Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 24
Found at i:3285697 original size:149 final size:149
Alignment explanation
Indices: 3285516--3285819 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
3285506 GAGTCGAGGG
3285516 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
3285581 ACTTGATCCCTATCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
3285646 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
3285665 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
3285730 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
3285795 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
3285814 TCTACG
1 TCTACG
3285820 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:3285842 original size:23 final size:23
Alignment explanation
Indices: 3285798--3285842 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3285788 ATCATTATAT
*
3285798 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
3285821 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
3285843 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:3289094 original size:18 final size:18
Alignment explanation
Indices: 3289071--3289105 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3289061 CTAGGAGATT
3289071 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
3289089 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
3289106 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:3289191 original size:21 final size:22
Alignment explanation
Indices: 3289162--3289205 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3289152 GTTGTATGAT
3289162 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
3289183 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
3289205 A
1 A
3289206 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:3290169 original size:149 final size:149
Alignment explanation
Indices: 3289988--3290291 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
3289978 GAGTCGAGGG
3289988 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
3290053 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
3290118 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
3290137 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
3290202 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
3290267 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
3290286 TCTACG
1 TCTACG
3290292 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:3290314 original size:23 final size:23
Alignment explanation
Indices: 3290270--3290314 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3290260 ATCATTATAT
*
3290270 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
3290293 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
3290315 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:3293054 original size:24 final size:25
Alignment explanation
Indices: 3293025--3293086 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 25
3293015 TCCATTTTAA
3293025 ACTTTAAAATCTTTTTTTTATT-TT
1 ACTTTAAAATCTTTTTTTTATTATT
*
3293049 ACTTT-AAATC--ATTTTTATTATT
1 ACTTTAAAATCTTTTTTTTATTATT
3293071 A-TTTAAATATCTTTTT
1 ACTTTAAA-ATCTTTTT
3293087 ACTAAAACCG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
21 11 0.35
22 5 0.16
23 8 0.26
24 5 0.16
25 2 0.06
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (25 bp):
ACTTTAAAATCTTTTTTTTATTATT
Found at i:3293063 original size:23 final size:25
Alignment explanation
Indices: 3293025--3293070 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3293015 TCCATTTTAA
*
3293025 ACTTTAAAATC-TTTTTTTTATTTT
1 ACTTTAAAATCATTTTTATTATTTT
3293049 ACTTT-AAATCATTTTTATTATT
1 ACTTTAAAATCATTTTTATTATT
3293071 ATTTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (25 bp):
ACTTTAAAATCATTTTTATTATTTT
Found at i:3298943 original size:18 final size:18
Alignment explanation
Indices: 3298920--3298969 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
3298910 CTGCGCTTAT
3298920 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
3298938 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
3298956 TTTTCAAAATCAAA
1 TTTTCAAAATCAAA
3298970 GATTGACTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (18 bp):
TTTTCAAAATCAAAACAG
Found at i:3299408 original size:21 final size:22
Alignment explanation
Indices: 3299382--3299428 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
3299372 AATATTTTTC
3299382 TTTATT-TTACTTTAAAT-CATT
1 TTTATTATTA-TTTAAATACATT
*
3299403 TTTATTATTATTTAAATATATT
1 TTTATTATTATTTAAATACATT
3299425 TTTA
1 TTTA
3299429 CCAAAACCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTATTATTTAAATACATT
Found at i:3299410 original size:24 final size:25
Alignment explanation
Indices: 3299365--3299427 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 25
3299355 TCCATTTTAA
*
3299365 ACTTTAAAATATTTTTCTTTATTTT
1 ACTTTAAAATATTTTTCATTATTTT
3299390 ACTTT-AAATCATTTTT-ATTA--TT
1 ACTTTAAAAT-ATTTTTCATTATTTT
3299412 A-TTTAAATATATTTTT
1 ACTTTAAA-ATATTTTT
3299428 ACCAAAACCC
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
21 3 0.09
22 11 0.32
23 2 0.06
24 7 0.21
25 11 0.32
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (25 bp):
ACTTTAAAATATTTTTCATTATTTT
Found at i:3317749 original size:23 final size:23
Alignment explanation
Indices: 3317719--3317775 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
3317709 TCTAGATAAT
3317719 TAATCTCCACCCTTGGATGTAAG
1 TAATCTCCACCCTTGGATGTAAG
3317742 TAATCTCCACCCTTGGATGTAAG
1 TAATCTCCACCCTTGGATGTAAG
3317765 TAATCTCCACC
1 TAATCTCCACC
3317776 ATTCATTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (23 bp):
TAATCTCCACCCTTGGATGTAAG
Found at i:3322271 original size:20 final size:20
Alignment explanation
Indices: 3322248--3322294 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3322238 TTCCAAAGAA
*
3322248 CTCTAGAGAAGTGTAGAACT
1 CTCTAGAGAAGAGTAGAACT
3322268 CTCTAGAGAAGAGTAGAACT
1 CTCTAGAGAAGAGTAGAACT
3322288 CTCTAGA
1 CTCTAGA
3322295 AGCTTGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (20 bp):
CTCTAGAGAAGAGTAGAACT
Found at i:3322295 original size:18 final size:18
Alignment explanation
Indices: 3322244--3322296 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
3322234 AGCATTCCAA
** *
3322244 AGAACTCTAGAGAAGTGT
1 AGAACTCTCTAGAAGAGT
3322262 AGAACTCTCTAGAGAAGAGT
1 AGAACTCTCT--AGAAGAGT
3322282 AGAACTCTCTAGAAG
1 AGAACTCTCTAGAAG
3322297 CTTGTGGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 13 0.43
20 17 0.57
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.21
Consensus pattern (18 bp):
AGAACTCTCTAGAAGAGT
Found at i:3325609 original size:6 final size:6
Alignment explanation
Indices: 3325598--3325628 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3325588 GACACGTATT
3325598 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
3325629 GCCGAGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3325636 original size:5 final size:5
Alignment explanation
Indices: 3325626--3325650 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3325616 ACCACGACCA
3325626 CGAGC CGAGC CGAGC CGAGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC
3325651 TTTGCCGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.40, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:3328046 original size:18 final size:18
Alignment explanation
Indices: 3328023--3328071 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
3328013 TGACCGGTCA
*
3328023 CGACCCGTTTACCCGACC
1 CGACCCGTTGACCCGACC
3328041 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
3328059 CGACCCGTTGACC
1 CGACCCGTTGACC
3328072 GGTGCTATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.16, C:0.49, G:0.20, T:0.14
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:3335290 original size:26 final size:26
Alignment explanation
Indices: 3335261--3335312 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3335251 TTTGACTGGT
*
3335261 TTGACC-GATCACGACCCGTTTACCCG
1 TTGACCTGA-CACGACCCGTTGACCCG
*
3335287 TTGACCTGACCCGACCCGTTGACCCG
1 TTGACCTGACACGACCCGTTGACCCG
3335313 ACCCGACCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.17, C:0.40, G:0.21, T:0.21
Consensus pattern (26 bp):
TTGACCTGACACGACCCGTTGACCCG
Found at i:3335305 original size:18 final size:18
Alignment explanation
Indices: 3335282--3335328 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
3335272 CGACCCGTTT
*
3335282 ACCCGTTGACCTGACCCG
1 ACCCGTTGACCCGACCCG
3335300 ACCCGTTGACCCGACCCG
1 ACCCGTTGACCCGACCCG
3335318 ACCCGTTGACC
1 ACCCGTTGACC
3335329 ATTGATCGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.47, G:0.21, T:0.15
Consensus pattern (18 bp):
ACCCGTTGACCCGACCCG
Found at i:3335328 original size:13 final size:13
Alignment explanation
Indices: 3335293--3335317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3335283 CCCGTTGACC
3335293 TGACCCGACCCGT
1 TGACCCGACCCGT
3335306 TGACCCGACCCG
1 TGACCCGACCCG
3335318 ACCCGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:3335382 original size:29 final size:29
Alignment explanation
Indices: 3335336--3335411 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
3335326 ACCATTGATC
* *** *
3335336 GGTGCTATTCTGGAAATTAATTCAGTTTT
1 GGTGCTATTTTGGAAATTAATTCAAAATG
*
3335365 GGTGCTATTTTGGGAATTAATTCAAAATG
1 GGTGCTATTTTGGAAATTAATTCAAAATG
*
3335394 GGTGCTATTTTGGTAATT
1 GGTGCTATTTTGGAAATT
3335412 TTTAAAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGAAATTAATTCAAAATG
Found at i:3335426 original size:27 final size:28
Alignment explanation
Indices: 3335365--3335430 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 28
3335355 ATTCAGTTTT
**
3335365 GGTGCTATTTTGGGAATTAATTCAAAATG
1 GGTGCTATTTTGGGAATT-ATTCAAAAAA
* *
3335394 GGTGCTATTTTGGTAATT-TTTAAAAAA
1 GGTGCTATTTTGGGAATTATTCAAAAAA
3335421 GGTGCTATTT
1 GGTGCTATTT
3335431 GTGTAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 16 0.48
29 17 0.52
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (28 bp):
GGTGCTATTTTGGGAATTATTCAAAAAA
Found at i:3338747 original size:22 final size:22
Alignment explanation
Indices: 3338719--3338769 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
3338709 GTTATGTAGT
3338719 AGTGTTTTCCTCCTTTACTTTC
1 AGTGTTTTCCTCCTTTACTTTC
3338741 AGTGTTTTCCTCCTTTACTTTC
1 AGTGTTTTCCTCCTTTACTTTC
3338763 AGTGTTT
1 AGTGTTT
3338770 CTAAAATCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.10, C:0.24, G:0.12, T:0.55
Consensus pattern (22 bp):
AGTGTTTTCCTCCTTTACTTTC
Found at i:3340451 original size:33 final size:33
Alignment explanation
Indices: 3340409--3340476 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
3340399 GTTGACATAT
3340409 TTGGTTGGTGACCAACTTATTGGAAAATTCATC
1 TTGGTTGGTGACCAACTTATTGGAAAATTCATC
*
3340442 TTGGTTGGTGGCCAACTTATTGGAAAATTCATC
1 TTGGTTGGTGACCAACTTATTGGAAAATTCATC
3340475 TT
1 TT
3340477 TGGTAGATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (33 bp):
TTGGTTGGTGACCAACTTATTGGAAAATTCATC
Found at i:3340488 original size:34 final size:33
Alignment explanation
Indices: 3340420--3340493 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
3340410 TGGTTGGTGA
* *
3340420 CCAACTTATTGGAAAATTCATCTTGGTTGGTGG
1 CCAACTTATTGGAAAATTCATCTTGGTAGATGG
3340453 CCAACTTATTGGAAAATTCATCTTTGGTAGATGG
1 CCAACTTATTGGAAAATTCATC-TTGGTAGATGG
3340487 CCAACTT
1 CCAACTT
3340494 TGCACATGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (33 bp):
CCAACTTATTGGAAAATTCATCTTGGTAGATGG
Found at i:3343949 original size:3 final size:3
Alignment explanation
Indices: 3343941--3343986 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3343931 GTGAGGCAAT
3343941 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3343987 GGAAATATCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3344223 original size:23 final size:23
Alignment explanation
Indices: 3344197--3344265 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
3344187 CACCACAGCT
* *
3344197 CGTATAACTGCATCGAAGTGCCA
1 CGTAGAACTGCACCGAAGTGCCA
* *
3344220 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAACTGCACCGAAGTGCCA
* * *
3344243 CATAGAATTGCACCGTAGTGCCA
1 CGTAGAACTGCACCGAAGTGCCA
3344266 TATAAGATTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAACTGCACCGAAGTGCCA
Found at i:3344275 original size:23 final size:23
Alignment explanation
Indices: 3344205--3344265 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
3344195 CTCGTATAAC
* *
3344205 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
*
3344228 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
*
3344251 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
3344266 TATAAGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:3344530 original size:31 final size:30
Alignment explanation
Indices: 3344487--3344545 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
3344477 ATTGTATAGG
*
3344487 CATATAATTTCCATACCTT-TATCACATAAA
1 CATATAATTTCCAT-CATTGTATCACATAAA
*
3344517 CATATCATGTTCCATCATTGTATCACATA
1 CATATAAT-TTCCATCATTGTATCACATA
3344546 GCTTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (30 bp):
CATATAATTTCCATCATTGTATCACATAAA
Found at i:3347364 original size:16 final size:16
Alignment explanation
Indices: 3347343--3347375 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3347333 TATGTTTGGT
3347343 TTGAAAGTTGACAAAG
1 TTGAAAGTTGACAAAG
*
3347359 TTGAAAGTTGGCAAAG
1 TTGAAAGTTGACAAAG
3347375 T
1 T
3347376 CGACATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.27
Consensus pattern (16 bp):
TTGAAAGTTGACAAAG
Found at i:3347422 original size:33 final size:34
Alignment explanation
Indices: 3347379--3347468 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 34
3347369 GCAAAGTCGA
3347379 CATCTTTGGTTGGTGGCCAACTTATTGGAAAATT
1 CATCTTTGGTTGGTGGCCAACTTATTGGAAAATT
*
3347413 CATC-TTGGTTGGTGGCCAATTTATTGGAAAATT
1 CATCTTTGGTTGGTGGCCAACTTATTGGAAAATT
* *
3347446 CATCTTTGGTAGGTGACCAACTT
1 CATCTTTGGTTGGTGGCCAACTT
3347469 TATAAGTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 32 0.63
34 19 0.37
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (34 bp):
CATCTTTGGTTGGTGGCCAACTTATTGGAAAATT
Found at i:3349069 original size:16 final size:16
Alignment explanation
Indices: 3349050--3349178 Score: 107
Period size: 16 Copynumber: 8.1 Consensus size: 16
3349040 AATTTAGCAA
3349050 AACCGAAATTAACCCG
1 AACCGAAATTAACCCG
* ** *
3349066 AACCAAAAGCAACAAC-
1 AACCGAAATTAAC-CCG
3349082 AACCGAAATTAACCCG
1 AACCGAAATTAACCCG
* **
3349098 AACCAAAAGCAACCCG
1 AACCGAAATTAACCCG
* *
3349114 AACCGAATTTAACACG
1 AACCGAAATTAACCCG
*
3349130 AACCGAATTTAACCCG
1 AACCGAAATTAACCCG
* ** *
3349146 ATCCGAAAGCAACCTG
1 AACCGAAATTAACCCG
*
3349162 AACCGAATTTAACCCG
1 AACCGAAATTAACCCG
3349178 A
1 A
3349179 TCCAAAAACA
Statistics
Matches: 84, Mismatches: 27, Indels: 4
0.73 0.23 0.03
Matches are distributed among these distances:
15 1 0.01
16 82 0.98
17 1 0.01
ACGTcount: A:0.45, C:0.31, G:0.12, T:0.12
Consensus pattern (16 bp):
AACCGAAATTAACCCG
Found at i:3349071 original size:32 final size:32
Alignment explanation
Indices: 3349050--3349133 Score: 125
Period size: 32 Copynumber: 2.6 Consensus size: 32
3349040 AATTTAGCAA
3349050 AACCGAAATTAACCCGAACCAAAAGCAACAAC
1 AACCGAAATTAACCCGAACCAAAAGCAACAAC
*
3349082 AACCGAAATTAACCCGAACCAAAAGCAAC-CC
1 AACCGAAATTAACCCGAACCAAAAGCAACAAC
* *
3349113 GAACCGAATTTAACACGAACC
1 -AACCGAAATTAACCCGAACC
3349134 GAATTTAACC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
31 1 0.02
32 47 0.98
ACGTcount: A:0.49, C:0.32, G:0.11, T:0.08
Consensus pattern (32 bp):
AACCGAAATTAACCCGAACCAAAAGCAACAAC
Found at i:3349112 original size:48 final size:48
Alignment explanation
Indices: 3349060--3349165 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
3349050 AACCGAAATT
3349060 AACCCGAACCAAAAGCAACAAC-AACCGAAATTAACCCGAACCAAAAGC
1 AACCCGAACCAAAAGCAAC-ACGAACCGAAATTAACCCGAACCAAAAGC
* *** * * *
3349108 AACCCGAACCGAATTTAACACGAACCGAATTTAACCCGATCCGAAAGC
1 AACCCGAACCAAAAGCAACACGAACCGAAATTAACCCGAACCAAAAGC
*
3349156 AACCTGAACC
1 AACCCGAACC
3349166 GAATTTAACC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 2 0.04
48 47 0.96
ACGTcount: A:0.45, C:0.33, G:0.12, T:0.09
Consensus pattern (48 bp):
AACCCGAACCAAAAGCAACACGAACCGAAATTAACCCGAACCAAAAGC
Found at i:3349166 original size:48 final size:48
Alignment explanation
Indices: 3349082--3349174 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
3349072 AAGCAACAAC
3349082 AACCGAAATTAACCCGAACCAAAAGCAACCCGAACCGAATTTAACACG
1 AACCGAAATTAACCCGAACCAAAAGCAACCCGAACCGAATTTAACACG
* * * *
3349130 AACCGAATTTAACCCGATCCGAAAGCAACCTGAACCGAATTTAAC
1 AACCGAAATTAACCCGAACCAAAAGCAACCCGAACCGAATTTAAC
3349175 CCGATCCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.43, C:0.30, G:0.13, T:0.14
Consensus pattern (48 bp):
AACCGAAATTAACCCGAACCAAAAGCAACCCGAACCGAATTTAACACG
Found at i:3349192 original size:27 final size:31
Alignment explanation
Indices: 3349130--3349195 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
3349120 ATTTAACACG
*
3349130 AACCGAATTTAACCCGATCCGAAAGCAACCTG
1 AACCGAATTTAACCCGATCCGAAA-CAACCTA
3349162 AACCGAATTTAACCCGATCC-AAA-AA-C-A
1 AACCGAATTTAACCCGATCCGAAACAACCTA
3349189 AACCGAA
1 AACCGAA
3349196 CAAATTGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 7 0.21
28 1 0.03
29 2 0.06
31 3 0.09
32 20 0.61
ACGTcount: A:0.44, C:0.30, G:0.12, T:0.14
Consensus pattern (31 bp):
AACCGAATTTAACCCGATCCGAAACAACCTA
Found at i:3351647 original size:20 final size:19
Alignment explanation
Indices: 3351622--3351674 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
3351612 AATAGCCTGA
*
3351622 GTGCATCGATGCATGGTCTT
1 GTGCATCGATGCATGGT-AT
3351642 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
*
3351661 ATGCATCGATGCAT
1 GTGCATCGATGCAT
3351675 AAAATGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:3354421 original size:44 final size:44
Alignment explanation
Indices: 3354366--3354462 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
3354356 GCTCTTGTGC
* * *
3354366 ATCGATGCACATTC-AAGGGCGTGCATCGGTGCATCAGTTGA-TGT
1 ATCGATGCACATTCAAAGGG-ATGCATCGGCGCA-CAGTTAAGTGT
*
3354410 ATCGATGCACATTCAAAGGGATGCATCGGCGCACTGTTAAGTGT
1 ATCGATGCACATTCAAAGGGATGCATCGGCGCACAGTTAAGTGT
3354454 ATCGATGCA
1 ATCGATGCA
3354463 TTAAGCACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 5 0.11
44 37 0.79
45 5 0.11
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (44 bp):
ATCGATGCACATTCAAAGGGATGCATCGGCGCACAGTTAAGTGT
Found at i:3357550 original size:14 final size:14
Alignment explanation
Indices: 3357531--3357561 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3357521 TGTCAATGAC
3357531 TTTACAACCATTAA
1 TTTACAACCATTAA
3357545 TTTACAACCATTAA
1 TTTACAACCATTAA
3357559 TTT
1 TTT
3357562 CAAACATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTACAACCATTAA
Found at i:3364015 original size:12 final size:12
Alignment explanation
Indices: 3364000--3364031 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3363990 TAATAATGTT
3364000 AATAATGATAAG
1 AATAATGATAAG
*
3364012 AATAATAATAAG
1 AATAATGATAAG
3364024 AATAATGA
1 AATAATGA
3364032 AATGCTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (12 bp):
AATAATGATAAG
Found at i:3369211 original size:13 final size:15
Alignment explanation
Indices: 3369190--3369232 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
3369180 CAGATAAAAT
3369190 TTTTATATAAATAAC
1 TTTTATATAAATAAC
*
3369205 TTTTATATAAATAAT
1 TTTTATATAAATAAC
*
3369220 TTTTATTTAAATA
1 TTTTATATAAATA
3369233 TTTAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTATATAAATAAC
Found at i:3370490 original size:93 final size:93
Alignment explanation
Indices: 3370331--3370509 Score: 313
Period size: 93 Copynumber: 1.9 Consensus size: 93
3370321 GTCACACCCA
* *
3370331 GAAGAGGAAGAGAAAGGGAATGAAAGCATCGAACTGAAAGTTGGACATGAGATCTAGACAATATT
1 GAAGAGGAAGAGAAAGGGAATGAAAGCATCAAACTGAAAGTTGGACATGAGATCTAGACAAGATT
3370396 TTTGGACTTGAAGAACAAAAACAACGAG
66 TTTGGACTTGAAGAACAAAAACAACGAG
* * *
3370424 GAAGAGGAAGAGAAATGGAATGAAAGCATCAAACTGAAAGTTGGACGTGAGATCTATACAAGATT
1 GAAGAGGAAGAGAAAGGGAATGAAAGCATCAAACTGAAAGTTGGACATGAGATCTAGACAAGATT
3370489 TTTGGACTTGAAGAACAAAAA
66 TTTGGACTTGAAGAACAAAAA
3370510 TAATGAGTGA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 81 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.18
Consensus pattern (93 bp):
GAAGAGGAAGAGAAAGGGAATGAAAGCATCAAACTGAAAGTTGGACATGAGATCTAGACAAGATT
TTTGGACTTGAAGAACAAAAACAACGAG
Found at i:3371304 original size:37 final size:37
Alignment explanation
Indices: 3371263--3371336 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3371253 CTTACAGAAG
3371263 TATGTTAAATAGCTGTGTTCTTGGTGTAATATTTCTT
1 TATGTTAAATAGCTGTGTTCTTGGTGTAATATTTCTT
3371300 TATGTTAAATAGCTGTGTTCTTGGTGTAATATTTCTT
1 TATGTTAAATAGCTGTGTTCTTGGTGTAATATTTCTT
3371337 CATTTCTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (37 bp):
TATGTTAAATAGCTGTGTTCTTGGTGTAATATTTCTT
Found at i:3382235 original size:45 final size:45
Alignment explanation
Indices: 3382178--3382357 Score: 193
Period size: 45 Copynumber: 3.8 Consensus size: 45
3382168 TAATAAGGTT
*
3382178 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATAATTTATTTTAAAATA
* * *
3382223 ATTTATTATAAAATAATTTATTATAAAATAGTTTACTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATAATTTATTTTAAAATA
*
3382268 AATTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTTT-AAATA
1 ATTTATTAT-AAA-AT--A---ATTTATTTTAAAATAATTTATTTTAAAATA
* *
3382319 ATTTATTAGTATGAATTGATTTATTTT-AAATAATTTATT
1 ATTTATTA-TA--AAATAATTTATTTTAAAATAATTTATT
3382358 AGTATGGATT
Statistics
Matches: 114, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
45 49 0.43
46 15 0.13
47 11 0.10
49 1 0.01
51 13 0.11
52 23 0.20
53 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (45 bp):
ATTTATTATAAAATAATTTATTTTAAAATAATTTATTTTAAAATA
Found at i:3382319 original size:14 final size:15
Alignment explanation
Indices: 3382178--3382357 Score: 175
Period size: 15 Copynumber: 11.5 Consensus size: 15
3382168 TAATAAGGTT
3382178 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
3382193 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
3382208 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
3382223 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
3382238 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
* *
3382253 GTTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
3382268 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
3382287 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
3382305 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
3382319 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
3382337 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
3382351 ATTTATT
1 ATTTATT
3382358 AGTATGGATT
Statistics
Matches: 140, Mismatches: 14, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
14 22 0.16
15 85 0.61
16 6 0.04
17 3 0.02
18 11 0.08
19 1 0.01
20 2 0.01
21 4 0.03
22 6 0.04
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:3382342 original size:18 final size:18
Alignment explanation
Indices: 3382319--3382375 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
3382309 ATTTTAAATA
3382319 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
3382337 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
3382351 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
3382369 ATTTATT
1 ATTTATT
3382376 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:3382344 original size:32 final size:32
Alignment explanation
Indices: 3382305--3382676 Score: 215
Period size: 32 Copynumber: 12.4 Consensus size: 32
3382295 TTTTAAAATA
*
3382305 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3382337 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
** **
3382369 ATTTATTTTAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTG
* * * * * *
3382398 ATTGTAGTTGTGTGGATTGATTTATTTTA-AAT-AATTT
1 ATT-TA-TT-T-T-AAATAATTTA--TTAGTATGGATTG
* * * * *
3382435 ATTAGTATGTATTGATTTATTT-TAAAATATGGATTG
1 ATT--TAT-T-TTAAATAATTTAT-TAGTATGGATTG
3382471 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3382503 ATTTATTTT-AA-AA--TA-T-G-A---ATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
3382525 ATTTATTTTAAAA----------TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3382547 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3382579 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3382601 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3382633 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3382665 ATTTATTTTAAA
1 ATTTATTTTAAA
3382677 ATATGGATTG
Statistics
Matches: 273, Mismatches: 23, Indels: 88
0.71 0.06 0.23
Matches are distributed among these distances:
19 1 0.00
22 43 0.16
23 6 0.02
25 2 0.01
26 4 0.01
27 1 0.00
28 5 0.02
29 4 0.01
30 9 0.03
31 10 0.04
32 143 0.52
33 4 0.01
34 8 0.03
35 2 0.01
36 19 0.07
37 7 0.03
38 5 0.02
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:3382397 original size:54 final size:54
Alignment explanation
Indices: 3382328--3382993 Score: 515
Period size: 54 Copynumber: 12.3 Consensus size: 54
3382318 AATTTATTAG
*
3382328 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
3382382 TATGGATTGATTTA--TT--AT--TGTAGTT-GTGTGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
** * * ** * * *
3382429 TAATTTATTAGTATGTA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAA
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * * *
3382483 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTGATTTATTTTAAAA
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
3382538 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
3382592 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * * ***
3382645 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTG
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAA
*
3382704 TATGGATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
3382758 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * ** ** * ** * * *
3382812 TATGAATTGACTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
* * * ***
3382866 TATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAA
3382924 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
3382978 TATGGATTGATTTATT
1 TATGGATTGATTTATT
3382994 ATTGTAGTTG
Statistics
Matches: 498, Mismatches: 82, Indels: 64
0.77 0.13 0.10
Matches are distributed among these distances:
47 4 0.01
48 26 0.05
49 3 0.01
50 6 0.01
51 1 0.00
52 8 0.02
53 26 0.05
54 296 0.59
55 29 0.06
56 15 0.03
57 15 0.03
58 68 0.14
59 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:3382456 original size:22 final size:22
Alignment explanation
Indices: 3382440--3382558 Score: 103
Period size: 22 Copynumber: 5.0 Consensus size: 22
3382430 AATTTATTAG
*
3382440 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3382462 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
3382486 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
*
3382516 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3382538 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
3382559 TAATTTATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
22 43 0.54
23 2 0.03
24 2 0.03
25 2 0.03
26 10 0.13
27 2 0.03
28 10 0.13
29 2 0.03
30 2 0.03
31 2 0.03
32 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:3382595 original size:22 final size:22
Alignment explanation
Indices: 3382570--3382612 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3382560 AATTTATTAG
3382570 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3382592 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
3382613 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:3382669 original size:296 final size:300
Alignment explanation
Indices: 3382305--3383088 Score: 1386
Period size: 296 Copynumber: 2.6 Consensus size: 300
3382295 TTTTAAAATA
*
3382305 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
*
3382370 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTGTGGATTGATTTATTTTAAATAATTT
66 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTT
*
3382435 ATTAGTATGTATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
131 ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
*
3382500 TTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTT
196 TTGATTTATTTTAAAATATGAATTGACTTATTTTAAAATATGGATTGATTTATTTTAAATAATTT
* *
3382565 ATTAGTATGGATTGATTTATTTT-AA-AA-TA-TGGATTG
261 ATTAGTATAGATTGATTTATTTTAAATAATTATTGGATAG
3382601 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
3382666 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTT
66 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTT
*
3382731 ATTAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
131 ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
3382796 TTGATTTATTTTAAAATATGAATTGACTTATTTTAAAATATGGATTGATTTATTTTAAATAATTT
196 TTGATTTATTTTAAAATATGAATTGACTTATTTTAAAATATGGATTGATTTATTTTAAATAATTT
*
3382861 ATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATAG
261 ATTAGTATAGATTGATTTATTTTAAATAA-TTA-TTGGATAG
* *
3382903 ATTGA-TTT--ATTATTGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATT
1 ATTTATTTTAAATAATT-TA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATT
3382964 GATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAAT
64 GATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAAT
3383029 TTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
129 TTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
3383089 TTGTAGTTGT
Statistics
Matches: 469, Mismatches: 11, Indels: 12
0.95 0.02 0.02
Matches are distributed among these distances:
296 277 0.59
297 2 0.00
298 2 0.00
299 5 0.01
300 169 0.36
301 5 0.01
302 9 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (300 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTT
ATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
TTGATTTATTTTAAAATATGAATTGACTTATTTTAAAATATGGATTGATTTATTTTAAATAATTT
ATTAGTATAGATTGATTTATTTTAAATAATTATTGGATAG
Found at i:3382681 original size:22 final size:22
Alignment explanation
Indices: 3382656--3382854 Score: 83
Period size: 22 Copynumber: 8.0 Consensus size: 22
3382646 AATTTATTAG
3382656 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
3382678 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
3382704 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
** *
3382728 TTTATTAATATGGATTGATTTATTTTAAAA
1 --TATGGAT-T-GATTTA-TT---TTAAAA
3382758 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
3382782 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
* *
3382812 TATGAATTGACTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3382834 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
3382855 TAATTTATTA
Statistics
Matches: 132, Mismatches: 21, Indels: 48
0.66 0.10 0.24
Matches are distributed among these distances:
22 41 0.31
23 4 0.03
24 7 0.05
25 7 0.05
26 33 0.25
27 4 0.03
28 20 0.15
29 4 0.03
30 4 0.03
31 4 0.03
32 4 0.03
ACGTcount: A:0.35, C:0.01, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:3382745 original size:32 final size:32
Alignment explanation
Indices: 3382703--3382810 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
3382693 TATTGTAGTT
3382703 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
3382735 ATATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
3382758 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
3382789 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
3382811 ATATGAATTG
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
22 14 0.22
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 35 0.54
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:3382862 original size:14 final size:14
Alignment explanation
Indices: 3382843--3382896 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
3382833 ATATGGATTG
3382843 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
3382857 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
3382875 ATTTATTTTAAATA
1 ATTTATTTTAAATA
3382889 ATTTATTT
1 ATTTATTT
3382897 GTATAGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:3382874 original size:32 final size:32
Alignment explanation
Indices: 3382838--3382976 Score: 184
Period size: 32 Copynumber: 4.5 Consensus size: 32
3382828 TTAAAATATG
3382838 GATTGATTTATTTTAAATAATTTATTAGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
*
3382870 GATTGATTTATTTTAAATAATTTATTTGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
* *
3382902 GATTGATTTA--TT--AT--TGTAGTT-GTATG
1 GATTGATTTATTTTAAATAATTTA-TTAGTATA
*
3382928 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATA
3382960 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
3382977 ATATGGATTG
Statistics
Matches: 95, Mismatches: 4, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
26 17 0.18
27 2 0.02
28 4 0.04
30 4 0.04
31 2 0.02
32 66 0.69
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAGTATA
Found at i:3382880 original size:18 final size:18
Alignment explanation
Indices: 3382857--3382914 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
3382847 ATTTTAAATA
3382857 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAGATTG
* *
3382875 ATTTATT--T-TA-AATA
1 ATTTATTAGTATAGATTG
*
3382889 ATTTATTTGTATAGATTG
1 ATTTATTAGTATAGATTG
3382907 ATTTATTA
1 ATTTATTA
3382915 TTGTAGTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 9 0.29
15 2 0.06
16 2 0.06
17 2 0.06
18 16 0.52
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (18 bp):
ATTTATTAGTATAGATTG
Found at i:3382924 original size:26 final size:26
Alignment explanation
Indices: 3382895--3383019 Score: 107
Period size: 26 Copynumber: 4.7 Consensus size: 26
3382885 AATAATTTAT
*
3382895 TTGTATAGATTGATTTATTATTGTAG
1 TTGTATGGATTGATTTATTATTGTAG
*
3382921 TTGTATGGATTGATTTATTTTAAATAATTTA-
1 TTGTATGGATTGATTTA--TT--AT--TGTAG
3382952 TTAGTATGGATTGATTTA-T-TT-TA-
1 TT-GTATGGATTGATTTATTATTGTAG
***
3382975 AAATATGGATTGATTTATTATTGTAG
1 TTGTATGGATTGATTTATTATTGTAG
3383001 TTGTATGGATTGATTTATT
1 TTGTATGGATTGATTTATT
3383020 TTAAATAATT
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
22 14 0.17
23 3 0.04
24 3 0.04
25 2 0.03
26 33 0.41
28 2 0.03
29 1 0.01
30 2 0.03
31 2 0.03
32 18 0.22
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.54
Consensus pattern (26 bp):
TTGTATGGATTGATTTATTATTGTAG
Found at i:3382970 original size:18 final size:18
Alignment explanation
Indices: 3382947--3382994 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
3382937 ATTTTAAATA
*
3382947 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
3382965 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
3382987 ATTTATTA
1 ATTTATTA
3382995 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:3382996 original size:80 final size:80
Alignment explanation
Indices: 3382902--3383073 Score: 344
Period size: 80 Copynumber: 2.1 Consensus size: 80
3382892 TATTTGTATA
3382902 GATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 GATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
3382967 TTATTTTAAAATATG
66 TTATTTTAAAATATG
3382982 GATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 GATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
3383047 TTATTTTAAAATATG
66 TTATTTTAAAATATG
3383062 GATTGATTTATT
1 GATTGATTTATT
3383074 TTAAATAATT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 92 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (80 bp):
GATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
TTATTTTAAAATATG
Found at i:3383061 original size:22 final size:22
Alignment explanation
Indices: 3383036--3383078 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3383026 AATTTATTAG
3383036 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3383058 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
3383079 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:3383073 original size:54 final size:54
Alignment explanation
Indices: 3382410--3383088 Score: 359
Period size: 54 Copynumber: 12.5 Consensus size: 54
3382400 TGTAGTTGTG
*
3382410 TGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
3382464 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
* ** ** * ** * * *
3382518 TGAATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATA
** ** * ** * * *
3382572 TGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATA
3382626 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
*
3382680 TGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA
1 TGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATA
* * * ** * * *
3382727 ---ATTTATTAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTT-AAATAA
1 TGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTATTTTAAAAT-A
** ** * ** * * * * *
3382782 TTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTGACTTATTTTAAAATA
1 TGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
*
3382836 TGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA
* * * *
3382894 TTTGTATAGATTGA-TTT--ATTATTGTAGTT-GTATGGATTGATTTATTTT-AAATAA
1 --TGGATTGATTTATTTTAAATAATT-TA-TTAGTATGGATTGATTTATTTTAAAAT-A
** ** * ** * * * ***
3382948 TTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTGTA
1 TGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATA
3383006 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
3383060 TGGATTGATTTATTTTAAATAATTTATTA
1 TGGATTGATTTATTTTAAATAATTTATTA
3383089 TTGTAGTTGT
Statistics
Matches: 493, Mismatches: 85, Indels: 94
0.73 0.13 0.14
Matches are distributed among these distances:
44 7 0.01
46 1 0.00
47 5 0.01
48 23 0.05
49 2 0.00
50 5 0.01
51 2 0.00
52 12 0.02
53 23 0.05
54 284 0.58
55 25 0.05
56 16 0.03
57 17 0.03
58 45 0.09
59 14 0.03
60 12 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
Found at i:3383137 original size:31 final size:31
Alignment explanation
Indices: 3383102--3383161 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
3383092 TAGTTGTATG
*
3383102 AATTATTTAAAT-TTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTT-AGTATTGCAAAACTAA
3383133 AATTATTTAAATCTTAGTATTGCAAAACT
1 AATTATTTAAATCTTAGTATTGCAAAACT
3383162 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTTAGTATTGCAAAACTAA
Found at i:3383198 original size:16 final size:16
Alignment explanation
Indices: 3383179--3383221 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
3383169 GTTTTAAAAA
3383179 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
3383195 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
* *
3383211 TTAGTTCATTT
1 TCAGTTTATTT
3383222 TAGCAGTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:3383878 original size:24 final size:25
Alignment explanation
Indices: 3383851--3383916 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 25
3383841 CATGCATGAA
3383851 TCCTTGGTCGCC-TGCATGGCGACC
1 TCCTTGGTCGCCGTGCATGGCGACC
3383875 TCCTTGGTCGCCGGGCGTGCATGGCGACC
1 TCCTTGGTCG-C---CGTGCATGGCGACC
3383904 TCCTTGGTCGCCG
1 TCCTTGGTCGCCG
3383917 GGCGTGCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
24 10 0.27
25 3 0.08
28 2 0.05
29 22 0.59
ACGTcount: A:0.06, C:0.36, G:0.33, T:0.24
Consensus pattern (25 bp):
TCCTTGGTCGCCGTGCATGGCGACC
Found at i:3383905 original size:29 final size:29
Alignment explanation
Indices: 3383863--3383933 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
3383853 CTTGGTCGCC
3383863 TGCATGGCGACCTCCTTGGTCGCCGGGCG
1 TGCATGGCGACCTCCTTGGTCGCCGGGCG
3383892 TGCATGGCGACCTCCTTGGTCGCCGGGCG
1 TGCATGGCGACCTCCTTGGTCGCCGGGCG
3383921 TGCATGGCGACCT
1 TGCATGGCGACCT
3383934 AGGAGGTCGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.08, C:0.34, G:0.37, T:0.21
Consensus pattern (29 bp):
TGCATGGCGACCTCCTTGGTCGCCGGGCG
Found at i:3383941 original size:29 final size:29
Alignment explanation
Indices: 3383863--3383963 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 29
3383853 CTTGGTCGCC
* **
3383863 TGCATGGCGACCTCCTTGGTCGCCGGGCG
1 TGCATGGCGACCTACGAGGTCGCCGGGCG
* **
3383892 TGCATGGCGACCTCCTTGGTCGCCGGGCG
1 TGCATGGCGACCTACGAGGTCGCCGGGCG
* * *
3383921 TGCATGGCGACCTAGGAGGTCGCTGGGAG
1 TGCATGGCGACCTACGAGGTCGCCGGGCG
*
3383950 TGCATAGCGACCTA
1 TGCATGGCGACCTA
3383964 TGGTTGGGTT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.13, C:0.30, G:0.38, T:0.20
Consensus pattern (29 bp):
TGCATGGCGACCTACGAGGTCGCCGGGCG
Found at i:3385904 original size:16 final size:16
Alignment explanation
Indices: 3385871--3385911 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3385861 GTTTATTTCA
3385871 GAATGATT-AAGCGTT
1 GAATGATTCAAGCGTT
*
3385886 GAATGATTCAAGTGTT
1 GAATGATTCAAGCGTT
*
3385902 GAATTATTCA
1 GAATGATTCA
3385912 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (16 bp):
GAATGATTCAAGCGTT
Found at i:3387385 original size:35 final size:36
Alignment explanation
Indices: 3387346--3387413 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
3387336 AAAGAGTGTA
*
3387346 TATCTATTTAATATTTA-ATATTTAAA-ATATATTAT
1 TATCTATTTAA-ATTTATATATTAAAAGATATATTAT
3387381 TATCTATTTAAATTTATATATTAAAAGATATAT
1 TATCTATTTAAATTTATATATTAAAAGATATAT
3387414 GGTTGGAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 5 0.17
35 19 0.63
36 6 0.20
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (36 bp):
TATCTATTTAAATTTATATATTAAAAGATATATTAT
Found at i:3387502 original size:83 final size:83
Alignment explanation
Indices: 3387352--3387504 Score: 218
Period size: 83 Copynumber: 1.8 Consensus size: 83
3387342 TGTATATCTA
* * * * *
3387352 TTTAATATTTAATATTTAAAATATATTATTATCTATTTAAATTTATATATTAAAAGATATATGGT
1 TTTAATATTTAATATTTAAAAGATATCATTATCTATTTAAATTTAGATATTAAAAGAGATATAGT
3387417 TGGAGTAAATATCTCATG
66 TGGAGTAAATATCTCATG
* * *
3387435 TTTAATATTTTAA-ATTTAAGAGATATCATTATCTGTTTAAATTTAGATATTAAAAGAGATTTAG
1 TTTAATA-TTTAATATTTAAAAGATATCATTATCTATTTAAATTTAGATATTAAAAGAGATATAG
3387499 TTGGAG
65 TTGGAG
3387505 AAAAACTCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 56 0.92
84 5 0.08
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (83 bp):
TTTAATATTTAATATTTAAAAGATATCATTATCTATTTAAATTTAGATATTAAAAGAGATATAGT
TGGAGTAAATATCTCATG
Found at i:3388551 original size:17 final size:17
Alignment explanation
Indices: 3388529--3388568 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3388519 CTCTTCTTTC
3388529 TCTCCCTTTTTCTTCCT
1 TCTCCCTTTTTCTTCCT
3388546 TCTCCCTTTTTCTTCCT
1 TCTCCCTTTTTCTTCCT
*
3388563 CCTCCC
1 TCTCCC
3388569 CGTGGAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (17 bp):
TCTCCCTTTTTCTTCCT
Found at i:3389751 original size:22 final size:21
Alignment explanation
Indices: 3389701--3389752 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3389691 TGACAGAGTT
* *
3389701 ACTGTAACAGGGTATCGGTAC
1 ACTGTAGCAGGGTATCGATAC
3389722 ACTGTAGCAGGGTATCGATACC
1 ACTGTAGCAGGGTATCGATA-C
*
3389744 CCTGTAGCA
1 ACTGTAGCA
3389753 TTCTGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGGGTATCGATAC
Found at i:3390749 original size:23 final size:23
Alignment explanation
Indices: 3390716--3390759 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3390706 GAGTCGAGGG
3390716 TCTACGCGGTCATTCGGGACAAT
1 TCTACGCGGTCATTCGGGACAAT
* *
3390739 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCATTCGGGACA
3390760 TATATGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCATTCGGGACAAT
Found at i:3390915 original size:24 final size:24
Alignment explanation
Indices: 3390888--3390933 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3390878 TACGGTTCAT
*
3390888 TTCTACGCGGTACTTCGGTGCAAA
1 TTCTACGCGGCACTTCGGTGCAAA
*
3390912 TTCTACGTGGCACTTCGGTGCA
1 TTCTACGCGGCACTTCGGTGCA
3390934 TTTATATGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (24 bp):
TTCTACGCGGCACTTCGGTGCAAA
Found at i:3395977 original size:20 final size:23
Alignment explanation
Indices: 3395937--3395977 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
3395927 TCAGAACTCA
3395937 TCATGACCACTTTGAGTTTAAAG
1 TCATGACCACTTTGAGTTTAAAG
3395960 TCATG-CCA-TTTG-GTTTAA
1 TCATGACCACTTTGAGTTTAA
3395978 CAAATGCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 3 0.17
23 5 0.28
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (23 bp):
TCATGACCACTTTGAGTTTAAAG
Found at i:3401503 original size:15 final size:15
Alignment explanation
Indices: 3401480--3401515 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3401470 TAAAATAATG
* *
3401480 TTTTTATAATTTGAA
1 TTTTAATAATTTAAA
3401495 TTTTAATAATTTAAA
1 TTTTAATAATTTAAA
3401510 TTTTAA
1 TTTTAA
3401516 AAATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTAATAATTTAAA
Found at i:3403328 original size:27 final size:27
Alignment explanation
Indices: 3403294--3403363 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
3403284 ACATTATATC
3403294 ATATTATTTAATATTTATATGTGTG-T
1 ATATTATTTAATATTTATATGTGTGAT
3403320 ATATCTATTT-ATA-TTATATGTGTGTAT
1 ATAT-TATTTAATATTTATATGTGTG-AT
3403347 ATATTTATTTAATATTT
1 ATA-TTATTTAATATTT
3403364 CTTAACCCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
25 11 0.29
26 7 0.18
27 14 0.37
28 4 0.11
29 2 0.05
ACGTcount: A:0.31, C:0.01, G:0.09, T:0.59
Consensus pattern (27 bp):
ATATTATTTAATATTTATATGTGTGAT
Found at i:3403351 original size:23 final size:25
Alignment explanation
Indices: 3403298--3403354 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
3403288 TATATCATAT
3403298 TATTTAATATTTATATGTGTGTATATC
1 TATTT-ATATTTATATGTGTGTATA-C
3403325 TATTTATA-TTATATGTGTGTATA-
1 TATTTATATTTATATGTGTGTATAC
3403348 TATTTAT
1 TATTTAT
3403355 TTAATATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.23
25 15 0.50
26 3 0.10
27 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.58
Consensus pattern (25 bp):
TATTTATATTTATATGTGTGTATAC
Found at i:3405288 original size:31 final size:32
Alignment explanation
Indices: 3405218--3405289 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
3405208 ACCGAATAAA
* * *
3405218 AAAAT-GATCAATTTGATATTGACTTAACTCG
1 AAAATCGATCAATTTAATATTGACTCAAATCG
3405249 AAAATCGATCAATTTAATATTGA-TCAGAATCG
1 AAAATCGATCAATTTAATATTGACTCA-AATCG
3405281 -AAATCGATC
1 AAAATCGATC
3405290 TGATATTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 16 0.44
32 20 0.56
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (32 bp):
AAAATCGATCAATTTAATATTGACTCAAATCG
Found at i:3412386 original size:27 final size:25
Alignment explanation
Indices: 3412327--3412386 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
3412317 ATTAGCTTCA
3412327 TGTATTTATATTATTATTTTTAAGT
1 TGTATTTATATTATTATTTTTAAGT
*
3412352 TATAATTTAT-TTCAATTATTTTTAATGT
1 TGT-ATTTATATT--ATTATTTTTAA-GT
3412380 TGTATTT
1 TGTATTT
3412387 TCTGCGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 4 0.14
26 6 0.21
27 15 0.52
28 4 0.14
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (25 bp):
TGTATTTATATTATTATTTTTAAGT
Found at i:3423194 original size:4 final size:4
Alignment explanation
Indices: 3423185--3423212 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3423175 CAACTATGTA
3423185 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
3423213 ACATGCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:3424699 original size:25 final size:24
Alignment explanation
Indices: 3424652--3424701 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
3424642 AAATATTAAC
3424652 AAATAAAATAATAAAAATAATATG
1 AAATAAAATAATAAAAATAATATG
*
3424676 AAATGAAAATAAATAAATATATATAT
1 AAAT-AAAAT-AATAAAAATA-ATAT
3424702 ATATATACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 5 0.23
26 9 0.41
27 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
AAATAAAATAATAAAAATAATATG
Found at i:3425965 original size:16 final size:17
Alignment explanation
Indices: 3425932--3425965 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3425922 CGGGATTTCA
*
3425932 TTTATTTTTTTATTATT
1 TTTATTGTTTTATTATT
3425949 TTTATTGTTTT-TTATT
1 TTTATTGTTTTATTATT
3425965 T
1 T
3425966 GACATCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTATTGTTTTATTATT
Found at i:3430297 original size:34 final size:33
Alignment explanation
Indices: 3430250--3430326 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 33
3430240 ATTACAGATC
*
3430250 TTATATTTAATTTTAAATTTCGAATAATATTATTT
1 TTAT-TTTAATTTTAAATTTCGAAT-ATATAATTT
*
3430285 TTATTTTTATTTTAAATTTCGAATATATAATTT
1 TTATTTTAATTTTAAATTTCGAATATATAATTT
*
3430318 GTATTTTAA
1 TTATTTTAA
3430327 AAACATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 15 0.39
34 19 0.50
35 4 0.11
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (33 bp):
TTATTTTAATTTTAAATTTCGAATATATAATTT
Found at i:3430877 original size:21 final size:21
Alignment explanation
Indices: 3430853--3430934 Score: 121
Period size: 21 Copynumber: 3.9 Consensus size: 21
3430843 ATAAAACCCT
*
3430853 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
3430874 GCGGGCTAGGAATGTAACCCT-
1 GCGGGCTAGGAATGTAA-CCTG
* *
3430895 GTGGGCTCGGAATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
3430916 GCGGGCTAGGAATGTAACC
1 GCGGGCTAGGAATGTAACC
3430935 CTGCAGAGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 3 0.06
21 48 0.89
22 3 0.06
ACGTcount: A:0.22, C:0.22, G:0.37, T:0.20
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:3430910 original size:42 final size:42
Alignment explanation
Indices: 3430847--3430938 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
3430837 TATGGTATAA
*
3430847 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGT
* *
3430889 AACCCTGTGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGT
3430931 AACCCTGC
1 AACCCTGC
3430939 AGAGATGGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.20
Consensus pattern (42 bp):
AACCCTGCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:3430970 original size:21 final size:21
Alignment explanation
Indices: 3430944--3430991 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3430934 CCTGCAGAGA
*
3430944 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
3430965 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
3430986 GGGCAT
1 TGGCAT
3430992 GTACTCCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.25
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:3432541 original size:254 final size:248
Alignment explanation
Indices: 3432084--3432586 Score: 952
Period size: 254 Copynumber: 2.0 Consensus size: 248
3432074 CCTGAGCACA
3432084 TGCCTTTGCTTGATCCTCTGAAGCATTTTCATTTAAACCTCAAATTAGCTTCAACCAAGATAACG
1 TGCCTTTGCTTGATCCTCTGAAGCATTTTCATTTAAACCTCAAATTAGCTTCAACCAAGATAACG
3432149 CTATTCTATCTACATAAACTCTGGTGGAGCAGCTCCAAGATAATCAATGCACATTGACTTCCAAT
66 CTATTCTATCTACATAAACTCTGGTGGAGCAGCTCCAAGATAATCAATGCACATTGACTTCCAAT
3432214 CACCATCGCCATACCAACATCATGTTTCCGTCGACGGGAAGCCCCATATGCATAGAGACATCCTC
131 CACCATCGCCATACCAACATCATGTTTCCGTCGACGGGAAGCCCCATATGCATAGAGACATCCTC
3432279 CAATGTAATTGTGGCCTCTCCACATGGAAGGTGAAAAGTGTGTGTCTCGGGCC
196 CAATGTAATTGTGGCCTCTCCACATGGAAGGTGAAAAGTGTGTGTCTCGGGCC
3432332 TGCCTTTGCTTGATCCTCTGAAGCATTTTCATTTAAAACCTCAAAATTAGCTTTCAACCAAGATA
1 TGCCTTTGCTTGATCCTCTGAAGCATTTTCATTT-AAACCTC-AAATTAGC-TTCAACCAAGATA
3432397 ACGCTATTCTATCTACATTAAACTCTGGTGGAGCAGCTCCAAGATAATCAATGCACATTGACTTC
63 ACGCTATTCTATCTACA-TAAACTCTGGTGGAGCAGCTCCAAGATAATCAATGCACATTGACTTC
3432462 CAATCACCATCCGCCATACCACACATCATGTTTCCGTCGACGGGAAGCCCCATATGCATAGAGAC
127 CAATCACCAT-CGCCATACCA-ACATCATGTTTCCGTCGACGGGAAGCCCCATATGCATAGAGAC
3432527 ATCCTCCAATGTAATTGTGGCCTCTCCACATGGAAGGTGAAAAGTGTGTGTCTCGGGCC
190 ATCCTCCAATGTAATTGTGGCCTCTCCACATGGAAGGTGAAAAGTGTGTGTCTCGGGCC
3432586 T
1 T
3432587 CCACCTCTCA
Statistics
Matches: 249, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
248 34 0.14
249 7 0.03
250 8 0.03
251 30 0.12
252 57 0.23
253 10 0.04
254 103 0.41
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (248 bp):
TGCCTTTGCTTGATCCTCTGAAGCATTTTCATTTAAACCTCAAATTAGCTTCAACCAAGATAACG
CTATTCTATCTACATAAACTCTGGTGGAGCAGCTCCAAGATAATCAATGCACATTGACTTCCAAT
CACCATCGCCATACCAACATCATGTTTCCGTCGACGGGAAGCCCCATATGCATAGAGACATCCTC
CAATGTAATTGTGGCCTCTCCACATGGAAGGTGAAAAGTGTGTGTCTCGGGCC
Found at i:3434258 original size:11 final size:10
Alignment explanation
Indices: 3434204--3434260 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
3434194 AGAGGTTCAA
3434204 ACCGGTTTT-
1 ACCGGTTTTC
*
3434213 ACCGATTTTC
1 ACCGGTTTTC
*
3434223 AGCCGGTTTAC
1 A-CCGGTTTTC
*
3434234 CCCGGTTTT-
1 ACCGGTTTTC
3434243 ACCGGTTTTC
1 ACCGGTTTTC
3434253 AGCCGGTT
1 A-CCGGTT
3434261 CTTCCTGTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 16 0.42
10 9 0.24
11 13 0.34
ACGTcount: A:0.12, C:0.28, G:0.23, T:0.37
Consensus pattern (10 bp):
ACCGGTTTTC
Found at i:3434565 original size:32 final size:33
Alignment explanation
Indices: 3434527--3434623 Score: 115
Period size: 35 Copynumber: 2.8 Consensus size: 33
3434517 CTTCGTTAAC
* *
3434527 ATAAAGATAAGTAACTA-AAATAATTTAGATGA
1 ATAAAGATGAGTAAATATAAATAATTTAGATGA
*
3434559 ATAAAGATGAGTAAATATTGAAATAATTTAGGTGA
1 ATAAAGATGAGTAAATA-T-AAATAATTTAGATGA
*
3434594 ACAAAGATGAGTAAATATTGAAATAATTTA
1 ATAAAGATGAGTAAATA-T-AAATAATTTA
3434624 TGTTAAAGAG
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 15 0.26
35 43 0.74
ACGTcount: A:0.53, C:0.02, G:0.15, T:0.30
Consensus pattern (33 bp):
ATAAAGATGAGTAAATATAAATAATTTAGATGA
Found at i:3434600 original size:35 final size:35
Alignment explanation
Indices: 3434544--3434623 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
3434534 TAAGTAACTA
*
3434544 AAATAATTTAGATGAATAAAGATGAGTAAATATTG
1 AAATAATTTAGATGAACAAAGATGAGTAAATATTG
*
3434579 AAATAATTTAGGTGAACAAAGATGAGTAAATATTG
1 AAATAATTTAGATGAACAAAGATGAGTAAATATTG
3434614 AAATAATTTA
1 AAATAATTTA
3434624 TGTTAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.51, C:0.01, G:0.16, T:0.31
Consensus pattern (35 bp):
AAATAATTTAGATGAACAAAGATGAGTAAATATTG
Found at i:3434658 original size:10 final size:10
Alignment explanation
Indices: 3434642--3434702 Score: 113
Period size: 10 Copynumber: 6.1 Consensus size: 10
3434632 AGTCTTATTA
3434642 CGATTCCATC
1 CGATTCCATC
*
3434652 TGATTCCATC
1 CGATTCCATC
3434662 CGATTCCATC
1 CGATTCCATC
3434672 CGATTCCATC
1 CGATTCCATC
3434682 CGATTCCATC
1 CGATTCCATC
3434692 CGATTCCATC
1 CGATTCCATC
3434702 C
1 C
3434703 CCAGATGGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 49 1.00
ACGTcount: A:0.20, C:0.39, G:0.10, T:0.31
Consensus pattern (10 bp):
CGATTCCATC
Found at i:3438081 original size:27 final size:27
Alignment explanation
Indices: 3438051--3438106 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
3438041 TGCTAAATGA
* *
3438051 TTCAAAAACCTAATAAACCAATATAAG
1 TTCAAAAACCAAATAAACAAATATAAG
* * *
3438078 TTCAACAACCAAATATATAAATATAAG
1 TTCAAAAACCAAATAAACAAATATAAG
3438105 TT
1 TT
3438107 TAAATATCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.27
Consensus pattern (27 bp):
TTCAAAAACCAAATAAACAAATATAAG
Found at i:3439345 original size:15 final size:15
Alignment explanation
Indices: 3439325--3439360 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3439315 TTGGAGGTTG
3439325 AGGAGGAATAAGATT
1 AGGAGGAATAAGATT
*
3439340 AGGAGGAATAGGATT
1 AGGAGGAATAAGATT
3439355 AGGAGG
1 AGGAGG
3439361 TCGGTTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.42, T:0.17
Consensus pattern (15 bp):
AGGAGGAATAAGATT
Found at i:3440117 original size:44 final size:44
Alignment explanation
Indices: 3440037--3440159 Score: 114
Period size: 44 Copynumber: 2.8 Consensus size: 44
3440027 AAAACCCGAC
* *
3440037 GGATGCATCGATGCATAGCTT-T-GTGCATCGATGCACAATC-AA-
1 GGATGCATCGATGC--ACCTTATAGTGTATCGATGCACAATCAAAG
* *
3440079 GGAGTGCATC-AGTGCATCTTCAT-GATGTATCGATGCACATTCAAAG
1 GGA-TGCATCGA-TGCACCTT-ATAG-TGTATCGATGCACAATCAAAG
3440125 GGATGCATCGATGCACCTTATAGTGTATCGATGCA
1 GGATGCATCGATGCACCTTATAGTGTATCGATGCA
3440160 TTATGCACAA
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
41 4 0.06
42 4 0.06
43 11 0.16
44 29 0.43
45 16 0.24
46 4 0.06
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
GGATGCATCGATGCACCTTATAGTGTATCGATGCACAATCAAAG
Found at i:3441348 original size:19 final size:18
Alignment explanation
Indices: 3441311--3441353 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
3441301 GAAACATTGA
*
3441311 ATGCA-TTTTATGCATCG
1 ATGCACTTTTATGCACCG
3441328 ATGCACTTTTAGTGCACCG
1 ATGCACTTTTA-TGCACCG
3441347 ATGCACT
1 ATGCACT
3441354 AAGGGTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 5 0.22
19 13 0.57
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (18 bp):
ATGCACTTTTATGCACCG
Found at i:3447145 original size:21 final size:21
Alignment explanation
Indices: 3447119--3447198 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 21
3447109 TTGTGCATAA
3447119 TGCATCGATACACTATGAAAG
1 TGCATCGATACACTATGAAAG
* * *
3447140 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAAAG
3447164 TGCATCGATACA-TCATGAATA-
1 TGCATCGATACACT-ATGAA-AG
*
3447185 TGCATCGATGCACT
1 TGCATCGATACACT
3447199 CCTTGAATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.02
21 25 0.54
22 2 0.04
23 1 0.02
24 17 0.37
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:3447189 original size:45 final size:44
Alignment explanation
Indices: 3447119--3447213 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 44
3447109 TTGTGCATAA
3447119 TGCATCGATACACTATGAAAGTGCATCGATGCA-TCCCTTTGAATG
1 TGCATCGATACACTATGAAAGTGCATCGATGCACT-CC-TTGAATG
3447164 TGCATCGATACA-TCATGAATA-TGCATCGATGCACTCCTTGAATG
1 TGCATCGATACACT-ATGAA-AGTGCATCGATGCACTCCTTGAATG
3447208 TGCATC
1 TGCATC
3447214 TATGCACAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
44 14 0.30
45 31 0.66
46 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGCATCGATGCACTCCTTGAATG
Found at i:3447220 original size:23 final size:22
Alignment explanation
Indices: 3447134--3447219 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 22
3447124 CGATACACTA
*
3447134 TGAAAGTGCATCGATGCATCCCTT
1 TGAATGTGCATCGATGCAT-CC-T
* *
3447158 TGAATGTGCATCGATACAT-CA
1 TGAATGTGCATCGATGCATCCT
*
3447179 TGAATATGCATCGATGCACTCCT
1 TGAATGTGCATCGATGCA-TCCT
*
3447202 TGAATGTGCATCTATGCA
1 TGAATGTGCATCGATGCA
3447220 CAAGGCCATA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 16 0.31
22 2 0.04
23 17 0.33
24 17 0.33
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (22 bp):
TGAATGTGCATCGATGCATCCT
Found at i:3449878 original size:20 final size:20
Alignment explanation
Indices: 3449853--3449890 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3449843 TTTGTGAAGG
3449853 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
3449873 GATGCATCGATGCACTCA
1 GATGCACCGATGCACTCA
3449891 CCATATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:3455567 original size:21 final size:21
Alignment explanation
Indices: 3455541--3455591 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3455531 GTGGGAGCGT
3455541 CTGGTGCATCGATGCATAGGG
1 CTGGTGCATCGATGCATAGGG
3455562 CTGGTGCATCGATGCATAGGG
1 CTGGTGCATCGATGCATAGGG
*
3455583 CTAGTGCAT
1 CTGGTGCAT
3455592 TGGTACACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (21 bp):
CTGGTGCATCGATGCATAGGG
Found at i:3459434 original size:31 final size:30
Alignment explanation
Indices: 3459396--3459458 Score: 108
Period size: 31 Copynumber: 2.1 Consensus size: 30
3459386 AGAGTTGTCA
3459396 TGAGATGAGGGAGAACTTATGTACTCACCAG
1 TGAGATGAGGGAGAACTTATGTACTCA-CAG
*
3459427 TGAGATGAGGGAGAACTTTTGTACTCACAG
1 TGAGATGAGGGAGAACTTATGTACTCACAG
3459457 TG
1 TG
3459459 GTTAAGAGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.25
Consensus pattern (30 bp):
TGAGATGAGGGAGAACTTATGTACTCACAG
Found at i:3467814 original size:11 final size:11
Alignment explanation
Indices: 3467798--3467827 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3467788 ATCTGAAGGT
3467798 TGATCCTCTGC
1 TGATCCTCTGC
3467809 TGATCCTCTGC
1 TGATCCTCTGC
3467820 TGATCCTC
1 TGATCCTC
3467828 CCCAGTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.37, G:0.17, T:0.37
Consensus pattern (11 bp):
TGATCCTCTGC
Found at i:3468740 original size:19 final size:20
Alignment explanation
Indices: 3468716--3468766 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3468706 AATGACCAAT
3468716 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
3468735 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
3468755 AAAATCGCAACG
1 AAAATCGCAACG
3468767 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:3468776 original size:20 final size:20
Alignment explanation
Indices: 3468753--3468806 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3468743 AACGCGATTT
*
3468753 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
3468773 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
3468793 AGAAAATCGCAACG
1 AGAAAATCGCAACG
3468807 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:3468866 original size:20 final size:20
Alignment explanation
Indices: 3468841--3469008 Score: 255
Period size: 20 Copynumber: 8.4 Consensus size: 20
3468831 TTTAGAAGAA
**
3468841 AATCGCAATGCGATTGATTG
1 AATCGCAATGCGATTGAGAG
* *
3468861 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
3468881 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
*
3468901 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
3468921 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
3468941 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
3468961 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
3468981 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
3469001 AATCGCAA
1 AATCGCAA
3469009 CGTTAAAAAG
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 138 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:3469024 original size:20 final size:20
Alignment explanation
Indices: 3469001--3469040 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3468991 CGATTGAGAG
*
3469001 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
3469021 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
3469041 TAGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:3469025 original size:40 final size:39
Alignment explanation
Indices: 3468901--3469028 Score: 116
Period size: 40 Copynumber: 3.2 Consensus size: 39
3468891 CGATTGAGAG
* ** ***
3468901 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGA
1 AATCGCAATGCGACTGAGAGAATCGCAACGTTAAAAAGA
* *
3468940 GAATCGCAATGCGACTGAGAGAATCGCAATGCGATT-TATAG-
1 -AATCGCAATGCGACTGAGAGAATCGCAA--CG-TTAAAAAGA
*
3468981 AATCGCAATGCGATTGAGAGAATCGCAACGTTAAAAAGAA
1 AATCGCAATGCGACTGAGAGAATCGCAACGTTAAAAAG-A
3469021 AATCGCAA
1 AATCGCAA
3469029 CGGTCAAAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
37 2 0.03
38 5 0.07
40 63 0.86
42 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (39 bp):
AATCGCAATGCGACTGAGAGAATCGCAACGTTAAAAAGA
Found at i:3469025 original size:60 final size:60
Alignment explanation
Indices: 3468836--3469028 Score: 233
Period size: 60 Copynumber: 3.2 Consensus size: 60
3468826 CGCGATTTAG
* * * *
3468836 AAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATCGCAATGCGATT
1 AAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAATCGCAATGCGAAT
* * * * * *
3468896 GAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACT
1 AAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAATCGCAATGCGAAT
* * * * ** *
3468956 GAGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAATCGCAACGTTAAA
1 AAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAATCGCAATGCGAAT
3469016 AAGAAAATCGCAA
1 AAGAAAATCGCAA
3469029 CGGTCAAAAG
Statistics
Matches: 113, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 113 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (60 bp):
AAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAATCGCAATGCGAAT
Found at i:3469129 original size:6 final size:6
Alignment explanation
Indices: 3469118--3469203 Score: 165
Period size: 6 Copynumber: 14.5 Consensus size: 6
3469108 GACACGTATT
3469118 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3469166 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
3469204 CGAGACGAGA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.06
6 75 0.94
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3469910 original size:6 final size:6
Alignment explanation
Indices: 3469894--3469931 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
3469884 TCTCGTCTCG
3469894 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
3469932 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:3470034 original size:20 final size:20
Alignment explanation
Indices: 3470009--3470048 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3469999 TTTTTAACTA
3470009 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGACCGTTGCGATT
*
3470029 TTCTTTTTACCGTTGCGATT
1 TTCTTTTGACCGTTGCGATT
3470049 CTCTCAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.20, G:0.17, T:0.53
Consensus pattern (20 bp):
TTCTTTTGACCGTTGCGATT
Found at i:3470064 original size:20 final size:20
Alignment explanation
Indices: 3470041--3470211 Score: 216
Period size: 20 Copynumber: 8.4 Consensus size: 20
3470031 CTTTTTACCG
3470041 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
3470061 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
3470081 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
*
3470101 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
* *
3470121 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
*
3470144 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
3470164 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
**
3470184 TTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
3470204 TTGCGATT
1 TTGCGATT
3470212 TTCTTCTAAA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
20 113 0.86
21 2 0.02
22 3 0.02
23 14 0.11
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:3470161 original size:83 final size:83
Alignment explanation
Indices: 3470054--3470232 Score: 268
Period size: 83 Copynumber: 2.2 Consensus size: 83
3470044 CGATTCTCTC
* * * * * ** *
3470054 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCG
1 AATCGCGTTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAATCG
3470119 CATTGCGATTTTCTTCTA
66 CATTGCGATTTTCTTCTA
* *
3470137 AATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAATCG
1 AATCGCGTTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAATCG
3470202 CATTGCGATTTTCTTCTA
66 CATTGCGATTTTCTTCTA
3470220 AATCGCGTTGCGA
1 AATCGCGTTGCGA
3470233 ACTTGGAAGC
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (83 bp):
AATCGCGTTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAATCG
CATTGCGATTTTCTTCTA
Found at i:3470309 original size:20 final size:20
Alignment explanation
Indices: 3470039--3470336 Score: 134
Period size: 20 Copynumber: 14.6 Consensus size: 20
3470029 TTCTTTTTAC
* *
3470039 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
3470059 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
3470079 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
3470099 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
3470119 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
3470142 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
3470162 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
3470182 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
3470202 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
3470225 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
3470246 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
3470264 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
3470286 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
3470306 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
3470325 CGTTGCGATTTT
1 CGTTGCGATTTT
3470337 ATTGGTCATT
Statistics
Matches: 223, Mismatches: 44, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 157 0.70
21 14 0.06
22 6 0.03
23 27 0.12
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:3470326 original size:19 final size:20
Alignment explanation
Indices: 3470286--3470336 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3470276 TTCTTTTTAA
*
3470286 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
3470306 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
3470325 CGTTGCGATTTT
1 CGTTGCGATTTT
3470337 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:3470716 original size:51 final size:50
Alignment explanation
Indices: 3470627--3470736 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 50
3470617 CACCCGTAGC
* * *
3470627 AGTAAAGCGCGCCCCTGCACCGCGCTATACGCTGATTTGGCGCCACGTGG
1 AGTATAGCGCGCCCCTGCACCGCGATATACGCTCATTTGGCGCCACGTGG
* *
3470677 AGTATAGCGCGCCCCCTGTC-CCGCGATATATGGTCATTTGGCGCCACGTGG
1 AGTATAGCGCG-CCCCTG-CACCGCGATATACGCTCATTTGGCGCCACGTGG
3470728 -GTATAGCGC
1 AGTATAGCGC
3470737 ATCCCATGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
50 19 0.36
51 33 0.62
52 1 0.02
ACGTcount: A:0.17, C:0.32, G:0.30, T:0.21
Consensus pattern (50 bp):
AGTATAGCGCGCCCCTGCACCGCGATATACGCTCATTTGGCGCCACGTGG
Found at i:3470894 original size:10 final size:10
Alignment explanation
Indices: 3470879--3470908 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3470869 TTTATCACAC
3470879 CAAATTCTCT
1 CAAATTCTCT
3470889 CAAATTCTCT
1 CAAATTCTCT
*
3470899 CAAATACTCT
1 CAAATTCTCT
3470909 ATCTTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:3470988 original size:17 final size:18
Alignment explanation
Indices: 3470951--3470989 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3470941 ATATTATGTA
3470951 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
3470969 TTTACTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
3470986 TTTA
1 TTTA
3470990 GTAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:3473227 original size:26 final size:24
Alignment explanation
Indices: 3473154--3473227 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
3473144 TTATATTTGT
3473154 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
** *
3473179 ATTTTTTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
3473203 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
3473228 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
24 4 0.11
25 17 0.46
26 16 0.43
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.64
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:3476968 original size:51 final size:50
Alignment explanation
Indices: 3476908--3477037 Score: 147
Period size: 51 Copynumber: 2.5 Consensus size: 50
3476898 CCCCTACGTG
*
3476908 GCATATAGCGCGGTGTAGGGGGCGCGCTATACCCCACGTGTAAC-CC-AGTCA
1 GCATATAGCGCGGT-TAGGGGGCGCGCTATACCCCACGTG--ACGCCAAATCA
* * * *
3476959 GCGTATAGCGCGGTACAGGGGGCACGCTATACTCCACGTGACGCCAAATCA
1 GCATATAGCGCGGT-TAGGGGGCGCGCTATACCCCACGTGACGCCAAATCA
*
3477010 GCATATAGCGCGGTTCAGGGGACGCGCT
1 GCATATAGCGCGGTT-AGGGGGCGCGCT
3477038 TTACTGCTAC
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
49 2 0.03
50 2 0.03
51 62 0.94
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.17
Consensus pattern (50 bp):
GCATATAGCGCGGTTAGGGGGCGCGCTATACCCCACGTGACGCCAAATCA
Done.