Multiple sequence alignment - TraesCS2D01G097600

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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 TraesCS2D01G097600 chr2D 100.000 3862 0 0 1 3862 49877305 49881166 0.000000e+00 7132
1 TraesCS2D01G097600 chr2D 97.872 94 2 0 1336 1429 650861392 650861485 3.090000e-36 163
2 TraesCS2D01G097600 chr2B 93.277 2484 102 25 1419 3862 77171600 77174058 0.000000e+00 3602
3 TraesCS2D01G097600 chr2B 90.711 1378 52 28 2 1339 77170262 77171603 0.000000e+00 1766
4 TraesCS2D01G097600 chr2B 83.962 212 27 2 2566 2771 1678618 1678828 3.040000e-46 196
5 TraesCS2D01G097600 chr2A 93.019 1676 84 13 1688 3338 51585128 51586795 0.000000e+00 2416
6 TraesCS2D01G097600 chr2A 95.765 1346 44 7 2 1339 51583509 51584849 0.000000e+00 2158
7 TraesCS2D01G097600 chr2A 94.906 530 17 4 3334 3862 51586874 51587394 0.000000e+00 821
8 TraesCS2D01G097600 chr2A 90.722 194 14 3 1419 1608 51584846 51585039 4.950000e-64 255
9 TraesCS2D01G097600 chr4D 92.328 378 29 0 36 413 312800701 312800324 4.390000e-149 538
10 TraesCS2D01G097600 chr4D 98.889 90 1 0 1336 1425 301528639 301528728 1.110000e-35 161
11 TraesCS2D01G097600 chr4A 90.741 378 35 0 36 413 163818733 163819110 4.450000e-139 505
12 TraesCS2D01G097600 chr4A 94.949 99 5 0 1336 1434 542275974 542276072 5.170000e-34 156
13 TraesCS2D01G097600 chr1B 89.153 378 41 0 37 414 543498119 543497742 4.520000e-129 472
14 TraesCS2D01G097600 chr1B 100.000 90 0 0 1336 1425 230031803 230031892 2.390000e-37 167
15 TraesCS2D01G097600 chr1D 88.889 378 42 0 37 414 404138644 404138267 2.100000e-127 466
16 TraesCS2D01G097600 chr1D 97.849 93 2 0 1330 1422 296532101 296532009 1.110000e-35 161
17 TraesCS2D01G097600 chr1A 88.624 378 43 0 37 414 499785376 499784999 9.780000e-126 460
18 TraesCS2D01G097600 chr3D 87.566 378 47 0 37 414 441147394 441147771 4.580000e-119 438
19 TraesCS2D01G097600 chr3A 87.302 378 48 0 37 414 581274016 581274393 2.130000e-117 433
20 TraesCS2D01G097600 chr3A 94.949 99 5 0 1328 1426 641169766 641169668 5.170000e-34 156
21 TraesCS2D01G097600 chr7A 86.512 215 20 5 2566 2773 605163720 605163508 1.080000e-55 228
22 TraesCS2D01G097600 chr7A 83.886 211 27 3 2567 2771 694564538 694564747 1.090000e-45 195
23 TraesCS2D01G097600 chr4B 85.915 213 21 5 2566 2771 391595363 391595573 6.500000e-53 219
24 TraesCS2D01G097600 chr7B 84.434 212 26 2 2566 2771 654701732 654701522 6.540000e-48 202
25 TraesCS2D01G097600 chr7D 100.000 89 0 0 1334 1422 570656714 570656802 8.580000e-37 165
26 TraesCS2D01G097600 chr5D 96.939 98 2 1 1334 1430 369431543 369431640 3.090000e-36 163
27 TraesCS2D01G097600 chr6B 96.875 96 3 0 1336 1431 504159544 504159639 1.110000e-35 161


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 TraesCS2D01G097600 chr2D 49877305 49881166 3861 False 7132.0 7132 100.000 1 3862 1 chr2D.!!$F1 3861
1 TraesCS2D01G097600 chr2B 77170262 77174058 3796 False 2684.0 3602 91.994 2 3862 2 chr2B.!!$F2 3860
2 TraesCS2D01G097600 chr2A 51583509 51587394 3885 False 1412.5 2416 93.603 2 3862 4 chr2A.!!$F1 3860

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
760 762 0.108186 TTATCCTGAGCTGTGGTGCG 60.108 55.0 0.00 0.0 38.13 5.34 F
1935 2008 0.468226 TCCCCGCGATCTAGCAATTT 59.532 50.0 8.23 0.0 36.85 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2638 2736 0.114954 AATTTGAGGCCTTGGGAGCA 59.885 50.0 6.77 0.0 0.00 4.26 R
2916 3015 0.388134 GTTTGTCTAGCGTCGGAGCA 60.388 55.0 5.88 0.0 40.15 4.26 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
28 29 5.003160 TGATCCTGGAGTTGTTTGTATGTG 58.997 41.667 1.52 0.00 0.00 3.21
241 242 1.068352 AGGAGGCCTTCAGGGTGTTT 61.068 55.000 15.31 0.00 37.43 2.83
419 420 1.304381 ATGGCCAAATGAGCACCGT 60.304 52.632 10.96 0.00 0.00 4.83
420 421 1.597797 ATGGCCAAATGAGCACCGTG 61.598 55.000 10.96 0.00 0.00 4.94
636 638 1.678101 GTATCCTGATTGCTGTTGGGC 59.322 52.381 0.00 0.00 0.00 5.36
716 718 3.143728 AGCCGGTGTTTCGTAATTCTTT 58.856 40.909 1.90 0.00 0.00 2.52
724 726 7.070183 GGTGTTTCGTAATTCTTTGACTCTTC 58.930 38.462 0.00 0.00 0.00 2.87
753 755 7.798596 ATTTTACAGATGTTATCCTGAGCTG 57.201 36.000 0.00 0.00 34.65 4.24
760 762 0.108186 TTATCCTGAGCTGTGGTGCG 60.108 55.000 0.00 0.00 38.13 5.34
763 765 3.720193 CTGAGCTGTGGTGCGTGC 61.720 66.667 0.00 0.00 38.13 5.34
989 1004 2.242196 CCTCTTAAGGCCTGGAATTCCA 59.758 50.000 25.53 25.53 38.79 3.53
1007 1022 2.158623 TCCATGTGCTTGTGGAAGAGTT 60.159 45.455 2.65 0.00 41.36 3.01
1014 1029 2.945668 GCTTGTGGAAGAGTTGAACACT 59.054 45.455 0.00 0.00 39.07 3.55
1015 1030 3.378427 GCTTGTGGAAGAGTTGAACACTT 59.622 43.478 7.72 7.72 35.01 3.16
1058 1095 1.203441 TCAAGGTGCTCTGCCTCCAT 61.203 55.000 0.00 0.00 34.81 3.41
1181 1218 4.686839 AGATCCTGTTTAAGCGCTTTTC 57.313 40.909 30.13 18.28 0.00 2.29
1330 1367 4.514066 GTGGTTTCAGTTCGACAAGGTATT 59.486 41.667 0.00 0.00 0.00 1.89
1331 1368 4.753107 TGGTTTCAGTTCGACAAGGTATTC 59.247 41.667 0.00 0.00 0.00 1.75
1333 1370 5.469084 GGTTTCAGTTCGACAAGGTATTCTT 59.531 40.000 0.00 0.00 35.79 2.52
1334 1371 6.347483 GGTTTCAGTTCGACAAGGTATTCTTC 60.347 42.308 0.00 0.00 32.41 2.87
1335 1372 5.462530 TCAGTTCGACAAGGTATTCTTCA 57.537 39.130 0.00 0.00 32.41 3.02
1336 1373 5.470368 TCAGTTCGACAAGGTATTCTTCAG 58.530 41.667 0.00 0.00 32.41 3.02
1337 1374 5.010719 TCAGTTCGACAAGGTATTCTTCAGT 59.989 40.000 0.00 0.00 32.41 3.41
1338 1375 6.208007 TCAGTTCGACAAGGTATTCTTCAGTA 59.792 38.462 0.00 0.00 32.41 2.74
1339 1376 6.308282 CAGTTCGACAAGGTATTCTTCAGTAC 59.692 42.308 0.00 0.00 32.41 2.73
1340 1377 6.208994 AGTTCGACAAGGTATTCTTCAGTACT 59.791 38.462 0.00 0.00 32.41 2.73
1341 1378 6.192234 TCGACAAGGTATTCTTCAGTACTC 57.808 41.667 0.00 0.00 32.41 2.59
1342 1379 5.125097 TCGACAAGGTATTCTTCAGTACTCC 59.875 44.000 0.00 0.00 32.41 3.85
1343 1380 5.662456 GACAAGGTATTCTTCAGTACTCCC 58.338 45.833 0.00 0.00 32.41 4.30
1344 1381 5.342866 ACAAGGTATTCTTCAGTACTCCCT 58.657 41.667 0.00 0.00 32.41 4.20
1345 1382 5.422650 ACAAGGTATTCTTCAGTACTCCCTC 59.577 44.000 0.00 0.00 32.41 4.30
1346 1383 4.548669 AGGTATTCTTCAGTACTCCCTCC 58.451 47.826 0.00 0.00 0.00 4.30
1347 1384 3.318557 GGTATTCTTCAGTACTCCCTCCG 59.681 52.174 0.00 0.00 0.00 4.63
1348 1385 2.599408 TTCTTCAGTACTCCCTCCGT 57.401 50.000 0.00 0.00 0.00 4.69
1349 1386 3.726557 TTCTTCAGTACTCCCTCCGTA 57.273 47.619 0.00 0.00 0.00 4.02
1350 1387 3.726557 TCTTCAGTACTCCCTCCGTAA 57.273 47.619 0.00 0.00 0.00 3.18
1351 1388 4.038271 TCTTCAGTACTCCCTCCGTAAA 57.962 45.455 0.00 0.00 0.00 2.01
1352 1389 3.760684 TCTTCAGTACTCCCTCCGTAAAC 59.239 47.826 0.00 0.00 0.00 2.01
1353 1390 3.446442 TCAGTACTCCCTCCGTAAACT 57.554 47.619 0.00 0.00 0.00 2.66
1354 1391 4.574674 TCAGTACTCCCTCCGTAAACTA 57.425 45.455 0.00 0.00 0.00 2.24
1355 1392 4.922206 TCAGTACTCCCTCCGTAAACTAA 58.078 43.478 0.00 0.00 0.00 2.24
1356 1393 5.513233 TCAGTACTCCCTCCGTAAACTAAT 58.487 41.667 0.00 0.00 0.00 1.73
1357 1394 6.662755 TCAGTACTCCCTCCGTAAACTAATA 58.337 40.000 0.00 0.00 0.00 0.98
1358 1395 7.293073 TCAGTACTCCCTCCGTAAACTAATAT 58.707 38.462 0.00 0.00 0.00 1.28
1359 1396 8.439971 TCAGTACTCCCTCCGTAAACTAATATA 58.560 37.037 0.00 0.00 0.00 0.86
1360 1397 9.071276 CAGTACTCCCTCCGTAAACTAATATAA 57.929 37.037 0.00 0.00 0.00 0.98
1361 1398 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
1362 1399 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
1363 1400 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1364 1401 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
1365 1402 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
1366 1403 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
1367 1404 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
1368 1405 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
1416 1453 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
1417 1454 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
1429 1466 5.605488 AGTTTACAGAGGGAGTAGAAACCAA 59.395 40.000 0.00 0.00 0.00 3.67
1489 1527 1.598132 CTGCTAGCATCACTCATGTGC 59.402 52.381 19.72 0.00 43.49 4.57
1523 1562 6.094048 AGGATTTCACCGAATACACAAATCTG 59.906 38.462 0.00 0.00 32.93 2.90
1544 1583 3.137533 GGAAGAGTGCATTGCCTATCTC 58.862 50.000 6.12 8.74 0.00 2.75
1602 1641 1.839994 TGCTTGGATTCTCCCAGGTAG 59.160 52.381 0.00 0.00 37.53 3.18
1603 1642 1.141858 GCTTGGATTCTCCCAGGTAGG 59.858 57.143 0.00 0.00 37.53 3.18
1604 1643 2.764269 CTTGGATTCTCCCAGGTAGGA 58.236 52.381 0.00 0.00 41.22 2.94
1605 1644 2.961536 TGGATTCTCCCAGGTAGGAA 57.038 50.000 0.00 0.00 41.22 3.36
1607 1646 2.844348 TGGATTCTCCCAGGTAGGAAAC 59.156 50.000 0.00 0.00 41.22 2.78
1608 1647 3.506031 TGGATTCTCCCAGGTAGGAAACT 60.506 47.826 0.00 0.00 41.22 2.66
1609 1648 4.265124 TGGATTCTCCCAGGTAGGAAACTA 60.265 45.833 0.00 0.00 41.22 2.24
1680 1749 6.072728 GCAACACAGGATCAAACATAGTTGTA 60.073 38.462 0.00 0.00 36.95 2.41
1686 1755 8.035394 ACAGGATCAAACATAGTTGTACTACTG 58.965 37.037 18.57 7.54 32.84 2.74
1702 1771 9.826574 TTGTACTACTGTGTTTTAGTTCATCTT 57.173 29.630 0.00 0.00 29.13 2.40
1814 1883 3.131396 GCAAACTTTTGAGTCCTCGAGA 58.869 45.455 15.71 0.00 40.55 4.04
1828 1897 4.035909 GTCCTCGAGATAAGTTCCAGAGAC 59.964 50.000 15.71 3.94 32.90 3.36
1935 2008 0.468226 TCCCCGCGATCTAGCAATTT 59.532 50.000 8.23 0.00 36.85 1.82
1936 2009 1.134220 TCCCCGCGATCTAGCAATTTT 60.134 47.619 8.23 0.00 36.85 1.82
1947 2020 7.437267 GCGATCTAGCAATTTTAGTTAGTGGTA 59.563 37.037 0.00 0.00 37.05 3.25
1954 2027 8.035984 AGCAATTTTAGTTAGTGGTAGAGAGTC 58.964 37.037 0.00 0.00 0.00 3.36
2047 2126 1.550524 TCACATGCCACACTCTAGGAC 59.449 52.381 0.00 0.00 0.00 3.85
2091 2170 7.559486 AGAGCATATGCCGAAGATATCATAAA 58.441 34.615 23.96 0.00 43.38 1.40
2181 2275 3.509442 AGGACATGGAAATTTGGCTCAA 58.491 40.909 0.00 0.00 0.00 3.02
2182 2276 4.098894 AGGACATGGAAATTTGGCTCAAT 58.901 39.130 0.00 0.00 0.00 2.57
2192 2286 4.730949 ATTTGGCTCAATGGAAGATGTG 57.269 40.909 0.00 0.00 0.00 3.21
2201 2295 2.957402 TGGAAGATGTGCTCCAAACT 57.043 45.000 0.00 0.00 0.00 2.66
2204 2298 4.517285 TGGAAGATGTGCTCCAAACTATC 58.483 43.478 0.00 0.00 0.00 2.08
2206 2301 4.574013 GGAAGATGTGCTCCAAACTATCTG 59.426 45.833 0.00 0.00 0.00 2.90
2259 2354 3.430790 GGTTGAATGATTTAGGGCAAGGC 60.431 47.826 0.00 0.00 0.00 4.35
2352 2447 0.912486 GATGTGGCCTACAAGGACCT 59.088 55.000 3.32 0.00 45.26 3.85
2512 2607 0.745845 CTCCCCTGTCTTTCCATGCG 60.746 60.000 0.00 0.00 0.00 4.73
2638 2736 3.196469 TGGAAGATCTCAAGAACGCAGAT 59.804 43.478 0.00 0.00 0.00 2.90
2665 2763 2.416680 AGGCCTCAAATTCAGAGAGC 57.583 50.000 0.00 9.71 35.09 4.09
2672 2770 4.323333 CCTCAAATTCAGAGAGCTCAGGAA 60.323 45.833 17.77 15.77 35.09 3.36
2752 2850 1.014564 GCAGTAGCCGAACTTCGCTT 61.015 55.000 5.61 0.00 38.82 4.68
2771 2869 1.169577 TGTTGAGTTGCGTTGGTGTT 58.830 45.000 0.00 0.00 0.00 3.32
2795 2893 0.103572 ACCTGTTGCTTGCTTGCTTG 59.896 50.000 3.47 0.00 0.00 4.01
2796 2894 1.219522 CCTGTTGCTTGCTTGCTTGC 61.220 55.000 3.47 0.00 0.00 4.01
2797 2895 0.249322 CTGTTGCTTGCTTGCTTGCT 60.249 50.000 10.35 0.00 0.00 3.91
2798 2896 0.528901 TGTTGCTTGCTTGCTTGCTG 60.529 50.000 10.35 0.00 0.00 4.41
2811 2909 1.945394 GCTTGCTGTATCCAGATGGTG 59.055 52.381 0.00 0.00 41.50 4.17
2840 2938 2.833794 TCACCGTATTAGCCTCATTGC 58.166 47.619 0.00 0.00 0.00 3.56
2924 3023 5.378292 TCTTGATATCAGTATGCTCCGAC 57.622 43.478 5.39 0.00 34.76 4.79
2929 3028 0.945099 TCAGTATGCTCCGACGCTAG 59.055 55.000 0.00 0.00 34.76 3.42
3061 3160 4.035278 GCTCTATATACATCGAGCACCC 57.965 50.000 13.92 0.00 45.08 4.61
3075 3174 1.274167 AGCACCCGACGAATCTACAAA 59.726 47.619 0.00 0.00 0.00 2.83
3082 3181 4.143179 CCCGACGAATCTACAAAGAACAAC 60.143 45.833 0.00 0.00 34.73 3.32
3084 3183 4.380678 CGACGAATCTACAAAGAACAACGA 59.619 41.667 0.00 0.00 34.73 3.85
3205 3304 5.393866 ACCCAAACAACATCCTTTATCTGT 58.606 37.500 0.00 0.00 0.00 3.41
3220 3319 5.929697 TTATCTGTGCAGAGAGTGTTTTG 57.070 39.130 19.31 0.00 41.33 2.44
3230 3329 4.051922 AGAGAGTGTTTTGTAGAACTGCG 58.948 43.478 0.00 0.00 0.00 5.18
3274 3373 9.807921 CAGTAAGGTTTACCCATTGGATATAAT 57.192 33.333 3.62 0.00 36.42 1.28
3287 3386 7.816031 CCATTGGATATAATCTGATTTGCAACC 59.184 37.037 8.38 7.15 0.00 3.77
3353 3536 6.182507 TGGGTACTGATTGTGTTCTAAGTT 57.817 37.500 0.00 0.00 0.00 2.66
3374 3557 3.560503 TGCTTGCTTAAATTACGTGTGC 58.439 40.909 0.00 0.00 0.00 4.57
3389 3572 0.249120 TGTGCGTAGTCCTTCATGGG 59.751 55.000 0.00 0.00 36.20 4.00
3390 3573 1.090052 GTGCGTAGTCCTTCATGGGC 61.090 60.000 0.00 0.00 41.82 5.36
3391 3574 1.220749 GCGTAGTCCTTCATGGGCA 59.779 57.895 0.00 0.00 44.59 5.36
3392 3575 1.090052 GCGTAGTCCTTCATGGGCAC 61.090 60.000 0.00 0.00 44.59 5.01
3393 3576 0.537188 CGTAGTCCTTCATGGGCACT 59.463 55.000 0.00 0.00 44.59 4.40
3394 3577 1.066143 CGTAGTCCTTCATGGGCACTT 60.066 52.381 0.00 0.00 44.59 3.16
3395 3578 2.633488 GTAGTCCTTCATGGGCACTTC 58.367 52.381 0.00 0.00 44.59 3.01
3396 3579 0.329596 AGTCCTTCATGGGCACTTCC 59.670 55.000 0.00 0.00 44.59 3.46
3576 3759 2.892852 CAAAGATGGAGCCACTTGGAAA 59.107 45.455 0.00 0.00 37.39 3.13
3591 3774 6.209391 CCACTTGGAAAACCTAGAAATGTCAT 59.791 38.462 0.00 0.00 37.39 3.06
3614 3797 9.134055 TCATCCTTGATCAATAATTGCATTACA 57.866 29.630 8.96 0.00 0.00 2.41
3824 4007 5.057819 TCGCACAACCTATGTTAAAAGTCA 58.942 37.500 0.00 0.00 41.46 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.895297 ACAAACAACTCCAGGATCAAACAT 59.105 37.500 0.00 0.00 0.00 2.71
19 20 5.468746 GCAACCTGTAAGAGACACATACAAA 59.531 40.000 0.00 0.00 33.33 2.83
28 29 3.003480 GGTGATGCAACCTGTAAGAGAC 58.997 50.000 0.00 0.00 37.24 3.36
241 242 0.106918 AGCCGTTTTGGTCCTTGTCA 60.107 50.000 0.00 0.00 41.21 3.58
673 675 6.481644 GGCTTTCCATTGATACTAGAAGAGTG 59.518 42.308 0.00 0.00 39.39 3.51
749 751 2.516930 AAAGCACGCACCACAGCT 60.517 55.556 0.00 0.00 39.37 4.24
763 765 1.536766 TCTGCCATTCACAAGCGAAAG 59.463 47.619 0.00 0.00 0.00 2.62
989 1004 3.213206 TCAACTCTTCCACAAGCACAT 57.787 42.857 0.00 0.00 0.00 3.21
1007 1022 0.953727 GCTCCATGTGCAAGTGTTCA 59.046 50.000 0.00 0.00 0.00 3.18
1014 1029 0.401356 TTCTCCTGCTCCATGTGCAA 59.599 50.000 11.00 0.00 40.13 4.08
1015 1030 0.035725 CTTCTCCTGCTCCATGTGCA 60.036 55.000 9.72 9.72 38.81 4.57
1076 1113 2.169832 TCTGCTTCTTCAGGAAACCG 57.830 50.000 0.00 0.00 34.91 4.44
1186 1223 4.494091 TGGGATCAAACCAAAGCAAAAA 57.506 36.364 0.00 0.00 34.44 1.94
1194 1231 5.602145 AGAATTGAACTTGGGATCAAACCAA 59.398 36.000 0.00 0.00 45.25 3.67
1304 1341 1.847818 TGTCGAACTGAAACCACTCG 58.152 50.000 0.00 0.00 0.00 4.18
1330 1367 3.726557 TTACGGAGGGAGTACTGAAGA 57.273 47.619 0.00 0.00 0.00 2.87
1331 1368 3.762823 AGTTTACGGAGGGAGTACTGAAG 59.237 47.826 0.00 0.00 0.00 3.02
1333 1370 3.446442 AGTTTACGGAGGGAGTACTGA 57.554 47.619 0.00 0.00 0.00 3.41
1334 1371 5.848833 ATTAGTTTACGGAGGGAGTACTG 57.151 43.478 0.00 0.00 0.00 2.74
1335 1372 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
1336 1373 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
1337 1374 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
1338 1375 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
1339 1376 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
1340 1377 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
1341 1378 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
1342 1379 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
1390 1427 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
1391 1428 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
1392 1429 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
1393 1430 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
1394 1431 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
1401 1438 8.975295 GGTTTCTACTCCCTCTGTAAACTAATA 58.025 37.037 0.00 0.00 0.00 0.98
1402 1439 7.456902 TGGTTTCTACTCCCTCTGTAAACTAAT 59.543 37.037 0.00 0.00 0.00 1.73
1403 1440 6.783977 TGGTTTCTACTCCCTCTGTAAACTAA 59.216 38.462 0.00 0.00 0.00 2.24
1404 1441 6.317312 TGGTTTCTACTCCCTCTGTAAACTA 58.683 40.000 0.00 0.00 0.00 2.24
1405 1442 5.152934 TGGTTTCTACTCCCTCTGTAAACT 58.847 41.667 0.00 0.00 0.00 2.66
1406 1443 5.479124 TGGTTTCTACTCCCTCTGTAAAC 57.521 43.478 0.00 0.00 0.00 2.01
1407 1444 5.842328 TCTTGGTTTCTACTCCCTCTGTAAA 59.158 40.000 0.00 0.00 0.00 2.01
1408 1445 5.245526 GTCTTGGTTTCTACTCCCTCTGTAA 59.754 44.000 0.00 0.00 0.00 2.41
1409 1446 4.771054 GTCTTGGTTTCTACTCCCTCTGTA 59.229 45.833 0.00 0.00 0.00 2.74
1410 1447 3.579151 GTCTTGGTTTCTACTCCCTCTGT 59.421 47.826 0.00 0.00 0.00 3.41
1411 1448 3.835395 AGTCTTGGTTTCTACTCCCTCTG 59.165 47.826 0.00 0.00 0.00 3.35
1412 1449 3.835395 CAGTCTTGGTTTCTACTCCCTCT 59.165 47.826 0.00 0.00 0.00 3.69
1413 1450 3.833070 TCAGTCTTGGTTTCTACTCCCTC 59.167 47.826 0.00 0.00 0.00 4.30
1414 1451 3.858135 TCAGTCTTGGTTTCTACTCCCT 58.142 45.455 0.00 0.00 0.00 4.20
1415 1452 4.618920 TTCAGTCTTGGTTTCTACTCCC 57.381 45.455 0.00 0.00 0.00 4.30
1416 1453 6.231211 TGATTTCAGTCTTGGTTTCTACTCC 58.769 40.000 0.00 0.00 0.00 3.85
1417 1454 6.128418 GCTGATTTCAGTCTTGGTTTCTACTC 60.128 42.308 9.21 0.00 45.45 2.59
1429 1466 5.163281 AGATGAAGTGCTGATTTCAGTCT 57.837 39.130 9.21 5.73 45.45 3.24
1448 1485 3.636153 GGAACCAAACTGAGGCTAGAT 57.364 47.619 0.00 0.00 0.00 1.98
1523 1562 3.137533 GAGATAGGCAATGCACTCTTCC 58.862 50.000 7.79 0.00 0.00 3.46
1544 1583 3.845775 CGTTTTTCACCATGTAATCGCAG 59.154 43.478 0.00 0.00 0.00 5.18
1615 1655 3.320610 TGGGATGTGGTTCTTTTGGAA 57.679 42.857 0.00 0.00 0.00 3.53
1632 1672 2.644992 GCGCCTCAAACAGTTGGG 59.355 61.111 0.00 0.00 35.29 4.12
1686 1755 9.827411 GGAAGTCAATAAGATGAACTAAAACAC 57.173 33.333 0.00 0.00 0.00 3.32
1702 1771 4.335416 CTGGAAGCAAAGGGAAGTCAATA 58.665 43.478 0.00 0.00 0.00 1.90
1706 1775 1.539157 CCTGGAAGCAAAGGGAAGTC 58.461 55.000 0.00 0.00 0.00 3.01
1814 1883 7.496346 TCCTTTGTATGTCTCTGGAACTTAT 57.504 36.000 0.00 0.00 0.00 1.73
1828 1897 5.830912 TGTTGTTTCTTGCTCCTTTGTATG 58.169 37.500 0.00 0.00 0.00 2.39
1877 1950 2.939103 GGTAGATGGATGTCACAGTTGC 59.061 50.000 0.00 0.00 0.00 4.17
1935 2008 7.525029 GCCAAAAGACTCTCTACCACTAACTAA 60.525 40.741 0.00 0.00 0.00 2.24
1936 2009 6.071503 GCCAAAAGACTCTCTACCACTAACTA 60.072 42.308 0.00 0.00 0.00 2.24
1947 2020 1.450360 AAGGGGCCAAAAGACTCTCT 58.550 50.000 4.39 0.00 0.00 3.10
1954 2027 7.669089 TTCCTATTAATAAAGGGGCCAAAAG 57.331 36.000 4.39 0.00 33.40 2.27
1986 2064 8.408601 CAAAATTTACTATTCTGTCAGGATGGG 58.591 37.037 9.17 2.64 36.16 4.00
2047 2126 7.664082 TGCTCTTGAAGAATAACTTTCTCTG 57.336 36.000 0.00 0.00 39.13 3.35
2091 2170 6.317140 CCTGTATCAACATGTTCTGCATAAGT 59.683 38.462 8.48 0.00 35.74 2.24
2175 2254 1.674962 GAGCACATCTTCCATTGAGCC 59.325 52.381 0.00 0.00 30.91 4.70
2181 2275 3.446442 AGTTTGGAGCACATCTTCCAT 57.554 42.857 0.00 0.00 31.71 3.41
2182 2276 2.957402 AGTTTGGAGCACATCTTCCA 57.043 45.000 0.00 0.00 0.00 3.53
2192 2286 2.035530 AGCAGCAGATAGTTTGGAGC 57.964 50.000 0.00 0.00 0.00 4.70
2201 2295 1.908619 TGGAACCAGAAGCAGCAGATA 59.091 47.619 0.00 0.00 0.00 1.98
2204 2298 0.809385 CATGGAACCAGAAGCAGCAG 59.191 55.000 0.00 0.00 0.00 4.24
2206 2301 0.524862 CACATGGAACCAGAAGCAGC 59.475 55.000 0.00 0.00 0.00 5.25
2352 2447 4.200838 TGTACAGATTTCGCCTTGATCA 57.799 40.909 0.00 0.00 0.00 2.92
2512 2607 9.612620 ATTCACAAGAAATTTCGACAGTTATTC 57.387 29.630 12.42 0.00 37.29 1.75
2638 2736 0.114954 AATTTGAGGCCTTGGGAGCA 59.885 50.000 6.77 0.00 0.00 4.26
2665 2763 4.572389 CCGACATTGTCCTTATTTCCTGAG 59.428 45.833 11.12 0.00 0.00 3.35
2672 2770 2.006888 CACGCCGACATTGTCCTTATT 58.993 47.619 11.12 0.00 0.00 1.40
2741 2839 2.629022 CAACTCAACAAGCGAAGTTCG 58.371 47.619 20.87 20.87 43.89 3.95
2752 2850 1.169577 AACACCAACGCAACTCAACA 58.830 45.000 0.00 0.00 0.00 3.33
2771 2869 2.891112 CAAGCAAGCAACAGGTTTCAA 58.109 42.857 0.00 0.00 0.00 2.69
2811 2909 2.934553 GCTAATACGGTGAACAAGGTCC 59.065 50.000 0.00 0.00 0.00 4.46
2840 2938 4.920340 CGGGACTGATTTATTCTCATCTCG 59.080 45.833 0.00 0.00 0.00 4.04
2916 3015 0.388134 GTTTGTCTAGCGTCGGAGCA 60.388 55.000 5.88 0.00 40.15 4.26
2920 3019 3.806316 ATTTTGTTTGTCTAGCGTCGG 57.194 42.857 0.00 0.00 0.00 4.79
2924 3023 7.924103 AGGTTAAAATTTTGTTTGTCTAGCG 57.076 32.000 13.76 0.00 0.00 4.26
2929 3028 9.982291 GAAGGAAAGGTTAAAATTTTGTTTGTC 57.018 29.630 13.76 4.22 0.00 3.18
3061 3160 4.380678 TCGTTGTTCTTTGTAGATTCGTCG 59.619 41.667 0.00 0.00 0.00 5.12
3075 3174 9.302345 CTCATGTATATAGTTGTTCGTTGTTCT 57.698 33.333 0.00 0.00 0.00 3.01
3082 3181 9.961265 TTAGGTTCTCATGTATATAGTTGTTCG 57.039 33.333 0.00 0.00 0.00 3.95
3205 3304 4.811024 CAGTTCTACAAAACACTCTCTGCA 59.189 41.667 0.00 0.00 0.00 4.41
3220 3319 5.028375 GGCATTAATTGTTCGCAGTTCTAC 58.972 41.667 0.00 0.00 0.00 2.59
3230 3329 4.946784 ACTGACTCGGCATTAATTGTTC 57.053 40.909 0.00 0.00 0.00 3.18
3274 3373 6.647334 TTATTCTTGTGGTTGCAAATCAGA 57.353 33.333 0.00 0.00 37.82 3.27
3316 3415 4.518970 TCAGTACCCAACAAAGAAGAATGC 59.481 41.667 0.00 0.00 0.00 3.56
3353 3536 3.560503 GCACACGTAATTTAAGCAAGCA 58.439 40.909 0.00 0.00 0.00 3.91
3374 3557 0.537188 AGTGCCCATGAAGGACTACG 59.463 55.000 7.87 0.00 41.22 3.51
3389 3572 2.888594 TCTATACAAGTGCGGAAGTGC 58.111 47.619 0.00 0.00 0.00 4.40
3390 3573 7.534085 TTTATTCTATACAAGTGCGGAAGTG 57.466 36.000 0.00 0.00 0.00 3.16
3391 3574 8.556213 TTTTTATTCTATACAAGTGCGGAAGT 57.444 30.769 0.00 0.00 0.00 3.01
3471 3654 9.383519 CTCTTGAATATTGTGGTTCTTTAGCTA 57.616 33.333 0.00 0.00 0.00 3.32
3576 3759 6.962182 TGATCAAGGATGACATTTCTAGGTT 58.038 36.000 0.00 0.00 38.69 3.50
3591 3774 9.752961 CAATGTAATGCAATTATTGATCAAGGA 57.247 29.630 14.54 5.19 41.51 3.36
3623 3806 4.297299 ACACAGCAGTTTGAGAAATGTG 57.703 40.909 0.00 0.00 41.68 3.21
3803 3986 8.129211 GGATATGACTTTTAACATAGGTTGTGC 58.871 37.037 2.37 0.00 38.99 4.57
3824 4007 2.310945 CCAAGCATCCTCCCATGGATAT 59.689 50.000 15.22 0.00 44.38 1.63


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

AutoCloner maintained by Alex Coulton.