Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 177 of 335
Found at i:53117022 original size:49 final size:51
Alignment explanation
Indices: 53116914--53117039 Score: 166
Period size: 49 Copynumber: 2.5 Consensus size: 51
53116904 TGGATACCCG
* * * *
53116914 GTGGCCTGCACATAGTACCACCCTTATAGTCAAAGCTATCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTAGACAAAGCTATCTTCTTCACAAA
* * *
53116965 GTGGCCTTCACATAGTACCACACTTGT-GACCAAGCTTTC-TCTTCTCAAA
1 GTGGCCTTCACATAGTACCACACTTGTAGACAAAGCTATCTTCTTCACAAA
*
53117014 GTGGCCTTCACATAGTACAACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
53117040 AGTCACTAGT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
49 34 0.51
50 9 0.13
51 24 0.36
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTAGACAAAGCTATCTTCTTCACAAA
Found at i:53119231 original size:31 final size:31
Alignment explanation
Indices: 53119196--53119258 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
53119186 AAGTTGTAGG
53119196 TATAAGGCTTCTGCATGAGATTGTCAACGAT
1 TATAAGGCTTCTGCATGAGATTGTCAACGAT
*
53119227 TATAAGGCTTCTGCATGAGATTGTCAGCGAT
1 TATAAGGCTTCTGCATGAGATTGTCAACGAT
53119258 T
1 T
53119259 GAATTGATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (31 bp):
TATAAGGCTTCTGCATGAGATTGTCAACGAT
Found at i:53120850 original size:23 final size:26
Alignment explanation
Indices: 53120822--53120871 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
53120812 AATATTTAAT
53120822 AAATT-AATAAT-ATT-TTAAATAAA
1 AAATTAAATAATAATTATTAAATAAA
*
53120845 AAATTAAATAATAATTATTTAATAAA
1 AAATTAAATAATAATTATTAAATAAA
53120871 A
1 A
53120872 TATCATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
24 6 0.26
25 3 0.13
26 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATTAAATAATAATTATTAAATAAA
Found at i:53122961 original size:23 final size:23
Alignment explanation
Indices: 53122933--53122979 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
53122923 AGAGAGAAAA
53122933 TTTTAAATAAGTGAAATGAATAG
1 TTTTAAATAAGTGAAATGAATAG
53122956 TTTTAAATAAGTGAAATGAATAG
1 TTTTAAATAAGTGAAATGAATAG
53122979 T
1 T
53122980 AAAATTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (23 bp):
TTTTAAATAAGTGAAATGAATAG
Found at i:53122990 original size:23 final size:22
Alignment explanation
Indices: 53122937--53122984 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
53122927 AGAAAATTTT
*
53122937 AAATAAGTGAAATGAATAGTTTT
1 AAATAAGTGAAATGAATAG-TTA
53122960 AAATAAGTGAAATGAATAG-TA
1 AAATAAGTGAAATGAATAGTTA
53122981 AAAT
1 AAAT
53122985 TTAAGTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
23 19 0.79
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (22 bp):
AAATAAGTGAAATGAATAGTTA
Found at i:53124808 original size:40 final size:40
Alignment explanation
Indices: 53124742--53124908 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
53124732 AAATTGAATG
* * *
53124742 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
53124781 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
53124821 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
53124861 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
53124901 ATATCCGG
1 ATATCCGG
53124909 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:53135644 original size:28 final size:27
Alignment explanation
Indices: 53135581--53135650 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
53135571 ATAGTGAGTC
*
53135581 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
53135608 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
53135636 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53135651 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:53139627 original size:29 final size:29
Alignment explanation
Indices: 53139595--53139667 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
53139585 CTTCGAGCTC
* *
53139595 GCACACCCAGTGCCGTATTTTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
53139624 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
53139653 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
53139668 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:53146277 original size:29 final size:29
Alignment explanation
Indices: 53146245--53146317 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
53146235 CTTCGAGCTC
* *
53146245 GCACACCCAGTGCCGTATTTTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
53146274 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
53146303 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
53146318 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:53152235 original size:21 final size:21
Alignment explanation
Indices: 53152211--53152252 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53152201 TTTGCCTAGG
*
53152211 ATGTAAATTGAATCAAATTGA
1 ATGTAAATTGAATAAAATTGA
* *
53152232 ATGTGAATTGTATAAAATTGA
1 ATGTAAATTGAATAAAATTGA
53152253 TGATTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (21 bp):
ATGTAAATTGAATAAAATTGA
Found at i:53152767 original size:24 final size:24
Alignment explanation
Indices: 53152740--53152877 Score: 102
Period size: 24 Copynumber: 5.7 Consensus size: 24
53152730 TGTTAAATTG
53152740 GCTCTTTGTGAGCTTCCTGATATT
1 GCTCTTTGTGAGCTTCCTGATATT
** *
53152764 GCTCGCT-TGAACTTCCTGATATT
1 GCTCTTTGTGAGCTTCCTGATATT
* * * * * *
53152787 AGTTATCTG-GAGCTTCCCGTTACATG
1 -GCTCTTTGTGAGCTT-CC-TGATATT
*
53152813 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTGTGAGCTTCCTGATATT
* *
53152837 GTTCTTTGTGAACTTCCTGATTATT
1 GCTCTTTGTGAGCTTCCTGA-TATT
*
53152862 GCTC-TTATGAGCTTCC
1 GCTCTTTGTGAGCTTCC
53152878 CATTATATAG
Statistics
Matches: 87, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
23 15 0.17
24 47 0.54
25 15 0.17
26 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.42
Consensus pattern (24 bp):
GCTCTTTGTGAGCTTCCTGATATT
Found at i:53157998 original size:40 final size:40
Alignment explanation
Indices: 53157871--53158000 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
53157861 ATGCTGGAAA
* *
53157871 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
53157911 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
53157951 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
53157991 TTATATCCGG
1 TTATATCCGG
53158001 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:53163090 original size:14 final size:14
Alignment explanation
Indices: 53163071--53163100 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
53163061 GCCAATCACG
53163071 ATACCCGAGTGGAA
1 ATACCCGAGTGGAA
53163085 ATACCCGAGTGGAA
1 ATACCCGAGTGGAA
53163099 AT
1 AT
53163101 GGGTATCCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (14 bp):
ATACCCGAGTGGAA
Found at i:53163174 original size:30 final size:31
Alignment explanation
Indices: 53163119--53163181 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
53163109 GGACTGCCAT
*
53163119 TGTCAGCAAGTAAGAATTTGATGCGGTTTGGG
1 TGTCAGCAAGTAAGAA-TGGATGCGGTTTGGG
53163151 TGTCAGCAAGTAAGAA-GGATGCGGTTTGGG
1 TGTCAGCAAGTAAGAATGGATGCGGTTTGGG
53163181 T
1 T
53163182 CGTGGTAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 14 0.47
32 16 0.53
ACGTcount: A:0.25, C:0.10, G:0.37, T:0.29
Consensus pattern (31 bp):
TGTCAGCAAGTAAGAATGGATGCGGTTTGGG
Found at i:53165983 original size:40 final size:40
Alignment explanation
Indices: 53165856--53165985 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
53165846 ATGCTGGAAA
* *
53165856 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
53165896 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
53165936 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
53165976 TTATATCCGG
1 TTATATCCGG
53165986 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:53177206 original size:19 final size:19
Alignment explanation
Indices: 53177172--53177210 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
53177162 AAGTTCGTAC
*
53177172 TTTGGCCCATTTTCTCTGTT
1 TTTGGCCCAGTTTCTC-GTT
53177192 TTTGGCCC-GTTTCTCGTT
1 TTTGGCCCAGTTTCTCGTT
53177210 T
1 T
53177211 ATTTCGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.03, C:0.26, G:0.18, T:0.54
Consensus pattern (19 bp):
TTTGGCCCAGTTTCTCGTT
Found at i:53181999 original size:45 final size:45
Alignment explanation
Indices: 53181935--53182028 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
53181925 TGCTCATTCT
*
53181935 CTGTGTATCTTAAGCTTCGCCTTATTTCTCTTTTGTTTCTACGTA
1 CTGTGTATCTTAAGCTTCGCCTTATTTCTCTTTGGTTTCTACGTA
53181980 CTGTGTATCTTAAGCTTCGCCTTATTTCTCTTTGGTTTCTACGTA
1 CTGTGTATCTTAAGCTTCGCCTTATTTCTCTTTGGTTTCTACGTA
53182025 CTGT
1 CTGT
53182029 ACGATCGATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.13, C:0.22, G:0.15, T:0.50
Consensus pattern (45 bp):
CTGTGTATCTTAAGCTTCGCCTTATTTCTCTTTGGTTTCTACGTA
Found at i:53195442 original size:27 final size:27
Alignment explanation
Indices: 53195346--53195444 Score: 67
Period size: 27 Copynumber: 3.7 Consensus size: 27
53195336 TTAGTTTACC
* * *
53195346 AAATTATTGAAATACCCTTGACTTT-TA
1 AAATTATCGAAATACCC-TCAATTTATA
* *
53195373 AAATTA-CCAAAGTACCCCCAATTTATA
1 AAATTATCGAAA-TACCCTCAATTTATA
* * ***
53195400 GAATTACCGTTTTACCCTCAATTTATA
1 AAATTATCGAAATACCCTCAATTTATA
*
53195427 AAATTATTGAAATACCCT
1 AAATTATCGAAATACCCT
53195445 TGTAGGGTAG
Statistics
Matches: 52, Mismatches: 17, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
26 7 0.13
27 44 0.85
28 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.35
Consensus pattern (27 bp):
AAATTATCGAAATACCCTCAATTTATA
Found at i:53195458 original size:27 final size:27
Alignment explanation
Indices: 53195435--53195596 Score: 198
Period size: 27 Copynumber: 6.0 Consensus size: 27
53195425 TAAAATTATT
*
53195435 GAAATACCCTTGTAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
*
53195462 GAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * * *
53195489 AAAATACCCCTGTAGAGTAGAATTATC
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
53195516 AAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
53195543 GAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * * *
53195570 TAGATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
53195597 ATTTTGCCCT
Statistics
Matches: 114, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 114 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAATTACC
Found at i:53195494 original size:54 final size:53
Alignment explanation
Indices: 53195436--53195597 Score: 218
Period size: 54 Copynumber: 3.0 Consensus size: 53
53195426 AAAATTATTG
*
53195436 AAATACCCTTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAGAAATACCA
1 AAATACCCCTGTAGGGTAGAATTACT-AAATACCCTTGTAGGGTAGAAATACCA
* * *
53195490 AAATACCCCTGTAGAGTAGAATTATCAAAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCCTGTAGGGTAGAATTA-CTAAATACCCTTGTAGGGTAGAAATACCA
* * *
53195544 AAATACCCCTATAGGGTAGAATTACCTAGATACCCTTGTGGGGTA-AAATTACCA
1 AAATACCCCTGTAGGGTAGAATTA-CTAAATACCCTTGTAGGGTAGAAA-TACCA
53195598 TTTTGCCCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 3 0.03
54 91 0.96
55 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (53 bp):
AAATACCCCTGTAGGGTAGAATTACTAAATACCCTTGTAGGGTAGAAATACCA
Found at i:53195594 original size:81 final size:81
Alignment explanation
Indices: 53195425--53195594 Score: 223
Period size: 81 Copynumber: 2.1 Consensus size: 81
53195415 CCTCAATTTA
** * * * *
53195425 TAAAATTATTGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAGAAATACCA
1 TAAAATTATCAAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTATAGGGTAGAAATACCA
53195490 AAATACCCCTGTAGAG
66 AAATACCCCTGTAGAG
* * *
53195506 TAGAATTATCAAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTATAGGGTAGAATTACCT
1 TAAAATTATCAAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTATAGGGTAGAAATACCA
* * * *
53195571 AGATACCCTTGTGGGG
66 AAATACCCCTGTAGAG
53195587 TAAAATTA
1 TAAAATTA
53195595 CCATTTTGCC
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (81 bp):
TAAAATTATCAAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTATAGGGTAGAAATACCA
AAATACCCCTGTAGAG
Found at i:53196036 original size:22 final size:22
Alignment explanation
Indices: 53195984--53196048 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
53195974 GCTAATTATT
* *
53195984 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
53196006 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
53196028 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
53196049 ACGTATTTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:53196224 original size:27 final size:26
Alignment explanation
Indices: 53196194--53196301 Score: 144
Period size: 27 Copynumber: 4.0 Consensus size: 26
53196184 ATTCTGTTAA
* *
53196194 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTG-TTCTG
*
53196221 GTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTCTGCCAC-AATATCTGTTCTG
53196248 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGT-TCTG
* *
53196275 GTGACTCTGTCACAATATCTGTTCTG
1 GTGGCTCTGCCACAATATCTGTTCTG
53196301 G
1 G
53196302 CAGCCATGTT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
26 14 0.19
27 53 0.72
28 7 0.09
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (26 bp):
GTGGCTCTGCCACAATATCTGTTCTG
Found at i:53196450 original size:25 final size:25
Alignment explanation
Indices: 53196422--53196483 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
53196412 CATCCACATT
* * *
53196422 CTGATTCTGATTCTGTTACTTGATA
1 CTGATTCTGATTCTGTCACCTAATA
* *
53196447 CTGATTCTGATTTTGTCACCTAATT
1 CTGATTCTGATTCTGTCACCTAATA
53196472 CTGATTCTGATT
1 CTGATTCTGATT
53196484 ATTATTTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (25 bp):
CTGATTCTGATTCTGTCACCTAATA
Found at i:53196554 original size:31 final size:32
Alignment explanation
Indices: 53196519--53196583 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
53196509 TGTTTCTTAT
* *
53196519 TCTG-TAATGGGCTAAGGCCCATTTGGTACTG
1 TCTGTTAATGGGCTAAGGCCCAATTGATACTG
53196550 TCTGTTATAATGGGCTAAGGCCCAATTGATACTG
1 TCTG-T-TAATGGGCTAAGGCCCAATTGATACTG
53196584 AAACTGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 4 0.14
34 25 0.86
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (32 bp):
TCTGTTAATGGGCTAAGGCCCAATTGATACTG
Found at i:53198342 original size:40 final size:40
Alignment explanation
Indices: 53198297--53198427 Score: 138
Period size: 40 Copynumber: 3.3 Consensus size: 40
53198287 CGGATTATAA
53198297 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
53198337 CCGGATAGAATGTCTCGCACGAATGCCTTTGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
53198377 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
53198417 CCGGATATAAT
1 CCGGATATAAT
53198428 TTCCGGCATA
Statistics
Matches: 70, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
39 1 0.01
40 69 0.99
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53208056 original size:28 final size:28
Alignment explanation
Indices: 53207987--53208058 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
53207977 AATAAGCCCG
* *
53207987 CACACTTAGTGCT-TAATAGTCGAACTCA
1 CACACTTAGTGCTAT-ATAATCAAACTCA
*
53208015 CACACTTAGTGCTATATAATCAAACTCG
1 CACACTTAGTGCTATATAATCAAACTCA
*
53208043 CGCACTTAGTGCTATA
1 CACACTTAGTGCTATA
53208059 CAATTTGAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (28 bp):
CACACTTAGTGCTATATAATCAAACTCA
Found at i:53210749 original size:4 final size:4
Alignment explanation
Indices: 53210740--53210768 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
53210730 ATGGAATTAA
53210740 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
53210769 ACACCCCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:53212273 original size:39 final size:40
Alignment explanation
Indices: 53212163--53212306 Score: 202
Period size: 39 Copynumber: 3.6 Consensus size: 40
53212153 TCGTTCAAAC
* * ** * *
53212163 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATCATAACTCGCACAATT
* *
53212203 GCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCATAACTCGCACAATT
53212243 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCATAACTCGCACAATT
53212282 GCCTTCGGG-CTTAGCCCGGATATCA
1 GCCTTCGGGACTTAGCCCGGATATCA
53212307 CTCGAACATT
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 53 0.56
40 41 0.44
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATCATAACTCGCACAATT
Found at i:53221812 original size:28 final size:29
Alignment explanation
Indices: 53221780--53221878 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
53221770 ATAATAAGCC
*
53221780 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
53221808 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
53221836 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
53221865 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53221879 CAATCTCATG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:53225746 original size:28 final size:29
Alignment explanation
Indices: 53225706--53225778 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
53225696 CCTCCGAGCT
** *
53225706 CGCACACCCAGTGCCGTAT-TTTCCAGCT
1 CGCACACTTAGTGCCGTATATTTCCAGCA
* *
53225734 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCA
53225763 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
53225779 ATCTCGTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCGTATATTTCCAGCA
Found at i:53225767 original size:29 final size:28
Alignment explanation
Indices: 53225648--53225777 Score: 91
Period size: 29 Copynumber: 4.5 Consensus size: 28
53225638 TACTCGATTT
* * *
53225648 CGCACACTTAGTGCCACGTAATTT-AAGCC
1 CGCACACTTAGTGCCA--TATTTTCCAGCA
** *** *
53225677 CGCACACACAGTGCCATACCCTCCGAGCT
1 CGCACACTTAGTGCCATATTTTCC-AGCA
** * *
53225706 CGCACACCCAGTGCCGTATTTTCCAGCT
1 CGCACACTTAGTGCCATATTTTCCAGCA
*
53225734 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATAT-TTTCCAGCA
53225763 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
53225778 GATCTCGTCA
Statistics
Matches: 80, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
27 3 0.04
28 19 0.24
29 58 0.73
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATTTTCCAGCA
Found at i:53233542 original size:29 final size:29
Alignment explanation
Indices: 53233510--53233587 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
53233500 ATACCCTCCG
** *
53233510 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* *
53233539 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
53233568 AGCACGCACACTTAGTGCCG
1 AGCTCGCACACTTAGTGCCG
53233588 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:53241764 original size:29 final size:29
Alignment explanation
Indices: 53241731--53241833 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
53241721 CCTCCGAACT
** * * *
53241731 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
53241760 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
53241789 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
53241818 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
53241834 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:53244984 original size:39 final size:40
Alignment explanation
Indices: 53244880--53245062 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
53244870 GCTACTCGTT
53244880 CAAATGCCTTCGGGAC--AGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
53244918 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
53244958 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
53244997 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
53245038 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53245063 CATCATTCGA
Statistics
Matches: 132, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
38 16 0.12
39 42 0.32
40 61 0.46
41 13 0.10
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:53245003 original size:79 final size:82
Alignment explanation
Indices: 53244880--53245062 Score: 247
Period size: 79 Copynumber: 2.3 Consensus size: 82
53244870 GCTACTCGTT
53244880 CAAATGCCTTCGGGAC--AGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
53244941 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
53244958 CAAATGCCTTC-GGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
*
53245021 GATATAGTCACTTAGCA
66 GATATAGTAACTTAGCA
53245038 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53245063 CATCATTCGA
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
77 4 0.04
78 14 0.15
79 51 0.55
80 23 0.25
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:53252094 original size:40 final size:40
Alignment explanation
Indices: 53251851--53252094 Score: 296
Period size: 40 Copynumber: 6.1 Consensus size: 40
53251841 GGAGTTTAAT
** * **
53251851 CGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATGGCC
1 CGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAACC
* *
53251891 CGGTTATAGTTACTCGCACAAATGCCTTCGGGACTTAACC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACC
*
53251931 CGGATCTAGTAACTCGCACAAATGCCTTCGGGACTTAACC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACC
*
53251971 CGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACC
* * **
53252011 CGGATTTAGTAACTCGCACAAATGCCTT-TGGATCTTAGTC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACC
* * *
53252051 CGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCC
1 CGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACC
53252091 CGGA
1 CGGA
53252095 CATCATTCGA
Statistics
Matches: 182, Mismatches: 18, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
39 4 0.02
40 167 0.92
41 11 0.06
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACC
Found at i:53254424 original size:40 final size:39
Alignment explanation
Indices: 53254259--53254442 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
53254249 AAATTGAATG
* * *
53254259 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
53254299 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
53254339 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
53254379 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
53254418 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
53254443 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:53254467 original size:80 final size:81
Alignment explanation
Indices: 53254299--53254487 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
53254289 GCTGGAAATT
* * * *
53254299 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
53254364 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
53254380 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
53254443 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
53254459 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
53254488 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:53257449 original size:6 final size:6
Alignment explanation
Indices: 53257438--53257463 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53257428 AACCAAAATT
53257438 AATTTA AATTTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AA
53257464 ACTTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:53259556 original size:68 final size:67
Alignment explanation
Indices: 53259484--53259633 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
53259474 CATCATGTGT
* * * *
53259484 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
53259546 ATGTAG
62 ATGTAG
** * *
53259552 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
53259617 AG
66 AG
53259619 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
53259634 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:53259589 original size:64 final size:64
Alignment explanation
Indices: 53259508--53259691 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
53259498 AGACATTATG
* *
53259508 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
53259572 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
53259637 AA
63 AA
* * * *
53259639 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
53259692 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53260778 original size:2 final size:2
Alignment explanation
Indices: 53260771--53260796 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53260761 GTATCATGAC
53260771 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
53260797 GACTAGTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53264003 original size:68 final size:67
Alignment explanation
Indices: 53263931--53264080 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
53263921 CATCATGTGT
* * * *
53263931 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
53263993 ATGTAG
62 ATGTAG
** * *
53263999 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
53264064 AG
66 AG
53264066 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
53264081 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:53264036 original size:64 final size:64
Alignment explanation
Indices: 53263955--53264138 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
53263945 AGACATTATG
* *
53263955 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
53264019 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
53264084 AA
63 AA
* * * *
53264086 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
53264139 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53269149 original size:18 final size:18
Alignment explanation
Indices: 53269126--53269165 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
53269116 CCAACTCTCT
53269126 AACTCAATTTGGGTCTAC
1 AACTCAATTTGGGTCTAC
53269144 AACTCAATTTGGGTCTAC
1 AACTCAATTTGGGTCTAC
53269162 AACT
1 AACT
53269166 ACTCCACTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (18 bp):
AACTCAATTTGGGTCTAC
Found at i:53269803 original size:36 final size:36
Alignment explanation
Indices: 53269756--53269825 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
53269746 CACTTTTTAG
*
53269756 ATTGAATTCATGTTATTGCCTTTGAAAGGTTGTGGC
1 ATTGAATTCATGTTATTGCCTTTCAAAGGTTGTGGC
53269792 ATTGAATTCATGTTATTGCCTTTCAAAGGTTGTG
1 ATTGAATTCATGTTATTGCCTTTCAAAGGTTGTG
53269826 ACATAGTCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (36 bp):
ATTGAATTCATGTTATTGCCTTTCAAAGGTTGTGGC
Found at i:53273881 original size:8 final size:8
Alignment explanation
Indices: 53273868--53273892 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53273858 AATAACATAT
53273868 ATTACCTA
1 ATTACCTA
53273876 ATTACCTA
1 ATTACCTA
53273884 ATTACCTA
1 ATTACCTA
53273892 A
1 A
53273893 CCATTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTACCTA
Found at i:53276614 original size:17 final size:17
Alignment explanation
Indices: 53276592--53276624 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53276582 AACTTAAGTA
53276592 TTGATATCC-ATAGCTAT
1 TTGATA-CCTATAGCTAT
53276609 TTGATACCTATAGCTA
1 TTGATACCTATAGCTA
53276625 CTCGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (17 bp):
TTGATACCTATAGCTAT
Found at i:53284964 original size:37 final size:37
Alignment explanation
Indices: 53284899--53285043 Score: 247
Period size: 37 Copynumber: 3.9 Consensus size: 37
53284889 AGCTCAGATG
* *
53284899 AAATCTCCACAC-AAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
53284935 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
53284972 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
53285009 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
53285044 ATATATTTCC
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 12 0.12
37 91 0.88
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:53285244 original size:48 final size:48
Alignment explanation
Indices: 53285189--53285433 Score: 463
Period size: 48 Copynumber: 5.1 Consensus size: 48
53285179 ACACATCGCC
*
53285189 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCCCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
53285237 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
53285285 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
53285333 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
53285381 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
53285429 TACAT
1 TACAT
53285434 CAATTTCAGC
Statistics
Matches: 194, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 194 1.00
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:53288927 original size:40 final size:40
Alignment explanation
Indices: 53288883--53289240 Score: 511
Period size: 40 Copynumber: 9.0 Consensus size: 40
53288873 GAATACACAT
* * *
53288883 CACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
53288923 CACCAGCACGAATGCTCTTTGGGACTTAACCCTGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * * ***
53288963 CTCTAGCACAAATGCTCTTTAAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
53289003 CACCAGCACAAATGCTCTTCGGGACTTAGCCCGGATACAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * * *
53289043 CACTAGCACGAATGCTCTTCGGGACTTAGCCTGGATACAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
53289083 CACTAGCACGAATGCTCTTCGGGACTTAGCCCGAATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
53289123 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
53289163 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
53289203 CACCAGCACAAATGCTCTTC-GGACTTAGCCCGGATATA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
53289241 TACAACTCTC
Statistics
Matches: 288, Mismatches: 30, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
39 18 0.06
40 270 0.94
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:53290560 original size:37 final size:37
Alignment explanation
Indices: 53290501--53290682 Score: 330
Period size: 37 Copynumber: 4.9 Consensus size: 37
53290491 AGCTCAGATG
* *
53290501 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
53290538 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
53290575 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC-
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
53290611 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
53290648 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
53290683 ATATATTTCC
Statistics
Matches: 141, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
36 36 0.26
37 105 0.74
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:53290644 original size:73 final size:74
Alignment explanation
Indices: 53290501--53290682 Score: 330
Period size: 73 Copynumber: 2.5 Consensus size: 74
53290491 AGCTCAGATG
* *
53290501 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
53290566 ACCCGGACA
66 ACCCGGACA
53290575 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC-AAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
53290639 ACCCGGACA
66 ACCCGGACA
*
53290648 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
53290683 ATATATTTCC
Statistics
Matches: 105, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 71 0.68
74 34 0.32
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (74 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
ACCCGGACA
Found at i:53290997 original size:94 final size:94
Alignment explanation
Indices: 53290829--53291112 Score: 438
Period size: 90 Copynumber: 3.1 Consensus size: 94
53290819 ACACATCGCC
* *
53290829 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATC-CATACATATTTCACACTAG
1 TACATATTTCACA-T-TCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
53290893 CCATTCGGCTTTACCACATATACATATCTCA
64 CCATTCGGCTTTACCACATATACATATCTCA
*
53290924 TACATATTTCACATTCCATTCGGCTTTACCACATATACATATCTCATACATACTTCACATTAGCC
1 TACATATTTCACATTCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCC
53290989 ATTCGGCTTTACCACATATACATATCTCA
66 ATTCGGCTTTACCACATATACATATCTCA
*
53291018 TACATATTTCACATTAGCCATTCGG------CACATATATATATCTCATACATATTTCACATTAG
1 TACATATTTCACATT--CCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
*
53291077 CCATTCGGCTTTACCACATATACATATCTTA
64 CCATTCGGCTTTACCACATATACATATCTCA
53291108 TACAT
1 TACAT
53291113 CAATTTCAGC
Statistics
Matches: 180, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
90 67 0.37
93 28 0.16
94 64 0.36
95 13 0.07
96 8 0.04
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (94 bp):
TACATATTTCACATTCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCC
ATTCGGCTTTACCACATATACATATCTCA
Found at i:53291010 original size:48 final size:48
Alignment explanation
Indices: 53290829--53291112 Score: 460
Period size: 48 Copynumber: 6.1 Consensus size: 48
53290819 ACACATCGCC
*
53290829 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATC-CA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
53290876 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
53290924 TACATATTTCACATT--CCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
53290970 TACATACTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
53291018 TACATATTTCACATTAGCCATTCGG------CACATATATATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
53291060 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
53291108 TACAT
1 TACAT
53291113 CAATTTCAGC
Statistics
Matches: 222, Mismatches: 6, Indels: 17
0.91 0.02 0.07
Matches are distributed among these distances:
42 41 0.18
46 45 0.20
47 45 0.20
48 91 0.41
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:53291047 original size:42 final size:42
Alignment explanation
Indices: 53291001--53291085 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
53290991 TCGGCTTTAC
53291001 CACATATACATATCTCATACATATTTCACATTAGCCATTCGG
1 CACATATACATATCTCATACATATTTCACATTAGCCATTCGG
*
53291043 CACATATATATATCTCATACATATTTCACATTAGCCATTCGG
1 CACATATACATATCTCATACATATTTCACATTAGCCATTCGG
53291085 C
1 C
53291086 TTTACCACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (42 bp):
CACATATACATATCTCATACATATTTCACATTAGCCATTCGG
Found at i:53294888 original size:25 final size:25
Alignment explanation
Indices: 53294852--53294902 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
53294842 CTAATTATGT
53294852 AAGCATAAAACGCATCTTGTAGATG
1 AAGCATAAAACGCATCTTGTAGATG
*
53294877 AAGCATAGAACGCATCTTGTAGATG
1 AAGCATAAAACGCATCTTGTAGATG
53294902 A
1 A
53294903 TGTTGACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (25 bp):
AAGCATAAAACGCATCTTGTAGATG
Found at i:53299458 original size:17 final size:17
Alignment explanation
Indices: 53299405--53299460 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
53299395 TTTGAACTTT
*
53299405 TCAAAAGTATTTTTGAG
1 TCAAAAGTATTTTTTAG
* *
53299422 ACAAAA--ATGTTTT-G
1 TCAAAAGTATTTTTTAG
53299436 -CAAAAGTATTTTTTAG
1 TCAAAAGTATTTTTTAG
53299452 TCAAAAGTA
1 TCAAAAGTA
53299461 GAAGCAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 5 0.16
14 1 0.03
15 11 0.35
16 1 0.03
17 13 0.42
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (17 bp):
TCAAAAGTATTTTTTAG
Found at i:53301244 original size:21 final size:19
Alignment explanation
Indices: 53301195--53301244 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
53301185 AAATAATCCC
*
53301195 CTGTATTTCATTTTTTATT
1 CTGTATTTAATTTTTTATT
*
53301214 CAGTATTTTAATTTTATTATTT
1 CTGTA-TTTAATTTT-TTA-TT
53301236 CTGTATTTA
1 CTGTATTTA
53301245 TAATCTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 7 0.28
22 6 0.24
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (19 bp):
CTGTATTTAATTTTTTATT
Found at i:53301952 original size:7 final size:7
Alignment explanation
Indices: 53301942--53301967 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53301932 ATAGTTAAAA
53301942 AATATAT
1 AATATAT
53301949 AATATAT
1 AATATAT
53301956 AATATAT
1 AATATAT
53301963 AATAT
1 AATAT
53301968 TTATTCGATT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATAT
Found at i:53304838 original size:30 final size:30
Alignment explanation
Indices: 53304782--53304840 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53304772 ACTCGAACAA
* * *
53304782 TTTACTCTATTCGGTTCAAATGAATTTCAT
1 TTTACTCGATTCGATTCAAATAAATTTCAT
53304812 TTTACTCGATTCGATTCGAAA-AAATTTCA
1 TTTACTCGATTCGATTC-AAATAAATTTCA
53304841 AATCGAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (30 bp):
TTTACTCGATTCGATTCAAATAAATTTCAT
Found at i:53304986 original size:40 final size:41
Alignment explanation
Indices: 53304917--53304998 Score: 148
Period size: 40 Copynumber: 2.0 Consensus size: 41
53304907 AGTCAATGAA
53304917 TATAGAGTGTTCCCCAATAGATATGAGATTGAAATTAACTT
1 TATAGAGTGTTCCCCAATAGATATGAGATTGAAATTAACTT
*
53304958 TATAGAGTGTT-CCCTATAGATATGAGATTGAAATTAACTT
1 TATAGAGTGTTCCCCAATAGATATGAGATTGAAATTAACTT
53304998 T
1 T
53304999 TTAAAAGATC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 29 0.73
41 11 0.28
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (41 bp):
TATAGAGTGTTCCCCAATAGATATGAGATTGAAATTAACTT
Found at i:53305655 original size:22 final size:22
Alignment explanation
Indices: 53305627--53305673 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
53305617 TTTAAGAGGA
*
53305627 CTTGATTCATTGATTTCTCATG
1 CTTGATTCATTGATTTCGCATG
53305649 CTTGATTCATTGATTTCGCATG
1 CTTGATTCATTGATTTCGCATG
53305671 CTT
1 CTT
53305674 TATTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.49
Consensus pattern (22 bp):
CTTGATTCATTGATTTCGCATG
Found at i:53306395 original size:2 final size:2
Alignment explanation
Indices: 53306388--53306425 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
53306378 TCATTGCCTT
53306388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53306426 CCTAAAAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53307075 original size:34 final size:34
Alignment explanation
Indices: 53307024--53307115 Score: 141
Period size: 34 Copynumber: 2.7 Consensus size: 34
53307014 CTCATCTTAG
*
53307024 TTAG-TAATTGAGTTGCTAGAATAAATGCTTATC
1 TTAGTTAATTGAGTTGCTAGAATAAATACTTATC
*
53307057 TTAGTTAATTGAGGTGCTAGAATAAATACTTATC
1 TTAGTTAATTGAGTTGCTAGAATAAATACTTATC
* *
53307091 TTAGTTAATTTAGTTGCTGGAATAA
1 TTAGTTAATTGAGTTGCTAGAATAA
53307116 TTTATTGTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 4 0.08
34 49 0.92
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (34 bp):
TTAGTTAATTGAGTTGCTAGAATAAATACTTATC
Found at i:53307139 original size:9 final size:9
Alignment explanation
Indices: 53307127--53307173 Score: 67
Period size: 9 Copynumber: 4.9 Consensus size: 9
53307117 TTATTGTTAC
53307127 ATGTGTTTA
1 ATGTGTTTA
53307136 ATGTGTGATTA
1 ATGTGT--TTA
53307147 ATGTGTTTA
1 ATGTGTTTA
53307156 ATGTGTTTTA
1 ATGTG-TTTA
53307166 ATGTGTTT
1 ATGTGTTT
53307174 GTTAAATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 17 0.49
10 9 0.26
11 9 0.26
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.55
Consensus pattern (9 bp):
ATGTGTTTA
Found at i:53307152 original size:20 final size:19
Alignment explanation
Indices: 53307127--53307173 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
53307117 TTATTGTTAC
53307127 ATGTGTTTAATGTGTGATTA
1 ATGTGTTTAATGTGT-ATTA
*
53307147 ATGTGTTTAATGTGTTTTA
1 ATGTGTTTAATGTGTATTA
53307166 ATGTGTTT
1 ATGTGTTT
53307174 GTTAAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.55
Consensus pattern (19 bp):
ATGTGTTTAATGTGTATTA
Found at i:53310318 original size:12 final size:12
Alignment explanation
Indices: 53310303--53310352 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
53310293 GAGTCTGTAA
*
53310303 AAAAATCGAAAG
1 AAAAATAGAAAG
*
53310315 AAAAATAGCAAG
1 AAAAATAGAAAG
*
53310327 AAAAAAAGAAAG
1 AAAAATAGAAAG
*
53310339 AAAAAGA-AAAG
1 AAAAATAGAAAG
53310350 AAA
1 AAA
53310353 CACGAGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
11 7 0.21
12 26 0.79
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (12 bp):
AAAAATAGAAAG
Found at i:53318804 original size:58 final size:58
Alignment explanation
Indices: 53318689--53318857 Score: 259
Period size: 58 Copynumber: 2.9 Consensus size: 58
53318679 GTGCCCACTA
* * * *
53318689 ACCGATCTCGCACACATAGTGCTCGATTGAA-GAACTCGTACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
* **
53318746 ACCGATCTCACACACATAGTTTTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
*
53318804 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTC
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTC
53318858 TAATCATTCG
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
57 26 0.26
58 74 0.74
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.24
Consensus pattern (58 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
Found at i:53318814 original size:29 final size:30
Alignment explanation
Indices: 53318671--53318825 Score: 103
Period size: 29 Copynumber: 5.4 Consensus size: 30
53318661 TCTCATTTCA
* *
53318671 CACACTTAGTGCC-C-ACTAACCGATCTCG
1 CACACATAGTGCCTCAATTAACCGATCTCG
* *
53318699 CACACATAGTG-CTCGATTGAA--GAACTCG
1 CACACATAGTGCCTCAATT-AACCGATCTCG
* * *
53318727 TACACACAGTGCCTCAATT-ACCGATCTCA
1 CACACATAGTGCCTCAATTAACCGATCTCG
** ** **
53318756 CACACATAGT-TTTCGGTTAAAGGAAT-TCG
1 CACACATAGTGCCTCAATTAACCG-ATCTCG
*
53318785 CACACACAGTGCCTCAATT-ACCGATCTCG
1 CACACATAGTGCCTCAATTAACCGATCTCG
53318814 CACACATAGTGC
1 CACACATAGTGC
53318826 TCGGTTAAAG
Statistics
Matches: 92, Mismatches: 25, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
27 2 0.02
28 32 0.35
29 50 0.54
30 8 0.09
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (30 bp):
CACACATAGTGCCTCAATTAACCGATCTCG
Found at i:53318845 original size:29 final size:29
Alignment explanation
Indices: 53318768--53318854 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
53318758 CACATAGTTT
53318768 TCGGTTAAAGGAATTCGCACACACAGTGCC
1 TCGGTTAAAGGAATTCGCACACACAGTG-C
** ** *
53318798 TCAATT-ACCG-ATCTCGCACACATAGTGC
1 TCGGTTAAAGGAAT-TCGCACACACAGTGC
*
53318826 TCGGTTAAAGGAATTTGCACACACAGTGC
1 TCGGTTAAAGGAATTCGCACACACAGTGC
53318855 CTCTAATCAT
Statistics
Matches: 43, Mismatches: 11, Indels: 7
0.70 0.18 0.11
Matches are distributed among these distances:
28 7 0.16
29 30 0.70
30 6 0.14
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (29 bp):
TCGGTTAAAGGAATTCGCACACACAGTGC
Found at i:53324919 original size:11 final size:9
Alignment explanation
Indices: 53324893--53324936 Score: 61
Period size: 9 Copynumber: 4.6 Consensus size: 9
53324883 TTGTTACATA
53324893 TGTTTAATG
1 TGTTTAATG
53324902 TGTTTAATG
1 TGTTTAATG
53324911 TGTGATTAATG
1 TGT--TTAATG
53324922 TGTTTTAATG
1 TG-TTTAATG
53324932 TGTTT
1 TGTTT
53324937 GTTAAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 15 0.47
10 8 0.25
11 8 0.25
12 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (9 bp):
TGTTTAATG
Found at i:53324921 original size:20 final size:21
Alignment explanation
Indices: 53324896--53324934 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53324886 TTACATATGT
53324896 TTAATGTG-TTTAATGTGTGA
1 TTAATGTGTTTTAATGTGTGA
53324916 TTAATGTGTTTTAATGTGT
1 TTAATGTGTTTTAATGTGT
53324935 TTGTTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (21 bp):
TTAATGTGTTTTAATGTGTGA
Found at i:53326675 original size:33 final size:33
Alignment explanation
Indices: 53326633--53326699 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
53326623 ATGGTCCATA
53326633 CAATAGTGCCAACCCATGGAAACAAAAACAAAG
1 CAATAGTGCCAACCCATGGAAACAAAAACAAAG
53326666 CAATAGTGCCAACCCATGGAAACAAAAACAAAG
1 CAATAGTGCCAACCCATGGAAACAAAAACAAAG
53326699 C
1 C
53326700 TCCAACTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.25, G:0.15, T:0.09
Consensus pattern (33 bp):
CAATAGTGCCAACCCATGGAAACAAAAACAAAG
Found at i:53331451 original size:35 final size:35
Alignment explanation
Indices: 53331401--53331531 Score: 104
Period size: 35 Copynumber: 3.6 Consensus size: 35
53331391 AGATAAATGG
*
53331401 GCACTAGTC-AGATAAATTGACTAAAGTTGCGCCCA
1 GCACTAGTCGA-ATAAATTGACTAAAGTTGCGCCAA
* * * * *
53331436 GCATTAGTCGAATAAATCGACAAATATAATGGTGTGCCTA
1 GCACTAGTCGAATAAATTGAC---TA-AA-GTTGCGCCAA
*
53331476 GCACTAGTC-AGATAAATTGACGAAAGTTGCGCCAA
1 GCACTAGTCGA-ATAAATTGACTAAAGTTGCGCCAA
* *
53331511 GCGCTAGTCGAATGAATTGAC
1 GCACTAGTCGAATAAATTGAC
53331532 AATGGTTTGC
Statistics
Matches: 75, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
35 41 0.55
36 4 0.05
37 1 0.01
38 2 0.03
39 3 0.04
40 24 0.32
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (35 bp):
GCACTAGTCGAATAAATTGACTAAAGTTGCGCCAA
Found at i:53341926 original size:23 final size:23
Alignment explanation
Indices: 53341885--53341936 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
53341875 TTTGTTTGTA
* *
53341885 TTTTTAAAATTTAAAATTTTTAT
1 TTTTTAAAATATAAAATTTTCAT
**
53341908 TTTTTAAAATATACTATTTTCAT
1 TTTTTAAAATATAAAATTTTCAT
*
53341931 ATTTTA
1 TTTTTA
53341937 TCTTTTATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTAAAATATAAAATTTTCAT
Found at i:53342083 original size:150 final size:150
Alignment explanation
Indices: 53341410--53342700 Score: 1945
Period size: 150 Copynumber: 8.6 Consensus size: 150
53341400 TTATTCAGTG
* *
53341410 ATTTTGGCCATTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATATTATTTTCG
1 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG
* * * *
53341475 TATTTTACTTTTTAAATTATTTTAGTACATAATATTTCAAATATATTATTTTAGTGTTTTTTATA
66 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTTATA
*
53341540 TTAATTTAGTAAGTAACCCTA
130 TTAATTTAGTAAATAACCCTA
* * *
53341561 ATTTTGACCTTTTGTTTGTATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCG
1 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG
*
53341626 TATTTTATTTTTTATATTATTTTAGTACATAATTTTTCAAATGTATTATTTTAGTGTTTTTTAAT
66 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTT-AT
* *
53341691 ATTAATTTATTAAATAACCCTT
129 ATTAATTTAGTAAATAACCCTA
*
53341713 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGAATTTTATTTTTTAAAATATACTATTTTCG
1 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG
*
53341778 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAATATTTTTTAAT
66 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTT-AT
*
53341843 ATTAATTTAGTAAATAACCCTG
129 ATTAATTTAGTAAATAACCCTA
***
53341865 ATTTTGGCCCTTTGTTTGTATTTTTAAAA-TTTAAAATTTTTATTTTTTAAAATATACTATTTTC
1 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGA-TTTTATTTTTTAAAATATACTATTTTC
* * * *
53341929 ATATTTTATCTTTTATATTATTTTAGTACATAATATTTTAAATGTATTATTTTAGTGTTTTTTAT
65 GTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGT-TTTTTTAT
* *
53341994 ATTAAATTAGTAAATAACCCTG
129 ATTAATTTAGTAAATAACCCTA
* * * **
53342016 A-TTTGGCCATTTGTTTGTATTTTTAAAATTTCCGGATTTTGTTTTTTAAAATATACTATTTTTA
1 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG
* *
53342080 TATTTTATATTTTATATTATTTTAGTACATAATGTTTTAAATGTATTATTTTAGTTTTTTTATAT
66 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATAT
*
53342145 TAATTTAGTAAATAACCCTG
131 TAATTTAGTAAATAACCCTA
*
53342165 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCAGATTTTATTTTTTAAAATATACTATTTTCG
1 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG
*
53342230 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAATTTTTTTAATA
66 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTT-ATA
* *
53342295 TTAATTTAGTAAATATCCCTT
130 TTAATTTAGTAAATAACCCTA
* * *
53342316 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGAATTCTATTTTTTAAAATATACTATTTTTG
1 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG
* * *
53342381 TA-TTTATCTTTTATATTATTTTAGTACATAATGTTTTAAATGTATTATTTTACTTTTTTTATAT
66 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATAT
*
53342445 TAAATTAGTAAATAACCCTA
131 TAATTTAGTAAATAACCCTA
* *
53342465 A-ATTGGCCCTTTGTTTGTATTTTTAAAATTTTC-GA---T-TTTTTTAAAATATATTATTTTCG
1 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG
* *
53342524 TATTTTATTTTTTATATTATTTTAGTACATAATATTTCAAATGTATTATTTCAGTTTTTTTTATA
66 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAG-TTTTTTTATA
* *
53342589 TTAATTTAGTAAGTAACTCTA
130 TTAATTTAGTAAATAACCCTA
* ** *
53342610 ATTTTGGCCATTTGTTTGTATTTTTAAAATTTTTAGATTTTATTTTTTAAAATATACTATTTTCA
1 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG
53342675 TATTTTA-TTTTTATATTATTTTAGTA
66 TATTTTATTTTTTATATTATTTTAGTA
53342701 AAAAACCGGC
Statistics
Matches: 1050, Mismatches: 77, Indels: 27
0.91 0.07 0.02
Matches are distributed among these distances:
143 23 0.02
144 47 0.04
145 29 0.03
146 29 0.03
147 3 0.00
148 31 0.03
149 52 0.05
150 295 0.28
151 264 0.25
152 277 0.26
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (150 bp):
ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCG
TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATAT
TAATTTAGTAAATAACCCTA
Found at i:53342766 original size:17 final size:16
Alignment explanation
Indices: 53342735--53342775 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
53342725 CCAAAAAAAA
53342735 TATTTTTTTCATATTT
1 TATTTTTTTCATATTT
*
53342751 TATTTCTTTTCGTATTT
1 TATTT-TTTTCATATTT
53342768 TATTTTTT
1 TATTTTTT
53342776 CATTAAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (16 bp):
TATTTTTTTCATATTT
Found at i:53342802 original size:15 final size:15
Alignment explanation
Indices: 53342746--53342807 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
53342736 ATTTTTTTCA
*
53342746 TATTTTATTTCTTTTCG
1 TATTTTA-TT-TTTTAG
*
53342763 TATTTTATTTTTTCAT
1 TATTTTATTTTTT-AG
***
53342779 TAAGATATTTTTTAG
1 TATTTTATTTTTTAG
53342794 TATTTTATTTTTTA
1 TATTTTATTTTTTA
53342808 TACTATTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
15 16 0.46
16 12 0.34
17 7 0.20
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (15 bp):
TATTTTATTTTTTAG
Found at i:53342805 original size:16 final size:16
Alignment explanation
Indices: 53342735--53342816 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 16
53342725 CCAAAAAAAA
53342735 TATTTTTTTCA-TATTT
1 TATTTTTTT-AGTATTT
*
53342751 TATTTCTTTTCGTATTT
1 TATTT-TTTTAGTATTT
* * ***
53342768 TATTTTTTCATTAAGA
1 TATTTTTTTAGTATTT
53342784 TA-TTTTTTAGTATTT
1 TATTTTTTTAGTATTT
*
53342799 TATTTTTTATACTATTT
1 TATTTTTT-TAGTATTT
53342816 T
1 T
53342817 TGTAAAATAG
Statistics
Matches: 49, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
15 10 0.20
16 17 0.35
17 22 0.45
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.70
Consensus pattern (16 bp):
TATTTTTTTAGTATTT
Found at i:53343294 original size:3 final size:3
Alignment explanation
Indices: 53343288--53343335 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
53343278 CGCCTCCTCT
*
53343288 TTC TTC TTC TTC TTC -TC TTC TTTC TT- TTC TTC TTC TCC TTC ATTC
1 TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC -TTC
53343333 TTC
1 TTC
53343336 CCGAAATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 4 0.10
3 29 0.74
4 6 0.15
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:53343310 original size:21 final size:22
Alignment explanation
Indices: 53343281--53343335 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
53343271 ATGCCGCCGC
53343281 CTCC-TCTTTCTTCTTCTTCTT
1 CTCCTTCTTTCTTCTTCTTCTT
53343302 CT-CTTCTTTCTT-TTCTTCTT
1 CTCCTTCTTTCTTCTTCTTCTT
*
53343322 CTCCTTCATTCTTC
1 CTCCTTCTTTCTTC
53343336 CCGAAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (22 bp):
CTCCTTCTTTCTTCTTCTTCTT
Found at i:53343467 original size:27 final size:28
Alignment explanation
Indices: 53343437--53343491 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
53343427 CTGCCAATGG
* *
53343437 CACCATCAGTGCCGCCTGTGGCA-GGCC
1 CACCACCAGTGCCGCCTGCGGCATGGCC
*
53343464 CACCACCAGTGCTGCCTGCGGCATGGCC
1 CACCACCAGTGCCGCCTGCGGCATGGCC
53343492 TTTGCCTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.15, C:0.42, G:0.29, T:0.15
Consensus pattern (28 bp):
CACCACCAGTGCCGCCTGCGGCATGGCC
Found at i:53346815 original size:18 final size:18
Alignment explanation
Indices: 53346792--53346837 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
53346782 ATACTTTCAT
*
53346792 ATATATATATATATGTAA
1 ATATATATATACATGTAA
*
53346810 ATATATCTATACATGTAA
1 ATATATATATACATGTAA
*
53346828 CTATATATAT
1 ATATATATAT
53346838 CTATTTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (18 bp):
ATATATATATACATGTAA
Found at i:53348186 original size:131 final size:129
Alignment explanation
Indices: 53347982--53348303 Score: 376
Period size: 131 Copynumber: 2.4 Consensus size: 129
53347972 TTCACAATTA
*
53347982 TTTAAGAATTCTTTAAAACGAAGGTGATATTCGATATTTGGCAATTCGTGGAATCGTGCCCTAAA
1 TTTAAAAATTCTTT-AAACGAAGGTGATATTCGATATTTGGCAATTCG-GGAATCGTGCCCTAAA
* ** * * * *
53348047 GTGTTGGGTTGCAATTTCTTGTTTGCTCAAAGTAGTCGAAGGTCCCTTTAGAATTTTAGC-CATG
64 GTGCTGGGTTGCAATTTCTCATTTGCTCAAAATAATCAAAGGTCCCTTTAGAATTTCA-CTCATG
53348111 TCT
128 T-T
* * * **
53348114 TTTAAAAATTCTTTAAACGAAGGCGATGTTCAATATTTGGCAATTCGCGGAATCGTGCCCTATCG
1 TTTAAAAATTCTTTAAACGAAGGTGATATTCGATATTTGGCAATTCG-GGAATCGTGCCCTAAAG
* * * *
53348179 TGCTGGGTTGCAATTTCTCATTTGTTCAAAATAATTAAAGGTCCCTTTTGAATTTCACTTATGTT
65 TGCTGGGTTGCAATTTCTCATTTGCTCAAAATAATCAAAGGTCCCTTTAGAATTTCACTCATGTT
* * * *
53348244 TTCTAAAAACTCTTCAAAACGAAGGTAATATTCGATGTTTGGCAATTCAGGGAATCGTGC
1 TT-TAAAAATTCTT-TAAACGAAGGTGATATTCGATATTTGGCAATTC-GGGAATCGTGC
53348304 TGGGTTGCGA
Statistics
Matches: 161, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
130 4 0.02
131 106 0.66
132 50 0.31
133 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (129 bp):
TTTAAAAATTCTTTAAACGAAGGTGATATTCGATATTTGGCAATTCGGGAATCGTGCCCTAAAGT
GCTGGGTTGCAATTTCTCATTTGCTCAAAATAATCAAAGGTCCCTTTAGAATTTCACTCATGTT
Found at i:53360528 original size:168 final size:168
Alignment explanation
Indices: 53359982--53360525 Score: 858
Period size: 168 Copynumber: 3.2 Consensus size: 168
53359972 AAAGACGGTG
* * * *
53359982 AATCTAGTCTTCATGAGGTTGCAGTGAAGCAGATTCAAGCCACCATCCTATCTCCCTAAAGTTGT
1 AATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCATCCTATCTCCCTAAAGTTGT
* * *
53360047 AGTGGAGTAGCCTGAAGATTGCAGATCTCGTCTACAGTGGAGCAGATCAAAGAAAACGAGCCTTA
66 AGTGGAGTAGGCTGAAGATTGCAGATCTCGTCTCCAGTGGAGCAGATCGAAGAAAACGAGCCTTA
53360112 ACCCCCTAAGTAGTAGGGCAACAGGCCGAAGATTGCAA
131 ACCCCCTAAGTAGTAGGGCAACAGGCCGAAGATTGCAA
* * *
53360150 AATCTTGTCTTCCTGAAGTTGCAATGAAGTAGA-TGTAAACCACCATCCTATCTCCCTAAAGTTG
1 AATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTG-AAGCCACCATCCTATCTCCCTAAAGTTG
*
53360214 TAGTGGGGTAGGCTGAAGATTGCAGATCTCGTCTCCAGTGGAGCAGATCGAAGAAAACGAGCCTT
65 TAGTGGAGTAGGCTGAAGATTGCAGATCTCGTCTCCAGTGGAGCAGATCGAAGAAAACGAGCCTT
53360279 AACCCCCTAAGTAGTAGGGCAACAGGCCGAAGATTGCAA
130 AACCCCCTAAGTAGTAGGGCAACAGGCCGAAGATTGCAA
* * *
53360318 AATCTTGTCTTCCTGAAGTTACAGTGAAGCAGATTTAAGCTACCATCCTATCTCCCTAAAGTTGT
1 AATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCATCCTATCTCCCTAAAGTTGT
* *
53360383 AGTAGAGTAGGCTGAAGATTGCAGATCTCGTCTCCAGTGGAGCAGATCGAAGAAAACAAGCCTTA
66 AGTGGAGTAGGCTGAAGATTGCAGATCTCGTCTCCAGTGGAGCAGATCGAAGAAAACGAGCCTTA
* *
53360448 ACCCTCTAAGTAGTAGGGCAACAGGCCGAAGATTGTAA
131 ACCCCCTAAGTAGTAGGGCAACAGGCCGAAGATTGCAA
* * * *
53360486 GATCTTG-CCTCTCTGAAGTTGCAGTGGAGCATATTGAAGC
1 AATCTTGTCTTC-CTGAAGTTGCAGTGAAGCAGATTGAAGC
53360526 TACTTGAAGA
Statistics
Matches: 345, Mismatches: 28, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
167 4 0.01
168 340 0.99
169 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (168 bp):
AATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCATCCTATCTCCCTAAAGTTGT
AGTGGAGTAGGCTGAAGATTGCAGATCTCGTCTCCAGTGGAGCAGATCGAAGAAAACGAGCCTTA
ACCCCCTAAGTAGTAGGGCAACAGGCCGAAGATTGCAA
Found at i:53361211 original size:5 final size:5
Alignment explanation
Indices: 53361203--53361228 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53361193 TCTTGTTTTG
53361203 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
53361229 CGAAAGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:53362018 original size:18 final size:18
Alignment explanation
Indices: 53361992--53362031 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53361982 TACTTTCATT
*
53361992 TATATATGTAAATATACA
1 TATACATGTAAATATACA
* *
53362010 TATACATGTAACTATATA
1 TATACATGTAAATATACA
53362028 TATA
1 TATA
53362032 TCTATTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (18 bp):
TATACATGTAAATATACA
Found at i:53363539 original size:132 final size:130
Alignment explanation
Indices: 53363199--53363577 Score: 465
Period size: 131 Copynumber: 2.9 Consensus size: 130
53363189 TAAGAATTCT
* * * * *
53363199 TTAAAACGAATGCGATATTCGATATTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGC
1 TTAAAACAAAAGCAATATTCGATATTTGGCAATTCGCGGAATCGTGCCCTATCGTGTTGGGTTGC
* * *
53363264 AATTTCTCGTTTGCTCAAAGTAATCGAAGGTCCCTTTAGAATTTCACCCATGTCTTTTAAAAATT
66 AATTTCTCGTTTGTTCAAA-TAATCGAAGGTCCCTTTAGAATTTCACTCATGTCTTTTAAAAACT
53363329 C
130 C
* * *
53363330 TTTAAACAAAAGCAATGTTCGATATTTGGCAATTCTCGGAATCGTGCCCTATCGTGTTGGGTTGC
1 TTAAAACAAAAGCAATATTCGATATTTGGCAATTCGCGGAATCGTGCCCTATCGTGTTGGGTTGC
* * *
53363395 AATTTCTCGTTTGTTCAACATAATCAAAGGTCCCTTTTGAATTTCACTTATG-CTTTCTAAAAAC
66 AATTTCTCGTTTGTTCAA-ATAATCGAAGGTCCCTTTAGAATTTCACTCATGTCTTT-TAAAAAC
53363459 TC
129 TC
* * * * * *
53363461 TTCAAAACGAAGGTAATATTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTG
1 TT-AAAACAAAAGCAATATTCGATATTTGGCAATTCGCGGAATCGTGCCCTATCGTGTTGGGTTG
* * * * *
53363526 CGATTTC-CTGTTTGTCCAAAATGATCGAAGATTCCTTTAGAATTTCACTCAT
65 CAATTTCTC-GTTTGTTC-AAATAATCGAAGGTCCCTTTAGAATTTCACTCAT
53363578 ACTCTCTAAA
Statistics
Matches: 212, Mismatches: 31, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
130 4 0.02
131 113 0.53
132 93 0.44
133 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (130 bp):
TTAAAACAAAAGCAATATTCGATATTTGGCAATTCGCGGAATCGTGCCCTATCGTGTTGGGTTGC
AATTTCTCGTTTGTTCAAATAATCGAAGGTCCCTTTAGAATTTCACTCATGTCTTTTAAAAACTC
Found at i:53364408 original size:10 final size:9
Alignment explanation
Indices: 53364395--53364510 Score: 74
Period size: 9 Copynumber: 12.3 Consensus size: 9
53364385 TTTTGATGCA
53364395 TTTTATAATT
1 TTTTATAA-T
*
53364405 TTTTATGAT
1 TTTTATAAT
*
53364414 TTTTATAAA
1 TTTTATAAT
* *
53364423 TATTATAAA
1 TTTTATAAT
53364432 TTTTAT-AT
1 TTTTATAAT
*
53364440 TTTTTTAAT
1 TTTTATAAT
*
53364449 TCTTAAATATAT
1 T-TT-TATA-AT
53364461 TTTTAT-AT
1 TTTTATAAT
*
53364469 TTTTATTAAA
1 TTTTA-TAAT
* *
53364479 ATTTATATTT
1 TTTTATA-AT
53364489 TTTTATAAT
1 TTTTATAAT
53364498 TTTTATTAAT
1 TTTTA-TAAT
53364508 TTT
1 TTT
53364511 CATTTTTTAT
Statistics
Matches: 82, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
8 13 0.16
9 33 0.40
10 29 0.35
11 4 0.05
12 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:53364428 original size:28 final size:27
Alignment explanation
Indices: 53364397--53364527 Score: 99
Period size: 26 Copynumber: 4.7 Consensus size: 27
53364387 TTGATGCATT
53364397 TTATAATTTTTTATGATTTTTATAAATA
1 TTATAATTTTTTAT-ATTTTTATAAATA
* * * *
53364425 TTATAA-ATTTTATATTTTTTTAATTC
1 TTATAATTTTTTATATTTTTATAAATA
*
53364451 TTAAATATATTTTTATATTTTTATTAAA-A
1 TTATA-AT-TTTTTATATTTTTA-TAAATA
* *
53364480 TTTATATTTTTTTATAATTTTTATTAAT-
1 -TTATAATTTTTTAT-ATTTTTATAAATA
*
53364508 TT-TCATTTTTTATATGTTTT
1 TTATAATTTTTTATAT-TTTT
53364528 TACCACATGT
Statistics
Matches: 81, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
25 2 0.02
26 27 0.33
27 9 0.11
28 16 0.20
29 20 0.25
30 7 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (27 bp):
TTATAATTTTTTATATTTTTATAAATA
Found at i:53364498 original size:17 final size:18
Alignment explanation
Indices: 53364462--53364504 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
53364452 TAAATATATT
53364462 TTTATATTTTTATTAAAA
1 TTTATATTTTTATTAAAA
*
53364480 TTTATATTTTT-TTATAA
1 TTTATATTTTTATTAAAA
*
53364497 TTTTTATT
1 TTTATATT
53364505 AATTTTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATATTTTTATTAAAA
Found at i:53364510 original size:47 final size:47
Alignment explanation
Indices: 53364395--53364520 Score: 118
Period size: 47 Copynumber: 2.7 Consensus size: 47
53364385 TTTTGATGCA
* * * *
53364395 TTTTATAATTTTT-TATGATTTTTATAAATATTA-TAAATTTTATATTT
1 TTTTATAATTTTTAT-TAATTTTTAT-ATTTTTATTAAAATTTATATTT
* *
53364442 TTTT--AATTCTTAAATATATTTTTATATTTTTATTAAAATTTATATTT
1 TTTTATAATT-TTTATTA-ATTTTTATATTTTTATTAAAATTTATATTT
*
53364489 TTTTATAATTTTTATTAATTTTCAT-TTTTTAT
1 TTTTATAATTTTTATTAATTTTTATATTTTTAT
53364521 ATGTTTTTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
45 4 0.06
46 15 0.23
47 36 0.56
48 5 0.08
49 4 0.06
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (47 bp):
TTTTATAATTTTTATTAATTTTTATATTTTTATTAAAATTTATATTT
Found at i:53364528 original size:28 final size:26
Alignment explanation
Indices: 53364396--53364529 Score: 80
Period size: 29 Copynumber: 4.9 Consensus size: 26
53364386 TTTGATGCAT
*
53364396 TTTATAATTTTTTATGATTTTTAT-AAA
1 TTTAT-ATTTTTTAT-ATTTTTTTAAAA
** *
53364423 TATTATAAATTTTATATTTTTTT-AAT
1 T-TTATATTTTTTATATTTTTTTAAAA
53364449 TCTTAAATATATTTTTATATTTTTATTAAAA
1 T-TT--ATAT-TTTTTATATTTTT-TTAAAA
53364480 TTTATATTTTTTTATAATTTTTATT--AA
1 TTTATA-TTTTTTAT-ATTTTT-TTAAAA
*
53364507 TTT-TCATTTTTTATATGTTTTTA
1 TTTAT-ATTTTTTATATTTTTTTA
53364530 CCACATGTAA
Statistics
Matches: 88, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
24 2 0.02
25 5 0.06
26 21 0.24
27 14 0.16
28 17 0.19
29 22 0.25
30 4 0.05
31 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
TTTATATTTTTTATATTTTTTTAAAA
Found at i:53369173 original size:30 final size:32
Alignment explanation
Indices: 53369106--53369174 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 32
53369096 GTTAATTTCA
* *
53369106 TTTTTCTAATATTATTTAATATTTTTATTTTAG
1 TTTTT-TAATATTAATTAATATTTTTATTCTAG
53369139 -TTTTTAAT-TTAATTAATATTTTT-TTCTAG
1 TTTTTTAATATTAATTAATATTTTTATTCTAG
53369168 TTTTTTA
1 TTTTTTA
53369175 TAACAGTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 5 0.15
30 20 0.61
31 4 0.12
32 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (32 bp):
TTTTTTAATATTAATTAATATTTTTATTCTAG
Found at i:53370535 original size:31 final size:31
Alignment explanation
Indices: 53370472--53370537 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
53370462 CGTTCCGGAG
53370472 TTAGCTTGCAATCCAGATTACATGCCATGGT
1 TTAGCTTGCAATCCAGATTACATGCCATGGT
53370503 TTAGCTTGCAATCCAGATTACATGCCATGGT
1 TTAGCTTGCAATCCAGATTACATGCCATGGT
53370534 TTAG
1 TTAG
53370538 GATCCATGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (31 bp):
TTAGCTTGCAATCCAGATTACATGCCATGGT
Found at i:53370756 original size:18 final size:18
Alignment explanation
Indices: 53370733--53370769 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
53370723 TTATACAATG
* *
53370733 TGCGTATCTTAACCTTTA
1 TGCGTATCCTAACCCTTA
53370751 TGCGTATCCTAACCCTTA
1 TGCGTATCCTAACCCTTA
53370769 T
1 T
53370770 ATATATATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.41
Consensus pattern (18 bp):
TGCGTATCCTAACCCTTA
Found at i:53373332 original size:49 final size:49
Alignment explanation
Indices: 53373274--53373721 Score: 770
Period size: 49 Copynumber: 9.1 Consensus size: 49
53373264 ATGAGATGTA
*
53373274 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
* *
53373323 TATATATGTGATAAGGCCTAATGGCCGATGTGACGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
*
53373372 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
*
53373421 AATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
*
53373470 TATATATGTGATAAGGCCTAATGGCCGAAGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
*
53373519 AATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
* * * *
53373568 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAATGTA
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
*
53373617 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
* *
53373666 TACATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
53373715 TATATAT
1 TATATAT
53373722 ATATGTGGTA
Statistics
Matches: 381, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 381 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
Found at i:53373856 original size:37 final size:37
Alignment explanation
Indices: 53373797--53373878 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
53373787 AGAAATATGT
53373797 TCCGGGTGA-GACCCGATGACTACGTGTGGAGATTACG
1 TCCGGGT-ACGACCCGATGACTACGTGTGGAGATTACG
* *
53373834 TCTGGGTACGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTACGACCCGATGACTACGTGTGGAGATTACG
53373871 TCCGGGTA
1 TCCGGGTA
53373879 AGACTTCGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 1 0.02
37 40 0.98
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (37 bp):
TCCGGGTACGACCCGATGACTACGTGTGGAGATTACG
Found at i:53378868 original size:29 final size:28
Alignment explanation
Indices: 53378818--53378873 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
53378808 ATTTCTCTCA
53378818 AAATATTATTGTTTTAATTTTATATTTTG
1 AAATATTATTGTTTTAATTTTAT-TTTTG
53378847 AAAT-TTATTTGTTTTCAA-TTTATTTTT
1 AAATATTA-TTGTTTT-AATTTTATTTTT
53378874 ATAATGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 7 0.28
29 16 0.64
30 2 0.08
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (28 bp):
AAATATTATTGTTTTAATTTTATTTTTG
Found at i:53382685 original size:46 final size:46
Alignment explanation
Indices: 53382618--53382849 Score: 322
Period size: 46 Copynumber: 5.0 Consensus size: 46
53382608 GTGTGCTCTC
* *
53382618 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACT
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
53382664 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
*
53382710 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * *
53382756 TGACAGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
53382802 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
53382848 TG
1 TG
53382850 TCAAAGATAA
Statistics
Matches: 173, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.01
46 172 0.99
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:53383150 original size:16 final size:17
Alignment explanation
Indices: 53383129--53383161 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53383119 ATGGTGGAGC
53383129 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
53383145 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
53383162 TACTTAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:53386489 original size:3 final size:3
Alignment explanation
Indices: 53386481--53386539 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
53386471 AGATTATTCG
* * * * *
53386481 TTA TTA TTA TTA TTA ATA TTA ATA ATA ATA TTA TTA TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
53386529 TTA TTG TTA TT
1 TTA TTA TTA TT
53386540 TACATTACCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:53391252 original size:7 final size:7
Alignment explanation
Indices: 53391240--53391265 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53391230 AAATGTTATA
53391240 AACAATC
1 AACAATC
53391247 AACAATC
1 AACAATC
53391254 AACAATC
1 AACAATC
53391261 AACAA
1 AACAA
53391266 AAAGTCTTAA
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:0.62, C:0.27, G:0.00, T:0.12
Consensus pattern (7 bp):
AACAATC
Found at i:53392265 original size:18 final size:18
Alignment explanation
Indices: 53392225--53392267 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
53392215 ATGCCGAAAA
53392225 TACTT-AGACATATTAAT
1 TACTTAAGACATATTAAT
53392242 TAACTTAAGACACT-TTAAT
1 T-ACTTAAGACA-TATTAAT
53392261 TACTTAA
1 TACTTAA
53392268 ACTAATCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 10 0.43
19 11 0.48
20 1 0.04
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (18 bp):
TACTTAAGACATATTAAT
Found at i:53393803 original size:25 final size:24
Alignment explanation
Indices: 53393762--53393831 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
53393752 GATTATGTAG
53393762 AAAGAATAAAGAAATGAAAAAAAAA
1 AAAGAA-AAAGAAATGAAAAAAAAA
* * *
53393787 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAAAAAAAA
*
53393812 AAAGAAAAGGAAA--AAAAAAA
1 AAAGAAAAAGAAATGAAAAAAA
53393832 GTGTTCATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 6 0.16
24 6 0.16
25 26 0.68
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAAAAAAAA
Found at i:53395020 original size:29 final size:29
Alignment explanation
Indices: 53394987--53395051 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
53394977 GTGACGAGAT
*
53394987 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
53395016 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
53395045 CGGCACT
1 TGGCACT
53395052 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:53401697 original size:25 final size:24
Alignment explanation
Indices: 53401656--53401718 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
53401646 GATTATGTAG
53401656 AAAGAATAAAGAAATGAAAAAAAAA
1 AAAGAA-AAAGAAATGAAAAAAAAA
* * *
53401681 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAAAAAAAA
*
53401706 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
53401719 AAAAAAGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 6 0.19
25 26 0.81
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAAAAAAAA
Found at i:53402916 original size:29 final size:29
Alignment explanation
Indices: 53402883--53402947 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
53402873 GTGACGAGAT
*
53402883 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
53402912 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
53402941 CGGCACT
1 TGGCACT
53402948 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:53406056 original size:48 final size:48
Alignment explanation
Indices: 53405985--53406081 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
53405975 ATATAATACC
*
53405985 AGAGAAAAATCACTATGAAATACCCAATTATAACAACCGCATTAAGAT
1 AGAGAAAAATCACAATGAAATACCCAATTATAACAACCGCATTAAGAT
53406033 AGAGAAAAATCACAATGAAATACCCAATTATAACAACCGCATTAAGAT
1 AGAGAAAAATCACAATGAAATACCCAATTATAACAACCGCATTAAGAT
53406081 A
1 A
53406082 TCTTTGCAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.20
Consensus pattern (48 bp):
AGAGAAAAATCACAATGAAATACCCAATTATAACAACCGCATTAAGAT
Found at i:53409049 original size:2 final size:2
Alignment explanation
Indices: 53409042--53409072 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
53409032 TCAGCTATGT
*
53409042 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53409073 GTAAGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:53409998 original size:40 final size:40
Alignment explanation
Indices: 53409943--53410198 Score: 374
Period size: 40 Copynumber: 6.4 Consensus size: 40
53409933 TGTGCATAGT
* * *
53409943 ATTCGTGCGGGTTATTGTAACTGGGTTAAGTCCCGAAGGC
1 ATTCGTGCTGGTTATTATAACCGGGTTAAGTCCCGAAGGC
*
53409983 ATTCGTGCTGGTTATTATAATCGGGTTAAGTCCCGAAGGC
1 ATTCGTGCTGGTTATTATAACCGGGTTAAGTCCCGAAGGC
* *
53410023 ATTCGTGCGGGTTATTATAACCGGGGTAAGTCCCGAAGGC
1 ATTCGTGCTGGTTATTATAACCGGGTTAAGTCCCGAAGGC
* *
53410063 ATTCGTG-TGGGTTATTATAATCGGGCTAAGTCCCGAAGGC
1 ATTCGTGCT-GGTTATTATAACCGGGTTAAGTCCCGAAGGC
* *
53410103 ATTCATG-TGGGTTATTATAACCGGGCTAAGTCCCGAAGGC
1 ATTCGTGCT-GGTTATTATAACCGGGTTAAGTCCCGAAGGC
*
53410143 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAA-GC
1 ATTCGTGCTGGTTATTATAACCGGGTTAAGTCCCGAAGGC
53410182 ATTCGTGCTGGTTATTA
1 ATTCGTGCTGGTTATTA
53410199 CATCCGAGCC
Statistics
Matches: 198, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
39 18 0.09
40 180 0.91
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (40 bp):
ATTCGTGCTGGTTATTATAACCGGGTTAAGTCCCGAAGGC
Found at i:53418549 original size:40 final size:40
Alignment explanation
Indices: 53418494--53418709 Score: 344
Period size: 40 Copynumber: 5.4 Consensus size: 40
53418484 TATGCATAGT
*
53418494 ATTCGTGCGGGTTATTGTAACCGGGTTAAGTCCCGAAGGC
1 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
* *
53418534 ATTCGTGCGGGTTATTGTAACCGGGTTAAGTCCCGAAGGT
1 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
*
53418574 ATTCGTGCGGGTTATTATAACCGGG-TAAGTCCGGAAGGC
1 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
* * * *
53418613 ATTTGTGCAGGTTATTATAACCGGGGTAAGTCCGGAAGGC
1 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
53418653 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
1 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
*
53418693 ATTCGTGCTGGTTATTA
1 ATTCGTGCGGGTTATTA
53418710 CATCCGAGCC
Statistics
Matches: 164, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 35 0.21
40 129 0.79
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (40 bp):
ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
Found at i:53418634 original size:79 final size:80
Alignment explanation
Indices: 53418492--53418709 Score: 348
Period size: 79 Copynumber: 2.7 Consensus size: 80
53418482 TATATGCATA
* * *
53418492 GTATTCGTGCGGGTTATTGTAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTGTAACCG
1 GTATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCAGGTTATTATAACCG
*
53418557 GGTTAAGTCCCGAAG
66 GGGTAAGTCCCGAAG
* *
53418572 GTATTCGTGCGGGTTATTATAACCGGG-TAAGTCCGGAAGGCATTTGTGCAGGTTATTATAACCG
1 GTATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCAGGTTATTATAACCG
*
53418636 GGGTAAGTCCGGAAG
66 GGGTAAGTCCCGAAG
* *
53418651 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTATTA
1 GTATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCAGGTTATTA
53418710 CATCCGAGCC
Statistics
Matches: 126, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
79 72 0.57
80 54 0.43
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (80 bp):
GTATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCAGGTTATTATAACCG
GGGTAAGTCCCGAAG
Found at i:53426071 original size:21 final size:21
Alignment explanation
Indices: 53426047--53426089 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53426037 ACTGGGTGGA
* * *
53426047 TAAGCTTTTACGAGCTTTTGT
1 TAAGCTCTTACAAGCTTCTGT
53426068 TAAGCTCTTACAAGCTTCTGT
1 TAAGCTCTTACAAGCTTCTGT
53426089 T
1 T
53426090 GGCATATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (21 bp):
TAAGCTCTTACAAGCTTCTGT
Found at i:53426383 original size:30 final size:30
Alignment explanation
Indices: 53426349--53426405 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
53426339 TTTGATAAGC
*
53426349 TTTTGTTTAACCTGTCGAACTTACTAAACT
1 TTTTGTTTAACCTGTCAAACTTACTAAACT
*
53426379 TTTTGTTTAAGCTGTCAAACTTACTAA
1 TTTTGTTTAACCTGTCAAACTTACTAA
53426406 GCTTCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.44
Consensus pattern (30 bp):
TTTTGTTTAACCTGTCAAACTTACTAAACT
Found at i:53427888 original size:191 final size:191
Alignment explanation
Indices: 53427563--53427944 Score: 728
Period size: 191 Copynumber: 2.0 Consensus size: 191
53427553 GCCATTTTAG
53427563 CATTCGAGGTAAGTTTGTATGTGATAAATTTCATTATAAAGGTATTTTAAATGATTAGATATTGC
1 CATTCGAGGTAAGTTTGTATGTGATAAATTTCATTATAAAGGTATTTTAAATGATTAGATATTGC
*
53427628 ATAAACTGTAATTACAAGACTATGGATATGTTCGACAATGATTCGATGACGATTCGGCATTCAAA
66 ATAAACTATAATTACAAGACTATGGATATGTTCGACAATGATTCGATGACGATTCGGCATTCAAA
*
53427693 ATCCCGATTGAAGCTTAGGAATAGATTTGGATATTAGTGACATGTCATTAGGGGATTATGT
131 ATCCCGATTGAACCTTAGGAATAGATTTGGATATTAGTGACATGTCATTAGGGGATTATGT
53427754 CATTCGAGGTAAGTTTGTATGTGATAAATTTCATTATAAAGGTATTTTAAATGATTAGATATTGC
1 CATTCGAGGTAAGTTTGTATGTGATAAATTTCATTATAAAGGTATTTTAAATGATTAGATATTGC
*
53427819 ATAAACTATAATTACAAGACTATGGATATGTTCGACAATGATTCGATGACGATTCGGCATTCGAA
66 ATAAACTATAATTACAAGACTATGGATATGTTCGACAATGATTCGATGACGATTCGGCATTCAAA
*
53427884 ATCCCGATTGAACCTTAGGAATAGTTTTGGATATTAGTGACATGTCATTAGGGGATTATGT
131 ATCCCGATTGAACCTTAGGAATAGATTTGGATATTAGTGACATGTCATTAGGGGATTATGT
53427945 GATTATGTGA
Statistics
Matches: 187, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
191 187 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (191 bp):
CATTCGAGGTAAGTTTGTATGTGATAAATTTCATTATAAAGGTATTTTAAATGATTAGATATTGC
ATAAACTATAATTACAAGACTATGGATATGTTCGACAATGATTCGATGACGATTCGGCATTCAAA
ATCCCGATTGAACCTTAGGAATAGATTTGGATATTAGTGACATGTCATTAGGGGATTATGT
Found at i:53450000 original size:79 final size:81
Alignment explanation
Indices: 53449825--53450008 Score: 270
Period size: 79 Copynumber: 2.3 Consensus size: 81
53449815 TCGAATGATG
*
53449825 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
53449889 TGTGCGAGTTACTAAA
66 TGTGCGAGTTACTAAA
* * **
53449905 TCCGGG-TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
53449967 TGTGCGAGTTACTATAA
66 TGTGCGAGTTACTA-AA
*
53449984 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53450009 AACGAGTAGC
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
78 31 0.33
79 51 0.54
80 13 0.14
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTAAA
Found at i:53450015 original size:40 final size:40
Alignment explanation
Indices: 53449825--53450008 Score: 252
Period size: 39 Copynumber: 4.7 Consensus size: 40
53449815 TCGAATGATG
* * *
53449825 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
53449865 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
53449905 TCCGGG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53449944 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53449984 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53450009 AACGAGTAGC
Statistics
Matches: 131, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
38 1 0.01
39 71 0.54
40 51 0.39
41 8 0.06
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.