Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 26
Found at i:4591265 original size:23 final size:23
Alignment explanation
Indices: 4591230--4591302 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
4591220 ATACTTTACA
*
4591230 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
4591253 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
4591276 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
4591299 ATAT
1 ATAT
4591303 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:4591770 original size:23 final size:23
Alignment explanation
Indices: 4591716--4591786 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
4591706 ATACTTTACA
* *
4591716 ATATAAGCACTACCTATTATATT
1 ATATAAGCGCTACCTATTACATT
4591739 ATA-AA-CGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
4591760 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
4591783 ATAT
1 ATAT
4591787 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 17 0.40
22 4 0.09
23 22 0.51
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:4592119 original size:974 final size:978
Alignment explanation
Indices: 4590339--4592130 Score: 3357
Period size: 974 Copynumber: 1.8 Consensus size: 978
4590329 TTATAATATG
4590339 TTGAAAGTGTCTATATATTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATATATTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
4590404 TTCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TTCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
*
4590469 AAAAAACTATTTGATCGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
131 AAAAAACTATTTGATCATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
4590534 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
4590599 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
4590664 AAAATATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGAAT
326 AAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGAAT
* *
4590729 AGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTCCCTATTACATTATATAAG
391 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
*
4590794 CGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCTATACTTTTTATAAAAATGA
456 CGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCTATACTTTTTATAAAAAGGA
*
4590859 TCGATACTTTTTTAAAGTTATGTAATTTATGTTTTAATTTTTTTTAATAGTGTTTCATGTTTTCC
521 TCGATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCC
4590924 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
586 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
4590989 AAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATAT
651 AAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATAT
4591054 ATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCC
716 ATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCC
4591119 TATAATTACTAAATTAATATCTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCACA
781 TATAATTACTAAATTAATATCTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCACA
4591184 GTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTA
846 GTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTA
4591249 CATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATT
911 CATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATT
4591314 ATA
976 ATA
* *
4591317 TTGAAAGTGTCTATA-CTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATATATTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
4591381 TTCAATTTTTTTTAATAGTTTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
* *
4591446 ACAAAAAATTATTTGATTATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
129 ACAAAAAACTATTTGATCATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
4591511 TTAACCAAAGATAATAATAAATATGT-A-ATATATGTTTATTGTTTTTAATTTAATAAT-A-ATA
194 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
4591572 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
259 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
* * *
4591637 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
324 TCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGA
*
4591702 ATAGATACTTTACAATATAAGCACTACCTATTATA-T-TATAAACGCTACCTATTACATTATATA
389 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
4591765 AGCGCTACCTATTACATCATATTTTTACCTA-TATATTGAAAGTGTCTATACTTTTTATAAAAAG
454 AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCTATACTTTTTATAAAAAG
4591829 GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTT
519 GATCGATAC-TTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTT
4591894 TCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAATTATTTGATTGTTTTGATATT
583 TCCACCTACAATATTAATTTAATAATTTCATTTGCAC-AAAAAATTATTTGATTGTTTTGATATT
4591959 TTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAAT
647 TTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAAT
4592024 ATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGA
712 ATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGA
4592089 CGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
777 CGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
4592131 GATGTACATA
Statistics
Matches: 795, Mismatches: 15, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
972 41 0.05
973 148 0.19
974 200 0.25
975 162 0.20
976 1 0.00
977 82 0.10
978 16 0.02
979 145 0.18
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (978 bp):
TTGAAAGTGTCTATATATTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
TTCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAACTATTTGATCATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGAAT
AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
CGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCTATACTTTTTATAAAAAGGA
TCGATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCC
ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
AAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATAT
ATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCC
TATAATTACTAAATTAATATCTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCACA
GTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTA
CATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATT
ATA
Found at i:4594942 original size:183 final size:183
Alignment explanation
Indices: 4594634--4595390 Score: 1268
Period size: 183 Copynumber: 4.1 Consensus size: 183
4594624 TACTTAAAAT
*
4594634 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAATC-AGTAT
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGA-TAT
* *
4594698 ATTTATACCGGTTATATTACAAAATTATCTATTATATTATAATTCTGGGTTCTGATGTGTAAATG
65 ATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATG
*
4594763 TTGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
130 TCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
4594817 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATA
4594882 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
4594947 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
** * * * * *
4595000 TTTCAACACATTATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTAATAAAACTGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATA
4595065 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
4595130 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* * *
4595183 TTCTGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATA
* **
4595248 TTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGATGT-TATTTCA
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAAT--
* * *
4595312 ATCGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCATTCTGGACATAAAG
129 GTCGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
4595367 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
4595391 GAAAACTTTG
Statistics
Matches: 545, Mismatches: 25, Indels: 7
0.94 0.04 0.01
Matches are distributed among these distances:
182 3 0.01
183 471 0.86
184 71 0.13
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:4596618 original size:12 final size:12
Alignment explanation
Indices: 4596601--4596664 Score: 83
Period size: 12 Copynumber: 5.3 Consensus size: 12
4596591 CTTGTTTGGA
4596601 TCATCATCATCG
1 TCATCATCATCG
*
4596613 TCATCATCATCA
1 TCATCATCATCG
*
4596625 TCGTCATCATCG
1 TCATCATCATCG
*
4596637 TCATCGTCATCG
1 TCATCATCATCG
* *
4596649 TCATCGTCATCT
1 TCATCATCATCG
4596661 TCAT
1 TCAT
4596665 TGTCAGCTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.22, C:0.33, G:0.09, T:0.36
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:4596620 original size:15 final size:15
Alignment explanation
Indices: 4596600--4596653 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
4596590 ACTTGTTTGG
4596600 ATCATCATCATCGTC
1 ATCATCATCATCGTC
4596615 ATCATCATCATCGTC
1 ATCATCATCATCGTC
*
4596630 ATCATCGTCATCGTC
1 ATCATCATCATCGTC
*
4596645 ATCGTCATC
1 ATCATCATC
4596654 GTCATCTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (15 bp):
ATCATCATCATCGTC
Found at i:4596682 original size:6 final size:6
Alignment explanation
Indices: 4596601--4596669 Score: 75
Period size: 6 Copynumber: 11.5 Consensus size: 6
4596591 CTTGTTTGGA
* * * * *
4596601 TCATCA TCATCG TCATCA TCATCA TCGTCA TCATCG TCATCG TCATCG
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG
* *
4596649 TCATCG TCATCT TCATTG TCA
1 TCATCG TCATCG TCATCG TCA
4596670 GCTTCATCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36
Consensus pattern (6 bp):
TCATCG
Found at i:4596691 original size:18 final size:18
Alignment explanation
Indices: 4596655--4596691 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4596645 ATCGTCATCG
*
4596655 TCATCTTCATTGTCAGCT
1 TCATCTTCATTGACAGCT
*
4596673 TCATCTTCATTGACCGCT
1 TCATCTTCATTGACAGCT
4596691 T
1 T
4596692 GGTTGTCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.30, G:0.11, T:0.43
Consensus pattern (18 bp):
TCATCTTCATTGACAGCT
Found at i:4598494 original size:200 final size:200
Alignment explanation
Indices: 4598151--4599089 Score: 1535
Period size: 200 Copynumber: 4.7 Consensus size: 200
4598141 TTTAAATTAG
* * * * *
4598151 TATCGACA-AAACATTAAACAGTGTCGATACA-TATTATATACCAATTCTCTCATAAAACCGGTA
1 TATCGACACAAAC-TAAAAAAGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTA
4598214 TACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGG
64 TACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGG
4598279 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGA
129 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGA
4598344 CCAAAAA
194 CCAAAAA
* *
4598351 TATCGACACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
* *
4598416 TTTATACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
4598481 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACC
4598546 AAAAA
196 AAAAA
4598551 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
*
4598616 CTTGTATCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
*
4598681 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCTTGTTTGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACC
4598746 AAAAA
196 AAAAA
* * * *
4598751 TATC-AGCACAAACTACAAAAGTGTTGACACATTATTTAGACCTATTATCTCATAAAA-CGGGAT
1 TATCGA-CACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTAT
* * * ** * *
4598814 ACTTGAACCGATTAGATTGAAAAATTACCTATTACATTACACTTTTGGGTTTCGATGTTTTTGGG
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGG
*
4598879 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGAC
130 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGAC
4598944 CAAAAA
195 CAAAAA
* *
4598950 TATCGACACAAACTACAAAAGTGTCGACACATTATTTATACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
* * * * * * *
4599015 CTTGCACCGATTAGATTGAAAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTTTAGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
4599080 TCGACACTTT
131 TCGACACTTT
4599090 GTAACATCCG
Statistics
Matches: 698, Mismatches: 36, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
199 184 0.26
200 506 0.72
201 8 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACC
AAAAA
Found at i:4599031 original size:399 final size:400
Alignment explanation
Indices: 4598151--4599089 Score: 1546
Period size: 399 Copynumber: 2.4 Consensus size: 400
4598141 TTTAAATTAG
* * * *
4598151 TATCGACA-AAACATTAAACAGTGTCGATACA-TATTATATACCAATTCTCTCATAAAACCGGTA
1 TATCGACACAAAC-TAAAAAAGTGTCGACACATTATT-TATACCTATTCTCTCATAAAACCGGTA
4598214 TACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGG
64 TACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGG
4598279 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGA
129 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGA
* *
4598344 CCAAAAATATCGACACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAAC
194 CCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTATCTCATAAAAC
* * * ** *
4598409 CGGTATATTTATACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTT
259 CGGGATATTGATACCGATTAGATTGAAAAATTACATATTACATTACACTTTTGGGTTTCGATGTT
*
4598474 TATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATT
324 TATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATT
4598539 CTGGACCAAAAA
389 CTGGACCAAAAA
*
4598551 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTATACCTATTCTCTCATAAAACCGGTATA
*
4598616 CTTGTATCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
*
4598681 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCTTGTTTGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACC
* * *
4598746 AAAAATATC-AGCACAAACTACAAAAGTGTTGACACATTATTTAGACCTATTATCTCATAAAA-C
196 AAAAATATCGA-CACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTATCTCATAAAACC
*
4598809 GGGATACTTGA-ACCGATTAGATTGAAAAATTACCTATTACATTACACTTTTGGGTTTCGATGTT
260 GGGATA-TTGATACCGATTAGATTGAAAAATTACATATTACATTACACTTTTGGGTTTCGATGTT
*
4598873 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATT
324 TATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATT
4598938 CTGGACCAAAAA
389 CTGGACCAAAAA
*
4598950 TATCGACACAAACTACAAAAGTGTCGACACATTATTTATACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTATACCTATTCTCTCATAAAACCGGTATA
* * * * * * *
4599015 CTTGCACCGATTAGATTGAAAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTTTAGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
4599080 TCGACACTTT
131 TCGACACTTT
4599090 GTAACATCCG
Statistics
Matches: 504, Mismatches: 31, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
399 260 0.52
400 236 0.47
401 8 0.02
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (400 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTATACCTATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTATGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACC
AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCG
GGATATTGATACCGATTAGATTGAAAAATTACATATTACATTACACTTTTGGGTTTCGATGTTTA
TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
GGACCAAAAA
Found at i:4599813 original size:21 final size:21
Alignment explanation
Indices: 4599787--4599830 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4599777 ATTTCTGGGT
* *
4599787 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
4599808 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
4599829 AA
1 AA
4599831 ACGACAGAAT
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:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:4600602 original size:31 final size:31
Alignment explanation
Indices: 4600564--4600719 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
4600554 AGGGTCGAGG
4600564 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
4600595 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
4600626 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
4600657 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
4600688 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
4600719 G
1 G
4600720 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:4603735 original size:21 final size:21
Alignment explanation
Indices: 4603709--4603752 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4603699 ATTTTTGGGT
* *
4603709 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
4603730 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
4603751 AA
1 AA
4603753 ACGACAGAAT
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:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:4604308 original size:21 final size:22
Alignment explanation
Indices: 4604264--4604309 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
4604254 TATATGGCCT
*
4604264 ATGATATGAAAGTGTATATGTGAA
1 ATGATATGAAA--GTATATATGAA
4604288 ATGATATGAAA-TATATATGAA
1 ATGATATGAAAGTATATATGAA
4604309 A
1 A
4604310 ACAAGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
24 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.33
Consensus pattern (22 bp):
ATGATATGAAAGTATATATGAA
Found at i:4604525 original size:31 final size:31
Alignment explanation
Indices: 4604487--4604642 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
4604477 AGGGTCGAGG
4604487 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
4604518 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
4604549 GTTTACATATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
4604580 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
4604611 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
4604642 G
1 G
4604643 GTCCTTCGGG
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:4607659 original size:21 final size:21
Alignment explanation
Indices: 4607633--4607676 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4607623 ATTTCTGGGT
* *
4607633 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
4607654 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
4607675 AA
1 AA
4607677 ACGACAGAAT
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:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:4608229 original size:23 final size:24
Alignment explanation
Indices: 4608186--4608232 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
4608176 ATATGGCCTG
*
4608186 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
4608210 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
4608233 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:4608448 original size:31 final size:31
Alignment explanation
Indices: 4608410--4608565 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
4608400 AGGGTCGAGG
4608410 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
4608441 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
4608472 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
4608503 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
4608534 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
4608565 G
1 G
4608566 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:4609475 original size:19 final size:19
Alignment explanation
Indices: 4609451--4609515 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
4609441 TTATATTCAC
*
4609451 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCTT
4609470 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
4609489 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
4609508 ATACAAAA
1 ATACAAAA
4609516 ATAACCCTAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:4611348 original size:33 final size:33
Alignment explanation
Indices: 4611311--4611376 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
4611301 CATCTTAATA
*
4611311 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
4611344 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
4611377 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:4611435 original size:21 final size:21
Alignment explanation
Indices: 4611410--4611474 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
4611400 CCCCTTATGC
* *
4611410 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
4611431 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
4611452 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
4611473 CT
1 CT
4611475 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:4613635 original size:17 final size:18
Alignment explanation
Indices: 4613613--4613655 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
4613603 ATATATCCAG
4613613 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
4613630 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
4613650 TATCAT
1 TATCAT
4613656 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:4613673 original size:20 final size:19
Alignment explanation
Indices: 4613618--4613664 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
4613608 TCCAGTATCA
4613618 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
4613637 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
4613658 TTTTACC
1 TTTTACC
4613665 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:4613826 original size:20 final size:20
Alignment explanation
Indices: 4613799--4613845 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
4613789 TTTGGTAACG
4613799 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
4613818 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
4613839 TTTTACC
1 TTTTACC
4613846 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:4613889 original size:181 final size:182
Alignment explanation
Indices: 4613585--4614057 Score: 696
Period size: 181 Copynumber: 2.6 Consensus size: 182
4613575 CGTACTTACG
* * *
4613585 AAAGTATCGACACTTTCAATATATCCAGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
4613650 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATAAATTTTTTAAAAGTATCGACACATTAT
*
4613715 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
** *
4613766 AAAGTATCGACACTTTCAATATATTTGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
4613831 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATAAATTTTTTAAAAGTATCGACACATTAT
** *
4613896 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * ** *
4613948 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGATTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
4614013 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGATAAATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATAAATTTTT
4614058 AATTTAGATC
Statistics
Matches: 260, Mismatches: 31, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
181 165 0.63
182 95 0.37
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATAAATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:4618000 original size:2 final size:2
Alignment explanation
Indices: 4617993--4618021 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4617983 ACCATCCTTT
4617993 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
4618022 CGGCACCAGC
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:4620280 original size:5 final size:5
Alignment explanation
Indices: 4620238--4620318 Score: 53
Period size: 5 Copynumber: 16.6 Consensus size: 5
4620228 GAAAAACAAG
* * * * * *
4620238 TAAAA TAAAG CAAAA GAAAA TAATA TAAAA AAGTAAA TAAAA T-AAA TAAAG
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA--AAA TAAAA TAAAA TAAAA
*
4620289 TAAAA TAAAA -CAAA T-AAA T-AAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA
4620319 GAAAAAAGGA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
4 15 0.25
5 40 0.68
7 4 0.07
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:4620284 original size:4 final size:4
Alignment explanation
Indices: 4620255--4620314 Score: 50
Period size: 4 Copynumber: 13.8 Consensus size: 4
4620245 AAGCAAAAGA
*
4620255 AAAT AATAT AAA- AAAGT AAAT AAAAT AAAT AAAGT AAAAT AAAAC AAAT
1 AAAT AA-AT AAAT AAA-T AAAT -AAAT AAAT AAA-T -AAAT -AAAT AAAT
4620304 AAAT AAAT AAA
1 AAAT AAAT AAA
4620315 ATAAGAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
3 3 0.06
4 25 0.52
5 17 0.35
6 3 0.06
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:4620285 original size:9 final size:9
Alignment explanation
Indices: 4620255--4620318 Score: 69
Period size: 9 Copynumber: 7.2 Consensus size: 9
4620245 AAGCAAAAGA
*
4620255 AAATAATAT
1 AAATAAAAT
*
4620264 AAA-AAAGT
1 AAATAAAAT
4620272 AAATAAAAT
1 AAATAAAAT
*
4620281 AAATAAAGT
1 AAATAAAAT
*
4620290 AAAATAAAAC
1 -AAATAAAAT
4620300 AAAT-AAAT
1 AAATAAAAT
4620308 AAATAAAAT
1 AAATAAAAT
4620317 AA
1 AA
4620319 GAAAAAAGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
8 13 0.29
9 25 0.56
10 7 0.16
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:4620294 original size:36 final size:35
Alignment explanation
Indices: 4620250--4620318 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
4620240 AAATAAAGCA
* *
4620250 AAAGAAAATAATATAAA-AAAGTAAATAAAATAAAT
1 AAAGAAAATAAAACAAATAAA-TAAATAAAATAAAT
4620285 AAAGTAAAATAAAACAAATAAATAAATAAAATAA
1 AAAG-AAAATAAAACAAATAAATAAATAAAATAA
4620319 GAAAAAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 4 0.13
36 23 0.77
37 3 0.10
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (35 bp):
AAAGAAAATAAAACAAATAAATAAATAAAATAAAT
Found at i:4620646 original size:2 final size:2
Alignment explanation
Indices: 4620639--4620674 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4620629 AAAAATAGTG
4620639 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
4620675 ACAAAACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4622887 original size:106 final size:100
Alignment explanation
Indices: 4622749--4622983 Score: 281
Period size: 100 Copynumber: 2.3 Consensus size: 100
4622739 GTATTGTTCT
* * * *
4622749 GAGTCCAATATCCTCCGCCGTGAAGTTTAAATTGGCTATGGAACTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTAT-GAA-----AAATTGTTTGTTGACAG
4622814 CCAGCCACCCCTTCGATGTGAAGTTGAGATTGTGTTGTCTC
60 CCAGCCACCCCTTCGATGTGAAGTTGAGATTGTGTTGTCTC
* * * * *
4622855 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAAAGTTGTTTGTTGACAGTCAGTC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTATGAAAAATTGTTTGTTGACAGCCAGCC
* * *
4622920 GCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTC
66 ACCCCTTCGATGTGAAGTTGAGATTGTGTTGTCTC
* * *
4622955 GAGTCTAATATTCTTTGCTGTGAAGTTGA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGA
4622984 GCTTGTGTTT
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
100 77 0.68
105 3 0.03
106 33 0.29
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (100 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTATGAAAAATTGTTTGTTGACAGCCAGCC
ACCCCTTCGATGTGAAGTTGAGATTGTGTTGTCTC
Found at i:4622928 original size:100 final size:100
Alignment explanation
Indices: 4622800--4622983 Score: 287
Period size: 100 Copynumber: 1.8 Consensus size: 100
4622790 AACTGGGAAA
4622800 TTGTTTGTTGACAGCCAGCCACCCCTTCGATGTGAAGTTGAGATTGTGTTGTCTCGAGTCCAATA
1 TTGTTTGTTGACAGCCAGCCACCCCTTCGATGTGAAGTTGAGATTGTGTTGTCTCGAGTCCAATA
4622865 TCCTTCGATGTGAAGTTGAAATTGACTCTGAAAAG
66 TCCTTCGATGTGAAGTTGAAATTGACTCTGAAAAG
* * * * * *
4622900 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATA
1 TTGTTTGTTGACAGCCAGCCACCCCTTCGATGTGAAGTTGAGATTGTGTTGTCTCGAGTCCAATA
* * *
4622965 TTCTTTGCTGTGAAGTTGA
66 TCCTTCGATGTGAAGTTGA
4622984 GCTTGTGTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 75 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (100 bp):
TTGTTTGTTGACAGCCAGCCACCCCTTCGATGTGAAGTTGAGATTGTGTTGTCTCGAGTCCAATA
TCCTTCGATGTGAAGTTGAAATTGACTCTGAAAAG
Found at i:4622976 original size:43 final size:43
Alignment explanation
Indices: 4622924--4623026 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
4622914 TCAGTCGCCC
4622924 CTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATT
1 CTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATT
* * *
4622967 CTTTGCTGTGAAGTTGAGCTTGTGTTTTCTTGAGTCTAATATT
1 CTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATT
4623010 CTTCGCTGTGAAGTTGA
1 CTTCGCTGTGAAGTTGA
4623027 AATTGACTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.44
Consensus pattern (43 bp):
CTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATT
Found at i:4623118 original size:67 final size:67
Alignment explanation
Indices: 4623010--4623159 Score: 273
Period size: 67 Copynumber: 2.2 Consensus size: 67
4623000 GTCTAATATT
* *
4623010 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGC
1 CTTCGCTGTGAAGTTGAAATTGACTCTGAAAGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCAC
4623075 CC
66 CC
*
4623077 CTTCGCTGTGAAGTTGAAATTGACTCTGAAAGAAACTGAAAAGTTGTTTGTTGATAGTCAGTCAC
1 CTTCGCTGTGAAGTTGAAATTGACTCTGAAAGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCAC
4623142 CC
66 CC
4623144 CTTCGCTGTGAAGTTG
1 CTTCGCTGTGAAGTTG
4623160 TGTTTGTGTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 80 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (67 bp):
CTTCGCTGTGAAGTTGAAATTGACTCTGAAAGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCAC
CC
Found at i:4623969 original size:7 final size:7
Alignment explanation
Indices: 4623957--4624001 Score: 67
Period size: 7 Copynumber: 6.6 Consensus size: 7
4623947 GAACCCATTT
4623957 TTTTTTC
1 TTTTTTC
4623964 TTTTTTC
1 TTTTTTC
4623971 TTTTGTTC
1 TTTT-TTC
4623979 TTTTTTC
1 TTTTTTC
4623986 -TTTTTC
1 TTTTTTC
4623992 TTTTTT-
1 TTTTTTC
4623998 TTTT
1 TTTT
4624002 CAAAATAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 10 0.28
7 19 0.53
8 7 0.19
ACGTcount: A:0.00, C:0.11, G:0.02, T:0.87
Consensus pattern (7 bp):
TTTTTTC
Found at i:4623979 original size:15 final size:14
Alignment explanation
Indices: 4623957--4624001 Score: 67
Period size: 13 Copynumber: 3.3 Consensus size: 14
4623947 GAACCCATTT
4623957 TTTTTTCTTTTTTC
1 TTTTTTCTTTTTTC
4623971 TTTTGTTCTTTTTTC
1 TTTT-TTCTTTTTTC
4623986 -TTTTTCTTTTTT-
1 TTTTTTCTTTTTTC
4623998 TTTT
1 TTTT
4624002 CAAAATAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.41
14 7 0.24
15 10 0.34
ACGTcount: A:0.00, C:0.11, G:0.02, T:0.87
Consensus pattern (14 bp):
TTTTTTCTTTTTTC
Found at i:4630682 original size:21 final size:21
Alignment explanation
Indices: 4630658--4630697 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4630648 TTCTTGGACC
*
4630658 ATCTTCATCTGATCTTCCAGG
1 ATCTTAATCTGATCTTCCAGG
**
4630679 ATCTTAATCTTTTCTTCCA
1 ATCTTAATCTGATCTTCCA
4630698 TTTTTTTCGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.28, G:0.07, T:0.45
Consensus pattern (21 bp):
ATCTTAATCTGATCTTCCAGG
Found at i:4634364 original size:5 final size:5
Alignment explanation
Indices: 4634354--4634479 Score: 50
Period size: 5 Copynumber: 25.0 Consensus size: 5
4634344 AAAAGAAGTG
* * ** * *
4634354 AATAA AATAA AGA-AA AA-CA AGTAA AATAA AGCAA AAGAA AATAA TATAA
1 AATAA AATAA A-ATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
* *
4634403 AA-AA GTGAATAA AAT-A AATAA AGTAA AATAA AA-CA AAT-A AATAA
1 AATAA ---AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
*
4634447 AATAA GAA-AA AAGGATA AATAA AATAA AGATAA
1 AATAA -AATAA AA-TA-A AATAA AATAA A-ATAA
4634480 TATTGACAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
4 18 0.20
5 58 0.63
6 9 0.10
7 5 0.05
8 2 0.02
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (5 bp):
AATAA
Found at i:4634413 original size:17 final size:18
Alignment explanation
Indices: 4634393--4634443 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
4634383 AGCAAAAGAA
*
4634393 AATAATATAAA-AAAGTG
1 AATAAAATAAATAAAGTG
*
4634410 AATAAAATAAATAAAGTAA
1 AATAAAATAAATAAAGT-G
*
4634429 AATAAAACAAATAAA
1 AATAAAATAAATAAA
4634444 TAAAATAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 10 0.34
18 5 0.17
19 14 0.48
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.20
Consensus pattern (18 bp):
AATAAAATAAATAAAGTG
Found at i:4634424 original size:9 final size:9
Alignment explanation
Indices: 4634354--4634474 Score: 54
Period size: 9 Copynumber: 13.2 Consensus size: 9
4634344 AAAAGAAGTG
4634354 AATAAAATA
1 AATAAAATA
*
4634363 AAGAAAA-A
1 AATAAAATA
4634371 CAAGTAAAATA
1 -AA-TAAAATA
* *
4634382 AAGCAAAAGAA
1 AA-TAAAA-TA
*
4634393 AATAATATA
1 AATAAAATA
* *
4634402 AA-AAAGTG
1 AATAAAATA
4634410 AATAAAATA
1 AATAAAATA
*
4634419 AATAAAGTAA
1 AATAAAAT-A
*
4634429 AATAAAACA
1 AATAAAATA
4634438 AAT-AAATAA
1 AATAAAAT-A
4634447 AATAAGAA-A
1 AATAA-AATA
**
4634456 AA-AGGATA
1 AATAAAATA
4634464 AATAAAATA
1 AATAAAATA
4634473 AA
1 AA
4634475 GATAATATTG
Statistics
Matches: 81, Mismatches: 20, Indels: 22
0.66 0.16 0.18
Matches are distributed among these distances:
7 1 0.01
8 13 0.16
9 39 0.48
10 22 0.27
11 6 0.07
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (9 bp):
AATAAAATA
Found at i:4634807 original size:2 final size:2
Alignment explanation
Indices: 4634800--4634837 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4634790 AGTGTATAAG
4634800 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
4634838 AAATAAAAAA
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:4634808 original size:35 final size:32
Alignment explanation
Indices: 4634744--4634809 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
4634734 AAATATAGAG
*
4634744 AATAGAAAAAAAATAGGTAAATATGTATATAA
1 AATAGAAAAAAAATAGGTAAATATATATATAA
4634776 AATA-AAACAAAAATAGTGTATAAGTATATATATA
1 AATAGAAA-AAAAATAG-GTA-AA-TATATATATA
4634810 TATATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 3 0.10
32 12 0.41
33 3 0.10
34 2 0.07
35 9 0.31
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.27
Consensus pattern (32 bp):
AATAGAAAAAAAATAGGTAAATATATATATAA
Found at i:4637643 original size:34 final size:32
Alignment explanation
Indices: 4637563--4637651 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
4637553 CAGTTATTTT
* * * *
4637563 TTTAAATAGTTATTATATTTTATATTAATATAA
1 TTTATATAATTATTAT-TTTTTTATTAAAATAA
*
4637596 -TTATATAAATATTATTTTTTTATTAAAATAA
1 TTTATATAATTATTATTTTTTTATTAAAATAA
*
4637627 TGTTTATATAATTATTATTTATTTA
1 --TTTATATAATTATTATTTTTTTA
4637652 AATTTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 14 0.30
32 12 0.26
34 20 0.43
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTTATTAAAATAA
Found at i:4640071 original size:34 final size:34
Alignment explanation
Indices: 4640028--4640133 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
4640018 ATAAATGTTT
4640028 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
4640062 TTAAAATAC-AATAATATTATTCGAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
4640095 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
4640129 TTAAA
1 TTAAA
4640134 TTCAAGTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.46
34 34 0.54
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:4640776 original size:127 final size:127
Alignment explanation
Indices: 4640545--4641205 Score: 1119
Period size: 127 Copynumber: 5.2 Consensus size: 127
4640535 TCCCCAGGAA
* *
4640545 CGCGTCCCCGGGAACGCGCCTTCACGGTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCC
1 CGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
*
4640610 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTAACAAAATAATGGAAGG
66 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
* * *
4640672 CGCGCCCCCGGGAATGCACCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCT
1 CGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
4640737 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
66 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
* * * *
4640799 TGCGCCCCCGGGAACGCGCATTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAATTCC
1 CGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
4640864 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
66 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
* ** * *
4640926 CGCGCCTCCGGGAACTTGCCTTCACGGTCCCCTAAGGAATAAAAGGTATTGACATGAATAGTTCT
1 CGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
4640991 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
66 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
4641053 CGCGCCCCCGGG-ACGGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTC
1 CGCGCCCCCGGGAAC-GCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTC
* *
4641117 CCGAGGGACATAAGTGA-AGTAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGA
65 CCGGGGGACATAAGTGACA-TAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
* *
4641180 CGCGCCCCCGAGAACACGCCTTCACG
1 CGCGCCCCCGGGAACGCGCCTTCACG
4641206 TGAATAGTAC
Statistics
Matches: 500, Mismatches: 31, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
126 3 0.01
127 495 0.99
128 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (127 bp):
CGCGCCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
Found at i:4642749 original size:71 final size:70
Alignment explanation
Indices: 4642650--4642791 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 70
4642640 CATGTGTTGA
*
4642650 ACATTTCTATAATATCTTAGAACACATAGCATCCTATAATCCATGCAATACCGTTCATATCACCA
1 ACATTTATATAATATCTTAGAACACATAGCATCCTATAATCCATGCAATACCGTTCATATCACCA
4642715 CAAGC
66 CAAGC
4642720 ACATTTATATACATATCTTAGAACACATAGCATCCTATAATCCATGCAATACCGTTCATATCACC
1 ACATTTATATA-ATATCTTAGAACACATAGCATCCTATAATCCATGCAATACCGTTCATATCACC
4642785 ACAAGC
65 ACAAGC
4642791 A
1 A
4642792 TATGCATCTT
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 10 0.14
71 60 0.86
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.28
Consensus pattern (70 bp):
ACATTTATATAATATCTTAGAACACATAGCATCCTATAATCCATGCAATACCGTTCATATCACCA
CAAGC
Found at i:4642934 original size:24 final size:24
Alignment explanation
Indices: 4642907--4642992 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 24
4642897 CACCACAGCT
*
4642907 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* * *
4642931 CGTAGAAATTATC-CCTAAG-GACCG
1 CGTAGAAATT-GCACCGAAGTG-CCA
4642955 CGTAGAAA-TGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
4642978 CATAG-AATTGTACCG
1 CGTAGAAATTGCACCG
4642993 TAGTTCCATA
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
22 3 0.06
23 19 0.40
24 25 0.52
25 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:4642992 original size:23 final size:23
Alignment explanation
Indices: 4642913--4642992 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
4642903 AGCTCGTATA
4642913 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
4642936 AAATTATC-CCTAAG-GACCGCGTAG
1 -AATT-GCACCGAAGTG-CCACGTAG
* *
4642960 AAATGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACGTAG
*
4642983 AATTGTACCG
1 AATTGCACCG
4642993 TAGTTCCATA
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
22 1 0.02
23 23 0.55
24 17 0.40
25 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:4644771 original size:3 final size:3
Alignment explanation
Indices: 4644759--4644806 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
4644749 TTTAATAATA
* * *
4644759 ATT ATA ATT ATT ATT AAT ATA ATAT ATT ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT ATT ATT
4644806 A
1 A
4644807 AATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:4644776 original size:19 final size:19
Alignment explanation
Indices: 4644750--4644793 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
4644740 ATTAATTTTT
4644750 TTAATAATAATTATAATTATTA
1 TTAAT-ATAA-TAT-ATTATTA
4644772 TTAATATAATATATTATTA
1 TTAATATAATATATTATTA
4644791 TTA
1 TTA
4644794 TTATTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 3 0.14
21 4 0.18
22 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATATAATATATTATTA
Found at i:4644786 original size:16 final size:16
Alignment explanation
Indices: 4644761--4644819 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
4644751 TAATAATAAT
4644761 TATAAT-TATTATTAA
1 TATAATATATTATTAA
*
4644776 TATAATATATTATTAT
1 TATAATATATTATTAA
* *
4644792 TATTATTTATTATTAAA
1 TATAATATATTATT-AA
4644809 TATATATATAT
1 TATA-ATATAT
4644820 ATATATTACA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 6 0.17
16 20 0.57
17 4 0.11
18 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATAATATATTATTAA
Found at i:4644790 original size:22 final size:22
Alignment explanation
Indices: 4644752--4644796 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
4644742 TAATTTTTTT
4644752 AATAATAATTATAATTATTATT
1 AATAATAATTATAATTATTATT
*
4644774 AAT-ATAATATATTATTATTATT
1 AATAATAAT-TATAATTATTATT
4644796 A
1 A
4644797 TTTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATAATAATTATAATTATTATT
Found at i:4646392 original size:21 final size:21
Alignment explanation
Indices: 4646367--4646421 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
4646357 TTGATATTTC
* *
4646367 TAAATAAATAAATATGTTATT
1 TAAATATATAAATATATTATT
* *
4646388 TAAATATATATATATATTCTT
1 TAAATATATAAATATATTATT
4646409 TAAAT-TATAAATA
1 TAAATATATAAATA
4646422 ACATGATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAATATATAAATATATTATT
Found at i:4651570 original size:2 final size:2
Alignment explanation
Indices: 4651563--4651642 Score: 146
Period size: 2 Copynumber: 41.0 Consensus size: 2
4651553 ATATCCTTTA
4651563 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4651604 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4651643 CCTTTGTTGT
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 74 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4651955 original size:22 final size:22
Alignment explanation
Indices: 4651929--4651972 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4651919 TATTATACTC
4651929 ATCCAGCAAAGAAAGAAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAA
*
4651951 ATCCAGCAAAGAAAGGAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAA
4651973 GAAAAAAAGA
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:0.66, C:0.14, G:0.16, T:0.05
Consensus pattern (22 bp):
ATCCAGCAAAGAAAGAAAAAAA
Found at i:4651990 original size:15 final size:14
Alignment explanation
Indices: 4651970--4652068 Score: 93
Period size: 14 Copynumber: 7.2 Consensus size: 14
4651960 AGAAAGGAAA
4651970 AAAGAAAAAAAGAGG
1 AAAGAAAAAAA-AGG
*
4651985 AAAGAATAAAAA--
1 AAAGAAAAAAAAGG
4651997 AAAGAAAAAAAAGG
1 AAAGAAAAAAAAGG
*
4652011 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAGG
4652025 AAA-AAGAAAAGAA--
1 AAAGAA-AAAA-AAGG
4652038 AAAGAAAAAAAA-G
1 AAAGAAAAAAAAGG
*
4652051 AAAAAGAAAAAAAGG
1 AAAGA-AAAAAAAGG
4652066 AAA
1 AAA
4652069 ATTGAATCAA
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
12 13 0.18
13 13 0.18
14 30 0.42
15 16 0.22
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (14 bp):
AAAGAAAAAAAAGG
Found at i:4651996 original size:1 final size:1
Alignment explanation
Indices: 4651992--4652063 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
4651982 AGGAAAGAAT
* ** * * * * * * *
4651992 AAAAAAAAGAAAAAAAAGGAAAGAAAAAAAAAGAAAAAGAAAAGAAAAAGAAAAAAAAGAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4652057 AAAAAAA
1 AAAAAAA
4652064 GGAAAATTGA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:4651996 original size:26 final size:24
Alignment explanation
Indices: 4651958--4652055 Score: 115
Period size: 26 Copynumber: 3.8 Consensus size: 24
4651948 AAAATCCAGC
4651958 AAAGAAAGGAAAAAAGAAAAAAAGAGG
1 AAAGAAA--AAAAAAGAAAAAAA-AGG
4651985 AAAGAATAAAAAAAAGAAAAAAAAGG
1 AAAG-A-AAAAAAAAGAAAAAAAAGG
*
4652011 AAAGAAAAAAAAAGAAAAAGAAAAG
1 AAAGAAAAAAAAAGAAAAA-AAAGG
*
4652036 AAAAAGAAAAAAAAGAAAAA
1 AAAGA-AAAAAAAAGAAAAA
4652056 GAAAAAAAGG
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
24 14 0.22
25 9 0.14
26 21 0.32
27 18 0.28
28 1 0.02
29 2 0.03
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (24 bp):
AAAGAAAAAAAAAGAAAAAAAAGG
Found at i:4652005 original size:57 final size:51
Alignment explanation
Indices: 4651940--4652060 Score: 129
Period size: 51 Copynumber: 2.3 Consensus size: 51
4651930 TCCAGCAAAG
* *
4651940 AAAGAAAAAAAATCCAGCAAAGAAAGGAAAAAAGAAAAA-AAGAGGAAAGAATAAAAA
1 AAAGAAAAAAAA---AGCAAAGAAA--AAAAAAGAAAAAGAA-AAGAAA-AAGAAAAA
*
4651997 AAAG-AAAAAAAAGGAAAGAAAAAAAAAGAAAAAGAAAAGAAAAAGAAAAA
1 AAAGAAAAAAAAAGCAAAGAAAAAAAAAGAAAAAGAAAAGAAAAAGAAAAA
4652047 AAAGAAAAAGAAAA
1 AAAGAAAAA-AAAA
4652061 AAAGGAAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
50 11 0.19
51 21 0.36
52 6 0.10
53 9 0.16
56 7 0.12
57 4 0.07
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (51 bp):
AAAGAAAAAAAAAGCAAAGAAAAAAAAAGAAAAAGAAAAGAAAAAGAAAAA
Found at i:4652009 original size:21 final size:20
Alignment explanation
Indices: 4651985--4652061 Score: 93
Period size: 20 Copynumber: 3.7 Consensus size: 20
4651975 AAAAAAGAGG
4651985 AAAGAATAAAAAAAAGAAAAA
1 AAAGAA-AAAAAAAAGAAAAA
*
4652006 AAAGGAAAGAAAAAAA-AAGAA
1 AAA-GAAA-AAAAAAAGAAAAA
*
4652027 AAAGAAAAGAAAAAGAAAAA
1 AAAGAAAAAAAAAAGAAAAA
4652047 AAAGAAAAAGAAAAA
1 AAAGAAAAA-AAAAA
4652062 AAGGAAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.12
20 16 0.33
21 16 0.33
22 10 0.21
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAAAAAAGAAAAA
Found at i:4652030 original size:6 final size:6
Alignment explanation
Indices: 4651985--4652061 Score: 69
Period size: 6 Copynumber: 13.5 Consensus size: 6
4651975 AAAAAAGAGG
*
4651985 AAAGAA TAAA-AA AAAGAA AAAAAA GGAAAG-A AAA-AA AAAGAA AAAG-A
1 AAAGAA -AAAGAA AAAGAA AAAGAA --AAAGAA AAAGAA AAAGAA AAAGAA
4652032 AAAGAA AAAG-- AAA-AA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
4652062 AAGGAAAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 19
0.74 0.03 0.24
Matches are distributed among these distances:
4 3 0.05
5 18 0.31
6 31 0.53
7 4 0.07
8 3 0.05
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:4652040 original size:41 final size:43
Alignment explanation
Indices: 4651962--4652069 Score: 136
Period size: 40 Copynumber: 2.6 Consensus size: 43
4651952 TCCAGCAAAG
* *
4651962 AAAGGAAAAAAGAAAAAAAGAGGAAAGAATAAAAAAAAGAAAAA
1 AAAGGAAAGAA-AAAAAAAGAGAAAAGAATAAAAAAAAGAAAAA
*
4652006 AAAGGAAAGAAAAAAAAAGA-AAAAGAA-AAGAAAAAGAAAAA
1 AAAGGAAAGAAAAAAAAAGAGAAAAGAATAAAAAAAAGAAAAA
4652047 AAA-GAAA-AAGAAAAAAAG-GAAAA
1 AAAGGAAAGAA-AAAAAAAGAGAAAA
4652070 TTGAATCAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
39 2 0.03
40 16 0.27
41 16 0.27
42 6 0.10
43 9 0.15
44 10 0.17
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (43 bp):
AAAGGAAAGAAAAAAAAAGAGAAAAGAATAAAAAAAAGAAAAA
Found at i:4652069 original size:21 final size:20
Alignment explanation
Indices: 4651968--4652069 Score: 93
Period size: 21 Copynumber: 5.0 Consensus size: 20
4651958 AAAGAAAGGA
*
4651968 AAAAAGAAAAAAAGAGGAAAG
1 AAAAAGAAAAAAAGA-AAAAG
*
4651989 AATAAA-AAAAAGAAAAAAAAGG
1 AA-AAAGAAAAA-AAGAAAAA-G
4652011 AAAGAA-AAAAAAAGAAAAAG
1 AAA-AAGAAAAAAAGAAAAAG
*
4652031 -AAAAGAAAAAGAAAAAAAAG
1 AAAAAGAAAAA-AAGAAAAAG
*
4652051 AAAAAGAAAAAAAGGAAAA
1 AAAAAGAAAAAAAGAAAAA
4652070 TTGAATCAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.03
19 7 0.10
20 15 0.22
21 28 0.41
22 16 0.24
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAAAGAAAAAG
Found at i:4657751 original size:184 final size:183
Alignment explanation
Indices: 4657438--4657805 Score: 648
Period size: 184 Copynumber: 2.0 Consensus size: 183
4657428 CCAATCAACA
4657438 TGTTATTTTGAAAAATAATGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAA
1 TGTTATTTTGAAAAATAATGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAA
*
4657503 ATTGTTGAAAAGCAAGAAAATGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATCTG
66 ATTGTTGAAAAGCAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATCTG
*
4657568 TAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
131 TAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
**
4657621 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTTATCTTTTCT-AAAATG
1 TGTTATTTTGAAAAATAAT--GAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
* * *
4657685 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTATTAAACTATTTCCTACATC
64 AAATTGTTGAAAAGCAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
4657750 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
129 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
4657805 T
1 T
4657806 TTCAAAGCCT
Statistics
Matches: 176, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
183 19 0.11
184 122 0.69
185 35 0.20
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (183 bp):
TGTTATTTTGAAAAATAATGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAA
ATTGTTGAAAAGCAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATCTG
TAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGT
Found at i:4657861 original size:48 final size:48
Alignment explanation
Indices: 4657785--4657881 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
4657775 TCCAAAAAGC
4657785 CTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGT
1 CTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGT
*
4657833 CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGT
1 CTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGT
4657881 C
1 C
4657882 CTGCAGTGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.39
Consensus pattern (48 bp):
CTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGT
Found at i:4657919 original size:76 final size:76
Alignment explanation
Indices: 4657833--4658133 Score: 503
Period size: 76 Copynumber: 3.9 Consensus size: 76
4657823 ATCTGTAAGT
*
4657833 CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGT
1 CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGT
4657898 TTCCAAAAAGC
66 TTCCAAAAAGC
*
4657909 CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAATGCATGATGT
1 CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGT
4657974 TTCCAAAAAGC
66 TTCCAAAAAGC
*
4657985 CTTCGGGAGCTTTTTGATGTCTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGT
1 CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGT
4658050 TTCCAAAAAGC
66 TTCCAAAAAGC
* * * * * *
4658061 CTTTGGGATCTTTTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 CTTCGGGAGCTTTTTGATGTTTTC-AAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATG
*
4658126 TTTTCAAA
65 TTTCCAAA
4658134 CATTTTCATC
Statistics
Matches: 212, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
76 169 0.80
77 43 0.20
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGT
TTCCAAAAAGC
Found at i:4658271 original size:3 final size:3
Alignment explanation
Indices: 4658259--4658306 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
4658249 TTTAATAATA
* * *
4658259 ATT ATA ATT ATT ATT AAT ATA ATAT ATT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT A-TT ATT
4658306 A
1 A
4658307 AATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:4658276 original size:19 final size:19
Alignment explanation
Indices: 4658250--4658319 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 19
4658240 ATTAATTTTT
4658250 TTAATAATAATTATAATTATTA
1 TTAAT-ATAA-TAT-ATTATTA
4658272 TTAATATAATATATTATTA
1 TTAATATAATATATTATTA
*
4658291 TT-AT-TATTAT-TTATTA
1 TTAATATAATATATTATTA
4658307 --AATAT-ATATATTA
1 TTAATATAATATATTA
4658320 CAAATTACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
15 5 0.12
16 10 0.23
17 5 0.12
18 2 0.05
19 9 0.21
20 3 0.07
21 4 0.09
22 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATATAATATATTATTA
Found at i:4658290 original size:22 final size:22
Alignment explanation
Indices: 4658252--4658296 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
4658242 TAATTTTTTT
4658252 AATAATAATTATAATTATTATT
1 AATAATAATTATAATTATTATT
*
4658274 AAT-ATAATATATTATTATTATT
1 AATAATAAT-TATAATTATTATT
4658296 A
1 A
4658297 TTATTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATAATAATTATAATTATTATT
Found at i:4659857 original size:2 final size:2
Alignment explanation
Indices: 4659845--4659885 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4659835 TGTTATTTAA
4659845 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4659886 TCTTTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4664328 original size:18 final size:18
Alignment explanation
Indices: 4664305--4664342 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4664295 GCCCTGGATG
4664305 TGATGGAGGTCATATAAT
1 TGATGGAGGTCATATAAT
4664323 TGATGGAGGTCATATAAT
1 TGATGGAGGTCATATAAT
4664341 TG
1 TG
4664343 TTACAGAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (18 bp):
TGATGGAGGTCATATAAT
Found at i:4666837 original size:24 final size:24
Alignment explanation
Indices: 4666792--4666837 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4666782 TTCCTAATCT
* *
4666792 AAAAATAGAAAACGGGACAGAAAA
1 AAAAAAAGAAAACAGGACAGAAAA
4666816 AAAAAAAGAAAACAAGGA-AGAA
1 AAAAAAAGAAAAC-AGGACAGAA
4666838 TCACCTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.72, C:0.07, G:0.20, T:0.02
Consensus pattern (24 bp):
AAAAAAAGAAAACAGGACAGAAAA
Found at i:4675731 original size:2 final size:2
Alignment explanation
Indices: 4675724--4675764 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
4675714 TTTTATCATA
* *
4675724 TC TC TC TC TC CC TC TC TC -C TC TT TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4675765 ATTCTCGGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:4679327 original size:16 final size:17
Alignment explanation
Indices: 4679308--4679339 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4679298 TTTAAAAACA
4679308 ATTTTTAAGA-AAAATC
1 ATTTTTAAGACAAAATC
4679324 ATTTTTAAGACAAAAT
1 ATTTTTAAGACAAAAT
4679340 GCCAGTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (17 bp):
ATTTTTAAGACAAAATC
Found at i:4681733 original size:3 final size:3
Alignment explanation
Indices: 4681725--4681788 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
4681715 CCTGTAAAAT
*
4681725 ATA ATA ATA ATA TTA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4681772 ATA ATA AT- ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA A
4681789 ATAAACAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 6 0.11
3 50 0.89
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4682211 original size:135 final size:133
Alignment explanation
Indices: 4681994--4682302 Score: 431
Period size: 135 Copynumber: 2.3 Consensus size: 133
4681984 AAGGGTAACT
* * * ** *
4681994 CGGCTCCTACATGATGA-GAAGATCTGGTCAGGTGATGACACGGCTCATACGTGATGAAGAGTTC
1 CGGCTCCTACGTGATGAGGAA-ATCTGGTCGGGGGATGACACAACTCATACGTGATAAAGAGTTC
* * *
4682058 TGGCCATCCTTAGGAAGGGAGATAACACGGTTCCTACGTGATGAGGACGTCTGGTTATCTATGGG
65 TGGCAATCCTTAGGAAGGGAGATAACACGGTTCCTACGTGATGAGGACGACTGGTTAT-TAGGGG
4682123 TGACA
129 TGACA
*
4682128 CGGCTCCTACGTGATGAGGAAATCTGGTCGGGGGGATGACACAACTCATACGTGATAAAGAGTTT
1 CGGCTCCTACGTGATGAGGAAATCTGGTC-GGGGGATGACACAACTCATACGTGATAAAGAGTTC
* * * *
4682193 TGGCAATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGATGACTGGTTATTAGGGGT
65 TGGCAATCCTTAGGAAGGGAGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATTAGGGGT
4682258 GACA
130 GACA
** *
4682262 CGGCTCCTACGTGATGAGGAGGTCTGCTCGGGGGATGACAC
1 CGGCTCCTACGTGATGAGGAAATCTGGTCGGGGGATGACAC
4682303 GGTTCCTACG
Statistics
Matches: 156, Mismatches: 17, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
133 12 0.08
134 60 0.38
135 84 0.54
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (133 bp):
CGGCTCCTACGTGATGAGGAAATCTGGTCGGGGGATGACACAACTCATACGTGATAAAGAGTTCT
GGCAATCCTTAGGAAGGGAGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATTAGGGGTG
ACA
Found at i:4682271 original size:42 final size:40
Alignment explanation
Indices: 4682224--4682323 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
4682214 ATAACTCGGT
*
4682224 TCCTACGTGATGAGGATGACTGGTTATTAGGGG-TGACACGGC
1 TCCTACGTGATGAGGATGACT-G--ATCAGGGGATGACACGGC
* * * * *
4682266 TCCTACGTGATGAGGAGGTCTGCTCGGGGGATGACACGGT
1 TCCTACGTGATGAGGATGACTGATCAGGGGATGACACGGC
4682306 TCCTACGTGATGAGGATG
1 TCCTACGTGATGAGGATG
4682324 GTTGTCCATC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 5 0.10
40 25 0.50
41 1 0.02
42 19 0.38
ACGTcount: A:0.20, C:0.18, G:0.37, T:0.25
Consensus pattern (40 bp):
TCCTACGTGATGAGGATGACTGATCAGGGGATGACACGGC
Found at i:4682388 original size:28 final size:28
Alignment explanation
Indices: 4682347--4682400 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4682337 AGGGATTATG
* **
4682347 GTTTCAAGAGAAACCGACTCAAAGATTT
1 GTTTCAAGAAAAACAAACTCAAAGATTT
4682375 GTTTCAAGAAAAACAAACTCAAAGAT
1 GTTTCAAGAAAAACAAACTCAAAGAT
4682401 GATGGTTTTC
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:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (28 bp):
GTTTCAAGAAAAACAAACTCAAAGATTT
Found at i:4682641 original size:65 final size:63
Alignment explanation
Indices: 4682570--4682708 Score: 188
Period size: 65 Copynumber: 2.2 Consensus size: 63
4682560 CAAAGATGGT
4682570 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCATAAAAGAAACTATCTCAAAAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTC--AAAAGAAACTATCTCAAAAGAGACA
*** * * * *
4682635 AAATTTTGTTTCCAAAGAAACATTTTCAATGATTTTTCAAAAGAAATTGTCTCAAGAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGACA
*
4682698 AAACTTTGTTT
1 AAATTTTGTTT
4682709 TTCAGAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
63 32 0.48
65 34 0.52
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.32
Consensus pattern (63 bp):
AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGACA
Found at i:4682708 original size:63 final size:64
Alignment explanation
Indices: 4682574--4682708 Score: 182
Period size: 63 Copynumber: 2.1 Consensus size: 64
4682564 GATGGTAAAT
*
4682574 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCATAAAAGAAACTATCTCAAAAGAGACAAAAT
1 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCA-AAAAGAAACTATCTCAAAAGAGACAAAAC
*** * * * *
4682639 TTTGTTTCCAAAGAAACATTTTCAATGATTTTTC-AAAAGAAATTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAAGAAACTATCTCAAAAGAGACAAAAC
4682702 TTTGTTT
1 TTTGTTT
4682709 TTCAGAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 32 0.52
65 30 0.48
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (64 bp):
TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAAGAAACTATCTCAAAAGAGACAAAAC
Found at i:4682956 original size:31 final size:31
Alignment explanation
Indices: 4682874--4682948 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
4682864 TCAAAATTCG
* *
4682874 TTTCAAGGGAAAC-GACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAAACTCAAAGAT-GTTTTA
4682905 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAACAAACTCAAAGATGTTT-TA
*
4682936 TTTCTAGAGAAAC
1 TTTCAAGAGAAAC
4682949 TGCCTCAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.67
32 10 0.26
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (31 bp):
TTTCAAGAGAAACAAACTCAAAGATGTTTTA
Found at i:4683004 original size:30 final size:29
Alignment explanation
Indices: 4682970--4683055 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 29
4682960 AAACAAAATT
* * * *
4682970 TGTTTTAATAGAAATGATCTCAAAGGTGGG
1 TGTTTCAAAAGAAATGA-CTCAAAGATAGG
* *
4683000 TGTTTCAAGAGAAACTAACTCAAAGATAGG
1 TGTTTCAAAAGAAA-TGACTCAAAGATAGG
*
4683030 TGTTTCAAAAGAAAGGACTCAAAGAT
1 TGTTTCAAAAGAAATGACTCAAAGAT
4683056 TTATTCACGA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 10 0.21
30 35 0.74
31 2 0.04
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (29 bp):
TGTTTCAAAAGAAATGACTCAAAGATAGG
Found at i:4683006 original size:97 final size:95
Alignment explanation
Indices: 4682806--4683027 Score: 234
Period size: 97 Copynumber: 2.3 Consensus size: 95
4682796 GATAAAACCT
* **
4682806 TGTTTCAAGAGAAACAAACTCAAAGATGATCTTGTTTTAAGAGAAAATGTCTCAAGAGTCAAAAT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-ATCTTGTTTTAAGAGAAAATGCCTCAAGAAACAAAAT
* *
4682871 TCGTTTCAAGGGAAACGACTCAAAGATGGTTT
65 TCGTTTCAAGAGAAACGACTCAAAGATGG-TG
* * *
4682903 TATTTCAAGAGAAACAAACTCAAAGAT-T-TTGTATTTCTAGAGAAACTGCCTCAAGGGAAACAA
1 TGTTTCAAGAGAAACAAACTCAAAGATATCTTGT-TTT-AAGAGAAAATGCCTCAA--GAAACAA
* * * * *
4682966 AATTTGTTTTAATAGAAATGATCTCAAAGGTGG-G
62 AATTCGTTTCAAGAGAAACGA-CTCAAAGATGGTG
*
4683000 TGTTTCAAGAGAAACTAACTCAAAGATA
1 TGTTTCAAGAGAAACAAACTCAAAGATA
4683028 GGTGTTTCAA
Statistics
Matches: 104, Mismatches: 15, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
94 4 0.04
95 4 0.04
96 14 0.13
97 51 0.49
98 21 0.20
99 10 0.10
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (95 bp):
TGTTTCAAGAGAAACAAACTCAAAGATATCTTGTTTTAAGAGAAAATGCCTCAAGAAACAAAATT
CGTTTCAAGAGAAACGACTCAAAGATGGTG
Found at i:4683292 original size:31 final size:32
Alignment explanation
Indices: 4683256--4683336 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 32
4683246 ATTTTTTCAT
*
4683256 TTTGTTTCAAGTGAAACAGACTTAAAGATCA-
1 TTTGTTTCAAGTGAAACAGACTCAAAGATCAG
** *
4683287 TTTGTTTCAAAAGAAAC-GACTCAAAGATGATG
1 TTTGTTTCAAGTGAAACAGACTCAAAGATCA-G
*
4683319 TTTGTTTCCAGTGAAACA
1 TTTGTTTCAAGTGAAACA
4683337 AATTCATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 11 0.28
31 15 0.38
32 14 0.35
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
TTTGTTTCAAGTGAAACAGACTCAAAGATCAG
Found at i:4683392 original size:36 final size:36
Alignment explanation
Indices: 4683352--4683489 Score: 165
Period size: 36 Copynumber: 3.8 Consensus size: 36
4683342 ATAATTTGGA
*
4683352 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
4683388 AAATTGTCTCAAACAAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
4683424 AAATTGTCTCAAGCGAGACAA-AGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACA-TTTGTTTTTAGAG
* *
4683459 AAAATGATCTCAAGTGAGACCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
4683490 AATGTGAACA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
35 9 0.10
36 76 0.86
37 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:4683736 original size:102 final size:102
Alignment explanation
Indices: 4683428--4683770 Score: 390
Period size: 102 Copynumber: 3.3 Consensus size: 102
4683418 TTAGAGAAAT
* * * * * *
4683428 TGTCTCAAGCGAGACAAAGTTTGTTTT-TGAGAAAATGATCTCAAGTGAGACCAACTTTGTTTAA
1 TGTCTCAAACAAGACGAAGTTTGTTTTAAGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAA
*
4683492 TGTGAACAAATTCAAAATTTGTATTTTCAAAGGAAAAA
66 TGTGAACAAATTCGAAATTTGTA-TTTCAAAGGAAAAA
* * * * * *
4683530 TGCCTCAAACGAGACGAA-TTTTTTTTAA-AGAAATAACAATCTCAAGTGAGATTAATTTTTGTT
1 TGTCTCAAACAAGACGAAGTTTGTTTTAAGAG-AA-AACGATCTCAAGTGAGATCAA-CTTTGTT
* *
4683593 TAAAGTGAATCAAATTCGAAATTTGTATATCAAAGGAAAAA
63 TAATGTGAA-CAAATTCGAAATTTGTATTTCAAAGGAAAAA
* * * *
4683634 TGTCTCAAGCAAGATGAAGTTTGTTTTAAGAGGAAGCGATCTCAAAG-GAGATCAACTTTGTTTA
1 TGTCTCAAACAAGACGAAGTTTGTTTTAAGAGAAAACGATCTC-AAGTGAGATCAACTTTGTTTA
4683698 ATGTGAACAAATTCGAAATTTGTATTTCAAAGGAAAAA
65 ATGTGAACAAATTCGAAATTTGTATTTCAAAGGAAAAA
* * *
4683736 TGTCTCAAACAATAAGAAATTTGTTTTGAA-AGAAA
1 TGTCTCAAACAAGACGAAGTTTGTTTT-AAGAGAAA
4683771 TTGTCTCAAG
Statistics
Matches: 202, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
101 9 0.04
102 74 0.37
103 33 0.16
104 55 0.27
105 29 0.14
106 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (102 bp):
TGTCTCAAACAAGACGAAGTTTGTTTTAAGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAA
TGTGAACAAATTCGAAATTTGTATTTCAAAGGAAAAA
Found at i:4683817 original size:35 final size:36
Alignment explanation
Indices: 4683752--4683870 Score: 159
Period size: 35 Copynumber: 3.3 Consensus size: 36
4683742 AAACAATAAG
* *
4683752 AAATTTGTTTTGAAAGAAATTGTCTCAAGCGAGACA
1 AAATTTGTTTTGAGAGAAACTGTCTCAAGCGAGACA
* *
4683788 AAATTTGTTTTTAGA-AAACTGTCTCAAGCGAGAGA
1 AAATTTGTTTTGAGAGAAACTGTCTCAAGCGAGACA
* * *
4683823 AAATTTGTTTTGAGATAAAGTGTCTCAAACGAGACAA
1 AAATTTGTTTTGAGAGAAACTGTCTCAAGCGAGAC-A
4683860 AAATTTGTTTT
1 AAATTTGTTTT
4683871 AAAATTCTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
35 32 0.44
36 29 0.40
37 12 0.16
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (36 bp):
AAATTTGTTTTGAGAGAAACTGTCTCAAGCGAGACA
Found at i:4684251 original size:16 final size:16
Alignment explanation
Indices: 4684230--4684269 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
4684220 CTCATGTAAT
**
4684230 ATGTATGTATGTGTTG
1 ATGTATGTATGCATTG
*
4684246 ATGTATATATGCATTG
1 ATGTATGTATGCATTG
4684262 ATGTATGT
1 ATGTATGT
4684270 TTTCTTGATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (16 bp):
ATGTATGTATGCATTG
Found at i:4692562 original size:3 final size:3
Alignment explanation
Indices: 4692554--4692610 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
4692544 CTACAAAATG
4692554 TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TTAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
4692598 TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA
4692611 ATAACACAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.16
3 38 0.78
4 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:4692579 original size:20 final size:20
Alignment explanation
Indices: 4692554--4692610 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
4692544 CTACAAAATG
4692554 TAATAATAATAATAAAATAA
1 TAATAATAATAATAAAATAA
*
4692574 TAATAATAATAAT-TAATAA
1 TAATAATAATAATAAAATAA
4692593 TAA-AATAA-AATAAAATAA
1 TAATAATAATAATAAAATAA
4692611 ATAACACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 3 0.09
18 10 0.29
19 8 0.24
20 13 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAATAATAATAATAAAATAA
Found at i:4692614 original size:14 final size:15
Alignment explanation
Indices: 4692555--4692632 Score: 76
Period size: 14 Copynumber: 5.3 Consensus size: 15
4692545 TACAAAATGT
4692555 AATAATAAT-AATAA
1 AATAATAATAAATAA
4692569 AATAATAAT-AATAA
1 AATAATAATAAATAA
4692583 TAATTAATAATAAAATAA
1 -AA-TAATAAT-AAATAA
4692601 AATAA-AATAAATAA
1 AATAATAATAAATAA
* *
4692615 CACAA-AATAAA-AA
1 AATAATAATAAATAA
4692628 AATAA
1 AATAA
4692633 AAAAAAAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.09
14 29 0.52
15 5 0.09
16 10 0.18
17 2 0.04
18 5 0.09
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAATAAATAA
Found at i:4692624 original size:32 final size:31
Alignment explanation
Indices: 4692555--4692639 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 31
4692545 TACAAAATGT
* *
4692555 AATAATAATAATAAAATAATAATAATAATAATT
1 AATAATAA-AATAAAATAA-AATAATAACAATA
4692588 AATAATAAAATAAAATAAAATAAATAACACA-A
1 AATAATAAAATAAAATAAAAT-AATAACA-ATA
* *
4692620 AATAAAAAAATAAAAAAAAA
1 AATAATAAAATAAAATAAAA
4692640 AGATCCAGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 3 0.07
32 34 0.74
33 9 0.20
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.22
Consensus pattern (31 bp):
AATAATAAAATAAAATAAAATAATAACAATA
Found at i:4700145 original size:40 final size:40
Alignment explanation
Indices: 4700090--4700171 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
4700080 ATGTCAGGAC
4700090 TAAAGTTAAATGCCTCAAAGTGTGAATTATTTGCTGCATG
1 TAAAGTTAAATGCCTCAAAGTGTGAATTATTTGCTGCATG
4700130 TAAAGTTAAATGCCTCAAAGTGTGAATTATTTGCTGCATG
1 TAAAGTTAAATGCCTCAAAGTGTGAATTATTTGCTGCATG
4700170 TA
1 TA
4700172 TGACTACCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (40 bp):
TAAAGTTAAATGCCTCAAAGTGTGAATTATTTGCTGCATG
Found at i:4701594 original size:21 final size:21
Alignment explanation
Indices: 4701565--4701608 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4701555 ATTAGATTGG
4701565 ATCCAAAATATT-TCAAAATTT
1 ATCCAAAAT-TTATCAAAATTT
* *
4701586 ATCCCAAATTTATCAATATTT
1 ATCCAAAATTTATCAAAATTT
4701607 AT
1 AT
4701609 AAAAAGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (21 bp):
ATCCAAAATTTATCAAAATTT
Found at i:4705166 original size:40 final size:41
Alignment explanation
Indices: 4705106--4705183 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
4705096 ATATATCAAA
* *
4705106 GATTTAATTGAGAAATAAGTACTCAAATTATATATTTTATT
1 GATTTAATTGAAAAATAAGTACTCAAACTATATATTTTATT
* *
4705147 GATTTAATT-AAAAATAAGTATTCAAACTATATCTTTT
1 GATTTAATTGAAAAATAAGTACTCAAACTATATATTTT
4705184 GTTCATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 24 0.73
41 9 0.27
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (41 bp):
GATTTAATTGAAAAATAAGTACTCAAACTATATATTTTATT
Found at i:4705349 original size:30 final size:30
Alignment explanation
Indices: 4705313--4705372 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4705303 TATGACACAG
4705313 AGTCATGAGCAAGATTAGATAATTGAATAT
1 AGTCATGAGCAAGATTAGATAATTGAATAT
4705343 AGTCATGAGCAAGATTAGATAATTGAATAT
1 AGTCATGAGCAAGATTAGATAATTGAATAT
4705373 GCTCAGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (30 bp):
AGTCATGAGCAAGATTAGATAATTGAATAT
Found at i:4712765 original size:41 final size:41
Alignment explanation
Indices: 4712712--4713136 Score: 480
Period size: 41 Copynumber: 10.4 Consensus size: 41
4712702 CAAAATAGTA
* * *
4712712 ACTTTAGCGGCGTTTTTATAAAAACGTCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* * * * *
4712753 ACTTTAGTGGCGTTTTTATATAAAACGCCACGATAGAGTAGT
1 ACTTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGACTCGT
** *
4712795 ACTTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTC-A
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
*** * * * *
4712835 ACTTTAGCATCGTTTTTATACAAAATGCCGCGATAGAGTAGT
1 ACTTTAGTGGCGTTTTTATAC-AAACGCCGCTATAGACTCGT
* *
4712877 ACTTTAGTGGCGTTTTTATACAAATGCCGCTATAGACTTGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* *
4712918 ACTTTAGTAGCGTTTTTATACAAACACCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* * * * * * *
4712959 AATTTTGTGGCATTTGTGTTTACAAATGCCGCTATAGGCTTGT
1 ACTTTAGTGGCGTTT-T-TATACAAACGCCGCTATAGACTCGT
*
4713002 ACTTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* *
4713043 ACATTAGTGGTGTTTTTATACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* *
4713084 ACATTAGTGGCG-TTTTATACAAACGCCGC--TAGACTTGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
4713122 ACTTTAGTGGCGTTT
1 ACTTTAGTGGCGTTT
4713137 GTTTTTTAAA
Statistics
Matches: 325, Mismatches: 53, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
38 19 0.06
39 2 0.01
40 37 0.11
41 181 0.56
42 54 0.17
43 32 0.10
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
Found at i:4713144 original size:125 final size:122
Alignment explanation
Indices: 4712715--4713136 Score: 474
Period size: 125 Copynumber: 3.4 Consensus size: 122
4712705 AATAGTAACT
* * * *
4712715 TTAGCGGCGTTTTTATAAAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTTATATAAAACG
1 TTAGCGGCGTTTTTATACAAACGCCGC-ATAGACTTGTACTTTAGTGGCGTTTTTATA-CAAACG
* * * * * *
4712780 CCACGATAGAGTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTC-AACT
64 CCGCTATAGACTAGTACTTTAGTAGCGTTTTTATACAAACGCCGCTATAGACTCGTACA
** * * * *
4712838 TTAGCATCGTTTTTATACAAAATGCCGCGATAGAGTAGTACTTTAGTGGCGTTTTTATACAAATG
1 TTAGCGGCGTTTTTATAC-AAACGCCGC-ATAGACTTGTACTTTAGTGGCGTTTTTATACAAACG
* *
4712903 CCGCTATAGACTTGTACTTTAGTAGCGTTTTTATACAAACACCGCTATAGACTCGTA-A
64 CCGCTATAGACTAGTACTTTAGTAGCGTTTTTATACAAACGCCGCTATAGACTCGTACA
* * * * * *
4712961 TTTTGTGGCATTTGTGTTTACAAATGCCGCTATAGGCTTGTACTTTAGTGGCGTTTTTATACAAA
1 -TTAGCGGCGTTT-T-TATACAAACGCCGC-ATAGACTTGTACTTTAGTGGCGTTTTTATACAAA
* * * * *
4713026 CGTCGCTATAGACTCGTACATTAGTGGTGTTTTTATACAAACGCCGCTATAGACTCGTACA
62 CGCCGCTATAGACTAGTACTTTAGTAGCGTTTTTATACAAACGCCGCTATAGACTCGTACA
*
4713087 TTAGTGGCG-TTTTATACAAACGCCGC-TAGACTTGTACTTTAGTGGCGTTT
1 TTAGCGGCGTTTTTATACAAACGCCGCATAGACTTGTACTTTAGTGGCGTTT
4713137 GTTTTTTAAA
Statistics
Matches: 253, Mismatches: 40, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
120 23 0.09
122 12 0.05
123 68 0.27
124 45 0.18
125 100 0.40
126 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (122 bp):
TTAGCGGCGTTTTTATACAAACGCCGCATAGACTTGTACTTTAGTGGCGTTTTTATACAAACGCC
GCTATAGACTAGTACTTTAGTAGCGTTTTTATACAAACGCCGCTATAGACTCGTACA
Found at i:4713546 original size:4 final size:4
Alignment explanation
Indices: 4713531--4713561 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
4713521 ACAGTAGAGA
*
4713531 GAGT GAGC GAGT GAGT GAGT GAGT GAGT GAG
1 GAGT GAGT GAGT GAGT GAGT GAGT GAGT GAG
4713562 GGGTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.52, T:0.19
Consensus pattern (4 bp):
GAGT
Found at i:4717727 original size:36 final size:36
Alignment explanation
Indices: 4717687--4717766 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
4717677 TGAACGGTTG
* * *
4717687 GGAATTTAATCAACATTCTACTTCTGCTGTTCAAGT
1 GGAATTTAATCAACATTCTACTGCTGATGTTCAACT
*
4717723 GGAATTTAATTAACATTCTACTGCTGATGTTCAACT
1 GGAATTTAATCAACATTCTACTGCTGATGTTCAACT
4717759 GGAATTTA
1 GGAATTTA
4717767 GTTACATTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (36 bp):
GGAATTTAATCAACATTCTACTGCTGATGTTCAACT
Found at i:4718660 original size:21 final size:21
Alignment explanation
Indices: 4718636--4718694 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
4718626 TGATTTATTA
**
4718636 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
4718657 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
4718678 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
4718695 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:4718910 original size:43 final size:44
Alignment explanation
Indices: 4718841--4719072 Score: 253
Period size: 43 Copynumber: 5.4 Consensus size: 44
4718831 CTATAGATAT
* *** * *
4718841 GACCTTTTGCGGCGTTTGTTCTAAAAAATGCCGCTATATAC-C-A
1 GACCTATTGCGGCGTTTGTGAGAAAAAACGCCGCTAAAT-CTCAA
* * *
4718884 GATCTTTTGCGGTGTTTGTGAG-AAAAACGCCGCTAAATCTCAA
1 GACCTATTGCGGCGTTTGTGAGAAAAAACGCCGCTAAATCTCAA
*
4718927 GACCTATTGCGGCGTTTGTG-GGAAAAACGCCGCTAAATCTCAA
1 GACCTATTGCGGCGTTTGTGAGAAAAAACGCCGCTAAATCTCAA
* *
4718970 CACCTATTGCGGCGTTTGTGAG-AAAAACTCCGCTAAATCTCAA
1 GACCTATTGCGGCGTTTGTGAGAAAAAACGCCGCTAAATCTCAA
* * *
4719013 CACCTATTGCGGCGTTTGTTG-G-AAAAATGCCGCTAAATATCAA
1 GACCTATTGCGGCGTTTG-TGAGAAAAAACGCCGCTAAATCTCAA
*
4719056 CACCTATTGCGGCGTTT
1 GACCTATTGCGGCGTTT
4719073 TTTGTTACCA
Statistics
Matches: 169, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 16 0.09
43 149 0.88
44 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (44 bp):
GACCTATTGCGGCGTTTGTGAGAAAAAACGCCGCTAAATCTCAA
Found at i:4718938 original size:86 final size:86
Alignment explanation
Indices: 4718841--4719072 Score: 315
Period size: 86 Copynumber: 2.7 Consensus size: 86
4718831 CTATAGATAT
* ** * * * * *
4718841 GACCTTTTGCGGCGTTTGTTCTAAAAAATGCCGCTATATAC-C-AGATCTTTTGCGGTGTTTGTG
1 GACCTATTGCGGCGTTTGTT-GGAAAAATGCCGCTAAAT-CTCAACACCTATTGCGGCGTTTGTG
4718904 AGAAAAACGCCGCTAAATCTCAA
64 AGAAAAACGCCGCTAAATCTCAA
* *
4718927 GACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGAG
1 GACCTATTGCGGCGTTTGTTGGAAAAATGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGAG
*
4718992 AAAAACTCCGCTAAATCTCAA
66 AAAAACGCCGCTAAATCTCAA
* *
4719013 CACCTATTGCGGCGTTTGTTGGAAAAATGCCGCTAAATATCAACACCTATTGCGGCGTTT
1 GACCTATTGCGGCGTTTGTTGGAAAAATGCCGCTAAATCTCAACACCTATTGCGGCGTTT
4719073 TTTGTTACCA
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
84 1 0.01
85 15 0.12
86 113 0.88
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (86 bp):
GACCTATTGCGGCGTTTGTTGGAAAAATGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGAG
AAAAACGCCGCTAAATCTCAA
Found at i:4720081 original size:18 final size:18
Alignment explanation
Indices: 4720045--4720078 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4720035 TTAGAGAGAC
*
4720045 AAAAAATATAATATCAAT
1 AAAAAATATAATATAAAT
4720063 AAAAAATATAA-ATAAA
1 AAAAAATATAATATAAA
4720079 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAATATAATATAAAT
Found at i:4722687 original size:56 final size:57
Alignment explanation
Indices: 4722625--4722737 Score: 183
Period size: 56 Copynumber: 2.0 Consensus size: 57
4722615 ATATGTGGCC
* *
4722625 CATTTGGTTTATAATAAAAGTTAGGGTAAATTATATAAAT-GTCATTAAAGTATGAA
1 CATTTGGGTTATAATAAAACTTAGGGTAAATTATATAAATGGTCATTAAAGTATGAA
* *
4722681 CATTTGGGTTATAATCAAACTTTGGGTAAATTATATAAATGGTCATTAAAGTATGAA
1 CATTTGGGTTATAATAAAACTTAGGGTAAATTATATAAATGGTCATTAAAGTATGAA
4722738 TAAATTTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 36 0.69
57 16 0.31
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (57 bp):
CATTTGGGTTATAATAAAACTTAGGGTAAATTATATAAATGGTCATTAAAGTATGAA
Found at i:4723239 original size:29 final size:29
Alignment explanation
Indices: 4723206--4723280 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
4723196 CATCGAAGTC
*
4723206 ATCATAATCAACGACAGAGTAACCATCTT
1 ATCATAACCAACGACAGAGTAACCATCTT
* *
4723235 ATCATAACCAACGACGGCGTAACCATCTT
1 ATCATAACCAACGACAGAGTAACCATCTT
*
4723264 GTCATAACCAACGACAG
1 ATCATAACCAACGACAG
4723281 TGAAGTCACC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (29 bp):
ATCATAACCAACGACAGAGTAACCATCTT
Found at i:4723529 original size:22 final size:22
Alignment explanation
Indices: 4723474--4723533 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
4723464 TAAGAGGTAG
* *
4723474 AATTATTCATGTGAATATGTGT
1 AATTATTCATATGAATAGGTGT
* * *
4723496 ATTTTTTTCATATGACTAGGTGT
1 A-ATTATTCATATGAATAGGTGT
4723519 AATTATTCATATGAA
1 AATTATTCATATGAA
4723534 AAGGCATGGC
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (22 bp):
AATTATTCATATGAATAGGTGT
Found at i:4723890 original size:22 final size:22
Alignment explanation
Indices: 4723849--4723902 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
4723839 TAAACCCCAA
4723849 AACCCAAAA--CCAAAACTGAT
1 AACCCAAAACTCCAAAACTGAT
*
4723869 AACCCAAAACTCCAAAATTGAT
1 AACCCAAAACTCCAAAACTGAT
*
4723891 AATCCAAAACTC
1 AACCCAAAACTC
4723903 AAATACTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 9 0.30
22 21 0.70
ACGTcount: A:0.52, C:0.30, G:0.04, T:0.15
Consensus pattern (22 bp):
AACCCAAAACTCCAAAACTGAT
Found at i:4724142 original size:21 final size:21
Alignment explanation
Indices: 4724100--4724148 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
4724090 CTCAAACTCT
*
4724100 CAAAA-TCCTAACCAATAAAC
1 CAAAACTCCAAACCAATAAAC
4724120 CATAAACTCCAAACCAA-AAAC
1 CA-AAACTCCAAACCAATAAAC
4724141 CAAAACTC
1 CAAAACTC
4724149 TTTCAGGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 9 0.35
22 9 0.35
ACGTcount: A:0.55, C:0.33, G:0.00, T:0.12
Consensus pattern (21 bp):
CAAAACTCCAAACCAATAAAC
Found at i:4735055 original size:63 final size:63
Alignment explanation
Indices: 4734901--4735057 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 63
4734891 TTCCCTTGAA
* * * * * * *
4734901 GTGCATCGATGCATTCAACAGTGCATCGATGCACCAATCACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACTC-CCTGTGCATCGATGCACCAATCACATTCAATGTTTCCATTATAAGGG
* * * *
4734965 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTACATTCAATGTTTCCATTA-ATATGG
1 G-TGCATCGATGCACTCCCTGTGCATCGATGCACCAATCACATTCAATGTTTCCATTATA-AGGG
4735029 GTGCATCGATGCACTCCCTGTGCATCGAT
1 GTGCATCGATGCACTCCCTGTGCATCGAT
4735058 ACACTCTGTA
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
63 27 0.35
64 37 0.47
65 14 0.18
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTCCCTGTGCATCGATGCACCAATCACATTCAATGTTTCCATTATAAGGG
Found at i:4736490 original size:14 final size:14
Alignment explanation
Indices: 4736471--4736497 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4736461 ATAGAGAGGG
4736471 TGTATCGATACATA
1 TGTATCGATACATA
4736485 TGTATCGATACAT
1 TGTATCGATACAT
4736498 TATGCCCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
TGTATCGATACATA
Found at i:4760129 original size:43 final size:43
Alignment explanation
Indices: 4760067--4760151 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
4760057 TCAACAATAT
*
4760067 ATGATAGTTAGACTCTGTAGAAATATGAATATAATTAGGTCTC
1 ATGATAGTTAGACTCTGTAGAAATATAAATATAATTAGGTCTC
*
4760110 ATGATAGTTAGACTGTGTAGAAATATAAATATAATTAGGTCT
1 ATGATAGTTAGACTCTGTAGAAATATAAATATAATTAGGTCT
4760152 TATTTTGTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (43 bp):
ATGATAGTTAGACTCTGTAGAAATATAAATATAATTAGGTCTC
Found at i:4765029 original size:15 final size:15
Alignment explanation
Indices: 4765009--4765039 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4764999 CAAAAAATAG
4765009 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
4765024 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
4765039 A
1 A
4765040 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:4765236 original size:20 final size:20
Alignment explanation
Indices: 4765200--4765237 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4765190 ATCCTATTCC
**
4765200 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
4765220 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
4765238 GTGAACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:4768867 original size:65 final size:65
Alignment explanation
Indices: 4768724--4768848 Score: 166
Period size: 65 Copynumber: 1.9 Consensus size: 65
4768714 AAGAGCCAGG
* *
4768724 AGTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAACCTGGGGTGTATCGATGTATGGTC
1 AGTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCTGGGGTGTATCGATGCAT-GTC
4768789 T
65 T
* * *
4768790 A-TGCATCGGTACACATAATGCATTCGATG-TTCAATAAAA-TTAGGTGTGTATCGATGCAT
1 AGTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCT-GGGGTGTATCGATGCAT
4768849 TCAATAGTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
63 1 0.02
64 25 0.47
65 26 0.49
66 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (65 bp):
AGTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCTGGGGTGTATCGATGCATGTCT
Found at i:4769200 original size:12 final size:13
Alignment explanation
Indices: 4769172--4769204 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4769162 TAAGATTTTC
*
4769172 TTTTGAAATTCAT
1 TTTTGAAATTCAA
4769185 TTTTGAAA-TCAA
1 TTTTGAAATTCAA
4769197 TTTTGAAA
1 TTTTGAAA
4769205 ATTACTCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (13 bp):
TTTTGAAATTCAA
Found at i:4770978 original size:13 final size:12
Alignment explanation
Indices: 4770949--4770982 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4770939 AATAGGCAAT
*
4770949 TTTTGAAAACTA
1 TTTTGAAAACAA
4770961 TTTTGAAAACAA
1 TTTTGAAAACAA
4770973 TGTTTGAAAA
1 T-TTTGAAAA
4770983 ATCAATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (12 bp):
TTTTGAAAACAA
Found at i:4771510 original size:44 final size:44
Alignment explanation
Indices: 4771461--4771563 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
4771451 TACACTCTTG
* * *
4771461 AGTGTATCGATGCACATTCAAGGCATGCATCGGTGCATCT-TCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACA-CTGTCAC
* * *
4771505 AGTGTATCGATGAATATTCAAGGAATGCATTGGTACACTGTCAC
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTGTCAC
4771549 AGTGTATCGATGCAC
1 AGTGTATCGATGCAC
4771564 TTTGCACAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
43 2 0.04
44 48 0.96
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTGTCAC
Found at i:4780806 original size:24 final size:25
Alignment explanation
Indices: 4780762--4780808 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
4780752 CATATTTTAG
*
4780762 TTTATTTTAGCTTACAAATTAATAT
1 TTTATTTTAGCTTAAAAATTAATAT
4780787 TTTA-TTTAGC-TAAAACATTAAT
1 TTTATTTTAGCTTAAAA-ATTAAT
4780809 TTAAGGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (25 bp):
TTTATTTTAGCTTAAAAATTAATAT
Done.