Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 155 of 163
Found at i:51601844 original size:89 final size:89
Alignment explanation
Indices: 51601641--51601851 Score: 244
Period size: 89 Copynumber: 2.4 Consensus size: 89
51601631 CCGATATAGA
* * * ** * **
51601641 AAGACAGGACCTACTATCTTTGATCTGTTTCACGCCGGTACATGAAAACAAGATCTGCTTTCCTT
1 AAGACAAGATCTACTATCTCTGATCTACTCCACGCCAATACATGAAAACAAGATCTGCTTTCCTT
*
51601706 GATCTGCTTCGCCACTAGTATGGG
66 GATCTGCTTCGCCACCAGTATGGG
* ** * * **
51601730 AAGGCAAGATCTGGTATCTCTGATCTACTCCACGCCAATACATGAAGACAAGATCTGTTTTTTTT
1 AAGACAAGATCTACTATCTCTGATCTACTCCACGCCAATACATGAAAACAAGATCTGCTTTCCTT
*
51601795 TATCTGCTTCGCCACCAGTATGGG
66 GATCTGCTTCGCCACCAGTATGGG
*
51601819 AAGACAAGATCTACTTTCT-TCGATCTACTCCAC
1 AAGACAAGATCTACTATCTCT-GATCTACTCCAC
51601852 CACCTGTACA
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
88 1 0.01
89 99 0.99
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (89 bp):
AAGACAAGATCTACTATCTCTGATCTACTCCACGCCAATACATGAAAACAAGATCTGCTTTCCTT
GATCTGCTTCGCCACCAGTATGGG
Found at i:51601889 original size:45 final size:43
Alignment explanation
Indices: 51601728--51601927 Score: 150
Period size: 45 Copynumber: 4.5 Consensus size: 43
51601718 CACTAGTATG
* * *
51601728 GGAAGGCAAGATCTGGTATCTCTGATCTACTCCACGCCAATACA
1 GGAAGACAAGATCTGGTATCT-TGATCTACTCCACACCAGTACA
* * * * * * **
51601772 TGAAGACAAGATCTGTTTTTTTTTATCTGCTTCGC-CACCAGTATG
1 GGAAGACAAGATCTG-GTATCTTGATCTAC-TC-CACACCAGTACA
** * *
51601817 GGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCTGTACA
1 GGAAGACAAGATCTGGTATCTT-GATCTACTCCA-CACCAGTACA
* * *
51601862 GGGAGACAAGATCTGGTATCTATGATCTACTTCACGCCAGTACA
1 GGAAGACAAGATCTGGTATCT-TGATCTACTCCACACCAGTACA
* *
51601906 TGAAGACAAGATCTGTTATCTT
1 GGAAGACAAGATCTGGTATCTT
51601928 TCAACCTGCT
Statistics
Matches: 119, Mismatches: 30, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
43 2 0.02
44 52 0.44
45 63 0.53
46 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
GGAAGACAAGATCTGGTATCTTGATCTACTCCACACCAGTACA
Found at i:51612362 original size:3 final size:3
Alignment explanation
Indices: 51612354--51612390 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
51612344 NNNNNNNNNN
*
51612354 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
51612391 AAAGGTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:51614070 original size:10 final size:9
Alignment explanation
Indices: 51614049--51614086 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
51614039 TTTGAATAAA
51614049 TTTAATTTT
1 TTTAATTTT
51614058 TTTAATTTCT
1 TTTAATTT-T
51614068 TTTAAATTTT
1 TTT-AATTTT
51614078 TTT-ATTTT
1 TTTAATTTT
51614086 T
1 T
51614087 GCCGATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 6 0.22
9 8 0.30
10 8 0.30
11 5 0.19
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTAATTTT
Found at i:51615622 original size:2 final size:2
Alignment explanation
Indices: 51615615--51615642 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51615605 ACATGAAAAC
51615615 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
51615643 TATGTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51619346 original size:4 final size:4
Alignment explanation
Indices: 51619337--51619379 Score: 50
Period size: 4 Copynumber: 10.0 Consensus size: 4
51619327 CAAACGAAAT
*
51619337 AAGA AAGAA AAGA AAGA AAGA ATAGA AAGA AGAAA AAGA AAGA
1 AAGA AAG-A AAGA AAGA AAGA A-AGA AAGA A-AGA AAGA AAGA
51619380 GACGCACGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 23 0.68
5 11 0.32
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:51619355 original size:13 final size:13
Alignment explanation
Indices: 51619337--51619379 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
51619327 CAAACGAAAT
51619337 AAGAAAGAAAAGA
1 AAGAAAGAAAAGA
*
51619350 AAGAAAGAATAGA
1 AAGAAAGAAAAGA
51619363 AAG-AAGAAAAAGA
1 AAGAAAG-AAAAGA
51619376 AAGA
1 AAGA
51619380 GACGCACGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 3 0.12
13 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (13 bp):
AAGAAAGAAAAGA
Found at i:51623220 original size:16 final size:16
Alignment explanation
Indices: 51623199--51623254 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
51623189 CAAAAGTAAT
51623199 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
51623215 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
* * *
51623231 GAAATAAATA-AATAAA
1 TAAA-AGATACAATTAA
51623247 TAAAAGAT
1 TAAAAGAT
51623255 GTGAGATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 27 0.79
17 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.23
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:51628579 original size:42 final size:44
Alignment explanation
Indices: 51628509--51628728 Score: 168
Period size: 42 Copynumber: 4.9 Consensus size: 44
51628499 GTTTGTGAAA
* *
51628509 TAAGCGCAGCTAAAGAACACT-A-CTTTTAGCGACGTTTTTGGC-C
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTGGCGC
* *
51628552 -ACGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTCTTCCTAAGCGCCGC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGC--GTT-TT--T--G-G-CGC
* *
51628604 TAAAGAGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TC-C
1 T-AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTGGCGC
* **
51628647 TAAGCGCCGCTAAAGAACATTATCTTTAGCGGCGTTTATT--TTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTGGCGC
* *
51628690 TTAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
51628729 TCTGTAAGCG
Statistics
Matches: 147, Mismatches: 14, Indels: 33
0.76 0.07 0.17
Matches are distributed among these distances:
41 1 0.01
42 61 0.41
43 40 0.27
44 3 0.02
45 2 0.01
47 1 0.01
49 2 0.01
50 1 0.01
51 3 0.02
52 3 0.02
54 30 0.20
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (44 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTGGCGC
Found at i:51628708 original size:43 final size:42
Alignment explanation
Indices: 51628610--51628747 Score: 190
Period size: 43 Copynumber: 3.2 Consensus size: 42
51628600 CCGCTAAAGA
* * *
51628610 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCTAAGC
1 GCCGCTAAAGAACATTATCTTTAGCGGCGTTTTTTTCTTAGC
51628652 GCCGCTAAAGAACATTATCTTTAGCGGCGTTTATTTTCTTAGC
1 GCCGCTAAAGAACATTATCTTTAGCGGCGTTT-TTTTCTTAGC
51628695 GCCGCTAAAGAACATGT-TCTTTAGCGGCG-TTTTTTCTGTAAGC
1 GCCGCTAAAGAACAT-TATCTTTAGCGGCGTTTTTTTCT-T-AGC
*
51628738 GCCGCAAAAG
1 GCCGCTAAAG
51628748 TTAGCGATGT
Statistics
Matches: 88, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
41 6 0.07
42 34 0.39
43 47 0.53
44 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (42 bp):
GCCGCTAAAGAACATTATCTTTAGCGGCGTTTTTTTCTTAGC
Found at i:51636989 original size:31 final size:32
Alignment explanation
Indices: 51636954--51637015 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
51636944 CGAATGTATT
* *
51636954 TAATTATTTTTTATATATAT-TTAATAAACAA
1 TAATTACTTTTTATATATATATAAATAAACAA
*
51636985 TAATTACTTTTTATTTATATATAAATAAACA
1 TAATTACTTTTTATATATATATAAATAAACA
51637016 CGCATCCCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (32 bp):
TAATTACTTTTTATATATATATAAATAAACAA
Found at i:51638980 original size:7 final size:7
Alignment explanation
Indices: 51638968--51638996 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
51638958 GATCCAATTG
51638968 ATTGAAT
1 ATTGAAT
51638975 ATTGAAT
1 ATTGAAT
51638982 ATTGAAT
1 ATTGAAT
51638989 ATTGAAT
1 ATTGAAT
51638996 A
1 A
51638997 ATATGAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (7 bp):
ATTGAAT
Found at i:51645134 original size:19 final size:19
Alignment explanation
Indices: 51645110--51645146 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
51645100 GAATGAAAGT
51645110 AGTTGTGGTAGTTAGCTGC
1 AGTTGTGGTAGTTAGCTGC
51645129 AGTTGTGGTAGTTAGCTG
1 AGTTGTGGTAGTTAGCTG
51645147 GTATTCTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.08, G:0.38, T:0.38
Consensus pattern (19 bp):
AGTTGTGGTAGTTAGCTGC
Found at i:51645156 original size:19 final size:19
Alignment explanation
Indices: 51645110--51645159 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
51645100 GAATGAAAGT
*
51645110 AGTTGTGGTAGTTAGCTGC
1 AGTTCTGGTAGTTAGCTGC
* *
51645129 AGTTGTGGTAGTTAGCTGGT
1 AGTTCTGGTAGTTAGCT-GC
51645149 A-TTCTGGTAGT
1 AGTTCTGGTAGT
51645160 AGTTAGTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (19 bp):
AGTTCTGGTAGTTAGCTGC
Found at i:51649206 original size:31 final size:31
Alignment explanation
Indices: 51649171--51649235 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
51649161 TGAATGGTTT
*
51649171 ATGAATTAACACATATTGGTAAGCGTGATAC
1 ATGAATTAACACATATTGATAAGCGTGATAC
51649202 ATGAATTAACACATATTGATAAGCGTGATAC
1 ATGAATTAACACATATTGATAAGCGTGATAC
51649233 ATG
1 ATG
51649236 CTTAGGCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (31 bp):
ATGAATTAACACATATTGATAAGCGTGATAC
Found at i:51649742 original size:51 final size:51
Alignment explanation
Indices: 51649666--51650448 Score: 1521
Period size: 51 Copynumber: 15.4 Consensus size: 51
51649656 AGTACTTCTA
*
51649666 ACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51649717 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51649768 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51649819 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51649870 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51649921 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51649972 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51650023 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51650074 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51650125 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51650176 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51650227 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
51650278 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
* *
51650329 ACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATCAGTG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
*
51650380 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGG
1 ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
*
51650431 ACAAGTGACAAGTGATAA
1 ACAAGTAACAAGTGATAA
51650449 ATGTGATCCG
Statistics
Matches: 725, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 725 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (51 bp):
ACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
Found at i:51664179 original size:21 final size:21
Alignment explanation
Indices: 51664135--51664179 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
51664125 ATCTTAAAAA
* *
51664135 AAATTTAATAGTAAAATATTT
1 AAATTTAATAGTAAAAAATAT
51664156 AAATTTAATTA-TAAAAAATAT
1 AAATTTAA-TAGTAAAAAATAT
51664177 AAA
1 AAA
51664180 ATCAATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATTTAATAGTAAAAAATAT
Found at i:51670798 original size:14 final size:14
Alignment explanation
Indices: 51670779--51670809 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
51670769 TTGACTTTAA
51670779 AAATTTAATTAATT
1 AAATTTAATTAATT
*
51670793 AAATTTATTTAATT
1 AAATTTAATTAATT
51670807 AAA
1 AAA
51670810 ACATCAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:51672793 original size:19 final size:20
Alignment explanation
Indices: 51672756--51672793 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
51672746 TTTAAAATAA
*
51672756 TTTAAATAGACAATTTTTTT
1 TTTAAATAGACAATATTTTT
*
51672776 TTTAAATA-TCAATATTTT
1 TTTAAATAGACAATATTTT
51672794 CTAATCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTAAATAGACAATATTTTT
Found at i:51678476 original size:164 final size:165
Alignment explanation
Indices: 51678289--51678619 Score: 655
Period size: 164 Copynumber: 2.0 Consensus size: 165
51678279 ATTTTTGTAT
51678289 ATTTTTAAATTTTTTAAAATCATGATCAAATTGAGATATTTATAAAACTTGAGGGTTAAATTTTT
1 ATTTTTAAATTTTTTAAAATCATGATCAAATTGAGATATTTATAAAACTTGAGGGTTAAATTTTT
51678354 TTAAATTATGACTAAATTAATATAATATGTAAAATATGAGAGTTGTTTGTGCCTAAAATGAAAAT
66 TTAAATTATGACTAAATTAATATAATATGTAAAATATGAGAGTTGTTTGTGCCTAAAATGAAAAT
51678419 AATTTATAATTGAGTCACTATATGGAGTTTACCCA
131 AATTTATAATTGAGTCACTATATGGAGTTTACCCA
51678454 ATTTTTAAA-TTTTTAAAATCATGATCAAATTGAGATATTTATAAAACTTGAGGGTTAAATTTTT
1 ATTTTTAAATTTTTTAAAATCATGATCAAATTGAGATATTTATAAAACTTGAGGGTTAAATTTTT
51678518 TTAAATTATGACTAAATTAATATAATATGTAAAATATGAGAGTTGTTTGTGCCTAAAATGAAAAT
66 TTAAATTATGACTAAATTAATATAATATGTAAAATATGAGAGTTGTTTGTGCCTAAAATGAAAAT
51678583 AATTTATAATTGAGTCACTATATGGAGTTTACCCA
131 AATTTATAATTGAGTCACTATATGGAGTTTACCCA
51678618 AT
1 AT
51678620 ACATAATCAT
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
164 157 0.95
165 9 0.05
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (165 bp):
ATTTTTAAATTTTTTAAAATCATGATCAAATTGAGATATTTATAAAACTTGAGGGTTAAATTTTT
TTAAATTATGACTAAATTAATATAATATGTAAAATATGAGAGTTGTTTGTGCCTAAAATGAAAAT
AATTTATAATTGAGTCACTATATGGAGTTTACCCA
Found at i:51679441 original size:2 final size:2
Alignment explanation
Indices: 51679434--51679460 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51679424 TCACAATTTA
51679434 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
51679461 CATTTTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51679567 original size:118 final size:119
Alignment explanation
Indices: 51679433--51679670 Score: 469
Period size: 118 Copynumber: 2.0 Consensus size: 119
51679423 CTCACAATTT
51679433 AATATATATATATATATATATATATATACATTTTTCACTTATTATTATTAATTGTTTCAAACTGT
1 AATATATATATATATATATATATATATACATTTTTCACTTATTATTATTAATTGTTTCAAACTGT
51679498 ACATTTTATTATTTATTGTATGTTAATTTTAAATACATCAGCAGAAACAATTAA
66 ACATTTTATTATTTATTGTATGTTAATTTTAAATACATCAGCAGAAACAATTAA
51679552 AATATATATA-ATATATATATATATATACATTTTTCACTTATTATTATTAATTGTTTCAAACTGT
1 AATATATATATATATATATATATATATACATTTTTCACTTATTATTATTAATTGTTTCAAACTGT
51679616 ACATTTTATTATTTATTGTATGTTAATTTTAAATACATCAGCAGAAACAATTAA
66 ACATTTTATTATTTATTGTATGTTAATTTTAAATACATCAGCAGAAACAATTAA
51679670 A
1 A
51679671 CTTTAATTGA
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 109 0.92
119 10 0.08
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (119 bp):
AATATATATATATATATATATATATATACATTTTTCACTTATTATTATTAATTGTTTCAAACTGT
ACATTTTATTATTTATTGTATGTTAATTTTAAATACATCAGCAGAAACAATTAA
Found at i:51682265 original size:7 final size:7
Alignment explanation
Indices: 51682253--51682278 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
51682243 TACTTAGCAG
51682253 TCAGCCA
1 TCAGCCA
51682260 TCAGCCA
1 TCAGCCA
51682267 TCAGCCA
1 TCAGCCA
51682274 TCAGC
1 TCAGC
51682279 TATATCCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.42, G:0.15, T:0.15
Consensus pattern (7 bp):
TCAGCCA
Found at i:51692543 original size:29 final size:29
Alignment explanation
Indices: 51692501--51692558 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
51692491 GATTATTAAA
*
51692501 CTAGTATTATTTTTTAATCTTCTTGAGGG
1 CTAGTATTATTTTTTAATCTTCTTCAGGG
*
51692530 CTAGTATTATTTTTTTATCTTCTTCAGGG
1 CTAGTATTATTTTTTAATCTTCTTCAGGG
51692559 TGTAGTGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.53
Consensus pattern (29 bp):
CTAGTATTATTTTTTAATCTTCTTCAGGG
Found at i:51694980 original size:20 final size:20
Alignment explanation
Indices: 51694943--51694982 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
51694933 AAATTTATAT
* *
51694943 TTTCTAAAAAATTATAAAAA
1 TTTCAAAAAAAATATAAAAA
*
51694963 TTTCAAAAAAAATCTAAAAA
1 TTTCAAAAAAAATATAAAAA
51694983 AATATAAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
TTTCAAAAAAAATATAAAAA
Found at i:51695035 original size:31 final size:29
Alignment explanation
Indices: 51694969--51695045 Score: 118
Period size: 31 Copynumber: 2.6 Consensus size: 29
51694959 AAAATTTCAA
*
51694969 AAAAAATCTAAAAAAATATAAAGTAAGAT
1 AAAAAATTTAAAAAAATATAAAGTAAGAT
51694998 AAAAAATTTAAAAATATATATAAAGTAAGAT
1 AAAAAATTTAAAAA-A-ATATAAAGTAAGAT
51695029 AAAAAATTTTAAAAAAA
1 AAAAAA-TTTAAAAAAA
51695046 AATTGTGCTC
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 13 0.30
30 2 0.05
31 21 0.48
32 8 0.18
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (29 bp):
AAAAAATTTAAAAAAATATAAAGTAAGAT
Found at i:51696725 original size:47 final size:47
Alignment explanation
Indices: 51696666--51696759 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
51696656 GTTAAATCAC
*
51696666 CTTAAAATAGATGGAAAATTTAATTTTTGCTAACTTTGTTGATGCGA
1 CTTAAAACAGATGGAAAATTTAATTTTTGCTAACTTTGTTGATGCGA
*
51696713 CTTAAAACAGATGGAAATTTTAATTTTTGCTAACTTTGTTGATGCGA
1 CTTAAAACAGATGGAAAATTTAATTTTTGCTAACTTTGTTGATGCGA
51696760 TATACATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (47 bp):
CTTAAAACAGATGGAAAATTTAATTTTTGCTAACTTTGTTGATGCGA
Found at i:51699776 original size:22 final size:22
Alignment explanation
Indices: 51699725--51699776 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
51699715 ATATGAAGTA
*
51699725 ATATTGTTGTTTAATGTACTAG
1 ATATTTTTGTTTAATGTACTAG
* *
51699747 ATAATTTTGTTTGATGTA-TAGG
1 ATATTTTTGTTTAATGTACTA-G
51699769 ATATTTTT
1 ATATTTTT
51699777 TTCTTGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (22 bp):
ATATTTTTGTTTAATGTACTAG
Found at i:51701755 original size:41 final size:41
Alignment explanation
Indices: 51701702--51701785 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
51701692 CTTTTAATTC
*
51701702 CACGTCAGTTATATAAAAAATTTGAAAAAAAAAATTCAAAT
1 CACGTCACTTATATAAAAAATTTGAAAAAAAAAATTCAAAT
* *
51701743 CACGTCACTTATATAAAAAATTTGAAAGAAAAATTTCAAAT
1 CACGTCACTTATATAAAAAATTTGAAAAAAAAAATTCAAAT
51701784 CA
1 CA
51701786 TTATTTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (41 bp):
CACGTCACTTATATAAAAAATTTGAAAAAAAAAATTCAAAT
Found at i:51705800 original size:15 final size:16
Alignment explanation
Indices: 51705760--51705800 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
51705750 GTATGTGAAA
51705760 GGGTTGCTGCTCTACCC
1 GGGTTGCTG-TCTACCC
*
51705777 TGG-TGCTGT-TACCC
1 GGGTTGCTGTCTACCC
51705791 GGGTTGCTGT
1 GGGTTGCTGT
51705801 GATTGCTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.33
15 7 0.33
16 5 0.24
17 2 0.10
ACGTcount: A:0.05, C:0.27, G:0.34, T:0.34
Consensus pattern (16 bp):
GGGTTGCTGTCTACCC
Found at i:51708792 original size:24 final size:22
Alignment explanation
Indices: 51708758--51708806 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
51708748 TGCATGCATG
51708758 CATACACAAGTACATACGTACGTA
1 CATACACAAGTACATACG--CGTA
* *
51708782 CATACATAAGTTCATACGCGTA
1 CATACACAAGTACATACGCGTA
51708804 CAT
1 CAT
51708807 TCATTTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
24 16 0.70
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (22 bp):
CATACACAAGTACATACGCGTA
Found at i:51712145 original size:2 final size:2
Alignment explanation
Indices: 51712140--51712286 Score: 294
Period size: 2 Copynumber: 73.5 Consensus size: 2
51712130 AAAACTTGCT
51712140 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
51712182 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
51712224 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
51712266 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
51712287 CCTGTTTCTG
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 145 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51718673 original size:9 final size:9
Alignment explanation
Indices: 51718659--51718690 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
51718649 TTTGGTTAAA
51718659 AATTACCCG
1 AATTACCCG
51718668 AATTACCCG
1 AATTACCCG
*
51718677 AATTAACCG
1 AATTACCCG
51718686 AATTA
1 AATTA
51718691 NNNNNNNNNN
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:51723191 original size:19 final size:19
Alignment explanation
Indices: 51723169--51723210 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
51723159 CCAAGATCTT
*
51723169 AAATTAATGTGGTCCAAAG
1 AAATTAATGTGGTCCAAAA
51723188 AAATTAATGTGGTCCAAAA
1 AAATTAATGTGGTCCAAAA
51723207 AAAT
1 AAAT
51723211 AATTAGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.26
Consensus pattern (19 bp):
AAATTAATGTGGTCCAAAA
Found at i:51729358 original size:40 final size:40
Alignment explanation
Indices: 51729303--51729382 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
51729293 CGCGGCGAAA
51729303 GAATGAAGGAATAACTGTATCAATTTTTTCATTTTACTTT
1 GAATGAAGGAATAACTGTATCAATTTTTTCATTTTACTTT
51729343 GAATGAAGGAATAACTGTATCAATTTTTTCATTTTACTTT
1 GAATGAAGGAATAACTGTATCAATTTTTTCATTTTACTTT
51729383 TATGGAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (40 bp):
GAATGAAGGAATAACTGTATCAATTTTTTCATTTTACTTT
Found at i:51729404 original size:47 final size:40
Alignment explanation
Indices: 51729303--51729416 Score: 147
Period size: 40 Copynumber: 2.7 Consensus size: 40
51729293 CGCGGCGAAA
*
51729303 GAATGAAGGAATAACTGTATCAATTTTTTCATTTTACTTT
1 GAATGAAGCAATAACTGTATCAATTTTTTCATTTTACTTT
*
51729343 GAATGAAGGAATAACTGTATCAATTTTTTCATTTTACTTTTAT
1 GAATGAAGCAATAACTGTATCAATTTTTTCATTTTAC--TT-T
51729386 GGAAATGAAATGCAATAACTGTATCAATTTT
1 -G-AATG-AA-GCAATAACTGTATCAATTTT
51729417 GTTTGGTAGG
Statistics
Matches: 66, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
40 37 0.56
42 2 0.03
43 1 0.02
44 1 0.02
45 4 0.06
46 2 0.03
47 19 0.29
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (40 bp):
GAATGAAGCAATAACTGTATCAATTTTTTCATTTTACTTT
Found at i:51730759 original size:13 final size:13
Alignment explanation
Indices: 51730741--51730765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51730731 ATCATCTCGT
51730741 GTATTCTTATTTA
1 GTATTCTTATTTA
51730754 GTATTCTTATTT
1 GTATTCTTATTT
51730766 GGAAATTGTT
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:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (13 bp):
GTATTCTTATTTA
Found at i:51732383 original size:14 final size:14
Alignment explanation
Indices: 51732364--51732393 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51732354 ATATCCAAAC
51732364 AATAACAATAGAAT
1 AATAACAATAGAAT
*
51732378 AATAACAATATAAT
1 AATAACAATAGAAT
51732392 AA
1 AA
51732394 CAAAATTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (14 bp):
AATAACAATAGAAT
Found at i:51732390 original size:11 final size:11
Alignment explanation
Indices: 51732375--51732420 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
51732365 ATAACAATAG
51732375 AATAATAACAA
1 AATAATAACAA
*
51732386 TATAATAACAA
1 AATAATAACAA
* *
51732397 AATTACAACAA
1 AATAATAACAA
51732408 AATAATAACAA
1 AATAATAACAA
51732419 AA
1 AA
51732421 CAACAATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.20
Consensus pattern (11 bp):
AATAATAACAA
Found at i:51732426 original size:22 final size:22
Alignment explanation
Indices: 51732381--51732435 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
51732371 ATAGAATAAT
* **
51732381 AACAATATAATAACAAAATTAC
1 AACAAAATAATAACAAAACAAC
51732403 AACAAAATAATAACAAAACAAC
1 AACAAAATAATAACAAAACAAC
*
51732425 AATAAAA-AATA
1 AACAAAATAATA
51732436 TTTAGGTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (22 bp):
AACAAAATAATAACAAAACAAC
Found at i:51736138 original size:5 final size:6
Alignment explanation
Indices: 51736121--51736148 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
51736111 TCCTTTTTGT
51736121 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
51736149 TTAATGCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:51751475 original size:20 final size:20
Alignment explanation
Indices: 51751452--51751489 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
51751442 ATTTTTTTGC
51751452 ATTTCG-AAATTGTTTTAAGA
1 ATTTCGAAAATT-TTTTAAGA
*
51751472 ATTTTGAAAATTTTTTAA
1 ATTTCGAAAATTTTTTAA
51751490 CAGATCTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (20 bp):
ATTTCGAAAATTTTTTAAGA
Found at i:51756547 original size:55 final size:54
Alignment explanation
Indices: 51756480--51756591 Score: 161
Period size: 55 Copynumber: 2.1 Consensus size: 54
51756470 TTATTTAAAC
* * * * *
51756480 AAAAAATATTTTTAATATAAAAAATTGATTTGTGCCTGTTAGATAGGCGCGATT
1 AAAAAATATTTTTAATATAAAAAATTGATTCGCGCCTGTCAAATAGGCGCAATT
*
51756534 AAAAAATATTTTTTAATATAAAAAATTGATTCGCGTCTGTCAAATAGGCGCAATT
1 AAAAAATA-TTTTTAATATAAAAAATTGATTCGCGCCTGTCAAATAGGCGCAATT
51756589 AAA
1 AAA
51756592 TTTTTTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 8 0.16
55 43 0.84
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (54 bp):
AAAAAATATTTTTAATATAAAAAATTGATTCGCGCCTGTCAAATAGGCGCAATT
Found at i:51756972 original size:60 final size:60
Alignment explanation
Indices: 51756896--51757014 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
51756886 ATACTAAACT
* * * *
51756896 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATTTT-AAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT-AATTTTAAAATAATTAC
*
51756956 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
51757015 TAAAAAACAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:51757037 original size:60 final size:60
Alignment explanation
Indices: 51756916--51757037 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
51756906 ACTTATAGCT
* * * **
51756916 TAATCCTAAATTACTAATAAATTAAATTTTAAATAATTACAAACACAAAAATTTATAACA
1 TAATCCTAAATTACTAACAAATTAAATTTTAAATAATTAAAAAAACAAAAATAAATAACA
*
51756976 TAATCCTAAATTACTAACAAATT-AATTTTAAAATAATTATAAAAAACAAAAA-AAATTACA
1 TAATCCTAAATTACTAACAAATTAAATTTT-AAATAATTA-AAAAAACAAAAATAAATAACA
51757036 TA
1 TA
51757038 TTCATACAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
59 6 0.11
60 38 0.70
61 10 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (60 bp):
TAATCCTAAATTACTAACAAATTAAATTTTAAATAATTAAAAAAACAAAAATAAATAACA
Found at i:51757154 original size:26 final size:27
Alignment explanation
Indices: 51757110--51757160 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
51757100 TATCTTTTTT
*
51757110 CTTTCTTTCTTTTTCTTCT-TCTTCTC
1 CTTTCTCTCTTTTTCTTCTCTCTTCTC
51757136 CTTTCTCTC-TTTTCTTTCTCTCTTC
1 CTTTCTCTCTTTTTC-TTCTCTCTTC
51757161 CAATGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 12 0.55
27 5 0.23
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (27 bp):
CTTTCTCTCTTTTTCTTCTCTCTTCTC
Found at i:51757489 original size:22 final size:24
Alignment explanation
Indices: 51757446--51757489 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
51757436 TAATAAAAAT
* *
51757446 AAAAAATAATATTTTATTTAAACC
1 AAAAAATAATATTTAATATAAACC
51757470 AAAAAA-AA-ATTTAATATAAA
1 AAAAAATAATATTTAATATAAA
51757490 AAATTCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 2 0.11
24 6 0.33
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAAATAATATTTAATATAAACC
Found at i:51770726 original size:1 final size:1
Alignment explanation
Indices: 51770670--51770706 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
51770660 GGGGGGGGGG
51770670 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
51770707 AGGCGTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:51774229 original size:21 final size:21
Alignment explanation
Indices: 51774205--51774245 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
51774195 CTGTAAAGAT
51774205 CCCTCTCTCCGCCGTCTCCAG
1 CCCTCTCTCCGCCGTCTCCAG
*
51774226 CCCTTTCTCCGCCGTCTCCA
1 CCCTCTCTCCGCCGTCTCCA
51774246 ATCCTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.56, G:0.12, T:0.27
Consensus pattern (21 bp):
CCCTCTCTCCGCCGTCTCCAG
Found at i:51774251 original size:21 final size:21
Alignment explanation
Indices: 51774205--51774251 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
51774195 CTGTAAAGAT
* *
51774205 CCCTCTCTCCGCCGTCTCCAG
1 CCCTTTCTCCGCCGTCTCCAA
51774226 CCCTTTCTCCGCCGTCTCCAA
1 CCCTTTCTCCGCCGTCTCCAA
*
51774247 TCCTT
1 CCCTT
51774252 CTTTCACGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.06, C:0.53, G:0.11, T:0.30
Consensus pattern (21 bp):
CCCTTTCTCCGCCGTCTCCAA
Found at i:51788041 original size:20 final size:20
Alignment explanation
Indices: 51787963--51788045 Score: 61
Period size: 20 Copynumber: 4.4 Consensus size: 20
51787953 CTATCTTCAA
51787963 AAATTTTAATCAGAACTTCT
1 AAATTTTAATCAGAACTTCT
* *
51787983 AAGTTTTAATTAG---TT-T
1 AAATTTTAATCAGAACTTCT
* * * *
51787999 -AATTTT-CTCAAAATTTTT
1 AAATTTTAATCAGAACTTCT
51788017 AAAATTTTAATCAGAACTTCT
1 -AAATTTTAATCAGAACTTCT
51788038 AAATTTTA
1 AAATTTTA
51788046 CTAATAATGA
Statistics
Matches: 46, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
14 2 0.04
15 5 0.11
16 1 0.02
17 4 0.09
18 1 0.02
20 25 0.54
21 8 0.17
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.47
Consensus pattern (20 bp):
AAATTTTAATCAGAACTTCT
Found at i:51793147 original size:31 final size:31
Alignment explanation
Indices: 51793089--51793147 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
51793079 CTTTTTCTGG
* *
51793089 TTTAATATACTATTTAGTACCTGAGTTTAAA
1 TTTAATATACAATTTAGTACCTAAGTTTAAA
* * *
51793120 TTTAATATTCAATTTGGTACTTAAGTTT
1 TTTAATATACAATTTAGTACCTAAGTTT
51793148 TTTTTTTCCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.49
Consensus pattern (31 bp):
TTTAATATACAATTTAGTACCTAAGTTTAAA
Found at i:51802207 original size:21 final size:21
Alignment explanation
Indices: 51802155--51802233 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
51802145 ATTTAATTTA
* *
51802155 ATTTAATATTTATGTTAATAGT
1 ATTTAATATTAAT-TTAATAAT
51802177 ATTT--TATTAATTTAATAAT
1 ATTTAATATTAATTTAATAAT
**
51802196 ATTTAATATTAAAGTAATTAA-
1 ATTTAATATTAATTTAA-TAAT
* *
51802217 GTTTAATAATAATTTAA
1 ATTTAATATTAATTTAA
51802234 CTCTCCCTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
19 11 0.24
20 6 0.13
21 22 0.48
22 7 0.15
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTAATATTAATTTAATAAT
Found at i:51805461 original size:19 final size:19
Alignment explanation
Indices: 51805435--51805484 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
51805425 ATACTAAATC
51805435 TGTTAAAAAATTTTCAAAA
1 TGTTAAAAAATTTTCAAAA
* * * *
51805454 TTTTAAAATAGTTTCGAAA
1 TGTTAAAAAATTTTCAAAA
*
51805473 TGTAAAAAAATT
1 TGTTAAAAAATT
51805485 ACATAAAATT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (19 bp):
TGTTAAAAAATTTTCAAAA
Found at i:51810299 original size:17 final size:17
Alignment explanation
Indices: 51810270--51810311 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
51810260 CAAACTGATT
51810270 ATTTTATTAATTTATTAG
1 ATTTTA-TAATTTATTAG
51810288 ATTTTATAATTTATTAG
1 ATTTTATAATTTATTAG
*
51810305 ATGTTAT
1 ATTTTAT
51810312 TTTTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (17 bp):
ATTTTATAATTTATTAG
Found at i:51820660 original size:15 final size:14
Alignment explanation
Indices: 51820638--51820676 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
51820628 GTAAAAGTAG
51820638 ATAATTAAATTATA
1 ATAATTAAATTATA
* *
51820652 TTAAATTAAAATATA
1 AT-AATTAAATTATA
51820667 ATAATTAAAT
1 ATAATTAAAT
51820677 CTCAAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATTAAATTATA
Found at i:51827111 original size:81 final size:80
Alignment explanation
Indices: 51826950--51827111 Score: 179
Period size: 81 Copynumber: 2.0 Consensus size: 80
51826940 TTAGCCCCCA
* * *
51826950 AAAATGAAAATTTTCAATTTAGTCTTATTATAAACAGAGAAACTATAAATTAATATAGAAAAATT
1 AAAATGAAAATTTTCAATTTAGTCCTATTATAAAAAGAGAAACTATAAATTAATATAGAAAAATC
*
51827015 GCACTTTGACCCCTC
66 GCACTTTGACACCTC
* * * *
51827030 AAAATGAAAAATTTTCAA-TTCGTTCCTCTTATAAATAAG-GAAATTATAAATTAATATATAGTA
1 AAAATG-AAAATTTTCAATTTAG-TCCTATTATAAA-AAGAGAAACTATAAATT-A-ATATAGAA
51827093 AAATCGCACTTT-A-ACCTC
61 AAATCGCACTTTGACACCTC
51827111 A
1 A
51827112 TAAAACTAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
80 9 0.13
81 38 0.55
82 4 0.06
83 18 0.26
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (80 bp):
AAAATGAAAATTTTCAATTTAGTCCTATTATAAAAAGAGAAACTATAAATTAATATAGAAAAATC
GCACTTTGACACCTC
Found at i:51829403 original size:196 final size:197
Alignment explanation
Indices: 51829059--51829451 Score: 779
Period size: 196 Copynumber: 2.0 Consensus size: 197
51829049 GTAATTGGTA
51829059 TTGATACAATTAAAATTAGGATACACGATGGGATGATTAAGACACTCTCAGATGTTAGGTATGTA
1 TTGATACAATTAAAATTAGGATACACGATGGGATGATTAAGACACTCTCAGATGTTAGGTATGTA
51829124 CTTGATTTACGAAAGAATCTCATCTCCTTGAGTATTTTAGACTTGAAAGGATGCGGAATCAACAT
66 CTTGATTTACGAAAGAATCTCATCTCCTTGAGTATTTTAGACTTGAAAGGATGCGGAATCAACAT
51829189 CGAGTCGAGCGACATTAAAGTATCTCGTAGAGCTCTCGTTTTGTTAAAAGGTAACATAATTGGCA
131 CGAGTCGAGCGACATTAAAGTATCTCGTAGAGCTCTCGTTTTGTTAAAAGGTAACATAATTGGCA
51829254 AT
196 AT
51829256 TTGATACAA-TAAAATTAGGATACACGATGGGATGATTAAGACACTCTCAGATGTTAGGTATGTA
1 TTGATACAATTAAAATTAGGATACACGATGGGATGATTAAGACACTCTCAGATGTTAGGTATGTA
51829320 CTTGATTTACGAAAGAATCTCATCTCCTTGAGTATTTTAGACTTGAAAGGATGCGGAATCAACAT
66 CTTGATTTACGAAAGAATCTCATCTCCTTGAGTATTTTAGACTTGAAAGGATGCGGAATCAACAT
51829385 CGAGTCGAGCGACATTAAAGTATCTCGTAGAGCTCTCGTTTTGTTAAAAGGTAACATAATTGGCA
131 CGAGTCGAGCGACATTAAAGTATCTCGTAGAGCTCTCGTTTTGTTAAAAGGTAACATAATTGGCA
51829450 AT
196 AT
51829452 CTTTATATTC
Statistics
Matches: 196, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
196 187 0.95
197 9 0.05
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (197 bp):
TTGATACAATTAAAATTAGGATACACGATGGGATGATTAAGACACTCTCAGATGTTAGGTATGTA
CTTGATTTACGAAAGAATCTCATCTCCTTGAGTATTTTAGACTTGAAAGGATGCGGAATCAACAT
CGAGTCGAGCGACATTAAAGTATCTCGTAGAGCTCTCGTTTTGTTAAAAGGTAACATAATTGGCA
AT
Found at i:51832375 original size:86 final size:88
Alignment explanation
Indices: 51832274--51832439 Score: 209
Period size: 89 Copynumber: 1.9 Consensus size: 88
51832264 ATTTGATACT
*
51832274 TTTTCTTAGTTTGGTATTTAA-ATTTTTT-GG-TCTAATTTGGTATTCA-AATTTGA-TATTTTT
1 TTTTCTTAGTTTGGTATTTAATATTTTTTGGGTTC-AATTTGGTA--CAGAACTTGACTATTTTT
**
51832334 TTTAATTTGGTACCTAAACTTGGCAC
63 CCTAATTTGGTACCTAAACTTGGCAC
*
51832360 TTTTCTTAAG-TTGGTATTTAATCTTTTTTGGGTTCAATTTGGTACATGAACTTGACTATTTTTC
1 TTTTCTT-AGTTTGGTATTTAATATTTTTTGGGTTCAATTTGGTACA-GAACTTGACTATTTTTC
51832424 CTAATTTGGTACCTAA
64 CTAATTTGGTACCTAA
51832440 TTATTTTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
86 20 0.29
87 8 0.12
88 17 0.25
89 24 0.35
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (88 bp):
TTTTCTTAGTTTGGTATTTAATATTTTTTGGGTTCAATTTGGTACAGAACTTGACTATTTTTCCT
AATTTGGTACCTAAACTTGGCAC
Found at i:51833530 original size:1 final size:1
Alignment explanation
Indices: 51833526--51833580 Score: 65
Period size: 1 Copynumber: 55.0 Consensus size: 1
51833516 TTAAAAAATT
* ** **
51833526 AAAAAAAAAAAAAAAAAAAAGAAAGGAAAATTAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
51833581 CCACCTTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.91, C:0.00, G:0.05, T:0.04
Consensus pattern (1 bp):
A
Found at i:51836475 original size:10 final size:10
Alignment explanation
Indices: 51836456--51836499 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
51836446 ATAAAAATAA
51836456 AAAAATATTTT
1 AAAAA-ATTTT
51836467 AAAAAATTTT
1 AAAAAATTTT
51836477 -AAAAA-TTT
1 AAAAAATTTT
51836485 --AAAATTTT
1 AAAAAATTTT
51836493 AAAAAAT
1 AAAAAAT
51836500 ATATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 4 0.13
8 6 0.20
9 5 0.17
10 10 0.33
11 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:51836482 original size:9 final size:9
Alignment explanation
Indices: 51836457--51836497 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
51836447 TAAAAATAAA
51836457 AAAATATTTT
1 AAAA-ATTTT
51836467 AAAAAATTTT
1 -AAAAATTTT
51836477 AAAAA-TTT
1 AAAAATTTT
51836485 -AAAATTTT
1 AAAAATTTT
51836493 AAAAA
1 AAAAA
51836498 ATATATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 4 0.14
8 6 0.21
9 9 0.32
10 5 0.18
11 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AAAAATTTT
Found at i:51838072 original size:23 final size:21
Alignment explanation
Indices: 51838044--51838085 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
51838034 TATTGTTTTG
*
51838044 ATTATTTTAATTATTTCTTAATA
1 ATTATTCTAATT-TTT-TTAATA
51838067 ATTATTCTAATTTTTTTAA
1 ATTATTCTAATTTTTTTAA
51838086 AAATATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATTCTAATTTTTTTAATA
Found at i:51841768 original size:18 final size:18
Alignment explanation
Indices: 51841741--51841784 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
51841731 GACGGGCCAG
*
51841741 TTTAAAATATTATGTTAT
1 TTTAAAATATTATGTAAT
*
51841759 TTTAATATATTATGTAAT
1 TTTAAAATATTATGTAAT
51841777 TTATAAAA
1 TT-TAAAA
51841785 CATAAAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
TTTAAAATATTATGTAAT
Found at i:51841916 original size:28 final size:27
Alignment explanation
Indices: 51841860--51841932 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
51841850 TTGTTTTTAT
51841860 ATAAAATTTTAATAAATGAAAAAATATA
1 ATAAAATTTTAA-AAATGAAAAAATATA
* *
51841888 ATAAAATTTTAAATATTAAATTAAA-ATA
1 ATAAAATTTTAAAAATGAAA--AAATATA
51841916 ATAGAAATATTTAAAAA
1 ATA-AAAT-TTTAAAAA
51841933 AAATAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 6 0.16
28 18 0.47
29 7 0.18
30 7 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (27 bp):
ATAAAATTTTAAAAATGAAAAAATATA
Found at i:51849612 original size:4 final size:4
Alignment explanation
Indices: 51849603--51849628 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
51849593 AACAATCGTT
51849603 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
51849629 TTAAACTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:51852731 original size:16 final size:16
Alignment explanation
Indices: 51852712--51852742 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51852702 TTGAAAAAGT
51852712 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
51852728 TTTCAAATTTATATG
1 TTTCAAATATATATG
51852743 CTTTTAACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:51859569 original size:18 final size:19
Alignment explanation
Indices: 51859546--51859589 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
51859536 ATTAGAAATT
*
51859546 AATATAAATTG-TTTATAA
1 AATATAAATTGATATATAA
*
51859564 AATATAATTTGAATATATAA
1 AATATAAATTG-ATATATAA
51859584 AATATA
1 AATATA
51859590 TTTTAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
AATATAAATTGATATATAA
Found at i:51864119 original size:2 final size:2
Alignment explanation
Indices: 51864112--51864148 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
51864102 TCACTTGGAG
51864112 AT 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 AT A
51864149 CTCACATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51864214 original size:2 final size:2
Alignment explanation
Indices: 51864209--51864249 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
51864199 ACTCTTGGAG
51864209 AT AT AT 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 AT AT AT A
51864250 CTCACATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51864997 original size:60 final size:60
Alignment explanation
Indices: 51864904--51865021 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
51864894 CGATCCCTAA
* *
51864904 CAAATTCAAGGACTAAGTATTATCTTAACCTTCGAGAAACACACTATTTATACAAATCTT
1 CAAATTCAAGGACTAAATATTACCTTAACCTTCGAGAAACACACTATTTATACAAATCTT
51864964 CAAATTCAAGGACTAAATATTACCTTAACCTTCGAGAAACACACTATTTATACAAATC
1 CAAATTCAAGGACTAAATATTACCTTAACCTTCGAGAAACACACTATTTATACAAATC
51865022 CCAACTATTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (60 bp):
CAAATTCAAGGACTAAATATTACCTTAACCTTCGAGAAACACACTATTTATACAAATCTT
Found at i:51865358 original size:60 final size:60
Alignment explanation
Indices: 51865265--51865382 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
51865255 CGATCCCTAA
* *
51865265 CAAATTCAAGGACTAAGTATTATCTTAACCTTCGAGAAACACACTATTTATACAAATCTT
1 CAAATTCAAGGACTAAATATTACCTTAACCTTCGAGAAACACACTATTTATACAAATCTT
51865325 CAAATTCAAGGACTAAATATTACCTTAACCTTCGAGAAACACACTATTTATACAAATC
1 CAAATTCAAGGACTAAATATTACCTTAACCTTCGAGAAACACACTATTTATACAAATC
51865383 CCAACTATTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (60 bp):
CAAATTCAAGGACTAAATATTACCTTAACCTTCGAGAAACACACTATTTATACAAATCTT
Found at i:51872102 original size:13 final size:13
Alignment explanation
Indices: 51872084--51872115 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
51872074 GTCAAAGGAA
51872084 AATACAAAGTGAT
1 AATACAAAGTGAT
51872097 AATACAAAGTGAT
1 AATACAAAGTGAT
51872110 AATACA
1 AATACA
51872116 GAAAATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.22
Consensus pattern (13 bp):
AATACAAAGTGAT
Found at i:51883978 original size:7 final size:7
Alignment explanation
Indices: 51883926--51883962 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
51883916 AAGGTGATTT
51883926 TTATTAA
1 TTATTAA
51883933 TTATTAA
1 TTATTAA
51883940 TTATTAA
1 TTATTAA
51883947 TTATTAA
1 TTATTAA
51883954 TTATTAA
1 TTATTAA
51883961 TT
1 TT
51883963 TAAGGATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTATTAA
Found at i:51888149 original size:15 final size:15
Alignment explanation
Indices: 51888129--51888178 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
51888119 ATTACCAAAA
51888129 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
51888144 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
51888159 GAGAATAGTTTATTAAAT
1 TAG---AGTTTATTAAAT
51888177 TA
1 TA
51888179 AAATAGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:51888197 original size:18 final size:18
Alignment explanation
Indices: 51888147--51888192 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
51888137 ATTAAATTAG
* *
51888147 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATTAAAAT
51888165 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATTAAAAT
51888183 AGATTTATTA
1 AG-TTTATTA
51888193 CTTAATTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (18 bp):
AGTTTATTAAATTAAAAT
Found at i:51888485 original size:26 final size:28
Alignment explanation
Indices: 51888433--51888494 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
51888423 TTTTTTTGGT
51888433 ATATTTTGATAAATGAAAAAAATTTATA
1 ATATTTTGATAAATGAAAAAAATTTATA
51888461 ATATTTTGATAAAT-AAAAAAA-TTATA
1 ATATTTTGATAAATGAAAAAAATTTATA
51888487 ATATTTTG
1 ATATTTTG
51888495 GTTATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 13 0.38
27 7 0.21
28 14 0.41
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (28 bp):
ATATTTTGATAAATGAAAAAAATTTATA
Found at i:51889144 original size:18 final size:19
Alignment explanation
Indices: 51889105--51889144 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
51889095 AATTACAAAA
*
51889105 AAAATTAAAAATAATTTTT
1 AAAATTAAAAATAATTTAT
*
51889124 AAAATTCAAAAT-ATTTAT
1 AAAATTAAAAATAATTTAT
51889142 AAA
1 AAA
51889145 GAATCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTAAAAATAATTTAT
Found at i:51889179 original size:9 final size:9
Alignment explanation
Indices: 51889165--51889208 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
51889155 TTTATATATT
51889165 TTTAAAAAA
1 TTTAAAAAA
51889174 TTTAAAAAA
1 TTTAAAAAA
*
51889183 ATTAAAAATA
1 TTTAAAAA-A
*
51889193 TATAAAAAA
1 TTTAAAAAA
*
51889202 GTTAAAA
1 TTTAAAA
51889209 CTTTTATAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:51889190 original size:19 final size:19
Alignment explanation
Indices: 51889168--51889208 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
51889158 ATATATTTTT
*
51889168 AAAAAATTTAAAAAAATTA
1 AAAAAATATAAAAAAATTA
* *
51889187 AAAATATATAAAAAAGTTA
1 AAAAAATATAAAAAAATTA
51889206 AAA
1 AAA
51889209 CTTTTATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAAATATAAAAAAATTA
Found at i:51895570 original size:30 final size:30
Alignment explanation
Indices: 51895499--51895570 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
51895489 CGCCTAGGGA
* * *
51895499 AGAGGCGGCACCCACTGGTCACGCCTTCGGC
1 AGAGGCGGCA-CCACCGGTCACGCCATCGCC
* *
51895530 AGAGGTGGCACCACCGGTCACGCCATCTCC
1 AGAGGCGGCACCACCGGTCACGCCATCGCC
*
51895560 ATAGGCGGCAC
1 AGAGGCGGCAC
51895571 TAGCCTGCAG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.19, C:0.38, G:0.31, T:0.12
Consensus pattern (30 bp):
AGAGGCGGCACCACCGGTCACGCCATCGCC
Found at i:51895724 original size:5 final size:5
Alignment explanation
Indices: 51895714--51895738 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
51895704 GGAGGATGGG
51895714 AGGGC AGGGC AGGGC AGGGC AGGGC
1 AGGGC AGGGC AGGGC AGGGC AGGGC
51895739 GAGGCGGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.60, T:0.00
Consensus pattern (5 bp):
AGGGC
Found at i:51896132 original size:16 final size:16
Alignment explanation
Indices: 51896113--51896177 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
51896103 TTTATTTTTT
51896113 TTATGTAATTTATTTG
1 TTATGTAATTTATTTG
**
51896129 TTATGTGAATTT-TAGG
1 TTATGT-AATTTATTTG
* *
51896145 TTGAT-TAGATTTGTTTT
1 TT-ATGTA-ATTTATTTG
51896162 TTATGTAATTTATTTG
1 TTATGTAATTTATTTG
51896178 GCATGTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
15 1 0.03
16 24 0.65
17 12 0.32
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (16 bp):
TTATGTAATTTATTTG
Found at i:51898849 original size:27 final size:27
Alignment explanation
Indices: 51898819--51898870 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
51898809 TTGGACTGTT
51898819 TTTA-TTGGACTTTTGATTTTAATTTTA
1 TTTATTTGG-CTTTTGATTTTAATTTTA
* *
51898846 TTTATTTGGCTTTTTATTTTTATTT
1 TTTATTTGGCTTTTGATTTTAATTT
51898871 ACTTGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.17, C:0.04, G:0.10, T:0.69
Consensus pattern (27 bp):
TTTATTTGGCTTTTGATTTTAATTTTA
Found at i:51900125 original size:12 final size:12
Alignment explanation
Indices: 51900108--51900133 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
51900098 TTACAACACT
51900108 AAAACTTAGAAC
1 AAAACTTAGAAC
51900120 AAAACTTAGAAC
1 AAAACTTAGAAC
51900132 AA
1 AA
51900134 GTTTTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAACTTAGAAC
Found at i:51900154 original size:14 final size:14
Alignment explanation
Indices: 51900135--51900164 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51900125 TTAGAACAAG
*
51900135 TTTTGTAATATAAA
1 TTTTGTAAAATAAA
51900149 TTTTGTAAAATAAA
1 TTTTGTAAAATAAA
51900163 TT
1 TT
51900165 AAATACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTTGTAAAATAAA
Found at i:51900225 original size:62 final size:62
Alignment explanation
Indices: 51900137--51900274 Score: 222
Period size: 62 Copynumber: 2.2 Consensus size: 62
51900127 AGAACAAGTT
*
51900137 TTGTAATATAAATTTTGTAAAATAAATTAAATACATTACAATATTAAAAATTGGAACAAACA
1 TTGTAATATAAATTTTGTAAAATAAATTAAATACATTACAACATTAAAAATTGGAACAAACA
* * * *
51900199 TTGTAATATAAATTTTGTTATATAAATTAAATACATTACAACATTAAAATTTGGAACAAACT
1 TTGTAATATAAATTTTGTAAAATAAATTAAATACATTACAACATTAAAAATTGGAACAAACA
*
51900261 TTGTAACATAAATT
1 TTGTAATATAAATT
51900275 AGGTACATTG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (62 bp):
TTGTAATATAAATTTTGTAAAATAAATTAAATACATTACAACATTAAAAATTGGAACAAACA
Found at i:51902030 original size:2 final size:2
Alignment explanation
Indices: 51902023--51902059 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
51902013 TTGAATTGGA
51902023 AT AT AT AT -T AT GA- 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
51902060 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 29 0.91
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51902234 original size:25 final size:25
Alignment explanation
Indices: 51902206--51902338 Score: 127
Period size: 25 Copynumber: 5.6 Consensus size: 25
51902196 TTTAGCGCGT
*
51902206 TATCTGATTATTAGCACATCTGTGC
1 TATCTGATTATTAGCACATCAGTGC
51902231 TATCTGATTATTAGCACATCAGTGC
1 TATCTGATTATTAGCACATCAGTGC
* * *
51902256 TATCTGATTACTAGCACGTCAATGC
1 TATCTGATTATTAGCACATCAGTGC
* *
51902281 TCTCTG--T-TTAGCACATCTGTGC
1 TATCTGATTATTAGCACATCAGTGC
* *
51902303 TCTCTG--TA-TAGCACTTCAGTGC
1 TATCTGATTATTAGCACATCAGTGC
*
51902325 TCTCTG-TTCATTAG
1 TATCTGATT-ATTAG
51902339 TGCATAACAA
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
22 36 0.39
23 2 0.02
24 1 0.01
25 54 0.58
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (25 bp):
TATCTGATTATTAGCACATCAGTGC
Found at i:51902303 original size:22 final size:22
Alignment explanation
Indices: 51902216--51902332 Score: 108
Period size: 22 Copynumber: 5.0 Consensus size: 22
51902206 TATCTGATTA
* *
51902216 TTAGCACATCTGTGCTATCTGATT
1 TTAGCACATCAGTGCTCTCTG--T
*
51902240 ATTAGCACATCAGTGCTATCTGAT
1 -TTAGCACATCAGTGCTCTCTG-T
* *
51902264 TACTAGCACGTCAATGCTCTCTGT
1 T--TAGCACATCAGTGCTCTCTGT
*
51902288 TTAGCACATCTGTGCTCTCTGT
1 TTAGCACATCAGTGCTCTCTGT
* *
51902310 ATAGCACTTCAGTGCTCTCTGT
1 TTAGCACATCAGTGCTCTCTGT
51902332 T
1 T
51902333 CATTAGTGCA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
22 37 0.47
23 1 0.01
24 3 0.04
25 37 0.47
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (22 bp):
TTAGCACATCAGTGCTCTCTGT
Found at i:51902330 original size:44 final size:46
Alignment explanation
Indices: 51902241--51902332 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 46
51902231 TATCTGATTA
51902241 TTAGCACATCAGTGCTATCTGATTACTAGCACGTCAATGCTCTCTGT
1 TTAGCACATCAGTGCTATCTGA-TACTAGCACGTCAATGCTCTCTGT
* * * *
51902288 TTAGCACATCTGTGCTCTCTG-TA-TAGCACTTCAGTGCTCTCTGT
1 TTAGCACATCAGTGCTATCTGATACTAGCACGTCAATGCTCTCTGT
51902332 T
1 T
51902333 CATTAGTGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
44 20 0.49
45 2 0.05
47 19 0.46
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (46 bp):
TTAGCACATCAGTGCTATCTGATACTAGCACGTCAATGCTCTCTGT
Found at i:51913953 original size:28 final size:28
Alignment explanation
Indices: 51913917--51913977 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
51913907 TGTCGAATTT
* *
51913917 TTTTAAAAAAATTACATGTATAGGCCGA
1 TTTTAAAAAAATTACAGGAATAGGCCGA
*
51913945 TTTTGAAAAAATTACAGGAATAGGCCGA
1 TTTTAAAAAAATTACAGGAATAGGCCGA
51913973 TTTTA
1 TTTTA
51913978 TGAAAATGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (28 bp):
TTTTAAAAAAATTACAGGAATAGGCCGA
Found at i:51918160 original size:48 final size:48
Alignment explanation
Indices: 51918108--51918267 Score: 194
Period size: 48 Copynumber: 3.3 Consensus size: 48
51918098 AACCAAAAAT
*
51918108 CCAAGACCAACTAGAGGAGGATGAACCCAAGGGAACCAAACAACTGAA
1 CCAAGACCAACTAGAGGAAGATGAACCCAAGGGAACCAAACAACTGAA
* * * *
51918156 CCAAGACCAACTAGAGGAAGATGAATCGAAGGGGACCAAACAACTAAA
1 CCAAGACCAACTAGAGGAAGATGAACCCAAGGGAACCAAACAACTGAA
* * * * * *
51918204 TCAAGATCAACTAGAGCAAGATGAACCCAAGGGAAACAAACTACAGAA
1 CCAAGACCAACTAGAGGAAGATGAACCCAAGGGAACCAAACAACTGAA
* * *
51918252 TCATGACCAACAAGAG
1 CCAAGACCAACTAGAG
51918268 TCGCAGGTGC
Statistics
Matches: 94, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 94 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (48 bp):
CCAAGACCAACTAGAGGAAGATGAACCCAAGGGAACCAAACAACTGAA
Found at i:51920945 original size:21 final size:21
Alignment explanation
Indices: 51920906--51920945 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51920896 ATGGAAATAT
*
51920906 AATTTATAATTATAGTTTTCA
1 AATTTATAATTATAATTTTCA
51920927 AATTTATTAATT-TAATTTT
1 AATTTA-TAATTATAATTTT
51920946 TTTGGTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
AATTTATAATTATAATTTTCA
Found at i:51921489 original size:29 final size:28
Alignment explanation
Indices: 51921423--51921494 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
51921413 ATTTTTTTTA
* *
51921423 AATATTTATATTATATTATTTTAATATTT
1 AATATTTTTA-TATATTATTTTAATATTG
* * *
51921452 AATAATTTTATATATTTTTTTATTTATTG
1 AATATTTTTATATATTATTTTA-ATATTG
51921481 AATATTTTTATATA
1 AATATTTTTATATA
51921495 GTCATCTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 11 0.31
29 25 0.69
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (28 bp):
AATATTTTTATATATTATTTTAATATTG
Found at i:51927661 original size:13 final size:13
Alignment explanation
Indices: 51927642--51927676 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
51927632 TTATTGACTT
51927642 AAGTCACACGGCC
1 AAGTCACACGGCC
* *
51927655 TAGTCACAAGGCC
1 AAGTCACACGGCC
51927668 AAGTCACAC
1 AAGTCACAC
51927677 ACCCGTGCGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.34, G:0.20, T:0.11
Consensus pattern (13 bp):
AAGTCACACGGCC
Found at i:51928976 original size:23 final size:23
Alignment explanation
Indices: 51928949--51928992 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
51928939 CCATATAACA
* *
51928949 GGAAGCTCATAAAGAGCCTATTG
1 GGAAGCTCACAAAAAGCCTATTG
51928972 GGAAGCTCACAAAAAGCCTAT
1 GGAAGCTCACAAAAAGCCTAT
51928993 CAAGAAGCTT
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:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (23 bp):
GGAAGCTCACAAAAAGCCTATTG
Found at i:51928999 original size:23 final size:23
Alignment explanation
Indices: 51928950--51929001 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
51928940 CATATAACAG
* * ***
51928950 GAAGCTCATAAAGAGCCTATTGG
1 GAAGCTCACAAAAAGCCTATCAA
51928973 GAAGCTCACAAAAAGCCTATCAA
1 GAAGCTCACAAAAAGCCTATCAA
51928996 GAAGCT
1 GAAGCT
51929002 TATCCGGGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (23 bp):
GAAGCTCACAAAAAGCCTATCAA
Found at i:51929264 original size:64 final size:64
Alignment explanation
Indices: 51929158--51929280 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 64
51929148 TCCGGAGAGC
*
51929158 CATATAACAAGACACTCATAAAGAGCTGCGATATGTCCGCAACACATGCAGGATCACTATCGAT
1 CATATAACAAGACACTCACAAAGAGCTGCGATATGTCCGCAACACATGCAGGATCACTATCGAT
* * **
51929222 CATATAACAGGACGCTCACAAAGAGCTGCTG-TATGTGTGCAACACATGCAGGATCACTA
1 CATATAACAAGACACTCACAAAGAGCTGC-GATATGTCCGCAACACATGCAGGATCACTA
51929281 CTGATCGAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
64 52 0.98
65 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (64 bp):
CATATAACAAGACACTCACAAAGAGCTGCGATATGTCCGCAACACATGCAGGATCACTATCGAT
Found at i:51933514 original size:23 final size:23
Alignment explanation
Indices: 51933488--51933562 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
51933478 ATAAGTGCAA
*
51933488 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
51933511 CACTGAAATGTAGCCGAAGCTAA
1 CACTGAAATGTAGCCGAAGCTAC
*
51933534 CACTGAAACGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
51933557 CACTGA
1 CACTGA
51933563 TCAATAACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:51933801 original size:18 final size:17
Alignment explanation
Indices: 51933775--51933813 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
51933765 ATTTTCCTTC
51933775 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
51933792 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
51933810 CACA
1 CACA
51933814 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:51938216 original size:5 final size:5
Alignment explanation
Indices: 51938208--51938233 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
51938198 AAGAGAATGT
51938208 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
51938234 AAAATGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:51943340 original size:9 final size:9
Alignment explanation
Indices: 51943326--51943362 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
51943316 TATAGTTTGA
51943326 TATTCGAAT
1 TATTCGAAT
51943335 TATTCGAAT
1 TATTCGAAT
*
51943344 TATTCGAGT
1 TATTCGAAT
51943353 TATTCGAAT
1 TATTCGAAT
51943362 T
1 T
51943363 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:51943439 original size:96 final size:97
Alignment explanation
Indices: 51943338--51943520 Score: 341
Period size: 96 Copynumber: 1.9 Consensus size: 97
51943328 TTCGAATTAT
51943338 TCGAATTATTCGAGTTATTCGAATTCGAAAACTCAACTCGATTCGAACTCAAAATTCGAAAAAAA
1 TCGAATTATTCGAGTTATTCGAATTCGAAAACTCAACTCGATTCGAACTCAAAATTCGAAAAAAA
51943403 -AATTCGAGTTGATTCGAATAATAGTTTAATA
66 TAATTCGAGTTGATTCGAATAATAGTTTAATA
* *
51943434 TCGAATTATTCGAGTTATTCGAATTTGAAAACTCAACTCGATTCGAACTCGAAATTCGAAAAAAA
1 TCGAATTATTCGAGTTATTCGAATTCGAAAACTCAACTCGATTCGAACTCAAAATTCGAAAAAAA
51943499 TAATTCGAGTTGATTCGAATAA
66 TAATTCGAGTTGATTCGAATAA
51943521 CTCGATTCGT
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 63 0.75
97 21 0.25
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (97 bp):
TCGAATTATTCGAGTTATTCGAATTCGAAAACTCAACTCGATTCGAACTCAAAATTCGAAAAAAA
TAATTCGAGTTGATTCGAATAATAGTTTAATA
Found at i:51948524 original size:28 final size:28
Alignment explanation
Indices: 51948493--51948585 Score: 147
Period size: 27 Copynumber: 3.4 Consensus size: 28
51948483 AAAAATAAAA
51948493 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
51948521 ATTTACCAAAATATTACAAC-TTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
*
51948548 ATTTACCAAAATATTAC--TTTTTTTATT
1 ATTTACCAAAATATTACAACTTTTTT-TT
51948575 ATTTACCAAAA
1 ATTTACCAAAA
51948586 AATATAAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
26 5 0.08
27 37 0.60
28 20 0.32
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:51948624 original size:6 final size:6
Alignment explanation
Indices: 51948591--51948632 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
51948581 CAAAAAATAT
*
51948591 AAAA-A AAAACA ACAACA AAAGACAA AAAACA AAAACA AAAAC
1 AAAACA AAAACA AAAACA AAA-AC-A AAAACA AAAACA AAAAC
51948633 TGACACAGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 4 0.12
6 20 0.62
7 4 0.12
8 4 0.12
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:51948628 original size:13 final size:13
Alignment explanation
Indices: 51948591--51948631 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
51948581 CAAAAAATAT
51948591 AAAA-AAAAAC-A
1 AAAACAAAAACAA
*
51948602 ACAACAAAAGACAA
1 AAAACAAAA-ACAA
51948616 AAAACAAAAACAA
1 AAAACAAAAACAA
51948629 AAA
1 AAA
51948632 CTGACACAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 3 0.12
12 4 0.16
13 9 0.36
14 9 0.36
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAACAAAAACAA
Found at i:51948689 original size:27 final size:27
Alignment explanation
Indices: 51948651--51948918 Score: 527
Period size: 27 Copynumber: 9.9 Consensus size: 27
51948641 CCTGATCACC
*
51948651 CCAATGCCATTGGCGGCACCAAAGGTG
1 CCAATGCCATTGGCGGCACCAATGGTG
51948678 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAATGGTG
51948705 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAATGGTG
51948732 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAATGGTG
51948759 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAATGGTG
51948786 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAATGGTG
51948813 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAATGGTG
51948840 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAATGGTG
51948867 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAATGGTG
51948894 CCAATGCCATTGGCGGCACCAATGG
1 CCAATGCCATTGGCGGCACCAATGG
51948919 AAAGACCAGG
Statistics
Matches: 240, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 240 1.00
ACGTcount: A:0.23, C:0.30, G:0.29, T:0.18
Consensus pattern (27 bp):
CCAATGCCATTGGCGGCACCAATGGTG
Found at i:51949433 original size:27 final size:27
Alignment explanation
Indices: 51949395--51949455 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
51949385 NNNNNNNNNN
51949395 GCATTGGCACCATTGGTGCCGCCAATG
1 GCATTGGCACCATTGGTGCCGCCAATG
51949422 GCATTGGCACCATTGGTGCCGCCAATG
1 GCATTGGCACCATTGGTGCCGCCAATG
51949449 GCATTGG
1 GCATTGG
51949456 GGTGATCAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.23
Consensus pattern (27 bp):
GCATTGGCACCATTGGTGCCGCCAATG
Found at i:51949613 original size:28 final size:28
Alignment explanation
Indices: 51949516--51949613 Score: 130
Period size: 28 Copynumber: 3.5 Consensus size: 28
51949506 TTTTTTTGAT
**
51949516 ATATTTTGGTAAATAATAAAAAA-AAGTA
1 ATATTTTGGTAAATAA-AAAAAAGTTGTA
51949544 ATAGTGTTTGGT-AA-AAAAAAAAGTTGTA
1 ATA-T-TTTGGTAAATAAAAAAAAGTTGTA
51949572 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
51949600 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
51949614 TTTTATTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
26 6 0.10
27 9 0.14
28 39 0.62
29 3 0.05
30 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:51950270 original size:291 final size:290
Alignment explanation
Indices: 51949747--51950328 Score: 1146
Period size: 291 Copynumber: 2.0 Consensus size: 290
51949737 TATAAGGCCA
51949747 TCTTCAAGAATTTGTAAAGGGTTACACACACGAACCCGGAGATTATTAAAAAAAATAAAAAAGCA
1 TCTTCAAGAATTTGTAAAGGGTTACACACACGAACCCGGAGATTATTAAAAAAAATAAAAAAGCA
51949812 GAATATTAAAGGTGATTTCATTTTTTTTTCTTTTCTAGATTTTTCTTTTCCCTTTTGCTTCATTT
66 GAATATTAAAGGTGATTTCATTTTTTTTTCTTTTCTAGATTTTTCTTTTCCCTTTTGCTTCATTT
51949877 TTGTACTCGAGATAAAATCAAAATGAGAGGATAGAGGGCTGAGAGTTACCTGTCATCTGAACGAT
131 TTGTACTCGAGATAAAATCAAAATGAGAGGATAGAGGGCTGAGAGTTACCTGTCATCTGAACGAT
*
51949942 GTCTACTCCGCTGTGATTGGAGCCAGACGAGCATTCGGAGAGCTCTTGAACAGCCAGTCTTCGAG
196 GTCTACTCCGCTGCGATTGGAGCCAGACGAGCATTCGGAGAGCTCTTGAACAGCCAGTCTTCGAG
51950007 GCGACGCATGGAGTTTCTTTTTCATTTGCT
261 GCGACGCATGGAGTTTCTTTTTCATTTGCT
51950037 TCTTCAAGAATTTGTAAAGGGTTACACACACGAACCCGGAGATTATTAAAAAAAATAAAAAAAGC
1 TCTTCAAGAATTTGTAAAGGGTTACACACACGAACCCGGAGATTATTAAAAAAAAT-AAAAAAGC
51950102 AGAATATTAAAGGTGATTTCATTTTTTTTTCTTTTCTAGATTTTTCTTTTCCCTTTTGCTTCATT
65 AGAATATTAAAGGTGATTTCATTTTTTTTTCTTTTCTAGATTTTTCTTTTCCCTTTTGCTTCATT
51950167 TTTGTACTCGAGATAAAATCAAAATGAGAGGATAGAGGGCTGAGAGTTACCTGTCATCTGAACGA
130 TTTGTACTCGAGATAAAATCAAAATGAGAGGATAGAGGGCTGAGAGTTACCTGTCATCTGAACGA
51950232 TGTCTACTCCGCTGCGATTGGAGCCAGACGAGCATTCGGAGAGCTCTTGAACAGCCAGTCTTCGA
195 TGTCTACTCCGCTGCGATTGGAGCCAGACGAGCATTCGGAGAGCTCTTGAACAGCCAGTCTTCGA
51950297 GGCGACGCATGGAGTTTCTTTTTCATTTGCT
260 GGCGACGCATGGAGTTTCTTTTTCATTTGCT
51950328 T
1 T
51950329 TAGGTTTTAA
Statistics
Matches: 290, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
290 56 0.19
291 234 0.81
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (290 bp):
TCTTCAAGAATTTGTAAAGGGTTACACACACGAACCCGGAGATTATTAAAAAAAATAAAAAAGCA
GAATATTAAAGGTGATTTCATTTTTTTTTCTTTTCTAGATTTTTCTTTTCCCTTTTGCTTCATTT
TTGTACTCGAGATAAAATCAAAATGAGAGGATAGAGGGCTGAGAGTTACCTGTCATCTGAACGAT
GTCTACTCCGCTGCGATTGGAGCCAGACGAGCATTCGGAGAGCTCTTGAACAGCCAGTCTTCGAG
GCGACGCATGGAGTTTCTTTTTCATTTGCT
Found at i:51956081 original size:2 final size:2
Alignment explanation
Indices: 51956074--51956100 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51956064 GATTCCATTG
51956074 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
51956101 CTTTTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51959787 original size:26 final size:26
Alignment explanation
Indices: 51959734--51959817 Score: 100
Period size: 26 Copynumber: 3.2 Consensus size: 26
51959724 CAAAAGAAAT
51959734 AAAAATA--TACCAAAATATACCCCGAAA
1 AAAAATATTTACCAAAATATA--CC-AAA
* *
51959761 AAAATTATTTATCAAAATATACCAAA
1 AAAAATATTTACCAAAATATACCAAA
*
51959787 AAAAATATTTACCAAAATATACAAAA
1 AAAAATATTTACCAAAATATACCAAA
51959813 AAAAA
1 AAAAA
51959818 AAAAAGAGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
26 31 0.62
27 8 0.16
29 11 0.22
ACGTcount: A:0.63, C:0.14, G:0.01, T:0.21
Consensus pattern (26 bp):
AAAAATATTTACCAAAATATACCAAA
Found at i:51960099 original size:14 final size:14
Alignment explanation
Indices: 51960080--51960119 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
51960070 TTGATTGCCA
51960080 GTAAAATATTTTCT
1 GTAAAATATTTTCT
51960094 GTAAAATGA-TTTCT
1 GTAAAAT-ATTTTCT
*
51960108 GGAAAATATTTT
1 GTAAAATATTTT
51960120 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (14 bp):
GTAAAATATTTTCT
Found at i:51960131 original size:34 final size:35
Alignment explanation
Indices: 51960088--51960154 Score: 127
Period size: 34 Copynumber: 1.9 Consensus size: 35
51960078 CAGTAAAATA
51960088 TTTTCTGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
51960122 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
51960155 CTGGTGTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 18 0.56
35 14 0.44
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:51960266 original size:20 final size:20
Alignment explanation
Indices: 51960241--51960279 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
51960231 GTTTTTACAT
51960241 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
51960261 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
51960280 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:51978223 original size:27 final size:27
Alignment explanation
Indices: 51978185--51978241 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
51978175 TAGTATTGGC
*
51978185 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTACCTGGGAGGCGCCAATGGTGGT
51978212 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTACCTGGGAGGCGCCAATGGTGGT
51978239 GCC
1 GCC
51978242 AATGCTGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.19
Consensus pattern (27 bp):
GCCTACCTGGGAGGCGCCAATGGTGGT
Found at i:51978255 original size:27 final size:27
Alignment explanation
Indices: 51978195--51978257 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
51978185 GCCTATCTGG
* *
51978195 GAGGCGCCAATGGTGGTGCCTACCTGG
1 GAGGCGCCAATGGTGGTGCCAACCTGA
*
51978222 GAGGCGCCAATGGTGGTGCCAATGCTGA
1 GAGGCGCCAATGGTGGTGCCAA-CCTGA
51978250 GA-GCGCCA
1 GAGGCGCCA
51978258 GGGGGCCGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.19, C:0.25, G:0.40, T:0.16
Consensus pattern (27 bp):
GAGGCGCCAATGGTGGTGCCAACCTGA
Found at i:51978654 original size:27 final size:27
Alignment explanation
Indices: 51978617--51978735 Score: 132
Period size: 22 Copynumber: 4.8 Consensus size: 27
51978607 ATATACCGAC
*
51978617 ATTACAATATTTATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTATAAT
*
51978644 ATTACAGTATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTATAAT
*
51978666 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTATAAT
51978693 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTATAAT
*
51978715 ATTACAATATTCATACTAAAT
1 ATTACAATATTCATACAAAAT
51978736 ATAGATAATT
Statistics
Matches: 80, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
22 30 0.38
23 10 0.12
24 2 0.03
25 1 0.01
26 8 0.10
27 29 0.36
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTATAAT
Found at i:51978684 original size:49 final size:49
Alignment explanation
Indices: 51978569--51978735 Score: 216
Period size: 49 Copynumber: 3.4 Consensus size: 49
51978559 ATTATCAAAT
* **
51978569 AATTACAATATTCATACAAAAAATTACAATATTACAATA-T-ATAC--CGA
1 AATTACAATATTCATAC--AAAATTATAATATTACAATATTCATACAAAAA
* * *
51978616 CATTACAATATTTATACAAAATTATAATATTACAGTATTCATACAAAAA
1 AATTACAATATTCATACAAAATTATAATATTACAATATTCATACAAAAA
*
51978665 AATTGCAATATTCATACAAAATTATAATATTACAATATTCATACAAAAA
1 AATTACAATATTCATACAAAATTATAATATTACAATATTCATACAAAAA
*
51978714 AATTACAATATTCATACTAAAT
1 AATTACAATATTCATACAAAAT
51978736 ATAGATAATT
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
45 18 0.17
46 1 0.01
47 19 0.18
49 66 0.63
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (49 bp):
AATTACAATATTCATACAAAATTATAATATTACAATATTCATACAAAAA
Done.