Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 148 of 198
Found at i:46948380 original size:15 final size:15
Alignment explanation
Indices: 46948360--46948396 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
46948350 TTTACAATTT
46948360 CAATTTCAATTCGTC
1 CAATTTCAATTCGTC
46948375 CAATTTCAATTCGTC
1 CAATTTCAATTCGTC
46948390 CATATTT
1 CA-ATTT
46948397 TTAATTCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.43
Consensus pattern (15 bp):
CAATTTCAATTCGTC
Found at i:46948736 original size:27 final size:27
Alignment explanation
Indices: 46948683--46948737 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
46948673 TATGTGCTAA
* * *
46948683 GAATCTTCCTCTTCTGTTGAGTTACCC
1 GAATCTTCCTCTTCTGGTAAGTAACCC
*
46948710 GAATCTTCCTCTTTTGGTAAGTAACCC
1 GAATCTTCCTCTTCTGGTAAGTAACCC
46948737 G
1 G
46948738 TAATGATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.38
Consensus pattern (27 bp):
GAATCTTCCTCTTCTGGTAAGTAACCC
Found at i:46951220 original size:18 final size:18
Alignment explanation
Indices: 46951193--46951236 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
46951183 ATAAATAAAA
46951193 TAAAGTAAGTAAAAGAAAC
1 TAAAG-AAGTAAAAGAAAC
46951212 TAAAGAAGTAAAAGAAAC
1 TAAAGAAGTAAAAGAAAC
*
46951230 AAAAGAA
1 TAAAGAA
46951237 CAGCAGAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.68, C:0.05, G:0.16, T:0.11
Consensus pattern (18 bp):
TAAAGAAGTAAAAGAAAC
Found at i:46952492 original size:18 final size:18
Alignment explanation
Indices: 46952469--46952504 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
46952459 GACACTGGGT
46952469 GTCATACTGTTACTTCGG
1 GTCATACTGTTACTTCGG
46952487 GTCATACTGTTACTTCGG
1 GTCATACTGTTACTTCGG
46952505 ATAGATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (18 bp):
GTCATACTGTTACTTCGG
Found at i:46953350 original size:27 final size:27
Alignment explanation
Indices: 46953320--46953372 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
46953310 ATGCATGAAT
*
46953320 GATTTATTAATGGTAAAATAGTGGTAA
1 GATTTAATAATGGTAAAATAGTGGTAA
*
46953347 GATTTAATGATGGTAAAATAGTGGTA
1 GATTTAATAATGGTAAAATAGTGGTA
46953373 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.36
Consensus pattern (27 bp):
GATTTAATAATGGTAAAATAGTGGTAA
Found at i:46953378 original size:2 final size:2
Alignment explanation
Indices: 46953371--46953395 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46953361 AAAATAGTGG
46953371 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46953396 GATGTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46971546 original size:16 final size:16
Alignment explanation
Indices: 46971525--46971558 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46971515 TACTTAAAAG
46971525 TTAAAACTAATTGTTA
1 TTAAAACTAATTGTTA
* *
46971541 TTAAAATTCATTGTTA
1 TTAAAACTAATTGTTA
46971557 TT
1 TT
46971559 GAATTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:46971659 original size:25 final size:25
Alignment explanation
Indices: 46971629--46971676 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
46971619 AAGATTACTT
46971629 ATTTGAATTTAATTACAAACAATTA
1 ATTTGAATTTAATTACAAACAATTA
46971654 ATTTGAATTTAATTACAAACAAT
1 ATTTGAATTTAATTACAAACAAT
46971677 CAAATCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTGAATTTAATTACAAACAATTA
Found at i:46971755 original size:8 final size:8
Alignment explanation
Indices: 46971742--46971774 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
46971732 ATTTAATTAC
46971742 TTTTAACT
1 TTTTAACT
46971750 TTTTAACT
1 TTTTAACT
46971758 TTTTAACT
1 TTTTAACT
46971766 TTTTAACT
1 TTTTAACT
46971774 T
1 T
46971775 AAATATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTAACT
Found at i:46972516 original size:9 final size:9
Alignment explanation
Indices: 46972484--46972517 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
46972474 ATGATCGTCG
*
46972484 TCGTCGTCA
1 TCGTCCTCA
*
46972493 TCGTCATCA
1 TCGTCCTCA
46972502 TCGTCCTCA
1 TCGTCCTCA
46972511 TCGTCCT
1 TCGTCCT
46972518 TTTTGCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.38, G:0.15, T:0.35
Consensus pattern (9 bp):
TCGTCCTCA
Found at i:46974499 original size:22 final size:22
Alignment explanation
Indices: 46974471--46974522 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
46974461 AGTGAAGCAC
*
46974471 CGTGGAGTCGTTGAGTC-GTGGA
1 CGTGGAGTCG-TGAATCGGTGGA
46974493 CGTGGAGTCGTGAATCGGTGGA
1 CGTGGAGTCGTGAATCGGTGGA
*
46974515 GGTGGAGT
1 CGTGGAGT
46974523 TGGATCCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.15, C:0.12, G:0.48, T:0.25
Consensus pattern (22 bp):
CGTGGAGTCGTGAATCGGTGGA
Found at i:46975442 original size:29 final size:30
Alignment explanation
Indices: 46975383--46975440 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46975373 TCCGAGCCTT
**
46975383 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATAAAAAAGTTTA
* *
46975413 GGGGCAAAATTGTAATTTTAAAAAAGTT
1 GGGGCAAAAATGTAATTATAAAAAAGTT
46975441 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATAAAAAAGTTTA
Found at i:46975946 original size:50 final size:50
Alignment explanation
Indices: 46975871--46976144 Score: 368
Period size: 50 Copynumber: 5.4 Consensus size: 50
46975861 NNNNNNNNNN
46975871 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
1 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
* * * ** *
46975921 TGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCTATGTAAGACCA
1 TGTCTGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCA
* **
46975972 TGTCTAGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCA
1 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
**
46976022 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCA
1 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
* * * * **
46976072 TGTCTGGGACATAGCATGGGCACCGATATGAGAACATCCCATGTAAGACCA
1 TGTCTGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCA
*
46976123 TGTCTGGGACATGGCTTTGGCA
1 TGTCTGGGACATGGCGTTGGCA
46976145 TGTTATTATC
Statistics
Matches: 195, Mismatches: 27, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
50 119 0.61
51 76 0.39
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
Found at i:46976046 original size:101 final size:100
Alignment explanation
Indices: 46975871--46976144 Score: 368
Period size: 101 Copynumber: 2.7 Consensus size: 100
46975861 NNNNNNNNNN
46975871 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
* * * *
46975936 ATGGGCACCGATATGAGAACATCCTATGTAAGACCA
66 ATTGGCACCGAGATGAG-ACATCCCACGTAAGACCA
* **
46975972 TGTCTAGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGC
1 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
* ** *
46976037 GTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCA
66 ATTGGCACCGAGATGAGACATCCCACGTAAGACCA
* * * * **
46976072 TGTCTGGGACATAGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTCTGGGACATGG
1 TGTCTGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTCTGGGACATGG
*
46976137 CTTTGGCA
65 CATTGGCA
46976145 TGTTATTATC
Statistics
Matches: 151, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
100 40 0.26
101 111 0.74
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (100 bp):
TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
ATTGGCACCGAGATGAGACATCCCACGTAAGACCA
Found at i:46977519 original size:9 final size:8
Alignment explanation
Indices: 46977500--46977529 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
46977490 TATTAATGAC
46977500 AAAATAAA
1 AAAATAAA
46977508 AAAATAAA
1 AAAATAAA
46977516 AAAATAAA
1 AAAATAAA
46977524 AGAAAT
1 A-AAAT
46977530 TATATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAATAAA
Found at i:46977996 original size:22 final size:23
Alignment explanation
Indices: 46977943--46977998 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
46977933 CCCGTTTTTA
* * *
46977943 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
46977966 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
46977988 ATTAAAATTAA
1 ATTAAAATTAA
46977999 TTATTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:46978011 original size:16 final size:16
Alignment explanation
Indices: 46977974--46978013 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
46977964 TTAATAAAAT
* * *
46977974 TAAAACTAATTGTTAT
1 TAAAATTAATTATTAG
46977990 TAAAATTAATTATTAG
1 TAAAATTAATTATTAG
46978006 TAAAATTA
1 TAAAATTA
46978014 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTATTAG
Found at i:46978119 original size:9 final size:9
Alignment explanation
Indices: 46978086--46978113 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
46978076 TTTATCAAAT
46978086 TATTAATTG
1 TATTAATTG
46978095 TATTAATTG
1 TATTAATTG
46978104 TATTAATTG
1 TATTAATTG
46978113 T
1 T
46978114 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:46978124 original size:68 final size:68
Alignment explanation
Indices: 46978001--46978211 Score: 390
Period size: 68 Copynumber: 3.1 Consensus size: 68
46977991 AAAATTAATT
*
46978001 ATTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACAT
1 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
46978064 TTG
66 TTG
46978067 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
1 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
46978132 TTG
66 TTG
*
46978135 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACAT
1 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
46978200 TTG
66 TTG
46978203 ATTAGTAAA
1 ATTAGTAAA
46978212 ACAAACTTGA
Statistics
Matches: 141, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
68 114 0.81
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (68 bp):
ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
TTG
Found at i:46978166 original size:9 final size:9
Alignment explanation
Indices: 46978154--46978181 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
46978144 TTTATCAAAT
46978154 TATTAATTG
1 TATTAATTG
46978163 TATTAATTG
1 TATTAATTG
46978172 TATTAATTG
1 TATTAATTG
46978181 T
1 T
46978182 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:46978318 original size:22 final size:24
Alignment explanation
Indices: 46978278--46978321 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
46978268 AAATAAACTT
46978278 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
46978302 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
46978322 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:46978735 original size:18 final size:19
Alignment explanation
Indices: 46978709--46978745 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
46978699 GATAAATTAT
*
46978709 ATTAGTAAAAATAT-TTTA
1 ATTAATAAAAATATATTTA
46978727 ATTAATAAAAATATATTTA
1 ATTAATAAAAATATATTTA
46978746 TAGGGATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTAATAAAAATATATTTA
Found at i:46983812 original size:9 final size:9
Alignment explanation
Indices: 46983798--46983847 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
46983788 TTTTTTCATA
46983798 AAAAATTAT
1 AAAAATTAT
*
46983807 AAAAATTCT
1 AAAAATTAT
*
46983816 AATAATTAT
1 AAAAATTAT
46983825 -AAAATTAAT
1 AAAAATT-AT
46983834 AAAAACTTAT
1 AAAAA-TTAT
46983844 AAAA
1 AAAA
46983848 GAGTCATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 5 0.15
9 17 0.50
10 10 0.29
11 2 0.06
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:46990838 original size:20 final size:20
Alignment explanation
Indices: 46990803--46990840 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46990793 GCTAACAAAA
**
46990803 TAGTCACTCAGGTTTCAATT
1 TAGTCACTCAACTTTCAATT
46990823 TAGTCACTCAACTTTCAA
1 TAGTCACTCAACTTTCAA
46990841 AAATGACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (20 bp):
TAGTCACTCAACTTTCAATT
Found at i:46991937 original size:3 final size:3
Alignment explanation
Indices: 46991929--46991988 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
46991919 TTATAGGATC
* *
46991929 TCT TCT TCT TCT TCT TCT TCT TCT TCT TAT TCT TCT TCT TAT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
46991977 TCT TCT TCT TCT
1 TCT TCT TCT TCT
46991989 GTTATTTGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:46992198 original size:30 final size:32
Alignment explanation
Indices: 46992132--46992202 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
46992122 ATGTTAGTGG
*
46992132 GTGACTGATTTGTCATTTTTTTTGAAAATGTTA
1 GTGACTGATTTGTCA-TTTTTTCGAAAATGTTA
*
46992165 GTGACTGGTTTGTCA-TTTTTCG-AAA-GTTGA
1 GTGACTGATTTGTCATTTTTTCGAAAATGTT-A
46992195 GTGACTGA
1 GTGACTGA
46992203 ATTGAAACCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 6 0.18
33 14 0.41
ACGTcount: A:0.23, C:0.08, G:0.24, T:0.45
Consensus pattern (32 bp):
GTGACTGATTTGTCATTTTTTCGAAAATGTTA
Found at i:46992288 original size:10 final size:10
Alignment explanation
Indices: 46992269--46992325 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
46992259 TAATTTACCC
46992269 AAAAATTTATT
1 AAAAA-TTATT
46992280 AAAAATTA-T
1 AAAAATTATT
46992289 AAAACATTATT
1 AAAA-ATTATT
*
46992300 TAAAATT-TGT
1 AAAAATTAT-T
46992310 AAAAATTATT
1 AAAAATTATT
46992320 AAAAAT
1 AAAAAT
46992326 AGTAAATAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 6 0.15
10 24 0.60
11 10 0.25
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
AAAAATTATT
Found at i:46992298 original size:20 final size:19
Alignment explanation
Indices: 46992269--46992357 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 19
46992259 TAATTTACCC
46992269 AAAAATTTATTAAAAATTAT
1 AAAAA-TTATTAAAAATTAT
* *
46992289 AAAACATTATTTAAAATTTGT
1 AAAA-ATTA-TTAAAAATTAT
46992310 AAAAATTATTAAAAA-TAGT
1 AAAAATTATTAAAAATTA-T
* * *
46992329 AAATAGTTGTTAAAAATTGT
1 AAA-AATTATTAAAAATTAT
46992349 AAATAATTA
1 AAA-AATTA
46992358 ACAAATTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.02
19 10 0.18
20 29 0.53
21 15 0.27
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (19 bp):
AAAAATTATTAAAAATTAT
Found at i:46992331 original size:9 final size:10
Alignment explanation
Indices: 46992269--46992357 Score: 51
Period size: 10 Copynumber: 8.8 Consensus size: 10
46992259 TAATTTACCC
*
46992269 AAAAATTTATT
1 AAAAA-TTAGT
46992280 AAAAATTA-T
1 AAAAATTAGT
*
46992289 AAAACATTATT
1 AAAA-ATTAGT
* *
46992300 TAAAATTTGT
1 AAAAATTAGT
*
46992310 AAAAATTATT
1 AAAAATTAGT
46992320 AAAAA-TAGT
1 AAAAATTAGT
*
46992329 AAATAGTT-GTT
1 AAA-AATTAG-T
46992340 AAAAATT-GT
1 AAAAATTAGT
46992349 AAATAATTA
1 AAA-AATTA
46992358 ACAAATTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
9 15 0.24
10 33 0.53
11 14 0.23
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (10 bp):
AAAAATTAGT
Found at i:46997692 original size:19 final size:18
Alignment explanation
Indices: 46997647--46997693 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
46997637 TAAATGCCAC
46997647 AATAATTTTCAAAATTTTT
1 AATAA-TTTCAAAATTTTT
*
46997666 ATTAAATTTCAAAAGTTTTT
1 AAT-AATTTCAAAA-TTTTT
46997686 AATAATTT
1 AATAATTT
46997694 TTTACAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (18 bp):
AATAATTTCAAAATTTTT
Found at i:46997773 original size:28 final size:28
Alignment explanation
Indices: 46997715--46997769 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
46997705 TAATATTGTT
* *
46997715 TTTAAAATTTTTATTAATTTTTCAATTA
1 TTTAAAATTTTTATTAATTTTTAAATAA
46997743 TTTAAATATTTTTA-TAA-TTTTAAATAA
1 TTTAAA-ATTTTTATTAATTTTTAAATAA
46997770 ATTTTGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 9 0.38
29 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTAAAATTTTTATTAATTTTTAAATAA
Found at i:46998493 original size:16 final size:15
Alignment explanation
Indices: 46998472--46998510 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
46998462 ATAAATTATA
46998472 TTAATAATTTATCATT
1 TTAATAATTTAT-ATT
*
46998488 TTAATAAATTATATT
1 TTAATAATTTATATT
*
46998503 TAAATAAT
1 TTAATAAT
46998511 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATAATTTATATT
Found at i:46999920 original size:19 final size:18
Alignment explanation
Indices: 46999888--46999925 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
46999878 CCGGATTTAG
46999888 TTTATAATTAATTTTAAAT
1 TTTATAATTAA-TTTAAAT
46999907 TTTATAA-TATATTTAAAT
1 TTTATAATTA-ATTTAAAT
46999925 T
1 T
46999926 AACAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATAATTAATTTAAAT
Found at i:47000457 original size:22 final size:22
Alignment explanation
Indices: 47000401--47000459 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
47000391 CTAGTCATTT
47000401 TATATTTT--AAATATATTTTA
1 TATATTTTAAAAATATATTTTA
**
47000421 TA-ATTAAAAATAATATATTTTA
1 TATATTTTAAA-AATATATTTTA
47000443 TATATTTTAAAAATATA
1 TATATTTTAAAAATATA
47000460 CAATTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 3 0.10
20 2 0.06
21 1 0.03
22 19 0.61
23 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTTTAAAAATATATTTTA
Found at i:47000465 original size:25 final size:26
Alignment explanation
Indices: 47000424--47000481 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
47000414 TATTTTATAA
* *
47000424 TTAAAAATAATATATTTTATATA-TT
1 TTAAAAATAATAAATTTTATAGAGTT
*
47000449 TTAAAAAT-ATACAATTTTTTAGAGTT
1 TTAAAAATAATA-AATTTTATAGAGTT
47000475 TTAAAAA
1 TTAAAAA
47000482 ACAAAATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 16 0.57
26 9 0.32
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (26 bp):
TTAAAAATAATAAATTTTATAGAGTT
Found at i:47001319 original size:23 final size:23
Alignment explanation
Indices: 47001276--47001322 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
47001266 CATTTATCTA
*
47001276 TTTTTGAATTTTTTATCTATTTT
1 TTTTTGAATTTTCTATCTATTTT
* *
47001299 TTTTTGAATTTTCTGTTTATTTT
1 TTTTTGAATTTTCTATCTATTTT
47001322 T
1 T
47001323 AGATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (23 bp):
TTTTTGAATTTTCTATCTATTTT
Found at i:47010160 original size:25 final size:25
Alignment explanation
Indices: 47010083--47010168 Score: 118
Period size: 26 Copynumber: 3.3 Consensus size: 25
47010073 AACTTTCTTG
* *
47010083 AAATTTTATCAGGGCTAAAATCGTTA
1 AAATTTTATC-GGGGTAAAATCGTCA
47010109 AAATTTTATCGGGGTTAAAATCGTCA
1 AAATTTTATCGGGG-TAAAATCGTCA
*
47010135 AAATTTTATCGGGGTAAAATCATCAA
1 AAATTTTATCGGGGTAAAATCGTC-A
47010161 AAATTTTA
1 AAATTTTA
47010169 CTAGAGTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
25 12 0.22
26 43 0.78
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (25 bp):
AAATTTTATCGGGGTAAAATCGTCA
Found at i:47011322 original size:25 final size:26
Alignment explanation
Indices: 47011287--47011335 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
47011277 TGTACATCAG
*
47011287 AATAATATCTTTAGA-AATTTTTTAA
1 AATAATATCTTCAGAGAATTTTTTAA
*
47011312 AATAATCTCTTCAGAGAATTTTTT
1 AATAATATCTTCAGAGAATTTTTT
47011336 CTATACAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (26 bp):
AATAATATCTTCAGAGAATTTTTTAA
Found at i:47011530 original size:31 final size:31
Alignment explanation
Indices: 47011474--47011551 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
47011464 TAGATTAAAT
47011474 TTAATATTAAATCT--TATTAAAATAATAACA
1 TTAATATTAAAT-TAATATTAAAATAATAACA
* * *
47011504 TTAA-ATTAAATTTAATATTAAGATAATCACT
1 TTAATATTAAA-TTAATATTAAAATAATAACA
47011535 TTAATATTAAATTAATA
1 TTAATATTAAATTAATA
47011552 AAATACAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.17
30 5 0.12
31 23 0.56
32 6 0.15
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (31 bp):
TTAATATTAAATTAATATTAAAATAATAACA
Found at i:47011550 original size:20 final size:18
Alignment explanation
Indices: 47011503--47011551 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
47011493 AAATAATAAC
47011503 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
47011520 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
47011540 ATTAAATTAATA
1 ATTAAATTAATA
47011552 AAATACAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:47020498 original size:21 final size:23
Alignment explanation
Indices: 47020460--47020501 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
47020450 CGGTCAAATT
*
47020460 TTTTAATAAATACTAAAAATTTA
1 TTTTAATAAATACAAAAAATTTA
47020483 TTTTAA-AAATA-AAAAAATT
1 TTTTAATAAATACAAAAAATT
47020502 AAAAAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTTAATAAATACAAAAAATTTA
Found at i:47020519 original size:12 final size:11
Alignment explanation
Indices: 47020504--47020533 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
47020494 AAAAAATTAA
47020504 AAAAAGTATTTT
1 AAAAA-TATTTT
47020516 AAAAATATTTT
1 AAAAATATTTT
47020527 AAAAATA
1 AAAAATA
47020534 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:47024132 original size:8 final size:8
Alignment explanation
Indices: 47024121--47024148 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
47024111 GACCAATTAA
47024121 AAAATTTT
1 AAAATTTT
47024129 AAAATTTT
1 AAAATTTT
47024137 AAAATTTT
1 AAAATTTT
47024145 AAAA
1 AAAA
47024149 AATCAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAAATTTT
Found at i:47024219 original size:33 final size:31
Alignment explanation
Indices: 47024155--47024223 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
47024145 AAAAAATCAA
* *
47024155 TTCAACCATCAATTCAATCAGTTTTAGCCGG
1 TTCAACCATCAATTCAACCACTTTTAGCCGG
* *
47024186 TTCAACCATCGATTCAACCTATCTTTTATCCGG
1 TTCAACCATCAATTCAACC-A-CTTTTAGCCGG
47024219 TTCAA
1 TTCAA
47024224 TCGGTTTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 17 0.53
32 1 0.03
33 14 0.44
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (31 bp):
TTCAACCATCAATTCAACCACTTTTAGCCGG
Found at i:47024400 original size:2 final size:2
Alignment explanation
Indices: 47024395--47024439 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
47024385 CCTTAGTAGA
47024395 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
47024437 AT A
1 AT A
47024440 AATCTTAGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47034384 original size:58 final size:58
Alignment explanation
Indices: 47034294--47034411 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
47034284 AGCGGCTGCA
47034294 TAATCATTTACGTAACACAAAAACGTTGTCATTTTATGCAGGAAAAACGGGCTTTTTT
1 TAATCATTTACGTAACACAAAAACGTTGTCATTTTATGCAGGAAAAACGGGCTTTTTT
47034352 TAATCATTTACGTAACACAAAAACGTTGTCATTTTATGCAGGAAAAACGGGCTTTTTT
1 TAATCATTTACGTAACACAAAAACGTTGTCATTTTATGCAGGAAAAACGGGCTTTTTT
47034410 TA
1 TA
47034412 TTCCTACATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (58 bp):
TAATCATTTACGTAACACAAAAACGTTGTCATTTTATGCAGGAAAAACGGGCTTTTTT
Found at i:47040671 original size:16 final size:16
Alignment explanation
Indices: 47040640--47040673 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47040630 CATTTTAATA
* *
47040640 TTATGTCTTTTTTATT
1 TTATGTCTTATATATT
47040656 TTATGTCTTATATATT
1 TTATGTCTTATATATT
47040672 TT
1 TT
47040674 GCATGCATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (16 bp):
TTATGTCTTATATATT
Found at i:47045301 original size:17 final size:18
Alignment explanation
Indices: 47045279--47045312 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
47045269 AAATTAAAAT
47045279 ATATAAAAATA-ATATAC
1 ATATAAAAATATATATAC
*
47045296 ATATAACAATATATATA
1 ATATAAAAATATATATA
47045313 AAACTTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
ATATAAAAATATATATAC
Found at i:47045767 original size:23 final size:23
Alignment explanation
Indices: 47045740--47045805 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
47045730 AAAAATATGT
*
47045740 TAAA-TTTAAATAATGATACATA
1 TAAATTTTAAATAATAATACATA
47045762 GTAAATTTTAAATAATAATACATA
1 -TAAATTTTAAATAATAATACATA
* *
47045786 TAAAACTTAAAATAATAATA
1 T-AAATTTTAAATAATAATA
47045806 TAAAAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.13
24 33 0.87
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.35
Consensus pattern (23 bp):
TAAATTTTAAATAATAATACATA
Found at i:47051114 original size:41 final size:41
Alignment explanation
Indices: 47051033--47051266 Score: 351
Period size: 41 Copynumber: 5.7 Consensus size: 41
47051023 TTAATTTAAA
* * *
47051033 CAGATTCACTGGCACTTAGCCCTGTTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAG-CCTGCTAGGCTTATAGCCTGATT
* *
47051076 CAGATCACCGACACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
47051117 TAGATCACCGGCATTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * *
47051158 CAGTTCACCGACACTTAGCCTGCTATGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
47051199 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTTATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
47051240 CAGATCACCGGCACTTAGCCTGCTAGG
1 CAGATCACCGGCACTTAGCCTGCTAGG
47051267 TTTTAAAACC
Statistics
Matches: 173, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 157 0.91
42 12 0.07
43 4 0.02
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:47051966 original size:2 final size:2
Alignment explanation
Indices: 47051959--47051998 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47051949 AAGCTTGCAC
47051959 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
47051999 TCGAAAACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47055846 original size:25 final size:25
Alignment explanation
Indices: 47055816--47055905 Score: 144
Period size: 25 Copynumber: 3.6 Consensus size: 25
47055806 TGTAAACAGT
* *
47055816 AAGCTCTTCCGAGCTAAATAACGGG
1 AAGCTCATGCGAGCTAAATAACGGG
47055841 AAGCTCATGCGAGCTAAATAACGGG
1 AAGCTCATGCGAGCTAAATAACGGG
* *
47055866 AAGCTCATGCGAGCTGAATAACGGA
1 AAGCTCATGCGAGCTAAATAACGGG
47055891 AAGCTCATGCGAGCT
1 AAGCTCATGCGAGCT
47055906 GCGGTGTGTC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (25 bp):
AAGCTCATGCGAGCTAAATAACGGG
Found at i:47055906 original size:25 final size:25
Alignment explanation
Indices: 47055794--47055906 Score: 138
Period size: 25 Copynumber: 4.6 Consensus size: 25
47055784 ATTCATGTAT
* * * *
47055794 GCTCATACGAGCTGTA-AACAGTAA
1 GCTCATGCGAGCTGAATAACGGGAA
* * *
47055818 GCTCTTCCGAGCTAAATAACGGGAA
1 GCTCATGCGAGCTGAATAACGGGAA
*
47055843 GCTCATGCGAGCTAAATAACGGGAA
1 GCTCATGCGAGCTGAATAACGGGAA
*
47055868 GCTCATGCGAGCTGAATAACGGAAA
1 GCTCATGCGAGCTGAATAACGGGAA
47055893 GCTCATGCGAGCTG
1 GCTCATGCGAGCTG
47055907 CGGTGTGTCC
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
24 12 0.15
25 66 0.85
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.19
Consensus pattern (25 bp):
GCTCATGCGAGCTGAATAACGGGAA
Found at i:47056234 original size:15 final size:16
Alignment explanation
Indices: 47056214--47056243 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47056204 CGAATGAATT
47056214 TAAGTCA-ATTCAATA
1 TAAGTCATATTCAATA
47056229 TAAGTCATATTCAAT
1 TAAGTCATATTCAAT
47056244 TTAGTCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (16 bp):
TAAGTCATATTCAATA
Found at i:47061291 original size:37 final size:37
Alignment explanation
Indices: 47061241--47061314 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
47061231 CTTATTTTTT
47061241 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
1 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
47061278 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
1 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
47061315 TGACCCGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (37 bp):
CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
Found at i:47064688 original size:25 final size:25
Alignment explanation
Indices: 47064559--47064751 Score: 78
Period size: 25 Copynumber: 7.7 Consensus size: 25
47064549 TCACGATATT
* *
47064559 TGGCTCTCATGAGCTTCTCGATTA-A
1 TGGCTCACATGAGCTTCCCG-TTACA
* * *
47064584 TGGATCTCTTGAGCTTCCCGTTTAC-
1 TGGCTCACATGAGCTTCCCG-TTACA
** **
47064609 -GGCTCGTATGAGCTTCCCAATA-A
1 TGGCTCACATGAGCTTCCCGTTACA
* *
47064632 TTGGCTCGCAAGAGCTTCCTAC-TATACA
1 -TGGCTCACATGAGCTTCC--CGT-TACA
47064660 --GCTCACATGAGCTTCCCGTTACA
1 TGGCTCACATGAGCTTCCCGTTACA
* ** *
47064683 TGGCTCATATGAGCTTCATGTTATA
1 TGGCTCACATGAGCTTCCCGTTACA
* * * * *
47064708 TTGCTCAAAAGAGCTACCCGTTTATA
1 TGGCTCACATGAGCTTCCCG-TTACA
47064734 T-GCTCACATGAGCATTCC
1 TGGCTCACATGAGC-TTCC
47064752 TGAATATGAG
Statistics
Matches: 127, Mismatches: 28, Indels: 25
0.71 0.16 0.14
Matches are distributed among these distances:
23 7 0.06
24 15 0.12
25 92 0.72
26 9 0.07
27 3 0.02
28 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCGTTACA
Found at i:47072082 original size:24 final size:24
Alignment explanation
Indices: 47072038--47072083 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
47072028 CAGCTCGCAA
*
47072038 GAGCATCCCGTTATTTAGCTCTAT
1 GAGCATCCCGTTATATAGCTCTAT
* *
47072062 GAGCATCCCGTTGTATGGCTCT
1 GAGCATCCCGTTATATAGCTCT
47072084 CACGAGCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (24 bp):
GAGCATCCCGTTATATAGCTCTAT
Found at i:47072130 original size:25 final size:26
Alignment explanation
Indices: 47072075--47072142 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
47072065 CATCCCGTTG
*
47072075 TATGGCTCTCACGAGC-TTCACGATA
1 TATGGCTCTCATGAGCTTTCACGATA
*
47072100 TTTGGCTCTCATGAGCTTTC-CGAT-
1 TATGGCTCTCATGAGCTTTCACGATA
**
47072124 TAATGGCTCTTTTGAGCTT
1 T-ATGGCTCTCATGAGCTT
47072143 CTCGTTTACG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 1 0.03
25 32 0.89
26 3 0.08
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.38
Consensus pattern (26 bp):
TATGGCTCTCATGAGCTTTCACGATA
Found at i:47072233 original size:25 final size:25
Alignment explanation
Indices: 47072205--47072256 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
47072195 ATCATCTAGT
47072205 TCACATAAGCTTCCA-GTTACATGGC
1 TCACATAAGCTT-CATGTTACATGGC
* *
47072230 TCACATGAGCTTCATGTTATATGGC
1 TCACATAAGCTTCATGTTACATGGC
47072255 TC
1 TC
47072257 GAAAGAGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (25 bp):
TCACATAAGCTTCATGTTACATGGC
Found at i:47073927 original size:13 final size:13
Alignment explanation
Indices: 47073879--47073964 Score: 50
Period size: 14 Copynumber: 6.4 Consensus size: 13
47073869 ATGTTCCAGC
* *
47073879 AAAAATGAAGAAAC
1 AAAAAT-AAAAAAT
* *
47073893 AAAAATACTAAAAC
1 AAAAATA-AAAAAT
*
47073907 AAAAA-AAAAGAT
1 AAAAATAAAAAAT
47073919 -AAAATAAAAAAT
1 AAAAATAAAAAAT
*
47073931 AAAAATAAAAACCT
1 AAAAATAAAAA-AT
*
47073945 AAAACTAAGAAATAT
1 AAAAATAA-AAA-AT
47073960 AAAAA
1 AAAAA
47073965 GCAAAGAACA
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
11 4 0.07
12 9 0.16
13 12 0.21
14 23 0.41
15 8 0.14
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.13
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:47078943 original size:2 final size:2
Alignment explanation
Indices: 47078936--47078977 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
47078926 GTAGACGTAG
47078936 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47078978 AAGTAAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47079172 original size:15 final size:14
Alignment explanation
Indices: 47079144--47079170 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47079134 ATGCGTCTTT
47079144 TTTTTTAATATTTA
1 TTTTTTAATATTTA
47079158 TTTTTTAATATTT
1 TTTTTTAATATTT
47079171 TACTATACGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:47085206 original size:31 final size:31
Alignment explanation
Indices: 47085141--47085206 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
47085131 AAAAAAACTC
* * *
47085141 ATTTAATTATTTATATCTTATTTTTTTATGT
1 ATTTAATTATTTAAATCTAATTTTTTTATAT
47085172 ATTTAATT-TTTAAATCTAACTTTATTTT-TAT
1 ATTTAATTATTTAAATCTAA-TTT-TTTTATAT
47085203 ATTT
1 ATTT
47085207 GTGCTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 9 0.30
31 17 0.57
32 4 0.13
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (31 bp):
ATTTAATTATTTAAATCTAATTTTTTTATAT
Found at i:47085290 original size:22 final size:23
Alignment explanation
Indices: 47085243--47085293 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
47085233 ATGAATGTTG
47085243 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTATCACATA-TATTAT
47085267 TTTAAATTTATCACATA-ATTAT
1 TTTAAATTTATCACATATATTAT
47085289 TTTAA
1 TTTAA
47085294 GTTTTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 10 0.37
24 17 0.63
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAATTTATCACATATATTAT
Found at i:47087046 original size:14 final size:14
Alignment explanation
Indices: 47087027--47087053 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47087017 TGGTAAAACT
47087027 CACTAAGATTAATC
1 CACTAAGATTAATC
47087041 CACTAAGATTAAT
1 CACTAAGATTAAT
47087054 TAATGTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (14 bp):
CACTAAGATTAATC
Found at i:47092795 original size:72 final size:72
Alignment explanation
Indices: 47092675--47092845 Score: 240
Period size: 72 Copynumber: 2.4 Consensus size: 72
47092665 AAAATTATAT
* * * *
47092675 ATAAACAACTATTGATAAAACTA-ATTTAATAAAAATAAGTAGAACATAACTTCAATATCTAAAG
1 ATAAACAACTATTGATAAAACTAGATTTAACAAAAATAAGTAGAACATAAATTCAATATCCAAAA
47092739 ACCAAAC
66 ACCAAAC
* * *
47092746 ATAAACAAATATTAATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGATTTA-ACAAAAATAAGTAGAACATAAATTCAATATCCAAA
47092810 AACCAAAC
65 AACCAAAC
*
47092818 ATAAATAACTATTGATAAAACTAG-TTTA
1 ATAAACAACTATTGATAAAACTAGATTTA
47092846 GCATTGTCAG
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
71 24 0.28
72 63 0.72
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTTAACAAAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:47093290 original size:18 final size:18
Alignment explanation
Indices: 47093269--47093316 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
47093259 TCCATATATT
*
47093269 TGAACATCATTTGAGATG
1 TGAACATCATTTGAAATG
47093287 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
47093305 TGAACATCATTT
1 TGAACATCATTT
47093317 CTCATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:47096013 original size:25 final size:25
Alignment explanation
Indices: 47095945--47096018 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 25
47095935 GAAGTGGAGA
* * *
47095945 AGAGGAACAAAGAACCAACACCAAC
1 AGAGGAACAAAGAACCAGCGCCAGC
47095970 AGAGGAACAAAGAACCAGCGCCAGC
1 AGAGGAACAAAGAACCAGCGCCAGC
* *
47095995 AGTGGAACAAAGAATCAGCGCCAG
1 AGAGGAACAAAGAACCAGCGCCAG
47096019 AGGAACACCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.47, C:0.26, G:0.24, T:0.03
Consensus pattern (25 bp):
AGAGGAACAAAGAACCAGCGCCAGC
Found at i:47098698 original size:6 final size:6
Alignment explanation
Indices: 47098687--47098713 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
47098677 GAAAGAAAAG
47098687 AAAGCC AAAGCC AAAGCC AAAGCC AAA
1 AAAGCC AAAGCC AAAGCC AAAGCC AAA
47098714 CGAAAACAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.30, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGCC
Found at i:47099724 original size:40 final size:40
Alignment explanation
Indices: 47099600--47099740 Score: 126
Period size: 40 Copynumber: 3.6 Consensus size: 40
47099590 CAACTTTGAA
* * *
47099600 TCGAGGAGACACTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATGAGACACTGGGTGTCAAATTATTACTTCGGATT-AT
* * * * *
47099641 TCAATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAG
1 TCGATGAGACACTGGGTGTCAAATTATTACTTCGGATTAT
* *
47099678 CCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTAT
1 TCGATGAGACACTGGGTGTCAAATTATTACTTCGGATTAT
* * * *
47099718 TTGATGAGGCACAGGGTGCCAAA
1 TCGATGAGACACTGGGTGTCAAA
47099741 CTGGTGTGTT
Statistics
Matches: 77, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
37 16 0.21
38 13 0.17
39 2 0.03
40 31 0.40
41 15 0.19
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAAATTATTACTTCGGATTAT
Found at i:47100219 original size:19 final size:19
Alignment explanation
Indices: 47100176--47100213 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
47100166 CCCGAACTCA
47100176 AATGTGGTGATGTTTATCC
1 AATGTGGTGATGTTTATCC
47100195 AATGTGGTGATGTTTATCC
1 AATGTGGTGATGTTTATCC
47100214 TTTGTGTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (19 bp):
AATGTGGTGATGTTTATCC
Found at i:47106276 original size:20 final size:18
Alignment explanation
Indices: 47106235--47106270 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47106225 CTCACTATAT
*
47106235 TTTTTATATTAGAATTTG
1 TTTTTATATTAGAACTTG
*
47106253 TTTTTATATTAGAGCTTG
1 TTTTTATATTAGAACTTG
47106271 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (18 bp):
TTTTTATATTAGAACTTG
Found at i:47108143 original size:35 final size:35
Alignment explanation
Indices: 47108097--47108165 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
47108087 TTAATTAATC
* *
47108097 AGCTTTGACAATTGGAGTTCCCGAACAGTCATTGG
1 AGCTTTGACAATTGGAGTTCCCAAACAGCCATTGG
47108132 AGCTTTGACAATTGGAGTTCCCAAACAGCCATTG
1 AGCTTTGACAATTGGAGTTCCCAAACAGCCATTG
47108166 AATTGGACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (35 bp):
AGCTTTGACAATTGGAGTTCCCAAACAGCCATTGG
Found at i:47108360 original size:32 final size:30
Alignment explanation
Indices: 47108293--47108377 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 30
47108283 TTATGGCGTC
* * *
47108293 TGAAGGGT-CTTTGGTGTGAACACTCAGAT
1 TGAATGGTCCTTTGGTGTGAACACTAAAAT
47108322 TCGAATGGTCCTTTGGGTGTGAACACTAAAAAT
1 T-GAATGGTCCTTT-GGTGTGAACACT-AAAAT
* *
47108355 TGAATGGTCCATTGATGTGAACA
1 TGAATGGTCCTTTGGTGTGAACA
47108378 AGAGTAGCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 1 0.02
30 6 0.13
31 13 0.28
32 23 0.49
33 4 0.09
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (30 bp):
TGAATGGTCCTTTGGTGTGAACACTAAAAT
Found at i:47112216 original size:26 final size:27
Alignment explanation
Indices: 47112172--47112233 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
47112162 GGTCCACCGA
47112172 GACAGTAAACACTGGGTAGTCTG-TCGG
1 GACAGTAAACACTGGGTAGTC-GATCGG
* *
47112199 GATAGTAAAC-GTGGGTAGTCGATCGG
1 GACAGTAAACACTGGGTAGTCGATCGG
47112225 GACAGTAAA
1 GACAGTAAA
47112234 TACGGGGACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.03
26 21 0.68
27 9 0.29
ACGTcount: A:0.31, C:0.15, G:0.34, T:0.21
Consensus pattern (27 bp):
GACAGTAAACACTGGGTAGTCGATCGG
Found at i:47121346 original size:35 final size:36
Alignment explanation
Indices: 47121305--47121373 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
47121295 AGCGTAAGTT
47121305 TGAAGAACCATTTTT-TTATT-GAAACCTTGTTTGAA
1 TGAAGAA-CATTTTTCTTATTGGAAACCTTGTTTGAA
* * *
47121340 TGAAGAACTTTTTTCTTCTTGGAACCCTTGTTTG
1 TGAAGAACATTTTTCTTATTGGAAACCTTGTTTG
47121374 TCATTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 6 0.21
35 11 0.38
36 12 0.41
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (36 bp):
TGAAGAACATTTTTCTTATTGGAAACCTTGTTTGAA
Found at i:47122529 original size:27 final size:26
Alignment explanation
Indices: 47122494--47122574 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 26
47122484 AAGGTCTTTC
47122494 GGGACAGTAAACACAGGTAAGTCTGCTT
1 GGGACAGTAAACAC-GGTAAGTCTG-TT
* *
47122522 -GGATAGTAAACACGAGTAAGTCCGTT
1 GGGACAGTAAACACG-GTAAGTCTGTT
*
47122548 GGGGCAGTAAACACGGGTAAGTCTGTT
1 GGGACAGTAAACAC-GGTAAGTCTGTT
47122575 AAGACAAAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 3 0.07
27 41 0.91
28 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (26 bp):
GGGACAGTAAACACGGTAAGTCTGTT
Found at i:47124963 original size:22 final size:22
Alignment explanation
Indices: 47124901--47124970 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
47124891 ATTGTTCAAA
* **
47124901 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
47124923 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
47124945 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
47124967 CATG
1 CATG
47124971 TGTAAGGTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:47126027 original size:29 final size:30
Alignment explanation
Indices: 47125984--47126050 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
47125974 TTGAAAATAT
* * *
47125984 CTCTATTTCATTCAA-AAAAAATTTAGA-AA
1 CTCTCTTTCAGTCAATAAAAAATTCA-ACAA
*
47126013 CTCTCTTTCAGTCAATAAAAACTTCAACAA
1 CTCTCTTTCAGTCAATAAAAAATTCAACAA
47126043 CTCTCTTT
1 CTCTCTTT
47126051 ACTTCAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (30 bp):
CTCTCTTTCAGTCAATAAAAAATTCAACAA
Found at i:47126078 original size:27 final size:30
Alignment explanation
Indices: 47126024--47126078 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
47126014 TCTCTTTCAG
*
47126024 TCAATAAAAACTTCAACAACTCTCTTTACT
1 TCAATAAAAACTTCAACAACCCTCTTTACT
*
47126054 TCAA-AAAAA-TTCACCAACCCT-TTTA
1 TCAATAAAAACTTCAACAACCCTCTTTA
47126079 ATATTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 10 0.43
29 5 0.22
30 4 0.17
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (30 bp):
TCAATAAAAACTTCAACAACCCTCTTTACT
Found at i:47130092 original size:13 final size:13
Alignment explanation
Indices: 47130074--47130099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47130064 TTACAGATGA
47130074 AATTAGGTTGACT
1 AATTAGGTTGACT
47130087 AATTAGGTTGACT
1 AATTAGGTTGACT
47130100 TAAATATGAA
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:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
AATTAGGTTGACT
Found at i:47131057 original size:24 final size:25
Alignment explanation
Indices: 47131030--47131091 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
47131020 ACATTTTCCA
47131030 TCAATTCATCCTTTGCA-TATATCG
1 TCAATTCATCCTTTGCATTATATCG
* *
47131054 TCAATTCAACCTTTGCATTTTATCG
1 TCAATTCATCCTTTGCATTATATCG
*
47131079 TTAATTCATCCTT
1 TCAATTCATCCTT
47131092 GCCACAGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (25 bp):
TCAATTCATCCTTTGCATTATATCG
Found at i:47138084 original size:20 final size:21
Alignment explanation
Indices: 47138040--47138082 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
47138030 ATAGGAGCTG
*
47138040 AACAAAAACCCATAAGGGTTA
1 AACAAAAACCCATAAGAGTTA
* *
47138061 AACAAAAACTCATATGAGTTA
1 AACAAAAACCCATAAGAGTTA
47138082 A
1 A
47138083 CAGAAGCTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (21 bp):
AACAAAAACCCATAAGAGTTA
Found at i:47138264 original size:18 final size:18
Alignment explanation
Indices: 47138241--47138276 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
47138231 TAATTTAATT
*
47138241 TCTTATTTTTAACAATAA
1 TCTTATTTTCAACAATAA
47138259 TCTTATTTTCAACAATAA
1 TCTTATTTTCAACAATAA
47138277 ATATTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (18 bp):
TCTTATTTTCAACAATAA
Found at i:47142139 original size:18 final size:17
Alignment explanation
Indices: 47142106--47142144 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
47142096 TTTTATAAAT
47142106 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
47142124 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
47142141 TGTG
1 TGTG
47142145 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:47142396 original size:23 final size:23
Alignment explanation
Indices: 47142370--47142468 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
47142360 AGTGTTATTG
47142370 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
47142393 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
47142416 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
47142439 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
47142462 ATCAGTG
1 ATCAGTG
47142469 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:47144398 original size:28 final size:28
Alignment explanation
Indices: 47144361--47144423 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
47144351 AGGGCTGATG
47144361 AATTTTTTGAA-GCAAAT-AGAGTT-ATTGA
1 AATTTTTTGAACG-AAATAAG-GTTCA-TGA
47144389 AATTTTTTGAACGAAATAAGGTTCATGA
1 AATTTTTTGAACGAAATAAGGTTCATGA
47144417 AATTTTT
1 AATTTTT
47144424 AAAGGATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (28 bp):
AATTTTTTGAACGAAATAAGGTTCATGA
Found at i:47144726 original size:2 final size:2
Alignment explanation
Indices: 47144719--47144750 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47144709 TAACTATAGA
47144719 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
47144751 TGATAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47145593 original size:363 final size:363
Alignment explanation
Indices: 47144928--47145657 Score: 1307
Period size: 363 Copynumber: 2.0 Consensus size: 363
47144918 AACAGAAAGC
* * *
47144928 AATAAATGAAAATAAGAAAAGGAACCTAAATATCTACCCCAGTTAATTAAAAAACGGTTGGATTC
1 AATAAATGAAAAGAAGAAAAGGAACCTAAATATCTACCCCAGTTAATTAAAAAACGGCTGGATAC
* *
47144993 CATTAATTCTCTCGATTTGTCATTTCAAAATCAAATTCGTTCTGATGATAGTAGTTTCCAAGGAT
66 CATTAATTCTCTCGATTTGTCATTTCAAAATCAAATTCATTCTGACGATAGTAGTTTCCAAGGAT
*
47145058 AAAACTTTATTTGCTATCTTCTTTTGAAATCATTTCCCTCAAATGCTCCTTCAGTCTGGATTTCT
131 AAAACTTTATTTGCTATCTTCTTTTGAAATCATTTCCCTCAAACGCTCCTTCAGTCTGGATTTCT
*
47145123 TGGCCATCTTCTCTCTGAAGCGAAATTATGAAGCTTCAGCTCTTCTCCCATCAAGTAAAAGGTTT
196 TGGCCATCTTCTCTCTGAAGCGAAACTATGAAGCTTCAGCTCTTCTCCCATCAAGTAAAAGGTTT
* *
47145188 CTCCTTTATCAAGAGCGTCTTTTGCTAGTCTATGTGCATGTGAGTTCCCTGATCTGTGAATATGC
261 CTCATCTATCAAGAGCGTCTTTTGCTAGTCTATGTGCATGTGAGTTCCCTGATCTGTGAATATGC
*
47145253 TGAAATATAATCTCTTGAAAACAAGGTTTCTTATTCTG
326 TGAAAGATAATCTCTTGAAAACAAGGTTTCTTATTCTG
* *
47145291 AATAAATGAAAGGAAGAAAAGGAACCTAAATATCTACCCCAGTTAATTCAAAAACGGCTGGATAC
1 AATAAATGAAAAGAAGAAAAGGAACCTAAATATCTACCCCAGTTAATTAAAAAACGGCTGGATAC
*
47145356 CATTAATTCTCTCGATTTGTCATTTCAAAATCCAATTCATTCTGACGATAGTAGTTTCCAAGGAT
66 CATTAATTCTCTCGATTTGTCATTTCAAAATCAAATTCATTCTGACGATAGTAGTTTCCAAGGAT
47145421 AAAACTTTATTTGCTATCTTCTTTTGAAATCATTTCCCTCAAACGCTCCTTCAGTCTGGATTTCT
131 AAAACTTTATTTGCTATCTTCTTTTGAAATCATTTCCCTCAAACGCTCCTTCAGTCTGGATTTCT
* *
47145486 TGGCCATCTTCTCTCTGAAGCGAAACTATGATGCTTCAGCTCTTCTCCCATCAGGTAAAAGGTTT
196 TGGCCATCTTCTCTCTGAAGCGAAACTATGAAGCTTCAGCTCTTCTCCCATCAAGTAAAAGGTTT
*
47145551 CTCATCTATCAAGAGCGTCTTTTGCTAGTCTATGTGCATGTGAGTTCCCTGATCTGTGCATATGC
261 CTCATCTATCAAGAGCGTCTTTTGCTAGTCTATGTGCATGTGAGTTCCCTGATCTGTGAATATGC
*
47145616 TGAAAGATAATCTCTTGAAAACAAGGTTTCTTATTTTG
326 TGAAAGATAATCTCTTGAAAACAAGGTTTCTTATTCTG
47145654 AATA
1 AATA
47145658 TCTCTGATAA
Statistics
Matches: 350, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
363 350 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (363 bp):
AATAAATGAAAAGAAGAAAAGGAACCTAAATATCTACCCCAGTTAATTAAAAAACGGCTGGATAC
CATTAATTCTCTCGATTTGTCATTTCAAAATCAAATTCATTCTGACGATAGTAGTTTCCAAGGAT
AAAACTTTATTTGCTATCTTCTTTTGAAATCATTTCCCTCAAACGCTCCTTCAGTCTGGATTTCT
TGGCCATCTTCTCTCTGAAGCGAAACTATGAAGCTTCAGCTCTTCTCCCATCAAGTAAAAGGTTT
CTCATCTATCAAGAGCGTCTTTTGCTAGTCTATGTGCATGTGAGTTCCCTGATCTGTGAATATGC
TGAAAGATAATCTCTTGAAAACAAGGTTTCTTATTCTG
Found at i:47156401 original size:14 final size:15
Alignment explanation
Indices: 47156372--47156404 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
47156362 TAACTTTTAC
47156372 CATTCATATCATGAAT
1 CATTCATA-CATGAAT
47156388 CATTCATA-ATGAAT
1 CATTCATACATGAAT
47156402 CAT
1 CAT
47156405 ATTGTCCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (15 bp):
CATTCATACATGAAT
Found at i:47161124 original size:23 final size:23
Alignment explanation
Indices: 47161094--47161143 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
47161084 TTGTGCAAGA
47161094 TTGAATGGCTTTATATGTATCAT
1 TTGAATGGCTTTATATGTATCAT
47161117 TTGAATGGCTTTATATGTATCAT
1 TTGAATGGCTTTATATGTATCAT
47161140 TTGA
1 TTGA
47161144 GCCTTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (23 bp):
TTGAATGGCTTTATATGTATCAT
Found at i:47164345 original size:19 final size:19
Alignment explanation
Indices: 47164321--47164370 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
47164311 CGAGTTTGGA
*
47164321 CGAACGGATCGCCTAAGGC
1 CGAACGGTTCGCCTAAGGC
47164340 CGAACGGTTCGCCTAAGGC
1 CGAACGGTTCGCCTAAGGC
*
47164359 AGAACGGTTCGC
1 CGAACGGTTCGC
47164371 GAGAGAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.24, C:0.30, G:0.32, T:0.14
Consensus pattern (19 bp):
CGAACGGTTCGCCTAAGGC
Found at i:47169014 original size:84 final size:84
Alignment explanation
Indices: 47168924--47169091 Score: 264
Period size: 84 Copynumber: 2.0 Consensus size: 84
47168914 CCACTACCAG
* **
47168924 TAGTTCCACCACTTAAATTCTGTCCACAATCTTGCAACTCATCATTGTCCTTCACATCACCTTCT
1 TAGTTCCACCACTTAAATTCTGTCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
47168989 CTTCTATTCACCACCTCTT
66 CTTCTATTCACCACCTCTT
* * *
47169008 TAGTTCCACCATTTAGATTCTGTCTACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
1 TAGTTCCACCACTTAAATTCTGTCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
* *
47169073 TTTTTATTCACCACCTCTT
66 CTTCTATTCACCACCTCTT
47169092 CATTAACCTC
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.23, C:0.35, G:0.05, T:0.38
Consensus pattern (84 bp):
TAGTTCCACCACTTAAATTCTGTCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
CTTCTATTCACCACCTCTT
Found at i:47169701 original size:228 final size:219
Alignment explanation
Indices: 47169313--47169747 Score: 683
Period size: 228 Copynumber: 1.9 Consensus size: 219
47169303 CTCTCCACCA
* * *
47169313 CCACCACCAACACTCTTAGACTGTTCGCTGCCTGAATCCCGTGACCATGTTGGTGACCTTGACTT
1 CCACCACCAACACTCTTAGACTGCTCACTGCCTGAATCCCGTGACCATGTTGGCGACCTTGACTT
* * *
47169378 AGACTTCGACTTGGAGCTTCTCCTCTTCAAATCCTCCTCCCTTGATTCCCCAACAACCCTGCCTG
66 AGACTTCGACTTGGAGCTTCTCCTCCTCAAATCCCCCTCCCTTGATTCCCCAACAACCCTCCCTG
*
47169443 CCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCTTCAGTTGCACCTTA
131 CCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCCTCAGTTGCACCTTA
47169508 CTACTACCTCTAGTCTCATCCATT
196 CTACTACCTCTAGTCTCATCCATT
47169532 CCACCACCAACACTCTTAGACTGCTCACTGCCTGAATCCCGTGACCATGTTGGCGACCTTGACAT
1 CCACCACCAACACTCTTAGACTGCTCACTGCCTGAATCCCGTGACCATGTTGGCGACCTTGAC--
*
47169597 TGACGTAGACATT-GCCTTGGAGCTTCTCCTCCTCAAATCTTCCCTCTCCCTTGATTCCCCAACA
64 T----TAGAC-TTCGACTTGGAGCTTCTCCTCCTCAAATC--CCC-CTCCCTTGATTCCCCAACA
*
47169661 ACCCTCCCTGCCCCCAAAGAATCCCTTGACCTTGTAGGTGAGCTCACATCCCTAACATCCCTCAG
121 ACCCTCCCTGCCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCCTCAG
*
47169726 TTGCACCTTACTACTCCCTCTA
186 TTGCACCTTACTACTACCTCTA
47169748 ACGTCATCAA
Statistics
Matches: 196, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
219 60 0.31
221 1 0.01
225 29 0.15
226 2 0.01
227 2 0.01
228 102 0.52
ACGTcount: A:0.21, C:0.38, G:0.14, T:0.27
Consensus pattern (219 bp):
CCACCACCAACACTCTTAGACTGCTCACTGCCTGAATCCCGTGACCATGTTGGCGACCTTGACTT
AGACTTCGACTTGGAGCTTCTCCTCCTCAAATCCCCCTCCCTTGATTCCCCAACAACCCTCCCTG
CCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCCTCAGTTGCACCTTA
CTACTACCTCTAGTCTCATCCATT
Found at i:47180140 original size:13 final size:13
Alignment explanation
Indices: 47180122--47180167 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
47180112 CATTTAATGG
*
47180122 AATCAGTTGGTCA
1 AATCAGTTAGTCA
* *
47180135 AATCAGTTAATAA
1 AATCAGTTAGTCA
*
47180148 AATCAGTTCGTCA
1 AATCAGTTAGTCA
47180161 AATCAGT
1 AATCAGT
47180168 CACTGCATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATCAGTTAGTCA
Found at i:47183091 original size:40 final size:40
Alignment explanation
Indices: 47183047--47183144 Score: 145
Period size: 34 Copynumber: 2.6 Consensus size: 40
47183037 TGTTTTGACA
*
47183047 AATAACAGATATAAACGAATATGAATTAAATAACACTTTC
1 AATAATAGATATAAACGAATATGAATTAAATAACACTTTC
47183087 AATAATAGATAT-----AA-ATGAATTAAATAACACTTTC
1 AATAATAGATATAAACGAATATGAATTAAATAACACTTTC
47183121 AATAATAGATATAAACGAATATGA
1 AATAATAGATATAAACGAATATGA
47183145 GTTATGAAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
34 32 0.63
35 2 0.04
39 2 0.04
40 15 0.29
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (40 bp):
AATAATAGATATAAACGAATATGAATTAAATAACACTTTC
Found at i:47186827 original size:100 final size:97
Alignment explanation
Indices: 47186636--47186833 Score: 308
Period size: 100 Copynumber: 2.0 Consensus size: 97
47186626 AAAATTCAAG
47186636 AGGATATTTGGCTATTTGGTTAAACGAGAAATCGAAACCCAACACATTAGGGCACGTTCCTCGAA
1 AGGATATTTGGCTATTTGGTTAAACGAGAAATCGAAACCCAACACATTAGGGCACGTTCCTCGAA
* *
47186701 TTTCCGAACGCGAAACATTGCCTTATTTTGAA
66 TTTCCAAACGCGAAACATTGCCTTATTTAGAA
*
47186733 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAA-CCAAGCACATTAGGGCACGTTTCCT
1 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAA-CACATTAGGGCACG-TTCCT
* *
47186797 CGAATTTCCAAACGCTAAATATTGCCTTATTTAGAA
62 CGAATTTCCAAACGCGAAACATTGCCTTATTTAGAA
47186833 A
1 A
47186834 AATCCTCATC
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
97 27 0.29
98 4 0.04
99 23 0.25
100 38 0.41
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (97 bp):
AGGATATTTGGCTATTTGGTTAAACGAGAAATCGAAACCCAACACATTAGGGCACGTTCCTCGAA
TTTCCAAACGCGAAACATTGCCTTATTTAGAA
Found at i:47187517 original size:30 final size:31
Alignment explanation
Indices: 47187468--47187532 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
47187458 ATATATGAAT
* *
47187468 TATAAAATATATGAAAAAATATGTATGTACA
1 TATAAAATATATGAAAAAATAAGTAAGTACA
* *
47187499 TATAAAGTATAT-AAAAAATAAGTAAGTATA
1 TATAAAATATATGAAAAAATAAGTAAGTACA
47187529 TATA
1 TATA
47187533 TATCAAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (31 bp):
TATAAAATATATGAAAAAATAAGTAAGTACA
Found at i:47191178 original size:50 final size:50
Alignment explanation
Indices: 47190947--47191177 Score: 277
Period size: 50 Copynumber: 4.6 Consensus size: 50
47190937 TGCCAAAGTT
* ** * * * *
47190947 ATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTAC--TGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGGTGCCAACGCC
* * ** * * *
47190996 ATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCC
** *
47191046 ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACACC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCC
*
47191096 ATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCC
47191146 ATGTCCCAGACATGGTCTTACATGGGACCTCT
1 ATGTCCCAGACATGGTCTTACATGGGACCTCT
47191178 TTACCCAAAT
Statistics
Matches: 157, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
48 1 0.01
49 29 0.18
50 127 0.81
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCC
Found at i:47193442 original size:22 final size:20
Alignment explanation
Indices: 47193394--47193500 Score: 80
Period size: 21 Copynumber: 5.5 Consensus size: 20
47193384 GTACATTATT
47193394 ATATTTTTTTGTATTCCCTC
1 ATATTTTTTTGTATTCCCTC
* *
47193414 GTATTTTTATGATACTT-CCTC
1 ATATTTTTTTG-TA-TTCCCTC
47193435 ATATTTTTTTAGTATTCCCTC
1 ATATTTTTTT-GTATTCCCTC
* * * *
47193456 ATAATATTTGGTAAT--CTC
1 ATATTTTTTTGTATTCCCTC
*
47193474 -TA-TTTTTTGTATTCACTC
1 ATATTTTTTTGTATTCCCTC
*
47193492 ATAATTTTT
1 ATATTTTTT
47193501 GGCACTCTCT
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
16 8 0.12
17 2 0.03
18 6 0.09
19 2 0.03
20 20 0.29
21 27 0.40
22 3 0.04
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.56
Consensus pattern (20 bp):
ATATTTTTTTGTATTCCCTC
Found at i:47193486 original size:36 final size:37
Alignment explanation
Indices: 47193439--47193511 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
47193429 TTCCTCATAT
* *
47193439 TTTTTTAGTATTCCCTCATAATATTTGGTAATCTCTA
1 TTTTTTAGTATTCACTCATAATATTTGGCAATCTCTA
* *
47193476 TTTTTT-GTATTCACTCATAATTTTTGGCACTCTCTA
1 TTTTTTAGTATTCACTCATAATATTTGGCAATCTCTA
47193512 ATATATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 26 0.81
37 6 0.19
ACGTcount: A:0.22, C:0.18, G:0.08, T:0.52
Consensus pattern (37 bp):
TTTTTTAGTATTCACTCATAATATTTGGCAATCTCTA
Found at i:47200608 original size:24 final size:24
Alignment explanation
Indices: 47200577--47200628 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
47200567 CTCCAAATCA
*
47200577 TTTTCCCCAAATCCCTAACTTAGT
1 TTTTCCCCAAATCCCTAACTTAAT
*
47200601 TTTTCCCCAATTCCCTAACTTAAT
1 TTTTCCCCAAATCCCTAACTTAAT
47200625 TTTT
1 TTTT
47200629 TCTTTCCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.02, T:0.44
Consensus pattern (24 bp):
TTTTCCCCAAATCCCTAACTTAAT
Found at i:47201589 original size:14 final size:14
Alignment explanation
Indices: 47201570--47201597 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47201560 TAGTAATTTA
47201570 AATTAGTTATGCTT
1 AATTAGTTATGCTT
47201584 AATTAGTTATGCTT
1 AATTAGTTATGCTT
47201598 GATGGTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
AATTAGTTATGCTT
Found at i:47202617 original size:17 final size:17
Alignment explanation
Indices: 47202595--47202628 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
47202585 TGAAACAGTG
47202595 ATTGGATCCTTATAAAA
1 ATTGGATCCTTATAAAA
47202612 ATTGGATCCTTATAAAA
1 ATTGGATCCTTATAAAA
47202629 GAAGTATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
ATTGGATCCTTATAAAA
Found at i:47204651 original size:21 final size:21
Alignment explanation
Indices: 47204615--47204662 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
47204605 ACTTAAAGCG
**
47204615 GAGGCAGCAGTGAGGGAAACA
1 GAGGCAGCAGAAAGGGAAACA
* *
47204636 GAGGCAGCAGAAAGGGTAGCA
1 GAGGCAGCAGAAAGGGAAACA
47204657 GAGGCA
1 GAGGCA
47204663 ATAAGAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.44, T:0.04
Consensus pattern (21 bp):
GAGGCAGCAGAAAGGGAAACA
Found at i:47205222 original size:18 final size:18
Alignment explanation
Indices: 47205195--47205281 Score: 54
Period size: 18 Copynumber: 4.7 Consensus size: 18
47205185 GTAAATAAAC
* *
47205195 ATTTATTATTTTAATAAG
1 ATTTAATATTTAAATAAG
47205213 ATTTAATA-TTAAATTTAATG
1 ATTTAATATTTAAA--TAA-G
* *
47205233 -TTT-ATCTTGTAAATAAAC
1 ATTTAATATT-TAAAT-AAG
* *
47205251 ATTTATTATTTTAATAAG
1 ATTTAATATTTAAATAAG
47205269 ATTTAATATTTAA
1 ATTTAATATTTAA
47205282 TTTAATTTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
17 4 0.08
18 23 0.45
19 16 0.31
20 8 0.16
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
ATTTAATATTTAAATAAG
Found at i:47205250 original size:56 final size:56
Alignment explanation
Indices: 47205160--47205287 Score: 240
Period size: 56 Copynumber: 2.3 Consensus size: 56
47205150 TTTGCAGCGC
47205160 TTAA-ATTAAATTTAATGTTTATCTTGTAAATAAACATTTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATGTTTATCTTGTAAATAAACATTTATTATTTTAATAAGAT
47205215 TTAATATTAAATTTAATGTTTATCTTGTAAATAAACATTTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATGTTTATCTTGTAAATAAACATTTATTATTTTAATAAGAT
*
47205271 TTAATATTTAATTTAAT
1 TTAATATTAAATTTAAT
47205288 TTAATACTAA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
55 4 0.06
56 67 0.94
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (56 bp):
TTAATATTAAATTTAATGTTTATCTTGTAAATAAACATTTATTATTTTAATAAGAT
Found at i:47205328 original size:11 final size:11
Alignment explanation
Indices: 47205276--47205328 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
47205266 AAGATTTAAT
47205276 ATTTAAT-TTA
1 ATTTAATATTA
*
47205286 ATTTAATACTA
1 ATTTAATATTA
*
47205297 ATCTTAATAGT-
1 AT-TTAATATTA
47205308 ATTT--TATTA
1 ATTTAATATTA
47205317 ATTTAATATTA
1 ATTTAATATTA
47205328 A
1 A
47205329 AGCGATTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
8 3 0.09
9 4 0.11
10 9 0.26
11 12 0.34
12 7 0.20
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (11 bp):
ATTTAATATTA
Found at i:47208166 original size:25 final size:25
Alignment explanation
Indices: 47208119--47208167 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
47208109 TTCCTAGCCA
* **
47208119 TATAATGGGAAGCTCATGTGAGCTG
1 TATAAAGGGAAGCTCATACGAGCTG
*
47208144 TATAAAGGGAAGCTCTTACGAGCT
1 TATAAAGGGAAGCTCATACGAGCT
47208168 AAATATCGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (25 bp):
TATAAAGGGAAGCTCATACGAGCTG
Found at i:47208605 original size:21 final size:22
Alignment explanation
Indices: 47208581--47208625 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
47208571 TGAATTTAAA
*
47208581 TCAATTTAATACAAT-TCATAT
1 TCAATTCAATACAATATCATAT
*
47208602 TCAATTCAATCCAATACTCATAT
1 TCAATTCAATACAATA-TCATAT
47208625 T
1 T
47208626 TGGAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (22 bp):
TCAATTCAATACAATATCATAT
Found at i:47226688 original size:18 final size:18
Alignment explanation
Indices: 47226667--47226704 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
47226657 GAAGACACTG
47226667 AAAAATGACAGCAATTCC
1 AAAAATGACAGCAATTCC
*
47226685 AAAAATGACGGCAATTCC
1 AAAAATGACAGCAATTCC
47226703 AA
1 AA
47226705 CTCGAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.13, T:0.16
Consensus pattern (18 bp):
AAAAATGACAGCAATTCC
Found at i:47229119 original size:75 final size:72
Alignment explanation
Indices: 47228996--47229141 Score: 220
Period size: 75 Copynumber: 2.0 Consensus size: 72
47228986 CAAGTCGCCT
* *
47228996 CTTGAAGCCCTTTTGTCTGACATGCAAGTAACAGGTACTGCTGCTTCCTGCTCTAAGAAAAGTGA
1 CTTGAAGCCCTTTTGTCAGACATGCAAGTAACAGATACTGCTGCTTCCTGCTCT---AAAAGTGA
*
47229061 TGATGGTTCC
63 TGATAGTTCC
* *
47229071 CTTGAAGCCCTTTTGTCAGACATGCAAGTCACAGATACTGCTTCTTCCTGCTCTAAAAGTGATGA
1 CTTGAAGCCCTTTTGTCAGACATGCAAGTAACAGATACTGCTGCTTCCTGCTCTAAAAGTGATGA
47229136 TAGTTC
66 TAGTTC
47229142 TCAACCTGGT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
72 16 0.24
75 50 0.76
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (72 bp):
CTTGAAGCCCTTTTGTCAGACATGCAAGTAACAGATACTGCTGCTTCCTGCTCTAAAAGTGATGA
TAGTTCC
Found at i:47235257 original size:2 final size:2
Alignment explanation
Indices: 47235250--47235274 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47235240 AAAAGCTATA
47235250 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
47235275 ATGCATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:47242513 original size:6 final size:6
Alignment explanation
Indices: 47242502--47242561 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
47242492 TCTGTCAAAT
47242502 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC
47242550 TCCTTC TCCTTC
1 TCCTTC TCCTTC
47242562 CGTTTTTTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCCTTC
Found at i:47248162 original size:22 final size:23
Alignment explanation
Indices: 47248112--47248170 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
47248102 TATATTTCGA
* *
47248112 TATTT-TATTATAAATATTTAAT
1 TATTTATATAATAAATATTAAAT
*
47248134 TAATTATATAATAAAT-TTAAAT
1 TATTTATATAATAAATATTAAAT
47248156 TATTTAT-TAGATAAA
1 TATTTATATA-ATAAA
47248171 ATGATAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 20 0.65
23 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TATTTATATAATAAATATTAAAT
Found at i:47255363 original size:29 final size:29
Alignment explanation
Indices: 47255330--47255387 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
47255320 TCCAACAGTT
47255330 ACTTCCCAACGGCTAATTCACACCCCCAA
1 ACTTCCCAACGGCTAATTCACACCCCCAA
*
47255359 ACTTCCTAACGGCTAATTCACACCCCCAA
1 ACTTCCCAACGGCTAATTCACACCCCCAA
47255388 CACTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.43, G:0.07, T:0.19
Consensus pattern (29 bp):
ACTTCCCAACGGCTAATTCACACCCCCAA
Found at i:47257657 original size:38 final size:38
Alignment explanation
Indices: 47257606--47257683 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
47257596 CTCAAAATAT
47257606 TATAATCATAATAATTAGGGCCTACGAGACCCGATACA
1 TATAATCATAATAATTAGGGCCTACGAGACCCGATACA
47257644 TATAATCATAATAATTAGGGCCTACGAGACCCGATACA
1 TATAATCATAATAATTAGGGCCTACGAGACCCGATACA
47257682 TA
1 TA
47257684 CTCATGCAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (38 bp):
TATAATCATAATAATTAGGGCCTACGAGACCCGATACA
Found at i:47265836 original size:21 final size:21
Alignment explanation
Indices: 47265812--47265851 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47265802 CAAACTAACG
*
47265812 TGGTTTTGCCTATTAACTTAA
1 TGGTTTTGACTATTAACTTAA
*
47265833 TGGTTTTGACTTTTAACTT
1 TGGTTTTGACTATTAACTT
47265852 TAGAAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.53
Consensus pattern (21 bp):
TGGTTTTGACTATTAACTTAA
Found at i:47268900 original size:13 final size:13
Alignment explanation
Indices: 47268882--47268906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47268872 GAAGCATCAG
47268882 ATTTTGATAACAT
1 ATTTTGATAACAT
47268895 ATTTTGATAACA
1 ATTTTGATAACA
47268907 CAAAACCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTTTGATAACAT
Found at i:47271656 original size:14 final size:14
Alignment explanation
Indices: 47271639--47271674 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
47271629 GTTAAAAATA
47271639 TATTATTAAATTAG
1 TATTATTAAATTAG
*
47271653 TATTATTAAATTAT
1 TATTATTAAATTAG
47271667 TATTATTA
1 TATTATTA
47271675 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TATTATTAAATTAG
Done.