Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 139 of 198
Found at i:44273073 original size:21 final size:21
Alignment explanation
Indices: 44273044--44273136 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
44273034 TTTGACGCTG
44273044 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGTAGC
* * * *
44273065 TTTTGCTTCCCTCGCTTTATC
1 CTCTGCTTCCCTCGCTGTAGC
*
44273086 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGTAGC
* * *
44273107 CTGTACTTCTCTCGCTGCT-GC
1 CTCTGCTTCCCTCGCTG-TAGC
44273128 CTCTGCTTC
1 CTCTGCTTC
44273137 TCTTACTGCC
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.04, C:0.41, G:0.16, T:0.39
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGTAGC
Found at i:44273131 original size:42 final size:42
Alignment explanation
Indices: 44273040--44273136 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
44273030 AACTTTTGAC
* * * *
44273040 GCTG-CTCTGCTTCCCTCGCTGTAGCTTTTGCTTCCCTCGCT
1 GCTGCCTCTGCTTCCCTCGCTGCAGCCTGTACTTCCCTCGCT
* * *
44273081 -TTATCCTCTGCTTCCCTCGCTGCAGCCTGTACTTCTCTCGCT
1 GCT-GCCTCTGCTTCCCTCGCTGCAGCCTGTACTTCCCTCGCT
44273123 GCTGCCTCTGCTTC
1 GCTGCCTCTGCTTC
44273137 TCTTACTGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
40 1 0.02
42 42 0.95
43 1 0.02
ACGTcount: A:0.04, C:0.40, G:0.18, T:0.38
Consensus pattern (42 bp):
GCTGCCTCTGCTTCCCTCGCTGCAGCCTGTACTTCCCTCGCT
Found at i:44273292 original size:66 final size:66
Alignment explanation
Indices: 44273163--44273294 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 66
44273153 GTTTTAAGCT
* * ** *
44273163 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGT
1 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTACATCCACTTTAAGTTGT
44273228 A
66 A
* * *
44273229 GCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTACCTCCACTTTAAGTTG
1 GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATGCTACATCCACTTTAAGTTG
44273293 TA
65 TA
44273295 TAATTTGCTC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 53 0.93
67 4 0.07
ACGTcount: A:0.16, C:0.26, G:0.17, T:0.41
Consensus pattern (66 bp):
GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTACATCCACTTTAAGTTGT
A
Found at i:44278861 original size:9 final size:9
Alignment explanation
Indices: 44278847--44279095 Score: 116
Period size: 9 Copynumber: 28.8 Consensus size: 9
44278837 AAAATTATGC
44278847 TATGTAAGT
1 TATGTAAGT
*
44278856 TTTGTAAGT
1 TATGTAAGT
* *
44278865 CATATAAGT
1 TATGTAAGT
44278874 TATGTAAG-
1 TATGTAAGT
44278882 T-TGTAAGT
1 TATGTAAGT
44278890 TATGTAAGT
1 TATGTAAGT
*
44278899 TAT-TTA-T
1 TATGTAAGT
* *
44278906 TATGAAAAT
1 TATGTAAGT
*
44278915 TAAGTAAGT
1 TATGTAAGT
*
44278924 TATGTAATT
1 TATGTAAGT
*
44278933 TACG-AA-T
1 TATGTAAGT
* **
44278940 AAT-TAAAAA
1 TATGT-AAGT
*
44278949 AATGTAAGT
1 TATGTAAGT
44278958 TATGTAAG-
1 TATGTAAGT
44278966 T-TGTAAGT
1 TATGTAAGT
44278974 TATGTAAGT
1 TATGTAAGT
*
44278983 TATGTATA-A
1 TATGTA-AGT
44278992 TAT-TAA-T
1 TATGTAAGT
** *
44278999 TAACTAACT
1 TATGTAAGT
*
44279008 TATGTAATT
1 TATGTAAGT
* *
44279017 TAAGTATAATAT
1 T-A-TGTAA-GT
44279029 TAATGTAAGT
1 T-ATGTAAGT
44279039 TATGTAAG-
1 TATGTAAGT
44279047 T-TGTAAGT
1 TATGTAAGT
44279055 TATGTAAGT
1 TATGTAAGT
*
44279064 TAT-TTA-T
1 TATGTAAGT
* *
44279071 TATGAAAAT
1 TATGTAAGT
*
44279080 TAAGTAAGT
1 TATGTAAGT
44279089 TATGTAA
1 TATGTAA
44279096 TTTACGAATA
Statistics
Matches: 182, Mismatches: 38, Indels: 40
0.70 0.15 0.15
Matches are distributed among these distances:
7 31 0.17
8 21 0.12
9 113 0.62
10 5 0.03
11 8 0.04
12 4 0.02
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.43
Consensus pattern (9 bp):
TATGTAAGT
Found at i:44278988 original size:34 final size:34
Alignment explanation
Indices: 44278847--44279144 Score: 94
Period size: 34 Copynumber: 8.9 Consensus size: 34
44278837 AAAATTATGC
* * *
44278847 TATGTAAGTTTTGTAAGTCATATAAGTTATGT-AAG
1 TATGTAAGTTATGTAAGT--TGTAAGTTATGTAAAT
* * *
44278882 T-TGTAAGTTATGTAAGTTATTTA-TTATGAAAAT
1 TATGTAAGTTATGTAAGTT-GTAAGTTATGTAAAT
* * * *
44278915 TAAGTAAGTTATGTAA-TT-TACGAATAAT-TAAAAA
1 TATGTAAGTTATGTAAGTTGTA--AGTTATGT-AAAT
* *
44278949 AATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAGTTGTAAGTTATGTAAAT
* * * *
44278983 TATGTATA-ATAT-TAA-TTAACTAACTTATGTAATT
1 TATGTA-AGTTATGTAAGTT--GTAAGTTATGTAAAT
* * *
44279017 TAAGTATA-ATAT-TAA--TGTAAGTTATGT-AAG
1 TATGTA-AGTTATGTAAGTTGTAAGTTATGTAAAT
* * *
44279047 T-TGTAAGTTATGTAAGTTATTTA-TTATGAAAAT
1 TATGTAAGTTATGTAAGTT-GTAAGTTATGTAAAT
* * * *
44279080 TAAGTAAGTTATGTAA-TT-TACGAATAAT-TAAAAA
1 TATGTAAGTTATGTAAGTTGTA--AGTTATGT-AAAT
*
44279114 AATGTAAGTTATGTAAGTTGTAAGTTATGTA
1 TATGTAAGTTATGTAAGTTGTAAGTTATGTA
44279145 TAATATTAAT
Statistics
Matches: 195, Mismatches: 41, Indels: 55
0.67 0.14 0.19
Matches are distributed among these distances:
28 1 0.01
29 6 0.03
30 5 0.03
31 11 0.06
32 14 0.07
33 20 0.10
34 126 0.65
35 8 0.04
36 4 0.02
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (34 bp):
TATGTAAGTTATGTAAGTTGTAAGTTATGTAAAT
Found at i:44279170 original size:156 final size:162
Alignment explanation
Indices: 44278869--44279200 Score: 595
Period size: 165 Copynumber: 2.1 Consensus size: 162
44278859 GTAAGTCATA
44278869 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
44278934 ACGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAAT
66 ACGAATAATTAAAAAAATGTAAG-T-TGTAAG-TGTAAGTTATGTAAGTTATGTATAATATTAAT
44278999 TAACTAACTTATGTAATTTAAGTATAATATTAATG
128 TAACTAACTTATGTAATTTAAGTATAATATTAATG
44279034 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
44279099 ACGAATAATTAAAAAAATGTAAG-T-T-A-TGTAAG-T-TGTAAGTTATGTATAATATTAATTAA
66 ACGAATAATTAAAAAAATGTAAGTTGTAAGTGTAAGTTATGTAAGTTATGTATAATATTAATTAA
44279158 CTAACTTATGTAATTTAAGTATAATATTAATG
131 CTAACTTATGTAATTTAAGTATAATATTAATG
44279190 TAAGTTATGTA
1 TAAGTTATGTA
44279201 TAATATTAAT
Statistics
Matches: 167, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
156 69 0.41
157 1 0.01
158 6 0.04
160 1 0.01
161 1 0.01
162 1 0.01
165 88 0.53
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.42
Consensus pattern (162 bp):
TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTT
ACGAATAATTAAAAAAATGTAAGTTGTAAGTGTAAGTTATGTAAGTTATGTATAATATTAATTAA
CTAACTTATGTAATTTAAGTATAATATTAATG
Found at i:44279190 original size:22 final size:22
Alignment explanation
Indices: 44279165--44279210 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
44279155 TAACTAACTT
*
44279165 ATGTAATTTAAGTATAATATTA
1 ATGTAAGTTAAGTATAATATTA
*
44279187 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTAAGTATAATATTA
44279209 AT
1 AT
44279211 TAACAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (22 bp):
ATGTAAGTTAAGTATAATATTA
Found at i:44279194 original size:56 final size:56
Alignment explanation
Indices: 44279132--44279578 Score: 423
Period size: 65 Copynumber: 7.5 Consensus size: 56
44279122 TTATGTAAGT
* * *
44279132 TGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
**
44279188 TGTAAGTTATGTATAATATTAATTAACAAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
44279244 TGTAATTAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
1 TGT-A--AGTTATGT-A--TA---ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
** *
44279309 TGTAAGTTATGTAATTTATGAATAATTATAAAAATGTAAGTTATGTAATTTATGTATAATACTAA
1 TGTAAGTTATG-----TAT-AAT-ATTA-ATTAAT-TAAGTTATGTAATTTATGTATAATATTAA
44279374 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
* * * *
44279430 TTAATTAAGTTATGTAATTTATGTATAATACTAATGTAAGTTATGT-ATAATAT-TAATTAATTA
1 -T--GTAAGTTATGT-A-TAATAT-TAAT--TAAT-TAAGTTATGTAAT-TTATGT-A-TAA-T-
* *
44279493 AGTTA
52 ATTAA
*
44279498 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
* * *
44279554 TGTAACTTATATATTA-ATTAATTAA
1 TGTAAGTTATGTATAATATTAATTAA
44279579 ATGATATGTA
Statistics
Matches: 330, Mismatches: 27, Indels: 69
0.77 0.06 0.16
Matches are distributed among these distances:
55 9 0.03
56 100 0.30
57 7 0.02
58 7 0.02
59 35 0.11
60 12 0.04
61 4 0.01
62 19 0.06
63 8 0.02
64 14 0.04
65 105 0.32
66 4 0.01
67 3 0.01
68 3 0.01
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (56 bp):
TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
Found at i:44279232 original size:34 final size:34
Alignment explanation
Indices: 44279187--44279554 Score: 248
Period size: 34 Copynumber: 11.7 Consensus size: 34
44279177 TATAATATTA
* **
44279187 ATGTAAGTTATGTATAATATTAATTAACAAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
44279221 ATGTAATTTATGTATAATATTAATGTAATT-AGTT
1 ATGTAATTTATGTATAATATTAAT-TAATTAAGTT
44279255 ATGTAATTTATG--T-ATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
*
44279286 ATGTAATTTATGTATAATATTAA-T--GTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
* *
44279317 ATGTAATTTATGAATAAT-TATAA-AAATGTAAGTT
1 ATGTAATTTATGTATAATAT-TAATTAAT-TAAGTT
* *
44279351 ATGTAATTTATGTATAATACTAA-T--GTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
* * * *
44279382 ATGT-A--TA-ATATTA-ATTAATTAAGTTATGTA
1 ATGTAATTTATGTATAATATTAATTAA-TTAAGTT
* *
44279412 AT-TTATGTA--T--AATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
* *
44279441 ATGTAATTTATGTATAATACTAA-T--GTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
* * * *
44279472 ATGT-A--TA-ATATTA-ATTAATTAAGTTATGTA
1 ATGTAATTTATGTATAATATTAATTAA-TTAAGTT
* *
44279502 AT-TTATGTA--T--AATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
44279531 ATGTAATTTATGTATAATATTAAT
1 ATGTAATTTATGTATAATATTAAT
44279555 GTAACTTATA
Statistics
Matches: 263, Mismatches: 35, Indels: 72
0.71 0.09 0.19
Matches are distributed among these distances:
26 8 0.03
27 10 0.04
28 4 0.02
29 18 0.07
30 50 0.19
31 72 0.27
32 7 0.03
33 3 0.01
34 88 0.33
35 3 0.01
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (34 bp):
ATGTAATTTATGTATAATATTAATTAATTAAGTT
Found at i:44279234 original size:90 final size:90
Alignment explanation
Indices: 44279132--44279578 Score: 625
Period size: 90 Copynumber: 4.9 Consensus size: 90
44279122 TTATGTAAGT
* * * *
44279132 TGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAATGTAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA
**
44279197 TGTATAATATTAATTAACAAAGTTA
66 TGTATAATATTAATTAATTAAGTTA
*
44279222 TGTAATTTATGTATAATATTAATGTAATT-AGTTATGTAATTTATGTATATTAATTAAT-TAAGT
1 TGTAATTTATGTATAATATTAAT-TAATTAAGTTATGTAATTTATGTATAAT-ATTAATGTAAGT
* *
44279285 TATGTAATTTATGTATAATATTAATGTAAGTTA
64 TATGT-A--TA-ATATTA-ATTAAT-TAAGTTA
* * *
44279318 TGTAATTTATGAATAAT-TATAA-AAATGTAAGTTATGTAATTTATGTATAATACTAATGTAAGT
1 TGTAATTTATGTATAATAT-TAATTAAT-TAAGTTATGTAATTTATGTATAATATTAATGTAAGT
44279381 TATGTATAATATTAATTAATTAAGTTA
64 TATGTATAATATTAATTAATTAAGTTA
*
44279408 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATACTAATGTAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA
44279473 TGTATAATATTAATTAATTAAGTTA
66 TGTATAATATTAATTAATTAAGTTA
*
44279498 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAACTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA
* *
44279563 TATATTA-ATTAATTAA
66 TGTATAATATTAATTAA
44279579 ATGATATGTA
Statistics
Matches: 322, Mismatches: 21, Indels: 29
0.87 0.06 0.08
Matches are distributed among these distances:
89 9 0.03
90 208 0.65
91 21 0.07
92 4 0.01
93 4 0.01
94 7 0.02
95 13 0.04
96 56 0.17
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (90 bp):
TGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA
TGTATAATATTAATTAATTAAGTTA
Found at i:44279473 original size:22 final size:22
Alignment explanation
Indices: 44279441--44279486 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
44279431 TAATTAAGTT
*
44279441 ATGTAATTTATGTATAATACTA
1 ATGTAAGTTATGTATAATACTA
*
44279463 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATACTA
44279485 AT
1 AT
44279487 TAATTAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATACTA
Found at i:44280887 original size:108 final size:107
Alignment explanation
Indices: 44280699--44280903 Score: 268
Period size: 108 Copynumber: 1.9 Consensus size: 107
44280689 CGTAAAGGCA
** * * *
44280699 AAACGACACCGTTTTGTTTAAAAACCCCGAATCTTTGCGGCGTTTTCACCATAGCGCCACTAATG
1 AAACGACACCGTTTCATTAAAAAACCCCGAATATTTGCGGCGTTTTCACCATAACGCCACTAATG
* * * *
44280764 TCGTTAATGTGCCAGGGAAAATGACACCGTTTGGTTTAATGT
66 CCGTTAATATGCCAGGCAAAACGACACCGTTTGGTTTAATGT
** * *
44280806 AAACGACACCGTTTCATTAAAAAAACCCCGACA-ATTTGCGGCGTTTTCGGCGTAATGCCACTAA
1 AAACGACACCGTTTCATT-AAAAAACCCCGA-ATATTTGCGGCGTTTTCACCATAACGCCACTAA
44280870 TGCCGTTAATATGCCAGGCAAAACGACACCGTTT
64 TGCCGTTAATATGCCAGGCAAAACGACACCGTTT
44280904 TATTTACAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
107 16 0.19
108 66 0.80
109 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (107 bp):
AAACGACACCGTTTCATTAAAAAACCCCGAATATTTGCGGCGTTTTCACCATAACGCCACTAATG
CCGTTAATATGCCAGGCAAAACGACACCGTTTGGTTTAATGT
Found at i:44281279 original size:6 final size:6
Alignment explanation
Indices: 44281270--44281299 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
44281260 GTATTTTGTT
44281270 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
44281300 TTTCTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:44281672 original size:15 final size:17
Alignment explanation
Indices: 44281633--44281665 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44281623 CTAACCCGAC
44281633 CCTCTTAAAACCCTAAA
1 CCTCTTAAAACCCTAAA
*
44281650 CCTCTTAAATCCCTAA
1 CCTCTTAAAACCCTAA
44281666 CTCTTAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.27
Consensus pattern (17 bp):
CCTCTTAAAACCCTAAA
Found at i:44288927 original size:23 final size:23
Alignment explanation
Indices: 44288901--44288992 Score: 80
Period size: 23 Copynumber: 3.9 Consensus size: 23
44288891 GGACTCACCA
44288901 CAGCTTGTATGAGCTTACCGTTT
1 CAGCTTGTATGAGCTTACCGTTT
* *
44288924 CAGC-TCTACGGAGCTTACCGTTT
1 CAGCTTGTA-TGAGCTTACCGTTT
*
44288947 CAGCTCG-ATAGAGCTTACCGTTTAT
1 CAGCTTGTAT-GAGCTTACCG-TT-T
* *
44288972 CAGCTCGGAATGAGCTTACCG
1 CAGCT-TGTATGAGCTTACCG
44288993 ATCATGGCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.05
23 32 0.57
24 2 0.04
25 6 0.11
26 11 0.20
27 2 0.04
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (23 bp):
CAGCTTGTATGAGCTTACCGTTT
Found at i:44292105 original size:62 final size:61
Alignment explanation
Indices: 44291987--44292167 Score: 186
Period size: 61 Copynumber: 2.9 Consensus size: 61
44291977 TTGGTCTTGT
* * * * *
44291987 AACAAAATTAGCCCTCTAATGTTTACATATTCTATCAATTT-GATACTAAATATAAAATAATTC
1 AACAAATTTAGTCCTC-AATGTTTACAAATTCTATCAATTTAG-TACTAAATCTAAAA-AAATC
* * *
44292050 AACAAATTTAGTCCTCAATGTTTACAAAATT-TATCATTTTAGTTCTAATTCTAAAAAAATC
1 AACAAATTTAGTCCTCAATGTTTAC-AAATTCTATCAATTTAGTACTAAATCTAAAAAAATC
* * * * * *
44292111 AATAAATTTATTCCTCAATATTTACAAATTCTGTCAATTTAGTCCTAACTCTAAAAA
1 AACAAATTTAGTCCTCAATGTTTACAAATTCTATCAATTTAGTACTAAATCTAAAAA
44292168 TTTTAAAAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
60 5 0.05
61 48 0.48
62 28 0.28
63 19 0.19
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.38
Consensus pattern (61 bp):
AACAAATTTAGTCCTCAATGTTTACAAATTCTATCAATTTAGTACTAAATCTAAAAAAATC
Found at i:44293361 original size:61 final size:61
Alignment explanation
Indices: 44293251--44293375 Score: 137
Period size: 61 Copynumber: 2.0 Consensus size: 61
44293241 TCAAAAATTG
* * * * * * *
44293251 TTAGAGTTAGGACTAAATTGATAGATTTTGTAAATGTTGATGGCCAAATTTATT-AATTCTT
1 TTAGAATTAGAACTAAAATGACAAATTCTGTAAATGTTGAGGGCCAAATTTATTAAATT-TT
* *
44293312 TTAGAATTAGAACTAAAATGACAAATTCTGTAAATAG-TGAGGGCTAAATTTGTTAAATTTT
1 TTAGAATTAGAACTAAAATGACAAATTCTGTAAAT-GTTGAGGGCCAAATTTATTAAATTTT
44293373 TTA
1 TTA
44293376 TATTTGGGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
61 48 0.91
62 5 0.09
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (61 bp):
TTAGAATTAGAACTAAAATGACAAATTCTGTAAATGTTGAGGGCCAAATTTATTAAATTTT
Found at i:44297667 original size:13 final size:13
Alignment explanation
Indices: 44297649--44297714 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
44297639 AACTTTGAAT
44297649 TATTTAGTGATAA
1 TATTTAGTGATAA
*
44297662 TATTTA--GA-AT
1 TATTTAGTGATAA
44297672 TATTTAGTGATAA
1 TATTTAGTGATAA
44297685 TATTTAG-GAT--
1 TATTTAGTGATAA
* *
44297695 GATTTAGTGACAA
1 TATTTAGTGATAA
44297708 TATTTAG
1 TATTTAG
44297715 GTAATGTCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 13 0.31
11 4 0.10
12 5 0.12
13 20 0.48
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:44297671 original size:23 final size:23
Alignment explanation
Indices: 44297645--44297714 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
44297635 TTTAAACTTT
44297645 GAATTATTTAGTGATAATATTTA
1 GAATTATTTAGTGATAATATTTA
44297668 GAATTATTTAGTGATAATATTTA
1 GAATTATTTAGTGATAATATTTA
* * *
44297691 GGATGATTTAGTGACAATATTTA
1 GAATTATTTAGTGATAATATTTA
44297714 G
1 G
44297715 GTAATGTCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.44
Consensus pattern (23 bp):
GAATTATTTAGTGATAATATTTA
Found at i:44297800 original size:16 final size:16
Alignment explanation
Indices: 44297779--44297848 Score: 113
Period size: 16 Copynumber: 4.4 Consensus size: 16
44297769 TTTGGTTCGC
*
44297779 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
44297795 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
44297811 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
*
44297827 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
44297843 TGTAAT
1 TGTAAT
44297849 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:44298090 original size:25 final size:25
Alignment explanation
Indices: 44298058--44298112 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
44298048 TAATTTAATC
*
44298058 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
44298082 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
44298107 ATATAT
1 ATATAT
44298113 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:44301742 original size:28 final size:28
Alignment explanation
Indices: 44301711--44301765 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
44301701 GCAAATCGGT
*
44301711 AGAAAAGAAAAGAAAATAAACAGAGGGC
1 AGAAAAGAAAAGAAAAGAAACAGAGGGC
*
44301739 AGAAAAGAAAAGAAAAGAAACGGAGGG
1 AGAAAAGAAAAGAAAAGAAACAGAGGG
44301766 AGCAAATCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.64, C:0.05, G:0.29, T:0.02
Consensus pattern (28 bp):
AGAAAAGAAAAGAAAAGAAACAGAGGGC
Found at i:44306653 original size:24 final size:25
Alignment explanation
Indices: 44306626--44306678 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
44306616 CAGCTCGAAA
*
44306626 GAGCATCTCGTTA-TTAGCTCTCAT
1 GAGCATCTCGATATTTAGCTCTCAT
*
44306650 GAGCATCTCGATATTTGGCTCTCAT
1 GAGCATCTCGATATTTAGCTCTCAT
44306675 GAGC
1 GAGC
44306679 TTTCCGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCATCTCGATATTTAGCTCTCAT
Found at i:44307404 original size:15 final size:16
Alignment explanation
Indices: 44307384--44307416 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
44307374 GCTTACTCTA
44307384 TTTTATTTCCTCT-TT
1 TTTTATTTCCTCTGTT
*
44307399 TTTTATTTTCTCTGTT
1 TTTTATTTCCTCTGTT
44307415 TT
1 TT
44307417 ATAGTATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTATTTCCTCTGTT
Found at i:44308184 original size:27 final size:26
Alignment explanation
Indices: 44308135--44308229 Score: 113
Period size: 25 Copynumber: 3.7 Consensus size: 26
44308125 CGTTTCGACC
* * **
44308135 CACAGCTTGTGTGAGTAAGCTAATTTT
1 CACAGCTCGTGTGAGCATTCTAA-TTT
44308162 CACAGCTCGTGTGAGCATTCTAA-TT
1 CACAGCTCGTGTGAGCATTCTAATTT
* *
44308187 CACAGCTCGTATGAGCATTCTGATTT
1 CACAGCTCGTGTGAGCATTCTAATTT
44308213 -ACAGCTCGTGTGAGCAT
1 CACAGCTCGTGTGAGCAT
44308230 ACATGTACAT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
25 39 0.65
26 2 0.03
27 19 0.32
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCATTCTAATTT
Found at i:44312197 original size:3 final size:3
Alignment explanation
Indices: 44312191--44312226 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
44312181 CTACTACTAC
44312191 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44312227 AATTGCTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:44313874 original size:132 final size:132
Alignment explanation
Indices: 44313634--44313919 Score: 518
Period size: 132 Copynumber: 2.2 Consensus size: 132
44313624 CGTTATTGTT
*
44313634 GATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
1 GATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATATTCAACCTACTCCACTACTGCTTA
*
44313699 AGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTTTATTGGGAAGATAAGATTCACCATCT
66 AGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCT
44313764 TC
131 TC
* *
44313766 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATATTTAACCTACTCCACTACTGCTTA
1 GATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATATTCAACCTACTCCACTACTGCTTA
* *
44313831 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCT
66 AGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCT
44313896 TC
131 TC
44313898 GATCTGCTCCACTACTGCTTAG
1 GATCTGCTCCACTACTGCTTAG
44313920 NNNNNNNNNN
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 148 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
GATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATATTCAACCTACTCCACTACTGCTTA
AGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCT
TC
Found at i:44324157 original size:132 final size:132
Alignment explanation
Indices: 44323920--44324800 Score: 1478
Period size: 132 Copynumber: 6.7 Consensus size: 132
44323910 NNNNNNNNNN
* * * *
44323920 ACTGTATTGGGAAGATAAGATTCACCATATTAGATCTGCTCCACTACTGCTTAGGATGACAGAAT
1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT
44323985 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
44324050 CC
131 CC
* *
44324052 ACTGTATTGGGAAGATAAGATTCACCATTTTCGATCTGCTCCACTACTGATTAGGGTAACAGAAT
1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT
44324117 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
44324182 CC
131 CC
* * * *
44324184 ACTATATTGGGAAGATAAGAATCACCATCTTCGATCTGCTCCGCTACTGCTTAGGGTGACAGAAT
1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT
* *
44324249 TTACAATCTTCAACCTACTCCACTACTGCTTAGGGT-AGTAGGACTAATGGCTTAAATCTGCTTC
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGA-TAGGACTAATGGCTTAAATCTGCTTC
44324313 TCC
130 TCC
* * *
44324316 ACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAAT
1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT
*
44324381 CTGCAATCTTCAACCTACTCCACAACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
44324446 CC
131 CC
* *
44324448 ACTGTATTGGGAAGATAAGATTCACCATGTTCAATCTGCTCCACTACTGATTAGGGTGACAGAAT
1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT
44324513 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
*
44324578 AC
131 CC
* * * * *
44324580 ACTGCATTGGGAAGATAAGATTCACCATCTTCGATATTCTCCACTACTGCTTAGGGTGGCAGAAT
1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT
*
44324645 TTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
44324710 CC
131 CC
*
44324712 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTATTGCA-TAGGGTGACAGAA
1 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTG-ATTAGGGTGACAGAA
* *
44324776 TCTGTAATCTTCAACCTATTCCACT
65 TCTGCAATCTTCAACCTACTCCACT
44324801 GCCAAATACA
Statistics
Matches: 698, Mismatches: 48, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 696 1.00
133 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAAT
CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
CC
Found at i:44324390 original size:44 final size:44
Alignment explanation
Indices: 44324349--44324682 Score: 159
Period size: 44 Copynumber: 7.6 Consensus size: 44
44324339 ACCATCTTTG
44324349 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA
* * * * * * *
44324393 ACCTACTCCACAACTGCTTAGGGTGATAGGA-CT--AATGGCTTAA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAAT--CTTCA
* * * * * * * * *
44324436 ATCTGCTTCTCCACTGTATT-GGGAAGATAAGATTC-ACCATGTTCA
1 ATCTGCTCCACTACTG-ATTAGGG-TGA-CAGAATCTGCAATCTTCA
44324481 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA
* * * * * *
44324525 ACCTACTCCACTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAAT--CTTCA
* * * * * * *
44324568 ATCTGCTTCTAC-ACTGCATT-GGGAAGATAAGATTC-ACCATCTTCG
1 ATCTGC-TCCACTACTG-ATTAGGG-TGA-CAGAATCTGCAATCTTCA
* * * * *
44324613 ATATTCTCCACTACTGCTTAGGGTGGCAGAATTTGCAATCTTCA
1 ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA
* * *
44324657 ACCTACTCCACTACTGCTTAGGGTGA
1 ATCTGCTCCACTACTGATTAGGGTGA
44324683 TAGGACTAAT
Statistics
Matches: 206, Mismatches: 62, Indels: 44
0.66 0.20 0.14
Matches are distributed among these distances:
41 6 0.03
43 46 0.22
44 111 0.54
45 37 0.18
46 2 0.01
47 4 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCA
Found at i:44325949 original size:21 final size:20
Alignment explanation
Indices: 44325923--44325968 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
44325913 GGTATAGCAG
44325923 GATCACCACATGCCCCAATCT
1 GATCACCACATGCCCC-ATCT
**
44325944 GATCACTTCATGCCCCATCT
1 GATCACCACATGCCCCATCT
44325964 GATCA
1 GATCA
44325969 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.39, G:0.11, T:0.24
Consensus pattern (20 bp):
GATCACCACATGCCCCATCT
Found at i:44326954 original size:13 final size:12
Alignment explanation
Indices: 44326936--44327052 Score: 54
Period size: 13 Copynumber: 9.0 Consensus size: 12
44326926 TGACTTCTCC
44326936 TTTTTCTTTTTCT
1 TTTTTCTTTTT-T
44326949 TTTTTCTTCTCTTT
1 TTTTTCTT-T-TTT
44326963 TTTTTCCTTTTTT
1 TTTTT-CTTTTTT
** *
44326976 TTTGACTTCGATTT
1 TTTTTCTT--TTTT
** *
44326990 TTTTGATTTTTAA
1 TTTTTCTTTTT-T
*
44327003 TTTTTGTTTTTT
1 TTTTTCTTTTTT
*
44327015 GTTTTTGTTTTTT
1 -TTTTTCTTTTTT
* *
44327028 TGTTTTGTTATTT
1 T-TTTTCTTTTTT
*
44327041 TTTTTGTTTTTT
1 TTTTTCTTTTTT
44327053 CCTTTTTTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
12 16 0.19
13 46 0.55
14 16 0.19
15 5 0.06
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:44326961 original size:12 final size:12
Alignment explanation
Indices: 44326929--44326975 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
44326919 TTCGCCTTGA
*
44326929 CTTCTCCTTTTT
1 CTTCTCTTTTTT
*
44326941 CTTTTTCTTTTTT
1 C-TTCTCTTTTTT
44326954 CTTCTCTTTTTT
1 CTTCTCTTTTTT
44326966 -TTC-CTTTTTT
1 CTTCTCTTTTTT
44326976 TTTGACTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 7 0.23
11 3 0.10
12 11 0.35
13 10 0.32
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTCTCTTTTTT
Found at i:44326984 original size:27 final size:25
Alignment explanation
Indices: 44326925--44326993 Score: 61
Period size: 25 Copynumber: 2.7 Consensus size: 25
44326915 GGTTTTCGCC
44326925 TTGACTTCTCCTTTTTCTTTTTCTTTT
1 TTGACTTCT-CTTTTT-TTTTTCTTTT
*
44326952 TT--CTTCTCTTTTTTTTCCTTTTTTT
1 TTGACTTCTCTTTTTTTT--TTCTTTT
**
44326977 TTGACTTCGATTTTTTT
1 TTGACTTCTCTTTTTTT
44326994 GATTTTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
23 3 0.09
24 6 0.17
25 13 0.37
27 13 0.37
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.72
Consensus pattern (25 bp):
TTGACTTCTCTTTTTTTTTTCTTTT
Found at i:44327013 original size:7 final size:7
Alignment explanation
Indices: 44326988--44327052 Score: 57
Period size: 7 Copynumber: 9.9 Consensus size: 7
44326978 TGACTTCGAT
44326988 TTTTTTG
1 TTTTTTG
* *
44326995 ATTTTTA
1 TTTTTTG
*
44327002 ATTTTTG
1 TTTTTTG
44327009 TTTTTTG
1 TTTTTTG
44327016 -TTTTTG
1 TTTTTTG
44327022 TTTTTT-
1 TTTTTTG
*
44327028 TGTTTTG
1 TTTTTTG
*
44327035 -TTATT-
1 TTTTTTG
44327040 TTTTTTG
1 TTTTTTG
44327047 TTTTTT
1 TTTTTT
44327053 CCTTTTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
6 18 0.39
7 28 0.61
ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83
Consensus pattern (7 bp):
TTTTTTG
Found at i:44327014 original size:8 final size:8
Alignment explanation
Indices: 44327003--44327052 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
44326993 TGATTTTTAA
44327003 TTTTTG-T
1 TTTTTGTT
44327010 TTTTTG--
1 TTTTTGTT
44327016 TTTTTGTT
1 TTTTTGTT
44327024 TTTTTGTT
1 TTTTTGTT
44327032 TTGTTAT-TT
1 TT-TT-TGTT
44327041 TTTTTGTT
1 TTTTTGTT
44327049 TTTT
1 TTTT
44327053 CCTTTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
6 6 0.16
7 7 0.18
8 18 0.47
9 6 0.16
10 1 0.03
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (8 bp):
TTTTTGTT
Found at i:44327059 original size:14 final size:12
Alignment explanation
Indices: 44326987--44327052 Score: 78
Period size: 13 Copynumber: 5.2 Consensus size: 12
44326977 TTGACTTCGA
44326987 TTTTTTTGATTTT
1 TTTTTTTG-TTTT
*
44327000 TAATTTTTGTTTT
1 T-TTTTTTGTTTT
44327013 TTGTTTTTGTTTT
1 TT-TTTTTGTTTT
*
44327026 TTTGTTTTGTTAT
1 TTT-TTTTGTTTT
44327039 TTTTTTTGTTTT
1 TTTTTTTGTTTT
44327051 TT
1 TT
44327053 CCTTTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
12 11 0.24
13 29 0.63
14 6 0.13
ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:44327062 original size:17 final size:17
Alignment explanation
Indices: 44326987--44327050 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
44326977 TTGACTTCGA
*
44326987 TTTTTTTGATTTT-TAAT
1 TTTTTTTG-TTTTGTTAT
* *
44327004 TTTTGTT-TTTTGTTTTT
1 TTTTTTTGTTTTG-TTAT
44327021 GTTTTTTTGTTTTGTTAT
1 -TTTTTTTGTTTTGTTAT
44327039 TTTTTTTGTTTT
1 TTTTTTTGTTTT
44327051 TTCCTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
15 4 0.11
17 20 0.53
18 9 0.24
19 5 0.13
ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83
Consensus pattern (17 bp):
TTTTTTTGTTTTGTTAT
Found at i:44331829 original size:11 final size:11
Alignment explanation
Indices: 44331813--44331837 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44331803 ATTTTTTAAC
44331813 TTTAAAATACT
1 TTTAAAATACT
44331824 TTTAAAATACT
1 TTTAAAATACT
44331835 TTT
1 TTT
44331838 TTTAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:44331857 original size:40 final size:40
Alignment explanation
Indices: 44331797--44331945 Score: 212
Period size: 40 Copynumber: 3.7 Consensus size: 40
44331787 TTTTATTTTA
* *
44331797 TTTTTT-A-TTTTTTAACTTTAAAATACTTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
* *
44331835 TTTTTTAATTTTTTTAATTTTAAAATTTTTTTTAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
44331875 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
44331915 TTTTTTAATTTTTATTTTAATTTTTAAAATA
1 TTTTTTAA--TTT-TTTTAA-TTTTAAAATA
44331946 AATTTTTGGT
Statistics
Matches: 99, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
38 6 0.06
39 1 0.01
40 73 0.74
42 3 0.03
43 6 0.06
44 10 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:44331877 original size:29 final size:28
Alignment explanation
Indices: 44331823--44331878 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
44331813 TTTAAAATAC
*
44331823 TTTTAAAATACTTTTTTTAATTTTTTTAA
1 TTTTAAAATA-TTTTTTTAATCTTTTTAA
44331852 TTTTAAAAT-TTTTTTTAAATACTTTTT
1 TTTTAAAATATTTTTTT-AAT-CTTTTT
44331879 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.29
28 3 0.12
29 14 0.58
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTAAAATATTTTTTTAATCTTTTTAA
Found at i:44331888 original size:8 final size:9
Alignment explanation
Indices: 44331834--44331895 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 9
44331824 TTTAAAATAC
44331834 TTTTTTTAA
1 TTTTTTTAA
44331843 TTTTTTTAA
1 TTTTTTTAA
**
44331852 -TTTTAAAA
1 TTTTTTTAA
44331860 TTTTTTTTAAATA
1 -TTTTTTT--A-A
44331873 CTTTTTTTAA
1 -TTTTTTTAA
44331883 TTTTTTTAA
1 TTTTTTTAA
44331892 TTTT
1 TTTT
44331896 AAAATATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
8 6 0.14
9 22 0.51
10 5 0.12
11 1 0.02
12 1 0.02
13 8 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:44332329 original size:3 final size:3
Alignment explanation
Indices: 44332323--44332349 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44332313 AAACTACTAT
44332323 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
44332350 AATTGCTAAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:44335363 original size:17 final size:17
Alignment explanation
Indices: 44335315--44335365 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
44335305 TTGTTTATTT
*
44335315 AATTTAATTA-ATTTT-
1 AATTAAATTATATTTTC
*
44335330 ATTTAAATT-TATTTTTC
1 AATTAAATTATA-TTTTC
44335347 AATTAAATTATATTTTC
1 AATTAAATTATATTTTC
44335364 AA
1 AA
44335366 CCAACTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 8 0.28
16 4 0.14
17 15 0.52
18 2 0.07
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTAAATTATATTTTC
Found at i:44336250 original size:29 final size:29
Alignment explanation
Indices: 44336208--44336267 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
44336198 CATACAAGTC
44336208 ATACATAAATTTTCTATCATCCATTCTGG
1 ATACATAAATTTTCTATCATCCATTCTGG
44336237 ATACATAAATTTTCTATCATCCATTCTGG
1 ATACATAAATTTTCTATCATCCATTCTGG
44336266 AT
1 AT
44336268 TAAGATGTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.42
Consensus pattern (29 bp):
ATACATAAATTTTCTATCATCCATTCTGG
Found at i:44343227 original size:59 final size:60
Alignment explanation
Indices: 44343124--44343256 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 60
44343114 TATATTAGTA
* * * * ** *
44343124 GTCACCTAATTATTAGTAAATTTTTTTTTTGGCCATTCAACTATG-AAAGTTGCAAAATG
1 GTCACCCAACTATTAGTAAATTTCTTTTTTGACCACCCAACTATGAAAAGTTACAAAATG
* * * *
44343183 GTCACCCCACTATTAGTAAATTTCTTTTTTGATCACCCAGCTATGAAAAGTTACAAAATT
1 GTCACCCAACTATTAGTAAATTTCTTTTTTGACCACCCAACTATGAAAAGTTACAAAATG
44343243 GTCACCCAACTATT
1 GTCACCCAACTATT
44343257 TAATTTTGTT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
59 36 0.59
60 25 0.41
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (60 bp):
GTCACCCAACTATTAGTAAATTTCTTTTTTGACCACCCAACTATGAAAAGTTACAAAATG
Found at i:44344164 original size:9 final size:9
Alignment explanation
Indices: 44344152--44344201 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 9
44344142 TAATGTTTTT
44344152 AATTTTAAA
1 AATTTTAAA
*
44344161 AATTTTGTTTAA
1 AA--TT-TTAAA
44344173 AATTTT-AA
1 AATTTTAAA
44344181 AATTTTAAA
1 AATTTTAAA
44344190 AA-TTTAAA
1 AATTTTAAA
44344198 AATT
1 AATT
44344202 AATTAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 16 0.46
9 9 0.26
10 2 0.06
11 2 0.06
12 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (9 bp):
AATTTTAAA
Found at i:44344181 original size:8 final size:8
Alignment explanation
Indices: 44344168--44344198 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
44344158 AAAAATTTTG
44344168 TTTAAAAT
1 TTTAAAAT
44344176 TTTAAAAT
1 TTTAAAAT
*
44344184 TTTAAAAA
1 TTTAAAAT
44344192 TTTAAAA
1 TTTAAAA
44344199 ATTAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TTTAAAAT
Found at i:44362095 original size:2 final size:2
Alignment explanation
Indices: 44362088--44362112 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44362078 AGTCATTTGA
44362088 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 A
44362113 AACAAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44367058 original size:22 final size:22
Alignment explanation
Indices: 44366976--44367055 Score: 112
Period size: 22 Copynumber: 3.7 Consensus size: 22
44366966 AATCTTCAAG
44366976 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
44366995 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
44367017 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
44367039 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
44367056 GATTTAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 13 0.24
22 30 0.55
23 12 0.22
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:44367302 original size:23 final size:23
Alignment explanation
Indices: 44367258--44367302 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
44367248 TCTTATTTTG
* *
44367258 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
44367281 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
44367303 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:44367732 original size:15 final size:16
Alignment explanation
Indices: 44367707--44367741 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
44367697 TTAAAATATG
44367707 TATATTTTTATTTTTT
1 TATATTTTTATTTTTT
44367723 TATA-TTTTATTTTTT
1 TATATTTTTATTTTTT
44367738 TATA
1 TATA
44367742 ATTCACACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATATTTTTATTTTTT
Found at i:44367777 original size:23 final size:22
Alignment explanation
Indices: 44367750--44367792 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
44367740 TAATTCACAC
*
44367750 ACATATATATTTTTCTTATATGT
1 ACATATATATATTT-TTATATGT
44367773 ACATATATATATTTTTATAT
1 ACATATATATATTTTTATAT
44367793 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
ACATATATATATTTTTATATGT
Found at i:44367882 original size:3 final size:3
Alignment explanation
Indices: 44367874--44367938 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
44367864 TCACATGACC
44367874 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
44367922 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
44367939 ATTCTTTAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:44371278 original size:2 final size:2
Alignment explanation
Indices: 44371271--44371296 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44371261 TATCAACATC
44371271 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
44371297 TCACTTTTAA
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:44371861 original size:40 final size:40
Alignment explanation
Indices: 44371817--44371955 Score: 133
Period size: 37 Copynumber: 3.5 Consensus size: 40
44371807 ACATATCAGT
*
44371817 TTGACACCCAGTGCCTCATCGGATAATTTGAAGTAGTAAA
1 TTGACACCCAGTGCCTCATCGGATAATCTGAAGTAGTAAA
* * * *
44371857 TTGACACCCAGCGTCTCATC-GATTAAACTG-A--AGTAAG
1 TTGACACCCAGTGCCTCATCGGA-TAATCTGAAGTAGTAAA
* * *
44371894 TTGGCACCCAGTGCCTCATCGAATAAATCTGAAGTAATAAA
1 TTGACACCCAGTGCCTCATCGGAT-AATCTGAAGTAGTAAA
* * *
44371935 TTGAAACCCGGTGTCTCATCG
1 TTGACACCCAGTGCCTCATCG
44371956 ACTCGAAGTC
Statistics
Matches: 77, Mismatches: 16, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
37 23 0.30
38 6 0.08
39 4 0.05
40 23 0.30
41 21 0.27
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (40 bp):
TTGACACCCAGTGCCTCATCGGATAATCTGAAGTAGTAAA
Found at i:44381274 original size:17 final size:18
Alignment explanation
Indices: 44381248--44381287 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
44381238 TTCTTCTCTC
*
44381248 AATTTTTTTTATTTT-AT
1 AATTTATTTTATTTTCAT
44381265 AATTTATTTTATTTTCAT
1 AATTTATTTTATTTTCAT
44381283 AATTT
1 AATTT
44381288 TAAAAATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
AATTTATTTTATTTTCAT
Found at i:44385250 original size:30 final size:30
Alignment explanation
Indices: 44385216--44385292 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
44385206 ACAGTAGAAC
* *
44385216 AAGATGAAGATTAAGAT-AATGTTAGAGATG
1 AAGATGAAGATCAAGATCAA-GGTAGAGATG
* *
44385246 AAGATCAAGATCAAGATCAAGGTAGAGCTG
1 AAGATGAAGATCAAGATCAAGGTAGAGATG
* *
44385276 GAGATGAAGATGAAGAT
1 AAGATGAAGATCAAGAT
44385293 GAAGATGATG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 37 0.95
31 2 0.05
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21
Consensus pattern (30 bp):
AAGATGAAGATCAAGATCAAGGTAGAGATG
Found at i:44385262 original size:36 final size:36
Alignment explanation
Indices: 44385215--44385298 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
44385205 CACAGTAGAA
* *
44385215 CAAGATGAAGATTAAGATA-ATGTTAGAGATGAAGAT
1 CAAGATGAAGATCAAGATAGA-GCTAGAGATGAAGAT
* * *
44385251 CAAGATCAAGATCAAGGTAGAGCTGGAGATGAAGAT
1 CAAGATGAAGATCAAGATAGAGCTAGAGATGAAGAT
*
44385287 GAAGATGAAGAT
1 CAAGATGAAGAT
44385299 GATGAGCCTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 39 0.98
37 1 0.03
ACGTcount: A:0.45, C:0.06, G:0.29, T:0.20
Consensus pattern (36 bp):
CAAGATGAAGATCAAGATAGAGCTAGAGATGAAGAT
Found at i:44385299 original size:12 final size:12
Alignment explanation
Indices: 44385241--44385300 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
44385231 ATAATGTTAG
*
44385241 AGATGAAGATCA
1 AGATGAAGATGA
* *
44385253 AGATCAAGATCA
1 AGATGAAGATGA
* * *
44385265 AGGT-AGAGCTGG
1 AGATGA-AGATGA
44385277 AGATGAAGATGA
1 AGATGAAGATGA
44385289 AGATGAAGATGA
1 AGATGAAGATGA
44385301 TGAGCCTGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 1 0.03
12 36 0.95
13 1 0.03
ACGTcount: A:0.45, C:0.07, G:0.32, T:0.17
Consensus pattern (12 bp):
AGATGAAGATGA
Found at i:44385632 original size:70 final size:70
Alignment explanation
Indices: 44385544--44385677 Score: 241
Period size: 70 Copynumber: 1.9 Consensus size: 70
44385534 ATTAAAAATA
44385544 ATTGTATTATATTTTTACATCAATAATATATTTATTTACAATTTACCAAAAAAATGAATAAATTA
1 ATTGTATTATATTTTTACATCAATAATATATTTATTTACAATTTACCAAAAAAATGAATAAATTA
44385609 TTTGT
66 TTTGT
* * *
44385614 ATTGTATTGTATTTTTACATCAATAATATATTTATTTACAATTTTCCCAAAAAATGAATAAATT
1 ATTGTATTATATTTTTACATCAATAATATATTTATTTACAATTTACCAAAAAAATGAATAAATT
44385678 GTTTTTTTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (70 bp):
ATTGTATTATATTTTTACATCAATAATATATTTATTTACAATTTACCAAAAAAATGAATAAATTA
TTTGT
Found at i:44386656 original size:20 final size:19
Alignment explanation
Indices: 44386615--44386674 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
44386605 TTTAAATATA
44386615 TATAAATATATTATTTTAT
1 TATAAATATATTATTTTAT
44386634 TATAAAGTATATTATTATT-T
1 TATAAA-TATATTATT-TTAT
44386654 TAT---TATATTAATTTTAT
1 TATAAATATATT-ATTTTAT
44386671 TATA
1 TATA
44386675 TTTTTATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 8 0.22
17 7 0.19
19 6 0.17
20 13 0.36
21 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATAAATATATTATTTTAT
Found at i:44386681 original size:11 final size:13
Alignment explanation
Indices: 44386621--44386676 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 13
44386611 TATATATAAA
44386621 TATATTATTTTAT
1 TATATTATTTTAT
* * *
44386634 TATA-AAGTATA-
1 TATATTATTTTAT
44386645 T-TATTATTTTAT
1 TATATTATTTTAT
44386657 TATATTAATTTTAT
1 TATATT-ATTTTAT
44386671 TATATT
1 TATATT
44386677 TTTATATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
10 2 0.06
11 5 0.15
12 5 0.15
13 8 0.24
14 13 0.39
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TATATTATTTTAT
Found at i:44395464 original size:24 final size:25
Alignment explanation
Indices: 44395405--44395466 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 25
44395395 TATTGTAAAA
*
44395405 ATTTGCACTTTGGTGCTTATCGATATT
1 ATTTGCACTTCGGTGCTTATC-A-ATT
44395432 ATTTTGCACTTCGGTGCTTATC-ATT
1 A-TTTGCACTTCGGTGCTTATCAATT
44395457 ATTTGCACTT
1 ATTTGCACTT
44395467 TGTACTTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 9 0.27
25 4 0.12
27 1 0.03
28 19 0.58
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (25 bp):
ATTTGCACTTCGGTGCTTATCAATT
Found at i:44396396 original size:15 final size:15
Alignment explanation
Indices: 44396376--44396406 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44396366 TCATATTTAA
44396376 ATCATTTCTAAACAT
1 ATCATTTCTAAACAT
44396391 ATCATTTCTAAACAT
1 ATCATTTCTAAACAT
44396406 A
1 A
44396407 CTCGGTTAAC
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:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (15 bp):
ATCATTTCTAAACAT
Found at i:44397020 original size:8 final size:8
Alignment explanation
Indices: 44397007--44397295 Score: 416
Period size: 8 Copynumber: 36.1 Consensus size: 8
44396997 ATCCATTTGG
*
44397007 ATGTATGC
1 ATGTATGT
44397015 ATGTATGT
1 ATGTATGT
44397023 ATGTATGT
1 ATGTATGT
44397031 ATGTATGT
1 ATGTATGT
*
44397039 ATGTGTGT
1 ATGTATGT
*
44397047 ATGTGTGT
1 ATGTATGT
*
44397055 ATGTGTGT
1 ATGTATGT
*
44397063 ATGTGTGT
1 ATGTATGT
*
44397071 ATGTGTGT
1 ATGTATGT
*
44397079 ATGTGTGT
1 ATGTATGT
*
44397087 ATGTGTGT
1 ATGTATGT
*
44397095 ATGTGTGT
1 ATGTATGT
*
44397103 ATGTGTGT
1 ATGTATGT
*
44397111 ATGTGTGT
1 ATGTATGT
*
44397119 ATGTGTGT
1 ATGTATGT
*
44397127 GTGTATGT
1 ATGTATGT
*
44397135 GTGTATGT
1 ATGTATGT
*
44397143 GTGTATGT
1 ATGTATGT
* *
44397151 GTGTGTGT
1 ATGTATGT
44397159 ATGTATGT
1 ATGTATGT
44397167 ATGTATGT
1 ATGTATGT
44397175 ATGTATGT
1 ATGTATGT
44397183 ATGTATGT
1 ATGTATGT
44397191 ATGTATGT
1 ATGTATGT
44397199 ATGTATGT
1 ATGTATGT
44397207 ATGTATGT
1 ATGTATGT
44397215 ATGTATGT
1 ATGTATGT
*
44397223 GTGTATGT
1 ATGTATGT
44397231 ATGTATGT
1 ATGTATGT
44397239 ATGTATGT
1 ATGTATGT
44397247 ATGTATGT
1 ATGTATGT
44397255 ATGTATGT
1 ATGTATGT
44397263 ATGTATGT
1 ATGTATGT
44397271 ATGTATGT
1 ATGTATGT
44397279 ATGTATGT
1 ATGTATGT
44397287 ATGTATGT
1 ATGTATGT
44397295 A
1 A
44397296 ACATTCCCCA
Statistics
Matches: 272, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 272 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.49
Consensus pattern (8 bp):
ATGTATGT
Found at i:44397410 original size:10 final size:10
Alignment explanation
Indices: 44397394--44397428 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
44397384 CTTCTACTTG
44397394 ATTTTATAAGT
1 ATTTTATAA-T
44397405 -TTTTATAAT
1 ATTTTATAAT
44397414 ATTTTATAAT
1 ATTTTATAAT
44397424 ATTTT
1 ATTTT
44397429 TTATTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.04
10 22 0.96
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:44397987 original size:6 final size:7
Alignment explanation
Indices: 44397970--44397995 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
44397960 TTTAAATTCG
44397970 AAAAAGT
1 AAAAAGT
44397977 AAAAAGT
1 AAAAAGT
44397984 AAAAAGT
1 AAAAAGT
44397991 AAAAA
1 AAAAA
44397996 AATACAAAAG
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:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAAGT
Found at i:44398312 original size:43 final size:43
Alignment explanation
Indices: 44398264--44398351 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
44398254 TATCAGCACG
* *** *
44398264 ATCTTGCTTAAAGTGATAGGTCCTTTTATCAACGATTAAATTT
1 ATCTTGCTCAAAGTGATAAAACCTTTTATCAACGATCAAATTT
* *
44398307 ATCTTGCTCAAAGTGATAAAACCTTTTATCGATGATCAAATTT
1 ATCTTGCTCAAAGTGATAAAACCTTTTATCAACGATCAAATTT
44398350 AT
1 AT
44398352 TCTCCATGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (43 bp):
ATCTTGCTCAAAGTGATAAAACCTTTTATCAACGATCAAATTT
Found at i:44400399 original size:14 final size:14
Alignment explanation
Indices: 44400380--44400406 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44400370 ACAAAACAAT
44400380 ATGACTAACTAAAC
1 ATGACTAACTAAAC
44400394 ATGACTAACTAAA
1 ATGACTAACTAAA
44400407 ATACGACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (14 bp):
ATGACTAACTAAAC
Found at i:44402632 original size:2 final size:2
Alignment explanation
Indices: 44402627--44402651 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44402617 CTATATATAT
44402627 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
44402652 AAGTATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44411081 original size:50 final size:51
Alignment explanation
Indices: 44410959--44411085 Score: 184
Period size: 51 Copynumber: 2.5 Consensus size: 51
44410949 AAAGGTCGCA
* * *
44410959 TGTGTAGTACCATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGCGAACCGGAAAGCTTCGATCACG
* **
44411010 TGTGTAGTACTATGTGCAGGCTACTATGTGAACCGGAAAG-TTTTATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGCGAACCGGAAAGCTTCGATCACG
*
44411060 TGTGTAGTACTATGTGAAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
44411086 CATGTATCGA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 33 0.48
51 36 0.52
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTATGCGAACCGGAAAGCTTCGATCACG
Found at i:44413315 original size:15 final size:14
Alignment explanation
Indices: 44413294--44413329 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
44413284 ATAATCCTTA
*
44413294 ATAATTATCTTAAT
1 ATAATTATCCTAAT
44413308 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
44413323 ATAATTA
1 ATAATTA
44413330 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:44417105 original size:84 final size:84
Alignment explanation
Indices: 44416964--44417119 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
44416954 GGCTCGTACA
* *
44416964 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCAATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCAATGCCACTGTCCCAGACAGGGT
44417029 CGTACACAAATCAACTACG
66 CGTACACAAATCAACTACG
44417048 ATGCC-ACTGTCCCAGACATGGTCTTACACGT-ATACACA-AGTCAATGCCAAC-GTCCCAGACA
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAT-CACATA-TCAATGCC-ACTGTCCCAGACA
* *
44417109 TGGTCTTACAC
62 GGGTCGTACAC
44417120 GAAAATACAT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
83 5 0.08
84 57 0.89
85 2 0.03
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCAATGCCACTGTCCCAGACAGGGT
CGTACACAAATCAACTACG
Found at i:44417119 original size:43 final size:41
Alignment explanation
Indices: 44416962--44417120 Score: 157
Period size: 43 Copynumber: 3.8 Consensus size: 41
44416952 AAGGCTCGTA
* *
44416962 CAATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCACATAT
1 CAATGCC-ACTGTCCCAGACATGGTCTTACACGTAA-CACA-AT
* *
44417005 CAATGCCACTGTCCCAGACAGGGTCGTACAC--AA-ATCAACT
1 CAATGCCACTGTCCCAGACATGGTCTTACACGTAACA-CAA-T
*
44417045 ACGATGCCACTGTCCCAGACATGGTCTTACACGTATACACAAGT
1 -CAATGCCACTGTCCCAGACATGGTCTTACACGTA-ACACAA-T
44417089 CAATGCCAAC-GTCCCAGACATGGTCTTACACG
1 CAATGCC-ACTGTCCCAGACATGGTCTTACACG
44417121 AAAATACATA
Statistics
Matches: 98, Mismatches: 9, Indels: 18
0.78 0.07 0.14
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 30 0.31
42 2 0.02
43 53 0.54
44 7 0.07
45 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (41 bp):
CAATGCCACTGTCCCAGACATGGTCTTACACGTAACACAAT
Found at i:44419881 original size:34 final size:34
Alignment explanation
Indices: 44419838--44419905 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
44419828 TCTATACTTG
44419838 GGTATCACGATACCCATTTCATGATGGGACAAAA
1 GGTATCACGATACCCATTTCATGATGGGACAAAA
*
44419872 GGTATCACGATACCCATTTCGTGATGGGACAAAA
1 GGTATCACGATACCCATTTCATGATGGGACAAAA
44419906 ATGGCACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (34 bp):
GGTATCACGATACCCATTTCATGATGGGACAAAA
Found at i:44421913 original size:15 final size:15
Alignment explanation
Indices: 44421893--44421924 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44421883 CATTTCACTA
*
44421893 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
44421908 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
44421923 TT
1 TT
44421925 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:44423583 original size:37 final size:35
Alignment explanation
Indices: 44423520--44423589 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 35
44423510 ATTTCCAAAA
*
44423520 TAATATCATTTTAATAGTTTAATATTAAATTTAATT
1 TAATATCATCTTAATAGTTTAATATT-AATTTAATT
*
44423556 TAATACTCATCTTAATAGTATT-TTATTAATTTAA
1 TAATA-TCATCTTAATAGT-TTAATATTAATTTAA
44423590 GATTAATGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 12 0.40
37 16 0.53
38 2 0.07
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (35 bp):
TAATATCATCTTAATAGTTTAATATTAATTTAATT
Found at i:44425502 original size:3 final size:3
Alignment explanation
Indices: 44425494--44425556 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
44425484 AAAACCCTAT
* *
44425494 AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
44425542 AA- AA- AAA AAG AAG AA
1 AAG AAG AAG AAG AAG AA
44425557 AATCTAAGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44425518 original size:21 final size:21
Alignment explanation
Indices: 44425494--44425556 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
44425484 AAAACCCTAT
44425494 AAGAAGAAGAAAAAGAAGAAG
1 AAGAAGAAGAAAAAGAAGAAG
44425515 AAGAAGAAGAAAAAGAAGAAG
1 AAGAAGAAGAAAAAGAAGAAG
44425536 AAGAAGAA-AAAAA-AAGAAG
1 AAGAAGAAGAAAAAGAAGAAG
44425555 AA
1 AA
44425557 AATCTAAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.19
20 5 0.12
21 29 0.69
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (21 bp):
AAGAAGAAGAAAAAGAAGAAG
Found at i:44429835 original size:20 final size:20
Alignment explanation
Indices: 44429793--44429842 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
44429783 AACCGATAAA
*
44429793 ATCGATACCAAGAGAAAATT
1 ATCGATACCAAGAGAAAAGT
*
44429813 ATCGATACCAA-ATAAAAGGT
1 ATCGATACCAAGAGAAAA-GT
*
44429833 ATCAATACCA
1 ATCGATACCA
44429843 TTTCATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20
Consensus pattern (20 bp):
ATCGATACCAAGAGAAAAGT
Found at i:44429944 original size:136 final size:136
Alignment explanation
Indices: 44429700--44429977 Score: 556
Period size: 136 Copynumber: 2.0 Consensus size: 136
44429690 TTGAGATGAA
44429700 AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC
1 AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC
44429765 TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA
66 TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA
44429830 GGTATC
131 GGTATC
44429836 AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC
1 AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC
44429901 TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA
66 TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA
44429966 GGTATC
131 GGTATC
44429972 AATACC
1 AATACC
44429978 GGTGATAGTA
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 142 1.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (136 bp):
AATACCATTTCATTTAATTCACCTGCAACAAAAGTTATCGATACTTAATTTTAACATTTAATGCC
TTGATTCAGTGACCATTAAACCGATAAAATCGATACCAAGAGAAAATTATCGATACCAAATAAAA
GGTATC
Found at i:44429971 original size:20 final size:20
Alignment explanation
Indices: 44429929--44429977 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
44429919 AACCGATAAA
*
44429929 ATCGATACCAAGAGAAAATT
1 ATCGATACCAAGAGAAAAGT
*
44429949 ATCGATACCAA-ATAAAAGGT
1 ATCGATACCAAGAGAAAA-GT
*
44429969 ATCAATACC
1 ATCGATACC
44429978 GGTGATAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.20
Consensus pattern (20 bp):
ATCGATACCAAGAGAAAAGT
Found at i:44431252 original size:17 final size:16
Alignment explanation
Indices: 44431230--44431263 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44431220 GGGGATAGCG
44431230 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
44431247 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
44431263 T
1 T
44431264 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:44444427 original size:16 final size:16
Alignment explanation
Indices: 44444406--44444437 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
44444396 GTGGAGTGGA
44444406 ACTCCACAGTTTTGGC
1 ACTCCACAGTTTTGGC
44444422 ACTCCACAGTTTTGGC
1 ACTCCACAGTTTTGGC
44444438 GAAGTTCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (16 bp):
ACTCCACAGTTTTGGC
Found at i:44455775 original size:10 final size:10
Alignment explanation
Indices: 44455762--44455801 Score: 57
Period size: 9 Copynumber: 4.2 Consensus size: 10
44455752 CTTTACAATA
44455762 TTTTATATTT
1 TTTTATATTT
44455772 TTTTATA-TT
1 TTTTATATTT
44455781 TTTTA-ATTT
1 TTTTATATTT
*
44455790 TTTTCTATTT
1 TTTTATATTT
44455800 TT
1 TT
44455802 AATAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 1 0.04
9 13 0.48
10 13 0.48
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTATATTT
Found at i:44455781 original size:17 final size:18
Alignment explanation
Indices: 44455759--44455804 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
44455749 ATTCTTTACA
44455759 ATATTTTAT-ATTTTTTT
1 ATATTTTATAATTTTTTT
*
44455776 ATATTTTTTAATTTTTTT
1 ATATTTTATAATTTTTTT
*
44455794 CTATTTT-TAAT
1 ATATTTTATAAT
44455805 AAATTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
ATATTTTATAATTTTTTT
Found at i:44455789 original size:18 final size:19
Alignment explanation
Indices: 44455762--44455801 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
44455752 CTTTACAATA
44455762 TTTTATATTTTTTTATATT
1 TTTTATATTTTTTTATATT
*
44455781 TTTTA-ATTTTTTTCTATT
1 TTTTATATTTTTTTATATT
44455799 TTT
1 TTT
44455802 AATAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTATATTTTTTTATATT
Found at i:44457130 original size:14 final size:13
Alignment explanation
Indices: 44457103--44457128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44457093 AAGATATAAC
44457103 CAGATTTTTTTTT
1 CAGATTTTTTTTT
44457116 CAGATTTTTTTTT
1 CAGATTTTTTTTT
44457129 TCTTTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
CAGATTTTTTTTT
Found at i:44459733 original size:25 final size:25
Alignment explanation
Indices: 44459704--44459762 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
44459694 ATTATATCTA
44459704 ATGTTTTATGAGATACTGACTTTTT
1 ATGTTTTATGAGATACTGACTTTTT
44459729 ATGTTTTATGAGATACTGACTTTTT
1 ATGTTTTATGAGATACTGACTTTTT
44459754 ATGTTTTAT
1 ATGTTTTAT
44459763 CTTGATTGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (25 bp):
ATGTTTTATGAGATACTGACTTTTT
Found at i:44462198 original size:41 final size:41
Alignment explanation
Indices: 44462137--44462323 Score: 313
Period size: 41 Copynumber: 4.6 Consensus size: 41
44462127 TTTAAACAGA
*
44462137 TTCACTGGCACTTCA-CCTGCTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTGATTCAG
* *
44462178 TTCACCGACACTTAGTCTGCTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
*
44462219 TTCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
*
44462260 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
44462301 TTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
44462324 ACGTAAAGTC
Statistics
Matches: 137, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
40 1 0.01
41 136 0.99
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.30
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
Found at i:44462346 original size:82 final size:82
Alignment explanation
Indices: 44462136--44462351 Score: 256
Period size: 82 Copynumber: 2.6 Consensus size: 82
44462126 ATTTAAACAG
* * * * ** * *
44462136 ATTCACTGGCACTTCA-CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAGTCTGCTA
1 ATTCACCGGCACTT-AGCCTGCTAGACGTAAAGCCTGAAACAGTTCACCGGCACTTAGCCTGCTA
44462200 GGCTTATAGCCTGATTCA
65 GGCTTATAGCCTGATTCA
* *** * **
44462218 GTTCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAG
1 ATTCACCGGCACTTAGCCTGCTAGACGTAAAGCCTGAAACAGTTCACCGGCACTTAGCCTGCTAG
44462283 GCTTATAGCCTGATTCA
66 GCTTATAGCCTGATTCA
*
44462300 ATTCACCGGCACTTAGCCTGCTAGACGTAAAGTCC-GAAACATTTCACCGGCA
1 ATTCACCGGCACTTAGCCTGCTAGACGTAAAG-CCTGAAACAGTTCACCGGCA
44462352 ATTAATCTGA
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
81 1 0.01
82 116 0.97
83 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (82 bp):
ATTCACCGGCACTTAGCCTGCTAGACGTAAAGCCTGAAACAGTTCACCGGCACTTAGCCTGCTAG
GCTTATAGCCTGATTCA
Found at i:44464074 original size:34 final size:31
Alignment explanation
Indices: 44464015--44464076 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
44464005 TGTTTTGTTT
44464015 TTATTATAATAACATTATAATATATAAATTA
1 TTATTATAATAACATTATAATATATAAATTA
* *
44464046 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAA-CATTAT-AAT-ATATAAA
44464077 ATCTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 11 0.42
32 5 0.19
33 3 0.12
34 7 0.27
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (31 bp):
TTATTATAATAACATTATAATATATAAATTA
Found at i:44474327 original size:46 final size:43
Alignment explanation
Indices: 44474001--44474781 Score: 232
Period size: 44 Copynumber: 18.0 Consensus size: 43
44473991 CAGATCGAGC
* ** * ** * *
44474001 CTTATCTCCCTGAAGTTACAGTAGAGTAGACTAATTAACCAAGT
1 CTTATCT-CCTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT
* * *
44474045 CTTATCCTCCTGAAGTTGCAAC-GAGGCAGACTAAAGATGGTAAAT
1 CTTAT-CTCCTGAAGTTGCAGCGGA-GCAGACTAAAGA-AGCAAAT
* * * **
44474090 CTTATCTCCTTGAAGTTTCAGTGGAGCAGATTAAAGCCG-ACAAT
1 CTTATCTCC-TGAAGTTGCAGCGGAGCAGACTAAAGAAGCA-AAT
* * * * * *
44474134 CCTATCTCGCTGAAGTTGCAGTGG-GCGGA-TTAA-AACCTTAGAT
1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGC--AAAT
* * * * * * * *
44474177 ATTATCTCTCTGAAGTTGTAG-AGAGCAGA-T--CGCATCTAGT
1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT
* ** *
44474217 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGT
1 CTTATCT-CCTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT
* *
44474261 CTTATCTTCCTAAAGTTGCAGC-GAGGCAGACTGAAAGATGGCAAAT
1 CTTATC-TCCTGAAGTTGCAGCGGA-GCAGACT-AAAGA-AGCAAAT
* * *
44474307 CTTATCTCCTTGAAGTTGCAGAGGAGCAGA-TTAA-AACCGACAAT
1 CTTATCTCC-TGAAGTTGCAGCGGAGCAGACTAAAGAAGC-A-AAT
* * ** * * *
44474351 CATATCTCCCTGAAGTTGCAGTGGAGC-GGGTTAA-AACCTTAGAT
1 CTTATCT-CCTGAAGTTGCAGCGGAGCAGACTAAAGAAGC--AAAT
* * * * * * *
44474395 CTTATCTCTCTGAAGTTGCAG-AGAGTAGA-T--CGCATCTAGT
1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT
* * * ** *
44474435 CTTATCTCCCTGACGTTGTAGTGGAGCAGACTAATTAAGCAAGT
1 CTTATCT-CCTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT
* * *
44474479 CTTATCCTCCTGAAGTTACAGC-GAGGCAGACTGAAGATGGCAAAT
1 CTTAT-CTCCTGAAGTTGCAGCGGA-GCAGACTAAAGA-AGCAAAT
* * * **
44474524 CTTATCTCCTTGAAGTTGCGGTGGAGCAGATTAAAGCCG-ACAAT
1 CTTATCTCC-TGAAGTTGCAGCGGAGCAGACTAAAGAAGCA-AAT
* * * * *
44474568 CCTATCTCGCTGAAGTTGCAGCGGA-CGGA-TTAA-AACCTTAGAT
1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGC--AAAT
* * * * * * *
44474611 CTTATCTCTCTAAAGTTGCAG-AGAGCAGA-T--CGCATCTACT
1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT
* * *
44474651 CTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGT
1 CTTATCTC-CTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT
* * *
44474695 CTTATCCTCTTGAAGTTGCAGC-GAGGCAGACTGAAGATGGCAAAT
1 CTTAT-CTCCTGAAGTTGCAGCGGA-GCAGACTAAAGA-AGCAAAT
* * * *
44474740 CTTATCTCCTTGAAATTGCAGTGGAGCAAACTAAATAAGCAA
1 CTTATCTCC-TGAAGTTGCAGCGGAGCAGACTAAAGAAGCAA
44474782 CACCTGATAA
Statistics
Matches: 544, Mismatches: 136, Indels: 114
0.69 0.17 0.14
Matches are distributed among these distances:
40 57 0.10
41 22 0.04
42 19 0.03
43 73 0.13
44 235 0.43
45 104 0.19
46 32 0.06
47 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
CTTATCTCCTGAAGTTGCAGCGGAGCAGACTAAAGAAGCAAAT
Found at i:44474676 original size:216 final size:216
Alignment explanation
Indices: 44474001--44474767 Score: 1246
Period size: 216 Copynumber: 3.5 Consensus size: 216
44473991 CAGATCGAGC
* * * * *
44474001 CTTATCTCCCTGAAGTTACAGTAGAGTAGACTAATTAACCAAGTCTTATCCTCCTGAAGTTGCAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG
* * *
44474066 CGAGGCAGACTAAAGATGGTAAATCTTATCTCCTTGAAGTTTCAGTGGAGCAGATTAAAGCCGAC
66 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGAC
* * *
44474131 AATCCTATCTCGCTGAAGTTGCAGTGGGCGGATTAAAACCTTAGATATTATCTCTCTGAAGTTGT
131 AATCCTATCTCGCTGAAGTTGCAGTGGACGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
44474196 AGAGAGCAGATCGCATCTAGT
196 AGAGAGCAGATCGCATCTAGT
* *
44474217 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCTTCCTAAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG
* *
44474282 CGAGGCAGACTGAAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGAGGAGCAGATTAAAACCGA
66 CGAGGCAGACTG-AAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGA
* * *
44474347 CAATCATATCTCCCTGAAGTTGCAGTGGAGCGGGTTAAAACCTTAGATCTTATCTCTCTGAAGTT
130 CAATCCTATCTCGCTGAAGTTGCAGTGGA-CGGATTAAAACCTTAGATCTTATCTCTCTGAAGTT
*
44474412 GCAGAGAGTAGATCGCATCTAGT
194 GCAGAGAGCAGATCGCATCTAGT
* * *
44474435 CTTATCTCCCTGACGTTGTAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTACAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG
*
44474500 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCGGTGGAGCAGATTAAAGCCGAC
66 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGAC
* *
44474565 AATCCTATCTCGCTGAAGTTGCAGCGGACGGATTAAAACCTTAGATCTTATCTCTCTAAAGTTGC
131 AATCCTATCTCGCTGAAGTTGCAGTGGACGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
*
44474630 AGAGAGCAGATCGCATCTACT
196 AGAGAGCAGATCGCATCTAGT
* * *
44474651 CTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGTCTTATCCTCTTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG
*
44474716 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAATTGCAGTGGAGCA
66 CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCA
44474768 AACTAAATAA
Statistics
Matches: 507, Mismatches: 42, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
216 232 0.46
217 149 0.29
218 126 0.25
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (216 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTGAAGTTGCAG
CGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGAC
AATCCTATCTCGCTGAAGTTGCAGTGGACGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
AGAGAGCAGATCGCATCTAGT
Found at i:44477915 original size:44 final size:43
Alignment explanation
Indices: 44477833--44477915 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
44477823 GCCTTGTGAG
*
44477833 TATTCGAAATAAGGACACACGGCCGTGTCCTAGCCTGTGTATA
1 TATTCGAAATAAGGACACACGGCCGTGTCCAAGCCTGTGTATA
* * *
44477876 TATTCGAAAATAGGGTCACACGGTCGTGTCGCAAG-CTGTG
1 TATTCG-AAATAAGGACACACGGCCGTGTC-CAAGCCTGTG
44477916 CTCGAAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 6 0.18
44 25 0.74
45 3 0.09
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (43 bp):
TATTCGAAATAAGGACACACGGCCGTGTCCAAGCCTGTGTATA
Found at i:44488791 original size:14 final size:14
Alignment explanation
Indices: 44488772--44488805 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
44488762 TAAGTTTAGT
44488772 TTTATTGTTTAAAG
1 TTTATTGTTTAAAG
*
44488786 TTTATTGTTTAAAT
1 TTTATTGTTTAAAG
44488800 TTTATT
1 TTTATT
44488806 TATTCCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (14 bp):
TTTATTGTTTAAAG
Found at i:44501684 original size:7 final size:7
Alignment explanation
Indices: 44501672--44501700 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
44501662 ATACAATAGA
44501672 TATTTAT
1 TATTTAT
44501679 TATTTAT
1 TATTTAT
44501686 TATTTAT
1 TATTTAT
44501693 TA-TTAT
1 TATTTAT
44501699 TA
1 TA
44501701 AATGAAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATTTAT
Found at i:44501959 original size:15 final size:16
Alignment explanation
Indices: 44501939--44501974 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
44501929 AAATAAAGTA
*
44501939 AAAGAATAAAA-AAAC
1 AAAGAAGAAAAGAAAC
44501954 AAAGAAGAAAAGAAAC
1 AAAGAAGAAAAGAAAC
44501970 AAAGA
1 AAAGA
44501975 CCATTCGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAC
Found at i:44502392 original size:17 final size:18
Alignment explanation
Indices: 44502370--44502403 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44502360 TAAATGAGTT
44502370 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
44502387 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
44502404 AAAAGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:44511259 original size:43 final size:43
Alignment explanation
Indices: 44511195--44511401 Score: 256
Period size: 43 Copynumber: 4.9 Consensus size: 43
44511185 TACCGTAACA
* * * *
44511195 ATGCC-ATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
** * * *
44511237 ATGCCAATAAGCCAGCCATGGTCTTACACGAAATCACATATCA
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
* * *
44511280 ATGGCAATATCCCAGACACGGTCTTACACGAAATCACATATCG
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
* *
44511323 ATGCCAATGTCCCAGACATGGTCTTACACGAAGTCTCATATCG
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
* *
44511366 ATGCCAA-ATCCCAGATATGGTCTTACACGTAATCTC
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTC
44511402 GGTAACCCTA
Statistics
Matches: 140, Mismatches: 24, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
42 30 0.21
43 110 0.79
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
Found at i:44513685 original size:29 final size:29
Alignment explanation
Indices: 44513643--44513700 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
44513633 ACCACTGCAA
*
44513643 ACGGCGGTGCCGTCACTGGAGATCGGTGG
1 ACGGCGGTGCCGTCACCGGAGATCGGTGG
44513672 ACGGCGGTGCCGTCACCGGAGATCGGTGG
1 ACGGCGGTGCCGTCACCGGAGATCGGTGG
44513701 CCGGTGCAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.26, G:0.45, T:0.16
Consensus pattern (29 bp):
ACGGCGGTGCCGTCACCGGAGATCGGTGG
Found at i:44514556 original size:11 final size:11
Alignment explanation
Indices: 44514532--44514569 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
44514522 TCTTATATTC
44514532 TTTATATTTTT
1 TTTATATTTTT
44514543 TTTAT-TTTTAT
1 TTTATATTTT-T
*
44514554 TTTATAATTTT
1 TTTATATTTTT
44514565 TTTAT
1 TTTAT
44514570 TTCCTTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 4 0.17
11 17 0.71
12 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATATTTTT
Found at i:44518955 original size:5 final size:5
Alignment explanation
Indices: 44518935--44518982 Score: 69
Period size: 5 Copynumber: 9.2 Consensus size: 5
44518925 TTTTTATGTT
*
44518935 TTATA TATATTA TTATA TTATA TTATA TTATA TTGTA TTATA TTATA T
1 TTATA T-TA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
44518983 AAGTAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 32 0.82
6 4 0.10
7 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:44519701 original size:3 final size:3
Alignment explanation
Indices: 44519693--44519757 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
44519683 AATAAGAATT
* * * * * *
44519693 TTA TTA TTA TTA TTA TTG TTA ATA TAA TAA TAA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
44519741 ATA TAA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
44519758 TTTAATGATT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:44519728 original size:27 final size:27
Alignment explanation
Indices: 44519698--44519757 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
44519688 GAATTTTATT
44519698 ATTATTATTATTGTTAATATAATAATA
1 ATTATTATTATTGTTAATATAATAATA
* *
44519725 ATTATTATTATTGTTAATATAATTATT
1 ATTATTATTATTGTTAATATAATAATA
44519752 ATTATT
1 ATTATT
44519758 TTTAATGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (27 bp):
ATTATTATTATTGTTAATATAATAATA
Found at i:44519746 original size:21 final size:22
Alignment explanation
Indices: 44519717--44519763 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
44519707 ATTGTTAATA
44519717 TAATAATAATTATTATTATTGT
1 TAATAATAATTATTATTATTGT
*
44519739 TAAT-ATAATTATTATTATTTT
1 TAATAATAATTATTATTATTGT
44519760 TAAT
1 TAAT
44519764 GATTGTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TAATAATAATTATTATTATTGT
Found at i:44528730 original size:17 final size:18
Alignment explanation
Indices: 44528708--44528741 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44528698 CAAATGAGTT
44528708 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
44528725 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
44528742 AAAAGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:44529094 original size:37 final size:36
Alignment explanation
Indices: 44529043--44529115 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
44529033 GAATATTAAC
* * * *
44529043 TTGAAAATGGAAAAGTTAATTTTGAATTGAATTGTGA
1 TTGAAAATGAAAAAGTGAA-ATTGAATTGAAATGTGA
*
44529080 TTGAAAGTGAAAAAGTGAAATTGAATTGAAATGTGA
1 TTGAAAATGAAAAAGTGAAATTGAATTGAAATGTGA
44529116 ATATGGAGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 15 0.48
37 16 0.52
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (36 bp):
TTGAAAATGAAAAAGTGAAATTGAATTGAAATGTGA
Found at i:44531111 original size:42 final size:42
Alignment explanation
Indices: 44531061--44531160 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
44531051 CTATACGAAT
** *
44531061 GGCACTAAGTGTGCGAAATTAAAATGACGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
44531103 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
44531145 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
44531161 TACCAAGATC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
Found at i:44539485 original size:29 final size:30
Alignment explanation
Indices: 44539450--44539506 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
44539440 CAATTCGATT
44539450 AAAAAATCATTAAAAATTTAA-AAAAATAA
1 AAAAAATCATTAAAAATTTAAGAAAAATAA
*
44539479 AAAAAATTATTAAAAATTTAAGAAAAAT
1 AAAAAATCATTAAAAATTTAAGAAAAAT
44539507 TTGGTTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (30 bp):
AAAAAATCATTAAAAATTTAAGAAAAATAA
Found at i:44554525 original size:27 final size:26
Alignment explanation
Indices: 44554495--44554570 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
44554485 AGAGATGGAA
44554495 GCCTTTATGGCAAATCTTGTAAAGAA-G
1 GCCTTTATGGCAAA-CTT-TAAAGAATG
* **
44554522 GCCTTTGTGGCGCACTTTAAAGAATG
1 GCCTTTATGGCAAACTTTAAAGAATG
* *
44554548 ACCTTTATGGCAACCTTCTAAAG
1 GCCTTTATGGCAAACTT-TAAAG
44554571 GAAACGCCTC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
25 7 0.18
26 16 0.41
27 16 0.41
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (26 bp):
GCCTTTATGGCAAACTTTAAAGAATG
Found at i:44557957 original size:18 final size:19
Alignment explanation
Indices: 44557914--44557958 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
44557904 AAATCAAAAT
44557914 ATTGTGAG-AGTTAAAAGC
1 ATTGTGAGTAGTTAAAAGC
44557932 A-TGATGAGTA-TTAAAAGC
1 ATTG-TGAGTAGTTAAAAGC
44557950 ATTGTGAGT
1 ATTGTGAGT
44557959 GAAAGAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 2 0.08
18 19 0.79
19 3 0.12
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (19 bp):
ATTGTGAGTAGTTAAAAGC
Found at i:44565166 original size:31 final size:30
Alignment explanation
Indices: 44565095--44565184 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
44565085 GTGACCAATT
44565095 AAAAAAA--ATAGTTAAGTGACCAAAAAAG
1 AAAAAAATCATAGTTAAGTGACCAAAAAAG
* *
44565123 AAACAAATTCATAGTTAAGTGGCCAAATTAAA-
1 AAA-AAAATCATAGTTAAGTGACCAAA--AAAG
* * *
44565155 AAAAAAATCATAATTGAGAGACCAGAAAAA
1 AAAAAAATCATAGTTAAGTGACCA-AAAAA
44565185 AATTTAACCC
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
28 3 0.06
29 3 0.06
30 3 0.06
31 32 0.65
32 5 0.10
33 3 0.06
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (30 bp):
AAAAAAATCATAGTTAAGTGACCAAAAAAG
Found at i:44566537 original size:27 final size:27
Alignment explanation
Indices: 44566499--44566560 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
44566489 GGTGCAGAAT
**
44566499 CATCATCATCATTTTCAACAACAGCAA
1 CATCATCATCATCATCAACAACAGCAA
**
44566526 CATCATCATCATCATCTGCAACAGCAA
1 CATCATCATCATCATCAACAACAGCAA
*
44566553 CAACATCA
1 CATCATCA
44566561 ACAGCAGTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.32, G:0.05, T:0.23
Consensus pattern (27 bp):
CATCATCATCATCATCAACAACAGCAA
Found at i:44571275 original size:20 final size:20
Alignment explanation
Indices: 44571250--44571300 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
44571240 AAATTATAAA
*
44571250 AATAAAAATTATTAAACTTT
1 AATAAAAATTATTAAAATTT
44571270 AATAAAAAGTT-TTAAAATTT
1 AATAAAAA-TTATTAAAATTT
*
44571290 ACTAAAAATTA
1 AATAAAAATTA
44571301 GAAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
AATAAAAATTATTAAAATTT
Found at i:44571323 original size:18 final size:18
Alignment explanation
Indices: 44571302--44571345 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
44571292 TAAAAATTAG
44571302 AAAAAATATAAAATTGTA
1 AAAAAATATAAAATTGTA
*
44571320 AAAAAATATAAAATTTTA
1 AAAAAATATAAAATTGTA
*
44571338 TAAAAATA
1 AAAAAATA
44571346 ATTAAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAAATATAAAATTGTA
Found at i:44579206 original size:195 final size:195
Alignment explanation
Indices: 44578874--44579267 Score: 754
Period size: 195 Copynumber: 2.0 Consensus size: 195
44578864 AACCACATAC
44578874 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCTGCACCGCTCACATCGAAAACACTACT
1 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCTGCACCGCTCACATCGAAAACACTACT
*
44578939 TATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCGGAATAACCAC
66 TATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCAC
*
44579004 AAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCATAACCATATTATAA
131 AAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATAA
44579069 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAG-TCGCACCGCTCACATCGAAAACACTAC
1 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCT-GCACCGCTCACATCGAAAACACTAC
44579133 TTATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCA
65 TTATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCA
44579198 CAAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATA
130 CAAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATA
44579263 A
195 A
44579264 TCAA
1 TCAA
44579268 GCAAAATAAC
Statistics
Matches: 196, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
194 1 0.01
195 195 0.99
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (195 bp):
TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCTGCACCGCTCACATCGAAAACACTACT
TATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCAC
AAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATAA
Found at i:44580028 original size:31 final size:31
Alignment explanation
Indices: 44579992--44580055 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
44579982 TTCACTTACT
*
44579992 TTACTTGTCACATCAATATCACATTCCACAA
1 TTACTTGTCACATCAACATCACATTCCACAA
44580023 TTACTTGTCACATCAACATCACATTCCACAA
1 TTACTTGTCACATCAACATCACATTCCACAA
44580054 TT
1 TT
44580056 CGACAAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (31 bp):
TTACTTGTCACATCAACATCACATTCCACAA
Found at i:44585251 original size:28 final size:28
Alignment explanation
Indices: 44585199--44585256 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
44585189 GTTCTCTCAA
*
44585199 AAATTAAAATTAAATTATATATTTTTAT
1 AAATTAAAATTAAATTATATATTTTAAT
44585227 AAATTAAAATATAAATTGAT-T-TTTTAAT
1 AAATTAAAAT-TAAATT-ATATATTTTAAT
44585255 AA
1 AA
44585257 CTTATATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 18 0.67
29 7 0.26
30 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AAATTAAAATTAAATTATATATTTTAAT
Found at i:44589264 original size:30 final size:29
Alignment explanation
Indices: 44589210--44589277 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
44589200 AGATTAGGAT
*
44589210 TAATTTAATTTTTCTTAAAATAAATAAAG
1 TAATTTAATTTTTATTAAAATAAATAAAG
* * *
44589239 TAATTTAGTTTTTATATAGAATAAATGAAG
1 TAATTTAATTTTTAT-TAAAATAAATAAAG
*
44589269 TAATATAAT
1 TAATTTAAT
44589278 ATTAAGATGC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (29 bp):
TAATTTAATTTTTATTAAAATAAATAAAG
Done.