Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000572.1 Hibiscus syriacus cultivar Beakdansim tig00001120_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: 2399138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1548421 original size:60 final size:60
Alignment explanation
Indices: 1548323--1548436 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 60
1548313 GATGGACCGT
* *
1548323 ACTGTGGTGCATGATGAGTAGATGGCGCCGGCGAGTGAGTCGGACCATGAGCCACCGGAG
1 ACTGCGGTGCATGATGAGTAGATGGCGCCGGCGAGTGAGTCGGACCATAAGCCACCGGAG
* *
1548383 ACTGCGGTGCATGATGAGTAGATGGCGCCGGTGAGTGAGTCGGTCCATAAGCCA
1 ACTGCGGTGCATGATGAGTAGATGGCGCCGGCGAGTGAGTCGGACCATAAGCCA
1548437 TGGGTGAGCC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.22, C:0.21, G:0.39, T:0.18
Consensus pattern (60 bp):
ACTGCGGTGCATGATGAGTAGATGGCGCCGGCGAGTGAGTCGGACCATAAGCCACCGGAG
Found at i:1557341 original size:2 final size:2
Alignment explanation
Indices: 1557334--1557365 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1557324 TTATACAAAT
1557334 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
1557366 ATTTTTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1565419 original size:2 final size:2
Alignment explanation
Indices: 1565412--1565440 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1565402 GTCAACTGTA
1565412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1565441 AATGATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1567772 original size:24 final size:24
Alignment explanation
Indices: 1567745--1567794 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1567735 CAATATCATC
1567745 CTTAGAATCATTATAATTGATCAA
1 CTTAGAATCATTATAATTGATCAA
1567769 CTTAGAATCATTATAATTGATCAA
1 CTTAGAATCATTATAATTGATCAA
1567793 CT
1 CT
1567795 CGCATGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (24 bp):
CTTAGAATCATTATAATTGATCAA
Found at i:1571723 original size:21 final size:21
Alignment explanation
Indices: 1571697--1571738 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1571687 GGAATTACAA
1571697 TGGCTGTAGGAATTTCAGCAG
1 TGGCTGTAGGAATTTCAGCAG
*
1571718 TGGCTGTAGGATTTTCAGCAG
1 TGGCTGTAGGAATTTCAGCAG
1571739 GTTTTGTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.31
Consensus pattern (21 bp):
TGGCTGTAGGAATTTCAGCAG
Found at i:1576544 original size:20 final size:20
Alignment explanation
Indices: 1576521--1576560 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1576511 GCACTGCTAC
1576521 GAGCCACAACGGACTGTTTT
1 GAGCCACAACGGACTGTTTT
1576541 GAGCCACAACGGACTGTTTT
1 GAGCCACAACGGACTGTTTT
1576561 TTACTTCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (20 bp):
GAGCCACAACGGACTGTTTT
Found at i:1603052 original size:18 final size:20
Alignment explanation
Indices: 1603017--1603059 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1603007 AGATATATAA
1603017 TTATACAAAATTAAACTT-T
1 TTATACAAAATTAAACTTCT
1603036 TTATA-AAAA-TAATACTTCT
1 TTATACAAAATTAA-ACTTCT
1603055 TTATA
1 TTATA
1603060 TCATTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.14
18 8 0.36
19 11 0.50
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATACAAAATTAAACTTCT
Found at i:1620897 original size:20 final size:21
Alignment explanation
Indices: 1620860--1620898 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1620850 TTGGATAGTT
*
1620860 TAATTGGATTTGAAATCCTGA
1 TAATTCGATTTGAAATCCTGA
1620881 TAATTCGATTT-AAATCCT
1 TAATTCGATTTGAAATCCT
1620899 AAAGAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (21 bp):
TAATTCGATTTGAAATCCTGA
Found at i:1623435 original size:14 final size:14
Alignment explanation
Indices: 1623416--1623442 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1623406 CAGTTGATAT
1623416 ATTTTTTGAATTTA
1 ATTTTTTGAATTTA
1623430 ATTTTTTGAATTT
1 ATTTTTTGAATTT
1623443 TTTAATCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
ATTTTTTGAATTTA
Found at i:1623588 original size:15 final size:15
Alignment explanation
Indices: 1623568--1623605 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1623558 AGTAGAGGGG
1623568 GAAATTAAATGTTAA
1 GAAATTAAATGTTAA
1623583 GAAATTAAATGTTAA
1 GAAATTAAATGTTAA
1623598 GAAATTAA
1 GAAATTAA
1623606 TCAATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (15 bp):
GAAATTAAATGTTAA
Found at i:1629701 original size:11 final size:10
Alignment explanation
Indices: 1629680--1629736 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
1629670 CATTTTTTAA
*
1629680 AAAAATAAAT
1 AAAAATGAAT
1629690 AAAAATGCAAT
1 AAAAATG-AAT
1629701 AAAAA-GAATT
1 AAAAATGAA-T
1629711 AAAAATGAAT
1 AAAAATGAAT
* *
1629721 AAAATTTAAT
1 AAAAATGAAT
1629731 AAAAAT
1 AAAAAT
1629737 ATAATGTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.68
11 11 0.28
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (10 bp):
AAAAATGAAT
Found at i:1630884 original size:21 final size:20
Alignment explanation
Indices: 1630851--1630894 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1630841 TTTTATTGAA
1630851 TTTTATTCATTTTAATTCAT
1 TTTTATTCATTTTAATTCAT
* *
1630871 TTTTATTGCATTTTTATTTAT
1 TTTTATT-CATTTTAATTCAT
1630892 TTT
1 TTT
1630895 AAAAAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTATTCATTTTAATTCAT
Found at i:1630893 original size:10 final size:10
Alignment explanation
Indices: 1630839--1630894 Score: 67
Period size: 10 Copynumber: 5.5 Consensus size: 10
1630829 TTTACATTAT
*
1630839 ATTTTTATTG
1 ATTTTTATTC
*
1630849 AATTTTATTC
1 ATTTTTATTC
*
1630859 ATTTTAATTC
1 ATTTTTATTC
1630869 ATTTTTATTGC
1 ATTTTTATT-C
*
1630880 ATTTTTATTT
1 ATTTTTATTC
1630890 ATTTT
1 ATTTT
1630895 AAAAAATGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
10 29 0.74
11 10 0.26
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:1635072 original size:31 final size:32
Alignment explanation
Indices: 1635027--1635086 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
1635017 TTAATCCTTT
*
1635027 AATTTTATATTTATCTATTTTATAAAAATTAA
1 AATTTTATATTTATCAATTTTATAAAAATTAA
*
1635059 AATTTTA-ATTTATCAATTTTATTAAAAT
1 AATTTTATATTTATCAATTTTATAAAAAT
1635087 CACATCGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (32 bp):
AATTTTATATTTATCAATTTTATAAAAATTAA
Found at i:1647779 original size:3 final size:3
Alignment explanation
Indices: 1647771--1647798 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1647761 TGCTCATCTT
1647771 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
1647799 AGGCCTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:1654970 original size:18 final size:17
Alignment explanation
Indices: 1654944--1654977 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1654934 TTAATTAAAT
*
1654944 AATATAATTACATAATTC
1 AATAGAATTAC-TAATTC
1654962 AATAGAATTACTAATT
1 AATAGAATTACTAATT
1654978 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (17 bp):
AATAGAATTACTAATTC
Found at i:1655189 original size:24 final size:25
Alignment explanation
Indices: 1655157--1655205 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
1655147 ATTAAAAAAT
*
1655157 AAATTATATATTATTTTTT-TTTTA
1 AAATAATATATTATTTTTTGTTTTA
*
1655181 AAATAATATATTCTTTTTTGTTTTA
1 AAATAATATATTATTTTTTGTTTTA
1655206 TGTTCCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
AAATAATATATTATTTTTTGTTTTA
Found at i:1665923 original size:4 final size:4
Alignment explanation
Indices: 1665914--1665941 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1665904 AGAGGTAATT
1665914 CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC
1665942 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (4 bp):
CATC
Found at i:1667327 original size:31 final size:31
Alignment explanation
Indices: 1667291--1667349 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1667281 AACTTAAAAG
* *
1667291 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1667322 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1667350 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1667400 original size:22 final size:22
Alignment explanation
Indices: 1667374--1667416 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1667364 TAATAAATTA
1667374 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1667396 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
1667417 CTAATACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1667428 original size:54 final size:54
Alignment explanation
Indices: 1667364--1667614 Score: 258
Period size: 54 Copynumber: 4.6 Consensus size: 54
1667354 ACAACTACAA
1667364 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
* * ** *
1667418 TAATACATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATTCATAC
** * ** * ** ** *
1667475 TTTTAAAATAAAT-CAATCCATACAAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATTCATAC
1667530 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA-TCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC-ATAC
1667584 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
1667615 CAACTACAAT
Statistics
Matches: 156, Mismatches: 30, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
53 1 0.01
54 100 0.64
55 13 0.08
56 10 0.06
57 12 0.08
58 20 0.13
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
Found at i:1667471 original size:80 final size:80
Alignment explanation
Indices: 1667379--1667695 Score: 494
Period size: 80 Copynumber: 3.9 Consensus size: 80
1667369 AATTATTTAA
* *
1667379 AATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACTAATACATTATTTAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCT-ATACAAATAAATTATTTAAAATAAATCAA
1667443 TCCATACAACTACAAT
65 TCCATACAACTACAAT
*
1667459 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAAT
*
1667524 CCATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
*
1667543 AAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCA
1667608 ATCCATACAACTACAAT
64 ATCCATACAACTACAAT
*
1667625 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAAT
1667690 CCATAC
66 CCATAC
1667696 TAATAAATTA
Statistics
Matches: 219, Mismatches: 9, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
80 139 0.63
81 2 0.01
82 2 0.01
84 2 0.01
85 2 0.01
86 72 0.33
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:1667505 original size:22 final size:22
Alignment explanation
Indices: 1667432--1667505 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
1667422 ACATTATTTA
*
1667432 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAA--A-T
***
1667457 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACAAAT
1667479 AAAATAAATCAATCCATACAAAT
1 -AAATAAATCAATCCATACAAAT
1667502 AAAT
1 AAAT
1667506 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
25 1 0.03
26 16 0.41
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:1667515 original size:32 final size:32
Alignment explanation
Indices: 1667476--1667617 Score: 187
Period size: 32 Copynumber: 4.8 Consensus size: 32
1667466 CAATCCATAT
1667476 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
1667508 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
1667540 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
1667562 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
1667594 TTTAAAATAAATCAATCCATACAA
1 TTTAAAATAAATCAATCCATACAA
1667618 CTACAATAAT
Statistics
Matches: 96, Mismatches: 4, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
22 16 0.17
23 1 0.01
24 1 0.01
26 3 0.03
28 3 0.03
30 1 0.01
31 2 0.02
32 69 0.72
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:1667550 original size:166 final size:166
Alignment explanation
Indices: 1667364--1667726 Score: 683
Period size: 166 Copynumber: 2.2 Consensus size: 166
1667354 ACAACTACAA
*
1667364 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACTAATACATTA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTA
1667428 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
65 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1667493 CATACAAATAAATTATTTAAAATAAATCAATCCATAC
130 CATACAAATAAATTATTTAAAATAAATCAATCCATAC
1667530 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
* *
1667595 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCT
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
1667660 ATACAAATAAATTATTTAAAATAAATCAATCCATAC
131 ATACAAATAAATTATTTAAAATAAATCAATCCATAC
1667696 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
1667727 CAACTACAAT
Statistics
Matches: 193, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
166 192 0.99
167 1 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (166 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATACAAATAAATTATTTAAAATAAATCAATCCATAC
Found at i:1667591 original size:22 final size:22
Alignment explanation
Indices: 1667542--1667590 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1667532 ATAAATTATT
**
1667542 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1667564 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
1667587 TAAA
1 TAAA
1667591 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1667629 original size:112 final size:111
Alignment explanation
Indices: 1667476--1667748 Score: 311
Period size: 112 Copynumber: 2.4 Consensus size: 111
1667466 CAATCCATAT
* *
1667476 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACAACTACA--A--T--AATAAATCAATCCATACTAATAAATTAT
*
1667541 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
60 TTAAAATAAATCAATCCATA-TTTAAAATAAATCAATCAATACTAATAAATTA
* * * *
1667594 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA--CT--AATAAAT-TATT
* * * *
1667659 T-ATACAAATAAAT---TATTTAAAATAAATCAATCCATACTAATAAATTA
61 TAAAATAAATCAATCCATATTTAAAATAAATCAATCAATACTAATAAATTA
1667706 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATC
1667749 TGTTGAGTTA
Statistics
Matches: 140, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
112 89 0.64
113 2 0.01
114 2 0.01
116 17 0.12
117 3 0.02
118 27 0.19
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (111 bp):
TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAATTATTTAAAA
TAAATCAATCCATATTTAAAATAAATCAATCAATACTAATAAATTA
Found at i:1667681 original size:32 final size:32
Alignment explanation
Indices: 1667642--1667729 Score: 158
Period size: 32 Copynumber: 2.8 Consensus size: 32
1667632 CAATCTATAT
*
1667642 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
1667674 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
1667706 TTTAAAATAAATCAATCCATACAA
1 TTTAAAATAAATCAATCCATACAA
1667730 CTACAATAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:1668854 original size:22 final size:22
Alignment explanation
Indices: 1668828--1668930 Score: 89
Period size: 22 Copynumber: 4.5 Consensus size: 22
1668818 TAAAAAATTA
*
1668828 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATAT
1668850 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
1668873 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
1668897 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1668919 TTTATAATAAAT
1 TTTAAAATAAAT
1668931 TATTTTAAAA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
22 34 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1668902 original size:15 final size:15
Alignment explanation
Indices: 1668873--1668960 Score: 97
Period size: 15 Copynumber: 5.5 Consensus size: 15
1668863 AATCCATACT
1668873 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1668887 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1668902 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
1668924 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1668939 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1668954 AATAAAT
1 AATAAAT
1668961 AACCTTATTA
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
14 9 0.14
15 37 0.58
17 1 0.02
18 3 0.05
19 3 0.05
20 1 0.02
22 10 0.16
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1668957 original size:52 final size:47
Alignment explanation
Indices: 1668793--1668983 Score: 203
Period size: 54 Copynumber: 3.9 Consensus size: 47
1668783 ACACAATCCA
* *
1668793 TATTTTAAAATAAATCAATCCATACTAAAAAATTATTTAAAATAAATCAATCT
1 TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAAT--A--AA--T
*
1668846 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 -TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAAT
1668894 TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAATCCATA----ATAATAAATTA-TTTAAAATAAAT
*
1668946 TATTTTAAAATAAAT-AA-CC-T--TATTAAATTATTTAAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAAT
1668984 TATTTTAATA
Statistics
Matches: 129, Mismatches: 3, Indels: 22
0.84 0.02 0.14
Matches are distributed among these distances:
42 8 0.06
43 9 0.07
47 24 0.19
48 1 0.01
49 1 0.01
50 4 0.03
51 12 0.09
52 28 0.22
54 42 0.33
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (47 bp):
TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAAT
Found at i:1672129 original size:12 final size:12
Alignment explanation
Indices: 1672112--1672162 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1672102 TTCAAAGAGG
1672112 TTTTATATTTAA
1 TTTTATATTTAA
1672124 TTTTATA-TTATA
1 TTTTATATTTA-A
*
1672136 TTTGAT-TTTAA
1 TTTTATATTTAA
1672147 TTTTA-ATATTAA
1 TTTTATAT-TTAA
1672159 TTTT
1 TTTT
1672163 TAAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:1672216 original size:23 final size:24
Alignment explanation
Indices: 1672151--1672211 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
1672141 TTTTAATTTT
1672151 AATATTAATTTTTAAAATAAATTA
1 AATATTAATTTTTAAAATAAATTA
1672175 AATATTAATTTTTAAAATAAATTA
1 AATATTAATTTTTAAAATAAATTA
1672199 AATATTAATTTTT
1 AATATTAATTTTT
1672212 TAATATTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATATTAATTTTTAAAATAAATTA
Found at i:1672561 original size:22 final size:23
Alignment explanation
Indices: 1672534--1672585 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1672524 AATATTTTCT
*
1672534 AAAAATAT-CATATA-ATTATAAA
1 AAAAATATGAATATATATT-TAAA
1672556 AAAAATTATGAATATATATTTAAA
1 AAAAA-TATGAATATATATTTAAA
1672580 AAAAAT
1 AAAAAT
1672586 TAAAAGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.19
23 4 0.15
24 14 0.54
25 3 0.12
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAATATGAATATATATTTAAA
Found at i:1672796 original size:31 final size:31
Alignment explanation
Indices: 1672759--1672818 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1672749 TAGTTGTATG
* *
1672759 AATTATTTAAATTTCAATATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGCAAAACTAA
1672790 AATTATTTAAATCTCAATATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
1672819 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAA
Found at i:1675790 original size:21 final size:21
Alignment explanation
Indices: 1675761--1675817 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
1675751 GAATTAATTA
* *
1675761 AATTAATTTAATTAATATTTT
1 AATTTATTTAATTAATATTGT
* **
1675782 AATTTATTTCATTTTTATTGT
1 AATTTATTTAATTAATATTGT
1675803 AATTTCAATTTAATT
1 AATTT--ATTTAATT
1675818 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 21 0.75
23 7 0.25
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (21 bp):
AATTTATTTAATTAATATTGT
Found at i:1676052 original size:32 final size:32
Alignment explanation
Indices: 1676016--1676076 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1676006 TTAATTTGAC
1676016 TTTGATAATTAAATCAATTAAATTTATTTATT
1 TTTGATAATTAAATCAATTAAATTTATTTATT
* * * *
1676048 TTTGATATTTTAATCAATTTATTTTATTT
1 TTTGATAATTAAATCAATTAAATTTATTT
1676077 GTATATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (32 bp):
TTTGATAATTAAATCAATTAAATTTATTTATT
Found at i:1682582 original size:60 final size:60
Alignment explanation
Indices: 1682509--1682623 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
1682499 GGTATGACTC
* * * *
1682509 TCATTTTAAATTAGCGCCT-AAACTT-TTAATTATTTTAATTTCATCCATAAACTATTACTA
1 TCATTCTAAATTAG-GCCTCAAACTTGTGAA-CATTTAAATTTCATCCATAAACTATTACTA
* *
1682569 TCATTCTAAATTAGTCCTCAAACTTGTGAACATTTAAATTTCATCCCTAAACTAT
1 TCATTCTAAATTAGGCCTCAAACTTGTGAACATTTAAATTTCATCCATAAACTAT
1682624 GACCTTAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.06
60 41 0.87
61 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (60 bp):
TCATTCTAAATTAGGCCTCAAACTTGTGAACATTTAAATTTCATCCATAAACTATTACTA
Found at i:1682636 original size:60 final size:61
Alignment explanation
Indices: 1682540--1682676 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 61
1682530 ACTTTTAATT
* * * * *
1682540 ATTTTAATTTCATCCATAAACTATTACTATCATTCTAAATT-AGTCCTCAAAC-TTGTGAAC
1 ATTTAAATTTCATCCCTAAACTATGACTATCATTCTAAATTGA-TCCCCAAACTTTGTAAAC
*
1682600 ATTTAAATTTCATCCCTAAACTATGACCT-T-AGTTCTAAATTGATCCCCAAACTTTTTAAAC
1 ATTTAAATTTCATCCCTAAACTATGA-CTATCA-TTCTAAATTGATCCCCAAACTTTGTAAAC
**
1682661 ATTCCAATTTCATCCC
1 ATTTAAATTTCATCCC
1682677 AAATTATACA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 1 0.02
60 41 0.63
61 23 0.35
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (61 bp):
ATTTAAATTTCATCCCTAAACTATGACTATCATTCTAAATTGATCCCCAAACTTTGTAAAC
Found at i:1682943 original size:59 final size:59
Alignment explanation
Indices: 1682797--1682945 Score: 133
Period size: 59 Copynumber: 2.5 Consensus size: 59
1682787 TTTGGATGAA
* * * *
1682797 TTTATGGAAGAAATTGGAATATTCAAAAGTTTGGGACCAATTTAGAATCAAGGTCATAG
1 TTTAGGGATGAAATTGGAATATTAAAAAGTTGGGGACCAATTTAGAATCAAGGTCATAG
* * * * * ** *
1682856 TTTAGGGATGAAATTAGACTCTTTAAAAGTTCGGGGACTAATTTAG--TTGAGATTCATAG
1 TTTAGGGATGAAATTGGAATATTAAAAAGTT-GGGGACCAATTTAGAATCAAG-GTCATAG
*
1682915 TTT-GAGTATGAAATTGGAATATTAAAAAGTT
1 TTTAG-GGATGAAATTGGAATATTAAAAAGTT
1682946 TAAAGATGAA
Statistics
Matches: 71, Mismatches: 16, Indels: 6
0.76 0.17 0.06
Matches are distributed among these distances:
58 4 0.06
59 55 0.77
60 12 0.17
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (59 bp):
TTTAGGGATGAAATTGGAATATTAAAAAGTTGGGGACCAATTTAGAATCAAGGTCATAG
Found at i:1694095 original size:23 final size:23
Alignment explanation
Indices: 1694076--1694120 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1694066 TATGTACTTC
*
1694076 TGTGTTGAATCATTCAGTACTGT
1 TGTGTTGAATCAATCAGTACTGT
* *
1694099 TTTGTTGAATCAATCAGCACTG
1 TGTGTTGAATCAATCAGTACTG
1694121 AATCATTCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (23 bp):
TGTGTTGAATCAATCAGTACTGT
Found at i:1694651 original size:15 final size:15
Alignment explanation
Indices: 1694631--1694717 Score: 67
Period size: 15 Copynumber: 6.1 Consensus size: 15
1694621 TATCGATGAA
1694631 TTTTATATAAATAAT
1 TTTTATATAAATAAT
* *
1694646 TTTTATTTAAGT-A-
1 TTTTATATAAATAAT
* *
1694659 -TAT-TATAGATGAAT
1 TTTTATATAAAT-AAT
*
1694673 TTGTATATAAATAAT
1 TTTTATATAAATAAT
*
1694688 TTGTATATAAATAAT
1 TTTTATATAAATAAT
*
1694703 TTTTAT-TTAATAAT
1 TTTTATATAAATAAT
1694717 T
1 T
1694718 AGAATTTCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
11 4 0.07
12 2 0.04
13 1 0.02
14 9 0.16
15 35 0.61
16 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTTATATAAATAAT
Found at i:1694716 original size:14 final size:15
Alignment explanation
Indices: 1694670--1694717 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1694660 ATTATAGATG
1694670 AATTTGTATATAAAT
1 AATTTGTATATAAAT
1694685 AATTTGTATATAAAT
1 AATTTGTATATAAAT
* *
1694700 AATTTTTAT-TTAAT
1 AATTTGTATATAAAT
1694714 AATT
1 AATT
1694718 AGAATTTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (15 bp):
AATTTGTATATAAAT
Found at i:1700424 original size:16 final size:13
Alignment explanation
Indices: 1700376--1700417 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1700366 TCAATTTTAT
*
1700376 AAAAT-TTTATAA
1 AAAATATTTAAAA
1700388 AAAATA-TTAAAA
1 AAAATATTTAAAA
1700400 AAAATATTTAAAA
1 AAAATATTTAAAA
1700413 GAAAA
1 -AAAA
1700418 CTCATTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 16 0.62
13 6 0.23
14 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AAAATATTTAAAA
Found at i:1701059 original size:2 final size:2
Alignment explanation
Indices: 1701054--1701088 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1701044 TAATACATAC
1701054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1701089 ATTTTCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1709505 original size:3 final size:3
Alignment explanation
Indices: 1709492--1709571 Score: 151
Period size: 3 Copynumber: 26.3 Consensus size: 3
1709482 TAATTGTTAA
1709492 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1709538 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1709572 CATTCTCTGA
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 73 0.96
4 3 0.04
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:1715119 original size:16 final size:16
Alignment explanation
Indices: 1715098--1715128 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1715088 TAGTTTAATT
*
1715098 TAAATAATTATTTTTA
1 TAAATAAATATTTTTA
1715114 TAAATAAATATTTTT
1 TAAATAAATATTTTT
1715129 TTTAAAAATT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAATAAATATTTTTA
Found at i:1715130 original size:19 final size:20
Alignment explanation
Indices: 1715098--1715137 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1715088 TAGTTTAATT
*
1715098 TAAATAATTATTTTTATAAA
1 TAAATAATTATTTTTAAAAA
*
1715118 TAAAT-ATTTTTTTTAAAAA
1 TAAATAATTATTTTTAAAAA
1715137 T
1 T
1715138 TAGAACGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAATAATTATTTTTAAAAA
Found at i:1719559 original size:2 final size:2
Alignment explanation
Indices: 1719507--1719545 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1719497 TCCCTCTATC
1719507 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 A
1719546 AAGAAATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1722871 original size:21 final size:21
Alignment explanation
Indices: 1722822--1722865 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1722812 GCGCAATACT
*
1722822 GGAGGTGGCTGTGGCGGCGGC
1 GGAGGTGGCTGTGGTGGCGGC
1722843 GGAGGTGGCTGTGGTGGCGGC
1 GGAGGTGGCTGTGGTGGCGGC
1722864 GG
1 GG
1722866 CTGTGGTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.05, C:0.16, G:0.64, T:0.16
Consensus pattern (21 bp):
GGAGGTGGCTGTGGTGGCGGC
Found at i:1739978 original size:21 final size:20
Alignment explanation
Indices: 1739954--1739998 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1739944 AAAAAAACCG
1739954 AACCTAACAGCGAAAATCTAA
1 AACC-AACAGCGAAAATCTAA
*
1739975 AACCGACAGCGAAAATCTAA
1 AACCAACAGCGAAAATCTAA
1739995 AACC
1 AACC
1739999 GAATTAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.51, C:0.27, G:0.11, T:0.11
Consensus pattern (20 bp):
AACCAACAGCGAAAATCTAA
Found at i:1739983 original size:20 final size:20
Alignment explanation
Indices: 1739960--1740000 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1739950 ACCGAACCTA
1739960 ACAGCGAAAATCTAAAACCG
1 ACAGCGAAAATCTAAAACCG
1739980 ACAGCGAAAATCTAAAACCG
1 ACAGCGAAAATCTAAAACCG
1740000 A
1 A
1740001 ATTAAATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (20 bp):
ACAGCGAAAATCTAAAACCG
Found at i:1741580 original size:22 final size:23
Alignment explanation
Indices: 1741533--1741588 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1741523 AATTTAGGAT
* * *
1741533 TTTAAAAGATTAGGGTTTGTAGA
1 TTTAAAAGTTTAAGGTATGTAGA
1741556 TTTAAAAGTTTAAGGTAT-TAGA
1 TTTAAAAGTTTAAGGTATGTAGA
1741578 TTTAAATAGTT
1 TTTAAA-AGTT
1741589 GATTGGGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.43
Consensus pattern (23 bp):
TTTAAAAGTTTAAGGTATGTAGA
Found at i:1744793 original size:23 final size:23
Alignment explanation
Indices: 1744756--1744814 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1744746 TTAATTGTTG
1744756 AATCTTA-TTTTATAATCTTTTA
1 AATCTTATTTTTATAATCTTTTA
1744778 AATCTTATTTTTATAATCTTTTA
1 AATCTTATTTTTATAATCTTTTA
1744801 AATCTTATTTTTAT
1 AATCTTATTTTTAT
1744815 TATCAATACT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 7 0.19
23 29 0.81
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (23 bp):
AATCTTATTTTTATAATCTTTTA
Found at i:1745177 original size:12 final size:12
Alignment explanation
Indices: 1745138--1745178 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1745128 TAAAAATAGA
*
1745138 TGTTATCGATTT
1 TGTTATTGATTT
1745150 TGTTATT--TTT
1 TGTTATTGATTT
1745160 T-TTATTGATTT
1 TGTTATTGATTT
1745171 TGTTATTG
1 TGTTATTG
1745179 TTGGGTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
9 5 0.20
10 4 0.16
11 4 0.16
12 12 0.48
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.68
Consensus pattern (12 bp):
TGTTATTGATTT
Found at i:1749696 original size:16 final size:17
Alignment explanation
Indices: 1749669--1749701 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1749659 ATAAATTAAA
1749669 TATTTAAATTAAAATCT
1 TATTTAAATTAAAATCT
*
1749686 TATTT-AATTAATATCT
1 TATTTAAATTAAAATCT
1749702 GAATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTAAATTAAAATCT
Found at i:1752734 original size:42 final size:42
Alignment explanation
Indices: 1752666--1752758 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
1752656 ATCGCGTTGT
*
1752666 GATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTAATTGC
1 GATTTTCCATTTCGCGCTGCGATAGTCTACAGTTGTAATTGC
* **
1752708 GATTTTCCATTTCGCGCTGCGGTAGTCTACAGTTGTCGTTGC
1 GATTTTCCATTTCGCGCTGCGATAGTCTACAGTTGTAATTGC
1752750 GATTTTCCA
1 GATTTTCCA
1752759 AATTCGTTGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.40
Consensus pattern (42 bp):
GATTTTCCATTTCGCGCTGCGATAGTCTACAGTTGTAATTGC
Found at i:1752767 original size:19 final size:19
Alignment explanation
Indices: 1752743--1752809 Score: 134
Period size: 19 Copynumber: 3.5 Consensus size: 19
1752733 TCTACAGTTG
1752743 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
1752762 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
1752781 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
1752800 TCGTTGCGAT
1 TCGTTGCGAT
1752810 AGTTAAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1753594 original size:21 final size:21
Alignment explanation
Indices: 1753570--1753623 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1753560 GAAATGGAAA
*
1753570 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
1753591 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1753612 ATCGCAACGCGA
1 ATCGCAACGCGA
1753624 AATGCGCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1753684 original size:21 final size:21
Alignment explanation
Indices: 1753644--1753684 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1753634 GAAATGGAAA
** *
1753644 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1753665 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1753685 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1753754 original size:22 final size:22
Alignment explanation
Indices: 1753726--1753819 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 22
1753716 AATTTGCAAA
*
1753726 ATCGCAACGACATCTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
1753748 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1753770 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
1753789 ATCGCAACGACAACTGTAGGCT
1 ATCGCAACGACAACTGTAGACT
1753811 ATCGCAACG
1 ATCGCAACG
1753820 CGAAATGCAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 13 0.23
20 2 0.04
21 2 0.04
22 40 0.70
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1754535 original size:182 final size:181
Alignment explanation
Indices: 1754316--1754906 Score: 785
Period size: 182 Copynumber: 3.3 Consensus size: 181
1754306 ATACAAATGA
* * * * ** *
1754316 AAAATATATCGCTTCATAACAATATTACAGGTAAAAATATGACAATACCGGTCTCAAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAA
1754381 AATCGGTAAAATGCTACCGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTC
66 AA-CGGTAAAATGCTACCGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTC
1754446 TGAATTTAAAAGAGAAGAAGTTATAGCGACTAAAAAGTGTCGACACTTTATG
130 TGAATTTAAAAGAGAAGAAGTTATAGCGACTAAAAAGTGTCGACACTTTATG
* * *
1754498 AAAATGTATCGATCTATAACAATATAACAACTAAAAATATGACAAAATCGGTTTCAAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAA
* * * * *
1754563 AACAGGT-AAATAACTACCGGATATATTGAAAGTGTCGATATTTTAATATAAATATCGACACTTT
66 AAC-GGTAAAAT-GCTACCGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* * * * * *
1754627 -TGAAATTTAAAAGGGAAGAAGTTATAGTGTCTATAAAGTGTCGATACTTTA-A
129 CTG-AATTTAAAAGAGAAGAAGTTATAGCGACTAAAAAGTGTCGACACTTTATG
** * * * **
1754679 AAAAAATATTGATCCATAATAATATTACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAA
* * * *
1754744 ACCGGTAAAATGCTA-CTAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATTGACAATTTC
66 AACGGTAAAATGCTACCGA-ATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTC
* *
1754808 TGAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATG
130 TGAATTTAAAAGAGAAGAAGTTATAGCGACTAAAAAGTGTCGACACTTTATG
* *
1754860 AAAATGTATCGATCGATAACAATATAACAACTAAAAATATGAGAAAA
1 AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAA
1754907 TAGGTCAAAA
Statistics
Matches: 346, Mismatches: 56, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
179 1 0.00
180 87 0.25
181 108 0.31
182 150 0.43
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (181 bp):
AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAA
AACGGTAAAATGCTACCGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCT
GAATTTAAAAGAGAAGAAGTTATAGCGACTAAAAAGTGTCGACACTTTATG
Found at i:1764464 original size:30 final size:29
Alignment explanation
Indices: 1764384--1764503 Score: 93
Period size: 30 Copynumber: 4.1 Consensus size: 29
1764374 TACCCTAAGG
1764384 GAACATCTTA-GGCCTG-AGAGCCTACCAA
1 GAACATCTTAGGGCC-GCAGAGCCTACCAA
* * ** *
1764412 GATAGAT-TTTGGGCCGTGGGGCCTACCTAA
1 GA-ACATCTTAGGGCCGCAGAGCCTACC-AA
* *
1764442 GAACATCTTAGGGCCGCAGGGCCTACCGA
1 GAACATCTTAGGGCCGCAGAGCCTACCAA
* *
1764471 GAATGATCTCAGGGCCGCAGAGCCTACCTAA
1 GAA-CATCTTAGGGCCGCAGAGCCTACC-AA
1764502 GA
1 GA
1764504 GTCACATTAG
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
28 5 0.07
29 22 0.31
30 42 0.58
31 3 0.04
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (29 bp):
GAACATCTTAGGGCCGCAGAGCCTACCAA
Found at i:1765526 original size:12 final size:12
Alignment explanation
Indices: 1765509--1765536 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1765499 AACGGTCAAC
1765509 GGTCAACGGTCG
1 GGTCAACGGTCG
1765521 GGTCAACGGTCG
1 GGTCAACGGTCG
1765533 GGTC
1 GGTC
1765537 GGGTCAGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:1765526 original size:19 final size:19
Alignment explanation
Indices: 1765502--1765552 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1765492 GAAAGTCAAC
1765502 GGTCAACGGTCAACGGTCG
1 GGTCAACGGTCAACGGTCG
*
1765521 GGTCAACGGTC--GGGTCG
1 GGTCAACGGTCAACGGTCG
1765538 GGTCAGACCGGTCAA
1 GGTCA-A-CGGTCAA
1765553 ACCGATTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 10 0.37
18 1 0.04
19 16 0.59
ACGTcount: A:0.20, C:0.25, G:0.39, T:0.16
Consensus pattern (19 bp):
GGTCAACGGTCAACGGTCG
Found at i:1765556 original size:9 final size:9
Alignment explanation
Indices: 1765538--1765636 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
1765528 GGTCGGGTCG
*
1765538 GGTCAGACC
1 GGTCAAACC
1765547 GGTCAAACC
1 GGTCAAACC
* *
1765556 GATTCAGACC
1 G-GTCAAACC
1765566 GGTCAAACC
1 GGTCAAACC
*
1765575 GGTTCGAACC
1 GG-TCAAACC
*
1765585 GGTTGAAACC
1 GG-TCAAACC
1765595 GGTCAAACC
1 GGTCAAACC
1765604 GGTCAGAACC
1 GGTCA-AACC
*
1765614 GGTTGAAAACC
1 GG-T-CAAACC
1765625 GGTCAAACC
1 GGTCAAACC
1765634 GGT
1 GGT
1765637 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1765562 original size:19 final size:19
Alignment explanation
Indices: 1765540--1765637 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
1765530 TCGGGTCGGG
*
1765540 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
1765559 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
1765578 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
1765597 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
1765617 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
1765637 T
1 T
1765638 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1765595 original size:29 final size:31
Alignment explanation
Indices: 1765563--1765637 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
1765553 ACCGATTCAG
1765563 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
1765592 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
1765622 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
1765638 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:1771898 original size:32 final size:31
Alignment explanation
Indices: 1771862--1771938 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1771852 TGGGGCCGTG
*
1771862 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
1771894 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
1771925 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1771939 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:1771921 original size:63 final size:63
Alignment explanation
Indices: 1771815--1771938 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
1771805 CCCTAAGGGA
* ** ** *
1771815 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTTGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
1771878 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
1771939 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:1772820 original size:7 final size:7
Alignment explanation
Indices: 1772808--1772850 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
1772798 GTCAAAGAAA
1772808 GTCAACG
1 GTCAACG
1772815 GTCAACG
1 GTCAACG
1772822 GTCAACG
1 GTCAACG
1772829 GTCAACG
1 GTCAACG
*
1772836 GTC--GG
1 GTCAACG
1772841 GTCAACG
1 GTCAACG
1772848 GTC
1 GTC
1772851 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 4 0.12
7 28 0.88
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1772845 original size:12 final size:12
Alignment explanation
Indices: 1772814--1772899 Score: 99
Period size: 12 Copynumber: 7.3 Consensus size: 12
1772804 GAAAGTCAAC
*
1772814 GGTCAACGGTCAAC
1 GGTCAACGGTC--G
1772828 GGTCAACGGTCG
1 GGTCAACGGTCG
1772840 GGTCAACGGTCG
1 GGTCAACGGTCG
*
1772852 GGTC--GGGTCG
1 GGTCAACGGTCG
1772862 GGTCAACGGTCG
1 GGTCAACGGTCG
*
1772874 GGTC--GGGTCG
1 GGTCAACGGTCG
1772884 GGTCAACGGTCG
1 GGTCAACGGTCG
1772896 GGTC
1 GGTC
1772900 GTGTCAGACC
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
10 18 0.29
12 34 0.54
14 11 0.17
ACGTcount: A:0.14, C:0.24, G:0.44, T:0.17
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:1772863 original size:22 final size:22
Alignment explanation
Indices: 1772835--1772900 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
1772825 AACGGTCAAC
1772835 GGTCGGGTCAACGGTCGGGTCG
1 GGTCGGGTCAACGGTCGGGTCG
1772857 GGTCGGGTCAACGGTCGGGTCG
1 GGTCGGGTCAACGGTCGGGTCG
1772879 GGTCGGGTCAACGGTCGGGTCG
1 GGTCGGGTCAACGGTCGGGTCG
1772901 TGTCAGACCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.18
Consensus pattern (22 bp):
GGTCGGGTCAACGGTCGGGTCG
Found at i:1772900 original size:5 final size:5
Alignment explanation
Indices: 1772847--1772887 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
1772837 TCGGGTCAAC
*
1772847 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
1772888 AACGGTCGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:1772919 original size:9 final size:9
Alignment explanation
Indices: 1772902--1772999 Score: 88
Period size: 9 Copynumber: 10.2 Consensus size: 9
1772892 GTCGGGTCGT
*
1772902 GTCAGACCG
1 GTCAAACCG
1772911 GTCAAACCG
1 GTCAAACCG
* *
1772920 ATTCAGACCG
1 -GTCAAACCG
1772930 GTCAAACCG
1 GTCAAACCG
*
1772939 GTTCGAACCG
1 G-TCAAACCG
*
1772949 GTTGAAACCG
1 G-TCAAACCG
1772959 GTCAAACCG
1 GTCAAACCG
1772968 GTCAGAACCG
1 GTCA-AACCG
*
1772978 GTTGAAAACCG
1 G-T-CAAACCG
1772989 GTCAAACCG
1 GTCAAACCG
1772998 GT
1 GT
1773000 TTCCAGCAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 35 0.48
10 30 0.41
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.15
Consensus pattern (9 bp):
GTCAAACCG
Found at i:1772925 original size:19 final size:19
Alignment explanation
Indices: 1772903--1773000 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
1772893 TCGGGTCGTG
*
1772903 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
1772922 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
1772941 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
1772960 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
1772980 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
1773000 T
1 T
1773001 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1772958 original size:29 final size:31
Alignment explanation
Indices: 1772926--1773000 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
1772916 ACCGATTCAG
1772926 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
1772955 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
1772985 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
1773001 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:1780623 original size:20 final size:21
Alignment explanation
Indices: 1780598--1780636 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1780588 TATTTCTCAT
1780598 CTTTC-TCTGAAATCTATTTC
1 CTTTCTTCTGAAATCTATTTC
*
1780618 CTTTCTTCTTAAATCTATT
1 CTTTCTTCTGAAATCTATT
1780637 ATGAGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.54
Consensus pattern (21 bp):
CTTTCTTCTGAAATCTATTTC
Found at i:1782736 original size:3 final size:3
Alignment explanation
Indices: 1782728--1782756 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1782718 AAAAATCTTA
1782728 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1782757 CAAACAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1785521 original size:52 final size:52
Alignment explanation
Indices: 1785442--1785548 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 52
1785432 GCATTTTATT
* *
1785442 GTTGTTTATACATCCCTAGTGTCGTCAC-CATTAATGTTTGGATATTGTTTAA
1 GTTGTTTACACATCCCTAGTGTCGTCACTCA-TAATGTTTGGATATTGTTCAA
* * * *
1785494 GTTGTTTACACTTTCCTAGTGTTGTCACTGATAATGTTTGGATATTGTTCAA
1 GTTGTTTACACATCCCTAGTGTCGTCACTCATAATGTTTGGATATTGTTCAA
1785546 GTT
1 GTT
1785549 ATATAAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (52 bp):
GTTGTTTACACATCCCTAGTGTCGTCACTCATAATGTTTGGATATTGTTCAA
Found at i:1795512 original size:31 final size:31
Alignment explanation
Indices: 1795477--1795581 Score: 165
Period size: 31 Copynumber: 3.4 Consensus size: 31
1795467 GGTTAACAAC
* * * *
1795477 TAGTGACCGATTTGTTATAAATCAATAACAT
1 TAGTGACCAATTTGCTATAAATCGATAACGT
*
1795508 TAGTGATCAATTTGCTATAAATCGATAACGT
1 TAGTGACCAATTTGCTATAAATCGATAACGT
1795539 TAGTGACCAATTTGCTATAAATCGATAACGT
1 TAGTGACCAATTTGCTATAAATCGATAACGT
1795570 TAGTGACCAATT
1 TAGTGACCAATT
1795582 CATTACTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Consensus pattern (31 bp):
TAGTGACCAATTTGCTATAAATCGATAACGT
Found at i:1795883 original size:26 final size:29
Alignment explanation
Indices: 1795827--1795885 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 29
1795817 TTGTAACAAC
*
1795827 AATATTATTCAAAATATAATTTAACTAAT
1 AATATTATTCAAAATATAAATTAACTAAT
1795856 AATA-TATTCAAAA-A-AAATTAACTAAT
1 AATATTATTCAAAATATAAATTAACTAAT
1795882 AATA
1 AATA
1795886 ATTTCAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 15 0.52
27 1 0.03
28 9 0.31
29 4 0.14
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (29 bp):
AATATTATTCAAAATATAAATTAACTAAT
Found at i:1797129 original size:20 final size:21
Alignment explanation
Indices: 1797104--1797155 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1797094 TTTTCCCAAT
1797104 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGTAAA
* **
1797124 TCGCAACGCGAATTGGGTAAA
1 TCGCAATGCGAATTAAGTAAA
1797145 TCGCAATGCGA
1 TCGCAATGCGA
1797156 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGTAAA
Found at i:1797169 original size:20 final size:20
Alignment explanation
Indices: 1797144--1797257 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
1797134 AATTGGGTAA
*
1797144 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1797164 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1797184 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
**
1797205 ATCGCAACGAAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1797225 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1797245 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1797258 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1797860 original size:19 final size:19
Alignment explanation
Indices: 1797813--1797854 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1797803 ACGAGAGAAT
*
1797813 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
1797832 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
1797851 CGCA
1 CGCA
1797855 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:1797872 original size:19 final size:19
Alignment explanation
Indices: 1797850--1798048 Score: 140
Period size: 19 Copynumber: 11.1 Consensus size: 19
1797840 GAAACAAAAA
*
1797850 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1797869 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1797888 TCACGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
1797907 TCGTGGTTGCGATTTTCATT
1 TCG-CGTTGCGATTTTCATT
*
1797927 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1797943 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1797960 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1797974 TCTCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1797988 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1798007 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1798027 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1798047 TC
1 TC
1798049 AACCAAAAGA
Statistics
Matches: 148, Mismatches: 19, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
14 34 0.23
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 57 0.39
20 48 0.32
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1797927 original size:39 final size:38
Alignment explanation
Indices: 1797855--1797939 Score: 134
Period size: 39 Copynumber: 2.2 Consensus size: 38
1797845 AAAAATCGCA
1797855 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCACG
* * *
1797893 TTGCGATTTTTATTTCGTGGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCG-CGTTGCGATTTTCATTTCACG
1797932 TTGCGATT
1 TTGCGATT
1797940 GTCTGGTCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
38 16 0.37
39 27 0.63
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCACG
Found at i:1797952 original size:33 final size:33
Alignment explanation
Indices: 1797910--1797986 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
1797900 TTTTATTTCG
* *
1797910 TGGTTGCGATTTTCATTTCGCGTTGCGATTGTC
1 TGGTTGCGATTGTCATTTCGCGTTGCGATTCTC
* *
1797943 TGGTCGCGATAGTCATTTCGCGTTGCGATTCTC
1 TGGTTGCGATTGTCATTTCGCGTTGCGATTCTC
*
1797976 TCGTTGCGATT
1 TGGTTGCGATT
1797987 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.10, C:0.21, G:0.27, T:0.42
Consensus pattern (33 bp):
TGGTTGCGATTGTCATTTCGCGTTGCGATTCTC
Found at i:1797980 original size:14 final size:14
Alignment explanation
Indices: 1797963--1797999 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1797953 AGTCATTTCG
1797963 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1797977 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1797991 CGTTGCGAT
1 CGTTGCGAT
1798000 AGTCATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.27, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1797999 original size:47 final size:48
Alignment explanation
Indices: 1797930--1798023 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 48
1797920 TTTCATTTCG
* *
1797930 CGTTGCGATTGTCTGGTCGCGATAGTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATTCTCT
*
1797977 CGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATTCTC
1798024 ATTATCTCGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
47 28 0.65
48 15 0.35
ACGTcount: A:0.11, C:0.26, G:0.26, T:0.38
Consensus pattern (48 bp):
CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:1798025 original size:20 final size:20
Alignment explanation
Indices: 1797991--1798048 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1797981 GCGATTCTCT
**
1797991 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1798011 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1798031 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1798049 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1801551 original size:14 final size:14
Alignment explanation
Indices: 1801532--1801567 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1801522 ATTGTTTAAT
1801532 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
* *
1801546 TGATTTGCAAAAGT
1 TGATTTGTAAAAGG
1801560 TGATTTGT
1 TGATTTGT
1801568 TTAATTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.25, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1801768 original size:19 final size:19
Alignment explanation
Indices: 1801746--1801896 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
1801736 CGAAATTAAA
1801746 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1801765 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1801780 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1801798 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1801812 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1801831 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1801846 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1801864 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1801883 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1801897 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1801792 original size:33 final size:32
Alignment explanation
Indices: 1801750--1801876 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
1801740 ATTAAATTCG
1801750 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1801783 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1801816 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1801849 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1801877 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1801851 original size:66 final size:66
Alignment explanation
Indices: 1801743--1801875 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1801733 ACGCGAAATT
*
1801743 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1801808 G
66 G
*
1801809 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1801874 G
66 G
1801875 A
1 A
1801876 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1804185 original size:12 final size:12
Alignment explanation
Indices: 1804168--1804192 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1804158 TCTTCGGGGA
1804168 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1804180 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1804192 C
1 C
1804193 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1804394 original size:24 final size:24
Alignment explanation
Indices: 1804367--1804420 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1804357 CTGAAACACC
* *
1804367 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1804391 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1804415 ATCAAA
1 ATCAAA
1804421 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1805502 original size:20 final size:20
Alignment explanation
Indices: 1805477--1805534 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1805467 ATTCATTTGA
1805477 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1805497 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1805517 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1805535 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1805577 original size:33 final size:33
Alignment explanation
Indices: 1805540--1805610 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
1805530 AAAATCGCAA
*
1805540 TGCGAAATGAAAATCGCATTGTGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1805573 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1805606 TGCGA
1 TGCGA
1805611 TAGCCATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:1805581 original size:14 final size:14
Alignment explanation
Indices: 1805562--1805611 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 14
1805552 ATCGCATTGT
1805562 GATTTTCTCGTTGC
1 GATTTTCTCGTTGC
1805576 GATTTTCATTTCGCATTGC
1 GATTTTC---TCG--TTGC
1805595 GATTTTCTCGTTGC
1 GATTTTCTCGTTGC
1805609 GAT
1 GAT
1805612 AGCCATTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 14 0.45
16 3 0.10
17 3 0.10
19 11 0.35
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
GATTTTCTCGTTGC
Found at i:1805594 original size:19 final size:19
Alignment explanation
Indices: 1805572--1805674 Score: 117
Period size: 19 Copynumber: 5.6 Consensus size: 19
1805562 GATTTTCTCG
1805572 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1805591 TTGCGATTTTC---TCG--
1 TTGCGATTTTCATTTCGCA
*** *
1805605 TTGCGATAGCCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
1805625 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
1805645 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1805664 TTGCGATTTTC
1 TTGCGATTTTC
1805675 TCGTTGCGAT
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
14 8 0.11
16 3 0.04
18 3 0.04
19 29 0.41
20 28 0.39
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1805611 original size:33 final size:33
Alignment explanation
Indices: 1805553--1805684 Score: 156
Period size: 33 Copynumber: 3.8 Consensus size: 33
1805543 GAAATGAAAA
*
1805553 TCGCATTGTGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
***
1805586 TCGCATTGCGATTTTCTCGTTGCGATAGCCATTT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCA-TT
*
1805620 TCGCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC----TCG--TTGCGATTTTCATT
1805659 TCGCATTGCGATTTTCTCGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
1805685 AGCCATTTCA
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
33 34 0.41
34 17 0.20
35 3 0.04
38 3 0.04
39 17 0.20
40 9 0.11
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:1805682 original size:73 final size:72
Alignment explanation
Indices: 1805563--1805703 Score: 246
Period size: 73 Copynumber: 1.9 Consensus size: 72
1805553 TCGCATTGTG
* * *
1805563 ATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATTTTCGCGTTG
1 ATTTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCA-TTTCACGTTG
1805628 CGATTTTC
65 CGATTTTC
1805636 ATTTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATTTCACGTTGC
1 ATTTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATTTCACGTTGC
1805701 GAT
66 GAT
1805704 AGTCTGTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
72 13 0.20
73 52 0.80
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (72 bp):
ATTTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATTTCACGTTGC
GATTTTC
Found at i:1805692 original size:33 final size:33
Alignment explanation
Indices: 1805553--1805703 Score: 149
Period size: 33 Copynumber: 4.4 Consensus size: 33
1805543 GAAATGAAAA
* ***
1805553 TCGCATTGTGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1805586 TCGCATTGCGATTTTCTCGTTGCGATAGCCATTT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCA-TT
* ***
1805620 TCGCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC----TCG--TTGCGATAGCCATT
1805659 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
* *
1805692 TCACGTTGCGAT
1 TCGCATTGCGAT
1805704 AGTCTGTTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
33 48 0.49
34 17 0.18
35 3 0.03
38 3 0.03
39 17 0.18
40 9 0.09
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:1805810 original size:14 final size:14
Alignment explanation
Indices: 1805791--1805827 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1805781 CATCAATTAA
1805791 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1805805 ACAAATCATCTTTT
1 ACAAATCAACATTT
1805819 ACAAATCAA
1 ACAAATCAA
1805828 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1807718 original size:20 final size:19
Alignment explanation
Indices: 1807695--1807762 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
1807685 GAAACTTAAA
1807695 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
1807715 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1807735 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1807754 ATCGCAACG
1 ATCGCAACG
1807763 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1807770 original size:14 final size:14
Alignment explanation
Indices: 1807751--1807808 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1807741 ATGCGAAATG
*
1807751 AAAATCGCAACGAC
1 AAAATCGCAACGAA
1807765 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
*
1807781 ATGAAATCGCAACGAT
1 A--AAATCGCAACGAA
1807797 AAAATCGCAACG
1 AAAATCGCAACG
1807809 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:1807793 original size:32 final size:33
Alignment explanation
Indices: 1807735--1807813 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1807725 GGAAATGGCT
1807735 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1807768 ATCGCAATGCGAAATG-AAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1807800 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1807814 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 28 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1807861 original size:14 final size:14
Alignment explanation
Indices: 1807842--1807899 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1807832 TTTCATTTCG
1807842 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1807856 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1807872 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1807888 CGTTGCGATTTT
1 CGTTGCGATTTT
1807900 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1807906 original size:33 final size:33
Alignment explanation
Indices: 1807825--1807915 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1807815 ACAAATCGCA
*
1807825 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1807858 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1807890 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1807916 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1807934 original size:20 final size:19
Alignment explanation
Indices: 1807900--1807954 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1807890 TTGCGATTTT
*
1807900 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1807919 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1807939 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1807955 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1808462 original size:18 final size:18
Alignment explanation
Indices: 1808436--1808480 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1808426 GTCGATCAGA
*
1808436 TGATGGCTCTGAGTGAGG
1 TGATGGCTCTGAGCGAGG
* *
1808454 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGAGCGAGG
1808472 TGATGGCTC
1 TGATGGCTC
1808481 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGAGCGAGG
Found at i:1810131 original size:22 final size:22
Alignment explanation
Indices: 1810101--1810144 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1810091 GATGGAGATA
*
1810101 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
1810123 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
1810145 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:1810358 original size:20 final size:20
Alignment explanation
Indices: 1810332--1810404 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
1810322 GATTATGTAT
1810332 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1810352 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
1810372 TATCGAGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1810392 TATCTCGTTGCGA
1 TATCGCGTTGCGA
1810405 TTTTGTATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1810439 original size:21 final size:20
Alignment explanation
Indices: 1810415--1810466 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1810405 TTTTGTATTA
*
1810415 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
1810436 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
1810456 TCGCATTGCGA
1 TCGCATTGCGA
1810467 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:1812014 original size:2 final size:2
Alignment explanation
Indices: 1812007--1812044 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1811997 ACACGCATGC
1812007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1812045 GCCTATGCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1821336 original size:13 final size:14
Alignment explanation
Indices: 1821320--1821354 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
1821310 TGTAATAATA
1821320 ATAATAAATA-AAT
1 ATAATAAATAGAAT
1821333 ATAATAAATAGGAAT
1 ATAATAAATA-GAAT
1821348 ATAATAA
1 ATAATAA
1821355 TATTATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
15 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
ATAATAAATAGAAT
Found at i:1825280 original size:34 final size:34
Alignment explanation
Indices: 1825242--1825310 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1825232 ATAATTGTCG
*
1825242 GTGGCCTATGAAGTCGACCGGTACTATAACGCAT
1 GTGGCCTATGAAGTCGACCGGTACTATAAAGCAT
1825276 GTGGCCTATGAAGTCGACCGGTACTATAAAGCAT
1 GTGGCCTATGAAGTCGACCGGTACTATAAAGCAT
1825310 G
1 G
1825311 CAAGTGCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (34 bp):
GTGGCCTATGAAGTCGACCGGTACTATAAAGCAT
Found at i:1825807 original size:23 final size:23
Alignment explanation
Indices: 1825761--1825812 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1825751 TTTATAAAAT
*
1825761 TTGATAAAATTTAAAGTATTTAA
1 TTGATAAAATTTAAAGTATATAA
*
1825784 TTGATTAAAATTTATA-TATATAA
1 TTGA-TAAAATTTAAAGTATATAA
1825807 -TGATAA
1 TTGATAA
1825813 TATTCGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 3 0.12
23 10 0.38
24 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (23 bp):
TTGATAAAATTTAAAGTATATAA
Found at i:1828151 original size:21 final size:21
Alignment explanation
Indices: 1828115--1828156 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1828105 TAACTCTCGA
**
1828115 AATTATATCATGTAACCCCTG
1 AATTATATCAAATAACCCCTG
*
1828136 AATTATATCAAATAACTCCTG
1 AATTATATCAAATAACCCCTG
1828157 TAACTCCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.33
Consensus pattern (21 bp):
AATTATATCAAATAACCCCTG
Done.