Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 376 of 427
Found at i:109350418 original size:15 final size:17
Alignment explanation
Indices: 109350385--109350419 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
109350375 TTGTTTGATA
109350385 AAAATAGATATTAATTT
1 AAAATAGATATTAATTT
109350402 AAAA-AGATATT-ATTT
1 AAAATAGATATTAATTT
109350417 AAA
1 AAA
109350420 TTTAATAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 7 0.39
17 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
AAAATAGATATTAATTT
Found at i:109351241 original size:22 final size:22
Alignment explanation
Indices: 109351203--109351247 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
109351193 ACATGTTAGA
* *
109351203 TGAAAACGTCTCTTGCAGGGAG
1 TGAAAACGTCTCCTGCAAGGAG
109351225 TGAAAACG-CTACCTGCAAGGAG
1 TGAAAACGTCT-CCTGCAAGGAG
109351247 T
1 T
109351248 TTTTTCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (22 bp):
TGAAAACGTCTCCTGCAAGGAG
Found at i:109357908 original size:14 final size:14
Alignment explanation
Indices: 109357889--109357925 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
109357879 AAATCGGGAA
109357889 CTTTGAAAACTTTT
1 CTTTGAAAACTTTT
109357903 CTTTGAAAACTTTT
1 CTTTGAAAACTTTT
*
109357917 CCTTGAAAA
1 CTTTGAAAA
109357926 TAAGGGCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.43
Consensus pattern (14 bp):
CTTTGAAAACTTTT
Found at i:109359851 original size:21 final size:21
Alignment explanation
Indices: 109359813--109359856 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
109359803 TTGTCTGTTC
* *
109359813 TTTCTTTCTTTTTCTATTTTA
1 TTTCTTTATTTTTCTATTATA
109359834 TTTCTTTATTCTTT-TATTATA
1 TTTCTTTATT-TTTCTATTATA
109359855 TT
1 TT
109359857 ATTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTCTTTATTTTTCTATTATA
Found at i:109360667 original size:46 final size:46
Alignment explanation
Indices: 109360602--109360770 Score: 207
Period size: 46 Copynumber: 3.7 Consensus size: 46
109360592 TTATCTTTGG
* * * * *
109360602 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTTATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTA-TTTCATAT
* *
109360648 CATGTTGCCATGGTATCTTTCAACCGTGGTCTT-GTTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTT-ATTTCATAT
* **
109360694 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTATTTCATAT
*
109360740 CAGGTTGCCATGGTATCTTTCAACCATGGTC
1 CATGTTGCCATGGTATCTTTCAACCATGGTC
109360771 CTTTCAACCA
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
45 6 0.06
46 101 0.94
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTATTTCATAT
Found at i:109360776 original size:15 final size:15
Alignment explanation
Indices: 109360756--109360785 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
109360746 GCCATGGTAT
109360756 CTTTCAACCATGGTC
1 CTTTCAACCATGGTC
109360771 CTTTCAACCATGGTC
1 CTTTCAACCATGGTC
109360786 TTACACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (15 bp):
CTTTCAACCATGGTC
Found at i:109363514 original size:46 final size:45
Alignment explanation
Indices: 109363454--109363717 Score: 346
Period size: 46 Copynumber: 6.0 Consensus size: 45
109363444 TTTGACATGA
* * * * * *
109363454 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
*** *
109363500 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
109363546 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
109363592 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT-TATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
109363636 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
109363674 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
109363718 AGAGCACACT
Statistics
Matches: 197, Mismatches: 11, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
38 34 0.17
40 3 0.02
42 3 0.02
43 1 0.01
44 36 0.18
45 4 0.02
46 116 0.59
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:109363681 original size:38 final size:39
Alignment explanation
Indices: 109363586--109363705 Score: 188
Period size: 38 Copynumber: 3.0 Consensus size: 39
109363576 ACATTTCATA
109363586 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTT
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC----T
109363629 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC-
1 -TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACT
109363668 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
109363706 ATTTCATATC
Statistics
Matches: 76, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
38 38 0.50
44 38 0.50
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (39 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACT
Found at i:109365870 original size:11 final size:11
Alignment explanation
Indices: 109365854--109365905 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
109365844 TATACTAAAT
109365854 AAATAATAATA
1 AAATAATAATA
*
109365865 AAATAAT-ATT
1 AAATAATAATA
* *
109365875 AAATATCTCATA
1 AAATA-ATAATA
*
109365887 AAATATTAATA
1 AAATAATAATA
109365898 AAATAATA
1 AAATAATA
109365906 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:109368806 original size:46 final size:45
Alignment explanation
Indices: 109368746--109369011 Score: 339
Period size: 46 Copynumber: 6.0 Consensus size: 45
109368736 TTTGACATGA
* * * * * *
109368746 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
*** *
109368792 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
109368838 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
109368884 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
109368930 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
109368968 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
109369012 AGAGCACACT
Statistics
Matches: 197, Mismatches: 13, Indels: 20
0.86 0.06 0.09
Matches are distributed among these distances:
38 34 0.17
40 3 0.02
43 1 0.01
44 3 0.02
45 4 0.02
46 149 0.76
47 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:109368975 original size:38 final size:38
Alignment explanation
Indices: 109368924--109368999 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
109368914 ACATTTTATA
109368924 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
109368962 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
109369000 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:109371164 original size:11 final size:11
Alignment explanation
Indices: 109371148--109371199 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
109371138 TATACTAAAT
109371148 AAATAATAATA
1 AAATAATAATA
*
109371159 AAATAAT-ATT
1 AAATAATAATA
* *
109371169 AAATATCTCATA
1 AAATA-ATAATA
*
109371181 AAATATTAATA
1 AAATAATAATA
109371192 AAATAATA
1 AAATAATA
109371200 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:109371730 original size:14 final size:15
Alignment explanation
Indices: 109371706--109371740 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
109371696 CTTTTATACT
109371706 AAATAATTAATAATA
1 AAATAATTAATAATA
109371721 AAATAA-TAATAATA
1 AAATAATTAATAATA
*
109371735 ATATAA
1 AAATAA
109371741 ATATCTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATTAATAATA
Found at i:109371756 original size:22 final size:21
Alignment explanation
Indices: 109371709--109371788 Score: 66
Period size: 20 Copynumber: 4.0 Consensus size: 21
109371699 TTATACTAAA
*
109371709 TAATT-AATAATA-AAATA-A
1 TAATTAAATAATATAAATATC
109371727 TAA-T-AATAATATAAATATC
1 TAATTAAATAATATAAATATC
*
109371746 TCATTAAAATAATAT--ATATC
1 TAATT-AAATAATATAAATATC
109371766 TAATTAAATAATCATAAAATATC
1 TAATTAAATAAT-AT-AAATATC
109371789 ATCAACATCA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
17 8 0.16
18 8 0.16
19 9 0.18
20 12 0.24
22 8 0.16
23 5 0.10
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (21 bp):
TAATTAAATAATATAAATATC
Found at i:109374587 original size:46 final size:46
Alignment explanation
Indices: 109374527--109374782 Score: 336
Period size: 46 Copynumber: 5.6 Consensus size: 46
109374517 TTTGACATGA
* * * * * * *
109374527 TGCCATAGTGTCTTTCAACTACGGTCTTACTTATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATA-TTTCATATCAGGT
** *
109374573 TGCCATGGTATCTTTCAACCATGGTCTT-GTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACAT-ATTTCATATCAGGT
* *
109374619 TGCCATGGTATCTTTCAACCATGGTATTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGT
* * *
109374665 TGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAGAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGT
*
109374711 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGT
109374757 TGCCATGGTATCTTTCAACCATGGTC
1 TGCCATGGTATCTTTCAACCATGGTC
109374783 CTTTCAACCA
Statistics
Matches: 190, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
45 6 0.03
46 184 0.97
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGT
Found at i:109374684 original size:92 final size:92
Alignment explanation
Indices: 109374571--109374782 Score: 381
Period size: 92 Copynumber: 2.3 Consensus size: 92
109374561 TTTCTGTCAT
* *
109374571 GTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACG-TTGCCATGGTATCTTTC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCA-GATTGCCATGGTATCTTTC
109374635 AACCATGGTATTACACATTTCATATCAG
65 AACCATGGTATTACACATTTCATATCAG
109374663 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAGATTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAGATTGCCATGGTATCTTTCA
*
109374728 ACCATGGTCTTACACATTTCATATCAG
66 ACCATGGTATTACACATTTCATATCAG
109374755 GTTGCCATGGTATCTTTCAACCATGGTC
1 GTTGCCATGGTATCTTTCAACCATGGTC
109374783 CTTTCAACCA
Statistics
Matches: 116, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
91 1 0.01
92 115 0.99
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (92 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAGATTGCCATGGTATCTTTCA
ACCATGGTATTACACATTTCATATCAG
Found at i:109374788 original size:15 final size:15
Alignment explanation
Indices: 109374768--109374797 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
109374758 GCCATGGTAT
109374768 CTTTCAACCATGGTC
1 CTTTCAACCATGGTC
109374783 CTTTCAACCATGGTC
1 CTTTCAACCATGGTC
109374798 TTACACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (15 bp):
CTTTCAACCATGGTC
Found at i:109376909 original size:11 final size:11
Alignment explanation
Indices: 109376893--109376920 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
109376883 ACTAAATAAT
109376893 TAATAATAAAA
1 TAATAATAAAA
109376904 TAATAATAAAA
1 TAATAATAAAA
109376915 TAATAA
1 TAATAA
109376921 AATATCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:109376947 original size:20 final size:21
Alignment explanation
Indices: 109376894--109376969 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 21
109376884 CTAAATAATT
*
109376894 AATAATAAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
109376913 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
109376934 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
109376955 TAATCATAAAATATC
1 -AATAATAAAATATC
109376970 ATCAACATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.26
20 12 0.26
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:109377437 original size:24 final size:24
Alignment explanation
Indices: 109377410--109377458 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
109377400 AGGGTATTAC
109377410 ATGTATTATACTTTATACACATGT
1 ATGTATTATACTTTATACACATGT
109377434 ATGTATTATACTTTATACACATGT
1 ATGTATTATACTTTATACACATGT
109377458 A
1 A
109377459 ATTAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (24 bp):
ATGTATTATACTTTATACACATGT
Found at i:109377978 original size:16 final size:15
Alignment explanation
Indices: 109377937--109377982 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
109377927 CCTGAAACTG
109377937 AATTAATAC-AAAAA
1 AATTAATACAAAAAA
*
109377951 AA-TAACTTCAAAAAA
1 AATTAA-TACAAAAAA
109377966 TAATTAATACAAAAAA
1 -AATTAATACAAAAAA
109377982 A
1 A
109377983 TTATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
13 3 0.12
14 4 0.15
15 6 0.23
16 10 0.38
17 3 0.12
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (15 bp):
AATTAATACAAAAAA
Found at i:109381512 original size:26 final size:26
Alignment explanation
Indices: 109381483--109381533 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
109381473 CAGAGAAGTT
109381483 CATTTAATGTGAGGGTGGACAGTAAA
1 CATTTAATGTGAGGGTGGACAGTAAA
109381509 CATTTAATGTGAGGGTGGACAGTAA
1 CATTTAATGTGAGGGTGGACAGTAA
109381534 GGAGGGATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.27
Consensus pattern (26 bp):
CATTTAATGTGAGGGTGGACAGTAAA
Found at i:109382504 original size:19 final size:20
Alignment explanation
Indices: 109382477--109382514 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
109382467 TTAGACATGA
109382477 ATCTATGATTTG-AGTTAAT
1 ATCTATGATTTGAAGTTAAT
*
109382496 ATCTCTGATTTGAAGTTAA
1 ATCTATGATTTGAAGTTAA
109382515 ATGCTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (20 bp):
ATCTATGATTTGAAGTTAAT
Found at i:109387301 original size:50 final size:47
Alignment explanation
Indices: 109387147--109387355 Score: 199
Period size: 49 Copynumber: 4.4 Consensus size: 47
109387137 ATAAATATTT
*
109387147 TTATT-CTTTTTGTAAACTTCCCTCATGCATTTGGAGCAGGGCCATTA
1 TTATTACTTTTTGTAAACCTCCC-CATGCATTTGGAGCAGGGCCATTA
* * * * * *
109387194 TTACTACTTTTCGTAAGCCTCCCCCATGCGTTTACGAGCAAGGCCATTA
1 TTATTACTTTTTGTAAACCT-CCCCATGCATTT-GGAGCAGGGCCATTA
* **
109387243 TTAGTACTTTTTGTAAACCTCCTCCAATGCATCTTGGAATAGGGCCATTA
1 TTATTACTTTTTGTAAACCTCC-CC-ATGCAT-TTGGAGCAGGGCCATTA
** * * *
109387293 TTATTACTTTCCGTAAGCCTTCCCATGCATATGGAGC-GGTGCCATTA
1 TTATTACTTTTTGTAAACCTCCCCATGCATTTGGAGCAGG-GCCATTA
109387340 TTATTAC-TTTTGTAAA
1 TTATTACTTTTTGTAAA
109387356 TTCTCCCTAT
Statistics
Matches: 129, Mismatches: 26, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
46 8 0.06
47 22 0.17
48 27 0.21
49 37 0.29
50 33 0.26
51 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (47 bp):
TTATTACTTTTTGTAAACCTCCCCATGCATTTGGAGCAGGGCCATTA
Found at i:109387596 original size:49 final size:49
Alignment explanation
Indices: 109387542--109387646 Score: 131
Period size: 49 Copynumber: 2.1 Consensus size: 49
109387532 CCATTATTAC
* * * *
109387542 TACTTTTTGTAAG-TTCTCTCTATATGTCTAGGAGCAGGGTTATAATTTT
1 TACTTTTTGTAAGCCTC-CCCTATACGTCTAGGAGCAAGGTTATAATTTT
* * *
109387591 TACTTTCTGTAAGCCTCCCCTATGCGTCTAGGAGTAAGGTTATAATTTT
1 TACTTTTTGTAAGCCTCCCCTATACGTCTAGGAGCAAGGTTATAATTTT
109387640 TACTTTT
1 TACTTTT
109387647 CGCAAGCTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 45 0.96
50 2 0.04
ACGTcount: A:0.22, C:0.16, G:0.17, T:0.45
Consensus pattern (49 bp):
TACTTTTTGTAAGCCTCCCCTATACGTCTAGGAGCAAGGTTATAATTTT
Found at i:109387606 original size:199 final size:196
Alignment explanation
Indices: 109387282--109387640 Score: 499
Period size: 199 Copynumber: 1.8 Consensus size: 196
109387272 CATCTTGGAA
* * * *
109387282 TAGGGCCATTATTATTACTTTCCGTAAGCCTTCCCATGCATATGGAGCGGTGCCATTATTATTAC
1 TAGGGCCATTATTACTACTTTCCATAAGCCTTCCCATGAATATGGAGCGGTGCCATTATTACTAC
* * *
109387347 TTTTGTAAATTCTCCCTATGTGTCTAAGAGCAAAGTTATAATTTTTTCTTTCTATAAGCCTTCCC
66 TTTTGTAAATTCTCCCTATATGTCTAAGAGCAAAGTTATAATTTTTACTTTCTATAAGCCTCCCC
* *
109387412 TATGCGTTTAGGAGTAGGGTTATAATTTTTTTAATTTTCGTAAGCCTCCCCCTATGAGTATGGGA
131 TATGCGTCTAGGAGTAAGGTTATAATTTTTTTAATTTTCGTAAGCCTCCCCCTATGAGTATGGGA
109387477 G
196 G
*
109387478 TAGGGCCATTATTACTAC-TTCTCATAAGCC-TCCTTCATGAATCTGAGAGCAGG-GCCATTATT
1 TAGGGCCATTATTACTACTTTC-CATAAGCCTTCC--CATGAATATG-GAGC-GGTGCCATTATT
* * * ** *
109387540 ACTACTTTTTGTAAGTTCTCTCTATATGTCTAGGAGCAGGGTTATAATTTTTACTTTCTGTAAGC
61 ACTAC-TTTTGTAAATTCTCCCTATATGTCTAAGAGCAAAGTTATAATTTTTACTTTCTATAAGC
109387605 CTCCCCTATGCGTCTAGGAGTAAGGTTATAATTTTT
125 CTCCCCTATGCGTCTAGGAGTAAGGTTATAATTTTT
109387641 ACTTTTCGCA
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
195 6 0.04
196 24 0.17
197 8 0.06
198 17 0.12
199 86 0.61
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (196 bp):
TAGGGCCATTATTACTACTTTCCATAAGCCTTCCCATGAATATGGAGCGGTGCCATTATTACTAC
TTTTGTAAATTCTCCCTATATGTCTAAGAGCAAAGTTATAATTTTTACTTTCTATAAGCCTCCCC
TATGCGTCTAGGAGTAAGGTTATAATTTTTTTAATTTTCGTAAGCCTCCCCCTATGAGTATGGGA
G
Found at i:109388341 original size:34 final size:34
Alignment explanation
Indices: 109388303--109388371 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
109388293 AATGTATCAC
109388303 AAAGAAAAGAAAGAAAAATAGAACACAAAACTTT
1 AAAGAAAAGAAAGAAAAATAGAACACAAAACTTT
109388337 AAAGAAAAGAAAGAAAAATAGAACACAAAACTTT
1 AAAGAAAAGAAAGAAAAATAGAACACAAAACTTT
109388371 A
1 A
109388372 CGTTGAAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.68, C:0.09, G:0.12, T:0.12
Consensus pattern (34 bp):
AAAGAAAAGAAAGAAAAATAGAACACAAAACTTT
Found at i:109389130 original size:16 final size:17
Alignment explanation
Indices: 109389101--109389133 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
109389091 ATTTAAAATA
*
109389101 AATTTAATTAATTTTTT
1 AATTAAATTAATTTTTT
109389118 AATTAAATT-ATTTTTT
1 AATTAAATTAATTTTTT
109389134 CAATCTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTAAATTAATTTTTT
Found at i:109389633 original size:28 final size:32
Alignment explanation
Indices: 109389592--109389654 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
109389582 TAGTAAAAAT
109389592 AAAATTATACTTTAA-CCTCT-AAAATTATAA
1 AAAATTATACTTTAATCCTCTAAAAATTATAA
* *
109389622 AAAATTA-A-TTTAATTCTTTAAAAATTATAA
1 AAAATTATACTTTAATCCTCTAAAAATTATAA
109389652 AAA
1 AAA
109389655 TATAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 4 0.14
30 20 0.69
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (32 bp):
AAAATTATACTTTAATCCTCTAAAAATTATAA
Found at i:109389945 original size:18 final size:18
Alignment explanation
Indices: 109389913--109389947 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
109389903 TCAAGGCAAG
**
109389913 TGTTTATGAGTTGTGTTT
1 TGTTTATGACATGTGTTT
109389931 TGTTTATGACATGTGTT
1 TGTTTATGACATGTGTT
109389948 GACATTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.03, G:0.26, T:0.57
Consensus pattern (18 bp):
TGTTTATGACATGTGTTT
Found at i:109392697 original size:3 final size:3
Alignment explanation
Indices: 109392683--109392738 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
109392673 GACAATAAAG
*
109392683 AAT AAT AGT AAT AAT AAT AAT -AT AGAT AAT AAT ATAT ATAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT A-AT AAT AAT
109392729 AAT AAT AAT A
1 AAT AAT AAT A
109392739 GTTAGAGATA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 4 0.09
3 33 0.70
4 10 0.21
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:109392700 original size:12 final size:13
Alignment explanation
Indices: 109392684--109392779 Score: 60
Period size: 12 Copynumber: 7.7 Consensus size: 13
109392674 ACAATAAAGA
109392684 ATAATAGTAATA-
1 ATAATAGTAATAG
*
109392696 ATAATAAT-ATAG
1 ATAATAGTAATAG
* *
109392708 ATAATAATATATAT
1 ATAATAGTA-ATAG
*
109392722 ATAA-AATAATA-
1 ATAATAGTAATAG
* *
109392733 ATAATAGTTAGAG
1 ATAATAGTAATAG
*
109392746 ATAAAAGATAATAG
1 ATAATAG-TAATAG
*
109392760 A-AGTAGTAATA-
1 ATAATAGTAATAG
109392771 ATAATAGTA
1 ATAATAGTA
109392780 TTAAAAAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
11 8 0.12
12 33 0.50
13 13 0.20
14 12 0.18
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (13 bp):
ATAATAGTAATAG
Found at i:109392729 original size:16 final size:15
Alignment explanation
Indices: 109392695--109392735 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
109392685 TAATAGTAAT
*
109392695 AATAATAATATAGAT
1 AATAATAATATAGAA
*
109392710 AATAATATATATATAA
1 AATAATA-ATATAGAA
109392726 AATAATAATA
1 AATAATAATA
109392736 ATAGTTAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
AATAATAATATAGAA
Found at i:109392906 original size:3 final size:3
Alignment explanation
Indices: 109392898--109392947 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
109392888 ATATGTATAT
109392898 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
109392946 AT
1 AT
109392948 GGTAAAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:109393001 original size:3 final size:3
Alignment explanation
Indices: 109392993--109393107 Score: 58
Period size: 3 Copynumber: 38.3 Consensus size: 3
109392983 TATAAATATG
* * * * *
109392993 ATA ATA ATA ATA ATG ATA ATG ACA ATA ATA ATA AT- ATA GTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
109393040 ATA A-A AGTA A-A ATTA ATA GTA A-A TTG ATA ATA ATA ATA ATGT ATG
1 ATA ATA A-TA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* *
109393085 TTA ATA ACA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA -ATA A
109393108 AGGATAGGAA
Statistics
Matches: 83, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
2 7 0.08
3 67 0.81
4 9 0.11
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:109393399 original size:33 final size:36
Alignment explanation
Indices: 109393333--109393399 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
109393323 GATATGAAAA
*
109393333 ATAAAAATAAAAATGATATAGTATTAAGGTATATGC
1 ATAAAAATAAAAATGATATAGTATTAAGATATATGC
* *
109393369 ATAACAATAAAAAT-ATA-A-TATTAATATATAT
1 ATAAAAATAAAAATGATATAGTATTAAGATATAT
109393400 ATACGAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 1 0.04
35 3 0.11
36 13 0.46
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (36 bp):
ATAAAAATAAAAATGATATAGTATTAAGATATATGC
Found at i:109393817 original size:17 final size:17
Alignment explanation
Indices: 109393769--109393819 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
109393759 AATACTATAT
*
109393769 AATATATATAATATACATA
1 AATATA-ATAATA-ACAAA
*
109393788 TATATAAGT-ATAACAAA
1 AATATAA-TAATAACAAA
109393805 AATATAATAATAACA
1 AATATAATAATAACA
109393820 GTAATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.04
17 16 0.59
18 4 0.15
19 6 0.22
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (17 bp):
AATATAATAATAACAAA
Found at i:109394425 original size:2 final size:2
Alignment explanation
Indices: 109394413--109394471 Score: 59
Period size: 2 Copynumber: 29.5 Consensus size: 2
109394403 ACCCCGAAGG
* * *
109394413 TA TA T- TA TA TA TA TA TA TA TA TA TT TA TT TT TA CT- TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA
109394455 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
109394472 GTATGTGTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
1 2 0.04
2 44 0.90
3 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (2 bp):
TA
Found at i:109406784 original size:34 final size:34
Alignment explanation
Indices: 109406741--109406811 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
109406731 GTTGAAAAGT
109406741 TAGCAGAAACTAGGGAAGAAATTCAACATAACAG
1 TAGCAGAAACTAGGGAAGAAATTCAACATAACAG
109406775 TAGCAGAAACTAGGGAAGAAATTCAACATAACAG
1 TAGCAGAAACTAGGGAAGAAATTCAACATAACAG
109406809 TAG
1 TAG
109406812 AGCTTGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.15
Consensus pattern (34 bp):
TAGCAGAAACTAGGGAAGAAATTCAACATAACAG
Found at i:109408436 original size:144 final size:144
Alignment explanation
Indices: 109408176--109408456 Score: 526
Period size: 144 Copynumber: 2.0 Consensus size: 144
109408166 AACTATTCAC
*
109408176 GCCAAAGGATTGCTAACCCTTCATGAGAATAAACTTCAGGCCCTAGTTCCGGTAACATGGTGTAA
1 GCCAAAGGATTGCTAACCATTCATGAGAATAAACTTCAGGCCCTAGTTCCGGTAACATGGTGTAA
109408241 TGCTAAACAAAAAGCCCTTGACAATGAGCTTTTACAGACAAAAGGTAATATTTGACATTAGAACC
66 TGCTAAACAAAAAGCCCTTGACAATGAGCTTTTACAGACAAAAGGTAATATTTGACATTAGAACC
109408306 TTCAAACTGTTCGG
131 TTCAAACTGTTCGG
*
109408320 GCCAAAGGATTGCTAACCATTCATGAGAATAAACTTCAGGCCCTTGTTCCGGTAACATGGTGTAA
1 GCCAAAGGATTGCTAACCATTCATGAGAATAAACTTCAGGCCCTAGTTCCGGTAACATGGTGTAA
* *
109408385 TGCTAAACAAAAAGCCCTTGACAATGAGTTTTTACAGACAAAGGGTAATATTTGACATTAGAACC
66 TGCTAAACAAAAAGCCCTTGACAATGAGCTTTTACAGACAAAAGGTAATATTTGACATTAGAACC
109408450 TTCAAAC
131 TTCAAAC
109408457 CAAATAGGTG
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 133 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (144 bp):
GCCAAAGGATTGCTAACCATTCATGAGAATAAACTTCAGGCCCTAGTTCCGGTAACATGGTGTAA
TGCTAAACAAAAAGCCCTTGACAATGAGCTTTTACAGACAAAAGGTAATATTTGACATTAGAACC
TTCAAACTGTTCGG
Found at i:109411815 original size:21 final size:19
Alignment explanation
Indices: 109411765--109411815 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
109411755 CCTATAAGAT
109411765 ATATTTTAATTGATACATAC
1 ATATTTT-ATTGATACATAC
109411785 A-ATTAATTATTGATTACATACC
1 ATATT--TTATTGA-TACATA-C
109411807 ATATTTTAT
1 ATATTTTAT
109411816 AATACTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
19 3 0.12
20 6 0.23
21 12 0.46
22 2 0.08
23 3 0.12
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (19 bp):
ATATTTTATTGATACATAC
Found at i:109412957 original size:16 final size:17
Alignment explanation
Indices: 109412931--109412963 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
109412921 GCCGGCCACG
109412931 GCGGTCGGCGCGACGGC
1 GCGGTCGGCGCGACGGC
*
109412948 GCGG-CGGCGCTACGGC
1 GCGGTCGGCGCGACGGC
109412964 AGGCGACGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.06, C:0.36, G:0.52, T:0.06
Consensus pattern (17 bp):
GCGGTCGGCGCGACGGC
Found at i:109414028 original size:25 final size:25
Alignment explanation
Indices: 109413999--109414046 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
109413989 ACGTCACTTC
*
109413999 TATATTTTTATTTCTCA-TATTATCT
1 TATATTTATATTTC-CATTATTATCT
109414024 TATATTTATATTTCCATTATTAT
1 TATATTTATATTTCCATTATTAT
109414047 ACCATATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.62
Consensus pattern (25 bp):
TATATTTATATTTCCATTATTATCT
Found at i:109414421 original size:3 final size:3
Alignment explanation
Indices: 109414415--109414441 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
109414405 CGTTTCGTAC
109414415 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
109414442 CGTTTTCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:109415151 original size:17 final size:17
Alignment explanation
Indices: 109415129--109415163 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
109415119 AAGAGGAAGA
109415129 TCGTGTTTCAAAGTATT
1 TCGTGTTTCAAAGTATT
109415146 TCGTGTTTCAAAGTATT
1 TCGTGTTTCAAAGTATT
109415163 T
1 T
109415164 TAAGTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (17 bp):
TCGTGTTTCAAAGTATT
Found at i:109415170 original size:17 final size:17
Alignment explanation
Indices: 109415133--109415175 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
109415123 GGAAGATCGT
**
109415133 GTTTCAAAGTATTTCGT
1 GTTTCAAAGTATTTCAA
*
109415150 GTTTCAAAGTATTTTAA
1 GTTTCAAAGTATTTCAA
109415167 GTTTTCAAA
1 G-TTTCAAA
109415176 TTTTTGACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (17 bp):
GTTTCAAAGTATTTCAA
Found at i:109417581 original size:46 final size:45
Alignment explanation
Indices: 109417530--109417616 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 45
109417520 GAAAAAAATT
109417530 ATAAAAAATTAAAATCAATAA-AATCTATAAATAT-TATTAAATTTTA
1 ATAAAAAATTAAAAT-AATAAGAAT-TATAAATATATA-TAAATTTTA
* *
109417576 ATAAAAAATTTAAATATTAAGAATTATAAATATATATAAAT
1 ATAAAAAATTAAAATAATAAGAATTATAAATATATATAAAT
109417617 CGTAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
45 18 0.49
46 19 0.51
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (45 bp):
ATAAAAAATTAAAATAATAAGAATTATAAATATATATAAATTTTA
Found at i:109417582 original size:45 final size:44
Alignment explanation
Indices: 109417532--109417626 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 44
109417522 AAAAAATTAT
**
109417532 AAAAAATTAAAATCAATAA-AATCTATAAATAT-TATTAAATTTTAA
1 AAAAAATTAAAAT-AATAAGAAT-TATAAATATATA-TAAATCGTAA
* *
109417577 TAAAAAATTTAAATATTAAGAATTATAAATATATATAAATCGTAA
1 -AAAAAATTAAAATAATAAGAATTATAAATATATATAAATCGTAA
109417622 AAAAA
1 AAAAA
109417627 TATAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
44 5 0.12
45 21 0.49
46 17 0.40
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (44 bp):
AAAAAATTAAAATAATAAGAATTATAAATATATATAAATCGTAA
Found at i:109417627 original size:21 final size:21
Alignment explanation
Indices: 109417603--109417676 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
109417593 TAAGAATTAT
*
109417603 AAATATATATAAATCGTAAAA
1 AAATATATAAAAATCGTAAAA
* *
109417624 AAATATAAAAAAATTTGTAAAA
1 AAATATATAAAAA-TCGTAAAA
***
109417646 TTTTATA-AAAAATCGTAAAA
1 AAATATATAAAAATCGTAAAA
109417666 AAAT-TATAAAA
1 AAATATATAAAA
109417677 TATATAGAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.05
20 12 0.29
21 16 0.39
22 11 0.27
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.30
Consensus pattern (21 bp):
AAATATATAAAAATCGTAAAA
Found at i:109417632 original size:10 final size:10
Alignment explanation
Indices: 109417619--109417704 Score: 50
Period size: 10 Copynumber: 8.5 Consensus size: 10
109417609 ATATAAATCG
109417619 TAAAAAAATA
1 TAAAAAAATA
*
109417629 TAAAAAAATT
1 TAAAAAAATA
** * *
109417639 TGTAAAATTT
1 TAAAAAAATA
*
109417649 TATAAAAAATCG
1 TA-AAAAAAT-A
109417661 TAAAAAAAT-
1 TAAAAAAATA
*
109417670 T-ATAAAATA
1 TAAAAAAATA
* *
109417679 TATAGAAATA
1 TAAAAAAATA
109417689 TAAAAAAATTA
1 TAAAAAAA-TA
109417700 TAAAA
1 TAAAA
109417705 TTTTATAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 9
0.71 0.17 0.11
Matches are distributed among these distances:
8 6 0.11
9 2 0.04
10 28 0.49
11 19 0.33
12 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:109417693 original size:28 final size:29
Alignment explanation
Indices: 109417623--109417724 Score: 120
Period size: 28 Copynumber: 3.5 Consensus size: 29
109417613 AAATCGTAAA
*
109417623 AAAAT-ATAAAAAAATTTGTAAAATTTTAT
1 AAAATCATAAAAAAA-TTATAAAATTTTAT
* *
109417652 AAAAAATCGTAAAAAAATTATAAAA-TATAT
1 --AAAATCATAAAAAAATTATAAAATTTTAT
109417682 AGAAAT-ATAAAAAAATTATAAAATTTTAT
1 A-AAATCATAAAAAAATTATAAAATTTTAT
109417711 AAAATCATAAAAAA
1 AAAATCATAAAAAA
109417725 TTGTAAAGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
28 21 0.34
29 17 0.27
30 4 0.06
31 12 0.19
32 8 0.13
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAATCATAAAAAAATTATAAAATTTTAT
Found at i:109417737 original size:59 final size:59
Alignment explanation
Indices: 109417624--109417739 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 59
109417614 AATCGTAAAA
* * *
109417624 AAATATAAAAAAATTTGTAAAATTTTATAAAAAATCGTAAAAAAATTATAAAATATATAG
1 AAATATAAAAAAATTTATAAAATTTTAT-AAAAATCATAAAAAAATTAAAAAATATATAG
*
109417684 AAATATAAAAAAA-TTATAAAATTTTAT-AAAATCATAAAAAATTGTAAAGAAATATA
1 AAATATAAAAAAATTTATAAAATTTTATAAAAATCATAAAAAAAT-TAAA-AAATATA
109417740 AATTTTGTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
57 14 0.28
58 3 0.06
59 20 0.40
60 13 0.26
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (59 bp):
AAATATAAAAAAATTTATAAAATTTTATAAAAATCATAAAAAAATTAAAAAATATATAG
Found at i:109417927 original size:18 final size:18
Alignment explanation
Indices: 109417904--109417958 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
109417894 GTCGTTAATT
109417904 TTTTATGATTTTATAAAA
1 TTTTATGATTTTATAAAA
* * * *
109417922 TTTTATAATTTTCTTATA
1 TTTTATGATTTTATAAAA
*
109417940 TTTTACGATTTTCATAAAA
1 TTTTATGATTTT-ATAAAA
109417959 AAATTCTAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTTATGATTTTATAAAA
Found at i:109418034 original size:11 final size:11
Alignment explanation
Indices: 109418008--109418048 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
109417998 TTAAAATTTA
*
109418008 ATAATTTTTCT
1 ATAATTTTTTT
109418019 A-AATTTTTTT
1 ATAATTTTTTT
109418029 ATAATTTTTTT
1 ATAATTTTTTT
*
109418040 CTAATTTTT
1 ATAATTTTT
109418049 AATAAGAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (11 bp):
ATAATTTTTTT
Found at i:109418224 original size:95 final size:91
Alignment explanation
Indices: 109418062--109418278 Score: 235
Period size: 95 Copynumber: 2.3 Consensus size: 91
109418052 AAGAGTAGGG
* * *
109418062 GCTTAATTGC-TTTTTTGAAAATTTTTAAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
1 GCTTAATTGCTTTTTTTGAAAA-ATTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
* * *
109418126 AATTGAGT-TAAAAAAAAAGATTACGTAA-TA
65 AATTAAGTGCAAAAAAAAA-A--A-G-AAGCA
* * *
109418156 GCTTAATTGCTTTTTTTGAAGAAATTTGAGGGCCTTTTTGATGCATTTTGAAAGTTTCGA-TGCT
1 GCTTAATTGCTTTTTTTGAA-AAATTTGAGGGCCTTTTTGATGCATTTTGAAAG-TTCAAGTACC
*
109418220 CAATTAAGTGCAAAAAAAAAAAGAAGCG
64 CAATTAAGTGCAAAAAAAAAAAGAAGCA
109418248 GCTTAATTGCTTTTTTTGAAAAAGTTTGAGG
1 GCTTAATTGCTTTTTTTGAAAAA-TTTGAGG
109418279 TCTTTTTACA
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
91 5 0.05
92 28 0.26
93 1 0.01
94 10 0.09
95 48 0.45
96 15 0.14
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (91 bp):
GCTTAATTGCTTTTTTTGAAAAATTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCA
ATTAAGTGCAAAAAAAAAAAGAAGCA
Found at i:109427677 original size:20 final size:22
Alignment explanation
Indices: 109427644--109427684 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
109427634 AAAAAAATCT
*
109427644 AAAAACTCATAAAATTATTTTA
1 AAAAACTCATAAAACTATTTTA
109427666 AAAAACT-A-AAAACTATTTT
1 AAAAACTCATAAAACTATTTT
109427685 TTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAACTCATAAAACTATTTTA
Found at i:109427829 original size:19 final size:19
Alignment explanation
Indices: 109427807--109427843 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
109427797 TTTTATGGTA
109427807 CTTTAAAAACTCAAAATTC
1 CTTTAAAAACTCAAAATTC
**
109427826 CTTTAAAATGTCAAAATT
1 CTTTAAAAACTCAAAATT
109427844 TTCATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (19 bp):
CTTTAAAAACTCAAAATTC
Found at i:109428071 original size:26 final size:27
Alignment explanation
Indices: 109428042--109428096 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
109428032 GTTATAATAA
* *
109428042 TTTTGGGGATTGTTTATGATTTTTTTT
1 TTTTGGGGATTCTTAATGATTTTTTTT
**
109428069 TTTTTTGGATTCTTAATGATTTTTTTT
1 TTTTGGGGATTCTTAATGATTTTTTTT
109428096 T
1 T
109428097 AAATTTCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.02, G:0.16, T:0.69
Consensus pattern (27 bp):
TTTTGGGGATTCTTAATGATTTTTTTT
Found at i:109428109 original size:17 final size:17
Alignment explanation
Indices: 109428089--109428128 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
109428079 TCTTAATGAT
109428089 TTTTTTTTAAATTTCTA
1 TTTTTTTTAAATTTCTA
** *
109428106 TTTTTTTTACTTTTTTA
1 TTTTTTTTAAATTTCTA
109428123 TTTTTT
1 TTTTTT
109428129 AAAATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTTTAAATTTCTA
Found at i:109436145 original size:20 final size:20
Alignment explanation
Indices: 109436120--109436160 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
109436110 TAGCACCACA
109436120 ATTCAAA-CAAAACATCAATC
1 ATTCAAACCAAAACAT-AATC
*
109436140 ATTCAAACCAAGACATAATC
1 ATTCAAACCAAAACATAATC
109436160 A
1 A
109436161 ACTTGTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (20 bp):
ATTCAAACCAAAACATAATC
Found at i:109436846 original size:45 final size:45
Alignment explanation
Indices: 109436733--109436846 Score: 106
Period size: 45 Copynumber: 2.5 Consensus size: 45
109436723 TCTTTCATTC
* * * *
109436733 ATGATATTACTCACTTCCGTCATGATGCCATAGCATCTTTCGGCT
1 ATGATCTTACTCGCTTCCGTCATGATGCCATAGAATCTTTCAGCT
* * * * * *
109436778 ATGGTCTTACAT-GTTTTCATCATGATGTCATA-AAGTCTTTTAGCT
1 ATGATCTTAC-TCGCTTCCGTCATGATGCCATAGAA-TCTTTCAGCT
109436823 ATGATCTTACTCGCTTCCGTCATG
1 ATGATCTTACTCGCTTCCGTCATG
109436847 TTTACAATAA
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
44 2 0.04
45 49 0.94
46 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (45 bp):
ATGATCTTACTCGCTTCCGTCATGATGCCATAGAATCTTTCAGCT
Found at i:109440844 original size:75 final size:75
Alignment explanation
Indices: 109440725--109440896 Score: 205
Period size: 75 Copynumber: 2.4 Consensus size: 75
109440715 CATGGCAAAG
** *
109440725 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
109440784 CCATACTGAGC
65 CCATACCGAGC
109440795 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
109440860 CATACCGAGT
66 CATACCGAGC
***
109440870 TAAAAAAATGTAGGTATGGTATT-TCAA
1 T-GTGAAATGTAGGTATGGTATTATCAA
109440897 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 1 0.01
75 46 0.53
76 18 0.21
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:109440863 original size:35 final size:35
Alignment explanation
Indices: 109440728--109440894 Score: 167
Period size: 35 Copynumber: 4.6 Consensus size: 35
109440718 GGCAAAGTGT
* **
109440728 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
109440763 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
109440798 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
109440838 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
*
109440874 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
109440895 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
35 64 0.55
36 21 0.18
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:109440886 original size:36 final size:35
Alignment explanation
Indices: 109440824--109440894 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
109440814 ATTATCAAAT
* *
109440824 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
*
109440859 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTT-AAAAAATGTAGGTATGGCATTTC
109440895 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (35 bp):
CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
Found at i:109453946 original size:12 final size:13
Alignment explanation
Indices: 109453923--109453951 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
109453913 GTATGAGCAC
109453923 TATAGTTTTATGA
1 TATAGTTTTATGA
109453936 TATAG-TTTATGA
1 TATAGTTTTATGA
109453948 TATA
1 TATA
109453952 TATTAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (13 bp):
TATAGTTTTATGA
Found at i:109460805 original size:62 final size:59
Alignment explanation
Indices: 109460700--109460831 Score: 149
Period size: 62 Copynumber: 2.2 Consensus size: 59
109460690 CAAAAATAAT
* * *
109460700 ATTATTTTAAT-AGATTTAATATTAAATTAAATTTAATGGTTATCTTGTAGATAAATATTCC
1 ATTAATTTAATAAGATTTAATATTAAATTAAATATAATGGTTATC-T-T-GATAAATATTAC
** * ** *
109460761 ATTAATTTAATAAGATTTAATATTAAATTTTATATGATTTTTATCTTGATAAATATTAT
1 ATTAATTTAATAAGATTTAATATTAAATTAAATATAATGGTTATCTTGATAAATATTAC
109460820 ATTAATTTAATA
1 ATTAATTTAATA
109460832 TTAAAGTGAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 22 0.36
60 1 0.02
61 11 0.18
62 27 0.44
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (59 bp):
ATTAATTTAATAAGATTTAATATTAAATTAAATATAATGGTTATCTTGATAAATATTAC
Found at i:109464180 original size:44 final size:45
Alignment explanation
Indices: 109464090--109464218 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
109464080 GACAGAACGA
*
109464090 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
109464136 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
109464180 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
109464219 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:109466072 original size:29 final size:29
Alignment explanation
Indices: 109466040--109466113 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
109466030 TAAATTACAT
*
109466040 TTTAGTCACTTATGTTTGATATGTTACGC
1 TTTAGTCACTTACGTTTGATATGTTACGC
109466069 TTTAGTCACTTACGTTTGATATGTTACGC
1 TTTAGTCACTTACGTTTGATATGTTACGC
109466098 TTTAGTCACTTACGTT
1 TTTAGTCACTTACGTT
109466114 ATCGTTTTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (29 bp):
TTTAGTCACTTACGTTTGATATGTTACGC
Found at i:109467052 original size:2 final size:2
Alignment explanation
Indices: 109467045--109467080 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
109467035 TCATTTCAAC
109467045 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
109467081 CGCCTAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109472992 original size:22 final size:23
Alignment explanation
Indices: 109472959--109473002 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
109472949 AATTATATCT
* *
109472959 AAAAAAATATTAATATTATCATG
1 AAAAAAATATTAAAAATATCATG
109472982 AAAAAAA-ATTAAAAATATCAT
1 AAAAAAATATTAAAAATATCAT
109473003 TCTATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAAATATTAAAAATATCATG
Found at i:109477366 original size:14 final size:14
Alignment explanation
Indices: 109477332--109477379 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
109477322 AAGAAACAAT
109477332 AAAGAAACAGAAAA-
1 AAAGAAA-AGAAAAG
109477346 AAA-AAAA-AAGAAG
1 AAAGAAAAGAA-AAG
109477359 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
109477373 AAAGAAA
1 AAAGAAA
109477380 GAATAGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.07
12 3 0.10
13 6 0.20
14 17 0.57
15 2 0.07
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:109481056 original size:16 final size:14
Alignment explanation
Indices: 109481020--109481071 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
109481010 CTCCCATTTC
*
109481020 TCTATATTTTAAAAT
1 TCTAAATTTT-AAAT
*
109481035 TATAAATTCTTAATAT
1 TCTAAATT-TTAA-AT
109481051 TCTAAATTTTAAAT
1 TCTAAATTTTAAAT
*
109481065 TTTAAAT
1 TCTAAAT
109481072 AATAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 8 0.26
15 12 0.39
16 11 0.35
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (14 bp):
TCTAAATTTTAAAT
Found at i:109492610 original size:42 final size:42
Alignment explanation
Indices: 109492545--109492656 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
109492535 AAAGCCCGAA
* * *
109492545 GGTTGAATAGAAGCTCATGAGAGCT-AAAAAAATACCCATAAG
1 GGTTGAACAGAAGCTTATAAGAGCTGAAAAAAA-ACCCATAAG
* **
109492587 GGTTGAACAGAAGCTTGTAAGAGCTGAACGAAAACCCATAAG
1 GGTTGAACAGAAGCTTATAAGAGCTGAAAAAAAACCCATAAG
109492629 GGTT-ATACAGAAGCTTA-ATAGAGCTGAA
1 GGTTGA-ACAGAAGCTTATA-AGAGCTGAA
109492657 CGGAAACTCA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.03
42 53 0.88
43 5 0.08
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (42 bp):
GGTTGAACAGAAGCTTATAAGAGCTGAAAAAAAACCCATAAG
Found at i:109492657 original size:42 final size:41
Alignment explanation
Indices: 109492578--109492685 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 41
109492568 CTAAAAAAAT
*
109492578 ACCCATAAGGGTTGAACAGAAGCTTGTAAGAGCTGAACGAAA
1 ACCCATAAGGGTT-AACAGAAGCTTATAAGAGCTGAACGAAA
*
109492620 ACCCATAAGGGTTATACAGAAGCTTA-ATAGAGCTGAACGGAA
1 ACCCATAAGGGTTA-ACAGAAGCTTATA-AGAGCTGAACGAAA
* * *
109492662 ACTCATATGAGTTAAACAGAAGCT
1 ACCCATAAGGGTT-AACAGAAGCT
109492686 CTTGAGAGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.03
42 55 0.95
43 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (41 bp):
ACCCATAAGGGTTAACAGAAGCTTATAAGAGCTGAACGAAA
Found at i:109500332 original size:6 final size:7
Alignment explanation
Indices: 109500317--109500342 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
109500307 TTTCTTTGTA
109500317 TTTGCTT
1 TTTGCTT
109500324 TTTGCTT
1 TTTGCTT
109500331 TTTGCTT
1 TTTGCTT
109500338 TTTGC
1 TTTGC
109500343 CAATATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (7 bp):
TTTGCTT
Found at i:109506871 original size:14 final size:15
Alignment explanation
Indices: 109506840--109506873 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
109506830 ATGTCTCAAG
109506840 TTTT-ATTATTTTAC
1 TTTTCATTATTTTAC
109506854 TTTTCATTATTTTA-
1 TTTTCATTATTTTAC
109506868 TTTTCA
1 TTTTCA
109506874 ACGAACTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTCATTATTTTAC
Found at i:109515250 original size:46 final size:46
Alignment explanation
Indices: 109515200--109515373 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
109515190 GTTGAGCATC
109515200 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
* *
109515246 CGAACTCGTTGAGTTGAGTTCGAGTT--C-T-TGAGATG-TAACTAGGTAT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--GT-T
* * * **
109515292 CCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 -CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
*
109515339 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
109515374 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
44 1 0.01
45 2 0.02
46 60 0.56
47 23 0.21
48 1 0.01
49 1 0.01
50 5 0.05
51 4 0.04
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
Found at i:109515356 original size:93 final size:93
Alignment explanation
Indices: 109515197--109515365 Score: 275
Period size: 93 Copynumber: 1.8 Consensus size: 93
109515187 ATGGTTGAGC
* **
109515197 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTG
*
109515262 AGTTCGAGTTCTTGAGATGTAACTAGGT
66 AGTCCGAGTTCTTGAGATGTAACTAGGT
* * *
109515290 ATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTG
109515355 AGTCCGAGTTC
66 AGTCCGAGTTC
109515366 ACTTATGGGC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTG
AGTCCGAGTTCTTGAGATGTAACTAGGT
Found at i:109516545 original size:14 final size:14
Alignment explanation
Indices: 109516526--109516557 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
109516516 TACCCCCCTC
109516526 TTCTTTCCCATGTT
1 TTCTTTCCCATGTT
109516540 TTCTTTCCCATGTT
1 TTCTTTCCCATGTT
109516554 TTCT
1 TTCT
109516558 AGAGTTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.28, G:0.06, T:0.59
Consensus pattern (14 bp):
TTCTTTCCCATGTT
Found at i:109518189 original size:21 final size:20
Alignment explanation
Indices: 109518152--109518190 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
109518142 TTATTTTTAC
*
109518152 TATTTTAAATATGAAATATT
1 TATTTTAAATATAAAATATT
*
109518172 TATTTATATATATAAAATA
1 TATTT-TAAATATAAAATA
109518191 AAGAAAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATTTTAAATATAAAATATT
Found at i:109528832 original size:2 final size:2
Alignment explanation
Indices: 109528825--109528867 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
109528815 ATATTAAATC
109528825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
109528867 A
1 A
109528868 AACAAGGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:109529183 original size:25 final size:23
Alignment explanation
Indices: 109529130--109529183 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
109529120 TTAATGATTT
* * *
109529130 TATATATTTTAATGATATATATG
1 TATATAGTTTAATCATATATATA
*
109529153 TGTATAGTTTAATACATCATATATA
1 TATATAGTTTAAT-CAT-ATATATA
109529178 TATATA
1 TATATA
109529184 ATATAACAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 11 0.46
24 2 0.08
25 11 0.46
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (23 bp):
TATATAGTTTAATCATATATATA
Found at i:109533434 original size:40 final size:40
Alignment explanation
Indices: 109533355--109533476 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 40
109533345 ATACTATTTG
* * * *
109533355 ATTCAGGGTTACCAAAGTATAAACAGGGGCATGCATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGC
* * * *
109533395 ATTTAGGGGTACCGGAGTACAAATAGGGGCACGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGC
*
109533435 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGCATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGC
109533475 AT
1 AT
109533477 CCAAGCAATA
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.20
Consensus pattern (40 bp):
ATTCAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGC
Found at i:109534836 original size:14 final size:14
Alignment explanation
Indices: 109534817--109534861 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
109534807 ATTGTGATTC
109534817 ATTATATGGATTTT
1 ATTATATGGATTTT
* *
109534831 ATTATAATAGATTTC
1 ATTAT-ATGGATTTT
*
109534846 ATTATATGAATTTT
1 ATTATATGGATTTT
109534860 AT
1 AT
109534862 ATTAACATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (14 bp):
ATTATATGGATTTT
Found at i:109534849 original size:15 final size:15
Alignment explanation
Indices: 109534814--109534851 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
109534804 ATAATTGTGA
*
109534814 TTCATTAT-ATGGAT
1 TTCATTATAATAGAT
*
109534828 TTTATTATAATAGAT
1 TTCATTATAATAGAT
109534843 TTCATTATA
1 TTCATTATA
109534852 TGAATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (15 bp):
TTCATTATAATAGAT
Found at i:109535309 original size:2 final size:2
Alignment explanation
Indices: 109535252--109535290 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
109535242 ATGTACAATT
*
109535252 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
109535291 CTAATTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:109537413 original size:63 final size:64
Alignment explanation
Indices: 109537331--109537471 Score: 167
Period size: 63 Copynumber: 2.2 Consensus size: 64
109537321 AGTAGTATAC
* *
109537331 GACACATAAAGTGCCTGAAACGACACATGAAGCACCTGAAAT-GACACATGAAGCGCCTGAAAT
1 GACACATAAAGCGCCTGAAACGACACATGAAGCACCTGAAATAGACACATAAAGCGCCTGAAAT
* * * * * *
109537394 GACACATGAAGCGCCTGAAATGACACATGAGGTACGTGAAATACGACACATAAAGTGCCTGATAT
1 GACACATAAAGCGCCTGAAACGACACATGAAGCACCTGAAATA-GACACATAAAGCGCCTGA-A-
*
109537459 AC
63 AT
109537461 GACACATAAAG
1 GACACATAAAG
109537472 TACCTGATCG
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 36 0.56
65 16 0.25
66 1 0.02
67 11 0.17
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (64 bp):
GACACATAAAGCGCCTGAAACGACACATGAAGCACCTGAAATAGACACATAAAGCGCCTGAAAT
Found at i:109537479 original size:23 final size:21
Alignment explanation
Indices: 109537329--109537478 Score: 138
Period size: 21 Copynumber: 7.0 Consensus size: 21
109537319 GAAGTAGTAT
*
109537329 ACGACACATAAAGTGCCTGAA
1 ACGACACATGAAGTGCCTGAA
**
109537350 ACGACACATGAAGCACCTGAA
1 ACGACACATGAAGTGCCTGAA
* *
109537371 ATGACACATGAAGCGCCTGAA
1 ACGACACATGAAGTGCCTGAA
* *
109537392 ATGACACATGAAGCGCCTGAA
1 ACGACACATGAAGTGCCTGAA
* * * *
109537413 ATGACACATGAGGTACGTGAAA
1 ACGACACATGAAGTGCCTG-AA
*
109537435 TACGACACATAAAGTGCCTGATA
1 -ACGACACATGAAGTGCCTGA-A
* *
109537458 TACGACACATAAAGTACCTGA
1 -ACGACACATGAAGTGCCTGA
109537479 TCGGCAAAGC
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
21 73 0.66
22 3 0.03
23 35 0.32
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.16
Consensus pattern (21 bp):
ACGACACATGAAGTGCCTGAA
Found at i:109537862 original size:13 final size:13
Alignment explanation
Indices: 109537844--109537868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109537834 AATTCACTTT
109537844 TATTTAATTCATA
1 TATTTAATTCATA
109537857 TATTTAATTCAT
1 TATTTAATTCAT
109537869 TTTTCAATCA
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTAATTCATA
Found at i:109538460 original size:12 final size:12
Alignment explanation
Indices: 109538445--109538472 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
109538435 GTTAATAATG
109538445 ATAATAATTATA
1 ATAATAATTATA
109538457 ATAATAATTATA
1 ATAATAATTATA
109538469 ATAA
1 ATAA
109538473 ATATCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATAATTATA
Found at i:109540359 original size:31 final size:31
Alignment explanation
Indices: 109540309--109540381 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
109540299 TTTTATTTTA
* * *
109540309 TTTTTAACAA-TCTAGTGAC-TCAAATAAATT
1 TTTTTAATAATTC-AGTGACTTAAAATAAAAT
109540339 TTTTTAAATAATTCAGTGACTTAAAATAAAAT
1 TTTTT-AATAATTCAGTGACTTAAAATAAAAT
109540371 TTTTTAATAAT
1 TTTTTAATAAT
109540382 ATAGTGGCCG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 5 0.14
31 16 0.43
32 16 0.43
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (31 bp):
TTTTTAATAATTCAGTGACTTAAAATAAAAT
Found at i:109555584 original size:2 final size:2
Alignment explanation
Indices: 109555579--109555611 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
109555569 AAAAAAAATA
109555579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
109555612 AAAGTTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:109555716 original size:27 final size:27
Alignment explanation
Indices: 109555686--109555742 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
109555676 ACATTACATT
109555686 AAAACAAGTTAAAATAAATAATATATA
1 AAAACAAGTTAAAATAAATAATATATA
* * * **
109555713 AAAATAATTTAAAATGAATGGTATATA
1 AAAACAAGTTAAAATAAATAATATATA
109555740 AAA
1 AAA
109555743 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (27 bp):
AAAACAAGTTAAAATAAATAATATATA
Found at i:109557338 original size:224 final size:224
Alignment explanation
Indices: 109556948--109557392 Score: 890
Period size: 224 Copynumber: 2.0 Consensus size: 224
109556938 ACAACCCAAA
109556948 ATCCGTGGGCACCAGAAAAGTGTGTTATCGGGCCTCCGTCTTAGTGAAATAAGTTCGAAAATAAT
1 ATCCGTGGGCACCAGAAAAGTGTGTTATCGGGCCTCCGTCTTAGTGAAATAAGTTCGAAAATAAT
109557013 TATTAAAAATAATTATGAGTCTAGTAGTGTGTTTAATTAGGTTTTAATTAAGTAAATTTAGCTTA
66 TATTAAAAATAATTATGAGTCTAGTAGTGTGTTTAATTAGGTTTTAATTAAGTAAATTTAGCTTA
109557078 ATTTAGAGTAATTAGTAAAAAGGATTAAATTGAATAAGGGTAAAAGTTTAATTATAGATTAAAGA
131 ATTTAGAGTAATTAGTAAAAAGGATTAAATTGAATAAGGGTAAAAGTTTAATTATAGATTAAAGA
109557143 AAAATTAGAAGGACTTAAGAGGAAATGGT
196 AAAATTAGAAGGACTTAAGAGGAAATGGT
109557172 ATCCGTGGGCACCAGAAAAGTGTGTTATCGGGCCTCCGTCTTAGTGAAATAAGTTCGAAAATAAT
1 ATCCGTGGGCACCAGAAAAGTGTGTTATCGGGCCTCCGTCTTAGTGAAATAAGTTCGAAAATAAT
109557237 TATTAAAAATAATTATGAGTCTAGTAGTGTGTTTAATTAGGTTTTAATTAAGTAAATTTAGCTTA
66 TATTAAAAATAATTATGAGTCTAGTAGTGTGTTTAATTAGGTTTTAATTAAGTAAATTTAGCTTA
109557302 ATTTAGAGTAATTAGTAAAAAGGATTAAATTGAATAAGGGTAAAAGTTTAATTATAGATTAAAGA
131 ATTTAGAGTAATTAGTAAAAAGGATTAAATTGAATAAGGGTAAAAGTTTAATTATAGATTAAAGA
109557367 AAAATTAGAAGGACTTAAGAGGAAAT
196 AAAATTAGAAGGACTTAAGAGGAAAT
109557393 TAAACCATTT
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 221 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (224 bp):
ATCCGTGGGCACCAGAAAAGTGTGTTATCGGGCCTCCGTCTTAGTGAAATAAGTTCGAAAATAAT
TATTAAAAATAATTATGAGTCTAGTAGTGTGTTTAATTAGGTTTTAATTAAGTAAATTTAGCTTA
ATTTAGAGTAATTAGTAAAAAGGATTAAATTGAATAAGGGTAAAAGTTTAATTATAGATTAAAGA
AAAATTAGAAGGACTTAAGAGGAAATGGT
Found at i:109557495 original size:5 final size:5
Alignment explanation
Indices: 109557485--109557530 Score: 83
Period size: 5 Copynumber: 9.0 Consensus size: 5
109557475 AATAATTAAG
109557485 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
109557531 ATAAAAGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 35 0.88
6 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:109559201 original size:39 final size:39
Alignment explanation
Indices: 109559094--109559228 Score: 121
Period size: 39 Copynumber: 3.4 Consensus size: 39
109559084 GACCTCGAGT
* * * *
109559094 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAT-TATTACTTCGGCTAG-TC
** ** * *
109559135 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAATTATTACTTCGGCTAGTC
*
109559173 CGATGAGACACTGGGTGTCAATTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAATTATTACTTCG-GCTAGTC
*
109559212 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
109559229 CCATATTGGT
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
38 18 0.24
39 36 0.49
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGGCTAGTC
Found at i:109560941 original size:133 final size:133
Alignment explanation
Indices: 109560748--109562042 Score: 1896
Period size: 133 Copynumber: 9.7 Consensus size: 133
109560738 TGATTTCAAC
* * * * * * * *
109560748 CTGCTCCAC-TGCAACTTCAGGGAGATAAGGCTAGTGGCTTCAATTTGGTCCGCTACTACCTCGG
1 CTGCTCC-CTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGG
* * * * ** * *
109560812 GAAGATAAGATTCGCCATATTCGATCTACTTCAGTGTTGCTCAGGGAGATAAGATCTACAATATT
65 GAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTT
109560877 CAGT
130 CAGT
* *
109560881 CTGCTCCCTTGCTATTTCAAGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
1 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
* *
109560946 AAGATAAGATTCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATATACAATCTTC
66 AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
109561011 AGT
131 AGT
* * *
109561014 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTACTCCTCTACGACCTCGGG
1 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
* * *
109561079 AAGATAAGATTTGCCATATTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCCTC
66 AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
109561144 AGT
131 AGT
* * * *
109561147 CTACTCCATTGCTACTTCTGGAAGATAAGACTGGTGGCTTAAATATGCTCCCCTACTACCTCGGG
1 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
109561212 AAGATAAGATTCGCCATCTTCGATCTGCTCCCACTACTGCTTAGGGAGATAAGATCTACAATCTT
66 AAGATAAGATTCGCCATCTTCGATCTGCT-CCACTACTGCTTAGGGAGATAAGATCTACAATCTT
109561277 CAGT
130 CAGT
* * *
109561281 CTGCTCCCTTGCTACTTCTGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCTTACTACCTCGGA
1 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
* * *
109561346 AAGATAAGATTCGCCATCTTTGATCTGCTCTACTACTACTTAGGGAGATAAGATCTACAATCTTC
66 AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
109561411 AGT
131 AGT
**
109561414 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCTACTACTACCTCGGG
1 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
*
109561479 AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTC
66 AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
109561544 AGT
131 AGT
* * * *
109561547 CTGCTCCCTTGCTACTTCTGAAAGATAAGACTGGTGGTTTAAATCTGCTCCCCTACTATCTCGGG
1 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
* * * *
109561612 AAGATAAGATTCGCCATCTTTGATTTGCTCCACTACTGCTTAGGGAGATATGATCTACAATCCTC
66 AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
109561677 AGT
131 AGT
* * *
109561680 CTGCTCCCTTGCCACTTCTGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGA
1 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
109561745 AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
66 AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
109561810 AGT
131 AGT
* * **
109561813 CTGCTCCCTTGCTACTTCAGGAAGATAAGAATGGTGGCTTAAATCTGCTCCCCTACTACCTTGAT
1 CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
* **
109561878 AAGATAAGATTTGTTATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
66 AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
*
109561943 AGC
131 AGT
* * * * * * * *
109561946 CTTGCTCTAC-TGCTGC-TCAGGGAGAGAAGGCTAGTAGCTTAAATCTGCTCCCTTACTACCTCA
1 C-TGCTC-CCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTC-
** *
109562009 GGG-AGATAAGATTCGCTGTCTTCGATCTACTCCA
63 GGGAAGATAAGATTCGCCATCTTCGATCTGCTCCA
109562043 TTGCTACCTC
Statistics
Matches: 1054, Mismatches: 103, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
132 1 0.00
133 915 0.87
134 137 0.13
135 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (133 bp):
CTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTCGGG
AAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
AGT
Found at i:109561927 original size:44 final size:44
Alignment explanation
Indices: 109560944--109561931 Score: 224
Period size: 44 Copynumber: 22.3 Consensus size: 44
109560934 TACTACCTCG
* * *
109560944 GGAAGATAAGATTCGCCATCTTTGATCTGCTCCACTACTGCTTA
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTGCTTA
* * * * * *
109560988 GGGAGATAAGATATACAATCTTC-AGTCTGCTCC-CTTGCTACTTCA
1 GGAAGATAAGATTTGCTATCTTCGA-TCTGCTCCAC-TACTGCTT-A
* * ** ** * * **
109561033 GGAAGATAAGA-CTGGTGGCTTAAATCTACTCCTCTAC-GACCTCG
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTG--CTTA
* *
109561077 GGAAGATAAGATTTGCCATATTCGATCTGCTCCACTACTGCTTA
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTGCTTA
* * * * * * * * * *
109561121 GGGAGATAAGATCTACAATCCTC-AGTCTACTCCATTGCTACTTCT
1 GGAAGATAAGATTTGCTATCTTCGA-TCTGCTCCACTACTGCTT-A
* * ** ** * * * **
109561166 GGAAGATAAGA-CTGGTGGCTTAAATATGCTCCCCTACTACCTCG
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACT-GCTTA
* *
109561210 GGAAGATAAGATTCGCCATCTTCGATCTGCTCCCACTACTGCTTA
1 GGAAGATAAGATTTGCTATCTTCGATCTGCT-CCACTACTGCTTA
* * * * * * *
109561255 GGGAGATAAGATCTACAATCTTC-AGTCTGCTCC-CTTGCTACTTCT
1 GGAAGATAAGATTTGCTATCTTCGA-TCTGCTCCAC-TACTGCTT-A
* * ** ** * * *
109561300 GGAAGATAAGA-CTGGTGGCTTAAATCTGCTCC-CTTACTACCTC
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCAC-TACTGCTTA
* * * * *
109561343 GGAAAGATAAGATTCGCCATCTTTGATCTGCTCTACTACTACTTA
1 GG-AAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTGCTTA
* * * * * *
109561388 GGGAGATAAGATCTACAATCTTC-AGTCTGCTCC-CTTGCTACTTCA
1 GGAAGATAAGATTTGCTATCTTCGA-TCTGCTCCAC-TACTGCTT-A
* * ** ** * * **
109561433 GGAAGATAAGA-CTGGTGGCTTAAATCTGCTCTACTACTACCTCG
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACT-GCTTA
* *
109561477 GGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTA
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTGCTTA
* * * * * * * *
109561521 GGGAGATAAGATCTACAATTTTC-AGTCTGCTCC-CTTGCTACTTCT
1 GGAAGATAAGATTTGCTATCTTCGA-TCTGCTCCAC-TACTGCTT-A
* * * * ** * * **
109561566 GAAAGATAAGA-CTGGTGGT-TTAAATCTGCTCCCCTACTATCTCG
1 GGAAGATAAGATTTGCT-ATCTTCGATCTGCTCCACTACT-GCTTA
* * * *
109561610 GGAAGATAAGATTCGCCATCTTTGATTTGCTCCACTACTGCTTA
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTGCTTA
* * * * * * * ** *
109561654 GGGAGATATGATCTACAATCCTC-AGTCTGCTCC-CTTGCCACTTCT
1 GGAAGATAAGATTTGCTATCTTCGA-TCTGCTCCAC-TACTGCTT-A
* * ** ** * * * *
109561699 GGAAGATAAGA-CTGGTGGCTTAAATCTGCTCCCCTACTACCTC
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTGCTTA
* *
109561742 GGAAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTA
1 GG-AAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTGCTTA
* * * * * *
109561787 GGGAGATAAGATCTACAATCTTC-AGTCTGCTCC-CTTGCTACTTCA
1 GGAAGATAAGATTTGCTATCTTCGA-TCTGCTCCAC-TACTGCTT-A
* * ** ** * *
109561832 GGAAGATAAGA-ATGGTGGCTTAAATCTGCTCCCCTACTACCTT-
1 GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACT-GCTTA
* *
109561875 GATAAGATAAGATTTGTTATCTTCGATCTGCTCCACTACTGCTTA
1 G-GAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTGCTTA
*
109561920 GGGAGATAAGAT
1 GGAAGATAAGAT
109561932 CTACAATCTT
Statistics
Matches: 657, Mismatches: 233, Indels: 108
0.66 0.23 0.11
Matches are distributed among these distances:
43 17 0.03
44 386 0.59
45 245 0.37
46 9 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
GGAAGATAAGATTTGCTATCTTCGATCTGCTCCACTACTGCTTA
Found at i:109562061 original size:666 final size:666
Alignment explanation
Indices: 109560748--109562067 Score: 1968
Period size: 666 Copynumber: 2.0 Consensus size: 666
109560738 TGATTTCAAC
* * * * * *
109560748 CTGCTCCACTGCAACTTCAGGGAGATAAGGCTAGTGGCTTCAATTTGGTCCGCTACTACCTCGGG
1 CTGCTCCACTGCAACTTCAGGAAGATAAGACTAGTGGCTTAAATCTGCTCCACTACTACCTCGGG
* * **
109560813 AAGATAAGATTCGCCATATTCGATCTACTTCAGTGTTGCTCAGGGAGATAAGATCTACAATATTC
66 AAGATAAGATTCGCCATATTCGATCTACTCCACTACTGCTCAGGGAGATAAGATCTACAATATTC
*
109560878 AGTCTGCTCCCTTGCTATTTCAAGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTC
131 AGTCTGCTCCCTTGCTACTTCAAGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTC
109560943 GGGAAGATAAGATTCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATATACAATC
196 GGGAAGATAAGATTCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATATACAATC
* * *
109561008 TTCAGTCTGCTCCCTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTACTCCTCTACGAC
261 CTCAGTCTGCTCCCTTGCCACTTCAGGAAGATAAGACTGGTGGCTTAAATCTACTCCCCTACGAC
* *
109561073 CTCGGGAAGATAAGATTTGCCATATTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
326 CTCGGAAAGATAAGATTCGCCATATTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
* *
109561138 ATCCTCAGTCTACTCCATTGCTACTTCTGGAAGATAAGACTGGTGGCTTAAATATGCTCCCCTAC
391 ATCCTCAGTCTACTCCATTGCTACTTCAGGAAGATAAGAATGGTGGCTTAAATATGCTCCCCTAC
*
109561203 TACCTCGGGAAGATAAGATTCGCCATCTTCGATCTGCTCCCACTACTGCTTAGGGAGATAAGATC
456 TACCTCGAGAAGATAAGATTCGCCATCTTCGATCTGCTCCCACTACTGCTTAGGGAGATAAGATC
* * * * * *
109561268 TACAATCTTCAGTCTGCTCCCTTGCTACTTCTGGAAGATAAGACTGGTGGCTTAAATCTGCTCCC
521 TACAATCTTCAGCCTGCTCACTTGCTACTTCAGGAAGAGAAGACTAGTAGCTTAAATCTGCTCCC
* * * *
109561333 TTACTACCTCGGAAAGATAAGATTCGCCATCTTTGATCTGCTCTACTACTACTTAGGGAGATAAG
586 TTACTACCTCGGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTACTCAGGGAGATAAG
109561398 ATCTACAATCTTCAGT
651 ATCTACAATCTTCAGT
* * *
109561414 CTGCTCC-CTTGCTACTTCAGGAAGATAAGACTGGTGGCTTAAATCTGCTCTACTACTACCTCGG
1 CTGCTCCAC-TGCAACTTCAGGAAGATAAGACTAGTGGCTTAAATCTGCTCCACTACTACCTCGG
* * * *
109561478 GAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTT
65 GAAGATAAGATTCGCCATATTCGATCTACTCCACTACTGCTCAGGGAGATAAGATCTACAATATT
* * *
109561543 CAGTCTGCTCCCTTGCTACTTC-TGAAAGATAAGACTGGTGGTTTAAATCTGCTCCCCTACTATC
130 CAGTCTGCTCCCTTGCTACTTCAAG-AAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACC
* * *
109561607 TCGGGAAGATAAGATTCGCCATCTTTGATTTGCTCCACTACTGCTTAGGGAGATATGATCTACAA
194 TCGGGAAGATAAGATTCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATATACAA
* * *
109561672 TCCTCAGTCTGCTCCCTTGCCACTTCTGGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACT
259 TCCTCAGTCTGCTCCCTTGCCACTTCAGGAAGATAAGACTGGTGGCTTAAATCTACTCCCCTACG
*
109561737 ACCTCGGAAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA
324 ACCTCGGAAAGATAAGATTCGCCATATTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA
* * * *
109561802 CAATCTTCAGTCTGCTCCCTTGCTACTTCAGGAAGATAAGAATGGTGGCTTAAATCTGCTCCCCT
389 CAATCCTCAGTCTACTCCATTGCTACTTCAGGAAGATAAGAATGGTGGCTTAAATATGCTCCCCT
* * * **
109561867 ACTACCTTGATAAGATAAGATTTGTTATCTTCGATCTGCT-CCACTACTGCTTAGGGAGATAAGA
454 ACTACCTCGAGAAGATAAGATTCGCCATCTTCGATCTGCTCCCACTACTGCTTAGGGAGATAAGA
* * *
109561931 TCTACAATCTTCAGCCTTGCTCTAC-TGCTGC-TCAGGGAGAGAAGGCTAGTAGCTTAAATCTGC
519 TCTACAATCTTCAGCC-TGCTC-ACTTGCTACTTCAGGAAGAGAAGACTAGTAGCTTAAATCTGC
* ** * * *
109561994 TCCCTTACTACCTCAGG-GAGATAAGATTCGCTGTCTTCGATCTACTCCATTGCTACCTCATGGA
582 TCCCTTACTACCTC-GGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTA-CTCAGGGA
109562058 GATAAGATCT
645 GATAAGATCT
109562068 GTGAATTCAC
Statistics
Matches: 584, Mismatches: 64, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
665 111 0.19
666 472 0.81
667 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (666 bp):
CTGCTCCACTGCAACTTCAGGAAGATAAGACTAGTGGCTTAAATCTGCTCCACTACTACCTCGGG
AAGATAAGATTCGCCATATTCGATCTACTCCACTACTGCTCAGGGAGATAAGATCTACAATATTC
AGTCTGCTCCCTTGCTACTTCAAGAAGATAAGACTGGTGGCTTAAATCTGCTCCCCTACTACCTC
GGGAAGATAAGATTCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATATACAATC
CTCAGTCTGCTCCCTTGCCACTTCAGGAAGATAAGACTGGTGGCTTAAATCTACTCCCCTACGAC
CTCGGAAAGATAAGATTCGCCATATTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
ATCCTCAGTCTACTCCATTGCTACTTCAGGAAGATAAGAATGGTGGCTTAAATATGCTCCCCTAC
TACCTCGAGAAGATAAGATTCGCCATCTTCGATCTGCTCCCACTACTGCTTAGGGAGATAAGATC
TACAATCTTCAGCCTGCTCACTTGCTACTTCAGGAAGAGAAGACTAGTAGCTTAAATCTGCTCCC
TTACTACCTCGGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTACTCAGGGAGATAAG
ATCTACAATCTTCAGT
Found at i:109578160 original size:127 final size:127
Alignment explanation
Indices: 109577987--109578215 Score: 359
Period size: 127 Copynumber: 1.8 Consensus size: 127
109577977 CATGCATTGA
* * * *
109577987 AATTTTAAAAGGATATTCGGTTATTTGGTCAAACGCTAAATTGAAACCCAGCACGTTAGGGCACG
1 AATTTTAAAAGGATATTCGGTAATTTGGTCAAACGCAAAATCGAAACCCAGCACGTTAGAGCACG
*
109578052 ATTTCTCGAATTTCCAAACATAAAATATTGCCTTGTTTTTTAATTGAAGAAAACACGGACAG
66 ATTTCTCGAATTTCCAAACACAAAATATTGCCTTGTTTTTTAATTGAAGAAAACACGGACAG
* * * **
109578114 AATTTTAAAAGGGTATTTGGTAATTTGGTCAAACGGAAAATCGAAACCCAGCACGTTAGAGCATT
1 AATTTTAAAAGGATATTCGGTAATTTGGTCAAACGCAAAATCGAAACCCAGCACGTTAGAGCACG
*
109578179 ATTTCTCGAATTTCCAAACACGAAATATTGCCTTGTT
66 ATTTCTCGAATTTCCAAACACAAAATATTGCCTTGTT
109578216 CTCGAAATGT
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
127 91 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (127 bp):
AATTTTAAAAGGATATTCGGTAATTTGGTCAAACGCAAAATCGAAACCCAGCACGTTAGAGCACG
ATTTCTCGAATTTCCAAACACAAAATATTGCCTTGTTTTTTAATTGAAGAAAACACGGACAG
Found at i:109578610 original size:25 final size:26
Alignment explanation
Indices: 109578547--109578600 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
109578537 ATAACCACTG
109578547 ATAGAAACATAAAGCAAATTAAAAATAA
1 ATAGAAA-AT-AAGCAAATTAAAAATAA
* *
109578575 ATAGAATATAAGCAATTTAAAAATAA
1 ATAGAAAATAAGCAAATTAAAAATAA
109578601 TAATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 2 0.08
28 6 0.25
ACGTcount: A:0.65, C:0.06, G:0.07, T:0.22
Consensus pattern (26 bp):
ATAGAAAATAAGCAAATTAAAAATAA
Found at i:109578936 original size:30 final size:28
Alignment explanation
Indices: 109578899--109578965 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
109578889 AAAAAATCTA
* *
109578899 AAATAAATAATATATATATATATAATTTT
1 AAATAAATAACATATATA-AAATAATTTT
* *
109578928 AGAATAAATAACGTATATAAAATTATTTT
1 A-AATAAATAACATATATAAAATAATTTT
109578957 AAATAAATA
1 AAATAAATA
109578966 GTAAAACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 8 0.24
29 10 0.30
30 15 0.45
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (28 bp):
AAATAAATAACATATATAAAATAATTTT
Found at i:109579010 original size:27 final size:27
Alignment explanation
Indices: 109578980--109579036 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
109578970 AACAAATTTT
* *
109578980 AATAAACATTACATTAAAATAAGTTAA
1 AATAAACAATACATAAAAATAAGTTAA
* * *
109579007 AATAAATAATATATAAAAATAATTTAA
1 AATAAACAATACATAAAAATAAGTTAA
109579034 AAT
1 AAT
109579037 GAATGGTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (27 bp):
AATAAACAATACATAAAAATAAGTTAA
Found at i:109579046 original size:27 final size:27
Alignment explanation
Indices: 109578995--109579051 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
109578985 ACATTACATT
109578995 AAAATAAGTTAAAATAAATAATATATA
1 AAAATAAGTTAAAATAAATAATATATA
* * **
109579022 AAAATAATTTAAAATGAATGGTATATA
1 AAAATAAGTTAAAATAAATAATATATA
109579049 AAA
1 AAA
109579052 TATTTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (27 bp):
AAAATAAGTTAAAATAAATAATATATA
Found at i:109597484 original size:27 final size:27
Alignment explanation
Indices: 109597449--109597500 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
109597439 TCATTGTTGC
* *
109597449 GTTTCAATTTTTATTTGCAAATCCTGT
1 GTTTCAATTTCTATTTGAAAATCCTGT
* *
109597476 GTTTGAATTTCTATTTTAAAATCCT
1 GTTTCAATTTCTATTTGAAAATCCT
109597501 AAATGGCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (27 bp):
GTTTCAATTTCTATTTGAAAATCCTGT
Found at i:109597598 original size:15 final size:15
Alignment explanation
Indices: 109597578--109597606 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
109597568 GTGTGTGTGT
109597578 TTATATATAAATATA
1 TTATATATAAATATA
109597593 TTATATATAAATAT
1 TTATATATAAATAT
109597607 GTAATATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATATATAAATATA
Found at i:109597613 original size:15 final size:15
Alignment explanation
Indices: 109597580--109597615 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
109597570 GTGTGTGTTT
*
109597580 ATATATAAATATATT
1 ATATATAAATATATA
*
109597595 ATATATAAATATGTA
1 ATATATAAATATATA
109597610 ATATAT
1 ATATAT
109597616 GCATGTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
ATATATAAATATATA
Found at i:109603819 original size:34 final size:35
Alignment explanation
Indices: 109603720--109603846 Score: 141
Period size: 35 Copynumber: 3.7 Consensus size: 35
109603710 TCCTCATTGA
* *
109603720 AATACCATACCTACATTTTACAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* * **
109603755 AATGCCATACCTACGTTTCTTAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
109603790 AATACCATACCTAC-TTTCACAACTCAGTATGAAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
* **
109603824 GATACCATACCTATGTTTCACAA
1 AATACCATACCTACATTTCACAA
109603847 ATTTTCCATT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
34 32 0.41
35 46 0.59
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:109607823 original size:42 final size:42
Alignment explanation
Indices: 109607773--109607885 Score: 136
Period size: 43 Copynumber: 2.7 Consensus size: 42
109607763 TTGAGATTAC
**
109607773 ATGTAAGACCATATCTGGGATATGGCATCGATATGAGAATTT
1 ATGTAAGACCATATCTGGGATATGGCATCGATATGAGAACCT
* * * **
109607815 GTGTAAGACCATAGCTGGGCTATTGGCATCGATATGAGGCCCT
1 ATGTAAGACCATATCTGGGATA-TGGCATCGATATGAGAACCT
* *
109607858 ATATAAGACCATATATGGGATATGGCAT
1 ATGTAAGACCATATCTGGGATATGGCAT
109607886 TGGTATAATT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 25 0.43
43 33 0.57
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (42 bp):
ATGTAAGACCATATCTGGGATATGGCATCGATATGAGAACCT
Found at i:109611591 original size:25 final size:25
Alignment explanation
Indices: 109611557--109611627 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
109611547 ATTGAGTCCA
*
109611557 TTTATCTTTATGCTTT-TTTTATTTT
1 TTTATTTTTAT-CTTTATTTTATTTT
* *
109611582 TTTATTTTTATTTTTATTTTGTTTT
1 TTTATTTTTATCTTTATTTTATTTT
* * *
109611607 TATATTTTGAACTTTATTTTA
1 TTTATTTTTATCTTTATTTTA
109611628 ATTATTATGG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 3 0.08
25 34 0.92
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTATTTTTATCTTTATTTTATTTT
Found at i:109611601 original size:17 final size:18
Alignment explanation
Indices: 109611581--109611614 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
109611571 TTTTTTATTT
109611581 TTTTATTTTTAT-TTTTA
1 TTTTATTTTTATATTTTA
*
109611598 TTTTGTTTTTATATTTT
1 TTTTATTTTTATATTTT
109611615 GAACTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTATTTTTATATTTTA
Found at i:109613586 original size:15 final size:15
Alignment explanation
Indices: 109613566--109613596 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109613556 TCTAAAGCCT
109613566 ATATAAACACACTAG
1 ATATAAACACACTAG
109613581 ATATAAACACACTAG
1 ATATAAACACACTAG
109613596 A
1 A
109613597 AGAAGACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
ATATAAACACACTAG
Found at i:109615130 original size:35 final size:35
Alignment explanation
Indices: 109615086--109615488 Score: 440
Period size: 35 Copynumber: 11.5 Consensus size: 35
109615076 TCCTCATTGA
109615086 AATACCATACCTACATTTCACAACTCGATATGGGA-
1 AATACCATACCTACATTTCACAACTCGATAT-GGAT
* **
109615121 AATGCCATACCTACATTTCTTAACTC-AGTATGGAT
1 AATACCATACCTACATTTCACAACTCGA-TATGGAT
* *
109615156 AATACCATACCTACATTTCTCAACTCGGTATGGAT
1 AATACCATACCTACATTTCACAACTCGATATGGAT
* * *
109615191 GATACCATACCTACGTTTCACAACT-TAGTATGGAT
1 AATACCATACCTACATTTCACAACTCGA-TATGGAT
* *
109615226 AATACCATACCTACATTTCTCAACTCGGTATGGAT
1 AATACCATACCTACATTTCACAACTCGATATGGAT
*
109615261 GATACCATACCTACATTTCACAACTCGATATGGAT
1 AATACCATACCTACATTTCACAACTCGATATGGAT
* * *
109615296 GATACCATACCTACATGTCACAACTCGGTATGGAT
1 AATACCATACCTACATTTCACAACTCGATATGGAT
* ** * *
109615331 GATACCATACCTATGTTTCACATCTCTG-TATGGTT
1 AATACCATACCTACATTTCACAACTC-GATATGGAT
* * *
109615366 AATACCATACCTACGTTTCACAACTCGGTATGGTT
1 AATACCATACCTACATTTCACAACTCGATATGGAT
* * * *
109615401 AATACCATACCTACGTATCATAGCTC-AGTATGGAT
1 AATACCATACCTACATTTCACAACTCGA-TATGGAT
* * *
109615436 GATGCCATACCTACATTTCACAACTCGGTATGG-T
1 AATACCATACCTACATTTCACAACTCGATATGGAT
* *
109615470 TATACCATACCTAAATTTC
1 AATACCATACCTACATTTC
109615489 GCACTTTGCC
Statistics
Matches: 315, Mismatches: 44, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
34 22 0.07
35 292 0.93
36 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCGATATGGAT
Found at i:109615199 original size:70 final size:70
Alignment explanation
Indices: 109615086--109615488 Score: 524
Period size: 70 Copynumber: 5.8 Consensus size: 70
109615076 TCCTCATTGA
* * * **
109615086 AATACCATACCTACATTTCACAACTCGATATGGGA-AATGCCATACCTACATTTCTTAACTCAGT
1 AATACCATACCTACATTTCACAACTCGGTAT-GGATGATACCATACCTACATTTCACAACTCAGT
109615150 ATGGAT
65 ATGGAT
* * *
109615156 AATACCATACCTACATTTCTCAACTCGGTATGGATGATACCATACCTACGTTTCACAACTTAGTA
1 AATACCATACCTACATTTCACAACTCGGTATGGATGATACCATACCTACATTTCACAACTCAGTA
109615221 TGGAT
66 TGGAT
*
109615226 AATACCATACCTACATTTCTCAACTCGGTATGGATGATACCATACCTACATTTCACAACTC-GAT
1 AATACCATACCTACATTTCACAACTCGGTATGGATGATACCATACCTACATTTCACAACTCAG-T
109615290 ATGGAT
65 ATGGAT
* * ** * *
109615296 GATACCATACCTACATGTCACAACTCGGTATGGATGATACCATACCTATGTTTCACATCTCTGTA
1 AATACCATACCTACATTTCACAACTCGGTATGGATGATACCATACCTACATTTCACAACTCAGTA
*
109615361 TGGTT
66 TGGAT
* * * * * * *
109615366 AATACCATACCTACGTTTCACAACTCGGTATGGTTAATACCATACCTACGTATCATAGCTCAGTA
1 AATACCATACCTACATTTCACAACTCGGTATGGATGATACCATACCTACATTTCACAACTCAGTA
109615431 TGGAT
66 TGGAT
* * * *
109615436 GATGCCATACCTACATTTCACAACTCGGTATGG-TTATACCATACCTAAATTTC
1 AATACCATACCTACATTTCACAACTCGGTATGGATGATACCATACCTACATTTC
109615489 GCACTTTGCC
Statistics
Matches: 295, Mismatches: 35, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
69 20 0.07
70 274 0.93
71 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (70 bp):
AATACCATACCTACATTTCACAACTCGGTATGGATGATACCATACCTACATTTCACAACTCAGTA
TGGAT
Found at i:109615269 original size:105 final size:105
Alignment explanation
Indices: 109615087--109615488 Score: 504
Period size: 105 Copynumber: 3.8 Consensus size: 105
109615077 CCTCATTGAA
* ** *
109615087 ATACCATACCTACATTTCACAACTC-GATATGGGA-AATGCCATACCTACATTTCTTAACTCAGT
1 ATACCATACCTACATTTCACAACTCAG-TAT-GGATAATACCATACCTACATTTCACAACTCGGT
*
109615150 ATGGATAATACCATACCTACATTTCTCAACTCGGTATGGATG
64 ATGGATAATACCATACCTACATTTCACAACTCGGTATGGATG
* * *
109615192 ATACCATACCTACGTTTCACAACTTAGTATGGATAATACCATACCTACATTTCTCAACTCGGTAT
1 ATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACTCGGTAT
* *
109615257 GGATGATACCATACCTACATTTCACAACTCGATATGGATG
66 GGATAATACCATACCTACATTTCACAACTCGGTATGGATG
* * * ** * *
109615297 ATACCATACCTACATGTCACAACTCGGTATGGATGATACCATACCTATGTTTCACATCTCTGTAT
1 ATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACTCGGTAT
* * * *
109615362 GGTTAATACCATACCTACGTTTCACAACTCGGTATGGTTA
66 GGATAATACCATACCTACATTTCACAACTCGGTATGGATG
* * * * * *
109615402 ATACCATACCTACGTATCATAGCTCAGTATGGATGATGCCATACCTACATTTCACAACTCGGTAT
1 ATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACTCGGTAT
* *
109615467 GG-TTATACCATACCTAAATTTC
66 GGATAATACCATACCTACATTTC
109615489 GCACTTTGCC
Statistics
Matches: 258, Mismatches: 37, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
104 20 0.08
105 237 0.92
106 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (105 bp):
ATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACTCGGTAT
GGATAATACCATACCTACATTTCACAACTCGGTATGGATG
Found at i:109616613 original size:32 final size:33
Alignment explanation
Indices: 109616572--109616640 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
109616562 CTCAATTAAG
*
109616572 ATAATACTTTTCCTAGACATTTTAAGTTATTT-
1 ATAATACTTTTCCTAGACATTATAAGTTATTTC
109616604 ATAATACTTTTCCTAGACATTATAAGTTATTTC
1 ATAATACTTTTCCTAGACATTATAAGTTATTTC
109616637 ATAA
1 ATAA
109616641 CTATTGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (33 bp):
ATAATACTTTTCCTAGACATTATAAGTTATTTC
Found at i:109623878 original size:28 final size:28
Alignment explanation
Indices: 109623846--109623929 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
109623836 AACTTCGATC
109623846 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
109623874 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
109623896 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
109623924 ACGTGT
1 ACGTGT
109623930 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:109623919 original size:50 final size:50
Alignment explanation
Indices: 109623790--109623973 Score: 253
Period size: 50 Copynumber: 3.7 Consensus size: 50
109623780 ATCTATTGTG
* * *
109623790 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * **
109623841 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
109623891 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
109623941 -GGTCACATGTGTAGTACTAAGTGTAGGCTACTA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
109623974 TGCGTACTAG
Statistics
Matches: 117, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
49 31 0.26
50 46 0.39
51 40 0.34
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:109627579 original size:25 final size:25
Alignment explanation
Indices: 109627530--109627584 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
109627520 ATTTAGAAAC
109627530 ATTTAAATAGCATCTAAAAAATTAA
1 ATTTAAATAGCATCTAAAAAATTAA
* * *
109627555 TTTTAAATAG-ATTTAAAAATTTTAA
1 ATTTAAATAGCATCTAAAAA-ATTAA
109627580 ATTTA
1 ATTTA
109627585 GAAACAACGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (25 bp):
ATTTAAATAGCATCTAAAAAATTAA
Found at i:109635860 original size:96 final size:96
Alignment explanation
Indices: 109635694--109635887 Score: 298
Period size: 96 Copynumber: 2.0 Consensus size: 96
109635684 GTGTCCGAGG
* * * * * *
109635694 AAGTCTGTTATCGATGGGAATGATCGAGTAGATACGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATCGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
109635759 AAAAGCCGAAGCCAAGAGGGCGAAGAGGAGC
66 AAAAGCCGAAGCCAAGAGGGCGAAGAGGAGC
*
109635790 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATCGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
* * *
109635855 TAAAGCCGAAGCCAAGAGGGCTAAGTGGAGC
66 AAAAGCCGAAGCCAAGAGGGCGAAGAGGAGC
109635886 AA
1 AA
109635888 AAAGAAGCGA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.34, C:0.18, G:0.35, T:0.13
Consensus pattern (96 bp):
AAGTCTGTCATCGAAGGGAACGATCGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
AAAAGCCGAAGCCAAGAGGGCGAAGAGGAGC
Done.