Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 21
Found at i:3600599 original size:2 final size:2
Alignment explanation
Indices: 3600592--3600616 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3600582 TTAGATAAGA
3600592 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3600617 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3600621 original size:2 final size:2
Alignment explanation
Indices: 3600616--3600654 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3600606 TCTCTCTCTC
3600616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3600655 CACAAATGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3604695 original size:31 final size:31
Alignment explanation
Indices: 3604657--3604781 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
3604647 AGGGTCGAGG
3604657 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3604688 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3604719 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3604750 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
3604781 G
1 G
3604782 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3608807 original size:31 final size:31
Alignment explanation
Indices: 3608769--3608879 Score: 179
Period size: 31 Copynumber: 3.6 Consensus size: 31
3608759 GGGTCGAGGG
*
3608769 TTTACCTATGTTATTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
*
3608800 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
3608831 TTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTTACCTATGTTCTTCGGGACATATGGACT-A
*
3608863 -TTACCTAGGTTCTTCGG
1 TTTACCTATGTTCTTCGG
3608880 AATCTATGGA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTA
Found at i:3642854 original size:30 final size:30
Alignment explanation
Indices: 3642818--3642890 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
3642808 CCCGAAGGAC
3642818 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3642848 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3642878 CTGTCCAGAGGTC
1 CTATCCAGAGGTC
3642891 CCGAAGAACC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3642907 original size:30 final size:30
Alignment explanation
Indices: 3642818--3642915 Score: 124
Period size: 30 Copynumber: 3.2 Consensus size: 30
3642808 CCCGAAGGAC
*
3642818 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
3642848 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
* * * * *
3642878 CTGTCCAGAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AA
3642909 CTATCCA
1 CTATCCA
3642916 TATGTTCCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 52 0.87
31 8 0.13
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAA
Found at i:3643914 original size:19 final size:19
Alignment explanation
Indices: 3643890--3643940 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
3643880 TATCACTGGG
3643890 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
3643909 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
3643928 ATGCATCGATGCA
1 ATGCATCGATGCA
3643941 CTAATTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCATGCCTT
Found at i:3651008 original size:22 final size:22
Alignment explanation
Indices: 3650967--3651033 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
3650957 CTCGTATAAA
3650967 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
3650990 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
3651012 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3651034 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:3651684 original size:2 final size:2
Alignment explanation
Indices: 3651677--3651728 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3651667 TCTCTTAAAC
3651677 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
3651719 AT AT AT AT AT
1 AT AT AT AT AT
3651729 TCACATGTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3652768 original size:21 final size:21
Alignment explanation
Indices: 3652744--3652788 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3652734 TCTTGTTCGT
* *
3652744 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3652765 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3652786 TTG
1 TTG
3652789 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:3654771 original size:21 final size:22
Alignment explanation
Indices: 3654742--3654794 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3654732 ATTCTGACTA
3654742 TCGCATTGCGATTTTCC-AAAT
1 TCGCATTGCGATTTTCCGAAAT
*
3654763 TCGCGTTGCGATTTTCCGAAA-
1 TCGCATTGCGATTTTCCGAAAT
*
3654784 TCGCAATGCGA
1 TCGCATTGCGA
3654795 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCGAAAT
Found at i:3654826 original size:20 final size:20
Alignment explanation
Indices: 3654803--3654868 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
3654793 GAATATGTAA
*
3654803 ATCGCAATGCGATT-TTGACT
1 ATCGCAACGCGATTCTT-ACT
3654823 ATCGCAACGCGATTCTTACT
1 ATCGCAACGCGATTCTTACT
* *
3654843 AT--CAACGCAATTCTGACT
1 ATCGCAACGCGATTCTTACT
*
3654861 GTCGCAAC
1 ATCGCAAC
3654869 ACTGAATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 15 0.38
20 22 0.56
21 2 0.05
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (20 bp):
ATCGCAACGCGATTCTTACT
Found at i:3655950 original size:15 final size:15
Alignment explanation
Indices: 3655930--3655966 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3655920 AGAAGAAAAA
3655930 GAAGAAAAAATCCCC
1 GAAGAAAAAATCCCC
*
3655945 GAAG-AAAAGTCCCC
1 GAAGAAAAAATCCCC
3655959 GAAGAAAA
1 GAAGAAAA
3655967 TGTCACAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.54, C:0.22, G:0.19, T:0.05
Consensus pattern (15 bp):
GAAGAAAAAATCCCC
Found at i:3658024 original size:18 final size:18
Alignment explanation
Indices: 3658001--3658035 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3657991 AGAAAAAGGC
*
3658001 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
3658019 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
3658036 CAACCGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:3658347 original size:140 final size:140
Alignment explanation
Indices: 3658095--3658364 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
3658085 AAACGTTGTA
*
3658095 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTACTA
*
3658160 TGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
3658225 TATGTGTATT
131 TATGTGTATT
3658235 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTACTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTACTA
3658300 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
3658365 CGCAACGCGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTACTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:3658360 original size:20 final size:20
Alignment explanation
Indices: 3658335--3658612 Score: 234
Period size: 20 Copynumber: 14.8 Consensus size: 20
3658325 TTACACATTC
*
3658335 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
3658355 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
3658375 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
3658394 A----A-AATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3658409 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* * *
3658429 ATATGACTACCGCAACG-TA
1 ATTTGACTATCGCAACGCGA
* *
3658448 A----A-AATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
3658463 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
3658483 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
3658503 ATTTGATTATCGCAACTG-GT
1 ATTTGACTATCGCAAC-GCGA
* * *
3658523 ATTTGATTATCGCAATGAGA
1 ATTTGACTATCGCAACGCGA
3658543 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
3658557 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
3658577 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
3658597 ATTTGACTATCGCAAC
1 ATTTGACTATCGCAAC
3658613 TAGAAAATTG
Statistics
Matches: 208, Mismatches: 30, Indels: 40
0.75 0.11 0.14
Matches are distributed among these distances:
14 27 0.13
15 6 0.03
16 1 0.00
18 1 0.00
19 6 0.03
20 166 0.80
21 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:3658430 original size:54 final size:54
Alignment explanation
Indices: 3658343--3658499 Score: 235
Period size: 54 Copynumber: 2.9 Consensus size: 54
3658333 TCATTTGAAT
*
3658343 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAAC-TCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGT-AAAA
* * * *
3658397 ATCGTAACGCGAATTTGACTATCGCAACACGAATATGACTACCGCAACGTAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTAAAA
* *
3658451 ATCGCAACGTGAATTTGTCTATCGCAACGCGAATTTGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
3658500 CGAATTTGAT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
54 90 0.99
55 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTAAAA
Found at i:3658537 original size:94 final size:94
Alignment explanation
Indices: 3658397--3658613 Score: 292
Period size: 94 Copynumber: 2.3 Consensus size: 94
3658387 CAACTCAAAA
* * *
3658397 ATCGTAACGCGAATTTGACTATCGCAACACGAATATGACTACCGCAACGTA-AAAATCGCAACGT
1 ATCGCAACGCGAATTTGACTATCGCAACTCGAATATGACTACCGCAACG-AGAAAATCGCAACGC
*
3658461 GAATTTGTCTATCGCAACGCGAATTTGACT
65 GAATTTGACTATCGCAACGCGAATTTGACT
* * * * * * *
3658491 ATCGCAACGCGAATTTGATTATCGCAACTGGTATTTGATTATCGCAATGAGAAAATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACTCGAATATGACTACCGCAACGAGAAAATCGCAACGCG
*
3658556 AATTTGACTATCGCAACGCGAATTTGATT
66 AATTTGACTATCGCAACGCGAATTTGACT
* *
3658585 ATCGCAACGGGTATTTGACTATCGCAACT
1 ATCGCAACGCGAATTTGACTATCGCAACT
3658614 AGAAAATTGC
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 1 0.01
94 106 0.99
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACTCGAATATGACTACCGCAACGAGAAAATCGCAACGCG
AATTTGACTATCGCAACGCGAATTTGACT
Found at i:3658549 original size:74 final size:74
Alignment explanation
Indices: 3658335--3658662 Score: 323
Period size: 74 Copynumber: 4.4 Consensus size: 74
3658325 TTACACATTC
* * *
3658335 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCA-AAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG-GTATTTGATTATCGCAACTGAGAAAAT
*
3658399 CGTAACGCGA
65 CGCAACGCGA
* * * ** *
3658409 ATTTGACTATCGCAACACGAATATGACTACCGCAAC-GTA----AAAATCGCAACGTGAATTTGT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGTATTTGATTATCGCAAC-TG-A---GA
**
3658469 CTATCGCAACGCGA
61 AAATCGCAACGCGA
*
3658483 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACTGGTATTTGATTATCGCAA-TGAGAAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAC-GGTATTTGATTATCGCAACTGAGAAAAT
3658547 CGCAACGCGA
65 CGCAACGCGA
* *
3658557 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACT-AGAAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAC-GGTATTTGATTATCGCAACTGAGAAAAT
* * * *
3658621 TGCAAAGTGT
65 CGCAACGCGA
* * *
3658631 ATTAGACTATTGCAACGCGAA-TTGACTTTCGC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGC
3658663 TTTGCGCTTT
Statistics
Matches: 210, Mismatches: 31, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
68 9 0.04
69 1 0.00
70 1 0.00
72 2 0.01
73 9 0.04
74 173 0.82
75 1 0.00
76 3 0.01
77 1 0.00
78 2 0.01
80 8 0.04
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (74 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGTATTTGATTATCGCAACTGAGAAAATC
GCAACGCGA
Found at i:3658681 original size:20 final size:20
Alignment explanation
Indices: 3658656--3658694 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3658646 CGCGAATTGA
* *
3658656 CTTTCGCTTTGCGCTTTTGT
1 CTTTCGCATTGCGATTTTGT
3658676 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
3658695 AGTTTAGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.23, G:0.21, T:0.51
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:3660361 original size:42 final size:42
Alignment explanation
Indices: 3660254--3660365 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 42
3660244 TCAAGAATGT
* * * * * *
3660254 TAGGAGAGACCTCTTCAACGATTACAGTGGCCTCTTGAACGG
1 TAGGGGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
3660296 T-GGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TAGGG-GAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
3660338 TAGGGGAGGCCTCTTGAACGATGACAGG
1 TAGGGGAGGCCTCTTGAACGATGACAGG
3660366 TGAGTCGGGC
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
41 2 0.04
42 47 0.90
43 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (42 bp):
TAGGGGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:3660944 original size:20 final size:20
Alignment explanation
Indices: 3660919--3660973 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
3660909 GCGATTCTTT
3660919 CGTTGCGATAGTAAAATTCG
1 CGTTGCGATAGTAAAATTCG
* **
3660939 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAAATTCG
* *
3660959 CATTGCGAAAGTAAA
1 CGTTGCGATAGTAAA
3660974 CTATTCTTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTAAAATTCG
Found at i:3661182 original size:20 final size:20
Alignment explanation
Indices: 3661157--3661204 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
3661147 TAGTTTACTT
3661157 TCGCAACGCGGAA-ATGACTA
1 TCGCAACGC-GAATATGACTA
*
3661177 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAATATGACTA
3661197 TCGCAACG
1 TCGCAACG
3661205 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATATGACTA
Found at i:3661419 original size:308 final size:308
Alignment explanation
Indices: 3660939--3661512 Score: 1017
Period size: 308 Copynumber: 1.9 Consensus size: 308
3660929 GTAAAATTCG
3660939 CGTTGCGATAGTCATTTTCGCATTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
1 CGTTGCGATAGTCATTTTCGCATTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
* *
3661004 TGAATTGCATTACTTTAACCAAAAGACAACCAAAAACAAATTATAACTTCACAGGGTTAAAGAAT
66 TGAATTGCATTAATTCAACCAAAAGACAACCAAAAACAAATTATAACTTCACAGGGTTAAAGAAT
*
3661069 AAACAGTTTAGCAGTATTGGCAGAAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATT
131 AAACAGTTTAGCAGTATTGACAGAAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATT
** *
3661134 TGCAGAAGAAGAATAGTTTACTTTCGCAACGCGGAA-ATGACTATCGCAACGCGAATTTGACTAT
196 TGCAGAAGAAGAATAGTTTACTTTCGCAACGC-GAATATGACTATCGCAACGCGAAAATAACTAT
3661198 CGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTCTTT
260 CGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTCTTT
* *
3661247 CGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAC
1 CGTTGCGATAGTCATTTTCGCATTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
*
3661312 TGGATTGCATTAATTCAACCAAAAGACAACCAAAAACAAA-TACTAACTTCACAGGGTTAAAGAA
66 TGAATTGCATTAATTCAACCAAAAGACAACCAAAAACAAATTA-TAACTTCACAGGGTTAAAGAA
*
3661376 TAAACAGTTTAGCAGTATTGACAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAAT
130 TAAACAGTTTAGCAGTATTGACAGAAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAAT
*
3661441 TTGCAGAAGAAGAATAGTTTACTTTCGCAACTCGAATATGACTATCGCAACGCGAAAATAACTAT
195 TTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAATATGACTATCGCAACGCGAAAATAACTAT
3661506 CGCAACG
260 CGCAACG
3661513 CGAAAATGAC
Statistics
Matches: 253, Mismatches: 11, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
307 5 0.02
308 248 0.98
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (308 bp):
CGTTGCGATAGTCATTTTCGCATTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
TGAATTGCATTAATTCAACCAAAAGACAACCAAAAACAAATTATAACTTCACAGGGTTAAAGAAT
AAACAGTTTAGCAGTATTGACAGAAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATT
TGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAATATGACTATCGCAACGCGAAAATAACTATC
GCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTCTTT
Found at i:3661490 original size:20 final size:20
Alignment explanation
Indices: 3661465--3661552 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
3661455 TAGTTTACTT
* *
3661465 TCGCAACTCGAATATGACTA
1 TCGCAACGCGAAAATGACTA
*
3661485 TCGCAACGCGAAAATAACTA
1 TCGCAACGCGAAAATGACTA
*
3661505 TCGCAACGCGAAAATGACAA
1 TCGCAACGCGAAAATGACTA
**
3661525 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
3661545 TCGCAACG
1 TCGCAACG
3661553 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:3661620 original size:20 final size:20
Alignment explanation
Indices: 3661595--3661642 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3661585 GTGATTCTTT
3661595 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
3661615 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
3661635 CGTTGCGA
1 CGTTGCGA
3661643 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3661813 original size:18 final size:18
Alignment explanation
Indices: 3661790--3661839 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
3661780 TTTACTAAGC
3661790 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
3661808 AATCTAAGTGACATGGTT
1 AATCTAAGTGAAATGGTT
3661826 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
3661840 TACGAGTAAA
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:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:3663586 original size:20 final size:20
Alignment explanation
Indices: 3663563--3663603 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3663553 TCTGAAACTT
3663563 AAAATTGCAACACGAAAATG
1 AAAATTGCAACACGAAAATG
3663583 AAAATTGCAACACGAAAATG
1 AAAATTGCAACACGAAAATG
3663603 A
1 A
3663604 CTTTCGCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATTGCAACACGAAAATG
Found at i:3663612 original size:20 final size:20
Alignment explanation
Indices: 3663569--3663639 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
3663559 ACTTAAAATT
**
3663569 GCAACACGAAAATGAAAATT-
1 GCAACACGAAAATG-ACTTTC
3663589 GCAACACGAAAATGACTTTC
1 GCAACACGAAAATGACTTTC
* ** *
3663609 GCAACGCGAATTTGACTATC
1 GCAACACGAAAATGACTTTC
*
3663629 GCAACGCGAAA
1 GCAACACGAAA
3663640 CTAAAATCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 3 0.07
20 40 0.93
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (20 bp):
GCAACACGAAAATGACTTTC
Found at i:3664063 original size:22 final size:22
Alignment explanation
Indices: 3664032--3664088 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
3664022 GATGGAGATA
*
3664032 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* * *
3664054 GACTGATTTCGTCAGAGCTGGG
1 GACGGATTTCGCCAGAGATGGG
*
3664076 GACGGATGTCGCC
1 GACGGATTTCGCC
3664089 TTAGAGAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.21, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:3664288 original size:20 final size:20
Alignment explanation
Indices: 3664254--3664391 Score: 186
Period size: 20 Copynumber: 6.9 Consensus size: 20
3664244 GCACTTTGAA
* *
3664254 AATCGCATTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
3664274 CATCGCGTTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
3664294 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
3664314 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
**
3664334 AATCTTGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* * *
3664354 ATTCGTGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
3664374 AATCGCATTGCGATAGTC
1 AATCGCGTTGCGATAGTC
3664392 GAAAAATCGC
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:3671219 original size:20 final size:20
Alignment explanation
Indices: 3671194--3671237 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3671184 TTTGTGCTGT
3671194 ACATCCTTAGGCACTTAGTG
1 ACATCCTTAGGCACTTAGTG
3671214 ACATCCTTAGGCACTTAGTG
1 ACATCCTTAGGCACTTAGTG
3671234 ACAT
1 ACAT
3671238 AGATATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (20 bp):
ACATCCTTAGGCACTTAGTG
Found at i:3674571 original size:4 final size:4
Alignment explanation
Indices: 3674562--3674596 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3674552 TGAAAGTGTA
3674562 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
3674597 AAGGTACCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3675037 original size:31 final size:31
Alignment explanation
Indices: 3674967--3675044 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
3674957 CTTTTAAAAC
** * *
3674967 TTGCAATACAGTCCCTTAACATTTAGTCTGT
1 TTGCAATATGGTCCCTCAACATTTAGTCCGT
3674998 TTGCAATATGGTCCCTCAACATTTAGTCCGT
1 TTGCAATATGGTCCCTCAACATTTAGTCCGT
*
3675029 TTGCAATATGTTCCCT
1 TTGCAATATGGTCCCT
3675045 GACGTAACTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (31 bp):
TTGCAATATGGTCCCTCAACATTTAGTCCGT
Found at i:3678434 original size:18 final size:16
Alignment explanation
Indices: 3678392--3678423 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3678382 TTACGAATAA
*
3678392 AAATATATATTTATAT
1 AAATGTATATTTATAT
3678408 AAATGTATATTTATAT
1 AAATGTATATTTATAT
3678424 TTAGATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AAATGTATATTTATAT
Found at i:3679173 original size:130 final size:130
Alignment explanation
Indices: 3678969--3679216 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
3678959 AATTTTCTTC
* *
3678969 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
3679034 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
3679099 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
3679164 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
3679217 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:3679664 original size:35 final size:35
Alignment explanation
Indices: 3679614--3679689 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
3679604 AATTGAATTT
* *
3679614 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
3679649 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
3679684 AATTGA
1 AATTGA
3679690 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:3681382 original size:24 final size:24
Alignment explanation
Indices: 3681354--3681424 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
3681344 GATTAATATT
3681354 TTGAAACACACCCATATATTTTTC
1 TTGAAACACACCCATATATTTTTC
* * * *
3681378 TTGAAGA-AGA---AGATAATATT-
1 TTGAA-ACACACCCATATATTTTTC
3681398 TTGAAACACACCCATATATTTTTC
1 TTGAAACACACCCATATATTTTTC
3681422 TTG
1 TTG
3681425 GAGGAGGACG
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 1 0.03
20 7 0.21
21 7 0.21
23 7 0.21
24 10 0.30
25 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (24 bp):
TTGAAACACACCCATATATTTTTC
Found at i:3683979 original size:22 final size:21
Alignment explanation
Indices: 3683951--3683994 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
3683941 AACGGTCAAC
3683951 GGTCAACGATCGGGTCGGGTCG
1 GGTCAACGATCGGGTC-GGTCG
*
3683973 GGTCAACGGTCGGGTCGGTCG
1 GGTCAACGATCGGGTCGGTCG
3683994 G
1 G
3683995 TCGGGTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (21 bp):
GGTCAACGATCGGGTCGGTCG
Found at i:3684024 original size:19 final size:18
Alignment explanation
Indices: 3683998--3684068 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 18
3683988 CGGTCGGTCG
3683998 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
*
3684016 GGTTCAGACCGGTTTCGAACC
1 GG-TCAGACCGG--TCAAACC
*
3684037 GGTCGAAACCGGTCAAACC
1 GGTC-AGACCGGTCAAACC
*
3684056 GATCAGAACCGGT
1 GGTCAG-ACCGGT
3684069 TGAAAACCGG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 3 0.07
19 24 0.56
20 2 0.05
21 14 0.33
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:3684077 original size:40 final size:39
Alignment explanation
Indices: 3684004--3684088 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 39
3683994 GTCGGGTCAG
* ***
3684004 ACCGGTCAAACCGGTTCAGACCGGTTTCGAACCGGTCGAA
1 ACCGGTCAAACCGGATCAGACCGGTTGAAAACCGGT-GAA
*
3684044 ACCGGTCAAACC-GATCAGAACCGGTTGAAAACCGGTTAA
1 ACCGGTCAAACCGGATCAG-ACCGGTTGAAAACCGGTGAA
3684083 ACCGGT
1 ACCGGT
3684089 TTCCAGCAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 13 0.33
40 26 0.67
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (39 bp):
ACCGGTCAAACCGGATCAGACCGGTTGAAAACCGGTGAA
Found at i:3691293 original size:17 final size:17
Alignment explanation
Indices: 3691267--3691311 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
3691257 TCAACGATCG
*
3691267 GGTCGAGTCGGATCAAC
1 GGTCGGGTCGGATCAAC
*
3691284 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGATCAAC
3691301 GGTCGGGTCGG
1 GGTCGGGTCGG
3691312 TCGGTCGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGATCAAC
Found at i:3691367 original size:10 final size:9
Alignment explanation
Indices: 3691319--3691409 Score: 56
Period size: 9 Copynumber: 9.3 Consensus size: 9
3691309 CGGTCGGTCG
*
3691319 GGTCAGACC
1 GGTCAAACC
*
3691328 TGTCAAACC
1 GGTCAAACC
*
3691337 GGTTCAGACC
1 GG-TCAAACC
*
3691347 GGTTTCGAACC
1 GG--TCAAACC
3691358 GGTCGAAACC
1 GGTC-AAACC
3691368 GGTCAAACC
1 GGTCAAACC
*
3691377 GATCAGAACC
1 GGTCA-AACC
*
3691387 GGTTGAAAACC
1 GG-T-CAAACC
*
3691398 GGTTAAACC
1 GGTCAAACC
3691407 GGT
1 GGT
3691410 TTCCAACAGC
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
9 27 0.42
10 22 0.34
11 15 0.23
12 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3700770 original size:19 final size:18
Alignment explanation
Indices: 3700746--3700785 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3700736 TTTATTTATA
*
3700746 ATTTTTAATAGTTTAATTT
1 ATTTTTAATAATTT-ATTT
*
3700765 ATTTTTTATAATTTATTT
1 ATTTTTAATAATTTATTT
3700783 ATT
1 ATT
3700786 GATATAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTTAATAATTTATTT
Found at i:3700776 original size:22 final size:21
Alignment explanation
Indices: 3700729--3700784 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
3700719 TCAATTCTAA
*
3700729 TTAACAGTTTATTTATAATTT
1 TTAATAGTTTATTTATAATTT
3700750 TTAATAGTTTAATTTAT--TTT
1 TTAATAGTTT-ATTTATAATTT
*
3700770 TT-ATAATTTATTTAT
1 TTAATAGTTTATTTAT
3700785 TGATATAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 6 0.19
19 6 0.19
20 5 0.16
21 9 0.28
22 6 0.19
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
TTAATAGTTTATTTATAATTT
Found at i:3701970 original size:27 final size:27
Alignment explanation
Indices: 3701902--3701970 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 27
3701892 AAACTCTTTA
*
3701902 ATATTTAATATTTA-ATAATTAAATT-
1 ATATATAATATTTATATAATTAAATTG
*
3701927 -TATATATTATTTATTATAAATTAAATTG
1 ATATATAATATTTA-TAT-AATTAAATTG
3701955 ATATATAATCATTTAT
1 ATATATAAT-ATTTAT
3701971 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
24 11 0.31
26 2 0.06
27 9 0.26
29 8 0.23
30 5 0.14
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
ATATATAATATTTATATAATTAAATTG
Found at i:3701981 original size:29 final size:29
Alignment explanation
Indices: 3701927--3701982 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
3701917 TAATTAAATT
* *
3701927 TATATATTATTTATTATAAATTAAATTGA
1 TATATATCATTTATTATAAATAAAATTGA
*
3701956 TATATAATCATTTATTTTAAA-AAAATT
1 TATAT-ATCATTTATTATAAATAAAATT
3701983 AACTGTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TATATATCATTTATTATAAATAAAATTGA
Found at i:3710908 original size:68 final size:68
Alignment explanation
Indices: 3710799--3710935 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
3710789 GATTCCACCG
3710799 TCGGAAACCCTCGAGTACATTGTTGAGATTGATAAAGTCTCTATTGCACCTGCATGATCTTGTTT
1 TCGGAAACCCTCGAGTACATTGTTGAGATTGATAAAGTCTCTATTGCACCTGCATGATCTTGTTT
3710864 TAT
66 TAT
3710867 TCGGAAACCCTCGAGTACATTGTTGAGATTGATAAAGTCTCTATTGCACCTGCATGATCTTGTTT
1 TCGGAAACCCTCGAGTACATTGTTGAGATTGATAAAGTCTCTATTGCACCTGCATGATCTTGTTT
3710932 TAT
66 TAT
3710935 T
1 T
3710936 ATAGTATATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (68 bp):
TCGGAAACCCTCGAGTACATTGTTGAGATTGATAAAGTCTCTATTGCACCTGCATGATCTTGTTT
TAT
Found at i:3711422 original size:41 final size:40
Alignment explanation
Indices: 3711375--3711454 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 40
3711365 AATGCAAATA
*
3711375 CGTAAATCGCAACGCAAATTTGGAAAATCGCAATGCGATTC
1 CGTAAATCGCAACGCAAATCT-GAAAATCGCAATGCGATTC
* * **
3711416 CGTAAATCGCAATGCGAATCTGACTATCGCAATGCGATT
1 CGTAAATCGCAACGCAAATCTGAAAATCGCAATGCGATT
3711455 TACATAGCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 16 0.47
41 18 0.53
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (40 bp):
CGTAAATCGCAACGCAAATCTGAAAATCGCAATGCGATTC
Found at i:3711424 original size:20 final size:19
Alignment explanation
Indices: 3711399--3711454 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
3711389 CAAATTTGGA
3711399 AAATCGCAATGCGATTCCG
1 AAATCGCAATGCGATTCCG
* *
3711418 TAAATCGCAATGCGAATCTG
1 -AAATCGCAATGCGATTCCG
*
3711438 ACTATCGCAATGCGATT
1 A-AATCGCAATGCGATT
3711455 TACATAGCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (19 bp):
AAATCGCAATGCGATTCCG
Found at i:3711655 original size:22 final size:22
Alignment explanation
Indices: 3711630--3711695 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
3711620 GGCGACATCC
3711630 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
3711652 GTCCCCATCGCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
3711674 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
3711696 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:3712098 original size:20 final size:20
Alignment explanation
Indices: 3712046--3712083 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3712036 CGATTTTCAT
3712046 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
3712066 TTCGCGTTGCGATAGTCA
1 TTCGCGTTGCGATAGTCA
3712084 TTTTCCTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:3713901 original size:34 final size:34
Alignment explanation
Indices: 3713810--3713903 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
3713800 ATAGTTTACT
* * * * *
3713810 ATCGCAACGCGAAAATGACTATCACAACGAGAGA
1 ATCGCAACGCGAAAATGAATATCGCAACAACAAA
* *
3713844 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAAATGAATATCGCAACAACAAA
3713877 ATCGCAACGCGAAAATGAATATCGCAA
1 ATCGCAACGCGAAAATGAATATCGCAA
3713904 TGCAAAAATG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGAATATCGCAACAACAAA
Found at i:3713912 original size:34 final size:34
Alignment explanation
Indices: 3713810--3713912 Score: 97
Period size: 34 Copynumber: 3.1 Consensus size: 34
3713800 ATAGTTTACT
* * * *
3713810 ATCGCAACGCGAAAATGACTATCACAA-CGAGAGA
1 ATCGCAACGCGAAAATGAATATCGCAAGC-ACAAA
* *
3713844 ATCGCAATGCG-AAATGAAAATCGCAA-CAACAAA
1 ATCGCAACGCGAAAATGAATATCGCAAGC-ACAAA
3713877 ATCGCAACGCGAAAATGAATATCGCAATGCA-AAA
1 ATCGCAACGCGAAAATGAATATCGCAA-GCACAAA
3713911 AT
1 AT
3713913 GACTATCGCA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
33 26 0.46
34 29 0.51
35 1 0.02
36 1 0.02
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGAATATCGCAAGCACAAA
Found at i:3713924 original size:20 final size:20
Alignment explanation
Indices: 3713877--3713926 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3713867 CAACAACAAA
* *
3713877 ATCGCAACGCGAAAATGAAT
1 ATCGCAATGCAAAAATGAAT
*
3713897 ATCGCAATGCAAAAATGACT
1 ATCGCAATGCAAAAATGAAT
3713917 ATCGCAATGC
1 ATCGCAATGC
3713927 GTTGCAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAATGCAAAAATGAAT
Found at i:3714515 original size:42 final size:42
Alignment explanation
Indices: 3714443--3714525 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
3714433 CATCCCCTAT
* *
3714443 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCACTCAAGAGGT-CCCTCCCAC
* * *
3714485 CGTTCAAGAGGCCACTGTCATCATTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCA
3714526 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCAC
Found at i:3716103 original size:33 final size:33
Alignment explanation
Indices: 3716057--3716120 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
3716047 TCGCAACGCG
**
3716057 GAAATGACTATCGCAACGAGAGAATCACAATAC
1 GAAATGAAAATCGCAACGAGAGAATCACAATAC
* *
3716090 GAAATGAAAATCGCAACGAGTGAATCGCAAT
1 GAAATGAAAATCGCAACGAGAGAATCACAAT
3716121 GCGATTCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATAC
Found at i:3716156 original size:20 final size:20
Alignment explanation
Indices: 3716131--3716199 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
3716121 GCGATTCTCT
3716131 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
* **
3716151 CGTTGCGATAGTCATTTCTA
1 CGTTGCGATAGTCAATTCCG
*
3716171 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCA-ATTCCG
3716191 CGTTGCGAT
1 CGTTGCGAT
3716200 TTCCGCGTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 38 0.95
21 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:3718666 original size:24 final size:24
Alignment explanation
Indices: 3718632--3718699 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
3718622 CTGAAAAATC
3718632 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3718656 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
3718680 ATCAAATTTCGAATATTGAC
1 ATCAAAATCCGAGTATTGAC
3718700 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3719512 original size:20 final size:20
Alignment explanation
Indices: 3719487--3719533 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3719477 AAATTCAGTA
*
3719487 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
3719507 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
3719527 TTGCGAT
1 TTGCGAT
3719534 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:3719543 original size:20 final size:20
Alignment explanation
Indices: 3719520--3719653 Score: 180
Period size: 20 Copynumber: 6.7 Consensus size: 20
3719510 CGATAGTCAG
*
3719520 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3719540 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
3719560 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3719580 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
3719600 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
3719621 ATTCG-AGTTGCGATTTACGT
1 ATTCGCA-TTGCGATTTACGT
*
3719641 ATTCGTATTGCGA
1 ATTCGCATTGCGA
3719654 ATTAGGAAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
20 85 0.85
21 15 0.15
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3719651 original size:61 final size:60
Alignment explanation
Indices: 3719520--3719653 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 60
3719510 CGATAGTCAG
* * **
3719520 ATTCGCGTTGCGATTTACGTATTCGCATTACGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTACGATTTACAAATTCGCATTGCGATTTACGT
* *
3719580 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG-AGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTACGA-TTTACAAATTCGCA-TTGCGATTTACGT
*
3719641 ATTCGTATTGCGA
1 ATTCGCATTGCGA
3719654 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 31 0.48
61 34 0.52
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (60 bp):
ATTCGCATTGCGATTTACGTAATCGCATTACGATTTACAAATTCGCATTGCGATTTACGT
Found at i:3719674 original size:41 final size:41
Alignment explanation
Indices: 3719520--3719674 Score: 172
Period size: 40 Copynumber: 3.8 Consensus size: 41
3719510 CGATAGTCAG
* * *
3719520 ATTCGCGTTGCGATTTACG-TATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGAAATTCGCATTGCGATTTACGT
*
3719560 ATTCGCATTGCGATTTACG-TATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGAAATTCGCATTGCGATTTACGT
* * *
3719600 AATCGCATTGCGATTTTCCAAATTCG-AGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGAAATTCGCA-TTGCGATTTACGT
* * * * *
3719641 ATTCGTATTGCGAATTAGGAAAATCGCAATGCGA
1 ATTCGCATTGCGATTTACGAAATTCGCATTGCGA
3719675 ATTTGGGAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
40 55 0.56
41 42 0.43
42 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGAAATTCGCATTGCGATTTACGT
Found at i:3719675 original size:21 final size:21
Alignment explanation
Indices: 3719649--3719695 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3719639 GTATTCGTAT
3719649 TGCGAATTAGGAAAATCGCAA
1 TGCGAATTAGGAAAATCGCAA
* *
3719670 TGCGAATTTGGGAAATCGCAA
1 TGCGAATTAGGAAAATCGCAA
3719691 TGCGA
1 TGCGA
3719696 TAGTCAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCGCAA
Found at i:3726714 original size:2 final size:2
Alignment explanation
Indices: 3726707--3726731 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3726697 TTCACTGTTG
3726707 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3726732 ACCATGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3731710 original size:23 final size:23
Alignment explanation
Indices: 3731656--3731702 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3731646 CATCGAAGTG
*
3731656 CCACATAG-AATGCCCCGAAGGA
1 CCACGTAGAAATGCCCCGAAGGA
* *
3731678 CTACGTAGAAATGTCCCGAAGGA
1 CCACGTAGAAATGCCCCGAAGGA
3731701 CC
1 CC
3731703 GTGTAGAACC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.30, G:0.23, T:0.13
Consensus pattern (23 bp):
CCACGTAGAAATGCCCCGAAGGA
Found at i:3732021 original size:45 final size:45
Alignment explanation
Indices: 3731933--3732035 Score: 102
Period size: 45 Copynumber: 2.3 Consensus size: 45
3731923 TATATCCTCG
* * *
3731933 TCACATAACTTATAATACATGTCCATATATTCACGTAGTTCAATT
1 TCACATAACTTATAATACATGTCCATATAATCACGTAGATCAATA
* * *
3731978 TCACATATCTTAT-ATCACATGTTCATATAAT-AGCTTAGATCAATA
1 TCACATAACTTATAAT-ACATGTCCATATAATCA-CGTAGATCAATA
* *
3732023 ACACATAGCTTAT
1 TCACATAACTTAT
3732036 CTTACTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 3 0.06
45 45 0.94
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (45 bp):
TCACATAACTTATAATACATGTCCATATAATCACGTAGATCAATA
Found at i:3732782 original size:20 final size:20
Alignment explanation
Indices: 3732757--3732807 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3732747 TTTACTTTGG
3732757 AGTATCGATACTGTTCATCC
1 AGTATCGATACTGTTCATCC
*
3732777 AGTATCGATACTGTTCATCT
1 AGTATCGATACTGTTCATCC
*
3732797 AGTACCGATAC
1 AGTATCGATAC
3732808 CCCTTGCCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTGTTCATCC
Found at i:3737426 original size:12 final size:12
Alignment explanation
Indices: 3737411--3737448 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
3737401 GAGAAAGGCA
3737411 GAGAGCGGGAAC
1 GAGAGCGGGAAC
3737423 GAGAGCGGGAAC
1 GAGAGCGGGAAC
*
3737435 GAGAGCGTGAAC
1 GAGAGCGGGAAC
3737447 GA
1 GA
3737449 CTACGAGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.34, C:0.16, G:0.47, T:0.03
Consensus pattern (12 bp):
GAGAGCGGGAAC
Found at i:3737513 original size:18 final size:18
Alignment explanation
Indices: 3737490--3737525 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3737480 TCTTGGAGCG
3737490 GCGGGAGAAGGAAAGAGA
1 GCGGGAGAAGGAAAGAGA
*
3737508 GCGGGAGAAGGAGAGAGA
1 GCGGGAGAAGGAAAGAGA
3737526 ACGAGAGCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.53, T:0.00
Consensus pattern (18 bp):
GCGGGAGAAGGAAAGAGA
Found at i:3742321 original size:3 final size:3
Alignment explanation
Indices: 3742313--3742337 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3742303 AAGCTCCTGT
3742313 TGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC T
3742338 AAGACAGGTG
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:0.00, C:0.32, G:0.32, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:3745481 original size:23 final size:23
Alignment explanation
Indices: 3745451--3745504 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
3745441 AGGACCATAA
3745451 AGATCCCTAAAAAAATACTCATC
1 AGATCCCTAAAAAAATACTCATC
* *
3745474 AGATCCCTAAACAAATATTCATC
1 AGATCCCTAAAAAAATACTCATC
3745497 AGATCCCT
1 AGATCCCT
3745505 GGAGTAGCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.43, C:0.28, G:0.06, T:0.24
Consensus pattern (23 bp):
AGATCCCTAAAAAAATACTCATC
Found at i:3746416 original size:64 final size:65
Alignment explanation
Indices: 3746322--3746461 Score: 178
Period size: 65 Copynumber: 2.2 Consensus size: 65
3746312 TTCAAAGGGA
* * **
3746322 TGCACCGATGCACTACTTCATGCATCGATGCACTCCT-AATTAAATTG-AATTTCGAATGCATTC
1 TGCACCGATGCACAAC-TCATGCATCGATGCACCCCTGAA-TAAATTGAAACATCGAATGCATTC
3746385 AG
64 AG
**
3746387 TGCACCGATGCACAAGC-CATGCATCGATGCACCCCTGAATATTTTGAAACATCGAATGCATTCA
1 TGCACCGATGCACAA-CTCATGCATCGATGCACCCCTGAATAAATTGAAACATCGAATGCATTCA
3746451 G
65 G
3746452 TGCACCGATG
1 TGCACCGATG
3746462 TGTGCACCGA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
64 23 0.35
65 42 0.64
66 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (65 bp):
TGCACCGATGCACAACTCATGCATCGATGCACCCCTGAATAAATTGAAACATCGAATGCATTCAG
Found at i:3746552 original size:76 final size:76
Alignment explanation
Indices: 3746389--3746543 Score: 201
Period size: 76 Copynumber: 2.1 Consensus size: 76
3746379 GCATTCAGTG
*
3746389 CACCGATGCACAAGCCATGCATCGATGCACCCCTGAATATTTTGAAACATCGAATGCATTCAGTG
1 CACCGATGCACAAGACATGCATCGATGCACCCCTGAATATTTTGAAACATCGAATGCATTCAGTG
**
3746454 CACCGATGTGTG
66 CACCGA-GTGCA
* * *
3746466 CACCGATGCACAAGACATGCATTGATGCA-CCCTGATTATTTTGAAACATCGAA-GCTGATT-TG
1 CACCGATGCACAAGACATGCATCGATGCACCCCTGAATATTTTGAAACATCGAATGC--ATTCAG
3746528 TGCACCGA-TGCA
64 TGCACCGAGTGCA
3746540 CACC
1 CACC
3746544 CTAGTGCACC
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
74 6 0.09
75 2 0.03
76 32 0.46
77 30 0.43
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (76 bp):
CACCGATGCACAAGACATGCATCGATGCACCCCTGAATATTTTGAAACATCGAATGCATTCAGTG
CACCGAGTGCA
Found at i:3750333 original size:18 final size:18
Alignment explanation
Indices: 3750307--3750347 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3750297 ACCATTGAAG
3750307 AAAGGGAAGTCTCTTACC
1 AAAGGGAAGTCTCTTACC
*
3750325 AAAGTGAAGTCTCTTACC
1 AAAGGGAAGTCTCTTACC
*
3750343 CAAGG
1 AAAGG
3750348 TAATACAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
AAAGGGAAGTCTCTTACC
Found at i:3752365 original size:23 final size:23
Alignment explanation
Indices: 3752339--3752399 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
3752329 CACCACAGCT
* *
3752339 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTACCA
* *
3752362 CGTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGAAGTACCA
3752385 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
3752400 TAGTTCCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTACCA
Found at i:3754375 original size:23 final size:22
Alignment explanation
Indices: 3754346--3754424 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
3754336 CACTACCTAG
*
3754346 TGCATCGATGCATCCCTTGAATG
1 TGCATCGATGCAT-CCTTGAATA
* *
3754369 TGCATCGATTCA-CCATGAATA
1 TGCATCGATGCATCCTTGAATA
* *
3754390 TGCACCGATGCAATCCTTGAGTA
1 TGCATCGATGC-ATCCTTGAATA
3754413 TGCATCGATGCA
1 TGCATCGATGCA
3754425 CTATACCATG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 16 0.35
22 2 0.04
23 28 0.61
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATA
Found at i:3766088 original size:64 final size:62
Alignment explanation
Indices: 3766011--3766150 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 62
3766001 TCTTTAACAT
* * *
3766011 GTGCATTGATGCACTACTCATACATCGATACACAAATTACCTTCGATGTTTTCATTTTAAAGG
1 GTGCATCGATGCACTACTCATACATCGATACACAAATTACATTCGATGTTTT-ATTTTAAAGA
* * * * * * *
3766074 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTTTTTTAAAGA
1 G-TGCATCGATGCACTACTCATACATCGATACACAAATTACATTCGATGTTTTATTTTAAAGA
3766137 GTGCATCGATGCAC
1 GTGCATCGATGCAC
3766151 ATTCAATATG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
62 13 0.20
63 10 0.15
64 43 0.65
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (62 bp):
GTGCATCGATGCACTACTCATACATCGATACACAAATTACATTCGATGTTTTATTTTAAAGA
Found at i:3766161 original size:64 final size:64
Alignment explanation
Indices: 3766033--3766172 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 64
3766023 ACTACTCATA
* * * **
3766033 CATCGATACACAAATTACCTTCGATGTTTTCATTTTAAAGGGATGCATCGATGCACTCCTTATG
1 CATCGATACACCAATTACATTCGATGTTTTCATTTTAAAGAGATGCATCGATGCACTCAATATG
* * *
3766097 CATCGATGCACCAATTGCATTCGATGTTTT-TTTTTAAAGAG-TGCATCGATGCACATTCAATAT
1 CATCGATACACCAATTACATTCGATGTTTTCATTTTAAAGAGATGCATCGATGCAC--TCAATAT
3766160 G
64 G
3766161 CATCGATACACC
1 CATCGATACACC
3766173 TTGCCCAGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
62 13 0.20
63 9 0.14
64 43 0.66
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (64 bp):
CATCGATACACCAATTACATTCGATGTTTTCATTTTAAAGAGATGCATCGATGCACTCAATATG
Found at i:3771565 original size:30 final size:30
Alignment explanation
Indices: 3771531--3771633 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
3771521 CCCGAAGGAC
3771531 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3771561 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3771591 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3771621 CTGTCCATAGGTC
1 CTATCCAGAGGTC
3771634 CCGAAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3771650 original size:60 final size:60
Alignment explanation
Indices: 3771531--3771650 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
3771521 CCCGAAGGAC
* * *
3771531 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAA
* * * *
3771591 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAA
3771651 ACTGTCCATA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAA
Found at i:3771657 original size:31 final size:31
Alignment explanation
Indices: 3771619--3771746 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
3771609 GATCCTCGGT
* *
3771619 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
3771650 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
3771681 TACTGTCCATATATCTCGAA-AGACATAGGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* *
3771713 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
3771744 AAC
1 AAC
3771747 CCTCGACTCT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.01
31 52 0.67
32 24 0.31
33 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:3773166 original size:21 final size:21
Alignment explanation
Indices: 3773136--3773180 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3773126 TTTTATTCGT
* *
3773136 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3773157 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3773178 TTG
1 TTG
3773181 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:3775285 original size:21 final size:21
Alignment explanation
Indices: 3775256--3775308 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3775246 ATTCTGACTA
3775256 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
3775277 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
3775298 TCGCAATGCGA
1 TCGCATTGCGA
3775309 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:3775361 original size:20 final size:20
Alignment explanation
Indices: 3775298--3775363 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
3775288 TTTTCCTAAT
3775298 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* **
3775318 TCGAAATGCGTTTACGTAAA
1 TCGCAATGCGAATACGTAAA
3775338 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
3775358 TCGCAA
1 TCGCAA
3775364 CGAGATTCTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3775373 original size:20 final size:20
Alignment explanation
Indices: 3775333--3775373 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3775323 ATGCGTTTAC
* *
3775333 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGAGAATCT
*
3775353 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGAGAATCT
3775373 G
1 G
3775374 ACTATCGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
GTAAATCGCAACGAGAATCT
Found at i:3776252 original size:24 final size:24
Alignment explanation
Indices: 3776225--3776278 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3776215 GTATTCTAAA
3776225 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3776249 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3776273 TTTGAT
1 TTTGAT
3776279 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:3778734 original size:20 final size:20
Alignment explanation
Indices: 3778705--3778785 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
3778695 AAATCACAAT
*
3778705 GCGAATATGACTATCGCAAC
1 GCGAAAATGACTATCGCAAC
* *
3778725 ACGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAC
* *
3778745 GCGGAATTGACTATCGCAAC
1 GCGAAAATGACTATCGCAAC
* *
3778765 GCGGAAATGACTACCGCAAC
1 GCGAAAATGACTATCGCAAC
3778785 G
1 G
3778786 AGAGAATCGC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
GCGAAAATGACTATCGCAAC
Found at i:3778756 original size:40 final size:40
Alignment explanation
Indices: 3778701--3778783 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
3778691 GCGGAAATCA
*
3778701 CAATGCGAATATGACTATCGCAACACGAAAATGACTATCG
1 CAATGCGAATATGACTATCGCAACACGAAAATGACTACCG
* *
3778741 CAATGCGGAAT-TGACTATCGCAACGCGGAAATGACTACCG
1 CAATGC-GAATATGACTATCGCAACACGAAAATGACTACCG
3778781 CAA
1 CAA
3778784 CGAGAGAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (40 bp):
CAATGCGAATATGACTATCGCAACACGAAAATGACTACCG
Found at i:3778814 original size:19 final size:19
Alignment explanation
Indices: 3778790--3778915 Score: 190
Period size: 19 Copynumber: 6.8 Consensus size: 19
3778780 GCAACGAGAG
3778790 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3778809 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3778828 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3778847 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3778866 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
3778880 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
3778900 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
3778916 TAGTTTCGCA
Statistics
Matches: 98, Mismatches: 3, Indels: 12
0.87 0.03 0.11
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 2 0.02
18 3 0.03
19 69 0.70
20 11 0.11
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3778987 original size:33 final size:33
Alignment explanation
Indices: 3778926--3779019 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
3778916 TAGTTTCGCA
*
3778926 TTGCGATTTTCATTTTCGCATTGTGATTCACTCG
1 TTGCGATTTTCA-TTTCGCATTGCGATTCACTCG
* *
3778960 TTGCGATTTTCATTTCGTATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCACTCG
** *
3778993 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCATTGCGAT
3779020 AGTCTGTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 31 0.60
34 21 0.40
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCACTCG
Found at i:3781123 original size:20 final size:20
Alignment explanation
Indices: 3781100--3781191 Score: 148
Period size: 20 Copynumber: 4.6 Consensus size: 20
3781090 GAAACTTAAA
*
3781100 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
3781120 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
3781140 ATCGCAATGCAAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
3781160 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
3781180 ATCGCAATGCGA
1 ATCGCAATGCGA
3781192 TTTTCATTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:3781203 original size:19 final size:20
Alignment explanation
Indices: 3781157--3781212 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
3781147 TGCAAAAATG
* *
3781157 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGATTTTC
3781177 ACTATCGCAATGCGATTTTC
1 ACTATCGCAATGCGATTTTC
* *
3781197 A-TTTCGCATTGCGATT
1 ACTATCGCAATGCGATT
3781213 CTTTCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (20 bp):
ACTATCGCAATGCGATTTTC
Found at i:3781242 original size:34 final size:34
Alignment explanation
Indices: 3781198--3781319 Score: 145
Period size: 34 Copynumber: 3.4 Consensus size: 34
3781188 GCGATTTTCA
*
3781198 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAA
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
* * *
3781232 ATTCACATTGCGATAGTTATTTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCG--A-TT-CTTTCG--TTGCGATAGTCAT
*
3781272 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
3781306 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
3781320 AGTAAACTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
34 37 0.50
36 5 0.07
37 4 0.05
38 6 0.08
40 22 0.30
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
Found at i:3781244 original size:20 final size:20
Alignment explanation
Indices: 3781219--3781322 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
3781209 GATTCTTTCG
** *
3781219 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCATTTTCGCA
*
3781239 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
3781259 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
3781279 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
3781293 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
3781313 TTGCGATAGT
1 TTGCGATAGT
3781323 AAACTATTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
14 7 0.10
16 6 0.08
18 6 0.08
20 52 0.73
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:3781294 original size:74 final size:73
Alignment explanation
Indices: 3781181--3781322 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 73
3781171 AATTTGACTA
** *
3781181 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCACATTGCGAT
1 TCGCAATGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCACATTGCGAT
3781246 AGTTATTT
66 AGTTATTT
* ** *
3781254 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGA
1 TCGCAATGCGATAGTCA-TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCACATTGCGA
3781319 TAGT
65 TAGT
3781323 AAACTATTCT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
73 14 0.23
74 47 0.77
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (73 bp):
TCGCAATGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCACATTGCGAT
AGTTATTT
Found at i:3783231 original size:20 final size:20
Alignment explanation
Indices: 3783208--3783261 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3783198 GAAACTTTAA
*
3783208 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
3783228 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3783248 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
3783262 TGAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3783330 original size:20 final size:20
Alignment explanation
Indices: 3783285--3783333 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3783275 GCGATTCTCT
3783285 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTTG
* *
3783305 CATTGCGATAGTC-ATTTTCG
1 CGTTGCGATAGTCAAATTT-G
3783325 CGTTGCGAT
1 CGTTGCGAT
3783334 TCACTCGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTTG
Found at i:3783726 original size:22 final size:22
Alignment explanation
Indices: 3783665--3783726 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
3783655 TGACCGTGAA
* *
3783665 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
3783687 TG-TTATCGTC---G-TGGGGAC
1 TGATT-TCGTCGGAGATGGGGAC
3783705 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
3783727 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 13 0.41
19 3 0.09
21 3 0.09
22 13 0.41
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:3783943 original size:20 final size:20
Alignment explanation
Indices: 3783920--3784027 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
3783910 GTGATAGTCA
*
3783920 TATTCACATTGCGATTTACG
1 TATTCGCATTGCGATTTACG
3783940 TATTCGCATTGCGATTTACG
1 TATTCGCATTGCGATTTACG
3783960 TATT--C---GC-A-TTACG
1 TATTCGCATTGCGATTTACG
* *
3783973 TATTCGCATTGCGATTTTCCA
1 TATTCGCATTGCGA-TTTACG
* * *
3783994 AATTCGCGTTGCGGTTTACG
1 TATTCGCATTGCGATTTACG
3784014 TATTCGCATTGCGA
1 TATTCGCATTGCGA
3784028 ATTAGGAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
13 9 0.13
14 1 0.01
15 3 0.04
18 3 0.04
19 1 0.01
20 38 0.55
21 14 0.20
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (20 bp):
TATTCGCATTGCGATTTACG
Found at i:3783973 original size:13 final size:13
Alignment explanation
Indices: 3783955--3783982 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3783945 GCATTGCGAT
3783955 TTACGTATTCGCA
1 TTACGTATTCGCA
3783968 TTACGTATTCGCA
1 TTACGTATTCGCA
3783981 TT
1 TT
3783983 GCGATTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (13 bp):
TTACGTATTCGCA
Found at i:3784048 original size:21 final size:21
Alignment explanation
Indices: 3784024--3784064 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3784014 TATTCGCATT
3784024 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
3784045 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
3784065 TGCAATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3796928 original size:31 final size:31
Alignment explanation
Indices: 3796892--3796958 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
3796882 GTTTCAAAAC
* * *
3796892 TAACAAATTAGTCACTAACA-TTATCGATTTG
1 TAACAAATTAGCCACTAA-AGTTATCAATTTA
*
3796923 TAACAACTTAGCCACTAAAGTTATCAATTTA
1 TAACAAATTAGCCACTAAAGTTATCAATTTA
3796954 TAACA
1 TAACA
3796959 TATGGTAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAACAAATTAGCCACTAAAGTTATCAATTTA
Found at i:3799853 original size:31 final size:31
Alignment explanation
Indices: 3799818--3799880 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3799808 AATACATTCT
* *
3799818 CCAACATTTAGTCTGTTTGGAATATCGTCCC
1 CCAACATTTAGTCCGTTTGCAATATCGTCCC
*
3799849 CCAACATTTAGTCCGTTTGCAATATGGTCCC
1 CCAACATTTAGTCCGTTTGCAATATCGTCCC
3799880 C
1 C
3799881 GACGTAACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (31 bp):
CCAACATTTAGTCCGTTTGCAATATCGTCCC
Found at i:3800145 original size:22 final size:24
Alignment explanation
Indices: 3800102--3800146 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
3800092 ACAGAAAAGC
*
3800102 CAAATAATATGATACTTATACAAA
1 CAAATAATATGATACATATACAAA
*
3800126 CAAA-AAT-TGATACATGTACAA
1 CAAATAATATGATACATATACAA
3800147 TTTTGAAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 3 0.16
24 4 0.21
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (24 bp):
CAAATAATATGATACATATACAAA
Found at i:3800544 original size:31 final size:31
Alignment explanation
Indices: 3800502--3800562 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
3800492 AATTTGTTTT
*
3800502 AATCGATGACGTTAATGATCAATTTGTTACA
1 AATCGACGACGTTAATGATCAATTTGTTACA
*
3800533 AATCGACGACGTTAGTGATCAATTTGTTAC
1 AATCGACGACGTTAATGATCAATTTGTTAC
3800563 CAATTTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (31 bp):
AATCGACGACGTTAATGATCAATTTGTTACA
Found at i:3808461 original size:3 final size:3
Alignment explanation
Indices: 3808453--3808497 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
3808443 ATTTTTTATT
* *
3808453 TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3808498 AACGAAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3822747 original size:31 final size:31
Alignment explanation
Indices: 3822709--3822771 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
3822699 CCCGAAGGAC
* *
3822709 CAGTCCATA-GATTCCAAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCAAAGAACATAGGTAAA
*
3822740 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCAAAGAACATAGGTAAA
3822771 C
1 C
3822772 CCTCGACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCAAAGAACATAGGTAAA
Found at i:3824640 original size:21 final size:22
Alignment explanation
Indices: 3824596--3824650 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
3824586 ATTATTACTA
*
3824596 TCGCAATGCG-ATTTTCCAATT
1 TCGCAATGCGAATTTCCCAATT
**
3824617 TCGCGTTGCGAATTTCCCAA-T
1 TCGCAATGCGAATTTCCCAATT
3824638 TCGCAATGCGAAT
1 TCGCAATGCGAAT
3824651 AAGTAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (22 bp):
TCGCAATGCGAATTTCCCAATT
Found at i:3824681 original size:21 final size:21
Alignment explanation
Indices: 3824638--3824751 Score: 83
Period size: 21 Copynumber: 5.5 Consensus size: 21
3824628 ATTTCCCAAT
* *
3824638 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
*
3824658 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
* **
3824679 TCGCAATGCG-ATACT-GACTA
1 TCGCAATGCGAAT-TTAGAAAA
* * *
3824699 TCGCAACGCG-ATAATACAAAA
1 TCGCAATGCGAAT-TTAGAAAA
*
3824720 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
3824741 TTGCAATGCGA
1 TCGCAATGCGA
3824752 TACTGACTAT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
20 30 0.41
21 42 0.57
22 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:3824689 original size:62 final size:61
Alignment explanation
Indices: 3824623--3824792 Score: 159
Period size: 62 Copynumber: 2.7 Consensus size: 61
3824613 AATTTCGCGT
* *
3824623 TGCGAATTTCCCAAT-TCGCAATGCGAATAAGT-AAATCGCAATGCGAATTTGGAAAATCGCAA
1 TGCGAA-TACCCAATATCGCAACGCG-ATAA-TAAAATCGCAATGCGAATTTGGAAAATCGCAA
** * *
3824685 TGCG-ATACTGACTATCGCAACGCGATAATACAAAATCGCAATGCGAATTTGGAAAATTGCAA
1 TGCGAATACCCAATATCGCAACGCGATAAT--AAAATCGCAATGCGAATTTGGAAAATCGCAA
** * *
3824747 TGCG-ATACTGACTATCGCAACGCGATAATACAAAATCGCAACGCGA
1 TGCGAATACCCAATATCGCAACGCGATAAT--AAAATCGCAATGCGA
3824793 TTCTGACTTT
Statistics
Matches: 97, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
59 1 0.01
60 8 0.08
61 10 0.10
62 78 0.80
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (61 bp):
TGCGAATACCCAATATCGCAACGCGATAATAAAATCGCAATGCGAATTTGGAAAATCGCAA
Found at i:3824771 original size:20 final size:20
Alignment explanation
Indices: 3824743--3824834 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
3824733 TTGGAAAATT
*
3824743 GCAATGCGATACTGACTATC
1 GCAACGCGATACTGACTATC
* *
3824763 GCAACGCGATAAT-ACAAAATC
1 GCAACGCGATACTGAC--TATC
* *
3824784 GCAACGCGATTCTGACTTTC
1 GCAACGCGATACTGACTATC
* *
3824804 GCAACGAGATTCTGACTATC
1 GCAACGCGATACTGACTATC
*
3824824 GCAACGAGATA
1 GCAACGCGATA
3824835 ATACAGAATC
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 41 0.69
21 14 0.24
22 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:3824786 original size:21 final size:21
Alignment explanation
Indices: 3824698--3824793 Score: 81
Period size: 21 Copynumber: 4.6 Consensus size: 21
3824688 GATACTGACT
3824698 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* * **
3824719 ATCGCAATGCGA-ATTTGGAAA
1 ATCGCAACGCGATA-ATACAAA
* * * *
3824740 ATTGCAATGCGATACTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
3824760 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
3824781 ATCGCAACGCGAT
1 ATCGCAACGCGAT
3824794 TCTGACTTTC
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
19 2 0.04
20 14 0.25
21 40 0.70
22 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:3824854 original size:61 final size:61
Alignment explanation
Indices: 3824655--3824856 Score: 255
Period size: 62 Copynumber: 3.3 Consensus size: 61
3824645 GCGAATAAGT
* * *
3824655 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAATGCG-ATTTGGAAAATTGCAACGAGATACTGACTATCGCAACGCGATAATACA
* *
3824717 AAATCGCAATGCGAATTTGGAAAATTGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAATGCG-ATTTGGAAAATTGCAACGAGATACTGACTATCGCAACGCGATAATACA
* ** * *
3824779 AAATCGCAACGCGATTCT-G-ACTTTCGCAACGAGATTCTGACTATCGCAACGAGATAATACA
1 AAATCGCAATGCGATT-TGGAAAATT-GCAACGAGATACTGACTATCGCAACGCGATAATACA
*
3824840 GAATCGCAATGCGATTT
1 AAATCGCAATGCGATTT
3824857 TCAAAGTTCG
Statistics
Matches: 128, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
60 4 0.03
61 50 0.39
62 74 0.58
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (61 bp):
AAATCGCAATGCGATTTGGAAAATTGCAACGAGATACTGACTATCGCAACGCGATAATACA
Found at i:3825601 original size:24 final size:24
Alignment explanation
Indices: 3825574--3825627 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3825564 GTATTCGAAA
* *
3825574 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTAGTCAATACCCGGAC
* *
3825598 TTTGATATTAGTCAATACTCGGAT
1 TTTGATATTAGTCAATACCCGGAC
3825622 TTTGAT
1 TTTGAT
3825628 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTAGTCAATACCCGGAC
Found at i:3825819 original size:12 final size:12
Alignment explanation
Indices: 3825802--3825826 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3825792 ATAAAATCCT
3825802 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3825814 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3825826 G
1 G
3825827 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3828144 original size:33 final size:33
Alignment explanation
Indices: 3828102--3828228 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
3828092 GGAAATGACT
3828102 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
*
3828135 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
3828168 ATCGCAATGCGAAATGAAAATCATAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
3828201 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCACAACG
3828229 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:3828158 original size:19 final size:19
Alignment explanation
Indices: 3828102--3828189 Score: 79
Period size: 19 Copynumber: 5.2 Consensus size: 19
3828092 GGAAATGACT
3828102 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
3828121 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3828135 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3828154 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3828168 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3828187 ATC
1 ATC
3828190 ATAACGAGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 20
0.67 0.08 0.25
Matches are distributed among these distances:
14 19 0.36
15 2 0.04
16 4 0.08
17 4 0.08
18 2 0.04
19 22 0.42
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3828280 original size:33 final size:33
Alignment explanation
Indices: 3828238--3828317 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
3828228 GCGAATTTAG
* *
3828238 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCATTGCGATTTTCA
* *
3828271 TTTCGCGTTGTGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCATTGCGATTTTCA
*
3828304 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
3828318 AGTCATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCATTGCGATTTTCA
Found at i:3828316 original size:19 final size:19
Alignment explanation
Indices: 3828257--3828317 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
3828247 GCGATTTTGT
3828257 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
* * *
3828276 CGTTGTGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
3828292 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
3828309 CATTGCGAT
1 CATTGCGAT
3828318 AGTCATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 5 0.16
16 7 0.22
17 7 0.22
19 13 0.41
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Done.