Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 13 of 27
Found at i:1826390 original size:22 final size:20
Alignment explanation
Indices: 1826322--1826384 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
1826312 TGTGATAAAA
1826322 TATTATAAAAATTAAAAAATT
1 TATTATAAAAA-TAAAAAATT
*
1826343 TAATATAAAATATATAACAAA-T
1 TATTATAAAA-ATA-AA-AAATT
1826365 TATTATAAAAATAAAAAATT
1 TATTATAAAAATAAAAAATT
1826385 GATATTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 14 0.39
22 13 0.36
23 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
TATTATAAAAATAAAAAATT
Found at i:1827958 original size:14 final size:13
Alignment explanation
Indices: 1827921--1827954 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1827911 TTATCATATT
*
1827921 ATTTTTTAATCTTA
1 ATTTTTTAA-CCTA
1827935 ATTTTTTAACCTA
1 ATTTTTTAACCTA
1827948 ATTTTTT
1 ATTTTTT
1827955 TAACAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTTTAACCTA
Found at i:1827964 original size:15 final size:14
Alignment explanation
Indices: 1827905--1827964 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
1827895 TTTAAATTAT
*
1827905 ATTTTTTTATCATA
1 ATTTTTTTAACATA
* *
1827919 TTATTTTTTAATCTTA
1 AT-TTTTTTAA-CATA
*
1827935 A-TTTTTTAACCTA
1 ATTTTTTTAACATA
1827948 ATTTTTTTAACAATA
1 ATTTTTTTAAC-ATA
1827963 AT
1 AT
1827965 ATTAAGCTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
13 4 0.11
14 18 0.50
15 11 0.31
16 3 0.08
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTTTTAACATA
Found at i:1828835 original size:12 final size:14
Alignment explanation
Indices: 1828803--1828838 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1828793 GAATTAATAA
*
1828803 AATAACATATATTT
1 AATAAAATATATTT
1828817 AATAAAATATATTT
1 AATAAAATATATTT
1828831 AA-AAAATA
1 AATAAAATA
1828839 AATAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAAAATATATTT
Found at i:1828863 original size:13 final size:13
Alignment explanation
Indices: 1828845--1828870 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1828835 AATAAATAAA
1828845 TGAATATATATTC
1 TGAATATATATTC
1828858 TGAATATATATTC
1 TGAATATATATTC
1828871 CTTTATAAAC
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:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TGAATATATATTC
Found at i:1835051 original size:2 final size:2
Alignment explanation
Indices: 1835040--1835070 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1835030 TCACGTTCGA
1835040 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1835071 TTGAGTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1839156 original size:21 final size:23
Alignment explanation
Indices: 1839132--1839180 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
1839122 ATTTTTTAAA
1839132 TTTAATACAT-ATAAA-AGAT-AT
1 TTTAATA-ATAATAAATAGATAAT
1839153 TTTAA-AATAATAAATAGATAAT
1 TTTAATAATAATAAATAGATAAT
1839175 TTTAAT
1 TTTAAT
1839181 TGAGGCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.08
20 6 0.25
21 9 0.38
22 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
TTTAATAATAATAAATAGATAAT
Found at i:1839542 original size:16 final size:17
Alignment explanation
Indices: 1839523--1839570 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1839513 TTTAAAATAA
1839523 AATTTTATA-TTTATTT
1 AATTTTATATTTTATTT
*
1839539 AATTTTTTATTTTATTT
1 AATTTTATATTTTATTT
*
1839556 ATAATTTA-ATTTTAT
1 A-ATTTTATATTTTAT
1839571 ATATTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.30
17 15 0.56
18 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTTTATATTTTATTT
Found at i:1842180 original size:2 final size:2
Alignment explanation
Indices: 1842175--1842199 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1842165 CTCTCTCATC
1842175 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1842200 GCTTTACTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1845202 original size:11 final size:10
Alignment explanation
Indices: 1845200--1845239 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
1845190 TTAAAATTAT
1845200 TTTTAAAAAA
1 TTTTAAAAAA
1845210 TTTTAAAACAA
1 TTTTAAAA-AA
1845221 TTTTTAAAAAA
1 -TTTTAAAAAA
1845232 TTTTAAAA
1 TTTTAAAA
1845240 CAATATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 16 0.57
11 4 0.14
12 8 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:1845205 original size:12 final size:10
Alignment explanation
Indices: 1845188--1845239 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
1845178 AATAATCATA
1845188 TTTTAAAATTAT
1 TTTTAAAA--AT
1845200 TTTTAAAAAAT
1 TTTT-AAAAAT
*
1845211 TTTAAAACAAT
1 TTTTAAA-AAT
*
1845222 TTTTAAAAAA
1 TTTTAAAAAT
1845232 TTTTAAAA
1 TTTTAAAA
1845240 CAATATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 13 0.37
11 14 0.40
12 4 0.11
13 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (10 bp):
TTTTAAAAAT
Found at i:1845215 original size:22 final size:22
Alignment explanation
Indices: 1845187--1845248 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
1845177 TAATAATCAT
**
1845187 ATTTTAAAATTATTTTTAAAAA
1 ATTTTAAAACAATTTTTAAAAA
1845209 ATTTTAAAACAATTTTTAAAAA
1 ATTTTAAAACAATTTTTAAAAA
*
1845231 ATTTTAAAACAATATTTA
1 ATTTTAAAACAATTTTTA
1845249 TCTCAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTAAAACAATTTTTAAAAA
Found at i:1846883 original size:14 final size:13
Alignment explanation
Indices: 1846859--1846893 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
1846849 TATATTATAG
1846859 TAAATTTAAAATT
1 TAAATTTAAAATT
1846872 TAAATATTAAAATT
1 TAAAT-TTAAAATT
1846886 TATAATTT
1 TA-AATTT
1846894 TTTTTACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 12 0.60
15 3 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:1849129 original size:14 final size:15
Alignment explanation
Indices: 1849105--1849133 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1849095 GGGTTTTTGA
1849105 TAAAAATATTAATTT
1 TAAAAATATTAATTT
1849120 TAAAAA-ATTAATTT
1 TAAAAATATTAATTT
1849134 AACAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAAATATTAATTT
Found at i:1849622 original size:17 final size:18
Alignment explanation
Indices: 1849601--1849659 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
1849591 TAATTCTCAT
*
1849601 AAAAATTTGAAACAATTA
1 AAAAATTTGAAAAAATTA
* **
1849619 AAAAAATTGAAAGGATTA
1 AAAAATTTGAAAAAATTA
*
1849637 AAAAATTTTAAAAAA-TA
1 AAAAATTTGAAAAAATTA
1849654 AAAAAT
1 AAAAAT
1849660 ACAAAATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
17 8 0.24
18 26 0.76
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (18 bp):
AAAAATTTGAAAAAATTA
Found at i:1850167 original size:16 final size:16
Alignment explanation
Indices: 1850138--1850170 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1850128 TAAAAATTAA
1850138 ATATAGATATAATATT
1 ATATAGATATAATATT
1850154 ATATA-ATATAAATATT
1 ATATAGATAT-AATATT
1850170 A
1 A
1850171 AAAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
ATATAGATATAATATT
Found at i:1850262 original size:28 final size:28
Alignment explanation
Indices: 1850199--1850266 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 28
1850189 TATGTTTAAA
*
1850199 AATATA-ATAAA-AAATATAAAATTATT
1 AATATATATAAATAAAAATAAAATTATT
* * *
1850225 AA-AAAT-TAAATAAAAATAATATTTTT
1 AATATATATAAATAAAAATAAAATTATT
1850251 AATATATATAAATAAA
1 AATATATATAAATAAA
1850267 TTAAATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
25 6 0.18
26 16 0.48
27 3 0.09
28 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
AATATATATAAATAAAAATAAAATTATT
Found at i:1850305 original size:7 final size:7
Alignment explanation
Indices: 1850293--1850319 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1850283 CAAATATAAA
1850293 TAAATTT
1 TAAATTT
1850300 TAAATTT
1 TAAATTT
1850307 TAAATTT
1 TAAATTT
1850314 TAAATT
1 TAAATT
1850320 AAATCAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TAAATTT
Found at i:1853518 original size:14 final size:14
Alignment explanation
Indices: 1853499--1853534 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1853489 ATGCTTGAGA
1853499 AATGAAATATATTT
1 AATGAAATATATTT
*
1853513 AATGAAATATTTTT
1 AATGAAATATATTT
1853527 AAT-AAATA
1 AATGAAATA
1853535 AAAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
AATGAAATATATTT
Found at i:1858989 original size:17 final size:17
Alignment explanation
Indices: 1858969--1859020 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
1858959 TGAATTTATT
1858969 TTATTATTTA-ATTAATA
1 TTATT-TTTATATTAATA
1858986 TTATTTTTATATTAATA
1 TTATTTTTATATTAATA
1859003 TTTATATTTTATAATTAA
1 -TTAT-TTTTAT-ATTAA
1859021 ATTTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 4 0.13
19 6 0.19
20 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTTTTATATTAATA
Found at i:1859010 original size:20 final size:19
Alignment explanation
Indices: 1858977--1859025 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1858967 TTTTATTATT
1858977 TAATT-AATATTAT-TTTTA
1 TAATTAAAT-TTATATTTTA
1858995 T-ATTAATATTTATATTTTA
1 TAATTAA-ATTTATATTTTA
1859014 TAATTAAATTTA
1 TAATTAAATTTA
1859026 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.11
18 6 0.22
19 13 0.48
20 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATTAAATTTATATTTTA
Found at i:1859244 original size:3 final size:3
Alignment explanation
Indices: 1859236--1859283 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
1859226 TAGCTAAATG
1859236 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1859282 TT
1 TT
1859284 TTTGAATGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1860327 original size:32 final size:32
Alignment explanation
Indices: 1860252--1860328 Score: 77
Period size: 32 Copynumber: 2.4 Consensus size: 32
1860242 TATAATATAA
1860252 ATTAATTAATATTAAAATTAAAAATAAAAATAT
1 ATTAATT-ATATTAAAATTAAAAATAAAAATAT
* * * *
1860285 AATACA-TATATTAAATATTTAAAAT-TAATTAT
1 ATTA-ATTATATTAAA-ATTAAAAATAAAAATAT
1860317 ATTAATTATATT
1 ATTAATTATATT
1860329 TGACGTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
31 1 0.03
32 22 0.61
33 12 0.33
34 1 0.03
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
ATTAATTATATTAAAATTAAAAATAAAAATAT
Found at i:1861217 original size:30 final size:29
Alignment explanation
Indices: 1861183--1861280 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 29
1861173 TAAATATAAT
**
1861183 ATAATTAAATGATACGAATATAATAAAAAA
1 ATAATTAAAT-ATAAAAATATAATAAAAAA
* *
1861213 ATAATTAAATATAATAA-GTAATAAGAACAA
1 ATAATTAAATATAAAAATATAATAA-AA-AA
1861243 ATAATTAAACATAATAAAAATATAATATAAAAA
1 ATAATT-AA-AT-ATAAAAATATAATA-AAAAA
1861276 ATAAT
1 ATAAT
1861281 AAAAACATTG
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
28 6 0.11
29 7 0.12
30 18 0.32
31 2 0.04
32 2 0.04
33 13 0.23
34 7 0.12
35 1 0.02
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (29 bp):
ATAATTAAATATAAAAATATAATAAAAAA
Found at i:1861284 original size:10 final size:10
Alignment explanation
Indices: 1861202--1861285 Score: 60
Period size: 10 Copynumber: 8.0 Consensus size: 10
1861192 TGATACGAAT
1861202 ATAATAAAAAA
1 ATAAT-AAAAA
* *
1861213 ATAATTAAAT
1 ATAATAAAAA
**
1861223 ATAATAAGTA
1 ATAATAAAAA
* *
1861233 ATAAGAACAA
1 ATAATAAAAA
* *
1861243 ATAATTAAAC
1 ATAATAAAAA
1861253 ATAATAAAAA
1 ATAATAAAAA
1861263 TATAATATAAAAA
1 -AT-A-ATAAAAA
1861276 ATAATAAAAA
1 ATAATAAAAA
1861286 CATTGATATA
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
10 37 0.67
11 8 0.15
12 3 0.05
13 7 0.13
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:1863552 original size:13 final size:13
Alignment explanation
Indices: 1863534--1863558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1863524 GTAAGAAAAT
1863534 AAAGGAAAAGAAA
1 AAAGGAAAAGAAA
1863547 AAAGGAAAAGAA
1 AAAGGAAAAGAA
1863559 GCGAAGAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGGAAAAGAAA
Found at i:1863678 original size:2 final size:2
Alignment explanation
Indices: 1863671--1863709 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1863661 CGATTCAAAT
1863671 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1863710 TTTTAAACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1868451 original size:2 final size:2
Alignment explanation
Indices: 1868444--1868468 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1868434 CTGATGTATG
1868444 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1868469 GTAATCAAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1875090 original size:19 final size:19
Alignment explanation
Indices: 1875048--1875091 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
1875038 TTAATTCATC
1875048 AAATTAATTATTTTATTTAT
1 AAATT-ATTATTTTATTTAT
1875068 -AATTATTATTTT-TTTATT
1 AAATTATTATTTTATTTA-T
1875086 AAATTA
1 AAATTA
1875092 ATCAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.18
18 9 0.41
19 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AAATTATTATTTTATTTAT
Found at i:1875635 original size:21 final size:21
Alignment explanation
Indices: 1875527--1875730 Score: 96
Period size: 21 Copynumber: 9.4 Consensus size: 21
1875517 AACACATTAT
1875527 TTTTAATATAATTTATAATAATGA
1 TTTTAATATAATTT-TAATAA--A
* * *
1875551 TCTTTGATATTATTTTAAT-TA
1 T-TTTAATATAATTTTAATAAA
* * **
1875572 TTTTAGATATGATTTCAATAGC
1 TTTTA-ATATAATTTTAATAAA
* * * * *
1875594 CTTGAATATGATTTTTGATAAT
1 TTTTAATAT-AATTTTAATAAA
1875616 TTTTAATATAATTTTAAT-AA
1 TTTTAATATAATTTTAATAAA
*
1875636 TTTTAGTTATAATTTTTAATATAA
1 TTTTA-ATATAA-TTTTAATA-AA
*
1875660 TTTTAATA-ATTTTTAATATAA
1 TTTTAATATAATTTTAATA-AA
* *
1875681 TATTAATA-AAATTTAATATAA
1 TTTTAATATAATTTTAATA-AA
*
1875702 TTTTAATA-ATTTTTTATATAAA
1 TTTTAATATA-ATTTTA-ATAAA
1875724 -TTTAATA
1 TTTTAATA
1875731 ACATTAATAT
Statistics
Matches: 140, Mismatches: 30, Indels: 23
0.73 0.16 0.12
Matches are distributed among these distances:
20 9 0.06
21 73 0.52
22 30 0.21
23 5 0.04
24 12 0.09
25 11 0.08
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTAATATAATTTTAATAAA
Found at i:1875648 original size:33 final size:31
Alignment explanation
Indices: 1875611--1875747 Score: 143
Period size: 33 Copynumber: 4.3 Consensus size: 31
1875601 ATGATTTTTG
1875611 ATAATTTTTAATATAATTTTAATAATTTTAGTT
1 ATAATTTTTAATATAATTTTAATAATTTTA--T
1875644 ATAATTTTTAATATAATTTTAATAATTTTTAAT
1 ATAATTTTTAATATAATTTTAATAA-TTTT-AT
* * *
1875677 ATAA-TATTAATAAAATTTAATATAATTTTA-
1 ATAATTTTTAATATAATTTTA-ATAATTTTAT
* * * *
1875707 ATAATTTTTTATATAAATTTAATAACATTAAT
1 ATAATTTTTAATATAATTTTAATAA-TTTTAT
1875739 ATAATTTTT
1 ATAATTTTT
1875748 CTAACTTTCA
Statistics
Matches: 88, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
30 8 0.09
31 15 0.17
32 26 0.30
33 34 0.39
34 4 0.05
35 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (31 bp):
ATAATTTTTAATATAATTTTAATAATTTTAT
Found at i:1875672 original size:42 final size:41
Alignment explanation
Indices: 1875650--1875746 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 41
1875640 AGTTATAATT
1875650 TTTAATATAATTTTAATAATTTTTAATATAATATTAATAAAA
1 TTTAATATAATTTTAATAA-TTTTAATATAATATTAATAAAA
* *
1875692 TTTAATATAATTTTAATAATTTTTTATATAA-ATTTAATAACA
1 TTTAATATAATTTTAATAA-TTTTAATATAATA-TTAATAAAA
1875734 -TTAATATAATTTT
1 TTTAATATAATTTT
1875747 TCTAACTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
41 14 0.27
42 38 0.73
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (41 bp):
TTTAATATAATTTTAATAATTTTAATATAATATTAATAAAA
Found at i:1875701 original size:54 final size:53
Alignment explanation
Indices: 1875606--1875709 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 53
1875596 TGAATATGAT
* * * *
1875606 TTTTGATAATTTTTAATATAATTTTAATAATTTTAGTTATAATTTTTAATATAA
1 TTTTAATAATTTTTAATATAATATTAATAAATTTAGATATAA-TTTTAATATAA
1875660 TTTTAATAATTTTTAATATAATATTAATAAAATTTA-ATATAATTTTAATA
1 TTTTAATAATTTTTAATATAATATTAAT-AAATTTAGATATAATTTTAATA
1875710 ATTTTTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
53 8 0.18
54 31 0.69
55 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (53 bp):
TTTTAATAATTTTTAATATAATATTAATAAATTTAGATATAATTTTAATATAA
Found at i:1875731 original size:21 final size:21
Alignment explanation
Indices: 1875644--1875731 Score: 115
Period size: 21 Copynumber: 4.2 Consensus size: 21
1875634 AATTTTAGTT
*
1875644 ATAATTTTTAATATAATTTTA
1 ATAATTTTTAATATAAATTTA
1875665 ATAATTTTTAATAT-AATATTA
1 ATAATTTTTAATATAAAT-TTA
** *
1875686 ATAAAATTTAATATAATTTTA
1 ATAATTTTTAATATAAATTTA
*
1875707 ATAATTTTTTATATAAATTTA
1 ATAATTTTTAATATAAATTTA
1875728 ATAA
1 ATAA
1875732 CATTAATATA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATAATTTTTAATATAAATTTA
Found at i:1875752 original size:20 final size:21
Alignment explanation
Indices: 1875729--1875767 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1875719 ATAAATTTAA
1875729 TAACATT-AATATAATTTTTC
1 TAACATTCAATATAATTTTTC
* *
1875749 TAACTTTCAATATTATTTT
1 TAACATTCAATATAATTTT
1875768 GATAACCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (21 bp):
TAACATTCAATATAATTTTTC
Found at i:1876188 original size:3 final size:3
Alignment explanation
Indices: 1876182--1876216 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1876172 TAAAAATCTT
* *
1876182 ATA ATA ATA ATA ATA ATA ATA AAA ATA AAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1876217 TAAATCGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1876374 original size:2 final size:2
Alignment explanation
Indices: 1876367--1876398 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1876357 CATATTCATA
1876367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1876399 TGTCGATCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1876678 original size:2 final size:2
Alignment explanation
Indices: 1876671--1876730 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
1876661 GCCAACCTGC
* * * *
1876671 AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AC AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1876713 AC AT AT AC AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1876731 CCCCGGCAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (2 bp):
AT
Found at i:1876700 original size:20 final size:20
Alignment explanation
Indices: 1876675--1876730 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1876665 ACCTGCATAT
*
1876675 ATATATATATATATATACAC
1 ATATATACATATATATACAC
* *
1876695 ATATATACATATACATATAC
1 ATATATACATATATATACAC
*
1876715 ATATACACATATATAT
1 ATATATACATATATAT
1876731 CCCCGGCAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATATACATATATATACAC
Found at i:1878590 original size:27 final size:28
Alignment explanation
Indices: 1878538--1878590 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1878528 TCAAACTCGA
* *
1878538 TAAATCTAACTGTTAAACCTGATTGACT
1 TAAATCTAAATGTTAAACATGATTGACT
1878566 TAAATCTAAAT-TTAAA-ATGACTTGA
1 TAAATCTAAATGTTAAACATGA-TTGA
1878591 ACCTGATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 3 0.14
27 9 0.41
28 10 0.45
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (28 bp):
TAAATCTAAATGTTAAACATGATTGACT
Found at i:1879276 original size:23 final size:22
Alignment explanation
Indices: 1879243--1879287 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1879233 TTGCATTATT
*
1879243 ATAATAAATTAAAATGTTAAAAA
1 ATAATAAATTAAAA-ATTAAAAA
*
1879266 ATAATATATTAAAAATTAAAAA
1 ATAATAAATTAAAAATTAAAAA
1879288 TTTATAAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAATAAATTAAAAATTAAAAA
Found at i:1882457 original size:2 final size:2
Alignment explanation
Indices: 1882450--1882477 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1882440 TAGGTATTTG
1882450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1882478 GAGTATGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1883107 original size:24 final size:24
Alignment explanation
Indices: 1883078--1883124 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1883068 AAGACATTGA
1883078 AAAAGA-CATATTAAATGAATATAT
1 AAAAGATCATATT-AATGAATATAT
* *
1883102 AAAAGATGATATTAATTAATATA
1 AAAAGATCATATTAATGAATATA
1883125 GCAATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (24 bp):
AAAAGATCATATTAATGAATATAT
Found at i:1883230 original size:2 final size:2
Alignment explanation
Indices: 1883223--1883266 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1883213 GCCAACCTGC
* *
1883223 AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1883265 AT
1 AT
1883267 CCCCACAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1895652 original size:21 final size:22
Alignment explanation
Indices: 1895609--1895655 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1895599 CTGTTCAGAC
* *
1895609 AAGTAGTACTCCACAGCAAGTG
1 AAGTAGTACTCCAAAACAAGTG
*
1895631 AAGTA-TACTCCAAAACAGGTG
1 AAGTAGTACTCCAAAACAAGTG
1895652 AAGT
1 AAGT
1895656 TTTAACAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (22 bp):
AAGTAGTACTCCAAAACAAGTG
Found at i:1897568 original size:27 final size:25
Alignment explanation
Indices: 1897533--1897609 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 25
1897523 CAAAAGCCAC
1897533 CCTTCGTGTTTGTCAAAAATGGTGG
1 CCTTCGTGTTTGTCAAAAATGGTGG
* *
1897558 TTCCTTTGTGTTTGTCAAAAATAGT-G
1 --CCTTCGTGTTTGTCAAAAATGGTGG
* * *
1897584 ACTTGGTGTTTGTCAAAATTGGTGG
1 CCTTCGTGTTTGTCAAAAATGGTGG
1897609 C
1 C
1897610 TAATTTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
24 19 0.45
25 1 0.02
26 1 0.02
27 21 0.50
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (25 bp):
CCTTCGTGTTTGTCAAAAATGGTGG
Found at i:1902971 original size:28 final size:28
Alignment explanation
Indices: 1902933--1903002 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 28
1902923 AAACAAGCCT
*
1902933 CCATATTTGACAAATC-CAAAGGA-AACCA
1 CCATTTTTGACAAATCACAAA--ATAACCA
1902961 CCATTTTTGACAAA-CACAAAATAACCA
1 CCATTTTTGACAAATCACAAAATAACCA
1902988 CCATTTTTGACAAAT
1 CCATTTTTGACAAAT
1903003 AAATGGGTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAATCACAAAATAACCA
Found at i:1906333 original size:18 final size:18
Alignment explanation
Indices: 1906310--1906345 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1906300 CCTACTTCCA
1906310 AAGTTATAAAATTCGGAT
1 AAGTTATAAAATTCGGAT
1906328 AAGTTATAAAATTCGGAT
1 AAGTTATAAAATTCGGAT
1906346 CGGGCCCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (18 bp):
AAGTTATAAAATTCGGAT
Found at i:1907043 original size:18 final size:19
Alignment explanation
Indices: 1907007--1907046 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1906997 CAACTTGATC
*
1907007 TAATTATTTTTTTGATTATA
1 TAATTATTTTTAT-ATTATA
1907027 TAATTATTTTTAT-TTATA
1 TAATTATTTTTATATTATA
1907045 TA
1 TA
1907047 TTAGATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TAATTATTTTTATATTATA
Found at i:1907778 original size:12 final size:12
Alignment explanation
Indices: 1907761--1907785 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1907751 CCAACCCAAA
1907761 TGAGTTATATTT
1 TGAGTTATATTT
1907773 TGAGTTATATTT
1 TGAGTTATATTT
1907785 T
1 T
1907786 ATTTTTAATG
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:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TGAGTTATATTT
Found at i:1908118 original size:79 final size:82
Alignment explanation
Indices: 1908015--1908204 Score: 237
Period size: 83 Copynumber: 2.3 Consensus size: 82
1908005 ACGTATATGT
* * *
1908015 TTAAAATATATAAATAAAAATAAGAGTA-C-TAAGTCCAAAAAGCTTGCCACATCTCA-TATATT
1 TTAAAATATATACATAAAAATAAGAGTACCGTAAATCCAAAAAGCTTACCACATCTCATTA-ATT
1908077 TATATTATTTTAA-TTAA
65 TATATTATTTTAATTTAA
* * * * * *
1908094 TTTAAATATATACATAAAAGTAAGAGTACCGAGTAAATCTAAATAGCTTATCACATCTTATTAAT
1 TTAAAATATATACATAAAAATAAGAGTACC--GTAAATCCAAAAAGCTTACCACATCTCATTAAT
1908159 TTATATTATTTTAATTTAA
64 TTATATTATTTTAATTTAA
1908178 TTAAAATATATACATAAAAATAA-AGTA
1 TTAAAATATATACATAAAAATAAGAGTA
1908205 ACATAAATAT
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
79 25 0.27
80 1 0.01
83 41 0.44
84 27 0.29
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.37
Consensus pattern (82 bp):
TTAAAATATATACATAAAAATAAGAGTACCGTAAATCCAAAAAGCTTACCACATCTCATTAATTT
ATATTATTTTAATTTAA
Found at i:1909024 original size:2 final size:2
Alignment explanation
Indices: 1909017--1909073 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
1909007 AGAGATATCG
** *
1909017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT CG AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1909058 AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT A
1909074 AAATGTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1915035 original size:5 final size:5
Alignment explanation
Indices: 1915027--1915112 Score: 67
Period size: 5 Copynumber: 17.8 Consensus size: 5
1915017 TATATATCAT
* *
1915027 ATATA ATATA A-A-A AAATA ATTAAA ATATA ATATA ATATA A-AT- ATATTA
1 ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATATA ATA-TA
* *
1915075 ATAT- GTAAA ATATTA A-ATA ATATA ATATA ATATA ATAT
1 ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA ATAT
1915113 TAAGTTAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
3 3 0.05
4 10 0.15
5 44 0.68
6 8 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:1915059 original size:24 final size:24
Alignment explanation
Indices: 1915027--1915109 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
1915017 TATATATCAT
*
1915027 ATATAATATAAAAAAATAATTAAA
1 ATATAATATAAATAAATAATTAAA
*
1915051 ATATAATATAATATAAATATATTAAT
1 ATATAATATAA-ATAAATA-ATTAAA
* * * *
1915077 ATGTAAAAT-ATTAAATAA-TATA
1 ATATAATATAAATAAATAATTAAA
1915099 ATATAATATAA
1 ATATAATATAA
1915110 TATTAAGTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
22 9 0.19
23 2 0.04
24 17 0.36
25 7 0.15
26 12 0.26
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (24 bp):
ATATAATATAAATAAATAATTAAA
Found at i:1916810 original size:20 final size:21
Alignment explanation
Indices: 1916765--1916803 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1916755 TAAATTATTA
*
1916765 AAATATTAATTTAAATTTAAT
1 AAATATTAAATTAAATTTAAT
*
1916786 TAATA-TAAATTAAATTTA
1 AAATATTAAATTAAATTTA
1916804 TCAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAAATTAAATTTAAT
Found at i:1926549 original size:132 final size:132
Alignment explanation
Indices: 1926312--1926563 Score: 450
Period size: 132 Copynumber: 1.9 Consensus size: 132
1926302 TAAATGAAAG
* *
1926312 TAGCTCAAAGGTTGGTAATATATCACACCATATAAGTGGCACAATCTTCCCATACTTGTCTATTT
1 TAGCTCAAAGGTGGGTAACATATCACACCATATAAGTGGCACAATCTTCCCATACTTGTCTATTT
* * *
1926377 CGTGAAGCTACAATCGAAACCTAACATCTGTTAAAGTAAATAGCTTTTTCGTGTGTGACATAGTA
66 CGTGAAGCTACAATCGAAACCAAACACCAGTTAAAGTAAATAGCTTTTTCGTGTGTGACATAGTA
1926442 TA
131 TA
1926444 TAGCTCAAAGGTGGGTAACATATCACACCATATAAGTGGCACAATCTTCCCATACTTGTCTATTT
1 TAGCTCAAAGGTGGGTAACATATCACACCATATAAGTGGCACAATCTTCCCATACTTGTCTATTT
*
1926509 CTTGAAGCTACAATCGAAACCAAACACCAGTTAAAGTAAATAGCTTTTTCGTGTG
66 CGTGAAGCTACAATCGAAACCAAACACCAGTTAAAGTAAATAGCTTTTTCGTGTG
1926564 ATATATTATA
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 114 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (132 bp):
TAGCTCAAAGGTGGGTAACATATCACACCATATAAGTGGCACAATCTTCCCATACTTGTCTATTT
CGTGAAGCTACAATCGAAACCAAACACCAGTTAAAGTAAATAGCTTTTTCGTGTGTGACATAGTA
TA
Found at i:1927879 original size:5 final size:6
Alignment explanation
Indices: 1927844--1927885 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
1927834 GGGAGGGGCT
*
1927844 TTTTCG TTTTAG TTTTAG TTTTAG TTTTAG -TTTAG -TTTAG TT
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TT
1927886 GCAAGGAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 10 0.29
6 24 0.71
ACGTcount: A:0.14, C:0.02, G:0.17, T:0.67
Consensus pattern (6 bp):
TTTTAG
Found at i:1928401 original size:15 final size:16
Alignment explanation
Indices: 1928362--1928404 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
1928352 TTTATAATAC
1928362 TATTATATTAAATATAA
1 TATTAT-TTAAATATAA
*
1928379 TATTATTTCAATA-AA
1 TATTATTTAAATATAA
1928394 TATTATTTAAA
1 TATTATTTAAA
1928405 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.50
16 6 0.25
17 6 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTATTTAAATATAA
Found at i:1928521 original size:10 final size:10
Alignment explanation
Indices: 1928501--1928576 Score: 66
Period size: 10 Copynumber: 7.3 Consensus size: 10
1928491 ATTATTAATA
1928501 TATTATAAATT
1 TATT-TAAATT
1928512 TATTTAAATT
1 TATTTAAATT
*
1928522 TATTTATATT
1 TATTTAAATT
*
1928532 TATTTATATT
1 TATTTAAATT
1928542 TA--TAAATAT
1 TATTTAAAT-T
1928551 GATAATTTAAATT
1 --T-ATTTAAATT
*
1928564 TATTTATATT
1 TATTTAAATT
1928574 TAT
1 TAT
1928577 ATATTATATT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
8 4 0.07
9 1 0.02
10 38 0.68
11 6 0.11
12 1 0.02
13 1 0.02
14 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (10 bp):
TATTTAAATT
Found at i:1928748 original size:19 final size:22
Alignment explanation
Indices: 1928705--1928762 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
1928695 AAATAAAATT
1928705 ATTATTATTATAAAAATATATA
1 ATTATTATTATAAAAATATATA
1928727 ATTA-TATTAT-AAAATATA-A
1 ATTATTATTATAAAAATATATA
*
1928746 ATT-TTATAATTAAAAAT
1 ATTATTATTA-TAAAAAT
1928763 TTTATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.25
20 9 0.28
21 11 0.34
22 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTATTATTATAAAAATATATA
Found at i:1928759 original size:20 final size:20
Alignment explanation
Indices: 1928685--1928760 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
1928675 TAATAACTTA
*
1928685 ATAATTAATAAAATAAAAT-T
1 ATAATT-ATATAATAAAATAT
*
1928705 ATTATTAT-T-ATAAAAATAT
1 ATAATTATATAAT-AAAATAT
*
1928724 ATAATTATATTATAAAATAT
1 ATAATTATATAATAAAATAT
*
1928744 A-AATTTTATAATTAAAA
1 ATAATTATATAA-TAAAA
1928761 ATTTTATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
17 2 0.04
18 5 0.11
19 18 0.39
20 19 0.41
21 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATTATATAATAAAATAT
Found at i:1928847 original size:17 final size:18
Alignment explanation
Indices: 1928811--1928858 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1928801 AAAGTTAACG
1928811 TATTTTTTAAATAAATTT
1 TATTTTTTAAATAAATTT
**
1928829 TATTTTTTATTTAAA-TT
1 TATTTTTTAAATAAATTT
*
1928846 TATTTTTAAAATA
1 TATTTTTTAAATA
1928859 TAATATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTTAAATAAATTT
Found at i:1930383 original size:17 final size:16
Alignment explanation
Indices: 1930339--1930386 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
1930329 ATATTTTTAT
1930339 AATTAAATTTAAATAAA
1 AATTAAA-TTAAATAAA
*
1930356 AATTATTATTAAATAATA
1 AATTA-AATTAAATAA-A
1930374 AATTAAATTAAAT
1 AATTAAATTAAAT
1930387 TAATTTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTAAATTAAATAAA
Found at i:1949164 original size:2 final size:2
Alignment explanation
Indices: 1949157--1949194 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1949147 GATAATCTTA
*
1949157 CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1949195 TACACACACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1950694 original size:1 final size:1
Alignment explanation
Indices: 1950688--1950717 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1950678 AGTAATAGTT
1950688 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1950718 GAGGTAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1951972 original size:26 final size:26
Alignment explanation
Indices: 1951941--1951995 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
1951931 AAGTTTATTA
*
1951941 TTTAATATA-ATCGTAATTTTAATAAT
1 TTTAATATAGAT-ATAATTTTAATAAT
1951967 TTTAATATAGATATAATTTTAATAAT
1 TTTAATATAGATATAATTTTAATAAT
1951993 TTT
1 TTT
1951996 TAATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTAATATAGATATAATTTTAATAAT
Found at i:1952045 original size:28 final size:26
Alignment explanation
Indices: 1951988--1952075 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 26
1951978 TATAATTTTA
1951988 ATAATTTTTAATTA-TTATTTGATATAAAT
1 ATAA-TTTTAATTATTTA-TT-ATAT-AAT
* *
1952017 ATAATTTTATTTTATTTTATTATTTAAT
1 ATAATTTTA-ATTA-TTTATTATATAAT
1952045 ATAAATTTTAATTATTTATTATATACAT
1 AT-AATTTTAATTATTTATTATATA-AT
1952073 ATA
1 ATA
1952076 CATATTTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
27 11 0.22
28 17 0.34
29 17 0.34
30 2 0.04
31 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (26 bp):
ATAATTTTAATTATTTATTATATAAT
Found at i:1952060 original size:20 final size:19
Alignment explanation
Indices: 1952030--1952067 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1952020 ATTTTATTTT
1952030 ATTTTATTATTTAATATAA
1 ATTTTATTATTTAATATAA
*
1952049 ATTTTAATTATTTATTATA
1 ATTTT-ATTATTTAATATA
1952068 TACATATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATTATTTAATATAA
Found at i:1952085 original size:30 final size:27
Alignment explanation
Indices: 1951988--1952086 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 27
1951978 TATAATTTTA
*
1951988 ATAATTTTTAATTA-TTATTTGATATAA-
1 ATAAATTTTAATTATTTA-TT-ATATAAT
* *
1952015 ATATAATTTTATTTTATTTTATTATTTAAT
1 ATA-AATTTTA-ATTA-TTTATTATATAAT
1952045 ATAAATTTTAATTATTTATTATATACAT
1 ATAAATTTTAATTATTTATTATATA-AT
1952073 ATACATATTTTAAT
1 ATA-A-ATTTTAAT
1952087 ATAATATTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
27 13 0.22
28 14 0.24
29 16 0.27
30 13 0.22
31 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (27 bp):
ATAAATTTTAATTATTTATTATATAAT
Found at i:1952091 original size:99 final size:96
Alignment explanation
Indices: 1951891--1952075 Score: 223
Period size: 99 Copynumber: 1.9 Consensus size: 96
1951881 TTATAAATTA
* *
1951891 AATTTTTTATTATCATTCAATATAAATATACTTTTATTTAAAGTTTATTATTTAATATAATCGTA
1 AATTTTTAATTATCATTCAATATAAATATAATTTTATTTAAAGTTTATTATTTAATATAA---TA
*
1951956 ATTTTAATAATTTTAATATAGATATAATTTTAAT
63 ATTTTAATAATTTTAATATACATATAATTTTAAT
* ** * *
1951990 AATTTTTAATTATTATTTGATATAAATATAATTTTATTT-TATTTTATTATTTAATAT-A-AATT
1 AATTTTTAATTATCATTCAATATAAATATAATTTTATTTAAAGTTTATTATTTAATATAATAATT
* *
1952052 TTAATTATTTATTATATACATATA
66 TTAATAATTT-TAATATACATATA
1952076 CATATTTTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
93 13 0.17
94 11 0.15
97 1 0.01
98 16 0.21
99 34 0.45
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (96 bp):
AATTTTTAATTATCATTCAATATAAATATAATTTTATTTAAAGTTTATTATTTAATATAATAATT
TTAATAATTTTAATATACATATAATTTTAAT
Found at i:1952661 original size:24 final size:24
Alignment explanation
Indices: 1952601--1952661 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
1952591 TTATTCATAA
1952601 AAAGATCATATTTATAAAAAATAATT
1 AAAGA-CATA-TTATAAAAAATAATT
**
1952627 AAAGATGTATTA-AAAAAATAATCT
1 AAAGACATATTATAAAAAATAAT-T
*
1952651 AACGACATATT
1 AAAGACATATT
1952662 TTTTCCCTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 10 0.34
24 12 0.41
25 2 0.07
26 5 0.17
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAGACATATTATAAAAAATAATT
Found at i:1953092 original size:15 final size:14
Alignment explanation
Indices: 1953023--1953129 Score: 67
Period size: 16 Copynumber: 7.4 Consensus size: 14
1953013 TATCACCAAA
* *
1953023 AAAATAAAATAAAT
1 AAAATTAAATAATT
* *
1953037 AAAATT-ATTAAAT
1 AAAATTAAATAATT
*
1953050 AAAAAT-AATAA-T
1 AAAATTAAATAATT
*
1953062 AAATTTAAATATATT
1 AAAATTAAATA-ATT
1953077 AAAATTCAAATAATT
1 AAAATT-AAATAATT
*
1953092 AAATTATTAAATTATT
1 AAA--ATTAAATAATT
1953108 AAATATTAAATATATT
1 AAA-ATTAAATA-ATT
1953124 ATAAAT
1 A-AAAT
1953130 ATATAAATTA
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
12 5 0.07
13 19 0.25
14 6 0.08
15 20 0.26
16 21 0.28
17 5 0.07
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATTAAATAATT
Found at i:1953100 original size:8 final size:8
Alignment explanation
Indices: 1953066--1953146 Score: 69
Period size: 8 Copynumber: 9.9 Consensus size: 8
1953056 AATAATAAAT
1953066 TTAAATATA
1 TTAAAT-TA
1953075 TTAAA--A
1 TTAAATTA
*
1953081 TTCAAATAA
1 TT-AAATTA
1953090 TTAAATTA
1 TTAAATTA
1953098 TTAAATTA
1 TTAAATTA
1953106 TTAAA-TA
1 TTAAATTA
1953113 TTAAATATA
1 TTAAAT-TA
*
1953122 TTATAAATA
1 TTA-AATTA
1953131 TATAAATTA
1 T-TAAATTA
*
1953140 TCAAATT
1 TTAAATT
1953147 TATATTTTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
6 3 0.05
7 10 0.16
8 23 0.38
9 21 0.34
10 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
TTAAATTA
Found at i:1953103 original size:16 final size:16
Alignment explanation
Indices: 1953038--1953124 Score: 87
Period size: 16 Copynumber: 5.6 Consensus size: 16
1953028 AAAATAAATA
*
1953038 AAAT-TATTAAATA-A
1 AAATATATTAAATATT
*
1953052 AAATAATAATAAAT-TT
1 AAAT-ATATTAAATATT
1953068 AAATATATTAAA-ATT
1 AAATATATTAAATATT
1953083 CAAATA-ATTAAATTATT
1 -AAATATATTAAA-TATT
1953100 AAAT-TATTAAATATT
1 AAATATATTAAATATT
1953115 AAATATATTA
1 AAATATATTA
1953125 TAAATATATA
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
14 4 0.07
15 23 0.38
16 31 0.51
17 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATATTAAATATT
Found at i:1954414 original size:25 final size:26
Alignment explanation
Indices: 1954360--1954420 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
1954350 ATTTTAAAAA
1954360 TATATAAATATTAATATAAAAATAATTT
1 TATAT-AAT-TTAATATAAAAATAATTT
*
1954388 TA-ATAATTTAATATATAAAT-ATATT
1 TATATAATTTAATATAAAAATAAT-TT
1954413 TATATAAT
1 TATATAAT
1954421 ATCTTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 2 0.07
25 16 0.53
26 8 0.27
27 2 0.07
28 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TATATAATTTAATATAAAAATAATTT
Found at i:1959476 original size:23 final size:21
Alignment explanation
Indices: 1959425--1959477 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
1959415 TGAATATCTG
*
1959425 TAATAAT-TAGATTTAATATT
1 TAATAATATAGATTTAAGATT
*
1959445 TTATAAATATAGATTTATAGATT
1 TAAT-AATATAGATTTA-AGATT
1959468 TGAATAATAT
1 T-AATAATAT
1959478 TTAAATTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.12
21 3 0.12
22 8 0.31
23 10 0.38
24 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (21 bp):
TAATAATATAGATTTAAGATT
Found at i:1959695 original size:17 final size:17
Alignment explanation
Indices: 1959669--1959706 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1959659 ATTAAATTTA
1959669 AATTTAAATAATAAT-AT
1 AATTTAAAT-ATAATAAT
*
1959686 AATTTTAATATAATAAT
1 AATTTAAATATAATAAT
1959703 AATT
1 AATT
1959707 AAACTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTAAATATAATAAT
Found at i:1961072 original size:22 final size:22
Alignment explanation
Indices: 1961047--1961089 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1961037 GAATTTCGAA
* * *
1961047 TCAACAAAAGTTAACATTTTTT
1 TCAAAAAAAATTAACAATTTTT
1961069 TCAAAAAAAATTAACAATTTT
1 TCAAAAAAAATTAACAATTTT
1961090 AAAAAAGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (22 bp):
TCAAAAAAAATTAACAATTTTT
Found at i:1961578 original size:5 final size:5
Alignment explanation
Indices: 1961568--1961600 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1961558 TATTATGTAA
1961568 TATTT TATTT TATTT TATTT TATTT T-TTT TATT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATT
1961601 ATTGTCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TATTT
Found at i:1962104 original size:5 final size:5
Alignment explanation
Indices: 1962085--1962224 Score: 101
Period size: 5 Copynumber: 27.6 Consensus size: 5
1962075 ATAGAATTAC
* * *
1962085 ATAAT ATATAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAAT ATATT AAAAA
1 ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT
* * ** *
1962137 AT-AT ATAAT ATATTAT AAAAT ATAAT GTAAT ATAAT ATAA- ATTTT A-AAA
1 ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
1962186 ATAATT ATGAT ATAA- A-AAT ATAAAAT ATAAT ATAAT ATA
1 ATAA-T ATAAT ATAAT ATAAT AT--AAT ATAAT ATAAT ATA
1962225 TAAATTATTA
Statistics
Matches: 105, Mismatches: 18, Indels: 24
0.71 0.12 0.16
Matches are distributed among these distances:
3 2 0.02
4 8 0.08
5 73 0.70
6 13 0.12
7 9 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:1962160 original size:47 final size:48
Alignment explanation
Indices: 1962092--1962226 Score: 154
Period size: 49 Copynumber: 2.8 Consensus size: 48
1962082 TACATAATAT
*
1962092 ATATATAATATA-ATATAATATAATATAATATAA-ATATA-TTAAAAA
1 ATATATAATATATATAAAATATAATATAATATAATATATATTTAAAAA
* * *
1962137 ATATATAATATATTATAAAATATAATGTAATATAATATAAATTTTAAAA
1 ATATATAATATA-TATAAAATATAATATAATATAATATATATTTAAAAA
*
1962186 ATA-ATTATGATATA-AAAATATAAAATATAATATAATATATA
1 ATATATAAT-ATATATAAAATAT--AATATAATATAATATATA
1962227 AATTATTAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
45 12 0.16
47 26 0.34
48 10 0.13
49 28 0.37
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (48 bp):
ATATATAATATATATAAAATATAATATAATATAATATATATTTAAAAA
Found at i:1965567 original size:18 final size:17
Alignment explanation
Indices: 1965533--1965565 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1965523 TAGAAATCTT
1965533 AAAATATTTTGATTTTA
1 AAAATATTTTGATTTTA
1965550 AAAATAATTTT-ATTTT
1 AAAAT-ATTTTGATTTT
1965566 TATTAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AAAATATTTTGATTTTA
Found at i:1965683 original size:3 final size:3
Alignment explanation
Indices: 1965675--1965713 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1965665 ATTGCTTTAT
1965675 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1965714 TGATATATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1965930 original size:15 final size:15
Alignment explanation
Indices: 1965887--1965933 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
1965877 TTTTTAAAAA
1965887 TAATATTTGATTAATTT
1 TAATATTT-A-TAATTT
1965904 ATAA-ATTT-TAATTT
1 -TAATATTTATAATTT
1965918 TAATATTTATAATTT
1 TAATATTTATAATTT
1965933 T
1 T
1965934 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.11
14 10 0.37
15 7 0.26
17 4 0.15
18 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TAATATTTATAATTT
Found at i:1966491 original size:13 final size:13
Alignment explanation
Indices: 1966464--1966503 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1966454 TCTCGACTTG
1966464 TTTAAA-TTATTA
1 TTTAAATTTATTA
*
1966476 TTTAAATTTTTTA
1 TTTAAATTTATTA
1966489 TTTAAATTTAATTA
1 TTTAAATTT-ATTA
1966503 T
1 T
1966504 AAATATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 6 0.25
13 14 0.58
14 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAAATTTATTA
Found at i:1966524 original size:20 final size:20
Alignment explanation
Indices: 1966492--1966531 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1966482 TTTTTTATTT
*
1966492 AAATTTAATTATAAATATAA
1 AAATTTAATTATAAAAATAA
1966512 AAATATTAA-TATAAAAATAA
1 AAAT-TTAATTATAAAAATAA
1966532 TTTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATTTAATTATAAAAATAA
Found at i:1966587 original size:50 final size:48
Alignment explanation
Indices: 1966495--1966593 Score: 112
Period size: 49 Copynumber: 2.0 Consensus size: 48
1966485 TTTATTTAAA
* *
1966495 TTTAATTATAAATATAAAAATATTAATATAAAAATAATTTTTAATATTT
1 TTTAATAATAAATATAAAAATATTAATATAAAAATAACTTTTAA-ATTT
* *
1966544 TTTAATAATAAA-ATAAAAACTGATTAAATTTATAAAT-ACTTTTAAATTT
1 TTTAATAATAAATATAAAAA-T-ATT-AATATAAAAATAACTTTTAAATTT
1966593 T
1 T
1966594 GACCCTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
48 7 0.16
49 17 0.40
50 10 0.23
51 9 0.21
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (48 bp):
TTTAATAATAAATATAAAAATATTAATATAAAAATAACTTTTAAATTT
Found at i:1966979 original size:2 final size:2
Alignment explanation
Indices: 1966974--1967009 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1966964 TGAAAATTGA
1966974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1967010 TCAAAAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1967238 original size:21 final size:21
Alignment explanation
Indices: 1967209--1967268 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
1967199 GGTACGAATG
*
1967209 ATATGATAATAAATAATTAAA
1 ATATAATAATAAATAATTAAA
*
1967230 ATATAATAA-AAA-AA-TAAT
1 ATATAATAATAAATAATTAAA
1967248 ATAATAA-AATAAATAAATTAA
1 AT-ATAATAATAAAT-AATTAA
1967269 TATTTATAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 7 0.22
19 9 0.28
20 3 0.09
21 10 0.31
22 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
ATATAATAATAAATAATTAAA
Found at i:1967243 original size:13 final size:12
Alignment explanation
Indices: 1967216--1967264 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
1967206 ATGATATGAT
*
1967216 AATAAATAATTAA
1 AATAAATAA-AAA
1967229 AATATAATAAAAA
1 AATA-AATAAAAA
*
1967242 AATAATATAATAA
1 AATAA-ATAAAAA
1967255 AATAAATAAA
1 AATAAATAAA
1967265 TTAATATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 5 0.16
13 21 0.68
14 5 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAAATAAAAA
Found at i:1967250 original size:16 final size:17
Alignment explanation
Indices: 1967229--1967263 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1967219 AAATAATTAA
1967229 AATATAATAAAA-AAAT
1 AATATAATAAAATAAAT
1967245 AATATAATAAAATAAAT
1 AATATAATAAAATAAAT
1967262 AA
1 AA
1967264 ATTAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AATATAATAAAATAAAT
Found at i:1967571 original size:12 final size:12
Alignment explanation
Indices: 1967554--1967607 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
1967544 AAAAATGATG
*
1967554 ATAATATTAAAT
1 ATAATATAAAAT
*
1967566 ATAATATAAAAA
1 ATAATATAAAAT
1967578 ATAAT-TAAAAT
1 ATAATATAAAAT
1967589 AT-A-ATAAAAT
1 ATAATATAAAAT
1967599 ATTAATATA
1 A-TAATATA
1967608 TATATATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 8 0.23
11 8 0.23
12 16 0.46
13 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:1967612 original size:22 final size:19
Alignment explanation
Indices: 1967566--1967634 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 19
1967556 AATATTAAAT
1967566 ATAATATAA-AAAATAATTA
1 ATAATATAATAAAAT-ATTA
1967585 A-AATATAATAAAATATTA
1 ATAATATAATAAAATATTA
1967603 ATATATATATATTTAAAAT-TTA
1 ATA-ATATA-A--TAAAATATTA
1967625 TATAATATAA
1 -ATAATATAA
1967635 ATTTATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
18 12 0.28
19 7 0.16
20 5 0.12
21 2 0.05
22 8 0.19
23 9 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATATAATAAAATATTA
Found at i:1967626 original size:15 final size:16
Alignment explanation
Indices: 1967608--1967645 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1967598 TATTAATATA
1967608 TATATATTTA-AAATT
1 TATATATTTATAAATT
*
1967623 TATATA-ATATAAATT
1 TATATATTTATAAATT
1967638 TATATATT
1 TATATATT
1967646 ACTACAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTATAAATT
Found at i:1967638 original size:22 final size:23
Alignment explanation
Indices: 1967593--1967639 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1967583 TAAAATATAA
*
1967593 TAAAATATTAATATATATATATT
1 TAAAATATTAATATATATAAATT
1967616 TAAAAT-TT-ATATAATATAAATT
1 TAAAATATTAATAT-ATATAAATT
1967638 TA
1 TA
1967640 TATATTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 12 0.55
23 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAAATATTAATATATATAAATT
Found at i:1967642 original size:32 final size:33
Alignment explanation
Indices: 1967582--1967644 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1967572 TAAAAAATAA
*
1967582 TTAAAATATAATAAAATATTAATATATATATAT
1 TTAAAATATAATAAAATATAAATATATATATAT
* * *
1967615 TTAAAAT-TTATATAATATAAATTTATATAT
1 TTAAAATATAATAAAATATAAATATATATAT
1967645 TACTACAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TTAAAATATAATAAAATATAAATATATATATAT
Found at i:1972171 original size:210 final size:210
Alignment explanation
Indices: 1971758--1972175 Score: 784
Period size: 210 Copynumber: 2.0 Consensus size: 210
1971748 ACTAAGGTGA
1971758 GAGGGAGCCTGAGTGTGATAAATTCACGTGTGTGCATGTGTATCTATATATTTCACCTGTTTCAG
1 GAGGGAGCCTGAGTGTGATAAATTCACGTGTGTGCATGTGTATCTATATATTTCACCTGTTTCAG
*
1971823 ACCTTCAATCTGAAGTTAATAACCACTATTACATATTCTAATTTTATCCTACTCAGGACTTGGAA
66 ACCTTCAATCTGAAGTTAATAACCAATATTACATATTCTAATTTTATCCTACTCAGGACTTGGAA
*
1971888 ACAAGATTTCTAAATACATATGTAAGGATTATATGGCAATTAATACAGTAAAATACAAATAAAGA
131 ACAAGATTTCTAAATACATATGTAAGGATTATATGGCAAGTAATACAGTAAAATACAAATAAAGA
*
1971953 TTGGGGGGGGGGGGG
196 TGGGGGGGGGGGGGG
*
1971968 GAGGGAGCCTGAGTGTGATAAATTCATGTGTGTGCATGTGTATCTATATATTTCACCTGTTTCAG
1 GAGGGAGCCTGAGTGTGATAAATTCACGTGTGTGCATGTGTATCTATATATTTCACCTGTTTCAG
1972033 ACCTTCAATCTGAAGTTAATAACCAATATTACATATTCTAATTTTATCCTACTCAGGACTT-GAA
66 ACCTTCAATCTGAAGTTAATAACCAATATTACATATTCTAATTTTATCCTACTCAGGACTTGGAA
*
1972097 ACAAGATTTCTAAATACATATGTAAGGATTATATGGCAAGTAATACAGTGAAATACAAATAAAGA
131 ACAAGATTTCTAAATACATATGTAAGGATTATATGGCAAGTAATACAGTAAAATACAAATAAAGA
1972162 TGGGGGGGGGGGGG
196 TGGGGGGGGGGGGG
1972176 TTGAATTTGA
Statistics
Matches: 203, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
209 79 0.39
210 124 0.61
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.31
Consensus pattern (210 bp):
GAGGGAGCCTGAGTGTGATAAATTCACGTGTGTGCATGTGTATCTATATATTTCACCTGTTTCAG
ACCTTCAATCTGAAGTTAATAACCAATATTACATATTCTAATTTTATCCTACTCAGGACTTGGAA
ACAAGATTTCTAAATACATATGTAAGGATTATATGGCAAGTAATACAGTAAAATACAAATAAAGA
TGGGGGGGGGGGGGG
Found at i:1976030 original size:14 final size:15
Alignment explanation
Indices: 1976006--1976051 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
1975996 GTATAATATG
1976006 AATAATATAAAATTA
1 AATAATATAAAATTA
*
1976021 AATAAT-TAAAATTT
1 AATAATATAAAATTA
*
1976035 AATAAAATATAAATTA
1 AATAATATA-AAATTA
1976051 A
1 A
1976052 TGAATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 12 0.46
15 8 0.31
16 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATAAAATTA
Found at i:1976436 original size:15 final size:13
Alignment explanation
Indices: 1976337--1976448 Score: 67
Period size: 11 Copynumber: 8.6 Consensus size: 13
1976327 TTTTAATATA
1976337 AAAATAATAA-TAT
1 AAAAT-ATAATTAT
*
1976350 TAAATATAATTACTT
1 AAAATATAATTA--T
1976365 AAAA-ATAA-TAT
1 AAAATATAATTAT
*
1976376 ACAATATAA-T-T
1 AAAATATAATTAT
*
1976387 AAAATATAAATTTT
1 AAAATAT-AATTAT
*
1976401 TAAATAT--TTAT
1 AAAATATAATTAT
1976412 AAAATATAATTAT
1 AAAATATAATTAT
*
1976425 ACAAATTATAATAAAT
1 A-AAA-TATAAT-TAT
1976441 AAAATATA
1 AAAATATA
1976449 TAAATATAAC
Statistics
Matches: 79, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
11 20 0.25
12 11 0.14
13 14 0.18
14 18 0.23
15 13 0.16
16 3 0.04
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATATAATTAT
Found at i:1977861 original size:102 final size:102
Alignment explanation
Indices: 1977685--1977892 Score: 371
Period size: 102 Copynumber: 2.0 Consensus size: 102
1977675 GTGTTAATGT
1977685 AAGTTGCAATAACCAACTAATCTAATATTTCAAGAGGCTCTCAACTTTCATCTTGAACAATCAAA
1 AAGTTGCAATAACCAACTAATCTAATATTTCAAGAGGCTCTCAACTTTCATCTTGAACAATCAAA
* *
1977750 ATGCGACTAAATTTCTCTGTTCGGTACTAAGAAAGCA
66 ATGCAACTAAATTTCTCTGTTCGATACTAAGAAAGCA
* *
1977787 AAGTTGCAATAACCAACTAGTCTAATATTTCAAGGGGCTCTCAACTTTCATCTTGAACAATCAAA
1 AAGTTGCAATAACCAACTAATCTAATATTTCAAGAGGCTCTCAACTTTCATCTTGAACAATCAAA
*
1977852 ATGCAACTAAATTTCTCTGTTCGATTCTAAGAAAGCA
66 ATGCAACTAAATTTCTCTGTTCGATACTAAGAAAGCA
1977889 AAGT
1 AAGT
1977893 ATCTGGCTGG
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (102 bp):
AAGTTGCAATAACCAACTAATCTAATATTTCAAGAGGCTCTCAACTTTCATCTTGAACAATCAAA
ATGCAACTAAATTTCTCTGTTCGATACTAAGAAAGCA
Found at i:1982678 original size:12 final size:13
Alignment explanation
Indices: 1982656--1982684 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1982646 TAATCACCAA
1982656 ATTTCATTTATTT
1 ATTTCATTTATTT
1982669 ATTT-ATTTATTT
1 ATTTCATTTATTT
1982681 ATTT
1 ATTT
1982685 TTAATTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTCATTTATTT
Found at i:1983123 original size:2 final size:2
Alignment explanation
Indices: 1983116--1983144 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1983106 AATCTCATTA
1983116 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1983145 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1984818 original size:23 final size:24
Alignment explanation
Indices: 1984768--1984822 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1984758 TTTTAAAAAA
*
1984768 TATATATTAAATTTATAATATTAAT
1 TATAT-TTAAATATATAATATTAAT
* *
1984793 TATATTTAAATATATTATATT-CT
1 TATATTTAAATATATAATATTAAT
1984816 TATATTT
1 TATATTT
1984823 TTGTAACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 8 0.30
24 14 0.52
25 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TATATTTAAATATATAATATTAAT
Found at i:1986334 original size:16 final size:17
Alignment explanation
Indices: 1986308--1986340 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1986298 TATATTTATG
*
1986308 AATAAATAAAATTTAAA
1 AATAAATAAAAATTAAA
1986325 AATAAA-AAAAATTAAA
1 AATAAATAAAAATTAAA
1986341 TTGTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAAATAAAAATTAAA
Found at i:1992441 original size:2 final size:2
Alignment explanation
Indices: 1992434--1992464 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1992424 ATTAGAAGTA
1992434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1992465 AATGTATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1993752 original size:21 final size:21
Alignment explanation
Indices: 1993713--1993752 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1993703 ATTAAAATAT
*
1993713 TATTTTATATTAATTTTTATA
1 TATTTTATATTAATATTTATA
1993734 TATTTTATAATTAA-ATTTA
1 TATTTTAT-ATTAATATTTA
1993753 AATAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATATTAATATTTATA
Found at i:1994628 original size:38 final size:38
Alignment explanation
Indices: 1994556--1994640 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 38
1994546 TATTAATAAA
*
1994556 AATTAAAATTTTATTTATATATTTATATATTTTAATTT
1 AATTAAAATTTTATTTATATATTAATATATTTTAATTT
* *
1994594 AATTAAAATATTT-TTTAT-TATTAAATAATATTTAAAATT
1 AATTAAAAT-TTTATTTATATATT-AAT-ATATTTTAATTT
1994633 AACTTAAA
1 AA-TTAAA
1994641 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 4 0.10
38 16 0.40
39 15 0.38
40 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (38 bp):
AATTAAAATTTTATTTATATATTAATATATTTTAATTT
Found at i:1995346 original size:35 final size:35
Alignment explanation
Indices: 1995282--1995373 Score: 87
Period size: 35 Copynumber: 2.5 Consensus size: 35
1995272 TAATTCAACT
* *
1995282 TATTTTAATTTAAA-TTATTATTTAATAATAAAAAA
1 TATTTTTATTTAAATTTA-TAATTAATAATAAAAAA
* * *
1995317 TATTTTTATTTAAATTTATAATTATTAATATATAA
1 TATTTTTATTTAAATTTATAATTAATAATAAAAAA
*
1995352 TAATTATTTATTATATATTTAT
1 T-ATT-TTTATT-TAAATTTAT
1995374 TTTATAAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
35 27 0.57
36 6 0.13
37 6 0.13
38 8 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
TATTTTTATTTAAATTTATAATTAATAATAAAAAA
Found at i:1996992 original size:22 final size:22
Alignment explanation
Indices: 1996967--1997008 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1996957 TATTTTTATT
1996967 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1996989 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1997009 ATATTGTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:2001965 original size:3 final size:3
Alignment explanation
Indices: 2001957--2001983 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2001947 ATAAAAATTC
2001957 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
2001984 TTGCGTACAT
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:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2004585 original size:14 final size:14
Alignment explanation
Indices: 2004566--2004594 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2004556 TTTATTAACA
2004566 TAATAATTAAAAGT
1 TAATAATTAAAAGT
2004580 TAATAATTAAAAGT
1 TAATAATTAAAAGT
2004594 T
1 T
2004595 TATTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAATAATTAAAAGT
Found at i:2006218 original size:2 final size:2
Alignment explanation
Indices: 2006211--2006244 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2006201 ATACACAAGC
2006211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2006245 GTTGATGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2012344 original size:2 final size:2
Alignment explanation
Indices: 2012332--2012367 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2012322 AAAGATATAA
*
2012332 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2012368 GAAAAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2012595 original size:2 final size:2
Alignment explanation
Indices: 2012588--2012613 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2012578 TTAAGCAAAA
2012588 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
2012614 GTGTGAAGAA
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:2012937 original size:2 final size:2
Alignment explanation
Indices: 2012930--2012959 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2012920 AAGTCAACAA
2012930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2012960 GCAAAGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2013711 original size:11 final size:12
Alignment explanation
Indices: 2013690--2013718 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2013680 AAGTTTGATA
2013690 ATTTATATATTT
1 ATTTATATATTT
2013702 ATTT-TATATTT
1 ATTTATATATTT
2013713 ATTTAT
1 ATTTAT
2013719 TTTATCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTATATATTT
Found at i:2014213 original size:25 final size:26
Alignment explanation
Indices: 2014158--2014217 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
2014148 ATGGTTATTT
* *
2014158 TTTATTATAAATATTTATGATTAATA
1 TTTATTATAAATAATTATGAATAATA
*
2014184 TTTATTATAATTAATTAT-AATAATA
1 TTTATTATAAATAATTATGAATAATA
2014209 TTTATTATA
1 TTTATTATA
2014218 TTTTTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTATTATAAATAATTATGAATAATA
Found at i:2014926 original size:22 final size:22
Alignment explanation
Indices: 2014901--2014964 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
2014891 AAAAAATTAG
2014901 TTTATATTTTATGTTTATAATT
1 TTTATATTTTATGTTTATAATT
* *
2014923 TTTATTATGTTATGATTAT-ATT
1 TTTA-TATTTTATGTTTATAATT
* * *
2014945 TATAAAATTTTATATTTATA
1 T-TTATATTTTATGTTTATA
2014965 TTAATTTTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTATATTTTATGTTTATAATT
Found at i:2015021 original size:29 final size:30
Alignment explanation
Indices: 2014985--2015056 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
2014975 TACGTTAATA
2014985 ATTTATATTATATAAAATTTTAAATA-TAT
1 ATTTATATTATATAAAATTTTAAATATTAT
* * * *
2015014 ATTTATATTATATTATATTTTAATTATTTT
1 ATTTATATTATATAAAATTTTAAATATTAT
*
2015044 ATATATATTATAT
1 ATTTATATTATAT
2015057 TCATATAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTATATTATATAAAATTTTAAATATTAT
Found at i:2015026 original size:5 final size:5
Alignment explanation
Indices: 2015011--2015062 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
2015001 ATTTTAAATA
* *
2015011 TATATT TATAT TATAT TATAT TTTAAT TATTT TATA- TATAT TATAT TCATAT
1 TATA-T TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT T-ATAT
2015063 AATCGTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 23 0.59
6 12 0.31
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Done.