Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008015.1 Hibiscus syriacus cultivar Beakdansim tig00110481_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 961110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:4533 original size:2 final size:2
Alignment explanation
Indices: 4521--4553 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4511 AAAATACATC
*
4521 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4554 ATTTAGGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13278 original size:13 final size:14
Alignment explanation
Indices: 13255--13286 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
13245 TTAGTAATAT
13255 TATATAAAAATTAA
1 TATATAAAAATTAA
13269 TATA-AAAAATTAA
1 TATATAAAAATTAA
13282 TATAT
1 TATAT
13287 TTAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATATAAAAATTAA
Found at i:18783 original size:24 final size:25
Alignment explanation
Indices: 18756--18806 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
18746 GTGATAAACA
* * *
18756 AACACAAATGAACGAACGT-AAATT
1 AACACAAACGAACAAACATAAAATT
18780 AACACAAACGAACAAACATAAAATT
1 AACACAAACGAACAAACATAAAATT
18805 AA
1 AA
18807 TTGATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.61, C:0.18, G:0.08, T:0.14
Consensus pattern (25 bp):
AACACAAACGAACAAACATAAAATT
Found at i:18956 original size:23 final size:23
Alignment explanation
Indices: 18913--18956 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
18903 TAATTGAGCT
*
18913 TTAAAATATTAATGAGTTTAAGG
1 TTAAAATATTAATAAGTTTAAGG
*
18936 TTAAAAT-TTATTAAGTCTTAA
1 TTAAAATATTAATAAGT-TTAA
18957 TATTTCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (23 bp):
TTAAAATATTAATAAGTTTAAGG
Found at i:20414 original size:35 final size:33
Alignment explanation
Indices: 20356--20422 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
20346 TAATGTATTG
*
20356 TTTGGTCAAAATAAGTACTTAAAGTTAATTTTTTT
1 TTTGGTAAAAATAAGTACTTAAAG-T-ATTTTTTT
*
20391 TTTGGTAAAAATAGGTA-TCTAAAGTATTTTTT
1 TTTGGTAAAAATAAGTACT-TAAAGTATTTTTT
20423 GATCAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 7 0.24
34 2 0.07
35 20 0.69
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.48
Consensus pattern (33 bp):
TTTGGTAAAAATAAGTACTTAAAGTATTTTTTT
Found at i:20430 original size:29 final size:29
Alignment explanation
Indices: 20388--20447 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
20378 AGTTAATTTT
* * *
20388 TTTTTTGGTAAAAATAGGTATCTAAAGTA
1 TTTTTTGATAAAAATAGGTACCTAAAATA
* *
20417 TTTTTTGATCAAAATATGTACCTAAAATA
1 TTTTTTGATAAAAATAGGTACCTAAAATA
20446 TT
1 TT
20448 CAATTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (29 bp):
TTTTTTGATAAAAATAGGTACCTAAAATA
Found at i:20951 original size:63 final size:63
Alignment explanation
Indices: 20877--21000 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
20867 TTTTACCCCT
* * *
20877 TCGTAAATAATAAATAGATAATGAATA-CAAAAATATTAAATGAGTACGAGGATAGAGGAAAGG
1 TCGTAAATAATAAATAGATAATAAATATC-AAAATATTAAATGAGTACGAAGAGAGAGGAAAGG
* * *
20940 TCGTGAATAATAAATAGGTAATAAATATCAAAATATTAAATGAGTATGAAGAGAGAGGAAA
1 TCGTAAATAATAAATAGATAATAAATATCAAAATATTAAATGAGTACGAAGAGAGAGGAAA
21001 TGTATCCACA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 53 0.98
64 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.23
Consensus pattern (63 bp):
TCGTAAATAATAAATAGATAATAAATATCAAAATATTAAATGAGTACGAAGAGAGAGGAAAGG
Found at i:22533 original size:23 final size:23
Alignment explanation
Indices: 22502--22580 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
22492 AATGATTCTA
*
22502 TCTTTGTGGCACGTTTATCTCTG
1 TCTTTGTGGTACGTTTATCTCTG
* * *
22525 CCTTTGTGGTACATCTATCTCTG
1 TCTTTGTGGTACGTTTATCTCTG
* *
22548 TTTTTGTGGTACGTTTATCTTTG
1 TCTTTGTGGTACGTTTATCTCTG
22571 TCTTTGTGGT
1 TCTTTGTGGT
22581 TCATTTGTCG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.09, C:0.18, G:0.22, T:0.52
Consensus pattern (23 bp):
TCTTTGTGGTACGTTTATCTCTG
Found at i:27523 original size:43 final size:43
Alignment explanation
Indices: 27476--27660 Score: 162
Period size: 43 Copynumber: 4.4 Consensus size: 43
27466 TAAATTACCT
* *
27476 ACTTATTGCAGCATTTAAAAGAAAAAAGACGCTAAATGTATGA
1 ACTTATTGCGGCATTTATAAGAAAAAAGACGCTAAATGTATGA
* * * *
27519 ACTTATTGCGGTATTTATAAGAAAAATGCCGCTAAATGTTTGA
1 ACTTATTGCGGCATTTATAAGAAAAAAGACGCTAAATGTATGA
* * ** *
27562 ACATATTGTGGCATTTATAAG--AAAACCCGCTAAATGTTTGA
1 ACTTATTGCGGCATTTATAAGAAAAAAGACGCTAAATGTATGA
* * * * * * *
27603 ACCTAATGCGACATTTGTAAGAAAAATGCCGCT-AATGTCTGA
1 ACTTATTGCGGCATTTATAAGAAAAAAGACGCTAAATGTATGA
*
27645 ACCTT-TTGCGACATTT
1 A-CTTATTGCGGCATTT
27661 TTTTATACAA
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
41 34 0.29
42 19 0.16
43 65 0.55
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (43 bp):
ACTTATTGCGGCATTTATAAGAAAAAAGACGCTAAATGTATGA
Found at i:34226 original size:15 final size:15
Alignment explanation
Indices: 34208--34238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34198 AAATTCTAAA
34208 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
34223 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
34238 T
1 T
34239 CTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:36528 original size:21 final size:21
Alignment explanation
Indices: 36502--36545 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
36492 ATTCTGGGCT
* *
36502 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
36523 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
36544 AG
1 AG
36546 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:36616 original size:23 final size:22
Alignment explanation
Indices: 36572--36616 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
36562 AATATCATGG
*
36572 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
36594 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
36617 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:37393 original size:31 final size:31
Alignment explanation
Indices: 37309--37430 Score: 124
Period size: 31 Copynumber: 3.9 Consensus size: 31
37299 GAGTCGAGGG
*
37309 TACCTATGTTCTACGGAACATATGGACATAA
1 TACCTATGTTCTACGGAACATATGGACATTA
*
37340 TTACCTATG-TCTTTC-GAGACATATGGACATTA
1 -TACCTATGTTC-TACGGA-ACATATGGACATTA
*
37372 TACCTATGTTCTAAGGAACATATGGACAGTT-
1 TACCTATGTTCTACGGAACATATGGACA-TTA
* * * *
37403 CACCTAGGTTCTTCGGAACCTATGGACA
1 TACCTATGTTCTACGGAACATATGGACA
37431 GTTGCCGAGG
Statistics
Matches: 76, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
31 47 0.62
32 29 0.38
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACATTA
Found at i:37471 original size:30 final size:30
Alignment explanation
Indices: 37430--37491 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
37420 ACCTATGGAC
*
37430 AGTTGCCGAGGATCTTTATGACCTCTGAAT
1 AGTTACCGAGGATCTTTATGACCTCTGAAT
*
37460 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGAAT
37490 AG
1 AG
37492 GTCCTGCGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGAAT
Found at i:41755 original size:21 final size:21
Alignment explanation
Indices: 41730--41770 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41720 TCTGGGCTAG
* *
41730 GGGAATCGGTACCCATTCAAA
1 GGGAACCGATACCCATTCAAA
*
41751 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
41771 GCGAATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAA
Found at i:41842 original size:23 final size:22
Alignment explanation
Indices: 41798--41842 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
41788 AATGTCATGG
*
41798 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
41820 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
41843 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:43103 original size:21 final size:21
Alignment explanation
Indices: 43077--43121 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43067 GATTTCTGGG
* *
43077 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
43098 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
43119 CAA
1 CAA
43122 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:44820 original size:25 final size:26
Alignment explanation
Indices: 44786--44836 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
44776 GAGTAGAGGG
44786 TCTACGCGGTCCTTCGGGATA-ATAT
1 TCTACGCGGTCCTTCGGGATATATAT
44811 TCTACGCGGTCCTTCGGGATATATAT
1 TCTACGCGGTCCTTCGGGATATATAT
44837 ATTCTTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (26 bp):
TCTACGCGGTCCTTCGGGATATATAT
Found at i:44986 original size:23 final size:23
Alignment explanation
Indices: 44942--44986 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
44932 ATCATTATAT
*
44942 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
44965 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
44987 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:45943 original size:31 final size:30
Alignment explanation
Indices: 45819--45943 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 30
45809 GAGTCGAGGG
45819 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG--T
*
45851 TACCTATG-TCTTTC-GAGACATATGGACAGT
1 TACCTATGTTC-TACGGA-ACATATGGACAGT
*
45881 ATACCTATGTTCTAAGGAACATATGGACAGT
1 -TACCTATGTTCTACGGAACATATGGACAGT
* * *
45912 TCACCTAGGTTCTTCGGAACCTATGGACAGT
1 T-ACCTATGTTCTACGGAACATATGGACAGT
45943 T
1 T
45944 GCCGAGGATC
Statistics
Matches: 80, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
30 2 0.03
31 52 0.65
32 26 0.32
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (30 bp):
TACCTATGTTCTACGGAACATATGGACAGT
Found at i:45981 original size:30 final size:30
Alignment explanation
Indices: 45930--46001 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
45920 GTTCTTCGGA
* * *
45930 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
45960 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
45990 ACCTCTGGATAG
1 ACCTCTGGATAG
46002 GTCCTGCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:50598 original size:38 final size:39
Alignment explanation
Indices: 50549--50625 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 39
50539 CCTCGTAATC
*
50549 GTTGGATACTATTTTAAAAA-ATATAAGGTAACAAGAGT
1 GTTGCATACTATTTTAAAAAGATATAAGGTAACAAGAGT
50587 GTTGCATACTATTTTAAAAAGATATAAGGTAACAAGAGT
1 GTTGCATACTATTTTAAAAAGATATAAGGTAACAAGAGT
50626 ATTATATATC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 19 0.51
39 18 0.49
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.31
Consensus pattern (39 bp):
GTTGCATACTATTTTAAAAAGATATAAGGTAACAAGAGT
Found at i:54024 original size:41 final size:41
Alignment explanation
Indices: 53930--54081 Score: 232
Period size: 41 Copynumber: 3.7 Consensus size: 41
53920 GATTCGCAAC
* * *
53930 GCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
*
53972 GCGATATGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
54013 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* *
54054 GCGACAGGCGAAGTTCACGTTGCGATTC
1 GCGATAGGCGAAGTTCGCGTTGCGATTC
54082 GACCACGACC
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 70 0.69
42 32 0.31
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (41 bp):
GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
Found at i:54103 original size:5 final size:5
Alignment explanation
Indices: 54081--54115 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
54071 CGTTGCGATT
54081 CGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
54116 GACAGGACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:55864 original size:20 final size:18
Alignment explanation
Indices: 55841--55892 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
55831 TTAATTTTAC
55841 AAATATAAAAAAATCAGAAA
1 AAATA-AAAAAAATC-GAAA
55861 AAATGCAAAAAAAATCGAAA
1 AAAT--AAAAAAAATCGAAA
*
55881 AATTAAAAAAAA
1 AAATAAAAAAAA
55893 ATTAGTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 8 0.28
20 11 0.38
21 9 0.31
22 1 0.03
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.13
Consensus pattern (18 bp):
AAATAAAAAAAATCGAAA
Found at i:55881 original size:19 final size:21
Alignment explanation
Indices: 55847--55894 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
55837 TTACAAATAT
*
55847 AAAAAAATCAGAAAAAATGCA
1 AAAAAAATCAGAAAAAATGAA
*
55868 AAAAAAATC-G-AAAAATTAA
1 AAAAAAATCAGAAAAAATGAA
55887 AAAAAAAT
1 AAAAAAAT
55895 TAGTATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
20 1 0.04
21 9 0.36
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (21 bp):
AAAAAAATCAGAAAAAATGAA
Found at i:55893 original size:20 final size:21
Alignment explanation
Indices: 55847--55893 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
55837 TTACAAATAT
**
55847 AAAAAAATCAGAAAAAATGCA
1 AAAAAAATCAGAAAAAATAAA
*
55868 AAAAAAATC-GAAAAATTAAA
1 AAAAAAATCAGAAAAAATAAA
55888 AAAAAA
1 AAAAAA
55894 TTAGTATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (21 bp):
AAAAAAATCAGAAAAAATAAA
Found at i:55931 original size:25 final size:25
Alignment explanation
Indices: 55903--55961 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
55893 ATTAGTATGA
55903 TTATTTATC-TAATTTAAATATATTT
1 TTATTTATCTTAATTT-AATATATTT
*
55928 TTATCTATCTTATAATTTAATATATTT
1 TTATTTATC-T-TAATTTAATATATTT
*
55955 TAATTTA
1 TTATTTA
55962 AAAAAAAGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 8 0.29
27 14 0.50
28 6 0.21
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTTATCTTAATTTAATATATTT
Found at i:56447 original size:10 final size:10
Alignment explanation
Indices: 56432--56486 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
56422 TTGAATTTAA
56432 AAAAAATCAG
1 AAAAAATCAG
*
56442 AAAAAAAT-ATA
1 -AAAAAATCA-G
56453 AAAAAATCAG
1 AAAAAATCAG
*
56463 AAAAAAT-AC
1 AAAAAATCAG
56472 AAAAAATCAG
1 AAAAAATCAG
56482 AAAAA
1 AAAAA
56487 TTACAAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
9 8 0.22
10 21 0.57
11 8 0.22
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.11
Consensus pattern (10 bp):
AAAAAATCAG
Found at i:56455 original size:21 final size:20
Alignment explanation
Indices: 56429--56486 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
56419 TACTTGAATT
56429 TAAAAAAAATCAGAAAAAAA
1 TAAAAAAAATCAGAAAAAAA
56449 TATAAAAAAATCAG-AAAAAA
1 TA-AAAAAAATCAGAAAAAAA
*
56469 TACAAAAAATCAGAAAAA
1 TAAAAAAAATCAGAAAAA
56487 TTACAAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 10 0.29
20 14 0.40
21 11 0.31
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (20 bp):
TAAAAAAAATCAGAAAAAAA
Found at i:56491 original size:19 final size:19
Alignment explanation
Indices: 56432--56494 Score: 83
Period size: 19 Copynumber: 3.2 Consensus size: 19
56422 TTGAATTTAA
56432 AAAAAATCAGAAAAAAATATA-
1 AAAAAATCAG--AAAAAT-TAC
*
56453 AAAAAATCAGAAAAAATAC
1 AAAAAATCAGAAAAATTAC
56472 AAAAAATCAGAAAAATTAC
1 AAAAAATCAGAAAAATTAC
56491 AAAA
1 AAAA
56495 CAATTAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.05
19 27 0.69
21 10 0.26
ACGTcount: A:0.75, C:0.08, G:0.05, T:0.13
Consensus pattern (19 bp):
AAAAAATCAGAAAAATTAC
Found at i:56513 original size:2 final size:2
Alignment explanation
Indices: 56506--56543 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56496 AATTAGTATT
56506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56544 ATTTTAATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58618 original size:7 final size:7
Alignment explanation
Indices: 58606--58636 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
58596 TTTAAACTAT
58606 AATAAAA
1 AATAAAA
58613 AATAAAA
1 AATAAAA
58620 AAT-AAA
1 AATAAAA
58626 AATAAAA
1 AATAAAA
58633 AATA
1 AATA
58637 TTTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAA
Found at i:58628 original size:13 final size:13
Alignment explanation
Indices: 58610--58636 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58600 AACTATAATA
58610 AAAAATAAAAAAT
1 AAAAATAAAAAAT
58623 AAAAATAAAAAAT
1 AAAAATAAAAAAT
58636 A
1 A
58637 TTTTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:61464 original size:2 final size:2
Alignment explanation
Indices: 61457--61504 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
61447 GTCGCAGCTG
61457 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
61499 CT CT CT
1 CT CT CT
61505 ACCACCTCCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:62936 original size:30 final size:30
Alignment explanation
Indices: 62880--62953 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
62870 AGTTAAATTG
** *
62880 ATATTTATCTATTGTTTAAGGGTCAAAAAA
1 ATATTTATCTAAAGTTTAAGGATCAAAAAA
**
62910 ATATTTCATCTAAAGTTTAA-GATCAAATTA
1 ATATTT-ATCTAAAGTTTAAGGATCAAAAAA
62940 ATATTATATCTAAA
1 ATATT-TATCTAAA
62954 ATTCACGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (30 bp):
ATATTTATCTAAAGTTTAAGGATCAAAAAA
Found at i:69227 original size:6 final size:6
Alignment explanation
Indices: 69218--69290 Score: 119
Period size: 6 Copynumber: 12.2 Consensus size: 6
69208 TATCTCTCTC
* *
69218 TATACA TATACA TATACA TGTACA TATATA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
69266 TGTACA TATACA TATACA TATACA T
1 TATACA TATACA TATACA TATACA T
69291 TGAATTCTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:69252 original size:30 final size:30
Alignment explanation
Indices: 69218--69290 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
69208 TATCTCTCTC
*
69218 TATACATATACATATACATGTACATATATA
1 TATACATATACATATACATGTACATATACA
69248 TATACATATACATATACATGTACATATACA
1 TATACATATACATATACATGTACATATACA
69278 TATACATATACAT
1 TATACATATACAT
69291 TGAATTCTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.36
Consensus pattern (30 bp):
TATACATATACATATACATGTACATATACA
Found at i:69561 original size:2 final size:2
Alignment explanation
Indices: 69556--69600 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
69546 ATATATTGCT
69556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69598 TA T
1 TA T
69601 TGTTTTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74236 original size:15 final size:16
Alignment explanation
Indices: 74216--74245 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
74206 TCTTTTCTTT
74216 TCTTTTT-ATTTTGAG
1 TCTTTTTAATTTTGAG
74231 TCTTTTTAATTTTGA
1 TCTTTTTAATTTTGA
74246 ATAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (16 bp):
TCTTTTTAATTTTGAG
Found at i:75929 original size:2 final size:2
Alignment explanation
Indices: 75922--75956 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
75912 AGATATTGAA
75922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75957 AAACAGTGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76968 original size:20 final size:20
Alignment explanation
Indices: 76940--77003 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
76930 CTATTATTAA
*
76940 ATTATATTAGGTTAATATTT
1 ATTACATTAGGTTAATATTT
76960 ATTACATTAGGTTAATATTT
1 ATTACATTAGGTTAATATTT
76980 ATTACATTAGGTTAATATTT
1 ATTACATTAGGTTAATATTT
77000 ATTA
1 ATTA
77004 TTAAGGTGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (20 bp):
ATTACATTAGGTTAATATTT
Found at i:82328 original size:93 final size:93
Alignment explanation
Indices: 82203--82385 Score: 219
Period size: 93 Copynumber: 2.0 Consensus size: 93
82193 CTAATTCAAT
* * * * * **
82203 CCGATTCAGGTTGGACATTTAGTTTTGGTGAGTGGCTCTTCCCTCAGTG-ATTTTCTACGTTCA-
1 CCGATTCAGGTCGCACATTTAATTTTGATGAGTGACTCTTCCAACAG-GAATTTTCTAC-TT-AT
*
82266 A-AAGAACTCAAACTCAAAACTTACTTAGAA
63 ATAAGAACTCAAAATCAAAACTTACTTAGAA
* *
82296 CCGATTCGGGTCGCACATTTAATTTTGATGAGTGACTCTTCCAACCGGAATTTTCTACTTATATA
1 CCGATTCAGGTCGCACATTTAATTTTGATGAGTGACTCTTCCAACAGGAATTTTCTACTTATATA
*
82361 AGGACTCAAAATCAAAACTTACTTA
66 AGAACTCAAAATCAAAACTTACTTA
82386 AGTTAAAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
91 1 0.01
92 4 0.05
93 71 0.93
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (93 bp):
CCGATTCAGGTCGCACATTTAATTTTGATGAGTGACTCTTCCAACAGGAATTTTCTACTTATATA
AGAACTCAAAATCAAAACTTACTTAGAA
Found at i:85129 original size:29 final size:29
Alignment explanation
Indices: 85086--85168 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
85076 CTCACCTAAC
85086 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
85116 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
85145 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
85169 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:89774 original size:28 final size:28
Alignment explanation
Indices: 89733--89814 Score: 128
Period size: 29 Copynumber: 2.9 Consensus size: 28
89723 CTCACCTAAC
89733 TAAATTGATGTAAGCAATGACATCATAAT
1 TAAA-TGATGTAAGCAATGACATCATAAT
*
89762 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATC-ATAAT
*
89791 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
89815 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
28 19 0.39
29 30 0.61
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.32
Consensus pattern (28 bp):
TAAATGATGTAAGCAATGACATCATAAT
Found at i:91598 original size:71 final size:72
Alignment explanation
Indices: 91460--91596 Score: 215
Period size: 71 Copynumber: 1.9 Consensus size: 72
91450 TTATATAATC
*
91460 AATATAAGATACAAATTATTGGGCGGAGAAAGCATTTTAAAATATATATAATTCAATTTAACAAA
1 AATATAAGATACAAATTATTGGACGGAGAAAGCATTTTAAAATATATATAATTCAATTTAACAAA
91525 AATGTTT
66 AATGTTT
* * * *
91532 AATATAATA-ACAAATTATTGGACGGAGAAAGTATTTTAAAATGTATATAATT-AGTTTAACAAA
1 AATATAAGATACAAATTATTGGACGGAGAAAGCATTTTAAAATATATATAATTCAATTTAACAAA
91595 AA
66 AA
91597 ATTTGATTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 12 0.20
71 40 0.67
72 8 0.13
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (72 bp):
AATATAAGATACAAATTATTGGACGGAGAAAGCATTTTAAAATATATATAATTCAATTTAACAAA
AATGTTT
Found at i:92352 original size:15 final size:15
Alignment explanation
Indices: 92332--92398 Score: 59
Period size: 15 Copynumber: 4.3 Consensus size: 15
92322 ATTTTTCTTC
92332 ATTTATATTATAATA
1 ATTTATATTATAATA
92347 ATTTAT-TTAATAATA
1 ATTTATATT-ATAATA
*
92362 ATACTAATACTTATAATA
1 AT--TTATA-TTATAATA
92380 ATTTTATATT-TAA-A
1 A-TTTATATTATAATA
92394 ATTTA
1 ATTTA
92399 AATATTTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
13 4 0.09
14 4 0.09
15 17 0.39
16 2 0.05
17 7 0.16
18 7 0.16
19 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTATATTATAATA
Found at i:92423 original size:23 final size:22
Alignment explanation
Indices: 92380--92423 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
92370 ACTTATAATA
**
92380 ATTTTATATTTAAAATTTAAAT
1 ATTTTATATTTAAAAAATAAAT
*
92402 ATTTATATTTTTAAAAAATAAA
1 ATTT-TATATTTAAAAAATAAA
92424 CAATTCTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTTATATTTAAAAAATAAAT
Found at i:93134 original size:32 final size:31
Alignment explanation
Indices: 93080--93145 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
93070 CAAAAAAATA
*
93080 TAAGATATAGTCACTTTCGTTTTTTATTTAAT
1 TAAGATATAGTCACTTTCG-TTTTTATATAAT
* *
93112 TAAGATAT-GATCATTTTTGTTTTTATATAAT
1 TAAGATATAG-TCACTTTCGTTTTTATATAAT
93143 TAA
1 TAA
93146 TACATGATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 15 0.50
32 15 0.50
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (31 bp):
TAAGATATAGTCACTTTCGTTTTTATATAAT
Found at i:93337 original size:27 final size:28
Alignment explanation
Indices: 93307--93392 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 28
93297 AAATAAAAAT
93307 AAAATATTTTTAAATTAAGTTAATA-AA
1 AAAATATTTTTAAATTAAGTTAATATAA
*
93334 AAAATATATTT-AA-TAAGTTAATATAA
1 AAAATATTTTTAAATTAAGTTAATATAA
* *
93360 AAAATATTTTTAAGTTAA--T-ATATAT
1 AAAATATTTTTAAATTAAGTTAATATAA
93385 AAAATATT
1 AAAATATT
93393 ATGAATTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
25 23 0.44
26 15 0.29
27 11 0.21
28 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (28 bp):
AAAATATTTTTAAATTAAGTTAATATAA
Found at i:93402 original size:25 final size:23
Alignment explanation
Indices: 93323--93402 Score: 72
Period size: 25 Copynumber: 3.3 Consensus size: 23
93313 TTTTTAAATT
*
93323 AAGTTAATAAAAAAATATATTTAAT-
1 AAGTTAATATAAAAA-ATA-TT-ATG
* *
93348 AAGTTAATATAAAAAATATTTTT
1 AAGTTAATATAAAAAATATTATG
93371 AAGTTAATATATATAAAATATTATG
1 AAGTTAATATA-A-AAAATATTATG
*
93396 AATTTAA
1 AAGTTAA
93403 GAATTTATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
22 1 0.02
23 13 0.28
24 4 0.09
25 29 0.62
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
AAGTTAATATAAAAAATATTATG
Found at i:101032 original size:121 final size:123
Alignment explanation
Indices: 100657--101166 Score: 768
Period size: 121 Copynumber: 4.2 Consensus size: 123
100647 TAATCAAAGC
100657 TGACACGTGTCACTCTATGATTGGGTAGAAAATAAA-TTAGTTAAATAAATTAAAATTAAT--AA
1 TGACACGTGTCACTCTATGATTGGGTAGAAAATAAATTTAGTTAAATAAATTAAAATTAATAAAA
* *
100719 AAATCCTCTAATTACGTGGTGACACGTGGCATGAATGACAT-TGGTCATGACCATGTAT
66 AAATCCTCCAATTACGTGGTGACACGTGGCATGAATGAAATGT-GTCATGACCATGTAT
* *
100777 TGACACGTGTCACTCTATGATTGGGTAGAAAACAAATTTAGTTAAATAAATAAAAAATTAATAAA
1 TGACACGTGTCACTCTATGATTGGGTAGAAAATAAATTTAGTTAAATAAAT-TAAAATTAATAAA
* *
100842 AAAATCCTCCAATTACGTGGTGACACGTGACACGAATGATAA-GTGTCATGACCATGTAT
65 AAAATCCTCCAATTACGTGGTGACACGTGGCATGAATGA-AATGTGTCATGACCATGTAT
* * * *
100901 TGACATGTGTCGCTCTATGATTGGATAGAAAATAAATTTAGTTAAATAAATTTAAATTAAT-AAA
1 TGACACGTGTCACTCTATGATTGGGTAGAAAATAAATTTAGTTAAATAAATTAAAATTAATAAAA
* *
100965 AAAT-CTGCAATTACGTGGTGACACGTGGCATGAATGAAATGTGCCATGACCATGTAT
66 AAATCCTCCAATTACGTGGTGACACGTGGCATGAATGAAATGTGTCATGACCATGTAT
*
101022 TGACACGTGTCACTCTATGATTGGGTAGAAAATAAATTTAGTTAAAT-AATTCAAATTAATAAAA
1 TGACACGTGTCACTCTATGATTGGGTAGAAAATAAATTTAGTTAAATAAATTAAAATTAATAAAA
* * * *
101086 AAATTCTCCAATTACGTGGTGACATGTGGCATGAATGACACGTGTCATGACCATGTAT
66 AAATCCTCCAATTACGTGGTGACACGTGGCATGAATGAAATGTGTCATGACCATGTAT
101144 TGACACGTGTCACTTCT-TGATTG
1 TGACACGTGTCAC-TCTATGATTG
101167 ATGGGTTAAT
Statistics
Matches: 355, Mismatches: 25, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
120 49 0.14
121 111 0.31
122 83 0.23
123 11 0.03
124 99 0.28
125 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (123 bp):
TGACACGTGTCACTCTATGATTGGGTAGAAAATAAATTTAGTTAAATAAATTAAAATTAATAAAA
AAATCCTCCAATTACGTGGTGACACGTGGCATGAATGAAATGTGTCATGACCATGTAT
Found at i:104369 original size:23 final size:23
Alignment explanation
Indices: 104325--104369 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
104315 TAATATAGTT
**
104325 TCTATTAAAAATTGATTTTTTGG
1 TCTATTAAAAATTGATAATTTGG
* *
104348 TCTATTAAAATTTTATAATTTG
1 TCTATTAAAAATTGATAATTTG
104370 ATAATTTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (23 bp):
TCTATTAAAAATTGATAATTTGG
Found at i:105553 original size:19 final size:18
Alignment explanation
Indices: 105521--105559 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
105511 TGTTAAATTA
*
105521 TATTAGGTTAATATTTAT
1 TATTAGGTTAATATTAAT
*
105539 TATTAAGGTTCATATTAAT
1 TATT-AGGTTAATATTAAT
105558 TA
1 TA
105560 AGATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (18 bp):
TATTAGGTTAATATTAAT
Found at i:114734 original size:17 final size:18
Alignment explanation
Indices: 114702--114736 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
114692 TTAAAATATA
114702 AAATTATATTTTTTAATAG
1 AAATTATA-TTTTTAATAG
114721 AAATTATA-TTTTAATA
1 AAATTATATTTTTAATA
114737 TAAACAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATTATATTTTTAATAG
Found at i:123519 original size:24 final size:20
Alignment explanation
Indices: 123492--123551 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 20
123482 ATGCATGGGT
123492 AATGCATCGATGCACATGTTAAAG
1 AATGCATCGATGCAC-TG-T--AG
*
123516 AATGCATCGATACACTGTAG
1 AATGCATCGATGCACTGTAG
*
123536 AATGTATCGATGCACT
1 AATGCATCGATGCACT
123552 TCGAGGGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 2 0.06
24 14 0.42
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (20 bp):
AATGCATCGATGCACTGTAG
Found at i:124144 original size:14 final size:14
Alignment explanation
Indices: 124125--124171 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
124115 GACATGGATA
124125 TGAAAGTGTATATG
1 TGAAAGTGTATATG
124139 TGAAAGTGTATATG
1 TGAAAGTGTATATG
*
124153 TGAAA-TGATATAAG
1 TGAAAGTG-TATATG
124167 TGAAA
1 TGAAA
124172 ATGGCCATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 2 0.06
14 29 0.94
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.32
Consensus pattern (14 bp):
TGAAAGTGTATATG
Found at i:130496 original size:38 final size:37
Alignment explanation
Indices: 130435--130515 Score: 117
Period size: 38 Copynumber: 2.2 Consensus size: 37
130425 TGATACTATT
*
130435 TTTTAAATCAAAACAAAACAAAATAATTATATTTAAG
1 TTTTAAATCAAAACAAAACAAAATAATTATATTTAAA
* * *
130472 TTTTAATATTAAATCAAAATAAAATAATTATATTTAAA
1 TTTTAA-ATCAAAACAAAACAAAATAATTATATTTAAA
130510 TTTTAA
1 TTTTAA
130516 GAAATAATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 6 0.15
38 33 0.85
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (37 bp):
TTTTAAATCAAAACAAAACAAAATAATTATATTTAAA
Found at i:131348 original size:2 final size:2
Alignment explanation
Indices: 131343--131404 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
131333 TCTAAAAATC
131343 AT AT AT AT AT AT AT AT A- AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131383 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
131405 TGATCACATA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134936 original size:5 final size:5
Alignment explanation
Indices: 134930--135023 Score: 134
Period size: 5 Copynumber: 18.8 Consensus size: 5
134920 ACAAAAAATG
* * * * * *
134930 TAATG TAATG TAATG TAATG TAATG TAATG TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
134980 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT
135024 TATGATCTCG
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 88 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:135134 original size:16 final size:15
Alignment explanation
Indices: 135096--135136 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
135086 TTAAAGCTAT
135096 ATATTATTTTAAATA
1 ATATTATTTTAAATA
135111 AT-TATATTTTATAATA
1 ATAT-TATTTTA-AATA
135127 ATATTATTTT
1 ATATTATTTT
135137 CACCTAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 9 0.39
16 12 0.52
17 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTATTTTAAATA
Found at i:137691 original size:16 final size:16
Alignment explanation
Indices: 137626--137692 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
137616 ATTGAAATTA
*
137626 ATAATAAAT-AAATAT
1 ATAATAATTAAAATAT
* *
137641 ATTATTAATTATTAA-AT
1 A-TAATAATTA-AAATAT
*
137658 ATAATAA-TAAATAAAT
1 ATAATAATTAAA-ATAT
137674 ATAATAATTAAAATAT
1 ATAATAATTAAAATAT
137690 ATA
1 ATA
137693 TTTTATAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
14 1 0.03
15 4 0.10
16 26 0.65
17 7 0.17
18 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATAATTAAAATAT
Found at i:137692 original size:32 final size:34
Alignment explanation
Indices: 137620--137692 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 34
137610 TTTCAAATTG
*
137620 AAAT-TAATAATAAATAAATATATTATTAATTATT
1 AAATATAATAATAAATAAATATA-TATTAATTATA
137654 AAATATAATAATAAATAAATATA-A-TAATTA-A
1 AAATATAATAATAAATAAATATATATTAATTATA
137685 AATATATA
1 AA-ATATA
137693 TTTTATAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 2 0.06
32 11 0.31
33 1 0.03
34 4 0.11
35 18 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATATAATAATAAATAAATATATATTAATTATA
Found at i:137693 original size:18 final size:16
Alignment explanation
Indices: 137620--137681 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
137610 TTTCAAATTG
137620 AAAT-TAATAATAAAT
1 AAATATAATAATAAAT
* *
137635 AAATATATTATTAATTATT
1 AAATATA--A-TAATAAAT
137654 AAATATAATAATAAAT
1 AAATATAATAATAAAT
137670 AAATATAATAAT
1 AAATATAATAAT
137682 TAAAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 4 0.10
16 20 0.51
17 1 0.03
18 1 0.03
19 13 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATAATAATAAAT
Found at i:137733 original size:25 final size:23
Alignment explanation
Indices: 137680--137737 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
137670 AAATATAATA
137680 ATTAAAATATATATTTTATAAAT
1 ATTAAAATATATATTTTATAAAT
* *
137703 AATAAATATAATATATTTTGTAAAT
1 ATTAAA-AT-ATATATTTTATAAAT
*
137728 TTTAAAATAT
1 ATTAAAATAT
137738 TAAAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 7 0.24
24 4 0.14
25 18 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAAAATATATATTTTATAAAT
Found at i:140485 original size:23 final size:23
Alignment explanation
Indices: 140451--140538 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 23
140441 ACATATTATA
*
140451 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
140474 TGGCACTTCGGTGCATCTCTCTACG
1 TGGCACTTCGGTGCA-AT-TCTACG
*
140499 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
*
140523 TGGCACTTTGGTGCAA
1 TGGCACTTCGGTGCAA
140539 ATTTATATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
23 17 0.33
24 16 0.31
25 17 0.33
26 2 0.04
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:141127 original size:21 final size:22
Alignment explanation
Indices: 141089--141132 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
141079 GTAGCAGTAT
141089 TGTAGCAGGGGAATCGATTCCC
1 TGTAGCAGGGGAATCGATTCCC
*
141111 TGTAGCA-GGGTATCGATTCCC
1 TGTAGCAGGGGAATCGATTCCC
141132 T
1 T
141133 ATTTGCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (22 bp):
TGTAGCAGGGGAATCGATTCCC
Found at i:141791 original size:22 final size:23
Alignment explanation
Indices: 141768--141809 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
141758 AATTCAAAAT
141768 ATATTA-TAATTA-TAATTAT-A
1 ATATTATTAATTATTAATTATAA
141788 ATATTATTAATTATTAATTATA
1 ATATTATTAATTATTAATTATA
141810 TTTAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 6 0.32
22 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATTATTAATTATTAATTATAA
Found at i:141822 original size:28 final size:27
Alignment explanation
Indices: 141770--141821 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
141760 TTCAAAATAT
141770 ATTATAATTATAATTATAATATTATTA
1 ATTATAATTATAATTATAATATTATTA
141797 ATTATTAATTAT-ATT-TAATA-TATTA
1 ATTA-TAATTATAATTATAATATTATTA
141822 TACATGTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.21
26 5 0.21
27 7 0.29
28 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTATAATTATAATTATAATATTATTA
Found at i:141904 original size:14 final size:14
Alignment explanation
Indices: 141885--141927 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
141875 TTATAAAATA
141885 TATATTTTAATTAC
1 TATATTTTAATTAC
* *
141899 TATATTTATTTATTAG
1 TATA-TT-TTAATTAC
141915 TATATTTTAATTA
1 TATATTTTAATTA
141928 TTTATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.42
15 4 0.17
16 10 0.42
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
TATATTTTAATTAC
Found at i:143115 original size:45 final size:45
Alignment explanation
Indices: 143066--143161 Score: 165
Period size: 45 Copynumber: 2.1 Consensus size: 45
143056 ACCTTTTTTT
*
143066 TCTTTTAGCTTTCTTGGGCATTTGTAAATCTACTTTATTTATTTC
1 TCTTTTAGCTTTCTTGGGCATTTGTAAATATACTTTATTTATTTC
*
143111 TCTTTCAGCTTTCTTGGGCATTTGTAAATATACTTTATTTATTTC
1 TCTTTTAGCTTTCTTGGGCATTTGTAAATATACTTTATTTATTTC
*
143156 TTTTTT
1 TCTTTT
143162 GATCGAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.57
Consensus pattern (45 bp):
TCTTTTAGCTTTCTTGGGCATTTGTAAATATACTTTATTTATTTC
Found at i:172651 original size:172 final size:174
Alignment explanation
Indices: 172365--172711 Score: 671
Period size: 172 Copynumber: 2.0 Consensus size: 174
172355 AGACATTATT
172365 GGTCCCCTAATCTACAAATTGAAAAATCATTACATTTTATTGCATCCACATAGAATCCTTCCATA
1 GGTCCCCTAATCTACAAATTGAAAAATCATTACATTTTATTGCATCCACATAGAATCCTTCCATA
172430 TATATGAAATAAACAGTTTTTGACACTTATATGTAGTTTAGATTTACCAACTTGTGTTTGGGGTT
66 TATATGAAATAAACAGTTTTTGACACTTATATGTAGTTTAGATTTACCAACTTGTGTTTGGGGTT
172495 AAGGTTGAATGAC-AGCTATGCTGAGA-GGCATCATCCACCTGA
131 AAGGTTGAATGACAAGCTATGCTGAGAGGGCATCATCCACCTGA
172537 GGTCCCCTAATCTACAAATTGAAAAATCATTACATTTTATTGCATCCACATAGAATCCTTCCATA
1 GGTCCCCTAATCTACAAATTGAAAAATCATTACATTTTATTGCATCCACATAGAATCCTTCCATA
172602 TATATGAAATAAACAGTTTTTGACACTTATATGTAGTTTAGATTTACCAACTTGTGTTTGGGGTT
66 TATATGAAATAAACAGTTTTTGACACTTATATGTAGTTTAGATTTACCAACTTGTGTTTGGGGTT
172667 AAGGTTGAATGACAGAGCTATGCTGAGAGGGCATCATCCACCTGA
131 AAGGTTGAATGACA-AGCTATGCTGAGAGGGCATCATCCACCTGA
172712 TTATGTTGCT
Statistics
Matches: 172, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
172 143 0.83
174 13 0.08
175 16 0.09
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (174 bp):
GGTCCCCTAATCTACAAATTGAAAAATCATTACATTTTATTGCATCCACATAGAATCCTTCCATA
TATATGAAATAAACAGTTTTTGACACTTATATGTAGTTTAGATTTACCAACTTGTGTTTGGGGTT
AAGGTTGAATGACAAGCTATGCTGAGAGGGCATCATCCACCTGA
Found at i:174609 original size:25 final size:23
Alignment explanation
Indices: 174581--174629 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 23
174571 ATAGCATAGT
174581 ATATATAATAAATATAGTTTTTGGA
1 ATATATAAT--ATATAGTTTTTGGA
174606 ATATATAATATATAGTTTTTGGA
1 ATATATAATATATAGTTTTTGGA
174629 A
1 A
174630 ACTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 15 0.62
25 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (23 bp):
ATATATAATATATAGTTTTTGGA
Found at i:174729 original size:35 final size:34
Alignment explanation
Indices: 174608--174733 Score: 146
Period size: 35 Copynumber: 3.5 Consensus size: 34
174598 TTTTTGGAAT
* *
174608 ATATAATATATAGTTTTTGGAAACTTATTTTTAAAAAC
1 ATATAATATATAGTTTTT--AAA--TAATTTTGAAAAC
* *
174646 ATATAATATATAGCTTTCAAA-ACGATTTTGAAAAC
1 ATATAATATATAGTTTTTAAATA--ATTTTGAAAAC
174681 ATATAATATATAGTTTTTAAGATAATTTTGAAAAC
1 ATATAATATATAGTTTTTAA-ATAATTTTGAAAAC
174716 ATATAATATATAGTTTTT
1 ATATAATATATAGTTTTT
174734 TAAAAAAATA
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
33 1 0.01
35 56 0.72
36 4 0.05
37 1 0.01
38 16 0.21
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.43
Consensus pattern (34 bp):
ATATAATATATAGTTTTTAAATAATTTTGAAAAC
Found at i:174909 original size:3 final size:3
Alignment explanation
Indices: 174901--174950 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
174891 TTATATAGTT
*
174901 TTA TTA TTA TTA TT- TATA TTA TTTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
174947 TTA T
1 TTA T
174951 ATTTATTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 1 0.02
3 37 0.88
4 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:176526 original size:20 final size:20
Alignment explanation
Indices: 176482--176696 Score: 130
Period size: 20 Copynumber: 10.6 Consensus size: 20
176472 AATGACCAAT
*
176482 AAAATCGCAACGCGATATA-
1 AAAATCGCAACGCGATTTAG
176501 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
176521 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
176541 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* * **
176561 AAAATCGCAATGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
176582 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
176605 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
176625 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
176645 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
176665 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
176685 AAAATCGCAACG
1 AAAATCGCAACG
176697 TTAAAAAGAA
Statistics
Matches: 153, Mismatches: 34, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
19 18 0.12
20 108 0.71
21 13 0.08
23 14 0.09
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:176662 original size:40 final size:40
Alignment explanation
Indices: 176586--176694 Score: 146
Period size: 40 Copynumber: 2.6 Consensus size: 40
176576 GCTTCCAAGT
*
176586 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTT---AGAAAATCGCAATGCGATTGAGAGAA
* * * *
176629 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAA
176669 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAAAATCGCAA
176695 CGTTAAAAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 45 0.78
43 13 0.22
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAA
Found at i:176706 original size:20 final size:20
Alignment explanation
Indices: 176683--176726 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
176673 AACGCGATTT
*
176683 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
176703 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
176723 AGAA
1 AGAA
176727 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:176813 original size:6 final size:6
Alignment explanation
Indices: 176802--176875 Score: 91
Period size: 6 Copynumber: 12.3 Consensus size: 6
176792 GACACGTATT
176802 ACCACG ACCACG ACCACG ACCACG ACCCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG A-CCACG ACCACG ACCACG ACCACG
*
176850 ACCCGCG ACC-CG ACC-CG ACCGACG AC
1 A-CCACG ACCACG ACCACG ACC-ACG AC
176876 GGCGGCGGCG
Statistics
Matches: 63, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
5 13 0.21
6 37 0.59
7 13 0.21
ACGTcount: A:0.28, C:0.53, G:0.19, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:176831 original size:25 final size:25
Alignment explanation
Indices: 176803--176875 Score: 107
Period size: 25 Copynumber: 3.0 Consensus size: 25
176793 ACACGTATTA
176803 CCACGACCACGACCACGACCACGAC
1 CCACGACCACGACCACGACCACGAC
176828 CCACGACCACGACCACGACC-CGAC
1 CCACGACCACGACCACGACCACGAC
*
176852 CCGCGACC-CGACC-CGACCGACGAC
1 CCACGACCACGACCACGACC-ACGAC
176876 GGCGGCGGCG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
22 5 0.11
23 5 0.11
24 15 0.33
25 20 0.44
ACGTcount: A:0.27, C:0.53, G:0.19, T:0.00
Consensus pattern (25 bp):
CCACGACCACGACCACGACCACGAC
Found at i:176833 original size:19 final size:19
Alignment explanation
Indices: 176802--176848 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
176792 GACACGTATT
176802 ACCACGA-CCACGACCACG
1 ACCACGACCCACGACCACG
176820 ACCACGACCCACGACCACG
1 ACCACGACCCACGACCACG
176839 ACCACGACCC
1 ACCACGACCC
176849 GACCCGCGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.32, C:0.53, G:0.15, T:0.00
Consensus pattern (19 bp):
ACCACGACCCACGACCACG
Found at i:176859 original size:31 final size:29
Alignment explanation
Indices: 176803--176875 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 29
176793 ACACGTATTA
176803 CCACGACCACGACCACGACCACGACCCACGA
1 CCACGACCACGACCACGACCACGA-CC-CGA
*
176834 CCACGACCACGACC-CGACCCGCGACCCGA
1 CCACGACCACGACCACGA-CCACGACCCGA
176863 CC-CGACCGACGAC
1 CCACGACC-ACGAC
176876 GGCGGCGGCG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 5 0.13
29 10 0.26
30 5 0.13
31 19 0.49
ACGTcount: A:0.27, C:0.53, G:0.19, T:0.00
Consensus pattern (29 bp):
CCACGACCACGACCACGACCACGACCCGA
Found at i:177617 original size:6 final size:6
Alignment explanation
Indices: 177538--177616 Score: 124
Period size: 6 Copynumber: 13.3 Consensus size: 6
177528 GCGCCGTCTC
177538 GTCG-G GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
* * *
177585 GTCGTG GTCGGG GTCGTG GTAGTG GTAGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
177617 AATACGTGTC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
5 4 0.06
6 66 0.94
ACGTcount: A:0.03, C:0.14, G:0.52, T:0.32
Consensus pattern (6 bp):
GTCGTG
Found at i:177713 original size:20 final size:20
Alignment explanation
Indices: 177688--177731 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
177678 TTTTTAACTA
*
177688 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
177708 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
177728 TTCT
1 TTCT
177732 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:177741 original size:20 final size:20
Alignment explanation
Indices: 177718--178056 Score: 130
Period size: 20 Copynumber: 16.6 Consensus size: 20
177708 TTCTTTTTAA
177718 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
177738 CGTTGCGA-TTCCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* ***
177757 CATTGCGATTCTAGAAAATCG
1 CGTTGCGATT-TTCTAAATCG
* * * **
177778 CATTGCGATTCTCTCAGCCG
1 CGTTGCGATTTTCTAAATCG
* *
177798 CATTGCGATTTTCTTCTAGATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
177821 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
177841 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
177861 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
177881 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
177901 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
177924 CGTTGCGAACTTT-GAAGCTCG
1 CGTTGCG-ATTTTCTAA-ATCG
** ** *
177945 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
177966 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
177984 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
178006 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
178026 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
178045 CGTTGCGATTTT
1 CGTTGCGATTTT
178057 ATTGGTCATT
Statistics
Matches: 251, Mismatches: 53, Indels: 31
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.01
19 33 0.13
20 136 0.54
21 47 0.19
22 7 0.03
23 25 0.10
24 1 0.00
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:177776 original size:40 final size:40
Alignment explanation
Indices: 177720--177910 Score: 231
Period size: 40 Copynumber: 4.7 Consensus size: 40
177710 CTTTTTAACG
* * *
177720 TTGCGATTTTCTAAATCGCGTTGCGATTC-CTCAATCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
* **
177759 TTGCGATTCTAGAAAATCGCATTGCGATTCTCTCAGCCGCA
1 TTGCGATTCTA-TAAATCGCATTGCGATTCTCTCAATCGCA
* * * *
177800 TTGCGATTTTCTTCTAGATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TTC-TATAAATCGCATTGCGATTCTCTCAATCGCA
*
177843 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
*
177883 TTGCGATTCTATCAATCGCATTGCGATT
1 TTGCGATTCTATAAATCGCATTGCGATT
177911 TTCTTCTAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 9 0.07
40 69 0.54
41 17 0.13
43 32 0.25
44 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (40 bp):
TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:177840 original size:103 final size:103
Alignment explanation
Indices: 177718--177931 Score: 304
Period size: 103 Copynumber: 2.1 Consensus size: 103
177708 TTCTTTTTAA
* * * * *
177718 CGTTGCGATTTTCTAAATCGCGTTGCGATTC-CTCAATCGCATTGCGATTCTAGAAAATCGCATT
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTA-AAAATCGCATT
* * *
177782 GCGATTCTCTCAGCCGCATTGCGATTTTCTTCTAGATCG
65 GCGATTCTATCAACCGCATTGCGATTTTCTTCTAAATCG
* **
177821 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTAAAAATCGCATTG
*
177886 CGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
66 CGATTCTATCAACCGCATTGCGATTTTCTTCTAAATCG
177924 CGTTGCGA
1 CGTTGCGA
177932 ACTTTGAAGC
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
103 79 0.81
104 19 0.19
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.35
Consensus pattern (103 bp):
CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTAAAAATCGCATTG
CGATTCTATCAACCGCATTGCGATTTTCTTCTAAATCG
Found at i:177859 original size:83 final size:83
Alignment explanation
Indices: 177728--177890 Score: 256
Period size: 83 Copynumber: 2.0 Consensus size: 83
177718 CGTTGCGATT
* *
177728 TTCTAAATCGCGTTGCGATTCCTCAATCGCATTGCGATTCTAGAAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCCTCAATCGCATTGCGATTCTAGAAAATCGCATTGCGATTCTATC
*
177793 AGCCGCATTGCGATTTTC
66 AACCGCATTGCGATTTTC
* *
177811 TTCTAGATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTA-TAAATCGCATTGCGATTCTAT
1 TTCTAAATCGCGTTGCGACTC-CTCAATCGCATTGCGATTCTAGAAAATCGCATTGCGATTCTAT
*
177875 CAATCGCATTGCGATT
65 CAACCGCATTGCGATT
177891 CTATCAATCG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
83 52 0.71
84 21 0.29
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCCTCAATCGCATTGCGATTCTAGAAAATCGCATTGCGATTCTATC
AACCGCATTGCGATTTTC
Found at i:177947 original size:21 final size:21
Alignment explanation
Indices: 177921--177973 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
177911 TTCTTCTAAA
*
177921 TCGCGTTGCGAACTTTGAAGC
1 TCGCGTTGCGAACTTGGAAGC
177942 TCGCGTTGCGAACTTGGAAGC
1 TCGCGTTGCGAACTTGGAAGC
177963 TCGCGTTGCGA
1 TCGCGTTGCGA
177974 TTTTCTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.25, G:0.32, T:0.26
Consensus pattern (21 bp):
TCGCGTTGCGAACTTGGAAGC
Found at i:178046 original size:19 final size:20
Alignment explanation
Indices: 178006--178056 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
177996 TTCTTTTTAA
*
178006 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
178026 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
178045 CGTTGCGATTTT
1 CGTTGCGATTTT
178057 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:179288 original size:24 final size:25
Alignment explanation
Indices: 179256--179302 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
179246 ACTGAAAATG
179256 ATAACCAAACAATTATTGACCACTT
1 ATAACCAAACAATTATTGACCACTT
179281 ATAA-CAAACAATTATTGACCAC
1 ATAACCAAACAATTATTGACCAC
179303 GTGTTTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.26
Consensus pattern (25 bp):
ATAACCAAACAATTATTGACCACTT
Found at i:187790 original size:27 final size:27
Alignment explanation
Indices: 187760--187813 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
187750 AAACGAACGA
187760 TAAACAAACACTAAAACAACGCTAAAC
1 TAAACAAACACTAAAACAACGCTAAAC
** **
187787 TAAATGAACACTAAATGAACGCTAAAC
1 TAAACAAACACTAAAACAACGCTAAAC
187814 GATTATGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (27 bp):
TAAACAAACACTAAAACAACGCTAAAC
Found at i:187890 original size:34 final size:34
Alignment explanation
Indices: 187845--187927 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
187835 CGTGAACATA
187845 TAAACGAACATGTTCGCGAATATTAAACTAACGC
1 TAAACGAACATGTTCGCGAATATTAAACTAACGC
*
187879 TAAACGGACATGTTCGCGAATATTAAACTAACGC
1 TAAACGAACATGTTCGCGAATATTAAACTAACGC
*
187913 TAAACAAACATGTTC
1 TAAACGAACATGTTC
187928 ATGAACATAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (34 bp):
TAAACGAACATGTTCGCGAATATTAAACTAACGC
Found at i:189201 original size:2 final size:2
Alignment explanation
Indices: 189194--189239 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
189184 TATGCATTTA
189194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
189236 AT AT
1 AT AT
189240 TTAATACTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:196436 original size:2 final size:2
Alignment explanation
Indices: 196431--196459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
196421 TCTCTCTCTC
196431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
196460 GCTCTTGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:204860 original size:20 final size:20
Alignment explanation
Indices: 204806--204861 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 20
204796 ACAATCTGAT
204806 AATTTT-AAAAAATTATTTAA
1 AATTTTAAAAAAATTA-TTAA
*
204826 AATTTAAAAATAAAATTA-TAA
1 AATTT-TAAA-AAAATTATTAA
204847 ATATTTTAAAAAAAT
1 A-ATTTTAAAAAAAT
204862 AAAATTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 10 0.33
21 7 0.23
22 6 0.20
23 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTTTAAAAAAATTATTAA
Found at i:204882 original size:26 final size:25
Alignment explanation
Indices: 204831--204884 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
204821 TTTAAAATTT
***
204831 AAAAATAAAATTATAAATATTTTAA
1 AAAAATAAAATTATAAATAACCTAA
*
204856 AAAAATAAAATTTTGAAATAACCTAA
1 AAAAATAAAATTAT-AAATAACCTAA
204882 AAA
1 AAA
204885 CTTTGAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (25 bp):
AAAAATAAAATTATAAATAACCTAA
Found at i:206516 original size:24 final size:24
Alignment explanation
Indices: 206488--206540 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
206478 CCTCTTCTCC
206488 GACCCCATACAAGAGGCCCCTTCT
1 GACCCCATACAAGAGGCCCCTTCT
*
206512 GACCCCTTACAAGAGGCCCCTTCT
1 GACCCCATACAAGAGGCCCCTTCT
206536 GACCC
1 GACCC
206541 AAACGCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.23, C:0.43, G:0.17, T:0.17
Consensus pattern (24 bp):
GACCCCATACAAGAGGCCCCTTCT
Found at i:213276 original size:20 final size:20
Alignment explanation
Indices: 213182--213550 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
213172 GATTTTCCAT
* ** *
213182 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
213202 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
213222 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
213242 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
213262 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
213282 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
213302 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
213322 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
213342 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
213362 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
213382 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
213402 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
213422 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
213442 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
213462 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
213482 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
213502 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
213522 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
213542 AATCACAAC
1 AATCGCAAC
213551 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:214263 original size:24 final size:24
Alignment explanation
Indices: 214224--214270 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
214214 AAATTTGGTC
214224 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
214248 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
214271 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:214462 original size:12 final size:12
Alignment explanation
Indices: 214445--214469 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
214435 ATATAATCCT
214445 GAAGAAGAAAAA
1 GAAGAAGAAAAA
214457 GAAGAAGAAAAA
1 GAAGAAGAAAAA
214469 G
1 G
214470 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:216797 original size:19 final size:19
Alignment explanation
Indices: 216775--217082 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
216765 CGGAAAATAC
*
216775 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
216794 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
216808 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
216828 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
216842 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
216861 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
216880 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
216894 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
216913 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
216932 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
216946 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
216965 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
216984 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
217003 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
217022 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
217036 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
217056 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
217075 AATCGCAA
1 AATCGCAA
217083 CGAGATAATC
Statistics
Matches: 249, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 12 0.05
17 18 0.07
18 6 0.02
19 140 0.56
20 24 0.10
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:216862 original size:33 final size:34
Alignment explanation
Indices: 216775--217104 Score: 276
Period size: 33 Copynumber: 9.5 Consensus size: 34
216765 CGGAAAATAC
* *
216775 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
216808 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
216842 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
216880 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
216913 AATCGCAATGCGAAATGAAAATCG-AACCGA-CAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CGATGAA
*
216946 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--ATGAA
216984 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
217022 AATCGCAA--CGAAA-G--AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C-G--ATGAA
*
217056 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
217089 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
217105 TATAAACGCA
Statistics
Matches: 257, Mismatches: 14, Indels: 52
0.80 0.04 0.16
Matches are distributed among these distances:
33 108 0.42
34 48 0.19
35 9 0.04
36 17 0.07
37 8 0.03
38 59 0.23
39 8 0.03
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:216890 original size:52 final size:53
Alignment explanation
Indices: 216803--217082 Score: 351
Period size: 52 Copynumber: 5.2 Consensus size: 53
216793 AAATCCCAAC
*
216803 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
216856 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
216908 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
216960 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
217017 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-G--A-GAAAATCGCAATGCGAA
217070 ATGAAAATCGCAA
1 ATGAAAATCGCAA
217083 CGAGATAATC
Statistics
Matches: 212, Mismatches: 8, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
51 2 0.01
52 121 0.57
53 53 0.25
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:216926 original size:71 final size:71
Alignment explanation
Indices: 216842--217082 Score: 348
Period size: 71 Copynumber: 3.4 Consensus size: 71
216832 GCAACGAGAG
*
216842 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
216907 AATGAA
66 AATGAA
* * *
216913 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
216973 TACGAAATGAA
61 TGCGAAATGAA
216984 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC-G
217049 AAATGAA
65 AAATGAA
217056 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
217083 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 21
0.83 0.05 0.12
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 78 0.52
72 37 0.25
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:217220 original size:19 final size:19
Alignment explanation
Indices: 217111--217212 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
217101 AAATTATAAA
217111 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
217130 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
217150 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
217166 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
217183 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
217202 CGCATTGCGAT
1 CGCATTGCGAT
217213 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:217338 original size:14 final size:14
Alignment explanation
Indices: 217319--217355 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
217309 CATCAATTAC
217319 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
217333 ACAAATCATCTTTT
1 ACAAATCAACTTTT
217347 ACAAATCAA
1 ACAAATCAA
217356 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:217367 original size:12 final size:12
Alignment explanation
Indices: 217350--217422 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
217340 ATCTTTTACA
217350 AATCAATTAAAC
1 AATCAATTAAAC
*
217362 AATCAA--AAATTG
1 AATCAATTAAA--C
**
217374 AATCAACTTTTAC
1 AATCAA-TTAAAC
217387 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
217400 AATCAA-AAAAC
1 AATCAATTAAAC
217411 AATCAATTAAAC
1 AATCAATTAAAC
217423 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:217384 original size:38 final size:38
Alignment explanation
Indices: 217336--217408 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
217326 AACTTTTACA
*
217336 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
217374 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
217409 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:219300 original size:14 final size:14
Alignment explanation
Indices: 219281--219337 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
219271 GCGAAATGAA
*
219281 AATCGCAACGACAG
1 AATCGCAACGAAAG
219295 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
219312 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
219328 AATCGCAACG
1 AATCGCAACG
219338 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:219308 original size:33 final size:33
Alignment explanation
Indices: 219262--219354 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
219252 GCGAAACCAA
*
219262 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
219295 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
219328 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
219355 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:219319 original size:19 final size:19
Alignment explanation
Indices: 219225--219359 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
219215 TAGTTTACTT
* *
219225 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
219245 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
219264 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
219283 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
219297 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
219316 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
219330 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
219349 TCGCAATGCGA
1 TCGCAACGCGA
219360 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:219377 original size:19 final size:19
Alignment explanation
Indices: 219355--219483 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
219345 AAAATCGCAA
219355 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
219374 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
219388 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
219407 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
219421 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
219440 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
219459 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
219479 TGCGA
1 TGCGA
219484 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:219397 original size:33 final size:33
Alignment explanation
Indices: 219355--219446 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
219345 AAAATCGCAA
219355 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
219388 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
219421 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
219447 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:219686 original size:93 final size:93
Alignment explanation
Indices: 219527--219906 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
219517 TTGAATGGAT
219527 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
219592 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
219620 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
219685 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
219713 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
219777 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
219805 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
219870 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
219898 AAATTTACT
1 AAATTTACT
219907 AAGCAATCTA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:219840 original size:185 final size:186
Alignment explanation
Indices: 219527--219906 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
219517 TTGAATGGAT
219527 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
219592 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
219657 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
219713 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
219777 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
219842 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
219898 AAATTTACT
1 AAATTTACT
219907 AAGCAATCTA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:221632 original size:14 final size:14
Alignment explanation
Indices: 221613--221702 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
221603 TTGAAATGAA
221613 AATCGCAACGAGAG
1 AATCGCAACGAGAG
221627 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
221644 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
221660 AATCGCAACGCGAAATGG
1 AATCGCAA--CGAGA--G
221678 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
221693 AATCGCAACG
1 AATCGCAACG
221703 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 26 0.41
15 1 0.02
16 10 0.16
17 10 0.16
18 1 0.02
19 16 0.25
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:221650 original size:33 final size:33
Alignment explanation
Indices: 221605--221719 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
221595 TCTTTTGGTT
221605 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
221638 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
221671 GAAATGGAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
221704 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
221720 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:221651 original size:19 final size:18
Alignment explanation
Indices: 221612--221724 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
221602 GTTGAAATGA
221612 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
221627 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
221644 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
221660 -AATCGCAACGCGAAATGG
1 AAATCGCAACGCGAGAT-G
221678 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
221693 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
221710 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
221725 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 14 0.18
17 11 0.14
18 1 0.01
19 28 0.35
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:221755 original size:14 final size:14
Alignment explanation
Indices: 221736--221790 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
221726 TTTGGTTTCG
221736 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
221750 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
221769 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
221783 CGTTGCGA
1 CGTTGCGA
221791 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Done.