Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 342 of 356
Found at i:109450770 original size:14 final size:15
Alignment explanation
Indices: 109450744--109450774 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
109450734 TCTAGGTTCA
109450744 TCAACACATTTTTCT
1 TCAACACATTTTTCT
109450759 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
109450773 TC
1 TC
109450775 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:109451545 original size:11 final size:11
Alignment explanation
Indices: 109451525--109451567 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
109451515 TTAGAATATA
*
109451525 CCCATTCCTTG
1 CCCATACCTTG
109451536 CCCATACCTTG
1 CCCATACCTTG
*
109451547 CCCATACC-TA
1 CCCATACCTTG
109451557 CCCATACCTTG
1 CCCATACCTTG
109451568 GAAAGATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.19, C:0.47, G:0.07, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:109452129 original size:18 final size:18
Alignment explanation
Indices: 109452106--109452178 Score: 101
Period size: 18 Copynumber: 4.1 Consensus size: 18
109452096 CATGTATGAC
*
109452106 ACTATTCACGTATACGGT
1 ACTATTCACGTATACAGT
*
109452124 ACTATTCACATATACAGT
1 ACTATTCACGTATACAGT
* *
109452142 ACTATTTATGTATACAGT
1 ACTATTCACGTATACAGT
*
109452160 ACTGTTCACGTATACAGT
1 ACTATTCACGTATACAGT
109452178 A
1 A
109452179 GTTAGGATTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (18 bp):
ACTATTCACGTATACAGT
Found at i:109452508 original size:14 final size:14
Alignment explanation
Indices: 109452489--109452523 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
109452479 TACACTGGAA
109452489 GAAAAGTTTCTAAC
1 GAAAAGTTTCTAAC
109452503 GAAAAGTTTCTAAC
1 GAAAAGTTTCTAAC
109452517 GAAAAGT
1 GAAAAGT
109452524 CTTGAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (14 bp):
GAAAAGTTTCTAAC
Found at i:109456245 original size:11 final size:11
Alignment explanation
Indices: 109456225--109456278 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
109456215 TTAGAATATA
*
109456225 CCCATTCCTTG
1 CCCATACCTTG
109456236 CCCATACCTTG
1 CCCATACCTTG
*
109456247 CCCATACCTTT
1 CCCATACCTTG
* *
109456258 TCCATACC-TA
1 CCCATACCTTG
109456268 CCCATACCTTG
1 CCCATACCTTG
109456279 GAAAGGTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
10 8 0.22
11 28 0.78
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:109456946 original size:29 final size:29
Alignment explanation
Indices: 109456909--109456967 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
109456899 TGACAATGTA
109456909 TGAGAAGAAAAATATATGTGGATGTAGTG
1 TGAGAAGAAAAATATATGTGGATGTAGTG
109456938 TGAGAAGAAAAATATATGTGGATGTAGTG
1 TGAGAAGAAAAATATATGTGGATGTAGTG
109456967 T
1 T
109456968 TCAAAATCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.29
Consensus pattern (29 bp):
TGAGAAGAAAAATATATGTGGATGTAGTG
Found at i:109459077 original size:23 final size:23
Alignment explanation
Indices: 109459051--109459096 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
109459041 ACATGGTCTG
109459051 CCACATTGGCCGATCACACAGCC
1 CCACATTGGCCGATCACACAGCC
109459074 CCACATTGGCCGATCACACAGCC
1 CCACATTGGCCGATCACACAGCC
109459097 ATGTGTCGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.43, G:0.17, T:0.13
Consensus pattern (23 bp):
CCACATTGGCCGATCACACAGCC
Found at i:109460571 original size:151 final size:151
Alignment explanation
Indices: 109460297--109460598 Score: 577
Period size: 151 Copynumber: 2.0 Consensus size: 151
109460287 CGTTGGCATC
109460297 GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATGAAGGTGAGTT
1 GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATGAAGGTGAGTT
*
109460362 CAAAAATCTCAGCCTTAAGTTTTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
66 CAAAAATCTCAGCCTTAAGTATTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
109460427 GAAAGCTAAGTCAAAAAAGTT
131 GAAAGCTAAGTCAAAAAAGTT
*
109460448 GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATTAAGGTGAGTT
1 GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATGAAGGTGAGTT
109460513 CAAAAATCTCAGCCTTAAGTATTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
66 CAAAAATCTCAGCCTTAAGTATTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
*
109460578 GCAAGCTAAGTCAAAAAAGTT
131 GAAAGCTAAGTCAAAAAAGTT
109460599 TAGCGATGAA
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 148 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (151 bp):
GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATGAAGGTGAGTT
CAAAAATCTCAGCCTTAAGTATTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
GAAAGCTAAGTCAAAAAAGTT
Found at i:109461335 original size:51 final size:51
Alignment explanation
Indices: 109461276--109461379 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
109461266 TAAAAACAGT
* *
109461276 AAGAAAAAGTTAAAATAAGAATAGAGATTTATTAAATGTTAAGGCCTGGTC
1 AAGAAAAAGTTAAAATAAGAATAGAGATTTATTAAATGTTAAAGCCTAGTC
*
109461327 AAGAAAAAGTTAAAATAAGAATAGAGGTTTATTAAATGTTAAAGCCTAGTC
1 AAGAAAAAGTTAAAATAAGAATAGAGATTTATTAAATGTTAAAGCCTAGTC
109461378 AA
1 AA
109461380 CGAAGGACAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (51 bp):
AAGAAAAAGTTAAAATAAGAATAGAGATTTATTAAATGTTAAAGCCTAGTC
Found at i:109465664 original size:87 final size:87
Alignment explanation
Indices: 109465515--109465685 Score: 272
Period size: 87 Copynumber: 2.0 Consensus size: 87
109465505 TTTTTTCAGC
109465515 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAA-C
1 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATC
*
109465579 CTATTAAATTGCATACTTCACGT
66 C-ACTAAATTGCATACTTCACGT
* * * **
109465602 AGTGTTAATGGATTGATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGTCTGCCGAATC
1 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATC
109465667 CACTAAATTGCATACTTCA
66 CACTAAATTGCATACTTCA
109465686 AGTGAAGAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
87 75 0.97
88 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (87 bp):
AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATC
CACTAAATTGCATACTTCACGT
Found at i:109466036 original size:153 final size:153
Alignment explanation
Indices: 109465755--109466056 Score: 453
Period size: 153 Copynumber: 2.0 Consensus size: 153
109465745 TTTAAGCATC
** * *
109465755 TTGCAATTTGACAATCCAAGAAACTGAAGCTTCGAAAGTCGAGTAAGAGATGCGGGTATGCTGAT
1 TTGCAATTTGACAATCCAAGAAACCCAAGCTTCGAAAGTCCAGTAAGAGATGCAGGTATGCTGAT
* *
109465820 GAAATTGTTATCACTAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACTTTGAATAT
66 GAAATTGTTATCACTAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACGTGGAATAT
* *
109465885 CTGCTTCACCAAGAGTGCACATG
131 CTCCTTCACAAAGAGTGCACATG
*
109465908 TTGCAATTTGACAA-CTCAAGAAACCCAAGCTTCGAGAGTCCAGTAAGAGATGCAGGTATGCTGA
1 TTGCAATTTGACAATC-CAAGAAACCCAAGCTTCGAAAGTCCAGTAAGAGATGCAGGTATGCTGA
* * ** *
109465972 TGAAGTTGTTATCACTAAGATCAAGATGTTTCAAAGAGGATAGACCAGAAATATCACGTGGAATA
65 TGAAATTGTTATCACTAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACGTGGAATA
*
109466037 TCTCCTTCACAAAGATTGCA
130 TCTCCTTCACAAAGAGTGCA
109466057 ATCCCTTAGA
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
152 1 0.01
153 132 0.99
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (153 bp):
TTGCAATTTGACAATCCAAGAAACCCAAGCTTCGAAAGTCCAGTAAGAGATGCAGGTATGCTGAT
GAAATTGTTATCACTAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACGTGGAATAT
CTCCTTCACAAAGAGTGCACATG
Found at i:109467295 original size:20 final size:21
Alignment explanation
Indices: 109467266--109467306 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
109467256 AAAATATATT
*
109467266 TTCCATTCAA-TTTTCCATCC
1 TTCCACTCAAGTTTTCCATCC
109467286 TTCCACTCAAGTTTTCCATCC
1 TTCCACTCAAGTTTTCCATCC
109467307 CCTCAGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.20, C:0.37, G:0.02, T:0.41
Consensus pattern (21 bp):
TTCCACTCAAGTTTTCCATCC
Found at i:109467922 original size:14 final size:15
Alignment explanation
Indices: 109467896--109467926 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
109467886 TCCAGGTTCA
109467896 TCAACACATTTTTCT
1 TCAACACATTTTTCT
109467911 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
109467925 TC
1 TC
109467927 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:109470728 original size:20 final size:20
Alignment explanation
Indices: 109470703--109470745 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
109470693 GAGATTCCAT
109470703 TCCAATTTTAGTTGGAAGAC
1 TCCAATTTTAGTTGGAAGAC
109470723 TCCAATTTTAGTTGGAAGAC
1 TCCAATTTTAGTTGGAAGAC
109470743 TCC
1 TCC
109470746 TAAGTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
TCCAATTTTAGTTGGAAGAC
Found at i:109472404 original size:7 final size:7
Alignment explanation
Indices: 109472392--109472423 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
109472382 TCTACCACAC
109472392 AAAAATA
1 AAAAATA
109472399 AAAAATA
1 AAAAATA
109472406 AAAAATA
1 AAAAATA
109472413 AAAAATA
1 AAAAATA
109472420 AAAA
1 AAAA
109472424 CCCAAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:109483909 original size:5 final size:5
Alignment explanation
Indices: 109483899--109483930 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
109483889 TTGTGTGTTC
109483899 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
109483931 TCACAACGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:109483918 original size:14 final size:14
Alignment explanation
Indices: 109483899--109483929 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
109483889 TTGTGTGTTC
109483899 TTTATTTTATTTTA
1 TTTATTTTATTTTA
109483913 TTTATTTTATTTTA
1 TTTATTTTATTTTA
109483927 TTT
1 TTT
109483930 TTCACAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:109485967 original size:18 final size:18
Alignment explanation
Indices: 109485944--109485979 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
109485934 AAATCTCTTC
109485944 TTCAAGGAAGCCATTGAG
1 TTCAAGGAAGCCATTGAG
109485962 TTCAAGGAAGCCATTGAG
1 TTCAAGGAAGCCATTGAG
109485980 ATATGCAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (18 bp):
TTCAAGGAAGCCATTGAG
Found at i:109500290 original size:57 final size:59
Alignment explanation
Indices: 109500221--109500335 Score: 180
Period size: 57 Copynumber: 2.0 Consensus size: 59
109500211 GTGCCCACTG
*
109500221 ACCGATCTCGCACACATAGTGCTCGGTT-GAAGAACTCGCACACACAGTGCCT-TAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCTAATT
* * *
109500278 ACCGATTTCGCACACATAGTGCTCGGTTAAAAGAATTTGCACACACAGTGCCTCTAAT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCTAAT
109500336 CATCCGCACA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 27 0.52
58 21 0.40
59 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (59 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCTAATT
Found at i:109504893 original size:12 final size:11
Alignment explanation
Indices: 109504843--109504910 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 11
109504833 ATTGAGTCCA
109504843 TTTATTTTATT
1 TTTATTTTATT
*
109504854 TTATTTTATTATT
1 TT-TATT-TTATT
* *
109504867 TTTGGTTTTAGT
1 TTT-ATTTTATT
109504879 TTTATTTCTATT
1 TTTATTT-TATT
109504891 TTTATGTTTATT
1 TTTAT-TTTATT
*
109504903 GTTATTTT
1 TTTATTTT
109504911 CTTAGACTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 8 0.17
12 27 0.59
13 11 0.24
ACGTcount: A:0.16, C:0.01, G:0.07, T:0.75
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:109504900 original size:24 final size:23
Alignment explanation
Indices: 109504842--109504910 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 23
109504832 CATTGAGTCC
109504842 ATTTAT-TTTATTTTATTTTATT
1 ATTTATGTTTATTTTATTTTATT
*
109504864 ATTTTTGGTTTTAGTTTTATTTCTATT
1 ATTTAT-G-TTTA-TTTTATTT-TATT
109504891 -TTTATGTTTATTGTTATTTT
1 ATTTATGTTTATT-TTATTTT
109504911 CTTAGACTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 5 0.13
23 3 0.08
24 10 0.26
25 5 0.13
26 12 0.31
27 4 0.10
ACGTcount: A:0.17, C:0.01, G:0.07, T:0.74
Consensus pattern (23 bp):
ATTTATGTTTATTTTATTTTATT
Found at i:109504911 original size:25 final size:24
Alignment explanation
Indices: 109504843--109504912 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
109504833 ATTGAGTCCA
*
109504843 TTTAT-TTTATTTTATTTTATTATT
1 TTTATGTTTATTTTATTTT-CTATT
*
109504867 TTT-GGTTTTAGTTTTA-TTTCTATT
1 TTTATG-TTTA-TTTTATTTTCTATT
109504891 TTTATGTTTATTGTTATTTTCT
1 TTTATGTTTATT-TTATTTTCT
109504913 TAGACTTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
23 2 0.05
24 17 0.46
25 13 0.35
26 5 0.14
ACGTcount: A:0.16, C:0.03, G:0.07, T:0.74
Consensus pattern (24 bp):
TTTATGTTTATTTTATTTTCTATT
Found at i:109517243 original size:29 final size:29
Alignment explanation
Indices: 109517201--109517260 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
109517191 ATTTCTTTTG
109517201 TTGAGAGGACATTTGCTCCTCCATAACTC
1 TTGAGAGGACATTTGCTCCTCCATAACTC
109517230 TTGAGAGGACATTTGCTCCTCCATAACTC
1 TTGAGAGGACATTTGCTCCTCCATAACTC
109517259 TT
1 TT
109517261 ATTCTCTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (29 bp):
TTGAGAGGACATTTGCTCCTCCATAACTC
Found at i:109518907 original size:39 final size:39
Alignment explanation
Indices: 109518849--109518923 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
109518839 TGAATTTTAA
* *
109518849 CTCGATTGGCATTAGTATTTTTGCATATGATGAAATTAG
1 CTCGATTGGCATCAATATTTTTGCATATGATGAAATTAG
109518888 CTCGATTGGCATCAATATTTTTGCATATGATGAAAT
1 CTCGATTGGCATCAATATTTTTGCATATGATGAAAT
109518924 CCATTCTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (39 bp):
CTCGATTGGCATCAATATTTTTGCATATGATGAAATTAG
Found at i:109529994 original size:23 final size:23
Alignment explanation
Indices: 109529968--109530065 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
109529958 ATAAGTGCCA
109529968 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
109529991 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
109530014 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
109530036 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
109530059 CACTGAT
1 CACTGAT
109530066 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:109530033 original size:45 final size:45
Alignment explanation
Indices: 109529975--109530063 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
109529965 CCACACTGAT
* *
109529975 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
109530020 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
109530064 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:109530300 original size:75 final size:75
Alignment explanation
Indices: 109530214--109530361 Score: 296
Period size: 75 Copynumber: 2.0 Consensus size: 75
109530204 CTATTCCTAA
109530214 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
109530279 CAACTTTCAT
66 CAACTTTCAT
109530289 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
1 GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
109530354 CAACTTTC
66 CAACTTTC
109530362 CTTCCACATT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (75 bp):
GTTCAACCGGGAATTTACACTTAACACTTTATTTTCAACACTTTATCACTTGAATAATTCATGAA
CAACTTTCAT
Found at i:109532769 original size:12 final size:12
Alignment explanation
Indices: 109532752--109532781 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
109532742 ACAGTCGAAA
*
109532752 ACAGATGCAAAT
1 ACAGATACAAAT
109532764 ACAGATACAAAT
1 ACAGATACAAAT
109532776 ACAGAT
1 ACAGAT
109532782 TTGAGCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (12 bp):
ACAGATACAAAT
Found at i:109541358 original size:14 final size:14
Alignment explanation
Indices: 109541339--109541368 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
109541329 ATAATCTTTA
*
109541339 AATTTTTTATATTT
1 AATTTTTTAAATTT
109541353 AATTTTTTAAATTT
1 AATTTTTTAAATTT
109541367 AA
1 AA
109541369 AAATTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTTTTAAATTT
Found at i:109544662 original size:12 final size:12
Alignment explanation
Indices: 109544645--109544670 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
109544635 AAGTGTGCCT
109544645 TCGAAAGACATC
1 TCGAAAGACATC
109544657 TCGAAAGACATC
1 TCGAAAGACATC
109544669 TC
1 TC
109544671 ATCGCATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.19
Consensus pattern (12 bp):
TCGAAAGACATC
Found at i:109549077 original size:2 final size:2
Alignment explanation
Indices: 109549070--109549100 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
109549060 AAGAGTTAAA
109549070 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
109549101 ACTAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:109551445 original size:3 final size:3
Alignment explanation
Indices: 109551439--109551700 Score: 98
Period size: 3 Copynumber: 87.0 Consensus size: 3
109551429 GATGAAAACG
** * *
109551439 ATA ATA ATA ATA ATA ATA ATA ATA CCA ACA ACGA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA
** **
109551484 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACGTA AGTAA ATA CGA A-A AGG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA A-T-A ATA ATA ATA ATA
* * * * *
109551532 A-A ATA TATA AT- GTA AT- ATA A-A TTA ATTA GT- TTA ATA AT- ATG
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
* * * * * *
109551573 ATG ATA ATA ATA GTG ATA AT- ACA ATA ACA ATA ATA A-A GTGGA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT--A ATA
* *
109551617 ATAA ATA ATA ATA ATA CATTA AGA ATA ATA ATA AT- ATA CTA ATA ATA
1 AT-A ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
109551664 ACA ATA ATA GAAA ATA ATA ATA AAA ATA ATA AAA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
109551701 CAAAAAATAT
Statistics
Matches: 196, Mismatches: 39, Indels: 48
0.69 0.14 0.17
Matches are distributed among these distances:
2 18 0.09
3 153 0.78
4 17 0.09
5 8 0.04
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:109551623 original size:25 final size:26
Alignment explanation
Indices: 109551576--109551632 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
109551566 TAATATGATG
*
109551576 ATAATAATAGTGATAATACAATAACA
1 ATAATAATAGTGAAAATACAATAACA
*
109551602 ATAATAA-AGTGGAAAATA-AATAATA
1 ATAATAATAGT-GAAAATACAATAACA
109551627 ATAATA
1 ATAATA
109551633 CATTAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26
Consensus pattern (26 bp):
ATAATAATAGTGAAAATACAATAACA
Found at i:109551645 original size:20 final size:20
Alignment explanation
Indices: 109551620--109551672 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
109551610 GTGGAAAATA
*
109551620 AATAATAATAATACATTAAG
1 AATAATAATAATACACTAAG
* *
109551640 AATAATAATAATATACTAAT
1 AATAATAATAATACACTAAG
*
109551660 AATAACAATAATA
1 AATAATAATAATA
109551673 GAAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAATAATAATACACTAAG
Found at i:109551660 original size:17 final size:17
Alignment explanation
Indices: 109551616--109551700 Score: 70
Period size: 17 Copynumber: 5.1 Consensus size: 17
109551606 TAAAGTGGAA
109551616 AATA-AATAATAATAAT
1 AATATAATAATAATAAT
*
109551632 ACAT-TAAGAATAATAAT
1 A-ATATAATAATAATAAT
* *
109551649 AATATACTAATAATAAC
1 AATATAATAATAATAAT
*
109551666 AATAATAGAAAATAATAAT
1 AAT-ATA-ATAATAATAAT
*
109551685 AA-A-AATAATAAAAAT
1 AATATAATAATAATAAT
109551700 A
1 A
109551701 CAAAAAATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
15 10 0.18
16 4 0.07
17 28 0.51
18 3 0.05
19 10 0.18
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (17 bp):
AATATAATAATAATAAT
Found at i:109551684 original size:22 final size:21
Alignment explanation
Indices: 109551619--109551700 Score: 74
Period size: 23 Copynumber: 3.7 Consensus size: 21
109551609 AGTGGAAAAT
* *
109551619 AAATAATAATAATACATTAAGAA
1 AAATAATAAAAATA-A-TAATAA
* *
109551642 TAATAATAATATACTAATAATAA
1 AAATAATAA-A-AATAATAATAA
*
109551665 CAATAATAGAAAATAATAATAA
1 AAATAATA-AAAATAATAATAA
109551687 AAATAATAAAAATA
1 AAATAATAAAAATA
109551701 CAAAAAATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 6 0.12
22 17 0.35
23 21 0.43
24 2 0.04
25 3 0.06
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAATAAAAATAATAATAA
Found at i:109551706 original size:9 final size:9
Alignment explanation
Indices: 109551619--109551719 Score: 53
Period size: 9 Copynumber: 10.7 Consensus size: 9
109551609 AGTGGAAAAT
109551619 AAATAATAA
1 AAATAATAA
*
109551628 TAATACATTAA
1 AAATA-A-TAA
*
109551639 GAATAATAA
1 AAATAATAA
* *
109551648 TAAT-ATAC
1 AAATAATAA
*
109551656 TAATAATAA
1 AAATAATAA
*
109551665 CAATAATAGAAA
1 AAATAAT---AA
109551677 ATAATAATAA
1 A-AATAATAA
109551687 AAATAATAA
1 AAATAATAA
109551696 AAATACA-AA
1 AAATA-ATAA
* *
109551705 AAATATTGA
1 AAATAATAA
109551714 AAATAA
1 AAATAA
109551720 AATAGCAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
8 7 0.10
9 45 0.62
10 6 0.08
11 7 0.10
12 2 0.03
13 6 0.08
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (9 bp):
AAATAATAA
Found at i:109554698 original size:35 final size:36
Alignment explanation
Indices: 109554659--109554728 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
109554649 CACACGCACA
109554659 TGTGT-CTCAAATATAAACTCAGTGAGTCACACACC
1 TGTGTACTCAAATATAAACTCAGTGAGTCACACACC
* * * *
109554694 TGTGTGACTCTAATATGAACTCGGTGAGTTACACA
1 TGTGT-ACTCAAATATAAACTCAGTGAGTCACACA
109554729 GCCTAGACAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.17
37 24 0.83
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (36 bp):
TGTGTACTCAAATATAAACTCAGTGAGTCACACACC
Found at i:109564909 original size:15 final size:17
Alignment explanation
Indices: 109564875--109564911 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
109564865 AGAAAAATAT
109564875 ATTTTCTATCCCTTCAA
1 ATTTTCTATCCCTTCAA
*
109564892 ATTTTC-AT-CCTTCCA
1 ATTTTCTATCCCTTCAA
109564907 ATTTT
1 ATTTT
109564912 TTTCACTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 2 0.11
17 6 0.32
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTCTATCCCTTCAA
Found at i:109579086 original size:22 final size:22
Alignment explanation
Indices: 109579058--109579102 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
109579048 TAAGTATACT
109579058 AGAACTCTAATTTATTCTAAAC
1 AGAACTCTAATTTATTCTAAAC
109579080 AGAACTCTAATTTATTCTAAAC
1 AGAACTCTAATTTATTCTAAAC
109579102 A
1 A
109579103 AGAAGTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (22 bp):
AGAACTCTAATTTATTCTAAAC
Found at i:109585360 original size:18 final size:18
Alignment explanation
Indices: 109585333--109585406 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 18
109585323 TACGACCATT
*
109585333 TATGGCACTATTCACGTA
1 TATGGTACTATTCACGTA
* *
109585351 TATGGAACTATTCATGTA
1 TATGGTACTATTCACGTA
* *
109585369 TACGGTACTATTTACGTA
1 TATGGTACTATTCACGTA
* *
109585387 TATAGTACTGTTCACGTA
1 TATGGTACTATTCACGTA
109585405 TA
1 TA
109585407 CAGTAGTTGG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (18 bp):
TATGGTACTATTCACGTA
Found at i:109601735 original size:27 final size:27
Alignment explanation
Indices: 109601696--109601750 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
109601686 ATGTTAGACA
109601696 CATGCCTGATTTGAAGAAGAATCTCAT
1 CATGCCTGATTTGAAGAAGAATCTCAT
* * *
109601723 CATGCTTGGTTTGAGGAAGAATCTCAT
1 CATGCCTGATTTGAAGAAGAATCTCAT
109601750 C
1 C
109601751 TCTTTAGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (27 bp):
CATGCCTGATTTGAAGAAGAATCTCAT
Found at i:109604420 original size:31 final size:32
Alignment explanation
Indices: 109604351--109604421 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 32
109604341 GATTCAGTGT
*
109604351 AATTATATAAATGAAACTTTAATTGTGATTCG
1 AATTATATAAATGAAACTTTAATTGTGACTCG
* *
109604383 AA-TATATACATGAAACTTTAATTTTGACTC-
1 AATTATATAAATGAAACTTTAATTGTGACTCG
109604413 AATTATATA
1 AATTATATA
109604422 TATATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 2 0.06
31 31 0.89
32 2 0.06
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (32 bp):
AATTATATAAATGAAACTTTAATTGTGACTCG
Found at i:109607347 original size:17 final size:16
Alignment explanation
Indices: 109607304--109607349 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
109607294 TGGTTTATTG
*
109607304 ATTTTAGTCATTTGTT
1 ATTTTAGTTATTTGTT
**
109607320 ATTTTTCTTATTTGTTT
1 ATTTTAGTTATTTG-TT
109607337 ATTTTAGTTATTT
1 ATTTTAGTTATTT
109607350 AAAGTTCCTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.70
Consensus pattern (16 bp):
ATTTTAGTTATTTGTT
Found at i:109608636 original size:53 final size:53
Alignment explanation
Indices: 109608573--109608680 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
109608563 TGCCATATCC
109608573 TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
1 TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
109608626 TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
1 TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
109608679 TT
1 TT
109608681 TGGACAAGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (53 bp):
TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
Found at i:109608844 original size:37 final size:38
Alignment explanation
Indices: 109608789--109608868 Score: 153
Period size: 37 Copynumber: 2.1 Consensus size: 38
109608779 ATGTAAGGAA
109608789 ATTAGAGAGTATTTAATGATGAATTCTAATGAATTTTT
1 ATTAGAGAGTATTTAATGATGAATTCTAATGAATTTTT
109608827 ATTA-AGAGTATTTAATGATGAATTCTAATGAATTTTT
1 ATTAGAGAGTATTTAATGATGAATTCTAATGAATTTTT
109608864 ATTAG
1 ATTAG
109608869 CATTGAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 37 0.90
38 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.45
Consensus pattern (38 bp):
ATTAGAGAGTATTTAATGATGAATTCTAATGAATTTTT
Found at i:109615946 original size:11 final size:12
Alignment explanation
Indices: 109615919--109615978 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
109615909 CTTCAAAAAG
* *
109615919 AAATAAAAGACA
1 AAATAAAATAAA
*
109615931 AAATAAAAT-TA
1 AAATAAAATAAA
109615942 AAATAAAATAAA
1 AAATAAAATAAA
109615954 AAAT-AAATATAA
1 AAATAAAATA-AA
* *
109615966 TAGTAAAATAAA
1 AAATAAAATAAA
109615978 A
1 A
109615979 GGGCTCAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 15 0.38
12 19 0.49
13 5 0.13
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:109621603 original size:30 final size:30
Alignment explanation
Indices: 109621568--109621625 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
109621558 CATGGCCATG
* *
109621568 ACACACGGGCGTATGG-TCTACCCGTGTGTC
1 ACACACAGGCATATGGATC-ACCCGTGTGTC
*
109621598 ACACACAGGCATGTGGATCACCCGTGTG
1 ACACACAGGCATATGGATCACCCGTGTG
109621626 GAAGTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (30 bp):
ACACACAGGCATATGGATCACCCGTGTGTC
Found at i:109629305 original size:18 final size:18
Alignment explanation
Indices: 109629282--109629410 Score: 150
Period size: 18 Copynumber: 7.2 Consensus size: 18
109629272 CCCAACTACT
*
109629282 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
109629300 GTATACATGAATAGTATC
1 GTATACGTGAATAGTACC
* **
109629318 GTATACGCGAATAGTGTC
1 GTATACGTGAATAGTACC
* *
109629336 GTATACATGAATAGTGCC
1 GTATACGTGAATAGTACC
*
109629354 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
109629372 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
109629390 GTATACATGAATAGTATC
1 GTATACGTGAATAGTACC
109629408 GTA
1 GTA
109629411 AACGGTCGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 94 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:109633042 original size:13 final size:13
Alignment explanation
Indices: 109632991--109633042 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
109632981 TTAAACCAAT
* *
109632991 CTTTTAAAAAACA
1 CTTTTCAAAAGCA
*
109633004 CTTCTCAAAAGCA
1 CTTTTCAAAAGCA
* *
109633017 CTTTTCCATAGCA
1 CTTTTCAAAAGCA
109633030 CTTTTCAAAAGCA
1 CTTTTCAAAAGCA
109633043 TTGTTAAACG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (13 bp):
CTTTTCAAAAGCA
Found at i:109636229 original size:11 final size:11
Alignment explanation
Indices: 109636213--109636237 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
109636203 GTAAAATTTT
109636213 AAATTAAAATA
1 AAATTAAAATA
109636224 AAATTAAAATA
1 AAATTAAAATA
109636235 AAA
1 AAA
109636238 ATTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATTAAAATA
Found at i:109640464 original size:16 final size:16
Alignment explanation
Indices: 109640443--109640474 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
109640433 CTCATGGTGC
*
109640443 TTATAAAAAGTTATAT
1 TTATAAAAAATTATAT
109640459 TTATAAAAAATTATAT
1 TTATAAAAAATTATAT
109640475 AAATAGCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TTATAAAAAATTATAT
Found at i:109648135 original size:20 final size:20
Alignment explanation
Indices: 109648110--109648156 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
109648100 CCTGGCGTTG
109648110 TTCTGGCACGTTCCAGAAGC
1 TTCTGGCACGTTCCAGAAGC
109648130 TTCTGGCACGTTCCAGAAGC
1 TTCTGGCACGTTCCAGAAGC
109648150 TTCTGGC
1 TTCTGGC
109648157 TTGTGTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.28
Consensus pattern (20 bp):
TTCTGGCACGTTCCAGAAGC
Found at i:109653432 original size:14 final size:15
Alignment explanation
Indices: 109653406--109653436 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
109653396 TCCAGGTTCA
109653406 TCAACACATTTTTCT
1 TCAACACATTTTTCT
109653421 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
109653435 TC
1 TC
109653437 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:109661925 original size:13 final size:13
Alignment explanation
Indices: 109661907--109661931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109661897 ATTTACAAGA
109661907 TTACATAATCAAT
1 TTACATAATCAAT
109661920 TTACATAATCAA
1 TTACATAATCAA
109661932 ATCTAAACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:109669314 original size:21 final size:21
Alignment explanation
Indices: 109669290--109669343 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
109669280 ATACTATTAT
* *
109669290 TATATTTATTTTTATTCCTAG
1 TATATTTATTTTTAATACTAG
* *
109669311 TATATTTATTATTAATATTAG
1 TATATTTATTTTTAATACTAG
*
109669332 TATATGTATTTT
1 TATATTTATTTT
109669344 GTTATACGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.61
Consensus pattern (21 bp):
TATATTTATTTTTAATACTAG
Found at i:109673742 original size:28 final size:28
Alignment explanation
Indices: 109673703--109673760 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
109673693 TGGTTCTGTG
109673703 ATATAAATCTTGGATATGGAGAGAGATT
1 ATATAAATCTTGGATATGGAGAGAGATT
* *
109673731 ATATAAATCTTGGATATGGATAGATATT
1 ATATAAATCTTGGATATGGAGAGAGATT
109673759 AT
1 AT
109673761 CCGACCTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (28 bp):
ATATAAATCTTGGATATGGAGAGAGATT
Found at i:109674964 original size:26 final size:26
Alignment explanation
Indices: 109674935--109675042 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
109674925 TGATACAAAT
*
109674935 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
109674961 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
109674987 TGATAATGGGTTTGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
109675013 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
109675039 TGAT
1 TGAT
109675043 GAGAATTTCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:109682022 original size:26 final size:26
Alignment explanation
Indices: 109681993--109682074 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
109681983 TGATACAAAT
*
109681993 TGATAATGGGTTAGGTAAATGCTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
109682019 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
109682045 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
109682071 TGAT
1 TGAT
109682075 GAGAATTTCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.34
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:109688024 original size:22 final size:21
Alignment explanation
Indices: 109687989--109688065 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 21
109687979 AAAAGGTATC
* *
109687989 TACAAATTAAATCTATAAGAT
1 TACAAATCATATCTATAAGAT
*
109688010 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TATAAGAT
* *
109688033 TGCATATCATATC--TAAGAT
1 TACAAATCATATCTATAAGAT
*
109688052 TGC-AATCATATCTA
1 TACAAATCATATCTA
109688066 AGATTGTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 8 0.17
19 9 0.20
21 3 0.07
22 17 0.37
23 9 0.20
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (21 bp):
TACAAATCATATCTATAAGAT
Found at i:109688081 original size:35 final size:37
Alignment explanation
Indices: 109688018--109688096 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
109688008 ATTACAAAAT
109688018 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
109688054 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
109688089 CATATCAT
1 CATATCAT
109688097 TGAAGATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:109688094 original size:14 final size:15
Alignment explanation
Indices: 109688039--109688094 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
109688029 AGATTGCATA
109688039 TCATATCTAAGATTG
1 TCATATCTAAGATTG
109688054 CAATCATATCTAAGATTG
1 ---TCATATCTAAGATTG
109688072 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
109688089 -CATATC
1 TCATATC
109688095 ATTGAAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 16 0.43
18 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:109688104 original size:17 final size:19
Alignment explanation
Indices: 109688025--109688096 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
109688015 AATCATATCT
109688025 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
109688044 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
109688062 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
109688079 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
109688097 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:109688568 original size:44 final size:45
Alignment explanation
Indices: 109688456--109688649 Score: 282
Period size: 45 Copynumber: 4.3 Consensus size: 45
109688446 TTATATCTAC
*
109688456 TATCTTTGATCTGCTCCCCGTCTAATATAGAGACGCCAAATCTGT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * *
109688501 TATCTTTGATCTGCTCCCTGTCTAATACAGAGACACCAAATCTGC
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* *
109688546 T-TCTTTAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * *
109688590 TATCTCTGATTTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* *
109688635 CATCTTGGATCTGCT
1 TATCTTTGATCTGCT
109688650 TCGATGTAAA
Statistics
Matches: 132, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 39 0.30
45 93 0.70
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (45 bp):
TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
Found at i:109688577 original size:89 final size:89
Alignment explanation
Indices: 109688458--109688633 Score: 280
Period size: 89 Copynumber: 2.0 Consensus size: 89
109688448 ATATCTACTA
* * * *
109688458 TCTTTGATCTGCTCCCCGTCTAATATAGAGACGCCAAATCTGTTATCTTTGATCTGCTCCCTGTC
1 TCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTCTGATCTGCTCCCCGTC
109688523 TAATACAGAGACACCAAATCTGCT
66 TAATACAGAGACACCAAATCTGCT
* *
109688547 TCTTTAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCTGATTTGCTCCCCGTC
1 TCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTCTGATCTGCTCCCCGTC
**
109688612 TAATACAGAGATGCCAAATCTG
66 TAATACAGAGACACCAAATCTG
109688634 TCATCTTGGA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (89 bp):
TCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTCTGATCTGCTCCCCGTC
TAATACAGAGACACCAAATCTGCT
Found at i:109688792 original size:78 final size:78
Alignment explanation
Indices: 109688663--109688957 Score: 457
Period size: 78 Copynumber: 3.8 Consensus size: 78
109688653 ATGTAAACAC
*
109688663 ATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
109688728 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* ***
109688741 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTATTCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
*
109688805 TTGGATCTGCTTTA
65 TTGGATCTGCTTCA
* *
109688819 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
109688884 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * **
109688897 ATGAAGGTCAGATCTGCTATGTCTTCGATTTGCTTCCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
109688958 TGTTTCTTCG
Statistics
Matches: 195, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
77 2 0.01
78 191 0.98
79 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:109689158 original size:78 final size:78
Alignment explanation
Indices: 109689029--109689322 Score: 464
Period size: 78 Copynumber: 3.8 Consensus size: 78
109689019 CGTAAACACG
* * * *
109689029 TGAAAGCCAAATCTGCTATGTCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAAACCATCTT
1 TGAAAGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTT
109689094 GGATCTGCTTCAA
66 GGATCTGCTTCAA
*
109689107 TGAAAGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 TGAAAGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
109689171 TGGATCTGCTTCAA
65 TGGATCTGCTTCAA
* *
109689185 TGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTT
1 TGAAAGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTT
109689250 GGATCTGCTTCAA
66 GGATCTGCTTCAA
* * * **
109689263 TGAAAGTCAGATCTACTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 TGAAAGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
109689323 TGTTTCTTCG
Statistics
Matches: 200, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
77 2 0.01
78 196 0.98
79 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (78 bp):
TGAAAGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTT
GGATCTGCTTCAA
Found at i:109689304 original size:365 final size:365
Alignment explanation
Indices: 109688553--109689427 Score: 1369
Period size: 365 Copynumber: 2.4 Consensus size: 365
109688543 TGCTTCTTTA
* * ** * * * * *
109688553 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATC-TCTGATTTGCTCCCCGTCTAATA
1 ATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTT-TCTTC-GATTTGTTCTCTG-ATAGTA
* * * * * *
109688617 CAGAGATGCCAAATCTGTCATCTTGGATCTGCTTC-GATGTAAACACATGAAGGTCAGATCTACT
63 CAGAGATGCCAAA----TCATCTTAGATCTGCTTCAG-TGTAAACACGTGAAAGCCAAATCTGCT
* *
109688681 ATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAA
123 ATGTCTTCGATATGCTCCCCGTCTAATACAGAGATGCCAAACCATCTTGGATCTGCTTCAATGAA
* **
109688746 GGTCCAATCTGTTATGTCTTCGATCTGCTATTCGTCTAATACAGAGATGCCAAATCATCTTGGAT
188 AGTCCAATCTGTTATGTCTTCGATCTGCTACCCGTCTAATACAGAGATGCCAAATCATCTTGGAT
*
109688811 CTGCTTTAATGAAGGTCAGATCTGCTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCA
253 CTGCTTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCA
* *
109688876 AATCATCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCG
318 AATCATCTTGGATCTGCTTCAATGAAAGTCAGATCTACTATGTCTTCG
*
109688924 ATTTGCT-TCCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGATAGTACA
1 ATCTGCTCT-CCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGATAGTACA
*
109688988 GAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATGTCTT
65 GAGATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACGTGAAAGCCAAATCTGCTATGTCTT
*
109689053 CGATTTGCTCCCCGTCTAATACAGAGATGCCAAACCATCTTGGATCTGCTTCAATGAAAGTCCAA
130 CGATATGCTCCCCGTCTAATACAGAGATGCCAAACCATCTTGGATCTGCTTCAATGAAAGTCCAA
*
109689118 TCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTC
195 TCTGTTATGTCTTCGATCTGCTACCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTC
*
109689183 AATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
260 AATGAAGGTCAGATCTGCTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATC
109689248 TTGGATCTGCTTCAATGAAAGTCAGATCTACTATGTCTTCG
325 TTGGATCTGCTTCAATGAAAGTCAGATCTACTATGTCTTCG
*
109689289 ATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGAAAGTACAG
1 ATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGATAGTACAG
* *
109689354 AGATTCCAAATCATCTTAGATCTGCTTCAGTGTAAACATGTGAAAGCCAAATCTGCTATGTCTTC
66 AGATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACGTGAAAGCCAAATCTGCTATGTCTTC
109689419 GATATGCTC
131 GATATGCTC
109689428 ATTGTCAACG
Statistics
Matches: 467, Mismatches: 33, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
365 402 0.86
366 2 0.00
369 17 0.04
370 12 0.03
371 34 0.07
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (365 bp):
ATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGATAGTACAG
AGATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACGTGAAAGCCAAATCTGCTATGTCTTC
GATATGCTCCCCGTCTAATACAGAGATGCCAAACCATCTTGGATCTGCTTCAATGAAAGTCCAAT
CTGTTATGTCTTCGATCTGCTACCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCA
ATGAAGGTCAGATCTGCTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCAATGAAAGTCAGATCTACTATGTCTTCG
Found at i:109689421 original size:287 final size:283
Alignment explanation
Indices: 109688751--109689269 Score: 727
Period size: 287 Copynumber: 1.8 Consensus size: 283
109688741 ATGAAGGTCC
* * *** * * *
109688751 AATCTGTTATGTCTTCGATCTGCTATTCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
1 AATCTGCTATGTCTTCGATTTGCTCCCCGTCAAATACAGAGATGCCAAACCATCTTAGATCTGCT
* * * *
109688816 TTAATGAAGGT-CAGATCTGCTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATC
66 TCAATGAAAGTCCA-ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
* * **
109688880 ATCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATTTGCTTCCCGTCGAATATG
130 ATCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCGAATACA
* * ** *
109688945 GAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGATAGTACAGAGATGCCAAATCATCTTAGAT
195 GAGATGCCAAATC--TATCTTCGATCTGTTCAATGAAAGTACA-AGATGCCAAATCATCTTAGAT
109689010 CTGCTTCAGCGTAAACACGTGAAAGCCA
257 CTGCTTCA-CGTAAACACGTGAAAGCCA
* *
109689038 AATCTGCTATGTCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAAACCATCTTGGATCTGCT
1 AATCTGCTATGTCTTCGATTTGCTCCCCGTCAAATACAGAGATGCCAAACCATCTTAGATCTGCT
*
109689103 TCAATGAAAGTCCAATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCA
66 TCAATGAAAGTCCAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCA
* *
109689168 TCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAG
131 TCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCGAATACAG
*
109689233 AGATGCCAAATC-ATCTTGGATCTGCTTCAATGAAAGT
196 AGATGCCAAATCTATCTTCGATCTG-TTCAATGAAAGT
109689270 CAGATCTACT
Statistics
Matches: 207, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
284 9 0.04
285 9 0.04
287 187 0.90
288 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (283 bp):
AATCTGCTATGTCTTCGATTTGCTCCCCGTCAAATACAGAGATGCCAAACCATCTTAGATCTGCT
TCAATGAAAGTCCAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCA
TCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCGAATACAG
AGATGCCAAATCTATCTTCGATCTGTTCAATGAAAGTACAAGATGCCAAATCATCTTAGATCTGC
TTCACGTAAACACGTGAAAGCCA
Found at i:109696332 original size:16 final size:16
Alignment explanation
Indices: 109696311--109696342 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
109696301 GAGTTACCGA
109696311 TTCATTTATCAGATAT
1 TTCATTTATCAGATAT
*
109696327 TTCATTTATCCGATAT
1 TTCATTTATCAGATAT
109696343 CTTTTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (16 bp):
TTCATTTATCAGATAT
Found at i:109700529 original size:18 final size:19
Alignment explanation
Indices: 109700491--109700529 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
109700481 TGGTTCAAGC
*
109700491 TTTCAATCTCATATATCAA
1 TTTCAATCTCACATATCAA
*
109700510 TTTCAAT-TCACATTTCAA
1 TTTCAATCTCACATATCAA
109700528 TT
1 TT
109700530 CTTAGTTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCACATATCAA
Found at i:109700988 original size:45 final size:45
Alignment explanation
Indices: 109700939--109701065 Score: 236
Period size: 45 Copynumber: 2.8 Consensus size: 45
109700929 AACAGTACGG
*
109700939 TAACAATATCCGACACACAAAGTGCCGAATCGGTAACGGTAACAA
1 TAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGTAACAA
*
109700984 TAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGTAACAG
1 TAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGTAACAA
109701029 TAACAATATTCGACACACAAAGTGCCGAATCGGTAAC
1 TAACAATATTCGACACACAAAGTGCCGAATCGGTAAC
109701066 AGTAGTAGTA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (45 bp):
TAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGTAACAA
Found at i:109701500 original size:15 final size:16
Alignment explanation
Indices: 109701463--109701512 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
109701453 CAATACACAT
109701463 TTCAATT-AA-TCATAA
1 TTCAATTCAATTCA-AA
* *
109701478 TTCCATTCCATTC-AA
1 TTCAATTCAATTCAAA
109701493 TTCAATTCAATTCAAA
1 TTCAATTCAATTCAAA
109701509 TTCA
1 TTCA
109701513 CTTTTCCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 19 0.68
16 7 0.25
17 2 0.07
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (16 bp):
TTCAATTCAATTCAAA
Found at i:109701823 original size:5 final size:6
Alignment explanation
Indices: 109701778--109701823 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
109701768 ACTTTTCCAA
* *
109701778 TCAATT T-ACATT TTAATT TTAATT TCAATT TCAATT TCAA-T TCAAT
1 TCAATT TCA-ATT TCAATT TCAATT TCAATT TCAATT TCAATT TCAAT
109701824 AACAATTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 6 0.17
6 29 0.81
7 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (6 bp):
TCAATT
Found at i:109706167 original size:17 final size:18
Alignment explanation
Indices: 109706145--109706179 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
109706135 GATATGATAC
*
109706145 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
109706162 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
109706180 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:109706460 original size:23 final size:23
Alignment explanation
Indices: 109706435--109706477 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
109706425 AAGGTATCTA
*
109706435 AAAATTAAATC-TCTAAGATTAC
1 AAAATCAAATCTTCTAAGATTAC
*
109706457 AAAATCATATCTTCTAAGATT
1 AAAATCAAATCTTCTAAGATT
109706478 GCATATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (23 bp):
AAAATCAAATCTTCTAAGATTAC
Found at i:109706505 original size:18 final size:19
Alignment explanation
Indices: 109706469--109706523 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
109706459 AATCATATCT
109706469 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
109706488 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
109706506 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
109706524 TGAAGATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:109706679 original size:21 final size:20
Alignment explanation
Indices: 109706642--109706680 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
109706632 TTGGACTTCA
**
109706642 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
109706662 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
109706681 TCTGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:109724378 original size:7 final size:7
Alignment explanation
Indices: 109724357--109724398 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
109724347 TTATTTTGTT
109724357 TTATTTA
1 TTATTTA
*
109724364 GT-TTTA
1 TTATTTA
109724370 TTATTTA
1 TTATTTA
109724377 TTATTTA
1 TTATTTA
109724384 TTATTTA
1 TTATTTA
109724391 TT-TTTA
1 TTATTTA
109724397 TT
1 TT
109724399 TTATTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:109726965 original size:21 final size:21
Alignment explanation
Indices: 109726941--109727004 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
109726931 TTTATAGATG
*
109726941 CCTCTGTTTTCTATTGAAAAT
1 CCTCTGTTTTCTTTTGAAAAT
* *
109726962 CCTCTATTTTCTTTTGGAAAT
1 CCTCTGTTTTCTTTTGAAAAT
*
109726983 CCTCTGTTCTCTTTTGAAAAT
1 CCTCTGTTTTCTTTTGAAAAT
109727004 C
1 C
109727005 AACAGTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.48
Consensus pattern (21 bp):
CCTCTGTTTTCTTTTGAAAAT
Found at i:109730179 original size:11 final size:11
Alignment explanation
Indices: 109730163--109730196 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
109730153 ATGCCAAATT
109730163 ATCAAGAATAA
1 ATCAAGAATAA
*
109730174 ATCAAGAACAA
1 ATCAAGAATAA
109730185 ATCAAGAATAA
1 ATCAAGAATAA
109730196 A
1 A
109730197 ACTAAATGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.65, C:0.12, G:0.09, T:0.15
Consensus pattern (11 bp):
ATCAAGAATAA
Found at i:109744189 original size:19 final size:22
Alignment explanation
Indices: 109744150--109744189 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
109744140 AGAAACCCAA
109744150 CCATATCCAACCGTATACACCC
1 CCATATCCAACCGTATACACCC
109744172 CCATA-CCAACC-T-TACACC
1 CCATATCCAACCGTATACACC
109744190 GTGTGGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.47, G:0.03, T:0.17
Consensus pattern (22 bp):
CCATATCCAACCGTATACACCC
Found at i:109744289 original size:27 final size:27
Alignment explanation
Indices: 109744251--109744390 Score: 153
Period size: 27 Copynumber: 5.2 Consensus size: 27
109744241 AGCATGGCTG
** *
109744251 CCAGA-ACAGATAATGTGATAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
109744277 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
109744305 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
*
109744332 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
* *
109744359 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
109744386 CCAGA
1 CCAGA
109744391 ACGCTTCCTC
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.05
27 82 0.80
28 16 0.16
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:109744315 original size:54 final size:54
Alignment explanation
Indices: 109744251--109744390 Score: 174
Period size: 54 Copynumber: 2.6 Consensus size: 54
109744241 AGCATGGCTG
* * *
109744251 CCAGAACAGATA-ATGTGATAGAGTCACCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * *
109744305 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
* * * *
109744359 CCAGATCAGATATTTGTGGCATAGCCACCAGA
1 CCAGAACAGATATATGTGACAGAGCCACCAGA
109744391 ACGCTTCCTC
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
54 59 0.78
55 17 0.22
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:109744522 original size:26 final size:27
Alignment explanation
Indices: 109744493--109744568 Score: 100
Period size: 26 Copynumber: 2.8 Consensus size: 27
109744483 CAAAATTAAC
*
109744493 CCTAGGGGTATAACAGTAATTTTGC-A
1 CCTAGGGGTATAACAGTAATTTTCCAA
109744519 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATAACAGTAATTTTCCA-A
* * *
109744547 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATAACAGTAATTT
109744569 AGCTACTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 24 0.55
28 20 0.45
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (27 bp):
CCTAGGGGTATAACAGTAATTTTCCAA
Found at i:109746046 original size:26 final size:26
Alignment explanation
Indices: 109746010--109746119 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
109746000 CATGAAATTC
109746010 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
109746036 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* **
109746062 TTATCATGGAACATTTACCTAACATA
1 TTATCATGAAACATTTACCTAACCCA
* *
109746088 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
109746114 TTATCA
1 TTATCA
109746120 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:109751988 original size:18 final size:18
Alignment explanation
Indices: 109751962--109751996 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
109751952 ACGTTGCAGT
109751962 CCAACTAGATTTTAAGTG
1 CCAACTAGATTTTAAGTG
*
109751980 CCAATTAGATTTTAAGT
1 CCAACTAGATTTTAAGT
109751997 ATATCTATTA
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:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (18 bp):
CCAACTAGATTTTAAGTG
Found at i:109757290 original size:36 final size:36
Alignment explanation
Indices: 109757243--109757315 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
109757233 ACTCTTTGTT
109757243 TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
1 TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
109757279 TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
1 TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
109757315 T
1 T
109757316 CAGACCAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (36 bp):
TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
Found at i:109760584 original size:13 final size:13
Alignment explanation
Indices: 109760566--109760590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109760556 GAGTATTAAA
109760566 TACTTATATCTAG
1 TACTTATATCTAG
109760579 TACTTATATCTA
1 TACTTATATCTA
109760591 ATGCATATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (13 bp):
TACTTATATCTAG
Found at i:109761695 original size:86 final size:84
Alignment explanation
Indices: 109761541--109761710 Score: 322
Period size: 86 Copynumber: 2.0 Consensus size: 84
109761531 ACAATCTACA
109761541 ACGTTTTCCGTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCATGC
1 ACGTTTTCCGTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCATGC
109761606 ATCCACAAATATTTGTTGT
66 ATCCACAAATATTTGTTGT
109761625 ACGTTTTCCAGGTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCAT
1 ACGTTTTCC--GTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCAT
109761690 GCATCCACAAATATTTGTTGT
64 GCATCCACAAATATTTGTTGT
109761711 CTTTGACTTT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 9 0.11
86 75 0.89
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.44
Consensus pattern (84 bp):
ACGTTTTCCGTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCATGC
ATCCACAAATATTTGTTGT
Found at i:109769627 original size:18 final size:18
Alignment explanation
Indices: 109769601--109769675 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
109769591 TACGACCGTT
*
109769601 TACGGTACTATTCATGTA
1 TACGGTACTATTCACGTA
* *
109769619 TATGGTACTATTCACTTA
1 TACGGTACTATTCACGTA
**
109769637 TACAATACTATTCACGTA
1 TACGGTACTATTCACGTA
*
109769655 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
109769673 TAC
1 TAC
109769676 AGTAGTTGGG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:109769656 original size:36 final size:36
Alignment explanation
Indices: 109769606--109769676 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
109769596 CCGTTTACGG
* * *
109769606 TACTATTCATGTATATGGTACTATTCACTTATACAA
1 TACTATTCACGTATACGGTACTATTCACGTATACAA
*
109769642 TACTATTCACGTATACGGTACTGTTCACGTATACA
1 TACTATTCACGTATACGGTACTATTCACGTATACA
109769677 GTAGTTGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
TACTATTCACGTATACGGTACTATTCACGTATACAA
Found at i:109774886 original size:153 final size:153
Alignment explanation
Indices: 109774605--109774906 Score: 408
Period size: 153 Copynumber: 2.0 Consensus size: 153
109774595 TTTAAGCATC
* * * * * *
109774605 TTGCAATTTACCAATGCAAGAAACTAAAGCTTGGAGAGTCTAGTAAGAGATGCAGGTATGTTGAT
1 TTGCAATTTACCAACGCAAGAAACCAAAGCTTCGAGAGTCCAATAAGAGATGCAGGTATGCTGAT
* * * *
109774670 GAAATTGTTAACACTAAGATTAAGATGTACCAAAGAGGATAGACCAGAAATATAACTTTGAATAT
66 GAAATTGTTAACACTAAGATCAAGATCTACCAAAGAGGATAGACCAGAAATATAACGTGGAATAT
* *
109774735 CTGCTTCACCAAGAGTGCACATG
131 CTCCTTCACAAAGAGTGCACATG
* * *
109774758 TTGCAATTTGA-CAACGTAAGAAACCCAAGCTTCGAGAGTCCAATAAGAGATGCAGGTATGCTGC
1 TTGCAATTT-ACCAACGCAAGAAACCAAAGCTTCGAGAGTCCAATAAGAGATGCAGGTATGCTGA
* ** *
109774822 TGAAATTGTTACCACTAAGATCAAGATCTGTCAAAGAGGATAGACCAGAAATATCACGTGGAATA
65 TGAAATTGTTAACACTAAGATCAAGATCTACCAAAGAGGATAGACCAGAAATATAACGTGGAATA
*
109774887 TCTCCTTCACAAAGATTGCA
130 TCTCCTTCACAAAGAGTGCA
109774907 GTCCCTTAGA
Statistics
Matches: 128, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
153 127 0.99
154 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (153 bp):
TTGCAATTTACCAACGCAAGAAACCAAAGCTTCGAGAGTCCAATAAGAGATGCAGGTATGCTGAT
GAAATTGTTAACACTAAGATCAAGATCTACCAAAGAGGATAGACCAGAAATATAACGTGGAATAT
CTCCTTCACAAAGAGTGCACATG
Found at i:109779488 original size:20 final size:20
Alignment explanation
Indices: 109779440--109779487 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
109779430 TTATAAATAA
*
109779440 TTTGAATTTT-AAAATTTAT
1 TTTGAATTTTGGAAATTTAT
109779459 TTTGAATTTTGGAAATTT-T
1 TTTGAATTTTGGAAATTTAT
*
109779478 TTTTAATTTT
1 TTTGAATTTT
109779488 TTTTGTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTGAATTTTGGAAATTTAT
Found at i:109779681 original size:18 final size:18
Alignment explanation
Indices: 109779660--109779696 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
109779650 AAATAATTTG
* *
109779660 AATAACTCGATTTGATTA
1 AATAACTCAATTTAATTA
109779678 AATAACTCAATTTAATTA
1 AATAACTCAATTTAATTA
109779696 A
1 A
109779697 CTCAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (18 bp):
AATAACTCAATTTAATTA
Found at i:109783492 original size:25 final size:23
Alignment explanation
Indices: 109783435--109783492 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
109783425 GATGATTCCT
*
109783435 AAAATAATTTAAAAAATAAAACA
1 AAAATAATTAAAAAAATAAAACA
109783458 ACTAAATAATTAAAAAAATAAAACTA
1 A--AAATAATTAAAAAAATAAAAC-A
109783484 AAAAGTAAT
1 AAAA-TAAT
109783493 ATCTTTGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 24 0.80
26 2 0.07
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAATTAAAAAAATAAAACA
Found at i:109784756 original size:21 final size:21
Alignment explanation
Indices: 109784730--109784784 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
109784720 ACAGCGGTGA
*
109784730 CGGTGAGATTAGTTACTGTAG
1 CGGTGAGATTAGATACTGTAG
*
109784751 CGGTGAGATTGGATACTGTAG
1 CGGTGAGATTAGATACTGTAG
109784772 CGGTGAGATTAGA
1 CGGTGAGATTAGA
109784785 AATAGCGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
CGGTGAGATTAGATACTGTAG
Found at i:109785837 original size:18 final size:19
Alignment explanation
Indices: 109785803--109785838 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
109785793 ATGATATTAA
109785803 TGATATACCTAAAAGGTAG
1 TGATATACCTAAAAGGTAG
109785822 TGATATACCT-AAAGGTA
1 TGATATACCTAAAAGGTA
109785839 TGAAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (19 bp):
TGATATACCTAAAAGGTAG
Found at i:109788227 original size:82 final size:82
Alignment explanation
Indices: 109788090--109788254 Score: 303
Period size: 82 Copynumber: 2.0 Consensus size: 82
109788080 AGACACTTAC
*
109788090 CATGATTTACAAGATTTAAATCATCACTAGGAATCACTGGAAAGGCCAACACTAGTGACCAGAGA
1 CATGATTTACAAGATTTAAATCATCACTAGGAATCACTGGAAAGGCCAACACTAGTGACCAAAGA
109788155 ACTAATTTTCATTTATA
66 ACTAATTTTCATTTATA
*
109788172 CATGATTTACAAGATTTAAATCATCACTAGGAATCACTGGAAAGGCCACCACTAGTGACCAAAGA
1 CATGATTTACAAGATTTAAATCATCACTAGGAATCACTGGAAAGGCCAACACTAGTGACCAAAGA
*
109788237 ACTAATTTTCTTTTATA
66 ACTAATTTTCATTTATA
109788254 C
1 C
109788255 TGTAATGAAC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.28
Consensus pattern (82 bp):
CATGATTTACAAGATTTAAATCATCACTAGGAATCACTGGAAAGGCCAACACTAGTGACCAAAGA
ACTAATTTTCATTTATA
Found at i:109791446 original size:15 final size:16
Alignment explanation
Indices: 109791426--109791457 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
109791416 TTTAAATATA
109791426 TAATAAAA-ATAAAAT
1 TAATAAAACATAAAAT
109791441 TAATAAAACATAAAAT
1 TAATAAAACATAAAAT
109791457 T
1 T
109791458 TTATCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATAAAACATAAAAT
Found at i:109794357 original size:21 final size:22
Alignment explanation
Indices: 109794331--109794373 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
109794321 ATGAAAAGTG
*
109794331 TATACATAATA-ATATTAAATA
1 TATACATAATATATATAAAATA
109794352 TATACATAATATATATAAAATA
1 TATACATAATATATATAAAATA
109794374 AACATATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
TATACATAATATATATAAAATA
Found at i:109794452 original size:20 final size:20
Alignment explanation
Indices: 109794429--109794488 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
109794419 AATACTACAT
109794429 AAATATGTACATATATATTA
1 AAATATGTACATATATATTA
**
109794449 AAATAAATACATAATAATATTA
1 AAATATGTACAT-AT-ATATTA
109794471 AAAGTATGTACATA-ATAT
1 AAA-TATGTACATATATAT
109794489 AGTGTTACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 14 0.42
21 2 0.06
22 10 0.30
23 7 0.21
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
AAATATGTACATATATATTA
Found at i:109794454 original size:24 final size:22
Alignment explanation
Indices: 109794396--109794539 Score: 74
Period size: 23 Copynumber: 6.1 Consensus size: 22
109794386 ATATATTAGA
* *
109794396 AATATTAAAATATATATATTAAT
1 AATATTAAAATAAATACA-TAAT
* * **
109794419 AATACT-ACATAAATATGTACAT
1 AATATTAAAATAAATACATA-AT
109794441 ATATATTAAAATAAATACATAAT
1 A-ATATTAAAATAAATACATAAT
**
109794464 AATATTAAAAGTATGTACATAAT
1 AATATTAAAA-TAAATACATAAT
* *
109794487 ATAGTGTTACAAATACATACATAATGT
1 A-A-TATTA-AAATAAATACATAA--T
* *
109794514 AGTTATTAAAAATATATACATAAT
1 A-ATATT-AAAATAAATACATAAT
109794538 AA
1 AA
109794540 AATATATGAA
Statistics
Matches: 93, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
21 2 0.02
22 20 0.22
23 23 0.25
24 13 0.14
25 13 0.14
26 19 0.20
27 3 0.03
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.35
Consensus pattern (22 bp):
AATATTAAAATAAATACATAAT
Found at i:109794533 original size:26 final size:25
Alignment explanation
Indices: 109794439--109794538 Score: 100
Period size: 25 Copynumber: 4.1 Consensus size: 25
109794429 AAATATGTAC
*
109794439 ATATA-TATT-AAAATAAATACATA
1 ATATAGTATTAAAAATATATACATA
* *
109794462 ATA-A-TATTAAAAGTATGTACATA
1 ATATAGTATTAAAAATATATACATA
* * *
109794485 ATATAGTGTTACAAATACATACATA
1 ATATAGTATTAAAAATATATACATA
*
109794510 ATGTAGTTATTAAAAATATATACATA
1 ATATAG-TATTAAAAATATATACATA
109794536 ATA
1 ATA
109794539 AAATATATGA
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
22 5 0.08
23 17 0.28
24 1 0.02
25 19 0.32
26 18 0.30
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (25 bp):
ATATAGTATTAAAAATATATACATA
Found at i:109794750 original size:15 final size:12
Alignment explanation
Indices: 109794710--109794836 Score: 65
Period size: 12 Copynumber: 10.7 Consensus size: 12
109794700 TAATAGTGAA
*
109794710 AATAATAAACAT
1 AATAATAAATAT
109794722 AATAATAAATAT
1 AATAATAAATAT
109794734 AATAATAGAA-AT
1 AATAATA-AATAT
* *
109794746 GATAAT-ACTAT
1 AATAATAAATAT
109794757 -ATAA-AAAGTAT
1 AATAATAAA-TAT
*
109794768 -ATATATACATAT
1 AATA-ATAAATAT
109794780 -ATAATAAA-AT
1 AATAATAAATAT
109794790 -AT-ATACCAATATT
1 AATAATA--AATA-T
*
109794803 AAAAATAAATAT
1 AATAATAAATAT
*
109794815 AATATTATAATACT
1 AATAATA-AATA-T
109794829 AATAATAA
1 AATAATAA
109794837 CAATATGAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
9 3 0.03
10 10 0.11
11 14 0.15
12 39 0.43
13 14 0.15
14 8 0.09
15 3 0.03
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:109794775 original size:22 final size:24
Alignment explanation
Indices: 109794711--109794794 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 24
109794701 AATAGTGAAA
*
109794711 ATAATAAACATA-ATA-ATAAATAT
1 ATAATAAA-ATATATATATACATAT
*
109794734 AATAATAGAAAT-GATA-ATAC-TAT
1 -ATAATA-AAATATATATATACATAT
*
109794757 ATAA-AAAGTATATATATACATAT
1 ATAATAAAATATATATATACATAT
109794780 ATAATAAAATATATA
1 ATAATAAAATATATA
109794795 CCAATATTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.06
21 4 0.08
22 8 0.16
23 10 0.20
24 23 0.46
25 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (24 bp):
ATAATAAAATATATATATACATAT
Found at i:109794931 original size:3 final size:3
Alignment explanation
Indices: 109794923--109794976 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
109794913 ACTAATATAT
* * * *
109794923 ATA ATA ATA ATA ATA TTG ATA ATA TTA ATA ATA TTA GA-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
109794968 ATA ATA ATA
1 ATA ATA ATA
109794977 TTTAATAAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:109794938 original size:18 final size:17
Alignment explanation
Indices: 109794915--109794973 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 17
109794905 AAACATACAC
109794915 TAATATATATAATAATAA
1 TAATAT-TATAATAATAA
*
109794933 TAATATTGATAATATTAA
1 TAATATT-ATAATAATAA
*
109794951 TAATATTAGAAATAATAA
1 TAATATTA-TAATAATAA
109794969 TAATA
1 TAATA
109794974 ATATTTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 2 0.06
18 34 0.94
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAATATTATAATAATAA
Found at i:109794953 original size:21 final size:20
Alignment explanation
Indices: 109794923--109794978 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 20
109794913 ACTAATATAT
109794923 ATAATAATAATAATATTG--
1 ATAATAATAATAATATTGAA
*
109794941 ATAATATTAATAATATTAGAA
1 ATAATAATAATAATATT-GAA
109794962 ATAATAATAATAATATT
1 ATAATAATAATAATATT
109794979 TAATAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 16 0.48
19 1 0.03
21 16 0.48
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
ATAATAATAATAATATTGAA
Found at i:109798361 original size:38 final size:37
Alignment explanation
Indices: 109798277--109798371 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
109798267 TATACGTACT
*
109798277 TATACATACTTAAATATATTTTTCATATTTCATAATTC
1 TATACATACTTAAATATATTTTGCATATTT-ATAATTC
* *
109798315 T-TATATACTTACATATATTTATGCATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TGCATATTTATA-ATTC
*
109798351 ATATACATACTTATATATATT
1 -TATACATACTTAAATATATT
109798372 CTTTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.08
37 19 0.40
38 25 0.52
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTGCATATTTATAATTC
Found at i:109805302 original size:86 final size:86
Alignment explanation
Indices: 109805157--109805420 Score: 420
Period size: 86 Copynumber: 3.1 Consensus size: 86
109805147 AGTAAAAATT
* * * * *
109805157 GAAGATAAACCTTGCCTCTCTTGGTCGTAGCAGAGCTGGTTGAAGTTATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
109805222 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* * *
109805243 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
109805308 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
*
109805329 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCTTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
* *
109805394 GTATTTGGCAGCGAAGCAGATC
66 GCA-TTGACAGCGAAGCAGATC
109805416 GAAGA
1 GAAGA
109805421 TGGCAGATTT
Statistics
Matches: 163, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
86 141 0.87
87 22 0.13
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (86 bp):
GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGATC
Found at i:109805344 original size:42 final size:42
Alignment explanation
Indices: 109805211--109805345 Score: 107
Period size: 42 Copynumber: 3.2 Consensus size: 42
109805201 GTTATCAGAT
109805211 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
* * * * * * * * *
109805253 CTTGCC-ACTCT-CGTTTG-TAG-TAGAGCTGGTTGAAGATAGCAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGA-AGCAGATCGAAG--A-CAAAC
109805297 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
109805339 CTTGCCT
1 CTTGCCT
109805346 CTCTCGTTTG
Statistics
Matches: 65, Mismatches: 18, Indels: 20
0.63 0.17 0.19
Matches are distributed among these distances:
40 1 0.02
41 13 0.20
42 21 0.32
43 2 0.03
44 14 0.22
45 13 0.20
46 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
Found at i:109805638 original size:45 final size:45
Alignment explanation
Indices: 109805445--109805643 Score: 118
Period size: 45 Copynumber: 4.4 Consensus size: 45
109805435 TCCCTGACAA
* * *
109805445 CAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGG
1 CAGTGGAATAGATTGAAGCCGATAACTCTACCTCCCTGTATCTGG
** * * * * *
109805490 CAGTGGAATAGATTGAAGATTGCAGATCT-TGCCTTCCTGTATTTGG
1 CAGTGGAATAGATTGAAG-CCG-ATAACTCTACCTCCCTGTATCTGG
* * * ** ** * * *
109805536 CAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGA-CT-A
1 CAGTGGAA-TAGATTGAAGCCGATA-ACTCTACCTCCCTGT-ATCTGG
* * *
109805581 CAGTGGAGTAGATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
1 CAGTGGAATAGATTGAAGCCGATAACTCTACCTCCCTGTATCTGG
109805626 CAGTGGAATAGATTGAAG
1 CAGTGGAATAGATTGAAG
109805644 ATTGCAGATC
Statistics
Matches: 109, Mismatches: 36, Indels: 18
0.67 0.22 0.11
Matches are distributed among these distances:
43 1 0.01
44 14 0.13
45 52 0.48
46 37 0.34
47 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (45 bp):
CAGTGGAATAGATTGAAGCCGATAACTCTACCTCCCTGTATCTGG
Found at i:109805643 original size:136 final size:134
Alignment explanation
Indices: 109805368--109805662 Score: 511
Period size: 136 Copynumber: 2.2 Consensus size: 134
109805358 GCAGAGCTGG
*
109805368 TTGAAGATAT-CAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
1 TTGAAGAT-TGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
109805432 ACCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGA
65 ACCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGA
109805497 ATAGA
130 ATAGA
109805502 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
* * *
109805567 CCTCCCTGTGACTACAGTGGAGTAGATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGG
66 CCTCCC--TGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGG
109805632 AATAGA
129 AATAGA
*
109805638 TTGAAGATTGCAGATCTTGTCTTCC
1 TTGAAGATTGCAGATCTTGCCTTCC
109805663 CATATTGGTG
Statistics
Matches: 153, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
133 1 0.01
134 68 0.44
136 84 0.55
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (134 bp):
TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
CCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGGAA
TAGA
Found at i:109806146 original size:176 final size:178
Alignment explanation
Indices: 109805647--109806285 Score: 675
Period size: 176 Copynumber: 3.6 Consensus size: 178
109805637 ATTGAAGATT
* * * * * * ***
109805647 GCAGATCTTGTCTTCCCATATTGGTGGCGAAATAGATCGAAGAAAGTAGATCTTGTCTTCATGTA
1 GCAGATCCTATCTTCCCATATTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCCCATA
* * * * *** *
109805712 TTGG-CGTGAAGTAGATCAAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGCGAAGTAGATCGC
* * *
109805775 AGAAAGCAGATATTGTCTTCATGTATTTGCGTGAAGAAGATCGAAGGTA
130 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTA
* * * *
109805824 GCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTATCTTTCCATA
1 GCAGATCCTATCTTCCCATATTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCCCATA
* *
109805887 TTGGTGGCGAAGTAGATCGAAGAAATCAGATCTTGTCTTCATGTATTAGCGCGAAGTAGATCGCA
66 TTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGCGAAGTAGATCGCA
*
109805952 GAAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTA
131 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTA
* * * *
109806000 GCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTGTCTTCCCATA
1 GCAGATCCTATCTTCCCATATTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCCCATA
* * *
109806063 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAA
66 TTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGCGAAGTAGATCGCA
* * * * * * * * *
109806128 GATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGACGAT-
131 GAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTA
* * * * * ***
109806175 GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTATCTTCATGTA
1 GCAGATCCTATCTTCCCATATTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCCCATA
* * * ** * *
109806240 TTGG-CGTGAAGTAGGTCGAAGATTGCAGATCTTGCCTTCCTGTATT
66 TTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATT
109806286 TGGCAGTGGA
Statistics
Matches: 393, Mismatches: 64, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
175 41 0.10
176 287 0.73
177 65 0.17
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (178 bp):
GCAGATCCTATCTTCCCATATTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCCCATA
TTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGCGAAGTAGATCGCA
GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTA
Found at i:109806237 original size:308 final size:308
Alignment explanation
Indices: 109805719--109806285 Score: 918
Period size: 308 Copynumber: 1.8 Consensus size: 308
109805709 GTATTGGCGT
109805719 GAAGTAGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAG
1 GAAGTAGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAG
* *
109805784 ATATTGTCTTCATGTATTTGCGTGAAGAAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGT
66 ATATTGTCTTCATGTATTGGCGTGAAGAAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
* * *
109805849 AGGAAGTGGATCGAAGATGCAGATCTTATCTTTCCATATTGGTGGCGAAGTAGATCGAAGAAATC
131 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGC
* * * *
109805914 AGATCTTGTCTTCATGTATTAGCGCGAAGTAGATCGCAGAAAGTAGATCTTGTCTTCATGTATTG
196 AGATCTTATCTTCATGTATTAGCGCGAAGTAGATCGAAGAAAGCAGATCTTGCCTTCATGTATTG
109805979 GCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAG
261 GCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAG
* *
109806027 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAG
1 GAAGTAGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAG
* * * *
109806092 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGT
66 ATATTGTCTTCATGTATTGGCGTGAAGAAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
* * *
109806157 AGGAAGTGGATCGACGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGCAGAAAGC
131 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGC
* * * ** *
109806222 AGATCTTATCTTCATGTATTGGCGTGAAGTAGGTCGAAGATTGCAGATCTTGCCTTCCTGTATT
196 AGATCTTATCTTCATGTATTAGCGCGAAGTAGATCGAAGAAAGCAGATCTTGCCTTCATGTATT
109806286 TGGCAGTGGA
Statistics
Matches: 235, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
308 235 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (308 bp):
GAAGTAGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAG
ATATTGTCTTCATGTATTGGCGTGAAGAAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGC
AGATCTTATCTTCATGTATTAGCGCGAAGTAGATCGAAGAAAGCAGATCTTGCCTTCATGTATTG
GCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAG
Found at i:109806279 original size:132 final size:134
Alignment explanation
Indices: 109805634--109806285 Score: 752
Period size: 132 Copynumber: 4.9 Consensus size: 134
109805624 GGCAGTGGAA
* * * * *
109805634 TAGATTGAAGATTGCAGATCTTGTCTTCCCATATTGGTGGCGAAATAGATCGAAGAAAGTAGATC
1 TAGATCGAAGAATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATC
* * *
109805699 TTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGA-TGCAGATCTTGTCTTCCCATATTGGTGGC
66 TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATTGCAGATCTTGTCTTCCTATATTGGTAGC
109805763 GAAG
131 GAAG
* * * *** * * * **
109805767 TAGATCGCAGAAAGCAGATATTGTCTTCATGTATT--TGCGTGAAGAAGATCGAAGGTAGCAGAT
1 TAGATCGAAGAATGCAGATCTTGTCTTCCCATATTGGTG-GCGAAGTAGATCGCAGAAAGCAGAT
* * * * * * *
109805830 CCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGA-TGCAGATCTTATCTTTCC-ATATTGGT
65 CTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATTGCAGATCTTGTC-TTCCTATATTGGT
*
109805892 GGCGAAG
128 AGCGAAG
*** * * *
109805899 TAGATCGAAGAAAT-CAGATCTTGTCTTCATGTATTAG-CGCGAAGTAGATCGCAGAAAGTAGAT
1 TAGATCGAAG-AATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGAT
* * * *
109805962 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAG
65 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATTGCAGATCTTGTCTTCCTATATTGGTAG
109806027 -GAAG
130 CGAAG
*
109806031 TGGATCGAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATC
1 TAGATCGAAGAATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATC
* * *
109806095 TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-
66 TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATTGCAGATCTTGTCTTCCTATATTGGTAGC
109806159 GAAG
131 GAAG
* * *
109806163 TGGATCGACG-ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGCAGAAAGCAGATC
1 TAGATCGAAGAATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATC
* * * *
109806227 TTATCTTCATGTATTGGCGTGAAGTAGGTCGAAGATTGCAGATCTTGCCTTCCTGTATT
66 TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATTGCAGATCTTGTCTTCCTATATT
109806286 TGGCAGTGGA
Statistics
Matches: 447, Mismatches: 61, Indels: 23
0.84 0.11 0.04
Matches are distributed among these distances:
130 2 0.00
131 22 0.05
132 369 0.83
133 54 0.12
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (134 bp):
TAGATCGAAGAATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATC
TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATTGCAGATCTTGTCTTCCTATATTGGTAGC
GAAG
Found at i:109806450 original size:143 final size:134
Alignment explanation
Indices: 109806258--109806532 Score: 345
Period size: 134 Copynumber: 2.0 Consensus size: 134
109806248 AAGTAGGTCG
* * *
109806258 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGAT
1 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGTCG---A-A---CAGATCGAAGATGGCAGAT
* * *
109806323 TTTACCTCCATGTGACCACATTGGAGTACATTGAAGCCGATAACTCTATCTCCATGTATTTGGCA
59 TTTACCTCC--CTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCATGTATTTGACA
*
109806388 GTGGAATAGATTA
122 GCGGAATAGATTA
* *
109806401 AAGATTGCAGATCTTGGCTTCTTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACC
1 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGTCGAA-CAGATCGAAGATGGCAGATTTTACC
* * *
109806465 TCCCTGACTACAGTGGAGTACATTGAAGCTGATAACTCTATCTCCCTGTATTTGACAGCGGAATA
65 TCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCATGTATTTGACAGCGGAATA
109806530 GAT
130 GAT
109806533 CGAAGATTAC
Statistics
Matches: 120, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
134 58 0.48
136 27 0.22
138 1 0.01
139 1 0.01
142 1 0.01
143 32 0.27
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (134 bp):
AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGTCGAACAGATCGAAGATGGCAGATTTTACCT
CCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCATGTATTTGACAGCGGAATAG
ATTA
Found at i:109806646 original size:40 final size:42
Alignment explanation
Indices: 109806541--109806655 Score: 155
Period size: 42 Copynumber: 2.8 Consensus size: 42
109806531 ATCGAAGATT
*
109806541 ACAGTCTTATCTCCCTAAGTAGTAGCGGAGCA-GACGAAACC
1 ACAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGGACGAAACC
* * *
109806582 ACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGGTC-ACATC
1 ACAG-TCTTATCTCCCTAAGTAGTAGTGGAGCAGGACGAAACC
*
109806624 -CAGTCTTATCTCCCTAAATAGTAGTGGAGCAG
1 ACAGTCTTATCTCCCTAAGTAGTAGTGGAGCAG
109806656 ACTAAAAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
40 28 0.42
41 7 0.10
42 30 0.45
43 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (42 bp):
ACAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGGACGAAACC
Found at i:109811552 original size:19 final size:19
Alignment explanation
Indices: 109811530--109811570 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
109811520 TTATTAATAA
109811530 TTTGAATTTTAAAAATTAT
1 TTTGAATTTTAAAAATTAT
**
109811549 TTTGAATTTTGGAAATTAT
1 TTTGAATTTTAAAAATTAT
109811568 TTT
1 TTT
109811571 TTATTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (19 bp):
TTTGAATTTTAAAAATTAT
Done.