Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008888.1 Hibiscus syriacus cultivar Beakdansim tig00112153_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: 1025554
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:272014 original size:42 final size:42
Alignment explanation
Indices: 271943--272061 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
271933 GATGCACCTG
* ** * *
271943 TCATCATTCAAGAGGTGCCTCCTATCGTTCAAGAGGC-CCATC
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCTCC-TC
* * *
271985 TCATTGTTCAAGAGGCCCCTCTCACCGTTCAAGAGGCTCCTG
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCTCCTC
*
272027 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAG
272062 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 63 0.97
43 2 0.03
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCTCCTC
Found at i:274005 original size:12 final size:12
Alignment explanation
Indices: 273990--274030 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
273980 AAGCCGGTTG
*
273990 TGATTGGGATTT
1 TGATTGCGATTT
**
274002 TGATTTTGATTT
1 TGATTGCGATTT
274014 TGATTGCGATTT
1 TGATTGCGATTT
274026 TGATT
1 TGATT
274031 TCCTTTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:274006 original size:6 final size:6
Alignment explanation
Indices: 273997--274031 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
273987 TTGTGATTGG
**
273997 GATTTT GATTTT GATTTT GATTGC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
274032 CCTTTTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:274038 original size:24 final size:24
Alignment explanation
Indices: 273990--274038 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
273980 AAGCCGGTTG
* **
273990 TGATTGGGATTTTGATTTTGATTT
1 TGATTGCGATTTTGATTTCCATTT
*
274014 TGATTGCGATTTTGATTTCCTTTT
1 TGATTGCGATTTTGATTTCCATTT
274038 T
1 T
274039 CTTGGCACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.14, C:0.06, G:0.20, T:0.59
Consensus pattern (24 bp):
TGATTGCGATTTTGATTTCCATTT
Found at i:276321 original size:24 final size:24
Alignment explanation
Indices: 276287--276340 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
276277 CTGAAACATC
276287 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
276311 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
276335 ATCAAA
1 ATCAAA
276341 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:276354 original size:24 final size:24
Alignment explanation
Indices: 276287--276354 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
276277 CTGAAACATC
* * *
276287 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
276311 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
276335 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
276355 TAGTACTCGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:277284 original size:19 final size:18
Alignment explanation
Indices: 277241--277287 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
277231 CAAAAGATTT
277241 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
277259 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
277278 GTGTTGCGAA
1 GTGTTGCGAA
277288 TTCGAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:277351 original size:21 final size:19
Alignment explanation
Indices: 277261--277339 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 19
277251 ACTAAAACCT
* *
277261 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
* *
277280 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTC-A
*
277300 GTTGC-AGATTTGAACTTCA
1 GTTGCGA-ATTTGAAATTCA
277319 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
277338 GT
1 GT
277340 GTTTCGAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
19 29 0.59
20 20 0.41
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:277364 original size:60 final size:57
Alignment explanation
Indices: 277261--277376 Score: 128
Period size: 60 Copynumber: 2.0 Consensus size: 57
277251 ACTAAAACCT
277261 GTTGCGAAATTAAATTCGTGTTGCGAATTCGAAAATCGAGTTGC-AGATTTGAACTTCA
1 GTTGCGAAATTAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGA-ATTTG-ACTTCA
* * * * *
277319 GTTGCGAATTTGAAATTCAGTGTTTCGAATTTGGCAAA-CGCGTTGCGAATTTGACTTC
1 GTTGCGAAATT-AAATTC-GTGTTGCGAA-TTCGAAAATCGAGTTGCGAATTTGACTTC
277377 TTTGTTGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
58 10 0.20
59 11 0.22
60 21 0.43
61 7 0.14
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (57 bp):
GTTGCGAAATTAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAATTTGACTTCA
Found at i:277417 original size:20 final size:20
Alignment explanation
Indices: 277319--277469 Score: 105
Period size: 20 Copynumber: 7.5 Consensus size: 20
277309 TTGAACTTCA
* *
277319 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGGAATTC-GC
* *
277340 GTTTCGAATTTGGCAA-ACGC
1 GTTGCGAATTTGG-AATTCGC
* **
277360 GTTGCGAATTT-GACTTCTTT
1 GTTGCGAATTTGGAATTC-GC
***
277380 GTTGCG-ATTCACATATTCGC
1 GTTGCGAATTTGGA-ATTCGC
277400 GTTGCGAATTTGGAATTCGC
1 GTTGCGAATTTGGAATTCGC
*
277420 GTTGCGAATTTGGAGTTCGC
1 GTTGCGAATTTGGAATTCGC
* *
277440 ATTGCGAATTT-GAGA-TCGT
1 GTTGCGAATTTGGA-ATTCGC
277459 GTTGCGAATTT
1 GTTGCGAATTT
277470 CTTGGTCATT
Statistics
Matches: 101, Mismatches: 22, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
18 1 0.01
19 20 0.20
20 59 0.58
21 19 0.19
22 2 0.02
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGGAATTCGC
Found at i:278029 original size:5 final size:5
Alignment explanation
Indices: 278019--278043 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
278009 TTAATTAGTA
278019 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
278044 TAATATATTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:278133 original size:2 final size:2
Alignment explanation
Indices: 278126--278165 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
278116 TTTAGTTATG
278126 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
278166 TGACAGGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:278928 original size:26 final size:26
Alignment explanation
Indices: 278861--278913 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
278851 AACTAATGAC
278861 AAGTAACTTACAATTAGTAATGTGAT
1 AAGTAACTTACAATTAGTAATGTGAT
278887 AAGTAACTTACAATTAGTAATGTGAT
1 AAGTAACTTACAATTAGTAATGTGAT
278913 A
1 A
278914 TGTACTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (26 bp):
AAGTAACTTACAATTAGTAATGTGAT
Found at i:287683 original size:125 final size:125
Alignment explanation
Indices: 287547--287806 Score: 341
Period size: 125 Copynumber: 2.1 Consensus size: 125
287537 TATTACATAT
* *
287547 TAACAACTAACTTTTAT-TTTATTGCATTCTAACTATTATTTATT-TATTTATTGTTTA-TCTTA
1 TAACCACTAACTTTTATATTTATTGCATT-TAA-TATTATTT-TTATATAT-TTGTTTACT-TTA
*
287609 -T-TATTTGACCTTGTGGTGACCCGATCCGGGGTAAAACCCACATTATTATGGTTCGAACTCTGC
61 TTCTATTCGACCTTGTGGTGACCCGATCCGGGGTAAAACCCACATTATTATGGTTCGAACTCTGC
* ** * *
287672 TAACCACTAACTTTTTTATTTATTTTATTTTATTTTATTTTTATATATTTGTTTACTTTATTCTA
1 TAACCACTAACTTTTATATTTATTGCATTTAATATTATTTTTATATATTTGTTTACTTTATTCTA
* * *
287737 TTCGACCTTTTGGTGACCCGATCCGGGGTAAGACCCACATTATTATGGTTCGGACTCTGC
66 TTCGACCTTGTGGTGACCCGATCCGGGGTAAAACCCACATTATTATGGTTCGAACTCTGC
287797 TAACCACTAA
1 TAACCACTAA
287807 TTGCTAACTT
Statistics
Matches: 119, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
123 12 0.10
124 13 0.11
125 85 0.71
126 9 0.08
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (125 bp):
TAACCACTAACTTTTATATTTATTGCATTTAATATTATTTTTATATATTTGTTTACTTTATTCTA
TTCGACCTTGTGGTGACCCGATCCGGGGTAAAACCCACATTATTATGGTTCGAACTCTGC
Found at i:292838 original size:28 final size:28
Alignment explanation
Indices: 292796--292849 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
292786 CACAAGAAGC
*
292796 TAACCTGAAACACATTACCTCCCCAAAT
1 TAACCAGAAACACATTACCTCCCCAAAT
* *
292824 TAACCAGAAATACATTACCTTCCCAA
1 TAACCAGAAACACATTACCTCCCCAA
292850 GTCAGCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.41, C:0.33, G:0.04, T:0.22
Consensus pattern (28 bp):
TAACCAGAAACACATTACCTCCCCAAAT
Found at i:294191 original size:43 final size:43
Alignment explanation
Indices: 294126--294340 Score: 229
Period size: 42 Copynumber: 5.0 Consensus size: 43
294116 ATAAGAAACT
* * *
294126 AAGCTTGAGGGACCAACGTGATATGTTGGGATTTCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
* ** *
294169 AAGCTTGAAGGACCAATATGATAAT-TAGGGGTTCCTTAATGAC
1 AAGCTTGAGGGACCAACGTGAT-ATGTAGGGGTTCCTTGATGAC
* * * *
294212 AAGCTTGAGGGACCAATGTGATATGTAGGGGTTCCTTAATTAT
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
** * *
294255 AA-CTCAAGGAACCAACATGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
* * * *
294297 AA-CTAGAGGGACCAACGTGATATGTTGGGGTTTCTAGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
294339 AA
1 AA
294341 TTAAGAAACT
Statistics
Matches: 144, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
42 71 0.49
43 71 0.49
44 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (43 bp):
AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
Found at i:296505 original size:43 final size:43
Alignment explanation
Indices: 296444--296658 Score: 337
Period size: 42 Copynumber: 5.0 Consensus size: 43
296434 ATATGAAACT
*
296444 AAGCTTGAGGGACTAACGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
*
296487 AAGCTTGAGGGACCAACGTGATATGTAGGGG-TCATTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTC-CTTGATGAC
* *
296530 AAGCTTGAGGGACCAACGTGATATGTAGGGTTTTCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
* *
296573 AA-CTCGAGGGACCAACATGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
*
296615 AA-CTAGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
296657 AA
1 AA
296659 CTAAGAAATT
Statistics
Matches: 159, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
42 80 0.50
43 78 0.49
44 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (43 bp):
AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
Found at i:296688 original size:84 final size:85
Alignment explanation
Indices: 296444--296666 Score: 263
Period size: 86 Copynumber: 2.6 Consensus size: 85
296434 ATATGAAACT
* * ** ** *
296444 AAGCTTGAGGGACTAACGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAGGGACCAACGTGAT
1 AAGCTAGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAA-CTCAAGAAACCAACATGAT
* *
296509 ATGT-AGGGGTCATTTGATGAC
65 ATGTAAGGGTTC-CTTGATGAC
* * * * **
296530 AAGCTTGAGGGACCAACGTGATATGTAGGGTTTTCTTGATGACAACTCGAGGGACCAACATGATA
1 AAGCTAGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAACTCAAGAAACCAACATGATA
*
296595 TGTAGGGGTTCCTTGATGAC
66 TGTAAGGGTTCCTTGATGAC
296615 AA-CTAGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAACT-AAGAAA
1 AAGCTAGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAACTCAAGAAA
296667 TTAAGCTTGA
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
83 3 0.02
84 41 0.34
85 31 0.25
86 47 0.39
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (85 bp):
AAGCTAGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAACTCAAGAAACCAACATGATA
TGTAAGGGTTCCTTGATGAC
Found at i:296806 original size:41 final size:42
Alignment explanation
Indices: 296700--296806 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
296690 TTTTGTTGAG
* * * *
296700 TAAGTCTTTCGGGCCAT-CAGTAAGTCTTTTGAGCATGAAGCT
1 TAAGTCCTTCGGGCCATCCA-TAAGTCTTTCGAGCAAGAAGCA
* * * *
296742 TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG-A
1 TAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAAGAAGCA
296783 TAAGTCCTTCGGGCCATCCATAAG
1 TAAGTCCTTCGGGCCATCCATAAG
296807 ACCTTCAGGC
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
41 21 0.40
42 31 0.58
43 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAAGAAGCA
Found at i:296984 original size:20 final size:20
Alignment explanation
Indices: 296959--297033 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
296949 TTTCTTGATG
296959 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCCTTCGGGCCATC
* * *
296979 AGTAAGTCTTTCGAG-CATG
1 AGTAAGTCCTTCGGGCCATC
296998 ATGTGTAAGTCCTTCGGGCCATC
1 A---GTAAGTCCTTCGGGCCATC
*
297021 TA-TAAGTCTTTCG
1 -AGTAAGTCCTTCG
297034 AGCAAGATGA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
19 4 0.09
20 23 0.53
22 12 0.28
23 3 0.07
24 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTAAGTCCTTCGGGCCATC
Found at i:297000 original size:42 final size:42
Alignment explanation
Indices: 296954--297067 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
296944 AAGATTTTCT
296954 TGATGAGTAAGTCCTTCGGGCCATC-AGTAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCATCTA-TAAGTCTTTCGAGCA
*
296996 TGATGTGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
* * * *
297038 AGATGA-TAAGTCTTTCAGGCCATCCATAAG
1 TGATGAGTAAGTCCTTCGGGCCATCTATAAG
297068 ACCCTCGGGC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 21 0.32
42 43 0.66
43 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (42 bp):
TGATGAGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
Found at i:297006 original size:22 final size:21
Alignment explanation
Indices: 296981--297053 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 21
296971 GGGCCATCAG
*
296981 TAAGTCTTTCGAGCATGATGTG
1 TAAGTCTTTCGAGCA-GATGTA
* * * *
297003 TAAGTCCTTCGGGC-CATCTA
1 TAAGTCTTTCGAGCAGATGTA
297023 TAAGTCTTTCGAGCAAGATG-A
1 TAAGTCTTTCGAGC-AGATGTA
297044 TAAGTCTTTC
1 TAAGTCTTTC
297054 AGGCCATCCA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 15 0.38
21 11 0.28
22 14 0.35
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (21 bp):
TAAGTCTTTCGAGCAGATGTA
Found at i:297080 original size:41 final size:41
Alignment explanation
Indices: 296955--297083 Score: 107
Period size: 42 Copynumber: 3.1 Consensus size: 41
296945 AGATTTTCTT
* * ** *
296955 GATGAGTAAGTCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCAT
1 GATGA-TAAGTCCTTCAGGCCATCCA-TAAGACCCTCGAGCAA
* * * * **
296997 GATGTGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCAA
1 GATG-ATAAGTCCTTCAGGCCATCCATAAGACCCTCGAGCAA
* *
297039 GATGATAAGTCTTTCAGGCCATCCATAAGACCCTCGGGCAA
1 GATGATAAGTCCTTCAGGCCATCCATAAGACCCTCGAGCAA
297080 GATG
1 GATG
297084 TTTTCAAATG
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 33 0.45
42 40 0.54
43 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (41 bp):
GATGATAAGTCCTTCAGGCCATCCATAAGACCCTCGAGCAA
Found at i:297339 original size:36 final size:36
Alignment explanation
Indices: 297253--297340 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 36
297243 TCTGTTTCTT
*
297253 TTGAAACAAAG-TTTGTCTCTCTTGAGACAGTTTATC
1 TTGAAAC-AAGTTTTGTCTCTCTTGAGACAGTTTACC
* *
297289 TTGAAA-AGAATTTTGTCTCTCTTGAGACAGTTTCCC
1 TTGAAACA-AGTTTTGTCTCTCTTGAGACAGTTTACC
297325 TTGAAACAAGTTTTGT
1 TTGAAACAAGTTTTGT
297341 TGCTTGAGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 1 0.02
35 1 0.02
36 42 0.93
37 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (36 bp):
TTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTACC
Found at i:297880 original size:21 final size:21
Alignment explanation
Indices: 297850--297889 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
297840 CTCGATTCTA
297850 TCACAAAAGGAGGTAGATCAG
1 TCACAAAAGGAGGTAGATCAG
* *
297871 TCACAGAAGGAGGTGGATC
1 TCACAAAAGGAGGTAGATC
297890 GCCATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.33, T:0.15
Consensus pattern (21 bp):
TCACAAAAGGAGGTAGATCAG
Found at i:297957 original size:109 final size:109
Alignment explanation
Indices: 297766--297979 Score: 331
Period size: 109 Copynumber: 2.0 Consensus size: 109
297756 ATTCAATCAT
* * * * *
297766 AGAAGGAGGTGGATTGGCATTTTTATTTCGTTCAAATCCATCGTATAAGGAGTTGGAGTAGCATC
1 AGAAGGAGGTGGATCGCCATTTTTATTTCGCTCAAATCCATCGCATAAGGAGTTAGAGTAGCATC
*
297831 AACTTTTTGCTCGATTCTATCACAAAAGGAGGTAGATCAGTCAC
66 AACTTTTTGATCGATTCTATCACAAAAGGAGGTAGATCAGTCAC
*
297875 AGAAGGAGGTGGATCGCCATTTTTTTTTCGCTCAAATCCATCGCATAAGGAGTTAGA-TCAGCAT
1 AGAAGGAGGTGGATCGCCATTTTTATTTCGCTCAAATCCATCGCATAAGGAGTTAGAGT-AGCAT
* *
297939 CAACTTTTTGATTGATTCTATCACAGAAGGAGGTAGATCAG
65 CAACTTTTTGATCGATTCTATCACAAAAGGAGGTAGATCAG
297980 CACTGACATC
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 1 0.01
109 94 0.99
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (109 bp):
AGAAGGAGGTGGATCGCCATTTTTATTTCGCTCAAATCCATCGCATAAGGAGTTAGAGTAGCATC
AACTTTTTGATCGATTCTATCACAAAAGGAGGTAGATCAGTCAC
Found at i:298161 original size:132 final size:132
Alignment explanation
Indices: 297871--298153 Score: 406
Period size: 132 Copynumber: 2.1 Consensus size: 132
297861 GGTAGATCAG
* * * * * *
297871 TCACAGAAGGAGGTGGATCGCCATTTTTTTTTCGCTCAAATCCATCGCATAAGGAGTTAGATCAG
1 TCACAGAAGGAGGTGGATCGACATTTTTATTTCACCCAAATCCATCGCATAAAGAGTTAGATCAA
** *
297936 CATCAACTTTTTGATTGATTCTATCACAGAAGGAGGTAGATCAGCACTGACATCTTGTTCGATTC
66 CATCAACTTTTTGATCAATTCTATCACAGAAGGAGGTAGATCACCACTGACATCTTGTTCGATTC
298001 CA
131 CA
* ** * *
298003 TCACAGAATGAAATGGATTGACATTTTTATTTCACCCAAATCCATCGCATAAAGAGTTGGATCAA
1 TCACAGAAGGAGGTGGATCGACATTTTTATTTCACCCAAATCCATCGCATAAAGAGTTAGATCAA
* *
298068 CATCAACTTTTTGCTCAATTCTATCACAGAAGGATGTAGATCACCACTGACAT-TATGTTCGATT
66 CATCAACTTTTTGATCAATTCTATCACAGAAGGAGGTAGATCACCACTGACATCT-TGTTCGATT
298132 CCA
130 CCA
298135 TCACAGAAGGAGGTGGATC
1 TCACAGAAGGAGGTGGATC
298154 AATATTTTCA
Statistics
Matches: 130, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
131 1 0.01
132 129 0.99
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (132 bp):
TCACAGAAGGAGGTGGATCGACATTTTTATTTCACCCAAATCCATCGCATAAAGAGTTAGATCAA
CATCAACTTTTTGATCAATTCTATCACAGAAGGAGGTAGATCACCACTGACATCTTGTTCGATTC
CA
Found at i:299540 original size:25 final size:24
Alignment explanation
Indices: 299486--299541 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
299476 TATTAATATT
299486 CTAACTTTTATTTTATTGTTCATA
1 CTAACTTTTATTTTATTGTTCATA
* * *
299510 CAAACTTTTATTTTTATTTTTCTTA
1 CTAACTTTTA-TTTTATTGTTCATA
299535 CTAACTT
1 CTAACTT
299542 ACTAACATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.25, C:0.14, G:0.02, T:0.59
Consensus pattern (24 bp):
CTAACTTTTATTTTATTGTTCATA
Found at i:299616 original size:14 final size:15
Alignment explanation
Indices: 299597--299633 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
299587 ATTTATGCAA
299597 TTTATTTCTA-TTT-T
1 TTTATTT-TAGTTTAT
299611 TTTATTTTAGTTTAT
1 TTTATTTTAGTTTAT
299626 TTTATTTT
1 TTTATTTT
299634 TCAGCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 10 0.48
15 9 0.43
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTATTTTAGTTTAT
Found at i:299693 original size:15 final size:15
Alignment explanation
Indices: 299624--299693 Score: 54
Period size: 15 Copynumber: 4.6 Consensus size: 15
299614 ATTTTAGTTT
*
299624 ATTTTATTTTTCAGC
1 ATTTTATTTTTCTGC
* ** *
299639 ACTTTAAATTTCAGC
1 ATTTTATTTTTCTGC
299654 ATTTTATTTTTCTGTC
1 ATTTTATTTTTCTG-C
299670 -TTTTAATTTTGT-TGC
1 ATTTT-ATTTT-TCTGC
299685 ATTTTATTT
1 ATTTTATTT
299694 CAATATTTCG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
15 31 0.70
16 12 0.27
17 1 0.02
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.61
Consensus pattern (15 bp):
ATTTTATTTTTCTGC
Found at i:307650 original size:33 final size:33
Alignment explanation
Indices: 307586--307675 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 33
307576 GTTAAATTTG
* * * * ** *
307586 GTTCAGGTTACTTTCGGATCGAATTCCAATTCG
1 GTTCGGGTTCCTTTCGGTTCGAGTTAAAATTCA
* *
307619 GTTCGGGTTTCTTTCGGTTTGAGTTAAAATTCA
1 GTTCGGGTTCCTTTCGGTTCGAGTTAAAATTCA
*
307652 GTTTGGGTTCCTTTCGGTTCGAGT
1 GTTCGGGTTCCTTTCGGTTCGAGT
307676 GGTTTTCGAT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.42
Consensus pattern (33 bp):
GTTCGGGTTCCTTTCGGTTCGAGTTAAAATTCA
Found at i:307699 original size:32 final size:32
Alignment explanation
Indices: 307663--307734 Score: 76
Period size: 32 Copynumber: 2.2 Consensus size: 32
307653 TTTGGGTTCC
* *
307663 TTTCGGTTCGAG-TG-GTTTTCGATTCGGGTTAT
1 TTTCGGTTCAAGTTGCGTTTTC--TTCGGGTTAA
* *
307695 TTTCGATTCAAGTTGCTTTTTCTTCGGGTTAA
1 TTTCGGTTCAAGTTGCGTTTTCTTCGGGTTAA
307727 TTTCGGTT
1 TTTCGGTT
307735 TAGGATGCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
32 26 0.79
33 2 0.06
34 5 0.15
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.50
Consensus pattern (32 bp):
TTTCGGTTCAAGTTGCGTTTTCTTCGGGTTAA
Found at i:308109 original size:18 final size:19
Alignment explanation
Indices: 308086--308149 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
308076 AATTTTTATT
308086 TTATT-TTATTAAAATATA
1 TTATTATTATTAAAATATA
308104 TTATTTAATTATTAAAAATATAA
1 TTA-TT-ATTATT-AAAATAT-A
**
308127 AAATTATTA-TAAAATATA
1 TTATTATTATTAAAATATA
308145 TTATT
1 TTATT
308150 TTAATTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
18 7 0.19
19 9 0.24
20 1 0.03
21 9 0.24
22 9 0.24
23 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTATTATTAAAATATA
Found at i:308117 original size:21 final size:21
Alignment explanation
Indices: 308091--308155 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
308081 TTATTTTATT
308091 TTATTAAAATATATTATTTAA
1 TTATTAAAATATATTATTTAA
** *
308112 TTATTAAAAATATAAAAATT-A
1 TTATT-AAAATATATTATTTAA
308133 TTA-TAAAATATATTATTTTAA
1 TTATTAAAATATATTA-TTTAA
308154 TT
1 TT
308156 GTTTATAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 9 0.26
20 3 0.09
21 12 0.34
22 11 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATTAAAATATATTATTTAA
Found at i:308147 original size:15 final size:15
Alignment explanation
Indices: 308129--308199 Score: 58
Period size: 14 Copynumber: 4.9 Consensus size: 15
308119 AAATATAAAA
308129 ATTATTATAAAATAT
1 ATTATTATAAAATAT
* * *
308144 ATTATT-TTAATTGT
1 ATTATTATAAAATAT
* *
308158 -TTATAATAAAATAA
1 ATTATTATAAAATAT
*
308172 ATAATTAT-AAATAT
1 ATTATTATAAAATAT
*
308186 ATTAGTATAAAATA
1 ATTATTATAAAATA
308200 AAATATTTTA
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
13 4 0.10
14 20 0.50
15 16 0.40
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATTATTATAAAATAT
Found at i:308184 original size:42 final size:40
Alignment explanation
Indices: 308093--308189 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 40
308083 ATTTTATTTT
* *
308093 ATTA-AAATATATTATTTAATTATTAAAAATATAAAAATT
1 ATTATAAATATATTATTTAATTATTAAAAATAAAAAAATA
* * *
308132 ATTATAAAATATATTATTTTAATTGTTTATAATAAAATAAATA
1 ATTAT-AAATATATTA-TTTAATTATTAAAAATAAAA-AAATA
308175 ATTATAAATATATTA
1 ATTATAAATATATTA
308190 GTATAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
39 4 0.08
41 10 0.20
42 26 0.53
43 9 0.18
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (40 bp):
ATTATAAATATATTATTTAATTATTAAAAATAAAAAAATA
Found at i:309799 original size:19 final size:19
Alignment explanation
Indices: 309777--309819 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
309767 AAGTGAGGGA
309777 AACCAAGATAAGTCTTCTC
1 AACCAAGATAAGTCTTCTC
*
309796 AACCAAGATAAGTCTTCTT
1 AACCAAGATAAGTCTTCTC
309815 AACCA
1 AACCA
309820 TAGCTACAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (19 bp):
AACCAAGATAAGTCTTCTC
Found at i:312476 original size:20 final size:21
Alignment explanation
Indices: 312439--312478 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
312429 AAATTAAGTT
312439 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
312460 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
312479 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:312788 original size:65 final size:64
Alignment explanation
Indices: 312694--312854 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 64
312684 GAATTAATTG
* * *** *
312694 AACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCATAAGCCATGCATCGATGCACTCAGAATATTTTC-A
* * **
312759 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCATAAGCCATGCATCGATGCACTCAGAATATTTTCA
*
312823 AACATCGAATGCATTTCATGCATCAATGCATA
1 AACATCGAATGCATTTCATGCATCGATGCATA
312855 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 30 0.36
65 53 0.64
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCATAAGCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:314949 original size:22 final size:20
Alignment explanation
Indices: 314890--314945 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 20
314880 CTTGGTCAAA
314890 ATTTTAAACGTAATTGATATTC
1 ATTTTAAAC--AATTGATATTC
*
314912 ATTTTAAACCATTGATA-TC
1 ATTTTAAACAATTGATATTC
314931 AATTTTCAAACAATT
1 -ATTTT-AAACAATT
314946 TGATTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.07
20 12 0.40
21 7 0.23
22 9 0.30
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.43
Consensus pattern (20 bp):
ATTTTAAACAATTGATATTC
Found at i:319504 original size:21 final size:21
Alignment explanation
Indices: 319462--319505 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
319452 ACCCCGGGAG
*
319462 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
319483 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
319504 CT
1 CT
319506 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:320322 original size:20 final size:21
Alignment explanation
Indices: 320285--320324 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
320275 AAATTACGTT
320285 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
320306 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
320325 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:320634 original size:65 final size:64
Alignment explanation
Indices: 320540--320700 Score: 223
Period size: 65 Copynumber: 2.5 Consensus size: 64
320530 GAATTAATTG
* * *** *
320540 AACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCATAAGCCATGCATCGATGCACTCAGAATATTTTC-A
* * **
320605 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCATAAGCCATGCATCGATGCACTCAGAATATTTTCA
320669 AACATCGAATGCATTTCATGCATCGATGCATA
1 AACATCGAATGCATTTCATGCATCGATGCATA
320701 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 31 0.37
65 53 0.63
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCATAAGCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:325612 original size:2 final size:2
Alignment explanation
Indices: 325605--325630 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
325595 TAGGAAAGAT
325605 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
325631 ATTAAAGGAA
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):
TA
Found at i:327017 original size:29 final size:28
Alignment explanation
Indices: 326971--327118 Score: 125
Period size: 29 Copynumber: 5.1 Consensus size: 28
326961 TTCGTAGAGG
* *
326971 ATCCCATACAGAAACAGGACGGAGATATA
1 ATCCCATACAGAATCAAGACGG-GATATA
* * * *
327000 ATCCCATATAGAATCAGGATGGAATATA
1 ATCCCATACAGAATCAAGACGGGATATA
* *
327028 ATCCCATGCAGAATCAAGATAGGGATATA
1 ATCCCATACAGAATCAAGA-CGGGATATA
** **
327057 ATCATATGTAGAATCAAGACGTGGATATA
1 ATCCCATACAGAATCAAGACG-GGATATA
* * *
327086 ATCCCATGCAAAATCAAGATAGGGATATA
1 ATCCCATACAGAATCAAGA-CGGGATATA
327115 ATCC
1 ATCC
327119 AATGCAAAAT
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
28 22 0.22
29 75 0.77
30 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCCCATACAGAATCAAGACGGGATATA
Found at i:327123 original size:29 final size:29
Alignment explanation
Indices: 327023--327128 Score: 126
Period size: 29 Copynumber: 3.7 Consensus size: 29
327013 TCAGGATGGA
* *
327023 ATATAATCCCATGCAGAATCAAGATAGGG
1 ATATAATCCAATGCAAAATCAAGATAGGG
* * *
327052 ATATAAT-CATATGTAGAATCAAGA-CGTGG
1 ATATAATCCA-ATGCAAAATCAAGATAG-GG
*
327081 ATATAATCCCATGCAAAATCAAGATAGGG
1 ATATAATCCAATGCAAAATCAAGATAGGG
327110 ATATAATCCAATGCAAAAT
1 ATATAATCCAATGCAAAAT
327129 AAATAATGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.03
29 61 0.94
30 2 0.03
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (29 bp):
ATATAATCCAATGCAAAATCAAGATAGGG
Found at i:343649 original size:2 final size:2
Alignment explanation
Indices: 343642--343724 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
343632 GATCCTGCCC
343642 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
343684 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
343725 GTACGTATGT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:347899 original size:3 final size:3
Alignment explanation
Indices: 347891--347963 Score: 101
Period size: 3 Copynumber: 24.3 Consensus size: 3
347881 TTTGATTTAT
* * * *
347891 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA GTA TTA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
347939 TTA CTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
347964 AATATATATA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:353099 original size:15 final size:15
Alignment explanation
Indices: 353079--353110 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
353069 ATTAATACCT
353079 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
353094 TTTTGCATACATTCA
1 TTTTGCATACATGCA
353109 TT
1 TT
353111 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:360406 original size:32 final size:31
Alignment explanation
Indices: 360365--360444 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
360355 ATGCTTGAAG
360365 AAAAAAAGAAGAAAAAAAAAGAAGAAGA-AAGA
1 AAAAAAAGAAGAAAAAAAAAGAA-AAGAGAA-A
* *
360397 AAAAAAAGAA-AAAAAGAAGGAAAAGAGAAA
1 AAAAAAAGAAGAAAAAAAAAGAAAAGAGAAA
360427 AAAGAAAA-AAGAAAAAAA
1 AAA-AAAAGAAGAAAAAAA
360445 GAAAAAGGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 10 0.24
31 22 0.52
32 10 0.24
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (31 bp):
AAAAAAAGAAGAAAAAAAAAGAAAAGAGAAA
Found at i:360408 original size:7 final size:7
Alignment explanation
Indices: 360366--360450 Score: 75
Period size: 7 Copynumber: 11.7 Consensus size: 7
360356 TGCTTGAAGA
360366 AAAAAAG
1 AAAAAAG
*
360373 AAGAAAAA
1 AA-AAAAG
360381 AAAAGAAG
1 AAAA-AAG
*
360389 AAGAAAG
1 AAAAAAG
360396 AAAAAA-
1 AAAAAAG
360402 AAGAAAA-
1 AA-AAAAG
*
360409 AAAGAAGG
1 AAA-AAAG
*
360417 AAAAGAG
1 AAAAAAG
360424 AAAAAAG
1 AAAAAAG
360431 AAAAAAG
1 AAAAAAG
360438 AAAAAAAG
1 -AAAAAAG
360446 AAAAA
1 AAAAA
360451 GGGGGTCAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
6 3 0.05
7 40 0.62
8 21 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:360450 original size:8 final size:8
Alignment explanation
Indices: 360362--360450 Score: 94
Period size: 8 Copynumber: 11.0 Consensus size: 8
360352 ATTATGCTTG
360362 AAGAAAAA
1 AAGAAAAA
360370 AAGAAGAAA
1 AAGAA-AAA
*
360379 AA-AAAAG
1 AAGAAAAA
*
360386 AAG-AAGA
1 AAGAAAAA
360393 AAGAAAAAA
1 AAG-AAAAA
360402 AAGAAAAA
1 AAGAAAAA
*
360410 AAGAAGGAA
1 AAGAA-AAA
360419 AAGAGAAAA
1 AAGA-AAAA
360428 AAG-AAAA
1 AAGAAAAA
360435 AAGAAAAA
1 AAGAAAAA
360443 AAGAAAAA
1 AAGAAAAA
360451 GGGGGTCAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
7 16 0.24
8 29 0.43
9 22 0.32
10 1 0.01
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:361643 original size:83 final size:82
Alignment explanation
Indices: 361364--361985 Score: 985
Period size: 83 Copynumber: 7.6 Consensus size: 82
361354 TGCAATGTAC
* *
361364 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGTAGAACCAATCATTAAAATT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATTT
*
361428 GGAAGATGATGTGCTCA
66 GGAAGATGATATGCTCA
*
361445 TAGCATCTTCTGGAAGTGTTCTTTGAGTTAT-TGATCTGGTTTGGTAAAACCAATCATTGAATTT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATTT
361509 GGAAGATGAATATGCTCA
66 GGAAGATG-ATATGCTCA
* *
361527 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAATT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATTT
*
361592 -GAAGATGATGTGCTCA
66 GGAAGATGATATGCTCA
*
361608 TAGCATC-TCTGGAAGTG-T-TTTGAGTTATCTGATCT-GTTTGGTAAAACCAATCATTGAATTT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATTT
361669 GGAAGATGAATATGCTCA
66 GGAAGATG-ATATGCTCA
*
361687 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATTT
361752 GGAAGATGA-ATGCTCA
66 GGAAGATGATATGCTCA
*
361768 TAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATC-GGTTTGGCAGAACCAATCATTGAATTT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATTT
*
361831 GGAAGAGTAATATGCTCA
66 GGAAGA-TGATATGCTCA
* *
361849 TAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATTT
* *
361914 GGAAGAGTAATGTGCTCA
66 GGAAGA-TGATATGCTCA
*
361932 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTAGGAACCA
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GAACCA
361986 CAGAACCAAT
Statistics
Matches: 505, Mismatches: 22, Indels: 25
0.91 0.04 0.05
Matches are distributed among these distances:
77 23 0.05
78 24 0.05
79 49 0.10
80 45 0.09
81 131 0.26
82 79 0.16
83 149 0.30
84 5 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (82 bp):
TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATTT
GGAAGATGATATGCTCA
Found at i:361698 original size:160 final size:164
Alignment explanation
Indices: 361364--361970 Score: 1016
Period size: 162 Copynumber: 3.7 Consensus size: 164
361354 TGCAATGTAC
* *
361364 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGTAGAACCAATCATTAAAATT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAATT
361428 GGAAGATGATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT-TGATCTGGTTTGGTAA
66 GGAAGATGATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGTAA
361492 AACCAATCATTGAATTTGGAAGATGAATATGCTCA
130 AACCAATCATTGAATTTGGAAGATGAATATGCTCA
361527 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAATT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAATT
361592 -GAAGATGATGTGCTCATAGCATC-TCTGGAAGTG-T-TTTGAGTTATCTGATCTGTTTGGTAAA
66 GGAAGATGATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGTAAA
361653 ACCAATCATTGAATTTGGAAGATGAATATGCTCA
131 ACCAATCATTGAATTTGGAAGATGAATATGCTCA
*
361687 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAATT
* * * *
361752 GGAAGATGA-ATGCTCATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATCGGTTTGGCAGA
66 GGAAGATGATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGTAAA
361815 ACCAATCATTGAATTTGGAAGA-GTAATATGCTCA
131 ACCAATCATTGAATTTGGAAGATG-AATATGCTCA
* * * *
361849 TAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAATT
*
361914 GGAAGAGTAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
66 GGAAGA-TGATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
361971 GTTTAGTAGG
Statistics
Matches: 421, Mismatches: 13, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
160 131 0.31
161 26 0.06
162 134 0.32
163 65 0.15
164 49 0.12
165 16 0.04
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (164 bp):
TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAATT
GGAAGATGATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGTAAA
ACCAATCATTGAATTTGGAAGATGAATATGCTCA
Found at i:362961 original size:32 final size:34
Alignment explanation
Indices: 362903--362965 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 34
362893 CCAGATAGAG
362903 TTCATAATGAGAAAACTCGTCATCTGAAGAAAGA
1 TTCATAATGAGAAAACTCGTCATCTGAAGAAAGA
* *
362937 TTCATAATG-G-AAATTTGTCATCTGAAGAA
1 TTCATAATGAGAAAACTCGTCATCTGAAGAA
362966 GGAAGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 17 0.63
33 1 0.04
34 9 0.33
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (34 bp):
TTCATAATGAGAAAACTCGTCATCTGAAGAAAGA
Found at i:363100 original size:19 final size:19
Alignment explanation
Indices: 363046--363103 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
363036 TTTGCCAGAT
363046 AGAGTTCATAATGAGAAGA
1 AGAGTTCATAATGAGAAGA
** *
363065 ACTCG-TCAT-CTGAAGAAGA
1 A-GAGTTCATAATG-AGAAGA
363084 AGAGTTCATAATGAGAAGA
1 AGAGTTCATAATGAGAAGA
363103 A
1 A
363104 TTTGTTCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
18 3 0.10
19 23 0.79
20 3 0.10
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (19 bp):
AGAGTTCATAATGAGAAGA
Found at i:363169 original size:111 final size:111
Alignment explanation
Indices: 362975--363216 Score: 475
Period size: 111 Copynumber: 2.2 Consensus size: 111
362965 AGGAAGAATA
*
362975 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAGCTTTG
1 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTAAATCCATCACTTGATGGATCAGCTTTG
363040 CCAGATAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG
66 CCAGATAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG
363086 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTAAATCCATCACTTGATGGATCAGCTTTG
1 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTAAATCCATCACTTGATGGATCAGCTTTG
363151 CCAGATAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG
66 CCAGATAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG
363197 AGTTCATAATGAGAAGAATT
1 AGTTCATAATGAGAAGAATT
363217 CGTCATCTGA
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 130 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (111 bp):
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTAAATCCATCACTTGATGGATCAGCTTTG
CCAGATAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG
Found at i:363192 original size:19 final size:18
Alignment explanation
Indices: 363170--363231 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
363160 GTTCATAATG
363170 AGAAGAACTCGTCATCTGA
1 AGAAGAA-TCGTCATCTGA
** *
363189 AGAAGAAGAGTTCATAATG-
1 AGAAGAATCG-TCAT-CTGA
363208 AGAAGAATTCGTCATCTGA
1 AGAAGAA-TCGTCATCTGA
363227 AGAAG
1 AGAAG
363232 GAAGAATAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 3 0.09
19 27 0.82
20 3 0.09
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (18 bp):
AGAAGAATCGTCATCTGA
Found at i:363208 original size:38 final size:39
Alignment explanation
Indices: 363157--363257 Score: 150
Period size: 38 Copynumber: 2.5 Consensus size: 39
363147 TTTGCCAGAT
363157 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GA
1 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGA
*
363195 AGAGTTCATAATGAGAAGAATTCGTCATCTGAAGAAGGA
1 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGA
363234 AGAATAAGTTCATAATGAGAAGAA
1 AG----AGTTCATAATGAGAAGAA
363258 TTTGTTCAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
38 35 0.61
39 4 0.07
43 18 0.32
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.22
Consensus pattern (39 bp):
AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGA
Found at i:363321 original size:154 final size:147
Alignment explanation
Indices: 363046--363418 Score: 529
Period size: 154 Copynumber: 2.5 Consensus size: 147
363036 TTTGCCAGAT
363046 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG-AGTTCATAATGAGAAGAATTTGTT
1 AGAGTTCATAATGAGAAGAA-TCGTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * *
363110 CAACCTTTTATTTAAATCCATCACTTGATGGATCAGCTTTGCCAGATAGAGTTCATAATGAGAAG
65 CAACCTTTTGTTTAAATCCATCACTTGATGGATCAACATTGCCAGATAGAGTTCATAATAAGAAG
363175 AACTCGTCATCTGAAGAAG-A
130 AA-T--TCATCTGAAGAAGAA
363195 AGAGTTCATAATGAGAAGAATTCGTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAATT
1 AGAGTTCATAATGAGAAGAA-TCGTCATCTGAAGAA-GAAG---AAGTTCATAATGAGAAGAATT
* * * *
363260 TGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATAA
61 TGTTCAACCTTTTGTTTAAATCCATCACTTGATGGATCAACATTGCCAGATAGAGTTCATAATAA
363325 GAAGAATTCATCTGAAGAAGAA
126 GAAGAATTCATCTGAAGAAGAA
* * **
363347 AAAGTTCATAATGAGAAGAAT--TCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
1 AGAGTTCATAATGAGAAGAATCGTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
363410 AACCTTTTG
66 AACCTTTTG
363419 CATAATTTAA
Statistics
Matches: 205, Mismatches: 13, Indels: 16
0.88 0.06 0.07
Matches are distributed among these distances:
145 32 0.16
148 4 0.02
149 47 0.23
150 4 0.02
151 14 0.07
152 20 0.10
153 1 0.00
154 83 0.40
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (147 bp):
AGAGTTCATAATGAGAAGAATCGTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGTTTAAATCCATCACTTGATGGATCAACATTGCCAGATAGAGTTCATAATAAGAAGA
ATTCATCTGAAGAAGAA
Found at i:363342 original size:16 final size:16
Alignment explanation
Indices: 363323--363382 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
363313 AGTTCATAAT
363323 AAGAAGAATTCATCTG
1 AAGAAGAATTCATCTG
*
363339 AAGAAGAAAAAGTTCATAATG
1 AAGAAG---AA-TTCAT-CTG
363360 -AGAAGAATTCATCTG
1 AAGAAGAATTCATCTG
363375 AAGAAGAA
1 AAGAAGAA
363383 GAAGTTCACA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 2 0.06
16 18 0.50
17 2 0.06
19 2 0.06
20 10 0.28
21 2 0.06
ACGTcount: A:0.52, C:0.08, G:0.20, T:0.20
Consensus pattern (16 bp):
AAGAAGAATTCATCTG
Found at i:363353 original size:36 final size:36
Alignment explanation
Indices: 363313--363401 Score: 151
Period size: 36 Copynumber: 2.5 Consensus size: 36
363303 TGCCAGGTAG
*
363313 AGTTCATAATAAGAAGAATTCATCTGAAGAAGAAAA
1 AGTTCATAATGAGAAGAATTCATCTGAAGAAGAAAA
*
363349 AGTTCATAATGAGAAGAATTCATCTGAAGAAGAAGA
1 AGTTCATAATGAGAAGAATTCATCTGAAGAAGAAAA
*
363385 AGTTCACAATGAGAAGA
1 AGTTCATAATGAGAAGA
363402 GCTTGTTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.21
Consensus pattern (36 bp):
AGTTCATAATGAGAAGAATTCATCTGAAGAAGAAAA
Found at i:363619 original size:118 final size:115
Alignment explanation
Indices: 363347--363621 Score: 290
Period size: 118 Copynumber: 2.3 Consensus size: 115
363337 TGAAGAAGAA
* *
363347 AAAGTTCATAATGAGAAGAATTCATCTGAAG-AAGAAGAAGTTCACAATGAGAAGAGCTTGTTCA
1 AAAGTTCATAATGAGAAGAAATCATCTGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTATTCA
* * * **
363411 ACCTTTTGCATAATTTAACAGTAGATAGATTAGCATCAACCTTTCCAGAG
66 ACCTTTTGAATAATTTAACAGAAGATAGAATAGCATCAACCTCCCCAGAG
* * *
363461 AAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAATAGCTTAT
1 AAAGTTCATAATGAGAAGAAATCATCTG---AAGAAAGAAGAAGTTCACAATGAGAAGAGCTTAT
* * * * *
363526 TTAATCTTTTGAATGACTCTATCACAGAAGA-A-AATAG-GTCAACATCATCCCCAGCAG
63 TCAACCTTTTGAAT-AAT-T-TAACAGAAGATAGAATAGCATCAAC--C-TCCCCAG-AG
363583 AAAGTTCATAATGAGAAGAAATC-TCTGAAGAAAGAAGAA
1 AAAGTTCATAATGAGAAGAAATCATCTGAAGAAAGAAGAA
363622 AGAGATTCAA
Statistics
Matches: 135, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
114 27 0.20
117 3 0.02
118 55 0.41
119 6 0.04
120 3 0.02
121 17 0.13
122 24 0.18
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (115 bp):
AAAGTTCATAATGAGAAGAAATCATCTGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTATTCA
ACCTTTTGAATAATTTAACAGAAGATAGAATAGCATCAACCTCCCCAGAG
Found at i:363783 original size:3 final size:3
Alignment explanation
Indices: 363775--363841 Score: 89
Period size: 3 Copynumber: 22.3 Consensus size: 3
363765 TTTGATTTAT
* * * *
363775 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA GTA TTA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
363823 TTA CTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
363842 ATATATATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:363866 original size:26 final size:24
Alignment explanation
Indices: 363779--363866 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 24
363769 ATTTATTTAT
* * * *
363779 TATTATTATTATTATCATTATTAT
1 TATTATTATAATTATAAATATTAC
* *
363803 TAGTATTATTATTATAAATATTAC
1 TATTATTATAATTATAAATATTAC
* *
363827 TATTATTATTATTATATATATATA-
1 TATTATTATAATTATAAATAT-TAC
363851 TATATATTAATAATTA
1 TAT-TATT-ATAATTA
363867 CAAGCCCAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 42 0.78
25 6 0.11
26 6 0.11
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (24 bp):
TATTATTATAATTATAAATATTAC
Found at i:368284 original size:21 final size:21
Alignment explanation
Indices: 368258--368299 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
368248 GAGCAGCTGC
368258 CCCTCAAATTTTTTTATCATT
1 CCCTCAAATTTTTTTATCATT
368279 CCCTCAAATTTTTTTATCATT
1 CCCTCAAATTTTTTTATCATT
368300 AAAGAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (21 bp):
CCCTCAAATTTTTTTATCATT
Found at i:368944 original size:190 final size:190
Alignment explanation
Indices: 368543--368951 Score: 495
Period size: 190 Copynumber: 2.1 Consensus size: 190
368533 AATTCATAGT
*
368543 CCTTTTGACTATTCCAAATTAAAAGATAATTTTTAATTTGAATATTAATAGGATAATTACTCTTT
1 CCTTTTGACTATTCCAAATT-AAAGATAATTTTTAATTCGAATATTAATAGGATAATTACTCTTT
* * * * *
368608 TAATAATTCAATTTAAAAATATATTTGTTATATTTTTAATTTTGAATATTAAAAGATAATTATAT
65 TAATAATCCAACTTAAAAATATATTTGTTACATTTTCAACTTTGAATATTAAAAGATAATTATAT
* * * *
368673 ACTTTTGTATAATTTAAATTAAAATAATATATGTTTAAATTTGAATAGTAAAATGAATTTA
130 ACTTTTATATAATTTAAATTAAAATAATACATATTTAAATTTGAATAGTAAAAGGAATTTA
* ** * *
368734 CCTTTTGACCATAGCAAATTAAATAT-ATTATTTAATTCGAATATTAGTAGGATAATTACT-TTT
1 CCTTTTGACTATTCCAAATTAAAGATAATT-TTTAATTCGAATATTAATAGGATAATTACTCTTT
* * *
368797 TGAAT-ATGCCAACTTAAAAATGTTTTTGTTACCTTTTCAACTTTGAATATT-AAAGATAATTAT
65 T-AATAAT-CCAACTTAAAAATATATTTGTTACATTTTCAACTTTGAATATTAAAAGATAATTAT
* * * *
368860 ATACTTTTATAT-ATTTCAAATTAAAATAATACATATTTAAGTTTGAATGGTAAAAGGAGTTTTG
128 ATACTTTTATATAATTT-AAATTAAAATAATACATATTTAAATTTGAATAGTAAAAGGA-ATTTA
* * *
368924 TCTTTTGAATATTTCAAATTAAAAGATA
1 CCTTTTGACTATTCCAAATT-AAAGATA
368952 TTGTTATCTC
Statistics
Matches: 183, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
188 4 0.02
189 68 0.37
190 89 0.49
191 22 0.12
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (190 bp):
CCTTTTGACTATTCCAAATTAAAGATAATTTTTAATTCGAATATTAATAGGATAATTACTCTTTT
AATAATCCAACTTAAAAATATATTTGTTACATTTTCAACTTTGAATATTAAAAGATAATTATATA
CTTTTATATAATTTAAATTAAAATAATACATATTTAAATTTGAATAGTAAAAGGAATTTA
Found at i:371676 original size:20 final size:20
Alignment explanation
Indices: 371651--371691 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
371641 TGGATCCACT
371651 AACCTAATGTTTAAATCGAG
1 AACCTAATGTTTAAATCGAG
371671 AACCTAATGTTTAAATCGAG
1 AACCTAATGTTTAAATCGAG
371691 A
1 A
371692 TCAAGTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (20 bp):
AACCTAATGTTTAAATCGAG
Found at i:375511 original size:18 final size:18
Alignment explanation
Indices: 375490--375561 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
375480 TTAATCAAAT
375490 AATATATATTAAAAATAA
1 AATATATATTAAAAATAA
* * *
375508 AATA-ATAATACTAATTAA
1 AATATATATTA-AAAATAA
*
375526 AATAT-TATATAAAATTAA
1 AATATATAT-TAAAAATAA
375544 AATATAT-TTAAACAATAA
1 AATATATATTAAA-AATAA
375562 TTAAAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 9 0.21
18 31 0.72
19 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATATATTAAAAATAA
Found at i:376420 original size:24 final size:25
Alignment explanation
Indices: 376391--376452 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 25
376381 AAGCTTTCCT
**
376391 TTCTTTTTTTTTTTTCTGTT-TTTC
1 TTCTTTTTTTTTTTTCTGTTCTCCC
* *
376415 TTC-TTTTCTGTTTTCTGTTCTCCC
1 TTCTTTTTTTTTTTTCTGTTCTCCC
*
376439 TTCTTTTTTGTTTT
1 TTCTTTTTTTTTTT
376453 GCAGGATCCG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 14 0.48
24 8 0.28
25 7 0.24
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (25 bp):
TTCTTTTTTTTTTTTCTGTTCTCCC
Found at i:376421 original size:16 final size:14
Alignment explanation
Indices: 376390--376428 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
376380 TAAGCTTTCC
376390 TTTCT-TTTTTTTT
1 TTTCTGTTTTTTTT
376403 TTTCTGTTTTTCTTCT
1 TTTCTGTTTTT-TT-T
376419 TTTCTGTTTT
1 TTTCTGTTTT
376429 CTGTTCTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 5 0.22
15 2 0.09
16 11 0.48
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (14 bp):
TTTCTGTTTTTTTT
Found at i:377135 original size:76 final size:76
Alignment explanation
Indices: 377009--377723 Score: 1256
Period size: 76 Copynumber: 9.4 Consensus size: 76
376999 GAAATATTGA
377009 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
377074 AGGCTTTTTGG
66 AGGCTTTTTGG
*
377085 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGACTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
377150 AGGCTTTTTGG
66 AGGCTTTTTGG
*
377161 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
377226 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
377237 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
377302 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
377313 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT-AAGAACATCAAAAAGATCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAA-AACATCAAAAAGCTCCCG
377377 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
377389 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT-AAGAACATCAAAAAGCTCTCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAA-AACATCAAAAAGCTCCCG
377453 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
377465 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
377530 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
377541 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT-AAGAACATCAAAAAGCTCTCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAA-AACATCAAAAAGCTCCCG
377605 AAGGCTTTTTTGG
65 AAGGC-TTTTTGG
*
377618 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
377683 AGGCTTTTTGG
66 AGGCTTTTTGG
377694 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
377724 TGAGAAATAG
Statistics
Matches: 613, Mismatches: 21, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
75 4 0.01
76 535 0.87
77 72 0.12
78 2 0.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:378417 original size:22 final size:22
Alignment explanation
Indices: 378390--378444 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
378380 CATAAAGTTT
*
378390 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
378412 TTATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
378434 TCATCTTTGAA
1 TCATCTTTGAA
378445 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:378883 original size:53 final size:54
Alignment explanation
Indices: 378803--378913 Score: 179
Period size: 53 Copynumber: 2.1 Consensus size: 54
378793 AGAATAGCAG
***
378803 GTTCGTAAAACATTTGACAGTGCATTCATCCTTT-CTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGTTTCTGCTCAGAT
*
378856 GTTCGTAAAACATTTGACAACACATTCATCTTTTACTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGTTTCTGCTCAGAT
378910 GTTC
1 GTTC
378914 TCAATCATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 30 0.57
54 23 0.43
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGTTTCTGCTCAGAT
Found at i:381233 original size:114 final size:114
Alignment explanation
Indices: 381033--381258 Score: 344
Period size: 114 Copynumber: 2.0 Consensus size: 114
381023 GATCATGCAG
* * * * *
381033 TTCATCTTTCAATTCCAATGATCAGTTCTGGGGTTCTTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCAGTTCTGGAGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
381098 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* ** * *
381147 TTCATCTTTTAAATCCAATGATTGGTTTTGGAGTTCATACCAAACCAGATCAGATAACTTAAAGA
1 TTCATCTTTCAAATCCAATGATCAGTTCTGGAGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
381212 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
381259 CGTGGCACTT
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCAGTTCTGGAGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:383430 original size:12 final size:12
Alignment explanation
Indices: 383413--383441 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
383403 TTGATTTAAA
383413 TTTTTTTCCTTT
1 TTTTTTTCCTTT
383425 TTTTTTTCCTTT
1 TTTTTTTCCTTT
383437 TTTTT
1 TTTTT
383442 CCTCCTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTCCTTT
Found at i:388892 original size:18 final size:18
Alignment explanation
Indices: 388871--388942 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
388861 TTAATCAAAT
388871 AATATATATTAAAAATAA
1 AATATATATTAAAAATAA
* * *
388889 AATA-ATAATACTAATTAA
1 AATATATATTA-AAAATAA
*
388907 AATAT-TATATAAAATTAA
1 AATATATAT-TAAAAATAA
388925 AATATAT-TTAAACAATAA
1 AATATATATTAAA-AATAA
388943 TTAAAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 9 0.21
18 31 0.72
19 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATATATTAAAAATAA
Found at i:389822 original size:24 final size:22
Alignment explanation
Indices: 389775--389833 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
389765 TTTCCTTTCT
**
389775 TTCTTTTT-TTTTCTGTTTTTC
1 TTCTTTTTGTTTTCTGTTTCCC
389796 TTCTTTTCTGTTTTCTGTTCTCCC
1 TTCTTTT-TGTTTTCTGTT-TCCC
389820 TTCTTTTTTGTTTT
1 TTC-TTTTTGTTTT
389834 GCAAGATCCG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 7 0.22
22 1 0.03
23 9 0.28
24 11 0.34
25 4 0.12
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.75
Consensus pattern (22 bp):
TTCTTTTTGTTTTCTGTTTCCC
Found at i:390219 original size:39 final size:39
Alignment explanation
Indices: 390200--390275 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
390190 TTATTATTAT
*
390200 TATTTTATTTAATGATAATAATATATATATATAATAATA
1 TATTTTATTTAATAATAATAATATATATATATAATAATA
390239 TATTTTATTTAATAATAATAATA-AT-TA-A-AATAATA
1 TATTTTATTTAATAATAATAATATATATATATAATAATA
390274 TA
1 TA
390276 ATGAAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
35 9 0.25
36 1 0.03
37 2 0.06
38 2 0.06
39 22 0.61
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (39 bp):
TATTTTATTTAATAATAATAATATATATATATAATAATA
Found at i:390235 original size:16 final size:17
Alignment explanation
Indices: 390214--390255 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
390204 TTATTTAATG
390214 ATAATAATATA-TATAT
1 ATAATAATATATTATAT
*
390230 ATAATAATATATTTTAT
1 ATAATAATATATTATAT
*
390247 TTAATAATA
1 ATAATAATA
390256 ATAATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATAATATATTATAT
Found at i:392252 original size:60 final size:60
Alignment explanation
Indices: 392171--392293 Score: 176
Period size: 60 Copynumber: 2.0 Consensus size: 60
392161 TACATGAATG
* * * * *
392171 GTCCCCCAATTATAGGGCATTATTTTGTTGATTCTTCT-GACTATTAAAAGTAACAAAATA
1 GTCCACCAATTATAGGACATTACTTAGTTGAGTCTT-TAGACTATTAAAAGTAACAAAATA
*
392231 GTCCACCAATTATAGGACATTACTTAGTTGAGTCTTTAGACTATTAAAAGTTACAAAATA
1 GTCCACCAATTATAGGACATTACTTAGTTGAGTCTTTAGACTATTAAAAGTAACAAAATA
392291 GTC
1 GTC
392294 ACTAGAGGTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (60 bp):
GTCCACCAATTATAGGACATTACTTAGTTGAGTCTTTAGACTATTAAAAGTAACAAAATA
Found at i:394973 original size:22 final size:22
Alignment explanation
Indices: 394922--394977 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
394912 AATGTAAACT
** *
394922 ATAAAAATATTCAAATATTATA
1 ATAAAAATATAAAAATACTATA
394944 A-AATAAATATAAAAATACTATA
1 ATAA-AAATATAAAAATACTATA
394966 ATAAAAAT-TAAA
1 ATAAAAATATAAA
394978 TTACTAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 6 0.21
22 21 0.72
23 2 0.07
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAAAATATAAAAATACTATA
Found at i:394982 original size:20 final size:20
Alignment explanation
Indices: 394945--394983 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
394935 AATATTATAA
*
394945 AATAAATATAAAAATACTAT
1 AATAAAAATAAAAATACTAT
* *
394965 AATAAAAATTAAATTACTA
1 AATAAAAATAAAAATACTA
394984 AAACAATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAAATAAAAATACTAT
Found at i:396164 original size:15 final size:15
Alignment explanation
Indices: 396144--396176 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
396134 GCTATGGGAA
396144 AGGGTGATAGAGGCT
1 AGGGTGATAGAGGCT
396159 AGGGTGATAGAGGCT
1 AGGGTGATAGAGGCT
396174 AGG
1 AGG
396177 TTGAGACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.48, T:0.18
Consensus pattern (15 bp):
AGGGTGATAGAGGCT
Found at i:399584 original size:38 final size:38
Alignment explanation
Indices: 399263--399604 Score: 447
Period size: 38 Copynumber: 9.0 Consensus size: 38
399253 ATTTATATAG
* *
399263 CTTTGTTATTCTTGACTCCCAT-GCGAAGAGAAGTCAAT
1 CTTTGTTATTCTTGACTTCC-TCGTGAAGAGAAGTCAAT
*
399301 CTTTGTTATTCTTGACTTCCTTGTGAAGAGAAGTCAAT
1 CTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAAT
* *
399339 CTTTGTTATTCCTGACTCCCTC-TCGAAGAGAAGTCAAT
1 CTTTGTTATTCTTGACTTCCTCGT-GAAGAGAAGTCAAT
* *
399377 CTTTGTTATTCTTGACTTCCTCATGAAGAAAAGTCAAT
1 CTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAAT
* * *
399415 CTTTGCTATTCCTGACTTCCTCGTGAAGAGAAGTAAAT
1 CTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAAT
** * * *
399453 CTTTGTTATTCCAGACTCCCTTGTGAAGAGGAGTCAAT
1 CTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAAT
*
399491 CTTTGTTATTCTTGACTTTCTCGTGAAGAGAAGTCAAT
1 CTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAAT
*
399529 CTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTCAAT
1 CTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAAT
** * *
399567 CTTTGTCCTTCTTGACTTTCTCGCGAAGATG-AGTCAAT
1 CTTTGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAAT
399605 ATTTTAGTGT
Statistics
Matches: 268, Mismatches: 32, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
37 2 0.01
38 264 0.99
39 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (38 bp):
CTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAAT
Found at i:399633 original size:45 final size:45
Alignment explanation
Indices: 399569--399877 Score: 392
Period size: 45 Copynumber: 6.9 Consensus size: 45
399559 AAGTCAATCT
*
399569 TTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTTTAGTG
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTTTAGTG
* * * * *
399614 TTGTCTTTATTGACTTTCTCGCGAAGAGGAGTTAATCTTTCAGTG
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTTTAGTG
*
399659 TTGTATCC--CTTGACTTTCTCGTGAAGAGGAGTCAATATTTTAGTG
1 TTG--TCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTTTAGTG
*
399704 TTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTTTAGTG
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTTTAGTG
* * * * *
399749 TTGTCTTTATTGACTTTCTAGCGAAGAGGAGTTAATCA-TTCAGTG
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAAT-ATTTTAGTG
* * * * *
399794 TTGTACTCCTTAACTTTCTCGTGAAGAGGAGTCAATCTTTTAGT-
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTTTAGTG
*
399838 TTGTCCTTCTTGACTTTCTTGCGAAGAGGAGTCAATATTT
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTT
399878 CAAATTTGGT
Statistics
Matches: 222, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
43 3 0.01
44 34 0.15
45 182 0.82
46 1 0.00
47 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (45 bp):
TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTTTAGTG
Found at i:399890 original size:135 final size:134
Alignment explanation
Indices: 399568--399877 Score: 541
Period size: 135 Copynumber: 2.3 Consensus size: 134
399558 GAAGTCAATC
399568 TTTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTTTAGTGTTGTCTTTATTGACTTTCT
1 TTTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTTTAGTGTTGTCTTTATTGACTTTCT
* * *
399633 CGCGAAGAGGAGTTAATCTTTCAGTGTTGTATCCCTTGACTTTCTCGTGAAGAGGAGTCAATATT
66 AGCGAAGAGGAGTTAATCATTCAGTGTTGTATCCCTTAACTTTCTCGTGAAGAGGAGTCAATATT
399698 TTAG
131 TTAG
399702 TGTTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTTTAGTGTTGTCTTTATTGACTTTC
1 T-TTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTTTAGTGTTGTCTTTATTGACTTTC
*
399767 TAGCGAAGAGGAGTTAATCATTCAGTGTTGTA-CTCCTTAACTTTCTCGTGAAGAGGAGTCAATC
65 TAGCGAAGAGGAGTTAATCATTCAGTGTTGTATC-CCTTAACTTTCTCGTGAAGAGGAGTCAATA
399831 TTTTAG
129 TTTTAG
* *
399837 TTTGTCCTTCTTGACTTTCTTGCGAAGAGGAGTCAATATTT
1 TTTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTT
399878 CAAATTTGGT
Statistics
Matches: 168, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
134 40 0.24
135 128 0.76
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (134 bp):
TTTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTTTAGTGTTGTCTTTATTGACTTTCT
AGCGAAGAGGAGTTAATCATTCAGTGTTGTATCCCTTAACTTTCTCGTGAAGAGGAGTCAATATT
TTAG
Found at i:399925 original size:135 final size:134
Alignment explanation
Indices: 399569--399916 Score: 366
Period size: 135 Copynumber: 2.6 Consensus size: 134
399559 AAGTCAATCT
* * * * **** *
399569 TTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTTTAGTGTTGTCTTTATTGACTTTCTC
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTTAAATGTTGTCTTCATTGAAGAGCTA
* * * *
399634 GCGAAGAGGAGTTAATCTTTCAGTGTTGTATCCCTTGACTTTCTCGTGAAGAGGAGTCAATATTT
66 GCGAAGA-GAATCAATCATTCAGTGTTGTATCCCTTAACTTTCTCGTGAAGAGGAGTCAATATTT
399699 TAGTG
130 TAGTG
* * * * ****
399704 TTGTCCTTCTTGACTTTCTCGCGAAGATGAGTCAATATTTTAGTGTTGTCTTTATTGACTTTCTA
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTTAAATGTTGTCTTCATTGAAGAGCTA
* * *
399769 GCGAAGAGGAGTTAATCATTCAGTGTTGTA-CTCCTTAACTTTCTCGTGAAGAGGAGTCAATCTT
66 GCGAAGA-GAATCAATCATTCAGTGTTGTATC-CCTTAACTTTCTCGTGAAGAGGAGTCAATATT
399833 TTAGT-
129 TTAGTG
*
399838 TTGTCCTTCTTGACTTTCTTGCGAAGAGGAGTCAATATTTCAAAT-TTGGTCTTCA-TGAAGAGC
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTT-AAATGTT-GTCTTCATTGAAGAGC
*
399901 -AGTGAAGCA-AATCAAT
64 TAGCGAAG-AGAATCAAT
399917 TCCGATTCAA
Statistics
Matches: 193, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
132 5 0.03
133 6 0.03
134 46 0.24
135 136 0.70
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (134 bp):
TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATATTTAAATGTTGTCTTCATTGAAGAGCTA
GCGAAGAGAATCAATCATTCAGTGTTGTATCCCTTAACTTTCTCGTGAAGAGGAGTCAATATTTT
AGTG
Found at i:399975 original size:21 final size:21
Alignment explanation
Indices: 399946--399986 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
399936 AAGAGCATCG
*
399946 AAGTGGATCAAAATTTTTCTT
1 AAGTAGATCAAAATTTTTCTT
399967 AAGTAGATCAAAATTTTTCT
1 AAGTAGATCAAAATTTTTCT
399987 CGAGTCTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (21 bp):
AAGTAGATCAAAATTTTTCTT
Found at i:400163 original size:133 final size:133
Alignment explanation
Indices: 399967--400417 Score: 583
Period size: 133 Copynumber: 3.4 Consensus size: 133
399957 AATTTTTCTT
* *
399967 AAGTAGATCAAAATTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAG-TAGATTTTTCTTC
1 AAGTGGATCAAAA--TTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGAT-GATTCTTCTTC
* * * *
400031 ATTCAGATTTGGTATTCTTGAAGAGCAGTGAAGCAAATCGATTCTGATTTAATCTTCCCTGAAGA
63 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
400096 GCAGTG
128 GCAGTG
* *
400102 AAGTTGATCAAAATTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTAGAGATGATTCTTCTTCTTT
1 AAGTGGATCAAAATTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGATGATTCTTCTTCTTT
* * *
400167 CATATTTGGTCTTCCTGAAGAGCA-TCGAAGCAAATCAAATTC-GATTCAATCTTCCCTAAAGAG
66 CAGATTTGGTCTTCCTGAAGAGCAGT-GAAGCAAATC-GATTCTGATTCAATCTTCCCTGAAGAG
*
400230 CAGCG
129 CAGTG
* * *
400235 AAGTGGATCAAATTTTTTCTCGAGTCTGATCTCCCATAAAGAGTAGCGGAGCA-GATTCTTCTT-
1 AAGTGGATCAAA--ATTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAG-ATGATTCTTCTTC
* * * *
400298 TTTCAGATTTGGTCTTCCTGAAGAGCGGTGAAGCAAATTGATTCTGATTCAACCTTCCCTGAATA
63 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
400363 GCA-TCG
128 GCAGT-G
*
400369 AAGTGGATCAAAATTTCTTGAGTCTGATCTCCCCTAACA-AGTAGTGGAG
1 AAGTGGATCAAAATTTCTCGAGTCTGATCTCCCCTAA-AGAGTAGTGGAG
400418 CATATCTCTC
Statistics
Matches: 278, Mismatches: 28, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
132 32 0.12
133 117 0.42
134 72 0.26
135 56 0.20
136 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (133 bp):
AAGTGGATCAAAATTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGATGATTCTTCTTCTTT
CAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGCA
GTG
Found at i:400582 original size:6 final size:6
Alignment explanation
Indices: 400573--400616 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
400563 TTATTATTAC
* *
400573 TTATAT TTATAT TTATAT TTATAT ATTTTAT TTTTAT TT-TAT TT
1 TTATAT TTATAT TTATAT TTATAT -TTATAT TTATAT TTATAT TT
400617 TACAAGTCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
5 5 0.14
6 26 0.72
7 5 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTATAT
Found at i:400594 original size:25 final size:24
Alignment explanation
Indices: 400551--400616 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
400541 CCGGAGTTTT
400551 TATTTATTATTATTA-TTAT-TACTTA
1 TATTTA-TATT-TTATTTATATA-TTA
*
400576 TATTTATATTTATATTTATATATTT
1 TATTTATATTT-TATTTATATATTA
*
400601 TATTTTTATTTTATTT
1 TATTTATATTTTATTT
400617 TACAAGTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
23 1 0.03
24 11 0.31
25 22 0.61
26 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTTATATTTTATTTATATATTA
Found at i:400614 original size:20 final size:20
Alignment explanation
Indices: 400574--400611 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
400564 TATTATTACT
400574 TATATTTATATTTATATTTA
1 TATATTTATATTTATATTTA
*
400594 TATATTT-TATTTTTATTT
1 TATATTTATATTTATATTT
400612 TATTTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATATTTATATTTATATTTA
Found at i:400618 original size:25 final size:28
Alignment explanation
Indices: 400547--400618 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
400537 TCTTCCGGAG
400547 TTTTTA-TTTATTATTATTATTATTACTTA
1 TTTTTATTTTATT-TTATTATTATTA-TTA
*
400576 TATTTATATTTATATTTA-TA-TATT-TTA
1 TTTTTAT-TTTAT-TTTATTATTATTATTA
400603 TTTTTATTTTATTTTA
1 TTTTTATTTTATTTTA
400619 CAAGTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
25 4 0.11
26 5 0.13
27 9 0.24
29 9 0.24
30 2 0.05
31 8 0.21
32 1 0.03
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTTTATTTTATTTTATTATTATTATTA
Found at i:404043 original size:16 final size:17
Alignment explanation
Indices: 404022--404053 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
404012 AATTCTTGAT
404022 TTTATTTAA-TAAAATG
1 TTTATTTAATTAAAATG
404038 TTTATTTAATTAAAAT
1 TTTATTTAATTAAAAT
404054 AATAATATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTATTTAATTAAAATG
Found at i:405647 original size:40 final size:39
Alignment explanation
Indices: 405498--405726 Score: 345
Period size: 39 Copynumber: 5.8 Consensus size: 39
405488 TCCATACCCA
* *
405498 ACTCGAAACAGAAGATTTTATCTCACTTGACATAGTTTC
1 ACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
405537 ACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
1 ACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
* * *
405576 ACTCGAAACAAAAGACTTTATCTTGCTTGAGATAGTTTC
1 ACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
*
405615 ACTCGAAATAGAAGATTTTTATCTCGCTTGAGATAGTTTC
1 ACTCGAAACAGAAGA-TTTTATCTCGCTTGAGATAGTTTC
*
405655 ACTCGAAACA-ACATATTTTTATCTCGCTTGAGATAGTTTC
1 ACTCGAAACAGA-AGA-TTTTATCTCGCTTGAGATAGTTTC
*
405695 ACTCGAAACAGAAGA-TTTATCTCACTTGAGAT
1 ACTCGAAACAGAAGATTTTATCTCGCTTGAGAT
405727 TATTTTTCTT
Statistics
Matches: 174, Mismatches: 13, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
38 16 0.09
39 87 0.50
40 70 0.40
41 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (39 bp):
ACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
Found at i:405995 original size:92 final size:92
Alignment explanation
Indices: 405854--406057 Score: 229
Period size: 92 Copynumber: 2.2 Consensus size: 92
405844 TCAAAACACG
* * *
405854 TCGAATTAGCCACGCCTCA-TATGAGGGACCAAAATTCCCAGTAGAGAATTCAT-GAGAATAA-C
1 TCGAATCAGCGACGCCTCACTATGAGGGACCAAAATTCCCAGTAGAGAATTCATAAAGAA-AAGC
* *
405916 TT-ATTCAACCTTGACTCGATTCTTGGCATT
65 TTGATTC--CCTT-ACTCGATTCATGACATT
* * * *
405946 TCGAATCAGCGACGCCTCACT-TGTGGGACCAACATTTCCAGTAGCGAATTCATAAAGAAAAGCT
1 TCGAATCAGCGACGCCTCACTATGAGGGACCAAAATTCCCAGTAGAGAATTCATAAAGAAAAGCT
* *
406010 TGTTTCCGTTACTCGATTCATGACATT
66 TGATTCCCTTACTCGATTCATGACATT
*
406037 TCGAATCAGCGATGCCTCACT
1 TCGAATCAGCGACGCCTCACT
406058 CGAGGGATGA
Statistics
Matches: 96, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
91 35 0.36
92 50 0.52
93 8 0.08
94 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (92 bp):
TCGAATCAGCGACGCCTCACTATGAGGGACCAAAATTCCCAGTAGAGAATTCATAAAGAAAAGCT
TGATTCCCTTACTCGATTCATGACATT
Found at i:409536 original size:17 final size:17
Alignment explanation
Indices: 409511--409557 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
409501 AAGAAACAAA
*
409511 AAAGGGAAAAATAA-GAG
1 AAAGAGAAAAA-AAGGAG
409528 AAAGAGAAAAAAATGGAG
1 AAAGAGAAAAAAA-GGAG
409546 AATAGAGAAAAA
1 AA-AGAGAAAAA
409558 GAAAGCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 10 0.38
18 5 0.19
19 9 0.35
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (17 bp):
AAAGAGAAAAAAAGGAG
Found at i:409538 original size:18 final size:19
Alignment explanation
Indices: 409517--409557 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
409507 CAAAAAAGGG
409517 AAAAATAAGAGAA-AGAGAA
1 AAAAAT-AGAGAATAGAGAA
*
409536 AAAAATGGAGAATAGAGAA
1 AAAAATAGAGAATAGAGAA
409555 AAA
1 AAA
409558 GAAAGCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (19 bp):
AAAAATAGAGAATAGAGAA
Found at i:409576 original size:41 final size:42
Alignment explanation
Indices: 409500--409629 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 42
409490 ACAACACAAA
* *
409500 AAAGAA-ACAAAAAAGGGAAA-AATAAGAGAAAGAGAAAAAAAT
1 AAAGAAGAGAAAAAAGAGAAAGAA-AA-AGAAAGAGAAAAAAAT
** * * * * *
409542 GGAGAATAGAGAAAA-AGAAAGCAAAAGATAGAGAAACAAAT
1 AAAGAAGAGAAAAAAGAGAAAGAAAAAGAAAGAGAAAAAAAT
* *
409583 AAAGAAGAGAAAAAAGAGAAAGAAAAAGAAAAAGAAAAGAA-
1 AAAGAAGAGAAAAAAGAGAAAGAAAAAGAAAGAGAAAAAAAT
409624 AAAGAA
1 AAAGAA
409630 ATAAAACATA
Statistics
Matches: 68, Mismatches: 17, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
41 31 0.46
42 30 0.44
43 7 0.10
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (42 bp):
AAAGAAGAGAAAAAAGAGAAAGAAAAAGAAAGAGAAAAAAAT
Found at i:409598 original size:12 final size:13
Alignment explanation
Indices: 409528--409620 Score: 59
Period size: 12 Copynumber: 7.1 Consensus size: 13
409518 AAAATAAGAG
409528 AAAGAGAAA-AAA
1 AAAGAGAAAGAAA
** *
409540 ATGGAGAATAGAGA
1 AAAGAGAA-AGAAA
409554 AAA-AGAAAGCAAA
1 AAAGAGAAAG-AAA
*
409567 AGATAGAGAAACAAA
1 A-A-AGAGAAAGAAA
*
409582 TAAAGA-AGAGAAA
1 -AAAGAGAAAGAAA
409595 AAAGAGAAAG-AA
1 AAAGAGAAAGAAA
*
409607 AAAGAAAAAGAAA
1 AAAGAGAAAGAAA
409620 A
1 A
409621 GAAAAAGAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
12 24 0.39
13 19 0.31
14 7 0.11
15 5 0.08
16 6 0.10
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (13 bp):
AAAGAGAAAGAAA
Found at i:409604 original size:18 final size:18
Alignment explanation
Indices: 409516--409623 Score: 66
Period size: 18 Copynumber: 6.0 Consensus size: 18
409506 ACAAAAAAGG
*
409516 GAAAAATAAGAGAAAG-A
1 GAAAAAAAAGAGAAAGAA
*
409533 GAAAAAAATGGAGAATAG-A
1 GAAAAAAA-AGAGAA-AGAA
409552 GAAAAAGAAAGCA-AAAGATA
1 GAAAAA-AAAG-AGAAAGA-A
* * *
409572 GAGAAACAA-ATAAAGAA
1 GAAAAAAAAGAGAAAGAA
*
409589 GAGAAAAAAGAGAAAGAA
1 GAAAAAAAAGAGAAAGAA
409607 -AAAGAAAAAGA-AAAGAA
1 GAAA-AAAAAGAGAAAGAA
409624 AAAGAAATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
17 25 0.34
18 26 0.35
19 14 0.19
20 9 0.12
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.05
Consensus pattern (18 bp):
GAAAAAAAAGAGAAAGAA
Found at i:409620 original size:11 final size:11
Alignment explanation
Indices: 409594--409630 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
409584 AAGAAGAGAA
*
409594 AAAAGAGAAAG
1 AAAAGAAAAAG
409605 AAAAAGAAAAAG
1 -AAAAGAAAAAG
409617 AAAAGAAAAAG
1 AAAAGAAAAAG
409628 AAA
1 AAA
409631 TAAAACATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:409621 original size:17 final size:18
Alignment explanation
Indices: 409593--409630 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
409583 AAAGAAGAGA
409593 AAAAAGAGAAAGAAAAAG
1 AAAAAGAGAAAGAAAAAG
409611 AAAAAGA-AAAGAAAAAG
1 AAAAAGAGAAAGAAAAAG
409628 AAA
1 AAA
409631 TAAAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAGAGAAAGAAAAAG
Found at i:409629 original size:6 final size:6
Alignment explanation
Indices: 409593--409630 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
409583 AAAGAAGAGA
*
409593 AAAAAG AGAAAG AAAAAG AAAAAG -AAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
409631 TAAAACATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:411928 original size:14 final size:15
Alignment explanation
Indices: 411909--411942 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
411899 TTTAAGAAAA
411909 TATAATAA-AATATT
1 TATAATAATAATATT
411923 TATAATAATAATATT
1 TATAATAATAATATT
411938 T-TAAT
1 TATAAT
411943 TCTTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATAATAATATT
Found at i:413672 original size:2 final size:2
Alignment explanation
Indices: 413665--413690 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
413655 TTAATAATAA
413665 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
413691 TAAATCCCAA
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:414265 original size:244 final size:244
Alignment explanation
Indices: 413815--414476 Score: 915
Period size: 244 Copynumber: 2.7 Consensus size: 244
413805 TATTGGATTG
* * * *
413815 AACAAGTTCTTCTCAATATGAACTTCTTCTCCCTCTCTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTT
* * * * * *
413880 CTT-ACTGAAAATGTTAAGT-CGTCTCCTTCTGTGGTGGACTTGAAAGGAACAAGTTCTTCTCAT
66 CTTCATTGGAAATGTTGA-TCCATCTCCTTCTGTGATGGAATTGAAAGGAACAAGTTCTTCTCAT
* * *
413943 TATGAAC--TTTTTCCTTTAGGGCAAGTTCTTCTCATTATGAACTCTTTTAGAAATGTCAATCCC
130 TATGAACTTTTTTTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTCAATCCC
* * * *
414006 TCAAGCGAGGTGTCACTGATTCAAAATG-CTGTGAATCGAGTGATAGGTCA
195 TCAACCAAGGTGTCACTGATTCAAAATGTC-ATGAATCGAGTGATAAGTCA
*
414056 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATTAGTTCTTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTT
* *
414121 CTTCATTGGAAATATTGATCCATCTCCTTCTGTGATAGAATTGAAAGGAACAAGTTCTTCTCATT
66 CTTCATTGGAAATGTTGATCCATCTCCTTCTGTGATGGAATTGAAAGGAACAAGTTCTTCTCATT
* **
414186 ATGAACTTTTTTTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTCAATTTCT
131 ATGAACTTTTTTTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTCAATCCCT
* *
414251 CAACCAATGTGTCACTGATTCGAAATGTCATGAATCGAGTGATAAGTCA
196 CAACCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGATAAGTCA
* *
414300 AACAAGCTCTTCTCATTATGAACTTCTTCTCCATATGTCGGATGAGTTCTTCTCATTATGAAC-T
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTT
* * * *
414364 CTCCATTGGAAATGTTGATCCATCTTCTTCTGTGATGGAATTGAAAAGAACAAATTCTTCTCATT
66 CTTCATTGGAAATGTTGATCCATCTCCTTCTGTGATGGAATTGAAAGGAACAAGTTCTTCTCATT
** * *
414429 ATGAACTTCTCCTTCCTCGTT-GGATGAGTTCTTCTCATTATTAACTCT
131 ATGAACTT-TTTTTCCT--TTAGGACGAGTTCTTCTCATTATGAACTCT
414477 CCATTGGAAA
Statistics
Matches: 374, Mismatches: 39, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
241 64 0.17
242 57 0.15
243 68 0.18
244 158 0.42
245 25 0.07
246 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (244 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTT
CTTCATTGGAAATGTTGATCCATCTCCTTCTGTGATGGAATTGAAAGGAACAAGTTCTTCTCATT
ATGAACTTTTTTTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTCAATCCCT
CAACCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGATAAGTCA
Found at i:414499 original size:111 final size:112
Alignment explanation
Indices: 414307--414513 Score: 330
Period size: 111 Copynumber: 1.9 Consensus size: 112
414297 TCAAACAAGC
* *
414307 TCTTCTCATTATGAACTTCTTCTCCATATGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTCCTCCATACGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
414372 GAAATGTTGATCCATCTTC-TTCTGTGATGGAATTGAAAAGAACAAAT
66 GAAATGTTGATCCATC-TCATTCTGTGATGGAATTGAAAAGAACAAAT
* *
414419 TCTTCTCATTATGAACTTCTCCTTCC-T-CGTTGGATGAGTTCTTCTCATTATTAACTCTCCATT
1 TCTTCTCATTATGAACTTCTCC-TCCATACGTCGGATGAGTTCTTCTCATTATGAACTCTCCATT
*
414482 GGAAATGTTGATTCATCTCATTCTGTGATGGA
65 GGAAATGTTGATCCATCTCATTCTGTGATGGA
414514 TCATAATTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
110 2 0.02
111 61 0.69
112 22 0.25
113 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (112 bp):
TCTTCTCATTATGAACTTCTCCTCCATACGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
GAAATGTTGATCCATCTCATTCTGTGATGGAATTGAAAAGAACAAAT
Found at i:415378 original size:12 final size:11
Alignment explanation
Indices: 415348--415406 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
415338 TCTCGAACCC
* *
415348 TTCTTTTTCTC
1 TTCTTTTTTTT
*
415359 TTCATTTTTTCT
1 TTC-TTTTTTTT
415371 TTCTTTTTTTT
1 TTCTTTTTTTT
415382 TTCTTTTTTTT
1 TTCTTTTTTTT
*
415393 TTATTTTTTATT
1 TTCTTTTTT-TT
415405 TT
1 TT
415407 TTCTCTTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
11 29 0.71
12 12 0.29
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:415381 original size:15 final size:14
Alignment explanation
Indices: 415363--415413 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
415353 TTTCTCTTCA
415363 TTTTTTCTTTCTTTT
1 TTTTTTCTTT-TTTT
415378 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
* *
415392 TTTATT-TTTTATT
1 TTTTTTCTTTTTTT
*
415405 TTTTCTCTT
1 TTTTTTCTT
415414 CAAGCATAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 10 0.32
14 11 0.35
15 10 0.32
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTCTTTTTTT
Found at i:426737 original size:25 final size:23
Alignment explanation
Indices: 426681--426738 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 23
426671 TTTTGCATGA
*
426681 AATAAT-ATAATAATAACTTTTTT
1 AATAATAAT-ATAATAACTTTTAT
*
426704 AAGAA-AATATAATAACATATTTAT
1 AATAATAATATAATAAC-T-TTTAT
426728 AATAATAATAT
1 AATAATAATAT
426739 TTTAATGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 8 0.29
23 7 0.25
24 8 0.29
25 5 0.18
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (23 bp):
AATAATAATATAATAACTTTTAT
Found at i:426938 original size:21 final size:21
Alignment explanation
Indices: 426909--426961 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
426899 ATTCTGACTA
426909 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
426930 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* *
426951 TCACAATGCGA
1 TCGCATTGCGA
426962 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:426983 original size:20 final size:20
Alignment explanation
Indices: 426954--427042 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
426944 TCCTAATTCA
*
426954 CAATGCGAATATGTAAATCG
1 CAATGCGAATACGTAAATCG
* ** *
426974 CAACGCGAATTTGGAAAATCG
1 CAATGCGAA-TACGTAAATCG
*
426995 CAATGCGATTACGTAAATCG
1 CAATGCGAATACGTAAATCG
427015 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
427035 CAATGCGA
1 CAATGCGA
427043 TTTACATAGC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 43 0.74
21 15 0.26
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:426999 original size:41 final size:40
Alignment explanation
Indices: 426954--427042 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 40
426944 TCCTAATTCA
* **
426954 CAATGCGAATATGTAAATCGCAACGCGAATTTGGAAAATCG
1 CAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAATCG
* * *
426995 CAATGCGATTACGTAAATCGCAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCGCAACGCGAATACGAAAATCG
427035 CAATGCGA
1 CAATGCGA
427043 TTTACATAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 16 0.38
41 26 0.62
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (40 bp):
CAATGCGAATACGTAAATCGCAACGCGAATACGAAAATCG
Found at i:427689 original size:20 final size:20
Alignment explanation
Indices: 427652--427709 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
427642 GATTCTTGCG
**
427652 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
427672 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
**
427692 TTGCGATTTTCATTTTCG
1 TTGCGATAGTCATTTTCG
427710 TGTTGCGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:427710 original size:20 final size:20
Alignment explanation
Indices: 427681--427720 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
427671 ATTGCGATAG
427681 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
427701 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
427721 AAAGTTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.55
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:429627 original size:20 final size:20
Alignment explanation
Indices: 429602--429651 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
429592 AGAATAGTTT
429602 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
429622 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
429642 ACTATCGCAA
1 ACTATCGCAA
429652 CGAGAGAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:429784 original size:20 final size:20
Alignment explanation
Indices: 429698--429776 Score: 124
Period size: 20 Copynumber: 4.0 Consensus size: 20
429688 GATTCTCTCG
**
429698 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
429718 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
429738 TTGCGATAGTCATTTGT-GCA
1 TTGCGATAGTCATTT-TCGCA
429758 TTGCGATAGTCATTTTCGC
1 TTGCGATAGTCATTTTCGC
429777 GTAGCGATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.02
20 53 0.96
21 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:429838 original size:33 final size:34
Alignment explanation
Indices: 429758--429848 Score: 103
Period size: 33 Copynumber: 2.7 Consensus size: 34
429748 CATTTGTGCA
* * * * *
429758 TTGCGATAGTCATTTTCGCGTAGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCAATTCTCTCG
** *
429792 TTGCGATTTTCA-TTTCGCATTGCAATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCAATTCTCTCG
429825 TTGCGATAGTCATTTTCGCGTTGC
1 TTGCGATAGTCATTTTCGCGTTGC
429849 GATTGTCATT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
33 25 0.56
34 20 0.44
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCAATTCTCTCG
Done.