Multiple sequence alignment - TraesCS2A01G361900

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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 TraesCS2A01G361900 chr2A 100.000 7763 0 0 1 7763 605806433 605798671 0.000000e+00 14336.0
1 TraesCS2A01G361900 chr2D 91.698 6986 291 98 3 6846 461307960 461301122 0.000000e+00 9420.0
2 TraesCS2A01G361900 chr2D 84.402 468 18 20 6888 7352 461301110 461300695 7.250000e-110 409.0
3 TraesCS2A01G361900 chr2D 93.822 259 13 1 7449 7707 461294004 461293749 3.400000e-103 387.0
4 TraesCS2A01G361900 chr2D 87.805 123 10 2 6547 6664 461293428 461293306 1.050000e-28 139.0
5 TraesCS2A01G361900 chr2D 93.333 90 5 1 7364 7453 461295374 461295286 1.760000e-26 132.0
6 TraesCS2A01G361900 chr2B 91.432 6863 314 92 590 7312 543196009 543189281 0.000000e+00 9164.0
7 TraesCS2A01G361900 chr2B 87.500 432 25 15 7293 7706 543189264 543188844 9.120000e-129 472.0
8 TraesCS2A01G361900 chr2B 86.239 436 52 6 1 433 627654008 627653578 4.240000e-127 466.0
9 TraesCS2A01G361900 chr2B 86.343 432 32 17 7205 7621 543165285 543164866 5.530000e-121 446.0
10 TraesCS2A01G361900 chr2B 88.761 347 25 2 6870 7209 543167749 543167410 5.610000e-111 412.0
11 TraesCS2A01G361900 chr2B 80.922 477 53 18 7252 7700 543058240 543057774 7.460000e-90 342.0
12 TraesCS2A01G361900 chr2B 89.080 174 9 4 6705 6873 543168190 543168022 2.840000e-49 207.0
13 TraesCS2A01G361900 chr2B 82.812 128 8 6 6747 6873 543142090 543141976 1.380000e-17 102.0
14 TraesCS2A01G361900 chr2B 81.667 120 21 1 486 604 543197001 543196882 1.780000e-16 99.0
15 TraesCS2A01G361900 chr2B 95.122 41 1 1 7710 7749 543188864 543188824 6.500000e-06 63.9
16 TraesCS2A01G361900 chr5D 85.337 416 48 11 4 408 293363346 293363759 1.200000e-112 418.0
17 TraesCS2A01G361900 chr5D 86.005 393 43 10 5 393 482213842 482214226 2.020000e-110 411.0
18 TraesCS2A01G361900 chr5A 84.615 416 48 9 12 413 6956210 6955797 4.360000e-107 399.0
19 TraesCS2A01G361900 chr3D 85.242 393 46 10 5 393 12627013 12627397 2.030000e-105 394.0
20 TraesCS2A01G361900 chr3D 85.242 393 46 10 5 393 253558833 253558449 2.030000e-105 394.0
21 TraesCS2A01G361900 chr7B 83.047 407 60 9 3 403 747427882 747428285 2.060000e-95 361.0
22 TraesCS2A01G361900 chr4D 83.047 407 56 11 3 403 47134211 47133812 2.660000e-94 357.0


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 TraesCS2A01G361900 chr2A 605798671 605806433 7762 True 14336.000000 14336 100.000000 1 7763 1 chr2A.!!$R1 7762
1 TraesCS2A01G361900 chr2D 461300695 461307960 7265 True 4914.500000 9420 88.050000 3 7352 2 chr2D.!!$R2 7349
2 TraesCS2A01G361900 chr2D 461293306 461295374 2068 True 219.333333 387 91.653333 6547 7707 3 chr2D.!!$R1 1160
3 TraesCS2A01G361900 chr2B 543188824 543197001 8177 True 2449.725000 9164 88.930250 486 7749 4 chr2B.!!$R5 7263
4 TraesCS2A01G361900 chr2B 543164866 543168190 3324 True 355.000000 446 88.061333 6705 7621 3 chr2B.!!$R4 916

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
770 1685 0.037697 TTCTACGCACGGCACATTCT 60.038 50.000 0.00 0.0 0.00 2.40 F
773 1688 0.108377 TACGCACGGCACATTCTGAT 60.108 50.000 0.00 0.0 0.00 2.90 F
775 1690 0.247814 CGCACGGCACATTCTGATTC 60.248 55.000 0.00 0.0 0.00 2.52 F
1655 2608 0.393537 CTGCCAGATTCCCTGACCAC 60.394 60.000 0.00 0.0 45.78 4.16 F
1996 2960 0.481128 TCCTTTCCAGTTTCCACCCC 59.519 55.000 0.00 0.0 0.00 4.95 F
2816 3824 0.607620 ACAGAGCTCACAGAGAAGGC 59.392 55.000 17.77 0.0 0.00 4.35 F
3660 4691 1.130561 GAATCAAAGAGGAAACCGCCG 59.869 52.381 0.00 0.0 0.00 6.46 F
4156 5187 1.000060 GACAACACACAATGCCTGCAT 60.000 47.619 0.00 0.0 38.46 3.96 F
5686 6763 0.034896 TGTTGAGCCTTTCGTCTCCC 59.965 55.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2954 0.326048 ACATGAGAGAGAGGGGGTGG 60.326 60.000 0.00 0.00 0.00 4.61 R
1992 2956 0.712979 TCACATGAGAGAGAGGGGGT 59.287 55.000 0.00 0.00 0.00 4.95 R
1994 2958 0.752054 GCTCACATGAGAGAGAGGGG 59.248 60.000 22.47 0.00 44.74 4.79 R
2779 3787 0.394565 GTCAGAGAGTGCCTTGGTGT 59.605 55.000 0.00 0.00 0.00 4.16 R
3803 4834 1.669604 TGTTTTGTTGTAGAGGCGCA 58.330 45.000 10.83 0.00 0.00 6.09 R
4156 5187 0.035317 ATGCGCTTTGTCTGAGGTGA 59.965 50.000 9.73 0.00 0.00 4.02 R
5170 6227 1.679680 CCGCTATCAGAAGGAACGGTA 59.320 52.381 0.00 0.00 36.41 4.02 R
5973 7050 0.323629 CCTTGCGGTCCAGGAACTTA 59.676 55.000 2.07 0.00 34.60 2.24 R
6796 7883 0.464452 AATACGTAGGGAGCAGTGCC 59.536 55.000 12.58 3.03 0.00 5.01 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
26 27 1.344114 GTGCCACACCAATTTCCATGT 59.656 47.619 0.00 0.00 0.00 3.21
28 29 1.066929 GCCACACCAATTTCCATGTCC 60.067 52.381 0.00 0.00 0.00 4.02
50 51 1.768684 TTCGCAGAACTCCAGGCCTT 61.769 55.000 0.00 0.00 45.90 4.35
90 91 0.402272 TAGGTGGTTGGAGGTTGGGT 60.402 55.000 0.00 0.00 0.00 4.51
119 120 1.453379 GACCCTCTGGACGATCCGA 60.453 63.158 0.00 0.00 40.17 4.55
124 125 2.029828 CCCTCTGGACGATCCGAAATAG 60.030 54.545 0.00 0.00 40.17 1.73
127 128 3.552875 TCTGGACGATCCGAAATAGACT 58.447 45.455 0.00 0.00 40.17 3.24
159 160 0.800683 CATTCCGCTTCGACGTGCTA 60.801 55.000 0.00 0.00 0.00 3.49
170 171 0.521659 GACGTGCTACTGACGCTCTC 60.522 60.000 0.00 0.00 40.56 3.20
213 214 4.715523 TTTGGCGGCCGCTTAGCT 62.716 61.111 45.23 0.00 41.60 3.32
257 259 2.174319 GCCTTCATCGCCGACCTTC 61.174 63.158 0.00 0.00 0.00 3.46
290 292 2.125269 ACTTATCGCCGCCGCTTT 60.125 55.556 0.00 0.00 0.00 3.51
385 387 1.279496 TGTTGAGCTATGCCCTCAGT 58.721 50.000 0.00 0.00 40.16 3.41
421 423 6.888430 ACTTGTTGTCGCTCTTTTATGTTAG 58.112 36.000 0.00 0.00 0.00 2.34
423 425 6.462073 TGTTGTCGCTCTTTTATGTTAGTC 57.538 37.500 0.00 0.00 0.00 2.59
425 427 6.365247 TGTTGTCGCTCTTTTATGTTAGTCTC 59.635 38.462 0.00 0.00 0.00 3.36
433 457 7.171678 GCTCTTTTATGTTAGTCTCTGTGTGTT 59.828 37.037 0.00 0.00 0.00 3.32
434 458 9.692749 CTCTTTTATGTTAGTCTCTGTGTGTTA 57.307 33.333 0.00 0.00 0.00 2.41
442 466 2.558795 GTCTCTGTGTGTTAGGCTCTGA 59.441 50.000 0.00 0.00 0.00 3.27
450 474 3.060602 GTGTTAGGCTCTGACAGTTGAC 58.939 50.000 1.59 0.00 30.83 3.18
456 480 4.826556 AGGCTCTGACAGTTGACTTTATC 58.173 43.478 1.59 0.00 0.00 1.75
457 481 4.530161 AGGCTCTGACAGTTGACTTTATCT 59.470 41.667 1.59 0.00 0.00 1.98
458 482 5.012561 AGGCTCTGACAGTTGACTTTATCTT 59.987 40.000 1.59 0.00 0.00 2.40
459 483 6.211584 AGGCTCTGACAGTTGACTTTATCTTA 59.788 38.462 1.59 0.00 0.00 2.10
467 494 6.708949 ACAGTTGACTTTATCTTAAAAGCGGA 59.291 34.615 0.00 0.00 39.59 5.54
469 496 6.935208 AGTTGACTTTATCTTAAAAGCGGAGT 59.065 34.615 0.00 0.00 39.59 3.85
474 501 8.161699 ACTTTATCTTAAAAGCGGAGTGAAAA 57.838 30.769 0.00 0.00 39.59 2.29
475 502 8.793592 ACTTTATCTTAAAAGCGGAGTGAAAAT 58.206 29.630 0.00 0.00 39.59 1.82
484 511 5.113502 AGCGGAGTGAAAATCTTTTTCAG 57.886 39.130 13.98 5.77 38.88 3.02
524 551 8.492782 AGATTAGATGTCCAACTCTTTCATCAT 58.507 33.333 0.00 0.00 37.80 2.45
525 552 8.674263 ATTAGATGTCCAACTCTTTCATCATC 57.326 34.615 0.00 0.00 37.80 2.92
551 578 1.088340 GGACTCGTCTCGACCGATCA 61.088 60.000 3.19 0.00 33.27 2.92
553 581 0.672711 ACTCGTCTCGACCGATCACA 60.673 55.000 3.19 0.00 33.27 3.58
588 616 1.879380 CCATTTCGAAGGCAGTGTTGA 59.121 47.619 0.00 0.00 0.00 3.18
629 1544 4.465632 AAAGGTTGAAACAACACCTTCC 57.534 40.909 14.89 0.00 39.61 3.46
676 1591 1.715585 CCACGGCGAGTAAATGCAG 59.284 57.895 16.62 0.00 0.00 4.41
742 1657 2.140717 GGCCGGATATACAAGAAACCG 58.859 52.381 5.05 0.00 40.03 4.44
770 1685 0.037697 TTCTACGCACGGCACATTCT 60.038 50.000 0.00 0.00 0.00 2.40
771 1686 0.735978 TCTACGCACGGCACATTCTG 60.736 55.000 0.00 0.00 0.00 3.02
772 1687 0.735978 CTACGCACGGCACATTCTGA 60.736 55.000 0.00 0.00 0.00 3.27
773 1688 0.108377 TACGCACGGCACATTCTGAT 60.108 50.000 0.00 0.00 0.00 2.90
774 1689 0.955428 ACGCACGGCACATTCTGATT 60.955 50.000 0.00 0.00 0.00 2.57
775 1690 0.247814 CGCACGGCACATTCTGATTC 60.248 55.000 0.00 0.00 0.00 2.52
839 1757 0.877071 CTTGTCATTCGCAGCCACTT 59.123 50.000 0.00 0.00 0.00 3.16
844 1762 0.445436 CATTCGCAGCCACTTCACTC 59.555 55.000 0.00 0.00 0.00 3.51
1047 1969 2.852075 TTCACGGGGCAGAAGGGT 60.852 61.111 0.00 0.00 0.00 4.34
1395 2336 2.329339 GCATTCGATTCAGGCCGC 59.671 61.111 0.00 0.00 0.00 6.53
1433 2374 2.857748 GAGGAGTTTGTTTGCGGTTTTG 59.142 45.455 0.00 0.00 0.00 2.44
1487 2439 4.095400 GCAGGAGGGAGGGAGGGA 62.095 72.222 0.00 0.00 0.00 4.20
1651 2604 1.198713 GTCTCTGCCAGATTCCCTGA 58.801 55.000 0.00 0.00 45.78 3.86
1654 2607 0.547471 TCTGCCAGATTCCCTGACCA 60.547 55.000 0.00 0.00 45.78 4.02
1655 2608 0.393537 CTGCCAGATTCCCTGACCAC 60.394 60.000 0.00 0.00 45.78 4.16
1656 2609 1.077429 GCCAGATTCCCTGACCACC 60.077 63.158 0.00 0.00 45.78 4.61
1657 2610 1.221840 CCAGATTCCCTGACCACCG 59.778 63.158 0.00 0.00 45.78 4.94
1658 2611 1.221840 CAGATTCCCTGACCACCGG 59.778 63.158 0.00 0.00 45.78 5.28
1659 2612 1.080354 AGATTCCCTGACCACCGGA 59.920 57.895 9.46 0.00 0.00 5.14
1662 2615 3.846405 TTCCCTGACCACCGGAGCT 62.846 63.158 9.46 0.00 0.00 4.09
1663 2616 4.087892 CCCTGACCACCGGAGCTG 62.088 72.222 9.46 0.00 0.00 4.24
1664 2617 3.314331 CCTGACCACCGGAGCTGT 61.314 66.667 9.46 0.00 0.00 4.40
1665 2618 2.743718 CTGACCACCGGAGCTGTT 59.256 61.111 9.46 0.00 0.00 3.16
1666 2619 1.669115 CTGACCACCGGAGCTGTTG 60.669 63.158 9.46 0.00 0.00 3.33
1668 2621 4.643387 ACCACCGGAGCTGTTGCC 62.643 66.667 9.46 0.00 40.80 4.52
1670 2623 4.988598 CACCGGAGCTGTTGCCGT 62.989 66.667 9.46 0.00 45.85 5.68
1671 2624 4.250305 ACCGGAGCTGTTGCCGTT 62.250 61.111 9.46 0.00 45.85 4.44
1672 2625 3.423154 CCGGAGCTGTTGCCGTTC 61.423 66.667 10.34 0.00 45.85 3.95
1673 2626 3.777925 CGGAGCTGTTGCCGTTCG 61.778 66.667 3.49 0.00 42.49 3.95
1675 2628 3.044305 GAGCTGTTGCCGTTCGCT 61.044 61.111 0.00 0.00 40.80 4.93
1677 2630 4.389576 GCTGTTGCCGTTCGCTGG 62.390 66.667 0.00 0.00 38.78 4.85
1702 2655 3.069729 CCTCTCGATTCCCGGATTAAACT 59.930 47.826 0.73 0.00 39.14 2.66
1756 2709 2.143925 CGAGTTCTTGGTGTTTCTCCC 58.856 52.381 0.00 0.00 0.00 4.30
1758 2711 2.106684 GAGTTCTTGGTGTTTCTCCCCT 59.893 50.000 0.00 0.00 0.00 4.79
1832 2790 3.023119 TCTTTTGCTTTGTGCCTTCAGA 58.977 40.909 0.00 0.00 42.00 3.27
1834 2792 2.057137 TTGCTTTGTGCCTTCAGAGT 57.943 45.000 0.00 0.00 42.00 3.24
1875 2839 3.976793 TTCTACATCGCCTAGGTTACG 57.023 47.619 11.31 5.75 0.00 3.18
1885 2849 2.477525 GCCTAGGTTACGTCTCGTTCAG 60.478 54.545 11.31 0.00 41.54 3.02
1888 2852 1.069378 GGTTACGTCTCGTTCAGCCG 61.069 60.000 0.00 0.00 41.54 5.52
1898 2862 1.225376 CGTTCAGCCGCCACAGTTTA 61.225 55.000 0.00 0.00 0.00 2.01
1904 2868 2.942376 CAGCCGCCACAGTTTATATCAA 59.058 45.455 0.00 0.00 0.00 2.57
1935 2899 1.506493 ACTCAGCAGCTCGAGTTTTG 58.494 50.000 15.13 11.30 39.45 2.44
1949 2913 6.311445 GCTCGAGTTTTGAACTTCTCATCATA 59.689 38.462 15.13 0.00 43.03 2.15
1958 2922 5.819379 TGAACTTCTCATCATACCATGAAGC 59.181 40.000 0.00 0.00 43.50 3.86
1961 2925 5.069119 ACTTCTCATCATACCATGAAGCGTA 59.931 40.000 0.00 0.00 43.50 4.42
1986 2950 2.012673 CAAAGCCGATCTCCTTTCCAG 58.987 52.381 4.94 0.00 0.00 3.86
1987 2951 1.280457 AAGCCGATCTCCTTTCCAGT 58.720 50.000 0.00 0.00 0.00 4.00
1990 2954 2.010497 GCCGATCTCCTTTCCAGTTTC 58.990 52.381 0.00 0.00 0.00 2.78
1991 2955 2.633488 CCGATCTCCTTTCCAGTTTCC 58.367 52.381 0.00 0.00 0.00 3.13
1992 2956 2.027192 CCGATCTCCTTTCCAGTTTCCA 60.027 50.000 0.00 0.00 0.00 3.53
1993 2957 3.003480 CGATCTCCTTTCCAGTTTCCAC 58.997 50.000 0.00 0.00 0.00 4.02
1994 2958 2.951229 TCTCCTTTCCAGTTTCCACC 57.049 50.000 0.00 0.00 0.00 4.61
1995 2959 1.423921 TCTCCTTTCCAGTTTCCACCC 59.576 52.381 0.00 0.00 0.00 4.61
1996 2960 0.481128 TCCTTTCCAGTTTCCACCCC 59.519 55.000 0.00 0.00 0.00 4.95
2047 3011 1.813862 GCCCGTGCCTGCTAAATCATA 60.814 52.381 0.00 0.00 0.00 2.15
2179 3152 2.024414 GCATCATGTTACCCCCTGTTC 58.976 52.381 0.00 0.00 0.00 3.18
2190 3163 1.375908 CCCTGTTCGCTGCTGCTAA 60.376 57.895 14.03 6.22 36.97 3.09
2191 3164 1.639298 CCCTGTTCGCTGCTGCTAAC 61.639 60.000 21.25 21.25 42.79 2.34
2193 3166 3.231734 TGTTCGCTGCTGCTAACAT 57.768 47.368 25.11 0.00 45.65 2.71
2194 3167 1.522668 TGTTCGCTGCTGCTAACATT 58.477 45.000 25.11 0.00 45.65 2.71
2195 3168 1.879380 TGTTCGCTGCTGCTAACATTT 59.121 42.857 25.11 0.00 45.65 2.32
2254 3237 2.027688 CAGTCGTTTATCGCTTCGTTCC 59.972 50.000 0.00 0.00 39.67 3.62
2286 3269 2.426522 TGCCATCTTCTCTCGGTTTTG 58.573 47.619 0.00 0.00 0.00 2.44
2302 3285 2.151502 TTTGAACAAGAACAGGGCCA 57.848 45.000 6.18 0.00 0.00 5.36
2315 3298 2.887568 GGCCATCGACTGTGCTCG 60.888 66.667 0.00 0.00 34.83 5.03
2316 3299 2.125912 GCCATCGACTGTGCTCGT 60.126 61.111 0.00 0.00 35.10 4.18
2317 3300 2.447887 GCCATCGACTGTGCTCGTG 61.448 63.158 0.00 0.00 35.10 4.35
2488 3488 4.383118 GCTACTTAAGAGCATCCCAAGACA 60.383 45.833 10.09 0.00 39.84 3.41
2491 3491 4.042187 ACTTAAGAGCATCCCAAGACACTT 59.958 41.667 10.09 0.00 33.66 3.16
2492 3492 2.777832 AGAGCATCCCAAGACACTTC 57.222 50.000 0.00 0.00 33.66 3.01
2493 3493 1.980765 AGAGCATCCCAAGACACTTCA 59.019 47.619 0.00 0.00 33.66 3.02
2494 3494 2.575279 AGAGCATCCCAAGACACTTCAT 59.425 45.455 0.00 0.00 33.66 2.57
2495 3495 3.009916 AGAGCATCCCAAGACACTTCATT 59.990 43.478 0.00 0.00 33.66 2.57
2496 3496 3.760684 GAGCATCCCAAGACACTTCATTT 59.239 43.478 0.00 0.00 0.00 2.32
2538 3539 2.281900 TGGCTGTTTGTACCGGCC 60.282 61.111 12.21 12.21 40.38 6.13
2589 3594 1.538687 GCTTGATTGGCTGGCCTTGT 61.539 55.000 13.05 0.00 36.94 3.16
2640 3645 1.079503 GTTTCATGTCCTCTGCGTCC 58.920 55.000 0.00 0.00 0.00 4.79
2668 3673 2.038387 AACTTCTTTGCCGTGACACT 57.962 45.000 3.68 0.00 0.00 3.55
2721 3729 5.235850 TGTTGTAATGCTTGGAGGAAGTA 57.764 39.130 0.00 0.00 33.73 2.24
2723 3731 5.880332 TGTTGTAATGCTTGGAGGAAGTATC 59.120 40.000 0.00 0.00 36.08 2.24
2779 3787 1.613928 TGAGTACGGGGATGGCCAA 60.614 57.895 10.96 0.00 35.15 4.52
2816 3824 0.607620 ACAGAGCTCACAGAGAAGGC 59.392 55.000 17.77 0.00 0.00 4.35
2898 3908 3.621268 TCAGTAATGCGTATTCAGTTGCC 59.379 43.478 0.69 0.00 0.00 4.52
2940 3950 7.686438 TGAGATAAATGCTGCTTTTCTACAA 57.314 32.000 15.61 0.61 0.00 2.41
2941 3951 8.284945 TGAGATAAATGCTGCTTTTCTACAAT 57.715 30.769 15.61 5.14 0.00 2.71
2998 4008 4.192429 AGCATTTTGTACATTTCTGCCC 57.808 40.909 13.41 0.00 0.00 5.36
3092 4102 3.368323 GGTGTTGGCATTGTATGGGAAAG 60.368 47.826 0.00 0.00 0.00 2.62
3121 4131 7.595819 TCCTTTCCACAATGTAGACATTTTT 57.404 32.000 5.14 0.00 43.48 1.94
3190 4200 6.431198 TTTCGCTCCATAGGTTTGAAATAC 57.569 37.500 0.00 0.00 0.00 1.89
3222 4251 5.796350 ACACGCTGGTCTAAATATTGAAC 57.204 39.130 0.00 0.00 0.00 3.18
3235 4264 8.999431 TCTAAATATTGAACTTGACTGTGTTCC 58.001 33.333 6.93 0.00 41.10 3.62
3269 4298 1.885887 TGTTTTGTCTGGCATGTAGGC 59.114 47.619 0.00 0.00 44.50 3.93
3277 4306 2.819608 TCTGGCATGTAGGCTGTTTTTC 59.180 45.455 0.00 0.00 44.55 2.29
3434 4463 6.204688 GTCATGTTTCAGTTTGTCATAGGTGA 59.795 38.462 0.00 0.00 0.00 4.02
3435 4464 6.942005 TCATGTTTCAGTTTGTCATAGGTGAT 59.058 34.615 0.00 0.00 36.60 3.06
3437 4466 5.705441 TGTTTCAGTTTGTCATAGGTGATCC 59.295 40.000 0.00 0.00 36.60 3.36
3549 4580 9.720769 CTTCTTTGTTCTAATACAAACTCCCTA 57.279 33.333 0.00 0.00 41.65 3.53
3621 4652 5.128919 CCCATGAAGAAGCTACTAGCAAAT 58.871 41.667 10.73 0.00 45.56 2.32
3657 4688 3.412386 AGTGGAATCAAAGAGGAAACCG 58.588 45.455 0.00 0.00 0.00 4.44
3660 4691 1.130561 GAATCAAAGAGGAAACCGCCG 59.869 52.381 0.00 0.00 0.00 6.46
3727 4758 5.448360 GCTCAAGAACAGGCATTACATTCTC 60.448 44.000 0.00 0.00 0.00 2.87
3735 4766 4.706476 CAGGCATTACATTCTCCCAAAAGA 59.294 41.667 0.00 0.00 0.00 2.52
3765 4796 7.799081 TGAGGAGAAGTCATTCACATGATAAT 58.201 34.615 0.00 0.00 41.64 1.28
3849 4880 1.757423 GCAAACACACAGGCCCCAAT 61.757 55.000 0.00 0.00 0.00 3.16
3885 4916 3.988976 AAGGATGTGTATGCAGTCTGT 57.011 42.857 0.93 0.00 0.00 3.41
4005 5036 6.096695 ACAAAAGTTCATACAAGCAAAACGT 58.903 32.000 0.00 0.00 0.00 3.99
4156 5187 1.000060 GACAACACACAATGCCTGCAT 60.000 47.619 0.00 0.00 38.46 3.96
4237 5268 2.600792 GCAAGAGAAAGCAGAACACACG 60.601 50.000 0.00 0.00 0.00 4.49
4277 5334 5.602628 TGAGATCTCATTCAGCAGAAGATG 58.397 41.667 21.67 0.00 37.14 2.90
4411 5468 4.520492 ACAGCCTTTCTTGGTGATTTACAG 59.480 41.667 0.00 0.00 0.00 2.74
4480 5537 3.031013 TCAATACCTGCCAGAAGATCGA 58.969 45.455 0.00 0.00 0.00 3.59
4783 5840 3.005155 CGGTAGCATGTGATGAGATCAGA 59.995 47.826 0.00 0.00 40.53 3.27
4839 5896 1.065199 GGGTGACATGCTCTCCATCAA 60.065 52.381 14.28 0.00 34.59 2.57
4865 5922 7.565680 AGAAACTGAGAAAGAGGAAACTGTTA 58.434 34.615 0.00 0.00 44.30 2.41
5161 6218 3.064900 AGAAGTAAAAGGCTGGCAGAG 57.935 47.619 20.86 0.00 0.00 3.35
5170 6227 0.037447 GGCTGGCAGAGGAGAAAACT 59.963 55.000 20.86 0.00 0.00 2.66
5174 6231 1.275291 TGGCAGAGGAGAAAACTACCG 59.725 52.381 0.00 0.00 0.00 4.02
5450 6524 3.769739 ACTTGTTGACATGTAGCAGGA 57.230 42.857 0.00 0.00 33.24 3.86
5515 6589 4.873746 AGTGGATATACTGATGAACCCG 57.126 45.455 0.00 0.00 0.00 5.28
5516 6590 4.223953 AGTGGATATACTGATGAACCCGT 58.776 43.478 0.00 0.00 0.00 5.28
5544 6618 0.173255 GTGGCCTAAAATGCATGCGT 59.827 50.000 14.09 10.53 0.00 5.24
5619 6693 7.170965 ACACTAATGAACCTGAATCATCAAGT 58.829 34.615 0.00 0.00 36.53 3.16
5650 6724 3.503363 TGCCTGCAATGAGAGTAAGTTTG 59.497 43.478 0.00 0.00 0.00 2.93
5682 6759 5.607119 TTCTAATTGTTGAGCCTTTCGTC 57.393 39.130 0.00 0.00 0.00 4.20
5686 6763 0.034896 TGTTGAGCCTTTCGTCTCCC 59.965 55.000 0.00 0.00 0.00 4.30
5732 6809 6.956299 TTGTTCTTATTACGTTACAGGAGC 57.044 37.500 0.00 0.00 0.00 4.70
5782 6859 1.227527 CCCCGCTCGTTATCATGCA 60.228 57.895 0.00 0.00 0.00 3.96
5939 7016 2.503356 TGGTTTTCACAGGTTGGCATTT 59.497 40.909 0.00 0.00 0.00 2.32
5973 7050 0.324614 TTGATCCCGCACTGTGTGAT 59.675 50.000 22.05 14.48 35.23 3.06
5980 7057 1.732259 CCGCACTGTGTGATAAGTTCC 59.268 52.381 22.05 0.00 35.23 3.62
6151 7228 2.012673 GCGAGGCATTGTCTCAAGATT 58.987 47.619 17.85 0.00 33.34 2.40
6189 7266 2.803203 CCATGTGAGGGATTGGCTG 58.197 57.895 0.00 0.00 0.00 4.85
6193 7270 1.357137 TGTGAGGGATTGGCTGTACA 58.643 50.000 0.00 0.00 0.00 2.90
6221 7298 3.869272 GCTCGCGGCCAATGAGTG 61.869 66.667 6.13 0.30 34.27 3.51
6223 7300 1.153647 CTCGCGGCCAATGAGTGTA 60.154 57.895 6.13 0.00 0.00 2.90
6258 7335 1.825090 TGCTGGAAAGAATCGTGCAT 58.175 45.000 0.00 0.00 33.84 3.96
6283 7360 2.285668 TGGAAGGAGGAGGCTGGG 60.286 66.667 0.00 0.00 0.00 4.45
6336 7413 1.470098 ACGAAACAGATTGCAGATGGC 59.530 47.619 0.00 0.00 45.13 4.40
6376 7453 1.880340 GAAGCTGTGGCGGATCTCG 60.880 63.158 0.00 0.00 44.37 4.04
6406 7483 0.108472 TCCACAGCAAGATCTCGCAG 60.108 55.000 8.66 1.91 0.00 5.18
6415 7492 1.094073 AGATCTCGCAGTGCCAATGC 61.094 55.000 7.13 7.13 40.35 3.56
6416 7493 2.056481 GATCTCGCAGTGCCAATGCC 62.056 60.000 11.97 0.00 40.67 4.40
6417 7494 2.825075 ATCTCGCAGTGCCAATGCCA 62.825 55.000 11.97 0.00 40.67 4.92
6418 7495 2.596923 TCGCAGTGCCAATGCCAA 60.597 55.556 11.97 0.00 40.67 4.52
6419 7496 1.940883 CTCGCAGTGCCAATGCCAAT 61.941 55.000 11.97 0.00 40.67 3.16
6420 7497 1.807981 CGCAGTGCCAATGCCAATG 60.808 57.895 11.97 0.00 40.67 2.82
6593 7676 3.322369 CGCACCACAGATTGTACTACAA 58.678 45.455 4.08 4.08 42.95 2.41
6626 7709 1.174712 ACCATGTCAACTGTGCAGCC 61.175 55.000 0.00 0.00 0.00 4.85
6640 7723 2.362120 AGCCCTGCACAAGCCATC 60.362 61.111 0.00 0.00 41.13 3.51
6644 7727 1.001764 CCTGCACAAGCCATCTGGA 60.002 57.895 0.00 0.00 41.13 3.86
6674 7757 9.016438 ACTAGTTTTTCCTTTTAACTGTCACAA 57.984 29.630 0.00 0.00 34.26 3.33
6691 7777 7.824289 ACTGTCACAATAGCATATTGTACTGTT 59.176 33.333 13.29 0.00 39.94 3.16
6728 7814 6.372659 CAGCATGTGGTTTCAGTATACTCTTT 59.627 38.462 1.26 0.00 0.00 2.52
6793 7880 4.919168 CCATGCATGTGTGTTTGACTTAAG 59.081 41.667 24.58 0.00 0.00 1.85
6796 7883 5.820131 TGCATGTGTGTTTGACTTAAGAAG 58.180 37.500 10.09 0.00 0.00 2.85
6810 7897 0.615850 AAGAAGGCACTGCTCCCTAC 59.384 55.000 0.00 0.00 44.46 3.18
6835 7930 6.924060 CGTATTATATATTAGCAGGTCAGGGC 59.076 42.308 0.00 0.00 0.00 5.19
6945 8316 6.131961 AGCAGGATTAATTAATGGAGCAACT 58.868 36.000 15.39 1.62 0.00 3.16
6946 8317 6.608808 AGCAGGATTAATTAATGGAGCAACTT 59.391 34.615 15.39 0.00 0.00 2.66
6958 8329 3.199946 TGGAGCAACTTAACCTAGGATGG 59.800 47.826 17.98 4.04 0.00 3.51
7038 8419 2.255252 CTTTTTGTCGGCCCTGCG 59.745 61.111 0.00 0.00 0.00 5.18
7048 8429 2.486966 GCCCTGCGCATTCTTCAC 59.513 61.111 12.24 0.00 37.47 3.18
7054 8435 2.099062 CGCATTCTTCACGCCTGC 59.901 61.111 0.00 0.00 0.00 4.85
7060 8441 0.516877 TTCTTCACGCCTGCGATTTG 59.483 50.000 19.52 6.41 42.83 2.32
7065 8446 1.079127 ACGCCTGCGATTTGCTACT 60.079 52.632 19.52 0.00 46.63 2.57
7072 8453 3.243873 CCTGCGATTTGCTACTCTGGATA 60.244 47.826 0.00 0.00 46.63 2.59
7189 8570 2.258286 GGTGCATGGTTTGGCGTC 59.742 61.111 0.00 0.00 0.00 5.19
7214 10724 2.290641 GTGTTTGACTGTAAGGTGCTGG 59.709 50.000 0.00 0.00 39.30 4.85
7284 10799 4.263506 ACTCCTGGTAATGTTTTCAGAGGG 60.264 45.833 0.00 0.00 0.00 4.30
7331 10882 4.124970 TCACATATGAACTCTGCATCTGC 58.875 43.478 10.38 0.00 42.50 4.26
7355 10918 6.672266 TTATCCTCTCTTGTGAGACTGTTT 57.328 37.500 1.76 0.00 43.73 2.83
7356 10919 7.577807 GCTTATCCTCTCTTGTGAGACTGTTTA 60.578 40.741 1.76 0.00 43.73 2.01
7362 10925 7.064371 CCTCTCTTGTGAGACTGTTTATTCATG 59.936 40.741 1.76 0.00 43.73 3.07
7415 10978 2.265739 GCAGTGGCTGTGATCGGA 59.734 61.111 0.00 0.00 36.96 4.55
7431 10994 1.006832 CGGATGTGGTTTCGTGGATC 58.993 55.000 0.00 0.00 0.00 3.36
7440 11003 1.993370 GTTTCGTGGATCTTCAGACCG 59.007 52.381 0.00 0.00 0.00 4.79
7541 12398 2.658538 CGACATCTTCGTCCTGCTG 58.341 57.895 0.00 0.00 43.24 4.41
7600 12463 4.678743 AAAACTGGCCCGCCCTCC 62.679 66.667 0.00 0.00 34.56 4.30
7617 12480 2.432444 CTCCGTTGATACCCTTTTGCA 58.568 47.619 0.00 0.00 0.00 4.08
7685 12552 0.179032 TGGCACGACCATTGTTCACT 60.179 50.000 0.00 0.00 46.36 3.41
7686 12553 0.238289 GGCACGACCATTGTTCACTG 59.762 55.000 0.00 0.00 38.86 3.66
7687 12554 0.944386 GCACGACCATTGTTCACTGT 59.056 50.000 0.00 0.00 0.00 3.55
7688 12555 1.333619 GCACGACCATTGTTCACTGTT 59.666 47.619 0.00 0.00 0.00 3.16
7689 12556 2.854424 GCACGACCATTGTTCACTGTTG 60.854 50.000 0.00 0.00 0.00 3.33
7690 12557 1.333619 ACGACCATTGTTCACTGTTGC 59.666 47.619 0.00 0.00 0.00 4.17
7691 12558 1.333308 CGACCATTGTTCACTGTTGCA 59.667 47.619 0.00 0.00 0.00 4.08
7692 12559 2.731217 GACCATTGTTCACTGTTGCAC 58.269 47.619 0.00 0.00 0.00 4.57
7693 12560 2.098614 ACCATTGTTCACTGTTGCACA 58.901 42.857 0.00 0.00 0.00 4.57
7694 12561 2.495270 ACCATTGTTCACTGTTGCACAA 59.505 40.909 0.00 0.00 42.09 3.33
7695 12562 3.117794 CCATTGTTCACTGTTGCACAAG 58.882 45.455 0.00 0.00 41.34 3.16
7696 12563 2.937469 TTGTTCACTGTTGCACAAGG 57.063 45.000 0.00 0.00 34.43 3.61
7697 12564 2.121291 TGTTCACTGTTGCACAAGGA 57.879 45.000 0.00 0.00 0.00 3.36
7698 12565 1.742831 TGTTCACTGTTGCACAAGGAC 59.257 47.619 0.00 0.00 0.00 3.85
7699 12566 1.065551 GTTCACTGTTGCACAAGGACC 59.934 52.381 0.00 0.00 0.00 4.46
7700 12567 0.254462 TCACTGTTGCACAAGGACCA 59.746 50.000 0.00 0.00 0.00 4.02
7701 12568 0.381801 CACTGTTGCACAAGGACCAC 59.618 55.000 0.00 0.00 0.00 4.16
7702 12569 0.751643 ACTGTTGCACAAGGACCACC 60.752 55.000 0.00 0.00 0.00 4.61
7703 12570 1.785041 CTGTTGCACAAGGACCACCG 61.785 60.000 0.00 0.00 41.83 4.94
7704 12571 1.822186 GTTGCACAAGGACCACCGT 60.822 57.895 0.00 0.00 41.83 4.83
7705 12572 1.077357 TTGCACAAGGACCACCGTT 60.077 52.632 0.00 0.00 41.83 4.44
7706 12573 1.098712 TTGCACAAGGACCACCGTTC 61.099 55.000 0.00 0.00 41.83 3.95
7707 12574 1.525077 GCACAAGGACCACCGTTCA 60.525 57.895 0.00 0.00 41.83 3.18
7708 12575 0.889186 GCACAAGGACCACCGTTCAT 60.889 55.000 0.00 0.00 41.83 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.318441 CTGGAGTTCTGCGAACAGGA 59.682 55.000 18.86 5.62 44.59 3.86
28 29 1.294659 GCCTGGAGTTCTGCGAACAG 61.295 60.000 18.86 10.44 45.95 3.16
84 85 2.359975 CCAGGCGAGGAACCCAAC 60.360 66.667 0.00 0.00 0.00 3.77
90 91 2.683933 GAGGGTCCAGGCGAGGAA 60.684 66.667 3.24 0.00 39.92 3.36
119 120 4.002982 TGCGCTGAATCACAAGTCTATTT 58.997 39.130 9.73 0.00 0.00 1.40
124 125 2.476854 GGAATGCGCTGAATCACAAGTC 60.477 50.000 9.73 0.00 0.00 3.01
127 128 0.447406 CGGAATGCGCTGAATCACAA 59.553 50.000 9.73 0.00 0.00 3.33
159 160 2.101582 ACAGTTTGAAGAGAGCGTCAGT 59.898 45.455 0.00 0.00 34.09 3.41
170 171 4.335315 TGCAAGTAACCAGACAGTTTGAAG 59.665 41.667 0.00 0.00 0.00 3.02
213 214 3.716195 CATCACGGTCCTGGGGCA 61.716 66.667 0.00 0.00 0.00 5.36
273 275 2.125269 AAAGCGGCGGCGATAAGT 60.125 55.556 36.87 15.29 46.35 2.24
304 306 1.661821 CGGCTCCTAATTCGGCTCG 60.662 63.158 0.00 0.00 0.00 5.03
375 377 2.114616 CTGAGGTTCTACTGAGGGCAT 58.885 52.381 0.00 0.00 0.00 4.40
385 387 4.558095 GCGACAACAAGTACTGAGGTTCTA 60.558 45.833 0.00 0.00 0.00 2.10
421 423 2.558795 TCAGAGCCTAACACACAGAGAC 59.441 50.000 0.00 0.00 0.00 3.36
423 425 2.297315 TGTCAGAGCCTAACACACAGAG 59.703 50.000 0.00 0.00 0.00 3.35
425 427 2.036475 ACTGTCAGAGCCTAACACACAG 59.964 50.000 6.91 0.00 36.63 3.66
433 457 5.717178 AGATAAAGTCAACTGTCAGAGCCTA 59.283 40.000 6.91 0.00 0.00 3.93
434 458 4.530161 AGATAAAGTCAACTGTCAGAGCCT 59.470 41.667 6.91 0.00 0.00 4.58
442 466 6.708949 TCCGCTTTTAAGATAAAGTCAACTGT 59.291 34.615 0.00 0.00 37.43 3.55
450 474 9.278734 GATTTTCACTCCGCTTTTAAGATAAAG 57.721 33.333 0.00 0.00 38.00 1.85
456 480 7.930513 AAAAGATTTTCACTCCGCTTTTAAG 57.069 32.000 0.00 0.00 34.80 1.85
457 481 7.976734 TGAAAAAGATTTTCACTCCGCTTTTAA 59.023 29.630 12.80 0.00 35.30 1.52
458 482 7.484975 TGAAAAAGATTTTCACTCCGCTTTTA 58.515 30.769 12.80 0.00 35.30 1.52
459 483 6.337356 TGAAAAAGATTTTCACTCCGCTTTT 58.663 32.000 12.80 0.00 37.21 2.27
588 616 8.379428 ACCTTTTGAATTATTAAGGGCATCTT 57.621 30.769 13.50 0.00 41.14 2.40
629 1544 4.836125 ACTACCTGCATTTCTGTTTGTG 57.164 40.909 0.00 0.00 0.00 3.33
676 1591 2.598439 CGTGCCGTAGATGTAGTACGAC 60.598 54.545 4.29 0.00 44.90 4.34
742 1657 2.781646 GCCGTGCGTAGAAATTTATTGC 59.218 45.455 0.00 0.00 0.00 3.56
770 1685 1.878069 CGCTGCGTGATCCGAATCA 60.878 57.895 14.93 0.00 39.63 2.57
771 1686 1.812214 GACGCTGCGTGATCCGAATC 61.812 60.000 33.96 10.78 41.37 2.52
772 1687 1.878522 GACGCTGCGTGATCCGAAT 60.879 57.895 33.96 3.65 41.37 3.34
773 1688 2.506217 GACGCTGCGTGATCCGAA 60.506 61.111 33.96 0.00 41.37 4.30
774 1689 4.492160 GGACGCTGCGTGATCCGA 62.492 66.667 33.96 0.00 41.37 4.55
839 1757 1.152631 TGGAGTGGACGTGGAGTGA 60.153 57.895 0.00 0.00 0.00 3.41
844 1762 1.153823 GATCGTGGAGTGGACGTGG 60.154 63.158 0.00 0.00 38.04 4.94
873 1791 2.280389 CGGTGATGATGGGCGAGG 60.280 66.667 0.00 0.00 0.00 4.63
879 1797 1.672881 GAGAAAAGGCGGTGATGATGG 59.327 52.381 0.00 0.00 0.00 3.51
934 1852 4.675029 GTCGTGGACGTGGGGTGG 62.675 72.222 0.00 0.00 40.80 4.61
963 1883 5.422145 GTCTCTCGGATATCCTACTCCTAC 58.578 50.000 19.61 5.66 0.00 3.18
964 1884 4.160065 CGTCTCTCGGATATCCTACTCCTA 59.840 50.000 19.61 0.00 35.71 2.94
965 1885 3.055675 CGTCTCTCGGATATCCTACTCCT 60.056 52.174 19.61 0.00 35.71 3.69
966 1886 3.264104 CGTCTCTCGGATATCCTACTCC 58.736 54.545 19.61 2.68 35.71 3.85
967 1887 2.674357 GCGTCTCTCGGATATCCTACTC 59.326 54.545 19.61 4.69 40.26 2.59
968 1888 2.702261 GCGTCTCTCGGATATCCTACT 58.298 52.381 19.61 0.00 40.26 2.57
995 1915 2.094234 GTGTTCTTGCTCCTCTCCTCTC 60.094 54.545 0.00 0.00 0.00 3.20
996 1916 1.899142 GTGTTCTTGCTCCTCTCCTCT 59.101 52.381 0.00 0.00 0.00 3.69
997 1917 1.620819 TGTGTTCTTGCTCCTCTCCTC 59.379 52.381 0.00 0.00 0.00 3.71
998 1918 1.722034 TGTGTTCTTGCTCCTCTCCT 58.278 50.000 0.00 0.00 0.00 3.69
999 1919 2.147150 GTTGTGTTCTTGCTCCTCTCC 58.853 52.381 0.00 0.00 0.00 3.71
1047 1969 1.691219 GGAATTCACCCAGCTCCCA 59.309 57.895 7.93 0.00 0.00 4.37
1319 2260 3.621461 GCGGAGGAAGATGGACCTAAAAA 60.621 47.826 0.00 0.00 36.57 1.94
1324 2265 2.427245 CGCGGAGGAAGATGGACCT 61.427 63.158 0.00 0.00 39.41 3.85
1395 2336 0.734253 CTCGCCTGAGAAGAACACGG 60.734 60.000 0.00 0.00 45.57 4.94
1433 2374 4.142966 CGAAATTCCCTGACGAAACCTAAC 60.143 45.833 0.00 0.00 0.00 2.34
1484 2436 0.250081 GCTCGGATCTCCACATTCCC 60.250 60.000 0.00 0.00 35.14 3.97
1485 2437 0.755686 AGCTCGGATCTCCACATTCC 59.244 55.000 0.00 0.00 35.14 3.01
1486 2438 1.601663 CGAGCTCGGATCTCCACATTC 60.602 57.143 28.40 0.00 35.14 2.67
1487 2439 0.387202 CGAGCTCGGATCTCCACATT 59.613 55.000 28.40 0.00 35.14 2.71
1651 2604 4.643387 GGCAACAGCTCCGGTGGT 62.643 66.667 0.00 0.35 35.13 4.16
1657 2610 4.090057 GCGAACGGCAACAGCTCC 62.090 66.667 0.00 0.00 42.87 4.70
1668 2621 2.202676 GAGAGGAGCCAGCGAACG 60.203 66.667 0.00 0.00 0.00 3.95
1670 2623 1.323271 AATCGAGAGGAGCCAGCGAA 61.323 55.000 0.00 0.00 34.46 4.70
1671 2624 1.729470 GAATCGAGAGGAGCCAGCGA 61.729 60.000 0.00 0.00 35.32 4.93
1672 2625 1.299773 GAATCGAGAGGAGCCAGCG 60.300 63.158 0.00 0.00 0.00 5.18
1673 2626 1.068921 GGAATCGAGAGGAGCCAGC 59.931 63.158 0.00 0.00 0.00 4.85
1675 2628 2.127869 CGGGAATCGAGAGGAGCCA 61.128 63.158 0.00 0.00 42.43 4.75
1677 2630 1.182385 ATCCGGGAATCGAGAGGAGC 61.182 60.000 0.00 0.00 42.43 4.70
1678 2631 1.333177 AATCCGGGAATCGAGAGGAG 58.667 55.000 0.00 0.00 42.43 3.69
1679 2632 2.670019 TAATCCGGGAATCGAGAGGA 57.330 50.000 0.00 0.00 42.43 3.71
1680 2633 3.069729 AGTTTAATCCGGGAATCGAGAGG 59.930 47.826 0.00 0.00 42.43 3.69
1758 2711 3.068691 CAGTCTTCTCCGCGGGGA 61.069 66.667 27.50 27.50 41.08 4.81
1784 2741 4.500116 GCTGTCCGAGGAGCGTCC 62.500 72.222 0.00 0.00 38.67 4.79
1832 2790 1.040646 TGTGGAGCAGAGAACGAACT 58.959 50.000 0.00 0.00 0.00 3.01
1875 2839 3.112709 GTGGCGGCTGAACGAGAC 61.113 66.667 11.43 0.00 35.47 3.36
1885 2849 4.364415 TTTTGATATAAACTGTGGCGGC 57.636 40.909 0.00 0.00 0.00 6.53
1888 2852 9.810231 CAAAATGTTTTTGATATAAACTGTGGC 57.190 29.630 6.85 0.00 36.64 5.01
1898 2862 9.199982 CTGCTGAGTTCAAAATGTTTTTGATAT 57.800 29.630 14.23 7.69 38.12 1.63
1904 2868 5.014808 AGCTGCTGAGTTCAAAATGTTTT 57.985 34.783 0.00 0.00 0.00 2.43
1935 2899 5.050499 CGCTTCATGGTATGATGAGAAGTTC 60.050 44.000 8.38 0.00 39.39 3.01
1949 2913 1.890876 TTGCTTGTACGCTTCATGGT 58.109 45.000 0.00 0.00 0.00 3.55
1958 2922 1.324736 GAGATCGGCTTTGCTTGTACG 59.675 52.381 0.00 0.00 0.00 3.67
1961 2925 0.326264 AGGAGATCGGCTTTGCTTGT 59.674 50.000 0.00 0.00 0.00 3.16
1986 2950 0.906066 GAGAGAGAGGGGGTGGAAAC 59.094 60.000 0.00 0.00 0.00 2.78
1987 2951 0.491823 TGAGAGAGAGGGGGTGGAAA 59.508 55.000 0.00 0.00 0.00 3.13
1990 2954 0.326048 ACATGAGAGAGAGGGGGTGG 60.326 60.000 0.00 0.00 0.00 4.61
1991 2955 0.829333 CACATGAGAGAGAGGGGGTG 59.171 60.000 0.00 0.00 0.00 4.61
1992 2956 0.712979 TCACATGAGAGAGAGGGGGT 59.287 55.000 0.00 0.00 0.00 4.95
1993 2957 1.412079 CTCACATGAGAGAGAGGGGG 58.588 60.000 14.32 0.00 44.74 5.40
1994 2958 0.752054 GCTCACATGAGAGAGAGGGG 59.248 60.000 22.47 0.00 44.74 4.79
1995 2959 1.409790 CAGCTCACATGAGAGAGAGGG 59.590 57.143 22.47 3.99 44.74 4.30
1996 2960 2.101783 ACAGCTCACATGAGAGAGAGG 58.898 52.381 22.47 10.68 44.74 3.69
2047 3011 1.933853 GCTTTTGCCGTCGTCAGATAT 59.066 47.619 0.00 0.00 40.15 1.63
2190 3163 4.875536 GCAAGTTGGAAAAGTGGAAAATGT 59.124 37.500 4.75 0.00 0.00 2.71
2191 3164 4.273235 GGCAAGTTGGAAAAGTGGAAAATG 59.727 41.667 4.75 0.00 0.00 2.32
2192 3165 4.450976 GGCAAGTTGGAAAAGTGGAAAAT 58.549 39.130 4.75 0.00 0.00 1.82
2193 3166 3.369997 GGGCAAGTTGGAAAAGTGGAAAA 60.370 43.478 4.75 0.00 0.00 2.29
2194 3167 2.169561 GGGCAAGTTGGAAAAGTGGAAA 59.830 45.455 4.75 0.00 0.00 3.13
2195 3168 1.760029 GGGCAAGTTGGAAAAGTGGAA 59.240 47.619 4.75 0.00 0.00 3.53
2286 3269 0.804989 CGATGGCCCTGTTCTTGTTC 59.195 55.000 0.00 0.00 0.00 3.18
2302 3285 1.080501 CCACACGAGCACAGTCGAT 60.081 57.895 0.00 0.00 42.85 3.59
2478 3478 4.990526 AGTGAAATGAAGTGTCTTGGGAT 58.009 39.130 0.00 0.00 0.00 3.85
2488 3488 2.175878 AGCGCAGAGTGAAATGAAGT 57.824 45.000 11.47 0.00 0.00 3.01
2491 3491 2.352651 GCAATAGCGCAGAGTGAAATGA 59.647 45.455 11.47 0.00 0.00 2.57
2492 3492 2.713011 GCAATAGCGCAGAGTGAAATG 58.287 47.619 11.47 0.00 0.00 2.32
2589 3594 4.141642 CCACATGATTGTACCTGAGATCCA 60.142 45.833 0.00 0.00 33.76 3.41
2640 3645 3.226347 CGGCAAAGAAGTTAAGCGAAAG 58.774 45.455 0.00 0.00 0.00 2.62
2721 3729 4.537135 TCGCCTTGTTCTCACTAAAGAT 57.463 40.909 0.00 0.00 0.00 2.40
2723 3731 4.245660 TCATCGCCTTGTTCTCACTAAAG 58.754 43.478 0.00 0.00 0.00 1.85
2779 3787 0.394565 GTCAGAGAGTGCCTTGGTGT 59.605 55.000 0.00 0.00 0.00 4.16
2875 3884 4.260375 GGCAACTGAATACGCATTACTGAG 60.260 45.833 0.00 0.00 0.00 3.35
2878 3887 3.605634 TGGCAACTGAATACGCATTACT 58.394 40.909 0.00 0.00 37.61 2.24
2898 3908 5.618056 TCTCAAGTAAAATGAAGCAGCTG 57.382 39.130 10.11 10.11 0.00 4.24
2940 3950 8.812972 CACCACCAAGTAGTACCACATATATAT 58.187 37.037 0.00 0.00 0.00 0.86
2941 3951 7.233962 CCACCACCAAGTAGTACCACATATATA 59.766 40.741 0.00 0.00 0.00 0.86
2998 4008 8.078596 GCAAATGTCCAAAATATTAGAGCCTAG 58.921 37.037 0.00 0.00 0.00 3.02
3003 4013 6.698766 GCCAGCAAATGTCCAAAATATTAGAG 59.301 38.462 0.00 0.00 0.00 2.43
3092 4102 5.705441 TGTCTACATTGTGGAAAGGAATCAC 59.295 40.000 4.26 0.00 0.00 3.06
3121 4131 5.567224 GCAAAACATGTCATCATCCAAAGGA 60.567 40.000 0.00 0.00 35.55 3.36
3222 4251 4.701956 ACACAAAAGGAACACAGTCAAG 57.298 40.909 0.00 0.00 0.00 3.02
3235 4264 6.034898 CCAGACAAAACAAGCTAACACAAAAG 59.965 38.462 0.00 0.00 0.00 2.27
3269 4298 9.520204 AATAGTTTGACAATGACAGAAAAACAG 57.480 29.630 0.00 0.00 0.00 3.16
3277 4306 9.912634 ACCAAATAAATAGTTTGACAATGACAG 57.087 29.630 0.52 0.00 38.51 3.51
3434 4463 2.633481 GACCAGGATAAGTTAGGCGGAT 59.367 50.000 0.00 0.00 0.00 4.18
3435 4464 2.037144 GACCAGGATAAGTTAGGCGGA 58.963 52.381 0.00 0.00 0.00 5.54
3437 4466 3.536956 TTGACCAGGATAAGTTAGGCG 57.463 47.619 0.00 0.00 0.00 5.52
3549 4580 6.257586 AGAACTCCTATTACTTGTCTCCTGT 58.742 40.000 0.00 0.00 0.00 4.00
3563 4594 6.886459 TGATTTGCTGCTTAAAGAACTCCTAT 59.114 34.615 0.00 0.00 0.00 2.57
3621 4652 4.908601 TTCCACTTCTTTGGCTATCTCA 57.091 40.909 0.00 0.00 36.48 3.27
3727 4758 6.040842 TGACTTCTCCTCAAATTTCTTTTGGG 59.959 38.462 0.00 0.00 44.16 4.12
3735 4766 7.449395 TCATGTGAATGACTTCTCCTCAAATTT 59.551 33.333 0.00 0.00 32.29 1.82
3765 4796 2.029110 GGCCTTCTTTGTTGCTGCATAA 60.029 45.455 1.84 0.00 0.00 1.90
3803 4834 1.669604 TGTTTTGTTGTAGAGGCGCA 58.330 45.000 10.83 0.00 0.00 6.09
3849 4880 8.918202 ACACATCCTTAAATTCTACTGTTTCA 57.082 30.769 0.00 0.00 0.00 2.69
3885 4916 7.884877 AGATGATGTGTTCTTAATGGTTCTTCA 59.115 33.333 0.00 0.00 0.00 3.02
4005 5036 4.834496 AGGAAATTTTCATCTGTGGCAAGA 59.166 37.500 11.09 0.00 0.00 3.02
4047 5078 0.902531 TTAGAACCTCCAGGGCTTCG 59.097 55.000 0.00 0.00 40.27 3.79
4156 5187 0.035317 ATGCGCTTTGTCTGAGGTGA 59.965 50.000 9.73 0.00 0.00 4.02
4201 5232 3.200825 TCTCTTGCCCCTTTATTCTCAGG 59.799 47.826 0.00 0.00 0.00 3.86
4237 5268 7.551974 TGAGATCTCATTTTCTTCATCAACTCC 59.448 37.037 21.67 0.00 34.14 3.85
4783 5840 4.338400 GTCCTTGGCAACTTTACTTCTTGT 59.662 41.667 0.00 0.00 37.61 3.16
4839 5896 6.418946 ACAGTTTCCTCTTTCTCAGTTTCTT 58.581 36.000 0.00 0.00 0.00 2.52
4865 5922 7.332182 GCTACTTGAAGCAGAGTTTATTACAGT 59.668 37.037 0.00 0.00 42.30 3.55
5161 6218 3.995048 CAGAAGGAACGGTAGTTTTCTCC 59.005 47.826 0.00 0.00 41.34 3.71
5170 6227 1.679680 CCGCTATCAGAAGGAACGGTA 59.320 52.381 0.00 0.00 36.41 4.02
5174 6231 2.427453 TCTCACCGCTATCAGAAGGAAC 59.573 50.000 0.00 0.00 0.00 3.62
5450 6524 2.885554 GCTTCCATGGAACCAACATCCT 60.886 50.000 23.63 0.00 37.85 3.24
5515 6589 4.668289 CATTTTAGGCCACCGTTTGATAC 58.332 43.478 5.01 0.00 0.00 2.24
5516 6590 3.129638 GCATTTTAGGCCACCGTTTGATA 59.870 43.478 5.01 0.00 0.00 2.15
5544 6618 4.211125 CTGAAGTAGGACTAGGCTGATCA 58.789 47.826 0.00 0.00 0.00 2.92
5677 6754 3.433343 TGTATACCAACAGGGAGACGAA 58.567 45.455 0.00 0.00 41.15 3.85
5682 6759 7.598759 ACTTAGTATGTATACCAACAGGGAG 57.401 40.000 0.00 0.00 41.15 4.30
5782 6859 3.262420 GCGAATGTGAGTATGTGTCCTT 58.738 45.455 0.00 0.00 0.00 3.36
5943 7020 0.882042 CGGGATCAAGAGGGCAATCG 60.882 60.000 0.00 0.00 0.00 3.34
5973 7050 0.323629 CCTTGCGGTCCAGGAACTTA 59.676 55.000 2.07 0.00 34.60 2.24
5980 7057 2.581354 CTCCTCCTTGCGGTCCAG 59.419 66.667 0.00 0.00 0.00 3.86
6024 7101 5.067805 ACAATCGAAGAGAAGCTTTTGGTTT 59.932 36.000 0.00 0.00 43.63 3.27
6151 7228 3.046374 GGCTCCATACTTCTTCCCCTAA 58.954 50.000 0.00 0.00 0.00 2.69
6189 7266 2.760385 AGCCTCTCCGCCCTGTAC 60.760 66.667 0.00 0.00 0.00 2.90
6213 7290 3.004862 TGCAGCATCACTACACTCATTG 58.995 45.455 0.00 0.00 0.00 2.82
6216 7293 2.837532 TTGCAGCATCACTACACTCA 57.162 45.000 0.00 0.00 0.00 3.41
6258 7335 1.553417 CCTCCTCCTTCCACCTCTTGA 60.553 57.143 0.00 0.00 0.00 3.02
6283 7360 0.108804 TCCGACCTCGCTGATTTCAC 60.109 55.000 0.00 0.00 38.18 3.18
6336 7413 0.108615 CGACTAGCTCCACCAACAGG 60.109 60.000 0.00 0.00 0.00 4.00
6376 7453 2.292103 TGCTGTGGAAAACAAACTGC 57.708 45.000 0.00 0.00 38.67 4.40
6406 7483 2.663796 TGGCATTGGCATTGGCAC 59.336 55.556 27.90 1.98 43.77 5.01
6415 7492 3.181483 GCTTCCTACAGATTTGGCATTGG 60.181 47.826 0.00 0.00 0.00 3.16
6416 7493 3.444742 TGCTTCCTACAGATTTGGCATTG 59.555 43.478 0.00 0.00 0.00 2.82
6417 7494 3.700538 TGCTTCCTACAGATTTGGCATT 58.299 40.909 0.00 0.00 0.00 3.56
6418 7495 3.370840 TGCTTCCTACAGATTTGGCAT 57.629 42.857 0.00 0.00 0.00 4.40
6419 7496 2.819608 GTTGCTTCCTACAGATTTGGCA 59.180 45.455 0.00 0.00 0.00 4.92
6420 7497 3.084786 AGTTGCTTCCTACAGATTTGGC 58.915 45.455 0.00 0.00 0.00 4.52
6626 7709 1.001764 TCCAGATGGCTTGTGCAGG 60.002 57.895 0.00 0.00 41.91 4.85
6640 7723 5.774498 AAAGGAAAAACTAGTTGCTCCAG 57.226 39.130 26.58 0.00 30.55 3.86
6644 7727 8.063200 ACAGTTAAAAGGAAAAACTAGTTGCT 57.937 30.769 9.34 0.00 32.35 3.91
6728 7814 9.139734 TCCTTTCTTTGTAGTAACAGAGAGTTA 57.860 33.333 0.00 0.00 44.85 2.24
6793 7880 1.153549 CGTAGGGAGCAGTGCCTTC 60.154 63.158 12.58 3.33 43.40 3.46
6796 7883 0.464452 AATACGTAGGGAGCAGTGCC 59.536 55.000 12.58 3.03 0.00 5.01
6810 7897 6.924060 GCCCTGACCTGCTAATATATAATACG 59.076 42.308 0.00 0.00 0.00 3.06
6835 7930 9.610705 ATGCATCTAGGAGTATTATATTGCAAG 57.389 33.333 4.94 0.00 39.49 4.01
6945 8316 6.833416 CACCAAAATGATCCATCCTAGGTTAA 59.167 38.462 9.08 0.00 0.00 2.01
6946 8317 6.364701 CACCAAAATGATCCATCCTAGGTTA 58.635 40.000 9.08 0.00 0.00 2.85
6958 8329 2.634982 TCTTGCGCACCAAAATGATC 57.365 45.000 11.12 0.00 31.94 2.92
7038 8419 1.709147 ATCGCAGGCGTGAAGAATGC 61.709 55.000 11.29 0.00 40.74 3.56
7048 8429 0.807667 AGAGTAGCAAATCGCAGGCG 60.808 55.000 7.46 7.46 46.13 5.52
7050 8431 1.134699 TCCAGAGTAGCAAATCGCAGG 60.135 52.381 0.00 0.00 46.13 4.85
7054 8435 4.855715 TCCTATCCAGAGTAGCAAATCG 57.144 45.455 0.00 0.00 0.00 3.34
7060 8441 6.906848 AGTATCCTATCCTATCCAGAGTAGC 58.093 44.000 0.00 0.00 0.00 3.58
7065 8446 8.798975 AACAAAAGTATCCTATCCTATCCAGA 57.201 34.615 0.00 0.00 0.00 3.86
7101 8482 7.961283 GCTTAAACAAATACTGCTACACCTAAC 59.039 37.037 0.00 0.00 0.00 2.34
7102 8483 7.662258 TGCTTAAACAAATACTGCTACACCTAA 59.338 33.333 0.00 0.00 0.00 2.69
7103 8484 7.162761 TGCTTAAACAAATACTGCTACACCTA 58.837 34.615 0.00 0.00 0.00 3.08
7104 8485 6.001460 TGCTTAAACAAATACTGCTACACCT 58.999 36.000 0.00 0.00 0.00 4.00
7105 8486 6.249035 TGCTTAAACAAATACTGCTACACC 57.751 37.500 0.00 0.00 0.00 4.16
7106 8487 7.148967 GCTTTGCTTAAACAAATACTGCTACAC 60.149 37.037 4.58 0.00 38.76 2.90
7107 8488 6.861055 GCTTTGCTTAAACAAATACTGCTACA 59.139 34.615 4.58 0.00 38.76 2.74
7189 8570 4.997395 AGCACCTTACAGTCAAACACATAG 59.003 41.667 0.00 0.00 0.00 2.23
7214 10724 1.544246 GTTGGTTCCACATTAGTGCCC 59.456 52.381 0.00 0.00 44.53 5.36
7259 10774 4.072131 TCTGAAAACATTACCAGGAGTGC 58.928 43.478 0.00 0.00 0.00 4.40
7260 10775 4.697352 CCTCTGAAAACATTACCAGGAGTG 59.303 45.833 0.00 0.00 0.00 3.51
7284 10799 1.282157 ACAACCCAAGGATCTACCAGC 59.718 52.381 0.00 0.00 42.04 4.85
7415 10978 3.007940 TCTGAAGATCCACGAAACCACAT 59.992 43.478 0.00 0.00 0.00 3.21
7431 10994 3.698382 GAGCATCGCGGTCTGAAG 58.302 61.111 6.13 0.00 39.15 3.02
7475 12332 0.670162 CCAGCCCAATATTCTTGCGG 59.330 55.000 0.00 0.00 0.00 5.69
7600 12463 3.500982 CACATGCAAAAGGGTATCAACG 58.499 45.455 0.00 0.00 0.00 4.10
7617 12480 3.005539 ACGAGAGGCCCAGCACAT 61.006 61.111 0.00 0.00 0.00 3.21
7647 12514 3.345808 CGTCCGTGTGGCCAGTTG 61.346 66.667 5.11 0.00 34.14 3.16
7669 12536 2.854424 GCAACAGTGAACAATGGTCGTG 60.854 50.000 0.00 0.00 0.00 4.35
7670 12537 1.333619 GCAACAGTGAACAATGGTCGT 59.666 47.619 0.00 0.00 0.00 4.34
7686 12553 1.381165 AACGGTGGTCCTTGTGCAAC 61.381 55.000 0.00 0.00 37.35 4.17
7687 12554 1.077357 AACGGTGGTCCTTGTGCAA 60.077 52.632 0.00 0.00 0.00 4.08
7688 12555 1.525077 GAACGGTGGTCCTTGTGCA 60.525 57.895 0.00 0.00 0.00 4.57
7689 12556 0.889186 ATGAACGGTGGTCCTTGTGC 60.889 55.000 0.00 0.00 0.00 4.57
7690 12557 1.266718 CAATGAACGGTGGTCCTTGTG 59.733 52.381 0.00 0.00 0.00 3.33
7691 12558 1.133915 ACAATGAACGGTGGTCCTTGT 60.134 47.619 0.50 0.50 0.00 3.16
7692 12559 1.604604 ACAATGAACGGTGGTCCTTG 58.395 50.000 0.00 0.00 0.00 3.61
7693 12560 1.953686 CAACAATGAACGGTGGTCCTT 59.046 47.619 0.00 0.00 0.00 3.36
7694 12561 1.604604 CAACAATGAACGGTGGTCCT 58.395 50.000 0.00 0.00 0.00 3.85
7695 12562 0.039527 GCAACAATGAACGGTGGTCC 60.040 55.000 0.00 0.00 0.00 4.46
7696 12563 0.665835 TGCAACAATGAACGGTGGTC 59.334 50.000 0.00 0.00 0.00 4.02
7697 12564 0.383949 GTGCAACAATGAACGGTGGT 59.616 50.000 0.00 0.00 36.32 4.16
7698 12565 3.177883 GTGCAACAATGAACGGTGG 57.822 52.632 0.00 0.00 36.32 4.61


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

AutoCloner maintained by Alex Coulton.