Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 6 of 143
Found at i:1935003 original size:14 final size:16
Alignment explanation
Indices: 1934974--1935023 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1934964 AATATGATTA
1934974 TTAGATATAAATAATT
1 TTAGATATAAATAATT
1934990 TTAGATA-AAA-AATT
1 TTAGATATAAATAATT
* * *
1935004 ATATTATATAAATATTT
1 TTA-GATATAAATAATT
1935021 TTA
1 TTA
1935024 TACTATGCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 6 0.22
15 6 0.22
16 10 0.37
17 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
TTAGATATAAATAATT
Found at i:1946679 original size:156 final size:156
Alignment explanation
Indices: 1945997--1946775 Score: 952
Period size: 156 Copynumber: 5.0 Consensus size: 156
1945987 ACAAAAGAAA
* * * *
1945997 TGTTCATAGTTCATTATCCTTGATTTGACTTTTATATCCCTATATCCATCCTCAAACACACGACT
1 TGTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACT
* * * *
1946062 AAAAATATAAATACAA-GCACAAGAAAATACCATTTTTTCCTTGGGGAGTAATTTCTCGGATGGC
66 CAAAATATAAATA-AATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGGC
* * *
1946126 TTCCTTGATATAGTTTCCTGAAAAGGA
130 TTCCTCGATACAGTTTCCTGAAAAGGG
*
1946153 TGCTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACT
1 TGTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACT
* * *
1946218 CAAAATATAAATATATGCACAAGAACTTACCATTTTCTCCTTGGGGAGTAACTTCTCAGATGGCT
66 CAAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGG--
1946283 TCTTCCTCGATACAGTTTCCTG-AAAGGG
129 -CTTCCTCGATACAGTTTCCTGAAAAGGG
* * ** * *
1946311 TGTTTC-TAGTTCATCATCCTTTATTTGAC-----CGTTCTTATCTCCATCCTAAAACACACAAC
1 TG-TTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAAC
* * * *
1946370 TAAAAATATAAATACAA-GCGCAAGAACATACCATTTTCTCGTTGGCGAGTAATTTCTCAGATGG
65 TCAAAATATAAATA-AATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGG
*
1946434 CTTCTTCCGCGATACAGTTTCCTGAAAAGGG
129 ---CTTCCTCGATACAGTTTCCTGAAAAGGG
* * * *
1946465 TGTTCCTAGTTTATTATCCTTGATTTGACTTTTATGTTCCTATCTCCATCCTCTAACACACAACT
1 TGTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACT
* * **
1946530 CAAAATATAAATAAATGCACGAGAGCATACCATTTTCTCCTTATGGAGTAATTTCTCAGATGGCT
66 CAAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGGCT
* * *
1946595 TCCTCGATTCAATTTCCTGAAAAAGG
131 TCCTCGATACAGTTTCCTGAAAAGGG
* * *
1946621 TGTTCGTAGTTCGTTATCCTTGATTTGACATTTATATTCCTATCTCTATCCTCAAACACACAACT
1 TGTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACT
* ** * * * * *
1946686 CAAGATATAAATATGTACACAAGAACATACCATTTTCACCTCGGAGAGTAATTCCTCAGATGGC-
66 CAAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGGCT
*
1946750 T--TCGATACAATTTCCTGAAAAGGG
131 TCCTCGATACAGTTTCCTGAAAAGGG
1946774 TG
1 TG
1946776 CTTGTAATTA
Statistics
Matches: 539, Mismatches: 70, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
153 130 0.24
154 29 0.05
155 2 0.00
156 248 0.46
158 30 0.06
159 100 0.19
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.34
Consensus pattern (156 bp):
TGTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACT
CAAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCAGATGGCT
TCCTCGATACAGTTTCCTGAAAAGGG
Found at i:1948054 original size:157 final size:156
Alignment explanation
Indices: 1947799--1948196 Score: 505
Period size: 157 Copynumber: 2.5 Consensus size: 156
1947789 TTTCAACTAG
* * *
1947799 TCGAAATCACTTTCTTTCCAGTAAAATAATTAAGTTGTAAAGTCTAAAAAC-AAAACTTCAATCA
1 TCGAAAACACTTTCTTT-CA-TAAAATAATTAAATTGTAAAGTCCAAAAACAAAAAC-TCAATCA
* * * * * * * *
1947863 CCATATTGATTTATAAACAGTAACATCACCTTAATCAACAGGATCAATTTATTAACTATAATATT
63 ACATATTGATTTATGAACAGTAAAATCACATTAATCAACAGGATCAACTCACTAACTATAACATT
1947928 AATTATAACATATGGGTTATTTCAA-ACAT
128 AATTATAACATATGGGTTATTTCAATA-AT
*
1947957 TCGAAAACACTTTTCTTTCATAAAATAATTAAATTGTAAAGTCCAAAAACAAAAACTCAATCAAT
1 TCGAAAACAC-TTTCTTTCATAAAATAATTAAATTGTAAAGTCCAAAAACAAAAACTCAATCAAC
* *
1948022 ATATTGATTTATGAATAGTAAAATCACATTAATCAACAGGATCAACTCACTACCTATAACATTAA
65 ATATTGATTTATGAACAGTAAAATCACATTAATCAACAGGATCAACTCACTAACTATAACATTAA
1948087 TTATAACATATGGGTTATTTCAATAAT
130 TTATAACATATGGGTTATTTCAATAAT
* * * ** * * *
1948114 TC-AAAATCACTTTCGTTCCGTAAAATAATTAAACTGTTAAAGTCGGAAAACATAACCCCAATCA
1 TCGAAAA-CACTTTC-TTTCATAAAATAATTAAATTG-TAAAGTCCAAAAACAAAAACTCAATCA
1948178 ACATATTGATTTATGAACA
63 ACATATTGATTTATGAACA
1948197 AGATGAAAGT
Statistics
Matches: 210, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
156 8 0.04
157 139 0.66
158 56 0.27
159 7 0.03
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.32
Consensus pattern (156 bp):
TCGAAAACACTTTCTTTCATAAAATAATTAAATTGTAAAGTCCAAAAACAAAAACTCAATCAACA
TATTGATTTATGAACAGTAAAATCACATTAATCAACAGGATCAACTCACTAACTATAACATTAAT
TATAACATATGGGTTATTTCAATAAT
Found at i:1949185 original size:3 final size:3
Alignment explanation
Indices: 1949138--1949171 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1949128 ATTATGATAG
1949138 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1949172 ATTCGAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1949612 original size:21 final size:22
Alignment explanation
Indices: 1949579--1949627 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
1949569 ATGTTATCTA
*
1949579 ATAAATAACTTAAATTAATTAT
1 ATAAATAACTTAAAATAATTAT
* *
1949601 ATAATTAA-TTAAAATATTTAT
1 ATAAATAACTTAAAATAATTAT
1949622 AATAAA
1 -ATAAA
1949628 AATATCGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATAACTTAAAATAATTAT
Found at i:1957509 original size:3 final size:3
Alignment explanation
Indices: 1957501--1957532 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1957491 GGATAGCCAT
*
1957501 TGA TGA TGA TGA TGA TGA CGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1957533 CGTTCTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:1969383 original size:45 final size:45
Alignment explanation
Indices: 1969319--1969409 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
1969309 ACTCTATGTG
1969319 CAAATTATCGGTAACATCAATAATCATCATGAACCCTTGAATCTA
1 CAAATTATCGGTAACATCAATAATCATCATGAACCCTTGAATCTA
*
1969364 CAAATTATCGGTAACATCAATAGTCATCATGAACCCTTGAATCTA
1 CAAATTATCGGTAACATCAATAATCATCATGAACCCTTGAATCTA
1969409 C
1 C
1969410 TAACTTACTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (45 bp):
CAAATTATCGGTAACATCAATAATCATCATGAACCCTTGAATCTA
Found at i:1970161 original size:8 final size:8
Alignment explanation
Indices: 1970150--1970188 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
1970140 AAATCTAAAA
*
1970150 TTAATATT
1 TTAAAATT
1970158 TTAAAATT
1 TTAAAATT
1970166 TTAAAATT
1 TTAAAATT
1970174 TATAAAA-T
1 T-TAAAATT
1970182 TTAAAAT
1 TTAAAAT
1970189 ATATATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 5 0.18
8 18 0.64
9 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TTAAAATT
Found at i:1970174 original size:16 final size:16
Alignment explanation
Indices: 1970145--1970193 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1970135 ATAAAAAATC
*
1970145 TAAAA-TTAATATTT-
1 TAAAATTTAAAATTTA
1970159 TAAAATTTTAAAATTTA
1 TAAAA-TTTAAAATTTA
*
1970176 TAAAATTTAAAATATA
1 TAAAATTTAAAATTTA
1970192 TA
1 TA
1970194 TAAAGAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.17
16 20 0.67
17 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATTTAAAATTTA
Found at i:1973094 original size:6 final size:6
Alignment explanation
Indices: 1973084--1973114 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1973074 TGATGTCTTT
*
1973084 GATGGT GATGGA GATGGA GATGGA GATGGA G
1 GATGGA GATGGA GATGGA GATGGA GATGGA G
1973115 GCTTGCATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.52, T:0.19
Consensus pattern (6 bp):
GATGGA
Found at i:1977194 original size:22 final size:20
Alignment explanation
Indices: 1977162--1977204 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
1977152 ATCAAAAAAT
*
1977162 AAATTTTTTAAGTTTTTATAA
1 AAATTTTTTAAATTTTT-TAA
1977183 AAATATTTTTAAATTTTTTAA
1 AAAT-TTTTTAAATTTTTTAA
1977204 A
1 A
1977205 TTATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AAATTTTTTAAATTTTTTAA
Found at i:1978158 original size:7 final size:7
Alignment explanation
Indices: 1978142--1978178 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1978132 ATATCTTTCC
1978142 TTTT-TT
1 TTTTCTT
1978148 TTTTCTT
1 TTTTCTT
1978155 TTTTCTT
1 TTTTCTT
1978162 TTTTCTT
1 TTTTCTT
1978169 TTTT-TT
1 TTTTCTT
1978175 TTTT
1 TTTT
1978179 ATGTTACTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 10 0.33
7 20 0.67
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (7 bp):
TTTTCTT
Found at i:1978192 original size:26 final size:25
Alignment explanation
Indices: 1978135--1978195 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
1978125 TGATGGGATA
*
1978135 TCTTTCCTTTTTTTTTTCTTTTTTCT
1 TCTTT-CTTTTTTTTTTCTTTTTACT
*
1978161 TTTTTCTTTTTTTTTT-TTATGTTACT
1 TCTTTCTTTTTTTTTTCTT-T-TTACT
1978187 TCTTTCTTT
1 TCTTTCTTT
1978196 GCTTATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.07
25 12 0.40
26 16 0.53
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (25 bp):
TCTTTCTTTTTTTTTTCTTTTTACT
Found at i:1980822 original size:46 final size:44
Alignment explanation
Indices: 1980772--1980919 Score: 156
Period size: 46 Copynumber: 3.2 Consensus size: 44
1980762 AGCACGTCTC
1980772 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACT-TGTGTGCTCTCTG-TTAGCACTTTGT
* * *
1980818 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCAC-TTGTGTGCTCTCTG-TTAGCACTTTGT
* *
1980864 GTGCTCTCTG-TTGCCAAGCACTTATGTGCTCTCTGTTAGTACTTTG-
1 GTGCTCTCTGATT----AGCACTTGTGTGCTCTCTGTTAGCACTTTGT
*
1980910 GTACTCTCTG
1 GTGCTCTCTG
1980920 CTTGTTCCGT
Statistics
Matches: 87, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
45 2 0.02
46 59 0.68
47 10 0.11
48 12 0.14
49 4 0.05
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (44 bp):
GTGCTCTCTGATTAGCACTTGTGTGCTCTCTGTTAGCACTTTGT
Found at i:1980862 original size:69 final size:66
Alignment explanation
Indices: 1980775--1980919 Score: 202
Period size: 69 Copynumber: 2.1 Consensus size: 66
1980765 ACGTCTCGTG
*
1980775 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACTTT
1980839 GTGTA
63 G-GTA
*
1980844 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCAAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTT--C-AGCACTTATGTGCTCTCTGTTAGTACTTT
1980909 GGTA
63 GGTA
1980913 CTCTCTG
1 CTCTCTG
1980920 CTTGTTCCGT
Statistics
Matches: 70, Mismatches: 2, Indels: 8
0.88 0.03 0.10
Matches are distributed among these distances:
68 2 0.03
69 39 0.56
70 11 0.16
71 13 0.19
72 5 0.07
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (66 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGT
A
Found at i:1980875 original size:23 final size:23
Alignment explanation
Indices: 1980751--1980873 Score: 167
Period size: 23 Copynumber: 5.3 Consensus size: 23
1980741 ACACTAGCGC
* *
1980751 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
1980774 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
1980797 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
1980820 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
1980843 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
1980866 GCTCTCTG
1 GCTCTCTG
1980874 TTGCCAAGCA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
23 87 0.97
24 3 0.03
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:1982021 original size:21 final size:20
Alignment explanation
Indices: 1981984--1982022 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1981974 TTTAATATAT
* *
1981984 TATAAATAATTTAAAAATTG
1 TATAAAAAAATTAAAAATTG
1982004 TATAAAAAAATTATAAAAT
1 TATAAAAAAATTA-AAAAT
1982023 CTTAATATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TATAAAAAAATTAAAAATTG
Found at i:1985008 original size:279 final size:281
Alignment explanation
Indices: 1984422--1985068 Score: 867
Period size: 279 Copynumber: 2.3 Consensus size: 281
1984412 TCTCTCTAAC
* * * ** *
1984422 AAGAAGATAAGGCGTTTCAGCATACTTGAACACACGTCTT-CTTATATTGACAACAATAATCATG
1 AAGAAGATAATGCGCTTCAACGCACTTGAACACACATCTTAC-TATATTGACAACAATAATCATG
* *
1984486 TCAATCGAATTAAAACTCAATCGACAAAATTGATACTTTAAATACAAGCTCTTTACAAATGGTGT
65 TCAATCGAACTAAAACTCAATCGACAAAATTGATACTTGAAATACAAGCTCTTTACAAATGGTGT
* * *
1984551 AGGACATTTGATGGATCACTCGCAATAAATTTTGAGTTAAAAAATGTGTACACTGTCTCTAAAAG
130 AGGACATTTGATGGATCACTCGCAAAAAATTTTGAGTTAAAAAATGTGTACACTATCCCTAAAAG
* * * *
1984616 TTAACAATCTTATTATAAATTCTGATCATATTTGCTTTTTTTGACATAATGTTTAAAATTATTCA
195 TT-ACAATATTATTATAAATTCTGATCATATTTGCTTTTTTTGACATAATATTTAAAACTACTCA
* *
1984681 TAGTCTCTCCTTAACCCATAAAT
259 TAATCTCTCCCTAACCCATAAAT
* * * *
1984704 AGGAGGATAATGCGCTTCAACGCACTTGAACTCACATCTTACTATATTGACAGCAATAATCATGT
1 AAGAAGATAATGCGCTTCAACGCACTTGAACACACATCTTACTATATTGACAACAATAATCATGT
* * *
1984769 CAGTCGAGCTAAAACTCAATCGA-AAAATTGATACTTGAAATACAAGCTTTTTACAAATGGTGTA
66 CAATCGAACTAAAACTCAATCGACAAAATTGATACTTGAAATACAAGCTCTTTACAAATGGTGTA
*
1984833 GGACATTTGATGGATCAC-CTGCAAAAAAATTTTGAGTTAAAAAATGTGTGCACTATCCCTAAAA
131 GGACATTTGATGGATCACTC-GC-AAAAAATTTTGAGTTAAAAAATGTGTACACTATCCCTAAAA
* * * *
1984897 G-T-CAATATTATTATAAGTTCTGTTCATATTTGTTTTTTTTGACATGATATTTAAAACTAC-CT
194 GTTACAATATTATTATAAATTCTGATCATATTTGCTTTTTTTGACATAATATTTAAAACTACTC-
1984959 ATAATCTCTCCCTAACCCATAAAT
258 ATAATCTCTCCCTAACCCATAAAT
* * * * * *
1984983 AAGAAGATAATGCTCTTCAACGCACTTGAACCCGCATCTTACTGTATTGACAATAAT-ATACATA
1 AAGAAGATAATGCGCTTCAACGCACTTGAACACACATCTTACTATATTGACAACAATAAT-CATG
*
1985047 TCAATCGAACTAAGACTCAATC
65 TCAATCGAACTAAAACTCAATC
1985069 AACTATTATT
Statistics
Matches: 319, Mismatches: 41, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
278 3 0.01
279 143 0.45
280 1 0.00
281 60 0.19
282 111 0.35
283 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (281 bp):
AAGAAGATAATGCGCTTCAACGCACTTGAACACACATCTTACTATATTGACAACAATAATCATGT
CAATCGAACTAAAACTCAATCGACAAAATTGATACTTGAAATACAAGCTCTTTACAAATGGTGTA
GGACATTTGATGGATCACTCGCAAAAAATTTTGAGTTAAAAAATGTGTACACTATCCCTAAAAGT
TACAATATTATTATAAATTCTGATCATATTTGCTTTTTTTGACATAATATTTAAAACTACTCATA
ATCTCTCCCTAACCCATAAAT
Found at i:1999420 original size:8 final size:8
Alignment explanation
Indices: 1999407--1999440 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
1999397 TTACTCGAAC
1999407 ATATATTT
1 ATATATTT
1999415 ATATATTT
1 ATATATTT
1999423 ATATATATGT
1 ATATAT-T-T
1999433 ATATATTT
1 ATATATTT
1999441 GAAGGAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.62
9 2 0.08
10 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
ATATATTT
Found at i:2003758 original size:31 final size:35
Alignment explanation
Indices: 2003712--2003776 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 35
2003702 TTTGATAGTT
2003712 TTTAAAAGAATTAATTATT-ATTT-TAAA-ATTAAA
1 TTTAAAAGAATTAATT-TTCATTTGTAAATATTAAA
2003745 TTTAAAA-AA-TAATTTTCATTTGTAAATATTAA
1 TTTAAAAGAATTAATTTTCATTTGTAAATATTAA
2003777 TATATAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
30 2 0.07
31 9 0.31
32 6 0.21
33 12 0.41
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (35 bp):
TTTAAAAGAATTAATTTTCATTTGTAAATATTAAA
Found at i:2011006 original size:18 final size:18
Alignment explanation
Indices: 2010969--2011022 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
2010959 TTTATTTAAA
*
2010969 TATAAA-ATTTTAAATTTT
1 TATAAATATTTTGAA-TTT
2010987 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
*
2011005 TAAAAATTATTTTGAATT
1 TATAAA-TATTTTGAATT
2011023 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:2024746 original size:28 final size:28
Alignment explanation
Indices: 2024667--2024754 Score: 104
Period size: 28 Copynumber: 3.0 Consensus size: 28
2024657 GTCCTTATAC
* *
2024667 TTTTTAAATTTCCAAATTTTAATCTCTCTA
1 TTTTTCAATTTCAAAATTTTAA--TCTCTA
* *
2024697 TATTTCTAATTTCAAGATTTTAATCTCTA
1 TTTTTC-AATTTCAAAATTTTAATCTCTA
*
2024726 TTTTTCAATTTCAAAAGTTTAATCTCTA
1 TTTTTCAATTTCAAAATTTTAATCTCTA
2024754 T
1 T
2024755 ATTGTGATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.42
29 11 0.22
30 4 0.08
31 14 0.28
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (28 bp):
TTTTTCAATTTCAAAATTTTAATCTCTA
Found at i:2026044 original size:17 final size:17
Alignment explanation
Indices: 2026024--2026057 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2026014 TATTTATTAT
2026024 GTATATCTATTATGTAA
1 GTATATCTATTATGTAA
2026041 GTATATCTATTATGTAA
1 GTATATCTATTATGTAA
2026058 ATGTAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (17 bp):
GTATATCTATTATGTAA
Found at i:2028901 original size:17 final size:18
Alignment explanation
Indices: 2028873--2028910 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2028863 GGATATTATA
2028873 TAATTATTGTTT-TATTGT
1 TAATTATTGTTTCTATT-T
2028891 TAATT-TTGTTTCTATTT
1 TAATTATTGTTTCTATTT
2028908 TAA
1 TAA
2028911 ATATATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.66
Consensus pattern (18 bp):
TAATTATTGTTTCTATTT
Found at i:2037208 original size:29 final size:28
Alignment explanation
Indices: 2037145--2037209 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
2037135 TACATAATAA
2037145 TGTAATTTTAATTTTTAAAAAATTAAAT
1 TGTAATTTTAATTTTTAAAAAATTAAAT
** * *
2037173 TAAAATTTT-ATTAGTTTAAAGAGTTAAAT
1 TGTAATTTTAATT--TTTAAAAAATTAAAT
2037202 TGTAATTT
1 TGTAATTT
2037210 AATCATTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 3 0.10
28 7 0.24
29 19 0.66
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (28 bp):
TGTAATTTTAATTTTTAAAAAATTAAAT
Found at i:2042215 original size:118 final size:115
Alignment explanation
Indices: 2042028--2042289 Score: 289
Period size: 118 Copynumber: 2.2 Consensus size: 115
2042018 AATTTTAGAC
* * *
2042028 TTTCGGGGGACAAAATAGTAATTTTGGAAAAAATTTGGGTTAAAGATGACATTTTAGACATTTTG
1 TTTCGGGGG-TAAAATGGTAATTTTGG-AAAAATTTGGGTTAAAAATGACATTTTAGACATTTTG
* ** *
2042093 GGATAACATGGTAATTTTT-ACAAAAATTCGGGATAAAAAATGAGG-TTTTTGGA
64 GGATAAAACAGTAATTTTTGA-AAAAA-TCGGGATAAAAAACG-GGATTTTTGGA
* *
2042146 TTTTCGGGGGTAAAATGGTAATTTTGG-AAATTTTGGGGTTAAAAAATGATATTTTAGACA-TTT
1 -TTTCGGGGGTAAAATGGTAATTTTGGAAAAATTT-GGGTT-AAAAATGACATTTTAGACATTTT
*
2042209 GAGGATAAAACAGTAATTTTTGAAAAAATCGGGATCAAAAACGGGATTTTTGGA
63 G-GGATAAAACAGTAATTTTTGAAAAAATCGGGATAAAAAACGGGATTTTTGGA
** *
2042263 CATCAGGGAGTAAAATGGTAATTTTGG
1 TTTC-GGGGGTAAAATGGTAATTTTGG
2042290 GAGTCCTGGT
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
116 10 0.08
117 51 0.41
118 53 0.43
119 10 0.08
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.34
Consensus pattern (115 bp):
TTTCGGGGGTAAAATGGTAATTTTGGAAAAATTTGGGTTAAAAATGACATTTTAGACATTTTGGG
ATAAAACAGTAATTTTTGAAAAAATCGGGATAAAAAACGGGATTTTTGGA
Found at i:2042307 original size:117 final size:118
Alignment explanation
Indices: 2042073--2042307 Score: 264
Period size: 117 Copynumber: 2.0 Consensus size: 118
2042063 TGGGTTAAAG
* ** *
2042073 ATGACATTTTAGACATTTTGGGATAACATGGTAATTTTTACAAAAATTCGGGATAAAAAATGAGG
1 ATGACATTTTAGACATTTTGGGATAAAACAGTAATTTTTACAAAAATTCGGGATAAAAAACGAGG
** * ** *
2042138 TTTTTGGATTTTCGGGGGTAAAATGGTAATTTTGGAAATTTTGGGGTTAAAAA
66 TTTTTGGATCATCGGGAGTAAAATGGTAATTTTGGAAATCCTGGGGTCAAAAA
* *
2042191 ATGATATTTTAGACA-TTTGAGGATAAAACAGTAATTTTTGA-AAAAA-TCGGGATCAAAAACG-
1 ATGACATTTTAGACATTTTG-GGATAAAACAGTAATTTTT-ACAAAAATTCGGGATAAAAAACGA
* * *
2042252 GGATTTTTGGA-CATCAGGGAGTAAAATGGTAATTTTGGGAGTCCTGGTGTCAAAAA
64 GG-TTTTTGGATCATC-GGGAGTAAAATGGTAATTTTGGAAATCCTGGGGTCAAAAA
2042308 TGGAATTTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
116 4 0.04
117 58 0.59
118 35 0.36
119 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (118 bp):
ATGACATTTTAGACATTTTGGGATAAAACAGTAATTTTTACAAAAATTCGGGATAAAAAACGAGG
TTTTTGGATCATCGGGAGTAAAATGGTAATTTTGGAAATCCTGGGGTCAAAAA
Found at i:2042335 original size:29 final size:29
Alignment explanation
Indices: 2042303--2042504 Score: 199
Period size: 29 Copynumber: 6.8 Consensus size: 29
2042293 TCCTGGTGTC
2042303 AAAAATGGAATTTTTGGAAGTTTAAGGGT
1 AAAAATGGAATTTTTGGAAGTTTAAGGGT
* * *
2042332 AAAAATGAAATTTTTGGAA-ATTCAGGGTT
1 AAAAATGGAATTTTTGGAAGTTTAAGGG-T
* * *
2042361 AAAAATGTAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTT-AAGGGT
* * *
2042391 AAAAATAGAATTTTTGGAAGTTTAGGGGC
1 AAAAATGGAATTTTTGGAAGTTTAAGGGT
* *
2042420 AAAAATGTAATTTTTGGAAGTTTCAAGGTT
1 AAAAATGGAATTTTTGGAAGTTT-AAGGGT
* **
2042450 AAAAATGGAATTTTGGAGAAGTTCGAGGGT
1 AAAAATGGAATTTTTG-GAAGTTTAAGGGT
* **
2042480 CAAAATACAATTTTTGGATAGTTTA
1 AAAAATGGAATTTTTGGA-AGTTTA
2042505 GGGACCTCTA
Statistics
Matches: 138, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
28 6 0.04
29 62 0.45
30 61 0.44
31 9 0.07
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTAAGGGT
Found at i:2042358 original size:88 final size:87
Alignment explanation
Indices: 2042254--2042504 Score: 235
Period size: 88 Copynumber: 2.8 Consensus size: 87
2042244 CAAAAACGGG
* * *
2042254 ATTTTTGGACATCAGGGAGT-AAAATGGTAA-TTTTGGGAGTC-CTG-GTGTCAAAAATGGAATT
1 ATTTTTGGAAATCAGGG-GTAAAAAT-GTAATTTTTGGAAGTCTC-GAG-GTCAAAAATAGAATT
*
2042315 TTTGGAAGTTTAAGGGTAAAAATGAA
62 TTTGGAAGTTTAAGGGCAAAAATGAA
* * *
2042341 ATTTTTGGAAATTCAGGGTTAAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATAGAATTTTT
1 ATTTTTGGAAA-TCAGGGGTAAAAATGTAATTTTTGGAAGTCTCGAGGTCAAAAATAGAATTTTT
* *
2042406 GGAAGTTTAGGGGCAAAAATGTA
65 GGAAGTTTAAGGGCAAAAATGAA
* * * * * *
2042429 ATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTGGAGAAGT-TCGAGGGTC-AAAATACAATT
1 ATTTTTGGAA--ATCAGGGGTAAAAATGTAATTTTTG-GAAGTCTCGA-GGTCAAAAATAGAATT
2042492 TTTGGATAGTTTA
62 TTTGGA-AGTTTA
2042505 GGGACCTCTA
Statistics
Matches: 139, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
87 15 0.11
88 67 0.48
89 43 0.31
90 14 0.10
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (87 bp):
ATTTTTGGAAATCAGGGGTAAAAATGTAATTTTTGGAAGTCTCGAGGTCAAAAATAGAATTTTTG
GAAGTTTAAGGGCAAAAATGAA
Found at i:2042393 original size:30 final size:30
Alignment explanation
Indices: 2042303--2042503 Score: 205
Period size: 30 Copynumber: 6.8 Consensus size: 30
2042293 TCCTGGTGTC
*
2042303 AAAAATGGAATTTTTGGAAGTTT-AAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGGT
* *
2042332 AAAAATGAAATTTTTGGAA-ATTC-AGGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGG-T
* *
2042361 AAAAATGTAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGGT
* * *
2042391 AAAAATAGAATTTTTGGAAGTTTAG-GGGC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGGT
* * *
2042420 AAAAATGTAATTTTTGGAAGTTTCAAGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGGT
*
2042450 AAAAATGGAATTTTGGAGAAG-TTCGAGGGT
1 AAAAATGGAATTTTTG-GAAGTTTCGAGGGT
* **
2042480 CAAAATACAATTTTTGGATAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
2042504 AGGGACCTCT
Statistics
Matches: 140, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.04
29 62 0.44
30 63 0.45
31 9 0.06
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGGT
Found at i:2042396 original size:59 final size:58
Alignment explanation
Indices: 2042303--2042503 Score: 228
Period size: 59 Copynumber: 3.4 Consensus size: 58
2042293 TCCTGGTGTC
* *
2042303 AAAAATGGAATTTTTGGAAGTTT-AAGGGTAAAAATGAAATTTTTGGAAATTCAGGGTT
1 AAAAATGTAATTTTTGGAAGTTTCAAGGTTAAAAATGAAATTTTTGGAAATTCAGGG-T
* * * *
2042361 AAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAAT-AGAATTTTTGGAAGTTTAGGGGC
1 AAAAATGTAATTTTTGGAAGTTTCAAGGTTAAAAATGA-AATTTTTGGAAATTCA-GGGT
*
2042420 AAAAATGTAATTTTTGGAAGTTTCAAGGTTAAAAATGGAA-TTTTGGAGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTTCAAGGTTAAAAATGAAATTTTTGGA-AA-TTC-AGGGT
* **
2042480 CAAAATACAATTTTTGGATAGTTT
1 AAAAATGTAATTTTTGGA-AGTTT
2042504 AGGGACCTCT
Statistics
Matches: 121, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
58 30 0.25
59 62 0.51
60 23 0.19
61 6 0.05
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
AAAAATGTAATTTTTGGAAGTTTCAAGGTTAAAAATGAAATTTTTGGAAATTCAGGGT
Found at i:2043749 original size:20 final size:20
Alignment explanation
Indices: 2043726--2043766 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2043716 TAACATTACC
*
2043726 AAAAAATATTTATTATTATT
1 AAAAAATATTTACTATTATT
2043746 AAAAAATATTTACTATTATT
1 AAAAAATATTTACTATTATT
2043766 A
1 A
2043767 TTACTGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAAAATATTTACTATTATT
Found at i:2043765 original size:3 final size:3
Alignment explanation
Indices: 2043759--2043812 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
2043749 AAATATTTAC
* * * **
2043759 TAT TAT TAT TAC TGT TAT TAT TAT TAA TGC TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
2043805 TAT TAT TA
1 TAT TAT TA
2043813 ATTAATGTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 39 0.95
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2044598 original size:11 final size:11
Alignment explanation
Indices: 2044582--2044635 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
2044572 ATAATAATAC
2044582 TAAATTTAAAT
1 TAAATTTAAAT
*
2044593 TAAATTAAAAT
1 TAAATTTAAAT
*
2044604 TAAAATTAAAAT
1 T-AAATTTAAAT
* *
2044616 TGAATTTAAAA
1 TAAATTTAAAT
2044627 TAAATTTAA
1 TAAATTTAA
2044636 TTTCAAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 26 0.70
12 11 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:2044603 original size:17 final size:16
Alignment explanation
Indices: 2044564--2044638 Score: 62
Period size: 17 Copynumber: 4.5 Consensus size: 16
2044554 ACTTTTCTTT
2044564 TTAAATTTATAA-TAATA
1 TTAAATTTA-AATTAA-A
*
2044581 CTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
*
2044597 TTAAAATTAAAATTAAAA
1 TT-AAATTTAAATT-AAA
* *
2044615 TTGAATTTAAAATAAA
1 TTAAATTTAAATTAAA
*
2044631 TTTAATTT
1 TTAAATTT
2044639 CAAAATGGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
16 14 0.29
17 29 0.60
18 5 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:2044609 original size:23 final size:22
Alignment explanation
Indices: 2044582--2044635 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
2044572 ATAATAATAC
2044582 TAAATTTAAATT-AAATTAAAA
1 TAAATTTAAATTGAAATTAAAA
* *
2044603 TTAAAATTAAAATTGAATTTAAAA
1 -T-AAATTTAAATTGAAATTAAAA
2044627 TAAATTTAA
1 TAAATTTAA
2044636 TTTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.30
23 11 0.41
24 8 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAATTTAAATTGAAATTAAAA
Found at i:2044611 original size:12 final size:11
Alignment explanation
Indices: 2044582--2044632 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 11
2044572 ATAATAATAC
*
2044582 TAAATTTAAAT
1 TAAATTAAAAT
2044593 TAAATTAAAAT
1 TAAATTAAAAT
2044604 TAAAATTAAAAT
1 T-AAATTAAAAT
*
2044616 TGAATTTAAAA-
1 T-AAATTAAAAT
2044627 TAAATT
1 TAAATT
2044633 TAATTTCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 4 0.11
11 12 0.34
12 19 0.54
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TAAATTAAAAT
Found at i:2045040 original size:91 final size:91
Alignment explanation
Indices: 2044895--2045721 Score: 1368
Period size: 91 Copynumber: 9.1 Consensus size: 91
2044885 TGATGTCGGG
* *
2044895 GCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
2044960 TCAAGAGGATAGGAAATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
**
2044986 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTAATATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* *
2045051 TCAAGAGGATAGGAAATGATGTCGGT
66 TCAAGAGGATAGGAAATGATGTTGAT
*
2045077 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAAACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
2045142 TCAAGAGGATAGGAAATGATGTTGGT
66 TCAAGAGGATAGGAAATGATGTTGAT
* *
2045168 GCTTCATCTTGCTCTTACTACAACTTCAAAGAGATAAAGACTTACTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
2045233 TCAAGAGGATAGGAAATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
* * * *
2045259 GCTTCATCTAGCTCTTACTACAACTTTAAAGAGATAAAGACTTACTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
2045324 TCAAGAGGATAGGAATTGATGTTTGAT
66 TCAAGAGGATAGGAAATGATG-TTGAT
*
2045351 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* * *
2045416 TCAAGAGGATAAGAATTGATGTTTAAT
66 TCAAGAGGATAGGAAATGATG-TTGAT
* *
2045443 GCTTCATCTTGCTTTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAGCTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* *
2045508 TCAAGAGGATAGGAAATGATATTGGT
66 TCAAGAGGATAGGAAATGATGTTGAT
* *
2045534 GCTTTATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCTAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
2045599 TCAAGAGGATAGG-GATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
* *
2045624 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAGCTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
2045689 TCAAGAGGATAGGAAATGATGTTTGAT
66 TCAAGAGGATAGGAAATGATG-TTGAT
2045716 GCTTCA
1 GCTTCA
2045722 AGGTAGCGGG
Statistics
Matches: 691, Mismatches: 42, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
90 83 0.12
91 425 0.62
92 183 0.26
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (91 bp):
GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
TCAAGAGGATAGGAAATGATGTTGAT
Found at i:2045427 original size:40 final size:40
Alignment explanation
Indices: 2045356--2045695 Score: 220
Period size: 40 Copynumber: 7.7 Consensus size: 40
2045346 TTGATGCTTC
2045356 ATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCT
1 ATCTAGCT-TTACTACAACTTCAGAGAGATAAAGACTTGCT
* * *
2045397 ATCCAACTTTACTACAACTTCA-AGAGGATAAGAATTGATGTTTAATGCTT
1 ATCTAGCTTTACTACAACTTCAGAGA-GAT-A-AA--GA---CT--TGC-T
*
2045447 CATCTTGCTTTTACTACAACTTCAGAGAGATAAAGACTTGCT
1 -ATCTAGC-TTTACTACAACTTCAGAGAGATAAAGACTTGCT
* *
2045489 ATCCAGCTTTACTACAACTTCA-AGAGGATAGGAAATGATATTGGTGCTTT
1 ATCTAGCTTTACTACAACTTCAGAGA-GAT---AAA-G--ACT--TGC--T
*
2045539 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCT
1 ATCTAGCT-TTACTACAACTTCAGAGAGATAAAGACTTGCT
* * *
2045580 ATCTAACTTTACTACAACTTCA-AGAGGATAGGGATGATGTTGATGCTT
1 ATCTAGCTTTACTACAACTTCAGAGA-GATA---AAGA--CT--TGC-T
2045628 CATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCT
1 -ATCTAGCT-TTACTACAACTTCAGAGAGATAAAGACTTGCT
*
2045670 ATCCAGCTTTACTACAACTTCA-AGAG
1 ATCTAGCTTTACTACAACTTCAGAGAG
2045696 GATAGGAAAT
Statistics
Matches: 239, Mismatches: 21, Indels: 80
0.70 0.06 0.24
Matches are distributed among these distances:
39 13 0.05
40 67 0.28
41 26 0.11
42 4 0.02
43 15 0.06
44 3 0.01
45 5 0.02
46 2 0.01
47 8 0.03
48 9 0.04
49 10 0.04
50 28 0.12
51 25 0.10
52 21 0.09
53 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (40 bp):
ATCTAGCTTTACTACAACTTCAGAGAGATAAAGACTTGCT
Found at i:2047902 original size:15 final size:15
Alignment explanation
Indices: 2047883--2047946 Score: 98
Period size: 15 Copynumber: 4.5 Consensus size: 15
2047873 TGACCTCTCT
2047883 TTTTTTTTGA-TTGA
1 TTTTTTTTGATTTGA
*
2047897 -TTTTTTTGATTTAA
1 TTTTTTTTGATTTGA
2047911 TTTTTTTTGATTTGA
1 TTTTTTTTGATTTGA
2047926 -TTTTTTTGATTTGA
1 TTTTTTTTGATTTGA
2047940 TTTTTTT
1 TTTTTTT
2047947 CACACGTCGA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
13 9 0.20
14 17 0.38
15 19 0.42
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (15 bp):
TTTTTTTTGATTTGA
Found at i:2047925 original size:29 final size:28
Alignment explanation
Indices: 2047883--2047946 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 28
2047873 TGACCTCTCT
2047883 TTTTTTTTGATTGATTTTTTTGATTTAA
1 TTTTTTTTGATTGATTTTTTTGATTTAA
*
2047911 TTTTTTTTGATTTGATTTTTTTGATTTGA
1 TTTTTTTTGA-TTGATTTTTTTGATTTAA
2047940 TTTTTTT
1 TTTTTTT
2047947 CACACGTCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (28 bp):
TTTTTTTTGATTGATTTTTTTGATTTAA
Found at i:2053080 original size:30 final size:30
Alignment explanation
Indices: 2053046--2053110 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
2053036 ACTCCGTCTA
* *
2053046 TTGTTAATTTTGTTATTATTTTAGAGATAT
1 TTGTTAATTTTATTATTATTTTAGAGACAT
2053076 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAGAGACAT
2053106 TTGTT
1 TTGTT
2053111 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAGAGACAT
Found at i:2053573 original size:17 final size:17
Alignment explanation
Indices: 2053551--2053590 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2053541 AATTAAATTG
2053551 TAATTTTAT-TATTTTAA
1 TAATTTTATATATTTT-A
2053568 TAA-TTTATATATTTTA
1 TAATTTTATATATTTTA
2053584 TAATTTT
1 TAATTTT
2053591 TAAAAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTTTATATATTTTA
Found at i:2053574 original size:16 final size:16
Alignment explanation
Indices: 2053555--2053589 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2053545 AAATTGTAAT
2053555 TTTAT-TATTTTAATAA
1 TTTATATATTTT-ATAA
2053571 TTTATATATTTTATAA
1 TTTATATATTTTATAA
2053587 TTT
1 TTT
2053590 TTAAAAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATATATTTTATAA
Found at i:2064918 original size:3 final size:3
Alignment explanation
Indices: 2064912--2064950 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2064902 CTCCTCCTCC
* * *
2064912 TCT TCT TCT TCT TCT TCA TCT TCT TCA TCT TCA TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2064951 CCATCATCGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.59
Consensus pattern (3 bp):
TCT
Found at i:2065013 original size:15 final size:15
Alignment explanation
Indices: 2064915--2065012 Score: 65
Period size: 15 Copynumber: 6.5 Consensus size: 15
2064905 CTCCTCCTCT
*
2064915 TCTTCTTCTTCTTCA
1 TCTTCTTCATCTTCA
2064930 TCTTCTTCATCTTCA
1 TCTTCTTCATCTTCA
* * *
2064945 TCTTCTCCATCATCG
1 TCTTCTTCATCTTCA
* * **
2064960 TCATCATCA-CCACTA
1 TCTTCTTCATCTTC-A
* *
2064975 TCTTCTTCGTCATCA
1 TCTTCTTCATCTTCA
*
2064990 TCCTCTTC-TCCTTCA
1 TCTTCTTCAT-CTTCA
2065005 TCTTCTTC
1 TCTTCTTC
2065013 TTCTACTTCG
Statistics
Matches: 62, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
14 3 0.05
15 57 0.92
16 2 0.03
ACGTcount: A:0.13, C:0.38, G:0.02, T:0.47
Consensus pattern (15 bp):
TCTTCTTCATCTTCA
Found at i:2067267 original size:6 final size:6
Alignment explanation
Indices: 2067231--2067334 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
2067221 GACTTTGATT
* * * *
2067231 TTTAAG TTTAAA -TTAAT TTTAAA TTT-TA TTTAGA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
2067275 TCTTAAA TTTAAA TTTATTTA TTTAAA TTT-AC TTTAAA TTTAAA TTT-AA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2067324 -TTAAA TTTAAA
1 TTTAAA TTTAAA
2067335 AATAATATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.05
5 18 0.23
6 49 0.63
7 2 0.03
8 5 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:2067268 original size:17 final size:16
Alignment explanation
Indices: 2067243--2067334 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
2067233 TAAGTTTAAA
*
2067243 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
*
2067260 TTAGATTTAAATTTAT
1 TTAAATTTAAATTTAT
2067276 CTTAAATTTAAATTTAT
1 -TTAAATTTAAATTTAT
2067293 TT--ATTTAAATTTACT
1 TTAAATTTAAATTTA-T
*
2067308 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAT
2067324 TTAAATTTAAA
1 TTAAATTTAAA
2067335 AATAATATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.16
15 3 0.04
16 18 0.27
17 35 0.52
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:2067325 original size:11 final size:11
Alignment explanation
Indices: 2067231--2067334 Score: 68
Period size: 11 Copynumber: 9.0 Consensus size: 11
2067221 GACTTTGATT
2067231 TTTAAGTTTAAA
1 TTTAA-TTTAAA
2067243 -TTAATTTTAAA
1 TTTAA-TTTAAA
* *
2067254 TTTTATTTAGA
1 TTTAATTTAAA
**
2067265 TTTAAATTTATC
1 TTT-AATTTAAA
*
2067277 TTAAATTTAAA
1 TTTAATTTAAA
2067288 TTTATTTATTTAAA
1 TTTA---ATTTAAA
*
2067302 TTTACTTTAAA
1 TTTAATTTAAA
2067313 TTTAAATTT-AA
1 TTT-AATTTAAA
*
2067324 TTAAATTTAAA
1 TTTAATTTAAA
2067335 AATAATATTA
Statistics
Matches: 72, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
10 5 0.07
11 42 0.58
12 14 0.19
14 11 0.15
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:2069409 original size:90 final size:89
Alignment explanation
Indices: 2069252--2069530 Score: 305
Period size: 90 Copynumber: 3.1 Consensus size: 89
2069242 CTTTGTAAGT
* * * * ** * * *
2069252 CCCTAAA-TTGTCCAAAAATTACATTTCAACCCCAAAACTTTCTGAAAACTATATTTTAACCCTA
1 CCCTAAACTTTTCC-AAAATCATATTTTAACCCCAAAA-TTTCCAAAAAATACATTTTAACCCCA
2069316 AAACTTTCTAAAAATTACATTTTAAC
64 AAACTTTCTAAAAATTACATTTTAAC
* ** * * *
2069342 CCCTAAACTTTTCCAAAATTATATTTTAACCTTAAAACTTTTCC-AAAATTGCATTTTGACCCCA
1 CCCTAAACTTTTCCAAAATCATATTTTAACCCCAAAA--TTTCCAAAAAATACATTTTAACCCCA
2069406 AAACTTTCTAAAAATTACATTTTAAC
64 AAACTTTCTAAAAATTACATTTTAAC
* *
2069432 CCCTAAACTTTTCCAAAATCATATTTTGACCCCAAAATTTCCAAAAAAATACATTTTTACCCCAA
1 CCCTAAACTTTTCCAAAATCATATTTTAACCCCAAAATTTCC-AAAAAATACATTTTAACCCCAA
*
2069497 AACTTTC-AACAATTACAATTTT-AC
65 AACTTTCTAAAAATTAC-ATTTTAAC
*
2069521 CCCCAAACTT
1 CCCTAAACTT
2069531 CCCTAAATCC
Statistics
Matches: 163, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
88 5 0.03
89 19 0.12
90 130 0.80
91 9 0.06
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (89 bp):
CCCTAAACTTTTCCAAAATCATATTTTAACCCCAAAATTTCCAAAAAATACATTTTAACCCCAAA
ACTTTCTAAAAATTACATTTTAAC
Found at i:2069525 original size:30 final size:29
Alignment explanation
Indices: 2069266--2069527 Score: 240
Period size: 30 Copynumber: 8.8 Consensus size: 29
2069256 AAATTGTCCA
* *
2069266 AAAATTACATTTCAACCCCAAAACTTTCTG
1 AAAATTACATTTTAACCCCAAAACTTTC-C
* * * *
2069296 AAAACTATATTTTAACCCTAAAACTTTCTA
1 AAAATTACATTTTAACCCCAAAACTTTC-C
*
2069326 AAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAAC-TTTCC
* **
2069356 AAAATTATATTTTAACCTTAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAAC-TTTCC
* * *
2069386 AAAATTGCATTTTGACCCCAAAACTTTCTA
1 AAAATTACATTTTAACCCCAAAACTTTC-C
*
2069416 AAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAAC-TTTCC
* * *
2069446 AAAATCATATTTTGACCCCAAAA-TTTCC
1 AAAATTACATTTTAACCCCAAAACTTTCC
* *
2069474 AAAAAAATACATTTTTACCCCAAAACTTT-C
1 --AAAATTACATTTTAACCCCAAAACTTTCC
*
2069504 AACAATTACAATTTTACCCCCAAA
1 AA-AATTAC-ATTTTAACCCCAAA
2069528 CTTCCCTAAA
Statistics
Matches: 189, Mismatches: 35, Indels: 16
0.79 0.15 0.07
Matches are distributed among these distances:
28 7 0.04
29 9 0.05
30 162 0.86
31 11 0.06
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATTACATTTTAACCCCAAAACTTTCC
Found at i:2069544 original size:29 final size:28
Alignment explanation
Indices: 2069516--2069599 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 28
2069506 CAATTACAAT
2069516 TTTACCCCCAAACTTCCCTAAATCCCAA
1 TTTACCCCCAAACTTCCCTAAATCCCAA
* * ** *
2069544 TTTAGACCCC-AATTTTACTAAAATTACC-A
1 TTTA-CCCCCAAACTTCCCT-AAA-TCCCAA
*
2069573 TTTACCCCCAAACTTCCTTAAATCCCA
1 TTTACCCCCAAACTTCCCTAAATCCCA
2069600 TTTTTAACAC
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
27 3 0.08
28 17 0.43
29 17 0.43
30 3 0.08
ACGTcount: A:0.33, C:0.36, G:0.01, T:0.30
Consensus pattern (28 bp):
TTTACCCCCAAACTTCCCTAAATCCCAA
Found at i:2069595 original size:28 final size:28
Alignment explanation
Indices: 2069507--2069595 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
2069497 AACTTTCAAC
* *
2069507 AATTACAATTTTACCCCCAAACTTCCCTA
1 AATTACCA-TTTACCCCCAAACTTCCTTA
* * ** * *
2069536 AA-TCCCAATTTAGACCCCAATTTTACTAA
1 AATTACC-ATTTA-CCCCCAAACTTCCTTA
2069565 AATTACCATTTACCCCCAAACTTCCTTA
1 AATTACCATTTACCCCCAAACTTCCTTA
2069593 AAT
1 AAT
2069596 CCCATTTTTA
Statistics
Matches: 43, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
28 20 0.47
29 20 0.47
30 3 0.07
ACGTcount: A:0.36, C:0.31, G:0.01, T:0.31
Consensus pattern (28 bp):
AATTACCATTTACCCCCAAACTTCCTTA
Found at i:2069624 original size:57 final size:57
Alignment explanation
Indices: 2069502--2069633 Score: 151
Period size: 57 Copynumber: 2.3 Consensus size: 57
2069492 CCCAAAACTT
* *
2069502 TCAACAATTACAATTTTACCCCCAAACTTCCCTAAATCCCAATTTAGACCCCAATTTTA
1 TCAA-AATTACAA-TTTACCCCCAAACTTCCCTAAATCCCAATTTAGACACCAATTTCA
* * * *
2069561 -CTAAAATTACCATTTACCCCCAAACTTCCTTAAATCCCATTTTTA-ACACCGATTTCA
1 TC-AAAATTACAATTTACCCCCAAACTTCCCTAAATCCCA-ATTTAGACACCAATTTCA
2069618 TCAAAATCTACAATTT
1 TCAAAAT-TACAATTT
2069634 TGCCCCCGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
57 40 0.65
58 20 0.32
59 2 0.03
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.33
Consensus pattern (57 bp):
TCAAAATTACAATTTACCCCCAAACTTCCCTAAATCCCAATTTAGACACCAATTTCA
Found at i:2071183 original size:12 final size:12
Alignment explanation
Indices: 2071165--2071200 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2071155 ATTCACGAAC
2071165 AAGCTCATTTAT
1 AAGCTCATTTAT
*
2071177 TAGCTCATTTAT
1 AAGCTCATTTAT
*
2071189 AAGCTCGTTTAT
1 AAGCTCATTTAT
2071201 GACTCGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (12 bp):
AAGCTCATTTAT
Found at i:2071949 original size:15 final size:15
Alignment explanation
Indices: 2071929--2071963 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2071919 TGTAATAAAT
2071929 TGAAAAATTAAGTGC
1 TGAAAAATTAAGTGC
2071944 TGAAAAATTAAGTGC
1 TGAAAAATTAAGTGC
2071959 TGAAA
1 TGAAA
2071964 TTGATAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (15 bp):
TGAAAAATTAAGTGC
Found at i:2072885 original size:17 final size:17
Alignment explanation
Indices: 2072865--2072914 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
2072855 TTTTTTAACA
2072865 TTATATTTTATATATTT
1 TTATATTTTATATATTT
2072882 TTATATTTT-TATACTTT
1 TTATATTTTATATA-TTT
*
2072899 TTACTTTTTTAT-TATT
1 TTA-TATTTTATATATT
2072915 AATAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 4 0.14
17 17 0.59
18 7 0.24
19 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATATTTTATATATTT
Found at i:2072888 original size:8 final size:8
Alignment explanation
Indices: 2072865--2072910 Score: 58
Period size: 8 Copynumber: 5.5 Consensus size: 8
2072855 TTTTTTAACA
2072865 TTATATTT
1 TTATATTT
2072873 TATATATTT
1 T-TATATTT
2072882 TTATATTT
1 TTATATTT
2072890 TTATACTTT
1 TTATA-TTT
2072899 TTACT-TTT
1 TTA-TATTT
2072907 TTAT
1 TTAT
2072911 TATTAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 1 0.03
8 19 0.54
9 14 0.40
10 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (8 bp):
TTATATTT
Found at i:2076997 original size:18 final size:16
Alignment explanation
Indices: 2076965--2077008 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
2076955 ATGGGATGAG
2076965 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
2076981 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
2076995 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
2077009 ACTCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:2077229 original size:16 final size:16
Alignment explanation
Indices: 2077188--2077230 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
2077178 AGGTTTAGGT
* *
2077188 TTAAAATTTTAATTAA
1 TTAAAAATTTATTTAA
2077204 TT-AAAA-TTATTTAA
1 TTAAAAATTTATTTAA
2077218 TTAAAAATTTATT
1 TTAAAAATTTATT
2077231 CTCATTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.39
15 7 0.30
16 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:2077370 original size:31 final size:29
Alignment explanation
Indices: 2077335--2077394 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2077325 GTGATCACTT
2077335 CGTAACAAAACAATAACATAAGTGACTAAAA
1 CGTAACAAAAC-A-AACATAAGTGACTAAAA
***
2077366 CGTAACATTTCAAACATAAGTGACTAAAA
1 CGTAACAAAACAAACATAAGTGACTAAAA
2077395 TATAACCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
30 1 0.04
31 8 0.31
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (29 bp):
CGTAACAAAACAAACATAAGTGACTAAAA
Found at i:2081565 original size:22 final size:23
Alignment explanation
Indices: 2081527--2081570 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
2081517 CAATTTAATT
2081527 TTTTTCTTTTATGTTCT-TTTAA
1 TTTTTCTTTTATGTTCTCTTTAA
*
2081549 TTTTTCTTTCT-TTTTCTCTTTA
1 TTTTTCTTT-TATGTTCTCTTTA
2081571 CTTTCCATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTTCTTTTATGTTCTCTTTAA
Found at i:2081568 original size:24 final size:24
Alignment explanation
Indices: 2081520--2081569 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2081510 TTTTGAGCAA
*
2081520 TTTAATTTTTTTCTTTTATGTTCT
1 TTTAATTTTTTTCTTTTATGCTCT
2081544 TTTAATTTTTCTTTCTTTT-T-CTCT
1 TTTAA-TTTT-TTTCTTTTATGCTCT
2081568 TT
1 TT
2081570 ACTTTCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 10 0.43
25 5 0.22
26 8 0.35
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTAATTTTTTTCTTTTATGCTCT
Found at i:2085467 original size:6 final size:6
Alignment explanation
Indices: 2085456--2085481 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2085446 TTGAACCGTA
2085456 AAAGAG AAAGAG AAAGAG AAAGAG AA
1 AAAGAG AAAGAG AAAGAG AAAGAG AA
2085482 CTTTCAATTA
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:2085715 original size:13 final size:15
Alignment explanation
Indices: 2085684--2085716 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
2085674 ATAATAATTT
2085684 AATTTTAATTTTGAA
1 AATTTTAATTTTGAA
2085699 AATTTT-ATTTT-AA
1 AATTTTAATTTTGAA
2085712 AATTT
1 AATTT
2085717 GATCATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 5 0.28
15 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
AATTTTAATTTTGAA
Found at i:2085717 original size:21 final size:20
Alignment explanation
Indices: 2085679--2085718 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2085669 TTTTCATAAT
*
2085679 AATTTAATTTTAATTTTGAA
1 AATTTAATTTTAAATTTGAA
*
2085699 AATTTTATTTTAAAATTTGA
1 AATTTAATTTT-AAATTTGA
2085719 TCATTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTTAATTTTAAATTTGAA
Found at i:2088980 original size:27 final size:24
Alignment explanation
Indices: 2088937--2088986 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2088927 CAAAACATCA
*
2088937 TTAAAAATAATTAAAAATACAAATT
1 TTAAAAATAAATAAAAATA-AAATT
2088962 TTAAAAATATAATATAAAATAAAAT
1 TTAAAAATA-AATA-AAAATAAAAT
2088987 CATATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 7 0.32
27 6 0.27
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
TTAAAAATAAATAAAAATAAAATT
Found at i:2090610 original size:32 final size:34
Alignment explanation
Indices: 2090574--2090640 Score: 102
Period size: 32 Copynumber: 2.0 Consensus size: 34
2090564 ATAGTTTATG
* *
2090574 TTTTTATAATTTTTAAATGGTTAAA-T-TAATTT
1 TTTTTATAATTTTTAAAGGGTCAAAGTGTAATTT
2090606 TTTTTATAATTTTTAAAGGGTCAAAGTGTAATTT
1 TTTTTATAATTTTTAAAGGGTCAAAGTGTAATTT
2090640 T
1 T
2090641 ACTATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 23 0.74
33 1 0.03
34 7 0.23
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.55
Consensus pattern (34 bp):
TTTTTATAATTTTTAAAGGGTCAAAGTGTAATTT
Found at i:2091975 original size:7 final size:7
Alignment explanation
Indices: 2091963--2091992 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2091953 ATGCTTGTGA
2091963 TATATGG
1 TATATGG
2091970 TATATGG
1 TATATGG
2091977 TATATGG
1 TATATGG
2091984 TATATGG
1 TATATGG
2091991 TA
1 TA
2091993 CTAACCCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (7 bp):
TATATGG
Found at i:2099089 original size:280 final size:274
Alignment explanation
Indices: 2098588--2099101 Score: 643
Period size: 277 Copynumber: 1.8 Consensus size: 274
2098578 GTATAAAATT
* * *
2098588 TATTAAAATGAAGGTTTGGTTGAATGGTAAAATTAAGGTTTTATTTATATAATTGGTGTGAATTC
1 TATTAAAATAAAGGTTTGGTTGAATGATAAAATTAAAGTTTTATTTATATAATTGGTGTGAATTC
** * *
2098653 AAATCTTACTGTATACTTATTTTAATTGGTTTTTGTTAAAATTAAAAGACTAAAATACCCTCAAA
66 AAATCCAACTATATACTTATTTTAATTGGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAA
* *
2098718 TAATATGATTCACTTTAATTAAGGAAGAACATTTTTGTAATTTCTCTAATCAAGTTGGTACCCGT
131 TAATATGATTCACTTTAATT-A--AAGAACATTTTTGTAATTTCACTAATCAAGTTGGTACCCGA
*
2098783 TTGACTCATGACACGAACTTAGAGATTTTATTAATAGTAAGTATATGTAGATATACAACTGATGG
193 TTGACTCATGACACCAACTTAGAGATTTTATTAATAGTAAGTATATGTAGATATACAACTGATGG
2098848 AGATAATAAATTGTACA
258 AGATAATAAATTGTACA
* * * * * *
2098865 TATTAAAATAAATGTTTGGTTGAGTGATAAATTTAAATTTTTATTTATATAGTTGGTGTGGATTC
1 TATTAAAATAAAGGTTTGGTTGAATGATAAAATTAAAGTTTTATTTATATAATTGGTGTGAATTC
* * * * * *
2098930 AATTCCAACTATATGCTTATTTTTATTTGTTTTTTTTGTTAAAATGAAAAGCCTAAAATACTCTC
66 AAATCCAACTATATACTTA-TTTTAATTG--GTTTTTGTTAAAATGAAAAGACTAAAATACCCTC
* * * * *** * *
2098995 GAATAATATGATTTATTTTAATT-ACGATTTTTTTTGTAATTTCACTAATCAAGTTGGTGCCTGA
128 AAATAATATGATTCACTTTAATTAAAGAACATTTTTGTAATTTCACTAATCAAGTTGGTACCCGA
*
2099059 TTGACTCATTACACCAACTCAGTAAGAGATTTTATTAATAGTA
193 TTGACTCATGACACCAACT---T-AGAGATTTTATTAATAGTA
2099102 TAGATATAAG
Statistics
Matches: 198, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
276 50 0.25
277 70 0.35
278 8 0.04
279 1 0.01
280 69 0.35
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (274 bp):
TATTAAAATAAAGGTTTGGTTGAATGATAAAATTAAAGTTTTATTTATATAATTGGTGTGAATTC
AAATCCAACTATATACTTATTTTAATTGGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAA
TAATATGATTCACTTTAATTAAAGAACATTTTTGTAATTTCACTAATCAAGTTGGTACCCGATTG
ACTCATGACACCAACTTAGAGATTTTATTAATAGTAAGTATATGTAGATATACAACTGATGGAGA
TAATAAATTGTACA
Found at i:2099308 original size:18 final size:20
Alignment explanation
Indices: 2099271--2099310 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2099261 GGCTCACTTC
2099271 TTATTTTTATAATATGTTATT
1 TTATTTTTATAATA-GTTATT
2099292 TTATTTTTAT-ATA-TTATT
1 TTATTTTTATAATAGTTATT
2099310 T
1 T
2099311 AATGTTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TTATTTTTATAATAGTTATT
Found at i:2100314 original size:14 final size:13
Alignment explanation
Indices: 2100270--2100344 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 13
2100260 TATTTTCTAC
*
2100270 TTTTATATAAT-T
1 TTTTATATAATAA
* *
2100282 TTTTAAATAAAAA
1 TTTTATATAATAA
2100295 TTTTTATATAATAA
1 -TTTTATATAATAA
* *
2100309 TATTTACATTATAA
1 T-TTTATATAATAA
* *
2100323 TGTTATATATTTAA
1 TTTTATATA-ATAA
2100337 TTTTATAT
1 TTTTATAT
2100345 GATATAAAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
12 9 0.19
13 6 0.13
14 32 0.68
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (13 bp):
TTTTATATAATAA
Found at i:2100350 original size:21 final size:22
Alignment explanation
Indices: 2100296--2100359 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
2100286 AAATAAAAAT
*
2100296 TTTTATATAATA-ATATTTACA
1 TTTTATATGATATATATTTACA
* *
2100317 TTATA-ATGTTATATATTTA-A
1 TTTTATATGATATATATTTACA
*
2100337 TTTTATATGATATAAAATTTACA
1 TTTTATATGATAT-ATATTTACA
2100360 ATATATTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 9 0.27
21 17 0.52
22 6 0.18
23 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (22 bp):
TTTTATATGATATATATTTACA
Found at i:2109487 original size:17 final size:19
Alignment explanation
Indices: 2109465--2109501 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
2109455 TTATAATATG
*
2109465 TTATTTTAT-TTTAT-ACA
1 TTATTTAATGTTTATCACA
2109482 TTATTTAATGTTTATCACA
1 TTATTTAATGTTTATCACA
2109501 T
1 T
2109502 AAAAATTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATTTAATGTTTATCACA
Found at i:2109558 original size:21 final size:22
Alignment explanation
Indices: 2109518--2109574 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
2109508 TGTCTATCTT
* *
2109518 TAAAATTTAAATAAGTATAAATA
1 TAAAATATAAAT-AGCATAAATA
* *
2109541 TTAAATA-AAATAGCATAATTA
1 TAAAATATAAATAGCATAAATA
2109562 TAAAATATAAATA
1 TAAAATATAAATA
2109575 ATATGAGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.50
22 9 0.32
23 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
TAAAATATAAATAGCATAAATA
Found at i:2110778 original size:11 final size:10
Alignment explanation
Indices: 2110742--2110795 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
2110732 AATATTAAAA
*
2110742 TTTTAACTTT
1 TTTTAAATTT
*
2110752 TTTTATATTT
1 TTTTAAATTT
2110762 TCTTTAGAATTT
1 T-TTTA-AATTT
2110774 TTTTATAATTT
1 TTTTA-AATTT
*
2110785 TTATAAATTT
1 TTTTAAATTT
2110795 T
1 T
2110796 AAAAAATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 15 0.41
11 17 0.46
12 5 0.14
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:2110832 original size:19 final size:19
Alignment explanation
Indices: 2110802--2110858 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
2110792 TTTTAAAAAA
2110802 TATAAA-ATTTTAAATTTT
1 TATAAATATTTTAAATTTT
*
2110820 TATAAATATTTTAAATATT
1 TATAAATATTTTAAATTTT
*
2110839 GA-AAATTATTTTAAACTTTT
1 TATAAA-TATTTTAAA-TTTT
2110859 CTTTTGTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 9 0.27
19 21 0.64
20 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:2117219 original size:7 final size:7
Alignment explanation
Indices: 2117209--2117240 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2117199 AAAAAGAAAA
2117209 TTTATAT
1 TTTATAT
2117216 TTTATAT
1 TTTATAT
2117223 TTTATAT
1 TTTATAT
2117230 TTTATAT
1 TTTATAT
2117237 TTTA
1 TTTA
2117241 AAAATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATAT
Found at i:2117286 original size:28 final size:28
Alignment explanation
Indices: 2117221--2117287 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
2117211 TATATTTTAT
*
2117221 ATTTT-ATATTTTATATTTTAAAAATAA
1 ATTTTAATAATTTATATTTTAAAAATAA
* *
2117248 A-TTAAAAAATTTATATTTTAAAAA-ACA
1 ATTTTAATAATTTATATTTTAAAAATA-A
2117275 ATTTTAATAATTT
1 ATTTTAATAATTT
2117288 TAAAATCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.09
27 20 0.62
28 9 0.28
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTTTAATAATTTATATTTTAAAAATAA
Found at i:2117602 original size:15 final size:16
Alignment explanation
Indices: 2117577--2117606 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2117567 AATTTAATCT
2117577 TAAAAATTATAAAATG
1 TAAAAATTATAAAATG
2117593 TAAAAA-TATAAAAT
1 TAAAAATTATAAAAT
2117607 TTAATTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAAAAATTATAAAATG
Found at i:2123259 original size:29 final size:30
Alignment explanation
Indices: 2123219--2123294 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
2123209 AGCCATGATC
2123219 AAAGTTTCATGTATATAATTG-A-ATTAAATT
1 AAAG-TTCATGTATA-AATTGTACATTAAATT
*
2123249 AAAGTTCATGTATCAAATTGTACATTGAATT
1 AAAGTTCATGTAT-AAATTGTACATTAAATT
*
2123280 AAAGTTTATGTATAA
1 AAAGTTCATGTATAA
2123295 TTTTGAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 14 0.34
30 8 0.20
31 19 0.46
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (30 bp):
AAAGTTCATGTATAAATTGTACATTAAATT
Found at i:2124245 original size:19 final size:20
Alignment explanation
Indices: 2124223--2124272 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2124213 TACTATAAAT
2124223 AAATAAAATAAA-CACATAA
1 AAATAAAATAAATCACATAA
* *
2124242 AAATAAAACAAATTACATAA
1 AAATAAAATAAATCACATAA
* *
2124262 TAATCAAATAA
1 AAATAAAATAA
2124273 TAAATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATAAAATAAATCACATAA
Found at i:2127374 original size:30 final size:30
Alignment explanation
Indices: 2127338--2127394 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
2127328 TGAGCTATAA
2127338 TGTAGAGATGGACCATTGAGGTCAGAATCC
1 TGTAGAGATGGACCATTGAGGTCAGAATCC
*
2127368 TGTAGAGATGGACCTTTGAGGTCAGAA
1 TGTAGAGATGGACCATTGAGGTCAGAA
2127395 ATGACTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.25
Consensus pattern (30 bp):
TGTAGAGATGGACCATTGAGGTCAGAATCC
Found at i:2128511 original size:18 final size:19
Alignment explanation
Indices: 2128476--2128516 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
2128466 ATTAAATAAT
*
2128476 TCGAGTTATTTGATTTAA-
1 TCGAGTTATTTGAATTAAC
2128494 TCGAGTT-TTTCGAATTAAC
1 TCGAGTTATTT-GAATTAAC
2128513 TCGA
1 TCGA
2128517 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 13 0.65
19 4 0.20
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGAGTTATTTGAATTAAC
Found at i:2133105 original size:21 final size:22
Alignment explanation
Indices: 2133079--2133119 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2133069 AATTAAATTT
*
2133079 AAATTT-TAAAATTAAAAAACA
1 AAATTTCTAAAAATAAAAAACA
2133100 AAATTTCTAAAAATAAAAAA
1 AAATTTCTAAAAATAAAAAA
2133120 AATTCAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATTTCTAAAAATAAAAAACA
Found at i:2133768 original size:17 final size:19
Alignment explanation
Indices: 2133735--2133769 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2133725 ATTGTTCGGA
2133735 TATTATATAACTTTTGTTT
1 TATTATATAACTTTTGTTT
2133754 TATTAT-TAA-TTTTGTT
1 TATTATATAACTTTTGTT
2133770 ACTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (19 bp):
TATTATATAACTTTTGTTT
Found at i:2139710 original size:46 final size:46
Alignment explanation
Indices: 2139643--2139736 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
2139633 TATATAACAA
*
2139643 TTGACTTTATTATTTTGGTGAAAAGATTTTCGACATCAAACATCCT
1 TTGACTTTATTATTTTGGTGAAAAGATTTTCGACATCAAACATACT
*
2139689 TTGACTTTATTATTTTGGTGAAAAGATTTTTGACATCAAACATACT
1 TTGACTTTATTATTTTGGTGAAAAGATTTTCGACATCAAACATACT
2139735 TT
1 TT
2139737 TAAGTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (46 bp):
TTGACTTTATTATTTTGGTGAAAAGATTTTCGACATCAAACATACT
Found at i:2150972 original size:15 final size:15
Alignment explanation
Indices: 2150952--2150986 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2150942 ATGATTTTAA
2150952 ATGGTGCTGCAACAC
1 ATGGTGCTGCAACAC
2150967 ATGGTGCTGCAACAC
1 ATGGTGCTGCAACAC
*
2150982 GTGGT
1 ATGGT
2150987 ATGGTAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (15 bp):
ATGGTGCTGCAACAC
Found at i:2153571 original size:132 final size:133
Alignment explanation
Indices: 2153327--2153571 Score: 284
Period size: 133 Copynumber: 1.8 Consensus size: 133
2153317 ATAATATATT
* * * *
2153327 TATTAATTAAAAATAAAAAAAATCTTAAAACAACCTGAAATAAAAATTACAAAAAGTAGTTAAGA
1 TATTAATTAAAAATAAAAAAAATCTTAAAACAACATAAAATAAAAAATACAAAAAGTAGTGAAGA
* * * * * **
2153392 GAAGAATTGAACTTTAGACTCAAAGATGAAATTATTATTATTTAATCAATGAGTTGATATGTTAA
66 GAAGAATTAAACTTGAGACTCAAAGATAAAATCAGTAACATTTAATCAATGAGTTGATATGTTAA
2153457 AAA
131 AAA
* *
2153460 TATTAATTAAAAATAAAAACAA-CTTAAAACAACATAAAATAAAAAAAATAC-AAATGTAAGTGG
1 TATTAATTAAAAATAAAAAAAATCTTAAAACAACATAAAAT--AAAAAATACAAAAAGT-AGT-G
* *
2153523 AAGAG-A-AATTAAACTTGAGACT-TAGGATAAAATCAGTAACATTTAATCA
62 AAGAGAAGAATTAAACTTGAGACTCAAAGATAAAATCAGTAACATTTAATCA
2153572 TCTAACTAAT
Statistics
Matches: 93, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
132 36 0.39
133 40 0.43
134 12 0.13
135 5 0.05
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (133 bp):
TATTAATTAAAAATAAAAAAAATCTTAAAACAACATAAAATAAAAAATACAAAAAGTAGTGAAGA
GAAGAATTAAACTTGAGACTCAAAGATAAAATCAGTAACATTTAATCAATGAGTTGATATGTTAA
AAA
Found at i:2154335 original size:27 final size:27
Alignment explanation
Indices: 2154289--2154360 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
2154279 ACACATTAAT
*
2154289 TTTAA-TTTAGTAT-ATAATATATAAAC
1 TTTAATTTTA-TATAATTATATATAAAC
*
2154315 TTTAATTTTATATAATTATATATAAAT
1 TTTAATTTTATATAATTATATATAAAC
2154342 TTTAATTTTCATA-AATTAT
1 TTTAATTTT-ATATAATTAT
2154361 TAATATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 8 0.20
27 30 0.73
28 3 0.07
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (27 bp):
TTTAATTTTATATAATTATATATAAAC
Found at i:2155191 original size:12 final size:12
Alignment explanation
Indices: 2155174--2155198 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2155164 TCGATTCGTT
2155174 TAAGCTCGTTTA
1 TAAGCTCGTTTA
2155186 TAAGCTCGTTTA
1 TAAGCTCGTTTA
2155198 T
1 T
2155199 TTATTAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TAAGCTCGTTTA
Found at i:2155614 original size:31 final size:32
Alignment explanation
Indices: 2155555--2155614 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2155545 TATTATTTTT
2155555 ATATAAATTAATCAAATTACCGAATTTTAAGC
1 ATATAAATTAATCAAATTACCGAATTTTAAGC
* *
2155587 ATATAAATTATTCAAA-TACTGAATTTTA
1 ATATAAATTAATCAAATTACCGAATTTTA
2155615 GATTAGTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (32 bp):
ATATAAATTAATCAAATTACCGAATTTTAAGC
Found at i:2161104 original size:14 final size:14
Alignment explanation
Indices: 2161085--2161129 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2161075 GACCACTCTT
2161085 AATTATAAAAAAAA
1 AATTATAAAAAAAA
* *
2161099 AATTATAATAATAA
1 AATTATAAAAAAAA
*
2161113 AATAATAAAATAAAA
1 AATTATAAAA-AAAA
2161128 AA
1 AA
2161130 AAACTTAAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AATTATAAAAAAAA
Found at i:2173153 original size:60 final size:60
Alignment explanation
Indices: 2173059--2173171 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
2173049 ATTTTTTTAA
* ***
2173059 TTTTATAAATAAAATTAAACTGACAAATTGTATAAATGTTGAGGGCTAAATTTATTGATT
1 TTTTATAAATAAAATTAAAATGACAAATTGTATAAACACTGAGGGCTAAATTTATTGATT
* * *
2173119 TTTTATAATTAGAATTAAAATGACAAATTTTATAAACACTGAGGGCTAAATTT
1 TTTTATAAATAAAATTAAAATGACAAATTGTATAAACACTGAGGGCTAAATTT
2173172 TTTTAAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (60 bp):
TTTTATAAATAAAATTAAAATGACAAATTGTATAAACACTGAGGGCTAAATTTATTGATT
Found at i:2177415 original size:21 final size:21
Alignment explanation
Indices: 2177389--2177429 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2177379 GCGGTGATAA
*
2177389 TGATGGTGATGGTGGCGATGT
1 TGATGGTGAGGGTGGCGATGT
*
2177410 TGATGGTGGGGGTGGCGATG
1 TGATGGTGAGGGTGGCGATG
2177430 GAGTTGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.54, T:0.29
Consensus pattern (21 bp):
TGATGGTGAGGGTGGCGATGT
Found at i:2177448 original size:3 final size:3
Alignment explanation
Indices: 2177440--2177477 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2177430 GAGTTGACTT
* *
2177440 TGG TGG TGG TGG TGA TGA TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
2177478 AAGAAGAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.05, C:0.00, G:0.61, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:2180429 original size:21 final size:21
Alignment explanation
Indices: 2180388--2180429 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2180378 TGTTGAAGTC
* *
2180388 GTAATTAGTTATTAGTTGATT
1 GTAATTAGTTATCAGTCGATT
2180409 GTAATTA-TTATCAGTACGATT
1 GTAATTAGTTATCAGT-CGATT
2180430 ATTTTTTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (21 bp):
GTAATTAGTTATCAGTCGATT
Found at i:2185738 original size:17 final size:15
Alignment explanation
Indices: 2185718--2185760 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2185708 GTAATTTAAC
2185718 CTTTTTTTTATTCTCTT
1 CTTTTTTTTATT-T-TT
2185735 CTTTTTTTTCATTTTT
1 CTTTTTTTT-ATTTTT
*
2185751 CATTTTTTTA
1 CTTTTTTTTA
2185761 ACGTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 1 0.04
16 10 0.42
17 10 0.42
18 3 0.12
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (15 bp):
CTTTTTTTTATTTTT
Found at i:2189905 original size:3 final size:3
Alignment explanation
Indices: 2189897--2189940 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2189887 TTTTGGCGGT
*
2189897 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2189941 GGAAAGGGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2196833 original size:19 final size:18
Alignment explanation
Indices: 2196808--2196862 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
2196798 TTAGGTATGA
2196808 ATGATTTTGGGGTTTAGG
1 ATGATTTTGGGGTTTAGG
*
2196826 ATTGATTTT-GAGTTTAGAG
1 A-TGATTTTGGGGTTTAG-G
**
2196845 ATGATAATGGGGTTTAGG
1 ATGATTTTGGGGTTTAGG
2196863 GTTTAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.42
Consensus pattern (18 bp):
ATGATTTTGGGGTTTAGG
Found at i:2196849 original size:18 final size:18
Alignment explanation
Indices: 2196808--2196849 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2196798 TTAGGTATGA
*
2196808 ATGATTTTGGGGTTTAGG
1 ATGATTTTGGAGTTTAGG
2196826 ATTGATTTT-GAGTTTAGAG
1 A-TGATTTTGGAGTTTAG-G
2196845 ATGAT
1 ATGAT
2196850 AATGGGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (18 bp):
ATGATTTTGGAGTTTAGG
Found at i:2199442 original size:7 final size:7
Alignment explanation
Indices: 2199430--2199480 Score: 66
Period size: 7 Copynumber: 7.1 Consensus size: 7
2199420 ATGATGCAGT
2199430 ATTTAAA
1 ATTTAAA
2199437 ATTTAAA
1 ATTTAAA
**
2199444 ATTTTTA
1 ATTTAAA
2199451 ATTTAAA
1 ATTTAAA
2199458 ATTTAAA
1 ATTTAAA
2199465 ATTTTAAA
1 A-TTTAAA
*
2199473 ATATAAA
1 ATTTAAA
2199480 A
1 A
2199481 AAAATTGTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
7 31 0.82
8 7 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
ATTTAAA
Found at i:2199455 original size:21 final size:21
Alignment explanation
Indices: 2199430--2199469 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2199420 ATGATGCAGT
2199430 ATTTAAAATTTAAAATTTTTA
1 ATTTAAAATTTAAAATTTTTA
2199451 ATTTAAAATTTAAAATTTT
1 ATTTAAAATTTAAAATTTT
2199470 AAAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAAAATTTAAAATTTTTA
Found at i:2208511 original size:58 final size:58
Alignment explanation
Indices: 2208423--2208568 Score: 172
Period size: 58 Copynumber: 2.5 Consensus size: 58
2208413 ATATATTATA
* * * **
2208423 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTACA-TATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAA-TAAATTAGC
* *
2208483 A-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAGC
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAGC
2208540 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
2208569 CATTAAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
56 3 0.04
57 16 0.21
58 43 0.57
59 8 0.11
60 5 0.07
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAGC
Found at i:2208707 original size:39 final size:44
Alignment explanation
Indices: 2208652--2208756 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 44
2208642 TTTCTTATGC
*
2208652 TATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-GAA-TA-T
1 TATTACAGC-TCTATTCCATTCCAACCAACAAACAATGAATTACT
*
2208691 TATTACAGCTCTATTCCATTCCAATCAACCAAACAATTGAATTACT
1 TATTACAGCTCTATTCCATTCCAACCAA-CAAACAA-TGAATTACT
*
2208737 GATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
2208757 ACACCTCTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.31
40 6 0.11
42 5 0.09
44 3 0.05
45 2 0.04
46 20 0.36
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (44 bp):
TATTACAGCTCTATTCCATTCCAACCAACAAACAATGAATTACT
Found at i:2208755 original size:46 final size:44
Alignment explanation
Indices: 2208663--2208756 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
2208653 ATTACAGCAT
* *
2208663 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
2208707 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
2208753 CATT
1 CATT
2208757 ACACCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:2208759 original size:16 final size:16
Alignment explanation
Indices: 2208738--2208777 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2208728 TGAATTACTG
2208738 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
2208754 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
2208770 ATTACAGC
1 ATTACAGC
2208778 GAACCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:2209586 original size:13 final size:12
Alignment explanation
Indices: 2209552--2209590 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2209542 AGCCTTTTTA
2209552 ATTATAAAAAAT
1 ATTATAAAAAAT
*
2209564 ATTTTCAAAAAAT
1 ATTAT-AAAAAAT
2209577 ATATATAAAAAAT
1 AT-TATAAAAAAT
2209590 A
1 A
2209591 AAATGAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 17 0.74
14 2 0.09
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
ATTATAAAAAAT
Found at i:2216124 original size:9 final size:9
Alignment explanation
Indices: 2216112--2216136 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2216102 ATATTTTTAT
2216112 AATTTTAAA
1 AATTTTAAA
2216121 AATTTTAAA
1 AATTTTAAA
2216130 AATTTTA
1 AATTTTA
2216137 TTATTTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTTTAAA
Found at i:2218164 original size:15 final size:16
Alignment explanation
Indices: 2218144--2218179 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2218134 AATCTTTTAA
2218144 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
2218159 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
2218175 AAATT
1 AAATT
2218180 TATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:2227183 original size:192 final size:191
Alignment explanation
Indices: 2226846--2227290 Score: 538
Period size: 192 Copynumber: 2.3 Consensus size: 191
2226836 CACGTCCTCT
** * * * *
2226846 TGCATTAACAACAATGTCCATACCAATCAAGCTAAGACTCAATCAACTTAGAATATCAACTTATA
1 TGCATT-ACAACAATACCCATACCAATCGAGCTAAGATTCAATCGACTTAGAATAT-AACTCATA
* *
2226911 AACTGTGTATAGAATGAAAATTGGGTGCAAAGTAGAATTAGGTTGAACGCCTAAAACTACTCATA
64 AACTATGTATAGAATGAAAATTGGGTGCAAAGTAGAATTAGGTTGAACACCTAAAACTACTCATA
* * *
2226976 GCCCCTCTCCAACTCATAAATAGGAGGATAATGTGA-TTCAACGCACTCGAATCCATATCCTTC
129 ACCCCTCTCCAACTCATAAATAGGAGGATAATG-CATTTCAACGCACTCAAATCCATATCCTTC
*
2227039 TGCATTGACAACAATACCCATACCAATCGAGCTAAGATTCAATCGACCTAGAATATAACTCATAA
1 TGCATT-ACAACAATACCCATACCAATCGAGCTAAGATTCAATCGACTTAGAATATAACTCATAA
* * *
2227104 ACTATGTATAGGATGAAAATTGGGTGCAAAGTAGAATTAGGTTGAATACCTAAAACTA-TCCGTA
65 ACTATGTATAGAATGAAAATTGGGTGCAAAGTAGAATTAGGTTGAACACCTAAAACTACT-CATA
* * * **
2227168 A-CTCTTTCTCAACTCATAAATAGGAGGATAATGCATTTCAACGTACTCAAATTTATATCCTTC
129 ACCCCTCTC-CAACTCATAAATAGGAGGATAATGCATTTCAACGCACTCAAATCCATATCCTTC
* ** ** * **
2227231 CGCATTAGCAATTATACTTATACTAATCGAGGGAAGAGTT-AATCGACTTAGAATATAACT
1 TGCATTA-CAACAATACCCATACCAATCGAGCTAAGA-TTCAATCGACTTAGAATATAACT
2227291 TGTATAGAAT
Statistics
Matches: 217, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
191 8 0.04
192 158 0.73
193 51 0.24
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (191 bp):
TGCATTACAACAATACCCATACCAATCGAGCTAAGATTCAATCGACTTAGAATATAACTCATAAA
CTATGTATAGAATGAAAATTGGGTGCAAAGTAGAATTAGGTTGAACACCTAAAACTACTCATAAC
CCCTCTCCAACTCATAAATAGGAGGATAATGCATTTCAACGCACTCAAATCCATATCCTTC
Found at i:2231379 original size:21 final size:21
Alignment explanation
Indices: 2231353--2231394 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2231343 AAAAATCCAG
2231353 ATCAAAATTAACTATTTGGAC
1 ATCAAAATTAACTATTTGGAC
2231374 ATCAAAATTAACTATTTGGAC
1 ATCAAAATTAACTATTTGGAC
2231395 TAAGTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (21 bp):
ATCAAAATTAACTATTTGGAC
Found at i:2234839 original size:24 final size:24
Alignment explanation
Indices: 2234794--2234840 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
2234784 AATTAACATC
2234794 AATTTTCCATGCAAAAAAGAAAAGA
1 AATTTTCCATG-AAAAAAGAAAAGA
2234819 AATTTTCTCATG-AAAAAGAAAA
1 AATTTTC-CATGAAAAAAGAAAA
2234841 CAAAATATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 7 0.33
26 4 0.19
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (24 bp):
AATTTTCCATGAAAAAAGAAAAGA
Found at i:2234846 original size:25 final size:24
Alignment explanation
Indices: 2234794--2234846 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
2234784 AATTAACATC
*
2234794 AATTTTCCATGCAAAAAAGAAAAGA
1 AATTTTCCATG-AAAAAAGAAAAAA
2234819 AATTTTCTCATG-AAAAAGAAAACAA
1 AATTTTC-CATGAAAAAAGAAAA-AA
2234844 AAT
1 AAT
2234847 ATCCTTCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 10 0.40
25 11 0.44
26 4 0.16
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (24 bp):
AATTTTCCATGAAAAAAGAAAAAA
Found at i:2238835 original size:7 final size:7
Alignment explanation
Indices: 2238799--2238859 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
2238789 AAACTGAACT
*
2238799 TTAAACC
1 TTAAATC
2238806 TTAAATC
1 TTAAATC
*
2238813 ATAAA-C
1 TTAAATC
2238819 TCTAAATC
1 T-TAAATC
2238827 TTAAATC
1 TTAAATC
** *
2238834 TTGGACC
1 TTAAATC
2238841 TTAAATC
1 TTAAATC
*
2238848 TTAAACC
1 TTAAATC
2238855 TTAAA
1 TTAAA
2238860 ACCCTAAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
6 1 0.02
7 39 0.93
8 2 0.05
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.34
Consensus pattern (7 bp):
TTAAATC
Found at i:2243170 original size:16 final size:16
Alignment explanation
Indices: 2243125--2243177 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
2243115 ATGACTCAAT
2243125 TAAAA-AATCTAAATC
1 TAAAATAATCTAAATC
* *
2243140 CAAAATAATCAAAATC
1 TAAAATAATCTAAATC
* *
2243156 TAGAATGATCTAAATC
1 TAAAATAATCTAAATC
*
2243172 TGAAAT
1 TAAAAT
2243178 TGACTCAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 4 0.14
16 25 0.86
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (16 bp):
TAAAATAATCTAAATC
Found at i:2261306 original size:15 final size:16
Alignment explanation
Indices: 2261286--2261320 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2261276 CACCGATCAT
2261286 AATAAAATACTA-ATA
1 AATAAAATACTAGATA
*
2261301 AATAAAATATTAGATA
1 AATAAAATACTAGATA
2261317 AATA
1 AATA
2261321 TATTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAAATACTAGATA
Found at i:2264014 original size:41 final size:40
Alignment explanation
Indices: 2263969--2264106 Score: 141
Period size: 41 Copynumber: 3.4 Consensus size: 40
2263959 ACTTTGTTCG
*
2263969 TGTTTAGTTTGTTTAATAAAGGAGCTTAAAAATTTTGCTCA
1 TGTTT-GTTTATTTAATAAAGGAGCTTAAAAATTTTGCTCA
* * * * * * * * *
2264010 TGTTTGTTTATTTAGCTTAATGAACTGAACATACTTTGTTCG
1 TGTTTGTTTATTTA-ATAAAGGAGCTTAA-AAATTTTGCTCA
*
2264052 TGTTTAGTTTGTTTAATAAAGGAGCTTAAAAATTTTGCTCA
1 TGTTT-GTTTATTTAATAAAGGAGCTTAAAAATTTTGCTCA
2264093 TGTTTGTTTATTTA
1 TGTTTGTTTATTTA
2264107 GCTTAATGAA
Statistics
Matches: 73, Mismatches: 21, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
40 16 0.22
41 27 0.37
42 22 0.30
43 8 0.11
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.48
Consensus pattern (40 bp):
TGTTTGTTTATTTAATAAAGGAGCTTAAAAATTTTGCTCA
Found at i:2264040 original size:83 final size:83
Alignment explanation
Indices: 2263945--2264117 Score: 337
Period size: 83 Copynumber: 2.1 Consensus size: 83
2263935 CATGAGCATA
2263945 AATGAACCGAACATACTTTGTTCGTGTTTAGTTTGTTTAATAAAGGAGCTTAAAAATTTTGCTCA
1 AATGAACCGAACATACTTTGTTCGTGTTTAGTTTGTTTAATAAAGGAGCTTAAAAATTTTGCTCA
2264010 TGTTTGTTTATTTAGCTT
66 TGTTTGTTTATTTAGCTT
*
2264028 AATGAACTGAACATACTTTGTTCGTGTTTAGTTTGTTTAATAAAGGAGCTTAAAAATTTTGCTCA
1 AATGAACCGAACATACTTTGTTCGTGTTTAGTTTGTTTAATAAAGGAGCTTAAAAATTTTGCTCA
2264093 TGTTTGTTTATTTAGCTT
66 TGTTTGTTTATTTAGCTT
2264111 AATGAAC
1 AATGAAC
2264118 GAGCAGAAAC
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 89 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (83 bp):
AATGAACCGAACATACTTTGTTCGTGTTTAGTTTGTTTAATAAAGGAGCTTAAAAATTTTGCTCA
TGTTTGTTTATTTAGCTT
Found at i:2271522 original size:16 final size:15
Alignment explanation
Indices: 2271501--2271559 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 15
2271491 AATCATTATA
2271501 TAATATTTTTTATTTT
1 TAATA-TTTTTATTTT
2271517 TAATA-TTTTATTTT
1 TAATATTTTTATTTT
*
2271531 ATAAGTATTTTTATTCT
1 -TAA-TATTTTTATTTT
2271548 TAATATTATTTA
1 TAATATT-TTTA
2271560 ACTCAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 9 0.24
15 7 0.18
16 14 0.37
17 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (15 bp):
TAATATTTTTATTTT
Done.