Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 90 of 204
Found at i:27572869 original size:9 final size:9
Alignment explanation
Indices: 27572855--27572885 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27572845 GTTAAACGAA
27572855 TCGAGTTAT
1 TCGAGTTAT
*
27572864 TCGAGTTAA
1 TCGAGTTAT
27572873 TCGAGTTAT
1 TCGAGTTAT
27572882 TCGA
1 TCGA
27572886 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:27572955 original size:9 final size:9
Alignment explanation
Indices: 27572938--27572974 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
27572928 TGAGTTTTCG
27572938 AATTCGAAT
1 AATTCGAAT
*
27572947 AACTCGAAT
1 AATTCGAAT
27572956 AATTCGAAT
1 AATTCGAAT
27572965 AATTCGAAT
1 AATTCGAAT
27572974 A
1 A
27572975 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:27576607 original size:96 final size:96
Alignment explanation
Indices: 27576433--27576608 Score: 212
Period size: 96 Copynumber: 1.8 Consensus size: 96
27576423 AGATATTCTG
* * **
27576433 GTTTGGCGAACACTTTCACTACCCAAAATTTCCAGCACATTGAATTCTCTATTATGGTGGAACCA
1 GTTTGGCGAACACTTTCACTACCCAAAATTTCCAGCACATTGAATCCTCTATTATAGCAGAACCA
*
27576498 TAGCGAATTCATATAACATGGAAATACTCTA
66 TAGCGAATACATATAACATGGAAATACTCTA
* * * * *
27576529 GTTTGGC-AGACACTTTCACTACTCATAACTTT-GAGCACCTTGAATCCTCTATTCTAGCAGAAC
1 GTTTGGCGA-ACACTTTCACTACCCA-AAATTTCCAGCACATTGAATCCTCTATTATAGCAGAAC
* *
27576592 CATAGTGGATACATATA
64 CATAGCGAATACATATA
27576609 TCAATTATAT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
95 1 0.02
96 60 0.91
97 5 0.08
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (96 bp):
GTTTGGCGAACACTTTCACTACCCAAAATTTCCAGCACATTGAATCCTCTATTATAGCAGAACCA
TAGCGAATACATATAACATGGAAATACTCTA
Found at i:27576770 original size:23 final size:23
Alignment explanation
Indices: 27576744--27576815 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
27576734 AATACGTTGT
* *
27576744 AAAGGCATTATAGATTATGCCAC
1 AAAGGCATTATAGAATACGCCAC
* * * *
27576767 AAAGGTATTTTGGAATACGTCAC
1 AAAGGCATTATAGAATACGCCAC
* * *
27576790 AAAGGCATTCTGGAATACGACAC
1 AAAGGCATTATAGAATACGCCAC
27576813 AAA
1 AAA
27576816 AGCTTATTCC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (23 bp):
AAAGGCATTATAGAATACGCCAC
Found at i:27582327 original size:106 final size:106
Alignment explanation
Indices: 27582142--27582353 Score: 406
Period size: 106 Copynumber: 2.0 Consensus size: 106
27582132 AATAATATTG
27582142 AAAAATTCAATACAAGTATGTTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
1 AAAAATTCAATACAAGTATGTTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
27582207 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
66 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
*
27582248 AAAAATTCAATACATGTATGTTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
1 AAAAATTCAATACAAGTATGTTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
*
27582313 ACAATAATGCTTGATTTGATACTTAGTGATTTCTGTGACAT
66 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
27582354 GCAAAATACT
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.32
Consensus pattern (106 bp):
AAAAATTCAATACAAGTATGTTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
Found at i:27584329 original size:26 final size:26
Alignment explanation
Indices: 27584300--27584355 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
27584290 TGGTTTCAAG
27584300 ATAACT-TCGCCAC-TATGGCTTTCCAA
1 ATAACTAT-GCCACATA-GGCTTTCCAA
*
27584326 ATAA-TATGCCACATAGGCTTTTCAA
1 ATAACTATGCCACATAGGCTTTCCAA
27584351 ATAAC
1 ATAAC
27584356 GTCCTACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (26 bp):
ATAACTATGCCACATAGGCTTTCCAA
Found at i:27585338 original size:118 final size:118
Alignment explanation
Indices: 27585130--27585357 Score: 343
Period size: 118 Copynumber: 1.9 Consensus size: 118
27585120 CCTACTACAG
* * *
27585130 ATAGTTTACTAATGTTTCCACTATATGTGACCCCCATGCAAGGTCTTCCTCTCACATCCTACTGT
1 ATAGTTTACTAATGTTTCAACTATATGTGACCCCCATACAAGGTCTTCCACTCACATCCTACTGT
* **
27585195 TCTTACATGTTTTAACATTCTTACTCTTCAACAATTGTAACATACAGAGATAT
66 TCTTACATATTTTAACATTCTTACTCTTCAACAATCATAACATACAGAGATAT
*
27585248 ATAGTTTACTAATGTCTT-AACTATATGTGACCCCCATACAAGGTCTTCCACTTACA-CCTTACT
1 ATAGTTTACTAATGT-TTCAACTATATGTGACCCCCATACAAGGTCTTCCACTCACATCC-TACT
* *
27585311 GTTCTTACGTATTTTAACATTTTTACTCTTCAACAATCATAACATAC
64 GTTCTTACATATTTTAACATTCTTACTCTTCAACAATCATAACATAC
27585358 TGACCTATAA
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
117 2 0.02
118 95 0.96
119 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.38
Consensus pattern (118 bp):
ATAGTTTACTAATGTTTCAACTATATGTGACCCCCATACAAGGTCTTCCACTCACATCCTACTGT
TCTTACATATTTTAACATTCTTACTCTTCAACAATCATAACATACAGAGATAT
Found at i:27586341 original size:31 final size:34
Alignment explanation
Indices: 27586271--27586344 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 34
27586261 AACCTCTCAC
* *
27586271 CTTCTTTTTGTTCTTTGCCTGCTACGTTCTTTCT
1 CTTCTTTTTGTTCTTTGACTGATACGTTCTTTCT
* *
27586305 ATTCTTTTTGTTC-TTGACT-AT-CGTTTTTTCT
1 CTTCTTTTTGTTCTTTGACTGATACGTTCTTTCT
27586336 CTTCTTTTT
1 CTTCTTTTT
27586345 TATTTGTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 17 0.49
32 1 0.03
33 5 0.14
34 12 0.34
ACGTcount: A:0.05, C:0.22, G:0.09, T:0.64
Consensus pattern (34 bp):
CTTCTTTTTGTTCTTTGACTGATACGTTCTTTCT
Found at i:27588605 original size:27 final size:27
Alignment explanation
Indices: 27588554--27588605 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
27588544 GGTGTTAATC
* *
27588554 AAAATTTATATCTTTTGGTTATTGATT
1 AAAAGTTATATCTTTTGATTATTGATT
* *
27588581 AAAAGTTATATCTTTTTATTTTTGA
1 AAAAGTTATATCTTTTGATTATTGA
27588606 CAAAGAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.56
Consensus pattern (27 bp):
AAAAGTTATATCTTTTGATTATTGATT
Found at i:27591603 original size:22 final size:22
Alignment explanation
Indices: 27591568--27591617 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
27591558 ACTATCGGTT
*
27591568 TTATTTTACTATTACTATTATTA
1 TTATTTAACTATTACTATTA-TA
*
27591591 TTATTTAAC-ATTATTATTATA
1 TTATTTAACTATTACTATTATA
27591612 TT-TTTA
1 TTATTTA
27591618 TTAATCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 4 0.16
22 9 0.36
23 8 0.32
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTTAACTATTACTATTATA
Found at i:27596442 original size:39 final size:39
Alignment explanation
Indices: 27596399--27596498 Score: 110
Period size: 39 Copynumber: 2.6 Consensus size: 39
27596389 CATGTTTTTG
* *
27596399 AGTATTGTGATATATACTTGAATGTTAAGTGATTATATA
1 AGTATTGTGATATATACTTAAATGTTAAGTGAATATATA
* * * *
27596438 AGTATTGTTATATATGCTTAAATGTTATGTGAATATATG
1 AGTATTGTGATATATACTTAAATGTTAAGTGAATATATA
* * * *
27596477 TGTAATGTGATACATGCTTAAA
1 AGTATTGTGATATATACTTAAA
27596499 AGTGAATATG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (39 bp):
AGTATTGTGATATATACTTAAATGTTAAGTGAATATATA
Found at i:27604476 original size:7 final size:7
Alignment explanation
Indices: 27604464--27604488 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27604454 ACACGGGTAG
27604464 GGGTTTA
1 GGGTTTA
27604471 GGGTTTA
1 GGGTTTA
27604478 GGGTTTA
1 GGGTTTA
27604485 GGGT
1 GGGT
27604489 GAAAGGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (7 bp):
GGGTTTA
Found at i:27606725 original size:70 final size:67
Alignment explanation
Indices: 27606606--27606738 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
27606596 TAAACAAATA
* ** *
27606606 TAATGGTTTTGCCTTTTAACTTAATGAGTAAACATTTATCAAAATGACGTAGCTTTGCCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAAAGACGTAGCTTTGCCTTTTAA
27606671 TT
66 TT
* *
27606673 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAAAGACGTAGTTTTGTCTTT
1 TAATGGTTTTGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAAAGACGTAGCTTTGCCTTT
27606738 T
63 T
27606739 CTTATTCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 19 0.33
68 3 0.05
69 2 0.04
70 33 0.58
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAAAGACGTAGCTTTGCCTTTTAA
TT
Found at i:27607634 original size:20 final size:20
Alignment explanation
Indices: 27607609--27607658 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
27607599 TTTTAGGGAT
*
27607609 GCCTATGTGGCATCTTGTCA
1 GCCTATGTGGCATCCTGTCA
* *
27607629 GCCTATATGACATCCTGTCA
1 GCCTATGTGGCATCCTGTCA
*
27607649 GCCTTTGTGG
1 GCCTATGTGG
27607659 TGTACTCTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (20 bp):
GCCTATGTGGCATCCTGTCA
Found at i:27607754 original size:27 final size:27
Alignment explanation
Indices: 27607696--27607767 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
27607686 ATGAACCGCT
27607696 TTTGTGGCATACTCTGTATATATAACC
1 TTTGTGGCATACTCTGTATATATAACC
* * **
27607723 GTTGTGGCATACTTTGTATATATGGCC
1 TTTGTGGCATACTCTGTATATATAACC
* *
27607750 TTTGTGACATATTCTGTA
1 TTTGTGGCATACTCTGTA
27607768 ATAATGACTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.43
Consensus pattern (27 bp):
TTTGTGGCATACTCTGTATATATAACC
Found at i:27612557 original size:2 final size:2
Alignment explanation
Indices: 27612550--27612579 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27612540 TTAGATATGA
27612550 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
27612580 GTCATATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27615147 original size:342 final size:342
Alignment explanation
Indices: 27614522--27615204 Score: 1348
Period size: 342 Copynumber: 2.0 Consensus size: 342
27614512 TCCTTTTTTA
27614522 ATCCCAGAATACTCGGATTTTTAAGTATATTTGAAAAAAATACATATTGGTGCTGACGAACAAAA
1 ATCCCAGAATACTCGGATTTTTAAGTATATTTGAAAAAAATACATATTGGTGCTGACGAACAAAA
27614587 TGTCAATAAAAAGAAAATCATTTTTTATAGACTGGACAATCATTAGAGGATGATAGAGGGTGGTG
66 TGTCAATAAAAAGAAAATCATTTTTTATAGACTGGACAATCATTAGAGGATGATAGAGGGTGGTG
27614652 CAGATGGTGAGATGGCTGGTACCAACATACAGTGTAGAAAACAAGTAATTTTGTACAAAATTTTA
131 CAGATGGTGAGATGGCTGGTACCAACATACAGTGTAGAAAACAAGTAATTTTGTACAAAATTTTA
27614717 CATTTGAGTTATTTTCATAAATAATCAATTTATTTGAATAAGTTATGAAAAAAAACTTTTAAGAA
196 CATTTGAGTTATTTTCATAAATAATCAATTTATTTGAATAAGTTATGAAAAAAAACTTTTAAGAA
27614782 TTAGGATATCCCAAACTAGGCGGCTAATTTTAATAAAATGACGTTTTCTTAAAAAAAAAGTTCAC
261 TTAGGATATCCCAAACTAGGCGGCTAATTTTAATAAAATGACGTTTTCTTAAAAAAAAAGTTCAC
27614847 TTATTAAATTAAAAAAT
326 TTATTAAATTAAAAAAT
* *
27614864 ATCCCAGAATACTCGTATTTTTAAGTATATTTGAAAAAAATACATATTGGTGTTGACGAACAAAA
1 ATCCCAGAATACTCGGATTTTTAAGTATATTTGAAAAAAATACATATTGGTGCTGACGAACAAAA
27614929 TGTCAATAAAAAGAAAATCATTTTTTATAGACTGGACAATCATTAGAGGATGATAGAGGGTGGTG
66 TGTCAATAAAAAGAAAATCATTTTTTATAGACTGGACAATCATTAGAGGATGATAGAGGGTGGTG
27614994 CAGATGGTGAGATGGCTGGTACCAACATACAGTGTAGAAAACAAGTAATTTTGTACAAAATTTTA
131 CAGATGGTGAGATGGCTGGTACCAACATACAGTGTAGAAAACAAGTAATTTTGTACAAAATTTTA
27615059 CATTTGAGTTATTTTCATAAATAATCAATTTATTTGAATAAGTTATGAAAAAAAACTTTTAAGAA
196 CATTTGAGTTATTTTCATAAATAATCAATTTATTTGAATAAGTTATGAAAAAAAACTTTTAAGAA
27615124 TTAGGATATCCCAAACTAGGCGGCTAATTTTAATAAAATGACGTTTTCTTAAAAAAAAAGTTCAC
261 TTAGGATATCCCAAACTAGGCGGCTAATTTTAATAAAATGACGTTTTCTTAAAAAAAAAGTTCAC
27615189 TTATTAAATTAAAAAA
326 TTATTAAATTAAAAAA
27615205 AAATATTCTC
Statistics
Matches: 339, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
342 339 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (342 bp):
ATCCCAGAATACTCGGATTTTTAAGTATATTTGAAAAAAATACATATTGGTGCTGACGAACAAAA
TGTCAATAAAAAGAAAATCATTTTTTATAGACTGGACAATCATTAGAGGATGATAGAGGGTGGTG
CAGATGGTGAGATGGCTGGTACCAACATACAGTGTAGAAAACAAGTAATTTTGTACAAAATTTTA
CATTTGAGTTATTTTCATAAATAATCAATTTATTTGAATAAGTTATGAAAAAAAACTTTTAAGAA
TTAGGATATCCCAAACTAGGCGGCTAATTTTAATAAAATGACGTTTTCTTAAAAAAAAAGTTCAC
TTATTAAATTAAAAAAT
Found at i:27616571 original size:29 final size:29
Alignment explanation
Indices: 27616521--27616577 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
27616511 AACCTTTACA
*
27616521 AAAGTGCTCAAATGAAAGCCAAATCTTTC
1 AAAGTGCTCAAATGAAAGCCAAAACTTTC
*
27616550 AAAGTGCTCAAAT-AAGGACCAAAACTTT
1 AAAGTGCTCAAATGAAAG-CCAAAACTTT
27616578 TTGAGAGCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (29 bp):
AAAGTGCTCAAATGAAAGCCAAAACTTTC
Found at i:27617701 original size:11 final size:12
Alignment explanation
Indices: 27617665--27617702 Score: 62
Period size: 11 Copynumber: 3.3 Consensus size: 12
27617655 CCATTTCAAT
27617665 TAAAATTTTATA
1 TAAAATTTTATA
27617677 TAAAA-TTTATA
1 TAAAATTTTATA
27617688 TAAAATTTTA-A
1 TAAAATTTTATA
27617699 TAAA
1 TAAA
27617703 TATATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATTTTATA
Found at i:27625133 original size:31 final size:31
Alignment explanation
Indices: 27625098--27625179 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
27625088 CTTAACCTAA
* ** *
27625098 TGACTTAAATAAAAACTTTTGAATAGTTTAG
1 TGACTTAAATGAAAACTTTCAAATAGTTCAG
*
27625129 TGACTTAAATGGAAACTTTCAAATAGTTCAG
1 TGACTTAAATGAAAACTTTCAAATAGTTCAG
**
27625160 TGACCAAAATGAAAACTTTC
1 TGACTTAAATGAAAACTTTC
27625180 CCATAATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAGTTCAG
Found at i:27625193 original size:31 final size:31
Alignment explanation
Indices: 27625104--27625194 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 31
27625094 CTAATGACTT
* ** * **
27625104 AAATAAAAACTTTTGAATAGTTTAGTGACTT
1 AAATGAAAACTTTCAAATAATTTAGTGACCA
* * *
27625135 AAATGGAAACTTTCAAATAGTTCAGTGACCA
1 AAATGAAAACTTTCAAATAATTTAGTGACCA
**
27625166 AAATGAAAACTTTCCCATAATTTAGTGAC
1 AAATGAAAACTTTCAAATAATTTAGTGAC
27625195 TAATAATGTA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (31 bp):
AAATGAAAACTTTCAAATAATTTAGTGACCA
Found at i:27625727 original size:15 final size:15
Alignment explanation
Indices: 27625689--27625726 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
27625679 GATTTCGTAT
* *
27625689 TTAAATTTTCAATAC
1 TTAACTTTTCAACAC
27625704 TTAACTTTTCAACAC
1 TTAACTTTTCAACAC
27625719 TT-ACTTTT
1 TTAACTTTT
27625727 TTAGTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAACTTTTCAACAC
Found at i:27630462 original size:12 final size:12
Alignment explanation
Indices: 27630445--27630470 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27630435 TCCAACTGAG
27630445 TTTTTGTTTGCT
1 TTTTTGTTTGCT
27630457 TTTTTGTTTGCT
1 TTTTTGTTTGCT
27630469 TT
1 TT
27630471 ATTAATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (12 bp):
TTTTTGTTTGCT
Found at i:27630643 original size:11 final size:11
Alignment explanation
Indices: 27630627--27630651 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27630617 AAAGTCGAAA
27630627 AAAAAACTAAG
1 AAAAAACTAAG
27630638 AAAAAACTAAG
1 AAAAAACTAAG
27630649 AAA
1 AAA
27630652 TGAGATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAACTAAG
Found at i:27632069 original size:18 final size:18
Alignment explanation
Indices: 27632003--27632069 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
27631993 GAAATGAGAA
27632003 AAAAAATAAATTT-AAATG
1 AAAAAA-AAATTTGAAATG
**
27632021 -AAATGAAATTTGAAATG
1 AAAAAAAAATTTGAAATG
*
27632038 AAAATATAAA-TTGAAATG
1 AAAA-AAAAATTTGAAATG
27632056 AAAAAAAAATTTGA
1 AAAAAAAAATTTGA
27632070 CAAGACATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
16 6 0.15
17 12 0.30
18 19 0.47
19 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (18 bp):
AAAAAAAAATTTGAAATG
Found at i:27632274 original size:25 final size:24
Alignment explanation
Indices: 27632240--27632293 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
27632230 TTAAATGAGA
* * *
27632240 AAAAATTTGAATTTAAATGAAATTT
1 AAAATTTTGAAATAAAATGAAA-TT
27632265 AAAATTTTGAAATAAAATGAAATT
1 AAAATTTTGAAATAAAATGAAATT
27632289 AAAAT
1 AAAAT
27632294 ATAAATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (24 bp):
AAAATTTTGAAATAAAATGAAATT
Found at i:27632331 original size:21 final size:21
Alignment explanation
Indices: 27632300--27632351 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
27632290 AAATATAAAT
27632300 TGAAATG--AAAA-AAAAAAC
1 TGAAATGAAAAAAGAAAAAAC
* *
27632318 TGAATATGAAAAAAGAATAAAT
1 TGAA-ATGAAAAAAGAAAAAAC
27632340 TGAAATGAAAAA
1 TGAAATGAAAAA
27632352 TAAATTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
21 12 0.43
22 9 0.32
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.17
Consensus pattern (21 bp):
TGAAATGAAAAAAGAAAAAAC
Found at i:27632355 original size:17 final size:17
Alignment explanation
Indices: 27632274--27632546 Score: 116
Period size: 18 Copynumber: 15.1 Consensus size: 17
27632264 TAAAATTTTG
* *
27632274 AAATAAAATGAAATTAA
1 AAATAAATTGAAATGAA
27632291 AATATAAATTGAAATGAAA
1 AA-ATAAATTGAAATG-AA
* *
27632310 AAAAAAACTGAATATGAAAAA
1 AAATAAATTGAA-ATG---AA
27632331 AGAATAAATTGAAATGAA
1 A-AATAAATTGAAATGAA
27632349 AAATAAATTGAAATGAAA
1 AAATAAATTGAAATG-AA
*
27632367 TGAAATGTAATTTGAAATG-A
1 --AAA--TAAATTGAAATGAA
** **
27632387 ATCTAAAACGAAATGAAA
1 AAATAAATTGAAATG-AA
*
27632405 GTTGAAATGAATATGAAATGAA
1 ----AAATAAAT-TGAAATGAA
*
27632427 AAAAAAATTGAAATGAGA
1 AAATAAATTGAAATGA-A
27632445 CAAA-AAATT-AATATGAA
1 -AAATAAATTGAA-ATGAA
27632462 AAATAAATTGAAAT-AA
1 AAATAAATTGAAATGAA
* *
27632478 TAAAAAAATTTTAAATGGAA
1 -AAATAAA-TTGAAAT-GAA
27632498 AAA-AAATT-AAATG--
1 AAATAAATTGAAATGAA
27632511 AAATGAAATGTGAAATG-A
1 AAAT-AAAT-TGAAATGAA
27632529 AAATGAAA-TGAAATGAA
1 AAAT-AAATTGAAATGAA
27632546 A
1 A
27632547 TGAAAAAAAA
Statistics
Matches: 202, Mismatches: 21, Indels: 66
0.70 0.07 0.23
Matches are distributed among these distances:
13 3 0.01
15 5 0.02
16 26 0.13
17 49 0.24
18 61 0.30
19 13 0.06
20 6 0.03
21 7 0.03
22 26 0.13
23 6 0.03
ACGTcount: A:0.62, C:0.01, G:0.13, T:0.23
Consensus pattern (17 bp):
AAATAAATTGAAATGAA
Found at i:27632365 original size:5 final size:5
Alignment explanation
Indices: 27632357--27632427 Score: 52
Period size: 5 Copynumber: 13.0 Consensus size: 5
27632347 AAAAATAAAT
* * * *
27632357 TGAAA TGAAA TGAAA TGTAATT TGAAA TGAATC TAAAA CGAAA TGAAA
1 TGAAA TGAAA TGAAA TG-AA-A TGAAA TGAA-A TGAAA TGAAA TGAAA
27632405 GTTGAAA TGAATA TGAAA TGAAA
1 --TGAAA TGAA-A TGAAA TGAAA
27632428 AAAAAATTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
5 33 0.63
6 12 0.23
7 7 0.13
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.25
Consensus pattern (5 bp):
TGAAA
Found at i:27632381 original size:22 final size:22
Alignment explanation
Indices: 27632340--27632387 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
27632330 AAGAATAAAT
27632340 TGAAATGAAAAATAAATTGAAA
1 TGAAATGAAAAATAAATTGAAA
** *
27632362 TGAAATGAAATGTAATTTGAAA
1 TGAAATGAAAAATAAATTGAAA
27632384 TGAA
1 TGAA
27632388 TCTAAAACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (22 bp):
TGAAATGAAAAATAAATTGAAA
Found at i:27632384 original size:28 final size:28
Alignment explanation
Indices: 27632357--27632442 Score: 93
Period size: 28 Copynumber: 3.1 Consensus size: 28
27632347 AAAAATAAAT
* *
27632357 TGAA-ATGAAATGAAATGTAATTTGAAA
1 TGAATATGAAATGAAATGAAAGTTGAAA
* * *
27632384 TGAATCTAAAACGAAATGAAAGTTGAAA
1 TGAATATGAAATGAAATGAAAGTTGAAA
** *
27632412 TGAATATGAAATGAAAAAAAAATTGAAA
1 TGAATATGAAATGAAATGAAAGTTGAAA
27632440 TGA
1 TGA
27632443 GACAAAAAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
27 4 0.09
28 43 0.91
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.24
Consensus pattern (28 bp):
TGAATATGAAATGAAATGAAAGTTGAAA
Found at i:27632461 original size:35 final size:34
Alignment explanation
Indices: 27632420--27632511 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 34
27632410 AATGAATATG
27632420 AAATGAAAAAAAAATTGAAATGAGACAAAAAA-TT
1 AAATGAAAAAAAAATTGAAATGAGA-AAAAAATTT
* * *
27632454 AATATGAAAAATAAATTGAAATAATAAAAAAATTTT
1 AA-ATGAAAAAAAAATTGAAATGAGAAAAAAA-TTT
*
27632490 AAATGGAAAAAAAATT-AAATGA
1 AAATGAAAAAAAAATTGAAATGA
27632512 AATGAAATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
34 13 0.27
35 32 0.65
36 4 0.08
ACGTcount: A:0.66, C:0.01, G:0.10, T:0.23
Consensus pattern (34 bp):
AAATGAAAAAAAAATTGAAATGAGAAAAAAATTT
Found at i:27632483 original size:52 final size:52
Alignment explanation
Indices: 27632273--27632531 Score: 140
Period size: 52 Copynumber: 4.7 Consensus size: 52
27632263 TTAAAATTTT
* * * **
27632273 GAAATAAAATGAAATTAAAATATAAAT-TGAAATGAAAAAAAAAACTGAATATG
1 GAAAAAAAATTAAATGAAAA-ATAAATATGAAATGAAAAAAAAATTTGAA-ATG
* *
27632326 AAAAAAGAATAAATTGAAATGAAAAATAAAT-TGAAATGAAATGAAATGTAATTTGAAATG
1 --GAAA-AA-AAATT-AAATGAAAAATAAATATGAAATGAAA--AAA--AAATTTGAAATG
* * *
27632386 AATCTAAAACGAAATGAAAGTTG--AAATGAATATGAAATGAAAAAAAAA-TTGAAATG
1 GA---AAAA--AAATTAAA--TGAAAAATAAATATGAAATGAAAAAAAAATTTGAAATG
* *
27632442 AGACAAAAAATTAATATGAAAAATAAAT-TGAAAT-AATAAAAAAATTTTAAATG
1 -GAAAAAAAATTAA-ATGAAAAATAAATATGAAATGAA-AAAAAAATTTGAAATG
*
27632495 GAAAAAAAATTAAATG--AAATGAAATGTGAAATGAAAA
1 GAAAAAAAATTAAATGAAAAAT-AAATATGAAATGAAAA
27632532 TGAAATGAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 50
0.71 0.07 0.22
Matches are distributed among these distances:
49 4 0.02
50 4 0.02
51 15 0.09
52 33 0.20
53 15 0.09
54 3 0.02
55 3 0.02
56 9 0.05
57 23 0.14
58 10 0.06
59 6 0.04
60 15 0.09
61 22 0.13
62 2 0.01
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (52 bp):
GAAAAAAAATTAAATGAAAAATAAATATGAAATGAAAAAAAAATTTGAAATG
Found at i:27632514 original size:5 final size:5
Alignment explanation
Indices: 27632501--27632551 Score: 66
Period size: 5 Copynumber: 9.6 Consensus size: 5
27632491 AATGGAAAAA
*
27632501 AAATT AAATG AAATG AAATGTG AAATG AAAATG AAATG AAATG AAATG
1 AAATG AAATG AAATG AAA--TG AAATG -AAATG AAATG AAATG AAATG
27632549 AAA
1 AAA
27632552 AAAAAAATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
5 32 0.76
6 5 0.12
7 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.22
Consensus pattern (5 bp):
AAATG
Found at i:27632554 original size:23 final size:22
Alignment explanation
Indices: 27632506--27632552 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
27632496 AAAAAAAATT
27632506 AAATGAAATGAAATGTGAAATGA
1 AAATGAAATGAAA-GTGAAATGA
27632529 AAATGAAATGAAA-TGAAATGA
1 AAATGAAATGAAAGTGAAATGA
27632550 AAA
1 AAA
27632553 AAAAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.46
23 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (22 bp):
AAATGAAATGAAAGTGAAATGA
Found at i:27632561 original size:17 final size:17
Alignment explanation
Indices: 27632278--27632561 Score: 97
Period size: 17 Copynumber: 15.4 Consensus size: 17
27632268 ATTTTGAAAT
* *
27632278 AAAATGAAATTAAAATAT
1 AAAATGAAATGAAAA-AA
*
27632296 AAATTGAAATGAAAAAA
1 AAAATGAAATGAAAAAA
27632313 AAAACTGAATATGAAAAAAGA
1 AAAA-TGAA-ATG-AAAAA-A
*
27632334 ATAAATTGAAATGAAAAAT
1 A-AAA-TGAAATGAAAAAA
*
27632353 AAATTGAAATGAAATGAAA
1 AAAATGAAATGAAA--AAA
**
27632372 TGTAATTTGAAATGAATCTAAAA
1 ---AAAATGAAATGAA---AAAA
* **
27632395 CGAAATGAAAGTTG-AAATG
1 -AAAATGAAA--TGAAAAAA
*
27632414 AATATGAAATGAAAAAA
1 AAAATGAAATGAAAAAA
* * *
27632431 AAATTGAAATGAGACAA
1 AAAATGAAATGAAAAAA
* *
27632448 AAAATTAATATGAAAAAT
1 AAAATGAA-ATGAAAAAA
*
27632466 AAATTGAAAT-AATAAAA
1 AAAATGAAATGAA-AAAA
* * *
27632483 AAATTTTAAATG-GAAAA
1 AAA-ATGAAATGAAAAAA
* **
27632500 AAAATTAAATGAAATGA
1 AAAATGAAATGAAAAAA
**
27632517 AATGTGAAATGAAAATGAA
1 AAAATGAAATGAAAA--AA
27632536 ATGAAATGAAATGAAAAAA
1 A--AAATGAAATGAAAAAA
27632555 AAAATGA
1 AAAATGA
27632562 TAAGACATAT
Statistics
Matches: 197, Mismatches: 44, Indels: 51
0.67 0.15 0.17
Matches are distributed among these distances:
16 11 0.06
17 70 0.36
18 44 0.22
19 13 0.07
20 10 0.05
21 23 0.12
22 20 0.10
23 5 0.03
25 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.13, T:0.23
Consensus pattern (17 bp):
AAAATGAAATGAAAAAA
Found at i:27633147 original size:22 final size:22
Alignment explanation
Indices: 27633092--27633156 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
27633082 ATATGTCTTG
**
27633092 TCAATTTTTTTTTCATTTCAAAT
1 TCAATTTAATTTTCATTTC-AAT
* *
27633115 TTAATTTAATTTTCATTTCACT
1 TCAATTTAATTTTCATTTCAAT
*
27633137 TCATTTTAATTTTCATTTCA
1 TCAATTTAATTTTCATTTCA
27633157 TTTAAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (22 bp):
TCAATTTAATTTTCATTTCAAT
Found at i:27633156 original size:17 final size:16
Alignment explanation
Indices: 27633102--27633159 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
27633092 TCAATTTTTT
* *
27633102 TTTCATTTCAAATTTAA
1 TTTCATTT-TAATTTCA
* *
27633119 TTTAATTTTCATTTCA
1 TTTCATTTTAATTTCA
*
27633135 CTTCATTTTAATTTTCA
1 TTTCATTTTAA-TTTCA
27633152 TTTCATTT
1 TTTCATTT
27633160 AAAATTTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTCATTTTAATTTCA
Found at i:27633188 original size:21 final size:20
Alignment explanation
Indices: 27633164--27633259 Score: 62
Period size: 20 Copynumber: 5.0 Consensus size: 20
27633154 TCATTTAAAA
27633164 TTTTTTC-CATTTAAATTTAT
1 TTTTTTCTCATTTAAATTT-T
*
27633184 TTTTTTCTCATTTCAA----
1 TTTTTTCTCATTTAAATTTT
27633200 TTTTTT-TCATATT-AATTTT
1 TTTTTTCTCAT-TTAAATTTT
* *
27633219 TTTTGTCTCATTTCAATTTAT
1 TTTTTTCTCATTTAAATTT-T
* *
27633240 TTATTTTTTCATTTCAATTT
1 TT-TTTTCTCATTTAAATTT
27633260 ATATTTTATT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
15 6 0.10
16 8 0.13
19 7 0.11
20 16 0.26
21 10 0.16
22 15 0.24
ACGTcount: A:0.21, C:0.11, G:0.01, T:0.67
Consensus pattern (20 bp):
TTTTTTCTCATTTAAATTTT
Found at i:27633202 original size:17 final size:17
Alignment explanation
Indices: 27633182--27633237 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 17
27633172 ATTTAAATTT
27633182 ATTTTTTTCTCATTTCA
1 ATTTTTTTCTCATTTCA
27633199 A-TTTTTT-TCATATT-A
1 ATTTTTTTCTCAT-TTCA
27633214 ATTTTTTTTGTCTCATTTCA
1 A--TTTTTT-TCTCATTTCA
27633234 ATTT
1 ATTT
27633238 ATTTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
15 6 0.19
16 8 0.25
17 1 0.03
18 8 0.25
19 3 0.09
20 6 0.19
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (17 bp):
ATTTTTTTCTCATTTCA
Found at i:27633222 original size:35 final size:36
Alignment explanation
Indices: 27633162--27633237 Score: 111
Period size: 35 Copynumber: 2.1 Consensus size: 36
27633152 TTTCATTTAA
*
27633162 AATTTTTTCCATTTAAATTTATTTTTTTCTCATTTC
1 AATTTTTTCCATTTAAATTTATTTTTGTCTCATTTC
*
27633198 AATTTTTTTCATATT-AATTT-TTTTTGTCTCATTTC
1 AATTTTTTCCAT-TTAAATTTATTTTTGTCTCATTTC
27633233 AATTT
1 AATTT
27633238 ATTTATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 19 0.51
36 16 0.43
37 2 0.05
ACGTcount: A:0.22, C:0.12, G:0.01, T:0.64
Consensus pattern (36 bp):
AATTTTTTCCATTTAAATTTATTTTTGTCTCATTTC
Found at i:27633232 original size:25 final size:22
Alignment explanation
Indices: 27633204--27633279 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
27633194 TTTCAATTTT
*
27633204 TTTCATATTAATTTTTTTTGTCTCA
1 TTTCA-ATTAATTTATTTT-T-TCA
*
27633229 TTTCAATTTATTTATTTTTTCA
1 TTTCAATTAATTTATTTTTTCA
*
27633251 TTTCAATTTATATTT-TATTTTCA
1 TTTCAA-TTA-ATTTATTTTTTCA
27633274 TTTCAA
1 TTTCAA
27633280 CTTTTATTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.20
23 16 0.36
24 15 0.33
25 5 0.11
ACGTcount: A:0.24, C:0.11, G:0.01, T:0.64
Consensus pattern (22 bp):
TTTCAATTAATTTATTTTTTCA
Found at i:27633275 original size:23 final size:22
Alignment explanation
Indices: 27633200--27633288 Score: 89
Period size: 22 Copynumber: 4.1 Consensus size: 22
27633190 CTCATTTCAA
27633200 TTTTTTTCATATT-AATTT-T-T
1 TTTTTTTCAT-TTCAATTTATAT
* *
27633220 TTTGTCTCATTTCAATTTAT-T
1 TTTTTTTCATTTCAATTTATAT
27633241 TATTTTTTCATTTCAATTTATAT
1 T-TTTTTTCATTTCAATTTATAT
27633264 TTTATTTTCATTTCAACTTT-TAT
1 TTT-TTTTCATTTCAA-TTTATAT
27633287 TT
1 TT
27633289 CATAGATCCT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.03
20 13 0.22
21 3 0.05
22 19 0.32
23 19 0.32
24 3 0.05
ACGTcount: A:0.21, C:0.10, G:0.01, T:0.67
Consensus pattern (22 bp):
TTTTTTTCATTTCAATTTATAT
Found at i:27635569 original size:89 final size:86
Alignment explanation
Indices: 27635496--27635827 Score: 305
Period size: 89 Copynumber: 3.7 Consensus size: 86
27635486 TCGAAAAATT
*
27635496 AATAATACGTAAC-AAATTAAATTTATAGATACAAGAAAATACAAACATTCTAGAATATTAATAC
1 AATAATAC--AACTAAATTAAATTTACAGATACAA-AAAATACAAACATTCTAGAA-ATTAATAC
*
27635560 GCGAAAATATAAAATTCAAACAACA
62 ACGAAAATATAAAATTCAAACAACA
* ** ** *
27635585 AACAATACAGACTAAATTAAATTTACAGACCCAACAAAATACAAACAGATGGGT-CAAATTAATA
1 AATAATACA-ACTAAATTAAATTTACAGATACAA-AAAATACAAAC--AT-TCTAGAAATTAATA
* * *
27635649 CACAAAAATTTAAAATTCAAATTAA-A
61 CACGAAAATATAAAATTCAAA-CAACA
* * *
27635675 AATAATACGGACTAAATTAAATTTACATATACAAAAAATACAAACATT-TAAAGAAATTATTACA
1 AATAATAC-AACTAAATTAAATTTACAGATACAAAAAATACAAACATTCT--AGAAATTAATACA
* *
27635739 CGAAAATATAAAATTGAAACCACA
63 CGAAAATATAAAATTCAAACAACA
* * *
27635763 AATAATACTGACTAAATTAAATTTACAAATATAAAAAAATACAAACATTCTAAAGAAA-TAATAC
1 AATAATAC-AACTAAATTAAATTTACAGATA-CAAAAAATACAAACATTCT--AGAAATTAATAC
27635827 A
62 A
27635828 AAAATTTTGA
Statistics
Matches: 201, Mismatches: 29, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
85 1 0.00
87 4 0.02
88 58 0.29
89 69 0.34
90 62 0.31
91 6 0.03
92 1 0.00
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.24
Consensus pattern (86 bp):
AATAATACAACTAAATTAAATTTACAGATACAAAAAATACAAACATTCTAGAAATTAATACACGA
AAATATAAAATTCAAACAACA
Found at i:27635682 original size:90 final size:87
Alignment explanation
Indices: 27635509--27635827 Score: 284
Period size: 90 Copynumber: 3.6 Consensus size: 87
27635499 AATACGTAAC
* * * ** *
27635509 AAATTAAATTTATAGATACAAGAAAATACAAACA-TTCTAGAATATTAATACGCGAAAATATAAA
1 AAATTAAATTTACAGACACAA-AAAATACAAACAGATAAAGAA-ATTAATACACGAAAATATAAA
*
27635573 ATTCAAACAACAAACAATACAGACT
64 ATTCAAACAA-AAATAATACAGACT
* ** * *
27635598 AAATTAAATTTACAGACCCAACAAAATACAAACAGAT-GGGTCAAATTAATACACAAAAATTTAA
1 AAATTAAATTTACAGACACAA-AAAATACAAACAGATAAAG--AAATTAATACACGAAAATATAA
* *
27635662 AATTCAAATTAAAAATAATACGGACT
63 AATTCAAA-CAAAAATAATACAGACT
* * ** *
27635688 AAATTAAATTTACATATACAAAAAATACAAACATTTAAAGAAATTATTACACGAAAATATAAAAT
1 AAATTAAATTTACAGACACAAAAAATACAAACAGATAAAGAAATTAATACACGAAAATATAAAAT
* * *
27635753 TGAAACCACAAATAATACTGACT
66 TCAAA-CAAAAATAATACAGACT
* * * **
27635776 AAATTAAATTTACAAATATAAAAAAATACAAACATTCTAAAGAAA-TAATACA
1 AAATTAAATTTACAGACA-CAAAAAATACAAACA-GATAAAGAAATTAATACA
27635828 AAAATTTTGA
Statistics
Matches: 191, Mismatches: 32, Indels: 14
0.81 0.14 0.06
Matches are distributed among these distances:
88 57 0.30
89 64 0.34
90 66 0.35
91 4 0.02
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.24
Consensus pattern (87 bp):
AAATTAAATTTACAGACACAAAAAATACAAACAGATAAAGAAATTAATACACGAAAATATAAAAT
TCAAACAAAAATAATACAGACT
Found at i:27638337 original size:18 final size:17
Alignment explanation
Indices: 27638316--27638350 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27638306 TTATTATTAA
*
27638316 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
27638334 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
27638351 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:27638405 original size:157 final size:157
Alignment explanation
Indices: 27638203--27638519 Score: 571
Period size: 157 Copynumber: 2.0 Consensus size: 157
27638193 TAGAATACCC
* *
27638203 TTAGCATAAATTTGTTTTCATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTCATAAATGATTATTGTTATTGTGATTTAAATTTTAATAAGATTATTA
* *
27638268 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
27638333 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
** *
27638360 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTGATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTCATAAATGATTATTGTTATTGTGATTTAAATTTTAATAAGATTATTA
27638425 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
27638490 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
27638517 TTA
1 TTA
27638520 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTCATAAATGATTATTGTTATTGTGATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:27638490 original size:16 final size:16
Alignment explanation
Indices: 27638453--27638494 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27638443 TTAATCATAT
*
27638453 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
27638469 TT-AAATATATTATAA
1 TTAAAATATATTATAA
27638484 TTAAAATATAT
1 TTAAAATATAT
27638495 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:27638501 original size:14 final size:15
Alignment explanation
Indices: 27638462--27638503 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
27638452 TTTAAACATA
*
27638462 ATTATTATTAAATAT
1 ATTATAATTAAATAT
27638477 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
27638491 A-TATAATTTAATA
1 ATTATAATTAAATA
27638504 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:27638739 original size:91 final size:91
Alignment explanation
Indices: 27638644--27638851 Score: 285
Period size: 91 Copynumber: 2.3 Consensus size: 91
27638634 TAATTATAAC
* * * *
27638644 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
27638708 TAATATATAATTTCATAAAATTCTTGA
65 TAATATATAATTTCATAAAATTCTTAA
* * *
27638735 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
27638800 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
27638826 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
27638852 CTAAAATCAA
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
91 82 0.78
92 22 0.21
93 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:27640288 original size:23 final size:23
Alignment explanation
Indices: 27640237--27640289 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
27640227 ACTTTACTGG
* * *
27640237 TTTTATTTTTTATGTTGTATTTA
1 TTTTAATTTTTATATTATATTTA
**
27640260 AATTAATTTTTATATTATATTTA
1 TTTTAATTTTTATATTATATTTA
27640283 TTTTAAT
1 TTTTAAT
27640290 ACTAATTTTG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTTAATTTTTATATTATATTTA
Found at i:27641233 original size:23 final size:23
Alignment explanation
Indices: 27641194--27641256 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
27641184 TGTACTGACT
27641194 AACAAATCAAGAACAATTTCCAG
1 AACAAATCAAGAACAATTTCCAG
27641217 CAGAC-AATCAA-AACAATTTCCAG
1 -A-ACAAATCAAGAACAATTTCCAG
*
27641240 AACAAATCAATAACAAT
1 AACAAATCAAGAACAAT
27641257 ATCAAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.06
22 7 0.19
23 18 0.50
24 7 0.19
25 2 0.06
ACGTcount: A:0.54, C:0.22, G:0.06, T:0.17
Consensus pattern (23 bp):
AACAAATCAAGAACAATTTCCAG
Found at i:27641265 original size:22 final size:22
Alignment explanation
Indices: 27641194--27641268 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 22
27641184 TGTACTGACT
*
27641194 AACAAATCAAGAACAATTTCCAGCA
1 AACAAATCAA-AACAATATCCA--A
* * *
27641219 GAC-AATCAAAACAATTTCCAG
1 AACAAATCAAAACAATATCCAA
27641240 AACAAATCAATAACAATAT-CAA
1 AACAAATCAA-AACAATATCCAA
27641262 AACAAAT
1 AACAAAT
27641269 TGCAACAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.05
22 15 0.35
23 18 0.42
24 6 0.14
25 2 0.05
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.17
Consensus pattern (22 bp):
AACAAATCAAAACAATATCCAA
Found at i:27652734 original size:16 final size:17
Alignment explanation
Indices: 27652709--27652759 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
27652699 GATACAAGCC
27652709 AGACAAGAAGTAGAAGA
1 AGACAAGAAGTAGAAGA
*
27652726 AGA-AAGAAGTAGAGAAA
1 AGACAAGAAGTAGA-AGA
27652743 AGACAAG-AG-AGAAGA
1 AGACAAGAAGTAGAAGA
27652758 AG
1 AG
27652760 GACATGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 4 0.13
16 13 0.43
17 10 0.33
18 3 0.10
ACGTcount: A:0.61, C:0.04, G:0.31, T:0.04
Consensus pattern (17 bp):
AGACAAGAAGTAGAAGA
Found at i:27658103 original size:44 final size:44
Alignment explanation
Indices: 27658038--27658239 Score: 121
Period size: 44 Copynumber: 4.6 Consensus size: 44
27658028 CTAAGCCTTG
* * *
27658038 TCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATAGCAGATCTTA
1 TCTCCCTAAGCAGTAGCGGAGTAGATTGAAGATAGCAGATCTTA
* ** * *
27658082 TCTCCCTAAGCAGTAGTGGAGTAGATCAAAGA-CGACAAATCTTA
1 TCTCCCTAAGCAGTAGCGGAGTAGATTGAAGATAG-CAGATCTTA
* * * * *
27658126 TCTTTCC-AAGACAGT-G-GGAAGCAGATTTAAGCCACTA--AG-CCTTG
1 TC-TCCCTAAG-CAGTAGCGG-AGTAGATTGAAG--A-TAGCAGATCTTA
* * * *
27658170 TCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATAGCAGATCTCA
1 TCTCCCTAAGCAGTAGCGGAGTAGATTGAAGATAGCAGATCTTA
* *
27658214 TCTCCCTAAGCAGTAGTGGAGCAGAT
1 TCTCCCTAAGCAGTAGCGGAGTAGAT
27658240 CAAAGACGGC
Statistics
Matches: 114, Mismatches: 30, Indels: 28
0.66 0.17 0.16
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 11 0.10
44 89 0.78
45 10 0.09
46 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.23
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGCGGAGTAGATTGAAGATAGCAGATCTTA
Found at i:27658171 original size:132 final size:132
Alignment explanation
Indices: 27657934--27658334 Score: 694
Period size: 132 Copynumber: 3.0 Consensus size: 132
27657924 CAGATCAGTA
* *
27657934 AAGATAGCAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
27657999 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
27658064 TG
131 TG
* *
27658066 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGACAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
*
27658131 CCAAGACAGTGGGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
27658196 TG
131 TG
*
27658198 AAGATAGCAGATCTCATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
* * * ** *
27658263 TCAAGATAGTGGGAAGTAGGTTTAAGCCACCGAGCCTTGTCTCCCTAAGCAGCAGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
27658328 TG
131 TG
27658330 AAGAT
1 AAGAT
27658335 TACAAATCCT
Statistics
Matches: 254, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 254 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (132 bp):
AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
TG
Found at i:27667322 original size:400 final size:401
Alignment explanation
Indices: 27666561--27667363 Score: 1518
Period size: 400 Copynumber: 2.0 Consensus size: 401
27666551 ACCTCTCACC
* *
27666561 ATACAGATAGTGCCTCCAAAATTTTAAGGTAAAAACTACGACAGCCAACTCGAGATCATGTGTCG
1 ATACAGATAGTGCCTCCAAAATTTTAAGGTAAAAACTACAACAACCAACTCGAGATCATGTGTCG
27666626 GATAATTCCCCTCGTGTGACTTAAGCTACCGGGACACATAAGCCACAACCTTACCATCTTGCATC
66 GATAATTCCCCTCGTGTGACTTAAGCTACCGGGACACATAAGCCACAACCTTACCATCTTGCATC
27666691 AATACACATCCCAAACCGACATGCGACGCATCACTATAAACCACGAAGTCCTTACCAGATTCAGG
131 AATACACATCCCAAACCGACATGCGACGCATCACTATAAACCACGAAGTCCTTACCAGATTCAGG
*
27666756 TTGTATCAAAACAAGAGCTTGAGTCAGAATAGACTTGAGCTTCTCAAAGCTCGATTATTGGTCAT
196 TTGTATCAAAACAAGAGCTTGAGGCAGAATAGACTTGAGCTTCTCAAAGCTCGATTATTGGTCAT
27666821 CAGTCTAGACAAAATGAGCATTCTTGCGTAAAAGCTTAGTTAGAGGAGTTCCAATCAATGAAAAC
261 CAGTCTAGACAAAATGAGCATTCTTGCGTAAAAGCTTAGTTAGAGGAGTTCCAATCAATGAAAAC
27666886 CCCTCAACAAACCTCCGATAATAACTCACAAGACTAGAAAACTGCGGATCTAAGAAATATTCTTA
326 CCCTCAACAAACCTCCGATAATAACTCACAAGACTAGAAAACTGCGGATCTAAGAAATATTCTTA
27666951 GGATGTTTCCA
391 GGATGTTTCCA
27666962 ATACAGATAGTGCCTCC-AAATTTTAAGGTAAAAACTACAACAACCAACTCGAGATCATGTGTCG
1 ATACAGATAGTGCCTCCAAAATTTTAAGGTAAAAACTACAACAACCAACTCGAGATCATGTGTCG
* *
27667026 GATAATTCCCCTCGTGTGACTTAAGCTGCTGGGACACATAAGCCACAACCTTACCATCTTGCATC
66 GATAATTCCCCTCGTGTGACTTAAGCTACCGGGACACATAAGCCACAACCTTACCATCTTGCATC
27667091 AATACACATCCCAAACCGACATGCGACGCATCACTATAAACCACGAAGTCCTTACCAGATTCAGG
131 AATACACATCCCAAACCGACATGCGACGCATCACTATAAACCACGAAGTCCTTACCAGATTCAGG
* *
27667156 TTGTATCAAAACAGGAGCTTGAGGCAGAATAGACTTGAGCTTCTCAAAGCTCGATTGTTGGTCAT
196 TTGTATCAAAACAAGAGCTTGAGGCAGAATAGACTTGAGCTTCTCAAAGCTCGATTATTGGTCAT
*
27667221 CAGTCTAGACAAAATGAGCATTCTTGCGTAAAAGCTTAGTTAGAGGAGTTCCAATTAATGAAAAC
261 CAGTCTAGACAAAATGAGCATTCTTGCGTAAAAGCTTAGTTAGAGGAGTTCCAATCAATGAAAAC
*
27667286 CCCTCAACAAACCTCCGATAATAACTCACCAGACTAGAAAACTGCGGATCTAAGAAATATTCTTA
326 CCCTCAACAAACCTCCGATAATAACTCACAAGACTAGAAAACTGCGGATCTAAGAAATATTCTTA
27667351 GGATGTTTCCA
391 GGATGTTTCCA
27667362 AT
1 AT
27667364 CAAGTACAAC
Statistics
Matches: 393, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
400 376 0.96
401 17 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (401 bp):
ATACAGATAGTGCCTCCAAAATTTTAAGGTAAAAACTACAACAACCAACTCGAGATCATGTGTCG
GATAATTCCCCTCGTGTGACTTAAGCTACCGGGACACATAAGCCACAACCTTACCATCTTGCATC
AATACACATCCCAAACCGACATGCGACGCATCACTATAAACCACGAAGTCCTTACCAGATTCAGG
TTGTATCAAAACAAGAGCTTGAGGCAGAATAGACTTGAGCTTCTCAAAGCTCGATTATTGGTCAT
CAGTCTAGACAAAATGAGCATTCTTGCGTAAAAGCTTAGTTAGAGGAGTTCCAATCAATGAAAAC
CCCTCAACAAACCTCCGATAATAACTCACAAGACTAGAAAACTGCGGATCTAAGAAATATTCTTA
GGATGTTTCCA
Found at i:27671873 original size:38 final size:39
Alignment explanation
Indices: 27671803--27671880 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
27671793 CAAGGAGGGG
27671803 AAAGAAAGAAAGAAAAAGTCAAAACGTAAGAAGAGAGAA
1 AAAGAAAGAAAGAAAAAGTCAAAACGTAAGAAGAGAGAA
* *
27671842 AAAGAAAGAAA-AAAAAGTCAAAATGTGAGAAGAGAGAA
1 AAAGAAAGAAAGAAAAAGTCAAAACGTAAGAAGAGAGAA
27671880 A
1 A
27671881 CGTGAAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 26 0.70
39 11 0.30
ACGTcount: A:0.67, C:0.04, G:0.23, T:0.06
Consensus pattern (39 bp):
AAAGAAAGAAAGAAAAAGTCAAAACGTAAGAAGAGAGAA
Found at i:27674584 original size:19 final size:19
Alignment explanation
Indices: 27674560--27674597 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
27674550 CTCTTTGTAA
*
27674560 ATCTTTAAATGGTAAAAGT
1 ATCTTTAAATGATAAAAGT
27674579 ATCTTTAAATGATAAAAGT
1 ATCTTTAAATGATAAAAGT
27674598 GAGGGGGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (19 bp):
ATCTTTAAATGATAAAAGT
Found at i:27675672 original size:114 final size:112
Alignment explanation
Indices: 27675214--27675830 Score: 498
Period size: 115 Copynumber: 5.4 Consensus size: 112
27675204 CGCTTATGGG
** ** ** * *
27675214 AAAA-CGCCGCAAAATATCTTAACCAAAGTGCACCGTTTTGGTCTTG-GTGTATGTTACAGTTAG
1 AAAAGCGCCGCAAAATATC-TAACCAAAACGCAGAGTTTT-GTCTTGAG-GTATACTAGAATTAG
* * * **
27675277 TGGCGTTTAAGGGAAAACGCCGCTAAAACATAATATTAGCGGCG-TTTTGTG
63 TGGCGCTTAAGGG-AAACGCCGCTAAAGCATACTATTAGCGGCGCTTTT-CA
** *
27675328 TGAAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTG
1 AAAAGCGCCGCAAAATATC-TAACCAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTG
* *
27675393 GCGC-AAAGGGAACACGCCGCTAAGGCATACTATTAGCGGCGC-TTTCA
65 GCGCTTAAGGGAA-ACGCCGCTAAAGCATACTATTAGCGGCGCTTTTCA
* * * * * *
27675440 GAGAAGCGCCGCAAAATTTGGTAACCAAAACGCA-ACGTTTTTGTCTTGATGTTTAC-AGTTATT
1 -AAAAGCGCCGCAAAATAT-CTAACCAAAACGCAGA-G-TTTTGTCTTGAGGTATACTAG-AATT
* * * * **
27675503 AGTGGCGAATATTAA--AAAACGCCGCTAAATCATAGTATTAGCGGCGCTTGGCA
61 AGTGGCG---CTTAAGGGAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTTCA
* * * * *
27675556 AAAAGCGCCGCAAAATATGCTCACCAAAACGCAGAGTTTTTTCATCAGGTATATTAGAATTAGTG
1 AAAAGCGCCGCAAAATAT-CTAACCAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTG
* *
27675621 GCGCTTATGGGAGAACGCCGCTAAAGCATACTATTAGCGGTGCTTTTCA
65 GCGCTTAAGGGA-AACGCCGCTAAAGCATACTATTAGCGGCGCTTTTCA
* * * * * *
27675670 AAAAGCGCCGCAAAATATATTAACAAAAACGCAGCGTTTAAGTCTTGATGTATACTGGAATTAGT
1 AAAAGCGCCGCAAAATAT-CTAACCAAAACGCAGAGTTT-TGTCTTGAGGTATACTAGAATTAGT
* * * * **
27675735 GGCG-TCCACGAGAAATCGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTG
64 GGCGCT-TAAGGGAAA-CGCCGCTAAAGCATACTATTAGCGGCGCTTTTCA
* *
27675785 ACAAGCGCCGAAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
1 AAAAGCGCCGCAAAATATC-TAACCAAAACGCAGAGTTTT-GTCTT
27675831 AACCATGCAT
Statistics
Matches: 402, Mismatches: 77, Indels: 47
0.76 0.15 0.09
Matches are distributed among these distances:
111 3 0.01
112 3 0.01
113 66 0.16
114 139 0.35
115 183 0.46
116 6 0.01
118 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (112 bp):
AAAAGCGCCGCAAAATATCTAACCAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGG
CGCTTAAGGGAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTTCA
Found at i:27675759 original size:229 final size:228
Alignment explanation
Indices: 27675289--27675825 Score: 648
Period size: 229 Copynumber: 2.4 Consensus size: 228
27675279 GCGTTTAAGG
* * **
27675289 GAAAACGCCGCTAAAACATAATATTAGCGGCGTTTTGTGTGAAGCGCCGCAAAATATCTTAACCA
1 GAAAACGCCGCTAAAACATAGTATTAGCGGCGCTTTGTGAAAAGCGCCGCAAAATATCTTAACCA
* * * *
27675354 AAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAGGC
66 AAACGCAGAGTTTTGTCATCAGGTATACTAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAAGC
* * * * **
27675419 ATACTATTAGCGGCGCTTTCAGAGAAGCGCCGCAAAATTTGGTAACCAAAACGCAACGTTTTTGT
131 ATACTATTAGCGGCGCTTTCAGAAAAGCGCCGCAAAATATAGTAACAAAAACGCAACGTTTAAGT
* ** * **
27675484 CTTGATGTTTACAGTTATTAGTGGCGAATATTA
196 CTTGATGTATACAGGAATTAGTGGCGAACACGA
* * * ** *
27675517 AAAAACGCCGCTAAATCATAGTATTAGCGGCGCTTGGCAAAAAGCGCCGCAAAATATGC-TCACC
1 GAAAACGCCGCTAAAACATAGTATTAGCGGCGCTTTGTGAAAAGCGCCGCAAAATAT-CTTAACC
* * * *
27675581 AAAACGCAGAGTTTTTTCATCAGGTATATTAGAATTAGTGGCGCTTATGGGAGA-ACGCCGCTAA
65 AAAACGCAGAGTTTTGTCATCAGGTATACTAGAATTAGTGGCGC-AAAGGGA-ACACGCCGCTAA
* * *
27675645 AGCATACTATTAGCGGTGCTTTTCA-AAAAGCGCCGCAAAATATATTAACAAAAACGCAGCGTTT
128 AGCATACTATTAGCGGCGC-TTTCAGAAAAGCGCCGCAAAATATAGTAACAAAAACGCAACGTTT
* **
27675709 AAGTCTTGATGTATACTGGAATTAGTGGCGTCCACGA
192 AAGTCTTGATGTATACAGGAATTAGTGGCGAACACGA
* * * * *
27675746 GAAATCGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGACAAGCGCCGAAAAATATCTTAACCA
1 GAAAACGCCGCTAAAACATAGTATTAGCGGCGCTTTGTGAAAAGCGCCGCAAAATATCTTAACCA
27675811 AAACGCAGAGTTTTG
66 AAACGCAGAGTTTTG
27675826 GTCTTAACCA
Statistics
Matches: 257, Mismatches: 47, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
228 92 0.36
229 159 0.62
230 6 0.02
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (228 bp):
GAAAACGCCGCTAAAACATAGTATTAGCGGCGCTTTGTGAAAAGCGCCGCAAAATATCTTAACCA
AAACGCAGAGTTTTGTCATCAGGTATACTAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAAGC
ATACTATTAGCGGCGCTTTCAGAAAAGCGCCGCAAAATATAGTAACAAAAACGCAACGTTTAAGT
CTTGATGTATACAGGAATTAGTGGCGAACACGA
Found at i:27681282 original size:21 final size:21
Alignment explanation
Indices: 27681256--27681306 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
27681246 CTACAACTTA
* *
27681256 AAGCAGATGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
*
27681277 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
*
27681298 AAGTAGAGG
1 AAGCAGAGG
27681307 TTCAAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.45, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:27683131 original size:21 final size:21
Alignment explanation
Indices: 27683106--27683164 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
27683096 TGTGCTAAAC
*
27683106 AGAAACCCATAAGGGTTGAAC
1 AGAAACCCATAAGGGTTGAAA
* * * *
27683127 GGAAACTCATAAGAGCTGAAA
1 AGAAACCCATAAGGGTTGAAA
27683148 AGAAACCCATAAGGGTT
1 AGAAACCCATAAGGGTT
27683165 AATTTCAAGC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (21 bp):
AGAAACCCATAAGGGTTGAAA
Found at i:27683228 original size:21 final size:21
Alignment explanation
Indices: 27683204--27683250 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
27683194 ACCCATTAGG
*
27683204 GTTAAATTGAAACTCATATGA
1 GTTAAATTGAAACTCATAAGA
*
27683225 GTT-AATTGAAGCTCATAAGA
1 GTTAAATTGAAACTCATAAGA
*
27683245 GCTAAA
1 GTTAAA
27683251 CGGAAAGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (21 bp):
GTTAAATTGAAACTCATAAGA
Found at i:27685151 original size:94 final size:95
Alignment explanation
Indices: 27684758--27685180 Score: 426
Period size: 94 Copynumber: 4.5 Consensus size: 95
27684748 AGATTCGAGG
* * * * * * * *
27684758 TTGTAGCTTTATCTTGCTCCACTACATCTTTAGGGAGATTAGATTTGCTATTGTAGTTTCAATCT
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTCC
** * *
27684823 ATTC-CATTACAACTTCAGGGATATAGGAT
66 AAACTCATTGCAACTTCAGGGGTATAGGAT
* * * * *** *
27684852 TTGTAGCTTCATCTTGC-CCTACTGCAGCTTTAGAGAGATAATACACGCCATTGTAGCTTCATTC
1 TTGTAGCTTCATCTTGCTCC-ACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTC
* * * *
27684916 CAAACT-ACTGTAACTTTAGGGGTATAAGAT
65 CAAACTCATTGCAACTTCAGGGGTATAGGAT
* * * * *
27684946 TTGTAGCTTCATTTTTCTCCACTGCAATTTCAGGGAGATAAAATTTGTTATTGTAGCTTCATTCC
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTCC
* *
27685011 AAAC-CATTGTAACTGT-AGGGGTATAGGAC
66 AAACTCATTGCAACT-TCAGGGGTATAGGAT
* * *
27685040 TTGTAGCTTTATCTTGCTCAACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGTTTCATTCC
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTCC
* *
27685105 -GACTCATTGCAACTTCAGGGGTACAGGAT
66 AAACTCATTGCAACTTCAGGGGTATAGGAT
* * **
27685134 TTATAGCTTCATCTTGCTTCACTAAAACTTCAGGGAGATAAGATTTG
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
27685181 TAGCTTCATC
Statistics
Matches: 268, Mismatches: 54, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
93 5 0.02
94 260 0.97
95 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (95 bp):
TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTGTAGCTTCATTCC
AAACTCATTGCAACTTCAGGGGTATAGGAT
Found at i:27685165 original size:44 final size:44
Alignment explanation
Indices: 27685115--27685222 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
27685105 GACTCATTGC
*
27685115 AACTTCAGGG-G-TACAGGATTTATAGCTTCATCTTGCTTCACTAA
1 AACTTCAGGGAGATA-A-GATTTATAGCTTCATCTTGCTCCACTAA
* **
27685159 AACTTCAGGGAGATAAGATTTGTAGCTTCATCTTGCTCCACTGT
1 AACTTCAGGGAGATAAGATTTATAGCTTCATCTTGCTCCACTAA
* *
27685203 AACTTCAGGTAGATGAGATT
1 AACTTCAGGGAGATAAGATT
27685223 CGCCATTGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 52 0.93
45 2 0.04
46 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (44 bp):
AACTTCAGGGAGATAAGATTTATAGCTTCATCTTGCTCCACTAA
Found at i:27690791 original size:29 final size:29
Alignment explanation
Indices: 27690758--27690849 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
27690748 GTGTGCTAAA
* *
27690758 CGATGGTCGTAACCGTCCCTTTTCATATT
1 CGATGGTCATAACCATCCCTTTTCATATT
* * *
27690787 CGATGGTTAAAACCATCCCTTTTCATTAAT
1 CGATGGTCATAACCATCCCTTTTCA-TATT
* * *
27690817 CGATGGTCATCACTATCCCTTTTAATATT
1 CGATGGTCATAACCATCCCTTTTCATATT
27690846 CGAT
1 CGAT
27690850 AGCCGAAGCT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 28 0.55
30 23 0.45
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (29 bp):
CGATGGTCATAACCATCCCTTTTCATATT
Found at i:27690822 original size:30 final size:29
Alignment explanation
Indices: 27690768--27690878 Score: 87
Period size: 29 Copynumber: 3.8 Consensus size: 29
27690758 CGATGGTCGT
* *
27690768 AACCGTCCCTTTTCATATTCGATGGTTAA
1 AACCATCCCTTTTCATAATCGATGGTTAA
* *
27690797 AACCATCCCTTTTCATTAATCGATGGTCAT
1 AACCATCCCTTTTCA-TAATCGATGGTTAA
* * * * * ***
27690827 CACTATCCCTTTTAATATTCGATAGCCGA
1 AACCATCCCTTTTCATAATCGATGGTTAA
* *
27690856 AGCTATCCCTTTTCATAATCGAT
1 AACCATCCCTTTTCATAATCGAT
27690879 AGCCGAATCT
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
29 42 0.65
30 23 0.35
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (29 bp):
AACCATCCCTTTTCATAATCGATGGTTAA
Found at i:27690861 original size:29 final size:29
Alignment explanation
Indices: 27690829--27690897 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
27690819 ATGGTCATCA
*
27690829 CTATCCCTTTTAATATTCGATAGCCGAAG
1 CTATCCCTTTTAATAATCGATAGCCGAAG
* *
27690858 CTATCCCTTTTCATAATCGATAGCCGAAT
1 CTATCCCTTTTAATAATCGATAGCCGAAG
*
27690887 CTACCCCTTTT
1 CTATCCCTTTT
27690898 CATTGGTCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (29 bp):
CTATCCCTTTTAATAATCGATAGCCGAAG
Found at i:27692606 original size:22 final size:22
Alignment explanation
Indices: 27692528--27692598 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
27692518 TTATCCACTA
* **
27692528 ATGAGAGCTTAGTACGTGAAAC
1 ATGAGAGCTTAGTACGTTAGCC
27692550 ATGAGAGCTTAGTACGTTAGCC
1 ATGAGAGCTTAGTACGTTAGCC
27692572 ATGAGAGCTTAGTACGTTAGCC
1 ATGAGAGCTTAGTACGTTAGCC
27692594 ATGAG
1 ATGAG
27692599 GGTTTAGTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.25
Consensus pattern (22 bp):
ATGAGAGCTTAGTACGTTAGCC
Found at i:27694264 original size:16 final size:16
Alignment explanation
Indices: 27694243--27694274 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27694233 TGTATAAAGC
27694243 TTGAAAACAAAGCAAA
1 TTGAAAACAAAGCAAA
27694259 TTGAAAACAAAGCAAA
1 TTGAAAACAAAGCAAA
27694275 GAATAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (16 bp):
TTGAAAACAAAGCAAA
Found at i:27697752 original size:2 final size:2
Alignment explanation
Indices: 27697745--27697795 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
27697735 TGGGCCCCTA
27697745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27697787 AT AT AT AT A
1 AT AT AT AT A
27697796 AGATAGATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27698316 original size:10 final size:10
Alignment explanation
Indices: 27698291--27698362 Score: 62
Period size: 10 Copynumber: 7.5 Consensus size: 10
27698281 GAAAATTATA
* *
27698291 AAAAAAACTA
1 AAAAAAATTT
27698301 AAAAAAATTT
1 AAAAAAATTT
27698311 AGAAAAAA-TT
1 A-AAAAAATTT
**
27698321 ATTAAAATTT
1 AAAAAAATTT
27698331 AAAAAAA-TT
1 AAAAAAATTT
27698340 AAAAAAA--T
1 AAAAAAATTT
*
27698348 AAAAAATTTT
1 AAAAAAATTT
27698358 AAAAA
1 AAAAA
27698363 TTAGAATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
8 7 0.14
9 13 0.25
10 25 0.49
11 6 0.12
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:27698316 original size:12 final size:11
Alignment explanation
Indices: 27698269--27698346 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 11
27698259 TTTTCTTATT
27698269 AAAATTTAGAAA
1 AAAATTTA-AAA
27698281 GAAAATTATAAAA
1 -AAAATT-TAAAA
*
27698294 AAAA-CTAAAA
1 AAAATTTAAAA
*
27698304 AAAATTTAGAA
1 AAAATTTAAAA
**
27698315 AAAA-TT-ATT
1 AAAATTTAAAA
27698324 AAAATTT-AAA
1 AAAATTTAAAA
27698334 AAAA-TTAAAA
1 AAAATTTAAAA
27698344 AAA
1 AAA
27698347 TAAAAAATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
9 6 0.11
10 24 0.45
11 8 0.15
12 4 0.08
13 9 0.17
14 2 0.04
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:27698336 original size:9 final size:9
Alignment explanation
Indices: 27698302--27698364 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
27698292 AAAAAACTAA
27698302 AAAAAATTT
1 AAAAAATTT
*
27698311 AGAAAAAATT
1 A-AAAAATTT
*
27698321 ATTAAAATTT
1 A-AAAAATTT
*
27698331 AAAAAAATT
1 AAAAAATTT
*
27698340 AAAAAA-AT
1 AAAAAATTT
27698348 AAAAAATTT
1 AAAAAATTT
*
27698357 TAAAAATT
1 AAAAAATT
27698365 AGAATTTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
8 7 0.16
9 21 0.49
10 15 0.35
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAAATTT
Found at i:27698361 original size:16 final size:17
Alignment explanation
Indices: 27698313--27698363 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
27698303 AAAAATTTAG
*
27698313 AAAAAATTATTAAAATTTA
1 AAAAAATT-TTAAAA-ATA
**
27698332 AAAAAATTAAAAAAAT-
1 AAAAAATTTTAAAAATA
27698348 AAAAAATTTTAAAAAT
1 AAAAAATTTTAAAAAT
27698364 TAGAATTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 14 0.52
17 1 0.04
18 4 0.15
19 8 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATTTTAAAAATA
Found at i:27698573 original size:21 final size:19
Alignment explanation
Indices: 27698546--27698612 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
27698536 GTACGATAAT
27698546 TTTTATAATTTTTTTTACGA
1 TTTTATAA-TTTTTTTACGA
*
27698566 TATTTAT-ATTTCTTTAC-A
1 T-TTTATAATTTTTTTACGA
*
27698584 TTTTGTATAATTTTCTTACGA
1 -TTT-TATAATTTTTTTACGA
27698605 TTTTATAA
1 TTTTATAA
27698613 AATTTTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
18 3 0.08
19 17 0.44
20 13 0.33
21 6 0.15
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTATAATTTTTTTACGA
Found at i:27698616 original size:21 final size:21
Alignment explanation
Indices: 27698574--27698618 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27698564 GATATTTATA
* *
27698574 TTTCTTTACATTTTGTATAAT
1 TTTCTTTACATTTTATAAAAT
27698595 TTTC-TTACGATTTTATAAAAT
1 TTTCTTTAC-ATTTTATAAAAT
27698616 TTT
1 TTT
27698619 ATAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTCTTTACATTTTATAAAAT
Found at i:27698626 original size:19 final size:20
Alignment explanation
Indices: 27698604--27698650 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
27698594 TTTTCTTACG
27698604 ATTTTATAAAATTT-TATAA
1 ATTTTATAAAATTTCTATAA
* * *
27698623 ATTTT-TTATATTTCTATAT
1 ATTTTATAAAATTTCTATAA
27698642 ATTTTATAA
1 ATTTTATAA
27698651 CTTGTTACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 6 0.27
19 14 0.64
20 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTATAAAATTTCTATAA
Found at i:27698635 original size:28 final size:27
Alignment explanation
Indices: 27698589--27698692 Score: 93
Period size: 29 Copynumber: 3.7 Consensus size: 27
27698579 TTACATTTTG
*
27698589 TATAATTTTCTTACGATTTTATAAAATTT
1 TATAATTTT-TTA-TATTTTATAAAATTT
*
27698618 TATAAATTTTTTATATTTCTAT-ATATTT
1 TAT-AATTTTTTATATTT-TATAAAATTT
* * *
27698646 TATAACTTGTTACTATTTTTATAAAAGTT
1 TATAATTTTTTA-TA-TTTTATAAAATTT
*
27698675 TACAATTTTTTATATTTT
1 TATAATTTTTTATATTTT
27698693 TTATGATTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
27 11 0.18
28 19 0.31
29 25 0.41
30 6 0.10
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.59
Consensus pattern (27 bp):
TATAATTTTTTATATTTTATAAAATTT
Found at i:27698693 original size:28 final size:28
Alignment explanation
Indices: 27698605--27698693 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
27698595 TTTCTTACGA
27698605 TTTTATAAAATTTTATAAATTTTTTATAT
1 TTTTATAAAATTTTA-AAATTTTTTATAT
* * * * *
27698634 TTCTAT-ATATTTTATAACTTGTTACTAT
1 TTTTATAAAATTTTAAAATTTTTTA-TAT
* *
27698662 TTTTATAAAAGTTTACAATTTTTTATAT
1 TTTTATAAAATTTTAAAATTTTTTATAT
27698690 TTTT
1 TTTT
27698694 TATGATTTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
27 7 0.15
28 22 0.47
29 18 0.38
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTATAAAATTTTAAAATTTTTTATAT
Found at i:27698800 original size:22 final size:21
Alignment explanation
Indices: 27698764--27698807 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
27698754 TATAGCTTTT
*
27698764 ATTTATTTTAATTTTTTATAA
1 ATTTATTTTAATTTTTAATAA
*
27698785 ATTTTTTTATAATTTTTAATAA
1 ATTTATTT-TAATTTTTAATAA
27698807 A
1 A
27698808 AGCAAGGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTATTTTAATTTTTAATAA
Found at i:27698911 original size:89 final size:88
Alignment explanation
Indices: 27698812--27698985 Score: 217
Period size: 89 Copynumber: 2.0 Consensus size: 88
27698802 AATAAAAGCA
* * * * * *
27698812 AGGGCTTAATTGCTTTTTTTGAAAAA-TTTTG-AGGATCTTTTTTATGTATTTTGAAAGTTCAAG
1 AGGGCTTAATTGC-TTTTTTAAAAAAGGTTTGAAGG-TCTTTTTGATGCACTTTAAAAGTTCAAG
* *
27698875 TACCCAATTGAGTGCAAAAAAATGT
64 TACCCAAATGAGTGAAAAAAAATGT
27698900 AGGGACTTAATTGCTTTTTTAAAAAAGGTTTGAAGGTCTTTTTGATGCACTTTAAAAGTTCAAGT
1 AGGG-CTTAATTGCTTTTTTAAAAAAGGTTTGAAGGTCTTTTTGATGCACTTTAAAAGTTCAAGT
**
27698965 ACTGAAATGAGTGAAAAAAAA
65 ACCCAAATGAGTGAAAAAAAA
27698986 AAAGCAGAAG
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
88 15 0.21
89 55 0.75
90 3 0.04
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (88 bp):
AGGGCTTAATTGCTTTTTTAAAAAAGGTTTGAAGGTCTTTTTGATGCACTTTAAAAGTTCAAGTA
CCCAAATGAGTGAAAAAAAATGT
Found at i:27705922 original size:24 final size:22
Alignment explanation
Indices: 27705895--27705940 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
27705885 TGTGTTTCAA
27705895 GAAACACGAAAAATAGTAATCTGT
1 GAAACACGAAAAAT--TAATCTGT
**
27705919 GAAAGTCGAAAAATTAATCTGT
1 GAAACACGAAAAATTAATCTGT
27705941 CGATGTCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (22 bp):
GAAACACGAAAAATTAATCTGT
Found at i:27710075 original size:4 final size:4
Alignment explanation
Indices: 27710066--27710115 Score: 91
Period size: 4 Copynumber: 12.5 Consensus size: 4
27710056 CTCATTTCAG
*
27710066 CACT CACT CACT CACT CACT CACT CACT CACT CACT CACT CACC CACT
1 CACT CACT CACT CACT CACT CACT CACT CACT CACT CACT CACT CACT
27710114 CA
1 CA
27710116 TCATTTCTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.26, C:0.52, G:0.00, T:0.22
Consensus pattern (4 bp):
CACT
Found at i:27710947 original size:16 final size:16
Alignment explanation
Indices: 27710909--27710950 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
27710899 TTATTGAGGT
*
27710909 TTGCTTCTATGAATTG
1 TTGCTTTTATGAATTG
27710925 TTGCTTTTATGAATTG
1 TTGCTTTTATGAATTG
27710941 TTGCTTTTAT
1 TTGCTTTTAT
27710951 CTGTGTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.57
Consensus pattern (16 bp):
TTGCTTTTATGAATTG
Found at i:27711561 original size:14 final size:14
Alignment explanation
Indices: 27711540--27711580 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
27711530 ATTTTTCCAA
*
27711540 AAAAATCATTTTCT
1 AAAAATCATTTTCC
*
27711554 AGAAATCATTTTCC
1 AAAAATCATTTTCC
*
27711568 AAAAATTATTTTC
1 AAAAATCATTTTC
27711581 AATGAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (14 bp):
AAAAATCATTTTCC
Found at i:27712250 original size:28 final size:29
Alignment explanation
Indices: 27712194--27712265 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
27712184 CAACGAGTTG
* * *
27712194 TTTTCTCATTTTCTCCCAACCTCTTTTTC
1 TTTTCTCATTTTCTCCAAACATCATTTTC
27712223 TTTTCTCATTTTCTCCAAACAT-ATTTTC
1 TTTTCTCATTTTCTCCAAACATCATTTTC
*
27712251 TTCTCTCATTTTCTC
1 TTTTCTCATTTTCTC
27712266 TCAAGCACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 19 0.49
29 20 0.51
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTCTCATTTTCTCCAAACATCATTTTC
Found at i:27713735 original size:79 final size:79
Alignment explanation
Indices: 27713626--27713854 Score: 289
Period size: 79 Copynumber: 2.9 Consensus size: 79
27713616 ACGCCTCCGT
* *** * * * *
27713626 GTTACTCTGTTGATGAA-GAATATGTGATATCTGATTATGTTAGATTGATTGTTACTGCTTTTGG
1 GTTACTTTGTTGAT-AAGGAATATACAATATCTGAATATGTTAGATTGATTGTTACTGATTCTGA
27713690 TTTATAATCCTCTAC
65 TTTATAATCCTCTAC
* *
27713705 GTTACTTTGTTGATAAGGAATGTACAATATCTGAATATGTTAGATTAATTGTTACTGATTCTGAT
1 GTTACTTTGTTGATAAGGAATATACAATATCTGAATATGTTAGATTGATTGTTACTGATTCTGAT
* *
27713770 TTATGATCTTCTAC
66 TTATAATCCTCTAC
* * * * *
27713784 GTTACTTTGTTGATGAGGAATATACGATATCTGAACATGTTAGATTGATTGTTAATGATTCTAAT
1 GTTACTTTGTTGATAAGGAATATACAATATCTGAATATGTTAGATTGATTGTTACTGATTCTGAT
27713849 TTATAA
66 TTATAA
27713855 CTGTGCATGT
Statistics
Matches: 129, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
78 2 0.02
79 127 0.98
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (79 bp):
GTTACTTTGTTGATAAGGAATATACAATATCTGAATATGTTAGATTGATTGTTACTGATTCTGAT
TTATAATCCTCTAC
Found at i:27719467 original size:13 final size:13
Alignment explanation
Indices: 27719449--27719474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27719439 CGAAATTATA
27719449 ATTATAATAATTT
1 ATTATAATAATTT
27719462 ATTATAATAATTT
1 ATTATAATAATTT
27719475 CGATAAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATAATAATTT
Found at i:27728881 original size:12 final size:12
Alignment explanation
Indices: 27728864--27728891 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
27728854 ACCAAAACAG
27728864 GTTTTTAGCGGC
1 GTTTTTAGCGGC
27728876 GTTTTTAGCGGC
1 GTTTTTAGCGGC
27728888 GTTT
1 GTTT
27728892 GTATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.32, T:0.46
Consensus pattern (12 bp):
GTTTTTAGCGGC
Found at i:27728925 original size:41 final size:40
Alignment explanation
Indices: 27728880--27729012 Score: 162
Period size: 40 Copynumber: 3.3 Consensus size: 40
27728870 AGCGGCGTTT
**
27728880 TTAGCGGCGTTTGTATAAAAAACGCCGCTAAAGATCGAGCA
1 TTAGCGGCGTTT-TATGGAAAACGCCGCTAAAGATCGAGCA
*
27728921 TTAGCGGCGCTTTT-TGGAAAACGCCGCTAAAGATCGAGTA
1 TTAGCGGCG-TTTTATGGAAAACGCCGCTAAAGATCGAGCA
* * * *
27728961 TTAGTGGCGATTTATGGAAAACGCCGCTAAA-AACAAGCA
1 TTAGCGGCGTTTTATGGAAAACGCCGCTAAAGATCGAGCA
*
27729000 TTAGCGGTGTTTT
1 TTAGCGGCGTTTT
27729013 CCAGAAAGCG
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
39 18 0.23
40 48 0.61
41 10 0.13
42 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (40 bp):
TTAGCGGCGTTTTATGGAAAACGCCGCTAAAGATCGAGCA
Found at i:27729133 original size:41 final size:40
Alignment explanation
Indices: 27729063--27729443 Score: 478
Period size: 41 Copynumber: 9.3 Consensus size: 40
27729053 TTGTGAGCTT
*
27729063 TCAGGGTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTG-GAAAGCGCCGCTAATGC
*
27729104 TTAGGGCTTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGG-AAAGCGCCGCTAATGC
27729145 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGA-AAGCGCCGCTAATGC
*
27729186 TCAGGGCTTTAGTGGCGTTTTTGAGAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTG-GAAAGCGCCGCTAATGC
*
27729227 TCAGTGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGA-AAGCGCCGCTAATGC
*
27729268 TCAGTGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGA-AAGCGCCGCTAATGC
* * *
27729309 TCAGTGCTTTAGCGGCATTTTTGTTAAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTG--GAAAGCGCCGCTAATGC
** * *
27729351 TCAGGGCTTTTAGCGGCGTTTTTTATAAAGCGCCGCAAATGT
1 TCAGGGC-TTTAGCGGCG-TTTTTGGAAAGCGCCGCTAATGC
** * **
27729393 TCTA--TTTTTTGCGGCGTTTTCTAAAAAGCGCCGCTAATGC
1 TC-AGGGCTTTAGCGGCGTTTT-TGGAAAGCGCCGCTAATGC
*
27729433 TCAGGGATTTA
1 TCAGGGCTTTA
27729444 AAATAATTTA
Statistics
Matches: 305, Mismatches: 23, Indels: 24
0.87 0.07 0.07
Matches are distributed among these distances:
39 5 0.02
40 31 0.10
41 214 0.70
42 39 0.13
43 11 0.04
44 5 0.02
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.31
Consensus pattern (40 bp):
TCAGGGCTTTAGCGGCGTTTTTGGAAAGCGCCGCTAATGC
Found at i:27729779 original size:15 final size:15
Alignment explanation
Indices: 27729744--27729812 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 15
27729734 TAAAAGTTGG
* *
27729744 GGTTTAAGGTTTAAA
1 GGTTTATGGGTTAAA
*
27729759 GG-TTATGTGTTAAA
1 GGTTTATGGGTTAAA
*
27729773 GGTTTATGGGTTTAA
1 GGTTTATGGGTTAAA
*
27729788 GGTTT-TAGGGTT-TA
1 GGTTTAT-GGGTTAAA
27729802 GGTTTA-GGGTT
1 GGTTTATGGGTT
27729813 TAGGGTTTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 5 0.11
14 18 0.40
15 22 0.49
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (15 bp):
GGTTTATGGGTTAAA
Found at i:27729806 original size:14 final size:13
Alignment explanation
Indices: 27729772--27729822 Score: 66
Period size: 13 Copynumber: 3.6 Consensus size: 13
27729762 TATGTGTTAA
27729772 AGGTTTATGGGTTT
1 AGGTTTA-GGGTTT
27729786 AAGGTTTTAGGGTTT
1 -AGG-TTTAGGGTTT
27729801 AGGTTTAGGGTTT
1 AGGTTTAGGGTTT
27729814 AGGGTTTAG
1 A-GGTTTAG
27729823 ATTAACTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.32
14 10 0.29
15 9 0.26
16 4 0.12
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (13 bp):
AGGTTTAGGGTTT
Found at i:27729816 original size:20 final size:21
Alignment explanation
Indices: 27729781--27729822 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
27729771 AAGGTTTATG
*
27729781 GGTTTAAGGTTTTAGGGTTTA
1 GGTTTAAGGGTTTAGGGTTTA
27729802 GGTTT-AGGGTTTAGGGTTTA
1 GGTTTAAGGGTTTAGGGTTTA
27729822 G
1 G
27729823 ATTAACTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (21 bp):
GGTTTAAGGGTTTAGGGTTTA
Found at i:27729822 original size:7 final size:7
Alignment explanation
Indices: 27729675--27729822 Score: 68
Period size: 7 Copynumber: 20.7 Consensus size: 7
27729665 ATGTTACCAT
*
27729675 TTTAAGG
1 TTTAGGG
*
27729682 TTTATGG
1 TTTAGGG
*
27729689 ATTATGGG
1 TTTA-GGG
27729697 TTTAGGG
1 TTTAGGG
* *
27729704 GTTACGG
1 TTTAGGG
*
27729711 TTTATGG
1 TTTAGGG
*
27729718 TTTATGG
1 TTTAGGG
*
27729725 TTTATGG
1 TTTAGGG
**
27729732 TTTAAAAG
1 TTT-AGGG
*
27729740 -TTGGGG
1 TTTAGGG
*
27729746 TTTAAGG
1 TTTAGGG
*
27729753 TTTAAAGG
1 TTT-AGGG
*
27729761 -TTATGTG
1 TTTA-GGG
* *
27729768 TTAAAGG
1 TTTAGGG
27729775 TTTATGGG
1 TTTA-GGG
*
27729783 TTTAAGGT
1 TTT-AGGG
27729791 TTTAGGG
1 TTTAGGG
27729798 TTTA-GG
1 TTTAGGG
27729804 TTTAGGG
1 TTTAGGG
27729811 TTTAGGG
1 TTTAGGG
27729818 TTTAG
1 TTTAG
27729823 ATTAACTAGT
Statistics
Matches: 108, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
6 8 0.07
7 76 0.70
8 23 0.21
9 1 0.01
ACGTcount: A:0.21, C:0.01, G:0.33, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:27730096 original size:21 final size:22
Alignment explanation
Indices: 27730078--27730155 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
27730068 GGATTAAGGG
*
27730078 TAGGGATTTAAGGTTTAAGTGT
1 TAGGGATTTAAGGTTTAAGAGT
* * *
27730100 TA-AGAGTTAAGGGTTAAGAGT
1 TAGGGATTTAAGGTTTAAGAGT
* * *
27730121 TAGGGATTTAGGGTTTATGATT
1 TAGGGATTTAAGGTTTAAGAGT
*
27730143 TAGGGATTCAAGG
1 TAGGGATTTAAGG
27730156 GTCGGGTTAG
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 17 0.40
22 26 0.60
ACGTcount: A:0.29, C:0.01, G:0.33, T:0.36
Consensus pattern (22 bp):
TAGGGATTTAAGGTTTAAGAGT
Found at i:27730102 original size:14 final size:14
Alignment explanation
Indices: 27730092--27730122 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27730082 GATTTAAGGT
*
27730092 TTAAGTGTTAAGAG
1 TTAAGGGTTAAGAG
27730106 TTAAGGGTTAAGAG
1 TTAAGGGTTAAGAG
27730120 TTA
1 TTA
27730123 GGGATTTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAAGAG
Found at i:27733060 original size:23 final size:24
Alignment explanation
Indices: 27733029--27733073 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
27733019 TCGGAACTTA
* *
27733029 ATTTATTTATTTTTATTATTTTAG
1 ATTTATTTATATTTATAATTTTAG
27733053 ATTT-TTTATATTTATAATTTT
1 ATTTATTTATATTTATAATTTT
27733074 TTTCCTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (24 bp):
ATTTATTTATATTTATAATTTTAG
Found at i:27733064 original size:16 final size:17
Alignment explanation
Indices: 27733038--27733075 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
27733028 AATTTATTTA
27733038 TTTTTATTATTT-TAGAT
1 TTTTTATTATTTATA-AT
27733055 TTTTTA-TATTTATAAT
1 TTTTTATTATTTATAAT
27733071 TTTTT
1 TTTTT
27733076 TCCTTATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTATTATTTATAAT
Found at i:27733966 original size:16 final size:16
Alignment explanation
Indices: 27733945--27733979 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
27733935 TGCCTACATG
27733945 TATATATATATTAGAT
1 TATATATATATTAGAT
27733961 TATATATATATTAGAT
1 TATATATATATTAGAT
27733977 TAT
1 TAT
27733980 TCAAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
TATATATATATTAGAT
Found at i:27734910 original size:27 final size:26
Alignment explanation
Indices: 27734880--27734936 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
27734870 AATTTCGAGG
*
27734880 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
* *
27734906 ATTTACGTTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
27734933 TTTA
1 TTTA
27734937 TTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:27735232 original size:43 final size:43
Alignment explanation
Indices: 27735168--27735463 Score: 441
Period size: 43 Copynumber: 6.9 Consensus size: 43
27735158 GTTTGTTCTA
* * * *
27735168 TAGCGGCGTTTGTGGGGAAAAGCGTCGCTGAAGGTCCTGGTCTT
1 TAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGGTCATGGTCTT
**
27735212 TAGCGGCGTTTGTGGAAAAAGCGCCATTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTT
* * *
27735255 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTT
*
27735298 TAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTT
* *
27735341 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTT
*
27735384 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTT
* *
27735427 TAGCGGCGTTTGTGG-GAAAGTGCCGCTAAAGGTCATG
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATG
27735464 ACTTTTAGCG
Statistics
Matches: 231, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
42 20 0.09
43 198 0.86
44 13 0.06
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTT
Found at i:27735272 original size:86 final size:86
Alignment explanation
Indices: 27735168--27735460 Score: 498
Period size: 86 Copynumber: 3.4 Consensus size: 86
27735158 GTTTGTTCTA
* *
27735168 TAGCGGCGTTTGTGGGGAAAAGCGTCGCTGAAGGTCCTGGTCTTTAGCGGCGTTTGTGGAAAAAG
1 TAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGAAAAAG
**
27735233 CGCCATTAAAGGTCATGGTCTT
65 CGCCGCTAAAGGTCATGGTCTT
* *
27735255 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGAAAAAGT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGAAAAAGC
27735320 GCCGCTAAAGGTCATGGTCTT
66 GCCGCTAAAGGTCATGGTCTT
27735341 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGAAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGAAAAAGC
*
27735406 GCCGCTAAAGGTCATGGTCTA
66 GCCGCTAAAGGTCATGGTCTT
*
27735427 TAGCGGCGTTTGTGGG-AAAGTGCCGCTAAAGGTC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
27735461 ATGACTTTTA
Statistics
Matches: 196, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
85 17 0.09
86 166 0.85
87 13 0.07
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.26
Consensus pattern (86 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGAAAAAGC
GCCGCTAAAGGTCATGGTCTT
Found at i:27735674 original size:2 final size:2
Alignment explanation
Indices: 27735667--27735696 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27735657 ATATAGACAC
27735667 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
27735697 AACAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27737597 original size:22 final size:21
Alignment explanation
Indices: 27737559--27737602 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
27737549 TTGATATTCT
27737559 TAATATTTGGTTAATATTAAA
1 TAATATTTGGTTAATATTAAA
* *
27737580 TAATGATTTTGTTGATATTAAA
1 TAAT-ATTTGGTTAATATTAAA
27737602 T
1 T
27737603 TTAACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (21 bp):
TAATATTTGGTTAATATTAAA
Found at i:27741141 original size:114 final size:114
Alignment explanation
Indices: 27740965--27741610 Score: 963
Period size: 114 Copynumber: 5.7 Consensus size: 114
27740955 AAAATAAGCA
** * * * *
27740965 TTAGCGGCGTTTTCCAGACAGCGCCGC-TAAAAACCTAAGCCCAACGACGCCGGTTTCCGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
27741029 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
27741078 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCATTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
27741143 TCGGGGATTTAGCAGCGTTCTTAAGAAAGCGCCGCTAATGCTCAGGACT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
27741192 TTAGCGCCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
27741257 TCGTGGATTTAGCGACGTTTTTAATAAAGCGCCGCTAATGTTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
** * * * * *
27741306 TTAGTAGTGATTTTGAGAAAGAGCCGCAAAAAAACCTAAGCCCAATGATGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
27741371 TCGTGGATTTAGCAGCGTTTTTAATAAAGCGCCGCTAATGTTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
*
27741420 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAA-CCCAACGACGCCTTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
27741484 TTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * *
27741533 TTCAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGACGCCGTTTTCTAATCT
1 TT-AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
27741598 TTCGGGGATTTAG
65 TTCGGGGATTTAG
27741611 TGGCACTTTT
Statistics
Matches: 480, Mismatches: 50, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
113 92 0.19
114 355 0.74
115 33 0.07
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:27741691 original size:91 final size:92
Alignment explanation
Indices: 27741529--27741711 Score: 323
Period size: 91 Copynumber: 2.0 Consensus size: 92
27741519 TAATGCTCAG
*
27741529 GGCTTTCAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGACGCCGTTTTCTA
1 GGCTTTCAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTA
*
27741594 ATCTTTCGGGGATTTAGTGGCACTTTT
66 AGCTTTCGGGGATTTAGTGGCACTTTT
*
27741621 GGCTTT-AGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
1 GGCTTTCAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTA
*
27741685 AGCTTTCGGGGATTTAGTGGCATTTTT
66 AGCTTTCGGGGATTTAGTGGCACTTTT
27741712 AATAAAGCGC
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 81 0.93
92 6 0.07
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (92 bp):
GGCTTTCAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTA
AGCTTTCGGGGATTTAGTGGCACTTTT
Found at i:27741760 original size:41 final size:41
Alignment explanation
Indices: 27741697--27741775 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
27741687 CTTTCGGGGA
* *
27741697 TTTAGTGGCATTTTTAATAAAGCGCCGCTAATGCTCAGTGC
1 TTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGTGC
* *
27741738 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAG
1 TTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAG
27741776 AGATTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGTGC
Found at i:27742024 original size:21 final size:21
Alignment explanation
Indices: 27741956--27742110 Score: 86
Period size: 21 Copynumber: 7.2 Consensus size: 21
27741946 TATCACTATA
27741956 GTTT-AGGGTATATGGTTT-AG
1 GTTTAAGGGT-TATGGTTTAAG
* * *
27741976 AGTTTAAGGTTTATGGATTATGG
1 -GTTTAAGGGTTATGGTTTA-AG
*
27741999 GTTTAGGGGTTATGGTTTAAG
1 GTTTAAGGGTTATGGTTTAAG
* *
27742020 GTTTAAAGGCTGA-GGTTTAAG
1 GTTT-AAGGGTTATGGTTTAAG
* * *
27742041 TTTTAAAGGTTAT-ATGTTAAGG
1 GTTTAAGGGTTATGGT-TTAA-G
* *
27742063 GTTTATGGGTTTAGGGTTTTAAG
1 GTTTAAGGG-TTATGG-TTTAAG
* *
27742086 GTTTAA-GTTTATGGTTTAGG
1 GTTTAAGGGTTATGGTTTAAG
27742106 GTTTA
1 GTTTA
27742111 GATTAACTAG
Statistics
Matches: 100, Mismatches: 24, Indels: 21
0.69 0.17 0.14
Matches are distributed among these distances:
20 16 0.16
21 36 0.36
22 33 0.33
23 10 0.10
24 4 0.04
25 1 0.01
ACGTcount: A:0.23, C:0.01, G:0.32, T:0.45
Consensus pattern (21 bp):
GTTTAAGGGTTATGGTTTAAG
Found at i:27742109 original size:14 final size:14
Alignment explanation
Indices: 27741956--27742110 Score: 91
Period size: 14 Copynumber: 10.9 Consensus size: 14
27741946 TATCACTATA
*
27741956 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
27741970 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
* *
27741984 GTTTATGGATTATGG
1 GTTTAGGGTTTAT-G
*
27741999 GTTTAGGGGTTATG
1 GTTTAGGGTTTATG
* *
27742013 GTTTAAGGTTTAAAG
1 GTTTAGGGTTT-ATG
* * *
27742028 GCTGA-GGTTTAAG
1 GTTTAGGGTTTATG
* *
27742041 TTTTAAAGGTTATAT-
1 GTTT-AGGGTT-TATG
*
27742056 GTTAAGGGTTTATGG
1 GTTTAGGGTTTAT-G
*
27742071 GTTTAGGGTTTTAAG
1 GTTTAGGG-TTTATG
*
27742086 GTTTA-AGTTTATG
1 GTTTAGGGTTTATG
27742099 GTTTAGGGTTTA
1 GTTTAGGGTTTA
27742111 GATTAACTAG
Statistics
Matches: 106, Mismatches: 26, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
13 17 0.16
14 47 0.44
15 36 0.34
16 6 0.06
ACGTcount: A:0.23, C:0.01, G:0.32, T:0.45
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:27742111 original size:7 final size:7
Alignment explanation
Indices: 27741956--27742111 Score: 57
Period size: 7 Copynumber: 21.9 Consensus size: 7
27741946 TATCACTATA
27741956 GTTTAGG
1 GTTTAGG
* *
27741963 GTATATG
1 GTTTAGG
*
27741970 GTTTAGA
1 GTTTAGG
*
27741977 GTTTAAG
1 GTTTAGG
*
27741984 GTTTATG
1 GTTTAGG
*
27741991 GATTATGG
1 GTTTA-GG
27741999 GTTTAGG
1 GTTTAGG
* *
27742006 GGTTATG
1 GTTTAGG
*
27742013 GTTTAAG
1 GTTTAGG
*
27742020 GTTTAAAG
1 GTTT-AGG
* *
27742028 GCTGA-G
1 GTTTAGG
*
27742034 GTTTAAG
1 GTTTAGG
* *
27742041 TTTTAAAG
1 GTTT-AGG
*
27742049 GTTATA-T
1 GTT-TAGG
*
27742056 GTTAAGG
1 GTTTAGG
27742063 GTTTATGG
1 GTTTA-GG
27742071 GTTTAGG
1 GTTTAGG
*
27742078 GTTTTAAG
1 G-TTTAGG
*
27742086 GTTTA-A
1 GTTTAGG
*
27742092 GTTTATG
1 GTTTAGG
27742099 GTTTAGG
1 GTTTAGG
27742106 GTTTAG
1 GTTTAG
27742112 ATTAACTAGT
Statistics
Matches: 111, Mismatches: 29, Indels: 18
0.70 0.18 0.11
Matches are distributed among these distances:
6 10 0.09
7 71 0.64
8 29 0.26
9 1 0.01
ACGTcount: A:0.23, C:0.01, G:0.32, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:27742258 original size:7 final size:7
Alignment explanation
Indices: 27742248--27742295 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
27742238 AATTTAAGGT
27742248 TTAGGGG
1 TTAGGGG
*
27742255 TTAGTGG
1 TTAGGGG
27742262 TTAGGGG
1 TTAGGGG
* *
27742269 TTAAGAG
1 TTAGGGG
*
27742276 TTAGGGAT
1 TTAGGG-G
27742284 TTAGGGG
1 TTAGGGG
27742291 TTAGG
1 TTAGG
27742296 ACTTAAGGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:27742305 original size:22 final size:22
Alignment explanation
Indices: 27742262--27742306 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
27742252 GGGTTAGTGG
* *
27742262 TTAGGGGTTAAGAGTTAGGGAT
1 TTAGGGGTTAAGACTTAAGGAT
*
27742284 TTAGGGGTTAGGACTTAAGGAT
1 TTAGGGGTTAAGACTTAAGGAT
27742306 T
1 T
27742307 CAAGGGTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (22 bp):
TTAGGGGTTAAGACTTAAGGAT
Found at i:27742641 original size:19 final size:18
Alignment explanation
Indices: 27742612--27742665 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
27742602 GGACCAAATT
*
27742612 ATAAGAAATAAAATTAAA
1 ATAAAAAATAAAATTAAA
* *
27742630 ATACAAAAATAAAAATGAA
1 ATA-AAAAATAAAATTAAA
27742649 ATAAAAACACTAAAATT
1 ATAAAAA-A-TAAAATT
27742666 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (18 bp):
ATAAAAAATAAAATTAAA
Found at i:27746620 original size:2 final size:2
Alignment explanation
Indices: 27746615--27746643 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27746605 GTGTGTTTTA
27746615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27746644 CACTGATTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27747067 original size:91 final size:91
Alignment explanation
Indices: 27746912--27747097 Score: 372
Period size: 91 Copynumber: 2.0 Consensus size: 91
27746902 GAATTTCCAT
27746912 TTTAATACGTCTTCAAATTAAATTATACATTTCTAAATTGGATTTGTGGTGTTTTTATAAGATTT
1 TTTAATACGTCTTCAAATTAAATTATACATTTCTAAATTGGATTTGTGGTGTTTTTATAAGATTT
27746977 TAATTTTAACTTTATTTTTTATGACC
66 TAATTTTAACTTTATTTTTTATGACC
27747003 TTTAATACGTCTTCAAATTAAATTATACATTTCTAAATTGGATTTGTGGTGTTTTTATAAGATTT
1 TTTAATACGTCTTCAAATTAAATTATACATTTCTAAATTGGATTTGTGGTGTTTTTATAAGATTT
27747068 TAATTTTAACTTTATTTTTTATGACC
66 TAATTTTAACTTTATTTTTTATGACC
27747094 TTTA
1 TTTA
27747098 GTGGCGCTTT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 95 1.00
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.52
Consensus pattern (91 bp):
TTTAATACGTCTTCAAATTAAATTATACATTTCTAAATTGGATTTGTGGTGTTTTTATAAGATTT
TAATTTTAACTTTATTTTTTATGACC
Found at i:27747141 original size:43 final size:42
Alignment explanation
Indices: 27747113--27747232 Score: 197
Period size: 43 Copynumber: 2.8 Consensus size: 42
27747103 GCTTTTATCA
27747113 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GTT
27747156 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTG-TT
*
27747199 AAAGCG-CGATTAAAGATCATGTTCTTTAGCGGCG
1 AAAGCGCCG-CTAAAGATCATGTTCTTTAGCGGCG
27747233 CTTTAAACAC
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
42 3 0.04
43 71 0.96
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGTT
Found at i:27747363 original size:22 final size:23
Alignment explanation
Indices: 27747328--27747370 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
27747318 TAGCGGCGCT
* *
27747328 AAAAAGCGCTGCTAAAGGCCTAA
1 AAAAAGCGCCGCTAAAAGCCTAA
27747351 AAAAAG-GCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
27747371 GTTTTGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (23 bp):
AAAAAGCGCCGCTAAAAGCCTAA
Done.