Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_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: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:3852015 original size:22 final size:22
Alignment explanation
Indices: 3851990--3852040 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3851980 CACCACAGCT
*
3851990 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
3852012 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
3852034 CGTAGAA
1 CGTAGAA
3852041 TTGTCCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:3852041 original size:22 final size:22
Alignment explanation
Indices: 3851998--3852043 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3851988 CTCGTATAAA
3851998 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3852020 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3852042 TG
1 TG
3852044 TCCATAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:3852288 original size:30 final size:30
Alignment explanation
Indices: 3852254--3852312 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3852244 ATCGCGTAGT
* *
3852254 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTACATACCTTTATCACATAGA
3852284 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
3852313 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGA
Found at i:3852826 original size:67 final size:68
Alignment explanation
Indices: 3852678--3852828 Score: 214
Period size: 68 Copynumber: 2.2 Consensus size: 68
3852668 CTTTTCTCAT
* * * *
3852678 GGGGAATCGGTTCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
3852743 GAG
66 GAG
* * * * *
3852746 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
3852810 GAG
66 GAG
3852813 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
3852829 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 23 0.31
68 51 0.69
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GAG
Found at i:3853900 original size:84 final size:83
Alignment explanation
Indices: 3853716--3854743 Score: 903
Period size: 84 Copynumber: 12.3 Consensus size: 83
3853706 CTGAATGAAA
* * * * *
3853716 TCGAACTCGAAAAGTCTTTGGTTGGCAGATATCCCTTCTCGACTTAAGCTATGTTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATG
3853781 TGCCTT-AGAGCTGAGCGTAG
64 TGCCTTGA-AGCTGAGCGTAG
* * * * * *
3853801 TAGAACTCGAAGGTCTTTGGTGACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
* *
3853866 CCCTTGAAGCTGAGTGTAA
66 -CCTTGAAGCTGAGCGTAG
* * * * * * *
3853885 TCAAACTTGAGGGTCTTTGGT---ATATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATATG
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
3853947 CCTT-AGAGCTGAGCGTAG
66 CCTTGA-AGCTGAGCGTAG
** * * * *
3853965 TCGAACTCGAAGGTCTTTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATTT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
*
3854030 GTCTCTG-AGCTGAGCGTAG
65 GCCT-TGAAGCTGAGCGTAG
* * *
3854049 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * *
3854114 GCCTTCAAAGCTGAGTGTAA
65 GCCTT-GAAGCTGAGCGTAG
* * * * * * *
3854134 TTGAAC-CTGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATTATA
1 TCGAACTC-GAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATG
3854198 TGCCTTTGAA-CTGAGCGTAG
64 TGCC-TTGAAGCTGAGCGTAG
* * * * * * * * *
3854218 TCGAACTCGAAGGTCTTTTGTTGGTAAATAACCCTTCTTGTCTTGAGCTATTCTGTAAATTTGGT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAA--TGAT
* * * *
3854283 TTTCCTCTG-AGCTGAGTGTAA
63 GTGCCT-TGAAGCTGAGCGTAG
* * * * * * *
3854304 TTGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTCCTAGCCCTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * *
3854369 ACCCTCGAAGCTGAGCATAG
65 -GCCTTGAAGCTGAGCGTAG
* * * * *
3854389 TCGAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAACTTATGATGCAAATG-TAT
1 TCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
*
3854453 GCCTTGGAGCTGAGCGTAG
65 GCCTTGAAGCTGAGCGTAG
* ** * * * *
3854472 TCGAACTCAAAGGTCTTTTGGTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * *
3854537 GCCCTCGAAGCTGAGTGTAA
65 G-CCTTGAAGCTGAGCGTAG
* * * ** *
3854557 TCAAACTCGAGGGTC-TT--TGGCAGATAACCCTTCTCGACTTAAGCTACACTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
*
3854619 CCTTGGAGCTGAGCGTAG
66 CCTTGAAGCTGAGCGTAG
* * * * * *
3854637 TCAAACTCAAAGGTATTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* *
3854702 GCCTTGGAGCTGAGCGTAA
65 GCCTTGAAGCTGAGCGTAG
* *
3854721 TTGAACTCGAAGGACTTTGGTGG
1 TCGAACTCGAAGGTCTTTGGTGG
3854744 GAACAATTCC
Statistics
Matches: 764, Mismatches: 149, Indels: 62
0.78 0.15 0.06
Matches are distributed among these distances:
79 1 0.00
80 52 0.07
81 78 0.10
83 102 0.13
84 297 0.39
85 167 0.22
86 67 0.09
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
CCTTGAAGCTGAGCGTAG
Found at i:3854730 original size:164 final size:165
Alignment explanation
Indices: 3853714--3854733 Score: 1016
Period size: 164 Copynumber: 6.1 Consensus size: 165
3853704 AGCTGAATGA
* * *
3853714 AATCGAACTCGAAAAGTCTTTGGTTGGCAGATATCCCTTCTCGACTTAAGCTATGTTGCAAATGA
1 AATCGAACTCG-AAGGTC-TT-GTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * *
3853779 TGTGCCTTAGAGCTGAGCGTAGTAGAACTCGAAGGTCTTTGGTGACATATAACCCTTCTAGCCTT
63 TATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTT
*
3853844 GAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGT
128 GAGTTATGCTGTAAATGATGTG-CCTTGAAGCTGAGCGT
* * * * * * *
3853883 AATCAAACTTGAGGGTC-T-TTGGTATATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATAT
1 AATCGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATAT
*
3853946 GCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGATAGATAACCCTTCTAGCCTTGA
66 GCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGA
* *
3854011 GTTATGCTGTAAATGATTTGTCTCTG-AGCTGAGCGT
130 GTTATGCTGTAAATGATGTGCCT-TGAAGCTGAGCGT
* *
3854047 AGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTC--TTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAT
* * * * * * * *
3854112 ATGCCTTCAAAGCTGAGTGTAATTGAAC-CTGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGAC
64 ATGCCTT-AGAGCTGAGCGTAGTCGAACTC-GAAGGTCTTTGG-TGACAGATAACCCTTCTAGCC
* * * * * *
3854176 TTAAGCTATGTTGCAAATTATATGCCTTTGAA-CTGAGCGT
126 TTGAGTTATGCTGTAAATGATGTGCC-TTGAAGCTGAGCGT
* * * * * * * *
3854216 AGTCGAACTCGAAGGTCTTTTGTTGGTAAATAACCCTTCTTGTCTTGAGCTATTCTGTAAATTTG
1 AATCGAACTCGAAGGTC--TTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAA--TG
* * * * * * * * *
3854281 GTTTTCCTCT-GAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTCCTAGC
62 ATATGCCT-TAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGC
* * * *
3854345 CCTGAGTTATGCTGTAAATGATGTACCCTCGAAGCTGAGCAT
125 CTTGAGTTATGCTGTAAATGATGT-GCCTTGAAGCTGAGCGT
* * *
3854387 AGTCGAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA-CTTATGATGCAAATG-
1 AATCGAACTCGAAGGTC-TT-GTTGGCAGATAACCCTTCTCGACTTAAGC-TATGCTGCAAATGA
* * *
3854450 TATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTAACAGATAACCCTTCTAGCCT
63 TATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCT
* * *
3854515 TGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGT
127 TGAGTTATGCTGTAAATGATGTG-CCTTGAAGCTGAGCGT
* * ** *
3854555 AATCAAACTCGAGGGTC-T-TTGGCAGATAACCCTTCTCGACTTAAGCTACACTGCAAATGATGT
1 AATCGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATAT
* * * * * * * * *
3854618 GCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTATTTGGTTGGCAGATAGCCCTTCTCGACTTAA
66 GCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGA
* * *
3854683 GTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGT
130 GTTATGCTGTAAATGATGTGCCTTGAAGCTGAGCGT
*
3854719 AATTGAACTCGAAGG
1 AATCGAACTCGAAGG
3854734 ACTTTGGTGG
Statistics
Matches: 711, Mismatches: 115, Indels: 55
0.81 0.13 0.06
Matches are distributed among these distances:
164 162 0.23
165 120 0.17
166 2 0.00
167 2 0.00
168 157 0.22
169 132 0.19
170 68 0.10
171 67 0.09
172 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (165 bp):
AATCGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATAT
GCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATGTGCCTTGAAGCTGAGCGT
Found at i:3860045 original size:5 final size:5
Alignment explanation
Indices: 3860035--3860073 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
3860025 AACAATGAAA
*
3860035 AAAAT AAAAT AAAAT AAAAT AAAAC AAAA- AAAAGT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAA
3860074 AACGAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
4 4 0.13
5 23 0.74
6 4 0.13
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:3860074 original size:10 final size:9
Alignment explanation
Indices: 3860021--3860075 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 9
3860011 AGAAAAGAGA
3860021 AAAAAACAAT
1 AAAAAA-AAT
*
3860031 GAAAAAAAT
1 AAAAAAAAT
3860040 AAAATAAAAT
1 AAAA-AAAAT
*
3860050 AAAATAAAAC
1 AAAA-AAAAT
3860060 AAAAAAAAGT
1 AAAAAAAA-T
3860070 AAAAAA
1 AAAAAA
3860076 CGAAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 10 0.26
10 29 0.74
ACGTcount: A:0.82, C:0.04, G:0.04, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:3861460 original size:63 final size:61
Alignment explanation
Indices: 3861322--3861478 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 61
3861312 AATATATATA
* * * *
3861322 TATATATATATATAAGTATTTTCAAAAACATATAATATATAATTTCAAAATGCTTTTAAAAAC
1 TATATA-ATATATAAATGTTTTC-AAAATATATAATATATAATTTCAAAATACTTTTAAAAAC
* * * * * * *
3861385 TATATGATATATAAATGTTTTCAAAATTATATACTGTATAGTTTTTAAAATATTTTTGAAAAC
1 TATATAATATATAAATGTTTTCAAAA-TATATAATATATA-ATTTCAAAATACTTTTAAAAAC
3861448 TATATAATATATAAATGTTTTCAAAATATAT
1 TATATAATATATAAATGTTTTCAAAATATAT
3861479 TTTCAAAACT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
61 4 0.05
62 29 0.36
63 47 0.59
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (61 bp):
TATATAATATATAAATGTTTTCAAAATATATAATATATAATTTCAAAATACTTTTAAAAAC
Found at i:3861507 original size:38 final size:38
Alignment explanation
Indices: 3861402--3861734 Score: 239
Period size: 37 Copynumber: 9.2 Consensus size: 38
3861392 TATATAAATG
* * * *
3861402 TTTTCAAAATTATATACTGTATA-GTTTTTAAAATAT-
1 TTTTCAAAACTATATAATATATATGTTTTCAAAATATA
*
3861438 TTTTGAAAACTATATAATATATAAATGTTTTCAAAATATA
1 TTTTCAAAACTATATAATATAT--ATGTTTTCAAAATATA
*
3861478 TTTTCAAAACTATATAATATATATGTTTTCACAA-ATA
1 TTTTCAAAACTATATAATATATATGTTTTCAAAATATA
* * * *
3861515 TTTTCAAAACCTATATATTATATAT-ATTT-AAAAAATG
1 TTTTCAAAA-CTATATAATATATATGTTTTCAAAATATA
* * *
3861552 TTTTAAAAAACTATA-AAT-TATATATTTTCAAAAT-GA
1 TTTT-CAAAACTATATAATATATATGTTTTCAAAATATA
* * * *
3861588 TTTTAAAAACTATATATTATATATATTTTCAAAATGT-
1 TTTTCAAAACTATATAATATATATGTTTTCAAAATATA
* *
3861625 TTTTAAAAACTATAT-A-ATATA-----T--AAATGT-
1 TTTTCAAAACTATATAATATATATGTTTTCAAAATATA
* *
3861653 TTTTAAAAACTATATAATATATAAATGTTTTC-AAA-ACA
1 TTTTCAAAACTATATAATATAT--ATGTTTTCAAAATATA
3861691 TTTTCAAAACTATAT-AT-TATAT-TTTGTCAAAA-ATA
1 TTTTCAAAACTATATAATATATATGTTT-TCAAAATATA
3861726 TTTTCAAAA
1 TTTTCAAAA
3861735 GATATATTAT
Statistics
Matches: 248, Mismatches: 24, Indels: 51
0.77 0.07 0.16
Matches are distributed among these distances:
28 21 0.08
29 1 0.00
30 5 0.02
32 1 0.00
33 3 0.01
34 4 0.02
35 34 0.14
36 35 0.14
37 64 0.26
38 47 0.19
39 12 0.05
40 21 0.08
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (38 bp):
TTTTCAAAACTATATAATATATATGTTTTCAAAATATA
Found at i:3861650 original size:28 final size:28
Alignment explanation
Indices: 3861619--3861688 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
3861609 TATATTTTCA
3861619 AAATGTTTTTAAAAACTATATAATATAT
1 AAATGTTTTTAAAAACTATATAATATAT
3861647 AAATGTTTTTAAAAACTATATAATATAT
1 AAATGTTTTTAAAAACTATATAATATAT
*
3861675 AAATGTTTTCAAAA
1 AAATGTTTTTAAAA
3861689 CATTTTCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (28 bp):
AAATGTTTTTAAAAACTATATAATATAT
Found at i:3861788 original size:22 final size:24
Alignment explanation
Indices: 3861749--3861793 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3861739 TATTATTATA
*
3861749 TATATATATATAATAAAATAAAAC
1 TATATATATATAATAAAACAAAAC
3861773 TATATATATAT-A-AAAACAAAA
1 TATATATATATAATAAAACAAAA
3861794 TAGCTCCGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 1 0.05
24 11 0.55
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
TATATATATATAATAAAACAAAAC
Found at i:3864415 original size:21 final size:22
Alignment explanation
Indices: 3864372--3864420 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3864362 CAAAATAATA
**
3864372 TATTT-ATAAAAATATTATTTT
1 TATTTAATAAAAATATTAAATT
3864393 TATTTAATAAAAATA-TAAATT
1 TATTTAATAAAAATATTAAATT
*
3864414 TAATTAA
1 TATTTAA
3864421 AAATAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTAATAAAAATATTAAATT
Found at i:3865693 original size:65 final size:66
Alignment explanation
Indices: 3865554--3865702 Score: 155
Period size: 65 Copynumber: 2.3 Consensus size: 66
3865544 TTCTGGTCAT
*
3865554 AGGGTATCGATACCATATGAAGGGGTATCGATACATCCTCTTGAACGAAAAATTACAGAATGTCA
1 AGGGTATCGATACCATATGAAGGGGTATCGATACA-CCTCCTGAACGAAAAATTACAGAATGTCA
*
3865619 GT
65 GC
** * *
3865621 ATTGTATCGATACCATAT-AGGGGGTATCGATAC-CC-CCTGAA-GATGAAAATTTCCAGAATGT
1 AGGGTATCGATACCATATGAAGGGGTATCGATACACCTCCTGAACGA--AAAA-TTACAGAATGT
3865682 -AGGC
63 CA-GC
*
3865686 AGGGTATCTATACCATA
1 AGGGTATCGATACCATA
3865703 GGCAGGGTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
62 2 0.03
63 5 0.07
64 7 0.10
65 25 0.36
66 14 0.20
67 16 0.23
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (66 bp):
AGGGTATCGATACCATATGAAGGGGTATCGATACACCTCCTGAACGAAAAATTACAGAATGTCAG
C
Found at i:3865706 original size:20 final size:20
Alignment explanation
Indices: 3865681--3865757 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
3865671 TTCCAGAATG
3865681 TAGGCAGGGTATCTATACCA
1 TAGGCAGGGTATCTATACCA
3865701 TAGGCAGGGTATCTATACCA
1 TAGGCAGGGTATCTATACCA
* *
3865721 TAGGTAGGGTATTTATACCA
1 TAGGCAGGGTATCTATACCA
* *
3865741 TAGACAGAGTATCTATA
1 TAGGCAGGGTATCTATA
3865758 TCTCAGTTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (20 bp):
TAGGCAGGGTATCTATACCA
Found at i:3866324 original size:22 final size:22
Alignment explanation
Indices: 3866296--3866372 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
3866286 GTTTATAGTA
* *
3866296 GTCCTTCGGGACATATCCAGTG
1 GTCCTTCAGGACGTATCCAGTG
3866318 GTCCTTCAGGACGTATCCAGTG
1 GTCCTTCAGGACGTATCCAGTG
3866340 GTCCTTCAGGACGTATCCAGTG
1 GTCCTTCAGGACGTATCCAGTG
3866362 GTCCTTCAGGA
1 GTCCTTCAGGA
3866373 AAAATATTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
GTCCTTCAGGACGTATCCAGTG
Found at i:3872121 original size:27 final size:26
Alignment explanation
Indices: 3872076--3872127 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
3872066 GATGAAGAAG
*
3872076 TTATATGAGATTAAAGAAAATGAGTTT
1 TTATATGAAATTAAAGAAAA-GAGTTT
**
3872103 TTATATGAAATTATGGAAAAGAGTT
1 TTATATGAAATTAAAGAAAAGAGTT
3872128 GATAAGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (26 bp):
TTATATGAAATTAAAGAAAAGAGTTT
Found at i:3872318 original size:19 final size:21
Alignment explanation
Indices: 3872278--3872320 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
3872268 GATGTATTGA
3872278 ATGAGTAGTAATGAGTTCAAGT
1 ATGAGTAG-AATGAGTTCAAGT
3872300 ATGAGTAG-ATGAGTT-AAGT
1 ATGAGTAGAATGAGTTCAAGT
3872319 AT
1 AT
3872321 ATGTAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
22 8 0.38
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (21 bp):
ATGAGTAGAATGAGTTCAAGT
Found at i:3872522 original size:66 final size:67
Alignment explanation
Indices: 3872396--3872563 Score: 186
Period size: 66 Copynumber: 2.5 Consensus size: 67
3872386 TTCCTGGTCA
3872396 TAGGGTATCGATACCATATGAAGGCGTATCGATACCTCCTCTTGAACGAAAAATTACAGAATGT-
1 TAGGGTATCGATACCATATGAAGGCGTATCGATACCTCCTCTTGAACGAAAAATTACAGAATGTA
3872460 CAG
66 C-G
* * * * *
3872463 TATGGTATCGATACCATAT-AGGGGGTATTGATACC-CC-CTTGAA-GATGAAAATTTCCAGAAT
1 TAGGGTATCGATACCATATGAAGGCGTATCGATACCTCCTCTTGAACGA--AAAA-TTACAGAAT
3872524 GTACG
63 GTACG
* * *
3872529 TAGGGTATCTATACCATAAGAAGG-GTATCTATACC
1 TAGGGTATCGATACCATATGAAGGCGTATCGATACC
3872564 ATAGGCAGGG
Statistics
Matches: 85, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
63 2 0.02
64 6 0.07
65 6 0.07
66 49 0.58
67 22 0.26
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (67 bp):
TAGGGTATCGATACCATATGAAGGCGTATCGATACCTCCTCTTGAACGAAAAATTACAGAATGTA
CG
Found at i:3872613 original size:20 final size:20
Alignment explanation
Indices: 3872529--3872601 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
3872519 AGAATGTACG
3872529 TAGGGTATCTATACCATAAGA
1 TAGGGTATCTATACCAT-AGA
*
3872550 -AGGGTATCTATACCATAGG
1 TAGGGTATCTATACCATAGA
*
3872569 CAGGGTATCTATACCATAGA
1 TAGGGTATCTATACCATAGA
3872589 TAGGGTATCTATA
1 TAGGGTATCTATA
3872602 TCTCAGTTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.04
20 46 0.96
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (20 bp):
TAGGGTATCTATACCATAGA
Found at i:3872899 original size:2 final size:2
Alignment explanation
Indices: 3872892--3872921 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3872882 ATGTACATGC
3872892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3872922 TATTGTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3873194 original size:22 final size:22
Alignment explanation
Indices: 3873156--3873255 Score: 146
Period size: 22 Copynumber: 4.5 Consensus size: 22
3873146 GTTTATAGTA
*
3873156 GTCCTTCGGGACATATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
3873178 GTCTTTTGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
3873200 GTCCTTCGGGTCGTATCCAATG
1 GTCCTTCGGGACGTATCCAGTG
3873222 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
3873244 GTCCTTTGGGAC
1 GTCCTTCGGGAC
3873256 AAATATTTAC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 68 1.00
ACGTcount: A:0.14, C:0.25, G:0.30, T:0.31
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:3878007 original size:3 final size:3
Alignment explanation
Indices: 3877999--3878035 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
3877989 AATATAGTAT
3877999 TAA TAA TAA -AA -AA TAAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA
3878036 TGAAAAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3878053 original size:2 final size:2
Alignment explanation
Indices: 3878046--3878128 Score: 73
Period size: 2 Copynumber: 42.0 Consensus size: 2
3878036 TGAAAAACAA
*
3878046 AT AT AT AT AT AT AT AT AT CAT AT AT -T AT AT AT -T AT AT AA AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
3878087 -T CT AA AA AA AG ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3878129 TTCTTAACCT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
1 3 0.04
2 64 0.91
3 3 0.04
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3878194 original size:26 final size:24
Alignment explanation
Indices: 3878112--3878195 Score: 60
Period size: 26 Copynumber: 3.1 Consensus size: 24
3878102 TATATATATA
*
3878112 TATATATATATATATATTTCTTAACC
1 TATATAT-TATATATATTT-TTAAAC
* *
3878138 TATACCGTATTATAATAAATTTTCAAAAC
1 TATA---TATTAT-ATATATTTT-TAAAC
3878167 TATATATCTATATATATTTTTAATAC
1 TATATAT-TATATATATTTTTAA-AC
3878193 TAT
1 TAT
3878196 GCTGTATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
25 2 0.04
26 20 0.43
27 3 0.07
28 4 0.09
29 17 0.37
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (24 bp):
TATATATTATATATATTTTTAAAC
Found at i:3879528 original size:21 final size:21
Alignment explanation
Indices: 3879502--3879542 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3879492 CCGCGTAGAA
3879502 ATGTCCCGAAGAACCACATAG
1 ATGTCCCGAAGAACCACATAG
*
3879523 ATGTCCCGAAGGACCACATA
1 ATGTCCCGAAGAACCACATA
3879543 TCACATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.29, G:0.20, T:0.15
Consensus pattern (21 bp):
ATGTCCCGAAGAACCACATAG
Found at i:3879660 original size:21 final size:21
Alignment explanation
Indices: 3879622--3879662 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3879612 CCAAAGTACC
*
3879622 ACATATATATTCCAAAGGATT
1 ACATATATATCCCAAAGGATT
* *
3879643 ACATATATGTCCCGAAGGAT
1 ACATATATATCCCAAAGGAT
3879663 CACGTAGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (21 bp):
ACATATATATCCCAAAGGATT
Found at i:3882406 original size:16 final size:17
Alignment explanation
Indices: 3882381--3882414 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3882371 TCAAGGTGTC
3882381 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
3882397 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
3882414 A
1 A
3882415 TAATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:3882653 original size:21 final size:21
Alignment explanation
Indices: 3882604--3882653 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3882594 GGCTAACATG
*
3882604 TCTTGCTCCTCTTAACTTCCT
1 TCTTGCTTCTCTTAACTTCCT
3882625 TCTTGCTTCTCTTAACTTCCT
1 TCTTGCTTCTCTTAACTTCCT
3882646 TCTTGCTT
1 TCTTGCTT
3882654 TCCGGAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.08, C:0.34, G:0.06, T:0.52
Consensus pattern (21 bp):
TCTTGCTTCTCTTAACTTCCT
Found at i:3883057 original size:25 final size:25
Alignment explanation
Indices: 3883009--3883058 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3882999 AAATTTATAA
* **
3883009 AATTTTAGAGAAAATAAACTTAAAT
1 AATTTTAGAGAAAACAAAAATAAAT
*
3883034 AATTTTATAGAAAACAAAAATAAAT
1 AATTTTAGAGAAAACAAAAATAAAT
3883059 TACCTATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (25 bp):
AATTTTAGAGAAAACAAAAATAAAT
Found at i:3884057 original size:17 final size:17
Alignment explanation
Indices: 3884035--3884068 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3884025 CACATTTCAT
3884035 ATCACAAAAGCATATAC
1 ATCACAAAAGCATATAC
3884052 ATCACAAAAGCATATAC
1 ATCACAAAAGCATATAC
3884069 TTGTGAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.24, G:0.06, T:0.18
Consensus pattern (17 bp):
ATCACAAAAGCATATAC
Found at i:3884335 original size:21 final size:21
Alignment explanation
Indices: 3884309--3884358 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
3884299 AATAGGTGTA
* *
3884309 CCAAAGTATCGCATATATGTT
1 CCAAAGGATCACATATATGTT
* *
3884330 CCAAAGGATTACATATATGTC
1 CCAAAGGATCACATATATGTT
*
3884351 CCGAAGGA
1 CCAAAGGA
3884359 CCACGTAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (21 bp):
CCAAAGGATCACATATATGTT
Found at i:3894214 original size:18 final size:18
Alignment explanation
Indices: 3894193--3894249 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
3894183 GTTCTCCTTT
3894193 ATTTTGAGTATAATAATA
1 ATTTTGAGTATAATAATA
3894211 ATTTTGAGTATAATAATA
1 ATTTTGAGTATAATAATA
*
3894229 ATTATT-ACTATAATAA-A
1 ATT-TTGAGTATAATAATA
3894246 ATTT
1 ATTT
3894250 ACATAAACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 1 0.03
17 4 0.11
18 30 0.81
19 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (18 bp):
ATTTTGAGTATAATAATA
Found at i:3894456 original size:2 final size:2
Alignment explanation
Indices: 3894449--3894493 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3894439 TAGGATTTCC
3894449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3894491 AT A
1 AT A
3894494 GTAATTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3896921 original size:33 final size:33
Alignment explanation
Indices: 3896873--3896937 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3896863 AATCATAATA
*
3896873 ACAAATATTAATTTTTTA-ATATAAAAAATTATG
1 ACAAATAATAATTTTTTATA-ATAAAAAATTATG
*
3896906 ACAAATAATATTTTTTTATAATAAAAAATTAT
1 ACAAATAATAATTTTTTATAATAAAAAATTAT
3896938 AAAAAAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (33 bp):
ACAAATAATAATTTTTTATAATAAAAAATTATG
Found at i:3898680 original size:10 final size:10
Alignment explanation
Indices: 3898665--3898695 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
3898655 TGCATAACAT
3898665 TTTAGTTGCA
1 TTTAGTTGCA
3898675 TTTAGTTGCA
1 TTTAGTTGCA
3898685 TTTAGTTGCA
1 TTTAGTTGCA
3898695 T
1 T
3898696 ATAGGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:3914068 original size:8 final size:7
Alignment explanation
Indices: 3914038--3914064 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3914028 TTTATACTCC
3914038 CTTTTTA
1 CTTTTTA
3914045 CTTTTTA
1 CTTTTTA
3914052 CTTTTTA
1 CTTTTTA
3914059 CTTTTT
1 CTTTTT
3914065 TACTACGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (7 bp):
CTTTTTA
Found at i:3916343 original size:23 final size:23
Alignment explanation
Indices: 3916304--3916360 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
3916294 GCAGGGAGAG
*
3916304 AAATAAAAATAAGGAAATAAAATA
1 AAAT-AAAATAAAGAAATAAAATA
*
3916328 AAATAAAATAAAGAAATAAAGTA
1 AAATAAAATAAAGAAATAAAATA
*
3916351 AAACAAAATA
1 AAATAAAATA
3916361 TTTTCCCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (23 bp):
AAATAAAATAAAGAAATAAAATA
Found at i:3916352 original size:13 final size:13
Alignment explanation
Indices: 3916302--3916352 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
3916292 ATGCAGGGAG
3916302 AGAAATAAAAATAA
1 AGAAAT-AAAATAA
*
3916316 GGAAATAAAAT--
1 AGAAATAAAATAA
3916327 A-AAATAAAATAA
1 AGAAATAAAATAA
*
3916339 AGAAATAAAGTAA
1 AGAAATAAAATAA
3916352 A
1 A
3916353 ACAAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.29
12 1 0.03
13 16 0.52
14 5 0.16
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.16
Consensus pattern (13 bp):
AGAAATAAAATAA
Found at i:3927196 original size:17 final size:17
Alignment explanation
Indices: 3927147--3927196 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
3927137 TTGTTCATAT
3927147 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
3927164 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
3927178 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
3927195 TT
1 TT
3927197 ACAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:3927738 original size:11 final size:12
Alignment explanation
Indices: 3927721--3927749 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3927711 AAAAATAAAC
3927721 TTAAAAACCAAG
1 TTAAAAACCAAG
3927733 TTAAAAACCAAG
1 TTAAAAACCAAG
3927745 TTAAA
1 TTAAA
3927750 TTATGAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (12 bp):
TTAAAAACCAAG
Found at i:3929407 original size:15 final size:15
Alignment explanation
Indices: 3929387--3929432 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
3929377 ATTTATATTG
3929387 ATTATTTGTAATATA
1 ATTATTTGTAATATA
* *
3929402 ATTATTTAT-AT-TG
1 ATTATTTGTAATATA
3929415 ATTATTTGTAATATA
1 ATTATTTGTAATATA
3929430 ATT
1 ATT
3929433 TAATACAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.36
14 4 0.16
15 12 0.48
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
ATTATTTGTAATATA
Found at i:3929407 original size:28 final size:28
Alignment explanation
Indices: 3929376--3929432 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3929366 GAATTTTCAA
3929376 TATTTATATTGATTATTTGTAATATAAT
1 TATTTATATTGATTATTTGTAATATAAT
3929404 TATTTATATTGATTATTTGTAATATAAT
1 TATTTATATTGATTATTTGTAATATAAT
3929432 T
1 T
3929433 TAATACAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (28 bp):
TATTTATATTGATTATTTGTAATATAAT
Found at i:3929420 original size:13 final size:13
Alignment explanation
Indices: 3929376--3929421 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
3929366 GAATTTTCAA
3929376 TATTTATATTGAT
1 TATTTATATTGAT
* *
3929389 TATTTGTAATATAAT
1 TATTTAT-AT-TGAT
3929404 TATTTATATTGAT
1 TATTTATATTGAT
3929417 TATTT
1 TATTT
3929422 GTAATATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 14 0.52
14 4 0.15
15 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (13 bp):
TATTTATATTGAT
Found at i:3930357 original size:20 final size:20
Alignment explanation
Indices: 3930332--3930372 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3930322 ATGCTATTTT
3930332 AAAAAAAAC-AAAAAAGCCA
1 AAAAAAAACAAAAAAAGCCA
3930351 AAAAAAAACAAAAAAAGCCA
1 AAAAAAAACAAAAAAAGCCA
3930371 AA
1 AA
3930373 TTTTCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.80, C:0.15, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAGCCA
Found at i:3940389 original size:15 final size:15
Alignment explanation
Indices: 3940369--3940403 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3940359 CAAAAATAAT
3940369 ATATATATATTAACA
1 ATATATATATTAACA
*
3940384 ATATATATCTTAACA
1 ATATATATATTAACA
3940399 ATATA
1 ATATA
3940404 AGCAAGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATATATATTAACA
Found at i:3944324 original size:12 final size:12
Alignment explanation
Indices: 3944317--3944348 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3944307 TAAAAATATC
3944317 TTTTAAAACATA
1 TTTTAAAACATA
*
3944329 TTTTAGAACATA
1 TTTTAAAACATA
3944341 TTTTAAAA
1 TTTTAAAA
3944349 AATTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (12 bp):
TTTTAAAACATA
Found at i:3952681 original size:19 final size:19
Alignment explanation
Indices: 3952657--3952698 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
3952647 TAAGAACATG
3952657 TTTGAAATCTTGATATGAT
1 TTTGAAATCTTGATATGAT
*
3952676 TTTGAAATCTTGGTATGAT
1 TTTGAAATCTTGATATGAT
3952695 TTTG
1 TTTG
3952699 TGTAGTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (19 bp):
TTTGAAATCTTGATATGAT
Found at i:3953001 original size:15 final size:16
Alignment explanation
Indices: 3952981--3953020 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3952971 TGAACAAGTG
3952981 TATGTGAAAAG-ACTC
1 TATGTGAAAAGAACTC
3952996 TATGTG-AAAGTAACTC
1 TATGTGAAAAG-AACTC
3953012 TATGTGAAA
1 TATGTGAAA
3953021 GTAACTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 6 0.27
16 10 0.45
17 2 0.09
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (16 bp):
TATGTGAAAAGAACTC
Found at i:3953013 original size:16 final size:16
Alignment explanation
Indices: 3952992--3953026 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3952982 ATGTGAAAAG
3952992 ACTCTATGTGAAAGTA
1 ACTCTATGTGAAAGTA
3953008 ACTCTATGTGAAAGTA
1 ACTCTATGTGAAAGTA
3953024 ACT
1 ACT
3953027 ATGTGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (16 bp):
ACTCTATGTGAAAGTA
Found at i:3953030 original size:14 final size:15
Alignment explanation
Indices: 3952995--3953033 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
3952985 TGAAAAGACT
3952995 CTATGTGAAAGTAAC
1 CTATGTGAAAGTAAC
3953010 TCTATGTGAAAGTAA-
1 -CTATGTGAAAGTAAC
3953025 CTATGTGAA
1 CTATGTGAA
3953034 TAAGAGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 9 0.39
16 14 0.61
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (15 bp):
CTATGTGAAAGTAAC
Found at i:3953197 original size:23 final size:21
Alignment explanation
Indices: 3953141--3953198 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
3953131 ACGAGGGTTT
*
3953141 TATGTGGTCATTCGGAACAAA
1 TATGTGGTCCTTCGGAACAAA
**
3953162 TATGTGG-CACTTCGGTGCAAA
1 TATGTGGTC-CTTCGGAACAAA
3953183 TCTATGTGGTCCTTCG
1 --TATGTGGTCCTTCG
3953199 AGACAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 16 0.53
23 12 0.40
24 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTTCGGAACAAA
Found at i:3953217 original size:44 final size:43
Alignment explanation
Indices: 3953140--3953231 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 43
3953130 GACGAGGGTT
* *
3953140 TTATGTGGTCATTCGGAACAAATATGTGGCACTTCGGTGCAAA
1 TTATGTGGTCATTCGGAACAAATATGCGACACTTCGGTGCAAA
* * *
3953183 TCTATGTGGTCCTTC-GAGACAATTATGCGACACTTTGGTGCAAA
1 T-TATGTGGTCATTCGGA-ACAAATATGCGACACTTCGGTGCAAA
3953227 TTATG
1 TTATG
3953232 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 7 0.17
44 35 0.83
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (43 bp):
TTATGTGGTCATTCGGAACAAATATGCGACACTTCGGTGCAAA
Found at i:3967629 original size:16 final size:16
Alignment explanation
Indices: 3967608--3967640 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3967598 CAGTTCTTTG
3967608 AATTGCATTATTTTTA
1 AATTGCATTATTTTTA
3967624 AATTGCATTATTTTTA
1 AATTGCATTATTTTTA
3967640 A
1 A
3967641 GGGTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
AATTGCATTATTTTTA
Found at i:3969138 original size:18 final size:20
Alignment explanation
Indices: 3969101--3969138 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3969091 TGGTCTAAAG
3969101 TATCAATATGTTTCTTCATAA
1 TATCAATA-GTTTCTTCATAA
3969122 TATCAATA-TTT-TTCATA
1 TATCAATAGTTTCTTCATA
3969139 TGATATTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
21 8 0.47
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (20 bp):
TATCAATAGTTTCTTCATAA
Found at i:3970987 original size:2 final size:2
Alignment explanation
Indices: 3970980--3971009 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3970970 CTCTTTGTCA
*
3970980 GT GT GT GT GT AT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
3971010 AATTGTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3977067 original size:22 final size:23
Alignment explanation
Indices: 3977039--3977093 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
3977029 TGTGTTCGGT
*
3977039 TCATTTATA-TTCCCAAACAAGC
1 TCATTTATAGTTCACAAACAAGC
*
3977061 TCATTTATATGTTCACAAATAAGC
1 TCATTTATA-GTTCACAAACAAGC
3977085 TCATTTATA
1 TCATTTATA
3977094 AGCTCGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.31
24 20 0.69
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.38
Consensus pattern (23 bp):
TCATTTATAGTTCACAAACAAGC
Found at i:3977111 original size:12 final size:12
Alignment explanation
Indices: 3977079--3977111 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3977069 ATGTTCACAA
*
3977079 ATAAGCTCATTT
1 ATAAGCTCGTTT
3977091 ATAAGCTCGTTT
1 ATAAGCTCGTTT
3977103 ATAAGCTCG
1 ATAAGCTCG
3977112 ATTAATTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (12 bp):
ATAAGCTCGTTT
Found at i:3982665 original size:2 final size:2
Alignment explanation
Indices: 3982658--3982692 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3982648 CAACAGTAGA
3982658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3982693 CCTTTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3987096 original size:22 final size:22
Alignment explanation
Indices: 3987048--3987101 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
3987038 TTTGAACATT
* *
3987048 TTAACGAACATGTTCGCAAACG
1 TTAAAGAACATGTTCGCAAACA
* **
3987070 CTAAAGAACATGTTCGTGAACA
1 TTAAAGAACATGTTCGCAAACA
3987092 TTAAACGAAC
1 TTAAA-GAAC
3987102 GCTAACAAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (22 bp):
TTAAAGAACATGTTCGCAAACA
Found at i:3987168 original size:23 final size:24
Alignment explanation
Indices: 3987137--3987204 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
3987127 AAATAAACGA
*
3987137 TAAATGAACATGTTCAC-AA-ATGC
1 TAAACGAACATGTTCACGAACAT-C
* *
3987160 TAAACGAACATGTTCGCGAACATT
1 TAAACGAACATGTTCACGAACATC
*
3987184 TAAACGAACATGTTCGCGAAC
1 TAAACGAACATGTTCACGAAC
3987205 GTTAAATGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 15 0.38
24 23 0.57
25 2 0.05
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
TAAACGAACATGTTCACGAACATC
Found at i:3987215 original size:23 final size:23
Alignment explanation
Indices: 3987132--3987215 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
3987122 ACATAAAATA
* * * *
3987132 AACGATAAATGAACATGTTCACA
1 AACGTTAAACGAACATGTTCGCG
* *
3987155 AATGCTAAACGAACATGTTCGCG
1 AACGTTAAACGAACATGTTCGCG
*
3987178 AACATTTAAACGAACATGTTCGCG
1 AAC-GTTAAACGAACATGTTCGCG
*
3987202 AACGTTAAATGAAC
1 AACGTTAAACGAAC
3987216 GAACATGAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 29 0.58
24 21 0.42
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (23 bp):
AACGTTAAACGAACATGTTCGCG
Found at i:3989815 original size:17 final size:17
Alignment explanation
Indices: 3989795--3989833 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3989785 TGAAAACCCA
3989795 ATAATATTA-ATGTGATG
1 ATAATATTATATGTG-TG
*
3989812 ATAATGTTATATGTGTG
1 ATAATATTATATGTGTG
3989829 ATAAT
1 ATAAT
3989834 CATAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (17 bp):
ATAATATTATATGTGTG
Found at i:4004094 original size:137 final size:136
Alignment explanation
Indices: 4003848--4004127 Score: 434
Period size: 137 Copynumber: 2.1 Consensus size: 136
4003838 ACCTAAGTGA
** * *
4003848 CGAAATGGTAATTCACAAACTCATTATGAATTTCATGGATGCACACATAGTGCCAAAAGTACATA
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATCCACACATAGTGCCAAAAGTACAAA
* *
4003913 TAGTACTGATACAAAAATGCAACATATGCATTAAACAAAATCGATTGATAACCTTCATACACAAA
66 TAGTACTAATACAAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCTTCATACACAAA
4003978 TATATGT
131 -ATATGT
* * *
4003985 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGTTCCACACCTAGTGCCGAAAGTACAAA
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATCCACACATAGTGCCAAAAGTACAAA
* *
4004050 TAGTACTAATACAAAAATGCAACATATGTATTAAACAAAATCGATCGATAACCTTCATACTCAAA
66 TAGTACTAATACAAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCTTCATACACAAA
*
4004115 GTATGT
131 ATATGT
*
4004121 TGAAATG
1 CGAAATG
4004128 CACCTATGAC
Statistics
Matches: 130, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
136 11 0.08
137 119 0.92
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (136 bp):
CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATCCACACATAGTGCCAAAAGTACAAA
TAGTACTAATACAAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCTTCATACACAAA
ATATGT
Found at i:4008568 original size:2 final size:2
Alignment explanation
Indices: 4008563--4008606 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4008553 ATACTTTTGC
4008563 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4008605 AT
1 AT
4008607 CTTACACATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4011338 original size:29 final size:29
Alignment explanation
Indices: 4011293--4011360 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
4011283 CCCAGTCACC
4011293 GAGTCAACCCATCCGAGTCAACTCGGTCT
1 GAGTCAACCCATCCGAGTCAACTCGGTCT
* * * *
4011322 GAGTCAACCCCTTCGAGTTAACTCGTTCT
1 GAGTCAACCCATCCGAGTCAACTCGGTCT
*
4011351 GAGTTAACCC
1 GAGTCAACCC
4011361 GTCTAAGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (29 bp):
GAGTCAACCCATCCGAGTCAACTCGGTCT
Found at i:4011356 original size:15 final size:15
Alignment explanation
Indices: 4011307--4011372 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
4011297 CAACCCATCC
*
4011307 GAGTCAACTCGGTCT
1 GAGTCAACTCGTTCT
* *
4011322 GAGTCAACCCCTTC-
1 GAGTCAACTCGTTCT
*
4011336 GAGTTAACTCGTTCT
1 GAGTCAACTCGTTCT
* *
4011351 GAGTTAACCCG-TCT
1 GAGTCAACTCGTTCT
*
4011365 AAGTCAAC
1 GAGTCAAC
4011373 CTGTTGAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
14 20 0.49
15 21 0.51
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (15 bp):
GAGTCAACTCGTTCT
Found at i:4011412 original size:28 final size:27
Alignment explanation
Indices: 4011371--4011428 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
4011361 GTCTAAGTCA
4011371 ACCTGTTGAATTTGACTCATTGACTTTG
1 ACCTGTTGAATTTGAC-CATTGACTTTG
* *
4011399 ACCTGTTGACTTTGACCGTTGACTTTG
1 ACCTGTTGAATTTGACCATTGACTTTG
4011426 ACC
1 ACC
4011429 AAAAAGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (27 bp):
ACCTGTTGAATTTGACCATTGACTTTG
Found at i:4011421 original size:13 final size:13
Alignment explanation
Indices: 4011375--4011428 Score: 72
Period size: 14 Copynumber: 4.0 Consensus size: 13
4011365 AAGTCAACCT
*
4011375 GTTGAATTTGACTC
1 GTTGACTTTGAC-C
*
4011389 ATTGACTTTGACC
1 GTTGACTTTGACC
4011402 TGTTGACTTTGACC
1 -GTTGACTTTGACC
4011416 GTTGACTTTGACC
1 GTTGACTTTGACC
4011429 AAAAAGTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
13 14 0.39
14 22 0.61
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (13 bp):
GTTGACTTTGACC
Found at i:4015486 original size:36 final size:36
Alignment explanation
Indices: 4015446--4015521 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
4015436 GACAATGGAG
4015446 ATAGCGACCAATGATAATCAACAATGGTGGTGAGCA
1 ATAGCGACCAATGATAATCAACAATGGTGGTGAGCA
4015482 ATAGCGACCAATGATAATCAACAATGGTGGTGAGCA
1 ATAGCGACCAATGATAATCAACAATGGTGGTGAGCA
4015518 ATAG
1 ATAG
4015522 TGAATGCCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (36 bp):
ATAGCGACCAATGATAATCAACAATGGTGGTGAGCA
Found at i:4016573 original size:15 final size:15
Alignment explanation
Indices: 4016553--4016771 Score: 157
Period size: 15 Copynumber: 14.7 Consensus size: 15
4016543 GACAAAATAC
*
4016553 AAAATATAATAACAT
1 AAAATACAATAACAT
4016568 AAAATACAATAACAT
1 AAAATACAATAACAT
* *
4016583 -AAATCAAAATACCA-
1 AAAAT-ACAATAACAT
4016597 AAAATTACAATAACAT
1 AAAA-TACAATAACAT
* *
4016613 AAAATATAATACCAT
1 AAAATACAATAACAT
*
4016628 AAATTACAATAACAT
1 AAAATACAATAACAT
* *
4016643 AAAATGCAATATCAT
1 AAAATACAATAACAT
*
4016658 AAAATACAATAATAT
1 AAAATACAATAACAT
4016673 AAAATGA-AATATA-A-
1 AAAAT-ACAATA-ACAT
4016687 AAAATTACAATAACAT
1 AAAA-TACAATAACAT
* *
4016703 AAAAT--AACACCAT
1 AAAATACAATAACAT
*** *
4016716 AAAATTTGAGAACAT
1 AAAATACAATAACAT
* *
4016731 AAAATTA-AATACCAG
1 AAAA-TACAATAACAT
*
4016746 AAAATACAAGAACAT
1 AAAATACAATAACAT
*
4016761 AAATTACAATA
1 AAAATACAATA
4016772 CTAAAAAATA
Statistics
Matches: 159, Mismatches: 31, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
13 11 0.07
14 12 0.08
15 124 0.78
16 12 0.08
ACGTcount: A:0.63, C:0.12, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAATACAATAACAT
Found at i:4016758 original size:30 final size:30
Alignment explanation
Indices: 4016560--4016782 Score: 181
Period size: 30 Copynumber: 7.5 Consensus size: 30
4016550 TACAAAATAT
* *
4016560 AATAACATAAAATACAATAACAT-AAATCAA
1 AATACCATAAAATACAATAACATAAAAT-TA
4016590 AATACCA-AAAATTACAATAACATAAAA-TA
1 AATACCATAAAA-TACAATAACATAAAATTA
* **
4016619 TAATACCATAAATTACAATAACATAAAATGC
1 -AATACCATAAAATACAATAACATAAAATTA
* * *
4016650 AATATCATAAAATACAATAATATAAAATGA
1 AATACCATAAAATACAATAACATAAAATTA
* *
4016680 AATA-TAAAAAATTACAATAACATAAAA-T-
1 AATACCATAAAA-TACAATAACATAAAATTA
* *** *
4016708 AACACCATAAAATTTGAGAACATAAAATTA
1 AATACCATAAAATACAATAACATAAAATTA
* *
4016738 AATACCAGAAAATACAAGAACAT-AAATTA
1 AATACCATAAAATACAATAACATAAAATTA
* *
4016767 CAATACTAAAAAATAC
1 -AATACCATAAAATAC
4016783 GATATCACAT
Statistics
Matches: 156, Mismatches: 27, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
28 14 0.09
29 22 0.14
30 114 0.73
31 6 0.04
ACGTcount: A:0.62, C:0.13, G:0.03, T:0.22
Consensus pattern (30 bp):
AATACCATAAAATACAATAACATAAAATTA
Found at i:4019945 original size:26 final size:26
Alignment explanation
Indices: 4019916--4019976 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
4019906 TGTTTTATGG
4019916 TTATGTTTTGTTGATCTAAGACATGC
1 TTATGTTTTGTTGATCTAAGACATGC
4019942 TTATGTTTTGTTGATCTAAGACATGC
1 TTATGTTTTGTTGATCTAAGACATGC
*
4019968 TTGTGTTTT
1 TTATGTTTT
4019977 TTGCACTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.51
Consensus pattern (26 bp):
TTATGTTTTGTTGATCTAAGACATGC
Found at i:4022756 original size:21 final size:21
Alignment explanation
Indices: 4022689--4022762 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
4022679 GGGTTAAGAC
* *
4022689 CTTTTGATTAAAGGACTT-AT
1 CTTTTCATGAAAGGACTTAAT
* * *
4022709 CCTTTCGATGAAATGACTTAAC
1 CTTTTC-ATGAAAGGACTTAAT
*
4022731 CTTTTCATGAAAGGATTTAAT
1 CTTTTCATGAAAGGACTTAAT
4022752 CTTTTCATGAA
1 CTTTTCATGAA
4022763 GAGAATTGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
20 4 0.09
21 33 0.77
22 6 0.14
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (21 bp):
CTTTTCATGAAAGGACTTAAT
Found at i:4027734 original size:2 final size:2
Alignment explanation
Indices: 4027729--4027776 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4027719 AATTTTTTTA
4027729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4027771 AT AT AT
1 AT AT AT
4027777 TCTCAACTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4028462 original size:60 final size:60
Alignment explanation
Indices: 4028396--4028559 Score: 197
Period size: 59 Copynumber: 2.7 Consensus size: 60
4028386 AGAATCTTAT
* * * *
4028396 TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTTATCTCAAAACTATGACTATGATTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCAAAACTATAACTATCATTC
* * * *
4028456 TAAATTAGTCCTTAAAC-TTTGAACATTCTAATTTCATCCCTAAACTATAACTTTCTTTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCAAAACTATAACTATCATTC
* * *
4028515 TAAATT-GATCCTCAAACTTTTGAATCTTCCAATTTCATCACCAAA
1 TAAATTAG-TCCTTAAACTTTTGAATATTCTAATTTCATC-CCAAA
4028560 TTCATCCAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
58 1 0.01
59 48 0.55
60 35 0.40
61 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCAAAACTATAACTATCATTC
Found at i:4028786 original size:60 final size:59
Alignment explanation
Indices: 4028691--4028871 Score: 175
Period size: 60 Copynumber: 3.0 Consensus size: 59
4028681 CGTACAGTTT
* * *
4028691 GGGATAAAATTGGAATGTTCAAAAAGTTTGGGGACTAATTTATAATGAAGGTCATAATTTG
1 GGGATAAAATTGAAATGTTC-AAAAGTTT-AGGACTAATTTAAAATGAAGGTCATAATTTG
* * * * *
4028752 GGGATGAAATTGAAATGCTCAAAAGTTTAAGGACTAATTTAGAATGATA-GTCATAGTTTA
1 GGGATAAAATTGAAATGTTCAAAAGTTT-AGGACTAATTTAAAATGA-AGGTCATAATTTG
* * * * * * *
4028812 GGGATTAAATTGAAATATTTATAAGTTTAGAGTCTAATTTAAAATGAGGGTCATACTTTG
1 GGGATAAAATTGAAATGTTCAAAAGTTTAG-GACTAATTTAAAATGAAGGTCATAATTTG
4028872 AGGACATGTG
Statistics
Matches: 99, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
59 2 0.02
60 79 0.80
61 18 0.18
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (59 bp):
GGGATAAAATTGAAATGTTCAAAAGTTTAGGACTAATTTAAAATGAAGGTCATAATTTG
Found at i:4041863 original size:21 final size:20
Alignment explanation
Indices: 4041831--4041870 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
4041821 TATCATAATC
4041831 ATTATCTTATTATTAATTTT
1 ATTATCTTATTATTAATTTT
4041851 ATTATCATTATTATTAATTT
1 ATTATC-TTATTATTAATTT
4041871 ATTTACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATCTTATTATTAATTTT
Found at i:4041864 original size:12 final size:12
Alignment explanation
Indices: 4041813--4041866 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
4041803 TTCATTACTA
*
4041813 ATTATTGTTATC
1 ATTATTATTATC
* *
4041825 ATAATCATTATC
1 ATTATTATTATC
4041837 -TTATTATTA--
1 ATTATTATTATC
4041846 ATT-TTATTATC
1 ATTATTATTATC
4041857 ATTATTATTA
1 ATTATTATTA
4041867 ATTTATTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
9 6 0.18
10 2 0.06
11 10 0.30
12 15 0.45
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:4045827 original size:17 final size:17
Alignment explanation
Indices: 4045802--4045866 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
4045792 ATAAACTATG
4045802 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
* **
4045819 TCCCAAAGGATGTCATCTGTA
1 TCCCGAAGGACCT-ATC---A
4045840 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
4045857 TCCCGAAGGA
1 TCCCGAAGGA
4045867 TGTAATCTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
17 21 0.55
18 3 0.08
20 3 0.08
21 11 0.29
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:4045843 original size:21 final size:20
Alignment explanation
Indices: 4045818--4045887 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
4045808 AGGACCTATC
4045818 ATCCCAAAGGATGTCATCTGT
1 ATCCCAAAGGATGT-ATCTGT
* **
4045839 ATCCCGAAGGACCTATC---
1 ATCCCAAAGGATGTATCTGT
*
4045856 ATCCCGAAGGATGTAATCTGT
1 ATCCCAAAGGATGT-ATCTGT
*
4045877 GTCCCAAAGGA
1 ATCCCAAAGGA
4045888 CCTATTATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 12 0.32
18 3 0.08
20 3 0.08
21 20 0.53
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCCCAAAGGATGTATCTGT
Found at i:4045853 original size:38 final size:38
Alignment explanation
Indices: 4045802--4045892 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
4045792 ATAAACTATG
*
4045802 TCCCGAAGGACCTATCATCCCAAAGGATGTCATCTGTA
1 TCCCGAAGGACCTATCATCCCAAAGGATGTAATCTGTA
* *
4045840 TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGACCTATCATCCCAAAGGATGTAATCTGTA
*
4045878 TCCCAAAGGACCTAT
1 TCCCGAAGGACCTAT
4045893 TATATGTCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (38 bp):
TCCCGAAGGACCTATCATCCCAAAGGATGTAATCTGTA
Found at i:4051370 original size:34 final size:31
Alignment explanation
Indices: 4051326--4051392 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 31
4051316 TTGTAAAGGA
*
4051326 GAAATGTTCTAGCTTAGCCCGTGTAAAAGCTAGG
1 GAAAGGTTCTAGCTTAGCCCG-G-AAAA-CTAGG
*
4051360 GAAAGGTTCTAGTTTAGCCCGGAAAACTAGG
1 GAAAGGTTCTAGCTTAGCCCGGAAAACTAGG
4051391 GA
1 GA
4051393 GTTTGTAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 7 0.23
32 4 0.13
33 1 0.03
34 19 0.61
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (31 bp):
GAAAGGTTCTAGCTTAGCCCGGAAAACTAGG
Found at i:4052909 original size:19 final size:20
Alignment explanation
Indices: 4052885--4052922 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
4052875 TAAAGATAAT
4052885 TTGATTTTG-AAATCAAAAG
1 TTGATTTTGAAAATCAAAAG
4052904 TTGATTTTGAAAATCAAAA
1 TTGATTTTGAAAATCAAAA
4052923 TGAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (20 bp):
TTGATTTTGAAAATCAAAAG
Found at i:4054408 original size:21 final size:22
Alignment explanation
Indices: 4054366--4054409 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4054356 AATCAGATTG
4054366 CCCAGGGGGTACAGATTCCCCC
1 CCCAGGGGGTACAGATTCCCCC
4054388 CCCAGGGGGTATC-GATTCCCCC
1 CCCAGGGGGTA-CAGATTCCCCC
4054410 TGTCTAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.16, C:0.41, G:0.27, T:0.16
Consensus pattern (22 bp):
CCCAGGGGGTACAGATTCCCCC
Found at i:4054802 original size:34 final size:32
Alignment explanation
Indices: 4054758--4054827 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
4054748 TTTTGTAAAG
*
4054758 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
4054792 GGGATAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
4054824 GGGA
1 GGGA
4054828 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:4055708 original size:20 final size:20
Alignment explanation
Indices: 4055683--4055762 Score: 124
Period size: 20 Copynumber: 4.0 Consensus size: 20
4055673 AAACCATTCA
4055683 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
*
4055703 GGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCTGTACCCCCT
*
4055723 GGGGGAAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
* *
4055743 AGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCTGTACCCCCT
4055763 AGGCAATCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:4055738 original size:40 final size:40
Alignment explanation
Indices: 4055683--4055762 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
4055673 AAACCATTCA
* *
4055683 GGGGGGAATCTGTACCCCCTGGGGGGAATCTGTTCCCCCT
1 GGGGGAAATCTGTACCCCCTAGGGGGAATCTGTTCCCCCT
4055723 GGGGGAAATCTGTACCCCCTAGGGGGAATCTGTTCCCCCT
1 GGGGGAAATCTGTACCCCCTAGGGGGAATCTGTTCCCCCT
4055763 AGGCAATCTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.23
Consensus pattern (40 bp):
GGGGGAAATCTGTACCCCCTAGGGGGAATCTGTTCCCCCT
Found at i:4056126 original size:21 final size:22
Alignment explanation
Indices: 4056100--4056153 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
4056090 TTTGAAATTA
*
4056100 CTCCCCCTT-ACTTTAACACTT
1 CTCCCCCTTAACCTTAACACTT
*
4056121 CTCCCCTTTAACACCTTAACACTT
1 CTCCCCCTT-A-ACCTTAACACTT
*
4056145 CCCCCCCTT
1 CTCCCCCTT
4056154 TTTGTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 8 0.31
24 18 0.69
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCCCCCTTAACCTTAACACTT
Found at i:4058147 original size:34 final size:32
Alignment explanation
Indices: 4058094--4058163 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
4058084 ACCTTACAAC
*
4058094 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
*
4058126 TCCCTAGCTTTTATACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTT-TACGGGCTAAACTAGAACCTT
4058160 TCCC
1 TCCC
4058164 CTTTACAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 23 0.68
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
Found at i:4058472 original size:21 final size:21
Alignment explanation
Indices: 4058446--4058487 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4058436 CCAGAATGGG
*
4058446 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
4058467 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
4058488 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:4058626 original size:20 final size:20
Alignment explanation
Indices: 4058601--4058638 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4058591 AACCATTCAG
4058601 GGGGGAATCTGTACCCCCGA
1 GGGGGAATCTGTACCCCCGA
*
4058621 GGGGGAATCTGTTCCCCC
1 GGGGGAATCTGTACCCCC
4058639 TAGGCAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCGA
Found at i:4059886 original size:23 final size:22
Alignment explanation
Indices: 4059828--4059888 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
4059818 CCAGGCTTTA
* *
4059828 ATCATTCATTACTAATTATTGTT
1 ATCATT-ATTATTAATTATTATT
* *
4059851 ATCATAATCATTATATTATTATT
1 ATCATTATTATTA-ATTATTATT
4059874 ATCATTATTATTAAT
1 ATCATTATTATTAAT
4059889 AATTTATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (22 bp):
ATCATTATTATTAATTATTATT
Found at i:4060531 original size:12 final size:11
Alignment explanation
Indices: 4060514--4060572 Score: 64
Period size: 12 Copynumber: 5.1 Consensus size: 11
4060504 GAAACAAAAC
4060514 AAAAAAAAGAA
1 AAAAAAAAGAA
*
4060525 GAAAAAAACGAA
1 -AAAAAAAAGAA
*
4060537 CAAAAAAAGAA
1 AAAAAAAAGAA
*
4060548 AAAAGCAAAGAA
1 AAAA-AAAAGAA
4060560 AAAAGAAAAGAA
1 AAAA-AAAAGAA
4060572 A
1 A
4060573 GAAGAGCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
11 12 0.30
12 28 0.70
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:4060541 original size:20 final size:20
Alignment explanation
Indices: 4060504--4060568 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
4060494 GGGGAGATTT
*
4060504 GAAACAAAACAAAAAAAAGAA
1 GAAA-AAAACAAAAAAAAAAA
* *
4060525 GAAAAAAACGAACAAAAAAA
1 GAAAAAAACAAAAAAAAAAA
* *
4060545 GAAAAAAGC-AAAGAAAAAA
1 GAAAAAAACAAAAAAAAAAA
4060564 GAAAA
1 GAAAA
4060569 GAAAGAAGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.34
20 21 0.55
21 4 0.11
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (20 bp):
GAAAAAAACAAAAAAAAAAA
Found at i:4060549 original size:19 final size:18
Alignment explanation
Indices: 4060515--4060568 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
4060505 AAACAAAACA
*
4060515 AAAAAAAGAAGAAAAAAAC
1 AAAAAAA-AAGAAAAAAGC
4060534 GAACAAAAAAAGAAAAAAGC
1 -AA-AAAAAAAGAAAAAAGC
4060554 AAAGAAAAAAGAAAA
1 AAA-AAAAAAGAAAA
4060569 GAAAGAAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 13 0.42
20 12 0.39
21 5 0.16
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAGC
Found at i:4064442 original size:12 final size:12
Alignment explanation
Indices: 4064425--4064475 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
4064415 GGACAACTTT
4064425 GTTTATGAGCTC
1 GTTTATGAGCTC
* *
4064437 GTTTATAAGTTC
1 GTTTATGAGCTC
*
4064449 GTTTACGAGCTC
1 GTTTATGAGCTC
4064461 GTTTATTGA-CTC
1 GTTTA-TGAGCTC
4064473 GTT
1 GTT
4064476 CATTTATGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 30 0.94
13 2 0.06
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.45
Consensus pattern (12 bp):
GTTTATGAGCTC
Found at i:4064700 original size:22 final size:21
Alignment explanation
Indices: 4064675--4064715 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4064665 AGAAAAACTA
*
4064675 ATAATTCAACATATAAATGAAT
1 ATAAATCAACA-ATAAATGAAT
*
4064697 ATAAATGAACAATAAATGA
1 ATAAATCAACAATAAATGA
4064716 GCACTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
ATAAATCAACAATAAATGAAT
Found at i:4064786 original size:24 final size:23
Alignment explanation
Indices: 4064754--4064863 Score: 98
Period size: 24 Copynumber: 4.5 Consensus size: 23
4064744 TTGTGAACGC
4064754 TAAATGAACACGTTCATAAGAATA
1 TAAATGAACACGTTC-TAAGAATA
*
4064778 TAAATGAACACGTTCCTAAGCATA
1 TAAATGAACACGTT-CTAAGAATA
*
4064802 TAAATGAA-ACCGTTC-ACGAATA
1 TAAATGAACA-CGTTCTAAGAATA
* *
4064824 TTAAATGAACATGTTCGTGAACAATAAA
1 -TAAATGAACACGTTC-T-AAGAAT--A
4064852 TAAATGAACACG
1 TAAATGAACACG
4064864 AACTGAACAT
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
22 5 0.07
23 14 0.20
24 34 0.49
25 1 0.01
26 4 0.06
27 11 0.16
28 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (23 bp):
TAAATGAACACGTTCTAAGAATA
Found at i:4068463 original size:2 final size:2
Alignment explanation
Indices: 4068456--4068491 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4068446 TATCTCCTTG
4068456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4068492 GATCATGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4068832 original size:20 final size:22
Alignment explanation
Indices: 4068793--4068834 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
4068783 ACTTTTAATA
4068793 TTAAATAATTAAAAATTATTTT
1 TTAAATAATTAAAAATTATTTT
*
4068815 TTAAAT-ATT-AATATTATTTT
1 TTAAATAATTAAAAATTATTTT
4068835 GTATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAAATAATTAAAAATTATTTT
Found at i:4075929 original size:63 final size:63
Alignment explanation
Indices: 4075816--4075941 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
4075806 TGGTAATAAA
* * *
4075816 GTGTGGATCACCATCCACACCTTTAAGGGGTTCTGTCTTAGCTAGAGCCACGTAAGGAAAGGC
1 GTGTGGATCACCATCCACACCTTCAAGGGGTTCGGTCTGAGCTAGAGCCACGTAAGGAAAGGC
** * * * *
4075879 GTGTGGATCGTCATCCACGCCTTCGAGGGGTTCGGTCTGAGCTGGCGCCACGTAAGGAAAGGC
1 GTGTGGATCACCATCCACACCTTCAAGGGGTTCGGTCTGAGCTAGAGCCACGTAAGGAAAGGC
4075942 TCGGATAGCG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.22
Consensus pattern (63 bp):
GTGTGGATCACCATCCACACCTTCAAGGGGTTCGGTCTGAGCTAGAGCCACGTAAGGAAAGGC
Found at i:4082548 original size:60 final size:59
Alignment explanation
Indices: 4082482--4082643 Score: 200
Period size: 60 Copynumber: 2.7 Consensus size: 59
4082472 TGGAAAATCA
** * * *
4082482 AAAAGTTTGGGGACCAATTTAGGATGAGGGTCATAGTTTAGGGATGAAACT-AGAATGTTC
1 AAAAGTTTAAGGACCAATTTAGAATGAGGGTTATAGTTT-GGGATGAAACTGA-AATATTC
* * *
4082542 AAAAGTTTAAGGACCAATTTTGAATGAGAGTTATAATTTGAGGATGAAACTGAAATATTC
1 AAAAGTTTAAGGACCAATTTAGAATGAGGGTTATAGTTTG-GGATGAAACTGAAATATTC
* *
4082602 AAAAGTTTAAGGACTAATTTAAAATGAGGGTTATAGTTTGGG
1 AAAAGTTTAAGGACCAATTTAGAATGAGGGTTATAGTTTGGG
4082644 GACGTATGAT
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.03
60 83 0.95
61 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (59 bp):
AAAAGTTTAAGGACCAATTTAGAATGAGGGTTATAGTTTGGGATGAAACTGAAATATTC
Found at i:4088040 original size:26 final size:26
Alignment explanation
Indices: 4088011--4088062 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
4088001 GATCTATTGG
4088011 TTTAAAA-TTAGTATTTTATATTTTTA
1 TTTAAAATTTAGTATTTT-TATTTTTA
4088037 TTTAAAATTTAGTATTTTTATTTTTA
1 TTTAAAATTTAGTATTTTTATTTTTA
4088063 ATACTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (26 bp):
TTTAAAATTTAGTATTTTTATTTTTA
Found at i:4089772 original size:2 final size:2
Alignment explanation
Indices: 4089761--4089792 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4089751 AAAGAAATTT
4089761 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4089793 AAATAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4091004 original size:182 final size:182
Alignment explanation
Indices: 4090633--4091290 Score: 853
Period size: 182 Copynumber: 3.6 Consensus size: 182
4090623 CCAAATAAAA
* * * * *
4090633 AATGTATCGATCCATATCAATATAATAGGTAAAAATATGACAACACCGGT-T-TAATTATGACAA
1 AATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTAA--AGGACAA
* * * * *
4090696 AACCGGTAAAGCA-CTACCAGATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATCGACACT
64 AACCGGTAAAG-AGCGACCAGATATATTGAAAGTGTCGA-TA-CTTTAATATAAGTATCGACACT
* * ** * *
4090759 TTGGGAATTTAAAAGAGAACCAGTAATAGCGCTTATAAAGTGTCGATACTTTATAAA
126 TTGGTAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAC
* * * * *
4090816 AATGTATCGATCCATAACGATATAACATGTAAAAATATGACAAAACCGGTGTCGAAATGATAAAA
1 AATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGACAAAA
* * *
4090881 CTGGTAAAGAGCTACCAGATATATTGAAAGTGTTGATACTTTAATATAAGTATCGACACTTTGGT
66 CCGGTAAAGAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGGT
4090946 AATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAC
131 AATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAC
*
4090998 AATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGAAAAAA
1 AATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGACAAAA
* * *
4091063 CCGGTATAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAATATAAGTATCAACACTTT-GT
66 CCGGTAAAGAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGGT
* * * *
4091127 GAATTTAAAAGAGAAGCATTTTTAGCACCTATAAA-TCGACGATACTTTATAAC
131 -AATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGT-GTCGATACTTTATAAC
* * *
4091180 AATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCGATCTCTAAAGGACAAAA
1 AATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGACAAAA
* * *
4091245 CTGATATAGAGCGACC-GTATATATTGAAAGTGTCGATACTTTAATA
66 CCGGTAAAGAGCGACCAG-ATATATTGAAAGTGTCGATACTTTAATA
4091291 AGTACGCATA
Statistics
Matches: 427, Mismatches: 41, Indels: 15
0.88 0.08 0.03
Matches are distributed among these distances:
181 7 0.02
182 334 0.78
183 83 0.19
184 1 0.00
185 2 0.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGACAAAA
CCGGTAAAGAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGGT
AATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAC
Found at i:4096065 original size:23 final size:22
Alignment explanation
Indices: 4096010--4096092 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 22
4096000 ACCAGAACCC
* *
4096010 CAAGGGGGTATCGATTCCCCTA
1 CAAGGGGGAATCGATTCCCCTT
* * *
4096032 C-ATGGGGAATCGATTTCCGTT
1 CAAGGGGGAATCGATTCCCCTT
*
4096053 CAAAGGGGGAATCGGTTCCCCTT
1 C-AAGGGGGAATCGATTCCCCTT
*
4096076 CAAGGGGGTATCGATTC
1 CAAGGGGGAATCGATTC
4096093 TCTCTGCACC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
21 16 0.33
22 15 0.31
23 17 0.35
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.25
Consensus pattern (22 bp):
CAAGGGGGAATCGATTCCCCTT
Found at i:4104340 original size:24 final size:24
Alignment explanation
Indices: 4104294--4104341 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4104284 ATTTCATATG
* * *
4104294 TAATTGGAGTTTGAATTTTAATTT
1 TAATTGGAGTTTCAATATAAATTT
*
4104318 TAATTTGAGTTTCAATATAAATTT
1 TAATTGGAGTTTCAATATAAATTT
4104342 CGGCTCCACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (24 bp):
TAATTGGAGTTTCAATATAAATTT
Found at i:4106099 original size:200 final size:198
Alignment explanation
Indices: 4105678--4106445 Score: 1006
Period size: 200 Copynumber: 3.8 Consensus size: 198
4105668 TAAAGTGTCC
* * * *
4105678 CATAAAGTGTCA-ATACATTTTTAAAAAGTATCGATCCCAAAATCATCGAAACTGAAAATTATAA
1 CATAAAGTGT-AGATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACCGATAATTATAA
*
4105742 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTT-TGAGAAAATAGAT-ATA
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCA-A
* * * *
4105805 CATAATGTATCAACACTTATGGAATTTGTGTCTATACGTTTTGTCCAAAATGAATGCCAAACGGG
129 CATAATGTATCGACACTT-T-TAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGGG
4105870 GTGCACA
192 GTGCACA
* *
4105877 CATAAAGTGTCGATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTAGATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACCGATAATTATAAT
* * ** * ** * * *
4105942 ATAATAGGTAATTTTGTAATATAACCAATATAAATATACCAGTTTTAT-ATGAGAATAGGTCTAC
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGA-GAAAATAGGTCAAC
* * *
4106006 ATAATGTGTCGACACTTTTGAATTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGT
130 ATAATGTATCGACACTTTT-AA-TTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGGGG
4106071 TGCACA
193 TGCACA
* *
4106077 CATAAAGTGTAGATACATTTTTAAAAAGTATTAATCCCAAAAACATCGAAACTGATAATTATAAT
1 CATAAAGTGTAGATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACCGATAATTATAAT
*
4106142 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACA
* *
4106207 TAATGTATCGACACGTTTTAGATTTGTTTCGATACATTTTGTCCAGAAATGAATGCCAAACGGGG
131 TAATGTATCGACAC-TTTTA-ATTTGTGTCGATACTTTTTGTCCA-AAATGAATGCCAAACGGGG
* **
4106272 TACAGG
193 TGCACA
* * * ** * * *
4106278 CACAAAGTGTCGATACA-TTTGAAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAAC
1 CATAAAGTGTAGATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACCGATAATTATAAT
* *
4106342 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACA
* *
4106407 TAATGTATCGACACGTTTAAATTTGCGTCGATACTTTTT
131 TAATGTATCGACAC-TTTTAATTTGTGTCGATACTTTTT
4106446 AAATAATGCA
Statistics
Matches: 495, Mismatches: 64, Indels: 20
0.85 0.11 0.03
Matches are distributed among these distances:
199 116 0.23
200 338 0.68
201 41 0.08
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
CATAAAGTGTAGATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACA
TAATGTATCGACACTTTTAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGGGGTGC
ACA
Found at i:4106439 original size:399 final size:399
Alignment explanation
Indices: 4105678--4106445 Score: 1116
Period size: 400 Copynumber: 1.9 Consensus size: 399
4105668 TAAAGTGTCC
* *
4105678 CATAAAGTGTCAATACATTTTTAAAAAGTATCGATCCCAAAATCATCGAAACTGAAAATTATAAT
1 CATAAAGTGTCAATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACTGAAAATTATAAT
4105743 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTTGAGAAAATAGATATACAT
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTTGAGAAAATAGATATACAT
* * * *
4105808 AATGTATCAACACTTATGGAATTTGTGTCTATACGTTTTGTCCAAAATGAATGCCAAACGGGGTG
131 AATGTATCAACACTTATAGAATTTGTGTCGATACATTTTGTCCAAAATGAATGCCAAACGGGGTA
* * *
4105873 CACACATAAAGTGTCGATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTA
196 CACACACAAAGTGTCGATACATTTTGAAAAAGTATCAATCCCAAAAACATCAAAACCCATAATTA
* * **
4105938 TAATATAATAGGTAATTTTGTAATATAACCAATATAAATATACCAGTTTTATATGAGAATAGGTC
261 TAACATAATAGGTAAATTTACAATATAACCAATATAAATATACCAGTTTTATATGAGAATAGGTC
* * * * *
4106003 TACATAATGTGTCGACACTTTTGAATTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAG
326 AACATAATGTATCGACACGTTTGAAATTTGCGTCGATACTTTTTGTCCAAAATGAATGCCAAAAG
4106068 GGTTGCACA
391 GGTTGCACA
* *
4106077 CATAAAGTGT-AGATACATTTTTAAAAAGTATTAATCCCAAAAACATCGAAACTGATAATTATAA
1 CATAAAGTGTCA-ATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACTGAAAATTATAA
*
4106141 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGA-A
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTT-TGAGAAAATAGAT-ATA
* * *
4106205 CATAATGTATCGACACGTTTTAG-ATTTGTTTCGATACATTTTGTCCAGAAATGAATGCCAAACG
128 CATAATGTATCAACAC-TTATAGAATTTGTGTCGATACATTTTGTCCA-AAATGAATGCCAAACG
** ** * *
4106269 GGGTACAGGCACAAAGTGTCGATACA-TTTGAAATTGTATCGATCCCAAAAACATCAAAACCGAT
191 GGGTACACACACAAAGTGTCGATACATTTTGAAAAAGTATCAATCCCAAAAACATCAAAACCCAT
* * ** **
4106333 AATTATAACGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACTGGTTTTATGA-GAGAA
256 AATTATAACATAATAGGTAAATTTACAATATAACCAATATAAATATACCAGTTTTAT-ATGAGAA
4106397 TAGGTCAACATAATGTATCGACACGTTT-AAATTTGCGTCGATACTTTTT
320 TAGGTCAACATAATGTATCGACACGTTTGAAATTTGCGTCGATACTTTTT
4106446 AAATAATGCA
Statistics
Matches: 327, Mismatches: 36, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
398 1 0.00
399 124 0.38
400 158 0.48
401 44 0.13
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (399 bp):
CATAAAGTGTCAATACATTTTTAAAAAGTATCAATCCCAAAAACATCGAAACTGAAAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTTGAGAAAATAGATATACAT
AATGTATCAACACTTATAGAATTTGTGTCGATACATTTTGTCCAAAATGAATGCCAAACGGGGTA
CACACACAAAGTGTCGATACATTTTGAAAAAGTATCAATCCCAAAAACATCAAAACCCATAATTA
TAACATAATAGGTAAATTTACAATATAACCAATATAAATATACCAGTTTTATATGAGAATAGGTC
AACATAATGTATCGACACGTTTGAAATTTGCGTCGATACTTTTTGTCCAAAATGAATGCCAAAAG
GGTTGCACA
Found at i:4108208 original size:87 final size:87
Alignment explanation
Indices: 4108103--4108265 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
4108093 AAATAGGTCA
* *
4108103 ATATAAACGTTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
4108168 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
4108190 ATATAAGCGCTACTTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
4108255 CCGGTTAAATG
66 CCGGTTAAATG
4108266 ATATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:4108237 original size:23 final size:23
Alignment explanation
Indices: 4108187--4108231 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4108177 TGCCTATTTT
* * *
4108187 ATTATATAAGCGCTACTTATTAC
1 ATTATATAAGCACTACCTAATAC
4108210 ATTATATAAGCACTACCTAATA
1 ATTATATAAGCACTACCTAATA
4108232 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:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCACTACCTAATAC
Found at i:4110716 original size:23 final size:22
Alignment explanation
Indices: 4110657--4110724 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
4110647 AACTAATGAA
* *
4110657 ACATACATTTACATACTTTCA-
1 ACATACAATCACATACTTTCAT
*
4110678 ACACACACATCTACATACTTTCAT
1 ACATACA-ATC-ACATACTTTCAT
4110702 ATCATACAATCACATACTTTCAT
1 A-CATACAATCACATACTTTCAT
4110725 CTCTTACCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 6 0.15
22 1 0.03
23 23 0.59
24 4 0.10
25 5 0.13
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (22 bp):
ACATACAATCACATACTTTCAT
Found at i:4110924 original size:21 final size:21
Alignment explanation
Indices: 4110873--4110946 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
4110863 GGGCCATATA
* *
4110873 AAATGTCCCGAAGTACCACGTAG
1 AAATGTCCCGAAGGACCAC--AT
* *
4110896 AAATGTCCTGAAGGACCATAT
1 AAATGTCCCGAAGGACCACAT
* *
4110917 ATATGTCCCGAATGACCACAT
1 AAATGTCCCGAAGGACCACAT
4110938 AAATGTCCC
1 AAATGTCCC
4110947 AAAAGATCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 26 0.62
23 16 0.38
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATGTCCCGAAGGACCACAT
Found at i:4114325 original size:20 final size:20
Alignment explanation
Indices: 4114302--4114350 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
4114292 CAACCCTTCG
4114302 GTATCGATATCAAGCATCTA
1 GTATCGATATCAAGCATCTA
** * *
4114322 GTATCGATATTGAGCCTTTA
1 GTATCGATATCAAGCATCTA
4114342 GTATCGATA
1 GTATCGATA
4114351 CTATTACCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (20 bp):
GTATCGATATCAAGCATCTA
Found at i:4117305 original size:41 final size:40
Alignment explanation
Indices: 4117243--4117320 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
4117233 AAAATATCAT
*
4117243 TCCTTTTTGAAATGGGATCGATCATTTTTGACAAAGATCTA
1 TCCTTTTTGAAATGGGATCGATC-CTTTTGACAAAGATCTA
* *
4117284 TCCTTTTTGTAAA-GGGGTCGATCCTTTTGAGAAAGAT
1 TCCTTTTTG-AAATGGGATCGATCCTTTTGACAAAGAT
4117321 ATCAATTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 12 0.36
41 18 0.55
42 3 0.09
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (40 bp):
TCCTTTTTGAAATGGGATCGATCCTTTTGACAAAGATCTA
Found at i:4122131 original size:38 final size:39
Alignment explanation
Indices: 4122089--4122165 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
4122079 AAATTGTCAT
** *
4122089 TTTCCTTTTTTTTT-TATTTCGTTGAAATAAGTTTAGTG
1 TTTCCTTTTTTTTTCTATTTCGCCGAAATAAGTCTAGTG
4122127 TTTCCTTTTTTTTTCTATTTCGCCGAAATAAGTCTAGTG
1 TTTCCTTTTTTTTTCTATTTCGCCGAAATAAGTCTAGTG
4122166 GATAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 14 0.40
39 21 0.60
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.56
Consensus pattern (39 bp):
TTTCCTTTTTTTTTCTATTTCGCCGAAATAAGTCTAGTG
Found at i:4122225 original size:17 final size:15
Alignment explanation
Indices: 4122194--4122228 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
4122184 AAAAACCGTA
4122194 AAATGTTTTTTTTAT
1 AAATGTTTTTTTTAT
4122209 AAATGATTTTTTGTTAT
1 AAATG-TTTTTT-TTAT
4122226 AAA
1 AAA
4122229 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 6 0.33
17 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (15 bp):
AAATGTTTTTTTTAT
Found at i:4124017 original size:33 final size:33
Alignment explanation
Indices: 4123980--4124046 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
4123970 AACTTAAATG
4123980 CAGTCATGTGCTTGTGATGTAGCGAAATGAAAA
1 CAGTCATGTGCTTGTGATGTAGCGAAATGAAAA
4124013 CAGTCATGTGCTTGTGATGTAGCGAAATGAAAA
1 CAGTCATGTGCTTGTGATGTAGCGAAATGAAAA
4124046 C
1 C
4124047 GGTCTGAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (33 bp):
CAGTCATGTGCTTGTGATGTAGCGAAATGAAAA
Found at i:4128423 original size:16 final size:17
Alignment explanation
Indices: 4128397--4128431 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4128387 CCGGATATCC
4128397 ATTCTAAAAATTCAGAT
1 ATTCTAAAAATTCAGAT
*
4128414 ATTC-AAAAATTCGGAT
1 ATTCTAAAAATTCAGAT
4128430 AT
1 AT
4128432 ACATTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (17 bp):
ATTCTAAAAATTCAGAT
Done.