Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 193 of 226
Found at i:61426149 original size:14 final size:14
Alignment explanation
Indices: 61426132--61426173 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
61426122 AACCCTTAAA
61426132 CCATAATCCCTAAT
1 CCATAATCCCTAAT
61426146 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
* *
61426161 TCATACTCCCTAA
1 CCATAATCCCTAA
61426174 ACCTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:61426170 original size:15 final size:15
Alignment explanation
Indices: 61426128--61426174 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
61426118 TCCCAACCCT
61426128 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
61426142 T-AATCCATAATCCC
1 TAAATCCATAATCCC
* *
61426156 TAAATTCATACTCCC
1 TAAATCCATAATCCC
61426171 TAAA
1 TAAA
61426175 CCTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 2 0.07
14 12 0.41
15 15 0.52
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:61426576 original size:41 final size:41
Alignment explanation
Indices: 61426524--61426835 Score: 392
Period size: 41 Copynumber: 7.6 Consensus size: 41
61426514 TAAAATGTTT
* * *
61426524 TTAGCGGCGCTTTTTGAAAAATGTCGCTAAAACCCCAAGCA
1 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAACCCCCAGCA
* * *
61426565 TTAGTGACGCTTTTTGAAAAACGCCGCTAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAACCCCCAGCA
* *
61426606 TTAGCGGTGCTTTTTGAAAAACGCCGCTAAAGCCCCCAGCA
1 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAACCCCCAGCA
* * *
61426647 TTAGCGGCGCTTTTTGAAAAACGCCGTTAAAGCCCTCAGCA
1 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAACCCCCAGCA
* * * *
61426688 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGCCCCCAGCG
1 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAACCCCCAGCA
* *
61426729 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAACCCCCAGCA
* * * * * **
61426770 TTAGCAGCGCTTTCTCAAAAACACCGCTAAATCCCTGAGCA
1 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAACCCCCAGCA
61426811 TTAGCGGCGCTTTTTTG-AAAACGCC
1 TTAGCGGCGC-TTTTTGAAAAACGCC
61426836 ACGAAAGCCC
Statistics
Matches: 239, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
41 235 0.98
42 4 0.02
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAACCCCCAGCA
Found at i:61432929 original size:18 final size:18
Alignment explanation
Indices: 61432908--61432947 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
61432898 TAGAGTTCGA
* *
61432908 AAATATATAAAAAGATAT
1 AAATAAATAAAAAGAAAT
*
61432926 AAATAAATAAAATGAAAT
1 AAATAAATAAAAAGAAAT
61432944 AAAT
1 AAAT
61432948 GTATTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AAATAAATAAAAAGAAAT
Found at i:61435384 original size:17 final size:17
Alignment explanation
Indices: 61435362--61435420 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
61435352 ATAATATGAT
61435362 TAAATAATTTAATAATA
1 TAAATAATTTAATAATA
** *
61435379 TAAATAATACAA-AATGT
1 TAAATAATTTAATAAT-A
61435396 TAAATTTAATTTAATAATA
1 TAAA--TAATTTAATAATA
61435415 TAAATA
1 TAAATA
61435421 GTAGATATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 3 0.09
17 16 0.50
19 10 0.31
20 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATAATTTAATAATA
Found at i:61435848 original size:33 final size:33
Alignment explanation
Indices: 61435802--61435876 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
61435792 AAACTAATCC
* * *
61435802 TCTCTCAAATTTGCTCTC-AGTTTCTTCTAAATT
1 TCTCTC-AATTTGCTCTCAAATTCCTTCAAAATT
61435835 TCCTCTCAATTTGCTCTCAAATTCCTTCAAAATT
1 T-CTCTCAATTTGCTCTCAAATTCCTTCAAAATT
61435869 TCTCTCAA
1 TCTCTCAA
61435877 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 19 0.51
34 18 0.49
ACGTcount: A:0.24, C:0.28, G:0.04, T:0.44
Consensus pattern (33 bp):
TCTCTCAATTTGCTCTCAAATTCCTTCAAAATT
Found at i:61435859 original size:22 final size:22
Alignment explanation
Indices: 61435802--61435878 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
61435792 AAACTAATCC
* *
61435802 TCTCTCAAATTTGCTCTCAGTT
1 TCTCTCAAATTTCCTCTCAATT
61435824 TCT-TCTAAATTTCCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
61435846 TGCTCTCAAA-TTCCT-TCAAAATT
1 T-CTCTCAAATTTCCTCTC--AATT
61435869 TCTCTCAAAT
1 TCTCTCAAAT
61435879 CCATATTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
21 4 0.09
22 31 0.66
23 10 0.21
24 2 0.04
ACGTcount: A:0.25, C:0.27, G:0.04, T:0.44
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:61435878 original size:11 final size:11
Alignment explanation
Indices: 61435802--61435878 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
61435792 AAACTAATCC
61435802 TCTCTCAAATT
1 TCTCTCAAATT
*
61435813 TGCTCTC-AGTT
1 T-CTCTCAAATT
61435824 TCT-TCTAAATT
1 TCTCTC-AAATT
61435835 TCCTCTC-AATT
1 T-CTCTCAAATT
61435846 TGCTCTCAAATT
1 T-CTCTCAAATT
*
61435858 CCT-TCAAAATT
1 TCTCTC-AAATT
61435869 TCTCTCAAAT
1 TCTCTCAAAT
61435879 CCATATTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
9 2 0.04
10 4 0.08
11 32 0.60
12 13 0.25
13 2 0.04
ACGTcount: A:0.25, C:0.27, G:0.04, T:0.44
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:61437745 original size:18 final size:18
Alignment explanation
Indices: 61437718--61437757 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
61437708 CAGGTGCGTT
* *
61437718 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
61437736 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
61437754 TCCT
1 TCCT
61437758 TTTTCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:61446088 original size:125 final size:127
Alignment explanation
Indices: 61445840--61446081 Score: 353
Period size: 125 Copynumber: 1.9 Consensus size: 127
61445830 NNNNNNNNNN
*
61445840 TGAAGCGTTTTTTTAAACTATTTGCTTAAAAACGTCAACTCGAAATTATTTCTTCCAAGACCAAC
1 TGAAGCGTTTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAAGACCAAC
* * * *
61445905 TGTAGAAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGCT
66 TGTAGAAAAAGCGCGTACACGAGGGCGCGACTTCAAAAATCCTTCTCATAAAGTATCCTGCT
* * * *
61445967 TGAAGCG-TTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTT-TTCCAGGACCTAC
1 TGAAGCGTTTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAAGACCAAC
* * * *
61446030 TGTAGCAAAAGCGCGTACACGTGGGTGCGACTTCAAAAATCCTTCTGATAAA
66 TGTAGAAAAAGCGCGTACACGAGGGCGCGACTTCAAAAATCCTTCTCATAAA
61446082 TCATCCTACT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
125 55 0.54
126 40 0.39
127 7 0.07
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (127 bp):
TGAAGCGTTTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAAGACCAAC
TGTAGAAAAAGCGCGTACACGAGGGCGCGACTTCAAAAATCCTTCTCATAAAGTATCCTGCT
Found at i:61450450 original size:17 final size:16
Alignment explanation
Indices: 61450412--61450450 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
61450402 ACCTCGTAGT
*
61450412 TTTGGTGAGCTCGCAG
1 TTTGGTGAGCTCGCAA
61450428 TCTTGGTGAGCTCGCACA
1 T-TTGGTGAGCTCGCA-A
61450446 TTTGG
1 TTTGG
61450451 AGAGTTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.90
18 1 0.05
ACGTcount: A:0.13, C:0.21, G:0.33, T:0.33
Consensus pattern (16 bp):
TTTGGTGAGCTCGCAA
Found at i:61452450 original size:13 final size:13
Alignment explanation
Indices: 61452428--61452458 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
61452418 AACAAGGTTG
*
61452428 TTGTTTAGTTACT
1 TTGTTAAGTTACT
61452441 TTGTTAAGTTACT
1 TTGTTAAGTTACT
61452454 TTGTT
1 TTGTT
61452459 GAAAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.61
Consensus pattern (13 bp):
TTGTTAAGTTACT
Found at i:61462588 original size:13 final size:13
Alignment explanation
Indices: 61462551--61462601 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
61462541 TTTGGCAATG
61462551 CTTTTGAAAAGTGA
1 CTTTTGAAAAGT-A
* *
61462565 C-GTAGAAAAGTA
1 CTTTTGAAAAGTA
* *
61462577 CTTTTGAGAAGTG
1 CTTTTGAAAAGTA
61462590 CTTTTGAAAAGT
1 CTTTTGAAAAGT
61462602 TTGGTTTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
12 2 0.07
13 26 0.90
14 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:61464702 original size:23 final size:23
Alignment explanation
Indices: 61464667--61464712 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
61464657 ATTAGTGGTT
**
61464667 ACATCATGAATGACGTGGGAAAA
1 ACATCATGAATGACAAGGGAAAA
61464690 ACATCATCG-ATGACAAGGGAAAA
1 ACATCAT-GAATGACAAGGGAAAA
61464713 GGTTTGACGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.15
Consensus pattern (23 bp):
ACATCATGAATGACAAGGGAAAA
Found at i:61466729 original size:15 final size:14
Alignment explanation
Indices: 61466709--61466758 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
61466699 TCATAAATTG
61466709 TAAAATATTTATTA
1 TAAAATATTTATTA
*
61466723 TTAAAATA-TTAATA
1 -TAAAATATTTATTA
61466737 T-AAATATTT-TTAA
1 TAAAATATTTATT-A
61466750 TAAAATATT
1 TAAAATATT
61466759 AAGAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 6 0.20
13 5 0.17
14 12 0.40
15 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAATATTTATTA
Found at i:61466757 original size:14 final size:14
Alignment explanation
Indices: 61466709--61466758 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
61466699 TCATAAATTG
*
61466709 TAAAATATTTATTAT
1 TAAAATATTT-TTAA
61466724 TAAAATA---TTAA
1 TAAAATATTTTTAA
61466735 TATAAATATTTTTAA
1 TA-AAATATTTTTAA
61466750 TAAAATATT
1 TAAAATATT
61466759 AAGAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
14 7 0.23
15 13 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAATATTTTTAA
Found at i:61466770 original size:26 final size:26
Alignment explanation
Indices: 61466710--61466772 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
61466700 CATAAATTGT
* *
61466710 AAAATATTTATTATTAAAATATTAAT
1 AAAATATTTATTAATAAAATATTAAG
61466736 ATAAATATTT-TTAATAAAATATTAAG
1 A-AAATATTTATTAATAAAATATTAAG
61466762 AAAATTATTTA
1 AAAA-TATTTA
61466773 AAATTATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 3 0.09
26 21 0.66
27 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AAAATATTTATTAATAAAATATTAAG
Found at i:61471090 original size:4 final size:4
Alignment explanation
Indices: 61471081--61471195 Score: 230
Period size: 4 Copynumber: 28.8 Consensus size: 4
61471071 CAATTAATGA
61471081 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
61471129 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
61471177 TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TAT
61471196 TGCTGAAAAG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 111 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:61472852 original size:50 final size:50
Alignment explanation
Indices: 61472753--61472940 Score: 225
Period size: 50 Copynumber: 3.6 Consensus size: 50
61472743 ATGAGATCCT
* *
61472753 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCT
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCCC
*
61472809 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCC
* * **
61472859 CTGTAAGACCATGTCTGGGACATGGC-TTGGGCACCGATATGAGAACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATT-GGCACCGAGATGAGAGGTCCC
* *
61472909 ATGTAAGACCATATCTGGGATATGGCATTGGC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGC
61472941 GGTACAAGAA
Statistics
Matches: 120, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
49 2 0.02
50 80 0.67
51 2 0.02
53 3 0.03
55 1 0.01
56 32 0.27
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCC
Found at i:61472971 original size:49 final size:49
Alignment explanation
Indices: 61472905--61473039 Score: 189
Period size: 49 Copynumber: 2.8 Consensus size: 49
61472895 ATATGAGAAC
*
61472905 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCGGTACAAGAAACA
1 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAACA
* * * *
61472954 TCTCATGTAAGATCATATCTGGGATATGACATTGGCAGTGCAAGAAACA
1 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAACA
* * * *
61473003 TCCCATGTAAGACCATCTTTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
61473040 TGTTATTATT
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 74 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (49 bp):
TCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAACA
Found at i:61475237 original size:24 final size:24
Alignment explanation
Indices: 61475210--61475255 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
61475200 CTAAACTATG
*
61475210 AGTAAGTTTTC-ATTTTTTTAATAA
1 AGTAA-TTTTCTATTTTTCTAATAA
61475234 AGTAATTTTCTATTTTTCTAAT
1 AGTAATTTTCTATTTTTCTAAT
61475256 TTTACTCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (24 bp):
AGTAATTTTCTATTTTTCTAATAA
Found at i:61475923 original size:16 final size:16
Alignment explanation
Indices: 61475904--61475946 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
61475894 GGTTTCCATC
61475904 TTTTCTATTTCTTCTCT
1 TTTTCT-TTTCTTCTCT
* *
61475921 TTTTCTTTTCTTTTCC
1 TTTTCTTTTCTTCTCT
*
61475937 TATTCTTTTC
1 TTTTCTTTTC
61475947 ATCATAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTCTTTTCTTCTCT
Found at i:61476883 original size:38 final size:38
Alignment explanation
Indices: 61476826--61476953 Score: 184
Period size: 38 Copynumber: 3.4 Consensus size: 38
61476816 ATTACGAAAC
* **
61476826 ACATGTTAAGCATGCCTACTACTACTATTGAACCCAAT
1 ACATGTTAAGCATGCCTACTGCTACTATTGAACTGAAT
** *
61476864 ACATGTTAAGCATATCTACTGTTACTATTGAACTGAAT
1 ACATGTTAAGCATGCCTACTGCTACTATTGAACTGAAT
* *
61476902 ACATGTTAAGCATGCCTAATGCTACTATTGAACTGAAA
1 ACATGTTAAGCATGCCTACTGCTACTATTGAACTGAAT
61476940 ACATGTTAAGCATG
1 ACATGTTAAGCATG
61476954 TTAATTGTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 79 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (38 bp):
ACATGTTAAGCATGCCTACTGCTACTATTGAACTGAAT
Found at i:61480768 original size:13 final size:13
Alignment explanation
Indices: 61480750--61480776 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
61480740 TTAATTTATA
61480750 TGTGTGAAAATTT
1 TGTGTGAAAATTT
61480763 TGTGTGAAAATTT
1 TGTGTGAAAATTT
61480776 T
1 T
61480777 ATCGTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:61481981 original size:42 final size:42
Alignment explanation
Indices: 61481857--61481981 Score: 103
Period size: 42 Copynumber: 2.9 Consensus size: 42
61481847 TTCTAAAATG
* * *
61481857 TGATATCGTGTAAGACCACGTCTGGGAC-GTTGGCATCG-ATT
1 TGATTTCGTGTAAGACCATGTCTGGGACAG-TGGCATCGTATA
* * ** **
61481898 TGAGATTTAAGTGTACGAATATGTCTGGGACA-TCGATATCGTATA
1 T--GATTT-CGTGTAAGACCATGTCTGGGACAGT-GGCATCGTATA
61481943 TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGT
1 TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGT
61481982 TATTTAGAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
41 1 0.02
42 25 0.40
43 11 0.18
44 22 0.35
45 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGTATA
Found at i:61484991 original size:71 final size:73
Alignment explanation
Indices: 61484891--61485082 Score: 262
Period size: 71 Copynumber: 2.6 Consensus size: 73
61484881 TAAAAAAACC
* * * ** *
61484891 CATAAAATTGATAACTGAAATAGTGAAAAAGTCATTACATAAATACAAAGTTTACTATTTAAATT
1 CATAAAATTGATAAATAAAATGGAAAAAAAGTCATTACATAAATACAAAGTTGACTATTTAAATT
*
61484956 GC-AATAA
66 GCAAAGAA
*
61484963 -ATAAAATTGATAAATAAAATGGCAAAAAAGTCATTACATAAATACAAAGTTGACTATTTAAATT
1 CATAAAATTGATAAATAAAATGGAAAAAAAGTCATTACATAAATACAAAGTTGACTATTTAAATT
61485027 GCAAAAGAA
66 GC-AAAGAA
*
61485036 CCCATAAAATTGATAAATAAAATGGAAAAAAATTCATTACATAAATA
1 --CATAAAATTGATAAATAAAATGGAAAAAAAGTCATTACATAAATA
61485083 TGAAATTATT
Statistics
Matches: 106, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
71 60 0.57
73 4 0.04
76 42 0.40
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (73 bp):
CATAAAATTGATAAATAAAATGGAAAAAAAGTCATTACATAAATACAAAGTTGACTATTTAAATT
GCAAAGAA
Found at i:61485317 original size:33 final size:33
Alignment explanation
Indices: 61485275--61485340 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
61485265 CTTGAGTTGA
* * *
61485275 GAGGAGTGAAGTACGATGGTGGGTATGGGCCGG
1 GAGGAGTGAAGTACGATAGTGGATATGAGCCGG
*
61485308 GAGGAGTGAAGTATGATAGTGGATATGAGCCGG
1 GAGGAGTGAAGTACGATAGTGGATATGAGCCGG
61485341 AAAGAGTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.08, G:0.47, T:0.20
Consensus pattern (33 bp):
GAGGAGTGAAGTACGATAGTGGATATGAGCCGG
Found at i:61487580 original size:103 final size:103
Alignment explanation
Indices: 61487370--61487660 Score: 403
Period size: 103 Copynumber: 2.8 Consensus size: 103
61487360 TACATTATAT
* *
61487370 AAAAATTACATTA--AAAAAATCACAAAACACTAAACTAAATACTAACAATTGATATAACCTAAT
1 AAAAATTACATTACTAAAAAATCACAAAACACT-AACTAAACACTAACAATTTATATAACCTAAT
*
61487433 CATAAATTACTAACAAAATAACTATAAAATTGTTTTTAA
65 CATAAATTACTAACAAAATAACTATAAAATTATTTTTAA
*
61487472 AAAAA-TACATTACTAAAAAATTACAAAACACATAACTAAACACTAACAATTTATATAACCTAAT
1 AAAAATTACATTACTAAAAAATCACAAAACAC-TAACTAAACACTAACAATTTATATAACCTAAT
**
61487536 CATAAATTACTAACAAAATAACTATAAAATTATTTTTTT
65 CATAAATTACTAACAAAATAACTATAAAATTATTTTTAA
* * *
61487575 TAAAATTACATTACTAAAAAATCACAAAACCCTACACTAAACACTAACAA-TT-TGTAACCTAAT
1 AAAAATTACATTACTAAAAAATCACAAAACACTA-ACTAAACACTAACAATTTATATAACCTAAT
* *
61487638 CCCATTAATTATTAACAAAATAA
65 --CATAAATTACTAACAAAATAA
61487661 ATAACTATAA
Statistics
Matches: 170, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
101 7 0.04
102 15 0.09
103 89 0.52
104 59 0.35
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.29
Consensus pattern (103 bp):
AAAAATTACATTACTAAAAAATCACAAAACACTAACTAAACACTAACAATTTATATAACCTAATC
ATAAATTACTAACAAAATAACTATAAAATTATTTTTAA
Found at i:61487932 original size:60 final size:60
Alignment explanation
Indices: 61487856--61487974 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
61487846 ATACTAAACT
*
61487856 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
* * *
61487916 AAACATAATAATTTATAACATAATCCTAAATTACTAACACATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
61487975 TAAAAAACAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:61496121 original size:18 final size:19
Alignment explanation
Indices: 61496098--61496133 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
61496088 CTATAGAAAA
*
61496098 TTATTTTTTATAA-ATATT
1 TTATTTTTAATAATATATT
61496116 TTATTTTTAATAATATAT
1 TTATTTTTAATAATATAT
61496134 AACATGGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTTTAATAATATATT
Found at i:61499983 original size:21 final size:21
Alignment explanation
Indices: 61499957--61500002 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
61499947 TTTATAAATA
61499957 TTTGAAAATTTAAAAAATTAT
1 TTTGAAAATTTAAAAAATTAT
* **
61499978 TTTG-AATTTTTGAAAATTAT
1 TTTGAAAATTTAAAAAATTAT
61499998 TTTGA
1 TTTGA
61500003 TTTTCCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (21 bp):
TTTGAAAATTTAAAAAATTAT
Found at i:61504264 original size:86 final size:86
Alignment explanation
Indices: 61504107--61504264 Score: 194
Period size: 86 Copynumber: 1.8 Consensus size: 86
61504097 GCACTTCAAA
* * *
61504107 TTTCAATTTAGTCCTTTTATAAATAAAAAAAATTTATAAAATCATATATGCTAAACTTGCACTTT
1 TTTCAATTTAGTCCTCTTATAAATAAAAAAAATTTATAAAATAATATATGCTAAAATTGCACTTT
*
61504172 GGCCCCCTTAAAATGAAAAGT
66 AGCCCCCTTAAAATGAAAAGT
* * * * *
61504193 TTTCAATTTAGTCCTCTTATAAGT-AAAGAAA-TTATAAATTAATATATAGAGTAAAATTTCACT
1 TTTCAATTTAGTCCTCTTATAAATAAAAAAAATTTATAAAATAATATAT-G-CTAAAATTGCACT
*
61504256 TTATCCCCC
64 TTAGCCCCC
61504265 CAAAAAAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 14 0.23
85 7 0.12
86 39 0.65
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (86 bp):
TTTCAATTTAGTCCTCTTATAAATAAAAAAAATTTATAAAATAATATATGCTAAAATTGCACTTT
AGCCCCCTTAAAATGAAAAGT
Found at i:61505404 original size:23 final size:23
Alignment explanation
Indices: 61505368--61505412 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
61505358 ACCGACAACA
*
61505368 CTCTCTCTCACCTTTAATTTCAT
1 CTCTCTCTCACCTTTAAATTCAT
61505391 CTCTCCTCTC-CCTTTAAATTCA
1 CTCT-CTCTCACCTTTAAATTCA
61505413 GACATCTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.44
Consensus pattern (23 bp):
CTCTCTCTCACCTTTAAATTCAT
Found at i:61505807 original size:3 final size:3
Alignment explanation
Indices: 61505799--61505828 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
61505789 GAAGCTATGG
61505799 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
61505829 TATACATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:61525414 original size:47 final size:47
Alignment explanation
Indices: 61525345--61525434 Score: 180
Period size: 47 Copynumber: 1.9 Consensus size: 47
61525335 TGAATTGGAA
61525345 AAGAGGAAGACCTAAACAAATCCATACAAGAAAACTGTTCATTTTCC
1 AAGAGGAAGACCTAAACAAATCCATACAAGAAAACTGTTCATTTTCC
61525392 AAGAGGAAGACCTAAACAAATCCATACAAGAAAACTGTTCATT
1 AAGAGGAAGACCTAAACAAATCCATACAAGAAAACTGTTCATT
61525435 ACCAAACTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (47 bp):
AAGAGGAAGACCTAAACAAATCCATACAAGAAAACTGTTCATTTTCC
Found at i:61531469 original size:2 final size:2
Alignment explanation
Indices: 61531462--61531507 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
61531452 ATTTTTAATA
*
61531462 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61531504 -T AT A
1 AT AT A
61531508 CATGACAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61539636 original size:30 final size:32
Alignment explanation
Indices: 61539568--61539636 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
61539558 AATATATATT
*
61539568 AATATTATAATATTATATCTTAATAATTAAGTA
1 AATA-TATAATATTATATATTAATAATTAAGTA
* *
61539601 TATATATTATATTATATATT-ATAA-TAAGTA
1 AATATATAATATTATATATTAATAATTAAGTA
61539631 AATATA
1 AATATA
61539637 ATAAAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 11 0.34
31 4 0.12
32 14 0.44
33 3 0.09
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (32 bp):
AATATATAATATTATATATTAATAATTAAGTA
Found at i:61540363 original size:24 final size:24
Alignment explanation
Indices: 61540336--61540382 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61540326 ATTGAAATGG
61540336 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
61540360 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
61540383 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:61540660 original size:40 final size:40
Alignment explanation
Indices: 61540602--61540677 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
61540592 GGGTGCCAAT
**
61540602 TTACTTCGGTTTAGCTGATGAGACACTGGATGTCAATTTA
1 TTACTTCGAATTAGCTGATGAGACACTGGATGTCAATTTA
* * * *
61540642 TTACTTCGAATTATCTGATGAGGCATTGGGTGTCAA
1 TTACTTCGAATTAGCTGATGAGACACTGGATGTCAA
61540678 ACTAGTGGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (40 bp):
TTACTTCGAATTAGCTGATGAGACACTGGATGTCAATTTA
Found at i:61542907 original size:28 final size:26
Alignment explanation
Indices: 61542874--61542928 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 26
61542864 ATTGTTTGTG
61542874 TATTAAT-TTTATTTATTTATACTATAAT
1 TATTAATATTTATTT-TTTAT--TATAAT
61542902 TATTAATATTTATTTTTTATTATAAT
1 TATTAATATTTATTTTTTATTATAAT
61542928 T
1 T
61542929 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 7 0.27
28 12 0.46
29 7 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
TATTAATATTTATTTTTTATTATAAT
Found at i:61546853 original size:21 final size:21
Alignment explanation
Indices: 61546827--61546868 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
61546817 ACGGGATAGG
*
61546827 TGACGTGACCCGTTAACTAGC
1 TGACGTGACCAGTTAACTAGC
61546848 TGACGTGACCAGTTAACTAGC
1 TGACGTGACCAGTTAACTAGC
61546869 CACATTGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (21 bp):
TGACGTGACCAGTTAACTAGC
Found at i:61549547 original size:2 final size:2
Alignment explanation
Indices: 61549540--61549576 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
61549530 ACATGATGTG
61549540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61549577 TCCACTATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61553533 original size:21 final size:21
Alignment explanation
Indices: 61553509--61553551 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
61553499 ACACAAAAAT
*
61553509 TTACAAATTAAT-ATGCAATTA
1 TTACAAATCAATGA-GCAATTA
61553530 TTACAAATCAATGAGCAATTA
1 TTACAAATCAATGAGCAATTA
61553551 T
1 T
61553552 AAGATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (21 bp):
TTACAAATCAATGAGCAATTA
Found at i:61554938 original size:28 final size:29
Alignment explanation
Indices: 61554899--61554966 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
61554889 GCTGATGGAC
61554899 AGAGAG-GAAGGAGAACGACTACTATGA-
1 AGAGAGTGAAGGAGAACGACTACTATGAT
*
61554926 AGAGAGTGAAGGAGAACGACTGCTATGAT
1 AGAGAGTGAAGGAGAACGACTACTATGAT
*
61554955 A-AGAGTGGAGGA
1 AGAGAGTGAAGGA
61554967 AAATGGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 6 0.16
28 30 0.81
29 1 0.03
ACGTcount: A:0.41, C:0.09, G:0.37, T:0.13
Consensus pattern (29 bp):
AGAGAGTGAAGGAGAACGACTACTATGAT
Found at i:61557323 original size:30 final size:29
Alignment explanation
Indices: 61557287--61557385 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 29
61557277 AAAATGTCTG
*
61557287 TTAGTGACTGCTTTTTTATTTTCGTAAAGT
1 TTAGTGACTGCTTTATTATTTTC-TAAAGT
* ** * *
61557317 TTAGTGATTGAGTTGTCACTTTTC-AAAGT
1 TTAGTGACTGCTTTATTA-TTTTCTAAAGT
* *
61557346 TTAGTGTCTGCTTTATTATTTTAATAAAAG-
1 TTAGTGACTGCTTTATTATTTT-CT-AAAGT
61557376 TTAGTGACTG
1 TTAGTGACTG
61557386 GCAATATACT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
28 4 0.08
29 17 0.33
30 22 0.42
31 9 0.17
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (29 bp):
TTAGTGACTGCTTTATTATTTTCTAAAGT
Found at i:61557950 original size:2 final size:2
Alignment explanation
Indices: 61557943--61557971 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61557933 CTTAATTATT
61557943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61557972 TCATATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61562005 original size:31 final size:31
Alignment explanation
Indices: 61561947--61562005 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
61561937 GGTGTAATTA
* * *
61561947 TATATATGAAACTTTGATTGTGGTTCAAATG
1 TATACATGAAACTTTAATTGTGATTCAAATG
* *
61561978 TATACATGCAACTTTAATTTTGATTCAA
1 TATACATGAAACTTTAATTGTGATTCAA
61562006 TCATACACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (31 bp):
TATACATGAAACTTTAATTGTGATTCAAATG
Found at i:61575402 original size:62 final size:62
Alignment explanation
Indices: 61575326--61575465 Score: 165
Period size: 62 Copynumber: 2.3 Consensus size: 62
61575316 TTCGAAGCAT
* *
61575326 AAACAATGAGTTACACGAACTGGACACATGCCTGTGCCCCT-GCCTGTGTGATCTTGTACCAC
1 AAACAATGAGTTACACGAACTGGACACACGCCCGTGCCCCTGGCC-GTGTGATCTTGTACCAC
* * ** * * * * *
61575388 AAACAGTGACTTACACGGCCTGGGCACACGCCCGTGTCCTTGGGCGTGTGGTCTTGTACCAC
1 AAACAATGAGTTACACGAACTGGACACACGCCCGTGCCCCTGGCCGTGTGATCTTGTACCAC
61575450 AAACAATGAGTTACAC
1 AAACAATGAGTTACAC
61575466 AGCCTGGGCA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 62 0.97
63 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (62 bp):
AAACAATGAGTTACACGAACTGGACACACGCCCGTGCCCCTGGCCGTGTGATCTTGTACCAC
Found at i:61575471 original size:62 final size:62
Alignment explanation
Indices: 61575371--61575500 Score: 181
Period size: 62 Copynumber: 2.1 Consensus size: 62
61575361 GCCCCTGCCT
* * * * *
61575371 GTGTGATCTTGTACCACAAACAGTGACTTACACGGCCTGGGCACACGCCCGTGT-CCTTGGGC
1 GTGTGGTCTTGTACCACAAACAATGACTTACACAGCCTGGGCACACACCCGTGTGCC-TGGCC
* *
61575433 GTGTGGTCTTGTACCACAAACAATGAGTTACACAGCCTGGGCACACACTCGTGTGCCTGGCC
1 GTGTGGTCTTGTACCACAAACAATGACTTACACAGCCTGGGCACACACCCGTGTGCCTGGCC
61575495 GTGTGG
1 GTGTGG
61575501 CGTCGACAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 58 0.97
63 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.23
Consensus pattern (62 bp):
GTGTGGTCTTGTACCACAAACAATGACTTACACAGCCTGGGCACACACCCGTGTGCCTGGCC
Found at i:61577571 original size:16 final size:16
Alignment explanation
Indices: 61577550--61577581 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61577540 GTTTTGTTGC
*
61577550 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
61577566 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
61577582 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:61579895 original size:17 final size:17
Alignment explanation
Indices: 61579875--61579909 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
61579865 AATTGGGTAG
61579875 AGAAAA-TAATTTAATTA
1 AGAAAATTAA-TTAATTA
61579892 AGAAAATTAATTAATTA
1 AGAAAATTAATTAATTA
61579909 A
1 A
61579910 TTAATGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
AGAAAATTAATTAATTA
Found at i:61580234 original size:17 final size:18
Alignment explanation
Indices: 61580197--61580240 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
61580187 AGTGACAATT
**
61580197 TATTTTTAGAATAAATTC
1 TATTTTTAGAATAAAAAC
61580215 TATTTTTAGAA-AAAAAC
1 TATTTTTAGAATAAAAAC
61580232 TATTCTTTA
1 TATT-TTTA
61580241 CACTTGGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (18 bp):
TATTTTTAGAATAAAAAC
Found at i:61580763 original size:39 final size:39
Alignment explanation
Indices: 61580716--61580795 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
61580706 TGAGTTAGTT
61580716 AAATTATTTGAGTCAATTCGAATAAGTAATTCGAGTTTG
1 AAATTATTTGAGTCAATTCGAATAAGTAATTCGAGTTTG
*
61580755 AAATTATTTGAGTCAATTTGAATAAGTAATTCGAGTTTG
1 AAATTATTTGAGTCAATTCGAATAAGTAATTCGAGTTTG
61580794 AA
1 AA
61580796 TCGAGTTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (39 bp):
AAATTATTTGAGTCAATTCGAATAAGTAATTCGAGTTTG
Found at i:61580795 original size:19 final size:19
Alignment explanation
Indices: 61580735--61580796 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
61580725 GAGTCAATTC
61580735 GAATAAGTAATTCGAGTTT
1 GAATAAGTAATTCGAGTTT
** * * *
61580754 GAAATTATTTGAGTC-AATTT
1 G-AA-TAAGTAATTCGAGTTT
61580774 GAATAAGTAATTCGAGTTT
1 GAATAAGTAATTCGAGTTT
61580793 GAAT
1 GAAT
61580797 CGAGTTGAAT
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 6 0.20
19 11 0.37
20 7 0.23
21 6 0.20
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (19 bp):
GAATAAGTAATTCGAGTTT
Found at i:61580921 original size:20 final size:20
Alignment explanation
Indices: 61580889--61580971 Score: 82
Period size: 20 Copynumber: 4.2 Consensus size: 20
61580879 ACAAAAATAA
*
61580889 AAAAAATT-CAAATAATTTT
1 AAAAAATTAAAAATAATTTT
* **
61580908 AAAAAATTCAAAATGTTTTT
1 AAAAAATTAAAAATAATTTT
*
61580928 CAAAAATTAAAAATAATTTT
1 AAAAAATTAAAAATAATTTT
*
61580948 -TAAAATTAAAAAT-ATTTAT
1 AAAAAATTAAAAATAATTT-T
61580967 AAAAA
1 AAAAA
61580972 TTCCAACATT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
18 4 0.08
19 21 0.40
20 27 0.52
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (20 bp):
AAAAAATTAAAAATAATTTT
Found at i:61580933 original size:39 final size:37
Alignment explanation
Indices: 61580890--61580974 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 37
61580880 CAAAAATAAA
* * *
61580890 AAAAATTCAAATAATTTTAAAAAATTCAAAATGTTTTT
1 AAAAATTCAAATAATTTT-AAAAATTAAAAATATTTAT
* *
61580928 CAAAAATTAAAAATAATTTTTAAAATTAAAAATATTTAT
1 -AAAAATT-CAAATAATTTTAAAAATTAAAAATATTTAT
61580967 AAAAATTC
1 AAAAATTC
61580975 CAACATTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
38 7 0.18
39 22 0.56
40 10 0.26
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (37 bp):
AAAAATTCAAATAATTTTAAAAATTAAAAATATTTAT
Found at i:61581693 original size:2 final size:2
Alignment explanation
Indices: 61581686--61581723 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
61581676 CTATAAAACA
61581686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61581724 CAACCACTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61582104 original size:34 final size:33
Alignment explanation
Indices: 61582065--61582209 Score: 118
Period size: 34 Copynumber: 4.2 Consensus size: 33
61582055 GTGGGTGGAG
*
61582065 AAGAAAAGGAGAGG-GAAAGGAGAAGAAAGAAAGA
1 AAGAAAAGGAAAGGAG-AAGGAGAA-AAAGAAAGA
* * *
61582099 AAGAAAAGGAAAGGAGAAGAAAGAAAAGGAGAGA
1 AAGAAAAGGAAAGGAGAAG-GAGAAAAAGAAAGA
*
61582133 AAGAAAAAGGAAAGGAGAAGAAAGAAAAAGAAAG-
1 AAG-AAAAGGAAAGGAGAAG-GAGAAAAAGAAAGA
*
61582167 GAGAAGAA-GAAGAGG-GAAGGAAGGAAAAAGAAAGA
1 AAGAA-AAGGAA-AGGAGAAGG-A-GAAAAAGAAAGA
*
61582202 AAAAAAAG
1 AAGAAAAG
61582210 AAGGTAAATT
Statistics
Matches: 92, Mismatches: 10, Indels: 17
0.77 0.08 0.14
Matches are distributed among these distances:
33 10 0.11
34 46 0.50
35 36 0.39
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (33 bp):
AAGAAAAGGAAAGGAGAAGGAGAAAAAGAAAGA
Found at i:61582113 original size:28 final size:28
Alignment explanation
Indices: 61582078--61582174 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
61582068 AAAAGGAGAG
61582078 GGAAAGGAGAAGAAAGAAAGAAAGAAAA
1 GGAAAGGAGAAGAAAGAAAGAAAGAAAA
*
61582106 GGAAAGGAGAAGAAAGAAA-AGGAGAGAAA
1 GGAAAGGAGAAGAAAGAAAGA-AAGA-AAA
* *
61582135 GAAAAAGGA-AAG-GAG-AAGAAAGAAAA
1 G-GAAAGGAGAAGAAAGAAAGAAAGAAAA
*
61582161 AGAAAGGAGAAGAA
1 GGAAAGGAGAAGAA
61582175 GAAGAGGGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
25 6 0.11
26 6 0.11
27 6 0.11
28 25 0.45
29 7 0.12
30 6 0.11
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (28 bp):
GGAAAGGAGAAGAAAGAAAGAAAGAAAA
Found at i:61582120 original size:20 final size:20
Alignment explanation
Indices: 61582095--61582187 Score: 108
Period size: 20 Copynumber: 5.0 Consensus size: 20
61582085 AGAAGAAAGA
61582095 AAGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
61582115 AAGAAAGAAAAGG--A-GAG
1 AAGAAAGAAAAGGAAAGGAG
*
61582132 AA-AGA-AAAAGGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
*
61582150 AAGAAAGAAAAAGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
* *
61582170 AAG-AAGAAGAGGGAAGGA
1 AAGAAAGAAAAGGAAAGGA
61582188 AGGAAAAAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.10
16 2 0.03
17 6 0.10
18 6 0.10
19 14 0.23
20 28 0.45
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAAAGGAAAGGAG
Found at i:61582185 original size:13 final size:13
Alignment explanation
Indices: 61582079--61582177 Score: 55
Period size: 15 Copynumber: 7.2 Consensus size: 13
61582069 AAAGGAGAGG
61582079 GAAAGGAGAAGAAA
1 GAAAGGAGAAG-AA
*
61582093 GAAAGAAAGAA-AA
1 GAAAG-GAGAAGAA
61582106 GGAAAGGAGAAGAAA
1 -GAAAGGAGAAG-AA
61582121 GAAAAGGAG-AGAAA
1 G-AAAGGAGAAG-AA
*
61582135 GAAAAAGGAAAGGAGAA
1 G--AAAGG--AGAAGAA
61582152 GAAA-GA-AA-AA
1 GAAAGGAGAAGAA
61582162 GAAAGGAGAAGAA
1 GAAAGGAGAAGAA
61582175 GAA
1 GAA
61582178 GAGGGAAGGA
Statistics
Matches: 70, Mismatches: 3, Indels: 25
0.71 0.03 0.26
Matches are distributed among these distances:
10 6 0.09
11 3 0.04
12 3 0.04
13 11 0.16
14 18 0.26
15 22 0.31
17 5 0.07
18 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (13 bp):
GAAAGGAGAAGAA
Found at i:61582194 original size:55 final size:54
Alignment explanation
Indices: 61582065--61582200 Score: 154
Period size: 55 Copynumber: 2.5 Consensus size: 54
61582055 GTGGGTGGAG
* * *
61582065 AAGAAAAGGAGAGGGAAAGGAGAAGAAA-GA-AAGAAAGAAAAGGAAAGGAGAAGA
1 AAGAAAAGGAGA--GAAAGAAAAAGAAAGGAGAAGAAAGAAAAAGAAAGGAGAAGA
61582119 AAGAAAAGGAGAGAAAGAAAAAGGAAAGGAGAAGAAAGAAAAAGAAAGGAGAAG-
1 AAGAAAAGGAGAGAAAGAAAAA-GAAAGGAGAAGAAAGAAAAAGAAAGGAGAAGA
* *
61582173 AAGAAGAGG-GAAGGAAGGAAAAAGAAAG
1 AAGAAAAGGAG-A-GAAAGAAAAAGAAAG
61582201 AAAAAAAAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
52 8 0.11
53 5 0.07
54 28 0.39
55 31 0.43
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (54 bp):
AAGAAAAGGAGAGAAAGAAAAAGAAAGGAGAAGAAAGAAAAAGAAAGGAGAAGA
Found at i:61582209 original size:9 final size:10
Alignment explanation
Indices: 61582094--61582211 Score: 67
Period size: 10 Copynumber: 11.0 Consensus size: 10
61582084 GAGAAGAAAG
61582094 AAAGAAAGAA
1 AAAGAAAGAA
* *
61582104 AAGGAAAGGA
1 AAAGAAAGAA
*
61582114 GAAGAAAGAAA
1 AAAGAAAG-AA
61582125 AGGAGAGAAAGAA
1 A--A-AGAAAGAA
*
61582138 AAAGGAAAGGA
1 AAA-GAAAGAA
*
61582149 GAAGAAAGAA
1 AAAGAAAGAA
61582159 AAAGAAAGGAGA
1 AAAGAAA-GA-A
**
61582171 AGAAGAAGAGGG
1 A-AAGAA-AGAA
* *
61582183 AAGGAAGGAA
1 AAAGAAAGAA
61582193 AAAGAAAGAA
1 AAAGAAAGAA
61582203 AAA-AAAGAA
1 AAAGAAAGAA
61582212 GGTAAATTTT
Statistics
Matches: 81, Mismatches: 18, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
9 6 0.07
10 39 0.48
11 16 0.20
12 3 0.04
13 10 0.12
14 7 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:61582211 original size:34 final size:35
Alignment explanation
Indices: 61582085--61582212 Score: 140
Period size: 34 Copynumber: 3.7 Consensus size: 35
61582075 GAGGGAAAGG
*
61582085 AGAAGAAAGAAAGAAAGAAAAGGAA-AGGAGAAGAA
1 AGAA-AAAGAAAGAAAGAAAAAGAAGAGGAGAAGAA
* *
61582120 AGAAAAGGAGAGAAAGAAAAAGGAA-AGGAGAAGAA
1 AGAAAAAGAAAGAAAGAAAAA-GAAGAGGAGAAGAA
* *
61582155 AGAAAAAGAAAG-GAGAAGAAGAAGAGG-GAAGGAA
1 AGAAAAAGAAAGAAAGAAAAAGAAGAGGAGAA-GAA
*
61582189 GGAAAAAGAAAGAAA-AAAAAGAAG
1 AGAAAAAGAAAGAAAGAAAAAGAAG
61582213 GTAAATTTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
33 6 0.08
34 45 0.57
35 28 0.35
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (35 bp):
AGAAAAAGAAAGAAAGAAAAAGAAGAGGAGAAGAA
Found at i:61582895 original size:301 final size:301
Alignment explanation
Indices: 61582541--61583603 Score: 1503
Period size: 301 Copynumber: 3.5 Consensus size: 301
61582531 AAAAATTGTA
*
61582541 TATTTAAAAAACACACTAAA-TTAATAAAGTTCAAACATAATGTACTAAAATAATGTAAAATAAT
1 TATTTAAAAAACACACTAAATTTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
* *
61582605 AAAATTAGAAAATA-TGATATTTTCTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGG
66 AAAATTAGAAAATAGT-ATATTTTTTAAAGTAATAAAATTCGG-GAAAAAAATACGAACAAAGGG
* * * *
61582669 TCGAAGTAA-GGTTTTTTACTAAATTTAAAAAAATAATTAATTAACACATTTCAAACATAATGTA
129 CCGAAATAAGGGTTTTTTACTAAATTTAAAAAAACAATTAATTAATACATTTCAAACATAATGTA
*
61582733 CTAAAATAATGTAAAAAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTTGGG
194 CTAAAATAATGTAAAAAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTTGGA
61582798 AAAAAAATATGAGCAAAGGGCCGAAATAAGAGTTTTTTTTAATT
259 AAAAAAATATGAGCAAAGGGCCGAAATAAG-GTTTTTTTTAATT
* * * *
61582842 TATCTAAAAAATACACTAAA-TTAATAAATTTAAAACATAATATACTAAAATAATGTAAAATAAT
1 TATTTAAAAAACACACTAAATTTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
*
61582906 AAAATTAGAAAATAGTATACTTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAATGGC
66 AAAATTAGAAAATAGTATA-TTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGC
* * *
61582971 CGAAATAAGGGTTTTTTACTAAATTTTAAAACAAGAATTAATTAATACATTTCAAACATAATATA
130 CGAAATAAGGGTTTTTTACTAAA-TTTAAAAAAACAATTAATTAATACATTTCAAACATAATGTA
* * *
61583036 CTAAAATAAAT-TAAACTAATAAAATACTAAAATAATATACTTTTATTGAAAGTAATAAAATTTG
194 CTAAAAT-AATGTAAA-AAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTTG
* *
61583100 AGAAAAAAAATATGAGCAATGGGCCGAAATAAGGATTTTTTTAAAATT
257 -GAAAAAAAATATGAGCAAAGGGCCGAAATAAGG-TTTTTTT-TAATT
* * * *
61583148 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAATATAATGTACTAAAATAATTTAAACTAA
1 TATTTAAAAAACACACTAAATTTA-ATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
61583213 TAAAA-T-----AT--TATATTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGC
65 TAAAATTAGAAAATAGTATATTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGC
* *
61583270 CGAAATAAGGGTTTTTTACTAATTTTTTTTAAAAAAACAGACCTAATTAATACATTTCAAACATA
130 CGAAATAAGGGTTTTTTACTAA----ATTTAAAAAAACA-A-TTAATTAATACATTTCAAACATA
61583335 ATGTACTAAAATAATGTAAAATAATAAAATTA-GAAAATAATAT-TTTTTATTGAAAGTAATAAA
189 ATGTACTAAAATAATGTAAAA-AATAAAA-TACGAAAATAATATATTTTTATTGAAAGTAATAAA
* * * * * *
61583398 AATCGGTAAAAATATACGAGCAAAGGGGCGAAATAAGGGTTTTTTTTAAATT
252 ATTTGGAAAAAAAATATGAGCAAAGGGCCGAAATAA-GGTTTTTTTT-AATT
61583450 TATTTAAAAAA-ACACTAAATTTAATTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTAA-TAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
*
61583514 TAAAATTAGAAAATAGTATATTTTTTAAAGTAATAAAATTCGGG-AAAAAATACGAATAAAGGGC
65 TAAAATTAGAAAATAGTATATTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGC
61583578 CGAAATAAGGGTTTTTTACTAAATTT
130 CGAAATAAGGGTTTTTTACTAAATTT
61583604 TTTTTGAAGT
Statistics
Matches: 680, Mismatches: 51, Indels: 59
0.86 0.06 0.07
Matches are distributed among these distances:
299 66 0.10
300 4 0.01
301 156 0.23
302 97 0.14
303 76 0.11
304 106 0.16
305 39 0.06
306 22 0.03
307 6 0.01
308 80 0.12
309 28 0.04
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (301 bp):
TATTTAAAAAACACACTAAATTTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
AAAATTAGAAAATAGTATATTTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCC
GAAATAAGGGTTTTTTACTAAATTTAAAAAAACAATTAATTAATACATTTCAAACATAATGTACT
AAAATAATGTAAAAAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTTGGAAA
AAAAATATGAGCAAAGGGCCGAAATAAGGTTTTTTTTAATT
Found at i:61583227 original size:454 final size:452
Alignment explanation
Indices: 61582541--61583594 Score: 1222
Period size: 454 Copynumber: 2.3 Consensus size: 452
61582531 AAAAATTGTA
* * *
61582541 TATTTAAAAAACACACTAAA-TTAA-TAAAGTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAA-ACAATAAATTTAATTAAATTTCAAACATAATATACTAAAATAATGTAAAATAA
* *
61582604 TAAAATTAGAAAAT-ATGATATTTTCTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGG
65 TAAAATTAGAAAATAAT-ATATTTTTTAAAGTAATAAAATTC-G-GAAAAAAATACGAACAAAGG
* * * * *
61582668 GTCGAAGTAAGG--TTTTTTACTAA---ATTT-AAAAA-A-A-T-AATTAATTAACACATTTCAA
127 GCCGAAATAAGGATTTTTTTA-AAATTTATTTAAAAAACACACTAAATTTATTTA-A-ATTTCAA
* * *
61582723 ACATAATGTACTAAAATAATGTAAAAAATAAAATACGAAAATAATATATTTTTATTGAAAGTAAT
189 ATATAATGTACTAAAATAAT-T-TAAACT--AAT---AAAATAATATA-TTTT-TT-AAAGTAAT
* * * *
61582788 AAAATTTGGGAAAAAAATATGAGCAAAGGGCCGAAATAAGAGTTTTTT-TTAA-TTTATCTAAAA
244 AAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTACTAATTTTATCTAAAA
61582851 AATAC-A-CTAAATTAATAAATTTAAAACATAATATACTAAAATAATGTAAAATAATAAAATTAG
309 AA-ACAACCT-AATTAATAAATTTAAAACATAATATACTAAAATAATGTAAAATAATAAAATTAG
* * *
61582914 AAAATAGTATACTTTT-TT-AAAGTAATAAAATTCGGGAAAAAAATACGAACAAATGGCCGAAAT
372 AAAATAATAT-CTTTTATTGAAAGTAATAAAAATCGGGAAAAAAATACGAACAAAGGGCCGAAAT
61582977 AAGGGTTTTTTACTAAA-
436 AAGGGTTTTTT-CTAAAT
* * * * *
61582994 T-TTTAAAACAAGAATTAA-TTAA-TACATTTCAAACATAATATACTAAAATAAAT-TAAACTAA
1 TATTTAAAAAAACAATAAATTTAATTAAATTTCAAACATAATATACTAAAAT-AATGTAAAATAA
* * * *
61583055 TAAAA-TACTAAAATAATATACTTTTATTGAAAGTAATAAAATTTGAGAAAAAAAATATGAGCAA
65 TAAAATTA-GAAAATAATATA-TTTT-TT-AAAGTAATAAAATTCG-G-AAAAAAATACGAACAA
*
61583119 TGGGCCGAAATAAGGATTTTTTTAAAATTTATTTAAAAAACACACTAAATTTATTTAAATTTCAA
124 AGGGCCGAAATAAGGATTTTTTTAAAATTTATTTAAAAAACACACTAAATTTATTTAAATTTCAA
*
61583184 ATATAATGTACTAAAATAATTTAAACTAATAAAATATTATATTTTTTAAAGTAATAAAATTCGGG
189 ATATAATGTACTAAAATAATTTAAACTAATAAAATAATATATTTTTTAAAGTAATAAAATTCGGG
* * *
61583249 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAATTTTTTTTAAAAAAACAGACCT
254 AAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTACTAATTTTATCTAAAAAAACA-ACCT
* * * *
61583314 AATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATT
318 AATTAATAAATTTAAAACATAATATACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATC
* * * * *
61583379 TTTTATTGAAAGTAATAAAAATCGGTAAAAATATACGAGCAAAGGGGCGAAATAAGGGTTTTTTT
383 TTTTATTGAAAGTAATAAAAATCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTC
61583444 TAAATT
448 TAAA-T
* *
61583450 TATTTAAAAAAACACTAAATTTAATTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
1 TATTTAAAAAAACAATAAATTTAATTAAATTTCAAACATAATATACTAAAATAATGTAAAATAAT
* * *
61583515 AAAATTAGAAAATAGTATATTTTTTAAAGTAATAAAATTCGGGAAAAAATACGAATAAAGGGCCG
66 AAAATTAGAAAATAATATATTTTTTAAAGTAATAAAATTCGGAAAAAAATACGAACAAAGGGCCG
*
61583580 AAATAAGGGTTTTTT
131 AAATAAGGATTTTTT
61583595 ACTAAATTTT
Statistics
Matches: 511, Mismatches: 59, Indels: 61
0.81 0.09 0.10
Matches are distributed among these distances:
450 2 0.00
451 105 0.21
452 24 0.05
453 24 0.05
454 148 0.29
455 55 0.11
456 23 0.05
457 18 0.04
458 15 0.03
459 56 0.11
460 4 0.01
461 27 0.05
462 2 0.00
463 8 0.02
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.31
Consensus pattern (452 bp):
TATTTAAAAAAACAATAAATTTAATTAAATTTCAAACATAATATACTAAAATAATGTAAAATAAT
AAAATTAGAAAATAATATATTTTTTAAAGTAATAAAATTCGGAAAAAAATACGAACAAAGGGCCG
AAATAAGGATTTTTTTAAAATTTATTTAAAAAACACACTAAATTTATTTAAATTTCAAATATAAT
GTACTAAAATAATTTAAACTAATAAAATAATATATTTTTTAAAGTAATAAAATTCGGGAAAAAAA
TACGAACAAAGGGCCGAAATAAGAGTTTTTTACTAATTTTATCTAAAAAAACAACCTAATTAATA
AATTTAAAACATAATATACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATCTTTTATTG
AAAGTAATAAAAATCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTCTAAAT
Found at i:61583415 original size:156 final size:153
Alignment explanation
Indices: 61582716--61583608 Score: 985
Period size: 152 Copynumber: 5.8 Consensus size: 153
61582706 TAATTAACAC
61582716 ATTTCAAACATAATGTACTAAAATAATGTAAAA-AATAAAA-TACGAAAATAATATATTTTTATT
1 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTA-GAAAATAATATA-TTTT-TT
* * * * *
61582779 GAAAGTAATAAAATTTGGGAAAAAAATATGAGCAAAGGGCCGAAATAAGAGTTTTTT-TTAA-TT
63 -AAAGTAATAAAATTCGGG-AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAATTT
* *
61582842 TATCTAAAAAATACACTAAA-TTAA-TAA
126 TTTTTAAAAAA-ACACTAAATTTAATTAA
* * *
61582869 ATTTAAAACATAATATACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATACTTTTTTAA
1 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATA-TTTTTTAA
* *
61582934 AGTAATAAAATTCGGGAAAAAAATACGAACAAATGGCCGAAATAAGGGTTTTTTACTAA---ATT
65 AGTAATAAAATTCGGG-AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAATTTTTT
* * * * *
61582996 TTAAAACAAGAATTAA-TTAA-TAC
129 TTAAAAAAACACTAAATTTAATTAA
* * *
61583019 ATTTCAAACATAATATACTAAAATAAAT-TAAACTAATAAAA-TACTAAAATAATATACTTTTAT
1 ATTTCAAACATAATGTACTAAAAT-AATGTAAAATAATAAAATTA-GAAAATAATATA-TTTT-T
* * * * * *
61583082 TGAAAGTAATAAAATTTGAGAAAAAAAATATGAGCAATGGGCCGAAATAAGGATTTTTT--TAAA
62 T-AAAGTAATAAAATTCG-G-GAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACT-AA
* * *
61583145 ATTTATTTAAAAAACACACTAAATTTATTTAA
123 TTTTTTTTAAAAAA-ACACTAAATTTAATTAA
* * *
61583177 ATTTCAAATATAATGTACTAAAATAATTTAAACTAATAAAA-T-----AT--TATATTTTTTAAA
1 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTAAA
61583234 GTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAATTTTTTT
66 GTAATAAAATTCGGG-AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAATTTTTTT
*
61583299 TAAAAAAACAGACCT-AA-TTAA-TAC
130 TAAAAAAAC--A-CTAAATTTAATTAA
*
61583323 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATTTTTTATTGA
1 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTT-TT-A
* * * * * * *
61583388 AAGTAATAAAAATCGGTAAAAATATACGAGCAAAGGGGCGAAATAAGGGTTTTTT-TTAAATTTA
64 AAGTAATAAAATTCGGGAAAAA-ATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAATTTTT
61583452 TTTAAAAAAACACTAAATTTAATTAA
128 TTTAAAAAAACACTAAATTTAATTAA
*
61583478 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTTAAA
1 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTAAA
*
61583543 GTAATAAAATTCGGGAAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTTACTAAATTTTTTT
66 GTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACT-AATTTTTTT
61583608 T
130 T
61583609 GAAGTTGCAG
Statistics
Matches: 630, Mismatches: 71, Indels: 77
0.81 0.09 0.10
Matches are distributed among these distances:
146 76 0.12
147 33 0.05
148 6 0.01
149 8 0.01
150 65 0.10
151 13 0.02
152 103 0.16
153 94 0.15
154 43 0.07
155 94 0.15
156 51 0.08
157 6 0.01
158 38 0.06
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (153 bp):
ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTAAA
GTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAATTTTTTTT
AAAAAAACACTAAATTTAATTAA
Found at i:61588726 original size:23 final size:23
Alignment explanation
Indices: 61588681--61588727 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
61588671 TAAAAATAAT
*
61588681 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
61588704 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
61588727 A
1 A
61588728 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:61588948 original size:24 final size:26
Alignment explanation
Indices: 61588916--61588965 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
61588906 AACTAAACTA
*
61588916 ACAACAAAAAATAATAA-AA-ATAAT
1 ACAAAAAAAAATAATAACAAGATAAT
*
61588940 ACAAAAAAACATAATAACAAGATAAT
1 ACAAAAAAAAATAATAACAAGATAAT
61588966 CCATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 2 0.09
26 5 0.23
ACGTcount: A:0.72, C:0.10, G:0.02, T:0.16
Consensus pattern (26 bp):
ACAAAAAAAAATAATAACAAGATAAT
Found at i:61589045 original size:3 final size:3
Alignment explanation
Indices: 61589039--61589069 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
61589029 CCTCCTCATC
*
61589039 CTT CTT CTT CTT CTT CTT CTT CTT CTC CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
61589070 AGCTGGACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:61589150 original size:27 final size:27
Alignment explanation
Indices: 61589101--61589187 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
61589091 ATAATACAAG
* * **
61589101 TGGTGCCGCCTGTGGCAGTGGCACCTT
1 TGGTGCCGCCTCTGACACAGGCACCTT
61589128 TGGTGCCGCCTCTGACACAGGCACCTT
1 TGGTGCCGCCTCTGACACAGGCACCTT
*
61589155 TGGTGCCGCCTCTGCCACAGGCACCTT
1 TGGTGCCGCCTCTGACACAGGCACCTT
61589182 TGGTGC
1 TGGTGC
61589188 TGCTTGTGGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.10, C:0.34, G:0.31, T:0.24
Consensus pattern (27 bp):
TGGTGCCGCCTCTGACACAGGCACCTT
Found at i:61590219 original size:18 final size:18
Alignment explanation
Indices: 61590198--61590232 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61590188 AATTAATTAA
*
61590198 TTTTATAAAATTTAAAAT
1 TTTTAAAAAATTTAAAAT
61590216 TTTTAAAAAATTTAAAA
1 TTTTAAAAAATTTAAAA
61590233 AAAATTAAAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTAAAAAATTTAAAAT
Found at i:61590925 original size:23 final size:24
Alignment explanation
Indices: 61590887--61590934 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
61590877 TTCTTGATTG
* *
61590887 AATTAAAACAATTATATAAAAATA
1 AATTAAAACAAATATAGAAAAATA
*
61590911 AATT-AAACAAATATAGAAATATA
1 AATTAAAACAAATATAGAAAAATA
61590934 A
1 A
61590935 TCTTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (24 bp):
AATTAAAACAAATATAGAAAAATA
Found at i:61595754 original size:21 final size:21
Alignment explanation
Indices: 61595728--61595770 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
61595718 TTGGAAAAGT
61595728 ACTAAGTCTCGTTTGAACCTA
1 ACTAAGTCTCGTTTGAACCTA
61595749 ACTAAGTCTCGTTTGAACCTA
1 ACTAAGTCTCGTTTGAACCTA
61595770 A
1 A
61595771 GAAATTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (21 bp):
ACTAAGTCTCGTTTGAACCTA
Found at i:61595913 original size:25 final size:25
Alignment explanation
Indices: 61595851--61595913 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
61595841 GACACACCAC
*
61595851 AGCTCGCAAGAGCATCCCATTATTT
1 AGCTCGAAAGAGCATCCCATTATTT
** *
61595876 AGCTCTTATGAGCATCCCATT-TTAT
1 AGCTCGAAAGAGCATCCCATTATT-T
*
61595901 GGCTCGAAAGAGC
1 AGCTCGAAAGAGC
61595914 TTCCTGATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
24 2 0.07
25 28 0.93
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (25 bp):
AGCTCGAAAGAGCATCCCATTATTT
Found at i:61597802 original size:42 final size:42
Alignment explanation
Indices: 61597756--61597848 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
61597746 GTGATAAATA
* * **
61597756 GAAACCCGTAAGGGTTGAACAGAAGCTCGTAAGAG-TTGAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTT-AACG
61597798 GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTTAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTTAACG
61597840 GAAACCCAT
1 GAAACCCAT
61597849 TAGAGTTGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTTAACG
Found at i:61597887 original size:21 final size:21
Alignment explanation
Indices: 61597741--61597906 Score: 84
Period size: 21 Copynumber: 7.9 Consensus size: 21
61597731 AATAGAAGCA
* * * *
61597741 CATAAGTGATAAATAGAAACC
1 CATAAGAGTTAAACAGAAACT
* * * *
61597762 CGTAAGGGTTGAACAGAAGCT
1 CATAAGAGTTAAACAGAAACT
* * * *
61597783 CGTAAGAGTTGAACGGAAACC
1 CATAAGAGTTAAACAGAAACT
* *
61597804 CATAAGGGTTAAACAGAAGCT
1 CATAAGAGTTAAACAGAAACT
* * *
61597825 CAAAAGAGCTT-AACGGAAACC
1 CATAAGAG-TTAAACAGAAACT
* *
61597846 CATTAGAGTTGAAC-GAAAACT
1 CATAAGAGTTAAACAG-AAACT
*
61597867 CATATGAGTTAAACAGAAACT
1 CATAAGAGTTAAACAGAAACT
* * * *
61597888 CGTGACAGCTAAACAGAAA
1 CATAAGAGTTAAACAGAAA
61597907 GTAAACACTA
Statistics
Matches: 108, Mismatches: 33, Indels: 8
0.72 0.22 0.05
Matches are distributed among these distances:
20 3 0.03
21 102 0.94
22 3 0.03
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
CATAAGAGTTAAACAGAAACT
Found at i:61599858 original size:40 final size:40
Alignment explanation
Indices: 61599799--61599875 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
61599789 TATTCACACG
61599799 ACCTAGCACACGAGCGTGTGGCTTGGCCGAGTGACCCTGC
1 ACCTAGCACACGAGCGTGTGGCTTGGCCGAGTGACCCTGC
* * * *
61599839 ACCTAGCACATGGGTGTGTGGCTTGGCCGTGTGACCC
1 ACCTAGCACACGAGCGTGTGGCTTGGCCGAGTGACCC
61599876 AAGTCAGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.16, C:0.30, G:0.34, T:0.21
Consensus pattern (40 bp):
ACCTAGCACACGAGCGTGTGGCTTGGCCGAGTGACCCTGC
Found at i:61600567 original size:23 final size:22
Alignment explanation
Indices: 61600524--61600567 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
61600514 TTTCAAGTCA
61600524 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
61600547 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
61600568 TTAATTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:61600817 original size:51 final size:51
Alignment explanation
Indices: 61600731--61600931 Score: 221
Period size: 51 Copynumber: 4.0 Consensus size: 51
61600721 ATAAATTATA
* * * * *
61600731 CCGGTTCACATAGTAGCCTGCACGTAGTAATACACATGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* * *
61600782 CCGATACACGTAGTAGCCTGCACAAAGTACTACACACGTGATCGA--AGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT
** * * *
61600833 CCGGTATGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
*
61600883 CTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
61600932 TCACTTTCAC
Statistics
Matches: 122, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
49 4 0.03
50 41 0.34
51 74 0.61
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:61600920 original size:101 final size:102
Alignment explanation
Indices: 61600739--61600923 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
61600729 TACCGGTTCA
* *
61600739 CATAGTAGCCTGCACGTAGTAATACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTAATACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
61600804 CAAAGTACTACACACGTGATCGAAGCTATCCGGTATG
66 CAAAGTACTACACACGTGATCGAAGCTATCCGGTATG
* * *
61600841 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTAATACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
*
61600904 ACATAGTACTACACACGTGA
65 ACAAAGTACTACACACGTGA
61600924 CCATCACTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 39 0.51
102 33 0.43
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTAATACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CAAAGTACTACACACGTGATCGAAGCTATCCGGTATG
Found at i:61602503 original size:28 final size:28
Alignment explanation
Indices: 61602463--61602518 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
61602453 GAACAAGTTA
61602463 ACCAATGGTCTAATTACCATTTAAGGAC
1 ACCAATGGTCTAATTACCATTTAAGGAC
61602491 ACCAATGGTCTAATTACCATTTAAGGAC
1 ACCAATGGTCTAATTACCATTTAAGGAC
61602519 CTCCAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (28 bp):
ACCAATGGTCTAATTACCATTTAAGGAC
Found at i:61611563 original size:50 final size:50
Alignment explanation
Indices: 61611461--61611700 Score: 221
Period size: 50 Copynumber: 4.7 Consensus size: 50
61611451 TAAAAAGATT
61611461 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTGTGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAGA---TGAGAGGTC
* *
61611517 CCATGTAAGACCATGTCTAGGACATGGCGTTGGCACTGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
** * * * * **
61611567 CCCCGTAAGACCATGTCTGGGACATGGCATAGGTACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
** * * * * * * **
61611617 CCATGTAAGACCATACCTGGGATATGGCATTGGTAGT-ACAAGAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
* *
61611666 CCATGTAATACCATGTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
61611701 TATTATTATC
Statistics
Matches: 153, Mismatches: 31, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
49 36 0.24
50 78 0.51
53 5 0.03
55 1 0.01
56 33 0.22
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
Found at i:61614295 original size:29 final size:29
Alignment explanation
Indices: 61614239--61614295 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
61614229 TTAAAAGAAA
*
61614239 TTATAGAAATAGGCCAAATTTTTGAAAAT
1 TTATAGAAATAGGCCAAATTTTGGAAAAT
* *
61614268 TTATAGAAATGGGCC-GATTTTGGTAAAA
1 TTATAGAAATAGGCCAAATTTTGG-AAAA
61614296 CGCTTATGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (29 bp):
TTATAGAAATAGGCCAAATTTTGGAAAAT
Found at i:61616446 original size:62 final size:59
Alignment explanation
Indices: 61616357--61616525 Score: 153
Period size: 59 Copynumber: 2.8 Consensus size: 59
61616347 CACTTTTTGT
* ** * *
61616357 GACC-TGAACTTGGTAATTTTTGTCACATTGGAGCCTGAATTTTTTATTATTATCTAAACTA
1 GACCTTGAACTTGGTAATTATTCCCACATTGGAGCCTGAA-CTTTT-TT-TTATCCAAACTA
* * * * **
61616418 GGCCTTGAACTTGGTAATTATTCCCACATTGGGGCTTGGACTTTTTTTTATCCAAGTTA
1 GACCTTGAACTTGGTAATTATTCCCACATTGGAGCCTGAACTTTTTTTTATCCAAACTA
** * *
61616477 GACCTTGAACTTGACAATTATTCCCACATTGG-GACTTGACCTTTTTTTT
1 GACCTTGAACTTGGTAATTATTCCCACATTGGAG-CCTGAACTTTTTTTT
61616526 TGTCCAAGTT
Statistics
Matches: 90, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
58 1 0.01
59 51 0.57
60 2 0.02
61 7 0.08
62 29 0.32
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (59 bp):
GACCTTGAACTTGGTAATTATTCCCACATTGGAGCCTGAACTTTTTTTTATCCAAACTA
Found at i:61616498 original size:59 final size:60
Alignment explanation
Indices: 61616420--61616536 Score: 175
Period size: 59 Copynumber: 2.0 Consensus size: 60
61616410 CTAAACTAGG
** *
61616420 CCTTGAACTTGGTAATTATTCCCACATTGGGGCTTGGA-C-TTTTTTTTATCCAAGTTAGA
1 CCTTGAACTTGACAATTATTCCCACATTGGGACTT-GACCTTTTTTTTTATCCAAGTTAGA
*
61616479 CCTTGAACTTGACAATTATTCCCACATTGGGACTTGACCTTTTTTTTTGTCCAAGTTA
1 CCTTGAACTTGACAATTATTCCCACATTGGGACTTGACCTTTTTTTTTATCCAAGTTA
61616537 ATCCTTGGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 2 0.04
59 33 0.63
60 17 0.33
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (60 bp):
CCTTGAACTTGACAATTATTCCCACATTGGGACTTGACCTTTTTTTTTATCCAAGTTAGA
Found at i:61617646 original size:20 final size:20
Alignment explanation
Indices: 61617602--61617649 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
61617592 ATATCTTTAT
* * *
61617602 AAATTTAAATGATTAAATTA
1 AAATTTTAAGGATTAAAGTA
61617622 AAATTTTAAGGATTAAAGTA
1 AAATTTTAAGGATTAAAGTA
*
61617642 TAATTTTA
1 AAATTTTA
61617650 TTATTATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (20 bp):
AAATTTTAAGGATTAAAGTA
Found at i:61621406 original size:17 final size:17
Alignment explanation
Indices: 61621384--61621418 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
61621374 TAATTAAGTT
61621384 AATTTTAAAGTTTTTAA
1 AATTTTAAAGTTTTTAA
*
61621401 AATTTTAAATTTTTTAA
1 AATTTTAAAGTTTTTAA
61621418 A
1 A
61621419 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTTAAAGTTTTTAA
Found at i:61632562 original size:11 final size:11
Alignment explanation
Indices: 61632546--61632574 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
61632536 CACTTTCATT
61632546 GCAACCAAGTG
1 GCAACCAAGTG
61632557 GCAACCAAGTG
1 GCAACCAAGTG
61632568 GCAACCA
1 GCAACCA
61632575 CACTAAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.24, T:0.07
Consensus pattern (11 bp):
GCAACCAAGTG
Found at i:61635566 original size:17 final size:18
Alignment explanation
Indices: 61635530--61635564 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61635520 ATAAGCATAC
*
61635530 ATTGTCATTGCATTTTTT
1 ATTGTCATTACATTTTTT
61635548 ATTGTCATTACATTTTT
1 ATTGTCATTACATTTTT
61635565 ATGTTAGTGC
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:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (18 bp):
ATTGTCATTACATTTTTT
Found at i:61640892 original size:5 final size:5
Alignment explanation
Indices: 61640882--61640908 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
61640872 ATGGAGGAAG
61640882 GATAT GATAT GATAT GATAT GATAT GA
1 GATAT GATAT GATAT GATAT GATAT GA
61640909 GAGATGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (5 bp):
GATAT
Found at i:61646013 original size:26 final size:26
Alignment explanation
Indices: 61645984--61646042 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
61645974 GTAAGTGATT
61645984 TGAAACTGATACATGCTATGATATTC
1 TGAAACTGATACATGCTATGATATTC
* *
61646010 TGAAACTGATATATGTTATGATATTC
1 TGAAACTGATACATGCTATGATATTC
61646036 TGAAACT
1 TGAAACT
61646043 AGTGTAGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (26 bp):
TGAAACTGATACATGCTATGATATTC
Found at i:61658783 original size:5 final size:5
Alignment explanation
Indices: 61658773--61658838 Score: 69
Period size: 5 Copynumber: 12.8 Consensus size: 5
61658763 GGGGTAGGAC
* * * *
61658773 ATGAT ATGAT ATGAT ATGTT ATGTT ATGAT ATGAGAT ATGAT AAGAT ATCAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT AT--GAT ATGAT ATGAT ATGAT
*
61658825 ATGAT AAGAT ATGA
1 ATGAT ATGAT ATGA
61658839 AATGTACTAC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
5 46 0.90
7 5 0.10
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.38
Consensus pattern (5 bp):
ATGAT
Found at i:61659362 original size:24 final size:24
Alignment explanation
Indices: 61659313--61659362 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
61659303 TTTTCCTTTG
*
61659313 TTAGGCTTGGCCTTGCCATTATCC
1 TTAGGCTTGGCCTTGCCATTAGCC
* *
61659337 TTAGGCTTTGCTTTAGCC-TTAGCC
1 TTAGGCTTGGCCTT-GCCATTAGCC
61659361 TT
1 TT
61659363 TCCTTTGCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.12, C:0.26, G:0.20, T:0.42
Consensus pattern (24 bp):
TTAGGCTTGGCCTTGCCATTAGCC
Found at i:61661608 original size:88 final size:88
Alignment explanation
Indices: 61661495--61661667 Score: 294
Period size: 88 Copynumber: 2.0 Consensus size: 88
61661485 ATTCTTTCCA
61661495 AAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAATATAACTATTTATAT
1 AAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAATATAACTATTTATAT
*
61661560 TAACAAAATT-GGTAAAATATTTC
66 TAA-AAAATTCAGTAAAATATTTC
* *
61661583 AAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAATATAACTATTTATAT
1 AAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAATATAACTATTTATAT
*
61661648 TAATAAATTCAGTAAAATAT
66 TAAAAAATTCAGTAAAATAT
61661668 ATACAATTAA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 5 0.06
88 75 0.94
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (88 bp):
AAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAATATAACTATTTATAT
TAAAAAATTCAGTAAAATATTTC
Found at i:61663047 original size:24 final size:24
Alignment explanation
Indices: 61662994--61663051 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
61662984 GGTGCAGATG
* *
61662994 AAGATGAAGACGAGGGTCGAGTTG
1 AAGATGAAGACGAGGGTCGAGGTA
* *
61663018 ATGATGAATAC-AGAGGTCGAGGTA
1 AAGATGAAGACGAG-GGTCGAGGTA
61663042 AAGATGAAGA
1 AAGATGAAGA
61663052 AGATAATCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.40, C:0.07, G:0.36, T:0.17
Consensus pattern (24 bp):
AAGATGAAGACGAGGGTCGAGGTA
Found at i:61665030 original size:323 final size:323
Alignment explanation
Indices: 61664436--61665083 Score: 1188
Period size: 323 Copynumber: 2.0 Consensus size: 323
61664426 TTTTAGGATA
* * * *
61664436 TGCATTTTCAGTAGACGCATGCTTCAAAGGGTCTTTAGTGTGCTTGAAAATGTACCCGGGATTAT
1 TGCATTTACAGTAGACGCATGCTTCAAAGGGTCTTTAATCTGCTTGAAAATGTACCCGAGATTAT
61664501 TGGGGTAAGGGATCTTAGCAGGATTTGAATTATGATGGATAGAAAGCGCGTCGAGTTGGGCGAGC
66 TGGGGTAAGGGATCTTAGCAGGATTTGAATTATGATGGATAGAAAGCGCGTCGAGTTGGGCGAGC
61664566 TTTCCTACTGACACGTTAGGGAAAGCACGCCTACCTAGACGCATTTTCCACTAGATACAAAGAAA
131 TTTCCTACTGACACGTTAGGGAAAGCACGCCTACCTAGACGCATTTTCCACTAGATACAAAGAAA
* * *
61664631 GCATGTTCAGCTAAGCGCGCTATCCCTGACATGTTAGCAGAAAAGCTCGCCCAGCTGAACGTGCT
196 GCACGTTCAGCTAAGCGCGCTATCCCTGACATGTCAGCAGAAAAGCTCACCCAGCTGAACGTGCT
*
61664696 TTCTGTCCACCACCATTCAAAGCCTACCAAGGTGCCCGGAGCCTGGGAATCATGGGTAAGATT
261 TTCTATCCACCACCATTCAAAGCCTACCAAGGTGCCCGGAGCCTGGGAATCATGGGTAAGATT
61664759 TGCATTTACAGTAGACGCATGCTTCAAAGGGTCTTTAATCTGCTTGAAAATGTACCCGAGATTAT
1 TGCATTTACAGTAGACGCATGCTTCAAAGGGTCTTTAATCTGCTTGAAAATGTACCCGAGATTAT
61664824 TGGGGTAAGGGATCTTAGCAGGATTTGAATTATGATGGATAGAAAGCGCGTCGAGTTGGGCGAGC
66 TGGGGTAAGGGATCTTAGCAGGATTTGAATTATGATGGATAGAAAGCGCGTCGAGTTGGGCGAGC
* *
61664889 TTTCCTACTGACACGTTAGGGAAAGCACGCCTACCTAGACGTATTTTCCACTAGATACAAAGAAT
131 TTTCCTACTGACACGTTAGGGAAAGCACGCCTACCTAGACGCATTTTCCACTAGATACAAAGAAA
* *
61664954 GCACGTTCAGCTAAGCGTGCTATCCCTGACATGTCAGCAGGAAAGCTCACCCAGCTGAACGTGCT
196 GCACGTTCAGCTAAGCGCGCTATCCCTGACATGTCAGCAGAAAAGCTCACCCAGCTGAACGTGCT
61665019 TTCTATCCACCACCATTCAAAGCCTACCAAGGTGCCCGGAGCCTGGGAATCATGGGTAAGATT
261 TTCTATCCACCACCATTCAAAGCCTACCAAGGTGCCCGGAGCCTGGGAATCATGGGTAAGATT
61665082 TG
1 TG
61665084 AGGCACCTCT
Statistics
Matches: 313, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
323 313 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (323 bp):
TGCATTTACAGTAGACGCATGCTTCAAAGGGTCTTTAATCTGCTTGAAAATGTACCCGAGATTAT
TGGGGTAAGGGATCTTAGCAGGATTTGAATTATGATGGATAGAAAGCGCGTCGAGTTGGGCGAGC
TTTCCTACTGACACGTTAGGGAAAGCACGCCTACCTAGACGCATTTTCCACTAGATACAAAGAAA
GCACGTTCAGCTAAGCGCGCTATCCCTGACATGTCAGCAGAAAAGCTCACCCAGCTGAACGTGCT
TTCTATCCACCACCATTCAAAGCCTACCAAGGTGCCCGGAGCCTGGGAATCATGGGTAAGATT
Found at i:61668951 original size:15 final size:15
Alignment explanation
Indices: 61668931--61668963 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
61668921 ACATATTAAA
61668931 TTTGTATGTTTT-TTT
1 TTTGTAT-TTTTCTTT
61668946 TTTGTATTTTTCTTT
1 TTTGTATTTTTCTTT
61668961 TTT
1 TTT
61668964 CTACGTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.06, C:0.03, G:0.09, T:0.82
Consensus pattern (15 bp):
TTTGTATTTTTCTTT
Found at i:61670588 original size:17 final size:17
Alignment explanation
Indices: 61670566--61670601 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
61670556 ATACCGTTTA
61670566 ATCAATGTTATTAGGAT
1 ATCAATGTTATTAGGAT
61670583 ATCAATGTTATTAGGAT
1 ATCAATGTTATTAGGAT
61670600 AT
1 AT
61670602 TGAGTTGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (17 bp):
ATCAATGTTATTAGGAT
Found at i:61670769 original size:27 final size:27
Alignment explanation
Indices: 61670739--61670796 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
61670729 TTTTAACCGA
61670739 AACTGAATCCCAACTCAACCACGTCTG
1 AACTGAATCCCAACTCAACCACGTCTG
61670766 AACTGAATCCCAACTCAACCACGTCTG
1 AACTGAATCCCAACTCAACCACGTCTG
61670793 AACT
1 AACT
61670797 CATTTACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.34, C:0.36, G:0.10, T:0.19
Consensus pattern (27 bp):
AACTGAATCCCAACTCAACCACGTCTG
Found at i:61674264 original size:22 final size:24
Alignment explanation
Indices: 61674236--61674297 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 24
61674226 TAAGCCCAGT
61674236 TAGCCCAAACCCAAA-ATTAA-CC
1 TAGCCCAAACCCAAACATTAAGCC
*
61674258 TAGCCCAAACCTAAACCCATTAAGCC
1 TAGCCCAAACCCAAA--CATTAAGCC
*
61674284 TAGCCCCAACCCAA
1 TAGCCCAAACCCAA
61674298 TCAGCCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 14 0.42
25 5 0.15
26 14 0.42
ACGTcount: A:0.40, C:0.40, G:0.06, T:0.13
Consensus pattern (24 bp):
TAGCCCAAACCCAAACATTAAGCC
Found at i:61679966 original size:39 final size:40
Alignment explanation
Indices: 61679910--61679994 Score: 95
Period size: 39 Copynumber: 2.1 Consensus size: 40
61679900 CAAATTCAAA
* *
61679910 AAAAAATCAGAAACAAAAAAGAGAA-GAAAAAAGA-AAAAT
1 AAAAAATCAGAAAC-AAAAAGAAAATGAAAAAAGAGAAAAG
* *
61679949 AAAAAATCA-AAGTCAAAATGAAAATGAAAAAAGAGAAAAG
1 AAAAAATCAGAA-ACAAAAAGAAAATGAAAAAAGAGAAAAG
61679989 AAAAAA
1 AAAAAA
61679995 GGAAAAGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
38 10 0.26
39 19 0.49
40 10 0.26
ACGTcount: A:0.75, C:0.05, G:0.13, T:0.07
Consensus pattern (40 bp):
AAAAAATCAGAAACAAAAAGAAAATGAAAAAAGAGAAAAG
Found at i:61679999 original size:13 final size:13
Alignment explanation
Indices: 61679924--61680003 Score: 56
Period size: 13 Copynumber: 6.2 Consensus size: 13
61679914 AATCAGAAAC
*
61679924 AAAAAA-GAGAAG
1 AAAAAAGGAAAAG
* *
61679936 AAAAAAGAAAAAT
1 AAAAAAGGAAAAG
**
61679949 AAAAAA-TCAAAG
1 AAAAAAGGAAAAG
** *
61679961 TCAAAATGAAAATG
1 AAAAAAGGAAAA-G
61679975 AAAAAAGAGAAAAG
1 AAAAAAG-GAAAAG
61679989 AAAAAAGGAAAAG
1 AAAAAAGGAAAAG
61680002 AA
1 AA
61680004 GAGGCCAAGG
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
12 13 0.25
13 20 0.39
14 13 0.25
15 5 0.10
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.06
Consensus pattern (13 bp):
AAAAAAGGAAAAG
Found at i:61680218 original size:35 final size:35
Alignment explanation
Indices: 61680178--61680247 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
61680168 ATCAAATGGA
61680178 TAGAGGCTACTGCATGCGTCAATGTCATCATATGC
1 TAGAGGCTACTGCATGCGTCAATGTCATCATATGC
61680213 TAGAGGCTACTGCATGCGTCAATGTCATCATATGC
1 TAGAGGCTACTGCATGCGTCAATGTCATCATATGC
61680248 CGATGGTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (35 bp):
TAGAGGCTACTGCATGCGTCAATGTCATCATATGC
Found at i:61682309 original size:87 final size:87
Alignment explanation
Indices: 61682158--61682513 Score: 586
Period size: 87 Copynumber: 4.1 Consensus size: 87
61682148 AGATCAGTGA
* *
61682158 AGATTGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
61682223 CTTCCTGCATTAACAGCGAAAC
66 CTTCCTGCATTGACAGCGAAGC
*
61682245 AGATCGAAAACAAAGACTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
61682310 CTTCCTGCATTGACAGCGAAGC
66 CTTCCTGCATTGACAGCGAAGC
* *
61682332 AGATCGAAAACAAAGCCTTGCCTCCATCGGTCGCAGTGGAGCTGGTTAAAGATAACAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
61682397 CTTCCTGCATTGATAGCGAAGC
66 CTTCCTGCATTGACAGCGAAGC
*
61682419 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * * * *
61682484 CCTCTTGCGTCGACAGTGAAGC
66 CTTCCTGCATTGACAGCGAAGC
61682506 AGATCGAA
1 AGATCGAA
61682514 GACGGCGAAT
Statistics
Matches: 250, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 250 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.23
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCATTGACAGCGAAGC
Found at i:61682354 original size:43 final size:43
Alignment explanation
Indices: 61682305--61682441 Score: 109
Period size: 42 Copynumber: 3.2 Consensus size: 43
61682295 GATAGCAGAT
*
61682305 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGC
* * * * * * * * * *
61682348 CTTGCC-TCCAT-CGGTCG-CAGTGGAGCTGGTTAAAGATAACAGAT
1 CTTGCCTTCC-TGC-ATTGACAGCGAAGCAGATCAAAAACAA-AG-C
*
61682392 CTTGCCTTCCTGCATTGATAGCGAAGCAGATCAAAAACAAAGC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGC
61682435 CTTGCCT
1 CTTGCCT
61682442 CCATCGGTTG
Statistics
Matches: 65, Mismatches: 22, Indels: 14
0.64 0.22 0.14
Matches are distributed among these distances:
42 18 0.28
43 18 0.28
44 11 0.17
45 18 0.28
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGC
Found at i:61682726 original size:130 final size:131
Alignment explanation
Indices: 61682503--61682920 Score: 640
Period size: 131 Copynumber: 3.2 Consensus size: 131
61682493 TCGACAGTGA
* *
61682503 AGCAGATCGAAGACGGCGAATCTTATCTTCCCCAAGAGTAGGAAAACAGATTTAAGCCACAAGTC
1 AGCAGATCGAAGACGGCAAATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAAGCCACAAGTC
* *
61682568 CTATGTCCCTGACCAGCAGTGGAGTAGGTTGGAAATTGCAGATCTTGCCTCCCTAAGCAGTAGCG
66 CTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAGTAGCG
61682633 G
131 G
* * *
61682634 AGTAGATCGAAGACGGAAAATCTTATCTTCCCCAAGAGTAGGGAAA-AGATTTAAGCCACCAGTC
1 AGCAGATCGAAGACGGCAAATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAAGCCACAAGTC
* * * *
61682698 CTATGTCCCTGACCAACATTGGAATAGGTTGAAAATTGCAGATCTTGTCTCCCTAAGTAGTAGCG
66 CTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAGTAGCG
61682763 G
131 G
* * * *
61682764 TGCAGATCGAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAACAAATTTAAGCCGCAAGTC
1 AGCAGATCGAAGACGGCAAATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAAGCCACAAGTC
* * * *
61682829 CTATGTCCCTGAGCAGCAGTGGAATAGGTTGGAAACTACAGATATTGTCTCCCTAAGCAGTAGCG
66 CTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAGTAGCG
61682894 G
131 G
**
61682895 AGCAGATCGAAGACGGTGAATCTTAT
1 AGCAGATCGAAGACGGCAAATCTTAT
61682921 ATTCAAGTGT
Statistics
Matches: 257, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
130 119 0.46
131 138 0.54
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (131 bp):
AGCAGATCGAAGACGGCAAATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAAGCCACAAGTC
CTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAGTAGCG
G
Found at i:61685200 original size:2 final size:2
Alignment explanation
Indices: 61685142--61685182 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
61685132 CATGTGCGTG
61685142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61685183 TCATTAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61685268 original size:10 final size:10
Alignment explanation
Indices: 61685249--61685278 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
61685239 TTGAAACTAA
61685249 ATATAAAAGT
1 ATATAAAAGT
*
61685259 ATATATAAGT
1 ATATAAAAGT
61685269 ATATAAAAGT
1 ATATAAAAGT
61685279 TAGGAAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (10 bp):
ATATAAAAGT
Found at i:61685394 original size:3 final size:3
Alignment explanation
Indices: 61685386--61685417 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
61685376 GCGCATAAAT
61685386 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
61685418 GATACAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:61685902 original size:23 final size:22
Alignment explanation
Indices: 61685872--61685916 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
61685862 AAATTAAATC
61685872 TCTAAGATTGCAAAATCATATCT
1 TCTAAGATTGC-AAATCATATCT
*
61685895 TCTAAGATTGCATATCATATCT
1 TCTAAGATTGCAAATCATATCT
61685917 AAGATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (22 bp):
TCTAAGATTGCAAATCATATCT
Found at i:61685919 original size:19 final size:19
Alignment explanation
Indices: 61685872--61685967 Score: 120
Period size: 19 Copynumber: 4.8 Consensus size: 19
61685862 AAATTAAATC
*
61685872 TCTAAGATTGCAAAATCATA
1 TCTAAGATTGC-ATATCATA
61685892 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTGCATATCATA
***
61685914 TCTAAGATTATTTATCATA
1 TCTAAGATTGCATATCATA
61685933 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
61685952 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
61685968 CTTGAAGATT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
19 48 0.73
22 7 0.11
23 11 0.17
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:61696575 original size:14 final size:14
Alignment explanation
Indices: 61696556--61696582 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
61696546 TGTTTGGAAC
61696556 AAATTTTACATTAT
1 AAATTTTACATTAT
61696570 AAATTTTACATTA
1 AAATTTTACATTA
61696583 CATCCTGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTTACATTAT
Found at i:61718672 original size:33 final size:32
Alignment explanation
Indices: 61718593--61718676 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
61718583 GGCTTCAGTT
*
61718593 TATATAATAT-ATATACATTTCTTTTATTATA
1 TATATAATATAATATACATTTATTTTATTATA
* **
61718624 TATATAGTATAAATATGTATTTATTTTAATGT-TA
1 TATATAATAT-AATATACATTTATTTT-AT-TATA
61718658 TATATAATATAATATACAT
1 TATATAATATAATATACAT
61718677 ATGCATGTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
31 9 0.21
33 19 0.45
34 13 0.31
35 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (32 bp):
TATATAATATAATATACATTTATTTTATTATA
Found at i:61718793 original size:25 final size:27
Alignment explanation
Indices: 61718724--61718795 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
61718714 TGGGTGTTGC
*
61718724 GTTATATAGTATATATATTTGAGTGGGTT
1 GTTATATA-TATA-ATATATGAGTGGGTT
* *
61718753 GTTGTATATATAATATATGCGTGGGTT
1 GTTATATATATAATATATGAGTGGGTT
61718780 -TTAT-TATATAATATAT
1 GTTATATATATAATATAT
61718796 ATAGGTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 12 0.31
26 3 0.08
27 13 0.33
28 4 0.10
29 7 0.18
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.49
Consensus pattern (27 bp):
GTTATATATATAATATATGAGTGGGTT
Found at i:61723346 original size:33 final size:33
Alignment explanation
Indices: 61723302--61723385 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
61723292 TGGTCTGTTG
* * *
61723302 GTTGGACTAGCTCTTATGAACACTGGTGTGATA
1 GTTGGATTAGCTCTTATGAACACTAGTATGATA
* *
61723335 GTTGGATTAGCTCTTATGAGCACTAGTATGATG
1 GTTGGATTAGCTCTTATGAACACTAGTATGATA
*
61723368 GTTGGATTAACTCTTATG
1 GTTGGATTAGCTCTTATG
61723386 TGGCATTGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (33 bp):
GTTGGATTAGCTCTTATGAACACTAGTATGATA
Found at i:61729695 original size:67 final size:63
Alignment explanation
Indices: 61729505--61729725 Score: 282
Period size: 63 Copynumber: 3.4 Consensus size: 63
61729495 GTATAATATG
*
61729505 TATATACATGTGGTTCGAATGTATGTTTCAATTTCTTTGAGCTGAATTTAATGTTATGAATTA
1 TATATATATGTGGTTCGAATGTATGTTTCAATTTCTTTGAGCTGAATTTAATGTTATGAATTA
** * * * *
61729568 TATATATATGACGTTCAAATGTATGTTACAAATTT-TTTTAGCTGAACTTAATGTTATGAATTA
1 TATATATATGTGGTTCGAATGTATGTTTC-AATTTCTTTGAGCTGAATTTAATGTTATGAATTA
* ** *
61729631 TATATACATACATGTGGTTCGAATATATGTTTCAATTTCTGCGAGCTGAATTTAATGTTGTGAAT
1 TATAT--AT--ATGTGGTTCGAATGTATGTTTCAATTTCTTTGAGCTGAATTTAATGTTATGAAT
61729696 TA
62 TA
*
61729698 TATATATATGTGGTTCGAATGTGTGTTT
1 TATATATATGTGGTTCGAATGTATGTTT
61729726 GCTATGAAGA
Statistics
Matches: 133, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
63 74 0.56
64 5 0.04
65 4 0.03
66 5 0.04
67 45 0.34
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (63 bp):
TATATATATGTGGTTCGAATGTATGTTTCAATTTCTTTGAGCTGAATTTAATGTTATGAATTA
Found at i:61734399 original size:33 final size:33
Alignment explanation
Indices: 61734362--61734480 Score: 105
Period size: 33 Copynumber: 3.3 Consensus size: 33
61734352 TCCCCCAAGG
61734362 GGTTGCTAAGTCTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTCTTGATTCCCCGATTCATTGGT
* *
61734395 GGTTGCTAAGTGC-TGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGT-CTTGATTCC-CCG-A--TT-CAT-TG---GT
* *
61734437 GGTTGCTATGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTCTTGATTCCCCGATTCATTGGT
61734470 GGTTGCTAAGT
1 GGTTGCTAAGT
61734481 GCTGATTGCA
Statistics
Matches: 68, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
33 29 0.43
34 4 0.06
35 1 0.01
36 2 0.03
37 4 0.06
38 4 0.06
39 2 0.03
40 1 0.01
41 3 0.04
42 18 0.26
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (33 bp):
GGTTGCTAAGTCTTGATTCCCCGATTCATTGGT
Found at i:61734454 original size:42 final size:41
Alignment explanation
Indices: 61734395--61734527 Score: 147
Period size: 42 Copynumber: 3.4 Consensus size: 41
61734385 ATTCATTGGT
61734395 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG-AAGG
* * * *
61734437 GGTTGCTATGTGTTGATTCC-CCG-A--TT-CAT-TG--GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
*
61734470 GGTTGCTAAGTGCTGATTGCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAA-GG
61734512 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
61734528 ATCCCCCGAG
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
33 18 0.25
34 3 0.04
35 1 0.01
36 2 0.03
37 4 0.05
38 4 0.05
39 2 0.03
40 1 0.01
41 3 0.04
42 35 0.48
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
Found at i:61734481 original size:75 final size:75
Alignment explanation
Indices: 61734358--61734533 Score: 298
Period size: 75 Copynumber: 2.3 Consensus size: 75
61734348 TGATTCCCCC
*
61734358 AAGGGGTTGCTAAGTCTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
61734423 TTAAATGTGA
66 TTAAATGTGA
* *
61734433 AAGGGGTTGCTATGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTGCACCGTATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
61734498 TTAAATGTGA
66 TTAAATGTGA
* * *
61734508 AGGGGGTTGCTAAGTGCTGAATCCCC
1 AAGGGGTTGCTAAGTGTTGATTCCCC
61734534 CGAGGGCTTG
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Done.