Multiple sequence alignment - TraesCS7A01G084100

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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 TraesCS7A01G084100 chr7A 100.000 2449 0 0 1 2449 48781296 48783744 0.000000e+00 4523.0
1 TraesCS7A01G084100 chr7A 98.507 67 1 0 1568 1634 48782925 48782991 4.280000e-23 119.0
2 TraesCS7A01G084100 chr2B 97.249 1636 41 4 1 1634 677291996 677293629 0.000000e+00 2769.0
3 TraesCS7A01G084100 chr2B 96.787 498 13 2 1 497 139361479 139360984 0.000000e+00 828.0
4 TraesCS7A01G084100 chr2B 97.720 307 7 0 1639 1945 139360993 139360687 1.670000e-146 529.0
5 TraesCS7A01G084100 chr2B 95.975 323 10 3 1630 1951 677293563 677293883 2.790000e-144 521.0
6 TraesCS7A01G084100 chr2B 88.474 321 31 5 1944 2260 470375627 470375309 1.370000e-102 383.0
7 TraesCS7A01G084100 chr2B 78.817 524 45 20 1944 2449 520500667 520500192 2.380000e-75 292.0
8 TraesCS7A01G084100 chr2B 77.799 527 51 18 1944 2449 520569927 520569446 5.190000e-67 265.0
9 TraesCS7A01G084100 chr2B 79.461 297 30 16 2157 2449 761524353 761524084 5.380000e-42 182.0
10 TraesCS7A01G084100 chr2B 75.638 431 40 20 2042 2449 660872 660484 1.170000e-33 154.0
11 TraesCS7A01G084100 chr2B 100.000 58 0 0 1577 1634 139360993 139360936 9.260000e-20 108.0
12 TraesCS7A01G084100 chrUn 88.528 1630 121 42 346 1947 96553495 96555086 0.000000e+00 1914.0
13 TraesCS7A01G084100 chrUn 92.263 517 35 5 1 513 96553068 96553583 0.000000e+00 728.0
14 TraesCS7A01G084100 chrUn 92.517 147 11 0 152 298 358480337 358480191 6.860000e-51 211.0
15 TraesCS7A01G084100 chr4D 93.431 1294 61 12 346 1634 459191838 459193112 0.000000e+00 1897.0
16 TraesCS7A01G084100 chr4D 93.567 513 33 0 1 513 459191335 459191847 0.000000e+00 765.0
17 TraesCS7A01G084100 chr4D 97.161 317 8 1 1630 1945 459193045 459193361 3.580000e-148 534.0
18 TraesCS7A01G084100 chr4D 100.000 39 0 0 1573 1611 101391974 101392012 3.380000e-09 73.1
19 TraesCS7A01G084100 chr1B 93.521 1281 65 13 346 1621 127025876 127024609 0.000000e+00 1890.0
20 TraesCS7A01G084100 chr1B 94.737 513 25 2 1 513 127026377 127025867 0.000000e+00 797.0
21 TraesCS7A01G084100 chr3B 93.282 1295 61 14 346 1634 8505360 8506634 0.000000e+00 1886.0
22 TraesCS7A01G084100 chr3B 92.368 511 38 1 1 511 597426778 597427287 0.000000e+00 726.0
23 TraesCS7A01G084100 chr3B 94.953 317 15 1 1630 1945 8506567 8506883 1.690000e-136 496.0
24 TraesCS7A01G084100 chr3B 90.596 319 22 7 1630 1944 564172745 564173059 1.350000e-112 416.0
25 TraesCS7A01G084100 chr3B 92.373 118 7 2 2334 2449 374881264 374881147 1.510000e-37 167.0
26 TraesCS7A01G084100 chr3B 93.162 117 2 3 2334 2449 736063082 736063193 1.510000e-37 167.0
27 TraesCS7A01G084100 chr3B 92.373 118 6 3 2334 2449 599521321 599521205 5.420000e-37 165.0
28 TraesCS7A01G084100 chr3B 94.186 86 3 2 1551 1635 564172728 564172812 1.980000e-26 130.0
29 TraesCS7A01G084100 chr2A 93.426 1217 64 7 346 1558 57826419 57827623 0.000000e+00 1790.0
30 TraesCS7A01G084100 chr2A 97.930 483 10 0 1 483 763971599 763971117 0.000000e+00 837.0
31 TraesCS7A01G084100 chr2A 98.065 310 5 1 1637 1946 763971125 763970817 2.770000e-149 538.0
32 TraesCS7A01G084100 chr3D 96.617 1064 30 4 574 1634 6991411 6992471 0.000000e+00 1760.0
33 TraesCS7A01G084100 chr3D 96.766 402 10 3 1235 1634 5544739 5545139 0.000000e+00 667.0
34 TraesCS7A01G084100 chr3D 96.865 319 9 1 1630 1947 5545072 5545390 1.290000e-147 532.0
35 TraesCS7A01G084100 chr3D 96.845 317 9 1 1630 1945 6992404 6992720 1.670000e-146 529.0
36 TraesCS7A01G084100 chr5A 92.910 1213 71 6 346 1554 570488812 570490013 0.000000e+00 1749.0
37 TraesCS7A01G084100 chr5A 92.687 1217 73 11 346 1558 564351963 564350759 0.000000e+00 1740.0
38 TraesCS7A01G084100 chr5A 88.060 134 13 3 2317 2449 155854116 155853985 3.260000e-34 156.0
39 TraesCS7A01G084100 chr7B 88.565 1303 92 27 346 1615 551484225 551482947 0.000000e+00 1528.0
40 TraesCS7A01G084100 chr7B 93.372 513 33 1 1 513 551484727 551484216 0.000000e+00 758.0
41 TraesCS7A01G084100 chr7B 83.048 525 46 15 1944 2449 129396558 129396058 1.040000e-118 436.0
42 TraesCS7A01G084100 chr7B 81.431 517 66 18 1948 2449 464617667 464617166 1.760000e-106 396.0
43 TraesCS7A01G084100 chr7B 80.460 522 86 13 1 513 269097849 269097335 3.820000e-103 385.0
44 TraesCS7A01G084100 chr2D 80.208 1637 226 52 346 1944 641119256 641117680 0.000000e+00 1138.0
45 TraesCS7A01G084100 chr2D 95.866 508 18 3 6 513 631749575 631749071 0.000000e+00 819.0
46 TraesCS7A01G084100 chr2D 93.177 513 35 0 1 513 469107942 469107430 0.000000e+00 754.0
47 TraesCS7A01G084100 chr2D 95.556 315 13 1 1630 1943 631747899 631747585 1.010000e-138 503.0
48 TraesCS7A01G084100 chr2D 93.827 81 4 1 1551 1630 330863243 330863163 1.190000e-23 121.0
49 TraesCS7A01G084100 chr2D 83.133 83 4 5 2261 2334 594861345 594861426 1.570000e-07 67.6
50 TraesCS7A01G084100 chr4B 79.719 1568 244 38 1 1521 535285854 535287394 0.000000e+00 1066.0
51 TraesCS7A01G084100 chr4B 81.885 541 73 15 1 520 449518309 449518845 1.350000e-117 433.0
52 TraesCS7A01G084100 chr4B 81.648 534 44 24 1944 2449 550468375 550468882 6.350000e-106 394.0
53 TraesCS7A01G084100 chr1A 93.957 513 31 0 1 513 35564011 35563499 0.000000e+00 776.0
54 TraesCS7A01G084100 chr1A 92.955 511 36 0 1 511 461966796 461966286 0.000000e+00 745.0
55 TraesCS7A01G084100 chr1A 87.968 374 29 9 1944 2306 40816956 40816588 6.260000e-116 427.0
56 TraesCS7A01G084100 chr1A 88.959 317 33 1 4 318 80284237 80283921 8.210000e-105 390.0
57 TraesCS7A01G084100 chr1A 93.750 64 4 0 1551 1614 385892638 385892575 2.000000e-16 97.1
58 TraesCS7A01G084100 chr6D 86.437 494 44 10 1944 2433 250667997 250667523 1.000000e-143 520.0
59 TraesCS7A01G084100 chr6D 94.000 50 3 0 1565 1614 175749425 175749376 2.610000e-10 76.8
60 TraesCS7A01G084100 chr1D 85.283 530 48 15 1941 2449 235329764 235330284 1.000000e-143 520.0
61 TraesCS7A01G084100 chr1D 92.617 298 22 0 1 298 80674254 80674551 1.740000e-116 429.0
62 TraesCS7A01G084100 chr1D 85.984 371 37 8 1944 2302 49870814 49870447 1.370000e-102 383.0
63 TraesCS7A01G084100 chr5B 84.902 510 64 11 9 513 173863479 173862978 1.010000e-138 503.0
64 TraesCS7A01G084100 chr5B 77.193 456 53 22 2021 2449 414532920 414532489 4.100000e-53 219.0
65 TraesCS7A01G084100 chr5B 92.308 117 7 2 2334 2449 414516261 414516146 5.420000e-37 165.0
66 TraesCS7A01G084100 chr6B 82.576 528 68 15 1 520 672729341 672729852 6.210000e-121 444.0
67 TraesCS7A01G084100 chr6B 88.283 367 28 7 1941 2297 521748994 521749355 2.250000e-115 425.0
68 TraesCS7A01G084100 chr6B 85.294 204 15 10 2249 2449 588498151 588498342 1.920000e-46 196.0
69 TraesCS7A01G084100 chr5D 90.938 320 27 1 1 318 538686715 538687034 1.740000e-116 429.0
70 TraesCS7A01G084100 chr5D 88.889 351 34 5 1944 2291 231879953 231880301 6.260000e-116 427.0
71 TraesCS7A01G084100 chr6A 82.171 516 53 23 1944 2449 438424144 438424630 8.150000e-110 407.0
72 TraesCS7A01G084100 chr6A 81.227 538 70 20 1 514 571574291 571574821 2.930000e-109 405.0
73 TraesCS7A01G084100 chr4A 79.854 412 51 18 2046 2449 381949184 381948797 3.100000e-69 272.0
74 TraesCS7A01G084100 chr4A 96.875 64 2 0 1551 1614 445298242 445298179 9.260000e-20 108.0
75 TraesCS7A01G084100 chr7D 87.568 185 17 3 2150 2334 176781144 176780966 2.470000e-50 209.0
76 TraesCS7A01G084100 chr7D 96.970 33 1 0 2325 2357 305674337 305674305 3.400000e-04 56.5


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 TraesCS7A01G084100 chr7A 48781296 48783744 2448 False 2321.000000 4523 99.253500 1 2449 2 chr7A.!!$F1 2448
1 TraesCS7A01G084100 chr2B 677291996 677293883 1887 False 1645.000000 2769 96.612000 1 1951 2 chr2B.!!$F1 1950
2 TraesCS7A01G084100 chr2B 139360687 139361479 792 True 488.333333 828 98.169000 1 1945 3 chr2B.!!$R6 1944
3 TraesCS7A01G084100 chrUn 96553068 96555086 2018 False 1321.000000 1914 90.395500 1 1947 2 chrUn.!!$F1 1946
4 TraesCS7A01G084100 chr4D 459191335 459193361 2026 False 1065.333333 1897 94.719667 1 1945 3 chr4D.!!$F2 1944
5 TraesCS7A01G084100 chr1B 127024609 127026377 1768 True 1343.500000 1890 94.129000 1 1621 2 chr1B.!!$R1 1620
6 TraesCS7A01G084100 chr3B 8505360 8506883 1523 False 1191.000000 1886 94.117500 346 1945 2 chr3B.!!$F3 1599
7 TraesCS7A01G084100 chr3B 597426778 597427287 509 False 726.000000 726 92.368000 1 511 1 chr3B.!!$F1 510
8 TraesCS7A01G084100 chr2A 57826419 57827623 1204 False 1790.000000 1790 93.426000 346 1558 1 chr2A.!!$F1 1212
9 TraesCS7A01G084100 chr2A 763970817 763971599 782 True 687.500000 837 97.997500 1 1946 2 chr2A.!!$R1 1945
10 TraesCS7A01G084100 chr3D 6991411 6992720 1309 False 1144.500000 1760 96.731000 574 1945 2 chr3D.!!$F2 1371
11 TraesCS7A01G084100 chr3D 5544739 5545390 651 False 599.500000 667 96.815500 1235 1947 2 chr3D.!!$F1 712
12 TraesCS7A01G084100 chr5A 570488812 570490013 1201 False 1749.000000 1749 92.910000 346 1554 1 chr5A.!!$F1 1208
13 TraesCS7A01G084100 chr5A 564350759 564351963 1204 True 1740.000000 1740 92.687000 346 1558 1 chr5A.!!$R2 1212
14 TraesCS7A01G084100 chr7B 551482947 551484727 1780 True 1143.000000 1528 90.968500 1 1615 2 chr7B.!!$R4 1614
15 TraesCS7A01G084100 chr7B 129396058 129396558 500 True 436.000000 436 83.048000 1944 2449 1 chr7B.!!$R1 505
16 TraesCS7A01G084100 chr7B 464617166 464617667 501 True 396.000000 396 81.431000 1948 2449 1 chr7B.!!$R3 501
17 TraesCS7A01G084100 chr7B 269097335 269097849 514 True 385.000000 385 80.460000 1 513 1 chr7B.!!$R2 512
18 TraesCS7A01G084100 chr2D 641117680 641119256 1576 True 1138.000000 1138 80.208000 346 1944 1 chr2D.!!$R3 1598
19 TraesCS7A01G084100 chr2D 469107430 469107942 512 True 754.000000 754 93.177000 1 513 1 chr2D.!!$R2 512
20 TraesCS7A01G084100 chr2D 631747585 631749575 1990 True 661.000000 819 95.711000 6 1943 2 chr2D.!!$R4 1937
21 TraesCS7A01G084100 chr4B 535285854 535287394 1540 False 1066.000000 1066 79.719000 1 1521 1 chr4B.!!$F2 1520
22 TraesCS7A01G084100 chr4B 449518309 449518845 536 False 433.000000 433 81.885000 1 520 1 chr4B.!!$F1 519
23 TraesCS7A01G084100 chr4B 550468375 550468882 507 False 394.000000 394 81.648000 1944 2449 1 chr4B.!!$F3 505
24 TraesCS7A01G084100 chr1A 35563499 35564011 512 True 776.000000 776 93.957000 1 513 1 chr1A.!!$R1 512
25 TraesCS7A01G084100 chr1A 461966286 461966796 510 True 745.000000 745 92.955000 1 511 1 chr1A.!!$R5 510
26 TraesCS7A01G084100 chr1D 235329764 235330284 520 False 520.000000 520 85.283000 1941 2449 1 chr1D.!!$F2 508
27 TraesCS7A01G084100 chr5B 173862978 173863479 501 True 503.000000 503 84.902000 9 513 1 chr5B.!!$R1 504
28 TraesCS7A01G084100 chr6B 672729341 672729852 511 False 444.000000 444 82.576000 1 520 1 chr6B.!!$F3 519
29 TraesCS7A01G084100 chr6A 571574291 571574821 530 False 405.000000 405 81.227000 1 514 1 chr6A.!!$F2 513

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
105 107 5.801947 CCAAGTTGACATTGTTATAGCTTGC 59.198 40.0 3.87 0.0 32.15 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2561 0.24691 TGTTACTAATGGCGCACCGA 59.753 50.0 10.83 0.0 39.7 4.69 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
105 107 5.801947 CCAAGTTGACATTGTTATAGCTTGC 59.198 40.000 3.87 0.00 32.15 4.01
479 734 7.405469 TGTTTAAATCATGTGTTTGTGATGC 57.595 32.000 8.45 0.00 35.38 3.91
697 1068 6.514947 TCTCAAACAATGTGCTGCTATTTTT 58.485 32.000 0.00 0.00 0.00 1.94
1060 1438 4.773674 TGAATGCAAGGTCTGGAAATGATT 59.226 37.500 0.00 0.00 0.00 2.57
1139 1541 4.977393 ACCGCAAGTTGGTGAGTT 57.023 50.000 4.75 0.00 38.60 3.01
1159 1561 1.455822 TTCTCACCCCAAAGGACCAT 58.544 50.000 0.00 0.00 39.89 3.55
1184 1586 0.111253 AAGAAGGCCAAGGTGGTGAG 59.889 55.000 5.01 0.00 40.46 3.51
1233 1635 8.303876 GCCATTCTCAAAGATGGTTTTAAACTA 58.696 33.333 7.79 1.74 36.59 2.24
1364 1767 4.820897 ACTATGCTCATCTCGTTGACAAA 58.179 39.130 0.00 0.00 0.00 2.83
1366 1769 2.832563 TGCTCATCTCGTTGACAAACA 58.167 42.857 0.00 0.00 35.94 2.83
1522 1934 3.874392 AGTGCCATTGGATTGCTTTAC 57.126 42.857 6.95 0.00 0.00 2.01
1627 2149 8.721133 TTGCTACCTGATTCTACCTTATGATA 57.279 34.615 0.00 0.00 0.00 2.15
1628 2150 8.901472 TGCTACCTGATTCTACCTTATGATAT 57.099 34.615 0.00 0.00 0.00 1.63
1629 2151 9.326489 TGCTACCTGATTCTACCTTATGATATT 57.674 33.333 0.00 0.00 0.00 1.28
1643 2165 9.592196 ACCTTATGATATTATTGGTTGATTGCT 57.408 29.630 0.88 0.00 0.00 3.91
1648 2170 8.945481 TGATATTATTGGTTGATTGCTTTTGG 57.055 30.769 0.00 0.00 0.00 3.28
1649 2171 8.756927 TGATATTATTGGTTGATTGCTTTTGGA 58.243 29.630 0.00 0.00 0.00 3.53
1650 2172 9.768662 GATATTATTGGTTGATTGCTTTTGGAT 57.231 29.630 0.00 0.00 0.00 3.41
1651 2173 7.852971 ATTATTGGTTGATTGCTTTTGGATG 57.147 32.000 0.00 0.00 0.00 3.51
1652 2174 4.686191 TTGGTTGATTGCTTTTGGATGT 57.314 36.364 0.00 0.00 0.00 3.06
1653 2175 3.992643 TGGTTGATTGCTTTTGGATGTG 58.007 40.909 0.00 0.00 0.00 3.21
1654 2176 2.738314 GGTTGATTGCTTTTGGATGTGC 59.262 45.455 0.00 0.00 0.00 4.57
1655 2177 2.738314 GTTGATTGCTTTTGGATGTGCC 59.262 45.455 0.00 0.00 37.10 5.01
1666 2188 3.663995 TGGATGTGCCAAATGAACTTG 57.336 42.857 0.00 0.00 45.87 3.16
1667 2189 2.288948 TGGATGTGCCAAATGAACTTGC 60.289 45.455 0.00 0.00 45.87 4.01
1668 2190 2.028748 GGATGTGCCAAATGAACTTGCT 60.029 45.455 0.00 0.00 36.34 3.91
1669 2191 3.193267 GGATGTGCCAAATGAACTTGCTA 59.807 43.478 0.00 0.00 36.34 3.49
1670 2192 3.641437 TGTGCCAAATGAACTTGCTAC 57.359 42.857 0.00 0.00 0.00 3.58
1671 2193 2.295909 TGTGCCAAATGAACTTGCTACC 59.704 45.455 0.00 0.00 0.00 3.18
1672 2194 2.558359 GTGCCAAATGAACTTGCTACCT 59.442 45.455 0.00 0.00 0.00 3.08
1673 2195 2.557924 TGCCAAATGAACTTGCTACCTG 59.442 45.455 0.00 0.00 0.00 4.00
1674 2196 2.819608 GCCAAATGAACTTGCTACCTGA 59.180 45.455 0.00 0.00 0.00 3.86
1675 2197 3.445096 GCCAAATGAACTTGCTACCTGAT 59.555 43.478 0.00 0.00 0.00 2.90
1676 2198 4.082026 GCCAAATGAACTTGCTACCTGATT 60.082 41.667 0.00 0.00 0.00 2.57
1677 2199 5.644644 CCAAATGAACTTGCTACCTGATTC 58.355 41.667 0.00 0.00 0.00 2.52
1678 2200 5.416952 CCAAATGAACTTGCTACCTGATTCT 59.583 40.000 0.00 0.00 0.00 2.40
1679 2201 6.599244 CCAAATGAACTTGCTACCTGATTCTA 59.401 38.462 0.00 0.00 0.00 2.10
1680 2202 7.414540 CCAAATGAACTTGCTACCTGATTCTAC 60.415 40.741 0.00 0.00 0.00 2.59
1681 2203 5.086104 TGAACTTGCTACCTGATTCTACC 57.914 43.478 0.00 0.00 0.00 3.18
1682 2204 4.777896 TGAACTTGCTACCTGATTCTACCT 59.222 41.667 0.00 0.00 0.00 3.08
1683 2205 5.248477 TGAACTTGCTACCTGATTCTACCTT 59.752 40.000 0.00 0.00 0.00 3.50
1684 2206 6.439375 TGAACTTGCTACCTGATTCTACCTTA 59.561 38.462 0.00 0.00 0.00 2.69
1685 2207 7.125811 TGAACTTGCTACCTGATTCTACCTTAT 59.874 37.037 0.00 0.00 0.00 1.73
1686 2208 6.821388 ACTTGCTACCTGATTCTACCTTATG 58.179 40.000 0.00 0.00 0.00 1.90
1687 2209 6.611642 ACTTGCTACCTGATTCTACCTTATGA 59.388 38.462 0.00 0.00 0.00 2.15
1688 2210 7.291182 ACTTGCTACCTGATTCTACCTTATGAT 59.709 37.037 0.00 0.00 0.00 2.45
1971 2527 2.359107 CCAGACATGTGGTGCGCT 60.359 61.111 9.73 0.00 32.32 5.92
1979 2539 4.039245 AGACATGTGGTGCGCTATTACTAT 59.961 41.667 9.73 0.00 0.00 2.12
1989 2549 9.181061 TGGTGCGCTATTACTATATACTAATGA 57.819 33.333 9.73 0.00 0.00 2.57
1998 2558 9.803315 ATTACTATATACTAATGACGCACCATG 57.197 33.333 0.00 0.00 0.00 3.66
2000 2560 7.090808 ACTATATACTAATGACGCACCATGTG 58.909 38.462 0.00 0.00 36.51 3.21
2001 2561 2.472695 ACTAATGACGCACCATGTGT 57.527 45.000 0.00 0.00 44.78 3.72
2187 2763 2.611473 CCAGGAGATAGTGCGCCATTAG 60.611 54.545 4.18 0.00 0.00 1.73
2190 2766 3.895656 AGGAGATAGTGCGCCATTAGTAA 59.104 43.478 4.18 0.00 0.00 2.24
2211 2787 8.446599 AGTAATTTTAACTAGTAATGGCGCAT 57.553 30.769 10.83 0.00 0.00 4.73
2313 2919 2.290641 CCATTACTAATTCAGGCGCACC 59.709 50.000 10.83 0.00 0.00 5.01
2317 2923 1.009829 CTAATTCAGGCGCACCACTC 58.990 55.000 10.83 0.00 39.06 3.51
2318 2924 0.392461 TAATTCAGGCGCACCACTCC 60.392 55.000 10.83 0.00 39.06 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
554 924 0.771755 ACCCCACTTTTCCCAGAGAC 59.228 55.000 0.00 0.00 0.00 3.36
697 1068 3.861840 AGCTAGCTTGAATTGCTCGTTA 58.138 40.909 12.68 0.00 41.46 3.18
904 1281 7.002879 AGTCATTAGCATAATGAAGGCAGAAT 58.997 34.615 12.50 0.00 38.27 2.40
1060 1438 7.102993 TCATCATCAACGTCAATAGAAAGGAA 58.897 34.615 0.00 0.00 0.00 3.36
1139 1541 1.227249 TGGTCCTTTGGGGTGAGAAA 58.773 50.000 0.00 0.00 36.25 2.52
1184 1586 4.825085 CACCTAGTGGATCCTCTAGAACTC 59.175 50.000 36.39 10.05 40.55 3.01
1233 1635 3.281727 TTTCACAAGAGCTTCACCACT 57.718 42.857 0.00 0.00 0.00 4.00
1364 1767 4.049393 GCTCTTGCCGTCTTGTGT 57.951 55.556 0.00 0.00 0.00 3.72
1513 1924 7.995289 TCACATTCCAAATATCGTAAAGCAAT 58.005 30.769 0.00 0.00 0.00 3.56
1522 1934 7.857389 CCATACAAGTTCACATTCCAAATATCG 59.143 37.037 0.00 0.00 0.00 2.92
1627 2149 7.334921 CACATCCAAAAGCAATCAACCAATAAT 59.665 33.333 0.00 0.00 0.00 1.28
1628 2150 6.649973 CACATCCAAAAGCAATCAACCAATAA 59.350 34.615 0.00 0.00 0.00 1.40
1629 2151 6.164876 CACATCCAAAAGCAATCAACCAATA 58.835 36.000 0.00 0.00 0.00 1.90
1630 2152 4.998672 CACATCCAAAAGCAATCAACCAAT 59.001 37.500 0.00 0.00 0.00 3.16
1631 2153 4.378774 CACATCCAAAAGCAATCAACCAA 58.621 39.130 0.00 0.00 0.00 3.67
1632 2154 3.803021 GCACATCCAAAAGCAATCAACCA 60.803 43.478 0.00 0.00 0.00 3.67
1633 2155 2.738314 GCACATCCAAAAGCAATCAACC 59.262 45.455 0.00 0.00 0.00 3.77
1634 2156 2.738314 GGCACATCCAAAAGCAATCAAC 59.262 45.455 0.00 0.00 34.01 3.18
1635 2157 2.367894 TGGCACATCCAAAAGCAATCAA 59.632 40.909 0.00 0.00 43.21 2.57
1636 2158 1.969208 TGGCACATCCAAAAGCAATCA 59.031 42.857 0.00 0.00 43.21 2.57
1637 2159 2.747396 TGGCACATCCAAAAGCAATC 57.253 45.000 0.00 0.00 43.21 2.67
1646 2168 2.288948 GCAAGTTCATTTGGCACATCCA 60.289 45.455 0.00 0.00 44.85 3.41
1647 2169 2.028748 AGCAAGTTCATTTGGCACATCC 60.029 45.455 0.00 0.00 39.30 3.51
1648 2170 3.308438 AGCAAGTTCATTTGGCACATC 57.692 42.857 0.00 0.00 39.30 3.06
1649 2171 3.056607 GGTAGCAAGTTCATTTGGCACAT 60.057 43.478 0.00 0.00 39.30 3.21
1650 2172 2.295909 GGTAGCAAGTTCATTTGGCACA 59.704 45.455 0.00 0.00 0.00 4.57
1651 2173 2.558359 AGGTAGCAAGTTCATTTGGCAC 59.442 45.455 0.00 0.00 0.00 5.01
1652 2174 2.557924 CAGGTAGCAAGTTCATTTGGCA 59.442 45.455 0.00 0.00 0.00 4.92
1653 2175 2.819608 TCAGGTAGCAAGTTCATTTGGC 59.180 45.455 0.00 0.00 0.00 4.52
1654 2176 5.416952 AGAATCAGGTAGCAAGTTCATTTGG 59.583 40.000 0.00 0.00 0.00 3.28
1655 2177 6.506500 AGAATCAGGTAGCAAGTTCATTTG 57.493 37.500 0.00 0.00 0.00 2.32
1656 2178 6.599638 GGTAGAATCAGGTAGCAAGTTCATTT 59.400 38.462 0.00 0.00 0.00 2.32
1657 2179 6.069963 AGGTAGAATCAGGTAGCAAGTTCATT 60.070 38.462 0.00 0.00 0.00 2.57
1658 2180 5.426833 AGGTAGAATCAGGTAGCAAGTTCAT 59.573 40.000 0.00 0.00 0.00 2.57
1659 2181 4.777896 AGGTAGAATCAGGTAGCAAGTTCA 59.222 41.667 0.00 0.00 0.00 3.18
1660 2182 5.346181 AGGTAGAATCAGGTAGCAAGTTC 57.654 43.478 0.00 0.00 0.00 3.01
1661 2183 5.763876 AAGGTAGAATCAGGTAGCAAGTT 57.236 39.130 0.00 0.00 0.00 2.66
1662 2184 6.611642 TCATAAGGTAGAATCAGGTAGCAAGT 59.388 38.462 0.00 0.00 0.00 3.16
1663 2185 7.055667 TCATAAGGTAGAATCAGGTAGCAAG 57.944 40.000 0.00 0.00 0.00 4.01
1664 2186 7.618019 ATCATAAGGTAGAATCAGGTAGCAA 57.382 36.000 0.00 0.00 0.00 3.91
1665 2187 8.901472 ATATCATAAGGTAGAATCAGGTAGCA 57.099 34.615 0.00 0.00 0.00 3.49
1852 2408 3.323243 CGTTCCTGTGTTTAGTAGGTGG 58.677 50.000 0.00 0.00 33.30 4.61
1957 2513 2.550978 AGTAATAGCGCACCACATGTC 58.449 47.619 11.47 0.00 0.00 3.06
1959 2515 7.258441 AGTATATAGTAATAGCGCACCACATG 58.742 38.462 11.47 0.00 0.00 3.21
1962 2518 9.234384 CATTAGTATATAGTAATAGCGCACCAC 57.766 37.037 18.37 1.22 32.19 4.16
1979 2539 5.270893 ACACATGGTGCGTCATTAGTATA 57.729 39.130 0.00 0.00 36.98 1.47
2000 2560 0.648958 GTTACTAATGGCGCACCGAC 59.351 55.000 10.83 0.00 39.70 4.79
2001 2561 0.246910 TGTTACTAATGGCGCACCGA 59.753 50.000 10.83 0.00 39.70 4.69
2052 2615 1.750930 CACTATCCCCTGATGCGCT 59.249 57.895 9.73 0.00 32.18 5.92
2058 2621 1.344953 AATGGCGCACTATCCCCTGA 61.345 55.000 10.83 0.00 0.00 3.86
2096 2659 2.751036 CCATGGATGTGGTGCGCA 60.751 61.111 5.66 5.66 34.46 6.09
2152 2728 0.906066 TCCTGGTGCGCCATTACTAA 59.094 50.000 21.54 0.00 45.05 2.24
2187 2763 8.339714 TGATGCGCCATTACTAGTTAAAATTAC 58.660 33.333 4.18 0.00 0.00 1.89
2190 2766 6.317642 TGTGATGCGCCATTACTAGTTAAAAT 59.682 34.615 4.18 0.00 32.63 1.82
2301 2898 2.045926 GGAGTGGTGCGCCTGAAT 60.046 61.111 18.96 0.00 33.96 2.57
2317 2923 3.560278 GTAATGGCGCACCGTCGG 61.560 66.667 10.83 10.48 39.70 4.79
2318 2924 2.508439 AGTAATGGCGCACCGTCG 60.508 61.111 10.83 0.00 39.70 5.12
2320 2926 2.125269 GGAGTAATGGCGCACCGT 60.125 61.111 10.83 0.00 39.70 4.83
2321 2927 2.895372 GGGAGTAATGGCGCACCG 60.895 66.667 10.83 0.00 39.70 4.94
2322 2928 2.112815 GTGGGAGTAATGGCGCACC 61.113 63.158 10.83 0.00 40.72 5.01
2323 2929 2.461110 CGTGGGAGTAATGGCGCAC 61.461 63.158 10.83 0.00 42.43 5.34
2324 2930 2.125310 CGTGGGAGTAATGGCGCA 60.125 61.111 10.83 0.00 0.00 6.09
2329 2935 2.461110 GCGCACCGTGGGAGTAATG 61.461 63.158 19.08 0.00 31.21 1.90
2330 2936 2.125269 GCGCACCGTGGGAGTAAT 60.125 61.111 19.08 0.00 31.21 1.89
2331 2937 4.382320 GGCGCACCGTGGGAGTAA 62.382 66.667 19.08 0.00 31.21 2.24


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

AutoCloner maintained by Alex Coulton.