Multiple sequence alignment - TraesCS7D01G168800

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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 TraesCS7D01G168800 chr7D 100.000 2411 0 0 1 2411 119650189 119647779 0.000000e+00 4453
1 TraesCS7D01G168800 chr7D 94.417 824 39 6 1594 2411 73099390 73098568 0.000000e+00 1260
2 TraesCS7D01G168800 chr3A 93.871 1452 79 8 1 1444 474675341 474676790 0.000000e+00 2180
3 TraesCS7D01G168800 chr3A 93.715 1448 81 8 1 1440 8667711 8669156 0.000000e+00 2161
4 TraesCS7D01G168800 chr3A 95.181 166 6 2 1430 1593 524819012 524818847 6.610000e-66 261
5 TraesCS7D01G168800 chr2A 93.595 1452 82 9 1 1444 96144894 96143446 0.000000e+00 2156
6 TraesCS7D01G168800 chr7B 93.301 1448 84 9 1 1440 608190404 608191846 0.000000e+00 2124
7 TraesCS7D01G168800 chr6B 93.025 1448 83 10 1 1440 694415420 694413983 0.000000e+00 2098
8 TraesCS7D01G168800 chr3D 94.182 825 40 8 1592 2411 338074187 338075008 0.000000e+00 1251
9 TraesCS7D01G168800 chr3D 94.061 825 42 6 1592 2411 244280115 244280937 0.000000e+00 1245
10 TraesCS7D01G168800 chr3D 94.053 824 44 4 1592 2411 576524248 576523426 0.000000e+00 1245
11 TraesCS7D01G168800 chr3D 95.181 166 6 2 1430 1593 107359741 107359576 6.610000e-66 261
12 TraesCS7D01G168800 chr5D 94.082 828 39 7 1589 2411 278402690 278403512 0.000000e+00 1249
13 TraesCS7D01G168800 chr5D 93.826 826 41 7 1592 2411 291043566 291042745 0.000000e+00 1234
14 TraesCS7D01G168800 chr5D 82.385 369 45 16 1430 1784 93875532 93875894 1.080000e-78 303
15 TraesCS7D01G168800 chr4D 93.939 825 44 6 1592 2411 394331698 394332521 0.000000e+00 1242
16 TraesCS7D01G168800 chr4D 93.932 824 41 9 1594 2411 56012363 56013183 0.000000e+00 1236
17 TraesCS7D01G168800 chr4D 95.181 166 6 2 1430 1593 320339599 320339764 6.610000e-66 261
18 TraesCS7D01G168800 chr2D 93.818 825 45 5 1592 2411 561011507 561012330 0.000000e+00 1236
19 TraesCS7D01G168800 chr1A 84.967 1051 127 15 143 1187 346751926 346750901 0.000000e+00 1037
20 TraesCS7D01G168800 chr1A 95.181 166 6 2 1430 1593 395874119 395873954 6.610000e-66 261
21 TraesCS7D01G168800 chr6D 95.783 166 5 2 1430 1593 88087772 88087607 1.420000e-67 267
22 TraesCS7D01G168800 chr1D 95.783 166 5 2 1430 1593 73929687 73929852 1.420000e-67 267
23 TraesCS7D01G168800 chr1D 95.181 166 6 2 1430 1593 330813109 330813274 6.610000e-66 261
24 TraesCS7D01G168800 chr2B 90.625 192 11 6 1430 1615 18859712 18859522 5.150000e-62 248


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 TraesCS7D01G168800 chr7D 119647779 119650189 2410 True 4453 4453 100.000 1 2411 1 chr7D.!!$R2 2410
1 TraesCS7D01G168800 chr7D 73098568 73099390 822 True 1260 1260 94.417 1594 2411 1 chr7D.!!$R1 817
2 TraesCS7D01G168800 chr3A 474675341 474676790 1449 False 2180 2180 93.871 1 1444 1 chr3A.!!$F2 1443
3 TraesCS7D01G168800 chr3A 8667711 8669156 1445 False 2161 2161 93.715 1 1440 1 chr3A.!!$F1 1439
4 TraesCS7D01G168800 chr2A 96143446 96144894 1448 True 2156 2156 93.595 1 1444 1 chr2A.!!$R1 1443
5 TraesCS7D01G168800 chr7B 608190404 608191846 1442 False 2124 2124 93.301 1 1440 1 chr7B.!!$F1 1439
6 TraesCS7D01G168800 chr6B 694413983 694415420 1437 True 2098 2098 93.025 1 1440 1 chr6B.!!$R1 1439
7 TraesCS7D01G168800 chr3D 338074187 338075008 821 False 1251 1251 94.182 1592 2411 1 chr3D.!!$F2 819
8 TraesCS7D01G168800 chr3D 244280115 244280937 822 False 1245 1245 94.061 1592 2411 1 chr3D.!!$F1 819
9 TraesCS7D01G168800 chr3D 576523426 576524248 822 True 1245 1245 94.053 1592 2411 1 chr3D.!!$R2 819
10 TraesCS7D01G168800 chr5D 278402690 278403512 822 False 1249 1249 94.082 1589 2411 1 chr5D.!!$F2 822
11 TraesCS7D01G168800 chr5D 291042745 291043566 821 True 1234 1234 93.826 1592 2411 1 chr5D.!!$R1 819
12 TraesCS7D01G168800 chr4D 394331698 394332521 823 False 1242 1242 93.939 1592 2411 1 chr4D.!!$F3 819
13 TraesCS7D01G168800 chr4D 56012363 56013183 820 False 1236 1236 93.932 1594 2411 1 chr4D.!!$F1 817
14 TraesCS7D01G168800 chr2D 561011507 561012330 823 False 1236 1236 93.818 1592 2411 1 chr2D.!!$F1 819
15 TraesCS7D01G168800 chr1A 346750901 346751926 1025 True 1037 1037 84.967 143 1187 1 chr1A.!!$R1 1044

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
420 424 0.187606 GTGGAAAGGACCAGGGGTTT 59.812 55.0 0.0 0.0 40.85 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1493 0.034337 TCTTTTTAGAGCACGGCGGT 59.966 50.0 13.24 0.0 0.0 5.68 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
57 58 1.344763 CGGAGCCTACTATTTGGGAGG 59.655 57.143 0.00 0.00 0.00 4.30
76 77 3.193782 AGGGAGCTAATTCAGAAAGGGT 58.806 45.455 0.00 0.00 0.00 4.34
80 81 5.010282 GGAGCTAATTCAGAAAGGGTTTCA 58.990 41.667 2.44 0.00 42.10 2.69
118 119 2.106166 GGAGCCAGGATCAAGATCATGT 59.894 50.000 19.50 5.91 45.20 3.21
137 139 1.829222 GTTAGACACTGGATTCCGGGA 59.171 52.381 15.99 0.00 33.40 5.14
160 162 1.202927 CCCCTCTGGAACTTTCAGCAA 60.203 52.381 0.00 0.00 35.39 3.91
189 191 6.723052 ACTCCCTTTAACTGCTACTACTACAA 59.277 38.462 0.00 0.00 0.00 2.41
233 235 2.125106 GTGGCGTGGGATGAGGAC 60.125 66.667 0.00 0.00 0.00 3.85
257 259 2.285950 CGTGCGAAGTTTCTTTTCGGAA 60.286 45.455 9.10 0.00 46.99 4.30
260 262 2.286772 GCGAAGTTTCTTTTCGGAAGCA 60.287 45.455 9.10 0.00 45.50 3.91
293 295 0.976641 TCTTGCAAGTCCCGATCAGT 59.023 50.000 25.19 0.00 0.00 3.41
375 379 6.044754 TCAAATCTGGGTATAATCTGGCTCAT 59.955 38.462 0.00 0.00 0.00 2.90
420 424 0.187606 GTGGAAAGGACCAGGGGTTT 59.812 55.000 0.00 0.00 40.85 3.27
432 436 0.264657 AGGGGTTTGCTTCCAACCTT 59.735 50.000 2.01 0.00 0.00 3.50
499 503 8.688747 TTGCCCAAATAAAATGAAGATTGTTT 57.311 26.923 0.00 0.00 0.00 2.83
510 514 0.317770 AGATTGTTTTGTGGCGCGTG 60.318 50.000 8.43 0.00 0.00 5.34
596 602 2.325583 TTTCTGCAACCGAACTGAGT 57.674 45.000 0.00 0.00 0.00 3.41
647 653 1.538047 TGCTTGTTCAATCTGGAGCC 58.462 50.000 0.00 0.00 0.00 4.70
687 693 1.002087 ACTCCGGCTGTGTAGAAAAGG 59.998 52.381 0.00 0.00 0.00 3.11
694 700 3.307480 GGCTGTGTAGAAAAGGCCTTCTA 60.307 47.826 20.79 14.47 36.95 2.10
700 706 5.416013 GTGTAGAAAAGGCCTTCTAAATGCT 59.584 40.000 20.79 9.30 39.13 3.79
728 734 2.158475 TGGCTGTTTGATTTCCTCACCT 60.158 45.455 0.00 0.00 32.17 4.00
785 791 0.890683 CCTTTGGCACATCTGGGAAC 59.109 55.000 0.00 0.00 39.30 3.62
887 894 5.464057 TGGTGAGACAACACTACATAAAACG 59.536 40.000 0.00 0.00 40.22 3.60
889 896 6.642131 GGTGAGACAACACTACATAAAACGTA 59.358 38.462 0.00 0.00 40.22 3.57
893 900 5.299148 ACAACACTACATAAAACGTAGGCA 58.701 37.500 0.00 0.00 40.58 4.75
905 912 0.461870 CGTAGGCATGTTGCTAGGCA 60.462 55.000 0.00 0.00 44.28 4.75
912 919 2.635714 CATGTTGCTAGGCATGAGTCA 58.364 47.619 0.00 0.00 43.60 3.41
920 927 3.808726 GCTAGGCATGAGTCATCTTCTTG 59.191 47.826 1.56 3.79 0.00 3.02
1065 1072 2.420372 TGTTGCTTGCAACGAAGTGTTA 59.580 40.909 26.49 9.58 45.00 2.41
1067 1074 2.010497 TGCTTGCAACGAAGTGTTACA 58.990 42.857 0.00 0.00 45.00 2.41
1078 1085 7.571613 GCAACGAAGTGTTACATGGTATTACAA 60.572 37.037 0.00 0.00 45.00 2.41
1123 1130 1.662876 CCATTCGGCACACTTTGAACG 60.663 52.381 0.00 0.00 0.00 3.95
1167 1174 5.506686 TGCATATCAGTCTAGTGTCAGAC 57.493 43.478 0.00 0.00 44.44 3.51
1190 1197 3.526534 GCCTCTCTATGGTGAACAAGAC 58.473 50.000 0.00 0.00 0.00 3.01
1199 1206 1.416401 GGTGAACAAGACCAGGTCTCA 59.584 52.381 23.17 13.49 42.59 3.27
1218 1225 1.590238 CATGTCCAAGATCGTTCGAGC 59.410 52.381 2.17 2.17 0.00 5.03
1224 1231 1.874345 AAGATCGTTCGAGCGTGGGT 61.874 55.000 21.11 6.46 0.00 4.51
1226 1233 2.537792 GATCGTTCGAGCGTGGGTGA 62.538 60.000 21.11 0.99 0.00 4.02
1249 1256 3.654414 GTTGTCTCCGACATCAAGTCTT 58.346 45.455 0.00 0.00 45.32 3.01
1278 1288 7.228108 GCTGTTAGTTTTACCCACTCTACTTTT 59.772 37.037 0.00 0.00 0.00 2.27
1318 1328 4.199310 ACTGAATGTAGCGGCACATAAAT 58.801 39.130 15.11 4.11 38.19 1.40
1459 1469 7.430992 AAAAATAAGTGAAGTACGGGAGTTC 57.569 36.000 0.56 0.56 43.33 3.01
1460 1470 5.733620 AATAAGTGAAGTACGGGAGTTCA 57.266 39.130 6.38 6.38 43.83 3.18
1461 1471 5.934402 ATAAGTGAAGTACGGGAGTTCAT 57.066 39.130 13.38 1.85 46.73 2.57
1462 1472 3.870633 AGTGAAGTACGGGAGTTCATC 57.129 47.619 13.38 7.74 46.73 2.92
1463 1473 3.162666 AGTGAAGTACGGGAGTTCATCA 58.837 45.455 13.38 0.00 46.73 3.07
1464 1474 3.576982 AGTGAAGTACGGGAGTTCATCAA 59.423 43.478 13.38 0.00 46.73 2.57
1465 1475 4.223032 AGTGAAGTACGGGAGTTCATCAAT 59.777 41.667 13.38 0.00 46.73 2.57
1466 1476 4.935808 GTGAAGTACGGGAGTTCATCAATT 59.064 41.667 13.38 0.00 46.73 2.32
1467 1477 5.411669 GTGAAGTACGGGAGTTCATCAATTT 59.588 40.000 13.38 0.00 46.73 1.82
1468 1478 5.642063 TGAAGTACGGGAGTTCATCAATTTC 59.358 40.000 6.38 0.00 41.66 2.17
1469 1479 5.422214 AGTACGGGAGTTCATCAATTTCT 57.578 39.130 0.00 0.00 43.33 2.52
1470 1480 6.540438 AGTACGGGAGTTCATCAATTTCTA 57.460 37.500 0.00 0.00 43.33 2.10
1471 1481 7.125792 AGTACGGGAGTTCATCAATTTCTAT 57.874 36.000 0.00 0.00 43.33 1.98
1472 1482 8.246430 AGTACGGGAGTTCATCAATTTCTATA 57.754 34.615 0.00 0.00 43.33 1.31
1473 1483 8.701895 AGTACGGGAGTTCATCAATTTCTATAA 58.298 33.333 0.00 0.00 43.33 0.98
1474 1484 9.321562 GTACGGGAGTTCATCAATTTCTATAAA 57.678 33.333 0.00 0.00 43.33 1.40
1475 1485 8.801882 ACGGGAGTTCATCAATTTCTATAAAA 57.198 30.769 0.00 0.00 43.33 1.52
1476 1486 9.408648 ACGGGAGTTCATCAATTTCTATAAAAT 57.591 29.630 0.00 0.00 43.33 1.82
1487 1497 9.575783 TCAATTTCTATAAAATAAAACCACCGC 57.424 29.630 0.00 0.00 0.00 5.68
1488 1498 8.813282 CAATTTCTATAAAATAAAACCACCGCC 58.187 33.333 0.00 0.00 0.00 6.13
1489 1499 5.738118 TCTATAAAATAAAACCACCGCCG 57.262 39.130 0.00 0.00 0.00 6.46
1490 1500 5.184711 TCTATAAAATAAAACCACCGCCGT 58.815 37.500 0.00 0.00 0.00 5.68
1491 1501 2.425578 AAAATAAAACCACCGCCGTG 57.574 45.000 0.00 0.00 39.91 4.94
1492 1502 0.038983 AAATAAAACCACCGCCGTGC 60.039 50.000 0.00 0.00 38.79 5.34
1493 1503 0.891904 AATAAAACCACCGCCGTGCT 60.892 50.000 0.00 0.00 38.79 4.40
1494 1504 1.303091 ATAAAACCACCGCCGTGCTC 61.303 55.000 0.00 0.00 38.79 4.26
1495 1505 2.386064 TAAAACCACCGCCGTGCTCT 62.386 55.000 0.00 0.00 38.79 4.09
1496 1506 2.386064 AAAACCACCGCCGTGCTCTA 62.386 55.000 0.00 0.00 38.79 2.43
1497 1507 2.386064 AAACCACCGCCGTGCTCTAA 62.386 55.000 0.00 0.00 38.79 2.10
1498 1508 2.047655 CCACCGCCGTGCTCTAAA 60.048 61.111 0.00 0.00 38.79 1.85
1499 1509 1.669760 CCACCGCCGTGCTCTAAAA 60.670 57.895 0.00 0.00 38.79 1.52
1500 1510 1.231958 CCACCGCCGTGCTCTAAAAA 61.232 55.000 0.00 0.00 38.79 1.94
1501 1511 0.165944 CACCGCCGTGCTCTAAAAAG 59.834 55.000 0.00 0.00 32.04 2.27
1502 1512 0.034337 ACCGCCGTGCTCTAAAAAGA 59.966 50.000 0.00 0.00 0.00 2.52
1503 1513 1.338769 ACCGCCGTGCTCTAAAAAGAT 60.339 47.619 0.00 0.00 0.00 2.40
1504 1514 2.093869 ACCGCCGTGCTCTAAAAAGATA 60.094 45.455 0.00 0.00 0.00 1.98
1505 1515 3.131396 CCGCCGTGCTCTAAAAAGATAT 58.869 45.455 0.00 0.00 0.00 1.63
1506 1516 4.202182 ACCGCCGTGCTCTAAAAAGATATA 60.202 41.667 0.00 0.00 0.00 0.86
1507 1517 4.748102 CCGCCGTGCTCTAAAAAGATATAA 59.252 41.667 0.00 0.00 0.00 0.98
1508 1518 5.107453 CCGCCGTGCTCTAAAAAGATATAAG 60.107 44.000 0.00 0.00 0.00 1.73
1509 1519 5.462398 CGCCGTGCTCTAAAAAGATATAAGT 59.538 40.000 0.00 0.00 0.00 2.24
1510 1520 6.562270 CGCCGTGCTCTAAAAAGATATAAGTG 60.562 42.308 0.00 0.00 0.00 3.16
1511 1521 6.479001 GCCGTGCTCTAAAAAGATATAAGTGA 59.521 38.462 0.00 0.00 0.00 3.41
1512 1522 7.011109 GCCGTGCTCTAAAAAGATATAAGTGAA 59.989 37.037 0.00 0.00 0.00 3.18
1513 1523 9.046296 CCGTGCTCTAAAAAGATATAAGTGAAT 57.954 33.333 0.00 0.00 0.00 2.57
1546 1556 7.035840 CAATATTGCCTAGCTCAAAAGATGT 57.964 36.000 1.74 0.00 0.00 3.06
1547 1557 8.158169 CAATATTGCCTAGCTCAAAAGATGTA 57.842 34.615 1.74 0.00 0.00 2.29
1548 1558 8.623903 CAATATTGCCTAGCTCAAAAGATGTAA 58.376 33.333 1.74 0.00 0.00 2.41
1549 1559 6.690194 ATTGCCTAGCTCAAAAGATGTAAG 57.310 37.500 0.00 0.00 0.00 2.34
1550 1560 5.165961 TGCCTAGCTCAAAAGATGTAAGT 57.834 39.130 0.00 0.00 0.00 2.24
1551 1561 4.937620 TGCCTAGCTCAAAAGATGTAAGTG 59.062 41.667 0.00 0.00 0.00 3.16
1552 1562 5.178797 GCCTAGCTCAAAAGATGTAAGTGA 58.821 41.667 0.00 0.00 0.00 3.41
1553 1563 5.643777 GCCTAGCTCAAAAGATGTAAGTGAA 59.356 40.000 0.00 0.00 0.00 3.18
1554 1564 6.183360 GCCTAGCTCAAAAGATGTAAGTGAAG 60.183 42.308 0.00 0.00 0.00 3.02
1555 1565 5.619625 AGCTCAAAAGATGTAAGTGAAGC 57.380 39.130 0.00 0.00 0.00 3.86
1556 1566 5.065914 AGCTCAAAAGATGTAAGTGAAGCA 58.934 37.500 0.00 0.00 0.00 3.91
1557 1567 5.049129 AGCTCAAAAGATGTAAGTGAAGCAC 60.049 40.000 0.00 0.00 34.10 4.40
1558 1568 5.277974 GCTCAAAAGATGTAAGTGAAGCACA 60.278 40.000 0.00 0.00 36.74 4.57
1559 1569 6.569226 GCTCAAAAGATGTAAGTGAAGCACAT 60.569 38.462 0.00 0.00 36.74 3.21
1560 1570 7.361201 GCTCAAAAGATGTAAGTGAAGCACATA 60.361 37.037 0.00 0.00 36.74 2.29
1561 1571 8.032952 TCAAAAGATGTAAGTGAAGCACATAG 57.967 34.615 0.00 0.00 36.74 2.23
1562 1572 7.877612 TCAAAAGATGTAAGTGAAGCACATAGA 59.122 33.333 0.00 0.00 36.74 1.98
1563 1573 7.840342 AAAGATGTAAGTGAAGCACATAGAG 57.160 36.000 0.00 0.00 36.74 2.43
1564 1574 6.537453 AGATGTAAGTGAAGCACATAGAGT 57.463 37.500 0.00 0.00 36.74 3.24
1565 1575 7.646548 AGATGTAAGTGAAGCACATAGAGTA 57.353 36.000 0.00 0.00 36.74 2.59
1566 1576 8.243961 AGATGTAAGTGAAGCACATAGAGTAT 57.756 34.615 0.00 0.00 36.74 2.12
1567 1577 8.700051 AGATGTAAGTGAAGCACATAGAGTATT 58.300 33.333 0.00 0.00 36.74 1.89
1568 1578 8.879342 ATGTAAGTGAAGCACATAGAGTATTC 57.121 34.615 0.00 0.00 36.74 1.75
1569 1579 8.067751 TGTAAGTGAAGCACATAGAGTATTCT 57.932 34.615 0.00 0.00 36.74 2.40
1570 1580 9.185680 TGTAAGTGAAGCACATAGAGTATTCTA 57.814 33.333 0.00 0.00 36.74 2.10
1589 1599 9.546909 GTATTCTAATAAATCACCATTCATGCG 57.453 33.333 0.00 0.00 0.00 4.73
1590 1600 7.566760 TTCTAATAAATCACCATTCATGCGT 57.433 32.000 0.00 0.00 0.00 5.24
1620 1630 5.928601 CGTCTCCAACGTATCTACTTTTC 57.071 43.478 0.00 0.00 46.42 2.29
1623 1633 6.183360 CGTCTCCAACGTATCTACTTTTCCTA 60.183 42.308 0.00 0.00 46.42 2.94
1638 1648 6.293698 ACTTTTCCTAACGCTTTTCCTCTTA 58.706 36.000 0.00 0.00 0.00 2.10
1725 1735 6.603997 AGAACTACCATGGTGTTGTTTTTGTA 59.396 34.615 28.17 1.17 34.98 2.41
1819 1831 2.297129 AAGACCTGCTGGAGAGGGC 61.297 63.158 17.64 0.00 39.20 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 4.726825 TGAATTAGCTCCCTCCCAAATAGT 59.273 41.667 0.00 0.00 0.00 2.12
48 49 3.788142 TCTGAATTAGCTCCCTCCCAAAT 59.212 43.478 0.00 0.00 0.00 2.32
57 58 5.010282 TGAAACCCTTTCTGAATTAGCTCC 58.990 41.667 0.00 0.00 40.32 4.70
76 77 0.468214 TTGCCGACACCCCATTGAAA 60.468 50.000 0.00 0.00 0.00 2.69
80 81 1.682005 CCATTGCCGACACCCCATT 60.682 57.895 0.00 0.00 0.00 3.16
118 119 2.241281 TCCCGGAATCCAGTGTCTAA 57.759 50.000 0.73 0.00 0.00 2.10
160 162 5.306114 AGTAGCAGTTAAAGGGAGTTTGT 57.694 39.130 0.00 0.00 0.00 2.83
189 191 4.141914 GGAGTCCGTCATAAGGAACTGAAT 60.142 45.833 0.00 0.00 40.86 2.57
233 235 2.372350 GAAAAGAAACTTCGCACGGTG 58.628 47.619 3.15 3.15 0.00 4.94
293 295 1.866015 AATCCTCTCCACCATGTCGA 58.134 50.000 0.00 0.00 0.00 4.20
317 319 4.119862 GCCGAGCTTATGTGACAAGATAA 58.880 43.478 0.00 0.00 0.00 1.75
319 321 2.093500 TGCCGAGCTTATGTGACAAGAT 60.093 45.455 0.00 0.00 0.00 2.40
321 323 1.725641 TGCCGAGCTTATGTGACAAG 58.274 50.000 0.00 0.00 0.00 3.16
322 324 2.093500 AGATGCCGAGCTTATGTGACAA 60.093 45.455 0.00 0.00 0.00 3.18
323 325 1.482182 AGATGCCGAGCTTATGTGACA 59.518 47.619 0.00 0.00 0.00 3.58
324 326 2.231215 AGATGCCGAGCTTATGTGAC 57.769 50.000 0.00 0.00 0.00 3.67
325 327 2.168313 TGAAGATGCCGAGCTTATGTGA 59.832 45.455 0.00 0.00 0.00 3.58
326 328 2.286294 GTGAAGATGCCGAGCTTATGTG 59.714 50.000 0.00 0.00 0.00 3.21
327 329 2.555199 GTGAAGATGCCGAGCTTATGT 58.445 47.619 0.00 0.00 0.00 2.29
432 436 4.269183 TCCAGTTTTTCTCTTGCAACTGA 58.731 39.130 11.53 2.97 46.08 3.41
510 514 2.548067 CCGGTAGGTAGACAATCATGCC 60.548 54.545 0.00 0.00 0.00 4.40
647 653 5.969435 GGAGTCCAAAACTTTCTTTAACACG 59.031 40.000 3.60 0.00 38.74 4.49
687 693 3.242870 CCATTGACGAGCATTTAGAAGGC 60.243 47.826 0.00 0.00 38.73 4.35
694 700 1.538047 ACAGCCATTGACGAGCATTT 58.462 45.000 0.00 0.00 0.00 2.32
700 706 3.057596 GGAAATCAAACAGCCATTGACGA 60.058 43.478 0.00 0.00 39.43 4.20
728 734 1.466856 GCATGAAGCTGGGATTCACA 58.533 50.000 0.00 0.00 39.36 3.58
785 791 6.074302 CCATTGTTACGAGTATCATTCTTCGG 60.074 42.308 0.00 0.00 33.17 4.30
789 795 9.832445 AAATACCATTGTTACGAGTATCATTCT 57.168 29.630 0.00 0.00 33.17 2.40
887 894 1.605710 CATGCCTAGCAACATGCCTAC 59.394 52.381 0.00 0.00 46.52 3.18
889 896 0.256752 TCATGCCTAGCAACATGCCT 59.743 50.000 11.66 0.00 46.52 4.75
893 900 3.136077 AGATGACTCATGCCTAGCAACAT 59.864 43.478 0.00 0.00 43.62 2.71
905 912 5.394005 CGGAGAGTTCAAGAAGATGACTCAT 60.394 44.000 4.83 0.00 33.60 2.90
912 919 2.234908 CCACCGGAGAGTTCAAGAAGAT 59.765 50.000 9.46 0.00 0.00 2.40
920 927 1.891616 GGAGTCCACCGGAGAGTTC 59.108 63.158 9.46 2.04 29.39 3.01
961 968 1.067706 CAAGGCGGCATCAACATTGAA 60.068 47.619 13.08 0.00 41.13 2.69
1065 1072 5.570320 AGCTCTGGTTTTGTAATACCATGT 58.430 37.500 7.27 0.00 43.15 3.21
1067 1074 5.105756 GCAAGCTCTGGTTTTGTAATACCAT 60.106 40.000 7.27 0.00 43.15 3.55
1078 1085 0.892814 GCCTCAGCAAGCTCTGGTTT 60.893 55.000 2.82 0.00 39.53 3.27
1114 1121 0.663153 GCTTGGCAGACGTTCAAAGT 59.337 50.000 0.00 0.00 0.00 2.66
1167 1174 0.824109 TGTTCACCATAGAGAGGCCG 59.176 55.000 0.00 0.00 0.00 6.13
1168 1175 2.501723 TCTTGTTCACCATAGAGAGGCC 59.498 50.000 0.00 0.00 0.00 5.19
1190 1197 2.482664 CGATCTTGGACATGAGACCTGG 60.483 54.545 0.00 0.00 0.00 4.45
1199 1206 1.799181 CGCTCGAACGATCTTGGACAT 60.799 52.381 1.02 0.00 34.06 3.06
1249 1256 4.139038 GAGTGGGTAAAACTAACAGCCAA 58.861 43.478 0.00 0.00 41.21 4.52
1278 1288 1.202639 AGTCCACGCTTGACATGTGAA 60.203 47.619 1.15 0.00 35.66 3.18
1394 1404 9.771534 ACTTCATAGATTAAGGAACATTAGAGC 57.228 33.333 0.00 0.00 0.00 4.09
1440 1450 4.768448 TGATGAACTCCCGTACTTCACTTA 59.232 41.667 0.00 0.00 0.00 2.24
1444 1454 4.819105 ATTGATGAACTCCCGTACTTCA 57.181 40.909 0.00 0.00 0.00 3.02
1445 1455 5.875359 AGAAATTGATGAACTCCCGTACTTC 59.125 40.000 0.00 0.00 0.00 3.01
1446 1456 5.805728 AGAAATTGATGAACTCCCGTACTT 58.194 37.500 0.00 0.00 0.00 2.24
1447 1457 5.422214 AGAAATTGATGAACTCCCGTACT 57.578 39.130 0.00 0.00 0.00 2.73
1448 1458 8.882415 TTATAGAAATTGATGAACTCCCGTAC 57.118 34.615 0.00 0.00 0.00 3.67
1449 1459 9.893634 TTTTATAGAAATTGATGAACTCCCGTA 57.106 29.630 0.00 0.00 0.00 4.02
1450 1460 8.801882 TTTTATAGAAATTGATGAACTCCCGT 57.198 30.769 0.00 0.00 0.00 5.28
1461 1471 9.575783 GCGGTGGTTTTATTTTATAGAAATTGA 57.424 29.630 0.00 0.00 0.00 2.57
1462 1472 8.813282 GGCGGTGGTTTTATTTTATAGAAATTG 58.187 33.333 0.00 0.00 0.00 2.32
1463 1473 7.703197 CGGCGGTGGTTTTATTTTATAGAAATT 59.297 33.333 0.00 0.00 0.00 1.82
1464 1474 7.148035 ACGGCGGTGGTTTTATTTTATAGAAAT 60.148 33.333 13.24 0.00 0.00 2.17
1465 1475 6.150809 ACGGCGGTGGTTTTATTTTATAGAAA 59.849 34.615 13.24 0.00 0.00 2.52
1466 1476 5.647225 ACGGCGGTGGTTTTATTTTATAGAA 59.353 36.000 13.24 0.00 0.00 2.10
1467 1477 5.064962 CACGGCGGTGGTTTTATTTTATAGA 59.935 40.000 16.16 0.00 40.58 1.98
1468 1478 5.267776 CACGGCGGTGGTTTTATTTTATAG 58.732 41.667 16.16 0.00 40.58 1.31
1469 1479 4.438472 GCACGGCGGTGGTTTTATTTTATA 60.438 41.667 23.86 0.00 44.54 0.98
1470 1480 3.673866 GCACGGCGGTGGTTTTATTTTAT 60.674 43.478 23.86 0.00 44.54 1.40
1471 1481 2.351544 GCACGGCGGTGGTTTTATTTTA 60.352 45.455 23.86 0.00 44.54 1.52
1472 1482 1.603425 GCACGGCGGTGGTTTTATTTT 60.603 47.619 23.86 0.00 44.54 1.82
1473 1483 0.038983 GCACGGCGGTGGTTTTATTT 60.039 50.000 23.86 0.00 44.54 1.40
1474 1484 1.582461 GCACGGCGGTGGTTTTATT 59.418 52.632 23.86 0.00 44.54 1.40
1475 1485 3.270000 GCACGGCGGTGGTTTTAT 58.730 55.556 23.86 0.00 44.54 1.40
1481 1491 1.231958 TTTTTAGAGCACGGCGGTGG 61.232 55.000 23.86 7.81 44.54 4.61
1483 1493 0.034337 TCTTTTTAGAGCACGGCGGT 59.966 50.000 13.24 0.00 0.00 5.68
1484 1494 1.369625 ATCTTTTTAGAGCACGGCGG 58.630 50.000 13.24 0.66 0.00 6.13
1485 1495 5.462398 ACTTATATCTTTTTAGAGCACGGCG 59.538 40.000 4.80 4.80 0.00 6.46
1486 1496 6.479001 TCACTTATATCTTTTTAGAGCACGGC 59.521 38.462 0.00 0.00 0.00 5.68
1487 1497 8.420374 TTCACTTATATCTTTTTAGAGCACGG 57.580 34.615 0.00 0.00 0.00 4.94
1522 1532 7.035840 ACATCTTTTGAGCTAGGCAATATTG 57.964 36.000 11.27 11.27 0.00 1.90
1523 1533 8.752005 TTACATCTTTTGAGCTAGGCAATATT 57.248 30.769 0.00 0.00 0.00 1.28
1524 1534 7.995488 ACTTACATCTTTTGAGCTAGGCAATAT 59.005 33.333 0.00 0.00 0.00 1.28
1525 1535 7.280876 CACTTACATCTTTTGAGCTAGGCAATA 59.719 37.037 0.00 0.00 0.00 1.90
1526 1536 6.094603 CACTTACATCTTTTGAGCTAGGCAAT 59.905 38.462 0.00 0.00 0.00 3.56
1527 1537 5.412594 CACTTACATCTTTTGAGCTAGGCAA 59.587 40.000 0.00 0.00 0.00 4.52
1528 1538 4.937620 CACTTACATCTTTTGAGCTAGGCA 59.062 41.667 0.00 0.00 0.00 4.75
1529 1539 5.178797 TCACTTACATCTTTTGAGCTAGGC 58.821 41.667 0.00 0.00 0.00 3.93
1530 1540 6.183360 GCTTCACTTACATCTTTTGAGCTAGG 60.183 42.308 0.00 0.00 0.00 3.02
1531 1541 6.369890 TGCTTCACTTACATCTTTTGAGCTAG 59.630 38.462 0.00 0.00 0.00 3.42
1532 1542 6.147821 GTGCTTCACTTACATCTTTTGAGCTA 59.852 38.462 0.00 0.00 0.00 3.32
1533 1543 5.049129 GTGCTTCACTTACATCTTTTGAGCT 60.049 40.000 0.00 0.00 0.00 4.09
1534 1544 5.149977 GTGCTTCACTTACATCTTTTGAGC 58.850 41.667 0.00 0.00 0.00 4.26
1535 1545 6.304356 TGTGCTTCACTTACATCTTTTGAG 57.696 37.500 0.00 0.00 35.11 3.02
1536 1546 6.882610 ATGTGCTTCACTTACATCTTTTGA 57.117 33.333 0.00 0.00 35.11 2.69
1537 1547 8.032952 TCTATGTGCTTCACTTACATCTTTTG 57.967 34.615 0.00 0.00 36.52 2.44
1538 1548 7.880195 ACTCTATGTGCTTCACTTACATCTTTT 59.120 33.333 0.00 0.00 36.52 2.27
1539 1549 7.390027 ACTCTATGTGCTTCACTTACATCTTT 58.610 34.615 0.00 0.00 36.52 2.52
1540 1550 6.940739 ACTCTATGTGCTTCACTTACATCTT 58.059 36.000 0.00 0.00 36.52 2.40
1541 1551 6.537453 ACTCTATGTGCTTCACTTACATCT 57.463 37.500 0.00 0.00 36.52 2.90
1542 1552 8.879342 AATACTCTATGTGCTTCACTTACATC 57.121 34.615 0.00 0.00 36.52 3.06
1543 1553 8.700051 AGAATACTCTATGTGCTTCACTTACAT 58.300 33.333 0.00 0.00 38.48 2.29
1544 1554 8.067751 AGAATACTCTATGTGCTTCACTTACA 57.932 34.615 0.00 0.00 35.11 2.41
1563 1573 9.546909 CGCATGAATGGTGATTTATTAGAATAC 57.453 33.333 0.00 0.00 0.00 1.89
1564 1574 9.283768 ACGCATGAATGGTGATTTATTAGAATA 57.716 29.630 0.00 0.00 0.00 1.75
1565 1575 8.077991 CACGCATGAATGGTGATTTATTAGAAT 58.922 33.333 0.00 0.00 33.59 2.40
1566 1576 7.066887 ACACGCATGAATGGTGATTTATTAGAA 59.933 33.333 14.76 0.00 34.88 2.10
1567 1577 6.542005 ACACGCATGAATGGTGATTTATTAGA 59.458 34.615 14.76 0.00 34.88 2.10
1568 1578 6.728200 ACACGCATGAATGGTGATTTATTAG 58.272 36.000 14.76 0.00 34.88 1.73
1569 1579 6.691754 ACACGCATGAATGGTGATTTATTA 57.308 33.333 14.76 0.00 34.88 0.98
1570 1580 5.581126 ACACGCATGAATGGTGATTTATT 57.419 34.783 14.76 0.00 34.88 1.40
1571 1581 5.125257 TCAACACGCATGAATGGTGATTTAT 59.875 36.000 12.05 0.00 37.62 1.40
1572 1582 4.457257 TCAACACGCATGAATGGTGATTTA 59.543 37.500 12.05 0.00 37.62 1.40
1573 1583 3.255395 TCAACACGCATGAATGGTGATTT 59.745 39.130 12.05 0.00 37.62 2.17
1574 1584 2.819019 TCAACACGCATGAATGGTGATT 59.181 40.909 12.05 2.62 37.62 2.57
1575 1585 2.435422 TCAACACGCATGAATGGTGAT 58.565 42.857 12.05 0.00 37.62 3.06
1576 1586 1.889545 TCAACACGCATGAATGGTGA 58.110 45.000 12.05 12.05 40.23 4.02
1577 1587 2.925578 ATCAACACGCATGAATGGTG 57.074 45.000 8.07 8.07 36.05 4.17
1578 1588 2.351418 CGTATCAACACGCATGAATGGT 59.649 45.455 0.00 0.00 34.78 3.55
1579 1589 2.351418 ACGTATCAACACGCATGAATGG 59.649 45.455 0.00 0.00 45.77 3.16
1580 1590 3.306973 AGACGTATCAACACGCATGAATG 59.693 43.478 0.00 0.00 45.77 2.67
1581 1591 3.521560 AGACGTATCAACACGCATGAAT 58.478 40.909 0.00 0.00 45.77 2.57
1582 1592 2.921121 GAGACGTATCAACACGCATGAA 59.079 45.455 5.07 0.00 45.77 2.57
1583 1593 2.526077 GAGACGTATCAACACGCATGA 58.474 47.619 5.07 0.00 45.77 3.07
1584 1594 1.588404 GGAGACGTATCAACACGCATG 59.412 52.381 12.92 0.00 45.77 4.06
1585 1595 1.203758 TGGAGACGTATCAACACGCAT 59.796 47.619 12.92 0.00 45.77 4.73
1586 1596 0.599060 TGGAGACGTATCAACACGCA 59.401 50.000 12.92 0.00 45.77 5.24
1587 1597 1.389106 GTTGGAGACGTATCAACACGC 59.611 52.381 12.92 0.00 45.77 5.34
1588 1598 1.647213 CGTTGGAGACGTATCAACACG 59.353 52.381 12.92 12.27 46.49 4.49
1620 1630 6.150474 TCCAAAATAAGAGGAAAAGCGTTAGG 59.850 38.462 0.00 0.00 0.00 2.69
1623 1633 5.535030 AGTCCAAAATAAGAGGAAAAGCGTT 59.465 36.000 0.00 0.00 32.30 4.84
1638 1648 9.158233 CAAATCATGCAAATTAGAGTCCAAAAT 57.842 29.630 0.00 0.00 0.00 1.82
1725 1735 6.940298 TCCATTCCGAGAACTTTTATTTCTGT 59.060 34.615 0.00 0.00 33.30 3.41
1781 1792 6.295292 GGTCTTGGCTCCACAAATTCTTATTT 60.295 38.462 0.00 0.00 34.29 1.40
1793 1805 1.673665 CAGCAGGTCTTGGCTCCAC 60.674 63.158 0.00 0.00 38.56 4.02
1887 1901 4.077184 CGTCAGCGGGGCTACCAA 62.077 66.667 0.00 0.00 36.40 3.67
1947 1963 5.822519 TGGATCGTGATAATTCTTTTCCCTG 59.177 40.000 0.00 0.00 0.00 4.45
1948 1964 5.823045 GTGGATCGTGATAATTCTTTTCCCT 59.177 40.000 0.00 0.00 0.00 4.20
1951 1967 6.475727 TCTCGTGGATCGTGATAATTCTTTTC 59.524 38.462 0.00 0.00 37.18 2.29
1986 2002 1.075659 GGAAGAACAGGGCTTGGCT 59.924 57.895 0.44 0.00 0.00 4.75
2017 2033 1.003718 CCCCAAACGGACTCCAGAC 60.004 63.158 0.00 0.00 0.00 3.51
2124 2140 1.654954 GACCAGCGAGCCTACGAAGA 61.655 60.000 0.00 0.00 35.09 2.87
2195 2211 6.470456 ACATAGTGGATACTAGGGATCAGA 57.530 41.667 8.63 0.00 43.56 3.27
2365 2381 1.210967 GGGGTTGTCGGATCATAACCA 59.789 52.381 16.41 0.00 43.33 3.67


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

AutoCloner maintained by Alex Coulton.