Multiple sequence alignment - TraesCS6A01G177200

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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 TraesCS6A01G177200 chr6A 100.000 2201 0 0 1 2201 196794409 196792209 0.000000e+00 4065
1 TraesCS6A01G177200 chr6A 90.303 165 15 1 1331 1494 115317413 115317249 4.760000e-52 215
2 TraesCS6A01G177200 chr6B 87.634 1399 99 18 2 1354 262464814 262466184 0.000000e+00 1557
3 TraesCS6A01G177200 chr6B 94.497 745 29 5 1458 2201 262466208 262466941 0.000000e+00 1138
4 TraesCS6A01G177200 chr6D 84.787 940 76 27 362 1275 149464480 149465378 0.000000e+00 881
5 TraesCS6A01G177200 chr6D 88.343 712 35 20 1492 2201 149465458 149466123 0.000000e+00 811
6 TraesCS6A01G177200 chr6D 86.070 201 11 2 1 201 149464296 149464479 1.330000e-47 200
7 TraesCS6A01G177200 chr7D 89.831 177 15 3 1327 1501 612886884 612887059 7.910000e-55 224
8 TraesCS6A01G177200 chr7D 90.964 166 14 1 1331 1495 312574292 312574127 2.840000e-54 222
9 TraesCS6A01G177200 chr7D 90.419 167 15 1 1331 1496 23497594 23497760 3.680000e-53 219
10 TraesCS6A01G177200 chr7D 90.419 167 15 1 1329 1494 56399640 56399806 3.680000e-53 219
11 TraesCS6A01G177200 chr3D 89.881 168 16 1 1331 1497 232137875 232137708 4.760000e-52 215
12 TraesCS6A01G177200 chr2D 90.303 165 15 1 1331 1494 134800141 134799977 4.760000e-52 215
13 TraesCS6A01G177200 chr4D 89.017 173 18 1 1330 1501 57386238 57386410 1.710000e-51 213
14 TraesCS6A01G177200 chr3B 86.559 186 23 2 1313 1497 68900230 68900046 1.030000e-48 204


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 TraesCS6A01G177200 chr6A 196792209 196794409 2200 True 4065.000000 4065 100.0000 1 2201 1 chr6A.!!$R2 2200
1 TraesCS6A01G177200 chr6B 262464814 262466941 2127 False 1347.500000 1557 91.0655 2 2201 2 chr6B.!!$F1 2199
2 TraesCS6A01G177200 chr6D 149464296 149466123 1827 False 630.666667 881 86.4000 1 2201 3 chr6D.!!$F1 2200

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
515 518 0.036765 GTGGGTTAGCATGGTGTCGA 60.037 55.0 7.89 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1795 1.517242 GCCACACTCAGACTGAAAGG 58.483 55.0 6.61 7.12 39.3 3.11 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
21 22 2.871453 AGGGTTATGGTGGTTGAACAC 58.129 47.619 0.00 0.00 40.60 3.32
28 29 0.812549 GGTGGTTGAACACGTTTGGT 59.187 50.000 0.00 0.00 42.23 3.67
39 40 3.848256 CACGTTTGGTGTCGAGGTCGA 62.848 57.143 0.00 0.00 41.11 4.20
123 124 5.147330 TGTCCTTCTACAGTTGTATGTGG 57.853 43.478 0.00 0.00 34.56 4.17
124 125 4.020573 TGTCCTTCTACAGTTGTATGTGGG 60.021 45.833 0.00 0.00 34.56 4.61
125 126 3.055385 TCCTTCTACAGTTGTATGTGGGC 60.055 47.826 0.00 0.00 34.56 5.36
126 127 3.307410 CCTTCTACAGTTGTATGTGGGCA 60.307 47.826 0.00 0.00 34.56 5.36
127 128 3.610040 TCTACAGTTGTATGTGGGCAG 57.390 47.619 0.00 0.00 34.56 4.85
128 129 2.236146 TCTACAGTTGTATGTGGGCAGG 59.764 50.000 0.00 0.00 34.56 4.85
216 217 1.294780 GCTGAGTAGCCACAGTGCT 59.705 57.895 0.00 0.00 44.33 4.40
221 222 0.038159 AGTAGCCACAGTGCTTCGTC 60.038 55.000 0.00 0.00 42.75 4.20
223 224 0.391228 TAGCCACAGTGCTTCGTCAA 59.609 50.000 0.00 0.00 42.75 3.18
236 239 1.732941 TCGTCAAACGATCAATGGGG 58.267 50.000 0.00 0.00 46.73 4.96
265 268 3.379445 GTGGCGAAGACCGAGGGA 61.379 66.667 0.00 0.00 41.76 4.20
302 305 3.128032 AAACCCGGGTGTCTGGTGG 62.128 63.158 31.05 0.00 37.74 4.61
487 490 2.146342 GCGACCAGATGGAATACATGG 58.854 52.381 5.72 0.00 40.72 3.66
515 518 0.036765 GTGGGTTAGCATGGTGTCGA 60.037 55.000 7.89 0.00 0.00 4.20
522 525 0.737367 AGCATGGTGTCGATGTCGTG 60.737 55.000 0.00 0.00 40.80 4.35
557 560 3.136009 TCGTGATCTAGGCCTCGATTA 57.864 47.619 20.02 13.85 0.00 1.75
600 603 3.071023 TCATCGTTCTTCAGGTCAAAGGT 59.929 43.478 0.00 0.00 0.00 3.50
682 693 1.301716 GCAAAGTCAGAGGTCGCCA 60.302 57.895 0.00 0.00 0.00 5.69
686 697 1.853963 AAGTCAGAGGTCGCCATAGT 58.146 50.000 0.00 0.00 0.00 2.12
710 722 0.370273 GACGACGAATGCGAGCAAAT 59.630 50.000 0.00 0.00 41.64 2.32
765 777 0.532573 GAGTCGTCCTGCCTCATTCA 59.467 55.000 0.00 0.00 0.00 2.57
767 779 0.037326 GTCGTCCTGCCTCATTCACA 60.037 55.000 0.00 0.00 0.00 3.58
774 786 3.009363 TCCTGCCTCATTCACAATGAAGA 59.991 43.478 0.83 0.00 46.49 2.87
782 794 5.493809 TCATTCACAATGAAGATGAGAGCA 58.506 37.500 0.00 0.00 44.47 4.26
819 831 2.809601 GACGCGTCACCGAGCATT 60.810 61.111 33.09 0.00 37.39 3.56
826 838 2.408704 GCGTCACCGAGCATTATCATAC 59.591 50.000 0.00 0.00 35.63 2.39
830 842 5.473931 GTCACCGAGCATTATCATACATCT 58.526 41.667 0.00 0.00 0.00 2.90
894 921 3.220222 CCGTGGAGGCTAGATGCA 58.780 61.111 0.00 0.00 45.15 3.96
981 1008 1.296715 GGTCCTGGCGATTGACACT 59.703 57.895 0.00 0.00 0.00 3.55
986 1013 2.434185 GGCGATTGACACTGCCGA 60.434 61.111 0.00 0.00 37.81 5.54
1037 1064 0.824759 GACAAGGGCGACAGTATCCT 59.175 55.000 0.00 0.00 0.00 3.24
1042 1070 1.523938 GGCGACAGTATCCTTGCCC 60.524 63.158 0.00 0.00 36.51 5.36
1098 1126 2.045634 GCAGAGCACCTCATGGCA 60.046 61.111 0.00 0.00 36.63 4.92
1140 1168 4.778143 GCGGACATTGTCGCCCCT 62.778 66.667 17.26 0.00 45.42 4.79
1153 1181 1.455217 GCCCCTACCGAGCTCTACA 60.455 63.158 12.85 0.00 0.00 2.74
1156 1184 0.395311 CCCTACCGAGCTCTACACCA 60.395 60.000 12.85 0.00 0.00 4.17
1161 1189 0.320374 CCGAGCTCTACACCAACCAA 59.680 55.000 12.85 0.00 0.00 3.67
1228 1257 3.254629 GCCACAAGCTCTTCATCCA 57.745 52.632 0.00 0.00 38.99 3.41
1240 1269 0.389817 TTCATCCACAACCGAGAGCG 60.390 55.000 0.00 0.00 37.24 5.03
1249 1279 1.403679 CAACCGAGAGCGAGAAGAGAT 59.596 52.381 0.00 0.00 40.82 2.75
1260 1290 2.416027 CGAGAAGAGATCTTTGCGGACA 60.416 50.000 0.00 0.00 38.96 4.02
1307 1361 2.044252 TCCGGCTAGCGACTCCTT 60.044 61.111 9.00 0.00 0.00 3.36
1339 1393 9.230122 GTATAGACTTTAGTATGTACTCCCTCC 57.770 40.741 0.00 0.00 37.73 4.30
1342 1396 5.267587 ACTTTAGTATGTACTCCCTCCGTT 58.732 41.667 0.00 0.00 37.73 4.44
1344 1398 3.666345 AGTATGTACTCCCTCCGTTCT 57.334 47.619 0.00 0.00 0.00 3.01
1345 1399 3.553904 AGTATGTACTCCCTCCGTTCTC 58.446 50.000 0.00 0.00 0.00 2.87
1346 1400 2.526888 ATGTACTCCCTCCGTTCTCA 57.473 50.000 0.00 0.00 0.00 3.27
1351 1405 4.773674 TGTACTCCCTCCGTTCTCAAATAA 59.226 41.667 0.00 0.00 0.00 1.40
1353 1407 4.833390 ACTCCCTCCGTTCTCAAATAAAG 58.167 43.478 0.00 0.00 0.00 1.85
1354 1408 4.286291 ACTCCCTCCGTTCTCAAATAAAGT 59.714 41.667 0.00 0.00 0.00 2.66
1355 1409 4.828829 TCCCTCCGTTCTCAAATAAAGTC 58.171 43.478 0.00 0.00 0.00 3.01
1356 1410 4.530946 TCCCTCCGTTCTCAAATAAAGTCT 59.469 41.667 0.00 0.00 0.00 3.24
1357 1411 5.012768 TCCCTCCGTTCTCAAATAAAGTCTT 59.987 40.000 0.00 0.00 0.00 3.01
1358 1412 5.705905 CCCTCCGTTCTCAAATAAAGTCTTT 59.294 40.000 2.81 2.81 0.00 2.52
1359 1413 6.877322 CCCTCCGTTCTCAAATAAAGTCTTTA 59.123 38.462 7.49 7.49 0.00 1.85
1361 1415 9.595823 CCTCCGTTCTCAAATAAAGTCTTTATA 57.404 33.333 16.47 2.92 34.88 0.98
1375 1429 8.622948 AAAGTCTTTATAGAGGTTCCAACAAG 57.377 34.615 0.00 0.00 0.00 3.16
1376 1430 7.317722 AGTCTTTATAGAGGTTCCAACAAGT 57.682 36.000 0.00 0.00 0.00 3.16
1378 1432 7.016268 AGTCTTTATAGAGGTTCCAACAAGTGA 59.984 37.037 0.00 0.00 0.00 3.41
1379 1433 7.117956 GTCTTTATAGAGGTTCCAACAAGTGAC 59.882 40.741 0.00 0.00 0.00 3.67
1381 1435 7.786046 TTATAGAGGTTCCAACAAGTGACTA 57.214 36.000 0.00 0.00 0.00 2.59
1382 1436 4.338379 AGAGGTTCCAACAAGTGACTAC 57.662 45.455 0.00 0.00 0.00 2.73
1384 1438 4.348168 AGAGGTTCCAACAAGTGACTACAT 59.652 41.667 0.00 0.00 0.00 2.29
1386 1440 5.548406 AGGTTCCAACAAGTGACTACATAC 58.452 41.667 0.00 0.00 0.00 2.39
1387 1441 5.307196 AGGTTCCAACAAGTGACTACATACT 59.693 40.000 0.00 0.00 0.00 2.12
1388 1442 6.495872 AGGTTCCAACAAGTGACTACATACTA 59.504 38.462 0.00 0.00 0.00 1.82
1389 1443 7.015877 AGGTTCCAACAAGTGACTACATACTAA 59.984 37.037 0.00 0.00 0.00 2.24
1390 1444 7.331193 GGTTCCAACAAGTGACTACATACTAAG 59.669 40.741 0.00 0.00 0.00 2.18
1391 1445 7.534723 TCCAACAAGTGACTACATACTAAGT 57.465 36.000 0.00 0.00 0.00 2.24
1392 1446 8.640063 TCCAACAAGTGACTACATACTAAGTA 57.360 34.615 0.00 0.00 0.00 2.24
1393 1447 9.081204 TCCAACAAGTGACTACATACTAAGTAA 57.919 33.333 0.00 0.00 0.00 2.24
1397 1451 9.403110 ACAAGTGACTACATACTAAGTAAAACG 57.597 33.333 0.00 0.00 0.00 3.60
1398 1452 9.616634 CAAGTGACTACATACTAAGTAAAACGA 57.383 33.333 0.00 0.00 0.00 3.85
1399 1453 9.837525 AAGTGACTACATACTAAGTAAAACGAG 57.162 33.333 0.00 0.00 0.00 4.18
1402 1456 9.002600 TGACTACATACTAAGTAAAACGAGTGA 57.997 33.333 0.00 0.00 0.00 3.41
1403 1457 9.831737 GACTACATACTAAGTAAAACGAGTGAA 57.168 33.333 0.00 0.00 0.00 3.18
1406 1460 8.699283 ACATACTAAGTAAAACGAGTGAATCC 57.301 34.615 0.00 0.00 0.00 3.01
1407 1461 7.487189 ACATACTAAGTAAAACGAGTGAATCCG 59.513 37.037 0.00 0.00 0.00 4.18
1408 1462 4.624452 ACTAAGTAAAACGAGTGAATCCGC 59.376 41.667 0.00 0.00 0.00 5.54
1409 1463 3.034721 AGTAAAACGAGTGAATCCGCA 57.965 42.857 0.00 0.00 0.00 5.69
1410 1464 2.735134 AGTAAAACGAGTGAATCCGCAC 59.265 45.455 0.00 0.00 39.05 5.34
1421 1475 6.851222 AGTGAATCCGCACTCTAAAATATG 57.149 37.500 0.00 0.00 45.54 1.78
1422 1476 6.349300 AGTGAATCCGCACTCTAAAATATGT 58.651 36.000 0.00 0.00 45.54 2.29
1423 1477 6.480320 AGTGAATCCGCACTCTAAAATATGTC 59.520 38.462 0.00 0.00 45.54 3.06
1424 1478 6.480320 GTGAATCCGCACTCTAAAATATGTCT 59.520 38.462 0.00 0.00 35.91 3.41
1425 1479 7.652105 GTGAATCCGCACTCTAAAATATGTCTA 59.348 37.037 0.00 0.00 35.91 2.59
1426 1480 7.652105 TGAATCCGCACTCTAAAATATGTCTAC 59.348 37.037 0.00 0.00 0.00 2.59
1427 1481 6.459670 TCCGCACTCTAAAATATGTCTACA 57.540 37.500 0.00 0.00 0.00 2.74
1428 1482 7.050970 TCCGCACTCTAAAATATGTCTACAT 57.949 36.000 0.63 0.63 40.22 2.29
1429 1483 6.923508 TCCGCACTCTAAAATATGTCTACATG 59.076 38.462 5.85 0.00 37.15 3.21
1430 1484 6.346919 CCGCACTCTAAAATATGTCTACATGC 60.347 42.308 5.85 0.00 37.15 4.06
1431 1485 6.200854 CGCACTCTAAAATATGTCTACATGCA 59.799 38.462 5.85 0.00 37.15 3.96
1432 1486 7.095481 CGCACTCTAAAATATGTCTACATGCAT 60.095 37.037 5.85 0.00 37.15 3.96
1433 1487 8.226448 GCACTCTAAAATATGTCTACATGCATC 58.774 37.037 0.00 0.00 37.15 3.91
1434 1488 8.715998 CACTCTAAAATATGTCTACATGCATCC 58.284 37.037 0.00 0.00 37.15 3.51
1435 1489 8.654997 ACTCTAAAATATGTCTACATGCATCCT 58.345 33.333 0.00 0.00 37.15 3.24
1436 1490 9.499479 CTCTAAAATATGTCTACATGCATCCTT 57.501 33.333 0.00 0.00 37.15 3.36
1440 1494 9.578576 AAAATATGTCTACATGCATCCTTATGT 57.421 29.630 0.00 0.00 40.39 2.29
1441 1495 9.578576 AAATATGTCTACATGCATCCTTATGTT 57.421 29.630 0.00 0.00 38.41 2.71
1442 1496 6.872628 ATGTCTACATGCATCCTTATGTTG 57.127 37.500 0.00 0.00 38.41 3.33
1443 1497 5.744171 TGTCTACATGCATCCTTATGTTGT 58.256 37.500 0.00 0.00 38.41 3.32
1444 1498 6.883744 TGTCTACATGCATCCTTATGTTGTA 58.116 36.000 0.00 0.00 38.41 2.41
1445 1499 7.334858 TGTCTACATGCATCCTTATGTTGTAA 58.665 34.615 0.00 0.00 38.41 2.41
1446 1500 7.992608 TGTCTACATGCATCCTTATGTTGTAAT 59.007 33.333 0.00 0.00 38.41 1.89
1447 1501 8.499162 GTCTACATGCATCCTTATGTTGTAATC 58.501 37.037 0.00 0.00 38.41 1.75
1448 1502 6.639632 ACATGCATCCTTATGTTGTAATCC 57.360 37.500 0.00 0.00 34.00 3.01
1449 1503 6.128486 ACATGCATCCTTATGTTGTAATCCA 58.872 36.000 0.00 0.00 34.00 3.41
1450 1504 6.779049 ACATGCATCCTTATGTTGTAATCCAT 59.221 34.615 0.00 0.00 34.00 3.41
1451 1505 7.288389 ACATGCATCCTTATGTTGTAATCCATT 59.712 33.333 0.00 0.00 34.00 3.16
1452 1506 7.658525 TGCATCCTTATGTTGTAATCCATTT 57.341 32.000 0.00 0.00 35.38 2.32
1453 1507 7.490840 TGCATCCTTATGTTGTAATCCATTTG 58.509 34.615 0.00 0.00 35.38 2.32
1454 1508 7.341512 TGCATCCTTATGTTGTAATCCATTTGA 59.658 33.333 0.00 0.00 35.38 2.69
1455 1509 8.196771 GCATCCTTATGTTGTAATCCATTTGAA 58.803 33.333 0.00 0.00 35.38 2.69
1459 1513 9.874205 CCTTATGTTGTAATCCATTTGAAATGT 57.126 29.630 15.93 1.43 0.00 2.71
1470 1524 8.655935 ATCCATTTGAAATGTCTAAAAGGACT 57.344 30.769 15.93 0.00 37.16 3.85
1471 1525 8.477419 TCCATTTGAAATGTCTAAAAGGACTT 57.523 30.769 15.93 0.00 37.16 3.01
1472 1526 9.581289 TCCATTTGAAATGTCTAAAAGGACTTA 57.419 29.630 15.93 0.00 37.16 2.24
1546 1600 6.082338 GCATCTCATTTTTATCTACGCATGG 58.918 40.000 0.00 0.00 0.00 3.66
1590 1644 1.539388 CGTTGCAGGCTTTTGTATGGA 59.461 47.619 0.00 0.00 0.00 3.41
1604 1658 6.746745 TTTGTATGGATTTAAGGGTTCGTC 57.253 37.500 0.00 0.00 0.00 4.20
1605 1659 5.423704 TGTATGGATTTAAGGGTTCGTCA 57.576 39.130 0.00 0.00 0.00 4.35
1606 1660 5.806818 TGTATGGATTTAAGGGTTCGTCAA 58.193 37.500 0.00 0.00 0.00 3.18
1607 1661 6.419791 TGTATGGATTTAAGGGTTCGTCAAT 58.580 36.000 0.00 0.00 0.00 2.57
1608 1662 7.566569 TGTATGGATTTAAGGGTTCGTCAATA 58.433 34.615 0.00 0.00 0.00 1.90
1609 1663 8.047911 TGTATGGATTTAAGGGTTCGTCAATAA 58.952 33.333 0.00 0.00 0.00 1.40
1610 1664 6.995511 TGGATTTAAGGGTTCGTCAATAAG 57.004 37.500 0.00 0.00 0.00 1.73
1611 1665 5.883673 TGGATTTAAGGGTTCGTCAATAAGG 59.116 40.000 0.00 0.00 0.00 2.69
1612 1666 5.298527 GGATTTAAGGGTTCGTCAATAAGGG 59.701 44.000 0.00 0.00 0.00 3.95
1634 1688 0.693622 TAAGGGGAATGGTTGCACGA 59.306 50.000 0.00 0.00 0.00 4.35
1703 1757 8.397906 TGCACTTACTGATTAAATAAGCATCAC 58.602 33.333 0.00 0.00 30.54 3.06
1750 1804 7.923414 ATTACATTTAGTCCACCTTTCAGTC 57.077 36.000 0.00 0.00 0.00 3.51
1837 1891 3.508952 TGGAGGAATTCTAAGAGGGGT 57.491 47.619 5.23 0.00 0.00 4.95
1996 2050 4.444876 GGGCCTCAGCAGTAAATGAATAGA 60.445 45.833 0.84 0.00 42.56 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.008194 TCGACCTCGACACCAAACG 60.008 57.895 0.00 0.00 44.22 3.60
39 40 2.117156 GGCCAATGAGCAGCGACAT 61.117 57.895 0.00 2.93 0.00 3.06
123 124 2.317149 CTACTGTAGCTGCCCCTGCC 62.317 65.000 1.26 0.00 36.33 4.85
124 125 1.144936 CTACTGTAGCTGCCCCTGC 59.855 63.158 1.26 0.00 38.26 4.85
145 146 1.616921 CCATGGAGGCCATCAGGTT 59.383 57.895 5.56 0.00 43.15 3.50
221 222 4.454728 AAATGACCCCATTGATCGTTTG 57.545 40.909 0.00 0.00 41.84 2.93
245 248 2.338620 CTCGGTCTTCGCCACACA 59.661 61.111 0.00 0.00 39.05 3.72
320 323 0.035439 TCATTCAACCGAAGCCCTCC 60.035 55.000 0.00 0.00 33.74 4.30
328 331 2.083774 GCTTCCACATCATTCAACCGA 58.916 47.619 0.00 0.00 0.00 4.69
333 336 2.173356 CCCCTAGCTTCCACATCATTCA 59.827 50.000 0.00 0.00 0.00 2.57
423 426 0.948623 CATCGACGACCACAAGCCAA 60.949 55.000 0.00 0.00 0.00 4.52
462 465 0.839277 ATTCCATCTGGTCGCCATGA 59.161 50.000 0.00 1.06 36.34 3.07
487 490 2.355115 CTAACCCACCAGCCCACC 59.645 66.667 0.00 0.00 0.00 4.61
530 533 2.298446 AGGCCTAGATCACGATCATGTG 59.702 50.000 1.29 0.00 40.22 3.21
546 549 2.843701 CAAGCTTCATAATCGAGGCCT 58.156 47.619 3.86 3.86 38.70 5.19
557 560 5.494724 TGATTCTTCACTAGCAAGCTTCAT 58.505 37.500 0.00 0.00 0.00 2.57
600 603 3.822192 CGCCGACACCATCTCCGA 61.822 66.667 0.00 0.00 0.00 4.55
682 693 1.533338 GCATTCGTCGTCGACCACTAT 60.533 52.381 19.29 5.28 46.03 2.12
686 697 2.503158 CGCATTCGTCGTCGACCA 60.503 61.111 19.29 3.91 46.03 4.02
710 722 0.897863 CTGCCCCCGAACCATTTTCA 60.898 55.000 0.00 0.00 0.00 2.69
765 777 5.558818 ACTTTCTGCTCTCATCTTCATTGT 58.441 37.500 0.00 0.00 0.00 2.71
767 779 7.148272 GCTTTACTTTCTGCTCTCATCTTCATT 60.148 37.037 0.00 0.00 0.00 2.57
782 794 1.339151 CGGGCCAGAGCTTTACTTTCT 60.339 52.381 4.39 0.00 39.73 2.52
819 831 8.255111 ACTGACTCCAAATCAGATGTATGATA 57.745 34.615 8.92 0.00 45.46 2.15
826 838 3.199508 AGGGACTGACTCCAAATCAGATG 59.800 47.826 8.92 0.00 45.46 2.90
830 842 2.978978 TCAAGGGACTGACTCCAAATCA 59.021 45.455 0.00 0.00 41.63 2.57
887 914 1.451207 AACGCGGGCAATGCATCTA 60.451 52.632 12.47 0.00 0.00 1.98
940 967 1.376037 CCTCTGAGCACGGGGTTTC 60.376 63.158 0.00 0.00 0.00 2.78
1031 1058 0.035458 CCATCGAGGGGCAAGGATAC 59.965 60.000 8.61 0.00 0.00 2.24
1037 1064 2.452116 CCTATCCATCGAGGGGCAA 58.548 57.895 17.40 0.00 38.24 4.52
1140 1168 1.180029 GGTTGGTGTAGAGCTCGGTA 58.820 55.000 8.37 0.00 0.00 4.02
1153 1181 2.414750 CAACGAAGGCTTGGTTGGT 58.585 52.632 34.09 12.17 43.08 3.67
1156 1184 0.106918 TCCACAACGAAGGCTTGGTT 60.107 50.000 20.10 20.10 31.44 3.67
1161 1189 1.404035 GTGTTTTCCACAACGAAGGCT 59.596 47.619 0.00 0.00 43.92 4.58
1228 1257 0.523966 CTCTTCTCGCTCTCGGTTGT 59.476 55.000 0.00 0.00 36.13 3.32
1240 1269 3.238108 TGTCCGCAAAGATCTCTTCTC 57.762 47.619 0.00 0.00 34.61 2.87
1249 1279 0.599204 GTCGTCCTTGTCCGCAAAGA 60.599 55.000 0.00 0.00 33.73 2.52
1260 1290 2.103771 CCTCATGATCATGGTCGTCCTT 59.896 50.000 30.54 0.00 39.24 3.36
1351 1405 7.661847 CACTTGTTGGAACCTCTATAAAGACTT 59.338 37.037 0.00 0.00 0.00 3.01
1353 1407 7.117956 GTCACTTGTTGGAACCTCTATAAAGAC 59.882 40.741 0.00 0.00 0.00 3.01
1354 1408 7.016268 AGTCACTTGTTGGAACCTCTATAAAGA 59.984 37.037 0.00 0.00 0.00 2.52
1355 1409 7.162082 AGTCACTTGTTGGAACCTCTATAAAG 58.838 38.462 0.00 0.00 0.00 1.85
1356 1410 7.074653 AGTCACTTGTTGGAACCTCTATAAA 57.925 36.000 0.00 0.00 0.00 1.40
1357 1411 6.681729 AGTCACTTGTTGGAACCTCTATAA 57.318 37.500 0.00 0.00 0.00 0.98
1358 1412 6.722590 TGTAGTCACTTGTTGGAACCTCTATA 59.277 38.462 0.00 0.00 0.00 1.31
1359 1413 5.542635 TGTAGTCACTTGTTGGAACCTCTAT 59.457 40.000 0.00 0.00 0.00 1.98
1361 1415 3.709653 TGTAGTCACTTGTTGGAACCTCT 59.290 43.478 0.00 0.00 0.00 3.69
1362 1416 4.067972 TGTAGTCACTTGTTGGAACCTC 57.932 45.455 0.00 0.00 0.00 3.85
1363 1417 4.706842 ATGTAGTCACTTGTTGGAACCT 57.293 40.909 0.00 0.00 0.00 3.50
1365 1419 7.871463 ACTTAGTATGTAGTCACTTGTTGGAAC 59.129 37.037 0.00 0.00 0.00 3.62
1366 1420 7.959175 ACTTAGTATGTAGTCACTTGTTGGAA 58.041 34.615 0.00 0.00 0.00 3.53
1367 1421 7.534723 ACTTAGTATGTAGTCACTTGTTGGA 57.465 36.000 0.00 0.00 0.00 3.53
1371 1425 9.403110 CGTTTTACTTAGTATGTAGTCACTTGT 57.597 33.333 0.00 0.00 0.00 3.16
1372 1426 9.616634 TCGTTTTACTTAGTATGTAGTCACTTG 57.383 33.333 0.00 0.00 0.00 3.16
1373 1427 9.837525 CTCGTTTTACTTAGTATGTAGTCACTT 57.162 33.333 0.00 0.00 0.00 3.16
1375 1429 9.059485 CACTCGTTTTACTTAGTATGTAGTCAC 57.941 37.037 0.00 0.00 0.00 3.67
1376 1430 9.002600 TCACTCGTTTTACTTAGTATGTAGTCA 57.997 33.333 0.00 0.00 0.00 3.41
1381 1435 7.487189 CGGATTCACTCGTTTTACTTAGTATGT 59.513 37.037 0.00 0.00 0.00 2.29
1382 1436 7.514747 GCGGATTCACTCGTTTTACTTAGTATG 60.515 40.741 0.00 0.00 0.00 2.39
1384 1438 5.801947 GCGGATTCACTCGTTTTACTTAGTA 59.198 40.000 0.00 0.00 0.00 1.82
1386 1440 4.624024 TGCGGATTCACTCGTTTTACTTAG 59.376 41.667 0.00 0.00 0.00 2.18
1387 1441 4.386652 GTGCGGATTCACTCGTTTTACTTA 59.613 41.667 0.00 0.00 34.29 2.24
1388 1442 3.185797 GTGCGGATTCACTCGTTTTACTT 59.814 43.478 0.00 0.00 34.29 2.24
1389 1443 2.735134 GTGCGGATTCACTCGTTTTACT 59.265 45.455 0.00 0.00 34.29 2.24
1390 1444 2.735134 AGTGCGGATTCACTCGTTTTAC 59.265 45.455 0.00 0.00 43.28 2.01
1391 1445 3.034721 AGTGCGGATTCACTCGTTTTA 57.965 42.857 0.00 0.00 43.28 1.52
1392 1446 1.878953 AGTGCGGATTCACTCGTTTT 58.121 45.000 0.00 0.00 43.28 2.43
1393 1447 3.606886 AGTGCGGATTCACTCGTTT 57.393 47.368 0.00 0.00 43.28 3.60
1399 1453 6.480320 AGACATATTTTAGAGTGCGGATTCAC 59.520 38.462 1.67 0.00 37.24 3.18
1402 1456 7.497595 TGTAGACATATTTTAGAGTGCGGATT 58.502 34.615 0.00 0.00 0.00 3.01
1403 1457 7.050970 TGTAGACATATTTTAGAGTGCGGAT 57.949 36.000 0.00 0.00 0.00 4.18
1404 1458 6.459670 TGTAGACATATTTTAGAGTGCGGA 57.540 37.500 0.00 0.00 0.00 5.54
1405 1459 6.346919 GCATGTAGACATATTTTAGAGTGCGG 60.347 42.308 0.00 0.00 34.26 5.69
1406 1460 6.200854 TGCATGTAGACATATTTTAGAGTGCG 59.799 38.462 0.00 0.00 34.26 5.34
1407 1461 7.482654 TGCATGTAGACATATTTTAGAGTGC 57.517 36.000 0.00 0.00 34.26 4.40
1408 1462 8.715998 GGATGCATGTAGACATATTTTAGAGTG 58.284 37.037 2.46 0.00 34.26 3.51
1409 1463 8.654997 AGGATGCATGTAGACATATTTTAGAGT 58.345 33.333 2.46 0.00 34.26 3.24
1410 1464 9.499479 AAGGATGCATGTAGACATATTTTAGAG 57.501 33.333 2.46 0.00 34.26 2.43
1414 1468 9.578576 ACATAAGGATGCATGTAGACATATTTT 57.421 29.630 2.46 0.00 36.43 1.82
1415 1469 9.578576 AACATAAGGATGCATGTAGACATATTT 57.421 29.630 2.46 0.00 36.43 1.40
1416 1470 9.006839 CAACATAAGGATGCATGTAGACATATT 57.993 33.333 2.46 0.00 36.43 1.28
1417 1471 8.159447 ACAACATAAGGATGCATGTAGACATAT 58.841 33.333 2.46 0.00 35.66 1.78
1418 1472 7.508687 ACAACATAAGGATGCATGTAGACATA 58.491 34.615 2.46 0.00 35.66 2.29
1419 1473 6.359804 ACAACATAAGGATGCATGTAGACAT 58.640 36.000 2.46 0.00 35.66 3.06
1420 1474 5.744171 ACAACATAAGGATGCATGTAGACA 58.256 37.500 2.46 0.00 35.66 3.41
1421 1475 7.786178 TTACAACATAAGGATGCATGTAGAC 57.214 36.000 2.46 0.00 38.69 2.59
1422 1476 7.661437 GGATTACAACATAAGGATGCATGTAGA 59.339 37.037 2.46 0.00 38.69 2.59
1423 1477 7.445096 TGGATTACAACATAAGGATGCATGTAG 59.555 37.037 2.46 0.00 38.69 2.74
1424 1478 7.286313 TGGATTACAACATAAGGATGCATGTA 58.714 34.615 2.46 0.00 37.51 2.29
1425 1479 6.128486 TGGATTACAACATAAGGATGCATGT 58.872 36.000 2.46 0.00 38.92 3.21
1426 1480 6.638096 TGGATTACAACATAAGGATGCATG 57.362 37.500 2.46 0.00 36.43 4.06
1427 1481 7.844493 AATGGATTACAACATAAGGATGCAT 57.156 32.000 0.00 0.00 36.43 3.96
1428 1482 7.341512 TCAAATGGATTACAACATAAGGATGCA 59.658 33.333 0.00 0.00 36.43 3.96
1429 1483 7.715657 TCAAATGGATTACAACATAAGGATGC 58.284 34.615 0.00 0.00 36.43 3.91
1433 1487 9.874205 ACATTTCAAATGGATTACAACATAAGG 57.126 29.630 14.70 0.00 0.00 2.69
1444 1498 9.093458 AGTCCTTTTAGACATTTCAAATGGATT 57.907 29.630 14.70 2.34 37.63 3.01
1445 1499 8.655935 AGTCCTTTTAGACATTTCAAATGGAT 57.344 30.769 14.70 4.99 37.63 3.41
1446 1500 8.477419 AAGTCCTTTTAGACATTTCAAATGGA 57.523 30.769 14.70 0.00 39.34 3.41
1463 1517 9.907229 CCCTCTGTTTCTAAATATAAGTCCTTT 57.093 33.333 0.00 0.00 0.00 3.11
1464 1518 9.280456 TCCCTCTGTTTCTAAATATAAGTCCTT 57.720 33.333 0.00 0.00 0.00 3.36
1465 1519 8.855804 TCCCTCTGTTTCTAAATATAAGTCCT 57.144 34.615 0.00 0.00 0.00 3.85
1466 1520 8.706521 ACTCCCTCTGTTTCTAAATATAAGTCC 58.293 37.037 0.00 0.00 0.00 3.85
1474 1528 8.877195 TGTAAACTACTCCCTCTGTTTCTAAAT 58.123 33.333 0.00 0.00 34.88 1.40
1475 1529 8.253867 TGTAAACTACTCCCTCTGTTTCTAAA 57.746 34.615 0.00 0.00 34.88 1.85
1476 1530 7.844493 TGTAAACTACTCCCTCTGTTTCTAA 57.156 36.000 0.00 0.00 34.88 2.10
1477 1531 7.844493 TTGTAAACTACTCCCTCTGTTTCTA 57.156 36.000 0.00 0.00 34.88 2.10
1478 1532 6.742559 TTGTAAACTACTCCCTCTGTTTCT 57.257 37.500 0.00 0.00 34.88 2.52
1479 1533 7.981102 AATTGTAAACTACTCCCTCTGTTTC 57.019 36.000 0.00 0.00 34.88 2.78
1480 1534 8.762481 AAAATTGTAAACTACTCCCTCTGTTT 57.238 30.769 0.00 0.00 36.69 2.83
1519 1573 6.486248 TGCGTAGATAAAAATGAGATGCAAC 58.514 36.000 0.00 0.00 0.00 4.17
1529 1583 8.846943 TCATACATCCATGCGTAGATAAAAAT 57.153 30.769 0.00 0.00 0.00 1.82
1590 1644 6.069705 TCCCTTATTGACGAACCCTTAAAT 57.930 37.500 0.00 0.00 0.00 1.40
1604 1658 5.715921 ACCATTCCCCTTATTCCCTTATTG 58.284 41.667 0.00 0.00 0.00 1.90
1605 1659 6.143206 CAACCATTCCCCTTATTCCCTTATT 58.857 40.000 0.00 0.00 0.00 1.40
1606 1660 5.715921 CAACCATTCCCCTTATTCCCTTAT 58.284 41.667 0.00 0.00 0.00 1.73
1607 1661 4.632655 GCAACCATTCCCCTTATTCCCTTA 60.633 45.833 0.00 0.00 0.00 2.69
1608 1662 3.885738 GCAACCATTCCCCTTATTCCCTT 60.886 47.826 0.00 0.00 0.00 3.95
1609 1663 2.359249 GCAACCATTCCCCTTATTCCCT 60.359 50.000 0.00 0.00 0.00 4.20
1610 1664 2.039418 GCAACCATTCCCCTTATTCCC 58.961 52.381 0.00 0.00 0.00 3.97
1611 1665 2.430694 GTGCAACCATTCCCCTTATTCC 59.569 50.000 0.00 0.00 0.00 3.01
1612 1666 2.099098 CGTGCAACCATTCCCCTTATTC 59.901 50.000 0.00 0.00 0.00 1.75
1634 1688 2.675075 CGCCCCCATTTGTCCGTT 60.675 61.111 0.00 0.00 0.00 4.44
1741 1795 1.517242 GCCACACTCAGACTGAAAGG 58.483 55.000 6.61 7.12 39.30 3.11
1750 1804 1.691196 TTTTGAAGGGCCACACTCAG 58.309 50.000 6.18 0.00 0.00 3.35
2013 2067 6.244552 ACTCATGGAAAGAAGATAGATGCA 57.755 37.500 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.