Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 26
Found at i:4184246 original size:20 final size:19
Alignment explanation
Indices: 4184221--4184270 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
4184211 GCCGAATGGT
*
4184221 TACATGATGTTTCGGCTAGA
1 TACATGATGTTTAGG-TAGA
*
4184241 TACATGA-CTTTAGGTAGA
1 TACATGATGTTTAGGTAGA
*
4184259 TACATAATGTTT
1 TACATGATGTTT
4184271 TAAAATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 10 0.40
19 8 0.32
20 7 0.28
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (19 bp):
TACATGATGTTTAGGTAGA
Found at i:4185000 original size:17 final size:17
Alignment explanation
Indices: 4184975--4185008 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4184965 ATATAATGCA
*
4184975 TATAATATAATGATGTG
1 TATAATATAAAGATGTG
*
4184992 TATATTATAAAGATGTG
1 TATAATATAAAGATGTG
4185009 AACTATAGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
TATAATATAAAGATGTG
Found at i:4187514 original size:25 final size:26
Alignment explanation
Indices: 4187475--4187534 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
4187465 CTTGGCTTGC
*
4187475 TTTCTTTTTGAATTTTT-TCTTTTTT
1 TTTCTTTTTGAATTTTTCTCTTCTTT
4187500 TTTCTTTTCTG-ATTTTTCTCTTCTTT
1 TTTCTTTT-TGAATTTTTCTCTTCTTT
*
4187526 TGTCTTTTT
1 TTTCTTTTT
4187535 CGTTCTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTCTTTTTGAATTTTTCTCTTCTTT
Found at i:4189974 original size:24 final size:23
Alignment explanation
Indices: 4189947--4190006 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
4189937 TCCAACTTTT
4189947 CTTTCTTTTTCTTCTTTTTGAGTG
1 CTTTCTTTTTCTTC-TTTTGAGTG
**
4189971 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTCTTTTGAGTG
4189994 CTTT-TATTTTCTT
1 CTTTCT-TTTTCTT
4190007 TGCTGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.08, C:0.17, G:0.10, T:0.65
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTG
Found at i:4189992 original size:23 final size:24
Alignment explanation
Indices: 4189954--4190006 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
4189944 TTTCTTTCTT
4189954 TTTCTTCTTTTTGAGTGCTTTCAA
1 TTTCTTCTTTTTGAGTGCTTTCAA
* *
4189978 TTTCTTC-TTTTGAGTGCTTTTAT
1 TTTCTTCTTTTTGAGTGCTTTCAA
4190001 TTTCTT
1 TTTCTT
4190007 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.64
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTGCTTTCAA
Found at i:4200011 original size:12 final size:13
Alignment explanation
Indices: 4199988--4200012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4199978 ACATACAACG
4199988 AAAATACAAAAAA
1 AAAATACAAAAAA
4200001 AAAATACAAAAA
1 AAAATACAAAAA
4200013 GAAGTTCAAG
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATACAAAAAA
Found at i:4207583 original size:19 final size:20
Alignment explanation
Indices: 4207542--4207592 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4207532 GAAACCCCTT
* *
4207542 TGAAAATACATAATTTTTGA
1 TGAAAATACATGATTTTTAA
4207562 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
4207581 TGAAGATACATG
1 TGAAAATACATG
4207593 CTCTTGACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4210028 original size:69 final size:69
Alignment explanation
Indices: 4209887--4210035 Score: 190
Period size: 69 Copynumber: 2.2 Consensus size: 69
4209877 ATTGAAGACA
* * * * *
4209887 TTTGATTTTCATTAGGCATATCTCTTGATTCTTGAAGGATCACGTCCCTTGGTTGAAAAATCGCT
1 TTTGATTTTCATTAGGAATAACTCTTGATTCTTGAAGGATCACGTCCCTTGGATGAAAAATCACC
*
4209952 TCCC
66 ACCC
* * * *
4209956 TTTGATTTTCATTAGGAATAACTCTTGATTCTTGAAGGATCACGTTCTTTGGATGAAGAATTACC
1 TTTGATTTTCATTAGGAATAACTCTTGATTCTTGAAGGATCACGTCCCTTGGATGAAAAATCACC
*
4210021 ACTC
66 ACCC
*
4210025 TTTGCTTTTCA
1 TTTGATTTTCA
4210036 AAAATCGCAC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (69 bp):
TTTGATTTTCATTAGGAATAACTCTTGATTCTTGAAGGATCACGTCCCTTGGATGAAAAATCACC
ACCC
Found at i:4212431 original size:8 final size:8
Alignment explanation
Indices: 4212420--4212449 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
4212410 TATTCTGATT
4212420 TTTTTTTC
1 TTTTTTTC
4212428 TTTTTTTC
1 TTTTTTTC
4212436 TTTTCTTTC
1 TTTT-TTTC
4212445 TTTTT
1 TTTTT
4212450 GCACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:4217297 original size:19 final size:21
Alignment explanation
Indices: 4217254--4217305 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
4217244 GAAACCCCTT
*
4217254 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTGTAAA
4217275 TGAAAATACATGA-TTGT-AA
1 TGAAAATACATGATTTGTAAA
*
4217294 TGAAGATACATG
1 TGAAAATACATG
4217306 CTCTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGATTTGTAAA
Found at i:4218334 original size:25 final size:26
Alignment explanation
Indices: 4218306--4218354 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4218296 TAGTTCATAT
*
4218306 CTTTATAAT-ATGCATATTCTTATTA
1 CTTTATAATAATGCATATACTTATTA
*
4218331 CTTTATAATAATTCATATACTTAT
1 CTTTATAATAATGCATATACTTAT
4218355 CTTATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (26 bp):
CTTTATAATAATGCATATACTTATTA
Found at i:4219517 original size:35 final size:37
Alignment explanation
Indices: 4219446--4219525 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
4219436 ATACTATTTC
*
4219446 CATCACCATAATCCATCTTCCATTATCACGCATATAT
1 CATCACCATAATCCATCTACCATTATCACGCATATAT
* * *
4219483 CATTACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCATATAT
4219518 CATCACCA
1 CATCACCA
4219526 AATTCTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 20 0.53
36 3 0.08
37 15 0.39
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCATATAT
Found at i:4223445 original size:35 final size:37
Alignment explanation
Indices: 4223376--4223455 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
4223366 ATACTATTTC
*
4223376 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
4223413 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
4223448 CATCACCA
1 CATCACCA
4223456 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:4224123 original size:20 final size:19
Alignment explanation
Indices: 4224087--4224125 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4224077 AGTAAATATG
**
4224087 TGAAAACATATGTTATGCA
1 TGAAAACATATAATATGCA
4224106 TGAAAATCATATAATATGCA
1 TGAAAA-CATATAATATGCA
4224126 AGTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (19 bp):
TGAAAACATATAATATGCA
Found at i:4225690 original size:2 final size:2
Alignment explanation
Indices: 4225679--4225707 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4225669 TAACTATAGG
4225679 TA TA -A 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
4225708 ATTAACTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4227590 original size:33 final size:33
Alignment explanation
Indices: 4227511--4227614 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
4227501 ATACAATCTG
* *
4227511 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
4227547 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
4227580 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
4227613 TC
1 TC
4227615 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:4230580 original size:11 final size:11
Alignment explanation
Indices: 4230566--4230619 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
4230556 CTCTTTTGAA
4230566 TTTCTTTTTCT
1 TTTCTTTTTCT
4230577 TTTCTTTTTCT
1 TTTCTTTTTCT
*
4230588 GATTCTTCTTT-T
1 -TTTCTT-TTTCT
*
4230600 TGTCTTTTTCT
1 TTTCTTTTTCT
*
4230611 TATCTTTTT
1 TTTCTTTTT
4230620 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 3 0.08
11 24 0.67
12 6 0.17
13 3 0.08
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:4234981 original size:11 final size:11
Alignment explanation
Indices: 4234967--4235020 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
4234957 CTCTTTTGAA
4234967 TTTCTTTTTCT
1 TTTCTTTTTCT
4234978 TTTCTTTTTCT
1 TTTCTTTTTCT
*
4234989 GATTCTTCTTT-T
1 -TTTCTT-TTTCT
*
4235001 TGTCTTTTTCT
1 TTTCTTTTTCT
*
4235012 TATCTTTTT
1 TTTCTTTTT
4235021 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 3 0.08
11 24 0.67
12 6 0.17
13 3 0.08
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:4236637 original size:2 final size:2
Alignment explanation
Indices: 4236626--4236658 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4236616 TAACTATAGG
4236626 TA TA -A 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
4236659 AATAACTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4239738 original size:19 final size:21
Alignment explanation
Indices: 4239688--4239739 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
4239678 GAAACCCCTT
4239688 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
4239709 TTAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
4239728 TGAAGATACATG
1 TGAAAATACATG
4239740 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:4246880 original size:19 final size:21
Alignment explanation
Indices: 4246837--4246888 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
4246827 GAAACCCCTT
4246837 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
4246858 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
4246877 TGAAGATACATG
1 TGAAAATACATG
4246889 CTCTTGGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:4259245 original size:19 final size:19
Alignment explanation
Indices: 4259214--4259255 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
4259204 AGGGGATACT
4259214 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
4259233 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
4259252 AATA
1 AATA
4259256 AAGAAAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:4259709 original size:19 final size:20
Alignment explanation
Indices: 4259668--4259718 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4259658 GAAACCCCTT
* *
4259668 TGAAAACACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
4259688 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
4259707 TGAAGATACATG
1 TGAAAATACATG
4259719 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4260741 original size:20 final size:19
Alignment explanation
Indices: 4260704--4260742 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4260694 AAGTAAAGAT
**
4260704 GTGAAAACATATGTTATGC
1 GTGAAAACATATAATATGC
4260723 GTGAAAATCATATAATATGC
1 GTGAAAA-CATATAATATGC
4260743 AAGTGAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
GTGAAAACATATAATATGC
Found at i:4264752 original size:18 final size:18
Alignment explanation
Indices: 4264731--4264766 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4264721 AAAGCACTCA
4264731 AAAAGAAAA-AAAGCAAAG
1 AAAAGAAAAGAAAG-AAAG
4264749 AAAAGAAAAGAAAGAAAG
1 AAAAGAAAAGAAAGAAAG
4264767 TAGAAGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAGAAAG
Found at i:4270836 original size:30 final size:31
Alignment explanation
Indices: 4270784--4270843 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
4270774 CTTAGCTTTA
**
4270784 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
4270814 TATTATGTTTTCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
4270844 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:4271777 original size:19 final size:20
Alignment explanation
Indices: 4271753--4271803 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
4271743 CGGCCAAGAG
* *
4271753 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
4271772 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
4271792 CATGTATTTTCA
1 CATGTATTTTCA
4271804 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:4288656 original size:13 final size:13
Alignment explanation
Indices: 4288632--4288663 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4288622 GAAAAGAATG
4288632 ATTAAT-AATGGA
1 ATTAATAAATGGA
4288644 ATTAATAAATGGA
1 ATTAATAAATGGA
4288657 A-TAATAA
1 ATTAATAA
4288664 TATAAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (13 bp):
ATTAATAAATGGA
Found at i:4297520 original size:23 final size:22
Alignment explanation
Indices: 4297493--4297547 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 22
4297483 TCTCTATTCC
*
4297493 ATCTTTATTTGATTTCATTTCTT
1 ATCTTTATTT-ATTTCATTTATT
4297516 ATCTTTA-TTATTTCATTTATT
1 ATCTTTATTTATTTCATTTATT
4297537 ATTCCTTTATT
1 A-T-CTTTATT
4297548 AATCATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.43
22 3 0.11
23 12 0.43
24 1 0.04
ACGTcount: A:0.20, C:0.13, G:0.02, T:0.65
Consensus pattern (22 bp):
ATCTTTATTTATTTCATTTATT
Found at i:4297548 original size:23 final size:21
Alignment explanation
Indices: 4297493--4297548 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
4297483 TCTCTATTCC
*
4297493 ATCTTTATTTGATTTCATTTCTT
1 ATCTTTA-TT-ATTTCATTTATT
4297516 ATCTTTATTATTTCATTTATT
1 ATCTTTATTATTTCATTTATT
4297537 ATTCCTTTATTA
1 A-T-CTTTATTA
4297549 ATCATATTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 12 0.40
22 3 0.10
23 15 0.50
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.64
Consensus pattern (21 bp):
ATCTTTATTATTTCATTTATT
Found at i:4297796 original size:20 final size:20
Alignment explanation
Indices: 4297771--4297816 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
4297761 GGAGTGCGAA
4297771 AAGAAAGAAAAGAC-AAAAAG
1 AAGAAA-AAAAGACAAAAAAG
**
4297791 AAGAAAAAAATTCAAAAAAG
1 AAGAAAAAAAGACAAAAAAG
4297811 AAGAAA
1 AAGAAA
4297817 TTCAAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.76, C:0.04, G:0.15, T:0.04
Consensus pattern (20 bp):
AAGAAAAAAAGACAAAAAAG
Found at i:4297819 original size:16 final size:17
Alignment explanation
Indices: 4297784--4297829 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
4297774 AAAGAAAAGA
*
4297784 CAAAAAGAAGAAAAAAATT
1 CAAAAAG-AG-AAGAAATT
4297803 CAAAAA-AGAAGAAATT
1 CAAAAAGAGAAGAAATT
4297819 CAAAAAGAGAA
1 CAAAAAGAGAA
4297830 TGCAAGCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 13 0.52
17 6 0.24
19 6 0.24
ACGTcount: A:0.72, C:0.07, G:0.13, T:0.09
Consensus pattern (17 bp):
CAAAAAGAGAAGAAATT
Found at i:4308354 original size:19 final size:20
Alignment explanation
Indices: 4308330--4308380 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
4308320 CGGCCAAGAG
* *
4308330 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
4308349 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
4308369 CATGTATTTTCA
1 CATGTATTTTCA
4308381 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:4308833 original size:19 final size:19
Alignment explanation
Indices: 4308793--4308834 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
4308783 ATCCTTTCTT
*
4308793 TATTTCATTTCATTCTTAA
1 TATTTCATTTCATTCATAA
4308812 TATTTCATTTCATTACAT-A
1 TATTTCATTTCATT-CATAA
4308831 TATT
1 TATT
4308835 ATTATTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTCATTTCATTCATAA
Found at i:4312293 original size:19 final size:20
Alignment explanation
Indices: 4312269--4312319 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
4312259 CGGCCAAGAG
* *
4312269 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
4312288 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
4312308 CATGTATTTTCA
1 CATGTATTTTCA
4312320 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:4312756 original size:19 final size:19
Alignment explanation
Indices: 4312732--4312773 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
4312722 ATCCTTTCTT
4312732 TATTTCATTTCATT-CTTAA
1 TATTTCATTTCATTACTT-A
4312751 TATTTCATTTCATTACTTA
1 TATTTCATTTCATTACTTA
4312770 TATT
1 TATT
4312774 ATTATTCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTCATTTCATTACTTA
Found at i:4314680 original size:321 final size:321
Alignment explanation
Indices: 4314098--4314714 Score: 1162
Period size: 321 Copynumber: 1.9 Consensus size: 321
4314088 TGAAGACACT
4314098 ATCAACAAAGGGAGTACTCTTGAAAATCTTTATATTGAATTTACTTTATATTAGTTATATACTAT
1 ATCAACAAAGGGAGTACTCTTGAAAATCTTTATATTGAATTTACTTTATATTAGTTATATACTAT
4314163 ATGCTTTTATAATACATTTTATGATAAGAATACTTGTTATGTAGTTAAAGAATAGCTTAGTATGA
66 ATGCTTTTATAATACATTTTATGATAAGAATACTTGTTATGTAGTTAAAGAATAGCTTAGTATGA
* *
4314228 ACACATCATGCACATTGATATTTAAACATGTTAGGATAGTCTGATAATCATATTAAACATGATTA
131 ACACAACATGCACATTGATATTTAAACATGTTAAGATAGTCTGATAATCATATTAAACATGATTA
4314293 TCATATATATACATCAAGGCAGCATCATTATAAACCATTTCATTAGTTCATATGCATTCATATTA
196 TCATATATATACATCAAGGCAGCATCATTATAAACCATTTCATTAGTTCATATGCATTCATATTA
* *
4314358 GCTTTTAAGCTTCATACATTATCTTGCACATATTTTCATCACCTGATGCAAGCACGTTTTC
261 GCTCTTAAGCTTCATACATTATCTTACACATATTTTCATCACCTGATGCAAGCACGTTTTC
* *
4314419 ATCAACAAAGGGAGTACTCTTGAACATCTTTATATTGGATTTACTTTATATTAGTTATATACTAT
1 ATCAACAAAGGGAGTACTCTTGAAAATCTTTATATTGAATTTACTTTATATTAGTTATATACTAT
4314484 ATGCTTTTATAATACATTTTATGATAAGAATACTTGTTATGTAGTTAAAGAATAGCTTAGTATGA
66 ATGCTTTTATAATACATTTTATGATAAGAATACTTGTTATGTAGTTAAAGAATAGCTTAGTATGA
* *
4314549 ACACAACATGCACATTGATATTTAAACATGTTAAGATAGTCTTATAATCATATTAAGCATGATTA
131 ACACAACATGCACATTGATATTTAAACATGTTAAGATAGTCTGATAATCATATTAAACATGATTA
4314614 TCATATATATACATCAAGGCAGCATCATTATAAACCATTTCATTAGTTCATATGCATTCATATTA
196 TCATATATATACATCAAGGCAGCATCATTATAAACCATTTCATTAGTTCATATGCATTCATATTA
4314679 GCTCTTAAGCTTCATACATTATCTTACACATATTTT
261 GCTCTTAAGCTTCATACATTATCTTACACATATTTT
4314715 GAGATGATAT
Statistics
Matches: 288, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
321 288 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (321 bp):
ATCAACAAAGGGAGTACTCTTGAAAATCTTTATATTGAATTTACTTTATATTAGTTATATACTAT
ATGCTTTTATAATACATTTTATGATAAGAATACTTGTTATGTAGTTAAAGAATAGCTTAGTATGA
ACACAACATGCACATTGATATTTAAACATGTTAAGATAGTCTGATAATCATATTAAACATGATTA
TCATATATATACATCAAGGCAGCATCATTATAAACCATTTCATTAGTTCATATGCATTCATATTA
GCTCTTAAGCTTCATACATTATCTTACACATATTTTCATCACCTGATGCAAGCACGTTTTC
Found at i:4320898 original size:168 final size:170
Alignment explanation
Indices: 4320587--4320901 Score: 483
Period size: 168 Copynumber: 1.9 Consensus size: 170
4320577 GGCACTTGTA
* *
4320587 CCTTAACAATTAATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCACAAGTGAATGGCTCAAAA
1 CCTTAACAAATAATTGTGGATCTAAGAAGGAAGCAAAACAACCTGCACAAGTGAATGGCTCAAAA
* * * *
4320652 AGAGAGGGTTAAGGGTGGTAAACGTTTGGGGTGAATAGGTGGGCTGTTTAAAATGAGGGATGGAA
66 AGAGAGGCTTAAGGGTGGTAAACGTATGAGGTGAATAGGTGGGCTGTTTAAAATGAGAGATGGAA
* *
4320717 GCGGAAGATGGTTGATATGTGATGTAAGGCTCTTCAGATG
131 GCGAAAAATGGTTGATATGTGATGTAAGGCTCTTCAGATG
* * *
4320757 CCTTAACAAATGATTGTGGATCTAAGAAGGAAG-TAAACAACCTGTACAAGTGAATGGCTCAAAA
1 CCTTAACAAATAATTGTGGATCTAAGAAGGAAGCAAAACAACCTGCACAAGTGAATGGCTCAAAA
* *
4320821 AGAGATGGCTTAA-GGTGGTAAATGTAT-AGGTGAATAGGTGGGTTGTTTAAAATGAGAGATGGA
66 AGAGA-GGCTTAAGGGTGGTAAACGTATGAGGTGAATAGGTGGGCTGTTTAAAATGAGAGATGGA
4320884 AGCGAAAAATGGTTGATA
130 AGCGAAAAATGGTTGATA
4320902 AGGCTATGGT
Statistics
Matches: 131, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
168 49 0.37
169 46 0.35
170 36 0.27
ACGTcount: A:0.36, C:0.10, G:0.30, T:0.24
Consensus pattern (170 bp):
CCTTAACAAATAATTGTGGATCTAAGAAGGAAGCAAAACAACCTGCACAAGTGAATGGCTCAAAA
AGAGAGGCTTAAGGGTGGTAAACGTATGAGGTGAATAGGTGGGCTGTTTAAAATGAGAGATGGAA
GCGAAAAATGGTTGATATGTGATGTAAGGCTCTTCAGATG
Found at i:4323848 original size:36 final size:36
Alignment explanation
Indices: 4323801--4323905 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
4323791 GATACAATAT
4323801 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
4323837 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
4323873 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
4323906 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:4323863 original size:11 final size:11
Alignment explanation
Indices: 4323804--4323888 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 11
4323794 ACAATATGTC
4323804 CATCACCATTAT
1 CATCACCA-TAT
*
4323816 CA-CGCCTATAT
1 CATCACC-ATAT
4323827 CATCACCATAGT
1 CATCACCATA-T
4323839 CCATCACCATTAT
1 -CATCACCA-TAT
4323852 CA-CACCTATAT
1 CATCACC-ATAT
4323863 CATCACCATATT
1 CATCACCATA-T
4323875 CCATCACCATAT
1 -CATCACCATAT
4323887 CA
1 CA
4323889 CGCCTATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 25 0.40
12 16 0.26
13 19 0.31
14 2 0.03
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:4325563 original size:24 final size:25
Alignment explanation
Indices: 4325528--4325582 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
4325518 ACTTGGAGCC
*
4325528 TCAA-TGATCACAACTTGTGGTACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
4325552 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
4325576 TCAAGTG
1 TCAAGTG
4325583 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:4327940 original size:20 final size:22
Alignment explanation
Indices: 4327915--4327954 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
4327905 TGAGTCATTG
*
4327915 TCAACTCCA-TAA-CTACATGT
1 TCAACTACATTAAGCTACATGT
4327935 TCAACTACATTAAGCTACAT
1 TCAACTACATTAAGCTACAT
4327955 TTGACATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.30
Consensus pattern (22 bp):
TCAACTACATTAAGCTACATGT
Found at i:4331246 original size:22 final size:22
Alignment explanation
Indices: 4331218--4331259 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4331208 TTGGTGCTGG
4331218 AAACAAGATAAAAAAAAGATTA
1 AAACAAGATAAAAAAAAGATTA
*
4331240 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
4331260 AAATGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.12
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:4335570 original size:9 final size:8
Alignment explanation
Indices: 4335558--4335627 Score: 90
Period size: 8 Copynumber: 8.8 Consensus size: 8
4335548 TTTTTTGAAA
4335558 TTTTTGTT
1 TTTTTGTT
4335566 TTTTTGTT
1 TTTTTGTT
4335574 TTTTTGTT
1 TTTTTGTT
4335582 TTTTTGTT
1 TTTTTGTT
4335590 TTTTTGCCTT
1 TTTTTG--TT
*
4335600 TTTTTGTG
1 TTTTTGTT
4335608 TTTTT-TT
1 TTTTTGTT
*
4335615 TGTTT-TT
1 TTTTTGTT
4335622 TTTTTG
1 TTTTTG
4335628 AAAAAACAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
7 11 0.20
8 36 0.65
10 8 0.15
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (8 bp):
TTTTTGTT
Found at i:4335978 original size:22 final size:22
Alignment explanation
Indices: 4335947--4335988 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4335937 TTTGTGCTGG
4335947 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
*
4335969 AAACATGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
4335989 AAATGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.17
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:4340298 original size:1 final size:1
Alignment explanation
Indices: 4340294--4340359 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
4340284 TTTTTTGAAA
* * * *** * * *
4340294 TTTTTGTTTTTTTTGTTTTTTTGTTTTTTTTTTGCCTTTTTTTGTGTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4340359 T
1 T
4340360 GAAAAAACAA
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (1 bp):
T
Found at i:4340306 original size:9 final size:9
Alignment explanation
Indices: 4340294--4340356 Score: 81
Period size: 9 Copynumber: 6.6 Consensus size: 9
4340284 TTTTTTGAAA
4340294 TTTTTGTTT
1 TTTTTGTTT
4340303 TTTTTGTTT
1 TTTTTGTTT
*
4340312 TTTTGTTTTT
1 TTTT-TGTTT
4340322 TTTTTGCCTTT
1 TTTTTG--TTT
4340333 TTTTGTGTTT
1 TTTT-TGTTT
4340343 TTTTTGTTT
1 TTTTTGTTT
4340352 TTTTT
1 TTTTT
4340357 TTTGAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
9 24 0.50
10 15 0.31
11 7 0.15
12 2 0.04
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:4340314 original size:11 final size:11
Alignment explanation
Indices: 4340294--4340358 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 11
4340284 TTTTTTGAAA
4340294 TTTTTGTTTTT-
1 TTTTT-TTTTTG
4340305 TTTGTTTTTTTG
1 TTT-TTTTTTTG
4340317 TTTTTTTTTTG
1 TTTTTTTTTTG
**
4340328 -CCTTTTTTTG
1 TTTTTTTTTTG
*
4340338 TGTTTTTTTTG
1 TTTTTTTTTTG
4340349 TTTTTTTTTT
1 TTTTTTTTTT
4340359 TGAAAAAACA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
10 8 0.17
11 33 0.72
12 5 0.11
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:4340324 original size:21 final size:21
Alignment explanation
Indices: 4340295--4340360 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
4340285 TTTTTGAAAT
*
4340295 TTTTGTTTTTTTTGTTTTTTTG
1 TTTT-TTTTTTTTCTTTTTTTG
**
4340317 TTTTTTTTTTGCCTTTTTTTG
1 TTTTTTTTTTTTCTTTTTTTG
*
4340338 TGTTTTTTTTGTTTTTTTTTTTG
1 T-TTTTTTTT-TTTCTTTTTTTG
4340361 AAAAAACAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.42
22 12 0.33
23 9 0.25
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTTTTCTTTTTTTG
Found at i:4340711 original size:22 final size:22
Alignment explanation
Indices: 4340680--4340721 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4340670 TTTGTGCTGG
4340680 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
*
4340702 AAACATGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
4340722 AAATGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.17
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:4345063 original size:12 final size:12
Alignment explanation
Indices: 4345048--4345079 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
4345038 TTTTTCTACC
4345048 TTTTTTTTGTGT
1 TTTTTTTTGTGT
4345060 TTTTTTTTGTGT
1 TTTTTTTTGTGT
4345072 TTTTTTTT
1 TTTTTTTT
4345080 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTTTTTTTGTGT
Found at i:4345432 original size:22 final size:22
Alignment explanation
Indices: 4345401--4345442 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4345391 TTGGTGCTGG
4345401 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
*
4345423 AAACATGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
4345443 AAATGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.17
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:4348926 original size:13 final size:13
Alignment explanation
Indices: 4348908--4348933 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4348898 AACTTGCTTC
4348908 TTTCTTTCTTTTT
1 TTTCTTTCTTTTT
4348921 TTTCTTTCTTTTT
1 TTTCTTTCTTTTT
4348934 CTCTTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTCTTTCTTTTT
Found at i:4348950 original size:19 final size:19
Alignment explanation
Indices: 4348912--4348951 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4348902 TGCTTCTTTC
* *
4348912 TTTCTTTTTTTTCTTTCTT
1 TTTCTCTTTTTTCTTGCTT
*
4348931 TTTCTCTTTTTTGTTGCTT
1 TTTCTCTTTTTTCTTGCTT
4348950 TT
1 TT
4348952 GTTGCAGCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTCTCTTTTTTCTTGCTT
Found at i:4360157 original size:14 final size:14
Alignment explanation
Indices: 4360140--4360171 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4360130 CAAAAAGAAG
4360140 AAGAAAAAAAACAA
1 AAGAAAAAAAACAA
*
4360154 AAGAAAAAAAAGAA
1 AAGAAAAAAAACAA
4360168 AAGA
1 AAGA
4360172 CTCCTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAACAA
Found at i:4360169 original size:20 final size:20
Alignment explanation
Indices: 4360132--4360169 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
4360122 TACTGCAACA
*
4360132 AAAAGAAGAAGAAAAAAAAC
1 AAAAGAAGAAAAAAAAAAAC
*
4360152 AAAAGAA-AAAAAAGAAAA
1 AAAAGAAGAAAAAAAAAAA
4360170 GACTCCTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAGAAGAAAAAAAAAAAC
Found at i:4360231 original size:21 final size:22
Alignment explanation
Indices: 4360202--4360242 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4360192 TGCAAAAGAG
4360202 AAAAAAAAAAGAAAA-AGAATC
1 AAAAAAAAAAGAAAAGAGAATC
*
4360223 AAAAGAAAAAGAAAAGAGAA
1 AAAAAAAAAAGAAAAGAGAA
4360243 ACAAGTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAGAAAAGAGAATC
Found at i:4360403 original size:16 final size:16
Alignment explanation
Indices: 4360369--4360429 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
4360359 TGTAAGTATC
* *
4360369 TTCATTTTCTTACTAT
1 TTCATTTCCTTATTAT
*
4360385 TTCATTTCCTTATTCT
1 TTCATTTCCTTATTAT
*
4360401 TTCATATT--TTCTTAT
1 TTCAT-TTCCTTATTAT
*
4360416 TTCATTACCTTATT
1 TTCATTTCCTTATT
4360430 CTTTTCTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 1 0.03
15 10 0.29
16 22 0.63
17 2 0.06
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCATTTCCTTATTAT
Found at i:4365285 original size:22 final size:19
Alignment explanation
Indices: 4365257--4365306 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 19
4365247 GTGCTACAAC
4365257 AAAAAAAGCAACAACAAAGAA
1 AAAAAAAGCAA-AA-AAAGAA
*
4365278 GAAAAAAAACAAAAAAAGAA
1 -AAAAAAAGCAAAAAAAGAA
4365298 AAGAAAAAG
1 AA-AAAAAG
4365307 ACTCCTACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 11 0.44
21 2 0.08
22 10 0.40
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAAGCAAAAAAAGAA
Found at i:4365298 original size:17 final size:20
Alignment explanation
Indices: 4365266--4365304 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
4365256 CAAAAAAAGC
4365266 AACAACAAAGAAGAAAA-AA
1 AACAACAAAGAAGAAAAGAA
4365285 AACAA-AAA-AAGAAAAGAA
1 AACAACAAAGAAGAAAAGAA
4365303 AA
1 AA
4365305 AGACTCCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 7 0.37
19 5 0.26
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (20 bp):
AACAACAAAGAAGAAAAGAA
Found at i:4365304 original size:20 final size:23
Alignment explanation
Indices: 4365257--4365306 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 23
4365247 GTGCTACAAC
4365257 AAAAAAAGCAACAACAAAGAAGA
1 AAAAAAAGCAACAACAAAGAAGA
4365280 AAAAAAA-CAA-AA-AAAGAA-A
1 AAAAAAAGCAACAACAAAGAAGA
*
4365299 AGAAAAAG
1 AAAAAAAG
4365307 ACTCCTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.28
20 6 0.24
21 2 0.08
22 3 0.12
23 7 0.28
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (23 bp):
AAAAAAAGCAACAACAAAGAAGA
Found at i:4367660 original size:53 final size:52
Alignment explanation
Indices: 4367580--4367685 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 52
4367570 TCGTGGGGTT
* * *
4367580 CATAACAGCATGTTTATAATTTGTTTTGTTAAATTCACGTGCACTCGCATTCA
1 CATAACAGCATGTTCATAATTTGTTTTGTT-AATTCACGTGCACCCACATTCA
* *
4367633 CATAACAGCATGTTCATCATTTGTTTTGTTAATTCACTTGCACCCACATTCA
1 CATAACAGCATGTTCATAATTTGTTTTGTTAATTCACGTGCACCCACATTCA
4367685 C
1 C
4367686 TTTACAACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 20 0.42
53 28 0.58
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (52 bp):
CATAACAGCATGTTCATAATTTGTTTTGTTAATTCACGTGCACCCACATTCA
Found at i:4367705 original size:52 final size:53
Alignment explanation
Indices: 4367580--4367705 Score: 155
Period size: 52 Copynumber: 2.4 Consensus size: 53
4367570 TCGTGGGGTT
* * * *
4367580 CATAACAGCATGTTTATAATTTGTTTTGTTAAATTCACGTGCACTCGCATTCA
1 CATAACAACATGTTTATCATTTGTTTTGTTAAATTCACGTGCACCCACATTCA
* * *
4367633 CATAACAGCATGTTCATCATTTGTTTTGTT-AATTCACTTGCACCCACATTCA
1 CATAACAACATGTTTATCATTTGTTTTGTTAAATTCACGTGCACCCACATTCA
* * *
4367685 CTTTACAACATGTTTTTCATT
1 CATAACAACATGTTTATCATT
4367706 ATCACTCATG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
52 35 0.56
53 28 0.44
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.41
Consensus pattern (53 bp):
CATAACAACATGTTTATCATTTGTTTTGTTAAATTCACGTGCACCCACATTCA
Found at i:4371943 original size:13 final size:11
Alignment explanation
Indices: 4371899--4371983 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
4371889 ACAATCTGTC
4371899 CATCACCATCAT
1 CATCACCAT-AT
*
4371911 CA-CGCCTATAT
1 CATCACC-ATAT
*
4371922 CATCGCCATAGT
1 CATCACCATA-T
4371934 CCATCACCATTAT
1 -CATCACCA-TAT
*
4371947 CA-CGCCTATAT
1 CATCACC-ATAT
4371958 CATCACCATATT
1 CATCACCATA-T
4371970 CCATCACCATAT
1 -CATCACCATAT
4371982 CA
1 CA
4371984 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 23 0.38
12 17 0.28
13 18 0.30
14 2 0.03
ACGTcount: A:0.31, C:0.38, G:0.05, T:0.27
Consensus pattern (11 bp):
CATCACCATAT
Found at i:4371943 original size:36 final size:35
Alignment explanation
Indices: 4371896--4372000 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 35
4371886 GAGACAATCT
*
4371896 GTCCATCACCATCATCACGCCTATATCATCGCCATA
1 GTCCATCACCAT-ATCACGCCTATATCATCACCATA
4371932 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCA-TATCACGCCTATATCATCACCATA
* *
4371968 TTCCATCACCATATCACGCCTATATTATCACCA
1 GTCCATCACCATATCACGCCTATATCATCACCA
4372001 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 21 0.32
36 43 0.66
37 1 0.02
ACGTcount: A:0.30, C:0.37, G:0.06, T:0.28
Consensus pattern (35 bp):
GTCCATCACCATATCACGCCTATATCATCACCATA
Found at i:4376237 original size:10 final size:10
Alignment explanation
Indices: 4376222--4376247 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4376212 ACTCAAAAAG
4376222 AAGAAAAGGA
1 AAGAAAAGGA
4376232 AAGAAAAGGA
1 AAGAAAAGGA
4376242 AAGAAA
1 AAGAAA
4376248 TAAAGTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGAAAAGGA
Found at i:4382520 original size:17 final size:15
Alignment explanation
Indices: 4382497--4382553 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
4382487 CTTTTTGAAA
*
4382497 TTCTTTTTTTTTTTC
1 TTCTTTTTTTTTTTT
*
4382512 TTCTATTTTGATTTTTT
1 TTCT-TTTT-TTTTTTT
4382529 TTCTTTTTTTCTTTTTT
1 TTC-TTTTTT-TTTTTT
4382546 TTCTTTTT
1 TTCTTTTT
4382554 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 4 0.11
16 9 0.26
17 21 0.60
18 1 0.03
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.84
Consensus pattern (15 bp):
TTCTTTTTTTTTTTT
Found at i:4382535 original size:9 final size:9
Alignment explanation
Indices: 4382503--4382553 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
4382493 GAAATTCTTT
4382503 TTTTTTTTC
1 TTTTTTTTC
**
4382512 TTCTATTTTGA
1 TT-T-TTTTTC
4382523 TTTTTTTTC
1 TTTTTTTTC
4382532 -TTTTTTTC
1 TTTTTTTTC
4382540 TTTTTTTTC
1 TTTTTTTTC
4382549 TTTTT
1 TTTTT
4382554 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 8 0.23
9 19 0.54
10 2 0.06
11 6 0.17
ACGTcount: A:0.04, C:0.10, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:4382833 original size:19 final size:19
Alignment explanation
Indices: 4382802--4382843 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
4382792 AGGGGATTAT
4382802 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
4382821 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
4382840 AATA
1 AATA
4382844 AAGAAAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:4388638 original size:11 final size:12
Alignment explanation
Indices: 4388624--4388652 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4388614 AAAAAAAAAC
4388624 AAAAAAA-GGCA
1 AAAAAAAGGGCA
4388635 AAAAAAAGGGCA
1 AAAAAAAGGGCA
4388647 AAAAAA
1 AAAAAA
4388653 CAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGGCA
Found at i:4388638 original size:21 final size:20
Alignment explanation
Indices: 4388613--4388678 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
4388603 TTTTTTTCAA
*
4388613 AAAAAAAAAACAAAAAAAGGC
1 AAAAAAAAAGCAAAAAAA-GC
*
4388634 AAAAAAAAGGGCAAAAAAA-C
1 AAAAAAAA-AGCAAAAAAAGC
*
4388654 AAAAAAAAAGCCAAAAAAGC
1 AAAAAAAAAGCAAAAAAAGC
4388674 AAAAA
1 AAAAA
4388679 TTTCAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 8 0.21
20 15 0.38
21 8 0.21
22 8 0.21
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCAAAAAAAGC
Found at i:4388639 original size:12 final size:12
Alignment explanation
Indices: 4388624--4388671 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
4388614 AAAAAAAAAC
4388624 AAAAAAAGGCAA
1 AAAAAAAGGCAA
*
4388636 AAAAAAGGGC--
1 AAAAAAAGGCAA
4388646 AAAAAAA--CAA
1 AAAAAAAGGCAA
*
4388656 AAAAAAAGCCAA
1 AAAAAAAGGCAA
4388668 AAAA
1 AAAA
4388672 GCAAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
8 1 0.03
10 13 0.43
12 16 0.53
ACGTcount: A:0.77, C:0.10, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGCAA
Found at i:4396746 original size:12 final size:11
Alignment explanation
Indices: 4396719--4396762 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
4396709 GTGCTACAAA
4396719 AAAAAGCAACAAG
1 AAAAAG-AA-AAG
4396732 AAAGAAGAAAAG
1 AAA-AAGAAAAG
4396744 AAAAGAGAAAAG
1 AAAA-AGAAAAG
4396756 AAAAAGA
1 AAAAAGA
4396763 CTCCTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.14
12 17 0.59
13 5 0.17
14 3 0.10
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:4396818 original size:14 final size:15
Alignment explanation
Indices: 4396784--4396830 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
4396774 AATTTGGAGT
4396784 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
4396799 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
4396813 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
4396830 G
1 G
4396831 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:4399342 original size:41 final size:40
Alignment explanation
Indices: 4399281--4399357 Score: 127
Period size: 41 Copynumber: 1.9 Consensus size: 40
4399271 ACACCACTTT
*
4399281 TGGGATATCAAGGGACCTAAATATTCAGAGCAAATTTACA
1 TGGGATATCAAGGGACCTAAATATTAAGAGCAAATTTACA
*
4399321 TGGGCATATCAAGGGACCTAAATATTAAGGGCAAATT
1 TGGG-ATATCAAGGGACCTAAATATTAAGAGCAAATT
4399358 CAATGATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (40 bp):
TGGGATATCAAGGGACCTAAATATTAAGAGCAAATTTACA
Found at i:4404017 original size:15 final size:15
Alignment explanation
Indices: 4404006--4404034 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4403996 ACTCAAAAAG
4404006 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
4404021 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
4404035 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:4408303 original size:45 final size:49
Alignment explanation
Indices: 4408248--4408356 Score: 138
Period size: 51 Copynumber: 2.3 Consensus size: 49
4408238 ATGACTAATG
4408248 AATAAAATAATAATAAACTAAACAT-ATA-TATTAA-C-TC-TAATTCCT
1 AATAAAATAATAAT-AACTAAACATAATATTATTAACCATCTTAATTCCT
* *
4408293 AATAAAATAATAATAACTAAAGATAATATTTTTAACCCAATCTTAATTCCT
1 AATAAAATAATAATAACTAAACATAATATTATTAA-CC-ATCTTAATTCCT
4408344 AATAAAATAATAA
1 AATAAAATAATAA
4408357 ATATAATCCT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
44 9 0.16
45 17 0.31
46 5 0.09
48 1 0.02
50 2 0.04
51 21 0.38
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (49 bp):
AATAAAATAATAATAACTAAACATAATATTATTAACCATCTTAATTCCT
Found at i:4409416 original size:9 final size:9
Alignment explanation
Indices: 4409402--4409428 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4409392 AAGTATGGGT
4409402 AGAAATATC
1 AGAAATATC
4409411 AGAAATATC
1 AGAAATATC
4409420 AGAAATATC
1 AGAAATATC
4409429 CGAGTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
AGAAATATC
Found at i:4412043 original size:9 final size:9
Alignment explanation
Indices: 4412031--4412070 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
4412021 TTTTTTGAAA
4412031 TTTTGGCTT
1 TTTTGGCTT
4412040 TTTTGGCTT
1 TTTTGGCTT
* *
4412049 TTTTTGTTT
1 TTTTGGCTT
4412058 TTTTGG-TT
1 TTTTGGCTT
4412066 TTTTG
1 TTTTG
4412071 AAAACAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.00, C:0.05, G:0.20, T:0.75
Consensus pattern (9 bp):
TTTTGGCTT
Found at i:4412427 original size:11 final size:11
Alignment explanation
Indices: 4412411--4412441 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
4412401 ACAAGGTAAG
4412411 AAACAAGATTA
1 AAACAAGATTA
4412422 AAACAAGATTA
1 AAACAAGATTA
4412433 AAACAAGAT
1 AAACAAGAT
4412442 AAAGAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (11 bp):
AAACAAGATTA
Found at i:4412455 original size:21 final size:22
Alignment explanation
Indices: 4412411--4412452 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4412401 ACAAGGTAAG
*
4412411 AAACAAGATTAAAACAAGATTA
1 AAACAAGATTAAAAAAAGATTA
4412433 AAACAAGA-TAAAGAAAAGAT
1 AAACAAGATTAAA-AAAAGAT
4412453 AAAGGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.67, C:0.07, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATTAAAAAAAGATTA
Found at i:4412961 original size:25 final size:22
Alignment explanation
Indices: 4412932--4412977 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4412922 TTTTTAACCC
4412932 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
4412957 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
4412978 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:4427788 original size:19 final size:19
Alignment explanation
Indices: 4427764--4427809 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
4427754 GATAGGACAT
4427764 TATCCATCGATTTTCTACA
1 TATCCATCGATTTTCTACA
4427783 TATCCATCGATTTTCTACA
1 TATCCATCGATTTTCTACA
4427802 TATCCATC
1 TATCCATC
4427810 CATGCCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.04, T:0.41
Consensus pattern (19 bp):
TATCCATCGATTTTCTACA
Found at i:4430582 original size:30 final size:30
Alignment explanation
Indices: 4430548--4430604 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
4430538 GTTTTCATTC
* *
4430548 ATCATTTCATCTAGCATTTTCACGTGTAAG
1 ATCATTGCATCTAGCACTTTCACGTGTAAG
*
4430578 ATCATTGCATCTAGGACTTTCACGTGT
1 ATCATTGCATCTAGCACTTTCACGTGT
4430605 TGTTAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (30 bp):
ATCATTGCATCTAGCACTTTCACGTGTAAG
Found at i:4437662 original size:17 final size:17
Alignment explanation
Indices: 4437623--4437665 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
4437613 GTGCTACAAC
4437623 AAAA-AAAACAACAAGA
1 AAAAGAAAACAACAAGA
4437639 AAGAAGAAAACAA-AAGA
1 AA-AAGAAAACAACAAGA
4437656 GAAAAGAAAA
1 -AAAAGAAAA
4437666 AGACTCCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAACAAGA
Found at i:4441329 original size:13 final size:13
Alignment explanation
Indices: 4441311--4441344 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
4441301 ACTATCTATT
4441311 CATCACCACCTTC
1 CATCACCACCTTC
4441324 CATCACCACCTTC
1 CATCACCACCTTC
4441337 CATCACCA
1 CATCACCA
4441345 TTTTCACGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (13 bp):
CATCACCACCTTC
Found at i:4446389 original size:17 final size:17
Alignment explanation
Indices: 4446369--4446418 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
4446359 ATAAAGTTAG
4446369 TTCATTAATTAAACTAC
1 TTCATTAATTAAACTAC
* * *
4446386 TTCATAAATCAAACTAG
1 TTCATTAATTAAACTAC
*
4446403 TTCATTTATTAAACTA
1 TTCATTAATTAAACTA
4446419 ACTCTTAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (17 bp):
TTCATTAATTAAACTAC
Found at i:4449701 original size:17 final size:17
Alignment explanation
Indices: 4449681--4449733 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
4449671 TTAATAAAGT
4449681 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
4449698 TAGTTCATAAATCAAAC
1 TAGTTCATTAATTAAAC
*
4449715 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
4449732 TA
1 TA
4449734 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:4450068 original size:17 final size:17
Alignment explanation
Indices: 4450046--4450081 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4450036 TGATTTGGAT
4450046 GAGTTTGAGCCAAGGAA
1 GAGTTTGAGCCAAGGAA
4450063 GAGTTTGAGCCAAGGAA
1 GAGTTTGAGCCAAGGAA
4450080 GA
1 GA
4450082 TTCCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (17 bp):
GAGTTTGAGCCAAGGAA
Found at i:4453033 original size:17 final size:17
Alignment explanation
Indices: 4453013--4453065 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
4453003 TTAATAAAGT
4453013 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
4453030 TAGTTCATAAATCAAAC
1 TAGTTCATTAATTAAAC
*
4453047 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
4453064 TA
1 TA
4453066 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:4453400 original size:17 final size:17
Alignment explanation
Indices: 4453378--4453413 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4453368 TGATTTGGAT
4453378 GAGTTTGAGCCAAGGAA
1 GAGTTTGAGCCAAGGAA
4453395 GAGTTTGAGCCAAGGAA
1 GAGTTTGAGCCAAGGAA
4453412 GA
1 GA
4453414 TTCCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (17 bp):
GAGTTTGAGCCAAGGAA
Found at i:4456363 original size:17 final size:17
Alignment explanation
Indices: 4456343--4456395 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
4456333 TTAATAAAGT
4456343 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
4456360 TAGTTCATAAATCAAAC
1 TAGTTCATTAATTAAAC
*
4456377 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
4456394 TA
1 TA
4456396 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:4465115 original size:5 final size:5
Alignment explanation
Indices: 4465102--4465147 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
4465092 CTGGAGTACA
*
4465102 AAAAG AAAA- TAAA- AAAAG AAAAG AAAA- AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
4465148 AGCCAAGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 10 0.27
5 27 0.73
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:4465118 original size:14 final size:14
Alignment explanation
Indices: 4465101--4465147 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
4465091 ACTGGAGTAC
*
4465101 AAAAAGAAAA-TAA
1 AAAAAGAAAAGAAA
4465114 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
4465128 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
4465142 AGAAAA
1 A-AAAA
4465148 AGCCAAGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 10 0.32
14 17 0.55
15 4 0.13
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:4465123 original size:19 final size:19
Alignment explanation
Indices: 4465102--4465148 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
4465092 CTGGAGTACA
*
4465102 AAAAGAAAATAAA-AAAAG
1 AAAAGAAAAAAAAGAAAAG
4465120 AAAAGAAAAAAAAGAAAAG
1 AAAAGAAAAAAAAGAAAAG
4465139 AAAAGAAAAA
1 AAAAGAAAAA
4465149 GCCAAGGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAAAAAGAAAAG
Found at i:4478181 original size:24 final size:24
Alignment explanation
Indices: 4478162--4478208 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
4478152 CAAAAGCAAT
*
4478162 AAAAAAA-GAGAAAAAGAAAGAAG
1 AAAAAAATAAGAAAAAGAAAGAAG
4478185 AAAAAAATAAGAAAAAGAAA-AAG
1 AAAAAAATAAGAAAAAGAAAGAAG
4478208 A
1 A
4478209 CTCCTACAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (24 bp):
AAAAAAATAAGAAAAAGAAAGAAG
Found at i:4478204 original size:6 final size:6
Alignment explanation
Indices: 4478165--4478208 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
4478155 AAGCAATAAA
*
4478165 AAAAGAG AAAAAG AAAGAAG AAAAA- AATAAG AAAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
4478209 CTCCTACAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 4 0.12
6 19 0.58
7 10 0.30
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:4482677 original size:23 final size:24
Alignment explanation
Indices: 4482648--4482694 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
4482638 CAACAAAAGC
4482648 AACAAAAAAAGAA-AG-AAGAAAAA
1 AACAAAAAAA-AAGAGAAAGAAAAA
4482671 AACAAAAAAAAAGAGAAAGAAAAA
1 AACAAAAAAAAAGAGAAAGAAAAA
4482695 GACTCCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.09
23 12 0.55
24 8 0.36
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (24 bp):
AACAAAAAAAAAGAGAAAGAAAAA
Found at i:4482683 original size:21 final size:22
Alignment explanation
Indices: 4482652--4482693 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4482642 AAAAGCAACA
4482652 AAAAAAGAAAGAAGAAA-AAAAC
1 AAAAAAGAAAG-AGAAAGAAAAC
4482674 AAAAAA-AAAGAGAAAGAAAA
1 AAAAAAGAAAGAGAAAGAAAA
4482694 AGACTCCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAGAGAAAGAAAAC
Found at i:4485991 original size:11 final size:11
Alignment explanation
Indices: 4485977--4486007 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4485967 CTTATCATCT
4485977 AATCATCATTC
1 AATCATCATTC
*
4485988 AATCATCCTTC
1 AATCATCATTC
4485999 AATCATCAT
1 AATCATCAT
4486008 CAAGGCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (11 bp):
AATCATCATTC
Found at i:4486706 original size:17 final size:18
Alignment explanation
Indices: 4486676--4486710 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4486666 AAAAAAAGAT
4486676 AAAAAGAAATAAGAAAAA
1 AAAAAGAAATAAGAAAAA
*
4486694 AAAAAGAGA-AAGAAAAA
1 AAAAAGAAATAAGAAAAA
4486711 GACTCCTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAAAGAAATAAGAAAAA
Found at i:4491106 original size:15 final size:16
Alignment explanation
Indices: 4491088--4491121 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4491078 AAAAAAAGAC
*
4491088 AAAAAGAAAGAAGAAAA
1 AAAAAGAGA-AAGAAAA
4491105 AAAAAGAGAAAGAAAA
1 AAAAAGAGAAAGAAAA
4491121 A
1 A
4491122 GACTCCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAGAGAAAGAAAA
Found at i:4496673 original size:33 final size:33
Alignment explanation
Indices: 4496594--4496697 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
4496584 ATACAATCTG
* *
4496594 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
4496630 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
4496663 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
4496696 TC
1 TC
4496698 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:4500703 original size:33 final size:33
Alignment explanation
Indices: 4500624--4500727 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
4500614 ATACAATCTG
* *
4500624 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
4500660 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
4500693 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
4500726 TC
1 TC
4500728 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:4501246 original size:12 final size:11
Alignment explanation
Indices: 4501229--4501289 Score: 68
Period size: 12 Copynumber: 5.2 Consensus size: 11
4501219 GTGATGCAAC
4501229 AAAAGAAACAAA
1 AAAAGAAA-AAA
4501241 AAAAGAAAAAA
1 AAAAGAAAAAA
*
4501252 AGAAAGAAGAAA
1 A-AAAGAAAAAA
*
4501264 AAAACAAAAAA
1 AAAAGAAAAAA
4501275 AAAGAGAAAGAAA
1 AAA-AGAAA-AAA
4501288 AA
1 AA
4501290 GACTCCTACA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 15 0.36
12 22 0.52
13 5 0.12
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:4501257 original size:24 final size:26
Alignment explanation
Indices: 4501230--4501289 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
4501220 TGATGCAACA
* *
4501230 AAAGAAACAAAAA-AAGAAAAAA-AG
1 AAAGAAAAAAAAACAAAAAAAAAGAG
4501254 AAAGAAGAAAAAAACAAAAAAAAAGAG
1 AAAGAA-AAAAAAACAAAAAAAAAGAG
4501281 AAAGAAAAA
1 AAAGAAAAA
4501290 GACTCCTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 6 0.19
25 6 0.19
26 11 0.35
27 8 0.26
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAAAAACAAAAAAAAAGAG
Found at i:4501263 original size:27 final size:27
Alignment explanation
Indices: 4501231--4501286 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
4501221 GATGCAACAA
4501231 AAGAAACAAAA-AAAGAAAAAA-AGAAAG
1 AAGAAA-AAAACAAA-AAAAAAGAGAAAG
4501258 AAGAAAAAAACAAAAAAAAAGAGAAAG
1 AAGAAAAAAACAAAAAAAAAGAGAAAG
4501285 AA
1 AA
4501287 AAAGACTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (27 bp):
AAGAAAAAAACAAAAAAAAAGAGAAAG
Found at i:4501272 original size:23 final size:24
Alignment explanation
Indices: 4501230--4501289 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
4501220 TGATGCAACA
* *
4501230 AAAGAAACAAAAAAAGAAAAAAAGAA
1 AAAGAAA-AAAACAA-AAAAAAAGAG
4501256 AGAAGAAAAAAACAAAAAAAAAGAG
1 A-AAGAAAAAAACAAAAAAAAAGAG
4501281 AAAGAAAAA
1 AAAGAAAAA
4501290 GACTCCTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 8 0.26
25 10 0.32
26 7 0.23
27 6 0.19
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (24 bp):
AAAGAAAAAAACAAAAAAAAAGAG
Found at i:4512175 original size:35 final size:36
Alignment explanation
Indices: 4512128--4512195 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
4512118 ATTTATAAGT
4512128 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
4512163 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
4512196 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:4516198 original size:19 final size:20
Alignment explanation
Indices: 4516174--4516222 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
4516164 TGTAGGAGTA
4516174 TTTTTTTCTT-TTCTTT-TTG
1 TTTTTTT-TTCTTCTTTCTTG
4516193 TTTTTTTTTCTTCTTTCTTG
1 TTTTTTTTTCTTCTTTCTTG
4516213 TTGTTTTTTT
1 TT-TTTTTTT
4516223 TGTTGTAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.07
19 13 0.48
20 5 0.19
21 7 0.26
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (20 bp):
TTTTTTTTTCTTCTTTCTTG
Found at i:4516199 original size:20 final size:23
Alignment explanation
Indices: 4516174--4516223 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
4516164 TGTAGGAGTA
*
4516174 TTTTTTTC-T-TTTCTTTTTGTT
1 TTTTTTTCTTCTTTCTTGTTGTT
4516195 TTTTTTTCTTCTTTCTTGTTGTT
1 TTTTTTTCTTCTTTCTTGTTGTT
4516218 TTTTTT
1 TTTTTT
4516224 GTTGTAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 8 0.31
22 1 0.04
23 17 0.65
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (23 bp):
TTTTTTTCTTCTTTCTTGTTGTT
Found at i:4520938 original size:45 final size:45
Alignment explanation
Indices: 4520889--4520979 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
4520879 GCCAATCTTG
*
4520889 TCCAAACAAGAAATAGAAATAATGTTTTTAGTCAAACTAGACACA
1 TCCAAACAAGAAATAGAAATAATGTTCTTAGTCAAACTAGACACA
4520934 TCCAAACAAGAAATAGAAATAATGTTCTTAGTCAAACTAGACACA
1 TCCAAACAAGAAATAGAAATAATGTTCTTAGTCAAACTAGACACA
4520979 T
1 T
4520980 AATAACAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.24
Consensus pattern (45 bp):
TCCAAACAAGAAATAGAAATAATGTTCTTAGTCAAACTAGACACA
Found at i:4525528 original size:22 final size:22
Alignment explanation
Indices: 4525503--4525554 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
4525493 CTTAAAATGC
*
4525503 ATGCATGGACGTAGGTTACAAT
1 ATGCATGGACGAAGGTTACAAT
* *
4525525 ATGCATGGTCGAATGTTACAAT
1 ATGCATGGACGAAGGTTACAAT
*
4525547 TTGCATGG
1 ATGCATGG
4525555 CCTCATGGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (22 bp):
ATGCATGGACGAAGGTTACAAT
Found at i:4528475 original size:23 final size:23
Alignment explanation
Indices: 4528421--4528475 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
4528411 TTCAATTGGC
*
4528421 ACATTCTTTTGAATTTCAAGAGGT
1 ACATTC-TTTGAATGTCAAGAGGT
4528445 ACATTCTTTGAAATGTCAA-AGG-
1 ACATTCTTTG-AATGTCAAGAGGT
4528467 ACATGTCTT
1 ACAT-TCTT
4528476 GTGGATCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.14
23 11 0.39
24 13 0.46
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (23 bp):
ACATTCTTTGAATGTCAAGAGGT
Found at i:4528532 original size:24 final size:24
Alignment explanation
Indices: 4528485--4528535 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4528475 TGTGGATCAC
* *
4528485 CAAAAGTCATGTTTATTAATTCTT
1 CAAAAGACATGTTTATTAAGTCTT
* *
4528509 CAAAAGACATGTTTCTTGAGTCTT
1 CAAAAGACATGTTTATTAAGTCTT
4528533 CAA
1 CAA
4528536 CTTGAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (24 bp):
CAAAAGACATGTTTATTAAGTCTT
Found at i:4529708 original size:23 final size:25
Alignment explanation
Indices: 4529670--4529723 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
4529660 TCTTTTTCTT
4529670 TTTCTTCCTTTTTGAGTGCTTTGAA
1 TTTCTTCCTTTTTGAGTGCTTTGAA
* *
4529695 TTTCTT-C-TTTTGAGTTCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTGAA
4529718 TTTCTT
1 TTTCTT
4529724 TGCTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.15, G:0.13, T:0.63
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTGAA
Found at i:4531891 original size:23 final size:23
Alignment explanation
Indices: 4531865--4531918 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
4531855 ATATAAAGTC
4531865 TGGGTCTTTGCTCTCTATAGCAT
1 TGGGTCTTTGCTCTCTATAGCAT
*
4531888 TGGGTCTTTTCTCTCTATAGCAT
1 TGGGTCTTTGCTCTCTATAGCAT
*
4531911 TGGTTCTT
1 TGGGTCTT
4531919 CTTTGAGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (23 bp):
TGGGTCTTTGCTCTCTATAGCAT
Found at i:4532291 original size:23 final size:23
Alignment explanation
Indices: 4532265--4532317 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
4532255 AAATCCAGCA
4532265 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
4532288 AAGAAATTGAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
*
4532311 AAAAAAA
1 AAGAAAA
4532318 AAGAAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.64, C:0.13, G:0.13, T:0.09
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:4532329 original size:20 final size:20
Alignment explanation
Indices: 4532306--4532343 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4532296 GAAAGCACTC
4532306 AAAAGAAAAAA-AAAGAAAAG
1 AAAA-AAAAAAGAAAGAAAAG
4532326 AAAAAAAAAAGAAAGAAA
1 AAAAAAAAAAGAAAGAAA
4532344 GTTGAAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAGAAAGAAAAG
Found at i:4532332 original size:16 final size:16
Alignment explanation
Indices: 4532306--4532343 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
4532296 GAAAGCACTC
4532306 AAAAG-AAAAAAAAAG
1 AAAAGAAAAAAAAAAG
4532321 AAAAGAAAAAAAAAAG
1 AAAAGAAAAAAAAAAG
4532337 -AAAGAAA
1 AAAAGAAA
4532344 GTTGAAGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAG
Done.