Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007889.1 Hibiscus syriacus cultivar Beakdansim tig00110271_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: 1663484
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1229258 original size:131 final size:131
Alignment explanation
Indices: 1229017--1229366 Score: 459
Period size: 131 Copynumber: 2.7 Consensus size: 131
1229007 ACAGAGTGGA
* * * * * *
1229017 CATCCACCGACTAGATCTCCTCATCACGTATGAGCCGTGTCACCCATAGATAATTAGTCGTCCTC
1 CATCCACCGACAAGATCTCCTCATCACGTAAGAGTCGTGTCACCCATAGATAATCAGACATCCTC
* * *
1229082 ATCACGTAGGAATAGTCTTATCATTCCTAAAGATGGTCTGCCGTCCTCATCACGTAGGAACCATG
66 ATCACGTAGGAATCGTGTTATCATTCCTAAAGATGGTATGCCGTCCTCATCACGTAGGAACCATG
1229147 T
131 T
* * *
1229148 CATCCACCGACAAGATCTCCTCATCACGTAGGAGTCGTGTCACCCATAGATAACCAGCCATCCTC
1 CATCCACCGACAAGATCTCCTCATCACGTAAGAGTCGTGTCACCCATAGATAATCAGACATCCTC
* *
1229213 ATCACGTAGGAATCGTGTTATCATTCCTAAAGATGGTATGTCGTCCTCATCATGTAGGAACCATG
66 ATCACGTAGGAATCGTGTTATCATTCCTAAAGATGGTATGCCGTCCTCATCACGTAGGAACCATG
1229278 T
131 T
* ** * * * * * * * *
1229279 CATCTATTGACCAGAACTCCTAATCACGTAAGA-TCTGTATCACCCTTAGATAGTCAAACTTCCT
1 CATCCACCGACAAGATCTCCTCATCACGTAAGAGTC-GTGTCACCCATAGATAATCAGACATCCT
1229343 CATCACGTAGGAATCGTGTTATCA
65 CATCACGTAGGAATCGTGTTATCA
1229367 CCTAAATTTA
Statistics
Matches: 192, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
130 2 0.01
131 190 0.99
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (131 bp):
CATCCACCGACAAGATCTCCTCATCACGTAAGAGTCGTGTCACCCATAGATAATCAGACATCCTC
ATCACGTAGGAATCGTGTTATCATTCCTAAAGATGGTATGCCGTCCTCATCACGTAGGAACCATG
T
Found at i:1229594 original size:3 final size:3
Alignment explanation
Indices: 1229570--1229644 Score: 75
Period size: 3 Copynumber: 25.7 Consensus size: 3
1229560 TTTTTTTGTT
* *
1229570 TTA TT- TTA TT- TTA TTA -TC TTA TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
1229615 TTA GTTA TTA TTA TCG TTA CTA TTA TTA TT
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
1229645 TACCTTTTGC
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
2 5 0.09
3 50 0.86
4 3 0.05
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1231104 original size:21 final size:21
Alignment explanation
Indices: 1231078--1231122 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1231068 GATTTCTGGG
* *
1231078 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1231099 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1231120 CAA
1 CAA
1231123 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1232775 original size:149 final size:149
Alignment explanation
Indices: 1232588--1232902 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
1232578 GAGTCGAGGG
* * *
1232588 TCTACCCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1232653 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
1232718 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
1232737 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1232802 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
1232867 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
1232886 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1232903 TGCAATTATA
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:1232903 original size:23 final size:23
Alignment explanation
Indices: 1232870--1232914 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1232860 ATTATTATAT
* *
1232870 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1232893 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1232915 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1236228 original size:21 final size:21
Alignment explanation
Indices: 1236202--1236246 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1236192 GATTTCTGGG
* *
1236202 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1236223 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1236244 CAA
1 CAA
1236247 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1237880 original size:149 final size:149
Alignment explanation
Indices: 1237699--1238013 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
1237689 GAGTCGAGGG
* *
1237699 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
1237764 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
1237829 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTACAAT
* *
1237848 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAATACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1237913 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
1237978 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTACAAT
1237997 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1238014 TGCAATTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTACAAT
Found at i:1238014 original size:23 final size:23
Alignment explanation
Indices: 1237981--1238025 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1237971 ATTATTATAT
*
1237981 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1238004 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1238026 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1240942 original size:43 final size:43
Alignment explanation
Indices: 1240870--1240952 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
1240860 CGAAGGGGCC
* * * *
1240870 ATCCACGATTTCAACTCCACAATGGAGGATATCGTGCCCACAG
1 ATCCACGATTTCAACTCAACAACGAAGGATATCATGCCCACAG
* *
1240913 ATCCACGATTTCAACTTAACAGCGAAGGATATCATGCCCA
1 ATCCACGATTTCAACTCAACAACGAAGGATATCATGCCCA
1240953 TCTACACAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.22
Consensus pattern (43 bp):
ATCCACGATTTCAACTCAACAACGAAGGATATCATGCCCACAG
Found at i:1241255 original size:116 final size:116
Alignment explanation
Indices: 1241094--1241416 Score: 493
Period size: 116 Copynumber: 2.8 Consensus size: 116
1241084 CAATACAAGC
* * * *
1241094 TTGGATTTTAACTTCACGACGAAGGATATTCAATTCAAAGCTCAACTTCATAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1241159 CCACGGTTTCAACTTCACGACGAAGGGAAACGTGCTCACCAGCAACATTCA
66 CCACGGTTTCAACTTCACGACGAAGGGAAACGTGCTCACCAGCAACATTCA
* * * *
1241210 TTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGTTCAACTTCACAATGAATGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * * *
1241275 CCACAGTTTCAATTTCACGACGAAGGGAATCGTGCTCACTAGCAACATTCA
66 CCACGGTTTCAACTTCACGACGAAGGGAAACGTGCTCACCAGCAACATTCA
* * *
1241326 TTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAAATTCACAACAAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* *
1241391 CCACGATTTCAACTTCACGAAGAAGG
66 CCACGGTTTCAACTTCACGACGAAGG
1241417 ATATCGTGCC
Statistics
Matches: 184, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
116 184 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (116 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAAACGTGCTCACCAGCAACATTCA
Found at i:1241586 original size:36 final size:36
Alignment explanation
Indices: 1241528--1241683 Score: 197
Period size: 36 Copynumber: 4.3 Consensus size: 36
1241518 GACTAATTTA
*
1241528 CTCAAAACAAAGTTTTGTCTCTCTTGAGACAGATTCT
1 CTCAAAACAAA-TTTTGTCTCTCTTGAGACAGATTCC
*
1241565 CTCAAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTCAAAACAAATTTTGTCTCTCTTGAGACAGATTCC
** *
1241601 CTTGACACAAATTTTGTCTCTCTTGAGACA-ATTTCC
1 CTCAAAACAAATTTTGTCTCTCTTGAGACAGA-TTCC
** *
1241637 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTCAAAACAAATTTTGTCTCTCTTGAGACAGATTCC
**
1241673 CTTGAAACAAA
1 CTCAAAACAAA
1241684 ATCTTTGAAT
Statistics
Matches: 109, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
36 98 0.90
37 11 0.10
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (36 bp):
CTCAAAACAAATTTTGTCTCTCTTGAGACAGATTCC
Found at i:1241630 original size:72 final size:73
Alignment explanation
Indices: 1241532--1241683 Score: 245
Period size: 72 Copynumber: 2.1 Consensus size: 73
1241522 AATTTACTCA
*
1241532 AAACAAAGTTTTGTCTCTCTTGAGACAGA-TTCTCTCAAAACAAATTTTGTCTCTCTTGAGACAG
1 AAACAAAGTTTTGTCTCTCTTGAGACA-ATTTCCCTCAAAACAAATTTTGTCTCTCTTGAGACAG
1241596 TTTCCCTTG
65 TTTCCCTTG
* **
1241605 ACACAAA-TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
1 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCCCTCAAAACAAATTTTGTCTCTCTTGAGACAGT
1241669 TTCCCTTG
66 TTCCCTTG
1241677 AAACAAA
1 AAACAAA
1241684 ATCTTTGAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
71 1 0.01
72 66 0.90
73 6 0.08
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (73 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAATTTCCCTCAAAACAAATTTTGTCTCTCTTGAGACAGT
TTCCCTTG
Found at i:1241631 original size:21 final size:21
Alignment explanation
Indices: 1241571--1241666 Score: 81
Period size: 21 Copynumber: 5.1 Consensus size: 21
1241561 TTCTCTCAAA
1241571 ACAAATTTTGTCTCTCTTGAG
1 ACAAATTTTGTCTCTCTTGAG
* *
1241592 AC--A-GTT-TC-C-CTTGAC
1 ACAAATTTTGTCTCTCTTGAG
1241607 ACAAATTTTGTCTCTCTTGAG
1 ACAAATTTTGTCTCTCTTGAG
*
1241628 AC-AA--TT-TC-C-CTTGAA
1 ACAAATTTTGTCTCTCTTGAG
1241643 ACAAATTTTGTCTCTCTTGAG
1 ACAAATTTTGTCTCTCTTGAG
1241664 ACA
1 ACA
1241667 GTTTCCCTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 24
0.66 0.07 0.28
Matches are distributed among these distances:
15 14 0.25
16 4 0.07
17 5 0.09
18 8 0.14
19 5 0.09
20 4 0.07
21 17 0.30
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (21 bp):
ACAAATTTTGTCTCTCTTGAG
Found at i:1241775 original size:17 final size:17
Alignment explanation
Indices: 1241753--1241812 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 17
1241743 AACTAAGTTT
1241753 TTTCTCTCTTGAGACAG
1 TTTCTCTCTTGAGACAG
* *
1241770 -TT-TCTCTTGAAACAAATT
1 TTTCTCTCTTGAGAC--A-G
1241788 TTGTCTCTCTTGAGACAG
1 TT-TCTCTCTTGAGACAG
1241806 TTTCTCT
1 TTTCTCT
1241813 TGAAACACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
15 10 0.30
16 2 0.06
17 6 0.18
18 2 0.06
19 2 0.06
20 1 0.03
21 10 0.30
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (17 bp):
TTTCTCTCTTGAGACAG
Found at i:1241784 original size:138 final size:138
Alignment explanation
Indices: 1241586--1241851 Score: 403
Period size: 138 Copynumber: 1.9 Consensus size: 138
1241576 TTTTGTCTCT
1241586 CTTGAGACAGTTTCCCTTGACACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTT
1 CTTGAGACAGTTTCCCTTGACACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTT
*
1241651 TGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATATGTTT-TCCTTGAAACAAAT
66 TGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACCTTTGAATATGTTTCT-CTTGAAACAAAT
1241714 TTCACCTCC
130 TTCACCTCC
** * * * *
1241723 CTTGAGACAGTTTCTTTTAGA-ACTAAGTTTTTTCTCTCTTGAGACAGTTTCTCTTGAAACAAAT
1 CTTGAGACAGTTTCCCTT-GACAC-AAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAT
* *
1241787 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAATATGTTTCTCTTGAAACAAA
64 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACCTTTGAATATGTTTCTCTTGAAACAAA
1241852 ATTTTGCCTC
Statistics
Matches: 116, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
137 18 0.16
138 70 0.60
139 27 0.23
140 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (138 bp):
CTTGAGACAGTTTCCCTTGACACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTT
TGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACCTTTGAATATGTTTCTCTTGAAACAAATT
TCACCTCC
Found at i:1241802 original size:36 final size:36
Alignment explanation
Indices: 1241698--1241819 Score: 149
Period size: 36 Copynumber: 3.4 Consensus size: 36
1241688 TTGAATATGT
* * *
1241698 TTTC-CTTGAAACAAATTTCACCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAG
* * *
1241733 TTTCT-TTTAGAACTAAGTTTTTTCTCTCTTGAGACAG
1 TTTCTCTTGA-AAC-AAATTTTATCTCTCTTGAGACAG
*
1241770 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAG
1241806 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
1241820 CCAACCTTTG
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
35 7 0.09
36 38 0.51
37 26 0.35
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAG
Found at i:1241877 original size:67 final size:68
Alignment explanation
Indices: 1241769--1241919 Score: 193
Period size: 67 Copynumber: 2.2 Consensus size: 68
1241759 TCTTGAGACA
* ** * *
1241769 GTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAC-CAACCTTTGAA
1 GTTTCTCTTGAAACAAAATTTTGCCTCTCCCGAGACAATTTCTCTTGAAACACAAAACCTTTGAA
1241832 TAT-
66 -ATC
1241835 GTTTCTCTTGAAACAAAATTTTGCCTC-CCCGAAGACAATTTCTCTTGAAACACAAAAAACCTTT
1 GTTTCTCTTGAAACAAAATTTTGCCTCTCCCG-AGACAATTTCTCTTGAAACAC--AAAACCTTT
1241899 GAAATC
63 GAAATC
1241905 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1241920 CGAAAAACCT
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
66 16 0.22
67 31 0.42
69 2 0.03
70 25 0.34
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (68 bp):
GTTTCTCTTGAAACAAAATTTTGCCTCTCCCGAGACAATTTCTCTTGAAACACAAAACCTTTGAA
ATC
Found at i:1241965 original size:34 final size:34
Alignment explanation
Indices: 1241873--1242027 Score: 210
Period size: 33 Copynumber: 4.5 Consensus size: 34
1241863 CCGAAGACAA
1241873 TTTCTCTTGAAACAC-AAAAAACCTTTG-AAATCG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAAAT-G
*
1241906 TTTCTCTTGAAACAC-GAAAAACCTTTG-AAATAG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAAAT-G
* *
1241939 TTTGTCTAGAAACACAAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAAATG
1241973 TTTCTCTTGAAACACAAAAAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAACAC---AAAAAAACCTTTGAAAATG
1242010 TTTCTCTTGAAACACAAA
1 TTTCTCTTGAAACACAAA
1242028 GACCTTCGAG
Statistics
Matches: 110, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
33 44 0.40
34 28 0.25
35 4 0.04
37 34 0.31
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (34 bp):
TTTCTCTTGAAACACAAAAAAACCTTTGAAAATG
Found at i:1242531 original size:3 final size:3
Alignment explanation
Indices: 1242523--1242553 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1242513 TATTTTTTAT
1242523 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1242554 ATTTTTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1248057 original size:43 final size:43
Alignment explanation
Indices: 1248009--1248091 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
1247999 ATAATGGGCC
* *
1248009 ATCCACGATTTCAACTCCACAACGGAGGATATCGTGCCCACAA
1 ATCCACGATTTCAACTCCACAACGAAGGATATCATGCCCACAA
* *
1248052 ATCCACGATTTCAACTTCACGACGAAGGATATCATGCCCA
1 ATCCACGATTTCAACTCCACAACGAAGGATATCATGCCCA
1248092 TCTACACAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACAACGAAGGATATCATGCCCACAA
Found at i:1248402 original size:116 final size:117
Alignment explanation
Indices: 1248233--1248555 Score: 492
Period size: 116 Copynumber: 2.8 Consensus size: 117
1248223 CAATACAAAC
* * *
1248233 TTGGATTTCAACTTCACGACGAAGAATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* *
1248298 CCACAG-TTTCAACTTCACGACGAAGGGAATCGTGATCACCAGCAACATTCG
66 CCACAGATTTCAACTTCACGAAGAAGGGAATCGTGATCACCAGCAACATTCA
* * * * *
1248349 TTGGATTTCAACTTCACGAAGAAGGATATCCAATTCAAGGTTCAATTTTACAACGAAGGGACCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* *
1248414 CCA-AGATTTCAATTTCAC-AATGAAGGGAATCGTGCTCACCAGCAACATTCA
66 CCACAGATTTCAACTTCACGAA-GAAGGGAATCGTGATCACCAGCAACATTCA
*
1248465 TTGGATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1248530 CCAC-GATTTCAACTTCACGAAGAAGG
66 CCACAGATTTCAACTTCACGAAGAAGG
1248556 ATATCATGCC
Statistics
Matches: 184, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
115 3 0.02
116 179 0.97
117 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (117 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACAGATTTCAACTTCACGAAGAAGGGAATCGTGATCACCAGCAACATTCA
Found at i:1248721 original size:21 final size:21
Alignment explanation
Indices: 1248696--1248796 Score: 64
Period size: 21 Copynumber: 5.4 Consensus size: 21
1248686 TGAGACAGTT
1248696 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
1248717 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
1248734 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* * *
1248753 TCTCTAGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
*
1248770 -C-ATTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
1248789 TCTCTTGA
1 TCTCTTGA
1248797 GACAGTTTCC
Statistics
Matches: 56, Mismatches: 12, Indels: 24
0.61 0.13 0.26
Matches are distributed among these distances:
15 12 0.21
16 2 0.04
17 6 0.11
18 8 0.14
19 6 0.11
20 2 0.04
21 20 0.36
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:1248721 original size:36 final size:36
Alignment explanation
Indices: 1248666--1248817 Score: 268
Period size: 36 Copynumber: 4.2 Consensus size: 36
1248656 AATTTACTCA
*
1248666 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
1248703 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
1248739 AAACAAATTTTGTCTCTCTAGAGACAGTTTCCATTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1248775 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1248811 AAACAAA
1 AAACAAA
1248818 ATCTTTGAAT
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 103 0.94
37 7 0.06
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1248943 original size:137 final size:137
Alignment explanation
Indices: 1248694--1248953 Score: 321
Period size: 137 Copynumber: 1.9 Consensus size: 137
1248684 CTTGAGACAG
*** * *
1248694 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTA
1 TTTCTCTTGAAACAAATTTCACCTCCCTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCTA
* ***
1248759 GAGACAGTTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTT
66 GAGACAGATTCCATTGAAACAAAAAATGTCTCTCTTGAGACAGTTT-CCTTGAAACAAAATCTTT
1248824 GAATATGT
130 GAATATGT
** **
1248832 TTTC-CTTGAAACAAATTTCACCTCCCTTGAGACAGTTTCTTTTAAAACTATGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCACCTCCCTTGAGACAGTTTCCCTTAAAAC-AAATTTTGTCTCTCT
* *
1248896 TGAGACAGATTCTC-TTGAAA-AAAAAAT-TCTCTTTTGAGACAGTTTTCCTTGAAACAAA
65 AGAGACAGATTC-CATTGAAACAAAAAATGTCTCTCTTGAGACAG-TTTCCTTGAAACAAA
1248954 GTTTTGTCTC
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
136 26 0.25
137 44 0.42
138 33 0.32
139 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (137 bp):
TTTCTCTTGAAACAAATTTCACCTCCCTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCTA
GAGACAGATTCCATTGAAACAAAAAATGTCTCTCTTGAGACAGTTTCCTTGAAACAAAATCTTTG
AATATGT
Found at i:1248971 original size:37 final size:36
Alignment explanation
Indices: 1248832--1248988 Score: 133
Period size: 37 Copynumber: 4.4 Consensus size: 36
1248822 TTGAATATGT
*** *
1248832 TTTC-CTTGAAACAAATTTCACCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * **
1248867 TTTCTTTTAAAACTATGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *** *
1248904 ATTCTCTTGAAA-AAAAAAT-TCTCTTTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
1248938 TTT-TCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTCT-CTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
1248975 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
1248989 CCAACCTTTG
Statistics
Matches: 92, Mismatches: 23, Indels: 12
0.72 0.18 0.09
Matches are distributed among these distances:
33 1 0.01
34 23 0.25
35 9 0.10
36 7 0.08
37 51 0.55
38 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1249002 original size:174 final size:174
Alignment explanation
Indices: 1248684--1249055 Score: 493
Period size: 173 Copynumber: 2.1 Consensus size: 174
1248674 TTTTGTCTCT
* * ***
1248684 CTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTT
1 CTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGATTCCCTTGAAACAAAAAA
*
1248749 TGTCTCTCTAGAGACAGTTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
66 TGTCTCTCTAGAGACAGTTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAA
*
1248814 CAAAATCTTTGAATATGTTT-TCCTTGAAAC-AAATTTCACCTCC
131 CAAAACCTTTGAATATGTTTCT-CTTGAAACAAAATTTCACCTCC
* ** *
1248857 CTTGAGACAGTTTCTTTTAAAACTATGTTTTGTCTCTCTTGAGACAGATTCTCTTGAAA-AAAAA
1 CTTGAGACAGTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGATTCCCTTGAAACAAAAA
* * *
1248921 AT-TCTCTTTTGAGACAGTTTTCC-TTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTG
65 ATGTCTCTCTAGAGACAG-TTTCCATTGAAACAAA-TTTTGTCTCTCTTGAGACAATTTCCCTTG
* **
1248984 AAACACCAACCTTTGAATATGTTTCTCTTGAAACAAAATTTTTCCTCC
128 AAACA-AAACCTTTGAATATGTTTCTCTTGAAACAAAATTTCACCTCC
* *
1249032 CTCGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCTCTTAAAACA
1249056 CAAAAAACCT
Statistics
Matches: 173, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
172 23 0.13
173 62 0.36
174 56 0.32
175 32 0.18
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (174 bp):
CTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGATTCCCTTGAAACAAAAAA
TGTCTCTCTAGAGACAGTTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAA
CAAAACCTTTGAATATGTTTCTCTTGAAACAAAATTTCACCTCC
Found at i:1249046 original size:67 final size:68
Alignment explanation
Indices: 1248939--1249088 Score: 191
Period size: 67 Copynumber: 2.2 Consensus size: 68
1248929 TTGAGACAGT
* * * *
1248939 TTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAC-CAACCTTTGAAT
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTCGAGACAATTTCTCTTGAAACACAAAACCTTTGAA-
1249002 AT-G
65 ATCG
*
1249005 TTTCTCTTGAAACAAAATTTT-TCCTCCCTCGAGACAGTTTCTCTTGAAACACAAAAAACCTTTG
1 TTTCTCTTGAAACAAAATTTTGT-CTCCCTCGAGACAATTTCTCTTGAAACAC--AAAACCTTTG
1249069 AAATCG
63 AAATCG
1249075 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
1249089 CGAAAAACCT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
66 5 0.07
67 41 0.56
69 2 0.03
70 25 0.34
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.36
Consensus pattern (68 bp):
TTTCTCTTGAAACAAAATTTTGTCTCCCTCGAGACAATTTCTCTTGAAACACAAAACCTTTGAAA
TCG
Found at i:1249134 original size:34 final size:34
Alignment explanation
Indices: 1249041--1249197 Score: 196
Period size: 33 Copynumber: 4.6 Consensus size: 34
1249031 CCTCGAGACA
1249041 GTTTCTCTTGAAACAC-AAAAAACCTTTG-AAAT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
*
1249073 CGTTTCTCTTGAAACAC-GAAAAACCTTTG-AAAT
1 -GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
1249106 CGTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
1 -GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
* *
1249141 GTTTCTCTTCAAACATAAAAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAAC----ACAAAAAAACCTTTGAAAAT
*
1249179 GTTTCTATTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
1249198 GATATTCTAG
Statistics
Matches: 111, Mismatches: 7, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
33 48 0.43
34 28 0.25
35 4 0.04
38 31 0.28
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
Found at i:1249396 original size:84 final size:83
Alignment explanation
Indices: 1249206--1249456 Score: 265
Period size: 84 Copynumber: 3.0 Consensus size: 83
1249196 AAGATATTCT
* * * *
1249206 AGTTCGACTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGACTACACTCAGC-TCAAAGGCACATAATTTGCAGCATAACTCAAGGCTATAAGGGTTAT
* *
1249271 CT---ACCAAATACCTTAG
65 CTCCAACCAAAGACCTTCG
* * * * * * * * *
1249287 AGTTCGATTTCATTCAGCTTAAAGGCGCATTATTTGCAGCATAGCTCAAGGCAATAAGGATTATC
1 AGTTCGACTACACTCAGCTCAAAGGCACATAATTTGCAGCATAACTCAAGGCTATAAGGGTTATC
1249352 TGCCAACCAAAGACCTTCG
66 T-CCAACCAAAGACCTTCG
* * *
1249371 AGTTCGACTACGCTCAGCTCCAAGGCACATAATTTGCAGCATAACTCAAGGCTGTAAGGGTTATC
1 AGTTCGACTACACTCAGCTCAAAGGCACATAATTTGCAGCATAACTCAAGGCTATAAGGGTTATC
** *
1249436 TACCAATTAAAGGCCTTCG
66 T-CCAACCAAAGACCTTCG
1249455 AG
1 AG
1249457 GGCACATCAT
Statistics
Matches: 136, Mismatches: 30, Indels: 5
0.80 0.18 0.03
Matches are distributed among these distances:
80 39 0.29
81 15 0.11
84 82 0.60
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (83 bp):
AGTTCGACTACACTCAGCTCAAAGGCACATAATTTGCAGCATAACTCAAGGCTATAAGGGTTATC
TCCAACCAAAGACCTTCG
Found at i:1249773 original size:3 final size:3
Alignment explanation
Indices: 1249765--1249789 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1249755 TCTTTTTTAT
1249765 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1249790 ATTTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1251608 original size:14 final size:14
Alignment explanation
Indices: 1251589--1251632 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
1251579 AATATAATTA
1251589 AATAATTAAATAAT
1 AATAATTAAATAAT
1251603 AATAA-TAAATAAAT
1 AATAATTAAAT-AAT
1251617 AATAATATAATATAAT
1 AATAAT-TAA-ATAAT
1251633 GTTTTTGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.19
14 13 0.50
16 6 0.23
17 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATAATTAAATAAT
Found at i:1251631 original size:17 final size:18
Alignment explanation
Indices: 1251589--1251631 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1251579 AATATAATTA
1251589 AATAAT-TAAATAATAAT
1 AATAATATAAATAATAAT
1251606 AATAA-ATAAATAATAAT
1 AATAATATAAATAATAAT
1251623 -ATAATATAA
1 AATAATATAA
1251632 TGTTTTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATATAAATAATAAT
Found at i:1252045 original size:84 final size:83
Alignment explanation
Indices: 1251949--1252211 Score: 268
Period size: 84 Copynumber: 3.2 Consensus size: 83
1251939 GAGTGTAATT
*
1251949 GAACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTTTCGACTTAAGCTATGCTTCAAATGATGTGC
1 GAACTCGAAGGTCTT-GGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGTGC
1252014 CTTGGAGCTGAGCGTAGTC
65 CTTGGAGCTGAGCGTAGTC
** * * * * * * *
1252033 GAACTCGAAGGTCTTTGG-TCACAGATAACCCTTGTAGCCTTGAGTTATGCTGT-AAATGATATA
1 GAACTCGAAGGTC-TTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT-TCAAATGATGT-
* * * * *
1252096 CCCTCGAAGCTGAGTGTAATC
63 GCCTTGGAGCTGAGCGTAGTC
** *
1252117 GAACTCGGGGGTC-T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCC
1 GAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGTGCC
1252179 ATT-GAGCTGAGCGTAGTC
66 -TTGGAGCTGAGCGTAGTC
*
1252197 GAACTCAAAGGTCTT
1 GAACTCGAAGGTCTT
1252212 TTGTTAGCAG
Statistics
Matches: 138, Mismatches: 34, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
80 24 0.17
81 35 0.25
82 1 0.01
83 33 0.24
84 43 0.31
85 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (83 bp):
GAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGTGCC
TTGGAGCTGAGCGTAGTC
Found at i:1252597 original size:106 final size:106
Alignment explanation
Indices: 1252412--1253220 Score: 1359
Period size: 106 Copynumber: 7.6 Consensus size: 106
1252402 TATTGTTCTA
* * *
1252412 AGTCCAATATCC-TCTGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1252476 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1252518 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1252583 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1252624 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1252689 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
1252730 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTGTTTTTTTTTTGA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG----TTTGTTGA
*
1252795 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
62 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1252840 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1252905 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1252946 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
1253011 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1253052 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1253117 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1253158 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTCTGTTGACA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1253221 GACAACTTTT
Statistics
Matches: 667, Mismatches: 31, Indels: 10
0.94 0.04 0.01
Matches are distributed among these distances:
106 565 0.85
107 2 0.00
110 100 0.15
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1258283 original size:14 final size:14
Alignment explanation
Indices: 1258264--1258308 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1258254 AATATAATTA
1258264 AATAATTAAATAAT
1 AATAATTAAATAAT
1258278 AATAA-TAAATAAAT
1 AATAATTAAAT-AAT
1258292 AATAATATAATATAAT
1 AATAAT-TAA-ATAAT
1258308 A
1 A
1258309 TTTTTGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.19
14 13 0.48
16 7 0.26
17 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATTAAATAAT
Found at i:1258306 original size:17 final size:18
Alignment explanation
Indices: 1258264--1258306 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1258254 AATATAATTA
1258264 AATAAT-TAAATAATAAT
1 AATAATATAAATAATAAT
1258281 AATAA-ATAAATAATAAT
1 AATAATATAAATAATAAT
1258298 -ATAATATAA
1 AATAATATAA
1258307 TATTTTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATATAAATAATAAT
Found at i:1259181 original size:28 final size:29
Alignment explanation
Indices: 1259149--1259208 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
1259139 TTTAACACCC
*
1259149 TAACCCGTATAATTAT-ATATATAAATTA
1 TAACCCATATAATTATAATATATAAATTA
*
1259177 TAACCTATATAATTATACATATATAAATTA
1 TAACCCATATAATTATA-ATATATAAATTA
1259207 TA
1 TA
1259209 GATGTCACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 14 0.50
30 14 0.50
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (29 bp):
TAACCCATATAATTATAATATATAAATTA
Found at i:1259192 original size:15 final size:16
Alignment explanation
Indices: 1259165--1259208 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
1259155 GTATAATTAT
1259165 ATATATAAATTATAAC
1 ATATATAAATTATAAC
*
1259181 CTATAT-AATTAT-AC
1 ATATATAAATTATAAC
1259195 ATATATAAATTATA
1 ATATATAAATTATA
1259209 GATGTCACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.29
15 12 0.50
16 5 0.21
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATAAATTATAAC
Found at i:1259937 original size:36 final size:37
Alignment explanation
Indices: 1259873--1259942 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
1259863 ATTTCTTATT
* *
1259873 AATATATTTATCATTTATTCCATAAGCTCGTAAGCTC
1 AATATACTTATCATTTAATCCATAAGCTCGTAAGCTC
*
1259910 AATATACTTGTCA-TTAATCCATAAGCTCGTAAG
1 AATATACTTATCATTTAATCCATAAGCTCGTAAG
1259943 TTTATTTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 19 0.63
37 11 0.37
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (37 bp):
AATATACTTATCATTTAATCCATAAGCTCGTAAGCTC
Found at i:1259975 original size:44 final size:44
Alignment explanation
Indices: 1259912--1260082 Score: 247
Period size: 44 Copynumber: 3.9 Consensus size: 44
1259902 GTAAGCTCAA
* * *
1259912 TATACTTGTCATTAATCCATAAGCTCGTAAGTTTATTTTACCAT
1 TATACTTATCATTATTCCATAAGCTCGTAAGCTTATTTTACCAT
*
1259956 TATACTTATCATTATTCCATAAGCTCTTAAGCTTATTTTACCAT
1 TATACTTATCATTATTCCATAAGCTCGTAAGCTTATTTTACCAT
*
1260000 TATACTTACCATT-TATCTCATAAGCTCGTAAGCTTATTTTACCCA-
1 TATACTTATCATTAT-TC-CATAAGCTCGTAAGCTTATTTTA-CCAT
*
1260045 TATACTTGTCATTATTCCATAAGCTCGTAAGCTTATTT
1 TATACTTATCATTATTCCATAAGCTCGTAAGCTTATTT
1260083 ACATGCTTAC
Statistics
Matches: 115, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.01
44 75 0.65
45 35 0.30
46 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (44 bp):
TATACTTATCATTATTCCATAAGCTCGTAAGCTTATTTTACCAT
Found at i:1260049 original size:89 final size:88
Alignment explanation
Indices: 1259912--1260082 Score: 263
Period size: 89 Copynumber: 1.9 Consensus size: 88
1259902 GTAAGCTCAA
** *
1259912 TATACTTGTCATTAATCCATAAGCTCGTAAGTTTATTTTACCATTATACTTATCATTATTCCATA
1 TATACTTACCATTAATCCATAAGCTCGTAAGCTTATTTTACCATTATACTTATCATTATTCCATA
*
1259977 AGCTCTTAAGCTTATTTTACCAT
66 AGCTCGTAAGCTTATTTTACCAT
* *
1260000 TATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTACCCA-TATACTTGTCATTATTCCA
1 TATACTTACCATTAATC-CATAAGCTCGTAAGCTTATTTTA-CCATTATACTTATCATTATTCCA
1260064 TAAGCTCGTAAGCTTATTT
64 TAAGCTCGTAAGCTTATTT
1260083 ACATGCTTAC
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
88 14 0.19
89 58 0.77
90 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (88 bp):
TATACTTACCATTAATCCATAAGCTCGTAAGCTTATTTTACCATTATACTTATCATTATTCCATA
AGCTCGTAAGCTTATTTTACCAT
Found at i:1265947 original size:3 final size:3
Alignment explanation
Indices: 1265939--1265968 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1265929 ATATTAAAAC
*
1265939 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1265969 AAGTTCAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1266643 original size:66 final size:66
Alignment explanation
Indices: 1266530--1266684 Score: 161
Period size: 66 Copynumber: 2.3 Consensus size: 66
1266520 GGGATAAAAG
* * * * *
1266530 TTTTGTTTCGAGTGAAACAATCTTAATGGTTGTGTTTAGAGGTAAACTATCTCTAGCGAGATGAA
1 TTTTGTTTCAAGAGAAACAATCTTAATGGTTGTGTTTAAAGGTAAACTATCTCGAGCGAGACGAA
1266595 A
66 A
* * *
1266596 TTTTGTTTCAAGAGAAACAATCTTCA-GGTTTGTGTTTCAAAGG-AAACTTTCTCGAGTGAGACG
1 TTTTGTTTCAAGAGAAACAATCTTAATGG-TTGTGTTT-AAAGGTAAACTATCTCGAGCGAGACG
*
1266659 AAG
64 AAA
* * * *
1266662 TTCTGTTTTAAAATAAACAATCT
1 TTTTGTTTCAAGAGAAACAATCT
1266685 CAAGTGAGAT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
65 2 0.03
66 68 0.92
67 4 0.05
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (66 bp):
TTTTGTTTCAAGAGAAACAATCTTAATGGTTGTGTTTAAAGGTAAACTATCTCGAGCGAGACGAA
A
Found at i:1270409 original size:6 final size:6
Alignment explanation
Indices: 1270398--1270426 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1270388 CTTACACGGG
1270398 AAAGAA AAAGAA AAAGAA AAAGAA AAAGA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGA
1270427 GGAGATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:1283032 original size:50 final size:51
Alignment explanation
Indices: 1282915--1283095 Score: 228
Period size: 49 Copynumber: 3.5 Consensus size: 51
1282905 CCCACTTTCA
* *
1282915 CTTTCTTTAGGGAGTATAG-ACTCGAACTTTTCTTCTTACGGGTTCG---CCT
1 CTTTCTCTAGGGAGTATAGAACTCGAAC-ATTCTTCTTAC-GGTTCGCTCCCT
*
1282964 CTTTCTCTATGGAGTATAGAACTCGAACATTCTTCTTACGGTTCGCTCCCT
1 CTTTCTCTAGGGAGTATAGAACTCGAACATTCTTCTTACGGTTCGCTCCCT
*
1283015 CTTTCTCTAGGG-GTATAGAACTCGAACACATTCTTCTTACGAGTTTGCTCCCT
1 CTTTCTCTAGGGAGTATAGAACTCG-A-ACATTCTTCTTACG-GTTCGCTCCCT
* *
1283068 CTTTCTTTAGGGAGTATACAACTCGAAC
1 CTTTCTCTAGGGAGTATAGAACTCGAAC
1283096 TTTATCAATC
Statistics
Matches: 117, Mismatches: 7, Indels: 13
0.85 0.05 0.09
Matches are distributed among these distances:
48 6 0.05
49 27 0.23
50 20 0.17
51 15 0.13
52 16 0.14
53 22 0.19
54 11 0.09
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (51 bp):
CTTTCTCTAGGGAGTATAGAACTCGAACATTCTTCTTACGGTTCGCTCCCT
Found at i:1283329 original size:159 final size:160
Alignment explanation
Indices: 1283130--1283621 Score: 716
Period size: 159 Copynumber: 3.1 Consensus size: 160
1283120 AAAGTATAAA
1283130 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTAT-AGACTCGAAC-A
* * * *
1283195 CCTTCAATAATTGTGTCTGCTCTCTATTCCTTCAGAG-GTATAAGACTCGAACATCTTCATCAAA
64 TCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCATCAAT
1283259 CG-GTCTGCTC-CTATTCCTTCAGAGAGTAAG
129 CGTGTCTGCTCTCTATTCCTTCAGAGAGTAAG
* * * *
1283289 ACTCAAACAACCTTCAACAATCGTGTTTTCTCCCTATTCCTTCAGAGAG--TAGACTCGAACATC
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGACTCGAACATC
* * *
1283352 TTCAACAATCGTGTCTGCTCCCTATTCCTTCAG-GAGTATAAGACTCGAACAATATTCAAC-ATC
66 TTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAAC-ATCTTCATCAATC
*
1283415 GTGTCTGCTCTCTATTTCTT-AGAGAGTATAAG
130 GTGTCTGCTCTCTATTCCTTCAGAGAG--TAAG
* *
1283447 ACTCGAACAATATTC-ACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGACTTGAACATC
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGACTCGAACATC
*
1283511 TTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCTTCAATCG
66 TTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCATCAATCG
1283576 TGTCTGCTCTCTATTCCTTCAGAGAGTATAAG
131 TGTCTGCTCTCTATTCCTTCAGAGAG--TAAG
1283608 ACTCGAAC-ATCTTC
1 ACTCGAACAATCTTC
1283622 TTCAAATGGG
Statistics
Matches: 298, Mismatches: 24, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
154 1 0.00
155 50 0.17
156 31 0.10
157 40 0.13
158 16 0.05
159 96 0.32
160 44 0.15
161 20 0.07
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (160 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGACTCGAACATC
TTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCATCAATCG
TGTCTGCTCTCTATTCCTTCAGAGAGTAAG
Found at i:1283333 original size:53 final size:54
Alignment explanation
Indices: 1283114--1283621 Score: 643
Period size: 53 Copynumber: 9.6 Consensus size: 54
1283104 TCGTATATCG
* *
1283114 CTTCAGAAAGTATAAAACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
1 CTTCAGAGAG-ATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* * * *
1283169 CTTCAGAGAGTATAAGACTCGAACAACCTTCAATAATTGTGTCTGCTCTCTATTC
1 CTTCAGAGAG-ATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* *
1283224 CTTCAGAG-GTATAAGACTCGAAC-ATCTTCATCAAACG-GTCTGCT-CCTATTC
1 CTTCAGAGAG-ATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* * * *
1283275 CTTCAGAGAG-TAAGACTCAAACAACCTTCAACAATCGTGTTTTCTCCCTATTC
1 CTTCAGAGAGATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
1283328 CTTCAGAGAG-T-AGACTCGAAC-ATCTTCAACAATCGTGTCTGCTCCCTATTC
1 CTTCAGAGAGATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* * *
1283379 CTTCAG-GAGTATAAGACTCGAACAATATTCAAC-ATCGTGTCTGCTCTCTATTT
1 CTTCAGAGAG-ATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
*
1283432 CTT-AGAGAGTATAAGACTCGAACAATATTC-ACAATCGTGTCTGCTCCCTATTC
1 CTTCAGAGAG-ATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* *
1283485 CTTCAGAGAG-TATAGACTTGAAC-ATCTTCAACAATCGTGTCTGCTCTCTATTC
1 CTTCAGAGAGATA-AGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
** *
1283538 CTTCAGAGAGTATAAGACTCGAAC-ATCTTCTTCAATCGTGTCTGCTCTCTATTC
1 CTTCAGAGAG-ATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
1283592 CTTCAGAGAGTATAAGACTCGAAC-ATCTTC
1 CTTCAGAGAG-ATAAGACTCGAACAATCTTC
1283622 TTCAAATGGG
Statistics
Matches: 405, Mismatches: 33, Indels: 31
0.86 0.07 0.07
Matches are distributed among these distances:
50 14 0.03
51 58 0.14
52 34 0.08
53 144 0.36
54 96 0.24
55 59 0.15
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (54 bp):
CTTCAGAGAGATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
Found at i:1283368 original size:210 final size:213
Alignment explanation
Indices: 1283114--1283616 Score: 725
Period size: 210 Copynumber: 2.4 Consensus size: 213
1283104 TCGTATATCG
* *
1283114 CTTCAGAAAGTATAAAACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAG
1 CTTCAGAGAG-ATAAGACTCGAAC-ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAG
* *
1283179 TATAAGACTCGAACAACCTTCAATAATTGTGTCTGCTCTCTATTCCTTCAGAG-GTATAAGACTC
64 TATAAGACTCGAACAACATTCAA-AATCGTGTCTGCTCTCTATTCCTT-AGAGAGTATAAGACTC
*
1283243 GAAC-ATCTTCATCAAACG-GTCTGCT-CCTATTCCTTCAGAGAGTA-AGACTCAAACAACCTTC
127 GAACAATATTCA-CAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGACTCAAAC-ACCTTC
* *
1283304 AACAATCGTGTTTTCTCCCTATTC
190 AACAATCGTGTCTGCTCCCTATTC
1283328 CTTCAGAGAG-T-AGACTCGAACATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAG-GAGTA
1 CTTCAGAGAGATAAGACTCGAACATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTA
* * *
1283390 TAAGACTCGAACAATATTCAACATCGTGTCTGCTCTCTATTTCTTAGAGAGTATAAGACTCGAAC
66 TAAGACTCGAACAACATTCAAAATCGTGTCTGCTCTCTATTCCTTAGAGAGTATAAGACTCGAAC
* ** *
1283455 AATATTCACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGACTTGAACATCTTCAACAAT
131 AATATTCACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGACTCAAACACCTTCAACAAT
*
1283520 CGTGTCTGCTCTCTATTC
196 CGTGTCTGCTCCCTATTC
** *
1283538 CTTCAGAGAGTATAAGACTCGAACATCTTCTTCAATCGTGTCTGCTCTCTATTCCTTCAGAGAGT
1 CTTCAGAGAG-ATAAGACTCGAACATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGT
1283603 ATAAGACTCGAACA
65 ATAAGACTCGAACA
1283617 TCTTCTTCAA
Statistics
Matches: 262, Mismatches: 18, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
207 4 0.02
208 41 0.16
209 37 0.14
210 91 0.35
211 17 0.06
212 2 0.01
213 43 0.16
214 27 0.10
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (213 bp):
CTTCAGAGAGATAAGACTCGAACATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTA
TAAGACTCGAACAACATTCAAAATCGTGTCTGCTCTCTATTCCTTAGAGAGTATAAGACTCGAAC
AATATTCACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGACTCAAACACCTTCAACAAT
CGTGTCTGCTCCCTATTC
Found at i:1283677 original size:107 final size:107
Alignment explanation
Indices: 1283122--1283729 Score: 474
Period size: 106 Copynumber: 5.7 Consensus size: 107
1283112 CGCTTCAGAA
* *
1283122 AGTATAAAACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
1 AGTATAAGACTCGAATAATCTT---CAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
* * * *
1283187 TCGAACAAC--CTTCAATAATTGTGTCTGCTCTCTATTCCTTCAGAG
63 TCGAACATCTTCTTC-A-AATCGTGTCTGCTCTCTATTTCTTTAGAG
* *
1283232 -GTATAAGACTCGAA-CATCTTCATCAAACG-GTCTGCT-CCTATTCCTTCAGAGAG--TAAGAC
1 AGTATAAGACTCGAATAATC-T--TCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
* * * * * * *
1283291 TCAAACAAC--CTTCAACAATCGTGTTTTCTCCCTATTCCTTCAGAG
63 TCGAACATCTTCTTC-A-AATCGTGTCTGCTCTCTATTTCTTTAGAG
*
1283336 AG--T-AGACTCGAA-CATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAG-GAGTATAAGAC
1 AGTATAAGACTCGAATAATCTT---CAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGAC
* *
1283396 TCGAACA--ATATTCAACATCGTGTCTGCTCTCTATTTC-TTAGAG
63 TCGAACATCTTCTTCAA-ATCGTGTCTGCTCTCTATTTCTTTAGAG
* *
1283439 AGTATAAGACTCGAACAATATTCACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTAT-AGACT
1 AGTATAAGACTCGAATAATCTT--CAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACT
* ** * *
1283503 TGAACATCTTCAAC-AATCGTGTCTGCTCTCTATTCCTTCAGAG
64 CGAACATCTTCTTCAAATCGTGTCTGCTCTCTATTTCTTTAGAG
** *
1283546 AGTATAAGACTCGAACATCTTCTTCAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACT
1 AGTATAAGACTCG-A-ATAATCTTCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACT
* * * * *
1283611 CGAACATCTTCTTCAAATGGGGT-TCGCTCCCTCTTTCTTTAGGG
64 CGAACATCTTCTTCAAATCGTGTCT-GCTCTCTATTTCTTTAGAG
* * * * * *
1283655 AGTAT-AGAATTCGAATAATCTTCCGCAAACGGGT-TCGCTCCCTCTTTCTT-AGGGAGTAT-AG
1 AGTATAAG-ACTCGAATAATCTT---CAATCGTGTCT-GCTCCCTATTCCTTCAGAGAGTATAAG
1283716 ACTCGAACATCTTC
61 ACTCGAACATCTTC
1283730 ATTTGCTTCA
Statistics
Matches: 415, Mismatches: 51, Indels: 66
0.78 0.10 0.12
Matches are distributed among these distances:
99 1 0.00
101 1 0.00
102 18 0.04
103 19 0.05
104 76 0.18
105 17 0.04
106 85 0.20
107 76 0.18
108 47 0.11
109 56 0.13
110 18 0.04
111 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (107 bp):
AGTATAAGACTCGAATAATCTTCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCG
AACATCTTCTTCAAATCGTGTCTGCTCTCTATTTCTTTAGAG
Found at i:1284106 original size:37 final size:37
Alignment explanation
Indices: 1284050--1284201 Score: 225
Period size: 37 Copynumber: 4.1 Consensus size: 37
1284040 CTGATGATCT
* * * *
1284050 GATGG-TTTGCTCCAATACTCTTCCGAGAAGGCTTAA
1 GATGGATTTGCTTCATTACTCTTCGGTGAAGGCTTAA
* *
1284086 AATGGATTTGCTTCATTACTCTTCAGTGAAGGCTTAA
1 GATGGATTTGCTTCATTACTCTTCGGTGAAGGCTTAA
*
1284123 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCATTACTCTTCGGTGAAGGCTTAA
1284160 GATGGATTTGCTTCATTACTCTTCGGTGAAGGCTTTAA
1 GATGGATTTGCTTCATTACTCTTCGGTGAAGGC-TTAA
1284198 GATG
1 GATG
1284202 ACTTTGCCCT
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
36 4 0.04
37 93 0.89
38 8 0.08
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (37 bp):
GATGGATTTGCTTCATTACTCTTCGGTGAAGGCTTAA
Found at i:1285491 original size:125 final size:122
Alignment explanation
Indices: 1285272--1285516 Score: 341
Period size: 125 Copynumber: 2.0 Consensus size: 122
1285262 CCGCAATATA
* **
1285272 TCTTATACTGGTACGAGCCTTCAAATACCCCAACATCTCCGATTGTAAGGCTCACTCAATGCCTT
1 TCTTATACTGGTACGAGCCTTCAAATACCCCAACACCTCAAATTGTAAGGCTCACTCAATGCCTT
* *
1285337 CTTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTTAGTTGTGCCCCAACATTG
66 CTTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTG
* *
1285394 TCTTATACTGGTACGAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTTC-ATG
1 TCTTATACTGGTACGAGCCTTC-AAATACCCCAACACCTCAAATTGTAAGGCTCA--C-TCAATG
* * *
1285458 CC-TCATTGGTTTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCGAACAT
62 CCTTC-TTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACAT
1285517 ATCACAACTT
Statistics
Matches: 108, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
122 22 0.20
123 27 0.25
124 2 0.02
125 55 0.51
126 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (122 bp):
TCTTATACTGGTACGAGCCTTCAAATACCCCAACACCTCAAATTGTAAGGCTCACTCAATGCCTT
CTTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTG
Found at i:1288987 original size:21 final size:21
Alignment explanation
Indices: 1288963--1289054 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
1288953 ATGCAAAGTA
*
1288963 GTCTTCAT-GTCTTTGTGAATG
1 GTCTTC-TCGTCTTTATGAATG
1288984 GTCTTCTCGTCTTTATGAATG
1 GTCTTCTCGTCTTTATGAATG
1289005 GTCTTCTCGTCTTTATGAATG
1 GTCTTCTCGTCTTTATGAATG
* * * *
1289026 GTCTTCTCATCCTTGTGCATG
1 GTCTTCTCGTCTTTATGAATG
1289047 GTCTTCTC
1 GTCTTCTC
1289055 ATCCTTGGTA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 1 0.02
21 64 0.98
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.47
Consensus pattern (21 bp):
GTCTTCTCGTCTTTATGAATG
Found at i:1293309 original size:54 final size:54
Alignment explanation
Indices: 1293228--1293418 Score: 301
Period size: 54 Copynumber: 3.5 Consensus size: 54
1293218 CCCACTTTCA
* **
1293228 CTTTCTTTAGGGAGTATAGAACTCGAACATTTTCTTCTTACGGGTTCGCTCCCT
1 CTTTCTCTAGGGAGTATAGAACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
*
1293282 CTTTCTCTATGGAGTATAGAACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
1 CTTTCTCTAGGGAGTATAGAACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
* * *
1293336 CTTTCTCTAGGGGGTATAGAACTCGAACACATTCTTCTTACGAGTTTGCTCCCT
1 CTTTCTCTAGGGAGTATAGAACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
* *
1293390 CTTTCTTTAGGGAGTATACAACTCGAACA
1 CTTTCTCTAGGGAGTATAGAACTCGAACA
1293419 TCTTTATCAA
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 126 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTTCTCTAGGGAGTATAGAACTCGAACACATTCTTCTTACGGGTTCGCTCCCT
Found at i:1293525 original size:55 final size:55
Alignment explanation
Indices: 1293439--1293961 Score: 818
Period size: 55 Copynumber: 9.6 Consensus size: 55
1293429 TCGTATATCG
* *
1293439 CTTCAGAAAGTATAAAACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* * * *
1293494 CTTCAGAGAGTATAAGACTCGAACAACCTTCAATAATTGTGTCTGCTCTCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* * *
1293549 CTTCAGAGAGTATAAGACTCGAAC-ATCTTCATCAAACGGGTCTGCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* * * *
1293603 CTTCAGAGAGTATAAGACTCAAACAACCTTCAACAATCGTGTTTTCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
1293658 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* * *
1293713 CTTCAGAGAGTATAAGACTCGAACAATATTCAACAATCGTGTCTGCTCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* *
1293768 CTTTAGAGAGTATAAGACTCGAACAATATTCAACAATCGTGTCTGCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* *
1293823 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCTGCTCTCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
** *
1293878 CTTCAGAGAGTATAAGACTCGAAC-ATCTTCTTCAATCGTGTCTGCTCTCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
1293932 CTTCAGAGAGTATAAGACTCGAAC-ATCTTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTC
1293962 TTCAAATGGG
Statistics
Matches: 430, Mismatches: 37, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
54 104 0.24
55 326 0.76
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
Found at i:1294447 original size:37 final size:37
Alignment explanation
Indices: 1294406--1294548 Score: 223
Period size: 37 Copynumber: 3.8 Consensus size: 37
1294396 TTGCTCCAAC
* * *
1294406 ACTCTTCCGAGAAGGCTTAAAATGGATTTGCTTCATT
1 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATT
* *
1294443 ACTCTTCAGTGAAGGCTTAAGATGGATTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATT
1294480 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATT
1 ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATT
*
1294517 ACTCTTCGGTGAAGGCTTAAGATTGACTTTGC
1 ACTCTTCGGTGAAGGCTTAAGATGGA-TTTGC
1294549 CCTAATCTCA
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
37 93 0.95
38 5 0.05
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATT
Found at i:1294516 original size:74 final size:74
Alignment explanation
Indices: 1294390--1294548 Score: 232
Period size: 74 Copynumber: 2.1 Consensus size: 74
1294380 CTGATGATCT
1294390 GATGG-TTTGCTCCAACACTCTTCCGAGAAGGCTTAAAATGGATTTGCTTCATTACTCTTCAGTG
1 GATGGATTTGCTCCAACACTCTTCCGAGAAGGCTTAAAATGGATTTGCTTCATTACTCTTCAGTG
1294454 AAGGCTTAA
66 AAGGCTTAA
* * * * *
1294463 GATGGATTTGCTTC-ACTACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCATTACTCTTCGGT
1 GATGGATTTGCTCCAAC-ACTCTTCCGAGAAGGCTTAAAATGGATTTGCTTCATTACTCTTCAGT
1294527 GAAGGCTTAA
65 GAAGGCTTAA
*
1294537 GATTGACTTTGC
1 GATGGA-TTTGC
1294549 CCTAATCTCA
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
73 7 0.09
74 65 0.84
75 5 0.06
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (74 bp):
GATGGATTTGCTCCAACACTCTTCCGAGAAGGCTTAAAATGGATTTGCTTCATTACTCTTCAGTG
AAGGCTTAA
Found at i:1298439 original size:3 final size:3
Alignment explanation
Indices: 1298426--1298455 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1298416 TTAATAGTAT
1298426 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1298456 TATATACCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1298739 original size:15 final size:15
Alignment explanation
Indices: 1298721--1298799 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 15
1298711 AAATATAAAA
1298721 ATTATTATAAAATAT
1 ATTATTATAAAATAT
* * *
1298736 ATTATT-TTAATTGT
1 ATTATTATAAAATAT
** * *
1298750 -TTAAAATATAATAA
1 ATTATTATAAAATAT
* *
1298764 ATAATTATAAAATTT
1 ATTATTATAAAATAT
*
1298779 ATTATTATAAAATTT
1 ATTATTATAAAATAT
1298794 ATTATT
1 ATTATT
1298800 TTAATTATTT
Statistics
Matches: 45, Mismatches: 17, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
13 3 0.07
14 8 0.18
15 34 0.76
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATTATTATAAAATAT
Found at i:1298756 original size:42 final size:43
Alignment explanation
Indices: 1298687--1298784 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
1298677 CTTATATGGT
* *
1298687 TAAAATATATT-CTTTAATTATTAAAAATATAA-AAATTATTA
1 TAAAATATATTATTTTAATTATTAAAAATATAATAAATAATTA
* *
1298728 TAAAATATATTATTTTAATTGTTTAAAATATAATAAATAATTA
1 TAAAATATATTATTTTAATTATTAAAAATATAATAAATAATTA
*
1298771 TAAAATTTATTATT
1 TAAAATATATTATT
1298785 ATAAAATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 11 0.22
42 18 0.36
43 21 0.42
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (43 bp):
TAAAATATATTATTTTAATTATTAAAAATATAATAAATAATTA
Found at i:1301378 original size:16 final size:17
Alignment explanation
Indices: 1301348--1301380 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1301338 AACCCGGTCC
1301348 AAAATAATATATTTATT
1 AAAATAATATATTTATT
*
1301365 AAAA-AATATTTTTATT
1 AAAATAATATATTTATT
1301381 CAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATAATATATTTATT
Found at i:1303448 original size:41 final size:42
Alignment explanation
Indices: 1303386--1303468 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
1303376 AGCGCATCAT
*
1303386 CTCTTTGAAAATATCAAA-TTTTTATTTTAAAATTTTATAAA
1 CTCTTTGAAAATATCAAATTTTTTATTTTAAAAATTTATAAA
*
1303427 CTCTTTGAAAATATCATATTTTTTATTTTAAAAATTTATAAA
1 CTCTTTGAAAATATCAAATTTTTTATTTTAAAAATTTATAAA
1303469 TTCATCATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 17 0.44
42 22 0.56
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (42 bp):
CTCTTTGAAAATATCAAATTTTTTATTTTAAAAATTTATAAA
Found at i:1304400 original size:151 final size:150
Alignment explanation
Indices: 1304154--1304457 Score: 484
Period size: 151 Copynumber: 2.0 Consensus size: 150
1304144 TCGGATATGT
1304154 TGAAAGTGTCGATAATTTAATATAAATATCGACACTTTATGAATTTAAAAGAGAAGAAGTTATAG
1 TGAAAGTGTCGATAATTTAATATAAATATCGACACTTTATGAATTTAAAAGAGAAGAAGTTATAG
**
1304219 CGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGCTAAAAATA
66 CGCCTAAAAAGTGTCGACACTTTAAAAAAATGTATCGATCCATAACAATATAACAGCTAAAAATA
*
1304284 TGATAAAACCGGTCTCAACAA
131 TGATAAAACCAGTCTCAA-AA
* * *
1304305 TGAAAGTGTCGATACTTTAATATAACTATCGACACTTT-TGGAATTTAAAAGAGAATAAGTTATA
1 TGAAAGTGTCGATAATTTAATATAAATATCGACACTTTAT-GAATTTAAAAGAGAAGAAGTTATA
* * * * *
1304369 GCGTCTATAAAGTGTCGATATTTTAAAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAT
65 GCGCCTAAAAAGTGTCGACACTTTAAAAAAATGTATCGATCCATAACAATATAACAGCTAAAAAT
1304434 ATGATAAAACCAGTCTCAAAA
130 ATGATAAAACCAGTCTCAAAA
1304455 TGA
1 TGA
1304458 CAACCGGTAA
Statistics
Matches: 141, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
150 6 0.04
151 135 0.96
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (150 bp):
TGAAAGTGTCGATAATTTAATATAAATATCGACACTTTATGAATTTAAAAGAGAAGAAGTTATAG
CGCCTAAAAAGTGTCGACACTTTAAAAAAATGTATCGATCCATAACAATATAACAGCTAAAAATA
TGATAAAACCAGTCTCAAAA
Found at i:1304919 original size:18 final size:19
Alignment explanation
Indices: 1304896--1304940 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1304886 TATTTAATAT
1304896 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
1304914 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
1304933 TTTTAGGT
1 TTATAGGT
1304941 TGTATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:1305727 original size:23 final size:23
Alignment explanation
Indices: 1305701--1305764 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1305691 CAGCTCATAT
1305701 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1305724 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCGA-AGTGCCACGTAG
*
1305747 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1305765 TATAATAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1305943 original size:103 final size:103
Alignment explanation
Indices: 1305787--1305992 Score: 349
Period size: 103 Copynumber: 2.0 Consensus size: 103
1305777 CATAAGGACT
* * *
1305787 ACATATCATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
* *
1305852 CACATGTTCTAAAGAATATATATATGTCCCGAAAGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
*
1305890 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
*
1305955 CACATGTTCCAAAGAATACATATATGTCCCGAAGGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
1305993 GCGTAGACCC
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (103 bp):
ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
Found at i:1307108 original size:21 final size:21
Alignment explanation
Indices: 1307084--1307128 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1307074 TTTTGTTCGT
* *
1307084 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1307105 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1307126 TTG
1 TTG
1307129 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1310125 original size:22 final size:23
Alignment explanation
Indices: 1310100--1310165 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
1310090 CACCACAGCT
*
1310100 CGTATAATTGCACCGAAGTG-CA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1310122 CGTAGAATTGCA-CGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1310144 CGTAGAATTGCA-CGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1310166 TATAATAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 6 0.16
22 32 0.84
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1310361 original size:103 final size:101
Alignment explanation
Indices: 1310181--1310391 Score: 350
Period size: 103 Copynumber: 2.1 Consensus size: 101
1310171 TAATGTCCAT
* * *
1310181 AAGGACTACATATCATTCCTTAAGAATCATATATATACTAGGGATCAAGTATGTGTCTCACCAGA
1 AAGGACCACATATCATTCCTTAAGAATCATATATATACCAAGGATCAAGTATGTGTCTCACCAGA
*
1310246 CTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 CTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1310282 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATAT--ATATACCAAGGATCAAGTATGTGTCTCACCA
*
1310347 GACTTCACATATGTTCCAAAGAATACATATATGTCCCG
64 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1310385 AAGGACC
1 AAGGACC
1310392 GTGTAGACCC
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 31 0.30
103 71 0.70
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (101 bp):
AAGGACCACATATCATTCCTTAAGAATCATATATATACCAAGGATCAAGTATGTGTCTCACCAGA
CTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1311508 original size:21 final size:21
Alignment explanation
Indices: 1311484--1311528 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1311474 TTTTGTTCGT
* *
1311484 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1311505 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1311526 TTG
1 TTG
1311529 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1314523 original size:23 final size:23
Alignment explanation
Indices: 1314497--1314588 Score: 148
Period size: 23 Copynumber: 4.0 Consensus size: 23
1314487 CACCACAGCT
*
1314497 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1314520 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1314543 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1314566 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1314589 TATAATAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1314731 original size:100 final size:102
Alignment explanation
Indices: 1314604--1314813 Score: 352
Period size: 100 Copynumber: 2.1 Consensus size: 102
1314594 TAATTTCCAT
* * * *
1314604 AAGGACTACATATCATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1314669 GACTTCACACATGTTCCAAAGAAT-ATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATAATATATGTCCCG
*
1314705 AAGGACCACATATC-TTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1314769 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATA-ATATATGTCCCG
1314807 AAGGACC
1 AAGGACC
1314814 GCGTAGACCC
Statistics
Matches: 102, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
100 70 0.69
101 13 0.13
102 19 0.19
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATAATATATGTCCCG
Found at i:1315920 original size:21 final size:21
Alignment explanation
Indices: 1315896--1315940 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1315886 TTTTGTTCGT
* *
1315896 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1315917 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1315938 TTG
1 TTG
1315941 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1318143 original size:9 final size:9
Alignment explanation
Indices: 1318131--1318180 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
1318121 AAGGAGTTAA
1318131 AGGAGGCAG
1 AGGAGGCAG
*
1318140 AGGAGGTAG
1 AGGAGGCAG
1318149 AGGAGGCAG
1 AGGAGGCAG
* *
1318158 AGGAAGTAG
1 AGGAGGCAG
1318167 AGGAGGCAG
1 AGGAGGCAG
*
1318176 TGGAG
1 AGGAG
1318181 AAAGAAGAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.34, C:0.06, G:0.54, T:0.06
Consensus pattern (9 bp):
AGGAGGCAG
Found at i:1318152 original size:18 final size:18
Alignment explanation
Indices: 1318131--1318180 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1318121 AAGGAGTTAA
1318131 AGGAGGCAGAGGAGGTAG
1 AGGAGGCAGAGGAGGTAG
*
1318149 AGGAGGCAGAGGAAGTAG
1 AGGAGGCAGAGGAGGTAG
*
1318167 AGGAGGCAGTGGAG
1 AGGAGGCAGAGGAG
1318181 AAAGAAGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.34, C:0.06, G:0.54, T:0.06
Consensus pattern (18 bp):
AGGAGGCAGAGGAGGTAG
Found at i:1319084 original size:191 final size:198
Alignment explanation
Indices: 1318625--1319415 Score: 1192
Period size: 191 Copynumber: 4.1 Consensus size: 198
1318615 AAAAAAGTGT
* *
1318625 AAAAACATAATTATAATATAATAGGTAAATTATTAATGT-ACTGGTCTAAATACCGGTTTTT-AG
1 AAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGTCTAAATACCGGTTTTTGAG
*
1318688 -AAACAAGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGTCGATACATCTTGTCCAGA-T-T
66 AAAACATGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGTCGATACATCTTGTCCAGATTGT
1318750 ATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAA-AAGTGTCGATCCCGAAAACA
131 ATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAAACA
1318814 TC-
196 TCG
* * * *
1318816 AAAAATATAATTATAATGTAATAAGTAAATTATTAATGTAACCGGTCTAAATATAC-ATTTTTGA
1 AAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGTCTAAATA-CCGGTTTTTGA
*
1318880 GAAAACATGTGTACAAAAAGTATCG-CACAAATAAAAAAAGTGTCGATAC-TCTTGTCCAGATTG
65 GAAAACATGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGTCGATACATCTTGTCCAGATTG
**
1318943 TATTTT-AAAACCAAGTGCACAAC-AAGTGTAAATACATTTAAAACAAGTGT-GATCCCG-AAAC
130 TATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAAAC
1319004 ATCG
195 ATCG
* * *
1319008 AAAAACATCATTATAATGTAATATGTAAAAT-TTAATGTAACCGGTCTAAATACCGGTTTTTGAG
1 AAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGTCTAAATACCGGTTTTTGAG
*
1319072 AAAACATGTGTACAAAAAGAATTGACACAAAT-AAAAAAGTGTCGATACATCTTGTCCAGATTGT
66 AAAACATGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGTCGATACATCTTGTCCAGATTGT
* * *
1319136 ATTTT-AAAACC-AGTGTACAACAAAGTG-CGCTACATTTAAAACAAGTGTCGATCACGAAAACA
131 ATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAAACA
1319198 TCG
196 TCG
* *
1319201 AAAAATATAA-T-TAATGTAATAGGTAAATTATTAATGTAACCGGTCTAAATATACCGATTTTTT
1 AAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGTCT-AA-ATACCG-GTTTTT
* * * *
1319264 GAGAAAACAGGTGTACAAAAAGTATCGAGACAAATAAAAAAAGTGTCGATACATCTTGTCCATAT
63 GAGAAAACATGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGTCGATACATCTTGTCCAGAT
1319329 TGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAA
128 TGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAA
1319394 ACATCG
193 ACATCG
1319400 AAAAACATAATTATAA
1 AAAAACATAATTATAA
1319416 CCAAATGTCT
Statistics
Matches: 539, Mismatches: 37, Indels: 38
0.88 0.06 0.06
Matches are distributed among these distances:
190 1 0.00
191 153 0.28
192 141 0.26
193 69 0.13
194 33 0.06
195 36 0.07
196 36 0.07
197 6 0.01
198 15 0.03
199 45 0.08
200 1 0.00
201 3 0.01
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (198 bp):
AAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGTCTAAATACCGGTTTTTGAG
AAAACATGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGTCGATACATCTTGTCCAGATTGT
ATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAAACA
TCG
Found at i:1322481 original size:23 final size:23
Alignment explanation
Indices: 1322431--1322475 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1322421 TGCCTATTTT
* * *
1322431 ATTATATAAGCGTTACCTATTAC
1 ATTATATAAGCGCTACCAAATAC
1322454 ATTATATAAGCGCTACCAAATA
1 ATTATATAAGCGCTACCAAATA
1322476 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCAAATAC
Found at i:1322522 original size:87 final size:87
Alignment explanation
Indices: 1322348--1322595 Score: 437
Period size: 87 Copynumber: 2.9 Consensus size: 87
1322338 AAAATAGGTA
1322348 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATG-TATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1322412 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* * *
1322434 ATATAAGCGTTACCTATTACATTATATAAGCGCTACCAAATATGTTATTGTATTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1322499 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
1322521 ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATA-TT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1322585 CCGGTTAAATG
66 CCGGTTAAATG
1322596 ATATAACTAA
Statistics
Matches: 153, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
86 55 0.36
87 98 0.64
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:1322568 original size:23 final size:23
Alignment explanation
Indices: 1322518--1322562 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1322508 TGCCTATTTT
*
1322518 ATTATATAAACGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
*
1322541 ATTATATAAGCGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
1322563 TGTTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:1323374 original size:18 final size:19
Alignment explanation
Indices: 1323335--1323378 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1323325 TATGTTCACG
*
1323335 GAATATAAGATTACCAGTGA
1 GAATAAAAGATTACCAG-GA
1323355 GAATAAAAGATTACCA-GA
1 GAATAAAAGATTACCAGGA
1323373 GAATAA
1 GAATAA
1323379 GATTAATGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.20
Consensus pattern (19 bp):
GAATAAAAGATTACCAGGA
Found at i:1324133 original size:20 final size:21
Alignment explanation
Indices: 1324083--1324133 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
1324073 CATTAGTATC
1324083 TAAATTATTATTTATTTATTT
1 TAAATTATTATTTATTTATTT
*
1324104 TAATATTTATTTTTTATTT-TTT
1 TAA-A-TTATTATTTATTTATTT
1324126 TAAATTAT
1 TAAATTAT
1324134 ACTTAATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 7 0.26
23 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TAAATTATTATTTATTTATTT
Found at i:1324438 original size:15 final size:16
Alignment explanation
Indices: 1324393--1324442 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
1324383 AAAATAAAAA
1324393 AATTGAAAGTTAAAGT
1 AATTGAAAGTTAAAGT
*
1324409 GATT-AAA-TTAGAAGT
1 AATTGAAAGTTA-AAGT
1324424 AATTGAAAGTT-AAGT
1 AATTGAAAGTTAAAGT
1324439 AATT
1 AATT
1324443 AAATTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 3 0.10
15 18 0.62
16 6 0.21
17 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (16 bp):
AATTGAAAGTTAAAGT
Found at i:1329443 original size:18 final size:18
Alignment explanation
Indices: 1329420--1329471 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1329410 GTGTGATTGT
1329420 TCATCTAAAAAGCATTTG
1 TCATCTAAAAAGCATTTG
1329438 TCATCTAAAAAGCATTTG
1 TCATCTAAAAAGCATTTG
*
1329456 TCGTCTTAAAAA-CATT
1 TCATC-TAAAAAGCATT
1329472 CATTTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (18 bp):
TCATCTAAAAAGCATTTG
Found at i:1330077 original size:127 final size:128
Alignment explanation
Indices: 1329825--1330185 Score: 372
Period size: 127 Copynumber: 2.8 Consensus size: 128
1329815 AATAATTTTA
* * * ** * * *
1329825 AGAGAG-AAATGATAATATCTAATTATTTCCAATTAAGAATAAATGA-ACTTTCATGCCTTAAAA
1 AGAGAGAAAACGATAATATCGAATGATTTCCAATCGAGAATAAATGACA-TCTCATACCTTAAAG
* * * * * * *
1329888 TAATCATTTATTACCCCAATTGAAATGAAAAGATATCACTATTTCGTCTTAAATTCATATTGATT
65 CAGTCA-TTATTACTCCAATCGAAATGAAAAGATATCACTATTTCATCTTAAAATCAAATTGATT
* * * * *
1329953 CGAGTGAAAACGATAGTATCTAATGATTTCCAATCGAG-A-AAATGACCTCTCATACCTTAAAGC
1 AGAGAGAAAACGATAATATCGAATGATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAGC
* * *
1330016 AGTTATTCATTGCTCCAATCGAAATGAAGAGATATCAC-ATTTCATCTTAAAAATCAAATTGATT
66 AGTCATT-ATTACTCCAATCGAAATGAAAAGATATCACTATTTCATCTT-AAAATCAAATTGATT
* * ** *
1330080 AGAGAGAAAACGGTAATATCGAATTATTTCCAATCGAGAATAAATGACATCTCATGGCTTAAAGT
1 AGAGAGAAAACGATAATATCGAATGATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAGC
* * *
1330145 AGTCATTATTACTCCAACCGAAATTAAAAGATATTACTATT
66 AGTCATTATTACTCCAATCGAAATGAAAAGATATCACTATT
1330186 CTTGATATCG
Statistics
Matches: 189, Mismatches: 37, Indels: 13
0.79 0.15 0.05
Matches are distributed among these distances:
126 11 0.06
127 92 0.49
128 31 0.16
129 55 0.29
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (128 bp):
AGAGAGAAAACGATAATATCGAATGATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAGC
AGTCATTATTACTCCAATCGAAATGAAAAGATATCACTATTTCATCTTAAAATCAAATTGATT
Found at i:1338603 original size:21 final size:21
Alignment explanation
Indices: 1338579--1338784 Score: 161
Period size: 21 Copynumber: 9.4 Consensus size: 21
1338569 CTTGAGGTAA
*
1338579 TGGAGATGGTAAGTGATGTAT
1 TGGAGATGGTAAGTGATGTAG
* *
1338600 TGGAGATGTTGA-TGATGTTGAGG
1 TGGAGATGGTAAGTGATG-T-A-G
*
1338623 TGGAGATGATAAGTGATGTAG
1 TGGAGATGGTAAGTGATGTAG
**
1338644 TGGAGATGGGGA-TGAATGTTGAG
1 TGGAGATGGTAAGTG-ATG-T-AG
1338667 ATGGAGATGGTAAGTGATGTAG
1 -TGGAGATGGTAAGTGATGTAG
* *
1338689 TGGAGATGTGATAAAT-TTG-AGG
1 TGGAGATG-G-TAAGTGATGTA-G
1338711 TGGAGATGGTAAGTGATGTAG
1 TGGAGATGGTAAGTGATGTAG
*
1338732 TGGAGATGGTGA-TGAATGTTGAG
1 TGGAGATGGTAAGTG-ATG-T-AG
*
1338755 ATGGAGATGGTAAGTGATGTGG
1 -TGGAGATGGTAAGTGATGTAG
1338777 TGGAGATG
1 TGGAGATG
1338785 TTGATGAATT
Statistics
Matches: 149, Mismatches: 17, Indels: 38
0.73 0.08 0.19
Matches are distributed among these distances:
20 13 0.09
21 59 0.40
22 20 0.13
23 21 0.14
24 32 0.21
25 4 0.03
ACGTcount: A:0.28, C:0.00, G:0.42, T:0.30
Consensus pattern (21 bp):
TGGAGATGGTAAGTGATGTAG
Found at i:1338681 original size:45 final size:45
Alignment explanation
Indices: 1338578--1338816 Score: 342
Period size: 45 Copynumber: 5.4 Consensus size: 45
1338568 GCTTGAGGTA
* *
1338578 ATGGAGATGGTAAGTGATGTATTGGAGATGTTGATG-ATGTTGAG
1 ATGGAGATGGTAAGTGATGTAGTGGAGATGGTGATGAATGTTGAG
* * *
1338622 GTGGAGATGATAAGTGATGTAGTGGAGATGGGGATGAATGTTGAG
1 ATGGAGATGGTAAGTGATGTAGTGGAGATGGTGATGAATGTTGAG
*
1338667 ATGGAGATGGTAAGTGATGTAGTGGAGAT-GTGATAAAT-TTGAG
1 ATGGAGATGGTAAGTGATGTAGTGGAGATGGTGATGAATGTTGAG
*
1338710 GTGGAGATGGTAAGTGATGTAGTGGAGATGGTGATGAATGTTGAG
1 ATGGAGATGGTAAGTGATGTAGTGGAGATGGTGATGAATGTTGAG
* * *
1338755 ATGGAGATGGTAAGTGATGTGGTGGAGATGTTGATGAATTTTGAGG
1 ATGGAGATGGTAAGTGATGTAGTGGAGATGGTGATGAATGTTGA-G
*
1338801 A-CGAGATGGTAAGTGA
1 ATGGAGATGGTAAGTGA
1338817 CGTAATAGAG
Statistics
Matches: 175, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
43 33 0.19
44 46 0.26
45 94 0.54
46 2 0.01
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.30
Consensus pattern (45 bp):
ATGGAGATGGTAAGTGATGTAGTGGAGATGGTGATGAATGTTGAG
Found at i:1338735 original size:88 final size:89
Alignment explanation
Indices: 1338578--1338816 Score: 374
Period size: 88 Copynumber: 2.7 Consensus size: 89
1338568 GCTTGAGGTA
* * *
1338578 ATGGAGATGGTAAGTGATGTATTGGAGATGTTGAT-GATGTTGAGGTGGAGATGATAAGTGATGT
1 ATGGAGATGGTAAGTGATGTAGTGGAGATGTTGATAAAT-TTGAGGTGGAGATGGTAAGTGATGT
1338642 AGTGGAGATGGGGATGAATGTTGAG
65 AGTGGAGATGGGGATGAATGTTGAG
1338667 ATGGAGATGGTAAGTGATGTAGTGGAGATG-TGATAAATTTGAGGTGGAGATGGTAAGTGATGTA
1 ATGGAGATGGTAAGTGATGTAGTGGAGATGTTGATAAATTTGAGGTGGAGATGGTAAGTGATGTA
*
1338731 GTGGAGATGGTGATGAATGTTGAG
66 GTGGAGATGGGGATGAATGTTGAG
* * **
1338755 ATGGAGATGGTAAGTGATGTGGTGGAGATGTTGATGAATTTTGAGGACGAGATGGTAAGTGA
1 ATGGAGATGGTAAGTGATGTAGTGGAGATGTTGAT-AAATTTGAGGTGGAGATGGTAAGTGA
1338817 CGTAATAGAG
Statistics
Matches: 139, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
88 81 0.58
89 35 0.25
90 23 0.17
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.30
Consensus pattern (89 bp):
ATGGAGATGGTAAGTGATGTAGTGGAGATGTTGATAAATTTGAGGTGGAGATGGTAAGTGATGTA
GTGGAGATGGGGATGAATGTTGAG
Found at i:1340106 original size:29 final size:29
Alignment explanation
Indices: 1340068--1340127 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
1340058 AGACCGGTTC
*
1340068 GACCGGTTGAACCAGTGAACCGATAGCAT
1 GACCGATTGAACCAGTGAACCGATAGCAT
* *
1340097 GACCGATTGAACCAGTGAACTGGTAGCAT
1 GACCGATTGAACCAGTGAACCGATAGCAT
1340126 GA
1 GA
1340128 TCGGTTCGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (29 bp):
GACCGATTGAACCAGTGAACCGATAGCAT
Found at i:1341134 original size:29 final size:28
Alignment explanation
Indices: 1341100--1341155 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1341090 AACTTAAAAG
* *
1341100 AGTTTTGCAATACTGAAATTTAAATAATT
1 AGTTTTACAATACT-AAAATTAAATAATT
*
1341129 AGTTTTATAATACTAAAATTAAATAAT
1 AGTTTTACAATACTAAAATTAAATAAT
1341156 CATCAACTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (28 bp):
AGTTTTACAATACTAAAATTAAATAATT
Found at i:1341209 original size:22 final size:22
Alignment explanation
Indices: 1341175--1341441 Score: 276
Period size: 22 Copynumber: 12.6 Consensus size: 22
1341165 CATAATAATT
1341175 TTTTAAAAT-AATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
1341196 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
1341218 TTTT-AAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
1341239 TTTTAAAATAAATC-A---ATA
1 TTTTAAAATAAATCAATTCATA
*
1341257 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
***
1341279 TTTTAAAAT-AATTTTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
*
1341301 -TTTAAAATAAGTCAATTCATA
1 TTTTAAAATAAATCAATTCATA
* ***
1341322 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
1341344 TTTTAAAATAAATCAA-TC-CA
1 TTTTAAAATAAATCAATTCATA
*
1341364 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
1341386 TTTT-AAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
1341407 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
1341429 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1341442 TTAAAATAGA
Statistics
Matches: 205, Mismatches: 21, Indels: 39
0.77 0.08 0.15
Matches are distributed among these distances:
18 18 0.09
19 1 0.00
20 15 0.07
21 64 0.31
22 104 0.51
23 3 0.01
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:1341222 original size:43 final size:44
Alignment explanation
Indices: 1341175--1341441 Score: 265
Period size: 43 Copynumber: 6.3 Consensus size: 44
1341165 CATAATAATT
*
1341175 TTTTAAAAT-AATCAATTCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCTATCTATA
*
1341218 TTTT-AAATAAATCAATCCATATTTTAAAATAAATC-A---ATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCTATCTATA
* * * * *
1341257 TTTTAAAATAAATCAATCCATATTTTAAAATAATTTTTTCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCTATCTATA
* * * *
1341301 -TTTAAAATAAGTCAATTCATATTTTAAAAT-AATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCTATCT-ATA
* * *
1341344 TTTTAAAATAAATCAA-TC-CATTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAAT-AAATCTATCTATA
*
1341386 TTTT-AAATAAATCAA-TCTATATTTTAAAATAAATCAAT-TCATA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAATCTATCT-ATA
1341429 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1341442 TTAAAATAGA
Statistics
Matches: 192, Mismatches: 17, Indels: 29
0.81 0.07 0.12
Matches are distributed among these distances:
39 7 0.04
40 29 0.15
41 13 0.07
42 32 0.17
43 83 0.43
44 28 0.15
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (44 bp):
TTTTAAAATAAATCAATTCATATTTTAAAATAAATCTATCTATA
Found at i:1350204 original size:26 final size:27
Alignment explanation
Indices: 1350146--1350204 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
1350136 AATTATCTAG
* * *
1350146 AATTTTATAAGTTTCATCCCCTCTTAA
1 AATTTTAAAAGTTTCATCCCATCATAA
*
1350173 AA-TTTAAAAGTTT-ATCCTATCATAA
1 AATTTTAAAAGTTTCATCCCATCATAA
1350198 AATTTTA
1 AATTTTA
1350205 CGTCCGTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 11 0.41
26 14 0.52
27 2 0.07
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.44
Consensus pattern (27 bp):
AATTTTAAAAGTTTCATCCCATCATAA
Found at i:1351295 original size:3 final size:3
Alignment explanation
Indices: 1351281--1351324 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
1351271 TTTAATACTT
* *
1351281 TGA TGT TGA TGA TGA TGA TGA TGA TGA TGA TAA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1351325 GTGGTGGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:1351948 original size:21 final size:21
Alignment explanation
Indices: 1351922--1351995 Score: 130
Period size: 21 Copynumber: 3.5 Consensus size: 21
1351912 GTTTTCAGAT
*
1351922 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACTTCGACTA
1351943 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
1351964 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
1351985 TCGCAATGCGA
1 TCGCAACGCGA
1351996 TTTTCTAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.18
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:1352050 original size:23 final size:23
Alignment explanation
Indices: 1352018--1352082 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
1352008 GTTGCGATAG
*
1352018 TCCAAGTTCGCGTTTCGATTTAT
1 TCCAAATTCGCGTTTCGATTTAT
1352041 TCCAAATTCGC-TTTGCGATTTAT
1 TCCAAATTCGCGTTT-CGATTTAT
*
1352064 TCCAAATTCGCGTTGCGAT
1 TCCAAATTCGCGTTTCGAT
1352083 AGTCGAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.08
23 33 0.87
24 2 0.05
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (23 bp):
TCCAAATTCGCGTTTCGATTTAT
Found at i:1352878 original size:6 final size:6
Alignment explanation
Indices: 1352867--1352892 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1352857 TCGTCTCGTC
1352867 TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TC
1352893 ATACGTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.46, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:1355088 original size:21 final size:21
Alignment explanation
Indices: 1355037--1355089 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1355027 ATTCTGACTA
1355037 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
1355058 TTGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1355079 TCGCAATGCGA
1 TCGCATTGCGA
1355090 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1355141 original size:20 final size:20
Alignment explanation
Indices: 1355079--1355144 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
1355069 TTTTCCTAAT
1355079 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** *
1355099 TCATAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1355119 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1355139 TCGCAA
1 TCGCAA
1355145 CGCAAATCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1355201 original size:20 final size:20
Alignment explanation
Indices: 1355138--1355204 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1355128 GAATACGTAA
* *
1355138 ATCGCAACGCAAATCTGACT
1 ATCGCAACGCGATTCTGACT
* *
1355158 ATCACAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1355178 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1355198 ATCGCAA
1 ATCGCAA
1355205 TACTGAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1356052 original size:24 final size:24
Alignment explanation
Indices: 1356025--1356078 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1356015 GTATTCGAAA
1356025 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1356049 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1356073 TTTGAT
1 TTTGAT
1356079 GATTTTTCAG
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:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1358984 original size:21 final size:22
Alignment explanation
Indices: 1358934--1359011 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 22
1358924 AATGTTGGGA
* *
1358934 GGGACCTCTTCAAC-GATGACAG
1 GGGA-CTCTTGAACGGATGATAG
* * *
1358956 TGGCCTCTTGAACGG-TGGTAG
1 GGGACTCTTGAACGGATGATAG
*
1358977 GGGACTCTTG-AGGGATGATAG
1 GGGACTCTTGAACGGATGATAG
*
1358998 GGGCCTCTTGAACG
1 GGGACTCTTGAACG
1359012 ATAGGGGAGG
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.07
21 34 0.81
22 5 0.12
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.23
Consensus pattern (22 bp):
GGGACTCTTGAACGGATGATAG
Found at i:1359036 original size:42 final size:41
Alignment explanation
Indices: 1358931--1359038 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
1358921 TAGAATGTTG
* * * *
1358931 GGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGT
1 GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT
* ** *
1358972 GGTAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGAT
1 GG-AGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT
1359014 AGG-GGAGGCCTCTTGAACGATGACA
1 -GGAGG-GGCCTCTTGAACGATGACA
1359039 AGTGAGTCGG
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
41 4 0.08
42 46 0.88
43 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (41 bp):
GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT
Found at i:1359543 original size:20 final size:20
Alignment explanation
Indices: 1359520--1359608 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 20
1359510 GAAACTTAAA
1359520 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1359540 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1359560 ATCGCAATGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1359580 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1359600 ATCGCAACG
1 ATCGCAACG
1359609 AGAGAATCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1359676 original size:34 final size:36
Alignment explanation
Indices: 1359633--1359738 Score: 108
Period size: 40 Copynumber: 2.8 Consensus size: 36
1359623 CTATTTTCAT
1359633 TTCGCATTGCGATTC-TTTCG-TTGCGATAGTCAAA
1 TTCGCATTGCGATTCATTTCGATTGCGATAGTCAAA
**
1359667 TTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATT
1 TTCGCATTGCGAT--TCA-TTTCG-ATTGCGATAGTCAAA
*
1359707 TTCGCGTTGCGATTTTCATTTCGCATTGCGAT
1 TTCGCATTGCGA--TTCATTTCG-ATTGCGAT
1359739 TCTCTCGTTG
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
34 13 0.21
36 2 0.03
38 5 0.08
39 14 0.23
40 26 0.43
42 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (36 bp):
TTCGCATTGCGATTCATTTCGATTGCGATAGTCAAA
Found at i:1359678 original size:20 final size:20
Alignment explanation
Indices: 1359653--1359795 Score: 165
Period size: 20 Copynumber: 7.5 Consensus size: 20
1359643 GATTCTTTCG
**
1359653 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1359673 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1359693 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
**
1359713 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1359732 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
1359746 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
1359766 TTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1359786 TTGCGATAGT
1 TTGCGATAGT
1359796 AAACTATTCT
Statistics
Matches: 106, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
17 2 0.02
18 4 0.04
19 13 0.12
20 74 0.70
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1359737 original size:93 final size:93
Alignment explanation
Indices: 1359625--1359795 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
1359615 TCTCAATGCT
*
1359625 ATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTC
1 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTC
1359690 GCATTGCGATAGTCATTTTCGCGTTGCG
66 GCATTGCGATAGTCATTTTCGCGTTGCG
** * *
1359718 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGTGATAGTCATTTTC
1 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTC
1359783 GCATTGCGATAGT
66 GCATTGCGATAGT
1359796 AAACTATTCT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (93 bp):
ATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTC
GCATTGCGATAGTCATTTTCGCGTTGCG
Found at i:1359759 original size:33 final size:35
Alignment explanation
Indices: 1359667--1359760 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 35
1359657 GATAGTCAAA
*
1359667 TTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTC
1 TTCGCGTTGCGATAGTCA-TTTCGCATTGCGATA-TC
**
1359704 ATTTTCGCGTTGCGATTTTCATTTCGCATTGCGAT-TC
1 ---TTCGCGTTGCGATAGTCATTTCGCATTGCGATATC
*
1359741 -TCTCGTTGCGATAGTCATTT
1 TTCGCGTTGCGATAGTCATTT
1359761 TCGCGTTGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
33 17 0.35
37 2 0.04
39 14 0.29
40 15 0.31
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (35 bp):
TTCGCGTTGCGATAGTCATTTCGCATTGCGATATC
Found at i:1360345 original size:18 final size:18
Alignment explanation
Indices: 1360322--1360371 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
1360312 CGGGTCGATC
1360322 AGGTGATGGCTCTGAGTG
1 AGGTGATGGCTCTGAGTG
*
1360340 AGGTGATGGCTCTAAGTG
1 AGGTGATGGCTCTGAGTG
1360358 AGGTGATGGCTCTG
1 AGGTGATGGCTCTG
1360372 GAAGTGGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.18, C:0.12, G:0.42, T:0.28
Consensus pattern (18 bp):
AGGTGATGGCTCTGAGTG
Found at i:1360380 original size:18 final size:18
Alignment explanation
Indices: 1360322--1360387 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
1360312 CGGGTCGATC
1360322 AGGTGATGGCTCTG-AGT
1 AGGTGATGGCTCTGAAGT
1360339 GAGGTGATGGCTCT-AAGT
1 -AGGTGATGGCTCTGAAGT
1360357 GAGGTGATGGCTCTGGAAGT
1 -AGGTGATGGCTCT-GAAGT
*
1360377 -GGTGATTGCTC
1 AGGTGATGGCTC
1360388 ATCATCCGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
18 40 0.91
20 4 0.09
ACGTcount: A:0.18, C:0.12, G:0.41, T:0.29
Consensus pattern (18 bp):
AGGTGATGGCTCTGAAGT
Found at i:1361822 original size:58 final size:59
Alignment explanation
Indices: 1361704--1361834 Score: 165
Period size: 58 Copynumber: 2.2 Consensus size: 59
1361694 AAAACTTAAA
* ** * **
1361704 ATCGCAACACGAAAATGAAAAGCGCAACACGAAAATGACTATCGCAACGCGAATTTGACT
1 ATCGCAACGCG-AAATGAAAAGCGCAACACGAAAATGAAAATCGCAACACGAAAATGACT
* *
1361764 ATCGCAACGCGAAATGAAAATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAATGAAAAGCGCAACACGAAAATGAAAATCGCAACACGAAAATGACT
*
1361822 ATCGTAACGCGAA
1 ATCGCAACGCGAA
1361835 TTTGACTATC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 35 0.56
59 17 0.27
60 10 0.16
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (59 bp):
ATCGCAACGCGAAATGAAAAGCGCAACACGAAAATGAAAATCGCAACACGAAAATGACT
Found at i:1361825 original size:20 final size:20
Alignment explanation
Indices: 1361704--1361851 Score: 147
Period size: 20 Copynumber: 7.5 Consensus size: 20
1361694 AAAACTTAAA
* **
1361704 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
* *
1361724 AGCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1361744 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
**
1361764 ATCGCAACGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
**
1361783 ATCGCAACGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
*
1361802 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1361822 ATCGTAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1361842 ATCGCAACGC
1 ATCGCAACGC
1361852 AAGAATCGCA
Statistics
Matches: 108, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
19 33 0.31
20 75 0.69
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1361831 original size:78 final size:75
Alignment explanation
Indices: 1361701--1361882 Score: 278
Period size: 78 Copynumber: 2.4 Consensus size: 75
1361691 TCTAAAACTT
* *
1361701 AAAATCGCAACACGAAAATGAAAAGCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTAT
1 AAAATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTAT
1361766 CGCAACGCGAAATG
65 CGCAACGC--AA-G
*
1361780 AAAATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACTATCGTAACGCGAATTTGACTATC
1 AAAATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATC
1361845 GCAACGCAAG
66 GCAACGCAAG
*
1361855 --AATCGCAAAGCGAAATGAAAATCGCAAC
1 AAAATCGCAACGCGAAATGAAAATCGCAAC
1361883 GACAGAATCG
Statistics
Matches: 99, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
73 27 0.27
75 1 0.01
76 2 0.02
78 56 0.57
79 13 0.13
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.14
Consensus pattern (75 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATC
GCAACGCAAG
Found at i:1362282 original size:22 final size:22
Alignment explanation
Indices: 1362229--1362285 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1362219 ATGATTTTGC
*
1362229 CAGAGATGGAGACTGATATCGT
1 CAGAGATGGGGACTGATATCGT
*
1362251 CAGAGATGGGGACTGATTTCGT
1 CAGAGATGGGGACTGATATCGT
*
1362273 TAGAGATGGGGAC
1 CAGAGATGGGGAC
1362286 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.28, C:0.12, G:0.37, T:0.23
Consensus pattern (22 bp):
CAGAGATGGGGACTGATATCGT
Found at i:1363781 original size:16 final size:15
Alignment explanation
Indices: 1363760--1363802 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1363750 TTAAAAACTA
1363760 ATATTTTATTAATATT
1 ATATTTTATTAA-ATT
1363776 ATATTTTAATTAAATT
1 ATATTTT-ATTAAATT
*
1363792 ACATTTATATT
1 ATATTT-TATT
1363803 TTTAACTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTTATTAAATT
Found at i:1363792 original size:22 final size:21
Alignment explanation
Indices: 1363767--1363831 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 21
1363757 CTAATATTTT
1363767 ATTAATATTATATTTTAATTAA
1 ATTAATATTATATTTTAATT-A
*
1363789 ATTACAT-TTATATTTTTAACTA
1 ATTA-ATATTATA-TTTTAATTA
*
1363811 ATTTATAATTATATATTTAAT
1 ATTAAT-ATTATAT-TTTAAT
1363832 ATTTTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
21 2 0.06
22 14 0.40
23 19 0.54
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAATATTATATTTTAATTA
Found at i:1363822 original size:23 final size:22
Alignment explanation
Indices: 1363773--1363855 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
1363763 TTTTATTAAT
* *
1363773 ATTATA-TTTTAATTAAATTACA
1 ATTATATTTTTAA-TAATTTATA
*
1363795 TTTATATTTTTAACTAATTTATA
1 ATTATATTTTTAA-TAATTTATA
* *
1363818 ATTATATATTTAATATTTTATA
1 ATTATATTTTTAATAATTTATA
*
1363840 ATT-TAATTTTTTATAA
1 ATTAT-ATTTTTAATAA
1363856 ATTAATTTAA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 1 0.02
22 24 0.49
23 24 0.49
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATATTTTTAATAATTTATA
Found at i:1363845 original size:15 final size:15
Alignment explanation
Indices: 1363819--1363861 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1363809 TAATTTATAA
1363819 TTATATATTTAATATT
1 TTATA-ATTTAATATT
*
1363835 TTATAATTTAATTTT
1 TTATAATTTAATATT
*
1363850 TTATAAATTAAT
1 TTATAATTTAAT
1363862 TTAATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATAATTTAATATT
Found at i:1369545 original size:29 final size:29
Alignment explanation
Indices: 1369503--1369569 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
1369493 TATGTTTATT
* * *
1369503 TATTTAATCGGTTTCTAATTTGTATCTTG
1 TATTTATTTGGTTTCTAAATTGTATCTTG
*
1369532 TATTTATTTGGTTTCTAAATTGTATGTTG
1 TATTTATTTGGTTTCTAAATTGTATCTTG
1369561 TATTTATTT
1 TATTTATTT
1369570 CAGTATATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (29 bp):
TATTTATTTGGTTTCTAAATTGTATCTTG
Found at i:1375284 original size:16 final size:16
Alignment explanation
Indices: 1375258--1375312 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1375248 AATAATTAAT
1375258 TAATAAATTTAAATAAA
1 TAAT-AATTTAAATAAA
*
1375275 TAATAATTTATATAAA
1 TAATAATTTAAATAAA
* *
1375291 T-ATTATTTTAATAAA
1 TAATAATTTAAATAAA
*
1375306 AAATAAT
1 TAATAAT
1375313 ATATATATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 11 0.35
16 16 0.52
17 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAATTTAAATAAA
Found at i:1375311 original size:31 final size:31
Alignment explanation
Indices: 1375244--1375330 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
1375234 AATTAGCACA
*
1375244 AAAAAATAA-TTA-ATTAATA-AATTTAAAT
1 AAAAAATAATTTATATAAATATAATTTAAAT
* * *
1375272 AAATAATAATTTATATAAATATTATTTTAAT
1 AAAAAATAATTTATATAAATATAATTTAAAT
*
1375303 AAAAAATAATATATATATATATATAATT
1 AAAAAATAAT-T-TATATAAATATAATT
1375331 ATATTAATCT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 8 0.17
29 3 0.06
30 6 0.13
31 16 0.34
32 1 0.02
33 13 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAAAATAATTTATATAAATATAATTTAAAT
Found at i:1376481 original size:200 final size:196
Alignment explanation
Indices: 1376048--1376540 Score: 542
Period size: 200 Copynumber: 2.5 Consensus size: 196
1376038 TAAATCGGTT
* * * *
1376048 TATTTATACCGGTAAAATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
1 TATTTATACCGGTTACATT-TTAATTTACCTATTACA-TATAATTATCAGTTTCGATGTTTTTGG
* * *
1376113 GATCGATACAATTT-TAAATGTATCGACACTTTATGCATGTATCTCGTTGGGCATTCATTCTGGA
64 GATCGATAC-TTTTATAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCATTCTGGA
* * * *
1376177 AAAAAGTATCGAAACATATTTAAAAAGTGTCAATACATTATGTTGACATATCCTCTCATAAAATC
128 AAAAAGTATCGAAACAAATTCAAAAAGTGTCAATACATTATGTTGACATATCCTCTAATAAAACC
*
1376242 GGTA
193 AGTA
* *
1376246 TATTTATTCCGGTTACATTTTAAATTTACCTATTACATCATAATTATCAGTTTCGATGTTTTTGA
1 TATTTATACCGGTTACATTTT-AATTTACCTATTACAT-ATAATTATCAGTTTCGATGTTTTTGG
* * *
1376311 GATCGATACTTTTAATAAATGTATCGGCACTTTATGCGTGCACCTCGTTTGGGCATTCATTTTGG
64 GATCGATACTTTT-ATAAATGTATCGACACTTTATGCATGCACCTCG-TTGGGCATTCATTCTGG
* * * * * * * * ** * *
1376376 ACAATAGGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTTATC-TGTTTTGTAAT-TA
127 A-AAAAAGTATCGAAACAAATTCAAAAAGTGTCAATACATTATGTTGA-CATATCCTCTAATAAA
1376439 ACCAGTA
190 ACCAGTA
**
1376446 TATTTATACCGGTTACATTGTTAATTTACCTATTACAGTATAATTATTTGTTTCGATGTTTTTGG
1 TATTTATACCGGTTACATT-TTAATTTACCTATTACA-TATAATTATCAGTTTCGATGTTTTTGG
* * * *
1376511 GGTTGATACTTTTAGAAAATATATCGACAC
64 GATCGATACTTTTA-TAAATGTATCGACAC
1376541 ATCTTTTTAC
Statistics
Matches: 247, Mismatches: 38, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
197 5 0.02
198 64 0.26
199 29 0.12
200 102 0.41
201 46 0.19
202 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (196 bp):
TATTTATACCGGTTACATTTTAATTTACCTATTACATATAATTATCAGTTTCGATGTTTTTGGGA
TCGATACTTTTATAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCATTCTGGAAAA
AAGTATCGAAACAAATTCAAAAAGTGTCAATACATTATGTTGACATATCCTCTAATAAAACCAGT
A
Done.