Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007973.1 Hibiscus syriacus cultivar Beakdansim tig00110410_pilon, 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: 1299094
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1129080 original size:55 final size:55
Alignment explanation
Indices: 1128966--1129086 Score: 138
Period size: 55 Copynumber: 2.2 Consensus size: 55
1128956 ACCGAAAGAG
* *
1128966 CACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTACATATTGG
1 CACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTACATATCGA
* * * * *
1129021 CACTATGTGTGCAGCC-CTACGTAATTCATAATGAGTTTGTGAA-TTACCGTATCGA
1 CACTATGTGTGCAACCTC-AAGAAATTCATAATGAGTTTATGAATTTA-CATATCGA
*
1129076 CACTACGTGTG
1 CACTATGTGTG
1129087 TGAAAACAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
54 4 0.07
55 52 0.93
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (55 bp):
CACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTACATATCGA
Found at i:1138130 original size:55 final size:55
Alignment explanation
Indices: 1138056--1138289 Score: 290
Period size: 55 Copynumber: 4.3 Consensus size: 55
1138046 TTACCGAATG
* * * *
1138056 GGCACTGTGTGTGGAACCTCAAGAAATTCATAATGAGTTTTTGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
* * **
1138111 GGCACTATGCGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTTTGTATT
1 GGCACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
* * * *
1138166 TGCACTATGTGTGCAACCTCACGAAATTTATAATGAGTTTATTAATTTCCGTATT
1 GGCACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
* * * * *
1138221 GGCACTATGTGTGCAACCCCACA-TAATTCGTAATGAGTTTATGAATTACCGTATC
1 GGCACTATGTGTGCAACCTCA-AGAAATTCATAATGAGTTTATGAATTTCCGTATT
*
1138276 GGCACTACGTGTGC
1 GGCACTATGTGTGC
1138290 GAAAATCACT
Statistics
Matches: 156, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
55 156 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (55 bp):
GGCACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
Found at i:1138281 original size:110 final size:110
Alignment explanation
Indices: 1138044--1138315 Score: 325
Period size: 110 Copynumber: 2.5 Consensus size: 110
1138034 TATATATTGC
* * * * * * *
1138044 AATTACCGAATGGGCACTGTGTGTGGAACCTCAAGAAATTCATAATGAGTTTTTGAATTTCTGTA
1 AATTACCGTATCGGCACTATGTGTGCAACCTCACGAAATTTATAATGAGTTTTTGAATTTCCGTA
*
1138109 TTGGCACTATGCGTGCAACCTCACGAAATTCATAATGAGTTTATG
66 TTGGCACTATGCGTGCAACCCCACGAAATTCATAATGAGTTTATG
*** **
1138154 AATTTTTGTATTTGCACTATGTGTGCAACCTCACGAAATTTATAATGAGTTTATT-AATTTCCGT
1 AATTACCGTATCGGCACTATGTGTGCAACCTCACGAAATTTATAATGAGTTT-TTGAATTTCCGT
* *
1138218 ATTGGCACTATGTGTGCAACCCCAC-ATAATTCGTAATGAGTTTATG
65 ATTGGCACTATGCGTGCAACCCCACGA-AATTCATAATGAGTTTATG
* **
1138264 AATTACCGTATCGGCACTACGTGTGCGAAAATCACTG-AATTTATAATGAGTT
1 AATTACCGTATCGGCACTATGTGTGC-AACCTCAC-GAAATTTATAATGAGTT
1138316 GAAATATCAA
Statistics
Matches: 136, Mismatches: 22, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
109 1 0.01
110 111 0.82
111 23 0.17
112 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (110 bp):
AATTACCGTATCGGCACTATGTGTGCAACCTCACGAAATTTATAATGAGTTTTTGAATTTCCGTA
TTGGCACTATGCGTGCAACCCCACGAAATTCATAATGAGTTTATG
Found at i:1142585 original size:7 final size:7
Alignment explanation
Indices: 1142581--1142763 Score: 83
Period size: 7 Copynumber: 25.1 Consensus size: 7
1142571 TTGTATATAG
1142581 TATATTA
1 TATATTA
1142588 TATTATTA
1 TA-TATTA
1142596 TATATTA
1 TATATTA
1142603 TATATTA
1 TATATTA
1142610 TATATCT-
1 TATAT-TA
* **
1142617 TGTAGCA
1 TATATTA
1142624 TAT-TTA
1 TATATTA
1142630 TACATATTA
1 T--ATATTA
*
1142639 TGTGATTA
1 TAT-ATTA
*
1142647 TCTATT-
1 TATATTA
1142653 TATTATATA
1 TA-TAT-TA
1142662 GTATATT-
1 -TATATTA
1142669 TATATTA
1 TATATTA
* **
1142676 CATAGAA
1 TATATTA
*
1142683 TACA-TA
1 TATATTA
1142689 TATTATTA
1 TA-TATTA
1142697 TATATT-
1 TATATTA
1142703 TATATATA
1 TATAT-TA
1142711 GTATATGTA
1 -TATAT-TA
*
1142720 TACATTA
1 TATATTA
1142727 TATCATTA
1 TAT-ATTA
1142735 TATATTTA
1 TATA-TTA
1142743 TATATTA
1 TATATTA
* *
1142750 CATAGTA
1 TATATTA
1142757 TAT-TTA
1 TATATTA
1142763 T
1 T
1142764 TGTAACACCC
Statistics
Matches: 134, Mismatches: 23, Indels: 39
0.68 0.12 0.20
Matches are distributed among these distances:
6 20 0.15
7 58 0.43
8 40 0.30
9 14 0.10
10 2 0.01
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (7 bp):
TATATTA
Found at i:1142599 original size:10 final size:9
Alignment explanation
Indices: 1142574--1142747 Score: 63
Period size: 9 Copynumber: 18.6 Consensus size: 9
1142564 CGATCCTTTG
*
1142574 TATATAGTA
1 TATATATTA
1142583 TATTATATTA
1 TA-TATATTA
1142593 T-TATA-TA
1 TATATATTA
1142600 TTATATATTA
1 -TATATATTA
* *
1142610 TATATCTTG
1 TATATATTA
*
1142619 TAGCATATTTA
1 TA-TATA-TTA
*
1142630 TACATATTA
1 TATATATTA
*
1142639 TGTGATTATCTA
1 TAT-A-TAT-TA
1142651 T-T-TATTA
1 TATATATTA
1142658 TATAGTA-TA
1 TATA-TATTA
*
1142667 TTTATATTA
1 TATATATTA
* * *
1142676 CATAGAATA
1 TATATATTA
*
1142685 CATATATTA
1 TATATATTA
1142694 TTATATATTTA
1 -TATATA-TTA
*
1142705 TATATAGTA
1 TATATATTA
* *
1142714 TATGTATACA
1 TATATAT-TA
1142724 TTATATCATTA
1 -TATAT-ATTA
1142735 TATAT-TTA
1 TATATATTA
1142743 TATAT
1 TATAT
1142748 TACATAGTAT
Statistics
Matches: 125, Mismatches: 22, Indels: 37
0.68 0.12 0.20
Matches are distributed among these distances:
7 5 0.04
8 19 0.15
9 45 0.36
10 35 0.28
11 16 0.13
12 5 0.04
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (9 bp):
TATATATTA
Found at i:1142709 original size:36 final size:37
Alignment explanation
Indices: 1142653--1142754 Score: 113
Period size: 38 Copynumber: 2.8 Consensus size: 37
1142643 ATTATCTATT
1142653 TATTA-TATAGTATATT-TATATTACATAGAATACA-TA
1 TATTATTATA-TAT-TTATATATTACATAGAATACATTA
* *
1142689 TATTATTATATATTTATATA-TAGTATATGTATACATTA
1 TATTATTATATATTTATATATTA-CATA-GAATACATTA
*
1142727 TATCATTATATATTTATATATTACATAG
1 TATTATTATATATTTATATATTACATAG
1142755 TATATTTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
35 4 0.07
36 15 0.27
37 11 0.20
38 24 0.43
39 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (37 bp):
TATTATTATATATTTATATATTACATAGAATACATTA
Found at i:1142729 original size:30 final size:28
Alignment explanation
Indices: 1142686--1142763 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 28
1142676 CATAGAATAC
1142686 ATATATT--ATTATATATTTATATATAGT
1 ATATATTACATTATATATTTATATAT-GT
* *
1142713 ATATGTATACATTATATCA-TTATATATTT
1 ATATAT-TACATTATAT-ATTTATATATGT
1142742 ATATATTACA-TAGTATATTTAT
1 ATATATTACATTA-TATATTTAT
1142764 TGTAACACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
27 8 0.19
28 12 0.29
29 6 0.14
30 15 0.36
31 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (28 bp):
ATATATTACATTATATATTTATATATGT
Found at i:1142985 original size:21 final size:22
Alignment explanation
Indices: 1142956--1142996 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1142946 AATACGATAT
1142956 GAATCGATT-CCCTACTACAAG
1 GAATCGATTCCCCTACTACAAG
*
1142977 GAATTGATTCCCCTACTACA
1 GAATCGATTCCCCTACTACA
1142997 GTACTGCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (22 bp):
GAATCGATTCCCCTACTACAAG
Found at i:1143599 original size:18 final size:18
Alignment explanation
Indices: 1143576--1143652 Score: 109
Period size: 18 Copynumber: 4.1 Consensus size: 18
1143566 ACTGAATATT
1143576 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1143594 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
*
1143616 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
1143634 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1143652 T
1 T
1143653 ATAACCCTCG
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
18 36 0.68
22 17 0.32
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1143620 original size:40 final size:40
Alignment explanation
Indices: 1143571--1143655 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
1143561 AGGGCACTGA
* *
1143571 ATATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACT
1 ATATATGTCCCGAAAGACCACTATGTCCCGAAGGACCACT
*
1143611 GTATATGTCCCGAAAGACCACTATGTCCCGAAGGACCACT
1 ATATATGTCCCGAAAGACCACTATGTCCCGAAGGACCACT
1143651 ATATA
1 ATATA
1143656 ACCCTCGACT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (40 bp):
ATATATGTCCCGAAAGACCACTATGTCCCGAAGGACCACT
Found at i:1143829 original size:18 final size:18
Alignment explanation
Indices: 1143806--1143876 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 18
1143796 CACAATTAGA
1143806 CCGAAGGACCACTATATC
1 CCGAAGGACCACTATATC
*
1143824 CCGAAGAACCACTGTATATGTC
1 CCGAAGGACCAC--TATA--TC
* *
1143846 CCGAAAGACCACTATGTC
1 CCGAAGGACCACTATATC
*
1143864 CTGAAGGACCACT
1 CCGAAGGACCACT
1143877 GTATAACCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 24 0.56
20 7 0.16
22 12 0.28
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.18
Consensus pattern (18 bp):
CCGAAGGACCACTATATC
Found at i:1143875 original size:40 final size:40
Alignment explanation
Indices: 1143806--1143881 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
1143796 CACAATTAGA
*
1143806 CCGAAGGACCACTATATCCCGAAGAACCACTGTATATGTC
1 CCGAAAGACCACTATATCCCGAAGAACCACTGTATATGTC
* * *
1143846 CCGAAAGACCACTATGTCCTGAAGGACCACTGTATA
1 CCGAAAGACCACTATATCCCGAAGAACCACTGTATA
1143882 ACCCTCGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (40 bp):
CCGAAAGACCACTATATCCCGAAGAACCACTGTATATGTC
Found at i:1143974 original size:226 final size:226
Alignment explanation
Indices: 1143580--1144021 Score: 839
Period size: 226 Copynumber: 2.0 Consensus size: 226
1143570 AATATTTGTC
* *
1143580 CCGAAGGACCACTATGTCCCGAAGGACCACTGTATATGTCCCGAAAGACCACTATGTCCCGAAGG
1 CCGAAGGACCACTATATCCCGAAGAACCACTGTATATGTCCCGAAAGACCACTATGTCCCGAAGG
1143645 ACCACTATATAACCCTCGACTCTTGGCATGCCAATTAGACCTACAGCTCTCATATTAAATAACAT
66 ACCACTATATAACCCTCGACTCTTGGCATGCCAATTAGACCTACAGCTCTCATATTAAATAACAT
1143710 GGGCTTAAATATGAATACATTTCTCATTTTCATATATTTTTCATCACTTTTCATATAAACACATA
131 GGGCTTAAATATGAATACATTTCTCATTTTCATATATTTTTCATCACTTTTCATATAAACACATA
1143775 TTTCACTTCACATGTACACATCACAATTAGA
196 TTTCACTTCACATGTACACATCACAATTAGA
*
1143806 CCGAAGGACCACTATATCCCGAAGAACCACTGTATATGTCCCGAAAGACCACTATGTCCTGAAGG
1 CCGAAGGACCACTATATCCCGAAGAACCACTGTATATGTCCCGAAAGACCACTATGTCCCGAAGG
* *
1143871 ACCACTGTATAACCCTCGACTCTTGGCATGCCAGTTAGACCTACAGCTCTCATATTAAATAACAT
66 ACCACTATATAACCCTCGACTCTTGGCATGCCAATTAGACCTACAGCTCTCATATTAAATAACAT
1143936 GGGCTTAAATATGAATACATTTCTCATTTTCATATATTTTTCATCACTTTTCATATAAACACATA
131 GGGCTTAAATATGAATACATTTCTCATTTTCATATATTTTTCATCACTTTTCATATAAACACATA
1144001 TTTCACTTCACATGTACACAT
196 TTTCACTTCACATGTACACAT
1144022 ATGATCATTT
Statistics
Matches: 211, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
226 211 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (226 bp):
CCGAAGGACCACTATATCCCGAAGAACCACTGTATATGTCCCGAAAGACCACTATGTCCCGAAGG
ACCACTATATAACCCTCGACTCTTGGCATGCCAATTAGACCTACAGCTCTCATATTAAATAACAT
GGGCTTAAATATGAATACATTTCTCATTTTCATATATTTTTCATCACTTTTCATATAAACACATA
TTTCACTTCACATGTACACATCACAATTAGA
Found at i:1145246 original size:7 final size:7
Alignment explanation
Indices: 1145228--1145280 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
1145218 TTGAGGATGT
1145228 TATATT-
1 TATATTA
1145234 TATATTA
1 TATATTA
1145241 TATATTA
1 TATATTA
*
1145248 TACCATTATA
1 TA-TA-T-TA
1145258 TATATTA
1 TATATTA
*
1145265 TTTATTA
1 TATATTA
1145272 TATATTA
1 TATATTA
1145279 TA
1 TA
1145281 CATAAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 6 0.15
7 25 0.64
8 2 0.05
9 2 0.05
10 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATTA
Found at i:1156272 original size:21 final size:21
Alignment explanation
Indices: 1156246--1156297 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1156236 GTGTAGATGC
1156246 AGAAGAGGTAAATATGATATT
1 AGAAGAGGTAAATATGATATT
1156267 AGAAGAGGTAAATATGATATT
1 AGAAGAGGTAAATATGATATT
*
1156288 GGAAGAGGTA
1 AGAAGAGGTA
1156298 CATGACGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (21 bp):
AGAAGAGGTAAATATGATATT
Found at i:1159205 original size:56 final size:54
Alignment explanation
Indices: 1159144--1159263 Score: 127
Period size: 56 Copynumber: 2.1 Consensus size: 54
1159134 TAGAATACAA
**
1159144 ATATTATTTTATATTTATATATAGTATATGTATA-CATTATAT-CATTATATATTTAT
1 ATATTATAGTATATTTATAT-TA-TATAT-TATACCATTATATACATTATATA-TTAT
* * *
1159200 ATATTACATAGTGTATTTATATTATATATTATACCATTATATATATTATTTATTAT
1 ATATT--ATAGTATATTTATATTATATATTATACCATTATATACATTATATATTAT
1159256 ATATTATA
1 ATATTATA
1159264 CATAAATTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
54 3 0.05
55 4 0.07
56 27 0.49
57 9 0.16
58 12 0.22
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (54 bp):
ATATTATAGTATATTTATATTATATATTATACCATTATATACATTATATATTAT
Found at i:1159229 original size:7 final size:7
Alignment explanation
Indices: 1159144--1159263 Score: 77
Period size: 7 Copynumber: 16.1 Consensus size: 7
1159134 TAGAATACAA
1159144 ATATTAT
1 ATATTAT
1159151 -T-TTAT
1 ATATTAT
1159156 AT-TTAT
1 ATATTAT
1159162 ATA-TAGT
1 ATATTA-T
1159169 ATATGTAT
1 ATAT-TAT
*
1159177 ACATTAT
1 ATATTAT
1159184 ATCATTAT
1 AT-ATTAT
1159192 ATATTTAT
1 ATA-TTAT
*
1159200 ATATTAC
1 ATATTAT
1159207 ATAGTGTATTT
1 ATA-T-TA--T
1159218 ATATTAT
1 ATATTAT
1159225 ATATTAT
1 ATATTAT
*
1159232 ACCATTATAT
1 A-TA-T-TAT
1159242 ATATTAT
1 ATATTAT
*
1159249 TTATTAT
1 ATATTAT
1159256 ATATTAT
1 ATATTAT
1159263 A
1 A
1159264 CATAAATTTA
Statistics
Matches: 91, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
5 4 0.04
6 10 0.11
7 40 0.44
8 21 0.23
9 8 0.09
10 5 0.05
11 3 0.03
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (7 bp):
ATATTAT
Found at i:1160956 original size:18 final size:19
Alignment explanation
Indices: 1160921--1160957 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1160911 CACGGAATGT
1160921 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1160941 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1160958 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1165118 original size:42 final size:42
Alignment explanation
Indices: 1165044--1165126 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1165034 GGAAGTGGTA
* *
1165044 GCTTTTGTGTCAATTAACATAAGACATAAAGAGCAGGTGATG
1 GCTTCTGTGTCAATTAACATAAGACATAAAGAGCAAGTGATG
* * * * *
1165086 GCTTCTGTGTCAATTAGCCTATGATATGAAGAGCAAGTGAT
1 GCTTCTGTGTCAATTAACATAAGACATAAAGAGCAAGTGAT
1165127 TTGCAATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (42 bp):
GCTTCTGTGTCAATTAACATAAGACATAAAGAGCAAGTGATG
Found at i:1168782 original size:23 final size:24
Alignment explanation
Indices: 1168715--1168785 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
1168705 TTTGTTTAGC
1168715 ATTCGTGAATATGTTCGTTTATAT
1 ATTCGTGAATATGTTCGTTTATAT
** * * *
1168739 ATTCGCCAACATGGTCATTTA-AT
1 ATTCGTGAATATGTTCGTTTATAT
*
1168762 ATTCGTGATTATGTTCGTTTATAT
1 ATTCGTGAATATGTTCGTTTATAT
1168786 GTTCAGAAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
23 17 0.49
24 18 0.51
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (24 bp):
ATTCGTGAATATGTTCGTTTATAT
Found at i:1172190 original size:31 final size:31
Alignment explanation
Indices: 1172138--1172225 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 31
1172128 TTTCAAATAA
* *
1172138 GTTTT-TTTGTTACTATTTTAGGTGTTTAAT
1 GTTTTCTTAGTTACCATTTTAGGTGTTTAAT
* * *
1172168 GTTTTGTTAGTTATCATTTTAGGTGTCTAAT
1 GTTTTCTTAGTTACCATTTTAGGTGTTTAAT
1172199 GTTTTCTTAGTTACCATTTTAGGTGTT
1 GTTTTCTTAGTTACCATTTTAGGTGTT
1172226 CGAACGCTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.17, C:0.07, G:0.18, T:0.58
Consensus pattern (31 bp):
GTTTTCTTAGTTACCATTTTAGGTGTTTAAT
Found at i:1174839 original size:16 final size:15
Alignment explanation
Indices: 1174818--1174852 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1174808 CACAGATGAG
*
1174818 ATGATCTGAGCGGACA
1 ATGATCTGAACGGA-A
1174834 ATGATCTGAACGGAA
1 ATGATCTGAACGGAA
1174849 ATGA
1 ATGA
1174853 GTCATCCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (15 bp):
ATGATCTGAACGGAA
Found at i:1178604 original size:18 final size:19
Alignment explanation
Indices: 1178581--1178616 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1178571 AAATGACTTG
1178581 ATTTTACTTA-ATTTAAAA
1 ATTTTACTTACATTTAAAA
1178599 ATTTTACTTACATTTAAA
1 ATTTTACTTACATTTAAA
1178617 CTATAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTACTTACATTTAAAA
Found at i:1179601 original size:21 final size:20
Alignment explanation
Indices: 1179576--1179614 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1179566 AATCAAATAG
1179576 TACAATAATATTATAAATATT
1 TACAATAATATT-TAAATATT
*
1179597 TACAATTATATTTAAATA
1 TACAATAATATTTAAATA
1179615 GAAACTCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TACAATAATATTTAAATATT
Found at i:1179932 original size:17 final size:16
Alignment explanation
Indices: 1179910--1179942 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1179900 AAACCGATCT
1179910 AAAAAACCGATAACCGA
1 AAAAAACCGA-AACCGA
1179927 AAAAAACCGAAACCGA
1 AAAAAACCGAAACCGA
1179943 TTTAGTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.61, C:0.24, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAACCGAAACCGA
Found at i:1180720 original size:27 final size:26
Alignment explanation
Indices: 1180663--1180719 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 26
1180653 CTCAAAACAT
1180663 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATA-TAATA
*
1180690 TATTATTTTAGTATTATTTTAATAAAATA
1 TATTATTTTA-TA-TA-TTTAATATAATA
1180719 T
1 T
1180720 TGATTATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 2 0.08
29 7 0.27
30 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TATTATTTTATATATTTAATATAATA
Found at i:1180786 original size:14 final size:13
Alignment explanation
Indices: 1180761--1180815 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 13
1180751 AATAATATAA
1180761 TATTATATTTTAT
1 TATTATATTTTAT
1180774 TATTATAATTTTAT
1 TATTAT-ATTTTAT
* *
1180788 TATTA-ATATATAA
1 TATTATAT-TTTAT
1180801 TATTATACTTTTAT
1 TATTATA-TTTTAT
1180815 T
1 T
1180816 TCAATAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
12 2 0.06
13 14 0.41
14 17 0.50
15 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATTTTAT
Found at i:1180832 original size:27 final size:27
Alignment explanation
Indices: 1180774--1180825 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1180764 TATATTTTAT
*
1180774 TATTATAATTTTATTATTAATATATAA
1 TATTATAATTTTATTATCAATATATAA
*
1180801 TATTATACTTTTATT-TCAATA-ATAA
1 TATTATAATTTTATTATCAATATATAA
1180826 ATAATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 5 0.22
27 14 0.61
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
TATTATAATTTTATTATCAATATATAA
Found at i:1180833 original size:40 final size:40
Alignment explanation
Indices: 1180750--1180835 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
1180740 TTTATAATTG
* ** *
1180750 TAATAATATAATATTATATTTTATTATTATAATTTTATTAT
1 TAAT-ATATAATATTATATTTTATTATAATAATTAAATAAT
1180791 TAATATATAATATTATACTTTTATT-TCAATAA-TAAATAAT
1 TAATATATAATATTATA-TTTTATTAT-AATAATTAAATAAT
1180831 TAATA
1 TAATA
1180836 AAATCAACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
40 24 0.62
41 15 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (40 bp):
TAATATATAATATTATATTTTATTATAATAATTAAATAAT
Found at i:1180997 original size:33 final size:34
Alignment explanation
Indices: 1180960--1181042 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
1180950 TTTTAACAGT
* *
1180960 ATTCTTATTTTAGTAAATAATTA-ATAATATATC
1 ATTCTTATTTTAATAAATAATTATATAATATATA
* *
1180993 ATTCTAATTTTAATAAATAATTATATAATTTATA
1 ATTCTTATTTTAATAAATAATTATATAATATATA
*
1181027 ATT-TTATTTAAATAAA
1 ATTCTTATTTTAATAAA
1181043 ATATATTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 32 0.74
34 11 0.26
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (34 bp):
ATTCTTATTTTAATAAATAATTATATAATATATA
Found at i:1181269 original size:21 final size:21
Alignment explanation
Indices: 1181240--1181306 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
1181230 ATTCTGACTA
*
1181240 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
1181261 TCGCGTTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
* *
1181282 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTCCCAAAT
1181303 TCGC
1 TCGC
1181307 AATGCGAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATTTCCCAAAT
Found at i:1181328 original size:20 final size:20
Alignment explanation
Indices: 1181303--1181396 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
1181293 TTTTCCTAAT
1181303 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1181323 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1181343 TCGCAATACGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1181364 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1181384 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1181397 CTGACTATCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 48 0.74
21 17 0.26
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1181365 original size:41 final size:41
Alignment explanation
Indices: 1181303--1181396 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
1181293 TTTTCCTAAT
* *
1181303 TCGCAATGCGAA-TACGTAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAATGCGAATACGTAAA
* *
1181343 TCGCAATACGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAATGCGAATACGTAAA
1181384 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1181397 CTGACTATCG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 11 0.23
41 37 0.77
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAATGCGAATACGTAAA
Found at i:1182010 original size:21 final size:21
Alignment explanation
Indices: 1181949--1182027 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
1181939 TTCTAAACTT
1181949 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
1181969 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
1181989 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
1182010 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
1182028 TTACAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1182041 original size:33 final size:33
Alignment explanation
Indices: 1182004--1182084 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
1181994 CGCAACGAGA
*
1182004 GAAATGAAAATCGCAACGAGAGAATTACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
* * * *
1182037 GAAATGGAAATCGCAACGATATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
**
1182070 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1182085 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAACGC
Found at i:1182144 original size:20 final size:19
Alignment explanation
Indices: 1182080--1182178 Score: 135
Period size: 19 Copynumber: 5.1 Consensus size: 19
1182070 GAAACCAAAA
*
1182080 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1182099 TCACGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1182118 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1182137 TCCGCGTTGCGATTTTCATTT
1 T-CGCGTTGCGATTTTCA-TT
*
1182158 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1182177 TC
1 TC
1182179 AACCAAAAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 38 0.54
20 29 0.41
21 3 0.04
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1184080 original size:94 final size:93
Alignment explanation
Indices: 1183870--1184243 Score: 614
Period size: 94 Copynumber: 4.1 Consensus size: 93
1183860 TAGATTGCTT
* * *
1183870 AGTAAATTTATTCGGCTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1183931 ATTTGTCTTT-TGTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1183958 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1184023 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
1184052 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1184117 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
1184146 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1184211 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1184239 AGTAA
1 AGTAA
1184244 TGCAATCCAT
Statistics
Matches: 272, Mismatches: 8, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
88 34 0.12
90 3 0.01
91 2 0.01
92 29 0.11
93 21 0.08
94 183 0.67
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1184363 original size:19 final size:19
Alignment explanation
Indices: 1184339--1184429 Score: 84
Period size: 19 Copynumber: 5.0 Consensus size: 19
1184329 TGGTTGAAAT
1184339 GAAAATCGCAACGCAAAAC
1 GAAAATCGCAACGCAAAAC
1184358 GAAAATCGCAACG----A-
1 GAAAATCGCAACGCAAAAC
* * *
1184372 GAGAATCGCAACGCGAAAT
1 GAAAATCGCAACGCAAAAC
*
1184391 GAAAATCGCAACGCGAAACC
1 GAAAATCGCAACGC-AAAAC
* *
1184411 AAAAATCGCAACGCGAAAC
1 GAAAATCGCAACGCAAAAC
1184430 TATAATCGCG
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
14 12 0.21
15 1 0.02
18 1 0.02
19 29 0.50
20 15 0.26
ACGTcount: A:0.48, C:0.25, G:0.20, T:0.07
Consensus pattern (19 bp):
GAAAATCGCAACGCAAAAC
Found at i:1184417 original size:20 final size:20
Alignment explanation
Indices: 1184375--1184429 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1184365 GCAACGAGAG
**
1184375 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACCAAA
1184394 AATCGCAACGCGAAACCAAA
1 AATCGCAACGCGAAACCAAA
1184414 AATCGCAACGCGAAAC
1 AATCGCAACGCGAAAC
1184430 TATAATCGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.07
Consensus pattern (20 bp):
AATCGCAACGCGAAACCAAA
Found at i:1184438 original size:19 final size:19
Alignment explanation
Indices: 1184375--1184438 Score: 85
Period size: 19 Copynumber: 3.3 Consensus size: 19
1184365 GCAACGAGAG
1184375 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
*
1184394 AATCGCAACGCGAAACCAAA
1 AATCGCAACGCGAAA-CTAA
*
1184414 AATCGCAACGCGAAACTAT
1 AATCGCAACGCGAAACTAA
1184433 AATCGC
1 AATCGC
1184439 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:1184457 original size:19 final size:19
Alignment explanation
Indices: 1184435--1184594 Score: 151
Period size: 19 Copynumber: 8.8 Consensus size: 19
1184425 GAAACTATAA
1184435 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1184454 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1184468 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1184487 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1184501 TCTCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
1184520 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1184539 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
**
1184559 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
1184580 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
1184595 AAGTTCCAGA
Statistics
Matches: 114, Mismatches: 14, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
14 19 0.17
16 6 0.05
17 6 0.05
19 51 0.45
20 18 0.16
21 14 0.12
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1184478 original size:14 final size:14
Alignment explanation
Indices: 1184459--1184513 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1184449 TCATTTCGCA
1184459 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1184473 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
1184492 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
1184506 TTGCGATT
1 TTGCGATT
1184514 TTCGTTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1184480 original size:33 final size:33
Alignment explanation
Indices: 1184438--1184570 Score: 194
Period size: 33 Copynumber: 3.8 Consensus size: 33
1184428 ACTATAATCG
*
1184438 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1184471 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
1184504 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCG------ATTCTCT
1184543 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
1184571 AGTCATTTTT
Statistics
Matches: 91, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
33 59 0.65
39 32 0.35
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1184551 original size:39 final size:37
Alignment explanation
Indices: 1184438--1184594 Score: 177
Period size: 33 Copynumber: 4.3 Consensus size: 37
1184428 ACTATAATCG
*
1184438 CGTTGCGATTTTCATTTCGCATTGCG----ATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCATTCTCT
1184471 CGTTGCGATTTTCATTTCGCGTTGCG----ATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCATTCTCT
*
1184504 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGA--TTCATTCTCT
* *
1184543 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCATTTCGCGTTGCGAT--TCA-TTCTCT
1184583 CGTTGCGATTTT
1 CGTTGCGATTTT
1184595 AAGTTCCAGA
Statistics
Matches: 110, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
33 57 0.52
37 1 0.01
39 36 0.33
40 16 0.15
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (37 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCATTCTCT
Found at i:1185071 original size:21 final size:21
Alignment explanation
Indices: 1185047--1185113 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1185037 TCATTCCTCG
1185047 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1185068 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1185089 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1185110 AGAG
1 AGAG
1185114 CCTGATTTAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1185071 original size:42 final size:42
Alignment explanation
Indices: 1184995--1185113 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1184985 GACTCGCCTG
* * * * * * *
1184995 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1185037 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1185079 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1185114 CCTGATTTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1186616 original size:19 final size:19
Alignment explanation
Indices: 1186594--1186659 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
1186584 AAAAATTACT
*
1186594 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1186613 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1186627 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1186646 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1186660 CTAAATTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1186728 original size:19 final size:19
Alignment explanation
Indices: 1186704--1186782 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
1186694 GATTCCCTCG
1186704 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1186723 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
*
1186737 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
**
1186756 TTGCGATAGTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1186776 TTGCGAT
1 TTGCGAT
1186783 AGACATTAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.15
17 6 0.12
19 19 0.40
20 10 0.21
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1186782 original size:39 final size:33
Alignment explanation
Indices: 1186674--1186762 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
1186664 ATTTGTGTAT
* * **
1186674 CGATTTTTATTTCGCTTTGCGATTCCCTCGTTG
1 CGATTTTCATTTCGCATTGCGATTATCTCGTTG
1186707 CGATTTTCATTTCGCATTGCGATTATCTCGTTG
1 CGATTTTCATTTCGCATTGCGATTATCTCGTTG
*
1186740 CGATTTTCATTTTGCATTGCGAT
1 CGATTTTCATTTCGCATTGCGAT
1186763 AGTCATTTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTGCGATTATCTCGTTG
Found at i:1189084 original size:14 final size:14
Alignment explanation
Indices: 1189065--1189091 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1189055 TCCCGTGGCA
1189065 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
1189079 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
1189092 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:1189325 original size:24 final size:24
Alignment explanation
Indices: 1189291--1189344 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1189281 CTGAAAAATC
1189291 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1189315 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1189339 ATCAAA
1 ATCAAA
1189345 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1189358 original size:24 final size:24
Alignment explanation
Indices: 1189291--1189358 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1189281 CTGAAAAATC
* * *
1189291 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1189315 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1189339 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1189359 TATACTCACA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1190321 original size:20 final size:20
Alignment explanation
Indices: 1190202--1190348 Score: 156
Period size: 20 Copynumber: 7.3 Consensus size: 20
1190192 CAGAATATCG
**
1190202 TTGCGATTTACAAAATCGCA
1 TTGCGATTTACGTAATCGCA
*
1190222 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* *
1190242 ATGCGA-ATACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* *
1190262 ATGCGA-ATACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
1190281 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
1190301 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* * *
1190321 TTGTGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAA-TCGCA
1190342 TTGCGAT
1 TTGCGAT
1190349 AATTCGCAAT
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.14
20 87 0.76
21 11 0.10
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:1190353 original size:15 final size:15
Alignment explanation
Indices: 1190333--1190364 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1190323 GTGATTTTCC
*
1190333 TAATTCGCATTGCGA
1 TAATTCGCAATGCGA
1190348 TAATTCGCAATGCGA
1 TAATTCGCAATGCGA
1190363 TA
1 TA
1190365 GTCAGAATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (15 bp):
TAATTCGCAATGCGA
Found at i:1190633 original size:24 final size:23
Alignment explanation
Indices: 1190545--1190642 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 23
1190535 AATTATACAT
*
1190545 TTAATATTTTAATAATATTATTCTCA
1 TTAATATTTTAAAAATATTA-T-T-A
* *
1190571 TAAATAATATTAAATAA-ATTATT-
1 TTAAT-ATTTTAAA-AATATTATTA
1190594 TTAATATTTTAAAAATATTATTA
1 TTAATATTTTAAAAATATTATTA
*
1190617 TTAAT-TTGTTAATAAATAATATTA
1 TTAATATT-TTAA-AAATATTATTA
1190641 TT
1 TT
1190643 TATTATATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
21 2 0.03
22 15 0.25
23 13 0.22
24 12 0.20
25 1 0.02
26 5 0.08
27 10 0.17
28 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (23 bp):
TTAATATTTTAAAAATATTATTA
Found at i:1192246 original size:13 final size:13
Alignment explanation
Indices: 1192223--1192254 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
1192213 ATATCTAATC
1192223 TTAATTAATAAATA
1 TTAA-TAATAAATA
1192237 TTAATAATAAATA
1 TTAATAATAAATA
1192250 TTAAT
1 TTAAT
1192255 CTAATGGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATAATAAATA
Found at i:1193793 original size:20 final size:20
Alignment explanation
Indices: 1193768--1193811 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1193758 TTATTGTCCA
1193768 CTTAATGATTTGTCGTCAAC
1 CTTAATGATTTGTCGTCAAC
*
1193788 CTTAATGATTTGTCGTCACC
1 CTTAATGATTTGTCGTCAAC
1193808 CTTA
1 CTTA
1193812 TTGACACACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (20 bp):
CTTAATGATTTGTCGTCAAC
Found at i:1194844 original size:41 final size:41
Alignment explanation
Indices: 1194707--1194903 Score: 136
Period size: 41 Copynumber: 4.8 Consensus size: 41
1194697 AAAATGATAC
** **
1194707 TTTAGCGGCGTTTTTAAACAAACGTCTTAATAGAG-GGTAA
1 TTTAGCGGCGTTTTTAAACAAACACCGCAATAGAGTGGTAA
* ** *
1194747 TTTAGCGGCGTTTATAGCTCAAACGCCGCAATAGAGAT-GT--
1 TTTAGCGGCGTTTTTA-AACAAACACCGCAATAGAG-TGGTAA
* * * *
1194787 TTATAGTGGCATTTTTTCAACAAACACCGCAATAGAGTGGTAC
1 TT-TAGCGGC-GTTTTTAAACAAACACCGCAATAGAGTGGTAA
* **
1194830 TTTAGCGGCGTTTTTAAACAAACGA-CGCTATAGAGAAGTAA
1 TTTAGCGGCGTTTTTAAACAAAC-ACCGCAATAGAGTGGTAA
* * *
1194871 TTTCGCGGCGTTTAATAAA-AAACATCGCAATAG
1 TTTAGCGGCGTTT-TTAAACAAACACCGCAATAG
1194904 TATTGTTTAT
Statistics
Matches: 123, Mismatches: 23, Indels: 21
0.74 0.14 0.13
Matches are distributed among these distances:
40 19 0.15
41 85 0.69
42 17 0.14
43 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAAACAAACACCGCAATAGAGTGGTAA
Found at i:1194939 original size:123 final size:122
Alignment explanation
Indices: 1194704--1194941 Score: 284
Period size: 123 Copynumber: 1.9 Consensus size: 122
1194694 CACAAAATGA
* * * **
1194704 TACTTTAGCGGCGTTTTTAAACAAACGTCTTAATAGAGGGTAATTTAGCGGCGTTTATAGCTCAA
1 TACTTTAGCGGCGTTTTTAAACAAACGACCTAATAGAGAGTAATTTAGCGGCGTTTATA-CAAAA
* * * *
1194769 ACGCCGCAATAGAGATGTTTATAGTGGCATTTTTTCAACAAACACCGCAATAGAGTGG
65 ACACCGCAATAGAGATGTTTATAGTGGCATTTGTGCAAAAAACACCGCAATAGAGTGG
*
1194827 TACTTTAGCGGCGTTTTTAAACAAACGACGCT-ATAGAGAAGTAATTTCGCGGCGTTTAATA-AA
1 TACTTTAGCGGCGTTTTTAAACAAACGAC-CTAATAGAG-AGTAATTTAGCGGCGTTT-ATACAA
* * * *
1194890 AAACATCGCAATAGTA-TTGTTTATAGTGGCGTTTGTGCAAAAAATACCGCAA
63 AAACACCGCAATAG-AGATGTTTATAGTGGCATTTGTGCAAAAAACACCGCAA
1194942 AAATATGAAC
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
123 76 0.78
124 18 0.19
125 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (122 bp):
TACTTTAGCGGCGTTTTTAAACAAACGACCTAATAGAGAGTAATTTAGCGGCGTTTATACAAAAA
CACCGCAATAGAGATGTTTATAGTGGCATTTGTGCAAAAAACACCGCAATAGAGTGG
Found at i:1195366 original size:22 final size:22
Alignment explanation
Indices: 1195340--1195390 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1195330 AAGTGTTTTT
1195340 TTGCTTTCGAATAGAAAAATAA
1 TTGCTTTCGAATAGAAAAATAA
1195362 TTGCTTTCGAATAGAAAAATAA
1 TTGCTTTCGAATAGAAAAATAA
*
1195384 TAGCTTT
1 TTGCTTT
1195391 TGAAAACGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
TTGCTTTCGAATAGAAAAATAA
Found at i:1196736 original size:21 final size:21
Alignment explanation
Indices: 1196691--1196738 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1196681 TAAGATCCCA
* **
1196691 ATGCTCCAATTGAATTTCGAG
1 ATGCTCCAATTAAATACCGAG
*
1196712 ATGCTCCAATTAAATACCGAT
1 ATGCTCCAATTAAATACCGAG
1196733 ATGCTC
1 ATGCTC
1196739 TAAAGCACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (21 bp):
ATGCTCCAATTAAATACCGAG
Found at i:1197639 original size:55 final size:56
Alignment explanation
Indices: 1197534--1197640 Score: 137
Period size: 55 Copynumber: 1.9 Consensus size: 56
1197524 TTCAATCCAC
* * *
1197534 AAACTAACACCTATGTGCTTTAATCAACGATTGAGCATCTCTATGTTTCAATTTAT
1 AAACTAACACCTATATGCTTTAATAAACGATTGAGCATCTCTATGCTTCAATTTAT
* * *
1197590 AAACTAACACCTCTAT-CTTTAATAAATGATTGAGCA-CTTTTATGCTTCAAT
1 AAACTAACACCTATATGCTTTAATAAACGATTGAGCATC-TCTATGCTTCAAT
1197641 CTAAAATTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 1 0.02
55 29 0.66
56 14 0.32
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (56 bp):
AAACTAACACCTATATGCTTTAATAAACGATTGAGCATCTCTATGCTTCAATTTAT
Found at i:1197684 original size:56 final size:56
Alignment explanation
Indices: 1197606--1197730 Score: 151
Period size: 56 Copynumber: 2.2 Consensus size: 56
1197596 ACACCTCTAT
* * * * * *
1197606 CTTTAATAAATGATTGAGCACTTTTATGCTTCAATCTAAAATTTGATACCTTTGTG
1 CTTTAATAAATGAGTCAACACTTATATGCTTCAATCTAAAATTTGACACCTATGTG
* * * * *
1197662 CTTTAATAAATGAGTCAACACTTATGTGCTTCACTTTAGAGTTTGACACCTATGTG
1 CTTTAATAAATGAGTCAACACTTATATGCTTCAATCTAAAATTTGACACCTATGTG
1197718 CTTTAATAAATGA
1 CTTTAATAAATGA
1197731 TGACTATATT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (56 bp):
CTTTAATAAATGAGTCAACACTTATATGCTTCAATCTAAAATTTGACACCTATGTG
Found at i:1209776 original size:15 final size:16
Alignment explanation
Indices: 1209716--1209797 Score: 60
Period size: 15 Copynumber: 5.1 Consensus size: 16
1209706 ATTACTTTGA
*
1209716 TTAATATATATATATAT
1 TTAATATAT-TTTATAT
* * * *
1209733 ATAATTTATTTTTTAG
1 TTAATATATTTTATAT
* *
1209749 TAATATATATTTTATTT
1 TTA-ATATATTTTATAT
1209766 TTAATAT-TTTTATAT
1 TTAATATATTTTATAT
*
1209781 TTAAT-TGTTTTATAT
1 TTAATATATTTTATAT
1209796 TT
1 TT
1209798 GTTTAGTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
14 1 0.02
15 22 0.44
16 9 0.18
17 18 0.36
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTAATATATTTTATAT
Found at i:1209779 original size:22 final size:23
Alignment explanation
Indices: 1209754--1209797 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1209744 TTTAGTAATA
*
1209754 TATATTTTATT-TTTAATATTTT
1 TATATTTAATTGTTTAATATTTT
*
1209776 TATATTTAATTGTTTTATATTT
1 TATATTTAATTGTTTAATATTT
1209798 GTTTAGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TATATTTAATTGTTTAATATTTT
Found at i:1210239 original size:28 final size:28
Alignment explanation
Indices: 1210194--1210247 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1210184 GGGTTTTATT
* *
1210194 GAAAATAGTTTCCGGAAAATG-AAATCTA
1 GAAAATAGTTTACAG-AAATGTAAATCTA
*
1210222 GAAAATATTTTACAGAAATGTAAATC
1 GAAAATAGTTTACAGAAATGTAAATC
1210248 ATTTTTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (28 bp):
GAAAATAGTTTACAGAAATGTAAATCTA
Found at i:1216219 original size:82 final size:82
Alignment explanation
Indices: 1216134--1216466 Score: 364
Period size: 82 Copynumber: 4.0 Consensus size: 82
1216124 CGATATCCAA
* * * * *
1216134 ATATATAACGGCGTTTTTGTAAAAATGCCGCTAAAAATGCGTACTTTAGTAGCGTTTATGTAAAA
1 ATATATAGCGGCGTTTTTATAAAAATGCCGCAAAAAACGCGTACTTTAGTGGCGTTTATG-AAAA
* *
1216199 AACATCGTAATA-TCCTA-
65 AACACCGTAATAGGCC-AG
* * * * *
1216216 ATATATAGCGGCATTTTTGTGAAAATGCCGCAAAAAACACGTACTTTAGTGGCGTTTATGCAAAA
1 ATATATAGCGGCGTTTTTATAAAAATGCCGCAAAAAACGCGTACTTTAGTGGCGTTTATGAAAAA
1216281 ACACCGTAATAGGCCAG
66 ACACCGTAATAGGCCAG
** * * * *
1216298 ATATATAGCGTAGTTTTTATGAAAATGCCACAAAAAATGCGTACTTTAGTGGCGTTTATGCAAAA
1 ATATATAGCGGCGTTTTTATAAAAATGCCGCAAAAAACGCGTACTTTAGTGGCGTTTATGAAAAA
1216363 ACACCGTAATAGGCCAG
66 ACACCGTAATAGGCCAG
* * * * * * * *
1216380 ATATATAGCGGCGTTTTTACAAAAACGCCTCTATAAACGCTTATTTTAGTGGCGTTTATGTATAA
1 ATATATAGCGGCGTTTTTATAAAAATGCCGCAAAAAACGCGTACTTTAGTGGCGTTTATG-AAAA
* * *
1216445 AACGCCGCAATAGCCCAG
65 AACACCGTAATAGGCCAG
1216463 ATAT
1 ATAT
1216467 GTAACCGCTA
Statistics
Matches: 215, Mismatches: 33, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
81 15 0.07
82 179 0.83
83 21 0.10
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (82 bp):
ATATATAGCGGCGTTTTTATAAAAATGCCGCAAAAAACGCGTACTTTAGTGGCGTTTATGAAAAA
ACACCGTAATAGGCCAG
Found at i:1216394 original size:41 final size:41
Alignment explanation
Indices: 1216266--1216405 Score: 101
Period size: 41 Copynumber: 3.4 Consensus size: 41
1216256 GTACTTTAGT
1216266 GGCGTTTATGCAAAAACACCGTAATAGGCCAGATATATAGC
1 GGCGTTTATGCAAAAACACCGTAATAGGCCAGATATATAGC
** * ** * * * *
1216307 GTAGTTTTTATG-AAAATGC-CACAAAAAATG-C-G-TACTTTAGT
1 G--GCGTTTATGCAAAA-ACAC-CGTAATAGGCCAGATA-TATAGC
1216348 GGCGTTTATGCAAAAACACCGTAATAGGCCAGATATATAGC
1 GGCGTTTATGCAAAAACACCGTAATAGGCCAGATATATAGC
* *
1216389 GGCGTTTTTACAAAAAC
1 GGCGTTTATGCAAAAAC
1216406 GCCTCTATAA
Statistics
Matches: 69, Mismatches: 20, Indels: 20
0.63 0.18 0.18
Matches are distributed among these distances:
39 13 0.19
40 8 0.12
41 27 0.39
42 8 0.12
43 13 0.19
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (41 bp):
GGCGTTTATGCAAAAACACCGTAATAGGCCAGATATATAGC
Found at i:1216935 original size:27 final size:27
Alignment explanation
Indices: 1216897--1216948 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1216887 TTTCTGCTTC
1216897 AATTTAGTTTTTGGTCATTCAATCTGG
1 AATTTAGTTTTTGGTCATTCAATCTGG
* *
1216924 AATTTGGTTTTTGGTCGTTCAATCT
1 AATTTAGTTTTTGGTCATTCAATCT
1216949 ATTTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (27 bp):
AATTTAGTTTTTGGTCATTCAATCTGG
Found at i:1221824 original size:37 final size:36
Alignment explanation
Indices: 1221772--1222254 Score: 479
Period size: 39 Copynumber: 13.1 Consensus size: 36
1221762 GCAAACGGTC
1221772 TTTGAAAATACGTATATAATATATAGTTTTTAAAAGCAT
1 TTTGAAAATA--TATATAATATATAGTTTTTAAAA-CAT
* *
1221811 TTTAAAAATGTATATAATATATAGTTTTTAAAACATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAACA-T
* *
1221848 TTTGAAAA-CTATATAATATATAATTTTTAAAACAT
1 TTTGAAAATATATATAATATATAGTTTTTAAAACAT
1221883 TTTAGAAAATATATATAATATATAGTTTTTAAAATCAT
1 TTT-GAAAATATATATAATATATAGTTTTTAAAA-CAT
*
1221921 TTTGAAAACT-TATATAATATATAGTTTTGAAAACATT
1 TTTGAAAA-TATATATAATATATAGTTTTTAAAACA-T
* *
1221958 TTTGAAAATTTATATAATATATAGTTTTGAAAACA-
1 TTTGAAAATATATATAATATATAGTTTTTAAAACAT
1221993 -TT-----TATATAT--TATATAGTTTTTTAAAAAACAT
1 TTTGAAAATATATATAATATATAG-TTTTT--AAAACAT
*
1222024 ATTGAAAATATATATAATATATAGTTTTTTAAAAAACAT
1 TTTGAAAATATATATAATATATAG-TTTTT--AAAACAT
*
1222063 ATTGAAAATATATATAATATATAGTTTTTTAAAAAACAT
1 TTTGAAAATATATATAATATATAG-TTTTT--AAAACAT
*
1222102 ATTGAAAATATATATAATATATAGTTTTTTAAAAACATT
1 TTTGAAAATATATATAATATATAG-TTTTT-AAAACA-T
* *
1222141 TTTGAAAATATATATATTATATAGTTTTTTAAAACGTT
1 TTTGAAAATATATATAATATATAG-TTTTTAAAAC-AT
** *
1222179 TTTGAAAATACGTATAATATATAGTTTTAAAAAACCAT
1 TTTGAAAATATATATAATATATAGTTTT-TAAAA-CAT
* * *
1222217 TTTGGAAACT-TATATATTATATA-TTTTTGAAAATAT
1 TTT-GAAAATATATATAATATATAGTTTTT-AAAACAT
1222253 TT
1 TT
1222255 GTTATATAAT
Statistics
Matches: 395, Mismatches: 24, Indels: 53
0.84 0.05 0.11
Matches are distributed among these distances:
27 7 0.02
28 4 0.01
29 6 0.02
30 6 0.02
32 2 0.01
34 2 0.01
35 4 0.01
36 38 0.10
37 133 0.34
38 59 0.15
39 134 0.34
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAACAT
Found at i:1221985 original size:25 final size:27
Alignment explanation
Indices: 1221957--1222012 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
1221947 TTGAAAACAT
1221957 TTTTG-AAA-ATTTATATAATATATAG
1 TTTTGAAAACATTTATATAATATATAG
*
1221982 TTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAACATTTATATAATATATAG
1222009 TTTT
1 TTTT
1222013 TTAAAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 5 0.18
26 3 0.11
27 20 0.71
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (27 bp):
TTTTGAAAACATTTATATAATATATAG
Found at i:1222272 original size:19 final size:19
Alignment explanation
Indices: 1222250--1222298 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1222240 TTTTTGAAAA
*
1222250 TATTTGTTATATAATA-TAT
1 TATTTATTAT-TAATATTAT
*
1222269 TATTTATTATTATTATTAT
1 TATTTATTATTAATATTAT
1222288 TATTTATTATT
1 TATTTATTATT
1222299 TATTTATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTATTATTAATATTAT
Found at i:1222276 original size:7 final size:7
Alignment explanation
Indices: 1222266--1222307 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
1222256 TTATATAATA
1222266 TATTATT
1 TATTATT
1222273 TATTA-T
1 TATTATT
1222279 TATTA-T
1 TATTATT
1222285 TATTATT
1 TATTATT
1222292 TATTATT
1 TATTATT
1222299 TATTTATT
1 TA-TTATT
1222307 T
1 T
1222308 CTTTTTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.36
7 15 0.45
8 6 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTATT
Found at i:1223554 original size:18 final size:19
Alignment explanation
Indices: 1223519--1223560 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1223509 TATATATATT
*
1223519 TTATTTTTATTTGTGTTTA
1 TTATTTTTATTTGCGTTTA
1223538 TTATTTTTATTT-CGTTTA
1 TTATTTTTATTTGCGTTTA
1223556 -TATTT
1 TTATTT
1223561 ATTTATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 5 0.23
19 12 0.55
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (19 bp):
TTATTTTTATTTGCGTTTA
Found at i:1223565 original size:4 final size:4
Alignment explanation
Indices: 1223556--1223601 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
1223546 ATTTCGTTTA
1223556 TATT TATT TATT TATT TATT TATGT T-TGT T-TT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TAT-T TAT-T TATT TATT TATT TATT TA
1223602 CTTAATAGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 2 0.05
4 36 0.90
5 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1223592 original size:32 final size:32
Alignment explanation
Indices: 1223534--1223601 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
1223524 TTTATTTGTG
*
1223534 TTTATTATTTTTATTTCGTTTATATTTATTTA
1 TTTATTATATTTATTTCGTTTATATTTATTTA
* *
1223566 TTTATT-TATTTATGTTTGTTTTTATTTATTTA
1 TTTATTATATTTAT-TTCGTTTATATTTATTTA
1223598 TTTA
1 TTTA
1223602 CTTAATAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTATTATATTTATTTCGTTTATATTTATTTA
Found at i:1223751 original size:19 final size:21
Alignment explanation
Indices: 1223722--1223774 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 21
1223712 TATTTTCATT
1223722 TTTTTACTTTTATTTTA-TA-C
1 TTTTTA-TTTTATTTTATTACC
1223742 TTTTTATTTTATTTTATTACC
1 TTTTTATTTTATTTTATTACC
1223763 TTTTTATCTTTA
1 TTTTTAT-TTTA
1223775 CCTTCTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.33
20 8 0.27
21 8 0.27
22 4 0.13
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTATTTTATTTTATTACC
Found at i:1223800 original size:9 final size:10
Alignment explanation
Indices: 1223780--1223813 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
1223770 CTTTACCTTC
1223780 TTTATATTTTT
1 TTTATA-TTTT
1223791 TTTATATTTT
1 TTTATATTTT
1223801 TTTAATATTTT
1 TTT-ATATTTT
1223812 TT
1 TT
1223814 ATTTCATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATATTTT
Found at i:1223945 original size:21 final size:20
Alignment explanation
Indices: 1223906--1223946 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1223896 TCGAATCGGA
*
1223906 TTTTTAAATTTCAATTTAAG
1 TTTTTAAATTTCAAATTAAG
*
1223926 TTTTTAATTTTCGAAATTAAG
1 TTTTTAAATTTC-AAATTAAG
1223947 ACAATCGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (20 bp):
TTTTTAAATTTCAAATTAAG
Found at i:1226643 original size:95 final size:94
Alignment explanation
Indices: 1226471--1226733 Score: 339
Period size: 95 Copynumber: 2.7 Consensus size: 94
1226461 ATTATAATAT
* * *
1226471 ATTATATATATACAATAAAACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACACCCCGGCTTTA
1 ATTATA-ATATAAAAT-AAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
1226536 TGGATAAGATTCAACTAGCCTGATAAAGGTG
64 TGGATAAGATTCAACTAGCCTGATAAAGGTG
*
1226567 ATTATAATATAAAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
1 ATTATAATATAAAATAAA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
* *
1226632 GGATAATATTCAGCTAGCCTGATAAAGGTG
65 GGATAAGATTCAACTAGCCTGATAAAGGTG
* * * * *
1226662 ATTATAATATCTATACAATGATA-TTAAGTTGACCCTCTAGAGCAATTGGTTACATGCCCCGGCT
1 ATTATAATA--TA-A-AAT-AAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCT
*
1226726 TTTTGGAT
61 TTATGGAT
1226734 TCATCTAGCC
Statistics
Matches: 148, Mismatches: 13, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
94 3 0.02
95 88 0.59
96 6 0.04
97 2 0.01
98 44 0.30
99 3 0.02
100 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (94 bp):
ATTATAATATAAAATAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
GATAAGATTCAACTAGCCTGATAAAGGTG
Found at i:1228005 original size:84 final size:84
Alignment explanation
Indices: 1227859--1228925 Score: 1016
Period size: 84 Copynumber: 12.9 Consensus size: 84
1227849 GAAACTATCG
* *
1227859 GCAGCATAACTCAAGGCGAGAAAGGTTATCTGT-CAACC-AAGACCTTCGAGTTCGACTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGACTACGCTC
* *
1227922 AGCTTCAAGGTATATCATTT
65 AGCTTCAAGGCACATCATTT
* * *
1227942 GCAGCATAGCTCAAGGCTAGAAGGGTTATCTTCCACCCAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * *
1228007 ACCTCAAGGCATATCATTT
66 GCTTCAAGGCACATCATTT
* * * * * *
1228026 TCAGCATAACTCAAGGCTAGAAGGGTTATATGCCGACCAAAGACCTTCAAGTTCTACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
*
1228091 GCTTCGAGGGCACATCATTT
66 GCTTC-AAGGCACATCATTT
** * * * * * ** * *
1228111 ATAGCATAACTTAACGCGATAATGGTTAT-TTGCCAATAAAAGACCTTCGAGTTTGATTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTT-CCAACCAAAGACCTTCGAGTTCGACTACGCTC
*
1228175 AGCTCCAAGGCACATCATTT
65 AGCTTCAAGGCACATCATTT
* *
1228195 GTAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * *
1228260 GCTCCAAGGCATATTA-TT
66 GCTTCAAGGCACATCATTT
* * * ** * *
1228278 GCAGCATAGCTCAAGGCTGGAAAGACTATCTGCC-A-C-----CCTTCGAGTTCGACTATGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* *
1228336 TCTTCCAGGCACATCATTT
66 GCTTCAAGGCACATCATTT
* * ** * * * *
1228355 GCAACATAGCTCAAGGAAAGAAGGGCTATTTTCCAACAAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
*
1228420 GC-TCTAAGGCATATCATTT
66 GCTTC-AAGGCACATCATTT
* * * * *
1228439 GCAGTATAGCTCAAGGCTAGAATGGCTATCTGCC-ACCAAAAGACCTTCGAGTTCGACTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACC-AAAGACCTTCGAGTTCGACTACGCTC
* * *
1228503 AGCTCCCAGGCCCATCATTT
65 AGCTTCAAGGCACATCATTT
* * *
1228523 GCAGTATAACTCAAGTCTAGAAGGGTTATCTGT-CAACCAAAGACCTTCGAGTTCGACTACACTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGACTACGCTC
1228587 AGC-TCTAAGGCACATCATTT
65 AGCTTC-AAGGCACATCATTT
* * *
1228607 GCAACATAACTCAAGGC-A-ATAGGGTTATTTTCCAACAAAAGACCTTCGAGTTCGACTACGCTC
1 GCAGCATAACTCAAGGCTAGA-AGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTC
* *
1228670 AGCTCCAAGGCACATTATTT
65 AGCTTCAAGGCACATCATTT
* * * * * * * * * *
1228690 GCAGCATAACTTAAGTCGAGAAAGGCTATATGCCAACCAAAGACCTTCGAGTTCGATTACACCCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
*
1228755 TC-TCAAAGGCACATCATTT
66 GCTTC-AAGGCACATCATTT
* * *
1228774 ACAGAATAACTCAAGGCTAGAAGGGTTATCTGT-CAA-CAAAGACCTTCGAGTTCAACTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGACTACGCTC
*
1228837 AGC-TCTAAGGTACATCATTT
65 AGCTTC-AAGGCACATCATTT
* * * * * ** * * *
1228857 ACAGCATAGCTTAAGGCAAGAATGACTATC-T---GCCAAAGACCTTCGAGTTTGACTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
1228918 GC-TCAAGG
66 GCTTCAAGG
1228926 GCATGTCAGA
Statistics
Matches: 809, Mismatches: 148, Indels: 58
0.80 0.15 0.06
Matches are distributed among these distances:
76 32 0.04
77 28 0.03
78 1 0.00
79 4 0.00
80 29 0.04
81 1 0.00
82 4 0.00
83 199 0.25
84 440 0.54
85 71 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (84 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
GCTTCAAGGCACATCATTT
Found at i:1228729 original size:167 final size:168
Alignment explanation
Indices: 1227859--1228993 Score: 1108
Period size: 167 Copynumber: 6.8 Consensus size: 168
1227849 GAAACTATCG
* * *
1227859 GCAGCATAACTCAAGGCGAGAAAGGTTATCTGTCAACC-AAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * * * *
1227923 GCT-TCAAGGTATATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTTCCACCCAAAGACC
66 GCTCT-AAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACC
* * *
1227987 TTCGAGTTTGACTACGCTCAAC-CTCAAGGCATATCATTT
130 TTCGAGTTCGACTACGCTCAGCTC-CAAGGCACATCATTT
* * * * *
1228026 TCAGCATAACTCAAGGCTAGAAGGGTTATATGCCGACCAAAGACCTTCAAGTTCTACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * ** * * * * * * *
1228091 GCTTCGAGGGCACATCATTTATAGCATAACTTAACGCGATAATGGTTATTTGCCAATAAAAGACC
66 GC-TCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACC
* *
1228156 TTCGAGTTTGATTACGCTCAGCTCCAAGGCACATCATTT
130 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
1228195 GTAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * * * * **
1228260 GCTCCAAGGCATATTA-TTGCAGCATAGCTCAAGGCTGGAAAGACTATCTGCC-AC------CCT
66 GCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
* *
1228317 TCGAGTTCGACTATGCTCATCTTCC-AGGCACATCATTT
131 TCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
* * ** * * * * *
1228355 GCAACATAGCTCAAGGAAAGAAGGGCTATTTTCCAACAAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * * * *
1228420 GCTCTAAGGCATATCATTTGCAGTATAGCTCAAGGCTAGAATGGCTATCTGCCACCAAAAGACCT
66 GCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
* *
1228485 TCGAGTTCGACTACGCTCAGCTCCCAGGCCCATCATTT
131 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * *
1228523 GCAGTATAACTCAAGTCTAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * *
1228588 GCTCTAAGGCACATCATTTGCAACATAACTCAAGGC-A-ATAGGGTTATTTTCCAACAAAAGACC
66 GCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGA-AGGGTTATCTGCCAACAAAAGACC
*
1228651 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTT
130 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * * * * * *
1228690 GCAGCATAACTTAAGTCGAGAAAGGCTATATGCCAACCAAAGACCTTCGAGTTCGATTACACCCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * * *
1228755 TCTCAAAGGCACATCATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCT
66 GCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
* * *
1228819 TCGAGTTCAACTACGCTCAGCTCTAAGGTACATCATTT
131 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * * ** * *
1228857 ACAGCATAGCTTAAGGCAAGAATGACTATCTG----CCAAAGACCTTCGAGTTTGACTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
** * * * * * **
1228918 GCTC-AAGGGCATGTCAGATTTACAGCATAGCTTAAGTCAAGAAAAGTTATCTGCCAACAAAA-A
66 GCTCTAA-GGCACATC--ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGA
1228981 -CTGTCGAGTTCGA
128 CCT-TCGAGTTCGA
1228994 TTCCATTCAG
Statistics
Matches: 803, Mismatches: 143, Indels: 46
0.81 0.14 0.05
Matches are distributed among these distances:
160 104 0.13
161 35 0.04
162 3 0.00
163 35 0.04
164 2 0.00
165 43 0.05
166 5 0.01
167 269 0.33
168 168 0.21
169 138 0.17
170 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (168 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
GCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
Found at i:1229632 original size:37 final size:36
Alignment explanation
Indices: 1229591--1229803 Score: 270
Period size: 37 Copynumber: 5.8 Consensus size: 36
1229581 TTGAAAATAC
1229591 GTATATAATATATAGTTTTTAAAA-ATGTATTAAAAAT
1 GTATATAATATATAGTTTTTAAAACAT-T-TTAAAAAT
*
1229628 GTATATAATATATAGTTTTTAAAACATTTTTGAAAA-
1 GTATATAATATATAGTTTTTAAAACA-TTTTAAAAAT
*
1229664 CTATATAATATATAGTTTTTAAAACATTTTAGAAAAT
1 GTATATAATATATAGTTTTTAAAACATTTTA-AAAAT
* *
1229701 ATATATAATATATAGTTTTTAAAATCATTTTGAAAACT
1 GTATATAATATATAGTTTTTAAAA-CATTTT-AAAAAT
* *
1229739 -TATATAATATATAGTTTTGAAAACATTTTTGAAAAT
1 GTATATAATATATAGTTTTTAAAACA-TTTTAAAAAT
* *
1229775 TTATATAATATATAGTTTTGAAAACATTT
1 GTATATAATATATAGTTTTTAAAACATTT
1229804 ATATATTATA
Statistics
Matches: 160, Mismatches: 8, Indels: 17
0.86 0.04 0.09
Matches are distributed among these distances:
35 4 0.03
36 38 0.24
37 104 0.65
38 12 0.08
39 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
GTATATAATATATAGTTTTTAAAACATTTTAAAAAT
Found at i:1229743 original size:110 final size:109
Alignment explanation
Indices: 1229580--1229948 Score: 354
Period size: 110 Copynumber: 3.3 Consensus size: 109
1229570 GCAAACGGTC
*
1229580 TTTGAAAATACGTATATAATATATAGTTTTTAAAA--ATGTATT-AAAAATGTATATAATATATA
1 TTTGAAAATA--TATATAATATATAGTTTTTAAAATCAT-T-TTGAAAAATATATATAATATATA
1229642 GTTTTTAAAACATTTTTGAAAACTATATAATATATAGTTTTTAAAACAT
62 GTTTTTAAAACATTTTTGAAAA-TATATAATATATAGTTTTTAAAACAT
*
1229691 TTTAGAAAATATATATAATATATAGTTTTTAAAATCATTTTGAAAACT-TATATAATATATAGTT
1 TTT-GAAAATATATATAATATATAGTTTTTAAAATCATTTTGAAAAATATATATAATATATAGTT
* *
1229755 TTGAAAACATTTTTGAAAATTTATATAATATATAGTTTTGAAAACA-
65 TTTAAAACATTTTTGAAAA--TATATAATATATAGTTTTTAAAACAT
*
1229801 -TT-----TATATAT--TATATAGTTTTTAAAAACATTTTGAATATATATATATATATATATATA
1 TTTGAAAATATATATAATATATAGTTTTTAAAATCATTTTG-A-A-A-A-ATATATATA-ATATA
*
1229858 TAGTTTTTTAAAACGTTTTTGAAAATACGTATAATATATAGTTTTTTAAAAAAACAT
60 TAG-TTTTTAAAACATTTTTGAAAATA--TATAATATATAG-TTTTT---AAAACAT
* *
1229915 TTTGGAAACT-TATATATTATAT-GTTTTTGAAAAT
1 TTT-GAAAATATATATAATATATAGTTTTT-AAAAT
1229949 ATTGTTTATA
Statistics
Matches: 218, Mismatches: 10, Indels: 49
0.79 0.04 0.18
Matches are distributed among these distances:
101 23 0.11
102 1 0.00
103 8 0.04
104 1 0.00
105 1 0.00
106 1 0.00
107 8 0.04
108 8 0.04
109 33 0.15
110 63 0.29
111 33 0.15
112 9 0.04
113 6 0.03
115 2 0.01
120 5 0.02
121 7 0.03
122 9 0.04
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (109 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAATCATTTTGAAAAATATATATAATATATAGTTT
TTAAAACATTTTTGAAAATATATAATATATAGTTTTTAAAACAT
Found at i:1229773 original size:74 final size:72
Alignment explanation
Indices: 1229592--1229947 Score: 333
Period size: 73 Copynumber: 4.8 Consensus size: 72
1229582 TGAAAATACG
* * *
1229592 TATATAATATATAGTTTTTAAAA-ATGTATTAAAAATGTATATAATATATAGTTTTTAAAACATT
1 TATATAATATATAGTTTTTAAAACAT-TTTTGAAAATATATATAATATATAGTTTTTAAAACA-T
1229656 TTTGAAAAC
64 TTTGAAAAC
*
1229665 TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCATT
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATAATATATAGTTTTTAAAA-CATT
1229730 TTGAAAAC
65 TTGAAAAC
* * *
1229738 TTATATAATATATAGTTTTGAAAACATTTTTGAAAATTTATATAATATATAGTTTTGAAAACA-T
1 -TATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATAATATATAGTTTTTAAAACATT
1229802 TT----A-
65 TTGAAAAC
1229805 TATAT--TATATAGTTTTTAAAAACA-TTTTGAATATATATATATATATATATATATAGTTTTTT
1 TATATAATATATAGTTTTT-AAAACATTTTTG---A-A-A-ATATATATA-ATATATAG-TTTTT
*
1229867 AAAACGTTTTTGAAAA-
57 AAAAC-ATTTTGAAAAC
* * *
1229883 TACGTATAATATATAGTTTTTTAAAAAAACATTTTGGAAACT-TATATATTATAT-GTTTTTGAA
1 TA--TATAATATATAG-TTTTT---AAAACATTTTTGAAAATATATATAATATATAGTTTTT-AA
1229946 AA
59 AA
1229948 TATTGTTTAT
Statistics
Matches: 241, Mismatches: 15, Indels: 50
0.79 0.05 0.16
Matches are distributed among these distances:
64 16 0.07
65 6 0.02
66 5 0.02
67 1 0.00
68 2 0.01
69 1 0.00
70 8 0.03
71 8 0.03
72 12 0.05
73 65 0.27
74 63 0.26
76 5 0.02
77 5 0.02
78 8 0.03
79 6 0.02
80 4 0.02
81 1 0.00
82 8 0.03
83 6 0.02
85 7 0.03
86 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (72 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATAATATATAGTTTTTAAAACATTT
TGAAAAC
Found at i:1229813 original size:27 final size:28
Alignment explanation
Indices: 1229764--1229831 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
1229754 TTTGAAAACA
1229764 TTTTTG-AAA-ATTTATATAATATATAG
1 TTTTTGAAAACATTTATATAATATATAG
*
1229790 -TTTTGAAAACATTTATATATTATATAG
1 TTTTTGAAAACATTTATATAATATATAG
*
1229817 TTTTTAAAAACATTT
1 TTTTTGAAAACATTT
1229832 TGAATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 5 0.14
26 3 0.08
27 16 0.43
28 13 0.35
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (28 bp):
TTTTTGAAAACATTTATATAATATATAG
Found at i:1229817 original size:64 final size:63
Alignment explanation
Indices: 1229728--1229853 Score: 175
Period size: 64 Copynumber: 2.0 Consensus size: 63
1229718 TTTAAAATCA
* *
1229728 TTTTGAAAACTTATATAATATATAG-TTTTGAAAACATTTTTGAAAATTTATATA-ATATATAG
1 TTTTGAAAACTTATATAATATATAGTTTTTAAAAACA-TTTTGAAAATATATATATATATATAG
* *
1229790 TTTTGAAAACATTTATATATTATATAGTTTTTAAAAACATTTTGAATATATATATATATATATA
1 TTTTGAAAAC--TTATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATATATATATA
1229854 TATATAGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
62 10 0.18
64 29 0.52
65 17 0.30
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (63 bp):
TTTTGAAAACTTATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATATATATATAG
Found at i:1229841 original size:28 final size:26
Alignment explanation
Indices: 1229773--1229845 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 26
1229763 ATTTTTGAAA
*
1229773 ATTTATATAATATATAGTTTTGAAAAC
1 ATTTATAT-ATATATAGTTTTAAAAAC
1229800 ATTTATATATTATATAGTTTTTAAAAAC
1 ATTTATATA-TATATAG-TTTTAAAAAC
1229828 ATTTTGAATATATATATA
1 A-TTT--ATATATATATA
1229846 TATATATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 1 0.03
27 15 0.38
28 10 0.25
29 3 0.08
30 6 0.15
31 5 0.12
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (26 bp):
ATTTATATATATATAGTTTTAAAAAC
Found at i:1229842 original size:2 final size:2
Alignment explanation
Indices: 1229835--1229859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1229825 AACATTTTGA
1229835 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1229860 GTTTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1229895 original size:44 final size:45
Alignment explanation
Indices: 1229803--1229897 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 45
1229793 TGAAAACATT
* *
1229803 TATATATTATATAGTTTTTAAAAACATTTTGAATATATATATATA
1 TATATATTATATAGTTTTTAAAAACATTTTGAAAATACATATATA
* * *
1229848 TATATA-TATATAGTTTTTTAAAACGTTTTTGAAAATACGTATA-A
1 TATATATTATATAGTTTTTAAAAAC-ATTTTGAAAATACATATATA
1229892 TATATA
1 TATATA
1229898 GTTTTTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
44 24 0.55
45 20 0.45
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (45 bp):
TATATATTATATAGTTTTTAAAAACATTTTGAAAATACATATATA
Found at i:1229936 original size:40 final size:39
Alignment explanation
Indices: 1229845--1229947 Score: 97
Period size: 39 Copynumber: 2.6 Consensus size: 39
1229835 ATATATATAT
* *
1229845 ATATATATATATATAGTTTTTT---AAAACGTTTTTGAAA
1 ATATATAT-TATATAGTTTTTTAAAAAAACATTTTGGAAA
*
1229882 ATACGTATAATATATAGTTTTTTAAAAAAACATTTTGGAAA
1 ATA--TATATTATATAGTTTTTTAAAAAAACATTTTGGAAA
* *
1229923 CTTATATATTATAT-GTTTTTGAAAA
1 -ATATATATTATATAGTTTTTTAAAA
1229948 TATTGTTTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
37 3 0.06
38 13 0.24
39 14 0.26
40 9 0.17
41 13 0.24
42 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (39 bp):
ATATATATTATATAGTTTTTTAAAAAAACATTTTGGAAA
Found at i:1229972 original size:16 final size:16
Alignment explanation
Indices: 1229947--1230002 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
1229937 GTTTTTGAAA
*
1229947 ATATTGTTTATATAAT
1 ATATTATTTATATAAT
* *
1229963 ATATTTTTTATATTAT
1 ATATTATTTATATAAT
*
1229979 -TATTATTTATATTAT
1 ATATTATTTATATAAT
*
1229994 TTATTATTT
1 ATATTATTT
1230003 TTTTTGTCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 14 0.39
16 22 0.61
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
ATATTATTTATATAAT
Found at i:1229990 original size:146 final size:141
Alignment explanation
Indices: 1229655--1229972 Score: 318
Period size: 149 Copynumber: 2.2 Consensus size: 141
1229645 TTTAAAACAT
* *
1229655 TTTTGAAAAC-TATATA-AT-ATATAGTTTTTAAAACATTTT--AGA-A-A-ATATATATAATAT
1 TTTTGAAAACATTTATATATAATATAGTTTTT-AAACATTTTGAATATATATATATATATAATAT
* *
1229712 ATAGTTTTTAAAATCATTTTGAAAACTTATATAATATATAGTTTTGAAAACATTTTTGAAAATTT
65 ATAGTTTTTAAAATCATTTTGAAAAC-TATATAATATATAGTTTTAAAAACATTTTTGAAAACTT
1229777 ATATAATATATAG
129 ATATAATATATAG
*
1229790 TTTTGAAAACATTTATATATTATATAGTTTTTAAAAACATTTTGAATATATATATATATATATAT
1 TTTTGAAAACATTTATATATAATATAGTTTTT--AAACATTTTGAATATATATATATATATA-AT
*
1229855 ATATAGTTTTTTAAAA-CGTTTTTGAAAA-TACGTATAATATATAGTTTTTTAAAAAAACA-TTT
63 ATATAG-TTTTTAAAATC-ATTTTGAAAACTA--TATAATATATAG--TTTT--AAAAACATTTT
* *
1229917 TGGAAACTTATATATTATAT-G
120 TGAAAACTTATATAATATATAG
* * *
1229938 TTTTTGAAAATATTGTTTATATAATATATTTTTTA
1 -TTTTGAAAACATT-TATATATAATATAGTTTTTA
1229973 TATTATTATT
Statistics
Matches: 152, Mismatches: 11, Indels: 27
0.80 0.06 0.14
Matches are distributed among these distances:
135 10 0.07
136 5 0.03
137 2 0.01
138 11 0.07
139 10 0.07
141 2 0.01
142 1 0.01
143 1 0.01
144 11 0.07
145 9 0.06
146 30 0.20
148 6 0.04
149 32 0.21
150 22 0.14
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (141 bp):
TTTTGAAAACATTTATATATAATATAGTTTTTAAACATTTTGAATATATATATATATATAATATA
TAGTTTTTAAAATCATTTTGAAAACTATATAATATATAGTTTTAAAAACATTTTTGAAAACTTAT
ATAATATATAG
Found at i:1231232 original size:10 final size:10
Alignment explanation
Indices: 1231217--1231287 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
1231207 TAGTTTTACA
*
1231217 TTTATTTGTT
1 TTTATTTATT
1231227 TTTA-TTATT
1 TTTATTTATT
1231236 TTTATTTCATT
1 TTTATTT-ATT
*
1231247 TATATTTATTT
1 TTTATTTA-TT
1231258 CTTTATTTA--
1 -TTTATTTATT
* *
1231267 TTTGTTTGTT
1 TTTATTTATT
1231277 TTTATTTATT
1 TTTATTTATT
1231287 T
1 T
1231288 ATTTACTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
8 6 0.12
9 8 0.17
10 16 0.33
11 11 0.23
12 7 0.15
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.76
Consensus pattern (10 bp):
TTTATTTATT
Found at i:1231254 original size:15 final size:14
Alignment explanation
Indices: 1231231--1231292 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
1231221 TTTGTTTTTA
*
1231231 TTATTTTTATTTCAT
1 TTATATTTATTTC-T
1231246 TTATATTTATTTCT
1 TTATATTTATTTCT
* *
1231260 TTATTTATTTGTTTGT
1 TTA--TATTTATTTCT
* *
1231276 TTTTATTTATTTAT
1 TTATATTTATTTCT
1231290 TTA
1 TTA
1231293 CTTAATAGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
14 15 0.39
15 12 0.32
16 11 0.29
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (14 bp):
TTATATTTATTTCT
Found at i:1231266 original size:4 final size:4
Alignment explanation
Indices: 1231236--1231292 Score: 50
Period size: 4 Copynumber: 15.0 Consensus size: 4
1231226 TTTTATTATT
* * *
1231236 TTTA TTTCA TTTA --TA TTTA TTTC TTTA TTTA TTTG TTT- GTT- TTTA
1 TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1231281 TTTA TTTA TTTA
1 TTTA TTTA TTTA
1231293 CTTAATAGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
2 2 0.05
3 4 0.09
4 34 0.77
5 4 0.09
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1231376 original size:12 final size:13
Alignment explanation
Indices: 1231361--1231392 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1231351 TAGTTCTGTT
1231361 TTTTATTCTT-TA
1 TTTTATTCTTATA
1231373 TTTTATTCTTATA
1 TTTTATTCTTATA
1231386 TTTTATT
1 TTTTATT
1231393 TATTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTATTCTTATA
Found at i:1231477 original size:21 final size:20
Alignment explanation
Indices: 1231429--1231483 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
1231419 CTATTTTCTT
*
1231429 TTTTTACTTTTATTTTATACT
1 TTTTTA-TTTTATTTTATACC
*
1231450 TTCTTTATTTTATTTTATTGCC
1 TT-TTTATTTTATTTTA-TACC
1231472 TTTTTATCTTTA
1 TTTTTAT-TTTA
1231484 CCTTCTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTATTTTATTTTATACC
Found at i:1232778 original size:20 final size:20
Alignment explanation
Indices: 1232755--1232909 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
1232745 GTTTCCAGAT
1232755 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
** *
1232775 TCGCATTGCGATTTTCCGACTA
1 TCGCAACGCGA--TTCTGACTA
* * * *
1232797 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
* *
1232817 TCGCAATGCGATTATGACTA
1 TCGCAACGCGATTCTGACTA
1232837 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
1232857 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
1232877 TCACAACGCGATGCTGACTA
1 TCGCAACGCGATTCTGACTA
*
1232897 TCGCAATGCGATT
1 TCGCAACGCGATT
1232910 TTCAAAGTGC
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
19 1 0.01
20 92 0.82
21 1 0.01
22 18 0.16
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1232860 original size:40 final size:40
Alignment explanation
Indices: 1232755--1232909 Score: 177
Period size: 40 Copynumber: 3.8 Consensus size: 40
1232745 GTTTCCAGAT
* *
1232755 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTCCGACTA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTAT--GACTA
* * * *
1232797 TCGCAATGCGAATATGTA-AATCGCAATGCGATTATGACTA
1 TCGCAACGCGATTCTG-ACTATCGCAATGCGATTATGACTA
* * *
1232837 TCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTATGACTA
* *
1232877 TCACAACGCGATGCTGACTATCGCAATGCGATT
1 TCGCAACGCGATTCTGACTATCGCAATGCGATT
1232910 TTCAAAGTGC
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 65 0.69
42 27 0.29
43 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
TCGCAACGCGATTCTGACTATCGCAATGCGATTATGACTA
Found at i:1233109 original size:22 final size:22
Alignment explanation
Indices: 1233084--1233148 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
1233074 GGCGACATCC
1233084 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1233106 GTCCCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1233128 GTCCTCATCTCC-AGCGAAATC
1 GTCCCCATCTCCGA-CGAAATC
1233149 CGTCTATCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.20
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1233159 original size:20 final size:22
Alignment explanation
Indices: 1233075--1233160 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
1233065 ACTCTCTAAG
* * *
1233075 GCGACATCCGTCCCCATCTCC-
1 GCGAAATCAGTCCTCATCTCCA
* *
1233096 GACGAAATCAGTCCCCATCTCCG
1 G-CGAAATCAGTCCTCATCTCCA
1233119 GCGAAATCAGTCCTCATCTCCA
1 GCGAAATCAGTCCTCATCTCCA
*
1233141 GCGAAATCCGT-CT-ATCTCCA
1 GCGAAATCAGTCCTCATCTCCA
1233161 TCTCTCAGAG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.12
21 3 0.05
22 47 0.81
23 1 0.02
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.21
Consensus pattern (22 bp):
GCGAAATCAGTCCTCATCTCCA
Found at i:1233589 original size:20 final size:20
Alignment explanation
Indices: 1233564--1233616 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1233554 CGATTTTCAT
1233564 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
* **
1233584 TTCGCGTTGTGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
1233604 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
1233617 TTTAAGTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:1235678 original size:20 final size:20
Alignment explanation
Indices: 1235626--1235679 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1235616 GATTCTCTTA
**
1235626 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCG
1235646 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
1235666 TTGCGATAGTCATT
1 TTGCGATAGTCATT
1235680 CGTGTTACGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:1237724 original size:19 final size:20
Alignment explanation
Indices: 1237700--1237763 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 20
1237690 GATTCTCTCA
1237700 TTGCGATAGTCAAATTC-CG
1 TTGCGATAGTCAAATTCGCG
**
1237719 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCG
*
1237739 TTGCGATAGTC--ATTCGTG
1 TTGCGATAGTCAAATTCGCG
1237757 TTGCGAT
1 TTGCGAT
1237764 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.30
19 15 0.38
20 13 0.32
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:1237742 original size:20 final size:19
Alignment explanation
Indices: 1237700--1237752 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
1237690 GATTCTCTCA
**
1237700 TTGCGATAGTCAAATTCCG
1 TTGCGATAGTCATTTTCCG
1237719 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTC-CG
1237739 TTGCGATAGTCATT
1 TTGCGATAGTCATT
1237753 CGTGTTGCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (19 bp):
TTGCGATAGTCATTTTCCG
Found at i:1238349 original size:42 final size:42
Alignment explanation
Indices: 1238278--1238359 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1238268 CTCCCCTATC
*
1238278 GTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCTCCTCCCACT
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTC-CCTCCCACT
* ** *
1238320 GTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
1238360 ACATTCTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (42 bp):
GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACT
Found at i:1239792 original size:14 final size:14
Alignment explanation
Indices: 1239754--1239815 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
1239744 TTGCTTGTTT
*
1239754 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
1239768 AATTGACTTGTAAA
1 AATTGATTTGTAAA
* *
1239782 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1239797 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1239811 TAATT
1 -AATT
1239816 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1239952 original size:20 final size:20
Alignment explanation
Indices: 1239916--1239967 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1239906 GTACACTTTT
*
1239916 GCAACGCTAAA-CTCAAAATC
1 GCAACGCGAAAGC-CAAAATC
*
1239936 GCAATGCGAAAGCCAAAATC
1 GCAACGCGAAAGCCAAAATC
1239956 GCAACGCGAAAG
1 GCAACGCGAAAG
1239968 TCAATTCGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.27, G:0.19, T:0.10
Consensus pattern (20 bp):
GCAACGCGAAAGCCAAAATC
Found at i:1240066 original size:20 final size:20
Alignment explanation
Indices: 1240010--1240234 Score: 204
Period size: 20 Copynumber: 11.8 Consensus size: 20
1240000 GCAATTTTCT
* ** *
1240010 CGTTACGATAGTCAAACACC
1 CGTTGCGATAGTCAAATTCG
*
1240030 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1240050 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1240070 CGTTGC-A-A-T---TTTCT
1 CGTTGCGATAGTCAAATTCG
* *
1240084 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
1240104 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1240124 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1240144 CGTTGCAATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1240164 TGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1240184 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
1240198 AGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1240218 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1240235 GAATGTGTAA
Statistics
Matches: 163, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
14 20 0.12
15 1 0.01
16 2 0.01
17 2 0.01
18 2 0.01
19 1 0.01
20 135 0.83
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1240093 original size:74 final size:74
Alignment explanation
Indices: 1239970--1240152 Score: 303
Period size: 74 Copynumber: 2.5 Consensus size: 74
1239960 CGCGAAAGTC
* * * *
1239970 AATTCGTGTTGCGATAGTCTAATACGCTTTGCAATTTTCTCGTTACGATAGTCAAACACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCAATTTTCTCGTTACGATAGTCAAACACCCGTTG
1240035 CGATAATCA
66 CGATAATCA
* * *
1240044 AATTCGCGTTGTGATAGTCAAATTCGCGTTGCAATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCAATTTTCTCGTTACGATAGTCAAACACCCGTTG
1240109 CGATAATCA
66 CGATAATCA
1240118 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCAAT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCAAT
1240153 AGTCATATTC
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 101 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATTCGCGTTGCAATTTTCTCGTTACGATAGTCAAACACCCGTTG
CGATAATCA
Found at i:1240171 original size:114 final size:114
Alignment explanation
Indices: 1240010--1240234 Score: 317
Period size: 114 Copynumber: 2.0 Consensus size: 114
1240000 GCAATTTTCT
*
1240010 CGTTACGATAGTCAAACACCCGTTGCGATAATCAAATTCGCGTTGTGATAGTCAAATTCGCGTTG
1 CGTTACGATAGTCAAACACCCGTTGCAATAATCAAATTCGCGTTGTGATAGTCAAATTCGCGTTG
*
1240075 CAATTTTCT-CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCG
66 CAATTTT-TGAGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCG
* ** * * * *
1240124 CGTTGCGATAGTCAAATTCGCGTTGCAATAGTCATATTCGTGTTGTGATAGTCAAATTCGCGTTG
1 CGTTACGATAGTCAAACACCCGTTGCAATAATCAAATTCGCGTTGTGATAGTCAAATTCGCGTTG
* * * *
1240189 CGATTTTTGAGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
66 CAATTTTTGAGTTGCGATAGTCAAATACCCGTTGCGATAATCAAAT
1240235 GAATGTGTAA
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
113 1 0.01
114 96 0.99
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (114 bp):
CGTTACGATAGTCAAACACCCGTTGCAATAATCAAATTCGCGTTGTGATAGTCAAATTCGCGTTG
CAATTTTTGAGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCG
Found at i:1240393 original size:140 final size:140
Alignment explanation
Indices: 1240205--1240474 Score: 531
Period size: 140 Copynumber: 1.9 Consensus size: 140
1240195 TTGAGTTGCG
*
1240205 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1240270 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1240335 AATACACATA
131 AATACACATA
1240345 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1240410 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1240475 TACAACGTTT
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 129 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1243207 original size:12 final size:12
Alignment explanation
Indices: 1243190--1243214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1243180 CGAAACACTA
1243190 ATGTAAGCAATG
1 ATGTAAGCAATG
1243202 ATGTAAGCAATG
1 ATGTAAGCAATG
1243214 A
1 A
1243215 ATCGTTCAAC
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:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (12 bp):
ATGTAAGCAATG
Found at i:1243790 original size:20 final size:20
Alignment explanation
Indices: 1243703--1243780 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
1243693 GAAATTCAGT
*
1243703 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
1243723 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
1243743 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1243763 GTTGCGATAGTCATAATC
1 GTTGCGATAGTCAGAATC
1243781 ACATTACGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1243797 original size:20 final size:20
Alignment explanation
Indices: 1243774--1243817 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1243764 TTGCGATAGT
*
1243774 CATAATCACATTACGATTTA
1 CATAATCACATTACAATTTA
* * *
1243794 CATATTCGCATTGCAATTTA
1 CATAATCACATTACAATTTA
1243814 CATA
1 CATA
1243818 TTCGCATTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (20 bp):
CATAATCACATTACAATTTA
Found at i:1243818 original size:20 final size:21
Alignment explanation
Indices: 1243789--1243832 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
1243779 TCACATTACG
1243789 ATTTACATATTCGCATTGC-A
1 ATTTACATATTCGCATTGCGA
1243809 ATTTACATATTCGCATTGCGA
1 ATTTACATATTCGCATTGCGA
1243830 ATT
1 ATT
1243833 CGGAAAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (21 bp):
ATTTACATATTCGCATTGCGA
Found at i:1243843 original size:21 final size:21
Alignment explanation
Indices: 1243819--1243871 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1243809 ATTTACATAT
*
1243819 TCGCATTGCGAATTCGGAAAA
1 TCGCAATGCGAATTCGGAAAA
* *
1243840 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTCGGAAAA
1243861 TCGCAATGCGA
1 TCGCAATGCGA
1243872 TAGTCAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTCGGAAAA
Found at i:1245652 original size:27 final size:26
Alignment explanation
Indices: 1245622--1245705 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 26
1245612 TTATAGTGAT
1245622 TTAGGGTTCTTGATTATTGCTTTCTTA
1 TTAGGGTT-TTGATTATTGCTTTCTTA
* * *
1245649 TTAGGGGTTTG-TT-TTGTTTTATAGTGA
1 TTAGGGTTTTGATTATTGCTTTCT--T-A
1245676 TTTAGGGTTTTTGATTATTGCTTTCTTA
1 -TTAGGG-TTTTGATTATTGCTTTCTTA
1245704 TT
1 TT
1245706 TTATGTTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
24 7 0.16
25 2 0.05
26 4 0.09
27 10 0.23
28 7 0.16
29 5 0.11
30 2 0.05
31 7 0.16
ACGTcount: A:0.14, C:0.06, G:0.21, T:0.58
Consensus pattern (26 bp):
TTAGGGTTTTGATTATTGCTTTCTTA
Found at i:1245659 original size:55 final size:55
Alignment explanation
Indices: 1245593--1245705 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
1245583 TTCACCAAAA
1245593 ATTAGGGGTTTGTTTTGTTTTATAGTGATTTAGGGTTCTTGATTATTGCTTTCTT
1 ATTAGGGGTTTGTTTTGTTTTATAGTGATTTAGGGTTCTTGATTATTGCTTTCTT
*
1245648 ATTAGGGGTTTGTTTTGTTTTATAGTGATTTAGGGTTTTTGATTATTGCTTTCTT
1 ATTAGGGGTTTGTTTTGTTTTATAGTGATTTAGGGTTCTTGATTATTGCTTTCTT
1245703 ATT
1 ATT
1245706 TTATGTTTAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.15, C:0.04, G:0.23, T:0.58
Consensus pattern (55 bp):
ATTAGGGGTTTGTTTTGTTTTATAGTGATTTAGGGTTCTTGATTATTGCTTTCTT
Done.