Multiple sequence alignment - TraesCS2B01G297200

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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 TraesCS2B01G297200 chr2B 100.000 4467 0 0 1 4467 415988105 415992571 0.000000e+00 8250
1 TraesCS2B01G297200 chr2B 94.922 768 35 3 3701 4467 53404407 53405171 0.000000e+00 1199
2 TraesCS2B01G297200 chr2D 96.135 1656 45 8 1403 3049 349734077 349732432 0.000000e+00 2686
3 TraesCS2B01G297200 chr2D 98.188 607 9 2 3052 3656 349732397 349731791 0.000000e+00 1059
4 TraesCS2B01G297200 chr2D 88.120 766 70 12 3701 4464 646079254 646080000 0.000000e+00 891
5 TraesCS2B01G297200 chr2D 95.423 437 11 3 866 1294 349734503 349734068 0.000000e+00 688
6 TraesCS2B01G297200 chr2D 94.565 184 6 3 702 882 349734707 349734525 9.460000e-72 281
7 TraesCS2B01G297200 chr2D 94.262 122 7 0 1288 1409 418057518 418057639 2.120000e-43 187
8 TraesCS2B01G297200 chr2D 93.684 95 4 2 3700 3794 315182219 315182311 1.680000e-29 141
9 TraesCS2B01G297200 chr2A 95.773 1656 49 10 1403 3049 465556387 465554744 0.000000e+00 2651
10 TraesCS2B01G297200 chr2A 97.231 650 17 1 3052 3700 465554709 465554060 0.000000e+00 1099
11 TraesCS2B01G297200 chr2A 87.143 770 77 13 3701 4467 773308996 773308246 0.000000e+00 854
12 TraesCS2B01G297200 chr2A 92.384 604 13 4 703 1289 465556982 465556395 0.000000e+00 830
13 TraesCS2B01G297200 chr2A 90.722 97 8 1 3698 3794 420141264 420141169 1.300000e-25 128
14 TraesCS2B01G297200 chr7A 97.554 695 14 3 1 694 717043735 717044427 0.000000e+00 1186
15 TraesCS2B01G297200 chr7A 91.417 769 61 4 3700 4467 733263023 733262259 0.000000e+00 1050
16 TraesCS2B01G297200 chr6B 97.131 697 15 4 1 694 687140592 687141286 0.000000e+00 1171
17 TraesCS2B01G297200 chr6B 92.857 126 9 0 1279 1404 44106402 44106527 2.740000e-42 183
18 TraesCS2B01G297200 chr5B 94.218 761 38 5 3711 4467 37977624 37976866 0.000000e+00 1157
19 TraesCS2B01G297200 chr5B 95.000 120 6 0 1288 1407 562793820 562793701 5.900000e-44 189
20 TraesCS2B01G297200 chrUn 96.562 698 19 4 1 695 61934431 61935126 0.000000e+00 1151
21 TraesCS2B01G297200 chrUn 96.562 698 19 4 1 695 379206554 379207249 0.000000e+00 1151
22 TraesCS2B01G297200 chrUn 96.343 629 20 3 69 695 410576965 410576338 0.000000e+00 1031
23 TraesCS2B01G297200 chrUn 96.869 511 14 2 186 695 393316529 393317038 0.000000e+00 854
24 TraesCS2B01G297200 chrUn 98.684 76 0 1 1 76 389858234 389858308 2.800000e-27 134
25 TraesCS2B01G297200 chr4B 96.667 690 17 5 1 687 223334462 223333776 0.000000e+00 1142
26 TraesCS2B01G297200 chr6A 93.108 769 49 3 3701 4467 601255941 601255175 0.000000e+00 1123
27 TraesCS2B01G297200 chr5A 97.561 615 13 2 71 684 640073622 640073009 0.000000e+00 1051
28 TraesCS2B01G297200 chr5A 93.275 342 23 0 3915 4256 686500865 686501206 5.160000e-139 505
29 TraesCS2B01G297200 chr5A 91.620 179 14 1 4287 4464 686501201 686501379 3.450000e-61 246
30 TraesCS2B01G297200 chr5A 84.252 254 22 13 997 1238 372931529 372931776 9.660000e-57 231
31 TraesCS2B01G297200 chr5A 85.161 155 23 0 1085 1239 649402042 649402196 4.620000e-35 159
32 TraesCS2B01G297200 chr1B 97.087 618 16 2 71 687 633696306 633696922 0.000000e+00 1040
33 TraesCS2B01G297200 chr3B 94.954 218 9 2 1 217 55212417 55212201 1.540000e-89 340
34 TraesCS2B01G297200 chr3B 91.667 132 10 1 1273 1404 545060678 545060808 9.870000e-42 182
35 TraesCS2B01G297200 chr5D 84.783 230 22 9 1021 1238 280309740 280309512 7.520000e-53 219
36 TraesCS2B01G297200 chr5D 95.763 118 5 0 1287 1404 486173645 486173528 1.640000e-44 191
37 TraesCS2B01G297200 chr4A 96.581 117 4 0 1288 1404 660714289 660714405 1.270000e-45 195
38 TraesCS2B01G297200 chr3D 93.701 127 8 0 1281 1407 401179055 401178929 1.640000e-44 191
39 TraesCS2B01G297200 chr7B 93.023 129 7 2 1284 1410 115517982 115517854 2.120000e-43 187
40 TraesCS2B01G297200 chr7B 94.309 123 6 1 1285 1407 199754610 199754731 2.120000e-43 187
41 TraesCS2B01G297200 chr7B 96.154 104 3 1 3700 3803 749675077 749675179 7.680000e-38 169


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 TraesCS2B01G297200 chr2B 415988105 415992571 4466 False 8250.000000 8250 100.000000 1 4467 1 chr2B.!!$F2 4466
1 TraesCS2B01G297200 chr2B 53404407 53405171 764 False 1199.000000 1199 94.922000 3701 4467 1 chr2B.!!$F1 766
2 TraesCS2B01G297200 chr2D 349731791 349734707 2916 True 1178.500000 2686 96.077750 702 3656 4 chr2D.!!$R1 2954
3 TraesCS2B01G297200 chr2D 646079254 646080000 746 False 891.000000 891 88.120000 3701 4464 1 chr2D.!!$F3 763
4 TraesCS2B01G297200 chr2A 465554060 465556982 2922 True 1526.666667 2651 95.129333 703 3700 3 chr2A.!!$R3 2997
5 TraesCS2B01G297200 chr2A 773308246 773308996 750 True 854.000000 854 87.143000 3701 4467 1 chr2A.!!$R2 766
6 TraesCS2B01G297200 chr7A 717043735 717044427 692 False 1186.000000 1186 97.554000 1 694 1 chr7A.!!$F1 693
7 TraesCS2B01G297200 chr7A 733262259 733263023 764 True 1050.000000 1050 91.417000 3700 4467 1 chr7A.!!$R1 767
8 TraesCS2B01G297200 chr6B 687140592 687141286 694 False 1171.000000 1171 97.131000 1 694 1 chr6B.!!$F2 693
9 TraesCS2B01G297200 chr5B 37976866 37977624 758 True 1157.000000 1157 94.218000 3711 4467 1 chr5B.!!$R1 756
10 TraesCS2B01G297200 chrUn 61934431 61935126 695 False 1151.000000 1151 96.562000 1 695 1 chrUn.!!$F1 694
11 TraesCS2B01G297200 chrUn 379206554 379207249 695 False 1151.000000 1151 96.562000 1 695 1 chrUn.!!$F2 694
12 TraesCS2B01G297200 chrUn 410576338 410576965 627 True 1031.000000 1031 96.343000 69 695 1 chrUn.!!$R1 626
13 TraesCS2B01G297200 chrUn 393316529 393317038 509 False 854.000000 854 96.869000 186 695 1 chrUn.!!$F4 509
14 TraesCS2B01G297200 chr4B 223333776 223334462 686 True 1142.000000 1142 96.667000 1 687 1 chr4B.!!$R1 686
15 TraesCS2B01G297200 chr6A 601255175 601255941 766 True 1123.000000 1123 93.108000 3701 4467 1 chr6A.!!$R1 766
16 TraesCS2B01G297200 chr5A 640073009 640073622 613 True 1051.000000 1051 97.561000 71 684 1 chr5A.!!$R1 613
17 TraesCS2B01G297200 chr5A 686500865 686501379 514 False 375.500000 505 92.447500 3915 4464 2 chr5A.!!$F3 549
18 TraesCS2B01G297200 chr1B 633696306 633696922 616 False 1040.000000 1040 97.087000 71 687 1 chr1B.!!$F1 616

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
119 122 1.030457 GCTGGCTGCTGCTGATTTAT 58.970 50.000 15.64 0.0 39.59 1.40 F
219 222 1.207089 CGGCCCTCACAAGATAACTGA 59.793 52.381 0.00 0.0 0.00 3.41 F
1250 1319 2.028112 TCGTCAGTACCGTACACTACCT 60.028 50.000 11.26 0.0 0.00 3.08 F
1304 1373 2.599408 ACTACTCCCTCAGTTCGGAA 57.401 50.000 0.00 0.0 36.43 4.30 F
2455 2533 0.729690 GCTTCATCTTTGCCGTCCTC 59.270 55.000 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1462 1.637553 ACGGTAGAAGTACTCCCTCCA 59.362 52.381 0.00 0.0 0.00 3.86 R
1394 1463 2.433662 ACGGTAGAAGTACTCCCTCC 57.566 55.000 0.00 0.0 0.00 4.30 R
2429 2507 1.171308 GCAAAGATGAAGCCAGCTGA 58.829 50.000 17.39 0.0 38.21 4.26 R
3185 3295 1.238439 CATTCGGCACAAGGAACACT 58.762 50.000 0.00 0.0 0.00 3.55 R
4069 4180 0.396435 CTGGTTGTACCTGGCAGTGA 59.604 55.000 14.43 0.0 39.58 3.41 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
119 122 1.030457 GCTGGCTGCTGCTGATTTAT 58.970 50.000 15.64 0.00 39.59 1.40
219 222 1.207089 CGGCCCTCACAAGATAACTGA 59.793 52.381 0.00 0.00 0.00 3.41
554 557 3.237268 ACTACCATGGAGGCAAAAACA 57.763 42.857 21.47 0.00 43.14 2.83
695 700 7.806680 ATTAGGGAGAGATTAGGGAAAGATC 57.193 40.000 0.00 0.00 0.00 2.75
696 701 4.498493 AGGGAGAGATTAGGGAAAGATCC 58.502 47.826 0.00 0.00 45.77 3.36
794 800 3.066900 CAGGTTGTAGCGCTCAGTATACT 59.933 47.826 16.34 0.00 0.00 2.12
795 801 3.315749 AGGTTGTAGCGCTCAGTATACTC 59.684 47.826 16.34 3.19 0.00 2.59
853 861 3.117738 ACAGATATCCAGAAAGCCCCAAG 60.118 47.826 0.00 0.00 0.00 3.61
898 959 3.894947 GACGGCTCCTCCTCTCGC 61.895 72.222 0.00 0.00 0.00 5.03
951 1014 6.377327 TCAAAATTCACTTCGAAAAGCTCT 57.623 33.333 0.00 0.00 37.12 4.09
1250 1319 2.028112 TCGTCAGTACCGTACACTACCT 60.028 50.000 11.26 0.00 0.00 3.08
1289 1358 5.148651 ACCGGATGCCATCTAAATACTAC 57.851 43.478 9.46 0.00 0.00 2.73
1291 1360 5.047235 ACCGGATGCCATCTAAATACTACTC 60.047 44.000 9.46 0.00 0.00 2.59
1293 1362 5.624738 CGGATGCCATCTAAATACTACTCCC 60.625 48.000 4.41 0.00 0.00 4.30
1294 1363 5.485708 GGATGCCATCTAAATACTACTCCCT 59.514 44.000 4.41 0.00 0.00 4.20
1296 1365 5.464069 TGCCATCTAAATACTACTCCCTCA 58.536 41.667 0.00 0.00 0.00 3.86
1297 1366 5.540337 TGCCATCTAAATACTACTCCCTCAG 59.460 44.000 0.00 0.00 0.00 3.35
1298 1367 5.540719 GCCATCTAAATACTACTCCCTCAGT 59.459 44.000 0.00 0.00 39.41 3.41
1299 1368 6.042208 GCCATCTAAATACTACTCCCTCAGTT 59.958 42.308 0.00 0.00 36.43 3.16
1300 1369 7.662897 CCATCTAAATACTACTCCCTCAGTTC 58.337 42.308 0.00 0.00 36.43 3.01
1301 1370 6.939132 TCTAAATACTACTCCCTCAGTTCG 57.061 41.667 0.00 0.00 36.43 3.95
1302 1371 5.826737 TCTAAATACTACTCCCTCAGTTCGG 59.173 44.000 0.00 0.00 36.43 4.30
1303 1372 3.947612 ATACTACTCCCTCAGTTCGGA 57.052 47.619 0.00 0.00 36.43 4.55
1304 1373 2.599408 ACTACTCCCTCAGTTCGGAA 57.401 50.000 0.00 0.00 36.43 4.30
1305 1374 3.103080 ACTACTCCCTCAGTTCGGAAT 57.897 47.619 0.00 0.00 36.43 3.01
1306 1375 3.442076 ACTACTCCCTCAGTTCGGAATT 58.558 45.455 0.00 0.00 36.43 2.17
1307 1376 4.607239 ACTACTCCCTCAGTTCGGAATTA 58.393 43.478 0.00 0.00 36.43 1.40
1308 1377 3.889520 ACTCCCTCAGTTCGGAATTAC 57.110 47.619 0.00 0.00 26.56 1.89
1309 1378 3.442076 ACTCCCTCAGTTCGGAATTACT 58.558 45.455 0.00 0.00 26.56 2.24
1310 1379 4.607239 ACTCCCTCAGTTCGGAATTACTA 58.393 43.478 0.00 0.00 26.56 1.82
1311 1380 4.645588 ACTCCCTCAGTTCGGAATTACTAG 59.354 45.833 0.00 0.00 26.56 2.57
1312 1381 4.607239 TCCCTCAGTTCGGAATTACTAGT 58.393 43.478 0.00 0.00 0.00 2.57
1313 1382 4.643784 TCCCTCAGTTCGGAATTACTAGTC 59.356 45.833 0.00 0.00 0.00 2.59
1314 1383 4.645588 CCCTCAGTTCGGAATTACTAGTCT 59.354 45.833 0.00 0.00 0.00 3.24
1315 1384 5.826737 CCCTCAGTTCGGAATTACTAGTCTA 59.173 44.000 0.00 0.00 0.00 2.59
1316 1385 6.320672 CCCTCAGTTCGGAATTACTAGTCTAA 59.679 42.308 0.00 0.00 0.00 2.10
1317 1386 7.419204 CCTCAGTTCGGAATTACTAGTCTAAG 58.581 42.308 0.00 0.00 0.00 2.18
1318 1387 7.282675 CCTCAGTTCGGAATTACTAGTCTAAGA 59.717 40.741 0.00 0.00 0.00 2.10
1319 1388 8.571461 TCAGTTCGGAATTACTAGTCTAAGAA 57.429 34.615 0.00 0.00 0.00 2.52
1320 1389 9.017509 TCAGTTCGGAATTACTAGTCTAAGAAA 57.982 33.333 0.00 0.00 0.00 2.52
1321 1390 9.804758 CAGTTCGGAATTACTAGTCTAAGAAAT 57.195 33.333 0.00 0.00 0.00 2.17
1322 1391 9.804758 AGTTCGGAATTACTAGTCTAAGAAATG 57.195 33.333 0.00 0.00 0.00 2.32
1323 1392 9.798994 GTTCGGAATTACTAGTCTAAGAAATGA 57.201 33.333 0.00 0.00 0.00 2.57
1390 1459 7.922505 TTCATTTTTGTGACAAGTAATTCCG 57.077 32.000 0.00 0.00 0.00 4.30
1391 1460 7.265647 TCATTTTTGTGACAAGTAATTCCGA 57.734 32.000 0.00 0.00 0.00 4.55
1392 1461 7.708051 TCATTTTTGTGACAAGTAATTCCGAA 58.292 30.769 0.00 0.00 0.00 4.30
1393 1462 8.356657 TCATTTTTGTGACAAGTAATTCCGAAT 58.643 29.630 0.00 0.00 0.00 3.34
1394 1463 7.922505 TTTTTGTGACAAGTAATTCCGAATG 57.077 32.000 0.00 0.00 0.00 2.67
1395 1464 5.621197 TTGTGACAAGTAATTCCGAATGG 57.379 39.130 0.00 0.00 0.00 3.16
1396 1465 4.900684 TGTGACAAGTAATTCCGAATGGA 58.099 39.130 0.00 0.00 44.61 3.41
1550 1626 4.863152 TGTTGTGATCATTCATACGCTG 57.137 40.909 0.00 0.00 33.56 5.18
1551 1627 3.622612 TGTTGTGATCATTCATACGCTGG 59.377 43.478 0.00 0.00 33.56 4.85
1552 1628 3.817709 TGTGATCATTCATACGCTGGA 57.182 42.857 0.00 0.00 33.56 3.86
1553 1629 4.135747 TGTGATCATTCATACGCTGGAA 57.864 40.909 0.00 0.00 33.56 3.53
1554 1630 4.122046 TGTGATCATTCATACGCTGGAAG 58.878 43.478 0.00 0.00 33.56 3.46
1555 1631 3.059325 GTGATCATTCATACGCTGGAAGC 60.059 47.826 0.00 0.00 45.71 3.86
1556 1632 6.085808 GTGATCATTCATACGCTGGAAGCC 62.086 50.000 0.00 0.00 46.17 4.35
1608 1684 5.602978 AGAGTATTTGGTCACTCGGGATAAT 59.397 40.000 0.00 0.00 44.77 1.28
1609 1685 6.099845 AGAGTATTTGGTCACTCGGGATAATT 59.900 38.462 0.00 0.00 44.77 1.40
1700 1776 6.040504 CCCAACTTTAAAGTAAAGAGGCTTGT 59.959 38.462 20.83 0.00 46.19 3.16
1744 1820 8.648698 TTTCACTTCCCATCAGAAAAATATGA 57.351 30.769 0.00 0.00 0.00 2.15
1842 1918 7.537596 AAAACCAAATGAATCATGTAGTCCA 57.462 32.000 0.00 0.00 0.00 4.02
2069 2146 5.296813 ACTTTGCCTGATAATTCGTGTTC 57.703 39.130 0.00 0.00 0.00 3.18
2091 2168 4.567959 TCATACTTCACATTGATCAGCACG 59.432 41.667 0.00 0.00 0.00 5.34
2269 2347 4.293662 AGAGGAAGAAACTGATGAACCC 57.706 45.455 0.00 0.00 0.00 4.11
2270 2348 3.009584 AGAGGAAGAAACTGATGAACCCC 59.990 47.826 0.00 0.00 0.00 4.95
2407 2485 5.988310 TCATTGGTGAAAATCTGCATTCT 57.012 34.783 0.00 0.00 0.00 2.40
2429 2507 3.262420 GTGTTTAGCCAGTCGATGTCAT 58.738 45.455 0.00 0.00 0.00 3.06
2455 2533 0.729690 GCTTCATCTTTGCCGTCCTC 59.270 55.000 0.00 0.00 0.00 3.71
2704 2782 3.216800 GGCACTAGAATCATCAATGGCA 58.783 45.455 0.00 0.00 32.93 4.92
2728 2806 2.627699 ACGTAGAAAGTTCCGTTGGGTA 59.372 45.455 0.00 0.00 33.83 3.69
2746 2824 3.498777 GGGTACTTTCTCAAGCAGTTGTC 59.501 47.826 0.00 0.00 34.98 3.18
2789 2867 4.708576 TGTTTTGGAGTATGTGGGTACA 57.291 40.909 0.00 0.00 41.89 2.90
3049 3127 8.109705 AGTAAATTTCATTGCCGCATGATATA 57.890 30.769 0.00 0.00 0.00 0.86
3050 3128 8.239314 AGTAAATTTCATTGCCGCATGATATAG 58.761 33.333 0.00 0.00 0.00 1.31
3185 3295 0.979665 CTTCCAGAAGCTCTCCCACA 59.020 55.000 0.00 0.00 0.00 4.17
3194 3304 0.398318 GCTCTCCCACAGTGTTCCTT 59.602 55.000 0.00 0.00 0.00 3.36
3554 3664 2.773661 TGGAGAGAAATATCTGCTGCCA 59.226 45.455 0.00 0.00 38.39 4.92
3700 3811 4.032960 TGTGTTCATAGGAGGCAACATT 57.967 40.909 0.00 0.00 41.41 2.71
3701 3812 4.406456 TGTGTTCATAGGAGGCAACATTT 58.594 39.130 0.00 0.00 41.41 2.32
3702 3813 4.832266 TGTGTTCATAGGAGGCAACATTTT 59.168 37.500 0.00 0.00 41.41 1.82
3703 3814 5.304101 TGTGTTCATAGGAGGCAACATTTTT 59.696 36.000 0.00 0.00 41.41 1.94
3786 3897 2.118732 TACACACCCGGCCTCTGA 59.881 61.111 0.00 0.00 0.00 3.27
3803 3914 5.762218 GCCTCTGAATAACTAAGATGCACAT 59.238 40.000 0.00 0.00 33.40 3.21
3887 3998 6.264292 TGCAACAAAACATCAACTACTACCAT 59.736 34.615 0.00 0.00 0.00 3.55
3930 4041 4.460382 ACGACGAGAAGGTTATCCTAACAA 59.540 41.667 0.00 0.00 44.35 2.83
4046 4157 2.498167 CAGCTAAGCTCCAAACAGTGT 58.502 47.619 0.00 0.00 36.40 3.55
4069 4180 2.814835 AACAAGGGAGCGGAACCGT 61.815 57.895 14.63 1.93 42.09 4.83
4201 4312 4.326826 CAACTTGCCATAGAAGAAGTCCA 58.673 43.478 0.00 0.00 0.00 4.02
4299 4410 1.409064 TCTGAGAACACAGACAACGCT 59.591 47.619 0.00 0.00 41.21 5.07
4452 4568 1.968017 CGCACCACCACTGAGCATT 60.968 57.895 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.284489 ACTCAAAATTAAGCTACTGTTGTTCCA 59.716 33.333 0.00 0.00 0.00 3.53
85 88 1.269936 GCCAGCAGCACACAAATTCTT 60.270 47.619 0.00 0.00 42.97 2.52
119 122 7.069826 TGGTACATCTGATCAATCATCACAGTA 59.930 37.037 0.00 0.00 36.51 2.74
311 314 5.975988 AAGGTTGGTGGTATGATCTATGT 57.024 39.130 0.00 0.00 0.00 2.29
554 557 7.662604 CCGATGTGGTACTAACTTAAAGTTT 57.337 36.000 0.00 0.00 39.51 2.66
585 589 5.985526 ACGCTTTTACGATTATGTTTTGC 57.014 34.783 0.00 0.00 36.70 3.68
690 695 0.759346 ATTTAGCCTCGCCGGATCTT 59.241 50.000 5.05 0.00 30.90 2.40
695 700 1.595382 CCTGATTTAGCCTCGCCGG 60.595 63.158 0.00 0.00 0.00 6.13
696 701 2.247437 GCCTGATTTAGCCTCGCCG 61.247 63.158 0.00 0.00 0.00 6.46
697 702 1.894282 GGCCTGATTTAGCCTCGCC 60.894 63.158 0.00 0.00 46.14 5.54
698 703 3.737824 GGCCTGATTTAGCCTCGC 58.262 61.111 0.00 0.00 46.14 5.03
783 789 0.882474 ATCGGCCGAGTATACTGAGC 59.118 55.000 33.87 12.28 0.00 4.26
825 831 3.181475 GCTTTCTGGATATCTGTCGGACA 60.181 47.826 10.88 10.88 0.00 4.02
853 861 2.427753 GAGCGGGATGGGATCACC 59.572 66.667 0.00 0.00 40.81 4.02
898 959 2.436646 ATTTGGCGCACGAGGGAG 60.437 61.111 10.83 0.00 0.00 4.30
951 1014 1.202582 GCCGAGACAAGAGAAGTAGCA 59.797 52.381 0.00 0.00 0.00 3.49
1250 1319 2.099592 CCGGTAGTGTTAATGCGAGGTA 59.900 50.000 0.00 0.00 0.00 3.08
1289 1358 4.645588 ACTAGTAATTCCGAACTGAGGGAG 59.354 45.833 0.00 0.00 33.01 4.30
1291 1360 4.645588 AGACTAGTAATTCCGAACTGAGGG 59.354 45.833 0.00 0.00 0.00 4.30
1293 1362 8.211116 TCTTAGACTAGTAATTCCGAACTGAG 57.789 38.462 0.00 0.00 0.00 3.35
1294 1363 8.571461 TTCTTAGACTAGTAATTCCGAACTGA 57.429 34.615 0.00 0.00 0.00 3.41
1296 1365 9.804758 CATTTCTTAGACTAGTAATTCCGAACT 57.195 33.333 0.00 0.00 0.00 3.01
1297 1366 9.798994 TCATTTCTTAGACTAGTAATTCCGAAC 57.201 33.333 0.00 0.00 0.00 3.95
1364 1433 9.619316 CGGAATTACTTGTCACAAAAATGAATA 57.381 29.630 0.00 0.00 0.00 1.75
1365 1434 8.356657 TCGGAATTACTTGTCACAAAAATGAAT 58.643 29.630 0.00 0.00 0.00 2.57
1366 1435 7.708051 TCGGAATTACTTGTCACAAAAATGAA 58.292 30.769 0.00 0.00 0.00 2.57
1367 1436 7.265647 TCGGAATTACTTGTCACAAAAATGA 57.734 32.000 0.00 0.00 0.00 2.57
1368 1437 7.922505 TTCGGAATTACTTGTCACAAAAATG 57.077 32.000 0.00 0.00 0.00 2.32
1369 1438 7.598493 CCATTCGGAATTACTTGTCACAAAAAT 59.402 33.333 0.00 0.00 0.00 1.82
1370 1439 6.920758 CCATTCGGAATTACTTGTCACAAAAA 59.079 34.615 0.00 0.00 0.00 1.94
1371 1440 6.263392 TCCATTCGGAATTACTTGTCACAAAA 59.737 34.615 0.00 0.00 38.83 2.44
1372 1441 5.765677 TCCATTCGGAATTACTTGTCACAAA 59.234 36.000 0.00 0.00 38.83 2.83
1373 1442 5.309638 TCCATTCGGAATTACTTGTCACAA 58.690 37.500 0.00 0.00 38.83 3.33
1374 1443 4.900684 TCCATTCGGAATTACTTGTCACA 58.099 39.130 0.00 0.00 38.83 3.58
1375 1444 4.332819 CCTCCATTCGGAATTACTTGTCAC 59.667 45.833 0.00 0.00 42.21 3.67
1376 1445 4.513442 CCTCCATTCGGAATTACTTGTCA 58.487 43.478 0.00 0.00 42.21 3.58
1377 1446 3.877508 CCCTCCATTCGGAATTACTTGTC 59.122 47.826 0.00 0.00 42.21 3.18
1378 1447 3.521937 TCCCTCCATTCGGAATTACTTGT 59.478 43.478 0.00 0.00 42.21 3.16
1379 1448 4.130118 CTCCCTCCATTCGGAATTACTTG 58.870 47.826 0.00 0.00 42.21 3.16
1380 1449 3.780850 ACTCCCTCCATTCGGAATTACTT 59.219 43.478 0.00 0.00 42.21 2.24
1381 1450 3.385115 ACTCCCTCCATTCGGAATTACT 58.615 45.455 0.00 0.00 42.21 2.24
1382 1451 3.840124 ACTCCCTCCATTCGGAATTAC 57.160 47.619 0.00 0.00 42.21 1.89
1383 1452 4.553678 AGTACTCCCTCCATTCGGAATTA 58.446 43.478 0.00 0.00 42.21 1.40
1384 1453 3.385115 AGTACTCCCTCCATTCGGAATT 58.615 45.455 0.00 0.00 42.21 2.17
1385 1454 3.047695 AGTACTCCCTCCATTCGGAAT 57.952 47.619 0.00 0.00 42.21 3.01
1386 1455 2.544844 AGTACTCCCTCCATTCGGAA 57.455 50.000 0.00 0.00 42.21 4.30
1387 1456 2.024273 AGAAGTACTCCCTCCATTCGGA 60.024 50.000 0.00 0.00 39.79 4.55
1388 1457 2.389715 AGAAGTACTCCCTCCATTCGG 58.610 52.381 0.00 0.00 0.00 4.30
1389 1458 3.318557 GGTAGAAGTACTCCCTCCATTCG 59.681 52.174 0.00 0.00 0.00 3.34
1390 1459 3.318557 CGGTAGAAGTACTCCCTCCATTC 59.681 52.174 0.00 0.00 0.00 2.67
1391 1460 3.297736 CGGTAGAAGTACTCCCTCCATT 58.702 50.000 0.00 0.00 0.00 3.16
1392 1461 2.244252 ACGGTAGAAGTACTCCCTCCAT 59.756 50.000 0.00 0.00 0.00 3.41
1393 1462 1.637553 ACGGTAGAAGTACTCCCTCCA 59.362 52.381 0.00 0.00 0.00 3.86
1394 1463 2.433662 ACGGTAGAAGTACTCCCTCC 57.566 55.000 0.00 0.00 0.00 4.30
1395 1464 3.619419 AGAACGGTAGAAGTACTCCCTC 58.381 50.000 0.00 0.00 0.00 4.30
1396 1465 3.735720 AGAACGGTAGAAGTACTCCCT 57.264 47.619 0.00 0.00 0.00 4.20
1397 1466 3.311048 CGTAGAACGGTAGAAGTACTCCC 59.689 52.174 0.00 0.00 38.08 4.30
1398 1467 4.528531 CGTAGAACGGTAGAAGTACTCC 57.471 50.000 0.00 0.00 38.08 3.85
1469 1545 3.687212 TGTAAATACGGACACCATGCAAG 59.313 43.478 0.00 0.00 0.00 4.01
1550 1626 6.399743 GCTAATATAGTACTTCCAGGCTTCC 58.600 44.000 0.00 0.00 0.00 3.46
1551 1627 6.072064 TCGCTAATATAGTACTTCCAGGCTTC 60.072 42.308 0.00 0.00 0.00 3.86
1552 1628 5.773680 TCGCTAATATAGTACTTCCAGGCTT 59.226 40.000 0.00 0.00 0.00 4.35
1553 1629 5.183522 GTCGCTAATATAGTACTTCCAGGCT 59.816 44.000 0.00 0.00 0.00 4.58
1554 1630 5.048224 TGTCGCTAATATAGTACTTCCAGGC 60.048 44.000 0.00 0.00 0.00 4.85
1555 1631 6.349445 CCTGTCGCTAATATAGTACTTCCAGG 60.349 46.154 0.00 0.00 0.00 4.45
1556 1632 6.349445 CCCTGTCGCTAATATAGTACTTCCAG 60.349 46.154 0.00 0.00 0.00 3.86
1557 1633 5.475909 CCCTGTCGCTAATATAGTACTTCCA 59.524 44.000 0.00 0.00 0.00 3.53
1558 1634 5.476254 ACCCTGTCGCTAATATAGTACTTCC 59.524 44.000 0.00 0.00 0.00 3.46
1744 1820 9.799106 CTGTTATACTGGAGAAAAATATGGGAT 57.201 33.333 0.00 0.00 0.00 3.85
1754 1830 4.529377 ACCGTTCCTGTTATACTGGAGAAA 59.471 41.667 5.72 0.00 45.12 2.52
1755 1831 4.091549 ACCGTTCCTGTTATACTGGAGAA 58.908 43.478 5.72 0.00 45.12 2.87
1842 1918 3.327757 TGACACTATTCCTGGAGTGCTTT 59.672 43.478 12.89 0.00 45.76 3.51
2012 2089 5.779529 ATTCAACACACTGAAGAAGCAAT 57.220 34.783 0.00 0.00 38.66 3.56
2057 2134 9.161629 TCAATGTGAAGTATGAACACGAATTAT 57.838 29.630 0.00 0.00 37.35 1.28
2069 2146 4.784394 GCGTGCTGATCAATGTGAAGTATG 60.784 45.833 0.00 0.00 0.00 2.39
2115 2193 3.260632 AGATGTGGCACAGTACATACACA 59.739 43.478 26.04 9.98 41.80 3.72
2165 2243 8.816144 CAGCTAAAAAGTTGTTGCTATCAAAAA 58.184 29.630 0.00 0.00 33.37 1.94
2407 2485 2.036604 TGACATCGACTGGCTAAACACA 59.963 45.455 0.00 0.00 32.21 3.72
2429 2507 1.171308 GCAAAGATGAAGCCAGCTGA 58.829 50.000 17.39 0.00 38.21 4.26
2471 2549 4.451900 AGTGAAAGAATGAAGGACAACGT 58.548 39.130 0.00 0.00 0.00 3.99
2704 2782 3.387397 CCAACGGAACTTTCTACGTTCT 58.613 45.455 0.00 0.00 46.35 3.01
2728 2806 2.213499 CCGACAACTGCTTGAGAAAGT 58.787 47.619 0.00 0.00 0.00 2.66
2746 2824 2.871633 TGCATACACAACTATGATGCCG 59.128 45.455 2.96 0.00 41.76 5.69
2841 2919 1.531423 AACAGCAGCAGATGACCAAG 58.469 50.000 0.00 0.00 34.60 3.61
2938 3016 5.192923 ACCAATTATCAAGTACTGGGGCTAA 59.807 40.000 0.00 0.00 0.00 3.09
3024 3102 4.717233 TCATGCGGCAATGAAATTTACT 57.283 36.364 6.82 0.00 31.22 2.24
3031 3109 5.308014 ACTTCTATATCATGCGGCAATGAA 58.692 37.500 6.82 3.54 39.90 2.57
3033 3111 5.179929 TGAACTTCTATATCATGCGGCAATG 59.820 40.000 6.82 6.42 0.00 2.82
3185 3295 1.238439 CATTCGGCACAAGGAACACT 58.762 50.000 0.00 0.00 0.00 3.55
3520 3630 1.074084 TCTCTCCAGACACGTCTTCCT 59.926 52.381 0.00 0.00 37.98 3.36
3554 3664 6.551975 TCTCAATTTGATGCATGTTATCCCAT 59.448 34.615 2.46 0.00 0.00 4.00
3674 3785 5.304101 TGTTGCCTCCTATGAACACATTTTT 59.696 36.000 0.00 0.00 0.00 1.94
3701 3812 5.993748 AAGAATGCCCTTTATCGGAAAAA 57.006 34.783 0.00 0.00 0.00 1.94
3702 3813 5.993748 AAAGAATGCCCTTTATCGGAAAA 57.006 34.783 0.00 0.00 34.85 2.29
3703 3814 7.340743 TCAATAAAGAATGCCCTTTATCGGAAA 59.659 33.333 12.97 0.00 44.24 3.13
3704 3815 6.831353 TCAATAAAGAATGCCCTTTATCGGAA 59.169 34.615 12.97 2.28 44.24 4.30
3705 3816 6.262273 GTCAATAAAGAATGCCCTTTATCGGA 59.738 38.462 12.97 11.47 44.24 4.55
3706 3817 6.263168 AGTCAATAAAGAATGCCCTTTATCGG 59.737 38.462 12.97 10.08 44.24 4.18
3786 3897 7.880160 TTTGGCTATGTGCATCTTAGTTATT 57.120 32.000 0.00 0.00 45.15 1.40
3887 3998 1.459455 CCGGGTGTTGCCAATGACAA 61.459 55.000 0.00 0.00 39.65 3.18
3930 4041 2.030562 CCTTGTGGAAGGCGTCGT 59.969 61.111 0.00 0.00 42.60 4.34
4046 4157 0.762418 TTCCGCTCCCTTGTTGAAGA 59.238 50.000 0.00 0.00 0.00 2.87
4069 4180 0.396435 CTGGTTGTACCTGGCAGTGA 59.604 55.000 14.43 0.00 39.58 3.41
4201 4312 2.159000 TGCTGATCGAGACATTGCATCT 60.159 45.455 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.