Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 24
Found at i:3241746 original size:23 final size:22
Alignment explanation
Indices: 3241698--3241746 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3241688 ACAGAATGTC
3241698 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
3241719 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
3241742 AAGGA
1 AAGGA
3241747 AAAATGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:3242656 original size:31 final size:31
Alignment explanation
Indices: 3242618--3242728 Score: 204
Period size: 31 Copynumber: 3.6 Consensus size: 31
3242608 AGGGTCCAGG
3242618 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3242649 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3242680 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
3242711 GATTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
3242729 AAATCTATGG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3242738 original size:62 final size:62
Alignment explanation
Indices: 3242618--3242742 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
3242608 AGGGTCCAGG
* * **
3242618 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAACATATGGACT
3242680 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAA-CATATGGACT
3242742 G
1 G
3242743 ATCCTTCGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 57 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAACATATGGACT
Found at i:3244653 original size:42 final size:42
Alignment explanation
Indices: 3244594--3244714 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
3244584 GTGAATCGGG
* *
3244594 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAAGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAAGGGC
** * *
3244636 CTCTTGAACGGTGGGAGGAGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGG-GACCTCTTGAACGATGACAAGGGC
* * *
3244678 CTCTTGAACGATAGGAGAGG-CCTCTTGAATGATGACA
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACA
3244715 GGTGAGTCGG
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
42 62 0.95
43 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAAGGGC
Found at i:3245208 original size:20 final size:20
Alignment explanation
Indices: 3245183--3245226 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3245173 AATAGTTTCT
3245183 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
3245203 GAAACTTAAAATCGCATCAC
1 GAAACTTAAAATCGCAACAC
3245223 GAAA
1 GAAA
3245227 AATGACTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.11, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:3245246 original size:21 final size:20
Alignment explanation
Indices: 3245193--3245262 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
3245183 GAAACTTAAA
* * **
3245193 ATCGCAACACGAAACTTAAA
1 ATCGCAACACGAAAATGACT
*
3245213 ATCGCATCACGAAAAATGACT
1 ATCGCAACACG-AAAATGACT
* **
3245234 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
3245254 ATCGCAACA
1 ATCGCAACA
3245263 AGATAATCGC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:3245383 original size:33 final size:34
Alignment explanation
Indices: 3245312--3245385 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
3245302 TAAATTCGCG
* * * *
3245312 TTGCGATTTTCATTTTTGCATTGTGATTTTCACG
1 TTGCGATTTTCATTTTCGCATTGCGATTATCACA
* *
3245346 TTGCGATTTTTA-TTTCGCATTGCGATTATCCCA
1 TTGCGATTTTCATTTTCGCATTGCGATTATCACA
3245379 TTGCGAT
1 TTGCGAT
3245386 AGTCAAATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTATCACA
Found at i:3245404 original size:20 final size:20
Alignment explanation
Indices: 3245379--3245442 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
3245369 GATTATCCCA
*
3245379 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAATTTCGCG
*
3245399 TTGCGATAGTC-ATTTCCGCA
1 TTGCGATAGTCAATTT-CGCG
* *
3245419 TTACGATAGTCATTTTCGCG
1 TTGCGATAGTCAATTTCGCG
3245439 TTGC
1 TTGC
3245443 TATTTTAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.08
20 30 0.83
21 3 0.08
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAATTTCGCG
Found at i:3247382 original size:20 final size:20
Alignment explanation
Indices: 3247359--3247414 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
3247349 TCTGAAACTT
3247359 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
3247379 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* * *
3247399 ACAATAGCAACGCGAA
1 AAAATCGCAACACGAA
3247415 TTTGACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.54, C:0.21, G:0.16, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:3248768 original size:20 final size:20
Alignment explanation
Indices: 3248743--3248781 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3248733 ACCGCGTTGC
3248743 GATTTACATATTCGCATTGT
1 GATTTACATATTCGCATTGT
3248763 GATTTACATATTCGCATTG
1 GATTTACATATTCGCATTG
3248782 CGATAGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
GATTTACATATTCGCATTGT
Found at i:3248797 original size:20 final size:20
Alignment explanation
Indices: 3248710--3248804 Score: 59
Period size: 20 Copynumber: 4.8 Consensus size: 20
3248700 TGACGCTTTG
3248710 AAAATCGCATTGCGATAGT-C
1 AAAATCGCATTGCGAT-GTAC
* * * *
3248730 AGAACCGCGTTGCGATTTAC
1 AAAATCGCATTGCGATGTAC
* * * *
3248750 ATATTCGCATTGTGATTTAC
1 AAAATCGCATTGCGATGTAC
* *
3248770 ATATTCGCATTGCGATAGT-C
1 AAAATCGCATTGCGAT-GTAC
*
3248790 AAAATCGCGTTGCGA
1 AAAATCGCATTGCGA
3248805 ATCTGGAAAC
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
19 1 0.02
20 57 0.97
21 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (20 bp):
AAAATCGCATTGCGATGTAC
Found at i:3248842 original size:20 final size:19
Alignment explanation
Indices: 3248819--3248864 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3248809 GGAAACTGAT
* *
3248819 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
3248839 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
3248858 TTGCGAT
1 TTGCGAT
3248865 TTTGTTGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:3248854 original size:19 final size:19
Alignment explanation
Indices: 3248830--3248866 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3248820 TGCGATACTG
*
3248830 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
3248849 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
3248867 TGTTGATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:3251606 original size:2 final size:2
Alignment explanation
Indices: 3251601--3251631 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3251591 AAACAGAGTA
3251601 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 A
3251632 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3251636 original size:2 final size:2
Alignment explanation
Indices: 3251631--3251659 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3251621 ATATATATAT
3251631 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3251660 AACCTGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3258592 original size:3 final size:3
Alignment explanation
Indices: 3258584--3258613 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3258574 AGGGTTCATG
3258584 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3258614 ATCGGAACCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3258865 original size:12 final size:13
Alignment explanation
Indices: 3258848--3258876 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3258838 TTTATTTGCG
3258848 AAAATTAAAA-TT
1 AAAATTAAAATTT
3258860 AAAATTAAAATTT
1 AAAATTAAAATTT
3258873 AAAA
1 AAAA
3258877 AACTCGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:3259035 original size:13 final size:14
Alignment explanation
Indices: 3259035--3259066 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3259025 ATAATAAAAG
3259035 AAAAGAA-AATAAT
1 AAAAGAACAATAAT
3259048 AAAA-AACAATAAT
1 AAAAGAACAATAAT
3259061 AAAAGA
1 AAAAGA
3259067 TTAGTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.12
13 14 0.82
14 1 0.06
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.12
Consensus pattern (14 bp):
AAAAGAACAATAAT
Found at i:3259038 original size:18 final size:18
Alignment explanation
Indices: 3259017--3259051 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3259007 CGAAGAAGGA
3259017 AAAAGAAAATAATAAAAG
1 AAAAGAAAATAATAAAAG
3259035 AAAAGAAAATAATAAAA
1 AAAAGAAAATAATAAAA
3259052 AACAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (18 bp):
AAAAGAAAATAATAAAAG
Found at i:3260522 original size:24 final size:24
Alignment explanation
Indices: 3260486--3260532 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3260476 AAAAAAACAA
* * *
3260486 AAATAAATGAAATTAAATTAAATT
1 AAATAAATAAAATAAAATAAAATT
*
3260510 AAATTAATAAAATAAAATAAAAT
1 AAATAAATAAAATAAAATAAAAT
3260533 AATATGATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATAAATAAAATAAAATAAAATT
Found at i:3260746 original size:36 final size:36
Alignment explanation
Indices: 3260603--3260899 Score: 246
Period size: 38 Copynumber: 7.9 Consensus size: 36
3260593 TTTAAAAAAA
* *
3260603 TTTTCAAAACTATATATTACATA-GTTTCCAAAATG
1 TTTTCAAAACTATATATTATATATGTTTTCAAAATG
* * *
3260638 TTTT-TAAA--A-ATATTATATAAGTTTTCAAAAAAAATA
1 TTTTCAAAACTATATATTATATATGTTTTC----AAAATG
* *
3260674 TTTTTAAAACTATATATTATATAAT-TTTACAAAAAATG
1 TTTTCAAAACTATATATTATAT-ATGTTTTC--AAAATG
* *
3260712 TTTTTAAAACTATATACTATATATGTTTTCAAAATG
1 TTTTCAAAACTATATATTATATATGTTTTCAAAATG
* * * **
3260748 TTTTAAAAACTATATAATATTTGAACATTTTCAAAATG
1 TTTTCAAAACTATATATTATAT--ATGTTTTCAAAATG
*
3260786 TTTTCAAAACTATATATTATATACGTATTTTCAAAATG
1 TTTTCAAAACTATATATTATATA--TGTTTTCAAAATG
*
3260824 TTTTCAAAAAAACTATATAATATATAAATGTTTTCAAACATG
1 TTTTC---AAAACTATAT-AT-TATATATGTTTTCAAA-ATG
*
3260866 TTTTCAAAACTATATATTATATATATTTTCAAAA
1 TTTTCAAAACTATATATTATATATGTTTTCAAAA
3260900 ACCATTTGAA
Statistics
Matches: 218, Mismatches: 23, Indels: 41
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.04
32 6 0.03
34 3 0.01
35 4 0.02
36 36 0.17
37 19 0.09
38 82 0.38
39 11 0.05
40 13 0.06
41 20 0.09
42 10 0.05
43 5 0.02
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (36 bp):
TTTTCAAAACTATATATTATATATGTTTTCAAAATG
Found at i:3260875 original size:39 final size:38
Alignment explanation
Indices: 3260668--3260925 Score: 231
Period size: 38 Copynumber: 6.8 Consensus size: 38
3260658 GTTTTCAAAA
* * * *
3260668 AAAATATTTTTAAAACTATATATTATAT-AAT-TTTAC
1 AAAATGTTTTCAAAACTATATAATATATAAATATTTTC
* * *
3260704 AAAAAATGTTTTTAAAACTATATACTATAT--ATGTTTTC
1 --AAAATGTTTTCAAAACTATATAATATATAAATATTTTC
* * * *
3260742 AAAATGTTTTAAAAACTATATAATATTTGAACATTTTC
1 AAAATGTTTTCAAAACTATATAATATATAAATATTTTC
* **
3260780 AAAATGTTTTCAAAACTATATATTATATACGTATTTTC
1 AAAATGTTTTCAAAACTATATAATATATAAATATTTTC
*
3260818 AAAATGTTTTCAAAAAAACTATATAATATATAAATGTTTTC
1 AAAATGTTTTC---AAAACTATATAATATATAAATATTTTC
*
3260859 AAACATGTTTTCAAAACTATAT-AT-TATATATATTTTC
1 AAA-ATGTTTTCAAAACTATATAATATATAAATATTTTC
*** *
3260896 AAAAACCATTTGAAAACTATATAATATATA
1 -AAAATGTTTTCAAAACTATATAATATATA
3260926 GAGGTATATG
Statistics
Matches: 185, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
36 25 0.14
37 27 0.15
38 85 0.46
39 14 0.08
41 26 0.14
42 8 0.04
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (38 bp):
AAAATGTTTTCAAAACTATATAATATATAAATATTTTC
Found at i:3262275 original size:106 final size:106
Alignment explanation
Indices: 3261665--3262279 Score: 1018
Period size: 106 Copynumber: 5.8 Consensus size: 106
3261655 AACCGTGGAT
*
3261665 GGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
1 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
* * * *
3261730 AATTGGCTCTGAAATCGGGAAATTATTTATTGACAACCAGC
66 AATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGC
*
3261771 GGTCCCTTCGGCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
1 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
* * *
3261836 AATTGGCTCTGAAATCGGGAAATTGTTTATTGACAACCAGC
66 AATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGC
*
3261877 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTAGTTGTGAAGTTGA
1 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
* *
3261942 AATTGCCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGC
66 AATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGC
* *
3261983 GGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGA
1 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
3262048 AATTGGCTCTGAAATTG-GAAAGTTGTTTATTGACAACCAGC
66 AATTGGCTCTGAAATTGAG-AAGTTGTTTATTGACAACCAGC
* *
3262089 GGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGA
1 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
* *
3262154 AATTGGCTTTGAAATTGAGAAGTTGTTTTTTGACAACCAGC
66 AATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGC
* * *
3262195 GGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGA
1 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
3262260 AATTGGCTCTGAAATT-AGAA
66 AATTGGCTCTGAAATTGAGAA
3262280 AGCCCATTCG
Statistics
Matches: 482, Mismatches: 25, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
105 5 0.01
106 476 0.99
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
AATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGC
Found at i:3264222 original size:5 final size:5
Alignment explanation
Indices: 3264198--3264257 Score: 66
Period size: 5 Copynumber: 11.6 Consensus size: 5
3264188 AAACAAAAAC
* * * *
3264198 AAATG AAATG AAATGA AATTA AATTA ATAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAAT-A AAATA AAATA A-AATA AAATA AAATA AAATA AAATA
3264250 AAATA AAA
1 AAATA AAA
3264258 AATAATATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
5 43 0.86
6 7 0.14
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:3264333 original size:29 final size:27
Alignment explanation
Indices: 3264284--3264347 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
3264274 CTATATAATA
* *
3264284 TATATATTCAAAAATATTTTTTAGAAAAC
1 TATATATTCAAAAATA-GTTTT-CAAAAC
*
3264313 TATATACTTTAAAAA-AGTTTTCAAAAC
1 TATATA-TTCAAAAATAGTTTTCAAAAC
3264340 TATATATT
1 TATATATT
3264348 ACATCGTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.06
27 11 0.35
28 4 0.13
29 7 0.23
30 7 0.23
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (27 bp):
TATATATTCAAAAATAGTTTTCAAAAC
Found at i:3264446 original size:39 final size:38
Alignment explanation
Indices: 3264374--3264548 Score: 173
Period size: 39 Copynumber: 4.6 Consensus size: 38
3264364 GTTTTTTAAA
3264374 ATATTATATAAGTTTTCAAAAAAAATGTTTTTAAAACTAT
1 ATATTATATAA-TTTTC-AAAAAAATGTTTTTAAAACTAT
3264414 ATATTATATAATTTTACAAAAAAATGTTTTTAAAACTAT
1 ATATTATATAATTTT-CAAAAAAATGTTTTTAAAACTAT
* * *
3264453 ATACTATATATGTTTTC---AAAATGTTTTAAAAACTAT
1 ATATTATATA-ATTTTCAAAAAAATGTTTTTAAAACTAT
* * * *
3264489 ATAATATTTAAACGTTTTC---AAAATATTTTCAAAACTAT
1 ATATTATAT-AA--TTTTCAAAAAAATGTTTTTAAAACTAT
3264527 ATATTATATATATTTTCAAAAA
1 ATATTATATA-ATTTTCAAAAA
3264549 CCATTTGCAA
Statistics
Matches: 116, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
36 30 0.26
37 2 0.02
38 30 0.26
39 38 0.33
40 16 0.14
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (38 bp):
ATATTATATAATTTTCAAAAAAATGTTTTTAAAACTAT
Found at i:3264523 original size:38 final size:36
Alignment explanation
Indices: 3264395--3264534 Score: 122
Period size: 38 Copynumber: 3.8 Consensus size: 36
3264385 GTTTTCAAAA
* *
3264395 AAAATGTTTTTAAAACTATATATTATATAA--TTTTAC
1 AAAATGTTTTAAAAACTATATAATATA-AACGTTTT-C
* * * *
3264431 AAAAAAATGTTTTTAAAACTATATACTATATATGTTTTC
1 ---AAAATGTTTTAAAAACTATATAATATAAACGTTTTC
3264470 AAAATGTTTTAAAAACTATATAATATTTAAACGTTTTC
1 AAAATGTTTTAAAAACTATATAATA--TAAACGTTTTC
* * *
3264508 AAAATATTTTCAAAACTATATATTATA
1 AAAATGTTTTAAAAACTATATAATATA
3264535 TATATTTTCA
Statistics
Matches: 88, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
36 25 0.28
38 32 0.36
39 27 0.31
40 4 0.05
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATAATATAAACGTTTTC
Found at i:3265567 original size:17 final size:18
Alignment explanation
Indices: 3265534--3265567 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3265524 CCGTTATTAG
3265534 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
3265552 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
3265568 GACTGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:3265778 original size:26 final size:26
Alignment explanation
Indices: 3265749--3265798 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3265739 TATCAAGTTC
3265749 AACTCAAACTCGAAATATAATATTGT
1 AACTCAAACTCGAAATATAATATTGT
**
3265775 AACTTGAACTCGAAATATAATATT
1 AACTCAAACTCGAAATATAATATT
3265799 AAAACTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (26 bp):
AACTCAAACTCGAAATATAATATTGT
Found at i:3265804 original size:26 final size:26
Alignment explanation
Indices: 3265755--3265815 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
3265745 GTTCAACTCA
**
3265755 AACTCGAAATATAATATTGTAACTTG
1 AACTCGAAATATAATATTAAAACTTG
3265781 AACTCGAAATATAATATTAAAACTTG
1 AACTCGAAATATAATATTAAAACTTG
3265807 AACTCGAAA
1 AACTCGAAA
3265816 AGGCTTGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.30
Consensus pattern (26 bp):
AACTCGAAATATAATATTAAAACTTG
Found at i:3266825 original size:33 final size:33
Alignment explanation
Indices: 3266783--3266847 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
3266773 TCACAATTCA
** *
3266783 AACTTTTAAACTTTGTTTGAAAAATTTAGTGTT
1 AACTTTTAAACTTAATTTGAAAAATATAGTGTT
*
3266816 AACTTTTAAACTTAATTTGAGAAATATAGTGT
1 AACTTTTAAACTTAATTTGAAAAATATAGTGT
3266848 ATAGTGGCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (33 bp):
AACTTTTAAACTTAATTTGAAAAATATAGTGTT
Found at i:3267552 original size:66 final size:66
Alignment explanation
Indices: 3267470--3267602 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
3267460 GATGAAGACT
3267470 GTGGGCTTGAGGTCAACGGTGATAGCGTTAGAGATTTGGCTTTCGGCTTGTTAGGTGTCAATGTT
1 GTGGGCTTGAGGTCAACGGTGATAGCGTTAGAGATTTGGCTTTCGGCTTGTTAGGTGTCAATGTT
3267535 G
66 G
3267536 GTGGGCTTGAGGTCAACGGTGATAGCGTTAGAGATTTGGCTTTCGGCTTGTTAGGTGTCAATGTT
1 GTGGGCTTGAGGTCAACGGTGATAGCGTTAGAGATTTGGCTTTCGGCTTGTTAGGTGTCAATGTT
3267601 G
66 G
3267602 G
1 G
3267603 AACTGTGGCT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.17, C:0.12, G:0.37, T:0.35
Consensus pattern (66 bp):
GTGGGCTTGAGGTCAACGGTGATAGCGTTAGAGATTTGGCTTTCGGCTTGTTAGGTGTCAATGTT
G
Found at i:3269713 original size:21 final size:22
Alignment explanation
Indices: 3269684--3269728 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3269674 TTATGAAATA
**
3269684 TTTTAAATCTTAAT-ATTTTAT
1 TTTTAAATCAAAATAATTTTAT
*
3269705 TTTTTAATCAAAATAATTTTAT
1 TTTTAAATCAAAATAATTTTAT
3269727 TT
1 TT
3269729 AGATGAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAATCAAAATAATTTTAT
Found at i:3274499 original size:3 final size:3
Alignment explanation
Indices: 3274484--3274526 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3274474 CTGTATTTAT
*
3274484 TAA TAA T-A GAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
3274527 TTTAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 30 0.86
4 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3274951 original size:35 final size:35
Alignment explanation
Indices: 3274905--3274971 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
3274895 CTTCTTCTTC
3274905 CTTCTTCAGATGAATTCTTCTCATTATGAACTCGA
1 CTTCTTCAGATGAATTCTTCTCATTATGAACTCGA
*
3274940 CTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 CTTCTTCAGATGAATTCTTCTCATTATGAACT
3274972 TTTTCTGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (35 bp):
CTTCTTCAGATGAATTCTTCTCATTATGAACTCGA
Found at i:3275081 original size:39 final size:40
Alignment explanation
Indices: 3275035--3275138 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 40
3275025 AAGGTTGAAC
3275035 AAATTCTTCTCATTATGAA-TTTCTTCTT-TCTCTTCAAAT
1 AAATTCTTCTCATTATGAACTTT-TTCTTCTCTCTTCAAAT
* *
3275074 AAATTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGAT
1 AAATTCTTCTCATTATGAACTTTTTCTTCTCTCTTCAAAT
* *
3275114 GAGTTCTTCTCATTATGAACTTTTT
1 AAATTCTTCTCATTATGAACTTTTT
3275139 TATGGAAAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
39 24 0.41
40 35 0.59
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (40 bp):
AAATTCTTCTCATTATGAACTTTTTCTTCTCTCTTCAAAT
Found at i:3275103 original size:159 final size:160
Alignment explanation
Indices: 3274756--3275153 Score: 550
Period size: 159 Copynumber: 2.5 Consensus size: 160
3274746 AAAGTTGAAC
* * ***
3274756 AAATTCTCCTTATTATGAACTTCTTT-TTCTTCAGATGAGTTCTTCTCATTATGAACTCACTCTG
1 AAATTCTTCTCATTATGAACTT-TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
* * *
3274820 GAAATGCTGATGATGATATATCTCCTTCTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTC
65 GAAAAGCTGATGATGATATATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAACTCTTC
*
3274885 TCATTATGAACTTCTTCTTCCTTCTTCAGAT
130 TCATTATGAACTTCTTCTTCCTTCTTCAAAT
* ***
3274916 GAATTCTTCTCATTATGAAC-TCGACTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
1 AAATTCTTCTCATTATGAACTTTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
* * *
3274980 AAAAGCTGATGTTGATCTATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCT
66 AAAAGCTGATGATGATATATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAACTCTTCT
* *
3275045 CATTATGAATTTCTTCTTTC-TCTTCAAAT
131 CATTATGAACTTCTTCTTCCTTCTTCAAAT
3275074 AAATTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTT
1 AAATTCTTCTCATTATGAAC--TTT-TTC-TTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTT
*
3275139 TATGGAAAAGCTGAT
61 TCTGGAAAAGCTGAT
3275154 CCATCGAGTG
Statistics
Matches: 208, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
158 27 0.13
159 114 0.55
160 17 0.08
161 1 0.00
162 1 0.00
163 30 0.14
164 18 0.09
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (160 bp):
AAATTCTTCTCATTATGAACTTTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
AAAAGCTGATGATGATATATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAACTCTTCT
CATTATGAACTTCTTCTTCCTTCTTCAAAT
Found at i:3275434 original size:113 final size:113
Alignment explanation
Indices: 3275077--3276607 Score: 2116
Period size: 113 Copynumber: 13.5 Consensus size: 113
3275067 TTCAAATAAA
* * ***
3275077 TTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTA-
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC--TCGAAC
* * * * * *
3275141 TGGAAAAGCTGATCCATCGAGTGATTAATTCGAGCGAAAAGTTGAACAAG
64 TGGTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* * * * **
3275191 TTCTTCTCATTATGGACTTCTTATTCCTTCTTCATATGAGTTCTTCTCATTATTAACTCTTTCAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC--GAAC
** * * *
3275256 TGGGGATGCTGATCCATCAAATGATGAATTCAAAC-AAAAGATTGAACAAA
64 TGGTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAG-TTGAACAAG
* * ***
3275306 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * * * *
3275371 GCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTAAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* **
3275419 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGCCCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * * *
3275484 GCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* **
3275532 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGCCCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * * *
3275597 GCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* * *
3275645 TTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
3275710 GTAATGCTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* *
3275758 TTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * *
3275823 GTAATGCTGATCTATTGAATCATGAATTCAAGCAAAAAGTTGAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* * **
3275871 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAATTCTTCTCATTATGAACTATAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * *
3275936 GTAATGCCGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* * *
3275984 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTTATTATGAACTCG-CCTT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAAC-T
* * * * *
3276048 GGCAATACTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAG
65 GGTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* **
3276097 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGCCCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * * *
3276162 GCAATGCTGGTCCATCGAATGATAAATTCAAGAAAAAAAGTTGAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAG-CAAAAAGTTGAACAAG
* * *
3276211 TTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
3276276 GTAATGCTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* *
3276324 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * *
3276389 GTAATGCTGATCTATTGAATCATGAATTCAAGCAAAAAGTTGAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* *
3276437 TTCATCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
3276502 GTAATGCTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAACAAG
66 GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
* * *
3276550 CTCTTCTTATTATGAACTTCTTCTTCCTTCTT-ATATGAGTTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
3276608 TTCTTGAAAT
Statistics
Matches: 1310, Mismatches: 99, Indels: 18
0.92 0.07 0.01
Matches are distributed among these distances:
112 27 0.02
113 1030 0.79
114 165 0.13
115 88 0.07
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
GTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAG
Found at i:3276595 original size:22 final size:24
Alignment explanation
Indices: 3276552--3276595 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3276542 TGAACAAGCT
3276552 CTTCTTATTATGAACTTCTTCTTC
1 CTTCTTATTATGAACTTCTTCTTC
*
3276576 CTTCTTA-TATG-AGTTCTTCT
1 CTTCTTATTATGAACTTCTTCT
3276596 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.55
Consensus pattern (24 bp):
CTTCTTATTATGAACTTCTTCTTC
Found at i:3277068 original size:22 final size:22
Alignment explanation
Indices: 3277043--3277098 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
3277033 GATAAAGCTT
* *
3277043 TCATCTTTGAAAAGAGAATTTG
1 TCATCTTTGAAAAGAGAATCTA
* *
3277065 TCATCTTTTAAAAAGGGAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
3277088 TCATCTTTGAA
1 TCATCTTTGAA
3277099 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3277557 original size:54 final size:53
Alignment explanation
Indices: 3277463--3277596 Score: 157
Period size: 54 Copynumber: 2.6 Consensus size: 53
3277453 GGAATAACTG
* * * * * *
3277463 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGA
1 GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGA
* *
3277516 TGTTCGTAAAACATTTGACAACACATTCTTCATCTCATGTGGTTTCAGCTCAGA
1 -GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGA
*
3277570 --T-GTAAAACACTTGACAACACATTCATC
1 GTTCGTAAAACATTTGACAACACATTCATC
3277597 CTTTTCTGTG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 24 0.34
51 1 0.01
54 45 0.64
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGA
Found at i:3277612 original size:40 final size:40
Alignment explanation
Indices: 3277568--3277647 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
3277558 TTTCAGCTCA
3277568 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
*
3277608 GATGTAAAACACTTGACAACAGATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
3277648 CTTCTGCTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
Found at i:3279778 original size:115 final size:114
Alignment explanation
Indices: 3279577--3279805 Score: 359
Period size: 115 Copynumber: 2.0 Consensus size: 114
3279567 ACGATCATGC
* * * * *
3279577 AATTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTATCGAACCAGATCAGATAACTCAAA
1 AATTCATATTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
3279642 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCA
* *
3279691 AATTCATATTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
1 AATTCATATTTCAAATCCAATGATTGG-TTCTGGGGTTCATACCAAACCAGATCAGATAACTCAA
* * *
3279756 GGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
65 AGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCA
3279806 CATGGCACTT
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
114 24 0.23
115 80 0.77
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (114 bp):
AATTCATATTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCA
Found at i:3279847 original size:115 final size:114
Alignment explanation
Indices: 3279621--3279847 Score: 280
Period size: 115 Copynumber: 2.0 Consensus size: 114
3279611 GTTCCTATCG
3279621 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCAT
* * ** **
3279686 GAGCAAATTCATATTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCA
66 GAGCAAATGCATATCTCAAATCTAATGATTGG-TACTGGAATTCATACCA
* * *
3279736 AACCAGATCAGATAACTCAAGGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCAT
* * *
3279801 GAGCACATGGCACT-TACTCCAAT-TAATGTTTGG-ACTGGAATATCATA
66 GAGCAAAT-GCA-TAT-CTCAAATCTAATGATTGGTACTGGAAT-TCATA
3279848 ATAGTTTTTC
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
114 4 0.04
115 74 0.77
116 12 0.12
117 6 0.06
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (114 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCAT
GAGCAAATGCATATCTCAAATCTAATGATTGGTACTGGAATTCATACCA
Found at i:3283978 original size:7 final size:7
Alignment explanation
Indices: 3283944--3283985 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
3283934 ATAAGAGTAT
3283944 AAATGCA
1 AAATGCA
* *
3283951 CAATGAA
1 AAATGCA
3283958 AAATGCA
1 AAATGCA
3283965 AAGATGCA
1 AA-ATGCA
3283973 AAATGC-
1 AAATGCA
3283979 AAATGCA
1 AAATGCA
3283986 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:3286327 original size:22 final size:21
Alignment explanation
Indices: 3286280--3286333 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
3286270 AAAATTAATC
*
3286280 AAATAATATATTAATATGATTA
1 AAATAATA-ATTAATATAATTA
* *
3286302 AAATAATAATTATTATTAATTT
1 AAATAATAATTAATA-TAATTA
3286324 AAATATATAA
1 AAATA-ATAA
3286334 CAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.22
22 17 0.63
23 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATAATAATTAATATAATTA
Found at i:3287293 original size:3 final size:3
Alignment explanation
Indices: 3287278--3287344 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
3287268 CTGTATTTAT
* * *
3287278 TAA TAA T-A GAA TAA TAA TAA TAA TAA TAA TAA TTA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3287325 TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TA
3287345 TTTAAATGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 3 0.05
3 52 0.91
4 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3292480 original size:32 final size:32
Alignment explanation
Indices: 3292423--3292592 Score: 263
Period size: 32 Copynumber: 5.4 Consensus size: 32
3292413 GTTCCTAAGA
*
3292423 ACATAGGTAA-C-TGTCCATATGTCCCGAAAT
1 ACATAGGTAATCTTGTCCATATGTCCCGAAAG
* *
3292453 ACATAGGTAATCTTGTCCATATATCCCGAAAT
1 ACATAGGTAATCTTGTCCATATGTCCCGAAAG
*
3292485 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
1 ACATAGGTAATCTTGTCCATATGTCCCGAAAG
* *
3292517 ACATAAGTAATCATGTCCATATGTCCCGAAAG
1 ACATAGGTAATCTTGTCCATATGTCCCGAAAG
*
3292549 ACATAGGTAATCTTGTCCATATGTCCCAAAAG
1 ACATAGGTAATCTTGTCCATATGTCCCGAAAG
3292581 ACATAGGTAATC
1 ACATAGGTAATC
3292593 CTCGACTCTT
Statistics
Matches: 129, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
30 10 0.08
31 1 0.01
32 118 0.91
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (32 bp):
ACATAGGTAATCTTGTCCATATGTCCCGAAAG
Found at i:3293149 original size:28 final size:30
Alignment explanation
Indices: 3293107--3293209 Score: 124
Period size: 30 Copynumber: 3.5 Consensus size: 30
3293097 AAAAATAATA
* * *
3293107 TTTTGATATATTAC-AATAAAGACCAAAAC
1 TTTTTATAAATTACAAAAAAAGACCAAAAC
*
3293136 -TTTTATAAATTACAAACAAATG-CC-AAAC
1 TTTTTATAAATTACAAA-AAAAGACCAAAAC
*
3293164 TTTTTATAAATTACAAAAAAATACCAAAAC
1 TTTTTATAAATTACAAAAAAAGACCAAAAC
3293194 TTTTTATAAATTACAA
1 TTTTTATAAATTACAA
3293210 CAAATGCCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
28 18 0.29
29 22 0.35
30 23 0.37
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (30 bp):
TTTTTATAAATTACAAAAAAAGACCAAAAC
Found at i:3293214 original size:29 final size:29
Alignment explanation
Indices: 3293107--3293351 Score: 176
Period size: 29 Copynumber: 8.5 Consensus size: 29
3293097 AAAAATAATA
* * * *
3293107 TTTTGATATATTACAATAAAGACCAAAAC
1 TTTTTATAAATTACAACAAATACCAAAAC
*
3293136 -TTTTATAAATTACAAACAAATGCC-AAAC
1 TTTTTATAAATTAC-AACAAATACCAAAAC
*
3293164 TTTTTATAAATTACAAAAAAATACCAAAAC
1 TTTTTATAAATTAC-AACAAATACCAAAAC
*
3293194 TTTTTATAAATTACAACAAATGCCAAAA-
1 TTTTTATAAATTACAACAAATACCAAAAC
*** * * ***
3293222 AAATTAAAAATTACAACTAATTA-CAATTG
1 TTTTTATAAATTACAAC-AAATACCAAAAC
* ***
3293251 TTTTTATAAATTACAACAAATTCCAATTG
1 TTTTTATAAATTACAACAAATACCAAAAC
* ***
3293280 TTTTTATAAATTACAACAAATTCCAATTG
1 TTTTTATAAATTACAACAAATACCAAAAC
* *
3293309 TTTTTATAAATTACAATCAAAGA-AAAAAC
1 TTTTTATAAATTACAA-CAAATACCAAAAC
* *
3293338 TTCTAATAAATTAC
1 TTTTTATAAATTAC
3293352 GACTTGAGAG
Statistics
Matches: 178, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
28 34 0.19
29 122 0.69
30 22 0.12
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTTTATAAATTACAACAAATACCAAAAC
Found at i:3293220 original size:87 final size:87
Alignment explanation
Indices: 3293107--3293351 Score: 201
Period size: 87 Copynumber: 2.8 Consensus size: 87
3293097 AAAAATAATA
* * * * *
3293107 TTTTGATATATTACAATAAA-GACCAAAACTTTTATAAATTACAAACAAATGCCAA-ACTTTTTA
1 TTTTTATAAATTACAACAAATG-CCAAAAATTTTATAAATTACAAACAAATGACAATACTTTTTA
3293170 TAAATTACAAAAAAATACCAAAAC
65 TAAATTAC-AAAAAATACCAAAAC
** * * * **
3293194 TTTTTATAAATTACAACAAATGCCAAAAAAATTAAAAATTAC-AACTAATTACAATTGTTTTTAT
1 TTTTTATAAATTACAACAAATGCCAAAAATTTTATAAATTACAAACAAATGACAATACTTTTTAT
* * ***
3293258 AAATTACAACAAATTCCAATTG
66 AAATTACAAAAAATACCAAAAC
* *** * * * * *
3293280 TTTTTATAAATTACAACAAATTCCAATTGTTTTTATAAATTACAATCAAA-GAAAAAACTTCTAA
1 TTTTTATAAATTACAACAAATGCCAA-AAATTTTATAAATTACAAACAAATGACAATACTTTTTA
3293344 TAAATTAC
65 TAAATTAC
3293352 GACTTGAGAG
Statistics
Matches: 121, Mismatches: 33, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
86 44 0.36
87 72 0.60
88 5 0.04
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.34
Consensus pattern (87 bp):
TTTTTATAAATTACAACAAATGCCAAAAATTTTATAAATTACAAACAAATGACAATACTTTTTAT
AAATTACAAAAAATACCAAAAC
Found at i:3305137 original size:200 final size:198
Alignment explanation
Indices: 3304794--3305190 Score: 719
Period size: 200 Copynumber: 2.0 Consensus size: 198
3304784 TAAGAAAAGC
3304794 CACTGTTTAGTGCACTTATCTCCGAAAGTCACCATTTTTGTTGCTGAAAGGAGCTTCAGATTTGA
1 CACTGTTTAGTGCACTTATCTCCGAAAGTCACCATTTTTGTTGCTGAAAGGAGCTTCAGATTTGA
3304859 GTGAGGAGAAGCTCAGATGCTATGCTGGCCACCAGAGTCAGCTGAGACCAAAGAATTAGATCTCA
66 GTGAGGAGAAGCTCAGATGCTATGCTGGCCACCAGAGTCAGCTGAGACCAAAGAATTAGATCTCA
3304924 ACAAAGGAGTGCCTTGATGC-ATGGCATTGTCTTGGGAGTTAAC-AACCATCAG-TCTTTGCAAC
131 ACAAAGGAGTGCCTTGATGCAATGGCATTGTCTTGGGAGTTAACAAACCATCAGTTCTTTGCAAC
3304986 TTA
196 TTA
3304989 CACTGTTTAGTGCACTTATCTCCGAAAAGTCACCATTTTTGTTGCTGAAAGGAGCTTCAGATTTG
1 CACTGTTTAGTGCACTTATCTCCG-AAAGTCACCATTTTTGTTGCTGAAAGGAGCTTCAGATTTG
*
3305054 AGTGAGGAGAAGCTCAGCATATGCTCTTGCTGGCCACCAGAGTCAGCTGAGACCAAAGAATTAGA
65 AGTGAGGAGAAGCTCAG---ATGCT-ATGCTGGCCACCAGAGTCAGCTGAGACCAAAGAATTAGA
3305119 TCTCAACAAAGGAGTGCCTTGATGCAATGGCATTGTCTTGGGAGTTAACAAACCATCAGTTCTTT
126 TCTCAACAAAGGAGTGCCTTGATGCAATGGCATTGTCTTGGGAGTTAACAAACCATCAGTTCTTT
3305184 GCAACTT
191 GCAACTT
3305191 TGAACATTTC
Statistics
Matches: 193, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
195 24 0.12
196 57 0.30
199 5 0.03
200 63 0.33
201 23 0.12
202 9 0.05
203 12 0.06
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (198 bp):
CACTGTTTAGTGCACTTATCTCCGAAAGTCACCATTTTTGTTGCTGAAAGGAGCTTCAGATTTGA
GTGAGGAGAAGCTCAGATGCTATGCTGGCCACCAGAGTCAGCTGAGACCAAAGAATTAGATCTCA
ACAAAGGAGTGCCTTGATGCAATGGCATTGTCTTGGGAGTTAACAAACCATCAGTTCTTTGCAAC
TTA
Found at i:3306327 original size:56 final size:56
Alignment explanation
Indices: 3306224--3306336 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 56
3306214 AAAAGAAAAG
3306224 TGAAGATCTAAAGAAGAATTATTTGTTCCACAAATATGAAGCTCCTTTATTCCGTT
1 TGAAGATCTAAAGAAGAATTATTTGTTCCACAAATATGAAGCTCCTTTATTCCGTT
3306280 TGAAGAATCTAAAGAAGAATTATTTGTTCCACAAATA-GAAGCTCCTTTATTCCGTT
1 TGAAG-ATCTAAAGAAGAATTATTTGTTCCACAAATATGAAGCTCCTTTATTCCGTT
3306336 T
1 T
3306337 TATTAATTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 25 0.45
57 31 0.55
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (56 bp):
TGAAGATCTAAAGAAGAATTATTTGTTCCACAAATATGAAGCTCCTTTATTCCGTT
Found at i:3309298 original size:26 final size:27
Alignment explanation
Indices: 3309253--3309307 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
3309243 ACCCGAACCG
*
3309253 AACCGAATCATAAAAATGAAGCC-TTTA
1 AACCGAACCATAAAAATGAA-CCGTTTA
*
3309280 AACCGAACCA-AAAACTGAACCGTTTA
1 AACCGAACCATAAAAATGAACCGTTTA
3309306 AA
1 AA
3309308 GCCAAACCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 14 0.56
27 9 0.36
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (27 bp):
AACCGAACCATAAAAATGAACCGTTTA
Found at i:3309322 original size:5 final size:5
Alignment explanation
Indices: 3309312--3309336 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3309302 TTTAAAGCCA
3309312 AACCG AACCG AACCG AACCG AACCG
1 AACCG AACCG AACCG AACCG AACCG
3309337 TTTTACTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:3313613 original size:9 final size:9
Alignment explanation
Indices: 3313601--3313633 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3313591 AAGTAAAATG
3313601 TTAAATAAA
1 TTAAATAAA
*
3313610 TTAAAT-AC
1 TTAAATAAA
3313618 TTAAATAAA
1 TTAAATAAA
3313627 TTAAATA
1 TTAAATA
3313634 CAAAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (9 bp):
TTAAATAAA
Found at i:3313632 original size:17 final size:17
Alignment explanation
Indices: 3313601--3313634 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3313591 AAGTAAAATG
3313601 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
3313618 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
3313635 AAAATATTAA
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:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:3314395 original size:45 final size:45
Alignment explanation
Indices: 3314331--3314420 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
3314321 CAAACCAGAG
3314331 GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATT
1 GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATT
3314376 GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATT
1 GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATT
3314421 CCTTTTTATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (45 bp):
GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATT
Found at i:3314578 original size:3 final size:3
Alignment explanation
Indices: 3314572--3314600 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3314562 AATAATTGAA
3314572 CTT CTT CTT CTT -TT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3314601 TATTTCCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:3314646 original size:125 final size:125
Alignment explanation
Indices: 3314376--3314720 Score: 610
Period size: 125 Copynumber: 2.8 Consensus size: 125
3314366 ATTTTATATT
3314376 GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATC
1 GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATC
3314441 TAATAATTGAA---CTTCTTC--TTCTTCTTCTTATTCTTTATTTCCCATCAAACCAGAG
66 TAATAATTGAACTTCTTCTTCTTTTCTTCTTCTTATTCTTTATTTCCCATCAAACCAGAG
* *
3314496 GAATAATGGCATGTGGTCTTACAATACGATTCCTAATTTTATATTTCTTTTTATCATTAAAAATC
1 GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATC
*
3314561 TAATAATTGAACTTCTTCTTCTTTTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAG
66 TAATAATTGAACTTCTTCTTCTTTTCTTCTTCTTATTCTTTATTTCCCATCAAACCAGAG
* *
3314621 GAATAATGGCACGTCGTCTTACAATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATC
1 GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATC
3314686 TAATAATTGAACTTCTTCTTCTTTTCTTCTTCTTA
66 TAATAATTGAACTTCTTCTTCTTTTCTTCTTCTTA
3314721 ATTTCTTCTT
Statistics
Matches: 212, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
120 74 0.35
123 7 0.03
125 131 0.62
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.45
Consensus pattern (125 bp):
GAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATC
TAATAATTGAACTTCTTCTTCTTTTCTTCTTCTTATTCTTTATTTCCCATCAAACCAGAG
Found at i:3314703 original size:3 final size:3
Alignment explanation
Indices: 3314697--3314745 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
3314687 AATAATTGAA
**
3314697 CTT CTT CTT CTT -TT CTT CTT CTT AAT -TT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3314743 CTT
1 CTT
3314746 TATTTCCCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
2 3 0.07
3 38 0.93
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3314716 original size:14 final size:14
Alignment explanation
Indices: 3314697--3314745 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
3314687 AATAATTGAA
3314697 CTTCTTCTTCTTTT
1 CTTCTTCTTCTTTT
**
3314711 CTTCTTCTTAATTT
1 CTTCTTCTTCTTTT
3314725 CTTCTTCTTCTTCTT
1 CTTCTTCTTCTT-TT
3314740 CTTCTT
1 CTTCTT
3314746 TATTTCCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 22 0.73
15 8 0.27
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (14 bp):
CTTCTTCTTCTTTT
Found at i:3314740 original size:282 final size:278
Alignment explanation
Indices: 3314172--3314862 Score: 796
Period size: 270 Copynumber: 2.5 Consensus size: 278
3314162 GATTTAACCC
* *
3314172 TCTTCTTCTTCTTCTTCTTCTTTATTTCCCATAAAACCAAAGAAATAATGGCATGTGGTCTTACA
1 TCTTCTTCTTCTTCTT-TTCTTTATTTCCCATCAAACCAGAGAAATAATGGCATGTGGTCTTACA
* *
3314237 ATACGCTTCTTAGTTTTATATTCCTTTTTATCATTAAAAATCTAATAATTGAA------CTTC--
65 ATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATCTAATAATTGAACTTCTTCTTCTT
* *
3314294 TTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGGAATAATGGCATGTGGTCTTACAATACG
130 TTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGGAATAATGGCACGTCGTCTTACAATACG
* * ** * * *
3314359 CTTCCTAATTTTATATTGAATAATGGCATGTGGTCTTACAATACGCTTCCTAATTTTATATTCCT
195 CTTCCTAATTTTATATTCAATAATAGCATGTAATCTAACAATACACTTCCT-ATCTTATATTCCT
*
3314424 TTTTATCATTAAAAATCTAATAATTGAACT
259 TTCTATCATT----A---AA-AA-T-AACT
*
3314454 TCTTCTTCTTCTTCTTATTCTTTATTTCCCATCAAACCAGAGGAATAATGGCATGTGGTCTTACA
1 TCTTCTTCTTCTTCTT-TTCTTTATTTCCCATCAAACCAGAGAAATAATGGCATGTGGTCTTACA
* *
3314519 ATACGATTCCTAATTTTATATTTCTTTTTATCATTAAAAATCTAATAATTGAACTTCTTCTTCTT
65 ATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATCTAATAATTGAACTTCTTCTTCTT
3314584 TTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGGAATAATGGCACGTCGTCTTACAATACG
130 TTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGGAATAATGGCACGTCGTCTTACAATACG
** ** * * *
3314649 CTTCCTAATTTTATATTCCTTTTTATCAT-TAAAAATCTAATAATTGA-ACTT-CT-TCTTCT-T
195 CTTCCTAATTTTATATTCAATAATAGCATGT---AATCTAACAA-T-ACACTTCCTATCTTATAT
*
3314709 TTC-TTCT-TC-TT---AAT---T
255 TCCTTTCTATCATTAAAAATAACT
*
3314724 TCTTCTTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGAAATAATGGCACGTGGTCTTACA
1 TCTTCTTCTTCTTCTT-TTCTTTATTTCCCATCAAACCAGAGAAATAATGGCATGTGGTCTTACA
*
3314789 ATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAATTCTAATAATTGAACTTCTTCTTCTT
65 ATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATCTAATAATTGAACTTCTTCTTCTT
*
3314854 CTTCGTCTT
130 -TTCTTCTT
3314863 ACAATACGCT
Statistics
Matches: 362, Mismatches: 33, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
270 125 0.35
271 7 0.02
274 1 0.00
275 2 0.01
282 110 0.30
286 2 0.01
287 2 0.01
288 7 0.02
289 4 0.01
290 89 0.25
292 8 0.02
293 4 0.01
294 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.45
Consensus pattern (278 bp):
TCTTCTTCTTCTTCTTTTCTTTATTTCCCATCAAACCAGAGAAATAATGGCATGTGGTCTTACAA
TACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATCTAATAATTGAACTTCTTCTTCTTT
TCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGGAATAATGGCACGTCGTCTTACAATACGC
TTCCTAATTTTATATTCAATAATAGCATGTAATCTAACAATACACTTCCTATCTTATATTCCTTT
CTATCATTAAAAATAACT
Found at i:3314785 original size:145 final size:145
Alignment explanation
Indices: 3314579--3314862 Score: 516
Period size: 145 Copynumber: 2.0 Consensus size: 145
3314569 GAACTTCTTC
*
3314579 TTCTTTTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGGAATAATGGCACGTCGTCTTACA
1 TTCTTTTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGAAATAATGGCACGTCGTCTTACA
3314644 ATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATCTAATAATTGAACTTCTTCTTCTT
66 ATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATCTAATAATTGAACTTCTTCTTCTT
*
3314709 -TTCTTCTTCTTAAT
131 CTTCGTCTTCTTAAT
*
3314723 TTCTTCTTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGAAATAATGGCACGTGGTCTTAC
1 TTCTT-TTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGAAATAATGGCACGTCGTCTTAC
*
3314788 AATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAATTCTAATAATTGAACTTCTTCTTCT
65 AATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATCTAATAATTGAACTTCTTCTTCT
3314853 TCTTCGTCTT
130 TCTTCGTCTT
3314863 ACAATACGCT
Statistics
Matches: 134, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
144 5 0.04
145 122 0.91
146 7 0.05
ACGTcount: A:0.24, C:0.23, G:0.07, T:0.47
Consensus pattern (145 bp):
TTCTTTTCTTCTTCTTCTTCTTTATTTCCCATCAAACCAGAGAAATAATGGCACGTCGTCTTACA
ATACGCTTCCTAATTTTATATTCCTTTTTATCATTAAAAATCTAATAATTGAACTTCTTCTTCTT
CTTCGTCTTCTTAAT
Found at i:3329024 original size:4 final size:4
Alignment explanation
Indices: 3329015--3329049 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3329005 CTGTTTCAAC
3329015 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
3329050 ACATGCATTG
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:3335464 original size:4 final size:4
Alignment explanation
Indices: 3335455--3335489 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3335445 TTCAACTATG
3335455 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
3335490 ACATGCATTG
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:3340756 original size:16 final size:16
Alignment explanation
Indices: 3340735--3340772 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
3340725 ACTGAATAAT
3340735 AGACTGGCTACTTGGA
1 AGACTGGCTACTTGGA
*
3340751 AGACTGGCTGCTTGGA
1 AGACTGGCTACTTGGA
3340767 AGACTG
1 AGACTG
3340773 CTTTGGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (16 bp):
AGACTGGCTACTTGGA
Found at i:3340780 original size:13 final size:15
Alignment explanation
Indices: 3340735--3340782 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
3340725 ACTGAATAAT
3340735 AGACTGGCTACTTGGA
1 AGACTGGCT-CTTGGA
3340751 AGACTGGCTGCTTGGA
1 AGACTGGCT-CTTGGA
3340767 AGACT-GCT-TTGGA
1 AGACTGGCTCTTGGA
3340780 AGA
1 AGA
3340783 AAAATGTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 8 0.26
15 3 0.10
16 20 0.65
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (15 bp):
AGACTGGCTCTTGGA
Found at i:3341828 original size:4 final size:4
Alignment explanation
Indices: 3341819--3341845 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3341809 GTCAACTATG
3341819 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
3341846 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:3347250 original size:18 final size:19
Alignment explanation
Indices: 3347227--3347264 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3347217 TATTTAAGTG
*
3347227 ATAAAAGCGA-TTAAATAA
1 ATAAAAGCAATTTAAATAA
3347245 ATAAAAGCAATTTAAATAA
1 ATAAAAGCAATTTAAATAA
3347264 A
1 A
3347265 AATAATAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
ATAAAAGCAATTTAAATAA
Found at i:3347871 original size:3 final size:3
Alignment explanation
Indices: 3347863--3347915 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
3347853 TTTTTCACTA
*
3347863 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT ATAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
3347908 TAT TAT TA
1 TAT TAT TA
3347916 AATTAAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3347916 original size:9 final size:9
Alignment explanation
Indices: 3347862--3347920 Score: 68
Period size: 9 Copynumber: 6.7 Consensus size: 9
3347852 ATTTTTCACT
3347862 ATATTATTA
1 ATATTATTA
*
3347871 TTATTATTA
1 ATATTATTA
*
3347880 TTATTATTA
1 ATATTATTA
*
3347889 TTATTA-TA
1 ATATTATTA
3347897 TATATTATTA
1 -ATATTATTA
3347907 ATATTATTA
1 ATATTATTA
3347916 A-ATTA
1 ATATTA
3347921 AATATTACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
8 6 0.13
9 38 0.83
10 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTATTA
Found at i:3349445 original size:27 final size:27
Alignment explanation
Indices: 3349377--3349447 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
3349367 TATTTTAATT
*
3349377 TTATATGTTTAATATT-TTAATTATTA
1 TTATATGTTTAATTTTATTAATTATTA
*
3349403 TTATTAT-TTTACTTTTATTAA-TATATA
1 TTA-TATGTTTAATTTTATTAATTAT-TA
*
3349430 TTATATGATTAATTTTAT
1 TTATATGTTTAATTTTAT
3349448 AAACTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
26 16 0.43
27 21 0.57
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (27 bp):
TTATATGTTTAATTTTATTAATTATTA
Found at i:3352730 original size:12 final size:13
Alignment explanation
Indices: 3352713--3352741 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3352703 ACATTCACAT
3352713 ATTTACA-TTTGC
1 ATTTACATTTTGC
3352725 ATTTACATTTTGC
1 ATTTACATTTTGC
3352738 ATTT
1 ATTT
3352742 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:3355447 original size:9 final size:9
Alignment explanation
Indices: 3355433--3355476 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
3355423 TATTATACTT
3355433 GAAAAAAAG
1 GAAAAAAAG
3355442 GAAAAAAAG
1 GAAAAAAAG
*
3355451 AAAAAAAAAAG
1 --GAAAAAAAG
*
3355462 GAAAAAAGG
1 GAAAAAAAG
3355471 GAAAAA
1 GAAAAA
3355477 TTAAACCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 22 0.73
11 8 0.27
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
GAAAAAAAG
Found at i:3358965 original size:75 final size:75
Alignment explanation
Indices: 3358886--3359137 Score: 294
Period size: 75 Copynumber: 3.3 Consensus size: 75
3358876 TTAACAAGAA
* * * *
3358886 CAAATGCTGGGGCATACTGAAAACCCCTCTT-AATCAGAATCATGAATGTTGATGTATTTTGAAC
1 CAAATGCTGGGGCATGCTGAAAGCCCCT-TTCAATCAGAATCAGGAATGTTGATGCATTTTGAAC
* *
3358950 ATTTATATCAG
65 GTTTGTATCAG
* * **
3358961 CAAATGCTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATGAGGAATATTGACACATTTTGAACG
1 CAAATGCTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATGTTGATGCATTTTGAACG
*
3359026 TTTGTATTAG
66 TTTGTATCAG
* *
3359036 CCAATGCTGGGGCATGCTGAAAGCACCTTTCAATCAAGAATCAGGAATGTTTG-TGCATTTTGAA
1 CAAATGCTGGGGCATGCTGAAAGCCCCTTTCAATC-AGAATCAGGAATG-TTGATGCATTTTGAA
* *
3359100 TGTTCGTATCAG
64 CGTTTGTATCAG
* *
3359112 CAAATG-TCGGGGCACGCTGAAGGCCC
1 CAAATGCT-GGGGCATGCTGAAAGCCC
3359138 ATATCATCTT
Statistics
Matches: 149, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
74 2 0.01
75 95 0.64
76 49 0.33
77 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (75 bp):
CAAATGCTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATGTTGATGCATTTTGAACG
TTTGTATCAG
Found at i:3360057 original size:54 final size:54
Alignment explanation
Indices: 3359978--3360089 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
3359968 AGATCCTCCC
* * * *
3359978 TTACCAGCATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTT
1 TTACCAGCATCTGAGCAGAAACCACAGGAAAGGATGAATGTATTGACAAATGTT
* * * * *
3360032 TTACTAGCATCTGAGCATAAACCACATGAGATGATGAATGTATTGACAAATGTT
1 TTACCAGCATCTGAGCAGAAACCACAGGAAAGGATGAATGTATTGACAAATGTT
3360086 TTAC
1 TTAC
3360090 GAACCAGTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (54 bp):
TTACCAGCATCTGAGCAGAAACCACAGGAAAGGATGAATGTATTGACAAATGTT
Found at i:3360488 original size:22 final size:22
Alignment explanation
Indices: 3360463--3360539 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
3360453 ATCTACACTT
3360463 TTCAAAGATGATAGACTCTTTC
1 TTCAAAGATGATAGACTCTTTC
* * *
3360485 TTCAAAGATGATAGCCTATCTC
1 TTCAAAGATGATAGACTCTTTC
* *
3360507 TTTAAAGATGATAGATTCTCTT-
1 TTCAAAGATGATAGACTCT-TTC
3360529 TTCAAAGATGA
1 TTCAAAGATGA
3360540 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGACTCTTTC
Found at i:3376570 original size:34 final size:35
Alignment explanation
Indices: 3376519--3376591 Score: 139
Period size: 34 Copynumber: 2.1 Consensus size: 35
3376509 CTTTTATTAT
3376519 TATTTTTAAAATTAAGCATAGAACTTTCAATTACA
1 TATTTTTAAAATTAAGCATAGAACTTTCAATTACA
3376554 TATTTTT-AAATTAAGCATAGAACTTTCAATTACA
1 TATTTTTAAAATTAAGCATAGAACTTTCAATTACA
3376588 TATT
1 TATT
3376592 AAGCATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 31 0.82
35 7 0.18
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.42
Consensus pattern (35 bp):
TATTTTTAAAATTAAGCATAGAACTTTCAATTACA
Found at i:3376589 original size:17 final size:17
Alignment explanation
Indices: 3376535--3376589 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3376525 TAAAATTAAG
3376535 CATAGAACTTTCAATTA
1 CATAGAACTTTCAATTA
** *
3376552 CAT--ATTTTTAAATTAA
1 CATAGAACTTTCAATT-A
3376568 GCATAGAACTTTCAATTA
1 -CATAGAACTTTCAATTA
3376586 CATA
1 CATA
3376590 TTAAGCATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
15 8 0.29
16 1 0.04
17 10 0.36
18 1 0.04
19 8 0.29
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (17 bp):
CATAGAACTTTCAATTA
Found at i:3380681 original size:51 final size:52
Alignment explanation
Indices: 3380597--3380700 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 52
3380587 AATTGATTGG
* * *
3380597 TAGTTAGATAATTACTTGCTGCCATGATTGAATTGGACTGTATATGTTATCT
1 TAGTTAGATAATTACTTGCTACCATGATCGAATTGGACTGTATATGTGATCT
* * * *
3380649 TAGTTAGATTATT-GTTGCTACCATGATCGAATTGGATTGTATGTGTGATCT
1 TAGTTAGATAATTACTTGCTACCATGATCGAATTGGACTGTATATGTGATCT
3380700 T
1 T
3380701 GGTTCTTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 33 0.73
52 12 0.27
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (52 bp):
TAGTTAGATAATTACTTGCTACCATGATCGAATTGGACTGTATATGTGATCT
Found at i:3381429 original size:93 final size:93
Alignment explanation
Indices: 3381222--3381416 Score: 329
Period size: 93 Copynumber: 2.1 Consensus size: 93
3381212 TGAGTGTTTC
* * *
3381222 TTTCTTGTTCGAATAGAGGAAAGAATGTTATACATGTTGAATTGTTTAAATCGATTTCCATATAG
1 TTTCTTGTTCGAATAGAGGAAAGAATGTTATACACGTTCAATTGTTTAAATCGATTGCCATATAG
3381287 ATTGCATGAATACATATGTGGTGAATTG
66 ATTGCATGAATACATATGTGGTGAATTG
*
3381315 CTTCTTGTTCGAATAGAGGAAAGAATGTTATACACGTTCAATTGTTT-AATCTGATTGCCATATA
1 TTTCTTGTTCGAATAGAGGAAAGAATGTTATACACGTTCAATTGTTTAAATC-GATTGCCATATA
*
3381379 GATTGCATGAATACGTATGTGGTGAATTG
65 GATTGCATGAATACATATGTGGTGAATTG
3381408 TTTCTTGTT
1 TTTCTTGTT
3381417 TAAATGGAGG
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 4 0.04
93 91 0.96
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (93 bp):
TTTCTTGTTCGAATAGAGGAAAGAATGTTATACACGTTCAATTGTTTAAATCGATTGCCATATAG
ATTGCATGAATACATATGTGGTGAATTG
Found at i:3382034 original size:19 final size:19
Alignment explanation
Indices: 3381998--3382036 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3381988 TTTTGAGTTC
*
3381998 TAATGATCTTGATCATGTT
1 TAATGATCTTGATAATGTT
* *
3382017 TAATGGTCTTGGTAATGTT
1 TAATGATCTTGATAATGTT
3382036 T
1 T
3382037 CCAAACCTCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.49
Consensus pattern (19 bp):
TAATGATCTTGATAATGTT
Found at i:3385742 original size:21 final size:21
Alignment explanation
Indices: 3385691--3385743 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3385681 ATTCTGACTA
3385691 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
3385712 TTGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
3385733 TCGCAATGCGA
1 TCGCATTGCGA
3385744 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:3385758 original size:20 final size:20
Alignment explanation
Indices: 3385733--3385826 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
3385723 TTTTCCTAAT
3385733 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
3385753 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
3385774 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3385794 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3385814 TCGCAATGCGAAT
1 TCGCAATGCGAAT
3385827 CTGACTATCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 49 0.75
21 16 0.25
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3385779 original size:41 final size:40
Alignment explanation
Indices: 3385733--3385826 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 40
3385723 TTTTCCTAAT
**
3385733 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAA
* *
3385774 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
3385814 TCGCAATGCGAAT
1 TCGCAATGCGAAT
3385827 CTGACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 18 0.37
41 31 0.63
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
Found at i:3386052 original size:22 final size:22
Alignment explanation
Indices: 3386026--3386087 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
3386016 ACATCCGTCC
3386026 CCATCTCCGACGAAATCAATC-
1 CCATCTCCGACGAAATCAATCT
* * *
3386047 CTCATCGCCGACGATATCAGTCT
1 C-CATCTCCGACGAAATCAATCT
*
3386070 CCATCTCCGGCGAAATCA
1 CCATCTCCGACGAAATCA
3386088 TTCACGGTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.27, C:0.37, G:0.15, T:0.21
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAATCT
Found at i:3386496 original size:20 final size:20
Alignment explanation
Indices: 3386424--3386530 Score: 112
Period size: 20 Copynumber: 5.5 Consensus size: 20
3386414 CGATTCTGTC
*
3386424 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
** **
3386443 GTTGCGATAGTCAAATTCGT
1 GTTGCGATTTTCATTTTCGT
**
3386463 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
3386483 GTTGCGATTTTCATTTTC--
1 GTTGCGATTTTCATTTTCGT
3386501 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
* *
3386521 TTTACGATTT
1 GTTGCGATTT
3386531 AAAGTTTAAG
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
18 18 0.24
19 11 0.15
20 46 0.61
ACGTcount: A:0.15, C:0.16, G:0.21, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:3386515 original size:38 final size:38
Alignment explanation
Indices: 3386422--3386530 Score: 112
Period size: 38 Copynumber: 2.8 Consensus size: 38
3386412 TGCGATTCTG
* **
3386422 TCGTTGCGATTTTCA-TTTCGCGTTGCGATAGTCAAAT
1 TCGTTGCGATTTTCATTTTCGTGTTGCGATTTTCAAAT
** **
3386459 TCGTGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTT
1 TC--GTTGCGATTTTCATTTTCGTGTTGCGATTTTCAAAT
* *
3386499 TCGTTGCGATTTTCATTTTCGTTTTACGATTT
1 TCGTTGCGATTTTCATTTTCGTGTTGCGATTT
3386531 AAAGTTTAAG
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
37 2 0.03
38 26 0.45
39 11 0.19
40 19 0.33
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.49
Consensus pattern (38 bp):
TCGTTGCGATTTTCATTTTCGTGTTGCGATTTTCAAAT
Found at i:3388494 original size:20 final size:20
Alignment explanation
Indices: 3388469--3388535 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
3388459 CAACAACAAA
3388469 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
3388489 ATCGCAATGTGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
3388509 ATCGCAATGC-AAATTTGACT
1 ATCGCAATGCGAAA-ATGACT
3388529 ATCGCAA
1 ATCGCAA
3388536 CGAAAGAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 3 0.07
20 40 0.93
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:3388610 original size:20 final size:20
Alignment explanation
Indices: 3388585--3388701 Score: 106
Period size: 20 Copynumber: 6.2 Consensus size: 20
3388575 TCTCTCGTTT
**
3388585 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
3388605 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
3388625 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCATTG
3388645 CGAT--T--TTGTT-G--TTG
1 CGATAGTCATT-TTCGCATTG
** *
3388659 CGATTTTCA-TTTCGCGTTG
1 CGATAGTCATTTTCGCATTG
*
3388678 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCATTG
3388698 CGAT
1 CGAT
3388702 TTTAAGTTTC
Statistics
Matches: 83, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
17 4 0.05
18 1 0.01
19 10 0.12
20 55 0.66
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:3389225 original size:18 final size:20
Alignment explanation
Indices: 3389187--3389228 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3389177 CTCGCCTGTC
3389187 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-CTCCCCT
3389208 ATCGTTCAAGA-G-TCCCCT
1 ATCGTTCAAGAGGCTCCCCT
3389226 ATC
1 ATC
3389229 ATCTCTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
20 1 0.05
21 11 0.52
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGTTCAAGAGGCTCCCCT
Found at i:3389260 original size:21 final size:23
Alignment explanation
Indices: 3389209--3389261 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
3389199 GCCTCCCCTA
*
3389209 TCGTTCAAGAGTCCCCTATCATC
1 TCGTTCAAGAGTCCCCTACCATC
*
3389232 TC-TT-AAGAGTCCCCTCCCA-C
1 TCGTTCAAGAGTCCCCTACCATC
3389252 -CGTTCAAGAG
1 TCGTTCAAGAG
3389262 GCCACTGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.04
20 3 0.12
21 18 0.69
22 2 0.08
23 2 0.08
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (23 bp):
TCGTTCAAGAGTCCCCTACCATC
Found at i:3390871 original size:20 final size:20
Alignment explanation
Indices: 3390846--3390974 Score: 215
Period size: 20 Copynumber: 6.5 Consensus size: 20
3390836 GCGATTCTCT
*
3390846 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
3390866 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
3390886 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
3390906 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
3390926 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
3390946 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCA-ATTCCG
3390966 CGTTGCGAT
1 CGTTGCGAT
3390975 TTCCGCGTTG
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
20 101 0.98
21 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:3393441 original size:24 final size:24
Alignment explanation
Indices: 3393407--3393460 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3393397 CTGAAAAATC
3393407 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3393431 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3393455 ATCAAA
1 ATCAAA
3393461 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3394346 original size:20 final size:20
Alignment explanation
Indices: 3394303--3394348 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3394293 AATTCAGTAT
* *
3394303 TGCGATAGTCAGAATCTCGT
1 TGCGATAGTCAGAATCGCGC
*
3394323 TGCGATAGTCAGATTCGCGC
1 TGCGATAGTCAGAATCGCGC
3394343 TGCGAT
1 TGCGAT
3394349 TTATATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGC
Found at i:3394366 original size:20 final size:20
Alignment explanation
Indices: 3394343--3394468 Score: 135
Period size: 20 Copynumber: 6.2 Consensus size: 20
3394333 AGATTCGCGC
** *
3394343 TGCGATTTATATATTTGCAT
1 TGCGATTTACGTATTCGCAT
*
3394363 TGCGATTTACGTATTCACAT
1 TGCGATTTACGTATTCGCAT
*
3394383 TACGATTTACGTATTCGCAT
1 TGCGATTTACGTATTCGCAT
* *
3394403 TGCGATTGACGTAATCGCAT
1 TGCGATTTACGTATTCGCAT
* ** *
3394423 TGCGATTTTCCAAATTCGCGT
1 TGCGA-TTTACGTATTCGCAT
*
3394444 TGCTATTTACGTATTCGCAT
1 TGCGATTTACGTATTCGCAT
3394464 TGCGA
1 TGCGA
3394469 ATTAGGAAAA
Statistics
Matches: 84, Mismatches: 21, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
20 71 0.85
21 13 0.15
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (20 bp):
TGCGATTTACGTATTCGCAT
Found at i:3396690 original size:51 final size:52
Alignment explanation
Indices: 3396606--3396709 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 52
3396596 AATTGATTGG
* * *
3396606 TAGTTAGATAATTACTTGCTGCCATGATTGAATTGGACTGTATATGTTATCT
1 TAGTTAGATAATTACTTGCTACCATGATCGAATTGGACTGTATATGTGATCT
* * * *
3396658 TAGTTAGATTATT-GTTGCTACCATGATCGAATTGGATTGTATGTGTGATCT
1 TAGTTAGATAATTACTTGCTACCATGATCGAATTGGACTGTATATGTGATCT
3396709 T
1 T
3396710 GGTTCTTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 33 0.73
52 12 0.27
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (52 bp):
TAGTTAGATAATTACTTGCTACCATGATCGAATTGGACTGTATATGTGATCT
Found at i:3397315 original size:49 final size:47
Alignment explanation
Indices: 3397262--3397413 Score: 118
Period size: 49 Copynumber: 3.2 Consensus size: 47
3397252 TTATACATGT
3397262 TGAATTGTTTAAATCGATTTCCATATAGATTGCATGAATACATATGTGG
1 TGAATTGTTT-AATCGATTTCCATATAGATTGCATGAATAC-TATGTGG
* * * * ** * *
3397311 TGAATTGCTT-CTTG--TTCGAATATAGGAAAGAATGTTATAC-ATGT--
1 TGAATTGTTTAATCGATTTC-CATATA-GATTGCATG-AATACTATGTGG
*
3397355 TGAATTGTTTAATCTGATTGCCATATAGATTGCATGAATACGTATGTGG
1 TGAATTGTTTAATC-GATTTCCATATAGATTGCATGAATAC-TATGTGG
3397404 TGAATTGTTT
1 TGAATTGTTT
3397414 CTTGTTTAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
44 9 0.12
45 8 0.11
46 16 0.21
47 17 0.23
48 6 0.08
49 19 0.25
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.40
Consensus pattern (47 bp):
TGAATTGTTTAATCGATTTCCATATAGATTGCATGAATACTATGTGG
Found at i:3397432 original size:93 final size:93
Alignment explanation
Indices: 3397225--3397419 Score: 338
Period size: 93 Copynumber: 2.1 Consensus size: 93
3397215 TGAGTGTTTA
*
3397225 CTTCTTGTTCGAATAGAGGAAAGAATGTTATACATGTTGAATTGTTTAAATCGATTTCCATATAG
1 CTTCTTGTTCGAATAGAGGAAAGAATGTTATACATGTTGAATTGTTTAAATCGATTGCCATATAG
3397290 ATTGCATGAATACATATGTGGTGAATTG
66 ATTGCATGAATACATATGTGGTGAATTG
*
3397318 CTTCTTGTTCGAATATAGGAAAGAATGTTATACATGTTGAATTGTTT-AATCTGATTGCCATATA
1 CTTCTTGTTCGAATAGAGGAAAGAATGTTATACATGTTGAATTGTTTAAATC-GATTGCCATATA
*
3397382 GATTGCATGAATACGTATGTGGTGAATTG
65 GATTGCATGAATACATATGTGGTGAATTG
*
3397411 TTTCTTGTT
1 CTTCTTGTT
3397420 TAAATGGAGG
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 4 0.04
93 93 0.96
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.40
Consensus pattern (93 bp):
CTTCTTGTTCGAATAGAGGAAAGAATGTTATACATGTTGAATTGTTTAAATCGATTGCCATATAG
ATTGCATGAATACATATGTGGTGAATTG
Found at i:3398029 original size:19 final size:19
Alignment explanation
Indices: 3398001--3398039 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3397991 TTTTGAGTTC
*
3398001 TAATGATCTTGATCATGTT
1 TAATGATCTTGATAATGTT
*
3398020 TAATGGTCTTGATAATGTT
1 TAATGATCTTGATAATGTT
3398039 T
1 T
3398040 CCAAACCTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.49
Consensus pattern (19 bp):
TAATGATCTTGATAATGTT
Found at i:3402231 original size:22 final size:21
Alignment explanation
Indices: 3402203--3402340 Score: 123
Period size: 22 Copynumber: 6.9 Consensus size: 21
3402193 TCAAGGGTTA
3402203 CAGTGGTCCTTCGGGACATAT
1 CAGTGGTCCTTCGGGACATAT
* *
3402224 CCAGTGGTTCTTCGGG--ATGT
1 -CAGTGGTCCTTCGGGACATAT
* *
3402244 -AGTGGTCATTCGAGACATATT
1 CAGTGGTCCTTCGGGACATA-T
*
3402265 CAGTGGTCCTTCGGG--ATGT
1 CAGTGGTCCTTCGGGACATAT
3402284 -AGTGGTCCTTCGGGACATAT
1 CAGTGGTCCTTCGGGACATAT
* *
3402304 CCAGTGGTCCTTAGGGACGTA-
1 -CAGTGGTCCTTCGGGACATAT
3402325 -A-TGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
3402341 AATATTCACT
Statistics
Matches: 94, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
18 38 0.40
19 2 0.02
20 10 0.11
21 1 0.01
22 43 0.46
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (21 bp):
CAGTGGTCCTTCGGGACATAT
Found at i:3402249 original size:18 final size:18
Alignment explanation
Indices: 3402226--3402338 Score: 82
Period size: 18 Copynumber: 5.8 Consensus size: 18
3402216 GGACATATCC
*
3402226 AGTGGTTCTTCGGGATGT
1 AGTGGTCCTTCGGGATGT
* * *
3402244 AGTGGTCATTCGAGACATATT
1 AGTGGTCCTTCG-G-GAT-GT
3402265 CAGTGGTCCTTCGGGATGT
1 -AGTGGTCCTTCGGGATGT
*
3402284 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGG--ATGT
* *
3402304 CCAGTGGTCCTTAGGGACGT
1 --AGTGGTCCTTCGGGATGT
*
3402324 AATGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
3402339 CAAATATTCA
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
18 37 0.50
19 2 0.03
20 9 0.12
21 2 0.03
22 24 0.32
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGATGT
Found at i:3402261 original size:40 final size:40
Alignment explanation
Indices: 3402204--3402340 Score: 211
Period size: 40 Copynumber: 3.4 Consensus size: 40
3402194 CAAGGGTTAC
*
3402204 AGTGGTCCTTCGGGACATATCCAGTGGTTCTTCGGGATGT
1 AGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGATGT
* * *
3402244 AGTGGTCATTCGAGACATATTCAGTGGTCCTTCGGGATGT
1 AGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGATGT
* *
3402284 AGTGGTCCTTCGGGACATATCCAGTGGTCCTTAGGGACGT
1 AGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGATGT
*
3402324 AATGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
3402341 AATATTCACT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.30
Consensus pattern (40 bp):
AGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGATGT
Found at i:3407424 original size:22 final size:21
Alignment explanation
Indices: 3407396--3407463 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 21
3407386 AGGGTTATAA
3407396 TGGTCCTTCGGAACATATCCAG
1 TGGTCCTTCGG-ACATATCCAG
*
3407418 TGGTCCTTCGGGAC--GT--AG
1 TGGTCCTTC-GGACATATCCAG
3407436 TGGTCCTTCGGA-ATATCCAG
1 TGGTCCTTCGGACATATCCAG
3407456 TGGTCCTT
1 TGGTCCTT
3407464 AGGGATGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
17 3 0.08
18 12 0.31
20 11 0.28
22 11 0.28
23 2 0.05
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.31
Consensus pattern (21 bp):
TGGTCCTTCGGACATATCCAG
Found at i:3407439 original size:18 final size:18
Alignment explanation
Indices: 3407416--3407487 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
3407406 GAACATATCC
3407416 AGTGGTCCTTCGGGACGT
1 AGTGGTCCTTCGGGACGT
* **
3407434 AGTGGTCCTTCGGAATAT
1 AGTGGTCCTTCGGGACGT
* *
3407452 CCAGTGGTCCTTAGGGATGT
1 --AGTGGTCCTTCGGGACGT
*
3407472 AATGGTCCTTCGGGAC
1 AGTGGTCCTTCGGGAC
3407488 AAATATTCAC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 28 0.65
20 15 0.35
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACGT
Found at i:3407460 original size:38 final size:40
Alignment explanation
Indices: 3407393--3407484 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 40
3407383 TCGAGGGTTA
*
3407393 TAATGGTCCTTCGGAACATATCCAGTGGTCCTTCGGGACG
1 TAATGGTCCTTCGGAACATATCCAGTGGTCCTTAGGGACG
* *
3407433 TAGTGGTCCTTCGG-A-ATATCCAGTGGTCCTTAGGGATG
1 TAATGGTCCTTCGGAACATATCCAGTGGTCCTTAGGGACG
3407471 TAATGGTCCTTCGG
1 TAATGGTCCTTCGG
3407485 GACAAATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 34 0.71
39 1 0.02
40 13 0.27
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.30
Consensus pattern (40 bp):
TAATGGTCCTTCGGAACATATCCAGTGGTCCTTAGGGACG
Found at i:3414657 original size:14 final size:14
Alignment explanation
Indices: 3414626--3414675 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3414616 AAGTCACATA
*
3414626 ATATTAATT-AATCG
1 ATATT-ATTGAATCT
*
3414640 ATATTATTGAATTT
1 ATATTATTGAATCT
*
3414654 ATATCATTGAATCT
1 ATATTATTGAATCT
3414668 ATATTATT
1 ATATTATT
3414676 TCTTAATGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 3 0.10
14 27 0.90
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (14 bp):
ATATTATTGAATCT
Found at i:3417369 original size:20 final size:19
Alignment explanation
Indices: 3417341--3417382 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3417331 ATATAAAAAA
*
3417341 TTATTTTTTATTAAATATTT
1 TTATATTTTATTAAAT-TTT
*
3417361 TTATATTTTATTTAATTTT
1 TTATATTTTATTAAATTTT
3417380 TTA
1 TTA
3417383 AATAATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATATTTTATTAAATTTT
Found at i:3422875 original size:23 final size:23
Alignment explanation
Indices: 3422836--3422880 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3422826 AATTAACTAT
*
3422836 ATAATAAATATATTAAATTTTAA
1 ATAATAAATATAATAAATTTTAA
3422859 ATAA-AAATATTAATAAATTTTA
1 ATAATAAATA-TAATAAATTTTA
3422881 TTAAACGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAATAAATATAATAAATTTTAA
Found at i:3423244 original size:12 final size:12
Alignment explanation
Indices: 3423227--3423257 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3423217 AAAAAAATAT
3423227 AATATAATTTTA
1 AATATAATTTTA
3423239 AATATAATTTTA
1 AATATAATTTTA
3423251 AA-ATAAT
1 AATATAAT
3423258 AATAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AATATAATTTTA
Found at i:3427863 original size:11 final size:11
Alignment explanation
Indices: 3427847--3427877 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3427837 TCTGTAACAC
3427847 ATCCGACCCGT
1 ATCCGACCCGT
3427858 ATCCGACCCGT
1 ATCCGACCCGT
3427869 ATCCGACCC
1 ATCCGACCC
3427878 AAATATGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.48, G:0.16, T:0.16
Consensus pattern (11 bp):
ATCCGACCCGT
Found at i:3428882 original size:21 final size:21
Alignment explanation
Indices: 3428848--3428887 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3428838 TGTTGTATAT
3428848 AGCCGTTAGGGATG-TTTTGG
1 AGCCGTTAGGGATGATTTTGG
*
3428868 AGCCGTTTGGGGATGATTTT
1 AGCCG-TTAGGGATGATTTT
3428888 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTAGGGATGATTTTGG
Found at i:3429105 original size:23 final size:23
Alignment explanation
Indices: 3429071--3429173 Score: 94
Period size: 23 Copynumber: 4.7 Consensus size: 23
3429061 TGCACTGCAT
3429071 GGTGCATCGATGCACTAGTGGCA
1 GGTGCATCGATGCACTAGTGGCA
* *
3429094 GGTGCATAGATGCACT-GCAGG--
1 GGTGCATCGATGCACTAG-TGGCA
*
3429115 GGTGCATGGATGCA--A-T-GCA
1 GGTGCATCGATGCACTAGTGGCA
*
3429134 TAGTGCATCGATGCACTAGTGGCA
1 -GGTGCATCGATGCACTAGTGGCA
*
3429158 GGTGCATGGATGCACT
1 GGTGCATCGATGCACT
3429174 TTGACACCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
17 1 0.02
20 12 0.19
21 13 0.21
22 2 0.03
23 32 0.51
24 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.22
Consensus pattern (23 bp):
GGTGCATCGATGCACTAGTGGCA
Found at i:3429124 original size:64 final size:64
Alignment explanation
Indices: 3429052--3429173 Score: 217
Period size: 64 Copynumber: 1.9 Consensus size: 64
3429042 TCGAAATGGA
* *
3429052 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGGCAGGTGCATAGATGCACTGCAGGG
1 GTGCATGGATGCAATGCATAGTGCATCGATGCACTAGTGGCAGGTGCATAGATGCACTGCAGGG
*
3429116 GTGCATGGATGCAATGCATAGTGCATCGATGCACTAGTGGCAGGTGCATGGATGCACT
1 GTGCATGGATGCAATGCATAGTGCATCGATGCACTAGTGGCAGGTGCATAGATGCACT
3429174 TTGACACCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (64 bp):
GTGCATGGATGCAATGCATAGTGCATCGATGCACTAGTGGCAGGTGCATAGATGCACTGCAGGG
Found at i:3429521 original size:24 final size:24
Alignment explanation
Indices: 3429494--3429542 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
3429484 CACCACAGGT
3429494 CGTATAAAT-TGCACCGAAGTGCCA
1 CGTA-AAATATGCACCGAAGTGCCA
*
3429518 CGTAGAATATGCACCGAAGTGCCA
1 CGTAAAATATGCACCGAAGTGCCA
3429542 C
1 C
3429543 ATAGAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (24 bp):
CGTAAAATATGCACCGAAGTGCCA
Found at i:3429547 original size:24 final size:23
Alignment explanation
Indices: 3429503--3429569 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
3429493 TCGTATAAAT
*
3429503 TGCACCGAAGTGCCACGTAGAATA
1 TGCACCGAAGTGCCACATAGAA-A
3429527 TGCACCGAAGTGCCACATAGAAA
1 TGCACCGAAGTGCCACATAGAAA
3429550 TGTC-CCGAAG-GACCACATAG
1 TG-CACCGAAGTG-CCACATAG
3429570 TATTGTCCCG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 1 0.03
23 17 0.43
24 22 0.55
ACGTcount: A:0.34, C:0.27, G:0.24, T:0.15
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAA
Found at i:3429565 original size:23 final size:23
Alignment explanation
Indices: 3429531--3429632 Score: 98
Period size: 23 Copynumber: 4.4 Consensus size: 23
3429521 AGAATATGCA
3429531 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
* *
3429554 CCGAAGGACCACATAGTATTGTC
1 CCGAAGGACCACATAGAAATGTC
** *
3429577 CCGAAGGACTGCGTAGAAATGTC
1 CCGAAGGACCACATAGAAATGTC
** * * *
3429600 CCGAAGGACTGCGTAGAATTATC
1 CCGAAGGACCACATAGAAATGTC
3429623 CCGAAGGACC
1 CCGAAGGACC
3429633 GCGTAAAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 1 0.01
23 67 0.99
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:3429594 original size:46 final size:46
Alignment explanation
Indices: 3429544--3429641 Score: 135
Period size: 46 Copynumber: 2.2 Consensus size: 46
3429534 AAGTGCCACA
* * *
3429544 TAGAAATGTCCCGAAGGACCACATAGTATTGTCCCGAAGGACTGCG
1 TAGAAATGTCCCGAAGGACCACATAGAATTATCCCGAAGGACCGCG
** *
3429590 TAGAAATGTCCCGAAGGACTGCGTAGAATTATCCCGAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACATAGAATTATCCCGAAGGACCGCG
3429636 TA-AAAT
1 TAGAAAT
3429642 CCTCGACTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 4 0.09
46 42 0.91
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (46 bp):
TAGAAATGTCCCGAAGGACCACATAGAATTATCCCGAAGGACCGCG
Found at i:3429636 original size:23 final size:23
Alignment explanation
Indices: 3429544--3429637 Score: 116
Period size: 23 Copynumber: 4.1 Consensus size: 23
3429534 AAGTGCCACA
* * *
3429544 TAGAAATGTCCCGAAGGACCACA
1 TAGAATTGTCCCGAAGGACCGCG
* *
3429567 TAGTATTGTCCCGAAGGACTGCG
1 TAGAATTGTCCCGAAGGACCGCG
* *
3429590 TAGAAATGTCCCGAAGGACTGCG
1 TAGAATTGTCCCGAAGGACCGCG
*
3429613 TAGAATTATCCCGAAGGACCGCG
1 TAGAATTGTCCCGAAGGACCGCG
3429636 TA
1 TA
3429638 AAATCCTCGA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCGCG
Done.