Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008226.1 Hibiscus syriacus cultivar Beakdansim tig00110860_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 835745
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:449177 original size:104 final size:105
Alignment explanation
Indices: 448996--449185 Score: 310
Period size: 104 Copynumber: 1.8 Consensus size: 105
448986 AATCACACCA
* * * *
448996 GAAGATTGTTCGAGTTCTACTCCCTGAAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTC
1 GAAGATTGTTCGAGTTCTACCCCCTGAAACCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATTC
449061 GAGTTCTACTCCCTGAAGCAAGAGAGTGAACCCGTAGGCG
66 GAGTTCTACTCCCTGAAGCAAGAGAGTGAACCCGTAGGCG
* **
449101 GAAGATTGTTCGAGTTCTACCCCCTG-AACCTAGAGGGAGCGAACTTGTAAGCAGAAGATTATTC
1 GAAGATTGTTCGAGTTCTACCCCCTGAAACCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATTC
449165 GAGTTCTACTCCCTGAAGCAA
66 GAGTTCTACTCCCTGAAGCAA
449186 TAGGGAGCGA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
104 53 0.68
105 25 0.32
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (105 bp):
GAAGATTGTTCGAGTTCTACCCCCTGAAACCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATTC
GAGTTCTACTCCCTGAAGCAAGAGAGTGAACCCGTAGGCG
Found at i:458692 original size:2 final size:2
Alignment explanation
Indices: 458685--458711 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
458675 TTTATTTGTT
458685 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
458712 TATTATCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:460067 original size:12 final size:12
Alignment explanation
Indices: 460032--460070 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
460022 TACATTATAC
460032 ATAATATAAATTCA
1 ATAAT-TAAATT-A
460046 ATAATT-AATTA
1 ATAATTAAATTA
460057 ATAATTAAATTA
1 ATAATTAAATTA
460069 AT
1 AT
460071 TACATCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.29
12 11 0.46
13 1 0.04
14 5 0.21
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAATTAAATTA
Found at i:460716 original size:10 final size:10
Alignment explanation
Indices: 460701--460736 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
460691 GAACCGGCTG
460701 AAAACCAGAA
1 AAAACCAGAA
* *
460711 AAAACCGGGA
1 AAAACCAGAA
460721 AAAACCAGAA
1 AAAACCAGAA
460731 AAAACC
1 AAAACC
460737 GGGATTTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.64, C:0.22, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAACCAGAA
Found at i:460726 original size:20 final size:20
Alignment explanation
Indices: 460701--460740 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
460691 GAACCGGCTG
460701 AAAACCAGAAAAAACCGGGA
1 AAAACCAGAAAAAACCGGGA
460721 AAAACCAGAAAAAACCGGGA
1 AAAACCAGAAAAAACCGGGA
460741 TTTTTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAACCAGAAAAAACCGGGA
Found at i:462673 original size:58 final size:58
Alignment explanation
Indices: 462578--462696 Score: 220
Period size: 58 Copynumber: 2.1 Consensus size: 58
462568 AATGTACCAT
462578 ATAAAATGGTAATAGAGTTCTTTGGCAGCCTACTTGAGCTAAAGATAGTTTTAGAGAC
1 ATAAAATGGTAATAGAGTTCTTTGGCAGCCTACTTGAGCTAAAGATAGTTTTAGAGAC
* *
462636 ATAATATGGTAATAGAGTTCTTTGGCAGCCTATTTGAGCTAAAGATAGTTTTAGAGAC
1 ATAAAATGGTAATAGAGTTCTTTGGCAGCCTACTTGAGCTAAAGATAGTTTTAGAGAC
462694 ATA
1 ATA
462697 CTGCTTCGAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (58 bp):
ATAAAATGGTAATAGAGTTCTTTGGCAGCCTACTTGAGCTAAAGATAGTTTTAGAGAC
Found at i:466721 original size:23 final size:23
Alignment explanation
Indices: 466687--466740 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
466677 AGAAATTACA
466687 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
* **
466710 CCGAAGGACCACGTAGATTTGTC
1 CCGAAGGACCACATAGAAATGTC
466733 CCGAAGGA
1 CCGAAGGA
466741 TCGCGTAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:466747 original size:23 final size:23
Alignment explanation
Indices: 466706--466749 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
466696 CACATAGAAA
466706 TGTCCCGAAGGACCACGTAGATT
1 TGTCCCGAAGGACCACGTAGATT
* *
466729 TGTCCCGAAGGATCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
466750 ACCCTCGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.20
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGATT
Found at i:467857 original size:64 final size:64
Alignment explanation
Indices: 467785--467993 Score: 217
Period size: 64 Copynumber: 3.3 Consensus size: 64
467775 CGATACATTG
** *
467785 GTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGTAATTCATGCATCGATCCATA
1 GTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATGCATCGATCCATA
467848 A
64 A
* ** *
467849 GTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGCATCGATGCATAA
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATCCATAA
* ** * * * * * * *
467913 GAAGTGCATCGATGCATCCCAGCAATAATAATACATCGAATATC-TTTTATGCACCGATGCATCA
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAAT-GCAATTCATGCATCGATCCATAA
467977 GTAGTGCATCGATGCAT
1 GTAGTGCATCGATGCAT
467994 AGCTTCATTA
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
64 118 0.96
65 5 0.04
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATCCATAA
Found at i:468314 original size:24 final size:24
Alignment explanation
Indices: 468287--468359 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
468277 ACATGCATAA
*
468287 GATATAT-ATATGTTCATGTGATAT
1 GATATATGATATG-ACATGTGATAT
*
468311 GATATGTGATATGACATGTGATAT
1 GATATATGATATGACATGTGATAT
* *
468335 GAGAACATGATATGA-A-GTGATAT
1 GA-TATATGATATGACATGTGATAT
468358 GA
1 GA
468360 GATACATGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
23 9 0.21
24 19 0.45
25 14 0.33
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (24 bp):
GATATATGATATGACATGTGATAT
Found at i:468319 original size:12 final size:12
Alignment explanation
Indices: 468301--468336 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
468291 TATATATGTT
468301 CATGTGATATGA
1 CATGTGATATGA
*
468313 TATGTGATATGA
1 CATGTGATATGA
468325 CATGTGATATGA
1 CATGTGATATGA
468337 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:468358 original size:23 final size:26
Alignment explanation
Indices: 468301--468369 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
468291 TATATATGTT
**
468301 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
468325 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
468350 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
468370 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:468499 original size:15 final size:15
Alignment explanation
Indices: 468481--468513 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
468471 GAGGGTATAA
468481 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
468496 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
468511 TAG
1 TAG
468514 GGGTCCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:474736 original size:64 final size:64
Alignment explanation
Indices: 474668--474884 Score: 197
Period size: 64 Copynumber: 3.4 Consensus size: 64
474658 TTGAAGGTGT
** **
474668 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
474731 C
64 C
** * **
474732 ATCGATATATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* * ** ** * * ** *
474796 ATCGATGCATAAGGAGTACATCGATATATCCCAGCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
*
474860 A-CTGATGCATTAGTAGTGCATCGAT
1 ATC-GATGCATAAGTAGTGCATCGAT
474885 TCATACCTTC
Statistics
Matches: 123, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
63 1 0.01
64 118 0.96
65 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:475227 original size:12 final size:12
Alignment explanation
Indices: 475197--475241 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
475187 ATATATGTTC
475197 ATGTGATATGAT
1 ATGTGATATGAT
475209 A--TGATATGAT
1 ATGTGATATGAT
*
475219 ATGTGATATGAC
1 ATGTGATATGAT
475231 ATGTGATATGA
1 ATGTGATATGA
475242 GAACATGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 10 0.33
12 20 0.67
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:475227 original size:17 final size:17
Alignment explanation
Indices: 475196--475241 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
475186 TATATATGTT
475196 CATGTGATATGATATGA
1 CATGTGATATGATATGA
* *
475213 TATGAT-ATGTGATATGA
1 CATG-TGATATGATATGA
475230 CATGTGATATGA
1 CATGTGATATGA
475242 GAACATGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
16 1 0.04
17 21 0.91
18 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (17 bp):
CATGTGATATGATATGA
Found at i:475263 original size:23 final size:26
Alignment explanation
Indices: 475222--475274 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 26
475212 ATATGATATG
475222 TGATATGACATGTGATATGAGA-ACA
1 TGATATGACATGTGATATGAGATACA
475247 TGATATGA-A-GTGATATGAGATACA
1 TGATATGACATGTGATATGAGATACA
475271 TGAT
1 TGAT
475275 CACAAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.41
24 8 0.30
25 8 0.30
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.30
Consensus pattern (26 bp):
TGATATGACATGTGATATGAGATACA
Found at i:475407 original size:15 final size:15
Alignment explanation
Indices: 475387--475419 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
475377 AGAAGTATAA
475387 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
475402 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
475417 TAG
1 TAG
475420 GGGTCCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:481015 original size:35 final size:37
Alignment explanation
Indices: 480952--481020 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 37
480942 TTTCGTCCTA
480952 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCAG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCAG
* *
480989 CTAGGATTC-AACTC-CTAAAATAGGATATAATT
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATT
481021 TTGCTATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 16 0.53
36 5 0.17
37 9 0.30
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCAG
Found at i:481529 original size:15 final size:15
Alignment explanation
Indices: 481509--481539 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
481499 ATTATATATA
481509 TATATTTATAATTAT
1 TATATTTATAATTAT
*
481524 TATATTTATTATTAT
1 TATATTTATAATTAT
481539 T
1 T
481540 GTACTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTTATAATTAT
Found at i:481735 original size:16 final size:16
Alignment explanation
Indices: 481716--481749 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
481706 CATGTATTTA
481716 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
481732 TATTATTTTACTTTAT
1 TATTATATTACATTAT
481748 TA
1 TA
481750 AATTATTTTT
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:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:481754 original size:21 final size:22
Alignment explanation
Indices: 481730--481780 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
481720 ATATTACATT
*
481730 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
481751 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
481773 ATTATTAT
1 ATTATTAT
481781 ATATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:483182 original size:5 final size:5
Alignment explanation
Indices: 483172--483199 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
483162 TCTTTTCATC
483172 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
483200 CATCACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:485121 original size:22 final size:22
Alignment explanation
Indices: 485098--485159 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
485088 CAAAAAGGGC
485098 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
485121 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
485142 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
485160 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:485150 original size:20 final size:20
Alignment explanation
Indices: 485098--485166 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
485088 CAAAAAGGGC
*
485098 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
485121 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
485142 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
485162 AAAAA
1 AAAAA
485167 AAAGGGACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 10 0.24
24 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:485806 original size:22 final size:22
Alignment explanation
Indices: 485778--485828 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
485768 CCCCATCAAT
485778 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
* *
485800 CCTTTGAGCATTAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
485822 CCTTTGA
1 CCTTTGA
485829 CCAAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:486781 original size:37 final size:37
Alignment explanation
Indices: 486688--486797 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
486678 ATGCTCACCA
*
486688 TTGTCTCTCTTGAGACAGTTTCTCTTAAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACT
* *
486724 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACT
* *
486761 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAAC
486798 ATTGAAAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 29 0.45
37 33 0.51
38 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACT
Found at i:486883 original size:37 final size:37
Alignment explanation
Indices: 486824--487098 Score: 168
Period size: 37 Copynumber: 7.9 Consensus size: 37
486814 TTGAAATGAG
*
486824 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
** *
486861 TTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* *
486899 ---------CATTGGAAACA-TTTCCCTTGAAA-TAAA
1 TTTTGTCTCCATT-GAGACAGTTTCCCTTGAAACAAAA
*
486926 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
486963 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
487001 ---------CATTGAAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATTG-AGACAGTTTCCCTTGAAACAAAA
* *
487028 TTTTGTCTCTC-TTGAGATAGTTTCCCTCGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
487065 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA
487099 TAAACATTGA
Statistics
Matches: 182, Mismatches: 25, Indels: 62
0.68 0.09 0.23
Matches are distributed among these distances:
27 5 0.03
29 30 0.16
30 9 0.05
35 7 0.04
36 31 0.17
37 94 0.52
38 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (37 bp):
TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACAAAA
Found at i:486899 original size:102 final size:102
Alignment explanation
Indices: 486723--487163 Score: 774
Period size: 102 Copynumber: 4.3 Consensus size: 102
486713 TAAAACAAAC
* *
486723 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
*
486788 AAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
** *
486825 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
* *
486890 AAACATAAACATTGGAAACATTTCCCTTGAAATAAAT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
486927 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
486992 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
*
487029 TTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
487094 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
** *
487131 TTCATCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
487164 TAAACATTGA
Statistics
Matches: 321, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 321 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
Found at i:487153 original size:65 final size:64
Alignment explanation
Indices: 487070--487227 Score: 271
Period size: 65 Copynumber: 2.5 Consensus size: 64
487060 CAAAATTTTG
*
487070 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA-TTCA
* *
487135 TCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCG
1 TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCA
*
487199 TCTCTCTTGAGACAGTTTCTCTTAAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACA
487228 AAATTTTGTC
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 30 0.34
65 58 0.66
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (64 bp):
TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCA
Found at i:487405 original size:37 final size:37
Alignment explanation
Indices: 487335--487406 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
487325 TGGAACTAAG
* * **
487335 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
487372 TTTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAA
487407 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:487993 original size:160 final size:160
Alignment explanation
Indices: 487729--488065 Score: 593
Period size: 160 Copynumber: 2.1 Consensus size: 160
487719 CAACACAAGT
* *
487729 TCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
1 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
487794 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
66 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
* *
487859 GACTGTCAACAAACAATTTCGGAGCCAATC
131 GAATGTCAACAAACAATTTCGGAGCCAAAC
487889 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
1 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
*
487954 ACTTCACATCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
66 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
* * *
488019 GAATGTCGACAAGCAATTTTGGAGCCAAAC
131 GAATGTCAACAAACAATTTCGGAGCCAAAC
*
488049 TCAACTTCACAGCGAAG
1 TCAACTTCACAACGAAG
488066 GATATTGGAC
Statistics
Matches: 168, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
160 168 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (160 bp):
TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
GAATGTCAACAAACAATTTCGGAGCCAAAC
Found at i:488218 original size:106 final size:104
Alignment explanation
Indices: 487889--488390 Score: 504
Period size: 106 Copynumber: 4.9 Consensus size: 104
487879 GGAGCCAATC
* * * * * *
487889 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCTCA-TTTCAGAGCCAATTTCA
* * * * *
487954 ACTTCACATCGAAGGATATTGGACCCAAGACAGCACAAGC
65 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * * * **
487994 TCAACTTCACAGCGAAGGGGCGGCTGAATGTCGACAAGCAA----T--TTT-GGAGCCAAACTCA
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAA-AAATTTCTCATTTCAGAGCCAATTTCA
488052 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
65 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* *
488092 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTCTCAAATTTCAGAGCCAATTTC
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCTC--ATTTCAGAGCCAATTTC
* *
488157 AACTTCGCAACGAAGGATATTGGACTCGAGACAACACAAGT
64 AACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * * *
488198 TCAACTTCATAATGAAGGGACGGCTGATTGTCAAC-AAGA-TT-TC-GTTCAGAGTCAATTTCAT
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCTCATTTCAGAGCCAATTTCAA
* * * *
488259 CTTCACAGCGAATGATATTAGACTCGAGACAGCACAAGC
66 CTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * * * *
488298 TCAACTTCACAGCGAAGGGGCGGTTGACTGTCAACAAATAATTTCCCAGTTCCAGAACCAATTTC
1 TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-AATTTCTCA-TTTCAGAGCCAATTTC
*
488363 AACTTCACAGCGGAGGATATTGGACTCG
64 AACTTCACAGCGAAGGATATTGGACTCG
488391 GAACAATATT
Statistics
Matches: 322, Mismatches: 59, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
97 1 0.00
98 75 0.23
99 3 0.01
100 77 0.24
101 3 0.01
102 1 0.00
103 4 0.01
104 3 0.01
105 37 0.11
106 118 0.37
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (104 bp):
TCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCTCATTTCAGAGCCAATTTCAA
CTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
Found at i:488316 original size:206 final size:202
Alignment explanation
Indices: 487888--488390 Score: 603
Period size: 206 Copynumber: 2.5 Consensus size: 202
487878 CGGAGCCAAT
* * *
487888 CTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTT
1 CTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAA-AATTTCCCAGTTTCAGAGCCAATTTC
* * * * * *
487953 AACTTCACATCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGC
65 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGC
* * *
488018 TGAATGTCGACAAGCAATTTTGGAGCCAAACTCAACTTCACAGCGAAGGATATTGGACTCGAGAC
130 TGAATGTCAACAAGCAATTTTAGAGCCAAACTCAACTTCACAGCGAAGGATATTAGACTCGAGAC
488083 AACACAAG
195 AACACAAG
* * *
488091 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTCTCAAATTTCAGAGCCAATTT
1 CTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-ATTTC-CCAGTTTCAGAGCCAATTT
* * * *
488156 CAACTTCGCAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCATAATGAAGGGACGG
64 CAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGG
* * * ** * *
488221 CTGATTGTCAACAAG-ATTTCGTTCAGAGTCAATTTCATCTTCACAGCGAATGATATTAGACTCG
129 CTGAATGTCAACAAGCAATT--TT-AGAGCCAAACTCAACTTCACAGCGAAGGATATTAGACTCG
*
488285 AGACAGCACAAG
191 AGACAACACAAG
* * * ** * *
488297 CTCAACTTCACAGCGAAGGGGCGGTTGACTGTCAACAAATAATTTCCCAGTTCCAGAACCAATTT
1 CTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AA-AATTTCCCAGTTTCAGAGCCAATTT
* *
488362 CAACTTCACAGCGGAGGATATTGGACTCG
64 CAACTTCACAACGAAGGATATTGGACTCG
488391 GAACAATATT
Statistics
Matches: 253, Mismatches: 40, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
202 1 0.00
203 44 0.17
204 83 0.33
205 2 0.01
206 115 0.45
207 7 0.03
208 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (202 bp):
CTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAATTTCCCAGTTTCAGAGCCAATTTCA
ACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCT
GAATGTCAACAAGCAATTTTAGAGCCAAACTCAACTTCACAGCGAAGGATATTAGACTCGAGACA
ACACAAG
Found at i:488914 original size:35 final size:37
Alignment explanation
Indices: 488851--488919 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 37
488841 TTTCGTCCTA
488851 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCAG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCAG
* *
488888 CTAGGATTC-AACTC-CTAAAATAGGATATAATT
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATT
488920 TTGCTATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 16 0.53
36 5 0.17
37 9 0.30
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCAG
Found at i:489426 original size:15 final size:15
Alignment explanation
Indices: 489408--489438 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
489398 TATATATATA
489408 TATATTTATAATTAT
1 TATATTTATAATTAT
*
489423 TATATTTATTATTAT
1 TATATTTATAATTAT
489438 T
1 T
489439 GTACTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTTATAATTAT
Found at i:489634 original size:16 final size:16
Alignment explanation
Indices: 489615--489648 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
489605 CATGTATTTA
489615 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
489631 TATTATTTTACTTTAT
1 TATTATATTACATTAT
489647 TA
1 TA
489649 AATTATTTTT
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:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:494440 original size:22 final size:22
Alignment explanation
Indices: 494415--494465 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
494405 CTACAGCGAC
494415 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
494437 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
494459 ATCCGTC
1 ATCCGTC
494466 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:494750 original size:19 final size:19
Alignment explanation
Indices: 494726--494767 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
494716 AATACCAAAT
494726 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
494745 TCGCAACGCGAAACTAAAA
1 TCGCAACGCGAAACTAAAA
494764 TCGC
1 TCGC
494768 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:495146 original size:14 final size:14
Alignment explanation
Indices: 495127--495162 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
495117 ATCATGTCTG
495127 TTTGTAGTGTATAA
1 TTTGTAGTGTATAA
495141 TTTGTAGTGTATAA
1 TTTGTAGTGTATAA
495155 TTTGTAGT
1 TTTGTAGT
495163 TTTTTGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (14 bp):
TTTGTAGTGTATAA
Found at i:497135 original size:21 final size:21
Alignment explanation
Indices: 497109--497153 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
497099 GATTTCTGGG
* *
497109 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
497130 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
497151 CAA
1 CAA
497154 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:498386 original size:32 final size:31
Alignment explanation
Indices: 498344--498471 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
498334 AGAGTCGAGG
498344 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
498375 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
498407 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
498438 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
498469 GTT
1 GTT
498472 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
31 54 0.66
32 28 0.34
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:498491 original size:30 final size:30
Alignment explanation
Indices: 498430--498526 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
498420 CTAAGGAACA
* * ***
498430 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
498461 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
498491 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
498521 TCTGGA
1 TATGGA
498527 TAGGTCATTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:498527 original size:30 final size:30
Alignment explanation
Indices: 498457--498529 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
498447 GGTTCTTCGG
* *
498457 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
498487 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
498517 GACCTCTGGATAG
1 GACCTCTGGATAG
498530 GTCATTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:499638 original size:4 final size:4
Alignment explanation
Indices: 499629--499670 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
499619 TTTTTCGGCA
* * *
499629 TTAT TTAT TTAT TTAT TTAT TGAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
499671 TCAACGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:499844 original size:21 final size:21
Alignment explanation
Indices: 499820--499872 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
499810 CCTATCATCA
499820 TTCAAGAGGCGC-CTCTTATCG
1 TTCAAGAGGC-CTCTCTTATCG
499841 TTCAAGAGGCCTCTCTTATCG
1 TTCAAGAGGCCTCTCTTATCG
499862 TTCAAGAGGCC
1 TTCAAGAGGCC
499873 CCTATCATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (21 bp):
TTCAAGAGGCCTCTCTTATCG
Found at i:501374 original size:14 final size:14
Alignment explanation
Indices: 501355--501394 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
501345 TTTTGATTAA
501355 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
501369 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
501383 TTGATTTGTAAA
1 TTGATTTGTAAA
501395 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:501387 original size:61 final size:64
Alignment explanation
Indices: 501304--501445 Score: 166
Period size: 67 Copynumber: 2.2 Consensus size: 64
501294 TTTTACATTG
501304 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-ATTTATTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTTATTTTCTTGATTAATTGATTTGTA
* ** * * *
501365 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTTGCTTGTTTAATTGATTT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAG-A--ATTTATTTT-CTTGATTAATTGATTT
501429 GTA
62 GTA
501432 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
501446 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
61 26 0.38
62 3 0.04
65 8 0.12
67 31 0.46
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (64 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTTATTTTCTTGATTAATTGATTTGTA
Found at i:501551 original size:20 final size:20
Alignment explanation
Indices: 501528--501570 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
501518 AATTTTCGGT
501528 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
501548 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
501568 TTG
1 TTG
501571 ATCGCAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:501799 original size:39 final size:39
Alignment explanation
Indices: 501745--501831 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
501735 TCAAGTTGTA
*
501745 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
*
501784 GATTTTGATTTCCTTTTGCTTGACACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
501823 GATTTTGAT
1 GATTTTGAT
501832 GAGCATCAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
Found at i:502122 original size:18 final size:18
Alignment explanation
Indices: 502099--502135 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
502089 CGAAATTTAT
502099 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
502117 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
502135 A
1 A
502136 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:503149 original size:24 final size:24
Alignment explanation
Indices: 503122--503175 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
503112 CCATCATATC
* *
503122 ATCAAAATCTGAGTATTAATCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* *
503146 ATCAAAGTCCGGGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
503170 ATCAAA
1 ATCAAA
503176 TTTGGAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:504107 original size:19 final size:20
Alignment explanation
Indices: 504085--504148 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 20
504075 AAACCTGTTA
504085 CGAAATT-AAATTCGCGTTG
1 CGAAATTGAAATTCGCGTTG
* *
504104 CGAATTTGAAATTC-AGTTG
1 CGAAATTGAAATTCGCGTTG
* **
504123 CGAATTTGACTTTCGCGTTG
1 CGAAATTGAAATTCGCGTTG
504143 C-AAATT
1 CGAAATT
504149 TGACTATCAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 26 0.70
20 11 0.30
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (20 bp):
CGAAATTGAAATTCGCGTTG
Found at i:504117 original size:20 final size:20
Alignment explanation
Indices: 504092--504151 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
504082 TTACGAAATT
504092 AAATTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
*
504112 AAATTC-AGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
** *
504131 ACTTTCGCGTTGCAAATTTG
1 AAATTCGCGTTGCGAATTTG
504151 A
1 A
504152 CTATCACGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTTG
Found at i:504141 original size:39 final size:40
Alignment explanation
Indices: 504095--504178 Score: 109
Period size: 39 Copynumber: 2.1 Consensus size: 40
504085 CGAAATTAAA
* *
504095 TTCGCGTTGCGAATTTGAA-ATTCA-GTTGCGAATTTGACT
1 TTCGCGTTGCAAATTTGAATA-TCACGTTGAGAATTTGACT
*
504134 TTCGCGTTGCAAATTTGACTATCACGTTGAGAATTTGACT
1 TTCGCGTTGCAAATTTGAATATCACGTTGAGAATTTGACT
*
504174 ATCGC
1 TTCGC
504179 AACGCGAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
39 20 0.51
40 19 0.49
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (40 bp):
TTCGCGTTGCAAATTTGAATATCACGTTGAGAATTTGACT
Found at i:504152 original size:20 final size:20
Alignment explanation
Indices: 504095--504178 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
504085 CGAAATTAAA
* **
504095 TTCGCGTTGCGAATTTGAAA
1 TTCGCGTTGCAAATTTGACT
* *
504115 TTC-AGTTGCGAATTTGACT
1 TTCGCGTTGCAAATTTGACT
504134 TTCGCGTTGCAAATTTGACT
1 TTCGCGTTGCAAATTTGACT
* *
504154 ATCACGTTG-AGAATTTGACT
1 TTCGCGTTGCA-AATTTGACT
*
504174 ATCGC
1 TTCGC
504179 AACGCGAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 17 0.31
20 37 0.69
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
TTCGCGTTGCAAATTTGACT
Found at i:505315 original size:71 final size:71
Alignment explanation
Indices: 505231--505375 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 71
505221 TCCATTTTAT
505231 ATCGCTTTTAACTGTTCAGACTATTACCCTTCAAGGATTTCGAATATTATGTTTTAACCTAGCAA
1 ATCGCTTTTAACTGTTCAGACTATTACCCTTCAAGGATTTCGAATATTATGTTTTAACCTAGCAA
505296 TGACAA
66 TGACAA
505302 ATCGCTTTTAACTGTTCAGACTATTACCCTTCAAGGATTTCGAATATTATGTTTTAACCTAGCAA
1 ATCGCTTTTAACTGTTCAGACTATTACCCTTCAAGGATTTCGAATATTATGTTTTAACCTAGCAA
*
505367 TGGCAA
66 TGACAA
505373 ATC
1 ATC
505376 ATGTTTCATG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (71 bp):
ATCGCTTTTAACTGTTCAGACTATTACCCTTCAAGGATTTCGAATATTATGTTTTAACCTAGCAA
TGACAA
Found at i:509634 original size:15 final size:15
Alignment explanation
Indices: 509610--509641 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
509600 TGGTAGATCC
*
509610 AAATCCAGAATGAGA
1 AAATCAAGAATGAGA
509625 AAATCAAGAATGAGA
1 AAATCAAGAATGAGA
509640 AA
1 AA
509642 GAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.09, G:0.19, T:0.12
Consensus pattern (15 bp):
AAATCAAGAATGAGA
Found at i:520346 original size:24 final size:23
Alignment explanation
Indices: 520317--520364 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
520307 CGATTCGGGT
*
520317 TCTTCTCCATCGTCATCATCATTC
1 TCTTCTCCATCATCATCATC-TTC
*
520341 TCTTCTTCATCATCATCATCTTC
1 TCTTCTCCATCATCATCATCTTC
520364 T
1 T
520365 TCATTATCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.17, C:0.35, G:0.02, T:0.46
Consensus pattern (23 bp):
TCTTCTCCATCATCATCATCTTC
Found at i:520352 original size:18 final size:18
Alignment explanation
Indices: 520329--520368 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
520319 TTCTCCATCG
520329 TCATCATCATTC-TCTTCT
1 TCATCATCA-TCATCTTCT
520347 TCATCATCATCATCTTCT
1 TCATCATCATCATCTTCT
520365 TCAT
1 TCAT
520369 TATCGTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (18 bp):
TCATCATCATCATCTTCT
Found at i:527528 original size:16 final size:17
Alignment explanation
Indices: 527509--527540 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
527499 TATTATTTTT
527509 ATTTAA-TAAAAAAATG
1 ATTTAATTAAAAAAATG
527525 ATTTAATTAAAAAAAT
1 ATTTAATTAAAAAAAT
527541 AATATATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
ATTTAATTAAAAAAATG
Found at i:527669 original size:27 final size:28
Alignment explanation
Indices: 527626--527695 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 28
527616 TTTTTCACCC
*
527626 TAAACCCGAATCCAACCC-AA-ATTTTTT
1 TAAACCCG-ACCCAACCCGAATATTTTTT
*
527653 TAAACCCGACCCAAACCCGAATGTTTTTT
1 TAAACCCGACCC-AACCCGAATATTTTTT
527682 TAAAAACCCGACCC
1 T--AAACCCGACCC
527696 GATCGGGTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 3 0.08
27 13 0.36
28 2 0.06
29 7 0.19
31 11 0.31
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.24
Consensus pattern (28 bp):
TAAACCCGACCCAACCCGAATATTTTTT
Found at i:529872 original size:2 final size:2
Alignment explanation
Indices: 529865--529893 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
529855 CATGCCCTAT
529865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
529894 GTTAGTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:532412 original size:2 final size:2
Alignment explanation
Indices: 532407--532436 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
532397 AAAAATATTA
532407 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
532437 TTTAAAAAAA
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:539676 original size:7 final size:7
Alignment explanation
Indices: 539660--539698 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
539650 GTCAAAGAAA
539660 GTCAACG
1 GTCAACG
*
539667 GTCAAGG
1 GTCAACG
539674 GTCAACG
1 GTCAACG
539681 GTCAACG
1 GTCAACG
539688 GTCAACG
1 GTCAACG
539695 GTCA
1 GTCA
539699 GGTCGGGTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.31, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:539713 original size:22 final size:22
Alignment explanation
Indices: 539687--539746 Score: 76
Period size: 17 Copynumber: 3.0 Consensus size: 22
539677 AACGGTCAAC
539687 GGTCAACGGTCAGGTCGGGTCG
1 GGTCAACGGTCAGGTCGGGTCG
539709 GGTCAA----C-GGTCGGGTCG
1 GGTCAACGGTCAGGTCGGGTCG
*
539726 GATCAACGGTCAGGTCGGGTC
1 GGTCAACGGTCAGGTCGGGTC
539747 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
21 1 0.03
22 15 0.47
ACGTcount: A:0.15, C:0.23, G:0.43, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCAGGTCGGGTCG
Found at i:539719 original size:17 final size:17
Alignment explanation
Indices: 539699--539747 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
539689 TCAACGGTCA
539699 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
*
539716 GGTCGGGTCGGATCAAC
1 GGTCGGGTCGGGTCAAC
*
539733 GGTCAGGTCGGGTCA
1 GGTCGGGTCGGGTCA
539748 GACCGGTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:539761 original size:9 final size:9
Alignment explanation
Indices: 539743--539831 Score: 70
Period size: 9 Copynumber: 9.3 Consensus size: 9
539733 GGTCAGGTCG
*
539743 GGTCAGACC
1 GGTCAAACC
539752 GGTCAAACC
1 GGTCAAACC
* * *
539761 GATTTAGACC
1 G-GTCAAACC
539771 GGTCAAACC
1 GGTCAAACC
*
539780 GGTTGAAACC
1 GG-TCAAACC
539790 GGTCAAACC
1 GGTCAAACC
539799 GGTCAGAACC
1 GGTCA-AACC
*
539809 GGTTGAAAACC
1 GG-T-CAAACC
*
539820 GGTTAAACC
1 GGTCAAACC
539829 GGT
1 GGT
539832 ATCCAGTAGC
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 35 0.55
10 21 0.33
11 7 0.11
12 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:539800 original size:19 final size:18
Alignment explanation
Indices: 539749--539831 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 18
539739 GTCGGGTCAG
* *
539749 ACCGGTCAAACCGATTTAG
1 ACCGGTCAAACCG-GTTAA
539768 ACCGGTCAAACCGGTTGAA
1 ACCGGTCAAACCGGTT-AA
*
539787 ACCGGTCAAACCGGTCAGA
1 ACCGGTCAAACCGGTTA-A
*
539806 ACCGGTTGAAAACCGGTTAA
1 ACCGG-T-CAAACCGGTTAA
539826 ACCGGT
1 ACCGGT
539832 ATCCAGTAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
18 3 0.05
19 36 0.65
20 7 0.13
21 9 0.16
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (18 bp):
ACCGGTCAAACCGGTTAA
Found at i:539810 original size:38 final size:39
Alignment explanation
Indices: 539749--539831 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 39
539739 GTCGGGTCAG
* * *
539749 ACCGGTCAAACCGATTTAGACCGG-T-CAAACCGGTTGAA
1 ACCGGTCAAACCGAGTCAGACCGGTTGAAAACCGGTT-AA
539787 ACCGGTCAAACCG-GTCAGAACCGGTTGAAAACCGGTTAA
1 ACCGGTCAAACCGAGTCAG-ACCGGTTGAAAACCGGTTAA
539826 ACCGGT
1 ACCGGT
539832 ATCCAGTAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
37 3 0.08
38 18 0.46
39 9 0.23
40 9 0.23
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (39 bp):
ACCGGTCAAACCGAGTCAGACCGGTTGAAAACCGGTTAA
Found at i:547025 original size:5 final size:5
Alignment explanation
Indices: 547015--547072 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
547005 AACGGTCAAC
* *
547015 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG
547064 GGTCG GGTC
1 GGTCG GGTC
547073 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:547044 original size:34 final size:35
Alignment explanation
Indices: 547001--547083 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
546991 GAAAGTCAAC
*
547001 GGTCAACGGTCAACGGTCGGGTC-GGGTCGGGTCG
1 GGTCAACGGTCAACGGTCGGGTCACGGTCGGGTCG
*
547035 GGTCAACGGTC--GGGTCGGGTCAACGGTCGGGTCG
1 GGTCAACGGTCAACGGTCGGGTC-ACGGTCGGGTCG
547069 GGTCAGACCGGTCAA
1 GGTCA-A-CGGTCAA
547084 ACCGATTCAG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
32 9 0.22
34 26 0.63
35 1 0.02
36 5 0.12
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (35 bp):
GGTCAACGGTCAACGGTCGGGTCACGGTCGGGTCG
Found at i:547045 original size:17 final size:17
Alignment explanation
Indices: 547025--547073 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
547015 GGTCGGGTCG
547025 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
547042 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
547059 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
547074 GACCGGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:547045 original size:22 final size:22
Alignment explanation
Indices: 547008--547072 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
546998 AACGGTCAAC
547008 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
* *
547030 GGTC--GGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
547052 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
547073 AGACCGGTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.11
22 27 0.77
24 4 0.11
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:547106 original size:28 final size:27
Alignment explanation
Indices: 547069--547157 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 27
547059 GGTCGGGTCG
* * *
547069 GGTCAGACCGGTCAAACCGATTCAGACC
1 GGTCAAACCGGTCAAACCG-GTCAAACC
*
547097 GGTCAAACCGGTTGAAACCGGTCAAACC
1 GGTCAAACCGG-TCAAACCGGTCAAACC
* *
547125 GGTCAGAACCGGTTGAAAACCGGTTAAACC
1 GGTCA-AACCGG-T-CAAACCGGTCAAACC
547155 GGT
1 GGT
547158 TTCCAGCAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 21 0.40
29 15 0.29
30 16 0.31
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (27 bp):
GGTCAAACCGGTCAAACCGGTCAAACC
Found at i:547114 original size:10 final size:10
Alignment explanation
Indices: 547075--547158 Score: 79
Period size: 9 Copynumber: 8.7 Consensus size: 10
547065 GTCGGGTCAG
547075 ACCGG-TCAA
1 ACCGGTTCAA
* *
547084 ACCGATTCAG
1 ACCGGTTCAA
547094 ACCGG-TCAA
1 ACCGGTTCAA
*
547103 ACCGGTTGAA
1 ACCGGTTCAA
547113 ACCGG-TCAA
1 ACCGGTTCAA
547122 ACCGG-TCAGA
1 ACCGGTTCA-A
*
547132 ACCGGTTGAAA
1 ACCGGTT-CAA
547143 ACCGGTT-AA
1 ACCGGTTCAA
547152 ACCGGTT
1 ACCGGTT
547159 TCCAGCAGCC
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
9 32 0.51
10 21 0.33
11 9 0.14
12 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:547126 original size:19 final size:19
Alignment explanation
Indices: 547075--547157 Score: 89
Period size: 19 Copynumber: 4.3 Consensus size: 19
547065 GTCGGGTCAG
* *
547075 ACCGGTCAAACCGATTCAG
1 ACCGGTCAAACCGGTTCAA
*
547094 ACCGGTCAAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAA
547113 ACCGGTCAAACCGG-TCAGA
1 ACCGGTCAAACCGGTTCA-A
*
547132 ACCGGTTGAAAACCGGTT-AA
1 ACCGG-T-CAAACCGGTTCAA
547152 ACCGGT
1 ACCGGT
547158 TTCCAGCAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
18 2 0.04
19 37 0.67
20 7 0.13
21 8 0.15
22 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:551337 original size:24 final size:23
Alignment explanation
Indices: 551311--551354 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
551301 TCCCCTAAGG
551311 GGGGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGGTTCCCATTCAAA
*
551334 GGGGGAATCGGTTCCCCTTCA
1 GGGGGAATCGGTTCCCATTCA
551355 TGAGAGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCATTCAAA
Found at i:556704 original size:15 final size:15
Alignment explanation
Indices: 556686--556717 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
556676 CCCTCAAGAA
556686 TTATACCCCAAATTC
1 TTATACCCCAAATTC
556701 TTATACCCCAAATTC
1 TTATACCCCAAATTC
556716 TT
1 TT
556718 GAGAACACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (15 bp):
TTATACCCCAAATTC
Found at i:559380 original size:20 final size:21
Alignment explanation
Indices: 559355--559447 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
559345 TTTTCCCAAT
*
559355 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
559375 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
559396 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
559416 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
559437 TCGCAATGCGA
1 TCGCAATGCGA
559448 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:559400 original size:41 final size:41
Alignment explanation
Indices: 559355--559447 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
559345 TTTTCCCAAT
559355 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
559396 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
559437 TCGCAATGCGA
1 TCGCAATGCGA
559448 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:559478 original size:41 final size:41
Alignment explanation
Indices: 559433--559510 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
559423 GCGAATTGGG
* * *
559433 AAAATCGCAATGCGATACTTACTATT-GCAATGCGATAATAA
1 AAAATCGCAACGAGATACTTACT-TTCGCAACGCGATAATAA
559474 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
559511 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 31 0.94
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTTTCGCAACGCGATAATAA
Found at i:559526 original size:20 final size:20
Alignment explanation
Indices: 559478--559529 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
559468 TAATAAAAAA
* *
559478 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
559498 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
559518 TCGCAACGCGAT
1 TCGCAACGCGAT
559530 TTACATAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:560105 original size:19 final size:19
Alignment explanation
Indices: 560081--560125 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
560071 GCAACGAGAT
560081 AATCGCAACGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
560100 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
560119 AATCGCA
1 AATCGCA
560126 TTGCGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:560186 original size:20 final size:19
Alignment explanation
Indices: 560121--560305 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
560111 GAAACTAAAA
*
560121 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
560140 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
560159 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
560178 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
560198 TCGCGTTGTGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
560214 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
560231 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
560245 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
560265 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
560284 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
560304 TC
1 TC
560306 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 49 0.36
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:560198 original size:39 final size:38
Alignment explanation
Indices: 560121--560305 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
560111 GAAACTAAAA
*
560121 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
560159 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * * **
560198 TCGCGTTGTGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
560231 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCA-TT
* *
560265 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
560304 TC
1 TC
560306 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
33 34 0.28
34 13 0.11
35 1 0.01
36 3 0.02
38 21 0.17
39 32 0.26
40 15 0.12
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:561814 original size:21 final size:21
Alignment explanation
Indices: 561790--561856 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
561780 TCATTCCTCG
561790 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
561811 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
561832 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
561853 AGAG
1 AGAG
561857 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:564236 original size:12 final size:12
Alignment explanation
Indices: 564219--564243 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
564209 TCTTCGGGGA
564219 CTTTTTCTTCTT
1 CTTTTTCTTCTT
564231 CTTTTTCTTCTT
1 CTTTTTCTTCTT
564243 C
1 C
564244 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:564452 original size:24 final size:24
Alignment explanation
Indices: 564418--564471 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
564408 CTGAAACATC
* *
564418 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
564442 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
564466 ATCAAA
1 ATCAAA
564472 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:565556 original size:20 final size:20
Alignment explanation
Indices: 565531--565588 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
565521 ATTCATTTGA
565531 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
565551 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
565571 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
565589 AGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:565644 original size:33 final size:35
Alignment explanation
Indices: 565607--565724 Score: 133
Period size: 33 Copynumber: 3.4 Consensus size: 35
565597 GAAATGAAAA
565607 TCGCATTGCGATTTTC-TCG-TTGCGATTTTCATT
1 TCGCATTGCGATTTTCTTCGATTGCGATTTTCATT
565640 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTC--TTCG-ATTGCGATTTTCATT
565675 TCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC--TTCG-ATTGCGATTTTCATT
565711 TCGCATTGCGATTT
1 TCGCATTGCGATTT
565725 CCATTTCGCG
Statistics
Matches: 75, Mismatches: 0, Indels: 15
0.83 0.00 0.17
Matches are distributed among these distances:
33 46 0.61
35 3 0.04
36 6 0.08
38 20 0.27
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (35 bp):
TCGCATTGCGATTTTCTTCGATTGCGATTTTCATT
Found at i:565648 original size:19 final size:19
Alignment explanation
Indices: 565607--565741 Score: 182
Period size: 19 Copynumber: 7.6 Consensus size: 19
565597 GAAATGAAAA
565607 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
565623 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
565640 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
565659 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
565675 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
565692 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
565711 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
565730 TCGCGTTGCGAT
1 TCGCATTGCGAT
565742 AGTCTGTTTT
Statistics
Matches: 107, Mismatches: 2, Indels: 17
0.85 0.02 0.13
Matches are distributed among these distances:
14 22 0.21
16 6 0.06
17 6 0.06
19 73 0.68
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:565663 original size:52 final size:52
Alignment explanation
Indices: 565607--565724 Score: 236
Period size: 52 Copynumber: 2.3 Consensus size: 52
565597 GAAATGAAAA
565607 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
565659 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
565711 TCGCATTGCGATTT
1 TCGCATTGCGATTT
565725 CCATTTCGCG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:567767 original size:20 final size:19
Alignment explanation
Indices: 567732--567798 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
567722 GAAACTTAAA
567732 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
567751 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
567771 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
567790 ATCGCAACG
1 ATCGCAACG
567799 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:567806 original size:14 final size:14
Alignment explanation
Indices: 567787--567844 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
567777 ATGCGAAATG
567787 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
567801 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
567817 ATGAAATCGCAACAAC
1 A--AAATCGCAACGAC
567833 AAAATCGCAACG
1 AAAATCGCAACG
567845 CGAAACATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 7 0.19
18 9 0.25
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:567829 original size:32 final size:33
Alignment explanation
Indices: 567771--567849 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
567761 GGAAATGGCT
* *
567771 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
567804 ATCGCAACGCGAAATG-AAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
567836 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
567850 CATTGCGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:567876 original size:19 final size:19
Alignment explanation
Indices: 567852--567980 Score: 91
Period size: 19 Copynumber: 7.3 Consensus size: 19
567842 ACGCGAAACA
567852 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
567871 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
567885 TTGCGATTTT-ATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
567903 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
567917 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
567936 TTGCGATAGACATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
** *
567956 TTGCGATAGTCATTTCGTG
1 TTGCGATTTTCATTTCGCG
567975 TTGCGA
1 TTGCGA
567981 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
14 16 0.18
15 6 0.07
16 6 0.07
17 5 0.06
18 11 0.12
19 28 0.31
20 17 0.19
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:567888 original size:14 final size:14
Alignment explanation
Indices: 567869--567926 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
567859 TTTCATTTCG
567869 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
567883 CGTTGCGATTTTATTT
1 CGTTGCGA-TTT-TGT
567899 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
567915 CGTTGCGATTTT
1 CGTTGCGATTTT
567927 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.53
15 3 0.08
16 4 0.11
17 3 0.08
18 8 0.21
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:567904 original size:32 final size:33
Alignment explanation
Indices: 567852--567942 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
567842 ACGCGAAACA
567852 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
567885 TTGCGATTTT-ATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
567917 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
567943 AGACATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:567961 original size:20 final size:19
Alignment explanation
Indices: 567927--567980 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
567917 TTGCGATTTT
*
567927 CATTTCGCATTGCGATAGA
1 CATTTCGCGTTGCGATAGA
*
567946 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGA
*
567966 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
567981 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGA
Found at i:568477 original size:18 final size:18
Alignment explanation
Indices: 568451--568495 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
568441 GTCGATCAGA
* *
568451 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
568469 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
568487 TGATGGCTC
1 TGATGGCTC
568496 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:569837 original size:20 final size:20
Alignment explanation
Indices: 569812--569849 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
569802 AATAGTTTCT
569812 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
569832 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
569850 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:570137 original size:22 final size:22
Alignment explanation
Indices: 570112--570155 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
570102 GATTTAGATA
570112 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
570134 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
570156 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:570436 original size:20 final size:20
Alignment explanation
Indices: 570323--570436 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
570313 CGCTTTGAAA
570323 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
570343 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
570363 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
570383 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
570404 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
570424 ATCGCATTGCGAT
1 ATCGCATTGCGAT
570437 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 56 0.73
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:570454 original size:21 final size:21
Alignment explanation
Indices: 570425--570517 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
570415 ATAGTAAGTA
570425 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
570446 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
570466 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
570487 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
570507 TCGCATTGCGA
1 TCGCATTGCGA
570518 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:570455 original size:41 final size:41
Alignment explanation
Indices: 570364--570498 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
570354 AAAGTCAGTA
* * * ** *
570364 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
570404 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
570446 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
570487 TCGCGTTGCGAT
1 TCGCGTTGCGAT
570499 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:570499 original size:41 final size:41
Alignment explanation
Indices: 570425--570517 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
570415 ATAGTAAGTA
570425 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
570466 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
570507 TCGCATTGCGA
1 TCGCATTGCGA
570518 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:576132 original size:29 final size:31
Alignment explanation
Indices: 576100--576167 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
576090 CTTTCATTTA
* *
576100 AGTCCCTTAAC-TTT-TAAAACTTTCAATAC
1 AGTCCCCTAACATTTGTAAAACTTGCAATAC
*
576129 AGTCCCCTAACATTTTGTAAAACTTGCAATAT
1 AGTCCCCTAACA-TTTGTAAAACTTGCAATAC
576161 AGTCCCC
1 AGTCCCC
576168 CAATATTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 10 0.30
31 3 0.09
32 20 0.61
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.34
Consensus pattern (31 bp):
AGTCCCCTAACATTTGTAAAACTTGCAATAC
Found at i:577284 original size:31 final size:31
Alignment explanation
Indices: 577249--577315 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
577239 TACAATACAT
577249 TCCCCTAACATTTAGTCCATTTGCAATATGG
1 TCCCCTAACATTTAGTCCATTTGCAATATGG
**
577280 TCCCCTAACATTTAGTCTGTTTGCAATATGG
1 TCCCCTAACATTTAGTCCATTTGCAATATGG
577311 TCCCC
1 TCCCC
577316 AATGTAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.36
Consensus pattern (31 bp):
TCCCCTAACATTTAGTCCATTTGCAATATGG
Found at i:581894 original size:2 final size:2
Alignment explanation
Indices: 581887--581970 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
581877 TATTCCAAGC
581887 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
581929 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
581971 ATCTAAATTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:589647 original size:22 final size:23
Alignment explanation
Indices: 589611--589671 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
589601 GTATCTTGAA
* *
589611 ATTTAATTTTTTTAAAATTATTT
1 ATTTAATTTTATTAAAAGTATTT
*
589634 ATTT-ATTTTATTAATAGTATTT
1 ATTTAATTTTATTAAAAGTATTT
589656 ATATTAAAATTTTATT
1 AT-TT--AATTTTATT
589672 CGTATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 17 0.55
23 6 0.19
26 8 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTAATTTTATTAAAAGTATTT
Found at i:590876 original size:2 final size:2
Alignment explanation
Indices: 590869--590903 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
590859 AAATAAATAA
590869 AT AT AT 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 AT AT AT A
590904 ATTTATTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:591097 original size:153 final size:156
Alignment explanation
Indices: 590908--591192 Score: 429
Period size: 155 Copynumber: 1.8 Consensus size: 156
590898 TATATAATTT
* * *
590908 ATTTAGAAATATCAGAAAAAACTTCTAGTTGCTTTAAGACAA-CCCTTTCTTAATAT-TAATAA-
1 ATTTAAAAATATCAGAAAAAACTTCTAGTTGCTTTAAGACAATCCCTTTCTTAATATAAAAAAAG
** *
590970 ATAAATAAAATATTAATAAATTATTTCTCTAAAAATAATTAAAAAA-AATA-AAATTAATATATA
66 ATAAAT-AAATATTAATAAAACATTTCTCTAAAAATAATTAAAAAATAAAATAAATTAATATATA
591033 TAATATATAAAAGTAGGATATTTATTA
130 TAATATATAAAAGTAGGATATTTATTA
*
591060 ATTTAAAAATATC-GAAAAATGACTTCTAGTTGCTTTAATACAATCCCTTTCTTAATATAAAAAA
1 ATTTAAAAATATCAGAAAAA--ACTTCTAGTTGCTTTAAGACAATCCCTTTCTTAATATAAAAAA
*
591124 AGATAAATAAATATTAATAAAACATTTCTCTAAAAATAATTAAAAAATAAAATAAATTAATATTT
64 AGATAAATAAATATTAATAAAACATTTCTCTAAAAATAATTAAAAAATAAAATAAATTAATATAT
591189 ATAA
129 ATAA
591193 AAATATCAGA
Statistics
Matches: 118, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
151 6 0.05
152 12 0.10
153 21 0.18
154 14 0.12
155 41 0.35
156 9 0.08
157 15 0.13
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (156 bp):
ATTTAAAAATATCAGAAAAAACTTCTAGTTGCTTTAAGACAATCCCTTTCTTAATATAAAAAAAG
ATAAATAAATATTAATAAAACATTTCTCTAAAAATAATTAAAAAATAAAATAAATTAATATATAT
AATATATAAAAGTAGGATATTTATTA
Found at i:592688 original size:3 final size:3
Alignment explanation
Indices: 592673--592748 Score: 111
Period size: 3 Copynumber: 25.0 Consensus size: 3
592663 TTTGGGCTTG
592673 TAA TAA TATA TAA TAA TAA TAA -AA TAAA TATA TAA TAA TAA T-A TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TA-A TAA TAA TAA TAA TAA
592719 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
592749 CCCAAATGAA
Statistics
Matches: 68, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.06
3 55 0.81
4 9 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:593465 original size:122 final size:122
Alignment explanation
Indices: 593075--593653 Score: 765
Period size: 122 Copynumber: 4.7 Consensus size: 122
593065 TTAAGGCAAG
* * * *
593075 GTTGAACAAATTCTTCTCATTATGAACTTGTTC-TCCTTCTTCAGATGAGTTCTTATCATTATAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGA
* ** * * * *
593139 ACTCTCTTTGGGAAATGAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTTACGCAAAAT
65 ACTCT-TCT-GG--A--AATGTTGATACTGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAA
* *
593203 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* *
593268 CT-TTCTTTGGAAAAATG-T-ATGA-TGATCTATCTCCTTCTGTGATAGAATCATGCAAAAG
66 CTCTTC--TGG--AAATGTTGAT-ACTGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAA
593326 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* *
593391 CACTTCTGGAAATGTTGATACTGATCTATCTTCTTCTGTGATAGAATCAAGCAAAAA
66 CTCTTCTGGAAATGTTGATACTGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAA
*
593448 GTTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAATTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGA
* *
593512 ACTCTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAA
65 ACTCTTCTGGAAATGTTGATACTGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAA
* * * * * *
593570 GTTAAATAAGTTCTTCTTATTATGAACTTTTTCTTCTTCTTCAGATGAATTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
593635 CTCTTCTGGAAATGTTGAT
66 CTCTTCTGGAAATGTTGAT
593654 CCATCGAGTA
Statistics
Matches: 413, Mismatches: 28, Indels: 26
0.88 0.06 0.06
Matches are distributed among these distances:
120 5 0.01
121 6 0.01
122 225 0.54
123 101 0.24
124 4 0.01
125 4 0.01
126 1 0.00
127 6 0.01
128 58 0.14
129 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (122 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTTCTGGAAATGTTGATACTGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAA
Found at i:594627 original size:18 final size:18
Alignment explanation
Indices: 594572--594626 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
594562 TATATAAAAG
*
594572 AATAAATTGAATTTCGAT
1 AATAAATTGAATTTCGAA
*
594590 AATAAATTGAATTTTGAA
1 AATAAATTGAATTTCGAA
594608 AATAAATTGAATTTC-AA
1 AATAAATTGAATTTCGAA
594625 AA
1 AA
594627 AGATAAACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 4 0.12
18 30 0.88
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (18 bp):
AATAAATTGAATTTCGAA
Found at i:595014 original size:11 final size:11
Alignment explanation
Indices: 595000--595034 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
594990 TATTTATTTA
595000 TTTTCTTTCTT
1 TTTTCTTTCTT
*
595011 TTTTTTTTCTT
1 TTTTCTTTCTT
595022 TTTTCTTT-TT
1 TTTTCTTTCTT
595032 TTT
1 TTT
595035 CAAACATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:595018 original size:15 final size:16
Alignment explanation
Indices: 595000--595035 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
594990 TATTTATTTA
595000 TTTTCTTTCTT-TTTT
1 TTTTCTTTCTTCTTTT
*
595015 TTTTCTTTTTTCTTTT
1 TTTTCTTTCTTCTTTT
595031 TTTTC
1 TTTTC
595036 AAACATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTCTTTCTTCTTTT
Found at i:602229 original size:15 final size:15
Alignment explanation
Indices: 602209--602240 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
602199 TGCAATAAAT
602209 AATGAATGTATGCAA
1 AATGAATGTATGCAA
602224 AATGAATGTATGCAA
1 AATGAATGTATGCAA
602239 AA
1 AA
602241 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:606072 original size:29 final size:28
Alignment explanation
Indices: 606030--606084 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 28
606020 ACTTCCAAGA
606030 AAATATATTAA-TTTTTATATTTTTAAT
1 AAATATATTAATTTTTTATATTTTTAAT
606057 AAATATATATATATTTTTTATATTTTTA
1 AAATATAT-TA-ATTTTTTATATTTTTA
606085 TATGTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 8 0.32
28 2 0.08
29 1 0.04
30 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
AAATATATTAATTTTTTATATTTTTAAT
Done.