Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 92 of 199
Found at i:28267215 original size:48 final size:48
Alignment explanation
Indices: 28267158--28267252 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
28267148 CAGTCACTCC
* * *
28267158 TTCAGTGCCTGCAACACCAACTCAACATTGGGCTCCAACTCCTGCACT
1 TTCAATGCCTACAACACCAACTCAACATTGGACTCCAACTCCTGCACT
* *
28267206 TTCAATGCCTACAACACCAACTCAACCTTGGACTCCAGCTCCTGCAC
1 TTCAATGCCTACAACACCAACTCAACATTGGACTCCAACTCCTGCAC
28267253 CTTGGGCACC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.22
Consensus pattern (48 bp):
TTCAATGCCTACAACACCAACTCAACATTGGACTCCAACTCCTGCACT
Found at i:28267398 original size:66 final size:66
Alignment explanation
Indices: 28267292--28267605 Score: 425
Period size: 66 Copynumber: 4.8 Consensus size: 66
28267282 GTAGCACCAA
* *
28267292 CACCGGCTACACCTTCTGTGCCAGCAACACCATATGAACCTTGGGCTCCAGCCCCTGCACCCTGG
1 CACCGACTACACCTTCTGTGCCAGCAACACCATCTGAACCTTGGGCTCCAGCCCCTGCACCCTGG
28267357 G
66 G
* * *
28267358 CACCGACTACACCTTCTGTGCTAGCAACACCATCTGAACCTTGGGCTCCAGGCCCTGCACCTTGG
1 CACCGACTACACCTTCTGTGCCAGCAACACCATCTGAACCTTGGGCTCCAGCCCCTGCACCCTGG
28267423 G
66 G
* * *
28267424 CACCAACTACACCTACTGTGCCAGCAACACCATCT-AACCCTTGTGCTCCAGCCCCTGCACCCTG
1 CACCGACTACACCTTCTGTGCCAGCAACACCATCTGAA-CCTTGGGCTCCAGCCCCTGCACCCTG
28267488 GG
65 GG
* * * * * *
28267490 CACCGGCTGCACCTTCTGTGCCAGCAACACGATCTCAACCTTGGGCTCCAGGCCCTGCACCATGG
1 CACCGACTACACCTTCTGTGCCAGCAACACCATCTGAACCTTGGGCTCCAGCCCCTGCACCCTGG
*
28267555 A
66 G
* * * *
28267556 CAGC-AGCTACACCTTCTGTGACAACAACACCATCTGACCCTTGGGCTCCA
1 CACCGA-CTACACCTTCTGTGCCAGCAACACCATCTGAACCTTGGGCTCCA
28267606 ACTCCATCTC
Statistics
Matches: 217, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
65 2 0.01
66 213 0.98
67 2 0.01
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.19
Consensus pattern (66 bp):
CACCGACTACACCTTCTGTGCCAGCAACACCATCTGAACCTTGGGCTCCAGCCCCTGCACCCTGG
G
Found at i:28270655 original size:18 final size:18
Alignment explanation
Indices: 28270627--28270673 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
28270617 CACACAAGAT
*
28270627 AACAATTCACACGA-ATTA
1 AACAGTTCACA-GAGATTA
* *
28270645 AACGGTTCACATAGATTA
1 AACAGTTCACAGAGATTA
28270663 AACAGTTCACA
1 AACAGTTCACA
28270674 TAAAATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (18 bp):
AACAGTTCACAGAGATTA
Found at i:28270674 original size:18 final size:18
Alignment explanation
Indices: 28270641--28270675 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28270631 ATTCACACGA
*
28270641 ATTAAACGGTTCACATAG
1 ATTAAACAGTTCACATAG
28270659 ATTAAACAGTTCACATA
1 ATTAAACAGTTCACATA
28270676 AAATAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (18 bp):
ATTAAACAGTTCACATAG
Found at i:28270688 original size:17 final size:17
Alignment explanation
Indices: 28270649--28270705 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
28270639 GAATTAAACG
* *
28270649 GTTCACATAGATTAAACA
1 GTTCACATAAAAT-AACA
*
28270667 GTTCACATAAAATAATA
1 GTTCACATAAAATAACA
* *
28270684 GTTCATATGAAATAACA
1 GTTCACATAAAATAACA
28270701 GTTCA
1 GTTCA
28270706 TTCAATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 22 0.67
18 11 0.33
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (17 bp):
GTTCACATAAAATAACA
Found at i:28270706 original size:17 final size:17
Alignment explanation
Indices: 28270663--28270706 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
28270653 ACATAGATTA
*
28270663 AACAGTTCACATAAAAT
1 AACAGTTCATATAAAAT
* *
28270680 AATAGTTCATATGAAAT
1 AACAGTTCATATAAAAT
28270697 AACAGTTCAT
1 AACAGTTCAT
28270707 TCAATATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.30
Consensus pattern (17 bp):
AACAGTTCATATAAAAT
Found at i:28272744 original size:40 final size:39
Alignment explanation
Indices: 28272699--28272774 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
28272689 GTTTGGAACA
*
28272699 AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTAGCC
1 AAAGCGCCACAAAAAATAGAGCATCAGCGGCG-TTTAGCC
* * **
28272739 AAAGCGCCGCTAAAGGTAGAGCATCAGCGGCGTTTA
1 AAAGCGCCACAAAAAATAGAGCATCAGCGGCGTTTA
28272775 TACGGAAGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (39 bp):
AAAGCGCCACAAAAAATAGAGCATCAGCGGCGTTTAGCC
Found at i:28273019 original size:82 final size:82
Alignment explanation
Indices: 28272876--28273237 Score: 447
Period size: 82 Copynumber: 4.4 Consensus size: 82
28272866 TTTAAACATT
* *
28272876 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTTGTTTAAGCGCC
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
*
28272941 GCTAATGCTCGGGTCTA
66 GCTAATGCTCGTGTCTA
*
28272958 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTTGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
* *
28273023 GCTAATGCTCCGAGTCTT
66 GCTAATGCT-CGTGTCTA
* * * * *
28273041 TAGCGGCGCTTTCGTCTAAGCGCCGCTAATGCTCCGAGTCTTTAGCGGCGTTTTCGTCTAAGCGC
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGGGTCTATAGCGGCGTTTTCGTATAAGCGC
* *
28273106 TGATAATGCTCTGTGTCTA
65 CGCTAATGCTC-GTGTCTA
* * * * ** *
28273125 TAGCGGCGTTTTCGCCTATGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTATATATGCGCC
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
* * *
28273190 GCTAATTCTCCTGTAT-
66 GCTAATGCTCGTGTCTA
* * *
28273206 TCAGCGGCGTTTGTATCTAAGCGCCGCGAATG
1 T-AGCGGCGTTTTTGTCTAAGCGCCGCTAATG
28273238 TATTAATCTT
Statistics
Matches: 242, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
81 1 0.00
82 99 0.41
83 72 0.30
84 70 0.29
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (82 bp):
TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
GCTAATGCTCGTGTCTA
Found at i:28273061 original size:42 final size:41
Alignment explanation
Indices: 28272876--28273195 Score: 424
Period size: 41 Copynumber: 7.7 Consensus size: 41
28272866 TTTAAACATT
*
28272876 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
* *
28272917 TAGCGGCGTTTTTGTTTAAGCGCCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
* *
28272958 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTTGGGTCTA
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
* * *
28272999 TAGCGGCGTTTTCGTATAAGCGCCGCTAATGCTCCGAGTCTT
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCT-CGGGTCTA
* * *
28273041 TAGCGGCGCTTTCGTCTAAGCGCCGCTAATGCTCCGAGTCTT
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCT-CGGGTCTA
* * *
28273083 TAGCGGCGTTTTCGTCTAAGCGCTGATAATGCTCTGTGTCTA
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTC-GGGTCTA
* * *
28273125 TAGCGGCGTTTTCGCCTATGCGCCGCTAATGCTCGGGTCTT
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
** * *
28273166 TAGCGGCGTTTTTATATATGCGCCGCTAAT
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAAT
28273196 TCTCCTGTAT
Statistics
Matches: 252, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
41 142 0.56
42 110 0.44
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.33
Consensus pattern (41 bp):
TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
Found at i:28273212 original size:41 final size:41
Alignment explanation
Indices: 28272877--28273237 Score: 150
Period size: 41 Copynumber: 8.7 Consensus size: 41
28272867 TTAAACATTT
* * * * * *
28272877 AGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTAT-
1 AGCGGCGTTTGTATATATGCGCCGCTAATGCTCCGGTAT-TC
* * * * * *
28272918 AGCGGCGTTTTTGTTTAAGCGCCGCTAATGCTCGGGTCTAT-
1 AGCGGCGTTTGTATATATGCGCCGCTAATGCTCCGGTAT-TC
* * * * ** *
28272959 AGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTTGGGTCTAT-
1 AGCGGCGTTTGTATATATGCGCCGCTAATGCTCCGGTAT-TC
* *
28273000 AGCGGCGTTTTCGTATA-A-GCGCCGCTAATGCTCCGAGTCTTT
1 AGCGGCG-TTT-GTATATATGCGCCGCTAATGCTCCG-GTATTC
* * *
28273042 AGCGGCGCTTTCGTCTA-A-GCGCCGCTAATGCTCCGAGTCTTT
1 AGCGGCG-TTT-GTATATATGCGCCGCTAATGCTCCG-GTATTC
* * * * *
28273084 AGCGGCGTTTTCGTCTA-A-GCGCTGATAATGCTCTGTGTCTAT-
1 AGCGGCG-TTT-GTATATATGCGCCGCTAATGCTCCG-GTAT-TC
*** * * *
28273126 AGCGGCGTTT-TCGCCTATGCGCCGCTAATGCTCGGGTCTTT
1 AGCGGCGTTTGT-ATATATGCGCCGCTAATGCTCCGGTATTC
* * *
28273167 AGCGGCGTTTTTATATATGCGCCGCTAATTCTCCTGTATTC
1 AGCGGCGTTTGTATATATGCGCCGCTAATGCTCCGGTATTC
* * *
28273208 AGCGGCGTTTGTATCTAAGCGCCGCGAATG
1 AGCGGCGTTTGTATATATGCGCCGCTAATG
28273238 TATTAATCTT
Statistics
Matches: 276, Mismatches: 34, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 166 0.60
42 105 0.38
43 3 0.01
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.32
Consensus pattern (41 bp):
AGCGGCGTTTGTATATATGCGCCGCTAATGCTCCGGTATTC
Found at i:28275383 original size:25 final size:22
Alignment explanation
Indices: 28275329--28275385 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
28275319 CACGATTTCA
*
28275329 TTTCCCCAATTTCCCAACTTCT
1 TTTCCCCAATTTCCCAACTTAT
*
28275351 TTTCCCCCAATTTCCCCCAAGTTAT
1 TTT-CCCCAATTT--CCCAACTTAT
28275376 TCTTCCCCAA
1 T-TTCCCCAA
28275386 AGTATTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 3 0.10
23 9 0.31
25 15 0.52
26 2 0.07
ACGTcount: A:0.19, C:0.42, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTCCCCAATTTCCCAACTTAT
Found at i:28275397 original size:14 final size:15
Alignment explanation
Indices: 28275361--28275399 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
28275351 TTTCCCCCAA
*
28275361 TTTCCCCCAAGTTAT
1 TTTCCCCAAAGTTAT
28275376 TCTTCCCCAAAG-TAT
1 T-TTCCCCAAAGTTAT
28275391 TTTCCCCAA
1 TTTCCCCAA
28275400 TTTCCCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (15 bp):
TTTCCCCAAAGTTAT
Found at i:28275658 original size:33 final size:33
Alignment explanation
Indices: 28275615--28275688 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
28275605 ATTTGCCATC
*
28275615 TATGATATTCGAGTTAAATGAGATGAGTGTTGGG
1 TATGA-ATTCGAGTTAAATGAGATGAGTGTTAGG
*
28275649 TATGAATTCGAGTTAAATGAGATTAGTGTTAGG
1 TATGAATTCGAGTTAAATGAGATGAGTGTTAGG
28275682 TATGAAT
1 TATGAAT
28275689 ATATGTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 33 0.87
34 5 0.13
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36
Consensus pattern (33 bp):
TATGAATTCGAGTTAAATGAGATGAGTGTTAGG
Found at i:28275951 original size:17 final size:17
Alignment explanation
Indices: 28275929--28275966 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28275919 ATCCCAGGAA
28275929 CTTGCAGCCTCTACTTC
1 CTTGCAGCCTCTACTTC
*
28275946 CTTGCAGCCTTTACTTC
1 CTTGCAGCCTCTACTTC
28275963 CTTG
1 CTTG
28275967 TGAACTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.37, G:0.13, T:0.39
Consensus pattern (17 bp):
CTTGCAGCCTCTACTTC
Found at i:28277668 original size:22 final size:22
Alignment explanation
Indices: 28277623--28277668 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
28277613 AACTTAATTA
*
28277623 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAACTGAC
28277645 ATTAATATTATACATAGA-TGAC
1 ATTAATATTATACATA-ACTGAC
28277667 AT
1 AT
28277669 AACTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (22 bp):
ATTAATATTATACATAACTGAC
Found at i:28277674 original size:56 final size:56
Alignment explanation
Indices: 28277611--28277949 Score: 363
Period size: 56 Copynumber: 5.6 Consensus size: 56
28277601 TGTAAGGGAT
*
28277611 ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAGATGAC
1 ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAATGAC
28277667 ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAATGAC
1 ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAATGAC
*
28277723 ATAACTTAATTAATTAATATTATACATAACTTACATAAATTAATTACTTAATATACATAAATTAC
1 ATAACTTAATTAATTAATATTATACATAACTTAC----ATTAA-TA--T--TATACATAAATGAC
* * * * *
28277788 ATAACTTACATTAATATGATACATAAATGACATAACTTAATTAATTAATATTATACATAACTTAC
1 ATAACTTA-ATTAAT-T-A-ATAT-TAT-ACATAACTT-A--CATTAATATTATACATAAATGAC
* * *
28277853 ATAAATTAATTAGTTAATATACATAAATTACATAACTTACATTAATATGATACATAAATGAC
1 ATAACTTAATTAATTAATAT---T--A-TACATAACTTACATTAATATTATACATAAATGAC
*
28277915 ATAACTTAGTTAATTAATATTATACATAACTTACA
1 ATAACTTAATTAATTAATATTATACATAACTTACA
28277950 ACTTACATAA
Statistics
Matches: 243, Mismatches: 17, Indels: 46
0.79 0.06 0.15
Matches are distributed among these distances:
56 102 0.42
57 1 0.00
59 1 0.00
60 5 0.02
61 5 0.02
62 37 0.15
63 3 0.01
64 6 0.02
65 51 0.21
66 7 0.03
67 2 0.01
68 1 0.00
69 5 0.02
70 7 0.03
71 9 0.04
72 1 0.00
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (56 bp):
ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAATGAC
Found at i:28277724 original size:22 final size:22
Alignment explanation
Indices: 28277679--28277724 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
28277669 AACTTAATTA
* *
28277679 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATGAC
28277701 ATTAATATTATACATAAATGAC
1 ATTAATATTATACATAAATGAC
28277723 AT
1 AT
28277725 AACTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTAATATTATACATAAATGAC
Found at i:28277759 original size:9 final size:9
Alignment explanation
Indices: 28277745--28278069 Score: 72
Period size: 9 Copynumber: 37.7 Consensus size: 9
28277735 ATTAATATTA
28277745 TACATAACT
1 TACATAACT
*
28277754 TACATAAAT
1 TACATAACT
*
28277763 TA-ATTACT
1 TACATAACT
28277771 TA-AT-A--
1 TACATAACT
*
28277776 TACATAAAT
1 TACATAACT
28277785 TACATAACT
1 TACATAACT
*
28277794 TACATTAATAT
1 TACA-TAA-CT
*
28277805 GATACATAAAT
1 --TACATAACT
*
28277816 GACATAACT
1 TACATAACT
28277825 TA-ATTAA-T
1 TACA-TAACT
*
28277833 TA-AT-ATT
1 TACATAACT
28277840 ATACATAACT
1 -TACATAACT
*
28277850 TACATAAAT
1 TACATAACT
* *
28277859 TA-ATTAGT
1 TACATAACT
28277867 TA-AT-A--
1 TACATAACT
*
28277872 TACATAAAT
1 TACATAACT
28277881 TACATAACT
1 TACATAACT
*
28277890 TACATTAATAT
1 TACA-TAA-CT
*
28277901 GATACATAAAT
1 --TACATAACT
*
28277912 GACATAACT
1 TACATAACT
**
28277921 TAGTTAA-T
1 TACATAACT
*
28277929 TA-AT-ATT
1 TACATAACT
28277936 ATACATAACT
1 -TACATAACT
28277946 TAC--AACT
1 TACATAACT
28277953 TACATAACT
1 TACATAACT
**
28277962 TACATATTTT
1 TACATA-ACT
*
28277972 TA-ATTA-T
1 TACATAACT
* *
28277979 T-CGTAAAT
1 TACATAACT
28277987 TACATAACT
1 TACATAACT
* *
28277996 TACTTAATT
1 TACATAACT
*
28278005 TTCATAA--
1 TACATAACT
*
28278012 TAAATAACT
1 TACATAACT
*
28278021 TACATAAAT
1 TACATAACT
* *
28278030 AAC-T-TCT
1 TACATAACT
28278037 TACATAACT
1 TACATAACT
** *
28278046 TATGTGACT
1 TACATAACT
28278055 TACATAACT
1 TACATAACT
28278064 TACATA
1 TACATA
28278070 GCATAATTTT
Statistics
Matches: 233, Mismatches: 48, Indels: 70
0.66 0.14 0.20
Matches are distributed among these distances:
5 4 0.02
6 6 0.03
7 27 0.12
8 32 0.14
9 131 0.56
10 13 0.06
11 6 0.03
12 6 0.03
13 8 0.03
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:28277811 original size:22 final size:21
Alignment explanation
Indices: 28277735--28277813 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 21
28277725 AACTTAATTA
28277735 ATTAATATTATACATAACTTAC
1 ATTAATA-TATACATAACTTAC
*
28277757 A-TAA-AT-TA-ATTACTTA-
1 ATTAATATATACATAACTTAC
*
28277773 ATATACATAAATTACATAACTTAC
1 AT-TA-ATATA-TACATAACTTAC
28277797 ATTAATATGATACATAA
1 ATTAATAT-ATACATAA
28277814 ATGACATAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
16 1 0.02
17 7 0.16
18 4 0.09
19 2 0.05
20 2 0.05
21 3 0.07
22 13 0.30
23 10 0.23
24 2 0.05
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.38
Consensus pattern (21 bp):
ATTAATATATACATAACTTAC
Found at i:28277821 original size:96 final size:96
Alignment explanation
Indices: 28277645--28277949 Score: 498
Period size: 96 Copynumber: 3.2 Consensus size: 96
28277635 CATAACTTAC
* *
28277645 ATTAATATTATACATAGA-TGACATAACTTAATTAATTAATAT---T--A-TACATAACTTACAT
1 ATTAATATTATACATA-ACTTACATAAATTAATTAATTAATATACATAAATTACATAACTTACAT
*
28277703 TAATATTATACATAAATGACATAACTTAATTA
65 TAATATGATACATAAATGACATAACTTAATTA
*
28277735 ATTAATATTATACATAACTTACATAAATTAATTACTTAATATACATAAATTACATAACTTACATT
1 ATTAATATTATACATAACTTACATAAATTAATTAATTAATATACATAAATTACATAACTTACATT
28277800 AATATGATACATAAATGACATAACTTAATTA
66 AATATGATACATAAATGACATAACTTAATTA
*
28277831 ATTAATATTATACATAACTTACATAAATTAATTAGTTAATATACATAAATTACATAACTTACATT
1 ATTAATATTATACATAACTTACATAAATTAATTAATTAATATACATAAATTACATAACTTACATT
*
28277896 AATATGATACATAAATGACATAACTTAGTTA
66 AATATGATACATAAATGACATAACTTAATTA
28277927 ATTAATATTATACATAACTTACA
1 ATTAATATTATACATAACTTACA
28277950 ACTTACATAA
Statistics
Matches: 202, Mismatches: 6, Indels: 8
0.94 0.03 0.04
Matches are distributed among these distances:
89 1 0.00
90 37 0.18
93 1 0.00
95 1 0.00
96 162 0.80
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (96 bp):
ATTAATATTATACATAACTTACATAAATTAATTAATTAATATACATAAATTACATAACTTACATT
AATATGATACATAAATGACATAACTTAATTA
Found at i:28277941 original size:152 final size:145
Alignment explanation
Indices: 28277611--28277949 Score: 430
Period size: 152 Copynumber: 2.2 Consensus size: 145
28277601 TGTAAGGGAT
* *
28277611 ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAGATGACATAACTTAA
1 ATAACTTAATTAATTAATATTATACATAACTTACATTAATATGATACATAAATGACATAACTTAA
28277676 TTAATTAATATTATACATAACTTACATTAATATTATACATAAATGACATAACTTAATTAATTAAT
66 TTAATTAATATTATACATAACTTACATTAATATTATACATAAATGACATAACTTAA-TAATTAAT
* * *
28277741 ATTATACATAACTTAC
130 ATGATACATAAATGAC
* *
28277757 ATAAATTAATTACTTAATATACATAAATTACATAACTTACATTAATATGATACATAAATGACATA
1 ATAACTTAATTAATTAATAT---T--A-TACATAACTTACATTAATATGATACATAAATGACATA
*
28277822 ACTTAATTAATTAATATTATACATAACTTACATAAATTAATTAGTTAATATACATAAATTACATA
60 ACTTAATTAATTAATATTATACATAACTTAC----ATTAA-TA--T--TATACATAAATGACATA
*
28277887 ACTT-A-CATTAATATGATACATAAATGAC
116 ACTTAATAATTAATATGATACATAAATGAC
*
28277915 ATAACTTAGTTAATTAATATTATACATAACTTACA
1 ATAACTTAATTAATTAATATTATACATAACTTACA
28277950 ACTTACATAA
Statistics
Matches: 166, Mismatches: 12, Indels: 24
0.82 0.06 0.12
Matches are distributed among these distances:
146 18 0.11
149 1 0.01
151 1 0.01
152 79 0.48
153 1 0.01
155 1 0.01
156 5 0.03
157 2 0.01
158 36 0.22
159 1 0.01
160 1 0.01
161 20 0.12
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (145 bp):
ATAACTTAATTAATTAATATTATACATAACTTACATTAATATGATACATAAATGACATAACTTAA
TTAATTAATATTATACATAACTTACATTAATATTATACATAAATGACATAACTTAATAATTAATA
TGATACATAAATGAC
Found at i:28278024 original size:34 final size:34
Alignment explanation
Indices: 28277949--28278027 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
28277939 CATAACTTAC
* * ***
28277949 AACTTACATAACTTACATATTTTTAATTATTCGT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
* * *
28277983 AAATTACATAACTTACTTAATTTTCATAATAAAT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
28278017 AACTTACATAA
1 AACTTACATAA
28278028 ATAACTTCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (34 bp):
AACTTACATAACTTACATAATTTTAATAATAAAT
Found at i:28278100 original size:25 final size:25
Alignment explanation
Indices: 28278071--28278126 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
28278061 ACTTACATAG
* *
28278071 CATAATTTTCATAATACACAACTTA
1 CATAATTTGCATAATAAACAACTTA
** *
28278096 CATAATTTGGGTAATAAATAACTTA
1 CATAATTTGCATAATAAACAACTTA
28278121 CATAAT
1 CATAAT
28278127 ACATAACTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (25 bp):
CATAATTTGCATAATAAACAACTTA
Found at i:28278126 original size:16 final size:16
Alignment explanation
Indices: 28278107--28278140 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28278097 ATAATTTGGG
28278107 TAATAAATAACTTACA
1 TAATAAATAACTTACA
*
28278123 TAATACATAACTTACA
1 TAATAAATAACTTACA
28278139 TA
1 TA
28278141 GCTTAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATAAATAACTTACA
Found at i:28283682 original size:66 final size:65
Alignment explanation
Indices: 28283574--28283738 Score: 197
Period size: 66 Copynumber: 2.5 Consensus size: 65
28283564 GAGCAAATTA
* * * * *
28283574 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTAATGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACAAAAG-TATGAAGAACTCCA
28283638 G
65 G
* *
28283639 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCA
28283704 G
65 G
* * * *
28283705 CAGCAGCTTAGAGCAGATGCGGCAGCAAGAGAAG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAG
28283739 TAGAGGCGGC
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 80 0.93
67 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:28283749 original size:21 final size:21
Alignment explanation
Indices: 28283723--28283787 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
28283713 TAGAGCAGAT
*
28283723 GCGGCAGCAAGAGAAGTAGAG
1 GCGGCAGCAAGAGAAGAAGAG
* *
28283744 GCGGCAGCGAGAGAAGAACAG
1 GCGGCAGCAAGAGAAGAAGAG
** * *
28283765 GCTACAGCAAGGGAAGCAGAG
1 GCGGCAGCAAGAGAAGAAGAG
28283786 GC
1 GC
28283788 TAAAGCGAGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.42, T:0.03
Consensus pattern (21 bp):
GCGGCAGCAAGAGAAGAAGAG
Found at i:28283788 original size:21 final size:21
Alignment explanation
Indices: 28283748--28283827 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
28283738 GTAGAGGCGG
* *
28283748 CAGCGAGAGAAGAACAGGCTA
1 CAGCGAGGGAAGAAGAGGCTA
* *
28283769 CAGCAAGGGAAGCAGAGGCTA
1 CAGCGAGGGAAGAAGAGGCTA
* * *
28283790 AAGCGAGGGAAAAAGAGGCTG
1 CAGCGAGGGAAGAAGAGGCTA
*
28283811 CAGCGAGGGAAGCAGAG
1 CAGCGAGGGAAGAAGAG
28283828 CAGCGTCAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.40, C:0.16, G:0.40, T:0.04
Consensus pattern (21 bp):
CAGCGAGGGAAGAAGAGGCTA
Found at i:28289309 original size:32 final size:31
Alignment explanation
Indices: 28289244--28289310 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
28289234 ACCTAAAATT
* * *
28289244 ATTAATTCTAATTATTTTAATATTTTATTTA
1 ATTAATTCTAATTATTTTAATATCTAATCTA
28289275 ATTAATTCCTAATTA-TTTAATTATCTAATCTA
1 ATTAATT-CTAATTATTTTAA-TATCTAATCTA
28289307 ATTA
1 ATTA
28289311 CAGTTTCCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTAATTCTAATTATTTTAATATCTAATCTA
Found at i:28291007 original size:16 final size:16
Alignment explanation
Indices: 28290959--28290999 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
28290949 TTCGCTGTAT
28290959 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
28290975 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
28290991 TGGAATAGA
1 TGGAATAGA
28291000 TGTGTAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.37, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:28291258 original size:16 final size:16
Alignment explanation
Indices: 28291221--28291262 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28291211 TTAATCATAT
*
28291221 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28291237 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28291252 TTAAAATATAT
1 TTAAAATATAT
28291263 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28291269 original size:14 final size:15
Alignment explanation
Indices: 28291230--28291271 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28291220 TTTAAACATA
*
28291230 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28291245 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28291259 A-TATAATTTAATA
1 ATTATAATTAAATA
28291272 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28291292 original size:45 final size:43
Alignment explanation
Indices: 28291242--28291413 Score: 111
Period size: 45 Copynumber: 4.1 Consensus size: 43
28291232 TATTATTAAA
28291242 TATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TATATTAT-ATTAAAATATATAATTTAATAAAATTCTTAATAAT
* *
28291286 TA-A-TAT-TCT----TATATGAATTTACTCAAA-TC---ATAA-
1 TATATTATAT-TAAAATATAT-AATTTAATAAAATTCTTAATAAT
* * * * *
28291319 TATATGATACTATAAAATATA-AA-TTAACATAATTATTAATTAAA
1 TATATTATA-T-TAAAATATATAATTTAATAAAATTCTTAA-TAAT
28291363 TATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TATATTAT-ATTAAAATATATAATTTAATAAAATTCTTAATAAT
28291407 TAATATT
1 T-ATATT
28291414 CTTATATGAA
Statistics
Matches: 94, Mismatches: 14, Indels: 39
0.64 0.10 0.27
Matches are distributed among these distances:
33 2 0.02
34 5 0.05
35 2 0.02
37 9 0.10
38 15 0.16
39 3 0.03
40 1 0.01
41 5 0.05
42 4 0.04
43 13 0.14
44 16 0.17
45 19 0.20
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.44
Consensus pattern (43 bp):
TATATTATATTAAAATATATAATTTAATAAAATTCTTAATAAT
Found at i:28291390 original size:14 final size:15
Alignment explanation
Indices: 28291340--28291392 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
28291330 ATAAAATATA
28291340 AATTAACATA-ATTATT
1 AATTAA-ATATATTA-T
28291356 AATTAAATATATTAT
1 AATTAAATATATTAT
28291371 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
28291384 AATTTAATA
1 AATTAAATA
28291393 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 9 0.26
14 4 0.12
15 11 0.32
16 10 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:28291522 original size:17 final size:17
Alignment explanation
Indices: 28291480--28291514 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28291470 AATTATTTTT
28291480 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
28291497 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
28291514 A
1 A
28291515 TTATTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:28291586 original size:119 final size:120
Alignment explanation
Indices: 28291221--28291591 Score: 604
Period size: 121 Copynumber: 3.1 Consensus size: 120
28291211 TTAATCATAT
28291221 TTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
28291286 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAA
65 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAA
*
28291342 TTAACATAATTATTAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAAATAATTATT-ATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
28291407 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAA
65 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAA
* * * *
28291463 TTAAATTAATTATTTTTAAATATAATT-TAA-TAAAAAATATAATTTAATAAAATTATTAAT-AT
1 TTAAAATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * * *
28291525 TAAATATTATTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAAT
65 T-AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAA
28291582 TTAAAATAAT
1 TTAAAATAAT
28291592 AAAATTTGAA
Statistics
Matches: 236, Mismatches: 11, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
118 3 0.01
119 88 0.37
120 20 0.08
121 125 0.53
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (120 bp):
TTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAA
Found at i:28291636 original size:20 final size:20
Alignment explanation
Indices: 28291589--28291627 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28291579 AATTTAAAAT
*
28291589 AATAAAATTTGAATCGATTA
1 AATAATATTTGAATCGATTA
* *
28291609 AATGATATTTGAATTGATT
1 AATAATATTTGAATCGATT
28291628 TGATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATATTTGAATCGATTA
Found at i:28294905 original size:5 final size:5
Alignment explanation
Indices: 28294895--28294925 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
28294885 CTCGAAAATT
28294895 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
28294926 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:28295213 original size:21 final size:21
Alignment explanation
Indices: 28295189--28295228 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28295179 GACTGCTGAC
*
28295189 GTGGCTAGTTAACTAGCTAAT
1 GTGGCCAGTTAACTAGCTAAT
*
28295210 GTGGCCAGTTAACTTGCTA
1 GTGGCCAGTTAACTAGCTA
28295229 TGTTGGACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (21 bp):
GTGGCCAGTTAACTAGCTAAT
Found at i:28302128 original size:29 final size:28
Alignment explanation
Indices: 28302083--28302158 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
28302073 CTCTTTCAAA
* *
28302083 TATTTTAACATTTTTAATTTATTTCAACT
1 TATTTCAACA-TTTTAATTTATTTAAACT
* *
28302112 TATTTCAATATTGTTAATTTATTTAAATT
1 TATTTCAACATT-TTAATTTATTTAAACT
*
28302141 TATTTTAACATTTTAATT
1 TATTTCAACATTTTAATT
28302159 GATATATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 8 0.20
29 32 0.80
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (28 bp):
TATTTCAACATTTTAATTTATTTAAACT
Found at i:28304068 original size:17 final size:17
Alignment explanation
Indices: 28304042--28304079 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28304032 ATCATTGTAA
*
28304042 ATATTTTATTATTTTAC
1 ATATTCTATTATTTTAC
*
28304059 ATATTCTATTATTTTAT
1 ATATTCTATTATTTTAC
28304076 ATAT
1 ATAT
28304080 ATTGCACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTCTATTATTTTAC
Found at i:28308288 original size:13 final size:14
Alignment explanation
Indices: 28308265--28308294 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
28308255 GTTTGAGTCC
28308265 GAAAAAGAGAAAAA
1 GAAAAAGAGAAAAA
28308279 GAAAAA-AGAAAAA
1 GAAAAAGAGAAAAA
28308292 GAA
1 GAA
28308295 GTGATGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
GAAAAAGAGAAAAA
Found at i:28308328 original size:7 final size:7
Alignment explanation
Indices: 28308304--28308345 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
28308294 AGTGATGTGA
28308304 AAAAATG
1 AAAAATG
28308311 AAAAGAT-
1 AAAA-ATG
28308318 AAAAATG
1 AAAAATG
28308325 AAAAATG
1 AAAAATG
28308332 AAAAA-G
1 AAAAATG
28308338 TAAAAATG
1 -AAAAATG
28308346 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.10
7 25 0.81
8 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:28308330 original size:21 final size:21
Alignment explanation
Indices: 28308304--28308345 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
28308294 AGTGATGTGA
28308304 AAAAATG-AAAAGATAAAAATG
1 AAAAATGAAAAAG-TAAAAATG
28308325 AAAAATGAAAAAGTAAAAATG
1 AAAAATGAAAAAGTAAAAATG
28308346 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAAGTAAAAATG
Found at i:28309724 original size:50 final size:50
Alignment explanation
Indices: 28309605--28310250 Score: 393
Period size: 50 Copynumber: 12.9 Consensus size: 50
28309595 ACTTCATCAG
* * * * * ** *
28309605 CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
1 CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * * * *
28309655 TATTGCAATTAAAAAGATTGAAGCCGCAACGGCGGATCTTACTTCCTT-A
1 CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * ** * * * ** *
28309704 GCAGTGCAGTGGAACGGATTGAAGCTACGACGGTGGATCTGGTTTCCCTGA
1 -CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * * * *
28309755 TATTGCAATTAAAAAGATTGAAGCCACAACGGTGGATCTTACTTCCTT-A
1 CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * * * * ** *
28309804 GCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
1 -CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * * * * * * ** *
28309855 TATTGCAATTAAAAGGATTGAAGCTACGACGGTGGATCTGGTTTCCCTGA
1 CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * * * * * * *
28309905 TATTGCAATTAAAAAGATTGAAGCCGCAACGACGAATCTTACTTCCTTAA
1 CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * ** * * **
28309955 CAGTGCAGTGGAACGGATTGAAGCTACGACGGCGGATCTGGTTTCCTTGA
1 CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * * *
28310005 TATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTT-A
1 CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * * * ** *
28310054 GCAGTGCAATGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
1 -CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * * * *
28310105 TATTGCAATTAAAAAGATTGAAGCCACAACGACGGATCTTACTTCCTT-A
1 CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
* * * * * * * * *
28310154 GCAGTGCAGTGGAACAGATTAAAGCTACGACGGCAGATCTG-GTGTCCCTGA
1 -CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACT-TCCTTGA
* * * *
28310205 TATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCC
1 CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCC
28310251 CTAACGGTGC
Statistics
Matches: 435, Mismatches: 151, Indels: 20
0.72 0.25 0.03
Matches are distributed among these distances:
49 5 0.01
50 425 0.98
51 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (50 bp):
CAGTGCAATGAAAAAGATTGAAGCCACAACGGCGGATCTGACTTCCTTGA
Found at i:28309766 original size:100 final size:100
Alignment explanation
Indices: 28309593--28309893 Score: 512
Period size: 100 Copynumber: 3.0 Consensus size: 100
28309583 ACCATAGATT
* *
28309593 TTACTTCATCAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
28309658 TGCAATTAAAAAGATTGAAGCCGCAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* *
28309693 TTACTTCCTTAGCAGTGCAGTGGAACGGATTGAAGCTACGACGGTGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
28309758 TGCAATTAAAAAGATTGAAGCCACAACGGTGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
28309793 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
* * * *
28309858 TGCAATTAAAAGGATTGAAGCTACGACGGTGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
28309893 T
1 T
28309894 GGTTTCCCTG
Statistics
Matches: 190, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 190 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:28309923 original size:100 final size:99
Alignment explanation
Indices: 28309819--28310311 Score: 558
Period size: 100 Copynumber: 4.9 Consensus size: 99
28309809 GCAGTGGAAC
* * ** * * *
28309819 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAGGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGGATCTGACTTCCCTGACAGTGCAATGAAAA-GATTGAAGCTACGA
*
28309884 CGGTGGATCTGGTTTCCCTGATATTGCAATTAAAA
65 CGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
* * * * * * * **
28309919 AGATTGAAGCCGCAACGACGAATCTTACTTCCTTAACAGTGCAGTGGAACGGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGGATCTGACTTCCCTGACAGTGCAAT-GAAAAGATTGAAGCTACGA
*
28309984 CGGCGGATCTGGTTTCCTTGATATTGCAATTAAAA
65 CGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
* * *
28310019 AGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTGCAATGGAACAGATTGAAGCTACG
1 AGATTGAAGCCACAACGGCGGATCTGACTTCCCTGA-CAGTGCAAT-GAAAAGATTGAAGCTACG
28310083 ACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
64 ACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
* * * * * *
28310119 AGATTGAAGCCACAACGACGGATCTTACTT-CCTTAGCAGTGCAGTGGAACAGATTAAAGCTACG
1 AGATTGAAGCCACAACGGCGGATCTGACTTCCCTGA-CAGTGCAAT-GAAAAGATTGAAGCTACG
* *
28310183 ACGGCAGATCTGGTGTCCCTGATATTGCAATTAAAA
64 ACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
* * * ** **
28310219 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACGGTGCGGTGGAGCAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGGATCTGACTTCCCTGACAGTGCAAT-GAAAAGATTGAAGCTACGA
* * *
28310284 CGGCAGATCTGGTTTCCCCGACATTGCA
65 CGGCGGATCTGGTTTCCCTGATATTGCA
28310312 GTTGAACAAA
Statistics
Matches: 350, Mismatches: 40, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
99 3 0.01
100 341 0.97
101 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (99 bp):
AGATTGAAGCCACAACGGCGGATCTGACTTCCCTGACAGTGCAATGAAAAGATTGAAGCTACGAC
GGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
Found at i:28310061 original size:250 final size:250
Alignment explanation
Indices: 28309619--28310143 Score: 942
Period size: 250 Copynumber: 2.1 Consensus size: 250
28309609 GCAGTGGAAC
28309619 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCGCAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCGCAA
* * * *
28309684 CGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACGGATTGAAGCTACGACGGTGGATCTGGTTT
66 CGACGAATCTTACTTCCTTAACAGTGCAGTGGAACGGATTGAAGCTACGACGGCGGATCTGGTTT
* *
28309749 CCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGGTGGATCTTACTTCCTTAGCAGTGCAGT
131 CCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAAT
28309814 GGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
196 GGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
* *
28309869 GGATTGAAGCTACGACGGTGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCGCAA
1 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCGCAA
28309934 CGACGAATCTTACTTCCTTAACAGTGCAGTGGAACGGATTGAAGCTACGACGGCGGATCTGGTTT
66 CGACGAATCTTACTTCCTTAACAGTGCAGTGGAACGGATTGAAGCTACGACGGCGGATCTGGTTT
*
28309999 CCTTGATATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAAT
131 CCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAAT
28310064 GGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
196 GGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
* * *
28310119 AGATTGAAGCCACAACGACGGATCT
1 AGATTGAAGCTACGACGGCGGATCT
28310144 TACTTCCTTA
Statistics
Matches: 261, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
250 261 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (250 bp):
AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCGCAA
CGACGAATCTTACTTCCTTAACAGTGCAGTGGAACGGATTGAAGCTACGACGGCGGATCTGGTTT
CCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAAT
GGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
Found at i:28310312 original size:150 final size:150
Alignment explanation
Indices: 28309708--28310327 Score: 634
Period size: 150 Copynumber: 4.1 Consensus size: 150
28309698 TCCTTAGCAG
* *
28309708 TGCAGTGGAACGGATTGAAGCTACGACGGTGGATCTGGTTTCCCTGATATTGCAATTAAAAAGAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGAT
* * *
28309773 TGAAGCCACAACGGTGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGC
66 TGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTACGACGGC
*
28309838 GGATCTGGTTTCCCTGATAT
131 GGATCTGGTTTCCCTGACAT
* * * *
28309858 TGCAAT-TAAAAGGATTGAAGCTACGACGGTGGATCTGGTTTCCCTGATATTGCAATTAAAAAGA
1 TGCAGTGGAACA-GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGA
* * * * *
28309922 TTGAAGCCGCAACGACGAATCTTACTTCCTTAACAGTGCAGTGGAACGGATTGAAGCTACGACGG
65 TTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTACGACGG
* *
28309987 CGGATCTGGTTTCCTTGATAT
130 CGGATCTGGTTTCCCTGACAT
* ** * * * *** * * * ** *
28310008 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTGCAATGGAACAGA
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-TATTGCAATTAAAAAGA
* * *** * * * * ** * * * *
28310072 TTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGA
65 TTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTACGACGG
*** * *
28310137 CGGATCTTACTT-CCTTAGCAG
130 CGGATCTGGTTTCCCTGA-CAT
* * *
28310158 TGCAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTGTCCCTGATATTGCAATTAAAAAGAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGAT
* * *
28310223 TGAAGCCACAACGGCGGATCTTACTTCCCTAACGGTGCGGTGGAGCAGATTGAAGCTACGACGGC
66 TGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTACGACGGC
* *
28310288 AGATCTGGTTTCCCCGACAT
131 GGATCTGGTTTCCCTGACAT
* *
28310308 TGCAGTTGAACAAATTGAAG
1 TGCAGTGGAACAGATTGAAG
28310328 ATTTCAGATC
Statistics
Matches: 367, Mismatches: 97, Indels: 12
0.77 0.20 0.03
Matches are distributed among these distances:
149 9 0.02
150 347 0.95
151 11 0.03
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (150 bp):
TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGAT
TGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTACGACGGC
GGATCTGGTTTCCCTGACAT
Found at i:28310327 original size:100 final size:100
Alignment explanation
Indices: 28309870--28310311 Score: 704
Period size: 100 Copynumber: 4.4 Consensus size: 100
28309860 CAATTAAAAG
* *
28309870 GATTGAAGCTACGACGGTGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCGCAAC
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
* *
28309935 GACGAATCTTACTTCCTTAACAGTGCAGTGGAACG
66 GACGGATCTTACTTCCTTAACAGTGCAGTGGAACA
*
28309970 GATTGAAGCTACGACGGCGGATCTGGTTTCCTTGATATTGCAATTAAAAAGATTGAAGCCACAAC
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
* * *
28310035 GGCGGATCTTACTTCCTTAGCAGTGCAATGGAACA
66 GACGGATCTTACTTCCTTAACAGTGCAGTGGAACA
28310070 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
*
28310135 GACGGATCTTACTTCCTTAGCAGTGCAGTGGAACA
66 GACGGATCTTACTTCCTTAACAGTGCAGTGGAACA
* * *
28310170 GATTAAAGCTACGACGGCAGATCTGGTGTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
* * * * *
28310235 GGCGGATCTTACTTCCCTAACGGTGCGGTGGAGCA
66 GACGGATCTTACTTCCTTAACAGTGCAGTGGAACA
* * *
28310270 GATTGAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCA
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCA
28310312 GTTGAACAAA
Statistics
Matches: 318, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 318 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (100 bp):
GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
GACGGATCTTACTTCCTTAACAGTGCAGTGGAACA
Found at i:28310811 original size:44 final size:44
Alignment explanation
Indices: 28310631--28310812 Score: 106
Period size: 44 Copynumber: 4.1 Consensus size: 44
28310621 CCCGGGCAAC
* *
28310631 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGT
** * **** * * *
28310675 AGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTCAG--GTT
1 AGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAG-T
* * * ** *
28310718 ACAGTGGAGTACATTGAAGCCAGTAAC---TC-TATCTCCCTGGGCAGC
1 --AGTGGAATAGATTAAAG--A-TAACAGATCTTATCTCCCTAAGCAGT
28310763 AGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGT
28310807 AGTGGA
1 AGTGGA
28310813 GCAGATAGAA
Statistics
Matches: 97, Mismatches: 29, Indels: 24
0.65 0.19 0.16
Matches are distributed among these distances:
40 4 0.04
41 1 0.01
42 1 0.01
43 17 0.18
44 57 0.59
45 14 0.14
46 1 0.01
47 1 0.01
48 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (44 bp):
AGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGT
Found at i:28312440 original size:17 final size:17
Alignment explanation
Indices: 28312414--28312451 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28312404 ATCATTGTAA
*
28312414 ATATTTTATTATTTTAC
1 ATATTCTATTATTTTAC
*
28312431 ATATTCTATTATTTTAT
1 ATATTCTATTATTTTAC
28312448 ATAT
1 ATAT
28312452 ATTGCACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTCTATTATTTTAC
Found at i:28316965 original size:14 final size:15
Alignment explanation
Indices: 28316946--28316975 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28316936 ATCAAAAATG
28316946 AAAAG-AAAAGAAAA
1 AAAAGAAAAAGAAAA
28316960 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
28316975 A
1 A
28316976 GAAAAAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:28317840 original size:15 final size:15
Alignment explanation
Indices: 28317820--28317848 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28317810 CTTTAAGTCA
28317820 AAAAAAATGAAAAAT
1 AAAAAAATGAAAAAT
28317835 AAAAAAATGAAAAA
1 AAAAAAATGAAAAA
28317849 GGAAATGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAAAAATGAAAAAT
Found at i:28318946 original size:4 final size:4
Alignment explanation
Indices: 28318937--28318967 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
28318927 CATTCTCAAA
28318937 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
28318968 ATTCTGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:28319350 original size:44 final size:44
Alignment explanation
Indices: 28319283--28319923 Score: 331
Period size: 44 Copynumber: 14.7 Consensus size: 44
28319273 AAAGAATTTC
* * *
28319283 AGATCTTATCTCCTTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
28319327 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA-
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
** * * * * * *
28319370 CTACCCTATCTCCCTGAAGA-TACAGTGGAGCGGATT-AAAATAA
1 AGATCTTATCTCCCTG-AGATTACAGTGGAGCAGATTGAAGACAG
* * * * * *
28319413 AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-TCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAG
* * **
28319457 -G-TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-A---CAG
* * * * *** *
28319503 -G-TCTTATCCCCCTGAGGTTAAAGTGGAGTAGGCCGAAGA-ATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA---G
* *
28319547 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
**
28319591 AGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGACA-
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
** * * * * *
28319634 CTATCCTATCTCCCTGA-AGTTACAGTGGAGTAGATT-AAAATAA
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAG
* * * * * *
28319677 AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-TCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAG
* * * ** *
28319721 -G-TCATATCTCCCTGAGGTTACAGTGGAGTAGA-CCAATGA-ATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-GACA---G
* *
28319765 AGATCTTATCTCCCTGAGATTACAGTGGAGCAAATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * * * * *
28319809 AGATCTTATCTCCTTGAGATTACAGCGGAGCAAATT-AAAATAA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * * * * *
28319852 AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-TCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAG
* *
28319896 -G-TCTTGTCTCCCTGAGGTTACAGTGGAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAG
28319924 TAGACCGAAG
Statistics
Matches: 461, Mismatches: 100, Indels: 75
0.72 0.16 0.12
Matches are distributed among these distances:
40 2 0.00
41 80 0.17
42 13 0.03
43 61 0.13
44 198 0.43
45 6 0.01
46 97 0.21
47 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
Found at i:28319421 original size:87 final size:88
Alignment explanation
Indices: 28319285--28319923 Score: 393
Period size: 87 Copynumber: 7.3 Consensus size: 88
28319275 AGAATTTCAG
* * * ***
28319285 ATCTTATCTCCTTGAGGTTACAGTGGAGCAGATT-GAAGCCAGAGATCTTATCTCCCTGAGATTA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG-GATCTTATCTCCCTGAGATTA
* * *
28319349 CAGTGGAGCAGATTGAAGACA-CT
65 CAGTAGAGTAGATCGAAGACAGCT
* * * * *
28319372 ACCCTATCTCCCTGAAGATACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCCCTGAGA-TTA
* *
28319436 CAGTAGAGTAGATCGCA-TCAG--
65 CAGTAGAGTAGATCGAAGACAGCT
* * * ** ** * *
28319457 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGG-TCTTATCCCCCTGAGGT
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AA-TAAAGGATCTTATCTCCCTGAGAT
* * **
28319521 TAAAGTGGAGTAGGCCGAAGAATTTCAG--
63 TACAGTAGAGTAGATCGAAG-A---CAGCT
* * ***
28319549 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-GAAGCCAGAGATCTTATCTCCCTGAGATTA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG-GATCTTATCTCCCTGAGATTA
* * *
28319613 CAGCAGAGCAGATTGAAGACA-CT
65 CAGTAGAGTAGATCGAAGACAGCT
* * *
28319636 ATCCTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCCCTGAGA-TTA
* *
28319700 CAGTAGAGTAGATCGCA-TCAG--
65 CAGTAGAGTAGATCGAAGACAGCT
* * * * ** **
28319721 GTCATATCTCCCTGAGGTTACAGTGGAGTAGACCAATGAATTTCA-GATCTTATCTCCCTGAGAT
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAA--AA-TAAAGGATCTTATCTCCCTGAGAT
* * * * * **
28319785 TACAGTGGAGCAAATTGAAGCCAGAG
63 TACAGTAGAGTAGATCGAAGACAGCT
* * * *
28319811 ATCTTATCTCCTTG-AGATTACAGCGGAGCAAATTAAAATAAAGGATCTTATCTCTCTGA-AGTT
1 ATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCCCTGAGA-TT
* *
28319874 ACAGTAGAGTAGATCGCA-TCAG--
64 ACAGTAGAGTAGATCGAAGACAGCT
* * *
28319896 GTCTTGTCTCCCTGAGGTTACAGTGGAG
1 ATCTTATCTCCCTGAAGTTACAGTGGAG
28319924 TAGACCGAAG
Statistics
Matches: 420, Mismatches: 102, Indels: 62
0.72 0.17 0.11
Matches are distributed among these distances:
85 77 0.18
86 11 0.03
87 188 0.45
88 53 0.13
89 5 0.01
90 53 0.13
92 33 0.08
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (88 bp):
ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCCCTGAGATTAC
AGTAGAGTAGATCGAAGACAGCT
Found at i:28319567 original size:264 final size:264
Alignment explanation
Indices: 28319235--28319794 Score: 978
Period size: 264 Copynumber: 2.1 Consensus size: 264
28319225 GTAGATCGCA
* *
28319235 TCAGGACTTATCTCCCTGAGGTTACAGTGGAGTAGGCCAAAGAATTTCAGATCTTATCTCCTTGA
1 TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGGCCAAAGAATTTCAGATCTTATCTCCCTGA
**
28319300 GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGA
66 GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGA
*
28319365 AGACACTACCCTATCTCCCTGAAGATACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTG
131 AGACACTACCCTATCTCCCTGAAGATACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTG
*
28319430 AAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAA-
196 AAGTTACAGTAGAGTAGATCGCATCAGGTCATATCTCCCTGAGGTTACAGTGGAGTAGACC-AAT
28319494 GAATT
260 GAATT
* * *
28319499 TCAGGTCTTATCCCCCTGAGGTTAAAGTGGAGTAGGCCGAAGAATTTCAGATCTTATCTCCCTGA
1 TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGGCCAAAGAATTTCAGATCTTATCTCCCTGA
28319564 GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGA
66 GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGA
* * *
28319629 AGACACTATCCTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATAAAGGATCTTATCTCTCTG
131 AGACACTACCCTATCTCCCTGAAGATACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTG
28319694 AAGTTACAGTAGAGTAGATCGCATCAGGTCATATCTCCCTGAGGTTACAGTGGAGTAGACCAATG
196 AAGTTACAGTAGAGTAGATCGCATCAGGTCATATCTCCCTGAGGTTACAGTGGAGTAGACCAATG
28319759 AATT
261 AATT
* *
28319763 TCAGATCTTATCTCCCTGAGATTACAGTGGAG
1 TCAGGTCTTATCTCCCTGAGGTTACAGTGGAG
28319795 CAAATTGAAG
Statistics
Matches: 279, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
263 2 0.01
264 277 0.99
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (264 bp):
TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGGCCAAAGAATTTCAGATCTTATCTCCCTGA
GGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGA
AGACACTACCCTATCTCCCTGAAGATACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTG
AAGTTACAGTAGAGTAGATCGCATCAGGTCATATCTCCCTGAGGTTACAGTGGAGTAGACCAATG
AATT
Found at i:28319866 original size:175 final size:174
Alignment explanation
Indices: 28319553--28319954 Score: 571
Period size: 175 Copynumber: 2.3 Consensus size: 174
28319543 TTTCAGATCT
* ** * *
28319553 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA---GAGATCTTATCTCCCTGAGATTACA
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG-AATTTCAGATCTTATCTCCCTGAGATTACA
* ** * * *
28319615 GCAGAGCAGATTGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATAAAGG
65 GCAGAGCAAATTGAAGACAAGATCCTATCTCCCTGAAGTTACAGCGGAGCAAATTAAAATAAAGG
28319680 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCA
130 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCA
28319725 TATCTCCCTGAGGTTACAGTGGAGTAGACC-AATGAATTTCAGATCTTATCTCCCTGAGATTACA
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAA-GAATTTCAGATCTTATCTCCCTGAGATTACA
** * * *
28319789 GTGGAGCAAATTGAAGCCAGAGATCTTATCTCCTTG-AGATTACAGCGGAGCAAATTAAAATAAA
65 GCAGAGCAAATTGAAGACA-AGATCCTATCTCCCTGAAG-TTACAGCGGAGCAAATTAAAATAAA
*
28319853 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCT
128 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCA
*
28319900 TGTCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCT
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCT
28319955 AAGCAGTAGT
Statistics
Matches: 205, Mismatches: 18, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
171 3 0.01
172 28 0.14
174 41 0.20
175 131 0.64
176 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (174 bp):
TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
CAGAGCAAATTGAAGACAAGATCCTATCTCCCTGAAGTTACAGCGGAGCAAATTAAAATAAAGGA
TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCA
Found at i:28319991 original size:218 final size:219
Alignment explanation
Indices: 28319158--28320105 Score: 974
Period size: 218 Copynumber: 4.3 Consensus size: 219
28319148 ATACCTATCC
* * * *
28319158 TATCTCCTTGA-AGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGT
1 TATCTCCCTGAGA-TTACAGCGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGT
* * *
28319222 AGAGTAGATCGCATCAGGACTTATCTCCCTGAGGTTACAGTGGAGTAGGCCAAAGAATTTCAGAT
65 AGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGAT
* ** ** *
28319287 CTTATCTCCTTGAGGTTACAGTGGAGCAGATTGA-AGCCA-GAGATCTTATCTCCCTGAGATTAC
130 CTTATCTCCCTGAGGTTA-AGTGGAGCAGACCGAGA-ATATCAGATCTTATCTCCCTGAGATTAC
* ** * *
28319350 AGTGGAGCAGATTGAAGACA-CTACCC
193 AGTGGAGCAGATTGAAGCCAGAGATCT
* *
28319376 TATCTCCCTGAAGA-TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGT
1 TATCTCCCTG-AGATTACAGCGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGT
*
28319440 AGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGGT
65 AGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGAT
* * * * *
28319505 CTTATCCCCCTGAGGTTAAAGTGGAGTAGGCCGAAGAATTTCAGATCTTATCTCCCTGAGGTTAC
130 CTTATCTCCCTGAGGTT-AAGTGGAGCAGACCG-AGAATATCAGATCTTATCTCCCTGAGATTAC
28319570 AGTGGAGCAGATTGAAGCCAGAGATCT
193 AGTGGAGCAGATTGAAGCCAGAGATCT
* * * * ** * * *
28319597 TATCTCCCTGAGATTACAGCAGAGCAGATT-GAAGACACTATCCTATCTCCCTGAAGTTACAGTG
1 TATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
*** * * * * * *
28319661 GAGTAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCA--TCAG
66 GAGTAGA-TCGCAT-CAGG-TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAG
* * * * *
28319721 GTCATATCTCCCTGAGGTTACAGTGGAGTAGACCAATGAATTTCAGATCTTATCTCCCTGAGATT
128 ATCTTATCTCCCTGAGGTTA-AGTGGAGCAGACCGA-GAATATCAGATCTTATCTCCCTGAGATT
*
28319786 ACAGTGGAGCAAATTGAAGCCAGAGATCT
191 ACAGTGGAGCAGATTGAAGCCAGAGATCT
* *
28319815 TATCTCCTTGAGATTACAGCGGAGCAAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
*
28319880 GAGTAGATCGCATCAGGTCTTGTCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
66 GAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
* * * * * * *
28319945 TTATCTCCCTAAGCAG-T-AGTGGAGCAGATCGAGGATACCA-ATCTTATTTCCCCGAGATTATA
131 TTATCTCCCTGAG--GTTAAGTGGAGCAGACCGAGAATATCAGATCTTATCTCCCTGAGATTACA
* * * *
28320007 GCGAAGCAGATAGAAGCCAGAAATCT
194 GTGGAGCAGATTGAAGCCAGAGATCT
* * * * * * * * * *
28320033 TATTTCCCTGA-AGTTGCAGTGGAGCGGATCAAAATGATA-GATCTCATCCCTCTGAAGTTGCAA
1 TATCTCCCTGAGA-TTACAGCGGAGCAGATTAAAAT-AAAGGATCTTATCTCTCTGAAGTTACAG
*
28320096 TAGAGCAGAT
64 TAGAGTAGAT
28320106 TTCATCAGAC
Statistics
Matches: 608, Mismatches: 99, Indels: 46
0.81 0.13 0.06
Matches are distributed among these distances:
216 28 0.05
217 6 0.01
218 357 0.59
219 45 0.07
220 93 0.15
221 45 0.07
222 4 0.01
223 30 0.05
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (219 bp):
TATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
GAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
TTATCTCCCTGAGGTTAAGTGGAGCAGACCGAGAATATCAGATCTTATCTCCCTGAGATTACAGT
GGAGCAGATTGAAGCCAGAGATCT
Found at i:28320304 original size:44 final size:44
Alignment explanation
Indices: 28320228--28320438 Score: 180
Period size: 44 Copynumber: 4.9 Consensus size: 44
28320218 AACTACAAGG
* * * * *
28320228 CACAAATCCTATCTCCCTGAAGTTGTAATAGAGTGGATTAAAAC
1 CACAGATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAAC
* * * *** *
28320272 CACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGA-TCGCAT
1 CACAGATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAAC
* ** *
28320315 C-CAG-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAA
1 CACAGATCTTATCTCCCTGAAGTTGCAGTAGAGTAGA-TTAA-AAC
* * * *
28320359 C-CA-ATCCTATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAAC
1 CACAGATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAAC
*
28320401 CACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 CACAGATCTTATCTCCCTGAAGTTGCAGTAGAGTAGAT
28320439 CGCATCAGGT
Statistics
Matches: 129, Mismatches: 32, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
41 27 0.21
42 6 0.05
43 7 0.05
44 89 0.69
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
CACAGATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAAC
Found at i:28320333 original size:41 final size:41
Alignment explanation
Indices: 28320237--28320466 Score: 131
Period size: 44 Copynumber: 5.4 Consensus size: 41
28320227 GCACAAATCC
* * ** * *
28320237 TATCTCCCTGAAGTTGTAATAGAGTGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TAGAATC-CAG-TCT
* * * *
28320281 TATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCCAGTCT
* * *
28320322 TATCTCCCTGAAGTTGCAGTGGAGTAGACAGA-AGAAACCAATCC
1 TATCTCCCTGAAGTTGCAGT--AG-AG-CAGATAGAATCCAGTCT
* * ** * *
28320366 TATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TAGAATC-CAG-TCT
* * * *
28320410 TATCTCTCTGAAGTTGCAGTAGAGTAGATCGCAT-CAGGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCCA-GTCT
*
28320451 TATCCCCCTGAAGTTG
1 TATCTCCCTGAAGTTG
28320467 TAGAGGGGCA
Statistics
Matches: 142, Mismatches: 35, Indels: 21
0.72 0.18 0.11
Matches are distributed among these distances:
40 2 0.01
41 42 0.30
42 9 0.06
43 9 0.06
44 76 0.54
45 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCCAGTCT
Found at i:28320398 original size:129 final size:129
Alignment explanation
Indices: 28320232--28320466 Score: 391
Period size: 129 Copynumber: 1.8 Consensus size: 129
28320222 ACAAGGCACA
* *
28320232 AATCCTATCTCCCTGAAGTTGTAATAGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAAGGTGCAATAGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
*
28320297 CAGTAGAGCAGATCGCATCCA-GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAACC
66 CAGTAGAGCAGATCGCAT-CAGGTCTTATCCCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAACC
* * *
28320361 AATCCTATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGGTGCAATAGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
*
28320426 CAGTAGAGTAGATCGCATCAGGTCTTATCCCCCTGAAGTTG
66 CAGTAGAGCAGATCGCATCAGGTCTTATCCCCCTGAAGTTG
28320467 TAGAGGGGCA
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
128 2 0.02
129 96 0.98
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (129 bp):
AATCCTATCTCCCTGAAGGTGCAATAGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
CAGTAGAGCAGATCGCATCAGGTCTTATCCCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAACC
Found at i:28320509 original size:129 final size:130
Alignment explanation
Indices: 28320232--28320545 Score: 343
Period size: 129 Copynumber: 2.4 Consensus size: 130
28320222 ACAAGGCACA
* * *
28320232 AATCCTATCTCCCTGAAGTTGTA-A-TAGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGT
1 AATCCTACCTCCCTGAAGGT-TACAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGT
* * *
28320295 TACAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAC
65 TACAGTAGAGCAGATCGCATCCAGTCTTATCCCCCTGAAGTTGCAGAGGAGCAGACAGAAGAAAC
28320360 C
130 C
* *
28320361 AATCCTATCTCCCTGAAGG-TGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
1 AATCCTACCTCCCTGAAGGTTACAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
* * * * *
28320425 GCAGTAGAGTAGATCGCAT-CAGGTCTTATCCCCCTGAAGTTGTAGAGGGGCAGACTA-AAGATG
66 ACAGTAGAGCAGATCGCATCCA-GTCTTATCCCCCTGAAGTTGCAGAGGAGCAGAC-AGAAGA-A
* *
28320488 GCG
128 ACC
* ** * * * * *
28320491 GATTTTACCTCCCT-AAGGTTACAGTGGAGTAGATTGAAGCCACAAATCCTATCTC
1 AATCCTACCTCCCTGAAGGTTACAGTGGAGTGGATTAAAACCACAGATCTTATCTC
28320546 CTCGATGTTG
Statistics
Matches: 156, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
127 1 0.01
128 3 0.02
129 110 0.71
130 42 0.27
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (130 bp):
AATCCTACCTCCCTGAAGGTTACAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
ACAGTAGAGCAGATCGCATCCAGTCTTATCCCCCTGAAGTTGCAGAGGAGCAGACAGAAGAAACC
Found at i:28322475 original size:29 final size:28
Alignment explanation
Indices: 28322415--28322509 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
28322405 CTCTTTTAAA
* **
28322415 TATTTTAACATTTTTAATTTATTTCGACT
1 TATTTCAACA-TTTTAATTTATTTAAACT
* *
28322444 TATTTCAATATTGTTAATTTATTTAAATT
1 TATTTCAACATT-TTAATTTATTTAAACT
* *
28322473 TATTTTAACATTTTAATTGATATATTATACT
1 TATTTCAACATTTTAATT--TAT-TTAAACT
28322504 TATTTC
1 TATTTC
28322510 TTAAATTATG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
28 8 0.15
29 31 0.60
30 3 0.06
31 10 0.19
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (28 bp):
TATTTCAACATTTTAATTTATTTAAACT
Found at i:28326931 original size:28 final size:28
Alignment explanation
Indices: 28326873--28326932 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
28326863 GTTTTATGAT
* *
28326873 TGAAAGCAACTTGTGTATGATTGACGGA
1 TGAAAGCAACTTGTGTATGATTGAAGAA
*
28326901 TGAAAGCGACTTGTGTATGATTGAAGAA
1 TGAAAGCAACTTGTGTATGATTGAAGAA
28326929 TGAA
1 TGAA
28326933 GTAAGGTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.28
Consensus pattern (28 bp):
TGAAAGCAACTTGTGTATGATTGAAGAA
Found at i:28328589 original size:19 final size:19
Alignment explanation
Indices: 28328549--28328590 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
28328539 TTTGACCAGT
* *
28328549 TTTTGGGTCTTGGTCTCGA
1 TTTTGGGTCTTGGGCTCCA
28328568 TTTTGGGCTCTTGGGC-CCA
1 TTTTGGG-TCTTGGGCTCCA
28328587 TTTT
1 TTTT
28328591 ACAATCTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.05, C:0.19, G:0.29, T:0.48
Consensus pattern (19 bp):
TTTTGGGTCTTGGGCTCCA
Found at i:28329891 original size:15 final size:15
Alignment explanation
Indices: 28329871--28329900 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28329861 TATGCATGCA
28329871 AAATATAAAAGACAT
1 AAATATAAAAGACAT
28329886 AAATATAAAAGACAT
1 AAATATAAAAGACAT
28329901 CAAGGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:28333850 original size:17 final size:17
Alignment explanation
Indices: 28333824--28333857 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28333814 ATTTAGATAT
*
28333824 ATATATTTGTAATTGTA
1 ATATAATTGTAATTGTA
*
28333841 ATATAATTGTATTTGTA
1 ATATAATTGTAATTGTA
28333858 CCCTAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
ATATAATTGTAATTGTA
Found at i:28334523 original size:21 final size:20
Alignment explanation
Indices: 28334486--28334535 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
28334476 CCAAATTTTG
28334486 TTTTAAAAA--ATTAGAAAA
1 TTTTAAAAATTATTAGAAAA
28334504 TTTTAAAAATTATATAGAAAA
1 TTTTAAAAATTAT-TAGAAAA
*
28334525 ATTTAAAAATT
1 TTTTAAAAATT
28334536 TAAAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
20 2 0.07
21 17 0.61
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (20 bp):
TTTTAAAAATTATTAGAAAA
Found at i:28334540 original size:7 final size:8
Alignment explanation
Indices: 28334521--28334555 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
28334511 AATTATATAG
28334521 AAAAATTT
1 AAAAATTT
28334529 AAAAATTT
1 AAAAATTT
28334537 AAAAATTT
1 AAAAATTT
28334545 -AAAATTT
1 AAAAATTT
28334552 AAAA
1 AAAA
28334556 GAATACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAAATTT
Found at i:28334542 original size:16 final size:15
Alignment explanation
Indices: 28334521--28334555 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
28334511 AATTATATAG
28334521 AAAAATTTAAAAATTT
1 AAAAATTT-AAAATTT
28334537 AAAAATTTAAAATTT
1 AAAAATTTAAAATTT
28334552 AAAA
1 AAAA
28334556 GAATACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATTTAAAATTT
Found at i:28335874 original size:23 final size:27
Alignment explanation
Indices: 28335832--28335899 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 27
28335822 CAAGCTAAAG
28335832 AACGGTAAGCTC-TATCGAGCT-A-A-
1 AACGGTAAGCTCATATCGAGCTGATAT
*
28335855 AACGGTAAGCTCATA-GGAGCTGATAT
1 AACGGTAAGCTCATATCGAGCTGATAT
*
28335881 ATCGGTAAGCTCATA-CGAG
1 AACGGTAAGCTCATATCGAG
28335900 TTGTGGTGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 17 0.45
24 3 0.08
25 1 0.03
26 17 0.45
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (27 bp):
AACGGTAAGCTCATATCGAGCTGATAT
Found at i:28343520 original size:19 final size:19
Alignment explanation
Indices: 28343493--28343539 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
28343483 ATAGTAATCC
28343493 ATCAA-CATTT-AACTAA-T
1 ATCAATCATTTCAA-TAATT
28343510 ATCATATCATTTCAATAATT
1 ATCA-ATCATTTCAATAATT
28343530 ATCAATCATT
1 ATCAATCATT
28343540 CATATTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.15
18 1 0.04
19 14 0.54
20 7 0.27
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
ATCAATCATTTCAATAATT
Found at i:28351372 original size:19 final size:18
Alignment explanation
Indices: 28351336--28351375 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28351326 TTTCCACTCG
*
28351336 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
28351354 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
28351373 TTT
1 TTT
28351376 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:28377162 original size:44 final size:44
Alignment explanation
Indices: 28377112--28377203 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
28377102 TATCGCATCA
* *
28377112 GATTGAAGCCAAAAATCTTATCT-CCTAGAGATTACAGCGGAGCT
1 GATTGAAGCCAAAAATCCTATCTCCCTA-AGATTACAGCGGAGCG
* ** *
28377156 GATTGAAGCTAGTAATCCTATCTCCCTAAGATTACAGTGGAGCG
1 GATTGAAGCCAAAAATCCTATCTCCCTAAGATTACAGCGGAGCG
28377200 GATT
1 GATT
28377204 AAAATGGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 37 0.90
45 4 0.10
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
GATTGAAGCCAAAAATCCTATCTCCCTAAGATTACAGCGGAGCG
Found at i:28377318 original size:142 final size:142
Alignment explanation
Indices: 28377062--28377396 Score: 539
Period size: 142 Copynumber: 2.4 Consensus size: 142
28377052 TTCCTAATCG
* *
28377062 AAAATGGTGGATCTTATCTCTCTGAAGTTACAGTAGAGTATATCGCATCAGATTGAAGCCAAAAA
1 AAAATGGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAAAAA
* *
28377127 TCTTATCTCCTAGAGATTACAGCGGAGCTGATTGAAGCTAGTAATCCTATCTCCCTAAGATTACA
66 TCTTATCTCCTAGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCACTAAGATTACA
28377192 GTGGAGCGGATT
131 GTGGAGCGGATT
* *
28377204 AAAATGGAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAA
1 AAAATGGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAAAAA
* *
28377269 TCTTATCTCCCT-GAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCATTGAGATTAC
66 TCTTATCT-CCTAGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCACTAAGATTAC
28377333 AGTGGAGCGGATT
130 AGTGGAGCGGATT
** *
28377346 AAAATAAAGGATCTTATCTCTTTGAAGTTACAGCT-GAGTAGATCGCATCAG
1 AAAATGGAGGATCTTATCTCTCTGAAGTTACAG-TAGAGTAGATCGCATCAG
28377397 GTCTTATCTC
Statistics
Matches: 179, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
142 175 0.98
143 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (142 bp):
AAAATGGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAAAAA
TCTTATCTCCTAGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCACTAAGATTACA
GTGGAGCGGATT
Found at i:28377320 original size:44 final size:44
Alignment explanation
Indices: 28377252--28377345 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
28377242 TAGATCGCAT
* *
28377252 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCCAGAAATCCTATCTCACTGAGATTACAGCGGAG
* * * *
28377296 CAGATTGAAGCTAGTAATCCTATCTCATTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGAAATCCTATCTCACTGAGATTACAGCGGAG
*
28377340 CGGATT
1 CAGATT
28377346 AAAATAAAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
CAGATTGAAGCCAGAAATCCTATCTCACTGAGATTACAGCGGAG
Found at i:28378179 original size:11 final size:11
Alignment explanation
Indices: 28378163--28378198 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
28378153 GGCCAATGGA
28378163 TTTTTTCATTC
1 TTTTTTCATTC
*
28378174 TTTTTTTATTC
1 TTTTTTCATTC
*
28378185 TTTTTTCTTTC
1 TTTTTTCATTC
28378196 TTT
1 TTT
28378199 CGGGTTCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTCATTC
Found at i:28384518 original size:17 final size:17
Alignment explanation
Indices: 28384496--28384529 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28384486 CCCTGGAAGA
28384496 CAGTCTTAAAGTAGCCC
1 CAGTCTTAAAGTAGCCC
28384513 CAGTCTTAAAGTAGCCC
1 CAGTCTTAAAGTAGCCC
28384530 TAGTTCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (17 bp):
CAGTCTTAAAGTAGCCC
Found at i:28384786 original size:22 final size:21
Alignment explanation
Indices: 28384761--28384802 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
28384751 TTAAATAAAT
*
28384761 TTTAGTTAATTTAGTTTAAGTA
1 TTTAATTAATTTAG-TTAAGTA
28384783 TTTAATTAATTTAGTTAAGT
1 TTTAATTAATTTAGTTAAGT
28384803 GTTAAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTTAGTTAAGTA
Found at i:28397983 original size:21 final size:21
Alignment explanation
Indices: 28397957--28398018 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
28397947 AGGGTAGATC
* *
28397957 AGCTCTTACGAGCTTTTGTTA
1 AGCTCTTATGAGCTTCTGTTA
*
28397978 AGCTCTTATGAGCTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTA
28397999 AGCTCTTATGAGCTTCTGTT
1 AGCTCTTATGAGCTTCTGTT
28398019 GATGTGTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTA
Found at i:28399892 original size:28 final size:29
Alignment explanation
Indices: 28399839--28399918 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
28399829 ATTTTTTACT
***
28399839 TTTTTAAAAATAATTTTAATGCTTTT-AA
1 TTTTTAAAAATAATTTTAAAAATTTTGAA
28399867 TTTTTAAAAATAATTTTAAAAATTTTTGAA
1 TTTTTAAAAATAATTTTAAAAA-TTTTGAA
28399897 -TTTTAAAAAT--TTTT-AAAATTTT
1 TTTTTAAAAATAATTTTAAAAATTTT
28399919 CAAAAGTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
25 4 0.09
26 4 0.09
27 4 0.09
28 19 0.40
29 14 0.30
30 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTTTAAAAATAATTTTAAAAATTTTGAA
Found at i:28399900 original size:17 final size:17
Alignment explanation
Indices: 28399878--28399910 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28399868 TTTTAAAAAT
28399878 AATTTTAAAAATTTTTG
1 AATTTTAAAAATTTTTG
28399895 AATTTTAAAAATTTTT
1 AATTTTAAAAATTTTT
28399911 AAAATTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTTAAAAATTTTTG
Found at i:28400722 original size:20 final size:21
Alignment explanation
Indices: 28400699--28400741 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
28400689 AATTTGAAAA
*
28400699 TTAAAATATTTATTT-TAATT
1 TTAAAATATTAATTTATAATT
*
28400719 TTAAATTATTAATTTATAATT
1 TTAAAATATTAATTTATAATT
28400740 TT
1 TT
28400742 TTTATGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAAATATTAATTTATAATT
Found at i:28417098 original size:13 final size:13
Alignment explanation
Indices: 28417076--28417110 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
28417066 AAGTGAATGA
*
28417076 AGTTTGATTTGTC
1 AGTTTAATTTGTC
28417089 AGTTTAATTTGTC
1 AGTTTAATTTGTC
28417102 AGTTTAATT
1 AGTTTAATT
28417111 GCATTACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (13 bp):
AGTTTAATTTGTC
Found at i:28421215 original size:24 final size:24
Alignment explanation
Indices: 28421152--28421219 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
28421142 CTCGGCTCGA
28421152 ATTATATATTAAATATATATTTTT
1 ATTATATATTAAATATATATTTTT
* *
28421176 ATT-TTTAATCAAATATATA-TTTT
1 ATTATAT-ATTAAATATATATTTTT
28421199 -TTATATATTAAATATATATTT
1 ATTATATATTAAATATATATTT
28421220 GATATGGGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 13 0.35
23 10 0.27
24 14 0.38
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATATATTAAATATATATTTTT
Found at i:28430365 original size:18 final size:17
Alignment explanation
Indices: 28430342--28430375 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28430332 CCACATTGAT
28430342 TAAAATTATAAAAAATTC
1 TAAAATT-TAAAAAATTC
*
28430360 TAAAATTTCAAAAATT
1 TAAAATTTAAAAAATT
28430376 ATATAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAATTTAAAAAATTC
Found at i:28436708 original size:19 final size:18
Alignment explanation
Indices: 28436672--28436720 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
28436662 TCAGAAATAA
28436672 AAAAATATAAAATTTATT
1 AAAAATATAAAATTTATT
28436690 AAAAAT-TACAAATTCTATT
1 AAAAATATA-AAATT-TATT
* *
28436709 TAAAATGTAAAA
1 AAAAATATAAAA
28436721 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 11 0.41
19 12 0.44
20 2 0.07
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAAATATAAAATTTATT
Found at i:28438326 original size:22 final size:23
Alignment explanation
Indices: 28438301--28438343 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
28438291 GCTTTATTTA
28438301 TTTATATAAA-AAAAAATATATT
1 TTTATATAAAGAAAAAATATATT
*
28438323 TTTATATAAAGAATAAATATA
1 TTTATATAAAGAAAAAATATA
28438344 AATAACACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TTTATATAAAGAAAAAATATATT
Found at i:28438328 original size:20 final size:23
Alignment explanation
Indices: 28438299--28438343 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 23
28438289 AAGCTTTATT
28438299 TATTTATATA-AAA-AA-AAATA
1 TATTTATATATAAAGAATAAATA
*
28438319 TATTTTTATATAAAGAATAAATA
1 TATTTATATATAAAGAATAAATA
28438342 TA
1 TA
28438344 AATAACACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 3 0.14
22 2 0.10
23 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TATTTATATATAAAGAATAAATA
Found at i:28439356 original size:3 final size:3
Alignment explanation
Indices: 28439338--28439383 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
28439328 ATAACATGTT
*
28439338 ATA A-A ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28439384 GCAAAGAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:28440039 original size:17 final size:17
Alignment explanation
Indices: 28440016--28440050 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28440006 ATTCAATTCG
*
28440016 AAAAAAAATAATTCTAAT
1 AAAAAAAGTAATT-TAAT
28440034 AAAAAAAGTAATTTAAT
1 AAAAAAAGTAATTTAAT
28440051 TTTTTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAAAAAGTAATTTAAT
Found at i:28440353 original size:20 final size:19
Alignment explanation
Indices: 28440298--28440354 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
28440288 AAATTATAAT
*
28440298 ATTATTTTAAAATTTAAAA
1 ATTATATTAAAATTTAAAA
*
28440317 A-TATA-TAAATTTCTTAAAA
1 ATTATATTAAA-AT-TTAAAA
28440336 ATTATATTAAAATGTTAAA
1 ATTATATTAAAAT-TTAAA
28440355 TTATATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.13
18 4 0.13
19 8 0.27
20 10 0.33
21 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTATATTAAAATTTAAAA
Found at i:28441690 original size:7 final size:7
Alignment explanation
Indices: 28441676--28441710 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
28441666 GTTACATTTG
28441676 AAATATA
1 AAATATA
*
28441683 ATATATA
1 AAATATA
28441690 AAA-ATA
1 AAATATA
28441696 AAATATA
1 AAATATA
28441703 AAATATA
1 AAATATA
28441710 A
1 A
28441711 GTGTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATATA
Found at i:28441701 original size:13 final size:14
Alignment explanation
Indices: 28441676--28441710 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
28441666 GTTACATTTG
*
28441676 AAATATAATATATA
1 AAATATAAAATATA
28441690 AAA-ATAAAATATA
1 AAATATAAAATATA
28441703 AAATATAA
1 AAATATAA
28441711 GTGTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATATAAAATATA
Found at i:28445700 original size:19 final size:19
Alignment explanation
Indices: 28445669--28445728 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
28445659 TTAAAAATAA
*
28445669 TTTTT-ATACTTTTTAATT
1 TTTTTAATAATTTTTAATT
*
28445687 TTTTTAATAATTTTTATAAT
1 TTTTTAATAATTTTTA-ATT
*
28445707 TTTTGAA-AA-TTTTAATT
1 TTTTTAATAATTTTTAATT
28445724 TTTTT
1 TTTTT
28445729 TACATTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 6 0.17
18 10 0.29
19 11 0.31
20 8 0.23
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTAATAATTTTTAATT
Found at i:28445719 original size:28 final size:28
Alignment explanation
Indices: 28445664--28445722 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
28445654 AAAAATTAAA
* **
28445664 AATAATTTTTATACTTTTTAATTTTTTT
1 AATAATTTTTATAATTTTTAATAATTTT
28445692 AATAATTTTTATAATTTTTGAA-AATTTT
1 AATAATTTTTATAATTTTT-AATAATTTT
28445720 AAT
1 AAT
28445723 TTTTTTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
AATAATTTTTATAATTTTTAATAATTTT
Found at i:28445729 original size:19 final size:19
Alignment explanation
Indices: 28445679--28445730 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
28445669 TTTTTATACT
28445679 TTTTAA-TTTTTTTAATAA
1 TTTTAATTTTTTTTAATAA
* * *
28445697 TTTTTATAATTTTTGAA-AA
1 TTTTAAT-TTTTTTTAATAA
28445716 TTTTAATTTTTTTTA
1 TTTTAATTTTTTTTA
28445731 CATTTAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 11 0.42
19 8 0.31
20 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTAATTTTTTTTAATAA
Found at i:28453372 original size:27 final size:27
Alignment explanation
Indices: 28453334--28453413 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
28453324 ACATGCCATA
28453334 AAAGAAAAGCCTTTGCGGTGAATTATG
1 AAAGAAAAGCCTTTGCGGTGAATTATG
*
28453361 AAAGAAAAGCCTTTGCCGTGAATTATG
1 AAAGAAAAGCCTTTGCGGTGAATTATG
* *
28453388 AAAGAAAAGCCTTTGTGGCGAATTAT
1 AAAGAAAAGCCTTTGCGGTGAATTAT
28453414 TGAAGGATCT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (27 bp):
AAAGAAAAGCCTTTGCGGTGAATTATG
Found at i:28456017 original size:45 final size:45
Alignment explanation
Indices: 28455953--28456043 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
28455943 TATTTGTATT
28455953 CTGCTTAAGATCTCTAAGGAACTCACTAAGTTCTTTTGAACTTAC
1 CTGCTTAAGATCTCTAAGGAACTCACTAAGTTCTTTTGAACTTAC
28455998 CTGCTTAAGATCTCTAAGGAACTCACTAAGTTCTTTTGAACTTAC
1 CTGCTTAAGATCTCTAAGGAACTCACTAAGTTCTTTTGAACTTAC
28456043 C
1 C
28456044 CTATTACTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (45 bp):
CTGCTTAAGATCTCTAAGGAACTCACTAAGTTCTTTTGAACTTAC
Found at i:28457086 original size:25 final size:26
Alignment explanation
Indices: 28457045--28457095 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
28457035 ATAATTTAAC
* *
28457045 TTTTAATATAAATATAGTATTAATAT
1 TTTTAATATAAATATAGCATAAATAT
28457071 TTTTAAT-TATAA-ATAGCATAAATAT
1 TTTTAATATA-AATATAGCATAAATAT
28457096 AAATATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTTAATATAAATATAGCATAAATAT
Found at i:28466721 original size:5 final size:5
Alignment explanation
Indices: 28466706--28466740 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
28466696 CATAAGCTCG
*
28466706 GGCCC GACCC GGCCC GGCCC GGCCC GGCCC GGCCC
1 GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC
28466741 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.03, C:0.60, G:0.37, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:28466821 original size:10 final size:11
Alignment explanation
Indices: 28466795--28466820 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28466785 AAAAATTAAA
28466795 AAAAATATTTT
1 AAAAATATTTT
28466806 AAAAATATTTT
1 AAAAATATTTT
28466817 AAAA
1 AAAA
28466821 TTAAAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:28466874 original size:40 final size:40
Alignment explanation
Indices: 28466787--28466931 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
28466777 ATTAAAACAA
* * **
28466787 AAATTAAAAAAAATATTTTAAAAATATTTTAAAATTA--AA
1 AAATTTAAAAAAATATTTTAAAAA-AATTTAAAATTATTTT
* * *
28466826 AAACTTTAAAAAAGTATTTTAAAAAAATTTAAATTTTTTTT
1 AAA-TTTAAAAAAATATTTTAAAAAAATTTAAAATTATTTT
* * * * *
28466867 AATTTTAAAATACTATTTTAAAAGTATTTTAAAATTATTTT
1 AAATTTAAAAAAATATTTTAAAA-AAATTTAAAATTATTTT
*
28466908 AAAATTAAAAAAAT-TTTTAAAAAA
1 AAATTTAAAAAAATATTTTAAAAAA
28466932 TAAAAATATT
Statistics
Matches: 83, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
39 13 0.16
40 45 0.54
41 25 0.30
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (40 bp):
AAATTTAAAAAAATATTTTAAAAAAATTTAAAATTATTTT
Found at i:28466912 original size:11 final size:11
Alignment explanation
Indices: 28466868--28466914 Score: 67
Period size: 11 Copynumber: 4.1 Consensus size: 11
28466858 ATTTTTTTTA
28466868 ATTTTAAAATACT
1 ATTTTAAAAT--T
*
28466881 ATTTTAAAAGT
1 ATTTTAAAATT
28466892 ATTTTAAAATT
1 ATTTTAAAATT
28466903 ATTTTAAAATT
1 ATTTTAAAATT
28466914 A
1 A
28466915 AAAAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 23 0.72
13 9 0.28
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (11 bp):
ATTTTAAAATT
Found at i:28466930 original size:19 final size:19
Alignment explanation
Indices: 28466897--28466942 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28466887 AAAGTATTTT
* *
28466897 AAAATTATTTTAAAATTAAA
1 AAAATT-TTTAAAAAATAAA
28466917 AAAATTTTTAAAAAATAAA
1 AAAATTTTTAAAAAATAAA
*
28466936 AATATTT
1 AAAATTT
28466943 ATTATATTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTTTTAAAAAATAAA
Found at i:28474101 original size:44 final size:44
Alignment explanation
Indices: 28473978--28474103 Score: 146
Period size: 44 Copynumber: 2.9 Consensus size: 44
28473968 TTTGATCTGC
* * *
28473978 TCCACTATTGCTTAGGGAGA-CAGATTCTACAATCTTCAACCTAT
1 TCCACTGTTGCCTAGGGAGATAAGATT-TACAATCTTCAACCTAT
** * * *
28474022 TCCACTGCAGTCTAGGGAGATAGGACTTACAATCTTCAACCTAT
1 TCCACTGTTGCCTAGGGAGATAAGATTTACAATCTTCAACCTAT
* *
28474066 TCCACTGTTGCCTAGGGAGATAAGATTTGCTATCTTCA
1 TCCACTGTTGCCTAGGGAGATAAGATTTACAATCTTCA
28474104 CCGATCTCTA
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
44 63 0.95
45 3 0.05
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
TCCACTGTTGCCTAGGGAGATAAGATTTACAATCTTCAACCTAT
Found at i:28475381 original size:43 final size:44
Alignment explanation
Indices: 28475342--28475427 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 44
28475332 TTTTTTCATT
* *
28475342 TTCATCATTTTTTTGACTCAAAGC-GCCTTTGCGGGTTTTCACA
1 TTCATCATTTTTTTGACTCAAAGCACCCTTTGCGAGTTTTCACA
* * * *
28475385 TTGATCTTTTTTTTTACTCAAGGCACCCTTTGCGAGTTTTCAC
1 TTCATCATTTTTTTGACTCAAAGCACCCTTTGCGAGTTTTCAC
28475428 CTTGGTCTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 20 0.56
44 16 0.44
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.44
Consensus pattern (44 bp):
TTCATCATTTTTTTGACTCAAAGCACCCTTTGCGAGTTTTCACA
Found at i:28489605 original size:17 final size:17
Alignment explanation
Indices: 28489583--28489627 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
28489573 AAGAAAACGA
28489583 TTTACGAAAACAACA-GT
1 TTTACGAAAACAA-ATGT
*
28489600 TTTACGCAAACAAATGT
1 TTTACGAAAACAAATGT
28489617 TTT-CGAAAACA
1 TTTACGAAAACA
28489628 CAAGTTCGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (17 bp):
TTTACGAAAACAAATGT
Found at i:28503440 original size:24 final size:24
Alignment explanation
Indices: 28503405--28503456 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28503395 ATAAAAAAAT
*
28503405 AAAAAGTAGTCCAAAATCAACAGA
1 AAAAAGTAGTCCAAAAGCAACAGA
* *
28503429 AAAAAGTTGTCCAAAAGCAATAGA
1 AAAAAGTAGTCCAAAAGCAACAGA
28503453 AAAA
1 AAAA
28503457 TATGAAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (24 bp):
AAAAAGTAGTCCAAAAGCAACAGA
Found at i:28503939 original size:7 final size:7
Alignment explanation
Indices: 28503929--28503980 Score: 97
Period size: 7 Copynumber: 7.6 Consensus size: 7
28503919 GGATTTTGTT
28503929 TTTTTTA
1 TTTTTTA
28503936 -TTTTTA
1 TTTTTTA
28503942 TTTTTTA
1 TTTTTTA
28503949 TTTTTTA
1 TTTTTTA
28503956 TTTTTTA
1 TTTTTTA
28503963 TTTTTTA
1 TTTTTTA
28503970 TTTTTTA
1 TTTTTTA
28503977 TTTT
1 TTTT
28503981 ACCTTACAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.14
7 38 0.86
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:28507499 original size:34 final size:35
Alignment explanation
Indices: 28507444--28507510 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
28507434 CAAACACTAG
* *
28507444 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTGTACAGAAAAGT
* *
28507479 AAAACATTTTCCCG-AAATCATTGTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTGTACAGAAAA
28507511 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTGTACAGAAAAGT
Found at i:28510349 original size:25 final size:25
Alignment explanation
Indices: 28510253--28510374 Score: 111
Period size: 25 Copynumber: 4.8 Consensus size: 25
28510243 ACAGCTTTTA
* * *
28510253 TGAGCATCCAGATATATGGCTCTTCG
1 TGAGCTTCCCGATATATGGCTCTT-T
* * *
28510279 TGAGTTTCCCGATAAAAGGCTCTTT
1 TGAGCTTCCCGATATATGGCTCTTT
** *
28510304 GTGAGCTTCCTAAT-TAAGGCTCTTT
1 -TGAGCTTCCCGATATATGGCTCTTT
**
28510329 TGAGCTTCCCGATATATGGCTCGCT
1 TGAGCTTCCCGATATATGGCTCTTT
*
28510354 TGAACTTCCCGATATATGGCT
1 TGAGCTTCCCGATATATGGCT
28510375 ATCCGGAGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
24 11 0.14
25 38 0.49
26 29 0.37
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
TGAGCTTCCCGATATATGGCTCTTT
Found at i:28512769 original size:19 final size:17
Alignment explanation
Indices: 28512747--28512795 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 17
28512737 TTTTATTTTT
28512747 ATTTTATTTTTATTATTAC
1 ATTTTATTTTTATTA--AC
28512766 ATTTTTAGTTTTTATTAAC
1 A-TTTTA-TTTTTATTAAC
28512785 ATTATTATTTT
1 ATT-TTATTTT
28512796 GTAATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.22
19 7 0.26
20 5 0.19
21 9 0.33
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTTTATTTTTATTAAC
Found at i:28514459 original size:23 final size:24
Alignment explanation
Indices: 28514430--28514503 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
28514420 AACGTAATCG
*
28514430 AACATGTTCACAAACAT-TAAATG
1 AACATGTTCACAAACATGTAAATA
* * *
28514453 AATATGTTCATAAACATGTAATTA
1 AACATGTTCACAAACATGTAAATA
* *
28514477 AACATGCTCACAAACAATGTTAATA
1 AACATGTTCACAAAC-ATGTAAATA
28514502 AA
1 AA
28514504 TAATAAACAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 15 0.38
24 16 0.40
25 9 0.22
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (24 bp):
AACATGTTCACAAACATGTAAATA
Found at i:28517483 original size:2 final size:2
Alignment explanation
Indices: 28517476--28517501 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28517466 AATATTTAAA
28517476 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
28517502 TTGGTGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28521558 original size:23 final size:21
Alignment explanation
Indices: 28521530--28521582 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
28521520 TATTATATAT
28521530 TATAAAAATTTAAAAATTGAATA
1 TATAAAAATTTAAAAA-TGAA-A
**
28521553 TATAAAAAAATAAAAATGAAA
1 TATAAAAATTTAAAAATGAAA
28521574 TA-AAAAATT
1 TATAAAAATT
28521583 AAGTTAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 3 0.12
22 4 0.15
23 14 0.54
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
TATAAAAATTTAAAAATGAAA
Found at i:28521636 original size:15 final size:14
Alignment explanation
Indices: 28521588--28521635 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
28521578 AAATTAAGTT
28521588 AAAAGTTAACATTT-
1 AAAAGTTAAC-TTTA
*
28521602 AAAAGCTTACTCTTTA
1 AAAAG-TTA-ACTTTA
28521618 AAAAGTTAACTTTA
1 AAAAGTTAACTTTA
28521632 AAAA
1 AAAA
28521636 ATATTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 14 0.48
15 9 0.31
16 6 0.21
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.33
Consensus pattern (14 bp):
AAAAGTTAACTTTA
Found at i:28521678 original size:23 final size:24
Alignment explanation
Indices: 28521647--28521696 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
28521637 TATTTTTTGT
*
28521647 AAATCT-AAAAGTACACAACAAATA
1 AAATCTAAAAAATACACAA-AAATA
*
28521671 AAAT-TAAAAAATATACAAAAATA
1 AAATCTAAAAAATACACAAAAATA
28521694 AAA
1 AAA
28521697 AAAGTCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.70, C:0.10, G:0.02, T:0.18
Consensus pattern (24 bp):
AAATCTAAAAAATACACAAAAATA
Found at i:28528418 original size:15 final size:13
Alignment explanation
Indices: 28528392--28528428 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
28528382 ATTTAAATAC
28528392 TTATA-TTTTAT-
1 TTATATTTTTATA
28528403 TTAATATTTTTATA
1 TT-ATATTTTTATA
28528417 TTATATTTTTAT
1 TTATATTTTTAT
28528429 TGTATTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 3 0.13
13 16 0.70
14 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATATTTTTATA
Done.