Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 33
Found at i:4979387 original size:17 final size:19
Alignment explanation
Indices: 4979355--4979389 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
4979345 AAAGAAATAA
4979355 AAAAGCAAATAAAAAAGAG
1 AAAAGCAAATAAAAAAGAG
4979374 AAAAG-AAA-AAAAAAGA
1 AAAAGCAAATAAAAAAGA
4979390 TAAGAAGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (19 bp):
AAAAGCAAATAAAAAAGAG
Found at i:4980476 original size:32 final size:32
Alignment explanation
Indices: 4980435--4980498 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
4980425 AAGAAATGAT
*
4980435 GAATGTTGGGGCATCTTTGGGGATTCAACATC
1 GAATGTTGGGGCATCTTTGGAGATTCAACATC
4980467 GAATGTTGGGGCATCTTTGGAGATTCAACATC
1 GAATGTTGGGGCATCTTTGGAGATTCAACATC
4980499 CTGAAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (32 bp):
GAATGTTGGGGCATCTTTGGAGATTCAACATC
Found at i:4980655 original size:35 final size:34
Alignment explanation
Indices: 4980616--4980703 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 34
4980606 CTAGATACAG
*
4980616 TTTTCTAAAACAAAATTTAGTATTGCTTGAGACAT
1 TTTTCTAAAA-AAAATTTAGTATCGCTTGAGACAT
* * *
4980651 TTTTCTAAAAACAATTTTGTCTCGCTTGAGACAAT
1 TTTTCTAAAAAAAATTTAGTATCGCTTGAGAC-AT
* *
4980686 TTCTCTCAAAATAAATTT
1 TTTTCT-AAAAAAAATTT
4980704 CATCTTGCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 18 0.41
35 17 0.39
36 9 0.20
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (34 bp):
TTTTCTAAAAAAAATTTAGTATCGCTTGAGACAT
Found at i:4980678 original size:34 final size:35
Alignment explanation
Indices: 4980600--4980683 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
4980590 ACAAAGCGTC
* *
4980600 GTCTCGCTAGATACAGTTTTCTAAAACAAAATTTA
1 GTCTCGCTTGAGACAGTTTTCTAAAACAAAATTTA
* * * * *
4980635 GTATTGCTTGAGACATTTTTCTAAAA-ACAATTTT
1 GTCTCGCTTGAGACAGTTTTCTAAAACAAAATTTA
4980669 GTCTCGCTTGAGACA
1 GTCTCGCTTGAGACA
4980684 ATTTCTCTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 19 0.47
35 21 0.52
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (35 bp):
GTCTCGCTTGAGACAGTTTTCTAAAACAAAATTTA
Found at i:4982333 original size:22 final size:22
Alignment explanation
Indices: 4982285--4982334 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
4982275 TATGCACGTG
4982285 TGATATGTGACAGAAGAGAAGA
1 TGATATGTGACAGAAGAGAAGA
* *
4982307 -AATATGTGATCATAAGAGAA-A
1 TGATATGTGA-CAGAAGAGAAGA
4982328 TGATATG
1 TGATATG
4982335 AGTACATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.46, C:0.04, G:0.26, T:0.24
Consensus pattern (22 bp):
TGATATGTGACAGAAGAGAAGA
Found at i:4995131 original size:22 final size:22
Alignment explanation
Indices: 4995103--4995146 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4995093 TTTTAGCATT
* *
4995103 TGGTACTGTTCACTATTGTTCA
1 TGGTACTATTCACTAATGTTCA
*
4995125 TGGTACTATTCATTAATGTTCA
1 TGGTACTATTCACTAATGTTCA
4995147 CAGTATTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (22 bp):
TGGTACTATTCACTAATGTTCA
Found at i:4998474 original size:196 final size:196
Alignment explanation
Indices: 4998127--4998518 Score: 759
Period size: 196 Copynumber: 2.0 Consensus size: 196
4998117 TTATAAGGTT
4998127 TAGGCTTCTGATAATCGTCTTGGAAATTATGTTTATGTAGATATTTAGCTTAAACAAGTTTTAGA
1 TAGGCTTCTGATAATCGTCTTGGAAATTATGTTTATGTAGATATTTAGCTTAAACAAGTTTTAGA
*
4998192 ACAATCAAAGATTAGGATCGAATCAAAGCAAGGCCAAGGTGAGTGTAATTTAATTTGTGCTTATG
66 ACAATCAAAGATTAGGATCGAATCAAAGCAAGGCCAAGGTGAGTGCAATTTAATTTGTGCTTATG
4998257 TTATTGAATAAGCATTGGCTTGCGATTAGCCAGTGATGGAGTTACTATGGTAAG-AGTGACTCCT
131 TTATTGAATAAGCATTGGCTTGCGATTAGCCAGTGATGGAGTTACTATGGTAAGAAGTGACTCCT
4998321 A
196 A
4998322 TAGGCTTCTGATAATCGTCTTGGAAATTATGTTTATGTAGATATTTAGCTTAAACAAGTTTTAGA
1 TAGGCTTCTGATAATCGTCTTGGAAATTATGTTTATGTAGATATTTAGCTTAAACAAGTTTTAGA
4998387 ACAATCAAAGAATTAGGATCGAATCAAAGCAAGGCCAAGGTGAGTGCAATTTAATTTGTGCTTAT
66 ACAATCAAAG-ATTAGGATCGAATCAAAGCAAGGCCAAGGTGAGTGCAATTTAATTTGTGCTTAT
4998452 GTTATTGAATAAGCATTGGCTTGCGATTAGCCAGTGATGGAGTTACTATGGTAAGAAGTGACTCC
130 GTTATTGAATAAGCATTGGCTTGCGATTAGCCAGTGATGGAGTTACTATGGTAAGAAGTGACTCC
4998517 TA
195 TA
4998519 AAATGTTACT
Statistics
Matches: 194, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
195 75 0.39
196 108 0.56
197 11 0.06
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.33
Consensus pattern (196 bp):
TAGGCTTCTGATAATCGTCTTGGAAATTATGTTTATGTAGATATTTAGCTTAAACAAGTTTTAGA
ACAATCAAAGATTAGGATCGAATCAAAGCAAGGCCAAGGTGAGTGCAATTTAATTTGTGCTTATG
TTATTGAATAAGCATTGGCTTGCGATTAGCCAGTGATGGAGTTACTATGGTAAGAAGTGACTCCT
A
Found at i:4999077 original size:22 final size:22
Alignment explanation
Indices: 4999059--4999104 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
4999049 TTCGGGATAT
4999059 ATACAGAGGTCCTTTGGGACAA
1 ATACAGAGGTCCTTTGGGACAA
* * *
4999081 ATACATAGGTCATTTGAGACAA
1 ATACAGAGGTCCTTTGGGACAA
4999103 AT
1 AT
4999105 TTCACATGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (22 bp):
ATACAGAGGTCCTTTGGGACAA
Found at i:4999816 original size:22 final size:22
Alignment explanation
Indices: 4999766--4999808 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
4999756 GATCGAAATT
*
4999766 ACTGTAGCAAGGGTATCGGTAC
1 ACTGTAGCAAGGGTATCGATAC
4999788 ACTGTAGC-AGGGTATCGATAC
1 ACTGTAGCAAGGGTATCGATAC
4999809 CCTTGTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (22 bp):
ACTGTAGCAAGGGTATCGATAC
Found at i:4999857 original size:10 final size:10
Alignment explanation
Indices: 4999842--4999883 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
4999832 TAGCATTCGG
4999842 TACTGTTCAT
1 TACTGTTCAT
4999852 TACTGTTCAT
1 TACTGTTCAT
*
4999862 GGTACTATTCAT
1 --TACTGTTCAT
4999874 TACTGTTCAT
1 TACTGTTCAT
4999884 ATCGTGTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 19 0.68
12 9 0.32
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (10 bp):
TACTGTTCAT
Found at i:4999872 original size:22 final size:22
Alignment explanation
Indices: 4999840--4999883 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4999830 TTTAGCATTC
*
4999840 GGTACTGTTCATTACTGTTCAT
1 GGTACTATTCATTACTGTTCAT
4999862 GGTACTATTCATTACTGTTCAT
1 GGTACTATTCATTACTGTTCAT
4999884 ATCGTGTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (22 bp):
GGTACTATTCATTACTGTTCAT
Found at i:5002124 original size:134 final size:132
Alignment explanation
Indices: 5001782--5002124 Score: 424
Period size: 134 Copynumber: 2.6 Consensus size: 132
5001772 TTAAAACAAA
* * *
5001782 TCCCTAAAGATGGCATGTTATCCTCATCACGTAGGAACCGTGTCATCCCCGACCAGACTTCCTCA
1 TCCCTAAAGATGGCATGTCATCCTCATCACGTAAGAACCGTGTCATCACCGACCAGAC-TCCTCA
* *
5001847 TCACGTAGGAGCAATGTCACCCTTAGATAACCAGTCGTCCTCATCGCGTAGGAACTGTGTTATCA
65 TCACGTAGGAGCAATGTCACCCCTAGATAACCAGTCGTCATCATCGCGTAGGAACTGTGTTATCA
5001912 CCC
130 CCC
* * * * *
5001915 TTCCTAAAGATGGTC-TATCGTCCTCATCAC-AAAGGAACTGTGTCATCCACCGACCAGACCTCC
1 TCCCTAAAGATGG-CATGTCATCCTCATCACGTAA-GAACCGTGTCAT-CACCGACCAGA-CTCC
* * *
5001978 TCATCACATAGGAGTC-ATGTTACCCCTAGATAACCA-TCCGTCATCATCGTGTAGGAACTGTGT
62 TCATCACGTAGGAG-CAATGTCACCCCTAGATAACCAGT-CGTCATCATCGCGTAGGAACTGTGT
5002041 TATCACCC
125 TATCACCC
* * *
5002049 TCCCTAAAGATGGCATGTCATCCTCATCGCGTAAGAACCGTGTCCATTACCAACCAGATCTCCTC
1 TCCCTAAAGATGGCATGTCATCCTCATCACGTAAGAACCGTGT-CATCACCGACCAGA-CTCCTC
*
5002114 ATCTCGTAGGA
64 ATCACGTAGGA
5002125 TTTGTGTCAC
Statistics
Matches: 177, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
132 1 0.01
133 37 0.21
134 132 0.75
135 7 0.04
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (132 bp):
TCCCTAAAGATGGCATGTCATCCTCATCACGTAAGAACCGTGTCATCACCGACCAGACTCCTCAT
CACGTAGGAGCAATGTCACCCCTAGATAACCAGTCGTCATCATCGCGTAGGAACTGTGTTATCAC
CC
Found at i:5002334 original size:3 final size:3
Alignment explanation
Indices: 5002326--5002408 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
5002316 GGTTTAAAAA
5002326 ATT ATT ATT ATT A-T ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5002372 A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5002409 ACAAGGTTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
2 6 0.08
3 71 0.92
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5005310 original size:203 final size:204
Alignment explanation
Indices: 5004958--5005363 Score: 796
Period size: 203 Copynumber: 2.0 Consensus size: 204
5004948 ATGCTATTTA
5004958 AAAAAAAAATTGTTATAAGAAGGCTTAATACTTAAAATGGCCCCACTAGTTTAGTCTGCGTCATT
1 AAAAAAAAATTGTTATAAGAAGGCTTAATACTTAAAATGGCCCCACTAGTTTAGTCTGCGTCATT
5005023 CTCATTTTGACCTTTTTACCATTTTTTCCATCAGTCTAACTCGTTAATTTTTAATTCGTTAAGAC
66 CTCATTTTGACCTTTTTACCATTTTTTCCATCAGTCTAACTCGTTAATTTTTAATTCGTTAAGAC
5005088 ATTATTCTTTGAATTGTTAATAAAAAATCGCATTGCTCAATCAAGTTTTGTTGCGTGTAATAGAT
131 ATTATTCTTTGAATTGTTAATAAAAAATCGCATTGCTCAATCAAGTTTTGTTGCGTGTAATAGAT
5005153 ATTTTTAGG
196 ATTTTTAGG
5005162 AAAAAAAAA-TGTTATAAGAAGGCTTAATACTTAAAATGGCCCCACTAGTTTAGTCTGCGTCATT
1 AAAAAAAAATTGTTATAAGAAGGCTTAATACTTAAAATGGCCCCACTAGTTTAGTCTGCGTCATT
5005226 CTCATTTTGACCTTTTTACCATTTTTTCCATCAGTCTAACTCGTTAATTTTTAATTCGTTAAGAC
66 CTCATTTTGACCTTTTTACCATTTTTTCCATCAGTCTAACTCGTTAATTTTTAATTCGTTAAGAC
*
5005291 ATTATTCTTTGATTTGTTAATAAAAAATCGCATTGCTCAATCAAGTTTTGTTGCGTGTAATAGAT
131 ATTATTCTTTGAATTGTTAATAAAAAATCGCATTGCTCAATCAAGTTTTGTTGCGTGTAATAGAT
5005356 ATTTTTAG
196 ATTTTTAG
5005364 ATTTTCCTTT
Statistics
Matches: 201, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
203 192 0.96
204 9 0.04
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (204 bp):
AAAAAAAAATTGTTATAAGAAGGCTTAATACTTAAAATGGCCCCACTAGTTTAGTCTGCGTCATT
CTCATTTTGACCTTTTTACCATTTTTTCCATCAGTCTAACTCGTTAATTTTTAATTCGTTAAGAC
ATTATTCTTTGAATTGTTAATAAAAAATCGCATTGCTCAATCAAGTTTTGTTGCGTGTAATAGAT
ATTTTTAGG
Found at i:5007214 original size:19 final size:18
Alignment explanation
Indices: 5007181--5007216 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5007171 AAAAAATTAC
*
5007181 CAAAAAAATTTAGATATT
1 CAAAAAAAATTAGATATT
5007199 CAAAACAAAATTAGATAT
1 CAAAA-AAAATTAGATAT
5007217 ATATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (18 bp):
CAAAAAAAATTAGATATT
Found at i:5007647 original size:168 final size:170
Alignment explanation
Indices: 5007364--5007706 Score: 672
Period size: 168 Copynumber: 2.0 Consensus size: 170
5007354 ATTTTTTAAG
5007364 TAAATATCTAATAAAGCATCATAAAATACAATTCATTTAGTTTTAGACGCCTTAATTTTCTTAAT
1 TAAATATCTAATAAAGCATCATAAAATACAATTCATTTAGTTTTAGACGCCTTAATTTTCTTAAT
5007429 TTATATCAAATATTTTTAATTTTTATTAAATAATTATTTGATATATTGATCGTATAAAATTTTAA
66 TTATATCAAATATTTTTAATTTTTATTAAATAATTATTTGATATATTGATCGTATAAAATTTTAA
5007494 CTCCACAAGAG-AATTAAAATACTACTTAATGTAATAAAT
131 CTCCACAAGAGAAATTAAAATACTACTTAATGTAATAAAT
5007533 TAAA-ATCTAATAAAGCATCATAAAATACAATTCATTTAGTTTTAGACGCCTTAATTTTCTTAAT
1 TAAATATCTAATAAAGCATCATAAAATACAATTCATTTAGTTTTAGACGCCTTAATTTTCTTAAT
5007597 TTATATCAAATATTTTTAATTTTTATTAAATAATTATTTGATATATTGATCGTATAAAATTTTAA
66 TTATATCAAATATTTTTAATTTTTATTAAATAATTATTTGATATATTGATCGTATAAAATTTTAA
5007662 CTCCACAAGAGAAATTAAAATACTACTTAATGTAATAAAT
131 CTCCACAAGAGAAATTAAAATACTACTTAATGTAATAAAT
5007702 TAAAT
1 TAAAT
5007707 TAAATTAAAA
Statistics
Matches: 172, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
168 136 0.79
169 36 0.21
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (170 bp):
TAAATATCTAATAAAGCATCATAAAATACAATTCATTTAGTTTTAGACGCCTTAATTTTCTTAAT
TTATATCAAATATTTTTAATTTTTATTAAATAATTATTTGATATATTGATCGTATAAAATTTTAA
CTCCACAAGAGAAATTAAAATACTACTTAATGTAATAAAT
Found at i:5019222 original size:19 final size:20
Alignment explanation
Indices: 5019200--5019245 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
5019190 CATGTTCCAA
5019200 AAAATGAATGAAAAAAA-TT
1 AAAATGAATGAAAAAAATTT
5019219 AAAATGAATGAAAAAAATTT
1 AAAATGAATGAAAAAAATTT
5019239 AAAATGA
1 AAAATGA
5019246 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (20 bp):
AAAATGAATGAAAAAAATTT
Found at i:5019252 original size:20 final size:19
Alignment explanation
Indices: 5019200--5019252 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
5019190 CATGTTCCAA
*
5019200 AAAATGAATGAAAAAAATT
1 AAAATGAATAAAAAAAATT
*
5019219 AAAATGAATGAAAAAAATTT
1 AAAATGAAT-AAAAAAAATT
5019239 AAAATG-ATAAAAAA
1 AAAATGAATAAAAAA
5019253 TATTGTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 6 0.19
19 11 0.35
20 14 0.45
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (19 bp):
AAAATGAATAAAAAAAATT
Found at i:5023697 original size:12 final size:12
Alignment explanation
Indices: 5023682--5023715 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
5023672 ACTGTTCATG
5023682 GTACTATTCACA
1 GTACTATTCACA
5023694 GTACTATTCACA
1 GTACTATTCACA
*
5023706 GTACTGTTCA
1 GTACTATTCA
5023716 TTACTGTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (12 bp):
GTACTATTCACA
Found at i:5034279 original size:51 final size:51
Alignment explanation
Indices: 5034210--5034313 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 51
5034200 TCCCAGTCCA
* ** * *
5034210 AGGGACAACAATAGTCCAATCAGTGGTGACTACGATGACCCACTCACACCT
1 AGGGACAACAATAATCCAATCAACGGTGACGACGAAGACCCACTCACACCT
* * *
5034261 AGGGACTACCATAATCCAATCAACGGTGACGACGAAGACCCACTTACACCT
1 AGGGACAACAATAATCCAATCAACGGTGACGACGAAGACCCACTCACACCT
5034312 AG
1 AG
5034314 CGGAAGCGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (51 bp):
AGGGACAACAATAATCCAATCAACGGTGACGACGAAGACCCACTCACACCT
Found at i:5035647 original size:3 final size:3
Alignment explanation
Indices: 5035641--5035704 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
5035631 TTCATTTGAA
* * * *
5035641 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAT TAT AAT AAT AAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5035686 TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
5035705 ATAAATTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 3 0.06
3 50 0.93
4 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5035687 original size:30 final size:30
Alignment explanation
Indices: 5035651--5035708 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
5035641 TATTATTTAT
5035651 ATTATTATTATTATTATAATTA-TAATAATA
1 ATTATTATTATTATT-TAATTATTAATAATA
*
5035681 ATTATTATTATTATTTTATTATTAATAA
1 ATTATTATTATTATTTAATTATTAATAA
5035709 ATTTTTACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTATTATTATTATTTAATTATTAATAATA
Found at i:5036015 original size:18 final size:19
Alignment explanation
Indices: 5035980--5036015 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5035970 CCCATCTTCC
*
5035980 GTGAGTCACCACAAGTTTG
1 GTGACTCACCACAAGTTTG
5035999 GTGACTCACCA-AAGTTT
1 GTGACTCACCACAAGTTT
5036016 ACTCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (19 bp):
GTGACTCACCACAAGTTTG
Found at i:5036925 original size:29 final size:30
Alignment explanation
Indices: 5036893--5036959 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
5036883 ATTTTATATG
*
5036893 TTTACTTTTA-TTATT-ATATATTATTTAA
1 TTTACTTTTATTTATTAAAATATTATTTAA
*
5036921 TTTTA-TTTTATTTATTAAAATCTTATTTAA
1 -TTTACTTTTATTTATTAAAATATTATTTAA
5036951 -TTACTTTTA
1 TTTACTTTTA
5036960 ACTTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 8 0.24
29 14 0.42
30 11 0.33
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTACTTTTATTTATTAAAATATTATTTAA
Found at i:5037191 original size:27 final size:28
Alignment explanation
Indices: 5037161--5037217 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
5037151 ATATTTCTAA
5037161 ATAAATAAATATTGTATTTATA-AA-TAT
1 ATAAATAAATATT-TATTTATATAATTAT
*
5037188 ATAAATTAATATTTATTTATATAATTAT
1 ATAAATAAATATTTATTTATATAATTAT
5037216 AT
1 AT
5037218 TTTGAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.30
27 14 0.52
28 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
ATAAATAAATATTTATTTATATAATTAT
Found at i:5037718 original size:16 final size:20
Alignment explanation
Indices: 5037692--5037742 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
5037682 TTTATTACTT
5037692 TTATATTATTTTATT-A-AT-
1 TTAT-TTATTTTATTCAGATA
5037710 TT-TTTATTTTATTCAGATA
1 TTATTTATTTTATTCAGATA
5037729 TTATTTATTTTATT
1 TTATTTATTTTATT
5037743 TGTCTGTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.34
17 2 0.07
18 4 0.14
19 2 0.07
20 11 0.38
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTATTTATTTTATTCAGATA
Found at i:5037737 original size:20 final size:17
Alignment explanation
Indices: 5037681--5037742 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 17
5037671 TCTTTCAAAT
*
5037681 TTTTATTACTTTTATATTA
1 TTTTATTA-ATTTAT-TTA
5037700 TTTTATTAATTT-TTTA
1 TTTTATTAATTTATTTA
5037716 TTTTATTCAGATATTATTTA
1 TTTTATT-A-AT-TTATTTA
5037736 TTTTATT
1 TTTTATT
5037743 TGTCTGTTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 10 0.26
17 2 0.05
18 5 0.13
19 10 0.26
20 11 0.29
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTATTAATTTATTTA
Found at i:5040396 original size:39 final size:39
Alignment explanation
Indices: 5040342--5040420 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
5040332 AAAAGAGTTC
5040342 ACTACTTTGTTCATCAGCACATTAAAATTTCCTCATGTT
1 ACTACTTTGTTCATCAGCACATTAAAATTTCCTCATGTT
5040381 ACTACTTTGTTCATCAGCACATTAAAATTTCCTCATGTT
1 ACTACTTTGTTCATCAGCACATTAAAATTTCCTCATGTT
5040420 A
1 A
5040421 ATCACATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.41
Consensus pattern (39 bp):
ACTACTTTGTTCATCAGCACATTAAAATTTCCTCATGTT
Found at i:5042556 original size:7 final size:7
Alignment explanation
Indices: 5042534--5042590 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
5042524 CTCATCCAGC
5042534 AAAGAAA
1 AAAGAAA
*
5042541 GAA-AAA
1 AAAGAAA
5042547 AAAGAAA
1 AAAGAAA
5042554 AAAGAAA
1 AAAGAAA
5042561 AAA-AAA
1 AAAGAAA
*
5042567 GAAAAAGAA
1 -AAAGA-AA
5042576 AAAGAAA
1 AAAGAAA
*
5042583 AAGGAAA
1 AAAGAAA
5042590 A
1 A
5042591 TTGAATCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
6 8 0.19
7 27 0.64
8 5 0.12
9 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:5042561 original size:6 final size:6
Alignment explanation
Indices: 5042534--5042590 Score: 64
Period size: 6 Copynumber: 9.5 Consensus size: 6
5042524 CTCATCCAGC
*
5042534 AAAGAA AGAAAAA AAAGAA AAA-AGA AAA-AA AAAGAA AAAGAA AAAGAA
1 AAAGAA A-AAGAA AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA
*
5042582 AAAGGA AAA
1 AAAGAA AAA
5042591 TTGAATCAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.11
6 35 0.78
7 5 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:5042564 original size:17 final size:16
Alignment explanation
Indices: 5042538--5042583 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
5042528 TCCAGCAAAG
5042538 AAAG-AAAAAAAAGAAA
1 AAAGAAAAAAAAAG-AA
5042554 AAAGAAAAAAAAAGAA
1 AAAGAAAAAAAAAGAA
5042570 AAAGAAAAAGAAAA
1 AAAGAAAAA-AAAA
5042584 AGGAAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAAGAA
Found at i:5045059 original size:115 final size:115
Alignment explanation
Indices: 5044857--5045196 Score: 565
Period size: 115 Copynumber: 3.0 Consensus size: 115
5044847 GTGCCATGTA
*
5044857 CTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTG
* *
5044922 GTTTAGTATGAACCCTAAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTG
5044972 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTG
5045037 GTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTG
* * * *
5045087 CTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTG
* * * * *
5045152 GTTTGGTAGGAACCAC-ATAACCAATCATTGGAATTAAAAGATGAA
66 GTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAA
5045197 CTGCATGATC
Statistics
Matches: 213, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
114 26 0.12
115 187 0.88
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (115 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTG
GTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTG
Found at i:5047365 original size:54 final size:51
Alignment explanation
Indices: 5047282--5047419 Score: 143
Period size: 50 Copynumber: 2.7 Consensus size: 51
5047272 AGCCACAAAA
* * * * *
5047282 AAAGGACGAATGTGTTGTCAAAGGCTTTACGAACATCTGAGCAGAAGCTACAAG
1 AAAGGAAGAATGTGTTGTCAAATGTTTTACGAAC-TC-GA-CAGAAACCACAAG
* * *
5047336 AAAGGAAGAATGTGTTTTCAAATGTTTTAC-ATCTCGACAGAAACCACAGG
1 AAAGGAAGAATGTGTTGTCAAATGTTTTACGAACTCGACAGAAACCACAAG
* * *
5047386 AAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 AAAGGAAGAATGTGTTGTCAAATGTTTTACGAAC
5047420 CAGTGATTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
50 36 0.51
51 4 0.06
52 2 0.03
53 2 0.03
54 26 0.37
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (51 bp):
AAAGGAAGAATGTGTTGTCAAATGTTTTACGAACTCGACAGAAACCACAAG
Found at i:5047814 original size:22 final size:22
Alignment explanation
Indices: 5047785--5047839 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
5047775 ATCTACACTC
5047785 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
5047807 TTTAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
5047829 TTCAAAGATGA
1 TTCAAAGATGA
5047840 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:5048436 original size:113 final size:113
Alignment explanation
Indices: 5048238--5049406 Score: 876
Period size: 113 Copynumber: 10.0 Consensus size: 113
5048228 TTTAGCAAAG
* * *
5048238 TTGAATTCATTATTCGATGGATTAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
* *
5048303 AGAAGGAAGAATAAGTTCATAATGAGAAGAACTGGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
5048351 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
5048416 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
* *
5048464 TTGAATTCATCATTCGATGGATCAGCATTACCAAGTCAAGTTCATAATAAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
*
5048529 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
5048577 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
* ****
5048642 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCATAATGAGAAGAAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA-ACT-TTTCG--C
* * * * * * * *** *
5048694 TT--TTTCAACTTTTCGCTTGAATTCATCATT-CGATGGATC-AG--CAT--TGCCAGGTCAAGT
1 TTGAATTCATC-ATTCG-ATGGA-TCAGCATTACCA-GG-TCAAGTTCATAATG--AGAAGAA-C
* * ** * ** ***
5048751 TCATAATG-AGAAGAACTCATCTGAAGAAG-GAAGAA--A-AAGTTCATAATGAGAAGAGCTTGT
58 TCAT-CTGAAGAAGGA---A---GAAGAAGTTCATAATGAGAAGAAC-T--TGTTCA-A-CTT-T
*
5048811 TCAAC
110 TC-GC
** * * * * *
5048816 TT-TTTGCTCAAATCCA-TC-ACTCGATGGATCAACATTTCCA-G-AAGAGTTCATAATGAGAAG
1 TTGAAT--TC--AT-CATTCGA-TGGAT-CAGC-A--TTACCAGGTCA-AGTTCATAATGAGAAG
* * *
5048876 AACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTCTC
55 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
* * * *
5048935 TTGAATTCATCATTTGATGGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
* * * * *
5049000 AGAAAGAATAAGAAGTTCATAATGTGAAGAATTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
* * * *
5049048 TTGAATTCATCACTCGATGGATCAACATTGCCAGGT-AGAGTTCATAATGAGAAGAACACATCTG
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCA-AGTTCATAATGAGAAGAACTCATCTG
* *
5049112 AAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT-TC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
* *** * * *
5049161 ATG-ATTCTATCACAGAAAAAGATAGATCAACATTAATTTGTCCAGAG-AAAGTTCATAATGAGA
1 TTGAATTC-AT--C---ATTCGATGGATCAGCATT-A-----CCAG-GTCAAGTTCATAATGAGA
* *
5049224 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTT-AC
53 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
* ** * * * *
5049285 AT-AATTCTATCACAGAATGAGATAGATCAGCATCAACTTTTCCAAAG-AAAGTTCATAATGAGA
1 TTGAATTC-AT--C---ATTCGATGGATCAG---C-A--TTACC-AGGTCAAGTTCATAATGAGA
5049348 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
53 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
5049407 GTATGATTCT
Statistics
Matches: 866, Mismatches: 113, Indels: 143
0.77 0.10 0.13
Matches are distributed among these distances:
112 9 0.01
113 488 0.56
114 10 0.01
115 11 0.01
116 18 0.02
117 19 0.02
118 29 0.03
119 9 0.01
120 7 0.01
121 2 0.00
122 18 0.02
123 16 0.02
124 177 0.20
125 13 0.02
126 7 0.01
127 7 0.01
128 13 0.02
129 9 0.01
130 2 0.00
131 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
Found at i:5048632 original size:226 final size:226
Alignment explanation
Indices: 5048238--5049406 Score: 1346
Period size: 226 Copynumber: 5.0 Consensus size: 226
5048228 TTTAGCAAAG
* * *
5048238 TTGAATTCATTATTCGATGGATTAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
* *
5048303 AGAAGGAAGAATAAGTTCATAATGAGAAGAACTGGTTCAACTTTTCGCTTGAATTCATCATTCGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGA
*
5048368 TGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
131 TGGATCAGCATTACCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
5048433 CATAATGAGAAGAACTTGTTCAACTTTTCGC
196 CATAATGAGAAGAACTTGTTCAACTTTTCGC
* *
5048464 TTGAATTCATCATTCGATGGATCAGCATTACCAAGTCAAGTTCATAATAAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
*
5048529 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGA
*
5048594 TGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
131 TGGATCAGCATTACCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
5048659 CATAATGAGAAGAACTTGTTCATAATGAGAAGAACTTTTTCAACTTTTCGC
196 CATAATGAGAAGAA------C-T--T-----G------TTCAACTTTTCGC
*
5048710 TTGAATTCATCATTCGATGGATCAGCATTGCCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
* * * ** * *
5048775 AGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACTTTTTGCTCAAATCCATCACTCGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGA
* * *
5048840 TGGATCAACATTTCCA-G-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGT
131 TGGATCAGCATTACCAGGTAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
5048903 TCATAATGAGAAGAACTTGTTCAAATTTTCTC
195 TCATAATGAGAAGAACTTGTTCAACTTTTCGC
* * * *
5048935 TTGAATTCATCATTTGATGGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
* * * * * *
5049000 AGAAAGAATAAGAAGTTCATAATGTGAAGAATTTGTTCAACTTTTTGCTTGAATTCATCACTCGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGA
* * * * *
5049065 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACACATCTGAAGAATGAAGAAGAAGTT
131 TGGATCAGCATTACCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
*
5049130 CATAATGAGAAGAACTTGTTCAATCTTTT-TC
196 CATAATGAGAAGAACTTGTTCAA-CTTTTCGC
* *** * * *
5049161 ATG-ATTCTATCACAGAAAAAGATAGATCAACATTAATTTGTCCAGAG-AAAGTTCATAATGAGA
1 TTGAATTC-AT--C---ATTCGATGGATCAGCATT-A-----CCAG-GTCAAGTTCATAATGAGA
* * *
5049224 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTT-ACAT-
53 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTG
** * * *
5049287 AATTCTATCACAGAATGAGATAGATCAGCATCAACTTTTCCAAAG-AAAGTTCATAATGAGAAGA
117 AATTC-AT--C---ATTCGATGGATCAG---C-A--TTACC-AGGTAAAGTTCATAATGAGAAGA
5049351 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
169 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
5049407 GTATGATTCT
Statistics
Matches: 824, Mismatches: 68, Indels: 80
0.85 0.07 0.08
Matches are distributed among these distances:
225 148 0.18
226 273 0.33
227 5 0.01
228 1 0.00
231 14 0.02
232 1 0.00
233 1 0.00
235 1 0.00
236 6 0.01
237 70 0.08
238 7 0.01
239 2 0.00
240 1 0.00
242 9 0.01
244 1 0.00
245 59 0.07
246 147 0.18
248 76 0.09
249 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (226 bp):
TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGA
TGGATCAGCATTACCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAACTTTTCGC
Found at i:5048670 original size:20 final size:20
Alignment explanation
Indices: 5048647--5048693 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5048637 TCTGAAGAAG
*
5048647 GAAGAAGAAGTTCATAATGA
1 GAAGAACAAGTTCATAATGA
**
5048667 GAAGAACTTGTTCATAATGA
1 GAAGAACAAGTTCATAATGA
5048687 GAAGAAC
1 GAAGAAC
5048694 TTTTTCAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.21
Consensus pattern (20 bp):
GAAGAACAAGTTCATAATGA
Found at i:5048694 original size:20 final size:20
Alignment explanation
Indices: 5048656--5048700 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
5048646 GGAAGAAGAA
5048656 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
5048676 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
*
5048696 TTTCA
1 GTTCA
5048701 ACTTTTCGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:5049061 original size:225 final size:224
Alignment explanation
Indices: 5048676--5049400 Score: 862
Period size: 225 Copynumber: 3.1 Consensus size: 224
5048666 AGAAGAACTT
* * * *
5048676 GTTCATAATGAGAAGAACTTTTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGC
1 GTTCATAATGAGAAGAACTTGTTCAAATTTTCTCTTGAATTCATCATTAGATGGATCAGCATTGC
* *
5048741 CAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAG
66 CAGGGCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAG
* *
5048806 CTTGTTCAACTTTTTGCTCAAATCCATCACTCGATGGATCAACATTTCCAGAAGAGTTCATAATG
131 CTTGTTCAACTTTTTGCT-TAATTCATCACTCGATGGATCAACATTTCCAGAAGAGTTCATAATG
5048871 AGAAGAACTCATCTGAAGAAAGAAGAAGAA
195 AGAAGAACTCATCTGAAGAAAGAAGAAGAA
*
5048901 GTTCATAATGAGAAGAACTTGTTCAAATTTTCTCTTGAATTCATCATTTGATGGATCAGCATTGC
1 GTTCATAATGAGAAGAACTTGTTCAAATTTTCTCTTGAATTCATCATTAGATGGATCAGCATTGC
* * * * *
5048966 CAGGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAATAAGAAGTTCATAATGTGAAGAA
66 CAGGGCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAG
* * *
5049031 TTTGTTCAACTTTTTGCTTGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAAT
131 CTTGTTCAACTTTTTGCTT-AATTCATCACTCGATGGATCAACATTTCCA-GAAGAGTTCATAAT
* *
5049096 GAGAAGAACACATCTGAAGAATGAAGAAGAA
194 GAGAAGAACTCATCTGAAGAAAGAAGAAGAA
* * ** *
5049127 GTTCATAATGAGAAGAACTTGTTC-AATCTTTTTCATG-ATTCTATCACAGAAAAAGATAGATCA
1 GTTCATAATGAGAAGAACTTGTTCAAAT-TTTCTCTTGAATTC-AT--C---ATTAGATGGATCA
* * *
5049190 ACATTAATTTGTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
59 GC----A-TTG-CCAGGGCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* * * *
5049255 ATAATGAGAAGAGCTTGTTCAACCTTTTACATAATTCTATCACAGAATGAGATAGATCAGCATCA
118 ATAATGAGAAGAGCTTGTTCAACTTTTTGCTTAATTC-ATCAC----T-CGAT-G----G-ATCA
* *
5049320 ACTTTTCCA-AAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
171 ACATTTCCAGAAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAA
5049375 GTTCATAATGAGAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTTGTTCAA
5049401 TCTTTTGTAT
Statistics
Matches: 428, Mismatches: 42, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
225 171 0.40
226 75 0.18
228 1 0.00
231 10 0.02
235 1 0.00
236 8 0.02
237 79 0.18
241 1 0.00
242 3 0.01
243 1 0.00
246 2 0.00
247 1 0.00
248 74 0.17
249 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (224 bp):
GTTCATAATGAGAAGAACTTGTTCAAATTTTCTCTTGAATTCATCATTAGATGGATCAGCATTGC
CAGGGCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAG
CTTGTTCAACTTTTTGCTTAATTCATCACTCGATGGATCAACATTTCCAGAAGAGTTCATAATGA
GAAGAACTCATCTGAAGAAAGAAGAAGAA
Found at i:5049226 original size:124 final size:124
Alignment explanation
Indices: 5049086--5049450 Score: 581
Period size: 124 Copynumber: 2.9 Consensus size: 124
5049076 TGCCAGGTAG
* *
5049086 AGTTCATAATGAGAAGAACACATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *
5049151 AATCTTTTTCATGATTCTATCACAGAAAAAGATAGATCAACATTAA-TTTGTCCAGAGAA
66 AATCTTTTTCATGATTCTATCACAGAAAGAGATAGATCAACATCAACTTT-TCCAAAGAA
*
5049210 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
5049275 AACCTTTTACATAATTCTATCACAGAATGAGATAGATCAGCATCAACTTTTCCAAAGAA
66 AATCTTTTTCATGATTCTATCACAGAAAGAGATAGATCAACATCAACTTTTCCAAAGAA
5049334 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
5049399 AATCTTTTGT-ATGATTCTATCACAGAAAGAGATAGATCAGCATCAACATTTC
66 AATCTTTT-TCATGATTCTATCACAGAAAGAGATAGATCAACATCAACTTTTC
5049451 TAAATTACAT
Statistics
Matches: 222, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
124 219 0.99
125 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (124 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AATCTTTTTCATGATTCTATCACAGAAAGAGATAGATCAACATCAACTTTTCCAAAGAA
Found at i:5049673 original size:3 final size:3
Alignment explanation
Indices: 5049667--5049727 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
5049657 TTCATTTGAA
* * * *
5049667 TAT TAT T-T ATAT TAT TAA TAT TAT TAT TAT AAT TAT TAT AAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5049712 TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TA
5049728 ATAAATATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.06
3 45 0.92
4 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5049731 original size:21 final size:21
Alignment explanation
Indices: 5049667--5049736 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 21
5049657 TTCATTTGAA
5049667 TATTATTTATATTATTAAT-AT
1 TATTATTT-TATTATTAATAAT
*
5049688 TATTATTATAATTATTATAATAAT
1 TATTATT-TTATTA-T-TAATAAT
*
5049712 TATTATTTTATTATTAATAAA
1 TATTATTTTATTATTAATAAT
5049733 TATT
1 TATT
5049737 TTTACAGGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 21 0.50
22 3 0.07
23 9 0.21
24 9 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTATTTTATTATTAATAAT
Found at i:5050047 original size:18 final size:19
Alignment explanation
Indices: 5050012--5050047 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5050002 CCATTCTTCC
*
5050012 GTGAGTCACCACAAGTTTG
1 GTGACTCACCACAAGTTTG
5050031 GTGACTCACCA-AAGTTT
1 GTGACTCACCACAAGTTT
5050048 ACTCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (19 bp):
GTGACTCACCACAAGTTTG
Found at i:5051474 original size:27 final size:27
Alignment explanation
Indices: 5051444--5051501 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
5051434 ATATTTCTAA
5051444 ATAAATAAATATTGTA-TTTATA-AATAT
1 ATAAATAAATATT-TATTTTATATAAT-T
*
5051471 ATAAATTAATATTTATTTTATATAATT
1 ATAAATAAATATTTATTTTATATAATT
5051498 ATAA
1 ATAA
5051502 TTTTGAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 23 0.82
28 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
ATAAATAAATATTTATTTTATATAATT
Found at i:5054588 original size:25 final size:25
Alignment explanation
Indices: 5054551--5054601 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5054541 ATTTATATAA
*
5054551 ATATTAATGATCATTTGTATATTTT
1 ATATTAATCATCATTTGTATATTTT
*
5054576 ATATTAGTCATCATTTGTATATTTT
1 ATATTAATCATCATTTGTATATTTT
5054601 A
1 A
5054602 CTTTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (25 bp):
ATATTAATCATCATTTGTATATTTT
Found at i:5060569 original size:10 final size:10
Alignment explanation
Indices: 5060554--5060595 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
5060544 TTTTATTGAT
5060554 TCCCTCTCCC
1 TCCCTCTCCC
*
5060564 TCCCTCTCTC
1 TCCCTCTCCC
5060574 TCCCTC-CCC
1 TCCCTCTCCC
*
5060583 -CTCTCTCCC
1 TCCCTCTCCC
5060592 TCCC
1 TCCC
5060596 CCTCTCTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 4 0.15
9 5 0.19
10 17 0.65
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (10 bp):
TCCCTCTCCC
Found at i:5060576 original size:14 final size:14
Alignment explanation
Indices: 5060557--5060603 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
5060547 TATTGATTCC
*
5060557 CTCTCCCTCCCTCT
1 CTCTCCCTCCCCCT
5060571 CTCTCCCTCCCCCT
1 CTCTCCCTCCCCCT
5060585 CTCTCCCTCCCCCT
1 CTCTCCCTCCCCCT
5060599 CTCTC
1 CTCTC
5060604 TCTCTAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (14 bp):
CTCTCCCTCCCCCT
Found at i:5060579 original size:20 final size:20
Alignment explanation
Indices: 5060554--5060601 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5060544 TTTTATTGAT
*
5060554 TCCCTCTCCCTCCCTCTCTC
1 TCCCTCTCCCTCCCTCCCTC
* *
5060574 TCCCTCCCCCTCTCTCCCTC
1 TCCCTCTCCCTCCCTCCCTC
*
5060594 CCCCTCTC
1 TCCCTCTC
5060602 TCTCTCTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (20 bp):
TCCCTCTCCCTCCCTCCCTC
Found at i:5060624 original size:249 final size:245
Alignment explanation
Indices: 5060325--5060801 Score: 679
Period size: 249 Copynumber: 1.9 Consensus size: 245
5060315 CAATATGACA
*
5060325 TCTCTCCCTCTCCCTCCCCTCCCCTCCCCCTCCCTAATATACAAAACACTTGGTCATATGATAAC
1 TCTCTCCCTCCCCCTCCCCTCCCCTCCCCCTCCCTAATATACAAAACACTTGGTCATATGATAAC
** * *
5060390 GGAATTGGGCAAATAATACAGGTGAGCGGATATATTTTTTAAAGGG-CTGTATCACGTGGATTTC
66 AAAATGGGGCAAATAATACAGGTGAGCGGATATATTTTTTAAAGGGTC-GTATCACGTGGATCTC
* * *
5060454 ACAACACGAATTATTTTAATATATTTTATTTAACGAGTTTCAATAAAAAATATTTTTTTTTTGAA
130 ACAACACGAATTATTTTAATATATTTTATTTAACGAGTTACAA-AAAAAAAATATTTTTTTTGAA
5060519 TTTTTTAAAAGCATT-AAAAATATTATTTTATTGATTCCCTCTCCCTCCCTC
194 TTTTTTAAAAGCATTAAAAAATATTATTTTATTGATTCCCTCTCCCTCCCTC
* * * * *
5060570 TCTCTCCCTCCCCCTCTCTCCCTCCCCCTCTCTCTCTCTAATATACACAACACTTGGTCATATTA
1 TCTCTCCCT-CCCC-CTC-CCCT-CCCCTCCCCCTCCCTAATATACAAAACACTTGGTCATATGA
** * * *
5060635 TGGCAAAATGGGGCAAATAATACAGGTGAGCGGATATATTTTTTAATGGGTCGTGTCACGTGGGT
62 TAACAAAATGGGGCAAATAATACAGGTGAGCGGATATATTTTTTAAAGGGTCGTATCACGTGGAT
*** *
5060700 CTCACAGGTCGAATTATTTTAATATATTTTATTTGACGAGTTACAAAAAAAAAATATTTTTTTTG
127 CTCACAACACGAATTATTTTAATATATTTTATTTAACGAGTTACAAAAAAAAAATATTTTTTTTG
5060765 AATTTTTTAAAAGCATTGAAAAAATATTATTTTATTG
192 AATTTTTTAAAAGCATT-AAAAAATATTATTTTATTG
5060802 TTGATGAAAC
Statistics
Matches: 203, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
245 9 0.04
246 3 0.01
247 3 0.01
248 38 0.19
249 131 0.65
250 19 0.09
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (245 bp):
TCTCTCCCTCCCCCTCCCCTCCCCTCCCCCTCCCTAATATACAAAACACTTGGTCATATGATAAC
AAAATGGGGCAAATAATACAGGTGAGCGGATATATTTTTTAAAGGGTCGTATCACGTGGATCTCA
CAACACGAATTATTTTAATATATTTTATTTAACGAGTTACAAAAAAAAAATATTTTTTTTGAATT
TTTTAAAAGCATTAAAAAATATTATTTTATTGATTCCCTCTCCCTCCCTC
Found at i:5063655 original size:16 final size:15
Alignment explanation
Indices: 5063631--5063660 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5063621 AATACAAGTT
5063631 AAAAAACATAATTAA
1 AAAAAACATAATTAA
5063646 AAAAAGACATAATTA
1 AAAAA-ACATAATTA
5063661 CAGTATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (15 bp):
AAAAAACATAATTAA
Found at i:5066019 original size:61 final size:61
Alignment explanation
Indices: 5065939--5066056 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 61
5065929 TACTATATGA
5065939 ATAAGTATCGATACCAGAAGCCAAAAGTGGATAAGTCATTCAAGGAGTATCGATACCCCTT
1 ATAAGTATCGATACCAGAAGCCAAAAGTGGATAAGTCATTCAAGGAGTATCGATACCCCTT
** * *
5066000 ATAAGTATCGATATTAGAAGCTAAAAGTGGATAAGTCATTCAAGGATTATCGATACC
1 ATAAGTATCGATACCAGAAGCCAAAAGTGGATAAGTCATTCAAGGAGTATCGATACC
5066057 TAAGGGGTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (61 bp):
ATAAGTATCGATACCAGAAGCCAAAAGTGGATAAGTCATTCAAGGAGTATCGATACCCCTT
Found at i:5067632 original size:13 final size:13
Alignment explanation
Indices: 5067614--5067638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5067604 CGCTAGGGGA
5067614 AGTTCTTGGTGGT
1 AGTTCTTGGTGGT
5067627 AGTTCTTGGTGG
1 AGTTCTTGGTGG
5067639 CTGAGGGAAG
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:0.08, C:0.08, G:0.40, T:0.44
Consensus pattern (13 bp):
AGTTCTTGGTGGT
Found at i:5079564 original size:24 final size:24
Alignment explanation
Indices: 5079537--5079619 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
5079527 TATATCAAAA
*
5079537 ATCAAAACATAATCCAAGTCAAGT
1 ATCAAAACAGAATCCAAGTCAAGT
* **
5079561 ATCAGATGAGAATCCAAGTCAAGT
1 ATCAAAACAGAATCCAAGTCAAGT
* ** *
5079585 ATCATATTAGAAT-CAATGTCAGGT
1 ATCAAAACAGAATCCAA-GTCAAGT
*
5079609 ATCATAACAGA
1 ATCAAAACAGA
5079620 TTTCATATCG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 3 0.06
24 46 0.94
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATCCAAGTCAAGT
Found at i:5081928 original size:12 final size:13
Alignment explanation
Indices: 5081910--5081976 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 13
5081900 TTGTATTTTT
5081910 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
*
5081923 -GTCAAAGTTAAC
1 GGTCAAAGTCAAC
* *
5081935 GGTCAACGGCAAC
1 GGTCAAAGTCAAC
*
5081948 GGT---GGTCAAC
1 GGTCAAAGTCAAC
*
5081958 GGTCAACAGTCAAT
1 GGTCAA-AGTCAAC
5081972 GGTCA
1 GGTCA
5081977 GGTCAATGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
10 8 0.20
12 11 0.27
13 12 0.29
14 10 0.24
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:5082007 original size:18 final size:18
Alignment explanation
Indices: 5081984--5082024 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5081974 TCAGGTCAAT
*
5081984 GGGTCGGATCAATGAGTC
1 GGGTCGGATCAACGAGTC
* *
5082002 GGGTCGGTTCAACGGGTC
1 GGGTCGGATCAACGAGTC
5082020 GGGTC
1 GGGTC
5082025 AAATGGGTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.20, G:0.44, T:0.22
Consensus pattern (18 bp):
GGGTCGGATCAACGAGTC
Found at i:5082017 original size:13 final size:13
Alignment explanation
Indices: 5082001--5082040 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5081991 ATCAATGAGT
*
5082001 CGGGTCGGTTCAA
1 CGGGTCGGGTCAA
5082014 CGGGTCGGGTCAAA
1 CGGGTCGGGTC-AA
*
5082028 TGGGTCGGGTCAA
1 CGGGTCGGGTCAA
5082041 ACTACCCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.17, C:0.20, G:0.42, T:0.20
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:5082034 original size:14 final size:14
Alignment explanation
Indices: 5082001--5082042 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
5081991 ATCAATGAGT
*
5082001 CGGGTCGGTTC-AA
1 CGGGTCGGGTCAAA
5082014 CGGGTCGGGTCAAA
1 CGGGTCGGGTCAAA
*
5082028 TGGGTCGGGTCAAA
1 CGGGTCGGGTCAAA
5082042 C
1 C
5082043 TACCCCAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.19, C:0.21, G:0.40, T:0.19
Consensus pattern (14 bp):
CGGGTCGGGTCAAA
Found at i:5083068 original size:19 final size:20
Alignment explanation
Indices: 5083044--5083089 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
5083034 TCGAGTGTTC
*
5083044 TATATG-ATCCTTCGGGACA
1 TATATGAATCCTTCGGAACA
*
5083063 TATATGTAATCCTTTGGAACA
1 TATATG-AATCCTTCGGAACA
5083084 TATATG
1 TATATG
5083090 CGGTTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
21 17 0.74
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
TATATGAATCCTTCGGAACA
Found at i:5083175 original size:21 final size:21
Alignment explanation
Indices: 5083054--5083184 Score: 84
Period size: 21 Copynumber: 6.1 Consensus size: 21
5083044 TATATGATCC
** *
5083054 TTCGGGACATATATGTAATCC
1 TTCGGGACATATATGTGGTCA
* * * *
5083075 TTTGGAACATATATGCGGTTA
1 TTCGGGACATATATGTGGTCA
* * * *
5083096 TTTGGGACACATATTTGGTCC
1 TTCGGGACATATATGTGGTCA
* * * *
5083117 TTTGGAATATATATGTGGTCC
1 TTCGGGACATATATGTGGTCA
*
5083138 TTAAGGAGA-ATTATATGTGGTCA
1 TT-CGG-GACA-TATATGTGGTCA
5083161 TTCGGGACATATATGTGGTCA
1 TTCGGGACATATATGTGGTCA
5083182 TTC
1 TTC
5083185 CGGAAAATTT
Statistics
Matches: 85, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
21 65 0.76
22 6 0.07
23 14 0.16
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (21 bp):
TTCGGGACATATATGTGGTCA
Found at i:5097117 original size:17 final size:17
Alignment explanation
Indices: 5097095--5097132 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5097085 TGCTTCACGT
*
5097095 TGAAGAAGAGAATAAGA
1 TGAAGAAGAGAAGAAGA
*
5097112 TGAAGAAGATAAGAAGA
1 TGAAGAAGAGAAGAAGA
5097129 TGAA
1 TGAA
5097133 TTGTCTGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.29, T:0.13
Consensus pattern (17 bp):
TGAAGAAGAGAAGAAGA
Found at i:5097497 original size:16 final size:16
Alignment explanation
Indices: 5097476--5097513 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
5097466 CCCACGTTGC
5097476 TTCCTCTATCATGTGA
1 TTCCTCTATCATGTGA
5097492 TTCCTCTATCATGTGA
1 TTCCTCTATCATGTGA
5097508 TTCCTC
1 TTCCTC
5097514 CATAGAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.16, C:0.29, G:0.11, T:0.45
Consensus pattern (16 bp):
TTCCTCTATCATGTGA
Found at i:5102047 original size:233 final size:234
Alignment explanation
Indices: 5101635--5102106 Score: 910
Period size: 233 Copynumber: 2.0 Consensus size: 234
5101625 CATCCAACTT
5101635 CTCCACATCAGAACAGTGGAGACCATCTAACATGATTTTCAAATCATTTAACCAAAGATCTGTCG
1 CTCCACATCAGAACAGTGGAGACCATCTAACATGATTTTCAAATCATTTAACCAAAGATCTGTCG
* *
5101700 CAATCGGACCTTCCTAGGCTTCTCCCTTAAATTCTGGAGCTCCTAATCCTCTCATCTCCTTTTCT
66 CAATCGGACCTTCCTAGGCTTCTCCCTTAAATTCTAGAGCTCCAAATCCTCTCATCTCCTTTTCT
5101765 ACATTTACTTTGAGAGTTGATGGAGCATGAGGTTGGAAACGCGTCAATACCGCATCTAACCGCTT
131 ACATTTACTTTGAGAGTTGATGGAGCATGAGGTTGGAAACGCGTCAATACCGCATCTAACCGCTT
5101830 CTAACATTCTAAAGAACACATCTTGATCACCTACAGGCA
196 CTAACATTCTAAAGAACACATCTTGATCACCTACAGGCA
5101869 CTCC-CATCAGAACAGTGGAGACCATCTAACATGATTTTCAAATCATTTAACCAAAGATCTGTCG
1 CTCCACATCAGAACAGTGGAGACCATCTAACATGATTTTCAAATCATTTAACCAAAGATCTGTCG
*
5101933 CAATCGGACCTTCCTAGGCTTCTCCTTTAAATTCTAGAGCTCCAAATCCTCTCATCTCCTTTTCT
66 CAATCGGACCTTCCTAGGCTTCTCCCTTAAATTCTAGAGCTCCAAATCCTCTCATCTCCTTTTCT
5101998 ACATTTACTTTGAGAGTTGATGGAGCATGAGGTTGGAAACGCGTCAATACCGCATCTAACCGCTT
131 ACATTTACTTTGAGAGTTGATGGAGCATGAGGTTGGAAACGCGTCAATACCGCATCTAACCGCTT
5102063 CTAACATTCTAAAGAACACATCTTGATCACCTACAGGCA
196 CTAACATTCTAAAGAACACATCTTGATCACCTACAGGCA
5102102 CTCCA
1 CTCCA
5102107 GAAGGTGCAT
Statistics
Matches: 234, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
233 230 0.98
234 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (234 bp):
CTCCACATCAGAACAGTGGAGACCATCTAACATGATTTTCAAATCATTTAACCAAAGATCTGTCG
CAATCGGACCTTCCTAGGCTTCTCCCTTAAATTCTAGAGCTCCAAATCCTCTCATCTCCTTTTCT
ACATTTACTTTGAGAGTTGATGGAGCATGAGGTTGGAAACGCGTCAATACCGCATCTAACCGCTT
CTAACATTCTAAAGAACACATCTTGATCACCTACAGGCA
Found at i:5102596 original size:12 final size:12
Alignment explanation
Indices: 5102559--5102605 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
5102549 ATTATATGGT
5102559 ATGAACAATACC
1 ATGAACAATACC
*
5102571 GTGAACAATA--
1 ATGAACAATACC
*
5102581 ATGAACAGTACC
1 ATGAACAATACC
*
5102593 ATGAACAGTACC
1 ATGAACAATACC
5102605 A
1 A
5102606 AATGCTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 8 0.27
12 22 0.73
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:5103253 original size:23 final size:23
Alignment explanation
Indices: 5103223--5103276 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
5103213 GCGCCGTAGT
*
5103223 GCCATATAATATTGTCCATAAGG
1 GCCATATAATATTGTCCATAAAG
5103246 GCCATATAATATTGTCCATAAAG
1 GCCATATAATATTGTCCATAAAG
*
5103269 ACCATATA
1 GCCATATA
5103277 GAAATTCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (23 bp):
GCCATATAATATTGTCCATAAAG
Found at i:5104991 original size:500 final size:509
Alignment explanation
Indices: 5104083--5105012 Score: 1241
Period size: 500 Copynumber: 1.8 Consensus size: 509
5104073 TCACTTAGAC
5104083 ACTTCTTATCTTTAATCCTCCATAACTCAAAACTCTTTGAGTTTCTAAGTCCCTTTTTCCTTCAT
1 ACTTCTTATCTTTAATCCTCCATAACTCAAAACTCTTTGAGTTTCTAAGTCCCTTTTTCCTTCAT
*
5104148 CATGTTTCCTAAGTCTTCCTTAACCAAAACCATACTTCAATTTTAAAGATTAACCAAAAGAAATC
66 CATGTTTCCTAAGTCTTCCTTAACCAAAACCATACTTAAATTTTAAAGATTAACCAAAAGAAATC
5104213 AAACTTACCTTGGCTTGGGTGCTTCACATTGGAGAAGAGAAGAAGATGAATTGTCTAGAAACTAT
131 AAACTTACCTTGGCTTGGGTGCTTCACATTGGAGAAGAGAAGAAGATGAA-TGTCTAGAAACTAT
* * * * * *
5104278 GTTTCCCCAATTATGATTCACATGGGTAATATAATACCCATTAATTATTATTTAATTATTTAATT
195 CTTTCCCAAATCATGATCCACATGGGTAATATAATACCCATCAATTATTATTT-ATTATTT-ACT
* * *
5104343 ATTACCCTATATTCAATGACCCCTTTACCCTTTTACTCTTCCTTCATTTATTAATTCATCCTACA
258 ATTA-CCTATATTCAATGACCCCTTTACCCCTTTACTCTTCCTTCATTTATTAAATCATCCAACA
* * *
5104408 CCAACATCTTTCAATTAATTCCTGAACTTTTCAATTTATTTAATCTGGTCATTGAATTTTAAAAT
322 CAAACATCTTTCAATTAATTCCTGAACTTTTCAATTTATCTAATATGGTCATTGAATTTTAAAAT
* * *
5104473 CTTACACTTTAATCACTAACATGGTATTGAGGATGTTACATATAACTTCTTATTCACACCTGTGA
387 CTCACACTTTAATCACTAACACGATATTGAGGATGTTACATATAACTTCTTATTCACACCTGTGA
5104538 CAAGTCAATTTCAGCTTCTAAATCCATTTATACATCTTTATTCAAATTTCATTTATCT
452 CAAGTCAATTTCAGCTTCTAAATCCATTTATACATCTTTATTCAAATTTCATTTATCT
** * * *
5104596 ACTTCTTATCTTTAATCCTTTATAACTTACAAA-TCTTTGAGTTTCTATGAT--CGTTTTCATCT
1 ACTTCTTATCTTTAATCCTCCATAACTCA-AAACTCTTTGAGTTTCTAAG-TCCCTTTTTC--CT
* * *
5104658 TCATCGTGTTTCCTAAGTCTTTCTTAACCAAAACCATACTTAAATTTT-AAGAATTAACCAAAAT
62 TCATCATGTTTCCTAAGTCTTCCTTAACCAAAACCATACTTAAATTTTAAAG-ATTAACCAAAAG
* * * *
5104722 AAATCAAA-TTCACCTTGGCTTGGG-GGTTCACGTTGGAGAAGAGAAGAAGAT-AA-GTTTGGAA
126 AAATCAAACTT-ACCTTGGCTTGGGTGCTTCACATTGGAGAAGAGAAGAAGATGAATGTCTAGAA
* * * *
5104783 ACTTATCTTT-TCAAATCATGCTCCACGTGGGTATTATAATACCCA-CAATTATTA-TT-TTA-T
190 AC-TATCTTTCCCAAATCATGATCCACATGGGTAATATAATACCCATCAATTATTATTTATTATT
* * * *
5104843 T-CT-TT-CCTTTGTTCAATGACCCTTTTGCCCCTTT-C-CTTCTCATTCATTTATTAAATCATC
254 TACTATTACCTATATTCAATGACCCCTTTACCCCTTTACTCTTC-C-TTCATTTATTAAATCATC
**
5104903 CAACACAAACATCTTTCAATTAATTCCTTCACTTTTCAATTTATCTAATATGGTCATTGAATTTT
317 CAACACAAACATCTTTCAATTAATTCCTGAACTTTTCAATTTATCTAATATGGTCATTGAA-TTT
**
5104968 TAAAAT-TCACACTTTGGTCACTAACACGATATTGAGGATGTTACA
381 TAAAATCTCACACTTTAATCACTAACACGATATTGAGGATGTTACA
5105013 CGTTAAGAAC
Statistics
Matches: 367, Mismatches: 40, Indels: 33
0.83 0.09 0.08
Matches are distributed among these distances:
498 4 0.01
499 2 0.01
500 130 0.35
501 9 0.02
502 2 0.01
503 1 0.00
505 2 0.01
506 3 0.01
508 2 0.01
509 8 0.02
510 36 0.10
511 6 0.02
512 8 0.02
513 71 0.19
514 83 0.23
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (509 bp):
ACTTCTTATCTTTAATCCTCCATAACTCAAAACTCTTTGAGTTTCTAAGTCCCTTTTTCCTTCAT
CATGTTTCCTAAGTCTTCCTTAACCAAAACCATACTTAAATTTTAAAGATTAACCAAAAGAAATC
AAACTTACCTTGGCTTGGGTGCTTCACATTGGAGAAGAGAAGAAGATGAATGTCTAGAAACTATC
TTTCCCAAATCATGATCCACATGGGTAATATAATACCCATCAATTATTATTTATTATTTACTATT
ACCTATATTCAATGACCCCTTTACCCCTTTACTCTTCCTTCATTTATTAAATCATCCAACACAAA
CATCTTTCAATTAATTCCTGAACTTTTCAATTTATCTAATATGGTCATTGAATTTTAAAATCTCA
CACTTTAATCACTAACACGATATTGAGGATGTTACATATAACTTCTTATTCACACCTGTGACAAG
TCAATTTCAGCTTCTAAATCCATTTATACATCTTTATTCAAATTTCATTTATCT
Found at i:5110422 original size:27 final size:27
Alignment explanation
Indices: 5110389--5110446 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
5110379 AATTCTTGTC
* *
5110389 ATTTTA-CAACATAGGGGTATTTTCATA
1 ATTTTACCAA-ATAGGAGTATTCTCATA
*
5110416 ATTTTACCAAATCGGAGTATTCTCATA
1 ATTTTACCAAATAGGAGTATTCTCATA
5110443 ATTT
1 ATTT
5110447 ATCATCCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (27 bp):
ATTTTACCAAATAGGAGTATTCTCATA
Found at i:5115852 original size:21 final size:21
Alignment explanation
Indices: 5115827--5115989 Score: 112
Period size: 21 Copynumber: 7.7 Consensus size: 21
5115817 AGTTTAGGGT
5115827 TATATGTGGTCCTTCGGGACA
1 TATATGTGGTCCTTCGGGACA
** ** *
5115848 TATATGTAATCCTTTAGAACA
1 TATATGTGGTCCTTCGGGACA
* *
5115869 TATATGTGGTTCTTAGGGACA
1 TATATGTGGTCCTTCGGGACA
* * * * *
5115890 CATATTTGGTCCTTTGGAATA
1 TATATGTGGTCCTTCGGGACA
* *
5115911 TATATATGGTCCTTAAGGAGA-A
1 TATATGTGGTCCTT-CGG-GACA
* **
5115933 TTATGTGTGGTCCTTCATGACA
1 -TATATGTGGTCCTTCGGGACA
*
5115955 TATATGTGGTCATTCGGGACA
1 TATATGTGGTCCTTCGGGACA
**
5115976 TATATAAGGTCCTT
1 TATATGTGGTCCTT
5115990 ATGGGCAATT
Statistics
Matches: 105, Mismatches: 33, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
21 88 0.84
22 4 0.04
23 13 0.12
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (21 bp):
TATATGTGGTCCTTCGGGACA
Found at i:5115877 original size:42 final size:42
Alignment explanation
Indices: 5115827--5115989 Score: 141
Period size: 42 Copynumber: 3.8 Consensus size: 42
5115817 AGTTTAGGGT
* **
5115827 TATATGTGGTCCTTCGGGACATATATGTAATCCTTTAGAACA
1 TATATGTGGTCCTTAGGGACATATATGTGGTCCTTTAGAACA
* * * * *
5115869 TATATGTGGTTCTTAGGGACACATATTTGGTCCTTTGGAATA
1 TATATGTGGTCCTTAGGGACATATATGTGGTCCTTTAGAACA
* * *
5115911 TATATATGGTCCTTAAGGAGA-ATTATGTGTGGTCCTTCATG-ACA
1 TATATGTGGTCCTT-AGG-GACA-TATATGTGGTCCTTTA-GAACA
* * **
5115955 TATATGTGGTCATTCGGGACATATATAAGGTCCTT
1 TATATGTGGTCCTTAGGGACATATATGTGGTCCTT
5115990 ATGGGCAATT
Statistics
Matches: 94, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
42 59 0.63
43 7 0.07
44 27 0.29
45 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (42 bp):
TATATGTGGTCCTTAGGGACATATATGTGGTCCTTTAGAACA
Found at i:5119423 original size:24 final size:27
Alignment explanation
Indices: 5119385--5119438 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
5119375 TTCATAGAAA
* *
5119385 ATATATTATTGTATT-ATTTTCAATTT
1 ATATATTATTGTATTAAATTTAAATTT
5119411 ATATATT-TT-TATTAAATTTAAATTT
1 ATATATTATTGTATTAAATTTAAATTT
5119436 ATA
1 ATA
5119439 AAATTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 14 0.56
26 7 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATATATTATTGTATTAAATTTAAATTT
Found at i:5119460 original size:13 final size:13
Alignment explanation
Indices: 5119442--5119485 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
5119432 ATTTATAAAA
5119442 TTTATATAATTTT
1 TTTATATAATTTT
* *
5119455 TTTATAAAATTTAA
1 TTTATATAATTT-T
5119469 TTTATATAATTTT
1 TTTATATAATTTT
5119482 TTTA
1 TTTA
5119486 CAAAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATATAATTTT
Found at i:5119461 original size:22 final size:22
Alignment explanation
Indices: 5119433--5119494 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 22
5119423 TAAATTTAAA
5119433 TTTATAAAATTTATATAATTTT
1 TTTATAAAATTTATATAATTTT
5119455 TTTATAAAATTTAATTTATATAATTTT
1 TTTAT--AA---AATTTATATAATTTT
*
5119482 TTTACAAAATTTA
1 TTTATAAAATTTA
5119495 ATGGGTAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 11 0.32
24 2 0.06
25 2 0.06
27 19 0.56
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATAAAATTTATATAATTTT
Found at i:5119471 original size:27 final size:27
Alignment explanation
Indices: 5119440--5119496 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
5119430 AAATTTATAA
*
5119440 AATTTATATAATTTTTTTATAAAATTT
1 AATTTATATAATTTTTTTACAAAATTT
5119467 AATTTATATAATTTTTTTACAAAATTT
1 AATTTATATAATTTTTTTACAAAATTT
5119494 AAT
1 AAT
5119497 GGGTAGATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
AATTTATATAATTTTTTTACAAAATTT
Found at i:5119492 original size:13 final size:13
Alignment explanation
Indices: 5119442--5119493 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
5119432 ATTTATAAAA
*
5119442 TTTATATAATTTT
1 TTTATAAAATTTT
*
5119455 TTTATAAAATTTAA
1 TTTATAAAATTT-T
*
5119469 TTTATATAATTTT
1 TTTATAAAATTTT
*
5119482 TTTACAAAATTT
1 TTTATAAAATTT
5119494 AATGGGTAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTATAAAATTTT
Found at i:5119587 original size:14 final size:14
Alignment explanation
Indices: 5119564--5119602 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
5119554 AAATTCTGAT
5119564 AATTTATGAAAATA
1 AATTTATGAAAATA
*
5119578 AATTTTTG-AAATA
1 AATTTATGAAAATA
*
5119591 AATTTGTGAAAA
1 AATTTATGAAAA
5119603 CAAAAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (14 bp):
AATTTATGAAAATA
Found at i:5121685 original size:31 final size:31
Alignment explanation
Indices: 5121650--5121732 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
5121640 AATTTTATGT
5121650 TAAAAAATAAATATATAAAAAAAT-TAAAAA
1 TAAAAAATAAATATATAAAAAAATATAAAAA
*
5121680 -ATAAAAATATAT-TATCAATAAAAATATAAAAA
1 TA-AAAAATAAATATAT-AA-AAAAATATAAAAA
*
5121712 -AAAAAATAAAATATATTAAAA
1 TAAAAAAT-AAATATATAAAAA
5121733 TTTAAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
29 4 0.09
30 11 0.25
31 15 0.34
32 11 0.25
33 3 0.07
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.25
Consensus pattern (31 bp):
TAAAAAATAAATATATAAAAAAATATAAAAA
Found at i:5122169 original size:50 final size:49
Alignment explanation
Indices: 5122081--5122205 Score: 169
Period size: 50 Copynumber: 2.5 Consensus size: 49
5122071 AACAGTAAAG
** *
5122081 CGCGCCCCTTGCATCGCGCTATACGCTGATGTGGCGCCACGTGGGGTATAA
1 CGCGCCCC-TGCATCGCGCTATACGCTGAACTGCCGCCACGT-GGGTATAA
* *
5122132 CGCGCCCCTGCATCGCGCTATACGGTGAACTGCCGCCACGTGGGTATAG
1 CGCGCCCCTGCATCGCGCTATACGCTGAACTGCCGCCACGTGGGTATAA
*
5122181 CGCGGCCCCTGCAGCGCGCTATACG
1 CGC-GCCCCTGCATCGCGCTATACG
5122206 TCACGTAGGG
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 10 0.15
50 49 0.73
51 8 0.12
ACGTcount: A:0.15, C:0.35, G:0.31, T:0.18
Consensus pattern (49 bp):
CGCGCCCCTGCATCGCGCTATACGCTGAACTGCCGCCACGTGGGTATAA
Found at i:5127982 original size:110 final size:111
Alignment explanation
Indices: 5127804--5128024 Score: 372
Period size: 110 Copynumber: 2.0 Consensus size: 111
5127794 ATTACAAAAA
* * * *
5127804 TTAATTCTTAATCTAATAATCATGCATTAAATGAATGAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATGAACTAAATATTAATAATAATTTAAATTA
*
5127869 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
5127915 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATGAACTAAATATTAATAATAATTTAAATTA
*
5127979 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
5128025 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 70 0.68
111 33 0.32
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATGAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:5128177 original size:20 final size:19
Alignment explanation
Indices: 5128149--5128188 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
5128139 CCTTAAAAAG
*
5128149 AGAGTATTTGAGAGAGATTT
1 AGAGAATTTGAGAGA-ATTT
5128169 AGAGAATTTGAGAGAATTT
1 AGAGAATTTGAGAGAATTT
5128188 A
1 A
5128189 ATGTGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAGAATTT
Found at i:5130071 original size:19 final size:20
Alignment explanation
Indices: 5130034--5130076 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
5130024 AAAATGTTTA
* *
5130034 AAAATATGAGGAATGATTT-
1 AAAATAAGAGGAATAATTTG
*
5130053 AAAATAAGAGGTATAATTTG
1 AAAATAAGAGGAATAATTTG
5130073 AAAA
1 AAAA
5130077 CATAGAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (20 bp):
AAAATAAGAGGAATAATTTG
Found at i:5156544 original size:25 final size:25
Alignment explanation
Indices: 5156484--5156544 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 25
5156474 TATATTTATA
*
5156484 TATAAATATAAAAAATTTAAATAGT
1 TATAAATAAAAAAAATTTAAATAGT
*
5156509 TAATTAGATAAAAAATAATTTAAATA-T
1 T-A-TAAATAAAAAA-AATTTAAATAGT
*
5156536 TATATATAA
1 TATAAATAA
5156545 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.23
26 2 0.07
27 11 0.37
28 10 0.33
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
TATAAATAAAAAAAATTTAAATAGT
Found at i:5156573 original size:36 final size:38
Alignment explanation
Indices: 5156516--5156595 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 38
5156506 AGTTAATTAG
*
5156516 ATAAAAAATAATTTAAATATTATATATA-ATTATAAAAA
1 ATAAAAAATAATTTAAATATTAAATATATATTA-AAAAA
* *
5156554 ATAAAAAAT-A-TTAAATATTAAATTTATATTAAAAAT
1 ATAAAAAATAATTTAAATATTAAATATATATTAAAAAA
5156590 ATAAAA
1 ATAAAA
5156596 CTTGTATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 24 0.63
37 5 0.13
38 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (38 bp):
ATAAAAAATAATTTAAATATTAAATATATATTAAAAAA
Found at i:5156591 original size:20 final size:20
Alignment explanation
Indices: 5156566--5156605 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5156556 AAAAAATATT
* *
5156566 AAATATTAAATTTATATTAA
1 AAATATAAAACTTATATTAA
*
5156586 AAATATAAAACTTGTATTAA
1 AAATATAAAACTTATATTAA
5156606 CACATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (20 bp):
AAATATAAAACTTATATTAA
Found at i:5160861 original size:24 final size:24
Alignment explanation
Indices: 5160833--5160878 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5160823 TAAGAATTCT
** *
5160833 AAATTATTTTATTTGATTGATATA
1 AAATTATGATATTTAATTGATATA
5160857 AAATTATGATATTTAATTGATA
1 AAATTATGATATTTAATTGATA
5160879 AATGTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (24 bp):
AAATTATGATATTTAATTGATATA
Found at i:5162489 original size:43 final size:44
Alignment explanation
Indices: 5162406--5162534 Score: 152
Period size: 44 Copynumber: 3.0 Consensus size: 44
5162396 CAGCTCGTAA
**
5162406 TTTGCACCGAAGTGCCACATAATTGTCATGAATGACCACATAGG
1 TTTGCACCGAAGTGCCACATAATTGTCACAAATGACCACATAGG
* *
5162450 TTTGCACCGAAGTGCCACAT-TTTGTCCCAAATGACCACATAGG
1 TTTGCACCGAAGTGCCACATAATTGTCACAAATGACCACATAGG
** * * * * *
5162493 TTTGCACATAAGTGTCACATAATTATCCCAGAGGACCACATA
1 TTTGCACCGAAGTGCCACATAATTGTCACAAATGACCACATA
5162535 ATTGTCCCGG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 36 0.49
44 37 0.51
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (44 bp):
TTTGCACCGAAGTGCCACATAATTGTCACAAATGACCACATAGG
Found at i:5162534 original size:21 final size:21
Alignment explanation
Indices: 5162508--5162556 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5162498 ACATAAGTGT
5162508 CACATAATTATCCCAGAGGAC
1 CACATAATTATCCCAGAGGAC
* *
5162529 CACATAATTGTCCCGGAGGAC
1 CACATAATTATCCCAGAGGAC
5162550 CACATAA
1 CACATAA
5162557 AACCCTCGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (21 bp):
CACATAATTATCCCAGAGGAC
Found at i:5163443 original size:20 final size:22
Alignment explanation
Indices: 5163417--5163474 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
5163407 CATTCTTCGG
5163417 GGTATCGATACTACCCTT-ACA
1 GGTATCGATACTACCCTTAACA
*
5163438 -GTATCGATAC--CTCTTCAACA
1 GGTATCGATACTACCCTT-AACA
5163458 GGTATCGATACTACCCT
1 GGTATCGATACTACCCT
5163475 CAAATTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 4 0.13
20 13 0.43
21 10 0.33
23 3 0.10
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (22 bp):
GGTATCGATACTACCCTTAACA
Found at i:5165633 original size:32 final size:32
Alignment explanation
Indices: 5165596--5165672 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
5165586 CGGGGCCACG
* *
5165596 GGGCCTACCTAAGAACAT-ATCTTAGGGTCGCA
1 GGGCCTACCTAAGAA-ATGATCTCAGGGCCGCA
**
5165628 GGGCCTACCCGAG-AATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
*
5165659 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
5165673 GTCACATTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
30 2 0.06
31 23 0.64
32 11 0.31
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (32 bp):
GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
Found at i:5173155 original size:21 final size:21
Alignment explanation
Indices: 5173128--5173220 Score: 73
Period size: 21 Copynumber: 4.3 Consensus size: 21
5173118 CACCGGAGTG
5173128 CCACATATTTGTCATGAAGGA
1 CCACATATTTGTCATGAAGGA
*
5173149 CCGCATAGGTTTG-CACTGAAGTG-
1 CCACATA--TTTGTCA-TGAAG-GA
**
5173172 CCACATATTTGTCCCGAAGGA
1 CCACATATTTGTCATGAAGGA
* ** *
5173193 CCACATAATTGTCCCGGAGGA
1 CCACATATTTGTCATGAAGGA
5173214 CCACATA
1 CCACATA
5173221 ATTATCCTGG
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.02
21 40 0.67
22 3 0.05
23 15 0.25
24 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
CCACATATTTGTCATGAAGGA
Found at i:5173163 original size:44 final size:44
Alignment explanation
Indices: 5173114--5173199 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
5173104 CAACTCGTAA
* * *
5173114 TTTGCACCGGAGTGCCACATATTTGTCATGAAGGACCGCATAGG
1 TTTGCACCGAAGTGCCACATATTTGTCACGAAGGACCACATAGG
* *
5173158 TTTGCACTGAAGTGCCACATATTTGTCCCGAAGGACCACATA
1 TTTGCACCGAAGTGCCACATATTTGTCACGAAGGACCACATA
5173200 ATTGTCCCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (44 bp):
TTTGCACCGAAGTGCCACATATTTGTCACGAAGGACCACATAGG
Found at i:5173178 original size:23 final size:21
Alignment explanation
Indices: 5173113--5173182 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
5173103 ACAACTCGTA
* *
5173113 ATTTGCACCGGAGTGCCACAT
1 ATTTGCACTGAAGTGCCACAT
*
5173134 ATTTGTCA-TGAAG-GACCGCAT
1 ATTTG-CACTGAAGTG-CCACAT
5173155 AGGTTTGCACTGAAGTGCCACAT
1 A--TTTGCACTGAAGTGCCACAT
5173178 ATTTG
1 ATTTG
5173183 TCCCGAAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
20 1 0.03
21 18 0.46
22 4 0.10
23 15 0.38
24 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (21 bp):
ATTTGCACTGAAGTGCCACAT
Found at i:5173221 original size:21 final size:21
Alignment explanation
Indices: 5173172--5173242 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
5173162 CACTGAAGTG
* *
5173172 CCACATATTTGTCCCGAAGGA
1 CCACATAATTGTCCCGGAGGA
5173193 CCACATAATTGTCCCGGAGGA
1 CCACATAATTGTCCCGGAGGA
* * *
5173214 CCACATAATTATCCTGGAGGT
1 CCACATAATTGTCCCGGAGGA
5173235 CCACATAA
1 CCACATAA
5173243 AACCCTCGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (21 bp):
CCACATAATTGTCCCGGAGGA
Found at i:5178489 original size:19 final size:19
Alignment explanation
Indices: 5178435--5178494 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
5178425 ACTCGTAATT
*
5178435 TGCACCGAAGTGCCACATAA
1 TGCACTGAAGTGCCACAT-A
5178455 TTGTCA-TGAAAG-GCCACATA
1 -TG-CACTG-AAGTGCCACATA
5178475 TGCACTGAAGTGCCACATA
1 TGCACTGAAGTGCCACATA
5178494 T
1 T
5178495 TTGTCCCGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 5 0.15
19 13 0.38
20 1 0.03
21 10 0.29
22 5 0.15
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (19 bp):
TGCACTGAAGTGCCACATA
Found at i:5179431 original size:21 final size:21
Alignment explanation
Indices: 5179407--5179458 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
5179397 TACCCTTACA
*
5179407 GTATCGATACCTCTTCAACAT
1 GTATCGATACCTCTTCAACAG
5179428 GTATCGATACCTCTTCAACAG
1 GTATCGATACCTCTTCAACAG
*
5179449 GTATCAATAC
1 GTATCGATAC
5179459 TACCCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (21 bp):
GTATCGATACCTCTTCAACAG
Found at i:5181943 original size:21 final size:20
Alignment explanation
Indices: 5181919--5181967 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5181909 ATCAAAATCA
* *
5181919 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
5181939 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
5181959 -CTTTCAAAA
1 TTTTTCAAAA
5181968 GAAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:5183172 original size:21 final size:22
Alignment explanation
Indices: 5183146--5183186 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5183136 CCAGGACAGG
5183146 GAGTATCGATA-CTCCTTTAAT
1 GAGTATCGATATCTCCTTTAAT
*
5183167 GAGTATCGATATTTCCTTTA
1 GAGTATCGATATCTCCTTTA
5183187 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (22 bp):
GAGTATCGATATCTCCTTTAAT
Found at i:5191416 original size:26 final size:24
Alignment explanation
Indices: 5191369--5191418 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
5191359 TACATGATTA
5191369 ATAATAATATATAATTTAATTTTT
1 ATAATAATATATAATTTAATTTTT
* *
5191393 ATAATATATATTATTATTTGATTTTT
1 ATAATA-ATA-TATAATTTAATTTTT
5191419 TTTTATAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
ATAATAATATATAATTTAATTTTT
Found at i:5191773 original size:30 final size:30
Alignment explanation
Indices: 5191733--5191798 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
5191723 ACGTAAGTGG
5191733 AAGACACTTCTT-TCAAGAAGCAT-TTTTCAA
1 AAGACACTTCTTGT-AAGAAGC-TCTTTTCAA
* *
5191763 AAGACGCTTCTTGTAAGAAGCTCTTTTCAG
1 AAGACACTTCTTGTAAGAAGCTCTTTTCAA
5191793 AAGACA
1 AAGACA
5191799 TTTTATACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 1 0.03
30 29 0.94
31 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (30 bp):
AAGACACTTCTTGTAAGAAGCTCTTTTCAA
Found at i:5192109 original size:23 final size:24
Alignment explanation
Indices: 5192057--5192114 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
5192047 TTAAAATGTT
* * *
5192057 ATATTCAAACATTTGAAAATCCAC
1 ATATTTAAACACTTGAAAACCCAC
*
5192081 ACATTTAAACACTTG-AAACCCAC
1 ATATTTAAACACTTGAAAACCCAC
5192104 ATATTTAAACA
1 ATATTTAAACA
5192115 ATATGGGCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (24 bp):
ATATTTAAACACTTGAAAACCCAC
Found at i:5192488 original size:17 final size:17
Alignment explanation
Indices: 5192462--5192494 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5192452 TAGATAAAAA
5192462 AAACCCTTATTAAATAT
1 AAACCCTTATTAAATAT
*
5192479 AAACCTTTATTAAATA
1 AAACCCTTATTAAATA
5192495 AAGGCTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (17 bp):
AAACCCTTATTAAATAT
Found at i:5192593 original size:13 final size:12
Alignment explanation
Indices: 5192573--5192613 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
5192563 ATGTTTTTAA
5192573 AAAGTGATTTTG
1 AAAGTGATTTTG
*
5192585 AAAGATGATGTTAG
1 AAAG-TGAT-TTTG
5192599 AAAGTGATTTTG
1 AAAGTGATTTTG
5192611 AAA
1 AAA
5192614 AGTTAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 10 0.40
13 8 0.32
14 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.34
Consensus pattern (12 bp):
AAAGTGATTTTG
Found at i:5192615 original size:13 final size:13
Alignment explanation
Indices: 5192567--5192616 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
5192557 TTAGTAATGT
*
5192567 TTTTAAAAAGTGA
1 TTTTGAAAAGTGA
5192580 TTTTG-AAAGATGA
1 TTTTGAAAAG-TGA
*
5192593 TGTT-AGAAAGTGA
1 TTTTGA-AAAGTGA
5192606 TTTTGAAAAGT
1 TTTTGAAAAGT
5192617 TAAGTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 4 0.13
13 21 0.70
14 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAGTGA
Found at i:5192945 original size:2 final size:2
Alignment explanation
Indices: 5192938--5192964 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5192928 CTTATAAACA
5192938 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5192965 ATAACTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5196319 original size:16 final size:17
Alignment explanation
Indices: 5196288--5196349 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 17
5196278 AATCAAATTA
*
5196288 GTTAATTTTCAGATCGG
1 GTTAATATTCAGATCGG
5196305 GTTAATATT-AGATC-G
1 GTTAATATTCAGATCGG
** *
5196320 GTCGA-ATTCAGGTCGG
1 GTTAATATTCAGATCGG
*
5196336 GTCAATATT-AGATC
1 GTTAATATTCAGATC
5196350 AGTTGACTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
14 3 0.08
15 8 0.22
16 14 0.39
17 11 0.31
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (17 bp):
GTTAATATTCAGATCGG
Found at i:5196369 original size:31 final size:31
Alignment explanation
Indices: 5196295--5196374 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
5196285 TTAGTTAATT
* * *
5196295 TTCAGATCGGGTTAATATTAGATCGGTCGAA
1 TTCAGGTCGGGTCAATATTAGATCAGTCGAA
* *
5196326 TTCAGGTCGGGTCAATATTAGATCAGTTGAC
1 TTCAGGTCGGGTCAATATTAGATCAGTCGAA
* *
5196357 TTCCGGTTGGGTCAATAT
1 TTCAGGTCGGGTCAATAT
5196375 CATATCGATT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (31 bp):
TTCAGGTCGGGTCAATATTAGATCAGTCGAA
Found at i:5196974 original size:16 final size:16
Alignment explanation
Indices: 5196937--5196975 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5196927 ATTCACATTA
* *
5196937 CTTTCGGTTCGATTTG
1 CTTTCAGTTCGAGTTG
5196953 -TTTCAGTTCGAGTTG
1 CTTTCAGTTCGAGTTG
5196968 CTTTCAGT
1 CTTTCAGT
5196976 CCAACTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (16 bp):
CTTTCAGTTCGAGTTG
Found at i:5200862 original size:25 final size:25
Alignment explanation
Indices: 5200831--5200880 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5200821 TTGGTTGGTC
5200831 AGGAATGTCATTCCCGGTAATCTTA
1 AGGAATGTCATTCCCGGTAATCTTA
5200856 AGGAATGTCATTCCCGGTAATCTTA
1 AGGAATGTCATTCCCGGTAATCTTA
5200881 CATTACCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (25 bp):
AGGAATGTCATTCCCGGTAATCTTA
Found at i:5201397 original size:18 final size:19
Alignment explanation
Indices: 5201374--5201426 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
5201364 CTAGTAATCC
*
5201374 TATTCT-CTGGTAATCTTT
1 TATTCTACTGGTAATATTT
5201392 TATTCTCACTGGTAATATTT
1 TATTCT-ACTGGTAATATTT
* *
5201412 TATCCAACTGGTAAT
1 TATTCTACTGGTAAT
5201427 TTTATATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.20
19 9 0.30
20 15 0.50
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (19 bp):
TATTCTACTGGTAATATTT
Found at i:5203995 original size:20 final size:19
Alignment explanation
Indices: 5203950--5203987 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5203940 TAAAATTATC
5203950 CCGAAGGACCTATGTATGA
1 CCGAAGGACCTATGTATGA
*
5203969 CTCGAAGGACCTTTGTATG
1 C-CGAAGGACCTATGTATG
5203988 TTCCGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (19 bp):
CCGAAGGACCTATGTATGA
Found at i:5208917 original size:20 final size:20
Alignment explanation
Indices: 5208892--5208943 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5208882 TATGAAATTA
5208892 TCCCGAAGGACCTATGTATG
1 TCCCGAAGGACCTATGTATG
*
5208912 TCCCGAAGGACCTTTGTATG
1 TCCCGAAGGACCTATGTATG
* *
5208932 TTCCAAAGGACC
1 TCCCGAAGGACC
5208944 GCGTAGAGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (20 bp):
TCCCGAAGGACCTATGTATG
Found at i:5209655 original size:2 final size:2
Alignment explanation
Indices: 5209648--5209677 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5209638 TTTCCATTAA
5209648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5209678 TCCTTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5210662 original size:15 final size:15
Alignment explanation
Indices: 5210627--5210655 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5210617 AATATGGAAG
5210627 AAGAAAGGAAATGAT
1 AAGAAAGGAAATGAT
5210642 AAGAAAGGAAATGA
1 AAGAAAGGAAATGA
5210656 ATTGAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (15 bp):
AAGAAAGGAAATGAT
Found at i:5211254 original size:19 final size:20
Alignment explanation
Indices: 5211216--5211258 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
5211206 GAAACCCCTT
*
5211216 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
5211236 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
5211255 TGAA
1 TGAA
5211259 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:5214598 original size:19 final size:22
Alignment explanation
Indices: 5214573--5214627 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
5214563 ATGTAAAAGT
5214573 CTTTTTCTT-TTT-TTTTTT-T
1 CTTTTTCTTCTTTCTTTTTTCT
*
5214592 GTTTTTCTTCTTTCTTTTTTCT
1 CTTTTTCTTCTTTCTTTTTTCT
5214614 CTTTTTCTTGCTTT
1 CTTTTTCTT-CTTT
5214628 TATTGCAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 8 0.27
20 3 0.10
21 6 0.20
22 9 0.30
23 4 0.13
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (22 bp):
CTTTTTCTTCTTTCTTTTTTCT
Found at i:5214609 original size:22 final size:22
Alignment explanation
Indices: 5214572--5214627 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 22
5214562 GATGTAAAAG
5214572 TCTTTTTCTT-TTT-TTTTTT-
1 TCTTTTTCTTCTTTCTTTTTTC
*
5214591 TGTTTTTCTTCTTTCTTTTTTC
1 TCTTTTTCTTCTTTCTTTTTTC
5214613 TCTTTTTCTTGCTTT
1 TCTTTTTCTT-CTTT
5214628 TATTGCAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 9 0.29
20 3 0.10
21 6 0.19
22 9 0.29
23 4 0.13
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (22 bp):
TCTTTTTCTTCTTTCTTTTTTC
Found at i:5214612 original size:7 final size:7
Alignment explanation
Indices: 5214574--5214622 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 7
5214564 TGTAAAAGTC
5214574 TTTTTCT
1 TTTTTCT
5214581 TTTTT-T
1 TTTTTCT
*
5214587 TTTTT-G
1 TTTTTCT
5214593 TTTTTCT
1 TTTTTCT
*
5214600 TCTTTCT
1 TTTTTCT
5214607 TTTTTCT
1 TTTTTCT
5214614 CTTTTTCT
1 -TTTTTCT
5214622 T
1 T
5214623 GCTTTTATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 11 0.31
7 18 0.50
8 7 0.19
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:5215413 original size:19 final size:20
Alignment explanation
Indices: 5215375--5215417 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
5215365 GAAACCCCTT
*
5215375 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
5215395 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
5215414 TGAA
1 TGAA
5215418 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:5220901 original size:2 final size:2
Alignment explanation
Indices: 5220896--5220924 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5220886 TTTGTGTGTG
5220896 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 T
5220925 CTATCTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5221013 original size:2 final size:2
Alignment explanation
Indices: 5221008--5221045 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5220998 TGCCATTAAT
5221008 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
5221046 ATGTCATGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5221720 original size:25 final size:25
Alignment explanation
Indices: 5221691--5221740 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5221681 TTATACCAAC
5221691 TAAGATACAATACTTATAGATCAAT
1 TAAGATACAATACTTATAGATCAAT
** * *
5221716 TAAGATGTACTACTTGTAGATCAAT
1 TAAGATACAATACTTATAGATCAAT
5221741 AATTTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (25 bp):
TAAGATACAATACTTATAGATCAAT
Found at i:5222621 original size:12 final size:13
Alignment explanation
Indices: 5222603--5222639 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
5222593 GATATCATAA
5222603 ATCAAAACAGAAT
1 ATCAAAACAGAAT
5222616 -TCAAAACAG-AT
1 ATCAAAACAGAAT
*
5222627 ATCATAACAGAAT
1 ATCAAAACAGAAT
5222640 CTAGATCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.19
Consensus pattern (13 bp):
ATCAAAACAGAAT
Done.