Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 83 of 129
Found at i:13394147 original size:18 final size:18
Alignment explanation
Indices: 13394124--13394285 Score: 121
Period size: 18 Copynumber: 9.2 Consensus size: 18
13394114 TATATTATAA
13394124 TATATTAATAAATAATAT
1 TATATTAATAAATAATAT
13394142 TATATTAATAAATAATA-
1 TATATTAATAAATAATAT
* *
13394159 TATAATTAAT--ATTATAA
1 TAT-ATTAATAAATAATAT
*
13394176 TATATTAATATAT-ATAT
1 TATATTAATAAATAATAT
13394193 TAATATTATAATAAATAATA-
1 T-ATA-T-TAATAAATAATAT
13394213 TACTATTAAT--AT-A-A-
1 TA-TATTAATAAATAATAT
13394227 TATATTAATAAATAATAT
1 TATATTAATAAATAATAT
** * *
13394245 TA-ACAAAATAATATTATAA
1 TATA-TTAATAA-ATAATAT
13394264 TATATTAATAAATAATAT
1 TATATTAATAAATAATAT
13394282 TATA
1 TATA
13394286 ATATATTAAT
Statistics
Matches: 116, Mismatches: 11, Indels: 34
0.72 0.07 0.21
Matches are distributed among these distances:
13 7 0.06
14 3 0.03
15 3 0.03
16 14 0.12
17 12 0.10
18 48 0.41
19 15 0.13
20 11 0.09
21 3 0.03
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATTAATAAATAATAT
Found at i:13394236 original size:31 final size:30
Alignment explanation
Indices: 13394120--13394305 Score: 149
Period size: 31 Copynumber: 6.3 Consensus size: 30
13394110 ATATTATATT
*
13394120 ATAATATATTAATAAATAATATTATATTAATAA
1 ATAATATA-TAAT-AAT-ATAATATATTAATAA
*
13394153 ATAATATATAATTA-AT-AT-TA-TAATATA
1 ATAATATATAATAATATAATATATTAATA-A
*
13394180 TTAATATAT-AT-AT-TAATAT-TATAATAA
1 ATAATATATAATAATATAATATAT-TAATAA
*
13394207 ATAATATACTATTAATATAATATATTAATAA
1 ATAATATA-TAATAATATAATATATTAATAA
* *
13394238 ATAATAT-TAACAAAATAATAT-TATAATATA
1 ATAATATATAATAATATAATATAT-TAATA-A
* * *
13394268 TTAATAAATAATATTATAATATATTAATAA
1 ATAATATATAATAATATAATATATTAATAA
13394298 ATAATATA
1 ATAATATA
13394306 AAGAAAATAA
Statistics
Matches: 123, Mismatches: 15, Indels: 33
0.72 0.09 0.19
Matches are distributed among these distances:
25 2 0.02
26 9 0.07
27 20 0.16
28 8 0.07
29 19 0.15
30 15 0.12
31 36 0.29
32 6 0.05
33 8 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (30 bp):
ATAATATATAATAATATAATATATTAATAA
Found at i:13394265 original size:60 final size:60
Alignment explanation
Indices: 13394193--13394315 Score: 176
Period size: 60 Copynumber: 2.0 Consensus size: 60
13394183 ATATATATAT
* * *
13394193 TAATATTATAATA-AATAATATACTATTAATATAATATATTAATAAATAATATTAACAAAA
1 TAATATTATAATATAATAATA-AATAATAATATAATATATTAATAAATAATATAAACAAAA
* * *
13394253 TAATATTATAATATATTAATAAATAATATTATAATATATTAATAAATAATATAAAGAAAA
1 TAATATTATAATATAATAATAAATAATAATATAATATATTAATAAATAATATAAACAAAA
13394313 TAA
1 TAA
13394316 ATGGTTTTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 50 0.89
61 6 0.11
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (60 bp):
TAATATTATAATATAATAATAAATAATAATATAATATATTAATAAATAATATAAACAAAA
Found at i:13394279 original size:103 final size:100
Alignment explanation
Indices: 13394103--13394291 Score: 242
Period size: 103 Copynumber: 1.9 Consensus size: 100
13394093 AATTTTATTT
* **
13394103 ATAAATAATATTATATTATAATATATTAATAAATAATATTATATTAATAAATAATATATAATTAA
1 ATAAATAATATTATAATATAATATATTAATAAATAATATTATAAAAATAAATAATATATAATTAA
*
13394168 TATTATAATA-TATTAATATATATATTAATATTATA
66 TATAATAATATTA-TAATATATATATTAATATTATA
*
13394203 ATAAATAATATACTATTAATATAATATATTAATAAATAATATTA-ACAAAAT-AATATTATAATA
1 ATAAATAATAT--TA-TAATATAATATATTAATAAATAATATTATA-AAAATAAATAATAT-ATA
13394266 TATTAATA-AATAATATTATAATATAT
61 -ATTAATATAATAATATTATAATATAT
13394292 TAATAAATAA
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
100 11 0.14
102 10 0.13
103 47 0.61
104 9 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (100 bp):
ATAAATAATATTATAATATAATATATTAATAAATAATATTATAAAAATAAATAATATATAATTAA
TATAATAATATTATAATATATATATTAATATTATA
Found at i:13394411 original size:9 final size:9
Alignment explanation
Indices: 13394394--13394467 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
13394384 AATTATTTTT
*
13394394 TAATATTAA
1 TAATTTTAA
13394403 TAATTTTAA
1 TAATTTTAA
*
13394412 TAA--TAAA
1 TAATTTTAA
*
13394419 TATTTTTAA
1 TAATTTTAA
13394428 TATATTTTAA
1 TA-ATTTTAA
*
13394438 TAA--TAAA
1 TAATTTTAA
13394445 TAATTTTTAA
1 TAA-TTTTAA
13394455 T-ATTTTAA
1 TAATTTTAA
13394463 TAATT
1 TAATT
13394468 ATATTAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
7 11 0.22
8 7 0.14
9 21 0.41
10 12 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TAATTTTAA
Found at i:13394411 original size:15 final size:15
Alignment explanation
Indices: 13394391--13394431 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
13394381 TATAATTATT
*
13394391 TTTTAATATTAATAA
1 TTTTAATATAAATAA
*
13394406 TTTTAATAATAAATAT
1 TTTTAAT-ATAAATAA
13394422 TTTTAATATA
1 TTTTAATATA
13394432 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:13394434 original size:26 final size:27
Alignment explanation
Indices: 13394399--13394466 Score: 108
Period size: 25 Copynumber: 2.7 Consensus size: 27
13394389 TTTTTTAATA
13394399 TTAATA-ATTTTAATAATAAAT-ATTT
1 TTAATATATTTTAATAATAAATAATTT
13394424 TTAATATATTTTAATAATAAATAATTT
1 TTAATATATTTTAATAATAAATAATTT
13394451 TT-A-ATATTTTAATAAT
1 TTAATATATTTTAATAAT
13394467 TATATTAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
25 19 0.46
26 16 0.39
27 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAATATATTTTAATAATAAATAATTT
Found at i:13394463 original size:25 final size:24
Alignment explanation
Indices: 13394399--13394466 Score: 100
Period size: 26 Copynumber: 2.7 Consensus size: 24
13394389 TTTTTTAATA
13394399 TTAATAATTTTAATAATAAATATTT
1 TTAAT-ATTTTAATAATAAATATTT
13394424 TTAATATATTTTAATAATAAATAATTT
1 TT-A-ATATTTTAATAATAAAT-ATTT
13394451 TTAATATTTTAATAAT
1 TTAATATTTTAATAAT
13394467 TATATTAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
25 15 0.38
26 17 0.43
27 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAATATTTTAATAATAAATATTT
Found at i:13397454 original size:10 final size:11
Alignment explanation
Indices: 13397428--13397460 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
13397418 TTAACAATAC
13397428 AAATTTTAAATA
1 AAATTTTAAA-A
13397440 AAA-TTTAAAA
1 AAATTTTAAAA
13397450 AAATTTTAAAA
1 AAATTTTAAAA
13397461 TATTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.20
11 13 0.65
12 3 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATTTTAAAA
Found at i:13399480 original size:30 final size:30
Alignment explanation
Indices: 13399446--13399506 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
13399436 TGTTCAGAAA
**
13399446 GTTCTTAGTGTATGTTAGCTGCTCATTAGT
1 GTTCTTAGTGTACATTAGCTGCTCATTAGT
*
13399476 GTTCTTAGTGTACATTAGCTGCTCTTTAGT
1 GTTCTTAGTGTACATTAGCTGCTCATTAGT
13399506 G
1 G
13399507 GGCTACTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.46
Consensus pattern (30 bp):
GTTCTTAGTGTACATTAGCTGCTCATTAGT
Found at i:13399729 original size:139 final size:139
Alignment explanation
Indices: 13399476--13399733 Score: 421
Period size: 139 Copynumber: 1.9 Consensus size: 139
13399466 GCTCATTAGT
13399476 GTTCTTAGTGTACATTAGCTGCTCTTTAGTGGGCTACTATATATGTTGTAGCATATATTGATGCT
1 GTTCTTAGTGTACATTAGCTGCTCTTTAGTGGGCTACTATATATGTTGTAGCATATATTGATGCT
* ** * **
13399541 CAAGTATGGAAATGACAGGGTCAGGTACAGTGATGCATGTATTTGGTAAATGCTCAAGCATATTT
66 CAAGTATGGAAATGACAGGGTCAGCTACAGCAATGCATGTACTCAGTAAATGCTCAAGCATATTT
13399606 GTTCAGAAA
131 GTTCAGAAA
*
13399615 GTTCTT-GATGTACATTGGCTGCTCTTTAGTGGGCTAAC-ATATATGTTGTAGCATATATTGATG
1 GTTCTTAG-TGTACATTAGCTGCTCTTTAGTGGGCT-ACTATATATGTTGTAGCATATATTGATG
13399678 CTCAAGTATGGAAATGACAGGGTCAGCTACAGCAATGCATGTACTCAGTAAATGCT
64 CTCAAGTATGGAAATGACAGGGTCAGCTACAGCAATGCATGTACTCAGTAAATGCT
13399734 ATGTAAAATA
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
138 1 0.01
139 107 0.97
140 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (139 bp):
GTTCTTAGTGTACATTAGCTGCTCTTTAGTGGGCTACTATATATGTTGTAGCATATATTGATGCT
CAAGTATGGAAATGACAGGGTCAGCTACAGCAATGCATGTACTCAGTAAATGCTCAAGCATATTT
GTTCAGAAA
Found at i:13402009 original size:12 final size:12
Alignment explanation
Indices: 13401992--13402016 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13401982 CAATAATATG
13401992 TAAAAAAATTAT
1 TAAAAAAATTAT
13402004 TAAAAAAATTAT
1 TAAAAAAATTAT
13402016 T
1 T
13402017 TATAATTCAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAAAATTAT
Found at i:13404867 original size:19 final size:19
Alignment explanation
Indices: 13404820--13404868 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
13404810 AGCCCAATGG
* *
13404820 AAGCCCAAATTTAGTGTTA
1 AAGCCTAAATTTAGTATTA
*
13404839 AA-ACTCAAATTTAGTATTA
1 AAGCCT-AAATTTAGTATTA
13404858 AAGCCTAAATT
1 AAGCCTAAATT
13404869 CGGTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 21 0.88
20 2 0.08
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (19 bp):
AAGCCTAAATTTAGTATTA
Found at i:13404948 original size:24 final size:26
Alignment explanation
Indices: 13404903--13404951 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
13404893 ATAAAATAGA
*
13404903 ATAACAAAAAATTAATACAAATAAAT
1 ATAACAAAAAACTAATACAAATAAAT
*
13404929 ATAAC-AAAAACTAA-AGAAATAAA
1 ATAACAAAAAACTAATACAAATAAA
13404952 AAAAAGGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.18
Consensus pattern (26 bp):
ATAACAAAAAACTAATACAAATAAAT
Found at i:13408840 original size:24 final size:24
Alignment explanation
Indices: 13408813--13408918 Score: 99
Period size: 24 Copynumber: 4.5 Consensus size: 24
13408803 GTTAACACCT
*
13408813 AAACCCTAAAATCTTAAAACCCTG
1 AAACCCTAAAATCTTAAAACCCTA
* * * *
13408837 AAACCTTAATAAT-TTGAAATCCTG
1 AAACCCTAA-AATCTTAAAACCCTA
*
13408861 AAACCCTAAAACCTTAAAACCCTA
1 AAACCCTAAAATCTTAAAACCCTA
* * * *
13408885 AAATCTTAAGA-CCTAAAACCCTA
1 AAACCCTAAAATCTTAAAACCCTA
13408908 AAACCCTAAAA
1 AAACCCTAAAA
13408919 CCATGAAAAC
Statistics
Matches: 65, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
23 21 0.32
24 41 0.63
25 3 0.05
ACGTcount: A:0.48, C:0.26, G:0.04, T:0.22
Consensus pattern (24 bp):
AAACCCTAAAATCTTAAAACCCTA
Found at i:13408872 original size:8 final size:8
Alignment explanation
Indices: 13408861--13409046 Score: 90
Period size: 8 Copynumber: 22.8 Consensus size: 8
13408851 TGAAATCCTG
13408861 AAACCCTA
1 AAACCCTA
*
13408869 AAACCTTA
1 AAACCCTA
13408877 AAACCCTA
1 AAACCCTA
* *
13408885 AAATCTTA
1 AAACCCTA
*
13408893 AGA-CCTA
1 AAACCCTA
13408900 AAACCCTA
1 AAACCCTA
13408908 AAACCCTA
1 AAACCCTA
*
13408916 AAACCATGA
1 AAACCCT-A
*
13408925 AAA-CTTAA
1 AAACCCT-A
** *
13408933 AAACTTTG
1 AAACCCTA
*
13408941 AAAGCCTA
1 AAACCCTA
* *
13408949 AAATCTTA
1 AAACCCTA
* **
13408957 TAACATTA
1 AAACCCTA
13408965 AAACCCTA
1 AAACCCTA
*
13408973 AAATCCTA
1 AAACCCTA
13408981 AAA-CCTA
1 AAACCCTA
*
13408988 AAATCCTA
1 AAACCCTA
* *
13408996 AGACCTTA
1 AAACCCTA
*
13409004 AAATCCTA
1 AAACCCTA
*
13409012 AAATCTAGCTA
1 AAA-C--CCTA
13409023 AAACCCTA
1 AAACCCTA
*
13409031 AATTACCCTT
1 AA--ACCCTA
13409041 AAACCC
1 AAACCC
13409047 AATGCCAACA
Statistics
Matches: 134, Mismatches: 35, Indels: 18
0.72 0.19 0.10
Matches are distributed among these distances:
7 12 0.09
8 102 0.76
9 6 0.04
10 8 0.06
11 6 0.04
ACGTcount: A:0.48, C:0.26, G:0.03, T:0.22
Consensus pattern (8 bp):
AAACCCTA
Found at i:13408901 original size:15 final size:16
Alignment explanation
Indices: 13408813--13409014 Score: 126
Period size: 16 Copynumber: 12.7 Consensus size: 16
13408803 GTTAACACCT
*
13408813 AAACCCTAAAATCTTA
1 AAACCCTAAAACCTTA
*
13408829 AAACCCTGAAACCTTA
1 AAACCCTAAAACCTTA
** * *
13408845 ATAA-TTTGAAATCC-TG
1 A-AACCCT-AAAACCTTA
13408861 AAACCCTAAAACCTTA
1 AAACCCTAAAACCTTA
*
13408877 AAACCCTAAAATCTTA
1 AAACCCTAAAACCTTA
* *
13408893 AGA-CCTAAAACCCTA
1 AAACCCTAAAACCTTA
*
13408908 AAACCCTAAAACCATGA
1 AAACCCTAAAACC-TTA
* * *
13408925 AAA-CTTAAAAACTTTG
1 AAACCCT-AAAACCTTA
* *
13408941 AAAGCCTAAAATCTTA
1 AAACCCTAAAACCTTA
* ** *
13408957 TAACATTAAAACCCTA
1 AAACCCTAAAACCTTA
*
13408973 AAATCCTAAAACC-TA
1 AAACCCTAAAACCTTA
* *
13408988 AAATCCTAAGACCTTA
1 AAACCCTAAAACCTTA
*
13409004 AAATCCTAAAA
1 AAACCCTAAAA
13409015 TCTAGCTAAA
Statistics
Matches: 139, Mismatches: 38, Indels: 18
0.71 0.19 0.09
Matches are distributed among these distances:
15 33 0.24
16 89 0.64
17 17 0.12
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.23
Consensus pattern (16 bp):
AAACCCTAAAACCTTA
Found at i:13408911 original size:39 final size:39
Alignment explanation
Indices: 13408861--13409032 Score: 111
Period size: 39 Copynumber: 4.3 Consensus size: 39
13408851 TGAAATCCTG
13408861 AAACCCTAAAACCTTAAAACCCTAAAATCTTAAGACCTA
1 AAACCCTAAAACCTTAAAACCCTAAAATCTTAAGACCTA
* *
13408900 AAACCCTAAAACCCTAAAACCATGAAAA-CTTAAAAACTTTGAAAGCCTA
1 AAACCCTAAAACCTTAAAACCCT-AAAATCTT---AA----G--A-CCTA
* * * * * *
13408949 AAATCTTATAACATTAAAACCCTAAAATCCTAAAACCTA
1 AAACCCTAAAACCTTAAAACCCTAAAATCTTAAGACCTA
* * *
13408988 AAATCCTAAGACCTTAAAATCCTAAAATC-T-AG--CTA
1 AAACCCTAAAACCTTAAAACCCTAAAATCTTAAGACCTA
13409023 AAACCCTAAA
1 AAACCCTAAA
13409033 TTACCCTTAA
Statistics
Matches: 103, Mismatches: 18, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
35 11 0.11
37 1 0.01
38 1 0.01
39 52 0.50
40 5 0.05
42 2 0.02
46 3 0.03
48 5 0.05
49 23 0.22
ACGTcount: A:0.50, C:0.25, G:0.03, T:0.22
Consensus pattern (39 bp):
AAACCCTAAAACCTTAAAACCCTAAAATCTTAAGACCTA
Found at i:13409909 original size:21 final size:20
Alignment explanation
Indices: 13409885--13409933 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
13409875 CCCAACTCTG
* *
13409885 TTTTCAAAGATCTAAATATTT
1 TTTTCAAAAACCTAAAT-TTT
*
13409906 TTTTGATAAAACCTAAATTTT
1 TTTTCA-AAAACCTAAATTTT
13409927 TTTTCAA
1 TTTTCAA
13409934 TTTTATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.57
22 9 0.39
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTTCAAAAACCTAAATTTT
Found at i:13411449 original size:3 final size:3
Alignment explanation
Indices: 13411443--13411482 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
13411433 TTAATGTCAC
13411443 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13411483 TATTTTCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13411608 original size:22 final size:21
Alignment explanation
Indices: 13411553--13411625 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
13411543 ATTATTATTA
*
13411553 TTATTATTATTATTTTTGTTTT
1 TTATTTTTATT-TTTTTGTTTT
*
13411575 TTATTTTCATTTTTTTGTTCTT
1 TTATTTTTATTTTTTTGTT-TT
* *
13411597 TT-TCTTTTATTTTGTTCTTTT
1 TTAT-TTTTATTTTTTTGTTTT
*
13411618 TTTTTTTT
1 TTATTTTT
13411626 TGCTCTAATC
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 17 0.40
22 26 0.60
ACGTcount: A:0.10, C:0.05, G:0.04, T:0.81
Consensus pattern (21 bp):
TTATTTTTATTTTTTTGTTTT
Found at i:13411611 original size:19 final size:18
Alignment explanation
Indices: 13411578--13411627 Score: 75
Period size: 19 Copynumber: 2.8 Consensus size: 18
13411568 TTGTTTTTTA
*
13411578 TTTTCATTTTTTTGTTCT
1 TTTTCTTTTTTTTGTTCT
13411596 TTTTCTTTTATTTTGTTCT
1 TTTTCTTTT-TTTTGTTCT
13411615 TTTT-TTTTTTTTG
1 TTTTCTTTTTTTTG
13411628 CTCTAATCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 5 0.17
18 12 0.40
19 13 0.43
ACGTcount: A:0.04, C:0.08, G:0.06, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTTTTGTTCT
Found at i:13411617 original size:28 final size:27
Alignment explanation
Indices: 13411573--13411626 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
13411563 TATTTTTGTT
13411573 TTTTATTTTCATTTTTTTGTTCTTTTTC
1 TTTTATTTTCATTTTTTT-TTCTTTTTC
* *
13411601 TTTTATTTT-GTTCTTTTTTTTTTTTT
1 TTTTATTTTCATT-TTTTTTTCTTTTT
13411627 GCTCTAATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.06, C:0.07, G:0.04, T:0.83
Consensus pattern (27 bp):
TTTTATTTTCATTTTTTTTTCTTTTTC
Found at i:13412531 original size:14 final size:14
Alignment explanation
Indices: 13412508--13412537 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13412498 TTTTACCCCA
*
13412508 TTTTATTTTTATTT
1 TTTTAGTTTTATTT
13412522 TTTTAGTTTTATTT
1 TTTTAGTTTTATTT
13412536 TT
1 TT
13412538 AAAAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTAGTTTTATTT
Found at i:13412699 original size:12 final size:12
Alignment explanation
Indices: 13412682--13412723 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
13412672 AAATTCTTTC
13412682 AATAAAATAAAA
1 AATAAAATAAAA
*
13412694 AATAAAA-ATAA
1 AATAAAATAAAA
13412705 AATGAAAAATAAAA
1 AAT--AAAATAAAA
13412719 AATAA
1 AATAA
13412724 TTTTTATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 9 0.36
13 4 0.16
14 6 0.24
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:13412705 original size:18 final size:18
Alignment explanation
Indices: 13412682--13412719 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
13412672 AAATTCTTTC
13412682 AATAAAATAAAAAATAAA
1 AATAAAATAAAAAATAAA
*
13412700 AATAAAATGAAAAATAAA
1 AATAAAATAAAAAATAAA
13412718 AA
1 AA
13412720 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (18 bp):
AATAAAATAAAAAATAAA
Found at i:13416716 original size:42 final size:42
Alignment explanation
Indices: 13416639--13416718 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
13416629 CAGATGAGCT
* *
13416639 TTTTAAAATTTTAAAAGCTATTAAGCCTCTGCTTAAAGGACC
1 TTTTAAAATTTTAAAAGCTATCAAGCCTCTACTTAAAGGACC
* * *
13416681 TTTTAAAATTTTAAAAGTTGTCAAGTCTCTACTTAAAG
1 TTTTAAAATTTTAAAAGCTATCAAGCCTCTACTTAAAG
13416719 AAGCCTTCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (42 bp):
TTTTAAAATTTTAAAAGCTATCAAGCCTCTACTTAAAGGACC
Found at i:13417766 original size:17 final size:18
Alignment explanation
Indices: 13417740--13417773 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13417730 TTTGTTTAGA
*
13417740 TTTTTCTTTTCT-TTTTC
1 TTTTTATTTTCTGTTTTC
13417757 TTTTTATTTTCTGTTTT
1 TTTTTATTTTCTGTTTT
13417774 GATTTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTATTTTCTGTTTTC
Found at i:13417803 original size:20 final size:21
Alignment explanation
Indices: 13417778--13417829 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
13417768 TGTTTTGATT
13417778 TTGATTTTATTTATT-TTCTG
1 TTGATTTTATTTATTGTTCTG
* * *
13417798 TTGATTTTTTTTGTTGTTTTG
1 TTGATTTTATTTATTGTTCTG
*
13417819 ATGATTTTATT
1 TTGATTTTATT
13417830 ATTATTATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.13, C:0.02, G:0.13, T:0.71
Consensus pattern (21 bp):
TTGATTTTATTTATTGTTCTG
Found at i:13417831 original size:3 final size:3
Alignment explanation
Indices: 13417825--13417877 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
13417815 TTTGATGATT
* *
13417825 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TG TTA TTA TTG TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
13417873 TTA TT
1 TTA TT
13417878 TTAAAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.93
4 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:13417901 original size:17 final size:17
Alignment explanation
Indices: 13417879--13417917 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
13417869 TTCATTATTT
13417879 TAAAAAT-AAGTAAAAAA
1 TAAAAATAAAGT-AAAAA
*
13417896 TAAAAATAAAGTCAAAA
1 TAAAAATAAAGTAAAAA
13417913 TAAAA
1 TAAAA
13417918 TGTAAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (17 bp):
TAAAAATAAAGTAAAAA
Found at i:13418206 original size:3 final size:3
Alignment explanation
Indices: 13418194--13418230 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
13418184 TTTAAACAAT
13418194 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
13418231 GAATTATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13421435 original size:49 final size:49
Alignment explanation
Indices: 13421363--13421461 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
13421353 GACTATTGGA
*
13421363 ACGGTAACTTCTTACGTCTAAATTAGAAATGATGAATAAAAAAAAAGTC
1 ACGGTAACTTCTTACGTCCAAATTAGAAATGATGAATAAAAAAAAAGTC
*
13421412 ACGGTAACTTCTTACTTCCAAATTAGAAATGATGAATAAAAAAAAAGTC
1 ACGGTAACTTCTTACGTCCAAATTAGAAATGATGAATAAAAAAAAAGTC
13421461 A
1 A
13421462 ATGGCATGCG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (49 bp):
ACGGTAACTTCTTACGTCCAAATTAGAAATGATGAATAAAAAAAAAGTC
Found at i:13429542 original size:13 final size:13
Alignment explanation
Indices: 13429524--13429550 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13429514 ATTAATAATC
13429524 ATAATCAATTAAA
1 ATAATCAATTAAA
13429537 ATAATCAATTAAA
1 ATAATCAATTAAA
13429550 A
1 A
13429551 CAAATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATCAATTAAA
Found at i:13431250 original size:19 final size:19
Alignment explanation
Indices: 13431226--13431265 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
13431216 TCAGATATAA
* *
13431226 TTTTATGACTATAATTAAG
1 TTTTATAACCATAATTAAG
13431245 TTTTATAACCATAATTAAG
1 TTTTATAACCATAATTAAG
13431264 TT
1 TT
13431266 ATGTCAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (19 bp):
TTTTATAACCATAATTAAG
Found at i:13431645 original size:23 final size:23
Alignment explanation
Indices: 13431617--13431666 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
13431607 AAAACATTTG
13431617 AAAATTTGGGATCTCG-ATCCCAA
1 AAAATTTGGGAT-TCGAATCCCAA
*
13431640 AAAATTTGGGATTTGAATCCCAA
1 AAAATTTGGGATTCGAATCCCAA
13431663 AAAA
1 AAAA
13431667 GCCTTACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (23 bp):
AAAATTTGGGATTCGAATCCCAA
Found at i:13443283 original size:10 final size:11
Alignment explanation
Indices: 13443261--13443287 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13443251 CAATTTCTAG
13443261 AAATTTATAAA
1 AAATTTATAAA
13443272 AAATTTATAAA
1 AAATTTATAAA
13443283 AAATT
1 AAATT
13443288 CCTTCCTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATTTATAAA
Found at i:13444129 original size:31 final size:32
Alignment explanation
Indices: 13444091--13444151 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
13444081 GAGCCAAAAG
*
13444091 TTAAAAAAT-GATGACTTGGAGTTAGCTGTAA
1 TTAAAAAATAGATGACTTGGACTTAGCTGTAA
*
13444122 TTAAAAAATGAGATGACTTGGTCTTAGCTG
1 TTAAAAAAT-AGATGACTTGGACTTAGCTG
13444152 AAGTCGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 9 0.35
33 17 0.65
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (32 bp):
TTAAAAAATAGATGACTTGGACTTAGCTGTAA
Found at i:13444223 original size:34 final size:33
Alignment explanation
Indices: 13444112--13444232 Score: 120
Period size: 33 Copynumber: 3.6 Consensus size: 33
13444102 TGACTTGGAG
* * * *
13444112 TTAGCTGTAATTA-AAAAATGAGATGACTTGGTC
1 TTAGCTG-AAGTAGAAAAATAAAATGACTTAGTC
* *
13444145 TTAGCTGAAGTCGAAAAACAAAATGACTTAGTC
1 TTAGCTGAAGTAGAAAAATAAAATGACTTAGTC
* *
13444178 TTAGCCGAAGTAGAGAAAATAAAATGACTTAGTG
1 TTAGCTGAAGTAGA-AAAATAAAATGACTTAGTC
*
13444212 TTAG-TGAAAGTAAAAAAATAA
1 TTAGCTG-AAGTAGAAAAATAA
13444233 TATAATTTGG
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
32 3 0.04
33 43 0.59
34 27 0.37
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (33 bp):
TTAGCTGAAGTAGAAAAATAAAATGACTTAGTC
Found at i:13444397 original size:32 final size:31
Alignment explanation
Indices: 13444336--13444465 Score: 109
Period size: 32 Copynumber: 4.0 Consensus size: 31
13444326 TAAAGGTGAC
* * * *
13444336 TGGACTAAGCCAAGATCAAAAAATGAAAATTA
1 TGGATTAAGCCAAGGTC-AAAAATAAAAATAA
*
13444368 TGGGATTAAGTCAAGGTCAAAAATAAAAATAA
1 T-GGATTAAGCCAAGGTCAAAAATAAAAATAA
* *
13444400 CAGGATTGAA-CCAAGGTCAAAAATTAAAATAA
1 -TGGATT-AAGCCAAGGTCAAAAATAAAAATAA
* * *
13444432 CTAGATTAAGCCAAGGTTAAAAAATAAAAGTAA
1 -TGGATTAAGCCAAGG-TCAAAAATAAAAATAA
13444465 T
1 T
13444466 TAGACTGAGC
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
31 2 0.03
32 50 0.62
33 28 0.35
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.21
Consensus pattern (31 bp):
TGGATTAAGCCAAGGTCAAAAATAAAAATAA
Found at i:13444455 original size:33 final size:32
Alignment explanation
Indices: 13444371--13444493 Score: 115
Period size: 32 Copynumber: 3.8 Consensus size: 32
13444361 AAAATTATGG
* *
13444371 GATTAAGTCAAGGTCAAAAATAAAAATAAC-A
1 GATTAAGCCAAGGTCAAAAATTAAAATAACTA
13444402 GGATTGAA-CCAAGGTCAAAAATTAAAATAACTA
1 -GATT-AAGCCAAGGTCAAAAATTAAAATAACTA
* * *
13444435 GATTAAGCCAAGGTTAAAAAATAAAAGTAATTA
1 GATTAAGCCAAGGTCAAAAATTAAAA-TAACTA
* * * * *
13444468 GACTGAGCCAAAGTCGAAAATGAAAA
1 GATTAAGCCAAGGTCAAAAATTAAAA
13444494 ATGACCAAAC
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
31 2 0.03
32 46 0.61
33 27 0.36
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.20
Consensus pattern (32 bp):
GATTAAGCCAAGGTCAAAAATTAAAATAACTA
Found at i:13444586 original size:32 final size:33
Alignment explanation
Indices: 13444550--13444650 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 33
13444540 GTTAAGGTTG
** *
13444550 AAAATAAAAGTGACTGGACTGAACCAAAG-TAA
1 AAAATAAAAGTGACTAAACTAAACCAAAGTTAA
* *
13444582 AAAATGAAAGTGACTAAACTAAACCAAGGTTAA
1 AAAATAAAAGTGACTAAACTAAACCAAAGTTAA
* * * * *
13444615 AAAATAAAAATGACTAAAATGAACTAAAGTTGA
1 AAAATAAAAGTGACTAAACTAAACCAAAGTTAA
13444648 AAA
1 AAA
13444651 TTACTAGGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
32 24 0.43
33 32 0.57
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (33 bp):
AAAATAAAAGTGACTAAACTAAACCAAAGTTAA
Found at i:13444629 original size:33 final size:32
Alignment explanation
Indices: 13444550--13444632 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
13444540 GTTAAGGTTG
** *
13444550 AAAATAAAAGTGACTGGACTGAACCAAAGTAA
1 AAAATAAAAGTGACTAAACTAAACCAAAGTAA
* *
13444582 AAAATGAAAGTGACTAAACTAAACCAAGGTTAA
1 AAAATAAAAGTGACTAAACTAAACCAAAG-TAA
*
13444615 AAAATAAAAATGACTAAA
1 AAAATAAAAGTGACTAAA
13444633 ATGAACTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 24 0.56
33 19 0.44
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (32 bp):
AAAATAAAAGTGACTAAACTAAACCAAAGTAA
Found at i:13444703 original size:59 final size:58
Alignment explanation
Indices: 13444640--13444861 Score: 225
Period size: 59 Copynumber: 3.8 Consensus size: 58
13444630 AAAATGAACT
* * * * * *
13444640 AAAGTTGAAAATTACTAGGTTTAAGCCTATGTCGAAAATGAAAATGATCGGACTGGGCC
1 AAAGTTAAAAATTACTAGGTCTAAGCCTAAGTCAAAAATGAAAATGA-CAGACTAGGCC
* **
13444699 AAAGTTAAAAATAACTAGGTCTAAGCCTAAGTCAAAAATGAAAATGACCAGACTAAACC
1 AAAGTTAAAAATTACTAGGTCTAAGCCTAAGTCAAAAATGAAAATGA-CAGACTAGGCC
* * * *
13444758 AAAG-TAAAAAATAGTTAGGTTTGAA-CCTAAGTCGAAAATGAAAATGACTAGACTAGGCC
1 AAAGTTAAAAATTA-CTAGGTCT-AAGCCTAAGTCAAAAATGAAAATGAC-AGACTAGGCC
* * *
13444817 -AAGATAAAAAATGACTAGGTCTGAGCCTAAGTCAAAAATGAAAAT
1 AAAG-TTAAAAATTACTAGGTCTAAGCCTAAGTCAAAAATGAAAAT
13444862 CAAACATTTT
Statistics
Matches: 133, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
58 12 0.09
59 113 0.85
60 8 0.06
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.22
Consensus pattern (58 bp):
AAAGTTAAAAATTACTAGGTCTAAGCCTAAGTCAAAAATGAAAATGACAGACTAGGCC
Found at i:13445166 original size:23 final size:23
Alignment explanation
Indices: 13445134--13445194 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
13445124 GTATGTAATG
*
13445134 AATGTCATGAATGCAATGCATGA
1 AATGTAATGAATGCAATGCATGA
13445157 AATGTAATGAATGCAATGCATGA
1 AATGTAATGAATGCAATGCATGA
13445180 AATGTAATGAATGCA
1 AATGTAATGAATGCA
13445195 TCCATAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (23 bp):
AATGTAATGAATGCAATGCATGA
Found at i:13445195 original size:18 final size:18
Alignment explanation
Indices: 13445126--13445192 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
13445116 TTTGCAATGT
*
13445126 ATGTAATGAATGTCATGA
1 ATGTAATGAATGACATGA
* * *
13445144 ATGCAATGCATGAAATGTA
1 ATGTAATGAATGACATG-A
13445163 ATG-AATGCAATG-CATGAA
1 ATGTAATG-AATGACATG-A
13445181 ATGTAATGAATG
1 ATGTAATGAATG
13445193 CATCCATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
18 28 0.72
19 11 0.28
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.28
Consensus pattern (18 bp):
ATGTAATGAATGACATGA
Found at i:13445866 original size:14 final size:14
Alignment explanation
Indices: 13445843--13445881 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
13445833 AAGTCCTTCT
13445843 TTTTTCTCATTTTCA
1 TTTTT-TCATTTTCA
13445858 TTTTTTCATTTTTCA
1 TTTTTTCA-TTTTCA
13445873 -TTTTTCATT
1 TTTTTTCATT
13445882 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 10 0.43
15 11 0.48
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTCATTTTCA
Found at i:13445870 original size:15 final size:15
Alignment explanation
Indices: 13445852--13445908 Score: 73
Period size: 15 Copynumber: 3.7 Consensus size: 15
13445842 TTTTTTCTCA
13445852 TTTTCATTTTTTCA-T
1 TTTTCA-TTTTTCATT
13445867 TTTTCATTTTTCATT
1 TTTTCATTTTTCATT
13445882 ATTTT-ATTTTTCACTT
1 -TTTTCATTTTTCA-TT
13445898 TTTTCATTTTT
1 TTTTCATTTTT
13445909 TTTCATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.18
15 19 0.50
16 12 0.32
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCATTTTTCATT
Found at i:13445901 original size:10 final size:9
Alignment explanation
Indices: 13445852--13445918 Score: 51
Period size: 9 Copynumber: 8.2 Consensus size: 9
13445842 TTTTTTCTCA
13445852 TTTTCA-TT
1 TTTTCATTT
13445860 TTTTCA--T
1 TTTTCATTT
13445867 TTTTCA--T
1 TTTTCATTT
*
13445874 TTTTCATTA
1 TTTTCATTT
13445883 TTTT-A--T
1 TTTTCATTT
*
13445889 TTTTCACTT
1 TTTTCATTT
13445898 TTTTCATTTT
1 TTTTCA-TTT
13445908 TTTTCATTT
1 TTTTCATTT
13445917 TT
1 TT
13445919 GCTTTACTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
6 4 0.08
7 15 0.30
8 7 0.14
9 16 0.32
10 8 0.16
ACGTcount: A:0.13, C:0.12, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTCATTT
Found at i:13445917 original size:31 final size:31
Alignment explanation
Indices: 13445842--13445917 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
13445832 TAAGTCCTTC
*
13445842 TTTTTTCTCATTTTCATTTTTTCATTTTTCA
1 TTTTTTTTCATTTTCATTTTTTCATTTTTCA
*
13445873 TTTTTCATT-ATTTT-A-TTTTTCACTTTTTTCA
1 TTTTT-TTTCATTTTCATTTTTTCA--TTTTTCA
13445904 TTTTTTTTCATTTT
1 TTTTTTTTCATTTT
13445918 TGCTTTACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 7 0.18
30 3 0.08
31 27 0.71
32 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (31 bp):
TTTTTTTTCATTTTCATTTTTTCATTTTTCA
Found at i:13445918 original size:8 final size:8
Alignment explanation
Indices: 13445852--13445909 Score: 70
Period size: 7 Copynumber: 7.5 Consensus size: 8
13445842 TTTTTTCTCA
13445852 TTTTCATT
1 TTTTCATT
13445860 TTTTCA-T
1 TTTTCATT
13445867 TTTTCA-T
1 TTTTCATT
13445874 TTTTCATT
1 TTTTCATT
13445882 ATTTT-A-T
1 -TTTTCATT
13445889 TTTTCACTT
1 TTTTCA-TT
13445898 TTTTCATT
1 TTTTCATT
13445906 TTTT
1 TTTT
13445910 TTCATTTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.09
7 16 0.36
8 14 0.31
9 11 0.24
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTCATT
Found at i:13446814 original size:10 final size:10
Alignment explanation
Indices: 13446799--13446825 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
13446789 AAAAAAGAAT
13446799 ATGTAATGAA
1 ATGTAATGAA
13446809 ATGTAATGAA
1 ATGTAATGAA
13446819 ATGTAAT
1 ATGTAAT
13446826 TGCCATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (10 bp):
ATGTAATGAA
Found at i:13450595 original size:12 final size:12
Alignment explanation
Indices: 13450578--13450602 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13450568 TTTTATCAAA
13450578 TTTATTTAAATT
1 TTTATTTAAATT
13450590 TTTATTTAAATT
1 TTTATTTAAATT
13450602 T
1 T
13450603 AAAAATAAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTAAATT
Found at i:13450910 original size:24 final size:23
Alignment explanation
Indices: 13450862--13450930 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
13450852 AATATATCAC
* *
13450862 AAATAAAT-AAATAATAATAATT
1 AAATAAATAAAATAATAAAAAAT
*
13450884 AAATAAATAAAACTCATAAAAAAT
1 AAATAAATAAAA-TAATAAAAAAT
* *
13450908 AAATAAACAAAATGAAGAAAAAA
1 AAATAAATAAAAT-AATAAAAAA
13450931 AATAATACCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 8 0.21
23 4 0.11
24 26 0.68
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.20
Consensus pattern (23 bp):
AAATAAATAAAATAATAAAAAAT
Found at i:13456479 original size:6 final size:6
Alignment explanation
Indices: 13456459--13456522 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
13456449 TTTTAAAATT
* *
13456459 TTTATA -TTATA TTTATC TTTATA TTTATA TTTA-A TGATTAT- TATATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T--TTATA TTTATA
* *
13456506 TTTATC TTTATT TTTAT
1 TTTATA TTTATA TTTAT
13456523 CATTGTGAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
5 10 0.21
6 33 0.70
7 4 0.09
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:13456480 original size:12 final size:12
Alignment explanation
Indices: 13456465--13456523 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
13456455 AATTTTTATA
13456465 TTATATTTATCT
1 TTATATTTATCT
*
13456477 TTATATTTATAT
1 TTATATTTATCT
13456489 TTA-ATGATTAT-T
1 TTATAT--TTATCT
*
13456501 ATATATTTATCT
1 TTATATTTATCT
*
13456513 TTATTTTTATC
1 TTATATTTATC
13456524 ATTGTGAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 6 0.15
12 27 0.69
13 6 0.15
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (12 bp):
TTATATTTATCT
Found at i:13456488 original size:18 final size:18
Alignment explanation
Indices: 13456459--13456522 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
13456449 TTTTAAAATT
13456459 TTTATA-TTATATTTATC
1 TTTATATTTATATTTATC
*
13456476 TTTATATTTATATTTAATG
1 TTTATATTTATATTT-ATC
* *
13456495 ATTAT-TATATATTTATC
1 TTTATATTTATATTTATC
*
13456512 TTTATTTTTAT
1 TTTATATTTAT
13456523 CATTGTGAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 12 0.32
18 20 0.53
19 6 0.16
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTATATTTATATTTATC
Found at i:13456718 original size:22 final size:22
Alignment explanation
Indices: 13456685--13456732 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
13456675 ACATATTAAT
13456685 TTTA-ATTAATTTAA-AATAATAA
1 TTTATATTAATTTAATAA-AA-AA
13456707 TTTATATT-ATTTAATAAAAAA
1 TTTATATTAATTTAATAAAAAA
13456728 TTTAT
1 TTTAT
13456733 TAAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.29
22 12 0.50
23 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATATTAATTTAATAAAAAA
Found at i:13456728 original size:27 final size:27
Alignment explanation
Indices: 13456654--13456728 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
13456644 AAATATATAT
* *
13456654 TAATATATATT-TTTAATAAAAACATAT
1 TAATTTATATTATTTAATAAAAA-ATAA
**
13456681 TAATTT-TA--A-TTAATTTAAAATAA
1 TAATTTATATTATTTAATAAAAAATAA
13456704 TAATTTATATTATTTAATAAAAAAT
1 TAATTTATATTATTTAATAAAAAAT
13456729 TTATTAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
23 9 0.24
24 10 0.27
26 3 0.08
27 15 0.41
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATTTATATTATTTAATAAAAAATAA
Found at i:13458699 original size:33 final size:33
Alignment explanation
Indices: 13458662--13458726 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
13458652 TTTTTAATTT
13458662 ATATATATATGAATTAATTTATATAT-AATTCAC
1 ATATATATAT-AATTAATTTATATATAAATTCAC
*
13458695 ATATATATATAATTTATTTATATATAAATTCA
1 ATATATATATAATTAATTTATATATAAATTCA
13458727 GATCAGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (33 bp):
ATATATATATAATTAATTTATATATAAATTCAC
Found at i:13459374 original size:2 final size:2
Alignment explanation
Indices: 13459367--13459391 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13459357 TCAGATATTT
13459367 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
13459392 GTGTATAATA
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:13459654 original size:12 final size:12
Alignment explanation
Indices: 13459630--13459662 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13459620 CCAACCAGGA
*
13459630 TTTTGTTTT-TT
1 TTTTTTTTTGTT
13459641 TTTTTTTTTGTT
1 TTTTTTTTTGTT
13459653 TTTTTTTTTG
1 TTTTTTTTTG
13459663 GAAAAGGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:13459654 original size:15 final size:16
Alignment explanation
Indices: 13459630--13459661 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13459620 CCAACCAGGA
13459630 TTTTGTTTTTTTTTTT
1 TTTTGTTTTTTTTTTT
13459646 TTTTGTTTTTTTTTTT
1 TTTTGTTTTTTTTTTT
13459662 GGAAAAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (16 bp):
TTTTGTTTTTTTTTTT
Found at i:13460319 original size:35 final size:35
Alignment explanation
Indices: 13460273--13460342 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
13460263 AAAGAGAGGA
13460273 GAATAGTGTACTTGATGCATATTTTATGTATATAC
1 GAATAGTGTACTTGATGCATATTTTATGTATATAC
13460308 GAATAGTGTACTTGATGCATATTTTATGTATATAC
1 GAATAGTGTACTTGATGCATATTTTATGTATATAC
13460343 TTGTATCCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (35 bp):
GAATAGTGTACTTGATGCATATTTTATGTATATAC
Found at i:13466063 original size:22 final size:23
Alignment explanation
Indices: 13466032--13466075 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
13466022 TTGTTGATGA
13466032 AAAAGGTG-TTATGAGAAATTTTT
1 AAAAGGTGTTTAT-AGAAATTTTT
13466055 AAAA-GTGTTTATAGAAATTTT
1 AAAAGGTGTTTATAGAAATTTT
13466076 CTTTCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (23 bp):
AAAAGGTGTTTATAGAAATTTTT
Found at i:13466724 original size:59 final size:58
Alignment explanation
Indices: 13466615--13467071 Score: 566
Period size: 59 Copynumber: 7.7 Consensus size: 58
13466605 TTTTTTGTAG
* *
13466615 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAA--TATTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATTTTTTTTTTG-AAATTTATTTCTAA
* * *
13466672 GGAAAATTGATACCTTCGACTTTTCC-CTAAAAATTTTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAA-TTTTTTTTTTGAAATTTATTTCTAA
* * * *
13466731 GGAAAATTGATACTTTTAACTTTTCCCCAAAAA-TATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAATTTATTTCTAA
* *
13466788 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAA-TTT-ATTTCTAA
** *
13466848 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTCAAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTTT-TGAAATTTATTTCTAA
* *
13466908 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAACTTTGATCT-TAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAA-TTT-ATTTCTAA
* * *
13466967 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTCTTTTTTGAAAATGTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTG-AAATTTATTTCTAA
*
13467026 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTCTTTTTTT
1 GGAAAATTGATACTTTCAACTTTT-CCTCAAAA-ATTT-TTTTTTT
13467072 TTGGAAAATT
Statistics
Matches: 350, Mismatches: 33, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
56 7 0.02
57 75 0.21
58 16 0.05
59 127 0.36
60 103 0.29
61 13 0.04
62 9 0.03
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAATTTATTTCTAA
Found at i:13466940 original size:27 final size:27
Alignment explanation
Indices: 13466910--13467000 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
13466900 ATTTTTAAGG
13466910 AAAATTGATACTTTCAACTTTTCCTCA
1 AAAATTGATACTTTCAACTTTTCCTCA
* ** * * *
13466937 AAAATAT-TTTTTTTGAAACTTTGATCTTAA
1 AAAAT-TGATACTTT-CAACTTT--TCCTCA
13466967 GGAAAATTGATACTTTCAACTTTTCCTCA
1 --AAAATTGATACTTTCAACTTTTCCTCA
13466996 AAAAT
1 AAAAT
13467001 CTCTTTTTTG
Statistics
Matches: 45, Mismatches: 12, Indels: 14
0.63 0.17 0.20
Matches are distributed among these distances:
27 14 0.31
28 7 0.16
29 4 0.09
30 4 0.09
31 7 0.16
32 9 0.20
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTCCTCA
Found at i:13467127 original size:10 final size:10
Alignment explanation
Indices: 13467105--13467163 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
13467095 AAGAAAATAG
13467105 AATAATAAAA
1 AATAATAAAA
13467115 AAT-ATAAATA
1 AATAATAAA-A
13467125 AATAATAAAA
1 AATAATAAAA
13467135 AATAA-AGAAA
1 AATAATA-AAA
*
13467145 AGTAA-AAAA
1 AATAATAAAA
13467154 AA-AATAAAA
1 AATAATAAAA
13467163 A
1 A
13467164 TAAAACTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
8 2 0.05
9 15 0.35
10 21 0.49
11 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (10 bp):
AATAATAAAA
Found at i:13467152 original size:17 final size:17
Alignment explanation
Indices: 13467098--13467168 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
13467088 TTATTTGAAG
* *
13467098 AAAATAGAATAATAAAA
1 AAAAAAGAAAAATAAAA
*
13467115 AATATAAATAAATAATAAAA
1 AA-A-AAAGAAA-AATAAAA
* *
13467135 AATAAAGAAAAGTAAAA
1 AAAAAAGAAAAATAAAA
*
13467152 AAAAAATAAAAATAAAA
1 AAAAAAGAAAAATAAAA
13467169 CTAAGATAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
17 22 0.52
18 7 0.17
19 4 0.10
20 9 0.21
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAAAAGAAAAATAAAA
Found at i:13467157 original size:6 final size:6
Alignment explanation
Indices: 13467098--13467168 Score: 56
Period size: 6 Copynumber: 11.5 Consensus size: 6
13467088 TTATTTGAAG
* * * *
13467098 AAAATA GAATAATAA AAAATA TAAATA AATAATA AAAA-A TAAAGA AAAGTA
1 AAAATA -AA-AAT-A AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA
13467149 AAAA-A AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAA
13467169 CTAAGATAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
5 9 0.17
6 26 0.50
7 11 0.21
8 5 0.10
9 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:13467179 original size:26 final size:24
Alignment explanation
Indices: 13467105--13467226 Score: 75
Period size: 21 Copynumber: 5.4 Consensus size: 24
13467095 AAGAAAATAG
*
13467105 AATAATAAAAAATATAAAT-AAA-T
1 AATAA-AAAAAATAAAAATAAAACT
* *
13467128 AAT--AAAAAAT--AAAGAAAAGT
1 AATAAAAAAAATAAAAATAAAACT
13467148 AA-AAAAAAAATAAAAATAAAACT
1 AATAAAAAAAATAAAAATAAAACT
* * * *
13467171 AAGATAAAAGAATATTAAATAAACCT
1 AATA-AAAAAAATA-AAAATAAAACT
*
13467197 AATAAAAAAAAT--AAAT-AAACA
1 AATAAAAAAAATAAAAATAAAACT
13467218 AATAAAAAA
1 AATAAAAAA
13467227 CATTCAAAGA
Statistics
Matches: 80, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.04
19 3 0.04
20 10 0.12
21 19 0.24
22 4 0.05
23 13 0.16
24 1 0.01
25 15 0.19
26 12 0.15
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.18
Consensus pattern (24 bp):
AATAAAAAAAATAAAAATAAAACT
Found at i:13468056 original size:6 final size:6
Alignment explanation
Indices: 13468045--13468077 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13468035 CTAGCCCTCC
*
13468045 AAAATA AAAATA AAAATA ATAATA AAAA-A AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
13468078 CCAGATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:13468197 original size:14 final size:17
Alignment explanation
Indices: 13468165--13468201 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
13468155 TAGATAAGTA
13468165 AAAATACAAAAATGAAT
1 AAAATACAAAAATGAAT
13468182 AAAATA-AAAAA-G-AT
1 AAAATACAAAAATGAAT
13468196 AAAATA
1 AAAATA
13468202 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 5 0.25
17 6 0.30
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAATACAAAAATGAAT
Found at i:13468306 original size:12 final size:12
Alignment explanation
Indices: 13468223--13468311 Score: 53
Period size: 12 Copynumber: 7.4 Consensus size: 12
13468213 ACATATTAGT
13468223 AATAATAC-ATA
1 AATAATACAATA
* *
13468234 AATATTAACAAAA
1 AATAAT-ACAATA
13468247 AATAAATA-AATA
1 AAT-AATACAATA
13468259 AATATATAC-ATA
1 AATA-ATACAATA
*
13468271 TATTAATAC-AT-
1 -AATAATACAATA
*
13468282 AATAATAATAATA
1 AATAAT-ACAATA
13468295 AATAATACAATA
1 AATAATACAATA
*
13468307 CATAA
1 AATAA
13468312 AATACAAAAG
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
10 5 0.08
11 7 0.12
12 31 0.52
13 15 0.25
14 2 0.03
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATACAATA
Found at i:13468311 original size:16 final size:15
Alignment explanation
Indices: 13468248--13468312 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
13468238 TTAACAAAAA
*
13468248 ATAAATAAATAAATAT
1 ATAAAT-AATAAATAC
* *
13468264 ATACATATATTAATAC
1 ATAAATA-ATAAATAC
13468280 AT-AATAAT-AATA-
1 ATAAATAATAAATAC
13468292 ATAAATAATACAATAC
1 ATAAATAATA-AATAC
13468308 ATAAA
1 ATAAA
13468313 ATACAAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 2 0.05
13 10 0.25
14 2 0.05
15 8 0.20
16 18 0.45
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAATAATAAATAC
Found at i:13468314 original size:65 final size:63
Alignment explanation
Indices: 13468180--13468322 Score: 155
Period size: 65 Copynumber: 2.2 Consensus size: 63
13468170 ACAAAAATGA
* * * * * *
13468180 ATAAAATAAAAAAGATAAAATATATATATATATACATATTAGTAATAATACATAAATATTAAC
1 ATAAAATAAAAAAGATAAAATATACATATATATACATAATAATAATAATAAATAAACAATAAC
* *
13468243 AAAAAATAAATAA-ATAAATATATACATATATTAATACATAATAATAATAATAAATAATACAAT-
1 ATAAAATAAAAAAGATAAA-ATATACATATA-T-ATACATAATAATAATAATAAATAA-ACAATA
13468306 AC
62 AC
*
13468308 ATAAAATACAAAAGA
1 ATAAAATAAAAAAGA
13468323 AGAAGAAAAG
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
62 5 0.08
63 21 0.33
64 1 0.02
65 33 0.52
66 4 0.06
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.29
Consensus pattern (63 bp):
ATAAAATAAAAAAGATAAAATATACATATATATACATAATAATAATAATAAATAAACAATAAC
Found at i:13471062 original size:15 final size:13
Alignment explanation
Indices: 13471042--13471079 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
13471032 CTCCAATTTG
13471042 TTATTATTTTTAT
1 TTATTATTTTTAT
13471055 CATTATTA-TTTTAT
1 --TTATTATTTTTAT
13471069 TTATTATTTTT
1 TTATTATTTTT
13471080 TCTCTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 6 0.27
15 6 0.27
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTATTTTTAT
Found at i:13472350 original size:68 final size:68
Alignment explanation
Indices: 13472252--13472392 Score: 187
Period size: 68 Copynumber: 2.1 Consensus size: 68
13472242 TCAGAAAGAT
* * *
13472252 ATTTTCGGATAATTGTAATACTTTTAGAAAATGCATTTTC-GAATAATTGCAATATTTTTCAGAA
1 ATTTTCGGATAATTGCAATACTTTTAGAAAATGCATTTTCAG-ATAATTACAATACTTTTCAGAA
13472316 ATGC
65 ATGC
* * * *
13472320 ATTTTCGGATAATTGCAAT-CTTTTTCGAAAATGCATTTTCAGATAATTATAATACTTTTCGGAG
1 ATTTTCGGATAATTGCAATAC-TTTTAGAAAATGCATTTTCAGATAATTACAATACTTTTCAGAA
13472384 ATGC
65 ATGC
13472388 ATTTT
1 ATTTT
13472393 TAGATATAGT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 1 0.02
68 62 0.97
69 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (68 bp):
ATTTTCGGATAATTGCAATACTTTTAGAAAATGCATTTTCAGATAATTACAATACTTTTCAGAAA
TGC
Found at i:13472398 original size:34 final size:34
Alignment explanation
Indices: 13472252--13472398 Score: 156
Period size: 34 Copynumber: 4.3 Consensus size: 34
13472242 TCAGAAAGAT
* * *
13472252 ATTTTCGGATAATTGTAATACTTTTAGAAAATGC
1 ATTTTCAGATAATTGCAATACTTTTCGAAAATGC
*
13472286 ATTTTC-GAATAATTGCAATATTTTTC-AGAAATGC
1 ATTTTCAG-ATAATTGCAATACTTTTCGA-AAATGC
*
13472320 ATTTTCGGATAATTGCAAT-CTTTTTCGAAAATGC
1 ATTTTCAGATAATTGCAATAC-TTTTCGAAAATGC
** * *
13472354 ATTTTCAGATAATTATAATACTTTTCGGAGATGC
1 ATTTTCAGATAATTGCAATACTTTTCGAAAATGC
*
13472388 ATTTTTAGATA
1 ATTTTCAGATA
13472399 TAGTGAAGAT
Statistics
Matches: 97, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
33 2 0.02
34 92 0.95
35 3 0.03
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (34 bp):
ATTTTCAGATAATTGCAATACTTTTCGAAAATGC
Found at i:13474848 original size:19 final size:20
Alignment explanation
Indices: 13474826--13474864 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
13474816 GAAAAAAAGT
13474826 GGAAAAAAAAAACAA-AAAA
1 GGAAAAAAAAAACAAGAAAA
13474845 GGAAAAAAAAAACAAGAAAA
1 GGAAAAAAAAAACAAGAAAA
13474865 AAGGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (20 bp):
GGAAAAAAAAAACAAGAAAA
Found at i:13474872 original size:19 final size:18
Alignment explanation
Indices: 13474829--13474916 Score: 59
Period size: 22 Copynumber: 4.3 Consensus size: 18
13474819 AAAAAGTGGA
*
13474829 AAAAAAAAACAAAAAAGG
1 AAAAAAAAAGAAAAAAGG
13474847 AAAAAAAAAACAAGAAAAAAGG
1 ---AAAAAAA-AAGAAAAAAGG
* *
13474869 AAAAGAGAAGACAAAAAGTG
1 AAAAAAAAAGA-AAAAAG-G
13474889 AAATTGAAAAAAGAAAAATAGG
1 AAA---AAAAAAGAAAAA-AGG
13474911 AAAAAA
1 AAAAAA
13474917 TTACTTTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
18 4 0.07
19 14 0.25
20 4 0.07
21 7 0.13
22 18 0.33
23 8 0.15
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAGG
Found at i:13474882 original size:23 final size:22
Alignment explanation
Indices: 13474828--13474872 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
13474818 AAAAAAGTGG
*
13474828 AAAAAAAA-AACAAAAAAGGAA
1 AAAAAAAACAAGAAAAAAGGAA
13474849 AAAAAAAACAAGAAAAAAGGAA
1 AAAAAAAACAAGAAAAAAGGAA
13474871 AA
1 AA
13474873 GAGAAGACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.00
Consensus pattern (22 bp):
AAAAAAAACAAGAAAAAAGGAA
Found at i:13475203 original size:16 final size:15
Alignment explanation
Indices: 13475168--13475224 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
13475158 AATGAGAAAA
13475168 AAAAAAT-AAAGAGAG
1 AAAAAATAAAAGA-AG
*
13475183 CAAAAAATAAAATAAGG
1 -AAAAAATAAAAGAA-G
*
13475200 AAAAAACAAAAGAAG
1 AAAAAATAAAAGAAG
13475215 -AAAAATAAAA
1 AAAAAATAAAA
13475225 AAATTGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 20 0.57
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.07
Consensus pattern (15 bp):
AAAAAATAAAAGAAG
Found at i:13475308 original size:2 final size:2
Alignment explanation
Indices: 13475301--13475329 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13475291 TGTAAATCTA
13475301 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13475330 TAATAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:13478539 original size:16 final size:16
Alignment explanation
Indices: 13478501--13478541 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
13478491 AAATGTAAAA
13478501 ATATATTTTTTAGCTT
1 ATATATTTTTTAGCTT
* * *
13478517 TTTTATTTTTTATCTT
1 ATATATTTTTTAGCTT
13478533 ATATATTTT
1 ATATATTTT
13478542 GATAATTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (16 bp):
ATATATTTTTTAGCTT
Found at i:13479522 original size:2 final size:2
Alignment explanation
Indices: 13479510--13479568 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
13479500 ACGACGCTCT
*
13479510 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13479551 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
13479569 GAAAGTATGT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:13480071 original size:29 final size:29
Alignment explanation
Indices: 13480029--13480096 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
13480019 AAAAAATTGA
* *
13480029 TTAAATGTTAAATG-ATTGAAAACAAATAT
1 TTAAATATTTAATGAATT-AAAACAAATAT
*
13480058 TTAAATATTTAATGAAATTAAAATAAATAT
1 TTAAATATTTAATG-AATTAAAACAAATAT
13480088 TTAAA-ATTT
1 TTAAATATTT
13480097 TGATTAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.47
30 15 0.44
31 3 0.09
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (29 bp):
TTAAATATTTAATGAATTAAAACAAATAT
Found at i:13480088 original size:30 final size:30
Alignment explanation
Indices: 13480047--13480111 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
13480037 TAAATGATTG
*
13480047 AAAACAAATATTT-AAATATTTAATGAAATT
1 AAAATAAATATTTAAAAT-TTTAATGAAATT
* *
13480077 AAAATAAATATTTAAAATTTTGATTAAATT
1 AAAATAAATATTTAAAATTTTAATGAAATT
13480107 AAAAT
1 AAAAT
13480112 TGCTTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATAAATATTTAAAATTTTAATGAAATT
Found at i:13480346 original size:3 final size:3
Alignment explanation
Indices: 13480338--13480428 Score: 100
Period size: 3 Copynumber: 31.7 Consensus size: 3
13480328 TTTTTAGGTG
* ** *
13480338 TAT TAT TAT TAT TAT TAT TGT GGT TGT TAT TAT TAT TAT TA- TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
13480384 TAT TA- TAT TA- TAT TAC AAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
13480429 ATCAGTGTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
2 8 0.11
3 68 0.89
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:13480718 original size:22 final size:24
Alignment explanation
Indices: 13480677--13480734 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
13480667 AGAAAGGCAC
13480677 GAGTTAATTTTTGAAGAAAGA-AT
1 GAGTTAATTTTTGAAGAAAGATAT
* *
13480700 GAGTGAATTTTTGCA-AAAGATAT
1 GAGTTAATTTTTGAAGAAAGATAT
13480723 GAGTTAATTTTT
1 GAGTTAATTTTT
13480735 AGGAGGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.40
Consensus pattern (24 bp):
GAGTTAATTTTTGAAGAAAGATAT
Found at i:13480820 original size:20 final size:21
Alignment explanation
Indices: 13480797--13480844 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
13480787 ATTTATTTGG
* *
13480797 GTTTGAATTTTTAGATTT-CA
1 GTTTGAAGTTTTAGATTTGAA
*
13480817 GTTTGAAGTTTTGGATTTGAA
1 GTTTGAAGTTTTAGATTTGAA
13480838 GTTTGAA
1 GTTTGAA
13480845 AATATGAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.50
Consensus pattern (21 bp):
GTTTGAAGTTTTAGATTTGAA
Found at i:13481179 original size:13 final size:13
Alignment explanation
Indices: 13481177--13481225 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
13481167 TCTATTTTAT
13481177 TTTTATTTTTCTA
1 TTTTATTTTTCTA
*
13481190 -TTTATTTTTTGCCA
1 TTTTA-TTTTT-CTA
*
13481204 TTTTATTTTTTTA
1 TTTTATTTTTCTA
13481217 TTTTATTTT
1 TTTTATTTT
13481226 ATTGATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.13
13 15 0.50
14 7 0.23
15 4 0.13
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTCTA
Found at i:13481185 original size:19 final size:17
Alignment explanation
Indices: 13481158--13481199 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
13481148 CGATCCCATG
13481158 TTTTTTTTTTCTATTTTA
1 TTTTTTTTTTCTA-TTTA
13481176 TTTTTATTTTTCTATTTA
1 TTTTT-TTTTTCTATTTA
13481194 TTTTTT
1 TTTTTT
13481200 GCCATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 8 0.35
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTTCTATTTA
Found at i:13481227 original size:33 final size:33
Alignment explanation
Indices: 13481158--13481228 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
13481148 CGATCCCATG
*
13481158 TTTT-TTTTTTCTATTTTATTTTTATTTTTCTA
1 TTTTATTTTTTCCATTTTATTTTTATTTTTCTA
13481190 -TTTATTTTTTGCCATTTTATTTTT-TTATTT-TA
1 TTTTATTTTTT-CCATTTTATTTTTATT-TTTCTA
13481222 TTTTATT
1 TTTTATT
13481229 GATTTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
31 3 0.09
32 10 0.29
33 21 0.62
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.79
Consensus pattern (33 bp):
TTTTATTTTTTCCATTTTATTTTTATTTTTCTA
Found at i:13481235 original size:28 final size:27
Alignment explanation
Indices: 13481175--13481235 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 27
13481165 TTTCTATTTT
13481175 ATTTTTATTTTTCTATTTATTTTTTGCC
1 ATTTTTATTTTTCTATTTATTTTTTG-C
*
13481203 A-TTTTATTTTTTTATTTTATTTTATTG-
1 ATTTTTATTTTTCTA-TTTATTTT-TTGC
13481230 ATTTTT
1 ATTTTT
13481236 TAAATTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 13 0.45
28 13 0.45
29 3 0.10
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.75
Consensus pattern (27 bp):
ATTTTTATTTTTCTATTTATTTTTTGC
Found at i:13482235 original size:22 final size:22
Alignment explanation
Indices: 13482194--13482235 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13482184 AAATCTAAGA
* * *
13482194 TTTTTCCTTTTTTTTTTTTTTC
1 TTTTTCCTTGTTTATATTTTTC
13482216 TTTTTCCTTGTTTATATTTT
1 TTTTTCCTTGTTTATATTTT
13482236 GTTTAGTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTTCCTTGTTTATATTTTTC
Found at i:13487394 original size:92 final size:91
Alignment explanation
Indices: 13487237--13487414 Score: 196
Period size: 92 Copynumber: 1.9 Consensus size: 91
13487227 TGTTAGCTAG
* * * * *
13487237 AATCTCCTTGTTGTCACTACTATTAATTCTAAATCACACTGTAATGCTTTATTAAAAGTGTTGAA
1 AATCTCCTTATTGTCACTACTATTAATTCTAAACCACACTGCAAAGCTTTATTAAAAGTGCTGAA
*
13487302 TCAGGCTTATGTGGGACATAAGCCAA
66 TCAGGCTTATGTGGCACATAAGCCAA
** * * * *
13487328 AATCTCCTTATTGTCACTGTTGTTGAATTCTAAACCACATTGCAAAGTTTTATT-GAAGATGCTG
1 AATCTCCTTATTGTCACTACTATT-AATTCTAAACCACACTGCAAAGCTTTATTAAAAG-TGCTG
** *
13487392 AATTGGGCTTATTTGGCACATAA
64 AATCAGGCTTATGTGGCACATAA
13487415 TATGTCTATA
Statistics
Matches: 70, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
91 23 0.33
92 47 0.67
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (91 bp):
AATCTCCTTATTGTCACTACTATTAATTCTAAACCACACTGCAAAGCTTTATTAAAAGTGCTGAA
TCAGGCTTATGTGGCACATAAGCCAA
Found at i:13492459 original size:16 final size:16
Alignment explanation
Indices: 13492440--13492493 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
13492430 TAAAAATATA
*
13492440 AAAAATTATATATATT
1 AAAAATTATATAAATT
13492456 -AAAATT-TA-AAATT
1 AAAAATTATATAAATT
*
13492469 TAAAATTAT-TAAATAT
1 AAAAATTATATAAAT-T
13492485 AAAAATTAT
1 AAAAATTAT
13492494 TACATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 4 0.12
14 8 0.25
15 11 0.34
16 9 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAATTATATAAATT
Found at i:13492489 original size:23 final size:23
Alignment explanation
Indices: 13492433--13492491 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
13492423 GCTGCCATAA
* *
13492433 AAATATAAAAAATTATATATATT
1 AAATATAAAAATTTAAATATATT
*
13492456 AAA-ATTTAAAATTTAAA-ATTATT
1 AAATA-TAAAAATTTAAATA-TATT
13492479 AAATATAAAAATT
1 AAATATAAAAATT
13492492 ATTACATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
22 2 0.07
23 26 0.90
24 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATATAAAAATTTAAATATATT
Found at i:13492494 original size:16 final size:16
Alignment explanation
Indices: 13492433--13492495 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
13492423 GCTGCCATAA
13492433 AAATATAAAAAATTA-T
1 AAATAT-AAAAATTATT
* * *
13492449 ATATATTAAAATT-TA
1 AAATATAAAAATTATT
*
13492464 AAAT-TTAAAATTATT
1 AAATATAAAAATTATT
13492479 AAATATAAAAATTATT
1 AAATATAAAAATTATT
13492495 A
1 A
13492496 CATAAATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 8 0.21
15 14 0.37
16 16 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATAAAAATTATT
Found at i:13493380 original size:132 final size:129
Alignment explanation
Indices: 13493203--13493585 Score: 371
Period size: 131 Copynumber: 2.9 Consensus size: 129
13493193 GCAAAATTTC
* * *
13493203 ATGAAGCCAATTGTAAGGGTACTTTAGTAA-ATAATATATAGTTAATTTTATATTATATTCAAAA
1 ATGAAG-CAATAGTAAGGGTATTTTAGTAATATAATATATAATTAATTTTATATTATATT-AAAA
*
13493267 TTTAATATGTAATTTAAATAAGGATATTATAATAAATTCTAAATAAAATGCCACAATATCAAATT
64 TTTAATATGTAATTT-AATAAGGAAATTATAATAAATT-TAAATAAAATGCCACAATATCAAATT
*
13493332 TTT
127 TAT
* * *
13493335 ATGAAGCAA-AGTCAAGGGTATTTTAGTAATTTAATATATAATTAATTTTATATTGTGTTAAAAT
1 ATGAAGCAATAGT-AAGGGTATTTTAGTAATATAATATATAATTAATTTTATATTATATTAAAAT
* * *** * *
13493399 TTCATATATAATTTAAT-AGGAGAATTATAATAATTATTTTTTTAAAAATACCAC-ATGTCAAAT
65 TTAATATGTAATTTAATAAGGA-AATTATAATAA--ATTTAAAT-AAAATGCCACAATATCAAAT
13493462 TTAT
126 TTAT
* ** * * *
13493466 ATGAAGCAATGGTAATCGTATTTTAGTAATATAATATGTGATTAGTTTTATATTATATTAAAATT
1 ATGAAGCAATAGTAAGGGTATTTTAGTAATATAATATATAATTAATTTTATATTATATTAAAATT
* * * * *
13493531 TGATACGTAATCTAATAAGAAGAGATTATAGGT-AATTTAAAAATAAAATGCCACA
66 TAATATGTAATTTAATAAG--GAAATTATA-ATAAATTT--AAATAAAATGCCACA
13493586 TGTTCAACTT
Statistics
Matches: 203, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
129 4 0.02
130 15 0.07
131 117 0.58
132 56 0.28
133 8 0.04
134 3 0.01
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (129 bp):
ATGAAGCAATAGTAAGGGTATTTTAGTAATATAATATATAATTAATTTTATATTATATTAAAATT
TAATATGTAATTTAATAAGGAAATTATAATAAATTTAAATAAAATGCCACAATATCAAATTTAT
Found at i:13493774 original size:22 final size:22
Alignment explanation
Indices: 13493709--13493767 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
13493699 TTTCGAGTTA
* *
13493709 AGGCCCAAGTTCAATCAGACTG
1 AGGCCCAATTTCAATCAGATTG
* *
13493731 AGGCCCAATTTCAAACAAATTG
1 AGGCCCAATTTCAATCAGATTG
13493753 AGGCCCAATTTCAAT
1 AGGCCCAATTTCAAT
13493768 TCGATTGGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (22 bp):
AGGCCCAATTTCAATCAGATTG
Found at i:13493936 original size:10 final size:10
Alignment explanation
Indices: 13493919--13493943 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13493909 ATGAAAATGA
13493919 AAAAAAATAC
1 AAAAAAATAC
13493929 AAAAAAATAC
1 AAAAAAATAC
13493939 AAAAA
1 AAAAA
13493944 TGAAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:13494065 original size:30 final size:30
Alignment explanation
Indices: 13494016--13494099 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
13494006 TGCACGGCAC
*
13494016 CACTGCCA-CCTTCTGTTCACCCTTACATA
1 CACTGCCACCCCTCTGTTCACCCTTACATA
* * *
13494045 CACTGCCACCCCTATGTTCACCCATGCATA
1 CACTGCCACCCCTCTGTTCACCCTTACATA
* *
13494075 CATTGCCACCTCTCTGTTCATCCCT
1 CACTGCCACCCCTCTGTTCA-CCCT
13494100 GTGCCCCTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
29 8 0.18
30 34 0.76
31 3 0.07
ACGTcount: A:0.19, C:0.43, G:0.08, T:0.30
Consensus pattern (30 bp):
CACTGCCACCCCTCTGTTCACCCTTACATA
Found at i:13498569 original size:37 final size:38
Alignment explanation
Indices: 13498528--13498601 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
13498518 ATATTTTTAA
*
13498528 TGATATTTAAAG-TTTTAAAATAAAAAATATTTTTTTG
1 TGATATTTAAAGATTTTAAAACAAAAAATATTTTTTTG
* * *
13498565 TGATATTTTAAGATTTTAAAACAATAATTATTTTTTT
1 TGATATTTAAAGATTTTAAAACAAAAAATATTTTTTT
13498602 AAAATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 11 0.34
38 21 0.66
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (38 bp):
TGATATTTAAAGATTTTAAAACAAAAAATATTTTTTTG
Found at i:13498906 original size:18 final size:18
Alignment explanation
Indices: 13498872--13498904 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
13498862 CAAAACTCCG
13498872 AGTATCAAATATTTTTTA
1 AGTATCAAATATTTTTTA
13498890 AGTATC--ATATTTTTT
1 AGTATCAAATATTTTTT
13498905 TTCAAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.60
18 6 0.40
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (18 bp):
AGTATCAAATATTTTTTA
Found at i:13500156 original size:2 final size:2
Alignment explanation
Indices: 13500145--13500184 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
13500135 TGGCTCTCAG
*
13500145 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13500185 TTAATTGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13500437 original size:14 final size:15
Alignment explanation
Indices: 13500414--13500444 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13500404 CCAACCAGGA
13500414 TTTTGTTTTTTTTTT
1 TTTTGTTTTTTTTTT
13500429 TTTTGTTTTTTTTTT
1 TTTTGTTTTTTTTTT
13500444 T
1 T
13500445 GGAAAAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (15 bp):
TTTTGTTTTTTTTTT
Found at i:13501099 original size:35 final size:35
Alignment explanation
Indices: 13501053--13501121 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
13501043 AAAGAGAGGA
13501053 AATAGTGTACTTGATGCATATTTTATGTATATACG
1 AATAGTGTACTTGATGCATATTTTATGTATATACG
13501088 AATAGTGTACTTGATGCATATTTTATGTATATAC
1 AATAGTGTACTTGATGCATATTTTATGTATATAC
13501122 TTGTATTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (35 bp):
AATAGTGTACTTGATGCATATTTTATGTATATACG
Found at i:13506851 original size:22 final size:23
Alignment explanation
Indices: 13506820--13506864 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
13506810 TTGTTGATGA
*
13506820 AAAAGGTG-TTATGAGAAATTTTT
1 AAAAGGTGTTTAT-AGAAAATTTT
13506843 AAAA-GTGTTTATAGAAAATTTT
1 AAAAGGTGTTTATAGAAAATTTT
13506865 CTTTCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (23 bp):
AAAAGGTGTTTATAGAAAATTTT
Found at i:13509571 original size:3 final size:3
Alignment explanation
Indices: 13509556--13509593 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
13509546 CTCCAATTTG
*
13509556 TTA TTA TTT TTA TTA TTA TTA TTA TT- TTA TTTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT
13509594 TTTTCTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:13509579 original size:18 final size:18
Alignment explanation
Indices: 13509556--13509593 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
13509546 CTCCAATTTG
13509556 TTATTATTTT-TATTATTA
1 TTATTATTTTAT-TTATTA
13509574 TTATTATTTTATTTATTA
1 TTATTATTTTATTTATTA
13509592 TT
1 TT
13509594 TTTTCTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTATTTTATTTATTA
Found at i:13510799 original size:33 final size:33
Alignment explanation
Indices: 13510755--13510862 Score: 103
Period size: 35 Copynumber: 3.2 Consensus size: 33
13510745 GTAAAAAAAT
* *
13510755 TACTTTCAGAAATATATTTTCGGATAATTGTAA
1 TACTTTTAGAAATATATTTTCGGATAATTGCAA
* *
13510788 TACTTTTAGAAAT-TGCATTTTTGAATAATTGCAA
1 TACTTTTAGAAATAT--ATTTTCGGATAATTGCAA
* * *
13510822 TATTTTTTCAGAAATACATTTTCGGATAACTGCAA
1 TA-CTTTT-AGAAATATATTTTCGGATAATTGCAA
13510857 T-CTTTT
1 TACTTTT
13510863 TCAAAAATGC
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
32 1 0.02
33 16 0.27
34 17 0.28
35 20 0.33
36 6 0.10
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (33 bp):
TACTTTTAGAAATATATTTTCGGATAATTGCAA
Found at i:13510856 original size:35 final size:34
Alignment explanation
Indices: 13510758--13510886 Score: 134
Period size: 34 Copynumber: 3.8 Consensus size: 34
13510748 AAAAAATTAC
* * *
13510758 TTTCAGAAATATATTTTCGGATAATTGTAATACT
1 TTTCAGAAATACATTTTCGGATAATTGCAATATT
* * *
13510792 TTT-AGAAATTGCATTTTTGAATAATTGCAATATTT
1 TTTCAGAAA-TACATTTTCGGATAATTGCAATA-TT
* *
13510827 TTTCAGAAATACATTTTCGGATAACTGCAATCTT
1 TTTCAGAAATACATTTTCGGATAATTGCAATATT
* * *
13510861 TTTCAAAAATGCATTTTCAGATAATT
1 TTTCAGAAATACATTTTCGGATAATT
13510887 ATTATACTTT
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
33 5 0.06
34 45 0.58
35 22 0.29
36 5 0.06
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (34 bp):
TTTCAGAAATACATTTTCGGATAATTGCAATATT
Found at i:13510885 original size:69 final size:69
Alignment explanation
Indices: 13510758--13510886 Score: 165
Period size: 69 Copynumber: 1.9 Consensus size: 69
13510748 AAAAAATTAC
* * * * *
13510758 TTTCAGAAATATATTTTCGGATAATTGTAATACTTTTAGAAATTGCATTTTTGAATAATTGCAAT
1 TTTCAGAAATACATTTTCGGATAACTGCAATACTTTTAGAAAATGCATTTTAGAATAATTGCAAT
13510823 ATTT
66 ATTT
13510827 TTTCAGAAATACATTTTCGGATAACTGCAAT-CTTTTTCA-AAAATGCATTTTCAG-ATAATT
1 TTTCAGAAATACATTTTCGGATAACTGCAATAC-TTTT-AGAAAATGCATTTT-AGAATAATT
13510887 ATTATACTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
68 1 0.02
69 49 0.94
70 2 0.04
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (69 bp):
TTTCAGAAATACATTTTCGGATAACTGCAATACTTTTAGAAAATGCATTTTAGAATAATTGCAAT
ATTT
Found at i:13513688 original size:15 final size:14
Alignment explanation
Indices: 13513670--13513717 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
13513660 AAAGAGAGCA
*
13513670 AAAAATAAAATAAGG
1 AAAAATAAAAGAA-G
13513685 AAAAAGTAAAAGAAG
1 AAAAA-TAAAAGAAG
13513700 AAAAATAAAA-AA-
1 AAAAATAAAAGAAG
13513712 AAAAAT
1 AAAAAT
13513718 TGAATTAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 6 0.19
13 2 0.06
14 5 0.16
15 11 0.35
16 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (14 bp):
AAAAATAAAAGAAG
Found at i:13513688 original size:16 final size:15
Alignment explanation
Indices: 13513636--13513709 Score: 55
Period size: 16 Copynumber: 4.8 Consensus size: 15
13513626 GAAAGATAAG
*
13513636 GAAAAAA-AACAAGGA
1 GAAAAAATAA-AAGAA
13513651 GAAAAAA-ATAAAGAGA
1 GAAAAAATA-AAAGA-A
*
13513667 GCAAAAAATAAAATAA
1 G-AAAAAATAAAAGAA
*
13513683 GGAAAAAGTAAAAGAA
1 -GAAAAAATAAAAGAA
13513699 G-AAAAATAAAA
1 GAAAAAATAAAA
13513710 AAAAAAATTG
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.18
15 12 0.24
16 16 0.33
17 11 0.22
18 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.07
Consensus pattern (15 bp):
GAAAAAATAAAAGAA
Found at i:13517612 original size:27 final size:25
Alignment explanation
Indices: 13517569--13517618 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
13517559 TATTTTGATA
*
13517569 ATTTTTTATAAATATATATTAATAT
1 ATTTTTTATAAAAATATATTAATAT
13517594 ATTTTTTCAATAAAAATATATTAAT
1 ATTTTTT--ATAAAAATATATTAAT
13517619 TCTAATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
27 15 0.68
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTTTATAAAAATATATTAATAT
Found at i:13518555 original size:2 final size:2
Alignment explanation
Indices: 13518537--13518577 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
13518527 ACGACGCTCT
*
13518537 TA TA T- TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13518578 GAAAGTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:13519073 original size:29 final size:29
Alignment explanation
Indices: 13519040--13519103 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
13519030 AAAAAATTGA
*
13519040 TTAAATGTTAAATG-ATTGAAAATAAATAT
1 TTAAATATTAAATGAATT-AAAATAAATAT
*
13519069 TTAAATATTTAATGAAATTAAAATAAATAT
1 TTAAATATTAAATG-AATTAAAATAAATAT
13519099 TTAAA
1 TTAAA
13519104 ATTTTGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 12 0.39
30 16 0.52
31 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (29 bp):
TTAAATATTAAATGAATTAAAATAAATAT
Done.