Multiple sequence alignment - TraesCS3D01G505000

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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 TraesCS3D01G505000 chr3D 100.000 1731 0 0 1691 3421 592576653 592578383 0.000000e+00 3197.0
1 TraesCS3D01G505000 chr3D 100.000 1366 0 0 1 1366 592574963 592576328 0.000000e+00 2523.0
2 TraesCS3D01G505000 chr3D 85.967 1582 169 31 1779 3352 592608431 592609967 0.000000e+00 1642.0
3 TraesCS3D01G505000 chr3D 89.753 527 44 8 706 1231 592607773 592608290 0.000000e+00 665.0
4 TraesCS3D01G505000 chr3D 91.176 136 10 2 1232 1366 6511857 6511723 2.100000e-42 183.0
5 TraesCS3D01G505000 chr3A 94.317 1742 73 10 1691 3421 724023062 724021336 0.000000e+00 2645.0
6 TraesCS3D01G505000 chr3A 86.596 1604 173 24 1785 3379 723661413 723659843 0.000000e+00 1733.0
7 TraesCS3D01G505000 chr3A 90.705 1022 59 25 1 1012 724024274 724023279 0.000000e+00 1328.0
8 TraesCS3D01G505000 chr3A 89.962 528 46 7 705 1231 723662079 723661558 0.000000e+00 675.0
9 TraesCS3D01G505000 chr3A 91.358 81 7 0 1286 1366 219452918 219452838 1.000000e-20 111.0
10 TraesCS3D01G505000 chr3A 96.429 56 2 0 1235 1290 219459760 219459705 3.640000e-15 93.5
11 TraesCS3D01G505000 chr3A 100.000 35 0 0 246 280 724024077 724024043 7.920000e-07 65.8
12 TraesCS3D01G505000 chr3B 93.956 1638 86 6 1691 3325 794840207 794838580 0.000000e+00 2464.0
13 TraesCS3D01G505000 chr3B 94.003 1434 62 9 1691 3120 794593173 794591760 0.000000e+00 2150.0
14 TraesCS3D01G505000 chr3B 94.427 951 44 8 286 1231 794594111 794593165 0.000000e+00 1454.0
15 TraesCS3D01G505000 chr3B 93.875 947 38 8 286 1231 794841126 794840199 0.000000e+00 1410.0
16 TraesCS3D01G505000 chr3B 87.940 995 98 13 1779 2772 794544101 794543128 0.000000e+00 1153.0
17 TraesCS3D01G505000 chr3B 89.753 527 49 5 706 1231 794544764 794544242 0.000000e+00 669.0
18 TraesCS3D01G505000 chr3B 84.642 293 27 13 1 280 794594446 794594159 3.360000e-70 276.0
19 TraesCS3D01G505000 chr3B 84.532 278 25 12 1 277 794841589 794841329 3.390000e-65 259.0
20 TraesCS3D01G505000 chr2B 89.362 141 13 2 1226 1366 24849057 24849195 3.510000e-40 176.0
21 TraesCS3D01G505000 chr2A 89.706 136 12 2 1232 1366 83638568 83638434 4.540000e-39 172.0
22 TraesCS3D01G505000 chr2A 85.246 122 17 1 1232 1352 754660421 754660542 1.290000e-24 124.0
23 TraesCS3D01G505000 chr2D 86.066 122 16 1 1232 1352 623406819 623406940 2.770000e-26 130.0
24 TraesCS3D01G505000 chr7B 84.874 119 18 0 3036 3154 119316560 119316442 1.670000e-23 121.0
25 TraesCS3D01G505000 chr7A 79.641 167 29 4 3036 3201 159729141 159729303 7.760000e-22 115.0


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 TraesCS3D01G505000 chr3D 592574963 592578383 3420 False 2860.000000 3197 100.000000 1 3421 2 chr3D.!!$F1 3420
1 TraesCS3D01G505000 chr3D 592607773 592609967 2194 False 1153.500000 1642 87.860000 706 3352 2 chr3D.!!$F2 2646
2 TraesCS3D01G505000 chr3A 724021336 724024274 2938 True 1346.266667 2645 95.007333 1 3421 3 chr3A.!!$R4 3420
3 TraesCS3D01G505000 chr3A 723659843 723662079 2236 True 1204.000000 1733 88.279000 705 3379 2 chr3A.!!$R3 2674
4 TraesCS3D01G505000 chr3B 794838580 794841589 3009 True 1377.666667 2464 90.787667 1 3325 3 chr3B.!!$R3 3324
5 TraesCS3D01G505000 chr3B 794591760 794594446 2686 True 1293.333333 2150 91.024000 1 3120 3 chr3B.!!$R2 3119
6 TraesCS3D01G505000 chr3B 794543128 794544764 1636 True 911.000000 1153 88.846500 706 2772 2 chr3B.!!$R1 2066

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
899 1119 1.065031 GCAACAAACTATGTGCGCCG 61.065 55.0 4.18 0.0 42.99 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2815 3114 0.528901 CCATGCATGCCATCCGTTTG 60.529 55.0 21.69 0.0 29.71 2.93 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
160 175 7.820872 AGCAAAATCAATGAATAGGGAAACAAG 59.179 33.333 0.00 0.00 0.00 3.16
209 224 1.535226 GCCGTGAACAGGAAAACAACC 60.535 52.381 0.00 0.00 0.00 3.77
222 237 3.791973 AAACAACCGCAAAATCAGTGA 57.208 38.095 0.00 0.00 0.00 3.41
228 243 2.948979 ACCGCAAAATCAGTGAAACAGA 59.051 40.909 0.00 0.00 41.43 3.41
345 561 4.285517 CCATGCTAGGATCACATAGGAAGT 59.714 45.833 0.00 0.00 34.81 3.01
481 698 7.499232 GGCTTAGTATTTATGTGGGCCATATAG 59.501 40.741 20.36 11.06 35.96 1.31
899 1119 1.065031 GCAACAAACTATGTGCGCCG 61.065 55.000 4.18 0.00 42.99 6.46
934 1154 4.693283 CCAAGATCACACTATAAAGGCGA 58.307 43.478 0.00 0.00 0.00 5.54
1079 1299 3.382546 GCAATATGCACCAACCATCTCTT 59.617 43.478 0.00 0.00 44.26 2.85
1085 1305 3.582647 TGCACCAACCATCTCTTCTCTAA 59.417 43.478 0.00 0.00 0.00 2.10
1159 1379 6.261118 GCCTTCTGCTATTATTGTTGTTCAG 58.739 40.000 0.00 0.00 36.87 3.02
1236 1456 9.764363 TTTAGTAATAGAGATTATGCACAGTGG 57.236 33.333 1.84 0.00 30.25 4.00
1237 1457 6.226787 AGTAATAGAGATTATGCACAGTGGC 58.773 40.000 1.84 0.00 30.25 5.01
1238 1458 1.945387 AGAGATTATGCACAGTGGCG 58.055 50.000 1.84 0.00 36.28 5.69
1239 1459 0.940126 GAGATTATGCACAGTGGCGG 59.060 55.000 1.84 0.00 36.28 6.13
1240 1460 0.541392 AGATTATGCACAGTGGCGGA 59.459 50.000 1.84 0.00 36.28 5.54
1241 1461 0.940126 GATTATGCACAGTGGCGGAG 59.060 55.000 1.84 0.00 36.28 4.63
1255 1475 3.248043 CGGAGCCAGGAATGTTGAA 57.752 52.632 0.00 0.00 0.00 2.69
1256 1476 1.755179 CGGAGCCAGGAATGTTGAAT 58.245 50.000 0.00 0.00 0.00 2.57
1257 1477 2.917933 CGGAGCCAGGAATGTTGAATA 58.082 47.619 0.00 0.00 0.00 1.75
1258 1478 3.278574 CGGAGCCAGGAATGTTGAATAA 58.721 45.455 0.00 0.00 0.00 1.40
1259 1479 3.313526 CGGAGCCAGGAATGTTGAATAAG 59.686 47.826 0.00 0.00 0.00 1.73
1260 1480 3.633986 GGAGCCAGGAATGTTGAATAAGG 59.366 47.826 0.00 0.00 0.00 2.69
1261 1481 3.633986 GAGCCAGGAATGTTGAATAAGGG 59.366 47.826 0.00 0.00 0.00 3.95
1262 1482 2.695147 GCCAGGAATGTTGAATAAGGGG 59.305 50.000 0.00 0.00 0.00 4.79
1263 1483 3.299503 CCAGGAATGTTGAATAAGGGGG 58.700 50.000 0.00 0.00 0.00 5.40
1277 1497 3.964108 GGGGGCCAAGTGTTGTTT 58.036 55.556 4.39 0.00 0.00 2.83
1278 1498 3.135027 GGGGGCCAAGTGTTGTTTA 57.865 52.632 4.39 0.00 0.00 2.01
1279 1499 0.966179 GGGGGCCAAGTGTTGTTTAG 59.034 55.000 4.39 0.00 0.00 1.85
1280 1500 0.317160 GGGGCCAAGTGTTGTTTAGC 59.683 55.000 4.39 0.00 0.00 3.09
1281 1501 1.328279 GGGCCAAGTGTTGTTTAGCT 58.672 50.000 4.39 0.00 0.00 3.32
1282 1502 1.686587 GGGCCAAGTGTTGTTTAGCTT 59.313 47.619 4.39 0.00 0.00 3.74
1283 1503 2.102420 GGGCCAAGTGTTGTTTAGCTTT 59.898 45.455 4.39 0.00 0.00 3.51
1284 1504 3.123050 GGCCAAGTGTTGTTTAGCTTTG 58.877 45.455 0.00 0.00 0.00 2.77
1285 1505 3.430236 GGCCAAGTGTTGTTTAGCTTTGT 60.430 43.478 0.00 0.00 0.00 2.83
1286 1506 4.180817 GCCAAGTGTTGTTTAGCTTTGTT 58.819 39.130 0.00 0.00 0.00 2.83
1287 1507 4.032786 GCCAAGTGTTGTTTAGCTTTGTTG 59.967 41.667 0.00 0.00 0.00 3.33
1288 1508 4.566360 CCAAGTGTTGTTTAGCTTTGTTGG 59.434 41.667 0.00 0.00 0.00 3.77
1289 1509 4.385358 AGTGTTGTTTAGCTTTGTTGGG 57.615 40.909 0.00 0.00 0.00 4.12
1290 1510 3.132111 AGTGTTGTTTAGCTTTGTTGGGG 59.868 43.478 0.00 0.00 0.00 4.96
1291 1511 3.131400 GTGTTGTTTAGCTTTGTTGGGGA 59.869 43.478 0.00 0.00 0.00 4.81
1292 1512 3.383185 TGTTGTTTAGCTTTGTTGGGGAG 59.617 43.478 0.00 0.00 0.00 4.30
1293 1513 2.593026 TGTTTAGCTTTGTTGGGGAGG 58.407 47.619 0.00 0.00 0.00 4.30
1294 1514 1.893137 GTTTAGCTTTGTTGGGGAGGG 59.107 52.381 0.00 0.00 0.00 4.30
1295 1515 0.251608 TTAGCTTTGTTGGGGAGGGC 60.252 55.000 0.00 0.00 0.00 5.19
1296 1516 2.150014 TAGCTTTGTTGGGGAGGGCC 62.150 60.000 0.00 0.00 0.00 5.80
1297 1517 2.676471 CTTTGTTGGGGAGGGCCG 60.676 66.667 0.00 0.00 33.83 6.13
1298 1518 4.293671 TTTGTTGGGGAGGGCCGG 62.294 66.667 0.00 0.00 33.83 6.13
1310 1530 2.438795 GGCCGGCCCGTCAAATTA 60.439 61.111 36.64 0.00 0.00 1.40
1311 1531 2.767445 GGCCGGCCCGTCAAATTAC 61.767 63.158 36.64 4.38 0.00 1.89
1312 1532 1.747745 GCCGGCCCGTCAAATTACT 60.748 57.895 18.11 0.00 0.00 2.24
1313 1533 1.712018 GCCGGCCCGTCAAATTACTC 61.712 60.000 18.11 0.00 0.00 2.59
1314 1534 1.093496 CCGGCCCGTCAAATTACTCC 61.093 60.000 0.85 0.00 0.00 3.85
1315 1535 0.391927 CGGCCCGTCAAATTACTCCA 60.392 55.000 0.00 0.00 0.00 3.86
1316 1536 1.745827 CGGCCCGTCAAATTACTCCAT 60.746 52.381 0.00 0.00 0.00 3.41
1317 1537 2.375146 GGCCCGTCAAATTACTCCATT 58.625 47.619 0.00 0.00 0.00 3.16
1318 1538 2.758423 GGCCCGTCAAATTACTCCATTT 59.242 45.455 0.00 0.00 0.00 2.32
1319 1539 3.194755 GGCCCGTCAAATTACTCCATTTT 59.805 43.478 0.00 0.00 0.00 1.82
1320 1540 4.399934 GGCCCGTCAAATTACTCCATTTTA 59.600 41.667 0.00 0.00 0.00 1.52
1321 1541 5.449999 GGCCCGTCAAATTACTCCATTTTAG 60.450 44.000 0.00 0.00 0.00 1.85
1322 1542 5.578776 CCCGTCAAATTACTCCATTTTAGC 58.421 41.667 0.00 0.00 0.00 3.09
1323 1543 5.124776 CCCGTCAAATTACTCCATTTTAGCA 59.875 40.000 0.00 0.00 0.00 3.49
1324 1544 6.258160 CCGTCAAATTACTCCATTTTAGCAG 58.742 40.000 0.00 0.00 0.00 4.24
1325 1545 6.258160 CGTCAAATTACTCCATTTTAGCAGG 58.742 40.000 0.00 0.00 0.00 4.85
1326 1546 6.093495 CGTCAAATTACTCCATTTTAGCAGGA 59.907 38.462 0.00 0.00 0.00 3.86
1327 1547 7.361713 CGTCAAATTACTCCATTTTAGCAGGAA 60.362 37.037 0.00 0.00 0.00 3.36
1328 1548 8.470002 GTCAAATTACTCCATTTTAGCAGGAAT 58.530 33.333 0.00 0.00 0.00 3.01
1329 1549 9.034800 TCAAATTACTCCATTTTAGCAGGAATT 57.965 29.630 0.00 0.00 0.00 2.17
1334 1554 9.693739 TTACTCCATTTTAGCAGGAATTAATCA 57.306 29.630 0.00 0.00 0.00 2.57
1335 1555 8.000780 ACTCCATTTTAGCAGGAATTAATCAC 57.999 34.615 0.00 0.00 0.00 3.06
1336 1556 7.068716 ACTCCATTTTAGCAGGAATTAATCACC 59.931 37.037 4.15 4.15 0.00 4.02
1337 1557 7.125391 TCCATTTTAGCAGGAATTAATCACCT 58.875 34.615 7.94 7.94 34.02 4.00
1338 1558 8.278639 TCCATTTTAGCAGGAATTAATCACCTA 58.721 33.333 11.99 0.14 32.35 3.08
1339 1559 8.352942 CCATTTTAGCAGGAATTAATCACCTAC 58.647 37.037 11.99 8.20 32.35 3.18
1340 1560 9.125026 CATTTTAGCAGGAATTAATCACCTACT 57.875 33.333 14.66 14.66 32.87 2.57
1341 1561 8.506168 TTTTAGCAGGAATTAATCACCTACTG 57.494 34.615 17.56 8.13 31.03 2.74
1342 1562 5.957771 AGCAGGAATTAATCACCTACTGA 57.042 39.130 11.99 0.00 32.35 3.41
1343 1563 5.675538 AGCAGGAATTAATCACCTACTGAC 58.324 41.667 11.99 0.74 32.35 3.51
1344 1564 5.189736 AGCAGGAATTAATCACCTACTGACA 59.810 40.000 11.99 0.00 32.35 3.58
1345 1565 6.058183 GCAGGAATTAATCACCTACTGACAT 58.942 40.000 11.99 0.00 32.35 3.06
1346 1566 6.017605 GCAGGAATTAATCACCTACTGACATG 60.018 42.308 11.99 0.00 32.35 3.21
1347 1567 6.017605 CAGGAATTAATCACCTACTGACATGC 60.018 42.308 11.99 0.00 32.35 4.06
1348 1568 5.822519 GGAATTAATCACCTACTGACATGCA 59.177 40.000 0.00 0.00 0.00 3.96
1349 1569 6.488006 GGAATTAATCACCTACTGACATGCAT 59.512 38.462 0.00 0.00 0.00 3.96
1350 1570 7.661437 GGAATTAATCACCTACTGACATGCATA 59.339 37.037 0.00 0.00 0.00 3.14
1351 1571 9.224267 GAATTAATCACCTACTGACATGCATAT 57.776 33.333 0.00 0.00 0.00 1.78
1352 1572 9.578576 AATTAATCACCTACTGACATGCATATT 57.421 29.630 0.00 0.00 0.00 1.28
1354 1574 9.710900 TTAATCACCTACTGACATGCATATTAG 57.289 33.333 0.00 0.00 0.00 1.73
1355 1575 5.541845 TCACCTACTGACATGCATATTAGC 58.458 41.667 0.00 0.00 0.00 3.09
1356 1576 5.305386 TCACCTACTGACATGCATATTAGCT 59.695 40.000 0.00 0.00 34.99 3.32
1357 1577 5.994054 CACCTACTGACATGCATATTAGCTT 59.006 40.000 0.00 0.00 34.99 3.74
1358 1578 5.994054 ACCTACTGACATGCATATTAGCTTG 59.006 40.000 0.00 0.00 43.13 4.01
1359 1579 6.183361 ACCTACTGACATGCATATTAGCTTGA 60.183 38.462 0.00 0.00 40.84 3.02
1360 1580 6.707608 CCTACTGACATGCATATTAGCTTGAA 59.292 38.462 0.00 0.00 40.84 2.69
1361 1581 7.389884 CCTACTGACATGCATATTAGCTTGAAT 59.610 37.037 0.00 0.00 40.84 2.57
1362 1582 7.578310 ACTGACATGCATATTAGCTTGAATT 57.422 32.000 0.00 0.00 40.84 2.17
1363 1583 7.646314 ACTGACATGCATATTAGCTTGAATTC 58.354 34.615 0.00 0.00 40.84 2.17
1364 1584 7.283807 ACTGACATGCATATTAGCTTGAATTCA 59.716 33.333 3.38 3.38 40.84 2.57
1365 1585 7.998580 TGACATGCATATTAGCTTGAATTCAA 58.001 30.769 19.45 19.45 40.84 2.69
2120 2413 8.863049 GTTGCAACGTAAGCTACTAAACTAATA 58.137 33.333 14.90 0.00 45.62 0.98
2195 2488 9.533253 CTTATTTTTGACTGGACATTTTCTTGT 57.467 29.630 0.00 0.00 0.00 3.16
2336 2629 1.357258 AAGAGAGTTGCAGCGATGCG 61.357 55.000 22.02 0.00 37.69 4.73
2563 2856 4.233123 CATGAGTGCTTGTTTGATGTGT 57.767 40.909 0.00 0.00 0.00 3.72
2564 2857 3.969117 TGAGTGCTTGTTTGATGTGTC 57.031 42.857 0.00 0.00 0.00 3.67
2641 2935 8.579006 TGATAAAAAGAATGCATGAACTGAAGT 58.421 29.630 0.00 0.00 0.00 3.01
2652 2946 7.660112 TGCATGAACTGAAGTTTTCACAATAT 58.340 30.769 0.00 0.00 38.56 1.28
2815 3114 3.552875 GAGGCCCCTACCTTTTCATTAC 58.447 50.000 0.00 0.00 41.32 1.89
2921 3223 3.308473 GGCAGGGTAGGAGACAAAAGAAT 60.308 47.826 0.00 0.00 0.00 2.40
3027 3332 4.022849 GCAGCCATGATAGGTGGAATAAAC 60.023 45.833 0.00 0.00 39.12 2.01
3028 3333 5.380043 CAGCCATGATAGGTGGAATAAACT 58.620 41.667 0.00 0.00 39.12 2.66
3117 3426 2.226912 GCAAATTGCATGCCACACAAAT 59.773 40.909 16.68 3.90 44.26 2.32
3118 3427 3.816091 CAAATTGCATGCCACACAAATG 58.184 40.909 16.68 2.73 0.00 2.32
3155 3464 0.601311 CCCCATCGCTACTTAGCTGC 60.601 60.000 6.68 0.00 46.85 5.25
3156 3465 0.390860 CCCATCGCTACTTAGCTGCT 59.609 55.000 7.57 7.57 46.85 4.24
3157 3466 1.495878 CCATCGCTACTTAGCTGCTG 58.504 55.000 13.43 0.00 46.85 4.41
3173 3482 1.828595 TGCTGGACGCCTAGTGAATTA 59.171 47.619 0.00 0.00 38.05 1.40
3201 3511 0.583438 CCTCGTCCTATTGCATTGCG 59.417 55.000 3.84 0.00 0.00 4.85
3295 3614 3.039011 TCTTTAGCAGGTATCCCACTCC 58.961 50.000 0.00 0.00 0.00 3.85
3389 3709 9.016243 AGCCTGGGTATCTATACATATACTACT 57.984 37.037 0.00 0.00 34.98 2.57
3417 3740 8.621286 AGTAAGGTGTGTTTCTCTTAATTTGTG 58.379 33.333 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 115 8.622948 TTTGTTGGTTTTCAGTTATGGTTTTT 57.377 26.923 0.00 0.00 0.00 1.94
129 144 5.875910 CCCTATTCATTGATTTTGCTGCAAA 59.124 36.000 22.84 22.84 0.00 3.68
144 159 6.665248 CCTTTTCTCCTTGTTTCCCTATTCAT 59.335 38.462 0.00 0.00 0.00 2.57
160 175 2.431454 CTCAGTTCAGGCCTTTTCTCC 58.569 52.381 0.00 0.00 0.00 3.71
209 224 4.161333 GGATCTGTTTCACTGATTTTGCG 58.839 43.478 0.00 0.00 36.99 4.85
222 237 2.554032 CAGTTCGCTTTGGGATCTGTTT 59.446 45.455 11.87 0.00 37.46 2.83
228 243 1.072331 AGACACAGTTCGCTTTGGGAT 59.928 47.619 0.00 0.00 0.00 3.85
280 454 4.142687 ACCTGATTTTTACATGCTACGTGC 60.143 41.667 0.00 0.00 43.25 5.34
281 455 5.106712 ACACCTGATTTTTACATGCTACGTG 60.107 40.000 0.00 0.00 0.00 4.49
282 456 5.001232 ACACCTGATTTTTACATGCTACGT 58.999 37.500 0.00 0.00 0.00 3.57
333 549 5.538849 TGTTGTGTGTACTTCCTATGTGA 57.461 39.130 0.00 0.00 0.00 3.58
345 561 6.926272 GCCCATTTTATCTTTTGTTGTGTGTA 59.074 34.615 0.00 0.00 0.00 2.90
793 1013 1.222567 ATGGGTGCTTAGGTTAGGGG 58.777 55.000 0.00 0.00 0.00 4.79
899 1119 5.458779 GTGTGATCTTGGCAGTAAAACAAAC 59.541 40.000 0.00 0.00 0.00 2.93
934 1154 3.303049 CTTAGTAAGGGACGGTATGGGT 58.697 50.000 1.60 0.00 0.00 4.51
1079 1299 5.127194 AGGTTACACTCATTGCGATTAGAGA 59.873 40.000 8.02 0.00 32.59 3.10
1085 1305 3.334583 ACAGGTTACACTCATTGCGAT 57.665 42.857 0.00 0.00 0.00 4.58
1159 1379 1.140852 TCGATGGGTGGAATGATGGTC 59.859 52.381 0.00 0.00 0.00 4.02
1223 1443 1.097547 GCTCCGCCACTGTGCATAAT 61.098 55.000 1.29 0.00 0.00 1.28
1224 1444 1.745115 GCTCCGCCACTGTGCATAA 60.745 57.895 1.29 0.00 0.00 1.90
1225 1445 2.125147 GCTCCGCCACTGTGCATA 60.125 61.111 1.29 0.00 0.00 3.14
1236 1456 0.960364 TTCAACATTCCTGGCTCCGC 60.960 55.000 0.00 0.00 0.00 5.54
1237 1457 1.755179 ATTCAACATTCCTGGCTCCG 58.245 50.000 0.00 0.00 0.00 4.63
1238 1458 3.633986 CCTTATTCAACATTCCTGGCTCC 59.366 47.826 0.00 0.00 0.00 4.70
1239 1459 3.633986 CCCTTATTCAACATTCCTGGCTC 59.366 47.826 0.00 0.00 0.00 4.70
1240 1460 3.628257 CCCCTTATTCAACATTCCTGGCT 60.628 47.826 0.00 0.00 0.00 4.75
1241 1461 2.695147 CCCCTTATTCAACATTCCTGGC 59.305 50.000 0.00 0.00 0.00 4.85
1242 1462 3.299503 CCCCCTTATTCAACATTCCTGG 58.700 50.000 0.00 0.00 0.00 4.45
1260 1480 0.966179 CTAAACAACACTTGGCCCCC 59.034 55.000 0.00 0.00 34.12 5.40
1261 1481 0.317160 GCTAAACAACACTTGGCCCC 59.683 55.000 0.00 0.00 34.12 5.80
1262 1482 1.328279 AGCTAAACAACACTTGGCCC 58.672 50.000 0.00 0.00 31.11 5.80
1263 1483 3.123050 CAAAGCTAAACAACACTTGGCC 58.877 45.455 0.00 0.00 31.11 5.36
1264 1484 3.780902 ACAAAGCTAAACAACACTTGGC 58.219 40.909 0.00 0.00 34.12 4.52
1265 1485 4.566360 CCAACAAAGCTAAACAACACTTGG 59.434 41.667 0.00 0.00 34.12 3.61
1266 1486 4.566360 CCCAACAAAGCTAAACAACACTTG 59.434 41.667 0.00 0.00 0.00 3.16
1267 1487 4.382577 CCCCAACAAAGCTAAACAACACTT 60.383 41.667 0.00 0.00 0.00 3.16
1268 1488 3.132111 CCCCAACAAAGCTAAACAACACT 59.868 43.478 0.00 0.00 0.00 3.55
1269 1489 3.131400 TCCCCAACAAAGCTAAACAACAC 59.869 43.478 0.00 0.00 0.00 3.32
1270 1490 3.366396 TCCCCAACAAAGCTAAACAACA 58.634 40.909 0.00 0.00 0.00 3.33
1271 1491 3.243737 CCTCCCCAACAAAGCTAAACAAC 60.244 47.826 0.00 0.00 0.00 3.32
1272 1492 2.962421 CCTCCCCAACAAAGCTAAACAA 59.038 45.455 0.00 0.00 0.00 2.83
1273 1493 2.593026 CCTCCCCAACAAAGCTAAACA 58.407 47.619 0.00 0.00 0.00 2.83
1274 1494 1.893137 CCCTCCCCAACAAAGCTAAAC 59.107 52.381 0.00 0.00 0.00 2.01
1275 1495 1.825641 GCCCTCCCCAACAAAGCTAAA 60.826 52.381 0.00 0.00 0.00 1.85
1276 1496 0.251608 GCCCTCCCCAACAAAGCTAA 60.252 55.000 0.00 0.00 0.00 3.09
1277 1497 1.382629 GCCCTCCCCAACAAAGCTA 59.617 57.895 0.00 0.00 0.00 3.32
1278 1498 2.118294 GCCCTCCCCAACAAAGCT 59.882 61.111 0.00 0.00 0.00 3.74
1279 1499 2.997315 GGCCCTCCCCAACAAAGC 60.997 66.667 0.00 0.00 0.00 3.51
1280 1500 2.676471 CGGCCCTCCCCAACAAAG 60.676 66.667 0.00 0.00 0.00 2.77
1281 1501 4.293671 CCGGCCCTCCCCAACAAA 62.294 66.667 0.00 0.00 0.00 2.83
1293 1513 2.438795 TAATTTGACGGGCCGGCC 60.439 61.111 38.57 38.57 31.60 6.13
1294 1514 1.712018 GAGTAATTTGACGGGCCGGC 61.712 60.000 31.78 30.32 34.27 6.13
1295 1515 1.093496 GGAGTAATTTGACGGGCCGG 61.093 60.000 31.78 12.53 0.00 6.13
1296 1516 0.391927 TGGAGTAATTTGACGGGCCG 60.392 55.000 27.06 27.06 0.00 6.13
1297 1517 2.052782 ATGGAGTAATTTGACGGGCC 57.947 50.000 0.00 0.00 0.00 5.80
1298 1518 4.450082 AAAATGGAGTAATTTGACGGGC 57.550 40.909 0.00 0.00 30.21 6.13
1299 1519 5.124776 TGCTAAAATGGAGTAATTTGACGGG 59.875 40.000 0.00 0.00 30.21 5.28
1300 1520 6.189677 TGCTAAAATGGAGTAATTTGACGG 57.810 37.500 0.00 0.00 30.21 4.79
1301 1521 6.093495 TCCTGCTAAAATGGAGTAATTTGACG 59.907 38.462 0.00 0.00 30.21 4.35
1302 1522 7.391148 TCCTGCTAAAATGGAGTAATTTGAC 57.609 36.000 0.00 0.00 30.21 3.18
1303 1523 8.593945 ATTCCTGCTAAAATGGAGTAATTTGA 57.406 30.769 0.00 0.00 30.21 2.69
1308 1528 9.693739 TGATTAATTCCTGCTAAAATGGAGTAA 57.306 29.630 0.00 0.00 0.00 2.24
1309 1529 9.120538 GTGATTAATTCCTGCTAAAATGGAGTA 57.879 33.333 0.00 0.00 0.00 2.59
1310 1530 7.068716 GGTGATTAATTCCTGCTAAAATGGAGT 59.931 37.037 0.00 0.00 0.00 3.85
1311 1531 7.286316 AGGTGATTAATTCCTGCTAAAATGGAG 59.714 37.037 10.90 0.00 0.00 3.86
1312 1532 7.125391 AGGTGATTAATTCCTGCTAAAATGGA 58.875 34.615 10.90 0.00 0.00 3.41
1313 1533 7.352079 AGGTGATTAATTCCTGCTAAAATGG 57.648 36.000 10.90 0.00 0.00 3.16
1314 1534 9.125026 AGTAGGTGATTAATTCCTGCTAAAATG 57.875 33.333 20.71 0.00 41.19 2.32
1315 1535 9.125026 CAGTAGGTGATTAATTCCTGCTAAAAT 57.875 33.333 21.22 6.39 41.08 1.82
1316 1536 8.325787 TCAGTAGGTGATTAATTCCTGCTAAAA 58.674 33.333 21.22 12.67 41.08 1.52
1317 1537 7.769044 GTCAGTAGGTGATTAATTCCTGCTAAA 59.231 37.037 21.22 14.23 41.08 1.85
1318 1538 7.093068 TGTCAGTAGGTGATTAATTCCTGCTAA 60.093 37.037 21.22 11.60 41.08 3.09
1319 1539 6.382859 TGTCAGTAGGTGATTAATTCCTGCTA 59.617 38.462 21.22 10.70 41.08 3.49
1320 1540 5.189736 TGTCAGTAGGTGATTAATTCCTGCT 59.810 40.000 18.26 18.26 43.11 4.24
1321 1541 5.428253 TGTCAGTAGGTGATTAATTCCTGC 58.572 41.667 17.76 16.61 37.56 4.85
1322 1542 6.017605 GCATGTCAGTAGGTGATTAATTCCTG 60.018 42.308 17.76 7.34 37.56 3.86
1323 1543 6.058183 GCATGTCAGTAGGTGATTAATTCCT 58.942 40.000 14.58 14.58 37.56 3.36
1324 1544 5.822519 TGCATGTCAGTAGGTGATTAATTCC 59.177 40.000 0.00 0.00 37.56 3.01
1325 1545 6.925610 TGCATGTCAGTAGGTGATTAATTC 57.074 37.500 0.00 0.00 37.56 2.17
1326 1546 9.578576 AATATGCATGTCAGTAGGTGATTAATT 57.421 29.630 10.16 0.00 37.56 1.40
1328 1548 9.710900 CTAATATGCATGTCAGTAGGTGATTAA 57.289 33.333 10.16 0.00 37.56 1.40
1329 1549 7.819415 GCTAATATGCATGTCAGTAGGTGATTA 59.181 37.037 10.16 0.00 37.56 1.75
1330 1550 6.652481 GCTAATATGCATGTCAGTAGGTGATT 59.348 38.462 10.16 0.00 37.56 2.57
1331 1551 6.013898 AGCTAATATGCATGTCAGTAGGTGAT 60.014 38.462 10.16 0.00 34.62 3.06
1332 1552 5.305386 AGCTAATATGCATGTCAGTAGGTGA 59.695 40.000 10.16 0.00 34.99 4.02
1333 1553 5.545588 AGCTAATATGCATGTCAGTAGGTG 58.454 41.667 10.16 0.00 34.99 4.00
1334 1554 5.815233 AGCTAATATGCATGTCAGTAGGT 57.185 39.130 10.16 5.39 34.99 3.08
1335 1555 6.226052 TCAAGCTAATATGCATGTCAGTAGG 58.774 40.000 10.16 0.00 33.91 3.18
1336 1556 7.719778 TTCAAGCTAATATGCATGTCAGTAG 57.280 36.000 10.16 3.72 33.91 2.57
1337 1557 8.681486 AATTCAAGCTAATATGCATGTCAGTA 57.319 30.769 10.16 0.00 33.91 2.74
1338 1558 7.283807 TGAATTCAAGCTAATATGCATGTCAGT 59.716 33.333 10.16 0.00 33.91 3.41
1339 1559 7.645402 TGAATTCAAGCTAATATGCATGTCAG 58.355 34.615 10.16 0.00 33.91 3.51
1340 1560 7.571080 TGAATTCAAGCTAATATGCATGTCA 57.429 32.000 10.16 0.00 33.91 3.58
1805 2095 5.844004 ACACAAAGGTATATCGATCCACTC 58.156 41.667 0.00 0.00 0.00 3.51
1888 2178 4.308458 TCGGCAACCCTGACCACG 62.308 66.667 0.00 0.00 0.00 4.94
2195 2488 6.126863 TCCTCTTTGATTCCTTTAAGCTGA 57.873 37.500 0.00 0.00 0.00 4.26
2257 2550 6.166279 TCTGTGTCATCATCCTTTCTTGTAC 58.834 40.000 0.00 0.00 0.00 2.90
2336 2629 6.643388 AGATGGTTTTTCCTTGCAATAATCC 58.357 36.000 0.00 2.32 37.07 3.01
2559 2852 6.513230 GCATTACAAATGAAGACACAGACACA 60.513 38.462 3.86 0.00 0.00 3.72
2560 2853 5.853282 GCATTACAAATGAAGACACAGACAC 59.147 40.000 3.86 0.00 0.00 3.67
2561 2854 5.530543 TGCATTACAAATGAAGACACAGACA 59.469 36.000 3.86 0.00 0.00 3.41
2562 2855 6.000891 TGCATTACAAATGAAGACACAGAC 57.999 37.500 3.86 0.00 0.00 3.51
2563 2856 6.822667 ATGCATTACAAATGAAGACACAGA 57.177 33.333 0.00 0.00 0.00 3.41
2564 2857 8.969121 TTAATGCATTACAAATGAAGACACAG 57.031 30.769 18.70 0.00 0.00 3.66
2624 2918 5.978919 TGTGAAAACTTCAGTTCATGCATTC 59.021 36.000 0.00 0.00 41.01 2.67
2625 2919 5.904941 TGTGAAAACTTCAGTTCATGCATT 58.095 33.333 0.00 0.00 41.01 3.56
2744 3039 7.378966 TCTATGTATGTTCTAGCAACATAGCC 58.621 38.462 19.44 13.29 44.87 3.93
2815 3114 0.528901 CCATGCATGCCATCCGTTTG 60.529 55.000 21.69 0.00 29.71 2.93
2868 3168 8.915036 TCTTTGTAGTTCTATACTCTTCCCATC 58.085 37.037 0.00 0.00 38.33 3.51
2921 3223 7.948034 TTTGGTGTTTCTTTCCTCTTTCTTA 57.052 32.000 0.00 0.00 0.00 2.10
2941 3243 0.031994 CGTGGGGCAGTTTCTTTTGG 59.968 55.000 0.00 0.00 0.00 3.28
2993 3297 4.822685 ATCATGGCTGCCAAAACAATTA 57.177 36.364 27.24 0.00 36.95 1.40
3027 3332 3.198872 GGACTCTATGGCTCCGAAAAAG 58.801 50.000 0.00 0.00 0.00 2.27
3028 3333 2.569853 TGGACTCTATGGCTCCGAAAAA 59.430 45.455 0.00 0.00 0.00 1.94
3117 3426 2.203480 GCTGGTTGGTGCCTTCCA 60.203 61.111 5.29 5.29 35.49 3.53
3118 3427 1.973812 GAGCTGGTTGGTGCCTTCC 60.974 63.158 0.00 0.00 0.00 3.46
3155 3464 3.520290 TGTAATTCACTAGGCGTCCAG 57.480 47.619 0.00 0.00 0.00 3.86
3156 3465 3.965379 TTGTAATTCACTAGGCGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
3157 3466 6.147328 GGATATTTGTAATTCACTAGGCGTCC 59.853 42.308 0.00 0.00 0.00 4.79
3173 3482 4.102524 TGCAATAGGACGAGGGATATTTGT 59.897 41.667 0.00 0.00 0.00 2.83
3295 3614 6.317789 TGAGTGTCAAGCAAAGATAAAAGG 57.682 37.500 0.00 0.00 0.00 3.11
3383 3703 8.930846 AGAGAAACACACCTTACTTAGTAGTA 57.069 34.615 0.00 0.00 35.78 1.82


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

AutoCloner maintained by Alex Coulton.