Multiple sequence alignment - TraesCS1A01G189700

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 TraesCS1A01G189700 chr1A 100.000 3567 0 0 1 3567 343398180 343394614 0.000000e+00 6588
1 TraesCS1A01G189700 chr1A 87.640 445 39 6 3125 3565 342878997 342878565 1.480000e-138 503
2 TraesCS1A01G189700 chr1A 77.854 438 61 18 2142 2569 343419535 343419124 4.600000e-59 239
3 TraesCS1A01G189700 chr1D 95.429 1400 39 11 1 1377 258339830 258341227 0.000000e+00 2207
4 TraesCS1A01G189700 chr1D 92.643 734 22 11 2834 3567 258345728 258346429 0.000000e+00 1027
5 TraesCS1A01G189700 chr1D 93.961 563 28 4 2087 2648 258341921 258342478 0.000000e+00 846
6 TraesCS1A01G189700 chr1D 92.020 589 30 9 1484 2068 258341229 258341804 0.000000e+00 811
7 TraesCS1A01G189700 chr1D 87.583 451 34 7 3125 3565 258356247 258356685 1.480000e-138 503
8 TraesCS1A01G189700 chr1D 97.354 189 5 0 2646 2834 258344584 258344772 4.440000e-84 322
9 TraesCS1A01G189700 chr1D 77.143 455 70 16 2124 2569 258094395 258094824 2.140000e-57 233
10 TraesCS1A01G189700 chr1D 99.130 115 1 0 1376 1490 247521067 247520953 1.300000e-49 207
11 TraesCS1A01G189700 chr1B 94.748 1409 41 14 1 1380 354924735 354923331 0.000000e+00 2161
12 TraesCS1A01G189700 chr1B 92.798 847 38 8 2090 2930 354922691 354921862 0.000000e+00 1205
13 TraesCS1A01G189700 chr1B 94.474 561 24 3 3008 3567 354660865 354660311 0.000000e+00 857
14 TraesCS1A01G189700 chr1B 90.610 607 31 16 1484 2088 354923332 354922750 0.000000e+00 782
15 TraesCS1A01G189700 chr1B 88.802 384 24 10 3187 3565 354545559 354545190 1.510000e-123 453
16 TraesCS1A01G189700 chr1B 83.046 348 42 10 34 370 629480882 629481223 2.080000e-77 300
17 TraesCS1A01G189700 chr1B 76.888 437 67 16 2142 2569 355103861 355103450 2.160000e-52 217
18 TraesCS1A01G189700 chr1B 88.182 110 13 0 2142 2251 354983566 354983457 8.040000e-27 132
19 TraesCS1A01G189700 chr5A 96.124 129 3 2 1365 1493 69844907 69844781 3.610000e-50 209
20 TraesCS1A01G189700 chr5A 97.541 122 3 0 1369 1490 528581270 528581391 3.610000e-50 209
21 TraesCS1A01G189700 chr5A 97.521 121 2 1 1371 1491 299768205 299768324 4.670000e-49 206
22 TraesCS1A01G189700 chr5A 98.291 117 1 1 1376 1492 9610329 9610214 1.680000e-48 204
23 TraesCS1A01G189700 chr2D 98.276 116 2 0 1370 1485 87031092 87030977 1.680000e-48 204
24 TraesCS1A01G189700 chr7A 95.349 129 3 2 1378 1503 269960427 269960299 6.040000e-48 202
25 TraesCS1A01G189700 chr3B 93.233 133 5 4 1354 1485 15806495 15806624 3.630000e-45 193
26 TraesCS1A01G189700 chr2A 95.833 120 4 1 1369 1488 35967943 35967825 3.630000e-45 193


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 TraesCS1A01G189700 chr1A 343394614 343398180 3566 True 6588.000000 6588 100.000000 1 3567 1 chr1A.!!$R2 3566
1 TraesCS1A01G189700 chr1D 258339830 258346429 6599 False 1042.600000 2207 94.281400 1 3567 5 chr1D.!!$F3 3566
2 TraesCS1A01G189700 chr1B 354921862 354924735 2873 True 1382.666667 2161 92.718667 1 2930 3 chr1B.!!$R5 2929
3 TraesCS1A01G189700 chr1B 354660311 354660865 554 True 857.000000 857 94.474000 3008 3567 1 chr1B.!!$R2 559

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
973 1004 1.194772 GCTCAAGTACGGTGCTTCAAC 59.805 52.381 8.59 0.0 0.0 3.18 F
1359 1393 0.878416 GTTTGGGCTTGCACGTATGA 59.122 50.000 0.00 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2455 2591 0.250901 GCTCTTTGACAGAAGGGGCA 60.251 55.0 0.0 0.0 0.0 5.36 R
2997 6202 0.105964 CGTCACTGTTTCCCTCCACA 59.894 55.0 0.0 0.0 0.0 4.17 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
223 233 9.378551 GAATCCTTGAAACCTTTACAAAGTTTT 57.621 29.630 0.00 0.00 34.01 2.43
421 431 5.075493 GCCATCAATCCATCCATTACTTCT 58.925 41.667 0.00 0.00 0.00 2.85
482 506 6.985188 TCTCTGTGTAATTTAAGATGTGGC 57.015 37.500 0.00 0.00 0.00 5.01
517 541 1.369209 CAGTTTGCACTGCCGAACG 60.369 57.895 0.00 0.00 44.16 3.95
531 555 1.732259 CCGAACGCTGCTAATTTGACT 59.268 47.619 0.00 0.00 0.00 3.41
533 557 2.668457 CGAACGCTGCTAATTTGACTCT 59.332 45.455 0.00 0.00 0.00 3.24
588 617 5.594199 TCCTTTTACTTCTTTAAGGCCCT 57.406 39.130 0.00 0.00 37.62 5.19
665 695 6.767524 AGGCATCCGTGTTTGATAAAATTA 57.232 33.333 0.00 0.00 0.00 1.40
767 797 8.184304 AGGCCAACATTTAGTTAAACAATGTA 57.816 30.769 5.01 0.00 39.66 2.29
896 927 8.286800 TGTTGGTCAAAGATAAGTATTGAAACG 58.713 33.333 0.00 0.00 35.07 3.60
973 1004 1.194772 GCTCAAGTACGGTGCTTCAAC 59.805 52.381 8.59 0.00 0.00 3.18
981 1012 3.863681 GGTGCTTCAACGAAATGCA 57.136 47.368 0.00 0.00 0.00 3.96
1229 1263 6.715347 AATCCATAAAGAAACCATAGTGCC 57.285 37.500 0.00 0.00 0.00 5.01
1359 1393 0.878416 GTTTGGGCTTGCACGTATGA 59.122 50.000 0.00 0.00 0.00 2.15
1384 1418 9.694137 GATAACATGTTCTAGTAATGTACTCCC 57.306 37.037 15.85 0.00 40.14 4.30
1385 1419 7.735326 AACATGTTCTAGTAATGTACTCCCT 57.265 36.000 4.92 0.00 40.14 4.20
1386 1420 7.349412 ACATGTTCTAGTAATGTACTCCCTC 57.651 40.000 0.00 0.00 40.14 4.30
1387 1421 6.324254 ACATGTTCTAGTAATGTACTCCCTCC 59.676 42.308 0.00 0.00 40.14 4.30
1388 1422 4.885907 TGTTCTAGTAATGTACTCCCTCCG 59.114 45.833 0.00 0.00 40.14 4.63
1389 1423 4.785346 TCTAGTAATGTACTCCCTCCGT 57.215 45.455 0.00 0.00 40.14 4.69
1390 1424 5.121380 TCTAGTAATGTACTCCCTCCGTT 57.879 43.478 0.00 0.00 40.14 4.44
1391 1425 5.128919 TCTAGTAATGTACTCCCTCCGTTC 58.871 45.833 0.00 0.00 40.14 3.95
1392 1426 3.029570 AGTAATGTACTCCCTCCGTTCC 58.970 50.000 0.00 0.00 32.47 3.62
1393 1427 1.946984 AATGTACTCCCTCCGTTCCA 58.053 50.000 0.00 0.00 0.00 3.53
1394 1428 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
1395 1429 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
1396 1430 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
1397 1431 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
1398 1432 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
1399 1433 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
1400 1434 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1401 1435 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
1402 1436 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
1403 1437 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
1404 1438 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
1405 1439 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
1406 1440 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
1407 1441 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
1408 1442 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
1409 1443 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
1410 1444 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
1411 1445 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
1412 1446 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
1413 1447 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
1414 1448 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
1415 1449 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
1416 1450 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
1417 1451 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
1418 1452 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
1419 1453 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
1420 1454 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
1421 1455 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
1422 1456 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
1423 1457 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
1424 1458 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
1425 1459 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
1426 1460 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
1427 1461 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
1428 1462 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
1429 1463 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
1430 1464 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
1431 1465 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
1457 1491 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
1458 1492 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
1459 1493 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
1460 1494 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
1461 1495 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
1462 1496 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
1463 1497 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
1464 1498 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
1465 1499 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
1466 1500 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
1467 1501 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
1468 1502 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
1469 1503 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
1470 1504 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
1471 1505 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
1472 1506 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
1473 1507 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
1474 1508 2.093783 CCTGCGACAAGTAATTCGGAAC 59.906 50.000 0.00 0.00 35.02 3.62
1498 1532 5.456186 CGGAGGGAGTAATATGTTTGGGAAT 60.456 44.000 0.00 0.00 0.00 3.01
1556 1590 5.741011 AGGTGCGTTTGATCCTAAGATTTA 58.259 37.500 0.00 0.00 30.90 1.40
1557 1591 6.357367 AGGTGCGTTTGATCCTAAGATTTAT 58.643 36.000 0.00 0.00 30.90 1.40
1558 1592 7.506114 AGGTGCGTTTGATCCTAAGATTTATA 58.494 34.615 0.00 0.00 30.90 0.98
1559 1593 8.157476 AGGTGCGTTTGATCCTAAGATTTATAT 58.843 33.333 0.00 0.00 30.90 0.86
1560 1594 8.443937 GGTGCGTTTGATCCTAAGATTTATATC 58.556 37.037 0.00 0.00 30.90 1.63
1561 1595 9.209175 GTGCGTTTGATCCTAAGATTTATATCT 57.791 33.333 0.00 0.00 43.01 1.98
1563 1597 9.646427 GCGTTTGATCCTAAGATTTATATCTCT 57.354 33.333 0.00 0.00 40.26 3.10
1588 1623 1.209261 CCCATATGTTTTGGTTGGCCC 59.791 52.381 0.00 0.00 31.99 5.80
1601 1636 0.960364 TTGGCCCGTGCTTCTCATTC 60.960 55.000 0.00 0.00 37.74 2.67
1719 1754 9.706691 TTCTTAATACCTTGACTTCAGTAACAG 57.293 33.333 0.00 0.00 0.00 3.16
1720 1755 9.085645 TCTTAATACCTTGACTTCAGTAACAGA 57.914 33.333 0.00 0.00 0.00 3.41
1721 1756 9.706691 CTTAATACCTTGACTTCAGTAACAGAA 57.293 33.333 0.00 0.00 0.00 3.02
1733 1768 8.398665 ACTTCAGTAACAGAAAACAGAATGAAC 58.601 33.333 0.00 0.00 39.69 3.18
1837 1872 4.067192 TGCATCATTGAGCATATTAGCGT 58.933 39.130 6.68 0.00 40.15 5.07
1841 1876 6.674037 GCATCATTGAGCATATTAGCGTAAGG 60.674 42.308 0.00 0.00 40.15 2.69
1877 1912 7.667043 TGATTTACTGTTTCTGTGACCATAC 57.333 36.000 0.00 0.00 0.00 2.39
1878 1913 7.220740 TGATTTACTGTTTCTGTGACCATACA 58.779 34.615 0.00 0.00 0.00 2.29
2137 2272 1.821216 AGCACGTAAACATTCTGGGG 58.179 50.000 0.00 0.00 0.00 4.96
2178 2313 7.031226 TGTTAAAGCATCTCCAAATCTATGC 57.969 36.000 0.00 0.00 43.97 3.14
2314 2450 5.948742 AAATTTGTTTGGTCCTTTCTCCA 57.051 34.783 0.00 0.00 0.00 3.86
2395 2531 4.511826 GTGCAGAAAGTACTATATGGCACC 59.488 45.833 20.18 9.19 42.24 5.01
2412 2548 2.169561 GCACCCCCTTGAAACAAAGAAA 59.830 45.455 0.00 0.00 0.00 2.52
2453 2589 1.318158 GGGCCCAACTGCTGAAGATG 61.318 60.000 19.95 0.00 0.00 2.90
2454 2590 0.322816 GGCCCAACTGCTGAAGATGA 60.323 55.000 0.00 0.00 30.34 2.92
2455 2591 1.684248 GGCCCAACTGCTGAAGATGAT 60.684 52.381 0.00 0.00 30.34 2.45
2485 2621 0.326264 TCAAAGAGCAGGAAGAGCCC 59.674 55.000 0.00 0.00 37.37 5.19
2533 2669 3.165071 TGATGGTAGCACTCACAGAGAA 58.835 45.455 0.00 0.00 33.32 2.87
2544 2680 4.578516 CACTCACAGAGAAGAGTCCGATAT 59.421 45.833 0.31 0.00 42.87 1.63
2559 2695 5.047847 GTCCGATATGAAATCGACCAAAGA 58.952 41.667 8.86 0.00 43.59 2.52
2584 2721 9.230932 GACGGTTAAATGTAGACACTAATACTC 57.769 37.037 0.00 0.00 0.00 2.59
2747 4996 4.156477 AGCTTAGGTATGGTGAGATCTCC 58.844 47.826 20.03 10.96 0.00 3.71
2809 5058 2.028045 CGACACTGATGACATTGTACGC 59.972 50.000 0.00 0.00 39.40 4.42
2826 5075 2.851195 ACGCCTTCTCAGTTTCATTGT 58.149 42.857 0.00 0.00 0.00 2.71
2851 6056 3.596046 AGGAATTGGGAGGGACAACAATA 59.404 43.478 0.00 0.00 33.54 1.90
2887 6092 5.750067 ACAATGATGACTTGACTGTTTTTGC 59.250 36.000 0.00 0.00 0.00 3.68
2930 6135 7.849804 TCAAGCCTAGATCTGTCATTTTTAC 57.150 36.000 5.18 0.00 0.00 2.01
2951 6156 3.736252 ACGAAGAAAACACTGATGACTCG 59.264 43.478 0.00 0.00 0.00 4.18
2973 6178 6.429624 TCGTGTCATGACTTGAATTTTGAAG 58.570 36.000 25.55 4.95 35.70 3.02
3113 6319 2.608546 CCCACGACGTTGTACTGAAAAA 59.391 45.455 8.44 0.00 0.00 1.94
3138 6344 2.159310 TCAACAAGAAAAGCCCACAACG 60.159 45.455 0.00 0.00 0.00 4.10
3185 6391 1.679305 GAGTCCTCGGTGGCTCAGA 60.679 63.158 12.51 0.00 38.22 3.27
3258 6464 3.979497 CCTTCCACCCCACCCCAC 61.979 72.222 0.00 0.00 0.00 4.61
3259 6465 3.979497 CTTCCACCCCACCCCACC 61.979 72.222 0.00 0.00 0.00 4.61
3376 6582 4.353437 ACCCGCTCCAACGACGAC 62.353 66.667 0.00 0.00 34.06 4.34
3379 6585 3.164011 CGCTCCAACGACGACGAC 61.164 66.667 15.32 0.00 42.66 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.817464 TGCTATTTGTAAGAAACACCACGT 59.183 37.500 0.00 0.00 38.00 4.49
64 65 6.479990 CACAGACAACTGAAGACAACAGATTA 59.520 38.462 0.00 0.00 46.03 1.75
223 233 4.764308 TGCAGGAGTTGTGCATAAAACATA 59.236 37.500 0.00 0.00 45.96 2.29
274 284 8.682936 AAATCGCCAAAATATCTCTAGATTGT 57.317 30.769 0.00 0.00 36.05 2.71
381 391 3.382083 TGGCACAGTAGATGAGGACTA 57.618 47.619 0.00 0.00 0.00 2.59
421 431 9.116067 ACAGCATACACAAACTTAAAAGTAAGA 57.884 29.630 0.00 0.00 39.36 2.10
474 498 6.835174 ACATCTGAGTATTATTGCCACATCT 58.165 36.000 0.00 0.00 0.00 2.90
481 505 6.909357 GCAAACTGACATCTGAGTATTATTGC 59.091 38.462 0.00 0.00 0.00 3.56
482 506 7.907045 GTGCAAACTGACATCTGAGTATTATTG 59.093 37.037 0.00 0.00 0.00 1.90
488 512 4.309933 CAGTGCAAACTGACATCTGAGTA 58.690 43.478 0.00 0.00 39.99 2.59
896 927 2.733956 TGGAATTGTAAGGCATCCACC 58.266 47.619 0.00 0.00 32.82 4.61
963 994 2.132740 TTGCATTTCGTTGAAGCACC 57.867 45.000 0.00 0.00 34.56 5.01
1137 1168 3.133721 AGCATAGAGGGTTCAGCTTACAG 59.866 47.826 0.00 0.00 0.00 2.74
1138 1169 3.107601 AGCATAGAGGGTTCAGCTTACA 58.892 45.455 0.00 0.00 0.00 2.41
1359 1393 9.435570 AGGGAGTACATTACTAGAACATGTTAT 57.564 33.333 11.95 11.45 39.59 1.89
1377 1411 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
1378 1412 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
1379 1413 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1380 1414 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
1381 1415 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
1382 1416 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1383 1417 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1384 1418 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1385 1419 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
1386 1420 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
1387 1421 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
1388 1422 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
1389 1423 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
1390 1424 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
1391 1425 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
1392 1426 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
1393 1427 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
1394 1428 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
1395 1429 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
1396 1430 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
1397 1431 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
1398 1432 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
1399 1433 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
1400 1434 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
1401 1435 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
1402 1436 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
1403 1437 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
1404 1438 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
1405 1439 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
1431 1465 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
1432 1466 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
1433 1467 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
1434 1468 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
1435 1469 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
1436 1470 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
1437 1471 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
1438 1472 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
1439 1473 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
1440 1474 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
1441 1475 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
1442 1476 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
1443 1477 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
1444 1478 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
1445 1479 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
1446 1480 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
1447 1481 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
1448 1482 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
1449 1483 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
1450 1484 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
1451 1485 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
1452 1486 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
1453 1487 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
1454 1488 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
1455 1489 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
1456 1490 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
1457 1491 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
1458 1492 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1459 1493 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1460 1494 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1461 1495 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
1462 1496 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1463 1497 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1464 1498 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1465 1499 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
1466 1500 1.856629 TTACTCCCTCCGTTCCGAAT 58.143 50.000 0.00 0.00 0.00 3.34
1467 1501 1.856629 ATTACTCCCTCCGTTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
1468 1502 2.734755 TATTACTCCCTCCGTTCCGA 57.265 50.000 0.00 0.00 0.00 4.55
1469 1503 2.626743 ACATATTACTCCCTCCGTTCCG 59.373 50.000 0.00 0.00 0.00 4.30
1470 1504 4.684484 AACATATTACTCCCTCCGTTCC 57.316 45.455 0.00 0.00 0.00 3.62
1471 1505 4.814771 CCAAACATATTACTCCCTCCGTTC 59.185 45.833 0.00 0.00 0.00 3.95
1472 1506 4.384868 CCCAAACATATTACTCCCTCCGTT 60.385 45.833 0.00 0.00 0.00 4.44
1473 1507 3.135895 CCCAAACATATTACTCCCTCCGT 59.864 47.826 0.00 0.00 0.00 4.69
1474 1508 3.389983 TCCCAAACATATTACTCCCTCCG 59.610 47.826 0.00 0.00 0.00 4.63
1475 1509 5.382664 TTCCCAAACATATTACTCCCTCC 57.617 43.478 0.00 0.00 0.00 4.30
1476 1510 7.898014 AAATTCCCAAACATATTACTCCCTC 57.102 36.000 0.00 0.00 0.00 4.30
1477 1511 8.679344 AAAAATTCCCAAACATATTACTCCCT 57.321 30.769 0.00 0.00 0.00 4.20
1526 1560 5.290493 AGGATCAAACGCACCTATTATCA 57.710 39.130 0.00 0.00 0.00 2.15
1556 1590 9.492730 ACCAAAACATATGGGAAAAAGAGATAT 57.507 29.630 7.80 0.00 42.48 1.63
1557 1591 8.893563 ACCAAAACATATGGGAAAAAGAGATA 57.106 30.769 7.80 0.00 42.48 1.98
1558 1592 7.797121 ACCAAAACATATGGGAAAAAGAGAT 57.203 32.000 7.80 0.00 42.48 2.75
1559 1593 7.441017 CAACCAAAACATATGGGAAAAAGAGA 58.559 34.615 7.80 0.00 42.48 3.10
1560 1594 6.650390 CCAACCAAAACATATGGGAAAAAGAG 59.350 38.462 7.80 0.00 42.48 2.85
1561 1595 6.529220 CCAACCAAAACATATGGGAAAAAGA 58.471 36.000 7.80 0.00 42.48 2.52
1563 1597 5.066593 GCCAACCAAAACATATGGGAAAAA 58.933 37.500 7.80 0.00 42.48 1.94
1588 1623 2.998670 ACATCACAGAATGAGAAGCACG 59.001 45.455 0.00 0.00 39.65 5.34
1706 1741 8.142994 TCATTCTGTTTTCTGTTACTGAAGTC 57.857 34.615 4.95 3.98 36.24 3.01
1707 1742 8.398665 GTTCATTCTGTTTTCTGTTACTGAAGT 58.601 33.333 4.95 0.00 36.24 3.01
1708 1743 7.584123 CGTTCATTCTGTTTTCTGTTACTGAAG 59.416 37.037 4.95 0.00 36.24 3.02
1711 1746 6.715464 ACGTTCATTCTGTTTTCTGTTACTG 58.285 36.000 0.00 0.00 0.00 2.74
1712 1747 6.920569 ACGTTCATTCTGTTTTCTGTTACT 57.079 33.333 0.00 0.00 0.00 2.24
1713 1748 9.737025 GTATACGTTCATTCTGTTTTCTGTTAC 57.263 33.333 0.00 0.00 0.00 2.50
1714 1749 9.701098 AGTATACGTTCATTCTGTTTTCTGTTA 57.299 29.630 0.00 0.00 0.00 2.41
1715 1750 8.603242 AGTATACGTTCATTCTGTTTTCTGTT 57.397 30.769 0.00 0.00 0.00 3.16
1716 1751 8.495949 CAAGTATACGTTCATTCTGTTTTCTGT 58.504 33.333 0.00 0.00 0.00 3.41
1717 1752 8.495949 ACAAGTATACGTTCATTCTGTTTTCTG 58.504 33.333 0.00 0.00 0.00 3.02
1718 1753 8.603242 ACAAGTATACGTTCATTCTGTTTTCT 57.397 30.769 0.00 0.00 0.00 2.52
1719 1754 9.314501 GAACAAGTATACGTTCATTCTGTTTTC 57.685 33.333 14.96 0.00 40.97 2.29
1720 1755 9.052759 AGAACAAGTATACGTTCATTCTGTTTT 57.947 29.630 19.47 1.64 43.20 2.43
1721 1756 8.603242 AGAACAAGTATACGTTCATTCTGTTT 57.397 30.769 19.47 1.40 43.20 2.83
1733 1768 8.912787 AGTACAATCAGAAGAACAAGTATACG 57.087 34.615 0.00 0.00 0.00 3.06
1841 1876 5.568620 ACAGTAAATCATAGTGATCCCCC 57.431 43.478 0.00 0.00 35.76 5.40
1877 1912 3.252458 GCTACCGCCCCATAAAATAGTTG 59.748 47.826 0.00 0.00 0.00 3.16
1878 1913 3.137728 AGCTACCGCCCCATAAAATAGTT 59.862 43.478 0.00 0.00 36.60 2.24
1931 1967 2.036958 TGTACCAGCCAATTCATCCG 57.963 50.000 0.00 0.00 0.00 4.18
2094 2229 8.555361 GCTTTACTTCAGAATGTCTGGAATATC 58.445 37.037 5.46 0.00 44.39 1.63
2137 2272 7.039993 TGCTTTAACATAAGAAAGAAGGGGAAC 60.040 37.037 0.00 0.00 35.12 3.62
2314 2450 9.982651 AGCGTGTTTCTATATGTCAAGTATAAT 57.017 29.630 0.00 0.00 0.00 1.28
2395 2531 6.348498 AGAACATTTTCTTTGTTTCAAGGGG 58.652 36.000 0.00 0.00 39.17 4.79
2412 2548 4.763793 CCTTCTGTCCATCACAAGAACATT 59.236 41.667 0.00 0.00 33.31 2.71
2453 2589 2.363683 CTCTTTGACAGAAGGGGCATC 58.636 52.381 0.00 0.00 0.00 3.91
2454 2590 1.615384 GCTCTTTGACAGAAGGGGCAT 60.615 52.381 0.00 0.00 0.00 4.40
2455 2591 0.250901 GCTCTTTGACAGAAGGGGCA 60.251 55.000 0.00 0.00 0.00 5.36
2485 2621 2.543777 TCTTTGTCTCTGGGGAAACG 57.456 50.000 0.00 0.00 0.00 3.60
2533 2669 3.889538 TGGTCGATTTCATATCGGACTCT 59.110 43.478 7.25 0.00 41.45 3.24
2544 2680 2.536761 ACCGTCTTTGGTCGATTTCA 57.463 45.000 0.00 0.00 37.91 2.69
2559 2695 7.912250 CGAGTATTAGTGTCTACATTTAACCGT 59.088 37.037 0.00 0.00 0.00 4.83
2598 2735 4.421948 GGTAAGTGGTGTAGTTCATCTCG 58.578 47.826 0.00 0.00 0.00 4.04
2747 4996 1.475280 CATGGTGTCAATGAAGGCCAG 59.525 52.381 5.01 0.00 0.00 4.85
2809 5058 5.065914 TCCTTCACAATGAAACTGAGAAGG 58.934 41.667 17.73 17.73 45.40 3.46
2826 5075 1.753903 TGTCCCTCCCAATTCCTTCA 58.246 50.000 0.00 0.00 0.00 3.02
2851 6056 8.853126 TCAAGTCATCATTGTTCTGAAAAATCT 58.147 29.630 2.79 0.00 0.00 2.40
2887 6092 7.227512 AGGCTTGATATCCAGTTATTTTCTTCG 59.772 37.037 5.75 0.00 0.00 3.79
2930 6135 3.736252 ACGAGTCATCAGTGTTTTCTTCG 59.264 43.478 0.00 0.00 0.00 3.79
2951 6156 7.377928 CACTCTTCAAAATTCAAGTCATGACAC 59.622 37.037 27.02 2.19 37.92 3.67
2994 6199 1.134220 TCACTGTTTCCCTCCACACAC 60.134 52.381 0.00 0.00 0.00 3.82
2995 6200 1.134220 GTCACTGTTTCCCTCCACACA 60.134 52.381 0.00 0.00 0.00 3.72
2996 6201 1.594331 GTCACTGTTTCCCTCCACAC 58.406 55.000 0.00 0.00 0.00 3.82
2997 6202 0.105964 CGTCACTGTTTCCCTCCACA 59.894 55.000 0.00 0.00 0.00 4.17
2998 6203 0.391597 TCGTCACTGTTTCCCTCCAC 59.608 55.000 0.00 0.00 0.00 4.02
2999 6204 1.124780 TTCGTCACTGTTTCCCTCCA 58.875 50.000 0.00 0.00 0.00 3.86
3000 6205 2.474410 ATTCGTCACTGTTTCCCTCC 57.526 50.000 0.00 0.00 0.00 4.30
3001 6206 4.935808 ACATAATTCGTCACTGTTTCCCTC 59.064 41.667 0.00 0.00 0.00 4.30
3005 6210 8.656849 AGATTACACATAATTCGTCACTGTTTC 58.343 33.333 0.00 0.00 30.77 2.78
3050 6256 6.491403 GGCCCATCAACAGTTATAAGATTGAT 59.509 38.462 10.77 10.77 39.90 2.57
3051 6257 5.827797 GGCCCATCAACAGTTATAAGATTGA 59.172 40.000 0.00 7.91 34.03 2.57
3113 6319 1.063266 TGGGCTTTTCTTGTTGAGGGT 60.063 47.619 0.00 0.00 0.00 4.34
3138 6344 2.804828 CTTCCCGCCTCCAGGTGTTC 62.805 65.000 5.45 0.00 43.97 3.18
3163 6369 0.107116 GAGCCACCGAGGACTCTAGA 60.107 60.000 0.00 0.00 41.22 2.43
3185 6391 3.728373 GCGGGAGGAATGGGGTGT 61.728 66.667 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.