Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_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: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 40
Found at i:3641755 original size:18 final size:18
Alignment explanation
Indices: 3641732--3641767 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3641722 GCTCATAAGG
*
3641732 TTATACATTTATTAGGAA
1 TTATACATTTATCAGGAA
3641750 TTATACATTTATCAGGAA
1 TTATACATTTATCAGGAA
3641768 ACATATATTG
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:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (18 bp):
TTATACATTTATCAGGAA
Found at i:3647130 original size:21 final size:21
Alignment explanation
Indices: 3647104--3647150 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3647094 AAAAGCTTAG
3647104 AATTTAGGTGAAGTGTGGGAA
1 AATTTAGGTGAAGTGTGGGAA
3647125 AATTTAGGTGAAGTGTGGGAA
1 AATTTAGGTGAAGTGTGGGAA
3647146 AATTT
1 AATTT
3647151 CGGAGTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (21 bp):
AATTTAGGTGAAGTGTGGGAA
Found at i:3648598 original size:16 final size:16
Alignment explanation
Indices: 3648547--3648598 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
3648537 AGTATAAATA
* *
3648547 AAAGTTTAAAAAAATC
1 AAAGTTTTAAAAAGTC
*
3648563 TACAAGTTTTCAACAAGTC
1 -A-AAGTTTT-AAAAAGTC
3648582 AAAGTTTTAAAAAGTC
1 AAAGTTTTAAAAAGTC
3648598 A
1 A
3648599 TGTAGACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 8 0.28
17 8 0.28
18 7 0.24
19 6 0.21
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (16 bp):
AAAGTTTTAAAAAGTC
Found at i:3649833 original size:21 final size:21
Alignment explanation
Indices: 3649807--3649853 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3649797 AAAAGCTTAG
3649807 AATTTAGGTGAAGTGTGGGAA
1 AATTTAGGTGAAGTGTGGGAA
3649828 AATTTAGGTGAAGTGTGGGAA
1 AATTTAGGTGAAGTGTGGGAA
3649849 AATTT
1 AATTT
3649854 CGGAGTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (21 bp):
AATTTAGGTGAAGTGTGGGAA
Found at i:3651301 original size:16 final size:16
Alignment explanation
Indices: 3651250--3651302 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
3651240 AGTATAAATA
* *
3651250 AAAGTTTAAAAAAATC
1 AAAGTTTTAAAAAGTC
*
3651266 TACAAGTTTTCAACAAGTC
1 -A-AAGTTTT-AAAAAGTC
3651285 AAAGTTTTAAAAAGTC
1 AAAGTTTTAAAAAGTC
3651301 AA
1 AA
3651303 TGTGACACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.30
17 8 0.27
18 7 0.23
19 6 0.20
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.28
Consensus pattern (16 bp):
AAAGTTTTAAAAAGTC
Found at i:3651890 original size:20 final size:20
Alignment explanation
Indices: 3651716--3651952 Score: 171
Period size: 20 Copynumber: 11.8 Consensus size: 20
3651706 AAATGACCAA
**
3651716 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACGCGAAAGT
* *
3651735 CAAATTCGCAACACG-AATT
1 CAAATTCGCAACGCGAAAGT
* *
3651754 CAAATTTCGCAACTC--AGGTT
1 CAAA-TTCGCAACGCGAAAG-T
*
3651774 CCAAATTCGCAATGCGAAAGT
1 -CAAATTCGCAACGCGAAAGT
*
3651795 CAAATTCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGA-AAGT
*
3651815 CAAATTCGCAACACGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
3651835 CAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
3651855 TAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* **
3651875 TAAATTCGCAACGCG-ATTT
1 CAAATTCGCAACGCGAAAGT
* * *
3651894 TAAGATTCGCAACGTGATAGT
1 CAA-ATTCGCAACGCGAAAGT
** * *
3651915 CCAAAAGCACAACGCGATAGT
1 -CAAATTCGCAACGCGAAAGT
3651936 CAAAATTCGCAACGCGA
1 C-AAATTCGCAACGCGA
3651953 TTTAAGATTC
Statistics
Matches: 178, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
19 27 0.15
20 115 0.65
21 32 0.18
22 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:3668770 original size:26 final size:26
Alignment explanation
Indices: 3668734--3668783 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3668724 ATTCCCCATC
*
3668734 TTCTTTTTCTTCACTTTTCTTCTTCT
1 TTCTTTCTCTTCACTTTTCTTCTTCT
3668760 TTCTTTCTCTTCACTTTTCTTCTT
1 TTCTTTCTCTTCACTTTTCTTCTT
3668784 TTCCTCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (26 bp):
TTCTTTCTCTTCACTTTTCTTCTTCT
Found at i:3673593 original size:11 final size:11
Alignment explanation
Indices: 3673579--3673617 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
3673569 AGTGTTATAT
3673579 AAGCTTAAAGA
1 AAGCTTAAAGA
* *
3673590 AAGCTTATA-T
1 AAGCTTAAAGA
3673600 AAGCTTAAAGA
1 AAGCTTAAAGA
3673611 AAGCTTA
1 AAGCTTA
3673618 TATAAGCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (11 bp):
AAGCTTAAAGA
Found at i:3673599 original size:21 final size:21
Alignment explanation
Indices: 3673573--3673629 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
3673563 TATTTGAGTG
3673573 TTATATAAGCTTAAAGAAAGC
1 TTATATAAGCTTAAAGAAAGC
3673594 TTATATAAGCTTAAAGAAAGC
1 TTATATAAGCTTAAAGAAAGC
3673615 TTATATAAGCTTAAA
1 TTATATAAGCTTAAA
3673630 ACACCAAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (21 bp):
TTATATAAGCTTAAAGAAAGC
Found at i:3673605 original size:10 final size:10
Alignment explanation
Indices: 3673573--3673627 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
3673563 TATTTGAGTG
3673573 TTATATAAGC
1 TTATATAAGC
* *
3673583 TTAAAGAAAGC
1 TTATA-TAAGC
3673594 TTATATAAGC
1 TTATATAAGC
* *
3673604 TTAAAGAAAGC
1 TTATA-TAAGC
3673615 TTATATAAGC
1 TTATATAAGC
3673625 TTA
1 TTA
3673628 AAACACCAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (10 bp):
TTATATAAGC
Found at i:3677733 original size:26 final size:26
Alignment explanation
Indices: 3677699--3677748 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3677689 ATAAGAGGAA
3677699 AAGAAGAAAACTGAAGAGAAAGAAAG
1 AAGAAGAAAACTGAAGAGAAAGAAAG
*
3677725 AAGAAGAAAAGTGAAGAGAAAGAA
1 AAGAAGAAAACTGAAGAGAAAGAA
3677749 GATGGGGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.66, C:0.02, G:0.28, T:0.04
Consensus pattern (26 bp):
AAGAAGAAAACTGAAGAGAAAGAAAG
Found at i:3680056 original size:3 final size:3
Alignment explanation
Indices: 3680048--3680082 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3680038 ATTAAAATTG
3680048 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3680083 TAGGATGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3680755 original size:2 final size:2
Alignment explanation
Indices: 3680748--3680773 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3680738 TAACCTAAGA
3680748 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
3680774 ACACACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3687798 original size:182 final size:184
Alignment explanation
Indices: 3687441--3687808 Score: 686
Period size: 183 Copynumber: 2.0 Consensus size: 184
3687431 ATTAAAATAG
* *
3687441 TTCGTTTGGAAAAGCATTCCTGTAACCCTTATATAGTTTTTTTTTTCTGTTTCTTAGATAACTAT
1 TTCGTTTGGAAAAGCATTCCTGTAACCCTTATAAAGTTTTTTTTTCCTGTTTCTTAGATAACTAT
3687506 TTTATTCACCAATACTTATAAGAGAAATATCATATTTATGTAATTATTTTTTATTTTTTATTTCA
66 TTTATTCACCAATACTTATAAGAGAAATATCATATTTATGTAATTATTTTTTATTTTTTATTTCA
3687571 TCCTGTAGTTTTAAATATTAGTTATATATTTAATAAAATTAATGGATATTATTA
131 TCCTGTAGTTTTAAATATTAGTTATATATTTAATAAAATTAATGGATATTATTA
*
3687625 TTCGTTTGGAAAAGCATTCCTGTAACCCTTATAAAG-TTTTTTTTCCTGTTTCTTATATAACTAT
1 TTCGTTTGGAAAAGCATTCCTGTAACCCTTATAAAGTTTTTTTTTCCTGTTTCTTAGATAACTAT
*
3687689 TTTATTCACCAATACTTATAAGAGAAATGTCATATTTATGTAATTATTTTTTATTTTTTATTTCA
66 TTTATTCACCAATACTTATAAGAGAAATATCATATTTATGTAATTATTTTTTATTTTTTATTTCA
3687754 TCC-GTAGTTTTAAATATTAGTTATATATTTAATAAAATTAATGGATATTATTA
131 TCCTGTAGTTTTAAATATTAGTTATATATTTAATAAAATTAATGGATATTATTA
3687807 TT
1 TT
3687809 AAATATTTGT
Statistics
Matches: 180, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
182 52 0.29
183 93 0.52
184 35 0.19
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.50
Consensus pattern (184 bp):
TTCGTTTGGAAAAGCATTCCTGTAACCCTTATAAAGTTTTTTTTTCCTGTTTCTTAGATAACTAT
TTTATTCACCAATACTTATAAGAGAAATATCATATTTATGTAATTATTTTTTATTTTTTATTTCA
TCCTGTAGTTTTAAATATTAGTTATATATTTAATAAAATTAATGGATATTATTA
Found at i:3696496 original size:23 final size:23
Alignment explanation
Indices: 3696461--3696559 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
3696451 AAATGCACGA
*
3696461 AGTGCCACATAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
* *
3696484 AGTGCCGCGTAGAATTGCACTGT
1 AGTGCCACGTAGAATTGCACCGT
3696507 AGTGCCACGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
*
3696530 AGTGTCACGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
3696553 AGTGCCA
1 AGTGCCA
3696560 TATAATAATG
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCGT
Found at i:3696700 original size:103 final size:103
Alignment explanation
Indices: 3696575--3696792 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
3696565 TAATGTCCAT
* *
3696575 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3696640 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
3696678 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3696743 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3696781 AAGGACCACATA
1 AAGGACCACATA
3696793 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3701224 original size:20 final size:21
Alignment explanation
Indices: 3701199--3701237 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3701189 CAGAACCCCA
3701199 GGGGGG-ATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3701219 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3701238 TCAAGGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.10, C:0.26, G:0.41, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3701273 original size:17 final size:18
Alignment explanation
Indices: 3701243--3701276 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3701233 CCCCTTCAAG
*
3701243 GGGGAATCGGTTCCCTCA
1 GGGGAATCGATTCCCTCA
3701261 GGGG-ATCGATTCCCTC
1 GGGGAATCGATTCCCTC
3701277 TGCACCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.24
Consensus pattern (18 bp):
GGGGAATCGATTCCCTCA
Found at i:3707377 original size:21 final size:20
Alignment explanation
Indices: 3707353--3707392 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3707343 TTTTGTTCGT
*
3707353 TTGAAGGGGTATCGGTTCCTC
1 TTGAAGGGGTA-CGATTCCTC
*
3707374 TTGAATGGGTACGATTCCT
1 TTGAAGGGGTACGATTCCT
3707393 TGCCCAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.35
Consensus pattern (20 bp):
TTGAAGGGGTACGATTCCTC
Found at i:3711637 original size:23 final size:23
Alignment explanation
Indices: 3711607--3711735 Score: 213
Period size: 23 Copynumber: 5.6 Consensus size: 23
3711597 TTCATATAAA
3711607 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCGCGTAGAAT
3711630 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCGCGTAGAAT
* *
3711653 TGCACCATAGTGCCGCATAGAAT
1 TGCACCGTAGTGCCGCGTAGAAT
* *
3711676 TGCACTGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCGCGTAGAAT
*
3711699 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCGCGTAGAAT
3711722 TGCACCGTAGTGCC
1 TGCACCGTAGTGCC
3711736 ATATAATAAT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 99 1.00
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.22
Consensus pattern (23 bp):
TGCACCGTAGTGCCGCGTAGAAT
Found at i:3711920 original size:102 final size:101
Alignment explanation
Indices: 3711752--3711968 Score: 328
Period size: 102 Copynumber: 2.1 Consensus size: 101
3711742 TAATGTCCAT
* * * *
3711752 AAGGACCAAATATCATTCCTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACCAG
1 AAGGACCACATATCATTCCTAAGAATCATATACATATACCAAGGATCAAGTA-GTGTCTCACCAG
*
3711817 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 ACTTCACACATGTTCCAAAGAATACATATAGGTCCCG
*
3711854 AAGGACCACATATCATTCCTTAAGAATCAATATACATATGCCAAGGATCAAGTA-TGTCTCACCA
1 AAGGACCACATATCATTCC-TAAGAATC-ATATACATATACCAAGGATCAAGTAGTGTCTCACCA
*
3711918 GACTTCACACATGTTCCAAAGAATACATATAGGTCTCG
64 GACTTCACACATGTTCCAAAGAATACATATAGGTCCCG
3711956 AAGGACCCACATA
1 AAGGA-CCACATA
3711969 GACCTCGACT
Statistics
Matches: 105, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
102 68 0.65
103 15 0.14
104 22 0.21
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (101 bp):
AAGGACCACATATCATTCCTAAGAATCATATACATATACCAAGGATCAAGTAGTGTCTCACCAGA
CTTCACACATGTTCCAAAGAATACATATAGGTCCCG
Found at i:3713132 original size:21 final size:21
Alignment explanation
Indices: 3713108--3713152 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3713098 TTTTGTTCGT
* *
3713108 TTGAAGGGGTATCGGTTCCTC
1 TTGAAGGGGTATCGATTCCCC
*
3713129 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
3713150 TTG
1 TTG
3713153 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:0.20, G:0.29, T:0.36
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:3713751 original size:2 final size:2
Alignment explanation
Indices: 3713744--3713791 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3713734 GATTATGCAG
3713744 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
3713786 AT AT AT
1 AT AT AT
3713792 TATTTGCTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3718204 original size:23 final size:24
Alignment explanation
Indices: 3718169--3718213 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
3718159 ATCATTTTAT
3718169 AAATCAATTAAAAAAGA-AGAAGA
1 AAATCAATTAAAAAAGATAGAAGA
*
3718192 AAAT-AATTCAAAACAGATAGAA
1 AAATCAATT-AAAAAAGATAGAA
3718214 TTAATGGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.16
Consensus pattern (24 bp):
AAATCAATTAAAAAAGATAGAAGA
Found at i:3722345 original size:185 final size:185
Alignment explanation
Indices: 3722033--3722402 Score: 722
Period size: 185 Copynumber: 2.0 Consensus size: 185
3722023 TATCCAGATT
3722033 CACAATTTAATATAAAAAAACTGACCAGTGATAAAATTAGTATATGACTGCTCATTGAAAGATAT
1 CACAATTTAATATAAAAAAACTGACCAGTGATAAAATTAGTATATGACTGCTCATTGAAAGATAT
3722098 AAAGTTGCAGAGTATTAACGTCTGATTGAATTGCTTAATTATTTGAAACTTAACACATGTCAGTC
66 AAAGTTGCAGAGTATTAACGTCTGATTGAATTGCTTAATTATTTGAAACTTAACACATGTCAGTC
3722163 AAATTTACTGAGGAAACAGTTCCATTTTCAAATACTAATGACACAAGCAAACAGA
131 AAATTTACTGAGGAAACAGTTCCATTTTCAAATACTAATGACACAAGCAAACAGA
3722218 CACAATTTAATATAAAAAAACTGACCAGTGATAAAATTAGTATATGACTGCTCATTGAAAGATAT
1 CACAATTTAATATAAAAAAACTGACCAGTGATAAAATTAGTATATGACTGCTCATTGAAAGATAT
3722283 AAAGTTGCAGAGTATTAACGTCTGATTGAATTGCTTAATTATTTGAAACTTAACACATGTCAGTC
66 AAAGTTGCAGAGTATTAACGTCTGATTGAATTGCTTAATTATTTGAAACTTAACACATGTCAGTC
* *
3722348 AAATTTATTGAGGAAACAGTTCCATTTTCAAATCCTAATGACACAAGCAAACAGA
131 AAATTTACTGAGGAAACAGTTCCATTTTCAAATACTAATGACACAAGCAAACAGA
3722403 TCAATAAGAA
Statistics
Matches: 183, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 183 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (185 bp):
CACAATTTAATATAAAAAAACTGACCAGTGATAAAATTAGTATATGACTGCTCATTGAAAGATAT
AAAGTTGCAGAGTATTAACGTCTGATTGAATTGCTTAATTATTTGAAACTTAACACATGTCAGTC
AAATTTACTGAGGAAACAGTTCCATTTTCAAATACTAATGACACAAGCAAACAGA
Found at i:3726889 original size:26 final size:26
Alignment explanation
Indices: 3726860--3726929 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 26
3726850 CTATAATCAC
3726860 TTGAATTTGCCTTCATTCAAGGAACT
1 TTGAATTTGCCTTCATTCAAGGAACT
3726886 TTGAATGTGGTCTGGCCTTCATTCAAGGAACT
1 TTGAA--T--T-T-GCCTTCATTCAAGGAACT
3726918 TTGAATTTGCCT
1 TTGAATTTGCCT
3726930 ATAATCACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
26 9 0.24
27 1 0.03
28 2 0.05
30 2 0.05
31 1 0.03
32 23 0.61
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (26 bp):
TTGAATTTGCCTTCATTCAAGGAACT
Found at i:3732954 original size:29 final size:30
Alignment explanation
Indices: 3732908--3732971 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
3732898 CTATTTTTGT
* *
3732908 CCCTAGAATTTTATAAGTTTAAGTTCG-CC
1 CCCTAGAATTTTAAAAGTTCAAGTTCGTCC
3732937 CCCTAGAATTTTAAAAGTTCAAGTTCGTCC
1 CCCTAGAATTTTAAAAGTTCAAGTTCGTCC
3732967 CCCTA
1 CCCTA
3732972 ACATTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (30 bp):
CCCTAGAATTTTAAAAGTTCAAGTTCGTCC
Found at i:3734163 original size:23 final size:21
Alignment explanation
Indices: 3734104--3734167 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
3734094 ATTATCCAAT
* * *
3734104 AAACTTCACATCCATAAT-AC
1 AAACTTGAAATCCATAATAAA
3734124 AAACTTGAAATCCATAATAAA
1 AAACTTGAAATCCATAATAAA
3734145 AAACTTGAAATCCCAATAATAAA
1 AAACTTGAAAT-CC-ATAATAAA
3734168 TCAAAGTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.42
21 12 0.32
22 2 0.05
23 8 0.21
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.23
Consensus pattern (21 bp):
AAACTTGAAATCCATAATAAA
Found at i:3738267 original size:41 final size:40
Alignment explanation
Indices: 3738205--3738394 Score: 222
Period size: 41 Copynumber: 4.7 Consensus size: 40
3738195 AATGCCATTA
* *
3738205 TATGAGTCATATTA-CGGCGTTTATAGAAAAACGCTACTAAAG
1 TATGAGTC-T-TTAGCGGCGTTTGTATAAAAACGC-ACTAAAG
*
3738247 TATGAGTCTTTAGCGGCGTTTGTCTAAAAACGCCACTAAAG
1 TATGAGTCTTTAGCGGCGTTTGTATAAAAACG-CACTAAAG
* * *
3738288 TACGAGTCTTTAGCGGCCTTTGTCTAAAAACGCACTAAAG
1 TATGAGTCTTTAGCGGCGTTTGTATAAAAACGCACTAAAG
*
3738328 TATGAGT-TTATAGCGGCGTTTGTACAAAAACGACACTAAAG
1 TATGAGTCTT-TAGCGGCGTTTGTATAAAAACG-CACTAAAG
* * *
3738369 TACGAGTCTTTAGTGGCGTTTATATA
1 TATGAGTCTTTAGCGGCGTTTGTATA
3738395 TAAAGTACAG
Statistics
Matches: 130, Mismatches: 13, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
39 2 0.02
40 36 0.28
41 81 0.62
42 11 0.08
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (40 bp):
TATGAGTCTTTAGCGGCGTTTGTATAAAAACGCACTAAAG
Found at i:3738331 original size:81 final size:82
Alignment explanation
Indices: 3738231--3738381 Score: 254
Period size: 81 Copynumber: 1.9 Consensus size: 82
3738221 GCGTTTATAG
*
3738231 AAAAACGCTACTAAAGTATGAGTCTT-TAGCGGCGTTTGT-CTAAAAACGCCACTAAAGTACGAG
1 AAAAACGCTACTAAAGTATGAGT-TTATAGCGGCGTTTGTAC-AAAAACGACACTAAAGTACGAG
3738294 TCTTTAGCGGCCTTTGTCT
64 TCTTTAGCGGCCTTTGTCT
3738313 AAAAACGC-ACTAAAGTATGAGTTTATAGCGGCGTTTGTACAAAAACGACACTAAAGTACGAGTC
1 AAAAACGCTACTAAAGTATGAGTTTATAGCGGCGTTTGTACAAAAACGACACTAAAGTACGAGTC
3738377 TTTAG
66 TTTAG
3738382 TGGCGTTTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
80 2 0.03
81 55 0.83
82 9 0.14
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (82 bp):
AAAAACGCTACTAAAGTATGAGTTTATAGCGGCGTTTGTACAAAAACGACACTAAAGTACGAGTC
TTTAGCGGCCTTTGTCT
Found at i:3744973 original size:84 final size:83
Alignment explanation
Indices: 3744874--3745029 Score: 208
Period size: 83 Copynumber: 1.9 Consensus size: 83
3744864 ACGACACATG
*
3744874 AATGTGTGTCATCTTT-TCTAATGACGTGTGCTTCAATGACACACAATGTA-AGTCATAAATGCG
1 AATGTGTGTCATCTTTAT-TAATGACG-GGGCTTCAATGACACACAATG-AGAGTCATAAATGCG
3744937 TGTCATAAATTATGACACACA
63 TGTCATAAATTATGACACACA
* * * * * *
3744958 AATGTTTGTCTTCTTTATTTATGACGGGGCTTCAATGACGCGCAATGAGCGTCATAAATGCGTGT
1 AATGTGTGTCATCTTTATTAATGACGGGGCTTCAATGACACACAATGAGAGTCATAAATGCGTGT
3745023 CATAAAT
66 CATAAAT
3745030 GCGCGTCATA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
82 1 0.02
83 40 0.63
84 21 0.33
85 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (83 bp):
AATGTGTGTCATCTTTATTAATGACGGGGCTTCAATGACACACAATGAGAGTCATAAATGCGTGT
CATAAATTATGACACACA
Found at i:3745024 original size:13 final size:13
Alignment explanation
Indices: 3745001--3745039 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3744991 AATGACGCGC
*
3745001 AATGAGCGTCATA
1 AATGCGCGTCATA
*
3745014 AATGCGTGTCATA
1 AATGCGCGTCATA
3745027 AATGCGCGTCATA
1 AATGCGCGTCATA
3745040 GATTTATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:3745999 original size:19 final size:20
Alignment explanation
Indices: 3745958--3745999 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
3745948 ATTAGTTTCA
* **
3745958 ATTTAATATATATATAATGT
1 ATTTAATATATAAATAAAAT
3745978 ATTTAA-ATATAAATAAAAT
1 ATTTAATATATAAATAAAAT
3745997 ATT
1 ATT
3746000 ATATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTTAATATATAAATAAAAT
Found at i:3757002 original size:587 final size:592
Alignment explanation
Indices: 3755836--3757014 Score: 1492
Period size: 587 Copynumber: 2.0 Consensus size: 592
3755826 TTACACATTA
* *
3755836 TGCACAGACAGGACGACTGAAACCTCTGGGCAAAACATGGGTACTAACTTCTAAATCAAACACTA
1 TGCACAGACAGGACGACTGAAACCTCTAGGCAAAACATGAGTACTAACTTCTAAATCAAACACTA
* * *
3755901 AAAGGTCTCCTCCGAGTCTCAGATCTACCCCCTCAATCCAAACTTTGTCCAGTCCTCAATTGTAC
66 AAAGGTCTCCTCCGAGTCTCAGATCTACCCCCTCAATCCAAACTCTATACAGTCCTCAATTGTAC
** * * *
3755966 TGTTGAGGGTATTGACAAACCCTGATTATCTCGAGCCCTCTTGGCCAGAGTCTAAGATGTCCTCG
131 TACTGAGGGTATCGACAAACCCTGACTATCTCGAGCCCTCTTGGCCAGAGTCTAAGATG--CGCG
* * * * * **
3756031 CTAACTGAGAGGCTCTGTCTTAAAGTCTCCCTGAACTATCTAGCATATTTATCTAAACCTCTCTC
194 CTAACTGAGAGGCTATGTCCTAAAGTCTCCATGAACTACCTACCATACCTATCTAAACCTCTCTC
*
3756096 CACTACTTCAGCCTGGTGGGTCATTTGGGAGAAGACCCTGAGAGGGTCGACTATAAGATGTGATA
259 CACTACTTCAGCCTGGTGGGTCAATTGGGAGAAGACCCTGAGAGGGTCGACTATAAGATGTGATA
* ** * *
3756161 AAATATCACCACGAAGGCCCTCTCTAAACCGATAACAACAACGTTCTTCTGTCGGGATCAATTCT
324 AAATATCACCACGAAGGCCATCTCTAAACCGATAACAACAACACTATTCTATCGGGATCAATTCT
3756226 GCAGCATACTTACTGAGCTTGAGGAACTCTTACTCCATCACTGAATGGTTACCCTGAGTCAAGTA
389 GCAG-ATAC-TACTGAGCTTGAGGAACTCTTACTCCATCACTGAATGGTTACCCTGAGTCAAGTA
* * * * *
3756291 CAAGAACTGCTCCATTAAGTCATCGGTATAAGTCTACCTAATGTACTTCAATATAAACTTCGAGA
452 CAAGAACTGCTCCATCAAGACATCGGTATAAGTCTACCTAATGTAATCCAATATAAACTTCGAAA
* ** * *
3756356 GGAACTACTCCCAAATCAACCTATCTGGCTCCATAGCCTTCTCGATTGTCTCCCACCAATCTATG
517 GGAACTACTCCCAAATCAACCTATCTGACTCCATAGCCGCCTCGATTATCTCCCACCAATCTATA
3756421 GCGTCACACTG
582 GCGTCACACTG
* * *
3756432 TGCACAGATAGGACGAGTGAAACCTCTAGGCAAAACGTGAGTACTAAC-TCTTAAATCAAACACT
1 TGCACAGACAGGACGACTGAAACCTCTAGGCAAAACATGAGTACTAACTTC-TAAATCAAACACT
* * * *
3756496 AAAA-GTTTCCTTCGGGTCTCAGATCTA-CCCCTTAATCCAAACTCTATACAGTCCTCCTTAATT
65 AAAAGGTCTCCTCCGAGTCTCAGATCTACCCCCTCAATCCAAACTCTATACAGTCCT-C--AATT
* *
3756559 GTACTACTGAGGGTCTCGACAAACCCTGACTGTCTC-AGGCCCTC-TGGCCAGAGTCTAAGATG-
127 GTACTACTGAGGGTATCGACAAACCCTGACTATCTCGA-GCCCTCTTGGCCAGAGTCTAAGATGC
* *
3756621 GC-CT-ACTGAGAGGCTATGTCCTAAAGTCTCCATGAACTGCCTACCCTACCTATCTAAACCTCT
191 GCGCTAACTGAGAGGCTATGTCCTAAAGTCTCCATGAACTACCTACCATACCTATCTAAACCTCT
* *
3756684 CTCCACTACTATC-TCCTGGTGGGTCAATTGGGAG-AGACCC-GAGAGGGTCGACTGTAAGATGT
256 CTCCACTACT-TCAGCCTGGTGGGTCAATTGGGAGAAGACCCTGAGAGGGTCGACTATAAGATGT
* *
3756746 GAT-AAA-ATCACCACGAATGCCATCTCTGAACCGATAACAACAACACTATTCTATCGGGATCAA
320 GATAAAATATCACCACGAAGGCCATCTCTAAACCGATAACAACAACACTATTCTATCGGGATCAA
* * * *
3756809 TTTTGTAG-TA-TACTTAGCTTGAGGAACTCTCACTTTTACTCCATCATTGAATGGTTACCCTGA
385 TTCTGCAGATACTACTGAGCTTGAGGAA--CT--C--TTACTCCATCACTGAATGGTTACCCTGA
* * * * * *
3756872 GTCAGGTGCAAGAACTGCTCCATCAAGACATCGGTGTAAGTTTA-C-AATGTAATCCAGTCTAAA
444 GTCAAGTACAAGAACTGCTCCATCAAGACATCGGTATAAGTCTACCTAATGTAATCCAATATAAA
* * *** * * * *
3756935 CTTCGAAAGGAACTGCTCCCAAGTTGGCCTCTCTGATTCTATAGCCGCCTCGATTATCTCTCACC
509 CTTCGAAAGGAACTACTCCCAAATCAACCTATCTGACTCCATAGCCGCCTCGATTATCTCCCACC
3757000 AATCTATAGCGTCAC
574 AATCTATAGCGTCAC
3757015 CCTTGAGTAG
Statistics
Matches: 504, Mismatches: 67, Indels: 33
0.83 0.11 0.05
Matches are distributed among these distances:
583 15 0.03
585 4 0.01
587 136 0.27
588 4 0.01
589 89 0.18
590 6 0.01
591 79 0.16
592 4 0.01
593 1 0.00
594 24 0.05
595 23 0.05
596 79 0.16
597 40 0.08
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (592 bp):
TGCACAGACAGGACGACTGAAACCTCTAGGCAAAACATGAGTACTAACTTCTAAATCAAACACTA
AAAGGTCTCCTCCGAGTCTCAGATCTACCCCCTCAATCCAAACTCTATACAGTCCTCAATTGTAC
TACTGAGGGTATCGACAAACCCTGACTATCTCGAGCCCTCTTGGCCAGAGTCTAAGATGCGCGCT
AACTGAGAGGCTATGTCCTAAAGTCTCCATGAACTACCTACCATACCTATCTAAACCTCTCTCCA
CTACTTCAGCCTGGTGGGTCAATTGGGAGAAGACCCTGAGAGGGTCGACTATAAGATGTGATAAA
ATATCACCACGAAGGCCATCTCTAAACCGATAACAACAACACTATTCTATCGGGATCAATTCTGC
AGATACTACTGAGCTTGAGGAACTCTTACTCCATCACTGAATGGTTACCCTGAGTCAAGTACAAG
AACTGCTCCATCAAGACATCGGTATAAGTCTACCTAATGTAATCCAATATAAACTTCGAAAGGAA
CTACTCCCAAATCAACCTATCTGACTCCATAGCCGCCTCGATTATCTCCCACCAATCTATAGCGT
CACACTG
Found at i:3758601 original size:13 final size:13
Alignment explanation
Indices: 3758583--3758609 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3758573 TGGTTAAGGC
3758583 AGTATCGATACTT
1 AGTATCGATACTT
3758596 AGTATCGATACTT
1 AGTATCGATACTT
3758609 A
1 A
3758610 AGGATGAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
AGTATCGATACTT
Found at i:3762219 original size:67 final size:69
Alignment explanation
Indices: 3762107--3762356 Score: 396
Period size: 70 Copynumber: 3.6 Consensus size: 69
3762097 TTTTTAAAAA
* * *
3762107 AAAACAATCCCACATGGCTAAGAAACATAGAAGAACATCCTAAAAGTTTAAAGA-AAAAGTATGA
1 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAGACAAAAATATGA
3762171 G-AC
66 GAAC
* * * *
3762174 AAAACAATCACACATGACTAAGAAACATAGAAGAGCACCCCAAAAGTTTAAAGAGTAAAAATATG
1 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAGA-CAAAAATATG
3762239 AGAAC
65 AGAAC
3762244 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAGAACAAAAATATG
1 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAG-ACAAAAATATG
3762309 AGAAC
65 AGAAC
*
3762314 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAA
1 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAA
3762357 CTTACTTCTA
Statistics
Matches: 168, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
67 49 0.29
69 10 0.06
70 108 0.64
71 1 0.01
ACGTcount: A:0.52, C:0.18, G:0.14, T:0.15
Consensus pattern (69 bp):
AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAGACAAAAATATGA
GAAC
Found at i:3772384 original size:24 final size:24
Alignment explanation
Indices: 3772352--3772400 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3772342 GATCGGAAAG
3772352 AATGAGCTTACATAGTCGTTGATC
1 AATGAGCTTACATAGTCGTTGATC
3772376 AATGAGCTTACATAGTCGTTGATC
1 AATGAGCTTACATAGTCGTTGATC
3772400 A
1 A
3772401 CTTTAGGCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (24 bp):
AATGAGCTTACATAGTCGTTGATC
Found at i:3780053 original size:2 final size:2
Alignment explanation
Indices: 3780046--3780098 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3780036 AGATGCACAT
3780046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3780088 TA TA TA TA TA T
1 TA TA TA TA TA T
3780099 GGGTATAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3784420 original size:35 final size:36
Alignment explanation
Indices: 3784381--3784448 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
3784371 TAATAACGTA
* * *
3784381 TATGGTTTTTTAACGATATGCACCTATA-ATATGTG
1 TATGGTTTTTGAACAACATGCACCTATATATATGTG
*
3784416 TATGGTTTTTGAACAACATGCAGCTATATATAT
1 TATGGTTTTTGAACAACATGCACCTATATATAT
3784449 ATATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (36 bp):
TATGGTTTTTGAACAACATGCACCTATATATATGTG
Found at i:3784557 original size:20 final size:20
Alignment explanation
Indices: 3784532--3784581 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
3784522 TCAGATGCAG
3784532 ATGTCTGTATCCCCATAATC
1 ATGTCTGTATCCCCATAATC
3784552 ATGTCTGTATCCCCATAATC
1 ATGTCTGTATCCCCATAATC
*
3784572 TTGTCTGTAT
1 ATGTCTGTAT
3784582 ATGCTGCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTCTGTATCCCCATAATC
Found at i:3786208 original size:23 final size:23
Alignment explanation
Indices: 3786173--3786231 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
3786163 ATCAAGTACA
* *
3786173 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
3786196 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
3786219 ATAATAAAATAGG
1 ATAATATAATAGG
3786232 CATTTAACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:3786305 original size:87 final size:87
Alignment explanation
Indices: 3786145--3786307 Score: 247
Period size: 87 Copynumber: 1.9 Consensus size: 87
3786135 TATGTTATAT
**
3786145 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATACAT
*
3786210 AGCGCTTATATAATAAAATAGG
66 AGCACTTATATAATAAAATAGG
* * *
3786232 CATTTAACCGGAAATATTATCATA-TATAATAACATATTAGGTAGCGCTTATATAATGTAATACA
1 CATTTAACCAGAAATATTATCA-AGTACAATAACATATTAGGTAGCGCTTATATAATATAATACA
*
3786296 TATCACTTATAT
65 TAGCACTTATAT
3786308 TTACCTATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 67 0.99
88 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (87 bp):
CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATACAT
AGCACTTATATAATAAAATAGG
Found at i:3786764 original size:201 final size:200
Alignment explanation
Indices: 3786325--3786828 Score: 744
Period size: 201 Copynumber: 2.5 Consensus size: 200
3786315 TTTTCTAACT
* * * * * **
3786325 AAACCAGTATATTTATATATGTAACATTGCAAATTTACCTATTACATTATAATTATAAGTTTCGA
1 AAACCGGTATATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
3786390 TGTTTTTGAGATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCAT
66 TGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCAT
* *
3786453 TCATTCTGGAAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTTT
130 TCATTCTGGAAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACATATTCT
3786518 CTCATA
195 CTCATA
* * * * *
3786524 AAACCGGTATATTTCTACTGGGTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTTGA
1 AAACCGGTATATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
3786589 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATT
66 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATT
* * * * *
3786654 CATTTTGGACAAAATGTATCGACACAAA-TTGAAAAAAGTGTCGATACATTCTGTTGACATATTC
131 CATTCTGGAAAAAAAGTATCGACACAAACTT--AAAAAGTGTCGATACATTATGTAGACATATTC
3786718 TCTCATA
194 TCTCATA
*
3786725 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
3786790 TATTTTTGGGATCGATACTTTTAATAAATGTATCGACAC
66 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACAC
3786829 ATATATTTAT
Statistics
Matches: 273, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
198 3 0.01
199 72 0.26
200 65 0.24
201 133 0.49
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (200 bp):
AAACCGGTATATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATT
CATTCTGGAAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACATATTCTC
TCATA
Found at i:3792134 original size:20 final size:20
Alignment explanation
Indices: 3792109--3792149 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3792099 TTAAAATCAG
3792109 TGTATATCTACCGATTACAT
1 TGTATATCTACCGATTACAT
* *
3792129 TGTATATTTACCTATTACAT
1 TGTATATCTACCGATTACAT
3792149 T
1 T
3792150 ATAATTATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.46
Consensus pattern (20 bp):
TGTATATCTACCGATTACAT
Found at i:3792171 original size:198 final size:197
Alignment explanation
Indices: 3791740--3792205 Score: 600
Period size: 197 Copynumber: 2.4 Consensus size: 197
3791730 ATTTATACCG
3791740 GTTACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATC
1 GTTACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATC
* ** * * *
3791805 GACACTTTATGCGTGCACCTCATTTGGCTTTTATTCTGGTCAAAATGTATCGACACAATTTAAAA
66 GACACTTTATGCGTGCACCTCATTGGGAATTCATTCTGGACAAAAAGTATCGACACAATTTAAAA
* *
3791870 AGTATAGATAAATTATACTGACCTATTTTCTAATTAACCAATATATTTCTACCGGTTACATTGTA
131 AGTATAGATAAATTATACTGACCTATTTTCTAATTAACCAATATATATCTACCGATTACATTGTA
3791935 AA
196 AA
*
3791937 GTTACATATTACATTATAATTATGGGTTTCGATG-TTTTGGGATCGATACAA-TTTAAATGTATT
1 GTTACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATC
* * *
3792000 GACACTTTATGTGTGCACCTCGTTGGGAATTCATTCTGGACAAAAAAGTATCGACACAAATTTAT
66 GACACTTTATGCGTGCACCTCATTGGGAATTCATTCTGGAC-AAAAAGTATCGACAC-AATTTAA
* * * * * * * *
3792065 AAAGTGTTGATACATTAT-GTAGACCTATTTTCT-CTTAAAATCAGTGTATATCTACCGATTACA
129 AAAGTATAGATAAATTATACT-GACCTATTTTCTAATT--AACCAATATATATCTACCGATTACA
*
3792128 TTGTATA
191 TTGTAAA
* * * * *
3792135 TTTACCTATTACATTATAATTATCGGTTTTGATGTTTTTGGGATCGATAC-TTTTAATAAATGTA
1 GTTACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACAATTT--TAAATGTA
3792199 TCGACAC
64 TCGACAC
3792206 ATTTGTTTAC
Statistics
Matches: 233, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
195 45 0.19
196 34 0.15
197 67 0.29
198 56 0.24
199 17 0.07
201 14 0.06
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (197 bp):
GTTACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATC
GACACTTTATGCGTGCACCTCATTGGGAATTCATTCTGGACAAAAAGTATCGACACAATTTAAAA
AGTATAGATAAATTATACTGACCTATTTTCTAATTAACCAATATATATCTACCGATTACATTGTA
AA
Found at i:3796491 original size:22 final size:22
Alignment explanation
Indices: 3796463--3796508 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3796453 GTTACATTAG
3796463 AACACAAACACATTAAGGAAAA
1 AACACAAACACATTAAGGAAAA
3796485 AACACAAACACATTAAGGAAAA
1 AACACAAACACATTAAGGAAAA
3796507 AA
1 AA
3796509 AAGAGTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.65, C:0.17, G:0.09, T:0.09
Consensus pattern (22 bp):
AACACAAACACATTAAGGAAAA
Found at i:3797129 original size:200 final size:201
Alignment explanation
Indices: 3796718--3797876 Score: 1559
Period size: 200 Copynumber: 5.8 Consensus size: 201
3796708 TGAAATTTAG
* * * *
3796718 AAAAA-TATCGACACAAATTTAAAAAGTTTTGATATATTATGTTGACCGCTTTTCTAATTAAACC
1 AAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
*
3796782 GGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * *
3796847 TTGGGATCGATACAATTT-TAAATGTATCGACACTTTATGCGTACACCTCGTTTGGGCATTGATT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATT
3796911 CTGGAC
196 CTGGAC
* * *
3796917 AAAAATTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAATC
1 AAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
*
3796982 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* *
3797047 TTGGGATCGATACATTTTATAAATGTATCGAAACTTTATGCTTGCACCTCGTTTGGGCATTCATT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATT
3797112 CTGGAC
196 CTGGAC
* *** * * ** * *
3797118 -AAAAGTATCGACACAAATTCCACTTGTGTCGATATATTATGTAGACCTATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
* * * * **
3797182 GGTATATATCTACTGGTTACATTTTAAATTTACCTATTACATTATAATTATATGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * * *
3797247 TTGGGATCGATATAATTT-TAAATGTATCGACAC-TTATTGCGTGCACCTCGTTTTGCCATTGAT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTA-TGCGTGCACCTCGTTTGGGCATTCAT
3797310 TCTGGAC
195 TCTGGAC
* * * * * *
3797317 AAAAAGTATCGACACAAATTAAAAAAATGTCGATACATTATGTT-AACTCTTTTATAATTAAATC
1 AAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
* ** * *
3797381 GATATATTTATACTTGTTATATTGTAGATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * *
3797446 TTGGGA-CGATACTTTTTATAAATGTATCGACACTTTATGCTTGGACCTCGTTTGGGCATTCATT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATT
3797510 CTGGAC
196 CTGGAC
* * * * *
3797516 AAAAAGTATCGACATAAATTCCACATGTGTCGATACATTATATTGACCGCTTTTCTAATTAAACC
1 AAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
* * * * *
3797581 GGAATATTTATACAGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAAAGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * *
3797646 TTTGGATCGATAC-TGTTTATAAATGTATCAACACTTTATGCGTGCACCTTGTTTGGGCATTCAT
131 TTGGGATCGATACAT-TTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCAT
3797710 TCTGGAC
195 TCTGGAC
* *
3797717 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCTG-TTTTCTAATT-AAC
1 AAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACC-GCTTTTCTAATTAAAC
* * *
3797780 CAGTATA-TTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGATGTT
65 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * *
3797844 TTTGGGGTCTATAC-TTTTAGAAAATATATCGAC
130 TTTGGGATCGATACATTTTA-TAAATGTATCGAC
3797877 GCATCTGTTT
Statistics
Matches: 840, Mismatches: 109, Indels: 22
0.87 0.11 0.02
Matches are distributed among these distances:
198 15 0.02
199 277 0.33
200 386 0.46
201 161 0.19
202 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (201 bp):
AAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATT
CTGGAC
Found at i:3797876 original size:599 final size:598
Alignment explanation
Indices: 3796718--3797876 Score: 1715
Period size: 599 Copynumber: 1.9 Consensus size: 598
3796708 TGAAATTTAG
* * * * * * *
3796718 AAAAATATCGACACAAATTTAAAAAGTTTTGATATATTATGTTGACCGCTTTTCTAATTAAACCG
1 AAAAATATCGACACAAATTAAAAAAATGTCGATACATTATGTTGAACGCTTTTATAATTAAACCG
*
3796783 GTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
66 ATATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
*
3796848 TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTACACCTCGTTTGGGCATTGATTCT
131 TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTACACCTCGTTTGGGCATTCATTCT
* * *
3796913 GGACAAAAATTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTA
196 GGACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATATTGACCGCTTTTCTAATTA
* * * ** *
3796978 AATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGAT
261 AACCGGAATATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAAA
*
3797043 GTTTTTGGGATCGATACATTTTATAAATGTATCGAAACTTTATGCTTGCACCTCGTTTGGGCATT
326 GTTTTTGGGATCGATACATTTTATAAATGTATCGAAACTTTATGCGTGCACCTCGTTTGGGCATT
** *
3797108 CATTCTGGACAAAAGTATCGACACAAATTCCACTTGTGTCGATATATTATGTAGACCTATTTTCT
391 CATTCTGGACAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTCT
* * * *
3797173 CATAAAACCGGTATATATCTACTGGTTACATTTTAAATTTACCTATTACATTATAATTATATGTT
456 AATAAAACCAGTATATATATACCGGTTACATTTTAAATTTACCTATTACATTATAATTATATGTT
*
3797238 TCGATGTTTTTGGGATCGATATAATTTTAAATGTATCGACACTTATTGCGTGCACCTCGTTTTGC
521 TCGATGTTTTTGGGATC-ATATAATTTTAAATATATCGACACTTATTGCGTGCACCTCGTTTTGC
3797303 CATTGATTCTGGAC
585 CATTGATTCTGGAC
* *
3797317 AAAAAGTATCGACACAAATTAAAAAAATGTCGATACATTATGTT-AACTCTTTTATAATTAAATC
1 AAAAA-TATCGACACAAATTAAAAAAATGTCGATACATTATGTTGAACGCTTTTATAATTAAACC
** *
3797381 GATATATTTATACTTGTTATATTGTAGATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
65 GATATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
** * **
3797446 TTGGGA-CGATACTTTTTATAAATGTATCGACACTTTATGCTTGGACCTCGTTTGGGCATTCATT
130 TTGGGATCGATACAATTT-TAAATGTATCGACACTTTATGCGTACACCTCGTTTGGGCATTCATT
* * * *
3797510 CTGGACAAAAAGTATCGACATAAATTCCACATGTGTCGATACATTATATTGACCGCTTTTCTAAT
194 CTGGACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATATTGACCGCTTTTCTAAT
*
3797575 TAAACCGGAATATTTATACAGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCA
259 TAAACCGGAATATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCA
* *
3797640 AAGTTTTTTGGATCGATAC-TGTTTATAAATGTATC-AACACTTTATGCGTGCACCTTGTTTGGG
324 AAGTTTTTGGGATCGATACAT-TTTATAAATGTATCGAA-ACTTTATGCGTGCACCTCGTTTGGG
* *
3797703 CATTCATTCTGGACAAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCTGT
387 CATTCATTCTGGAC-AAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTAT
*
3797768 TTTCTAAT-TAACCAGTATAT-TATACCGGTTACATTGTT-AATTTACCTATTACATTATAATTA
451 TTTCTAATAAAACCAGTATATATATACCGGTTACATT-TTAAATTTACCTATTACATTATAATTA
* *
3797830 T-TGGTTTCGATGTTTTTGGGGTC-TATACTTTTAGAAAATATATCGAC
515 TAT-GTTTCGATGTTTTTGGGATCATATAATTTT---AAATATATCGAC
3797877 GCATCTGTTT
Statistics
Matches: 501, Mismatches: 49, Indels: 20
0.88 0.09 0.04
Matches are distributed among these distances:
596 8 0.02
597 1 0.00
598 69 0.14
599 338 0.67
600 85 0.17
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (598 bp):
AAAAATATCGACACAAATTAAAAAAATGTCGATACATTATGTTGAACGCTTTTATAATTAAACCG
ATATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTACACCTCGTTTGGGCATTCATTCT
GGACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATATTGACCGCTTTTCTAATTA
AACCGGAATATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAAA
GTTTTTGGGATCGATACATTTTATAAATGTATCGAAACTTTATGCGTGCACCTCGTTTGGGCATT
CATTCTGGACAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTCT
AATAAAACCAGTATATATATACCGGTTACATTTTAAATTTACCTATTACATTATAATTATATGTT
TCGATGTTTTTGGGATCATATAATTTTAAATATATCGACACTTATTGCGTGCACCTCGTTTTGCC
ATTGATTCTGGAC
Found at i:3798335 original size:19 final size:19
Alignment explanation
Indices: 3798311--3798356 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
3798301 TCATCACATG
3798311 CAAAATTATAAATCGTATA
1 CAAAATTATAAATCGTATA
*
3798330 CAAAATTATAAATCTTATA
1 CAAAATTATAAATCGTATA
3798349 CAAAATTA
1 CAAAATTA
3798357 ACCCTACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (19 bp):
CAAAATTATAAATCGTATA
Found at i:3799924 original size:18 final size:18
Alignment explanation
Indices: 3799901--3799939 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3799891 TCCTCCTCAT
*
3799901 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTATTC
3799919 TTCCTCCATCTTTTATTC
1 TTCCTCCATCTTTTATTC
3799937 TTC
1 TTC
3799940 ATATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTATTC
Found at i:3800669 original size:22 final size:23
Alignment explanation
Indices: 3800641--3800696 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
3800631 AACCTGCATT
*
3800641 TATAATAAAAT-TTATCATTTTA
1 TATAATAAAATATTATCAGTTTA
*
3800663 TATAATAACTATATTATCAGTTTA
1 TATAATAA-AATATTATCAGTTTA
*
3800687 TATAAAAAAA
1 TATAATAAAA
3800697 CAAAAATGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (23 bp):
TATAATAAAATATTATCAGTTTA
Found at i:3803237 original size:181 final size:182
Alignment explanation
Indices: 3802621--3803462 Score: 1361
Period size: 182 Copynumber: 4.6 Consensus size: 182
3802611 TACGCGTACT
*
3802621 TATTAAAGTATCGACACTTTCAACATATCCAGTAGCGCTTTACC-GTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
*
3802685 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCAACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * * *
3802750 TTACATGCGCTATTACTGCTTCCCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
3802802 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
*
3802867 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGACACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
3802932 TTATAGGCGCTATTA-TTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTT-CTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *
3802984 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTATCAGTTTTGTCATTTCGAAACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
* * * *
3803049 ATTTTGTCTTATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATTGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
*
3803114 TTATAGGCTCTA-TACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
3803165 TATTAAAGTATCGACACTTTAAACATATCCGATAGTGTTTTACCAGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
**
3803230 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATTAATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
3803295 TTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
** * * *
3803347 T-TTCAATCTAATTGATACTTTCAACATATCCGGTAGCGCTTTACC-GTTTTTTTTCATTTCGAG
1 TATT-AAAGT-ATCGACACTTTCAACATATCCGGTAGCGCTTTACCAG--TTTTGTCATTTCGAG
* *
3803410 ACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTT
62 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
3803463 TATTTGTATC
Statistics
Matches: 612, Mismatches: 41, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
181 211 0.34
182 309 0.50
183 29 0.05
184 63 0.10
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:3803286 original size:363 final size:363
Alignment explanation
Indices: 3802621--3803462 Score: 1366
Period size: 363 Copynumber: 2.3 Consensus size: 363
3802611 TACGCGTACT
*
3802621 TATTAAAGTATCGACACTTTCAACATATCCAGTAGCGCTTTACCGTTTTGTCATTTCGAGACCGG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGTTTTGTCATTTCGAGACCGG
3802686 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCAACACTT
66 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCAACACTT
*
3802751 TACATGCGCTATTACTGCTTCCCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGA
131 TACAGGCGCTATTACTGCTTCCCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGA
* *
3802816 CACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATTT
196 CACTTTAAACATATCCGATAGCGCTTTACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATTT
*
3802881 TTACCTGTTATATTGTTATGGATCGACACATTTTTATAAAGTATCGACACTTTATAGGCGCTATT
261 TTACCTGTTATATTGTTATGGATCAACACATTTTTATAAAGTATCGACACTTTATAGGCGCTATT
3802946 A-TTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
326 ACTT-CTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *
3802984 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTATCAGTTTTGTCATTTCGAAACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTA-CCGTTTTGTCATTTCGAGACCG
* * * **
3803049 ATTTTGTCTTATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATTGACACT
65 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCAACACT
* * * *
3803114 TTATAGGCTCTA-TACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
130 TTACAGGCGCTATTACTGCTTCCCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
* *
3803178 ACACTTTAAACATATCCGATAGTGTTTTACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATT
195 ACACTTTAAACATATCCGATAGCGCTTTACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATT
* *
3803243 TTTACCTGTTATATTGTTATGGATTAATACATTTTTATAAAGTATCGACACTTTATAGGCGCTAT
260 TTTACCTGTTATATTGTTATGGATCAACACATTTTTATAAAGTATCGACACTTTATAGGCGCTAT
3803308 TACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
325 TACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
** * * *
3803347 T-TTCAATCTAATTGATACTTTCAACATATCCGGTAGCGCTTTACCGTTTTTTTTCATTTCGAGA
1 TATT-AAAGT-ATCGACACTTTCAACATATCCGGTAGCGCTTTACCG--TTTTGTCATTTCGAGA
* *
3803411 CCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTT
62 CCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
3803463 TATTTGTATC
Statistics
Matches: 441, Mismatches: 32, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
362 2 0.00
363 256 0.58
364 122 0.28
365 61 0.14
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (363 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGTTTTGTCATTTCGAGACCGG
TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCAACACTT
TACAGGCGCTATTACTGCTTCCCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGA
CACTTTAAACATATCCGATAGCGCTTTACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATTT
TTACCTGTTATATTGTTATGGATCAACACATTTTTATAAAGTATCGACACTTTATAGGCGCTATT
ACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:3805443 original size:11 final size:11
Alignment explanation
Indices: 3805429--3805480 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
3805419 ACTCGATTTT
3805429 AAGCTCGAATC
1 AAGCTCGAATC
*
3805440 AAGCTCAAATC
1 AAGCTCGAATC
*
3805451 AAGCTCAAATC
1 AAGCTCGAATC
*
3805462 AAACTCGAATC
1 AAGCTCGAATC
3805473 AAGCTCGA
1 AAGCTCGA
3805481 CTCTTAGCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.17
Consensus pattern (11 bp):
AAGCTCGAATC
Found at i:3807711 original size:11 final size:11
Alignment explanation
Indices: 3807695--3807757 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
3807685 GTATTATAGA
3807695 ATTTTTAATAT
1 ATTTTTAATAT
3807706 ATTTTTAA-A-
1 ATTTTTAATAT
3807715 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
3807726 ATCAATAGTGT
1 ATTTTTAATAT
3807737 ATTTTTAATAT
1 ATTTTTAATAT
3807748 ATTTTTAATA
1 ATTTTTAATA
3807758 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:3808431 original size:3 final size:3
Alignment explanation
Indices: 3808423--3808449 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3808413 ATATAAGAAT
3808423 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
3808450 GACTGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3810461 original size:2 final size:2
Alignment explanation
Indices: 3810454--3810491 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3810444 CATTCACAAC
3810454 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
3810492 CTAGAATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3815361 original size:23 final size:23
Alignment explanation
Indices: 3815343--3815403 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
3815333 CTCGTATAAA
3815343 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
3815366 TGCACCGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
3815389 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
3815404 TATAAAATGT
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:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3816884 original size:20 final size:20
Alignment explanation
Indices: 3816856--3816913 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
3816846 TTCCCCTTGA
* *
3816856 AGTGTATCGATGTATTCTAC
1 AGTGCATCGATGCATTCTAC
3816876 AGTGCATCGATGCATTCTTTGAC
1 AGTGCATCGATGCATTC--T-AC
3816899 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3816914 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
22 1 0.03
23 3 0.09
24 13 0.41
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:3821240 original size:32 final size:31
Alignment explanation
Indices: 3821199--3821265 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
3821189 GGAAATTTAA
* *
3821199 TTCGGGTCGGGTCAAAATTGGATCGGTTGGCT
1 TTCGGGTCGGGTCAAAATCGAATCGGTTGG-T
* *
3821231 TTCGGGTCGGGTTAATATCGAATCGGTTGGT
1 TTCGGGTCGGGTCAAAATCGAATCGGTTGGT
3821262 TTCG
1 TTCG
3821266 AGTTGGGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 5 0.16
32 26 0.84
ACGTcount: A:0.15, C:0.15, G:0.36, T:0.34
Consensus pattern (31 bp):
TTCGGGTCGGGTCAAAATCGAATCGGTTGGT
Found at i:3821274 original size:31 final size:31
Alignment explanation
Indices: 3821220--3821304 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
3821210 TCAAAATTGG
* *
3821220 ATCGGTTGGCTTTCGGGTCGGGTTAATATCGA
1 ATCGGTTGG-TTTCGAGTTGGGTTAATATCGA
* *
3821252 ATCGGTTGGTTTCGAGTTGGGTTAGTATCGG
1 ATCGGTTGGTTTCGAGTTGGGTTAATATCGA
* * *
3821283 GTCGGTTTGTTTCGATTTGGGT
1 ATCGGTTGGTTTCGAGTTGGGT
3821305 GGGTCAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 37 0.80
32 9 0.20
ACGTcount: A:0.12, C:0.12, G:0.36, T:0.40
Consensus pattern (31 bp):
ATCGGTTGGTTTCGAGTTGGGTTAATATCGA
Found at i:3821684 original size:2 final size:2
Alignment explanation
Indices: 3821679--3821704 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3821669 AAAATACATA
3821679 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
3821705 TTTTATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3821807 original size:10 final size:11
Alignment explanation
Indices: 3821782--3821811 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3821772 ACCCTAGATT
3821782 TTTTTATATTA
1 TTTTTATATTA
3821793 TTTTTATATTA
1 TTTTTATATTA
3821804 -TTTTATAT
1 TTTTTATAT
3821812 CTGTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:3822428 original size:16 final size:16
Alignment explanation
Indices: 3822391--3822461 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
3822381 TTGATTTTGA
* * *
3822391 TTCGGATTATTTTCTG
1 TTCGGGTTACTTTCAG
3822407 TTCGGGTTACTTTCAG
1 TTCGGGTTACTTTCAG
*
3822423 TTCGGGTTGAC-TTCGG
1 TTCGGGTT-ACTTTCAG
* *
3822439 TTTGAGGTT-CTTTCAA
1 TTCG-GGTTACTTTCAG
3822455 TTCGGGT
1 TTCGGGT
3822462 CGATTTCGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
15 4 0.09
16 34 0.77
17 6 0.14
ACGTcount: A:0.11, C:0.15, G:0.27, T:0.46
Consensus pattern (16 bp):
TTCGGGTTACTTTCAG
Found at i:3822452 original size:32 final size:33
Alignment explanation
Indices: 3822411--3822472 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
3822401 TTTCTGTTCG
* *
3822411 GGTTACTTTCAGTTCGGGTTGACTTCGGTTTGA
1 GGTTACTTTCAATTCGGGTCGACTTCGGTTTGA
*
3822444 GGTT-CTTTCAATTCGGGTCGATTTCGGTT
1 GGTTACTTTCAATTCGGGTCGACTTCGGTT
3822473 CAATTATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.11, C:0.16, G:0.29, T:0.44
Consensus pattern (33 bp):
GGTTACTTTCAATTCGGGTCGACTTCGGTTTGA
Found at i:3825920 original size:2 final size:2
Alignment explanation
Indices: 3825913--3825938 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3825903 AATTTTCTTA
3825913 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
3825939 TACATTTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3838933 original size:45 final size:45
Alignment explanation
Indices: 3838870--3838973 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
3838860 CTCGAAGGCT
* * **
3838870 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG
*
3838915 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACTCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG
*
3838960 CTTTGAAAACATCA
1 TTTTGAAAACATCA
3838974 AAAAGCTCCG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG
Found at i:3839001 original size:75 final size:73
Alignment explanation
Indices: 3838908--3839048 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 73
3838898 TATGGATGAC
*
3838908 CCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACTCGAAGGCTTTGAAAACATC
1 CCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC
3838973 AAAAAGCT
66 AAAAAGCT
* * ** *
3838981 CCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACA
1 CCGAAGG--TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
3839046 TCA
64 TCA
3839049 TGCACTGTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 7 0.12
75 53 0.88
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (73 bp):
CCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC
AAAAAGCT
Found at i:3839041 original size:120 final size:120
Alignment explanation
Indices: 3838785--3839170 Score: 601
Period size: 120 Copynumber: 3.2 Consensus size: 120
3838775 TGAAAACATC
* * ** * * * *
3838785 ACCCGAAGGTTTTGATAATATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTGATAACA
1 ACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACACGAAGGCTTTGAAAACA
*
3838850 TCAAACAGCTCTCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
66 TCAAAAAGCTC-CGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
*
3838906 ACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACTCGAAGGCTTTGAAAACA
1 ACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACACGAAGGCTTTGAAAACA
3838971 TCAAAAAGCTCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
66 TCAAAAAGCTCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* *
3839026 ACCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACACGAAGGCTTTGAAAAAT
1 ACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACACGAAGGCTTTG-AAAAC
* **
3839091 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTATAGGTCTTACAGATG
65 ATCAAAAAGCT-CCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
*
3839148 ACCCGAAGGCTTTGAAAACATCA
1 ACCCGAAGGTTTTGAAAACATCA
3839171 AAAAGCTCCC
Statistics
Matches: 247, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
120 101 0.41
121 82 0.33
122 64 0.26
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (120 bp):
ACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACACGAAGGCTTTGAAAACA
TCAAAAAGCTCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
Found at i:3839047 original size:45 final size:45
Alignment explanation
Indices: 3838981--3839088 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 45
3838971 TCAAAAAGCT
* **
3838981 CCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGAC
1 CCGAAGG--TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGAC
3839028 CCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGAC
1 CCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGAC
* *
3839073 ACGAAGGCTTTGAAAA
1 CCGAAGGTTTTGAAAA
3839089 ATATCAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 49 0.88
47 7 0.12
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (45 bp):
CCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGAC
Found at i:3839301 original size:151 final size:151
Alignment explanation
Indices: 3839027--3839397 Score: 541
Period size: 151 Copynumber: 2.5 Consensus size: 151
3839017 TTATGGATGA
* *
3839027 CCCGAAGG-TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACACGAAGGCTTTGAAAAAT
1 CCCGAAGGTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTG-AAAAC
* * *
3839091 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTATAGGTCTTACAGATGACCCGAAG
65 ATCAAAAAGATCCCGAAGGCTTTTTGAAAACATCATGCACTATAGGGCTTACAGATGACCCGAAG
3839156 GCTTTGAAAACATCAAAAAGCT
130 GCTTTGAAAACATCAAAAAGCT
* * * *
3839178 CCCGAAGGCTTTTTGAAAA-ATCATGAACTGAAGGGCTTACAGATGACCCGAAGACTTTGAAAAC
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
*
3839242 ATCAAAAAGATCCTGAAGGCTTTTTGAAAACATCATGCACTGA-AGGGCTTACAGATGACCCGAA
65 ATCAAAAAGATCCCGAAGGCTTTTTGAAAACATCATGCACT-ATAGGGCTTACAGATGACCCGAA
3839306 GGCTTTGAAAACATCAAAAAGCT
129 GGCTTTGAAAACATCAAAAAGCT
* * ** * *
3839329 CTCGAAGGATTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGATGGTTTTGAAAAC
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
3839394 ATCA
65 ATCA
3839398 TGCACTGTAG
Statistics
Matches: 195, Mismatches: 21, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
151 110 0.56
152 76 0.39
153 9 0.05
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (151 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACA
TCAAAAAGATCCCGAAGGCTTTTTGAAAACATCATGCACTATAGGGCTTACAGATGACCCGAAGG
CTTTGAAAACATCAAAAAGCT
Found at i:3839323 original size:76 final size:76
Alignment explanation
Indices: 3839027--3839397 Score: 534
Period size: 76 Copynumber: 4.9 Consensus size: 76
3839017 TTATGGATGA
* *
3839027 CCCGAAGG--TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACACGAAGGCTTTGAAAAA
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTG-AAAA
*
3839090 TATCAAAAAGCT
65 CATCAAAAAGCT
*
3839102 CCCGAAGGCTTTTTGAAAACATCCTGCACT-ATAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGA-AGGTCTTACAGATGACCCGAAGGCTTTGAAAA
3839166 CATCAAAAAGCT
65 CATCAAAAAGCT
* * *
3839178 CCCGAAGGCTTTTTGAAAA-ATCATGAACTGAAGGGCTTACAGATGACCCGAAGACTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
*
3839242 ATCAAAAAGAT
66 ATCAAAAAGCT
* *
3839253 CCTGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
3839318 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * * ** * *
3839329 CTCGAAGGATTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGATGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
3839394 ATCA
66 ATCA
3839398 TGCACTGTAG
Statistics
Matches: 268, Mismatches: 23, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
75 75 0.28
76 147 0.55
77 46 0.17
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:3843859 original size:72 final size:72
Alignment explanation
Indices: 3843742--3843881 Score: 235
Period size: 72 Copynumber: 1.9 Consensus size: 72
3843732 ATATAATAGT
* * *
3843742 ATAACAGGCTAGCTGAATATTATCCATAAAGTCGGGGCGATTAACCAATTGCTTTAGAGGGACAA
1 ATAACAGACTAGCTGAATATTATCCATAAAGCCGGGGCCATTAACCAATTGCTTTAGAGGGACAA
3843807 CTCGAGC
66 CTCGAGC
* *
3843814 ATAACAGACTAGCTGAATATTATCCATAAAGCCGGGGCCATTAACCAATTGCTTTAGGGGGATAA
1 ATAACAGACTAGCTGAATATTATCCATAAAGCCGGGGCCATTAACCAATTGCTTTAGAGGGACAA
3843879 CTC
66 CTC
3843882 AAGCTTTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (72 bp):
ATAACAGACTAGCTGAATATTATCCATAAAGCCGGGGCCATTAACCAATTGCTTTAGAGGGACAA
CTCGAGC
Found at i:3845894 original size:13 final size:13
Alignment explanation
Indices: 3845878--3845912 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
3845868 GCAAAGATGC
3845878 AAATATAAAATGA
1 AAATATAAAATGA
3845891 AAATAT-AAATGA
1 AAATATAAAATGA
3845903 AAATATAAAA
1 AAATATAAAA
3845913 ATGCAAATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (13 bp):
AAATATAAAATGA
Found at i:3845955 original size:20 final size:21
Alignment explanation
Indices: 3845897--3845942 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
3845887 ATGAAAATAT
3845897 AAATG-AAA-ATATAAAAATGC
1 AAATGCAAACATA-AAAAATGC
3845917 AAATGCAAACATAAAAAATGC
1 AAATGCAAACATAAAAAATGC
3845938 AAATG
1 AAATG
3845943 TAATGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.21
21 16 0.67
22 3 0.12
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (21 bp):
AAATGCAAACATAAAAAATGC
Found at i:3848275 original size:15 final size:15
Alignment explanation
Indices: 3848255--3848300 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3848245 ATTTTCACAC
3848255 AAAAATTAATATATA
1 AAAAATTAATATATA
*
3848270 AAAAATTAA-AAATA
1 AAAAATTAATATATA
*
3848284 TAAACATTAATATATA
1 -AAAAATTAATATATA
3848300 A
1 A
3848301 GGATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATTAATATATA
Found at i:3848310 original size:30 final size:31
Alignment explanation
Indices: 3848259--3848318 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
3848249 TCACACAAAA
3848259 ATTAATATATAAAAAATTAAAAAT-ATAAAC
1 ATTAATATATAAAAAATTAAAAATAATAAAC
**
3848289 ATTAATATAT-AAGGATATAAAAATAATAAA
1 ATTAATATATAAAAAAT-TAAAAATAATAAA
3848319 GGATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 17 0.65
31 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (31 bp):
ATTAATATATAAAAAATTAAAAATAATAAAC
Found at i:3848327 original size:17 final size:18
Alignment explanation
Indices: 3848299--3848332 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3848289 ATTAATATAT
3848299 AAGGATATAAAAATAATA
1 AAGGATATAAAAATAATA
3848317 AAGGATA-AAAAATAAT
1 AAGGATATAAAAATAAT
3848333 TGAATGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
AAGGATATAAAAATAATA
Found at i:3848867 original size:17 final size:19
Alignment explanation
Indices: 3848837--3848871 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3848827 AATTCCAAGA
3848837 AAATATATTAATTTTTTAT
1 AAATATATTAATTTTTTAT
3848856 AAATATA-T-ATTTTTTA
1 AAATATATTAATTTTTTA
3848872 CATTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATATATTAATTTTTTAT
Found at i:3848877 original size:25 final size:27
Alignment explanation
Indices: 3848849--3848901 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 27
3848839 ATATATTAAT
*
3848849 TTTTTATAAAT-ATATATTT-TTTACA
1 TTTTTATAAATAAGATATTTATTTACA
3848874 TTTTTATAAATAAGATATTTATTTACA
1 TTTTTATAAATAAGATATTTATTTACA
3848901 T
1 T
3848902 AGAAATATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 11 0.44
26 7 0.28
27 7 0.28
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTTATAAATAAGATATTTATTTACA
Found at i:3850849 original size:10 final size:10
Alignment explanation
Indices: 3850834--3850858 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3850824 CTTATCCTTT
3850834 AGGCTTTGAG
1 AGGCTTTGAG
3850844 AGGCTTTGAG
1 AGGCTTTGAG
3850854 AGGCT
1 AGGCT
3850859 ATAAATACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.12, G:0.40, T:0.28
Consensus pattern (10 bp):
AGGCTTTGAG
Found at i:3855959 original size:20 final size:20
Alignment explanation
Indices: 3855934--3855971 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3855924 ATTATGTTAA
3855934 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
3855954 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
3855972 TCAAGGGGAA
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:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:3857538 original size:23 final size:23
Alignment explanation
Indices: 3857508--3857567 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
3857498 CATTTTATAT
*
3857508 GGCACTTCGGTGTAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
3857531 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
3857554 AGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3857568 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:3863858 original size:3 final size:3
Alignment explanation
Indices: 3863845--3863915 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
3863835 GTAATTATTT
* * * *
3863845 ATA ATA A-A ATA ATA TTA ATA TTA ATA ATA TTA ATA ATA TTA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3863891 ATA TATA ATA ATA ATA ATA ATA ATA
1 ATA -ATA ATA ATA ATA ATA ATA ATA
3863916 TTTTTAAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
2 4 0.07
3 50 0.88
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:3864149 original size:45 final size:45
Alignment explanation
Indices: 3864097--3864337 Score: 167
Period size: 45 Copynumber: 5.0 Consensus size: 45
3864087 TTTAAGATCT
3864097 TGCACTGAAGGTCTTATAGATGACCCGAAGGCTTTGAAAACATCA
1 TGCACTGAAGGTCTTATAGATGACCCGAAGGCTTTGAAAACATCA
* * * *
3864142 TGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGATAATATCATAGA
1 TGCACTGAAGGTCTTATAGATGACCCGAAGGCTTTGA-AA-A-CAT-CA
* ** * * * * *
3864191 TGACCCCAAAGGTTTTGATAACATCAAAAAGCACCTGAAGGCTTTTTGAAAACTTCC
1 TG-CACTGAAGGTCTT-AT-AGAT------G-ACCCGAAGGC--TTTGAAAACATCA
* * * *
3864248 TGCACTGTAGGTCTTATGGATGACCTGAAGGTTTTGAAAACATCA
1 TGCACTGAAGGTCTTATAGATGACCCGAAGGCTTTGAAAACATCA
* * *
3864293 TGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
1 TGCACTGAAGGTCTTATAGATGACCCGAAGGCTTTGAAAACATCA
3864338 AAAAGCTCCC
Statistics
Matches: 149, Mismatches: 31, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
45 85 0.57
46 2 0.01
47 10 0.07
48 4 0.03
49 3 0.02
50 9 0.06
51 1 0.01
52 3 0.02
54 2 0.01
55 2 0.01
56 8 0.05
57 2 0.01
58 3 0.02
59 8 0.05
60 2 0.01
61 5 0.03
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (45 bp):
TGCACTGAAGGTCTTATAGATGACCCGAAGGCTTTGAAAACATCA
Found at i:3864201 original size:30 final size:29
Alignment explanation
Indices: 3864159--3864216 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
3864149 AAGGTCTTAC
*
3864159 AGATGACCCAAAGGTTTTGATAATATCAT
1 AGATGACCCAAAGGTTTTGATAACATCAT
3864188 AGATGACCCCAAAGGTTTTGATAACATCA
1 AGATGA-CCCAAAGGTTTTGATAACATCA
3864217 AAAAGCACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (29 bp):
AGATGACCCAAAGGTTTTGATAACATCAT
Found at i:3864418 original size:45 final size:46
Alignment explanation
Indices: 3864345--3864459 Score: 153
Period size: 45 Copynumber: 2.5 Consensus size: 46
3864335 TCAAAAAGCT
* **
3864345 CCCGAAGGCTTTTTGAAAACATTC-TGCACTGTAGGTCTTATGGATGA
1 CCCGAAGGC-TTTTAAAAACA-TCATGCACTGTAGGTCTTACAGATGA
3864392 CCCGAAGG-TTTTAAAAACATCATGCACTGTAGGTCTTACAGATGA
1 CCCGAAGGCTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGA
* *
3864437 CCCGAAGGCTTTGAAAAATATCA
1 CCCGAAGGCTTTTAAAAACATCA
3864460 AAAAACTCCT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
44 2 0.03
45 39 0.64
46 12 0.20
47 8 0.13
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (46 bp):
CCCGAAGGCTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGA
Found at i:3864418 original size:121 final size:121
Alignment explanation
Indices: 3864188--3864535 Score: 527
Period size: 121 Copynumber: 2.9 Consensus size: 121
3864178 ATAATATCAT
* * * *
3864188 AGATGACCCCAAAGGTTTTGATAACATCAAAAAGCACCTGAAGGCTTTTTGAAAAC-TTCCTGCA
1 AGATGA-CCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATT-CTGCA
*
3864252 CTGTAGGTCTTATGGATGACCTGAAGGTTTTGAAAACATCATGCACTGTAGGACTTAC
64 CTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTAC
*
3864310 AGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATTCTGCACT
1 AGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATTCTGCACT
* *
3864375 GTAGGTCTTATGGATGACCCGAAGGTTTTAAAAACATCATGCACTGTAGGTCTTAC
66 GTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTAC
* * *
3864431 AGATGACCCGAAGGCTTTGAAAAATATCAAAAAACTCCTGAAGGCTTTTTGAAAACATCCTGCAC
1 AGATGACCCGAAGGCTTTG-AAAACATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATTCTGCAC
** * *
3864496 TGTAGGTCTTACAGATGACTCGAAGGCTTTGAAAACATCA
65 TGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCA
3864536 AAAAGCTCCC
Statistics
Matches: 207, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
121 123 0.59
122 84 0.41
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (121 bp):
AGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATTCTGCACT
GTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTAC
Found at i:3864583 original size:76 final size:76
Alignment explanation
Indices: 3864392--3864687 Score: 398
Period size: 76 Copynumber: 3.9 Consensus size: 76
3864382 TTATGGATGA
*
3864392 CCCGAAGG--TTTTAAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAA
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTG-AAAA
* *
3864455 TATCAAAAAACT
65 CATCAAAAAGCT
* * *
3864467 CCTGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACTCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
3864532 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
3864543 CCCGAAGGCTTTTTGAAAACATCATGTACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
3864608 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * * ** * * * *
3864619 CTCGAAGGCTTTTTGAAAACATCCTGCCCTGTAGATCTTATGGAAGACTCGAATGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
3864684 ATCA
66 ATCA
3864688 TGCACTGTAG
Statistics
Matches: 194, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
75 7 0.04
76 140 0.72
77 47 0.24
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:3867139 original size:3 final size:3
Alignment explanation
Indices: 3867126--3867186 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
3867116 GTAATTATTT
* * *
3867126 ATA ATA A-A ATA ATA TTA ATA TTA ATA ATA ATA ATA TATA ATA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
*
3867171 ATA ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA A
3867187 ATATTTTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3867148 original size:26 final size:28
Alignment explanation
Indices: 3867126--3867190 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
3867116 GTAATTATTT
3867126 ATAATAA-A-ATAATATTAATATTAATA
1 ATAATAATATATAATATTAATATTAATA
*
3867152 ATAATAATATATAATATTAATAATAATA
1 ATAATAATATATAATATTAATATTAATA
*
3867180 AAAATAA-ATAT
1 ATAATAATATAT
3867191 TTTTAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 7 0.20
27 5 0.14
28 23 0.66
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
ATAATAATATATAATATTAATATTAATA
Found at i:3867169 original size:22 final size:21
Alignment explanation
Indices: 3867127--3867180 Score: 92
Period size: 22 Copynumber: 2.6 Consensus size: 21
3867117 TAATTATTTA
3867127 TAATAA-AATAATATTAATAT
1 TAATAATAATAATATTAATAT
3867147 TAATAATAATAATATATAATAT
1 TAATAATAATAATAT-TAATAT
3867169 TAATAATAATAA
1 TAATAATAATAA
3867181 AAATAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 6 0.19
21 8 0.25
22 18 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATAATAATAATATTAATAT
Found at i:3867189 original size:22 final size:22
Alignment explanation
Indices: 3867121--3867191 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
3867111 ATTTTGTAAT
*
3867121 TATTTATAATAA-AATAATATTAA
1 TATTAATAATAATAA-AATA-TAA
*
3867144 TATTAATAATAATAATATATAA
1 TATTAATAATAATAAAATATAA
3867166 TATTAATAATAATAAAA-ATAAA
1 TATTAATAATAATAAAATAT-AA
3867188 TATT
1 TATT
3867192 TTTAAAATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.05
22 25 0.58
23 14 0.33
24 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTAATAATAATAAAATATAA
Found at i:3868924 original size:21 final size:21
Alignment explanation
Indices: 3868899--3868938 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3868889 CATATAGCTT
3868899 CTTTTCATATAATTCATATCA
1 CTTTTCATATAATTCATATCA
3868920 CTTTTCATATAATTCATAT
1 CTTTTCATATAATTCATAT
3868939 GTTCACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (21 bp):
CTTTTCATATAATTCATATCA
Found at i:3869315 original size:20 final size:19
Alignment explanation
Indices: 3869290--3869362 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 19
3869280 CTTGAAGTGC
3869290 ATCGATGCATCCTACCGTGT
1 ATCGATGCATCCTA-CGTGT
3869310 ATCGATGCATCCCTTAACGTGT
1 ATCGATGCAT-CC-T-ACGTGT
*
3869332 GCATCGATGCACTCCT-CATGT
1 --ATCGATGCA-TCCTACGTGT
3869353 ATCGATGCAT
1 ATCGATGCAT
3869363 TAATTGCATT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
18 1 0.02
19 9 0.20
20 10 0.22
21 6 0.13
22 6 0.13
23 2 0.04
24 11 0.24
25 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (19 bp):
ATCGATGCATCCTACGTGT
Found at i:3869338 original size:24 final size:22
Alignment explanation
Indices: 3869286--3869347 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 22
3869276 TCCCCTTGAA
*
3869286 GTGCATCGATGCATCCTACCGT
1 GTGCATCGATGCATCCTAACGT
3869308 GT--ATCGATGCATCCCTTAACGT
1 GTGCATCGATGCAT-CC-TAACGT
3869330 GTGCATCGATGCACTCCT
1 GTGCATCGATGCA-TCCT
3869348 CATGTATCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
20 10 0.29
21 2 0.06
22 9 0.26
23 1 0.03
24 11 0.32
25 1 0.03
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (22 bp):
GTGCATCGATGCATCCTAACGT
Found at i:3872737 original size:27 final size:27
Alignment explanation
Indices: 3872695--3872764 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
3872685 GGCTATGAAT
*
3872695 TTTGTCCCGAAA-GACCTATGTACTGTA
1 TTTGTCCC-AAATGACCTACGTACTGTA
3872722 TTTGTCCCAAATGACCTACGTACTGTA
1 TTTGTCCCAAATGACCTACGTACTGTA
*
3872749 TTTGTCCCGAATGACC
1 TTTGTCCCAAATGACC
3872765 ACTCCTTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 3 0.08
27 37 0.93
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (27 bp):
TTTGTCCCAAATGACCTACGTACTGTA
Found at i:3873461 original size:24 final size:23
Alignment explanation
Indices: 3873412--3873473 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
3873402 CCTTGAAGTA
*
3873412 CATCGATGCAT-CC-TACCGTGT
1 CATCGATGCATCCCTTATCGTGT
3873433 -ATCGATGCATCCCTTATCGTGT
1 CATCGATGCATCCCTTATCGTGT
3873455 GCATCGATGCA-CTCCTTAT
1 -CATCGATGCATC-CCTTAT
3873474 GCATCGATGC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 10 0.29
21 2 0.06
22 7 0.20
23 1 0.03
24 15 0.43
ACGTcount: A:0.19, C:0.31, G:0.18, T:0.32
Consensus pattern (23 bp):
CATCGATGCATCCCTTATCGTGT
Found at i:3876836 original size:27 final size:27
Alignment explanation
Indices: 3876799--3876868 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
3876789 GGCTATGAAT
* *
3876799 TTTGTCCCGAAAGACCTATGTACTATA
1 TTTGTCCCGAATGACCTACGTACTATA
* *
3876826 TTTGTCACGAATGACCTACGTACTGTA
1 TTTGTCCCGAATGACCTACGTACTATA
3876853 TTTGTCCCGAATGACC
1 TTTGTCCCGAATGACC
3876869 ACTCCTTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (27 bp):
TTTGTCCCGAATGACCTACGTACTATA
Found at i:3877564 original size:24 final size:23
Alignment explanation
Indices: 3877512--3877568 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
3877502 TCCCCTTGAA
* *
3877512 GTGCATCGATGC-TTCCTACCGT
1 GTGCATCGATGCATCCCTAACGT
3877534 GT--ATCGATGCATCCCTTAACGT
1 GTGCATCGATGCATCCC-TAACGT
3877556 GTGCATCGATGCA
1 GTGCATCGATGCA
3877569 CTCCTTATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 8 0.28
21 3 0.10
22 9 0.31
24 9 0.31
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (23 bp):
GTGCATCGATGCATCCCTAACGT
Found at i:3877574 original size:24 final size:23
Alignment explanation
Indices: 3877512--3877575 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
3877502 TCCCCTTGAA
* *
3877512 GTGCATCGATGCTTCC-TACCGT
1 GTGCATCGATGCATCCTTAACGT
3877534 GT--ATCGATGCATCCCTTAACGT
1 GTGCATCGATGCAT-CCTTAACGT
3877556 GTGCATCGATGCACTCCTTA
1 GTGCATCGATGCA-TCCTTA
3877576 TGCATCGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 9 0.26
21 2 0.06
22 9 0.26
24 14 0.40
25 1 0.03
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.31
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTAACGT
Found at i:3881628 original size:24 final size:22
Alignment explanation
Indices: 3881576--3881629 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
3881566 TCCCCTTGAA
* *
3881576 GTGCATCGATGCATCCTACCGT
1 GTGCATCGATACATCCTAACGT
3881598 GT--ATCGATACATCCATTAACGT
1 GTGCATCGATACATCC--TAACGT
3881620 GTGCATCGAT
1 GTGCATCGAT
3881630 GCACTCCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 11 0.42
22 9 0.35
24 6 0.23
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (22 bp):
GTGCATCGATACATCCTAACGT
Found at i:3889778 original size:22 final size:20
Alignment explanation
Indices: 3889738--3889779 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3889728 CTTGAAGTGC
*
3889738 ATCGATGCATCCTAACGTGT
1 ATCGATACATCCTAACGTGT
3889758 ATCGATACATCCCTTAACGTGT
1 ATCGATACAT-CC-TAACGTGT
3889780 GCATCGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (20 bp):
ATCGATACATCCTAACGTGT
Found at i:3889796 original size:24 final size:23
Alignment explanation
Indices: 3889734--3889797 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
3889724 TCCCCTTGAA
3889734 GTGCATCGATGCATCC-TAACGT
1 GTGCATCGATGCATCCTTAACGT
*
3889756 GT--ATCGATACATCCCTTAACGT
1 GTGCATCGATGCAT-CCTTAACGT
3889778 GTGCATCGATGCACTCCTTA
1 GTGCATCGATGCA-TCCTTA
3889798 TGCATCGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 9 0.26
21 2 0.06
22 10 0.29
24 13 0.37
25 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTAACGT
Found at i:3893739 original size:17 final size:17
Alignment explanation
Indices: 3893717--3893753 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3893707 TCCGCATATT
*
3893717 ACAGTTAAATGCAAATG
1 ACAGTTAAATGAAAATG
3893734 ACAGTTAAATGAAAATG
1 ACAGTTAAATGAAAATG
3893751 ACA
1 ACA
3893754 TATTTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (17 bp):
ACAGTTAAATGAAAATG
Found at i:3899324 original size:37 final size:36
Alignment explanation
Indices: 3899219--3899328 Score: 168
Period size: 36 Copynumber: 3.0 Consensus size: 36
3899209 GATTATTTCC
* *
3899219 ATGCAAATTCAGCCGTCCCAAAAGAGTAGTGAAGCA
1 ATGCAAATTCAGCCTTCACAAAAGAGTAGTGAAGCA
*
3899255 AAGCAAA-TCAAGCCTTCACAAAAGAGTAGTGAAGCA
1 ATGCAAATTC-AGCCTTCACAAAAGAGTAGTGAAGCA
3899291 ATGCAAATTCAGCCTTCACAAAAAGAGTAGTGAAGCA
1 ATGCAAATTCAGCCTTCAC-AAAAGAGTAGTGAAGCA
3899328 A
1 A
3899329 GATCAGATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
35 2 0.03
36 45 0.67
37 20 0.30
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (36 bp):
ATGCAAATTCAGCCTTCACAAAAGAGTAGTGAAGCA
Found at i:3904331 original size:12 final size:12
Alignment explanation
Indices: 3904314--3904376 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
3904304 AAAAAAATTA
3904314 ATTAAATAAAAT
1 ATTAAATAAAAT
*
3904326 ATTAAAAATTAAAT
1 ATT--AAATAAAAT
3904340 AGTTAAATAAAAT
1 A-TTAAATAAAAT
* *
3904353 ACT-AACAAAAT
1 ATTAAATAAAAT
*
3904364 ATTAAATATAAT
1 ATTAAATAAAAT
3904376 A
1 A
3904377 ATATATACCT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 9 0.22
12 11 0.28
13 9 0.22
14 9 0.22
15 2 0.05
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:3908556 original size:20 final size:20
Alignment explanation
Indices: 3908531--3908623 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
3908521 TTTTCCCAAT
3908531 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
3908551 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
3908571 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
3908592 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
3908613 TCGCAATGCGA
1 TCGCAATGCGA
3908624 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:3908573 original size:41 final size:41
Alignment explanation
Indices: 3908528--3908623 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
3908518 CGATTTTCCC
3908528 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
3908569 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
3908610 AAATCGCAATGCGA
1 AATTCGCAATGCGA
3908624 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:3908577 original size:21 final size:20
Alignment explanation
Indices: 3908531--3908623 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
3908521 TTTTCCCAAT
*
3908531 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
3908551 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
3908571 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
3908592 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
3908613 TCGCAATGCGA
1 TCGCAATGCGA
3908624 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:3908636 original size:41 final size:41
Alignment explanation
Indices: 3908550--3908684 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
3908540 GAATAAGTAA
* * *
3908550 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
3908591 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
3908632 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
3908673 TTCGCAACGCGA
1 ATCGCAACGCGA
3908685 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:3908637 original size:20 final size:20
Alignment explanation
Indices: 3908612--3908705 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
3908602 AATTGGGAAA
*
3908612 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
3908632 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
3908653 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
3908673 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3908693 TTCGCAACGCGAT
1 ATCGCAACGCGAT
3908706 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3909289 original size:19 final size:19
Alignment explanation
Indices: 3909265--3909309 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3909255 GCAACGAGAT
*
3909265 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
3909284 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
3909303 AATCGCA
1 AATCGCA
3909310 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:3909327 original size:19 final size:19
Alignment explanation
Indices: 3909305--3909527 Score: 223
Period size: 19 Copynumber: 12.1 Consensus size: 19
3909295 GAAACCAAAA
*
3909305 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3909324 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3909343 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3909362 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3909381 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
3909400 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
3909420 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
3909436 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
3909453 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
3909467 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
3909486 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
3909506 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3909526 TC
1 TC
3909528 AACCAAAAGA
Statistics
Matches: 174, Mismatches: 17, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
14 19 0.11
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 97 0.56
20 49 0.28
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3909452 original size:33 final size:33
Alignment explanation
Indices: 3909415--3909502 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
3909405 GTTGCGATTT
* *
3909415 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
3909448 TCATTTCGCGTTGTGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
3909481 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
3909503 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:3909504 original size:20 final size:20
Alignment explanation
Indices: 3909470--3909527 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
3909460 GTGATTCTCT
**
3909470 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
3909490 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
3909510 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
3909528 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:3911581 original size:42 final size:42
Alignment explanation
Indices: 3911521--3911643 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
3911511 GCTCGACTCG
* * *
3911521 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
3911563 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
3911605 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
3911644 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:3911601 original size:21 final size:21
Alignment explanation
Indices: 3911577--3911643 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3911567 TCATTCCTCG
3911577 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3911598 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3911619 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3911640 AGAG
1 AGAG
3911644 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3913029 original size:14 final size:14
Alignment explanation
Indices: 3912996--3913031 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
3912986 GATTGTTTAA
*
3912996 TTGATTTGTAAATG
1 TTGATTTGTAAAAG
3913010 -TGATTTGTAAAAG
1 TTGATTTGTAAAAG
3913023 TTGATTTGT
1 TTGATTTGT
3913032 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:3913039 original size:13 final size:13
Alignment explanation
Indices: 3912984--3913040 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
3912974 TGCTTATTTT
*
3912984 TTGA-TTGTTTAA
1 TTGATTTGTTAAA
3912996 TTGATTTG-TAAA
1 TTGATTTGTTAAA
*
3913008 TGTGATTTGTAAAA
1 T-TGATTTGTTAAA
*
3913022 GTTGATTTGTTTAA
1 -TTGATTTGTTAAA
3913036 TTGAT
1 TTGAT
3913041 GTTAACATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 8 0.22
13 15 0.41
14 13 0.35
15 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (13 bp):
TTGATTTGTTAAA
Done.