Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008164.1 Hibiscus syriacus cultivar Beakdansim tig00110744_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: 2577652
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1563898 original size:46 final size:46
Alignment explanation
Indices: 1563846--1564357 Score: 749
Period size: 46 Copynumber: 11.1 Consensus size: 46
1563836 TTATTCGTTA
* * *
1563846 ATTTCATTTATGGTATCATTTCATGCCTT-ATGGCATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAAT-GCATCCTTTCATGC
* *
1563892 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
1563938 ATTTTATTTATGACATCCTTTCATGCCTTAATGCATTCATTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
1563984 ATTTTATTTATGGCATCCATTCATTCCTTAATGCATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
1564030 ATTTTATTCATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1564076 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCAT-CTGTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCT-TTCATGC
* * **
1564122 ATTTTATTTATAGCATCCTTTCATGCCTTAATGCATCCGTTCATAT
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
1564168 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCGTCCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
1564214 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
1564260 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * ** * * *
1564306 ATTTTTAGTTATGGTATTTTTTCAAGCCTTAATGCATACATTCATGC
1 A-TTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1564353 ATTTT
1 ATTTT
1564358 TAGTTATGTA
Statistics
Matches: 426, Mismatches: 36, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
45 2 0.00
46 381 0.89
47 43 0.10
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (46 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:1563906 original size:26 final size:26
Alignment explanation
Indices: 1563873--1563963 Score: 104
Period size: 26 Copynumber: 3.7 Consensus size: 26
1563863 ATTTCATGCC
1563873 TTATGGCATCCTTTCATGCATTTCAT
1 TTATGGCATCCTTTCATGCATTTCAT
1563899 TTATGGCATCCTTTCATGC----C-T
1 TTATGGCATCCTTTCATGCATTTCAT
* * *
1563920 TAAT-GCATCATTTCATGCATTTTAT
1 TTATGGCATCCTTTCATGCATTTCAT
*
1563945 TTATGACATCCTTTCATGC
1 TTATGGCATCCTTTCATGC
1563964 CTTAATGCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
20 13 0.25
21 4 0.08
22 1 0.02
25 4 0.08
26 31 0.58
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (26 bp):
TTATGGCATCCTTTCATGCATTTCAT
Found at i:1564774 original size:19 final size:20
Alignment explanation
Indices: 1564716--1564774 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
1564706 ATCGATACCC
*
1564716 CTACCATGGTATCAATACTA
1 CTACTATGGTATCAATACTA
**
1564736 CTATACTATGGTATTGATACT-
1 C--TACTATGGTATCAATACTA
1564757 CTACTATGGTATCAATAC
1 CTACTATGGTATCAATAC
1564775 CATTTTTGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 15 0.47
20 1 0.03
21 1 0.03
22 15 0.47
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (20 bp):
CTACTATGGTATCAATACTA
Found at i:1570463 original size:22 final size:22
Alignment explanation
Indices: 1570436--1570478 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1570426 GGGTATCGAT
1570436 ACAAGAGGATAATACCGATACC
1 ACAAGAGGATAATACCGATACC
*
1570458 ACAAGAGGATAATATCGATAC
1 ACAAGAGGATAATACCGATAC
1570479 TATAATTAGG
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:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (22 bp):
ACAAGAGGATAATACCGATACC
Found at i:1571784 original size:22 final size:21
Alignment explanation
Indices: 1571734--1571785 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1571724 ATTTTTTGAC
1571734 TAAATTATATTTTATCATTTGT
1 TAAATTA-ATTTTATCATTTGT
*
1571756 T-ATTTAATTTTAATCAATTT-T
1 TAAATTAATTTT-ATC-ATTTGT
1571777 TAAATTAAT
1 TAAATTAAT
1571786 ACACATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 11 0.44
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
TAAATTAATTTTATCATTTGT
Found at i:1572216 original size:76 final size:76
Alignment explanation
Indices: 1572114--1572265 Score: 200
Period size: 76 Copynumber: 2.0 Consensus size: 76
1572104 AAAATGAACA
* *
1572114 TTTAATCTTTTCAAAATCATTTTTTAATAGCAATTCCAAATAG-AAAGTTTTAAACTGCACTTTT
1 TTTAATCTTTTCAAAATCA-TTTTTAATAACAATTCCAAATAGTAAA-TTTTAAACTACACTTTT
1572178 CAAAAATACTTTT
64 CAAAAATACTTTT
* * * * *
1572191 TTTAATACTTTTCAAAATC-TTTTTAATAACAATTTCAAATGGTTAATTTTAGACTACACTTTTG
1 TTTAAT-CTTTTCAAAATCATTTTTAATAACAATTCCAAATAGTAAATTTTAAACTACACTTTTC
1572255 AAAAATACTTT
65 AAAAATACTTT
1572266 AAAAAATATT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
76 46 0.70
77 8 0.12
78 12 0.18
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (76 bp):
TTTAATCTTTTCAAAATCATTTTTAATAACAATTCCAAATAGTAAATTTTAAACTACACTTTTCA
AAAATACTTTT
Found at i:1576863 original size:104 final size:104
Alignment explanation
Indices: 1576673--1576867 Score: 257
Period size: 104 Copynumber: 1.9 Consensus size: 104
1576663 GATATAGAGT
* * * * *
1576673 TGAATTCATGCATTATACAACAAGGAAATGTGTGGAGTTTCTGCGCCTGGATCAACTCCTTAACT
1 TGAATTCATGCATTAAACAACAAGGAAATATGTGGAGTTCCTGCACCTGGATCAACGCCTTAACT
* * *
1576738 GCTGCCATTAACGTAGCTCGTGTATTTATTCATCATTGA
66 ACTGACATTAACGTAGATCGTGTATTTATTCATCATTGA
* * *
1576777 TGAATTCATGCATTAAACAATAAGGAAATATGTGTAGTCTCCT-CATCTGGATCAACGCCTTAAC
1 TGAATTCATGCATTAAACAACAAGGAAATATGTGGAGT-TCCTGCACCTGGATCAACGCCTTAAC
* *
1576841 TACTGACATTAATGTGGATCGTGTATT
65 TACTGACATTAACGTAGATCGTGTATT
1576868 CACACATCAC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 74 0.96
105 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (104 bp):
TGAATTCATGCATTAAACAACAAGGAAATATGTGGAGTTCCTGCACCTGGATCAACGCCTTAACT
ACTGACATTAACGTAGATCGTGTATTTATTCATCATTGA
Found at i:1579197 original size:4 final size:4
Alignment explanation
Indices: 1579190--1579216 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1579180 GAACATACAA
1579190 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1579217 CACACGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1581761 original size:20 final size:20
Alignment explanation
Indices: 1581736--1581781 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1581726 GTTGTTATGG
1581736 CTGTTAAGGAATGTTGGAAT
1 CTGTTAAGGAATGTTGGAAT
1581756 CTGTTAAGGAATGTTGGAAT
1 CTGTTAAGGAATGTTGGAAT
1581776 CTGTTA
1 CTGTTA
1581782 TGAATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (20 bp):
CTGTTAAGGAATGTTGGAAT
Found at i:1584437 original size:12 final size:12
Alignment explanation
Indices: 1584420--1584444 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1584410 GTCTGTTAAC
1584420 CTAACAACCTAG
1 CTAACAACCTAG
1584432 CTAACAACCTAG
1 CTAACAACCTAG
1584444 C
1 C
1584445 AACTAACTCA
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:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CTAACAACCTAG
Found at i:1588919 original size:12 final size:12
Alignment explanation
Indices: 1588902--1588926 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1588892 GTATGTTAAC
1588902 CTAACAACCTAG
1 CTAACAACCTAG
1588914 CTAACAACCTAG
1 CTAACAACCTAG
1588926 C
1 C
1588927 AACTAACTCA
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:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CTAACAACCTAG
Found at i:1590662 original size:16 final size:16
Alignment explanation
Indices: 1590641--1590673 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1590631 ACACTTTAAC
1590641 TCATCTTTACGACATG
1 TCATCTTTACGACATG
1590657 TCATCTTTACGACATG
1 TCATCTTTACGACATG
1590673 T
1 T
1590674 ATATTATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (16 bp):
TCATCTTTACGACATG
Found at i:1605627 original size:28 final size:28
Alignment explanation
Indices: 1605595--1605655 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 28
1605585 TCATCTTTGA
1605595 CTTA-TGGAAGATGATAAGGGTTAGGTGT
1 CTTATTGGAAGATGATAA-GGTTAGGTGT
1605623 CTTATTTTGGAAGATGATAAGGTTAGGTGT
1 CTTA--TTGGAAGATGATAAGGTTAGGTGT
1605653 CTT
1 CTT
1605656 GGTTTAATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 4 0.13
30 13 0.43
31 13 0.43
ACGTcount: A:0.26, C:0.05, G:0.31, T:0.38
Consensus pattern (28 bp):
CTTATTGGAAGATGATAAGGTTAGGTGT
Found at i:1605657 original size:25 final size:27
Alignment explanation
Indices: 1605599--1605655 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 27
1605589 CTTTGACTTA
1605599 TGGAAGATGATAAGGGTTAGGTGTCTTATTT
1 TGGAAGATGATAAGGGTTAGGTGTC----TT
1605630 TGGAAGATGATAA-GGTTAGGTGTCTT
1 TGGAAGATGATAAGGGTTAGGTGTCTT
1605656 GGTTTAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 2 0.08
30 11 0.42
31 13 0.50
ACGTcount: A:0.26, C:0.04, G:0.33, T:0.37
Consensus pattern (27 bp):
TGGAAGATGATAAGGGTTAGGTGTCTT
Found at i:1608003 original size:2 final size:2
Alignment explanation
Indices: 1607996--1608028 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1607986 CTGATAGTTG
1607996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1608029 GATGCTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1615639 original size:20 final size:20
Alignment explanation
Indices: 1615614--1615657 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1615604 TGATAATGGG
1615614 AGAACAATATCGACACTAGA
1 AGAACAATATCGACACTAGA
* *
1615634 AGAACAATATCGATACTTGA
1 AGAACAATATCGACACTAGA
1615654 AGAA
1 AGAA
1615658 TAGTATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (20 bp):
AGAACAATATCGACACTAGA
Found at i:1615699 original size:25 final size:25
Alignment explanation
Indices: 1615671--1615732 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
1615661 TATTGATACT
* *
1615671 TCCTAGATCTGACACTAGATAAAAG
1 TCCTAAATCTGACACTAGAGAAAAG
* * *
1615696 TCCTAAATCCGACGCTAGAGAAAGG
1 TCCTAAATCTGACACTAGAGAAAAG
*
1615721 TCTTAAATCTGA
1 TCCTAAATCTGA
1615733 TGCCAGAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (25 bp):
TCCTAAATCTGACACTAGAGAAAAG
Found at i:1622590 original size:20 final size:21
Alignment explanation
Indices: 1622551--1622596 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1622541 GTAAACATAA
1622551 AGTATCGATACTTATTATTCC
1 AGTATCGATACTTATTATTCC
1622572 AGTATCGATACTT-TTATTCC
1 AGTATCGATACTTATTATTCC
1622592 AGTAT
1 AGTAT
1622597 GCATCTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (21 bp):
AGTATCGATACTTATTATTCC
Found at i:1622944 original size:20 final size:21
Alignment explanation
Indices: 1622900--1622945 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1622890 GCATAAATAT
*
1622900 AAGTATCAATAATGTCTATAT
1 AAGTATCAATAATGTCTATAC
* *
1622921 AAGTATCAATACT-TTTATAC
1 AAGTATCAATAATGTCTATAC
1622941 AAGTA
1 AAGTA
1622946 ACGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (21 bp):
AAGTATCAATAATGTCTATAC
Found at i:1622977 original size:20 final size:20
Alignment explanation
Indices: 1622949--1623029 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
1622939 ACAAGTAACG
*
1622949 AATTTGACAAAACCGATTGGA
1 AATTTGACAAAACCGATT-AA
* *
1622970 AA-TTGACAAAACTGGTTAA
1 AATTTGACAAAACCGATTAA
*
1622989 AATTTGACAAAACCAATTAA
1 AATTTGACAAAACCGATTAA
*
1623009 AATTTGACAAAATCGATTAA
1 AATTTGACAAAACCGATTAA
1623029 A
1 A
1623030 TATAAATAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
19 3 0.06
20 46 0.90
21 2 0.04
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.26
Consensus pattern (20 bp):
AATTTGACAAAACCGATTAA
Found at i:1623459 original size:21 final size:21
Alignment explanation
Indices: 1623430--1623483 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1623420 TGAAATGTAT
*
1623430 CAAATGTATCGATACCTTACA
1 CAAAAGTATCGATACCTTACA
1623451 CAAAAGTATCGATACCTTACA
1 CAAAAGTATCGATACCTTACA
1623472 CAAAAGTATCGA
1 CAAAAGTATCGA
1623484 AACTTCAGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (21 bp):
CAAAAGTATCGATACCTTACA
Found at i:1625102 original size:2 final size:2
Alignment explanation
Indices: 1625095--1625131 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1625085 AAATGTATCG
1625095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1625132 CATACTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1625381 original size:108 final size:108
Alignment explanation
Indices: 1625239--1625653 Score: 390
Period size: 108 Copynumber: 3.7 Consensus size: 108
1625229 ATGTACATGG
* * *
1625239 TAATATGTTGATAA-AGGTTGATAACAAATAAAGTAATTAACCGGTTATGTTATTGTCGGATTTC
1 TAATATGTTGATAATA--TTGATAACAAATTAAGTAATTAACCGATTATGTTATCGTCGGATTTC
1625303 TAAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACC
64 TAAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACC
* * * *
1625348 TAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATC-TTGGAATTTCT
1 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCGATTATGTTATCGTCGG-ATTTCT
* *** * * *
1625412 AAGGCACCATCAGCTTTAAAAAGGTGATACCTATTACGTTACATAAGC-TCTACC
65 AAGGCCCCATCAGC-TT-AAACTTTGGTAAC-A-T---TT---TAGGCGT-TACC
* * * * * * *
1625466 TAATTTGTT-ATTATGGTTGATAACAAATCAAATAATTAACCGGTTACGTTATCGTCGGATTTCT
1 TAATATGTTGATAAT-ATTGATAACAAATTAAGTAATTAACCGATTATGTTATCGTCGGATTTCT
* * *
1625530 ATGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGTCGTTACC
65 AAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACC
* * *
1625574 TAATATGTTGATAATAATGATAAC-AATGTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCT
1 TAATATGTTGATAATATTGATAACAAAT-TAAGTAATTAACCGATTATGTTATCGTCGGATTTCT
* *
1625638 ATGGCCCAATCAGCTT
65 AAGGCCCCATCAGCTT
1625654 TAAAAATGTG
Statistics
Matches: 242, Mismatches: 46, Indels: 37
0.74 0.14 0.11
Matches are distributed among these distances:
107 6 0.02
108 116 0.48
109 21 0.09
110 9 0.04
111 3 0.01
112 1 0.00
114 1 0.00
115 3 0.01
116 8 0.03
117 7 0.03
118 64 0.26
119 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (108 bp):
TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCGATTATGTTATCGTCGGATTTCTA
AGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACC
Found at i:1625652 original size:226 final size:226
Alignment explanation
Indices: 1625239--1625743 Score: 784
Period size: 226 Copynumber: 2.2 Consensus size: 226
1625229 ATGTACATGG
* * *
1625239 TAATATGTTGATAAAGGTTGATAACAAAT-AAAGTAATTAACCGGTTATGTTATTGTCGGATTTC
1 TAATATGTT-ATTATGGTTGATAACAAATCAAA-TAATTAACCGGTTATGTTATCGTCGGATTTC
*
1625303 TAAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGA
64 TAAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATAATGA
*
1625368 TAACAAATTAAGTAATTAACCTATTTTGTTATCTTGGAATTTCTAAGGCACCATCAGCTTTAAAA
129 TAACAAATTAAGTAATTAACCTATTTTGTTATCTCGGAATTTCTAAGGCACCATCAGCTTTAAAA
* *
1625433 AGGTGATACCTATTACGTTACATAAGCTCTACC
194 AGGTGATACCTATTACATTACATAAGCGCTACC
* *
1625466 TAATTTGTTATTATGGTTGATAACAAATCAAATAATTAACCGGTTACGTTATCGTCGGATTTCTA
1 TAATATGTTATTATGGTTGATAACAAATCAAATAATTAACCGGTTATGTTATCGTCGGATTTCTA
* * *
1625531 TGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGTCGTTACCTAATATGTTGATAATAATGATA
66 AGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATAATGATA
*
1625596 AC-AATGTAAGTAATTAACCTATTTTGTTATCGTCGG-ATTTCTATGGC-CCAATCAGCTTTAAA
131 ACAAAT-TAAGTAATTAACCTATTTTGTTATC-TCGGAATTTCTAAGGCACC-ATCAGCTTTAAA
* *
1625658 AATGTGCTACCTATTACATTACATAAGCGCTACC
193 AAGGTGATACCTATTACATTACATAAGCGCTACC
* *
1625692 TAATATGTTATTATGGTTGATAACAAATCAAGTAATTAACTGGTTATGTTAT
1 TAATATGTTATTATGGTTGATAACAAATCAAATAATTAACCGGTTATGTTAT
1625744 TATCGTAATC
Statistics
Matches: 255, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
225 5 0.02
226 236 0.93
227 14 0.05
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (226 bp):
TAATATGTTATTATGGTTGATAACAAATCAAATAATTAACCGGTTATGTTATCGTCGGATTTCTA
AGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATAATGATA
ACAAATTAAGTAATTAACCTATTTTGTTATCTCGGAATTTCTAAGGCACCATCAGCTTTAAAAAG
GTGATACCTATTACATTACATAAGCGCTACC
Found at i:1626712 original size:23 final size:22
Alignment explanation
Indices: 1626685--1626741 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
1626675 TAAATCAAAG
*
1626685 AAAAACATAAGAAAACAAATAAT
1 AAAAA-ATAAAAAAACAAATAAT
* *
1626708 CAAAAATCAAAAAAATAAATAAT
1 AAAAAAT-AAAAAAACAAATAAT
1626731 AAAAAAATAAA
1 -AAAAAATAAA
1626742 TCGAAAGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 20 0.71
24 6 0.21
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAAATAAAAAAACAAATAAT
Found at i:1626903 original size:45 final size:44
Alignment explanation
Indices: 1626813--1626908 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 44
1626803 AATAAACAAT
* *
1626813 AATACATCAAAAGGAAAAGAAAGAATAAATAAAAAATAAGAAAAA
1 AATAAATCAAAAGGAAAAGAAAGAATAAATAAAAAATAA-CAAAA
*
1626858 AATAAATCAAAGAGGAAAA-AAATGAAATAAA-ACAAAA-AACAAAA
1 AATAAATCAAA-AGGAAAAGAAA-G-AATAAATAAAAAATAACAAAA
1626902 AATAAAT
1 AATAAAT
1626909 TGAAATTGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
44 11 0.24
45 15 0.33
46 13 0.29
47 6 0.13
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.11
Consensus pattern (44 bp):
AATAAATCAAAAGGAAAAGAAAGAATAAATAAAAAATAACAAAA
Found at i:1627035 original size:28 final size:27
Alignment explanation
Indices: 1626988--1627040 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
1626978 TTCGAATAAA
*
1626988 AATAAATTAGGGATTAAAATGTAAAAAT
1 AATAAATTAGGGATCAAAAT-TAAAAAT
* *
1627016 AATAAATTTGGGATCCAAATTAAAA
1 AATAAATTAGGGATCAAAATTAAAA
1627041 TACTACAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.28
Consensus pattern (27 bp):
AATAAATTAGGGATCAAAATTAAAAAT
Found at i:1628067 original size:15 final size:16
Alignment explanation
Indices: 1628028--1628067 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
1628018 AAAAAAAAAA
1628028 TAATAAT-AATAATAG
1 TAATAATAAATAATAG
1628043 TAATAATAAATAATAG
1 TAATAATAAATAATAG
1628059 T-ATAATAAA
1 TAATAATAAA
1628068 ATCTATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAATAATAAATAATAG
Found at i:1628111 original size:35 final size:35
Alignment explanation
Indices: 1628071--1628377 Score: 120
Period size: 37 Copynumber: 8.5 Consensus size: 35
1628061 TAATAAAATC
1628071 TATATAATATATATATTTCAAAAATATTTTT-AAA
1 TATATAATATATATATTTCAAAAATATTTTTAAAA
* *
1628105 -ATAT-ATAT-TATA-TT-AAAAAAAGTTGTTTAAAC
1 TATATAATATATATATTTCAAAAATA-TT-TTTAAAA
* *
1628137 TATATATTACATAGT-TTTCAAAAAATATTTTTAAAA
1 TATATAATATATA-TATTTC-AAAAATATTTTTAAAA
* * * *
1628173 -ACCAT-ATATTATATATTTTAAGAATGTTTTTAAAAA
1 TA-TATAATA-TATATATTTCAAAAATATTTTT-AAAA
* * *
1628209 CTATATATTATTTA-ATTTTC-AAAATGTTTTTAAAGAA
1 -TATATAATATATATA-TTTCAAAAATATTTTT-AA-AA
* * *
1628246 TTATATATTATATA-ATTTTC-AAAATGA-TTTCAAAC
1 -TATATAATATATATA-TTTCAAAAAT-ATTTTTAAAA
* *
1628281 TATATAATATATACATTTTCAAAAAAATTGTTTTCAAAACTA
1 TATATAATATATATA-TTTCAAAAATA-T-TTTT--AAA--A
** *
1628323 TATATATTATATATATATTTCAAAAAATCATTTGCAAAC
1 TATATA--ATATATATATTTC-AAAAAT-ATTTTTAAAA
1628362 TATATAATATATATAT
1 TATATAATATATATAT
1628378 ATATATAAAA
Statistics
Matches: 209, Mismatches: 31, Indels: 63
0.69 0.10 0.21
Matches are distributed among these distances:
29 6 0.03
30 4 0.02
31 7 0.03
32 6 0.03
33 8 0.04
34 14 0.07
35 24 0.11
36 41 0.20
37 48 0.23
38 12 0.06
39 6 0.03
40 3 0.01
41 3 0.01
42 6 0.03
43 6 0.03
44 14 0.07
45 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (35 bp):
TATATAATATATATATTTCAAAAATATTTTTAAAA
Found at i:1628125 original size:31 final size:31
Alignment explanation
Indices: 1628077--1628186 Score: 80
Period size: 31 Copynumber: 3.4 Consensus size: 31
1628067 AATCTATATA
**
1628077 ATATA-TATATTTCAAAAATATTTTTAAAAT
1 ATATATTATATTAAAAAAATATTTTTAAAAT
* *
1628107 ATATATTATATTAAAAAAAGT-TGTTTAAACT
1 ATATATTATATTAAAAAAA-TATTTTTAAAAT
* *
1628138 ATATATTACATAGTTTTCAAAAAATATTTTTAAAAACC
1 ATATATT--ATA---TTAAAAAAATATTTTT-AAAA-T
1628176 ATATATTATAT
1 ATATATTATAT
1628187 ATTTTAAGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
30 5 0.08
31 26 0.42
32 1 0.02
33 4 0.06
35 1 0.02
36 15 0.24
37 3 0.05
38 7 0.11
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (31 bp):
ATATATTATATTAAAAAAATATTTTTAAAAT
Found at i:1628264 original size:73 final size:69
Alignment explanation
Indices: 1628133--1628304 Score: 184
Period size: 73 Copynumber: 2.4 Consensus size: 69
1628123 AAAGTTGTTT
* *
1628133 AAACTATATATTACATAGTTTTCAAAAAATATTTTTAAAAACCATATATTATATATTTT-AAGAA
1 AAACTATATATTATATAATTTTC--AAAATATTTTTAAAAACCATATATTATATATTTTCAA-AA
*
1628197 TGTTTTTAA
63 TG-ATTT-A
* * **
1628206 AAACTATATATTATTTAATTTTCAAAATGTTTTTAAAGAATTATATATTATATAATTTTCAAAAT
1 AAACTATATATTATATAATTTTCAAAATATTTTTAAA-AACCATATATTATAT-ATTTTCAAAAT
*
1628271 GATTTC
64 GATTTA
*
1628277 AAACTATATAATATATACATTTTCAAAA
1 AAACTATATATTATATA-ATTTTCAAAA
1628305 AAATTGTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
71 28 0.33
72 26 0.31
73 29 0.34
74 2 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (69 bp):
AAACTATATATTATATAATTTTCAAAATATTTTTAAAAACCATATATTATATATTTTCAAAATGA
TTTA
Found at i:1628362 original size:41 final size:39
Alignment explanation
Indices: 1628247--1628381 Score: 136
Period size: 42 Copynumber: 3.4 Consensus size: 39
1628237 TTTAAAGAAT
*
1628247 TATATATTATATA-ATTTTC--AAAATGATTTCAAACTA
1 TATATATTATATATATTTTCAAAAAATCATTTCAAACTA
* **
1628283 TATA-A-TATATACATTTTCAAAAAAATTGTTTTCAAAACTA
1 TATATATTATATATATTTTC-AAAAAA-TCATTTC-AAACTA
1628323 TATATATTATATATATATTTCAAAAAATCATTTGCAAACTA
1 TATATATTATATATAT-TTTCAAAAAATCATTT-CAAACTA
1628364 TATAATATATATATATAT
1 TAT-ATAT-TATATATAT
1628382 ATAAAATATA
Statistics
Matches: 83, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
34 6 0.07
35 7 0.08
36 4 0.05
38 4 0.05
39 6 0.07
40 10 0.12
41 14 0.17
42 19 0.23
43 13 0.16
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (39 bp):
TATATATTATATATATTTTCAAAAAATCATTTCAAACTA
Found at i:1629412 original size:170 final size:170
Alignment explanation
Indices: 1629197--1629758 Score: 750
Period size: 170 Copynumber: 3.3 Consensus size: 170
1629187 TATTGGAATT
* * * * * * *
1629197 GAACTTGAAGGTTTTTGCTGACAGATAACCCTTCTCACCTTGAGTTATGCTATAAATTGGATATC
1 GAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTGATATG
1629262 CCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAAATAGCCCCCTCGCCTTGAGC
66 CCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAAATAGCCCCCTCGCCTTGAGC
*
1629327 TATGCTGTAAATTTGATGTGACTCTAAGCTAAATGTAATC
131 TATGCTGTAAATTTGATGTGACTCTGAGCTAAATGTAATC
* * *
1629367 GATCTCGAAGGTCTTGGTTGACAGATAACTCTTCTCGCCTTGAGTTATGTTATAAATTTGATATG
1 GAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTGATATG
* * * * * * *
1629432 CCTTTGAGTTGAATGTAATCGAACTCAAAGGTCTTTTGTTGATAGATATCCCTCATTGCCTTGAG
66 CCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAAATAGCCC-CCTCGCCTTGAG
* *
1629497 CTATGCTGTAAATTTGATGT-ACGTCTGAGCTGAATGTAAAC
130 CTATGCTGTAAATTTGATGTGAC-TCTGAGCTAAATGTAATC
* * *
1629538 GAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCATGAGTTATACTGTAAATTTGATATG
1 GAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTGATATG
* * **
1629603 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAAATAGGCCTTCTCGCCTTGAG
66 CCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAAATA-GCCCCCTCGCCTTGAG
* * * * * * *
1629667 CTATGTTTTAAATTTGATGTGCCTTTGATCTTACTGTAATC
130 CTATGCTGTAAATTTGATGTGACTCTGAGCTAAATGTAATC
* * *
1629708 AAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCT
1 GAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCT
1629759 GCCAATATTT
Statistics
Matches: 339, Mismatches: 49, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
170 202 0.60
171 137 0.40
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (170 bp):
GAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTGATATG
CCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAAATAGCCCCCTCGCCTTGAGC
TATGCTGTAAATTTGATGTGACTCTGAGCTAAATGTAATC
Found at i:1629595 original size:256 final size:255
Alignment explanation
Indices: 1629215--1629759 Score: 666
Period size: 256 Copynumber: 2.1 Consensus size: 255
1629205 AGGTTTTTGC
** * * *
1629215 TGACAGATAACCCTTCTCACCTTGAGTTATGCTATAAATTGGATATCCCTTTGAGCTGAATGTAA
1 TGACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATTGGATATACCTCTGAGCTGAATGTAA
* * * * * *
1629280 TCGAACTCGAAGGTCTTTTGTTGAAAAATAGCCCCCTCGCCTTGAGCTATGCTGTAAATTTGATG
66 ACGAACTCGAAGGTCTTTGGTTGAAAAATAACCCCCTCGCCATGAGCTATACTGTAAATTTGATA
* *
1629345 TGACTCTAAGCTAAATGTAATCGATCTCGAAGGTCTTGGTTGACAGATA-ACTCTTCTCGCCTTG
131 TGACTCTAAGCTAAATGTAATCGAACTCGAAGGTCTTGGTTGACAAATAGAC-CTTCTCGCCTTG
* * *
1629409 AGTTATGTTATAAATTTGATATGCCTTTGAGT-TGAATGTAATCGAACTCAAAGGTCTTTTGT
195 AGCTATGTTATAAATTTGATATGCCTTTGA-TCTGAATGTAATCAAACTCAAAGGTC-TTGGT
* * * * * *
1629471 TGATAGATATCCC-TCATTGCCTTGAGCTATGCTGTAAATTTGATGTACGTCTGAGCTGAATGTA
1 TGACAGATAACCCTTC-TTGCCTTGAGTTATGCTGTAAATTGGATATACCTCTGAGCTGAATGTA
* * * *
1629535 AACGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCATGAGTTATACTGTAAATTTGA
65 AACGAACTCGAAGGTCTTTGGTTGAAAAATAACCC-CCTCGCCATGAGCTATACTGTAAATTTGA
* * * * * * *
1629599 TATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAAATAGGCCTTCTCGCCTT
129 TATGACTCTAAGCTAAATGTAATCGAACTCGAAGGTCTTGGTTGACAAATAGACCTTCTCGCCTT
* * * * *
1629664 GAGCTATGTTTTAAATTTGATGTGCCTTTGATCTTACTGTAATCAAACTCGAAGGTCTTGGT
194 GAGCTATGTTATAAATTTGATATGCCTTTGATCTGAATGTAATCAAACTCAAAGGTCTTGGT
*
1629726 TGGCAGATAACCCTTCTTGCCTTGAGTTATGCTG
1 TGACAGATAACCCTTCTTGCCTTGAGTTATGCTG
1629760 CCAATATTTC
Statistics
Matches: 242, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
255 48 0.20
256 193 0.80
257 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (255 bp):
TGACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATTGGATATACCTCTGAGCTGAATGTAA
ACGAACTCGAAGGTCTTTGGTTGAAAAATAACCCCCTCGCCATGAGCTATACTGTAAATTTGATA
TGACTCTAAGCTAAATGTAATCGAACTCGAAGGTCTTGGTTGACAAATAGACCTTCTCGCCTTGA
GCTATGTTATAAATTTGATATGCCTTTGATCTGAATGTAATCAAACTCAAAGGTCTTGGT
Found at i:1629684 original size:85 final size:84
Alignment explanation
Indices: 1629154--1629759 Score: 604
Period size: 85 Copynumber: 7.1 Consensus size: 84
1629144 TCTCAACTTA
* * * * * * * * * *
1629154 AGCTATGCTGTAAATTTGACACGCCCTTGAGCTTATTGGAATTGAACTTGAAGGTTTTTGCTGAC
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
*
1629219 AGATAACCCTTCTCACCTTG
66 AGAT-ACCCTTCTCGCCTTG
* * * *
1629239 AGTTATGCTATAAATTGGATATCCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGA
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGA
* * *
1629304 AAAATAGCCC-CCTCGCCTTG
65 CAGATA-CCCTTCTCGCCTTG
* * * * * * *
1629324 AGCTATGCTGTAAATTTGATGTGACTCTAAGCTAAATGTAATCGATCTCGAAGGTCTTGGTTGAC
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
*
1629389 AGATAACTCTTCTCGCCTTG
66 AGAT-ACCCTTCTCGCCTTG
* * * * *
1629409 AGTTATGTTATAAATTTGATATGCCTTTGAGTTGAATGTAATCGAACTCAAAGGTCTTTTGTTGA
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGA
* *
1629474 TAGATATCCC-TCATTGCCTTG
65 CAGATA-CCCTTC-TCGCCTTG
* * * * * *
1629495 AGCTATGCTGTAAATTTGATGTACGTCTGAGCTGAATGTAAACGAACTCGAAGGTCTTGGTTGAC
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
*
1629560 AGATAACCCTTCTCGCCATG
66 AGAT-ACCCTTCTCGCCTTG
* * *
1629580 AGTTATACTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGAC
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
* *
1629645 AAATAGGCCTTCTCGCCTTG
66 AGATA-CCCTTCTCGCCTTG
* * * * * * * * *
1629665 AGCTATGTTTTAAATTTGATGTGCCTTTGATCTTACTGTAATCAAACTCGAAGGTCTTGGTTGGC
1 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
*
1629730 AGATAACCCTTCTTGCCTTG
66 AGAT-ACCCTTCTCGCCTTG
*
1629750 AGTTATGCTG
1 AGCTATGCTG
1629760 CCAATATTTC
Statistics
Matches: 419, Mismatches: 91, Indels: 22
0.79 0.17 0.04
Matches are distributed among these distances:
84 13 0.03
85 323 0.77
86 83 0.20
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (84 bp):
AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
AGATACCCTTCTCGCCTTG
Found at i:1631022 original size:95 final size:95
Alignment explanation
Indices: 1630826--1631078 Score: 349
Period size: 95 Copynumber: 2.7 Consensus size: 95
1630816 GGCTAGTTGG
* * *
1630826 ATCCATAAAGTCGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAA-C---A-AG-ATATAA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTA
* *
1630885 TAATAACCTTTATCAGGCTAGTTGAATATT
66 TAATAACCTTTAACAGGCTAGCTGAATATT
* * *
1630915 ATTCATAAAGCCGGGGCATTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTA
* * *
1630980 TAATCACCTTTAAGAGGCTAGCTGAATCTT
66 TAATAACCTTTAACAGGCTAGCTGAATATT
*
1631010 ATCCATAAAGCCGGGGCATTTAACCAATTGTTTTAGAGGGACAACTCAAGCTTTATTGTATA-TA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTA
1631074 TAATA
66 TAATA
1631079 TTATAATCTG
Statistics
Matches: 142, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
89 45 0.32
90 1 0.01
93 1 0.01
94 7 0.05
95 88 0.62
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATAACCTTTAACAGGCTAGCTGAATATT
Found at i:1634749 original size:13 final size:13
Alignment explanation
Indices: 1634714--1634998 Score: 79
Period size: 13 Copynumber: 21.2 Consensus size: 13
1634704 AAAAATATTT
*
1634714 AAATAAATCAAAGA
1 AAATAAAT-AAAAA
*
1634728 AAA-ACATAAGAAA
1 AAATAAATAA-AAA
*
1634741 AAAT-AATAAATCA
1 AAATAAATAAA-AA
*
1634754 AAAGAAA-AAAAA
1 AAATAAATAAAAA
*
1634766 CAATAAATAAAAA
1 AAATAAATAAAAA
1634779 AAATAAATAATAAAA
1 AAATAAAT-A-AAAA
1634794 AAATAAATCAAAAGGGA
1 AAATAAAT-AAAA---A
1634811 AAATAAAATAAAATA
1 AAAT-AAATAAAA-A
* * *
1634826 TATTAAATAAATCA
1 AAATAAATAAA-AA
*
1634840 AAA-AAA-GAAAA
1 AAATAAATAAAAA
* *
1634851 AAAT-AATACGACA
1 AAATAAATA-AAAA
**
1634864 AAAGGAA-AAAAA
1 AAATAAATAAAAA
*
1634876 GAATAAATAAAAA
1 AAATAAATAAAAA
* * *
1634889 ATAAGAAACAAATA
1 A-AATAAATAAAAA
* * *
1634903 AATTAAAGAGAAA
1 AAATAAATAAAAA
1634916 AAATGAAATAAAACA
1 AAAT-AAATAAAA-A
* *
1634931 AAACACAA-AAAAT
1 AAATA-AATAAAAA
*
1634944 ATATAAA-AATAAA
1 AAATAAATAA-AAA
1634957 AAA-AAATTAAAAA
1 AAATAAA-TAAAAA
* *
1634970 AATTAAA-AAAATT
1 AAATAAATAAAA-A
1634983 AAATCAAATAAAAA
1 AAAT-AAATAAAAA
1634997 AA
1 AA
1634999 TGAATAATTA
Statistics
Matches: 194, Mismatches: 49, Indels: 56
0.65 0.16 0.19
Matches are distributed among these distances:
11 6 0.03
12 28 0.14
13 70 0.36
14 51 0.26
15 26 0.13
17 9 0.05
18 4 0.02
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (13 bp):
AAATAAATAAAAA
Found at i:1634760 original size:20 final size:19
Alignment explanation
Indices: 1634735--1634796 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 19
1634725 AGAAAAACAT
1634735 AAGAAAAAATAATAAATCAA
1 AAGAAAAAATAATAAAT-AA
*
1634755 AAGAAAAAAAACAATAAATAA
1 AAG--AAAAAATAATAAATAA
*
1634776 AAAAAATAAATAATAAA-AA
1 AAGAAA-AAATAATAAATAA
1634795 AA
1 AA
1634797 TAAATCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
19 7 0.19
20 12 0.33
21 4 0.11
22 13 0.36
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.13
Consensus pattern (19 bp):
AAGAAAAAATAATAAATAA
Found at i:1634779 original size:16 final size:16
Alignment explanation
Indices: 1634758--1634796 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1634748 AAATCAAAAG
1634758 AAAAAAAAC-AATAAAT
1 AAAAAAAACAAAT-AAT
*
1634774 AAAAAAAATAAATAAT
1 AAAAAAAACAAATAAT
1634790 AAAAAAA
1 AAAAAAA
1634797 TAAATCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAAACAAATAAT
Found at i:1634780 original size:17 final size:16
Alignment explanation
Indices: 1634733--1634801 Score: 61
Period size: 18 Copynumber: 4.1 Consensus size: 16
1634723 AAAGAAAAAC
*
1634733 ATAAGAAAAAATAATAA
1 ATAATAAAAAA-AATAA
*
1634750 ATCAA-AAGAAAAAAAACA
1 AT-AATAA-AAAAAATA-A
1634768 ATAAATAAAAAAAATAA
1 AT-AATAAAAAAAATAA
1634785 ATAAT-AAAAAAATAA
1 ATAATAAAAAAAATAA
1634800 AT
1 AT
1634802 CAAAAGGGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
15 12 0.27
16 3 0.07
17 10 0.22
18 18 0.40
19 2 0.04
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (16 bp):
ATAATAAAAAAAATAA
Found at i:1634953 original size:10 final size:9
Alignment explanation
Indices: 1634937--1634999 Score: 65
Period size: 9 Copynumber: 6.8 Consensus size: 9
1634927 AACAAAACAC
1634937 AAAAAATATA
1 AAAAAAT-TA
* *
1634947 TAAAAATAAA
1 AAAAAAT-TA
1634957 AAAAAATTA
1 AAAAAATTA
1634966 AAAAAATTA
1 AAAAAATTA
1634975 AAAAAATTA
1 AAAAAATTA
*
1634984 AATCAAA-TA
1 AA-AAAATTA
1634993 AAAAAAT
1 AAAAAAT
1635000 GAATAATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
8 3 0.07
9 25 0.56
10 17 0.38
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAAATTA
Found at i:1634960 original size:9 final size:9
Alignment explanation
Indices: 1634921--1634998 Score: 57
Period size: 9 Copynumber: 8.2 Consensus size: 9
1634911 AGAAAAAATG
1634921 AAATAAAACA
1 AAATAAAA-A
* *
1634931 AAACACAAA
1 AAATAAAAA
*
1634940 AAATATATAA
1 AAATA-AAAA
1634950 AAATAAAAAA
1 AAAT-AAAAA
1634960 AAATTAAAAA
1 AAA-TAAAAA
*
1634970 AATTAAAAA
1 AAATAAAAA
* **
1634979 AATTAAATC
1 AAATAAAAA
1634988 AAATAAAAA
1 AAATAAAAA
1634997 AA
1 AA
1634999 TGAATAATTA
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
9 26 0.49
10 25 0.47
11 2 0.04
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (9 bp):
AAATAAAAA
Found at i:1634970 original size:19 final size:19
Alignment explanation
Indices: 1634937--1634998 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 19
1634927 AACAAAACAC
*
1634937 AAAAAATATATAAAAATAAA
1 AAAAAAT-TAAAAAAATAAA
*
1634957 AAAAAATTAAAAAAAT-TA
1 AAAAAATTAAAAAAATAAA
*
1634975 AAAAAATTAAATCAAATAAA
1 AAAAAATTAAA-AAAATAAA
1634995 AAAA
1 AAAA
1634999 TGAATAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.33
19 12 0.33
20 12 0.33
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAAATTAAAAAAATAAA
Found at i:1636204 original size:30 final size:28
Alignment explanation
Indices: 1636139--1636211 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
1636129 ATAATAATAT
1636139 AATATATATATATATCAAAAATATTTTAA
1 AATATATAT-TATATCAAAAATATTTTAA
* *
1636168 ACTATATATTATATTAAACAA-AGTTTTAA
1 AATATATATTATATCAAA-AATA-TTTTAA
1636197 AGATATATATTATAT
1 A-ATATATATTATAT
1636212 AGTTTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 9 0.24
29 17 0.45
30 12 0.32
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (28 bp):
AATATATATTATATCAAAAATATTTTAA
Found at i:1636267 original size:35 final size:36
Alignment explanation
Indices: 1636191--1636369 Score: 195
Period size: 37 Copynumber: 4.9 Consensus size: 36
1636181 TTAAACAAAG
* *
1636191 TTTTAAAGA-TATATATTATATAGTTTTCAAAAAATAT
1 TTTTAAAAACTATATATTATATAATTTTC--AAAATAT
* *
1636228 TTTTAAAAACCATATATTATAT-ATTTTCAAAATGT
1 TTTTAAAAACTATATATTATATAATTTTCAAAATAT
1636263 TTTTAAAAACTATATATTATATAATTTTCAAAATAT
1 TTTTAAAAACTATATATTATATAATTTTCAAAATAT
* *
1636299 TTTTAAAAAATTATATACTATATAATTTTCAAAA-AT
1 TTTT-AAAAACTATATATTATATAATTTTCAAAATAT
* * *
1636335 GATTT-CAAACTATATAATATATACATTTTTCAAAA
1 -TTTTAAAAACTATATATTATATA-A-TTTTCAAAA
1636370 AAATTGTTTT
Statistics
Matches: 124, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
35 42 0.34
36 19 0.15
37 52 0.42
38 11 0.09
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATAATTTTCAAAATAT
Found at i:1636381 original size:40 final size:37
Alignment explanation
Indices: 1636200--1636440 Score: 136
Period size: 37 Copynumber: 6.4 Consensus size: 37
1636190 GTTTTAAAGA
* * *
1636200 TATATATTATATAGTTTTCAAAAAATAT-TTTTAAAAAC
1 TATATAATATATAATTTTCAAAAAAT-TGTTTT-CAAAC
* * ** **
1636238 CATATATTATAT-ATTTTCAAAATGTT-TTTAAAAAC
1 TATATAATATATAATTTTCAAAAAATTGTTTTCAAAC
* * ** *
1636273 TATATATTATATAATTTTCAAAATATT-TTTAAAAAAT
1 TATATAATATATAATTTTCAAAAAATTGTTT-TCAAAC
* *
1636310 TATATACTATATAATTTTC-AAAAA-TGATTTCAAAC
1 TATATAATATATAATTTTCAAAAAATTGTTTTCAAAC
1636345 TATATAATATATACATTTTTCAAAAAAATTGTTTTCAAAAC
1 TATATAATATATA-A-TTTTC-AAAAAATTGTTTTC-AAAC
* ** *
1636386 TATGTATATTATATATATATTT-AAAAAATCATTTGCAAAC
1 TA--TATAATATATA-AT-TTTCAAAAAATTGTTTTCAAAC
1636426 TAATATATATATATA
1 T-ATATA-ATATATA
1636441 TATATAAGAT
Statistics
Matches: 167, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
35 32 0.19
36 27 0.16
37 38 0.23
38 11 0.07
39 9 0.05
40 17 0.10
41 18 0.11
42 1 0.01
43 14 0.08
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (37 bp):
TATATAATATATAATTTTCAAAAAATTGTTTTCAAAC
Found at i:1636441 original size:40 final size:39
Alignment explanation
Indices: 1636310--1636445 Score: 111
Period size: 40 Copynumber: 3.5 Consensus size: 39
1636300 TTTAAAAAAT
* *
1636310 TATATACTATATA-AT-TTTCAAAAATGATTTCAAACTA
1 TATATACTATATATATATTTAAAAAATCATTTCAAACTA
* * **
1636347 TATA-A-TATATACATTTTTCAAAAAAATTGTTTTCAAAACTA
1 TATATACTATATATATATTT--AAAAAA-TCATTTC-AAACTA
* *
1636388 TGTATATTATATATATATTTAAAAAATCATTTGCAAACTAA
1 TATATACTATATATATATTTAAAAAATCATTT-CAAACT-A
1636429 TATATA-TATATATATAT
1 TATATACTATATATATAT
1636446 AAGATAAATA
Statistics
Matches: 81, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
35 6 0.07
36 3 0.04
37 7 0.09
39 5 0.06
40 26 0.32
41 22 0.27
42 1 0.01
43 11 0.14
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (39 bp):
TATATACTATATATATATTTAAAAAATCATTTCAAACTA
Found at i:1643502 original size:20 final size:20
Alignment explanation
Indices: 1643479--1643528 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1643469 CGAAAAGGTA
1643479 GTATTGATACCATGGTAAGG
1 GTATTGATACCATGGTAAGG
1643499 GTATTGATACCATGGTAAGG
1 GTATTGATACCATGGTAAGG
1643519 GTATTGATAC
1 GTATTGATAC
1643529 TAGGTAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32
Consensus pattern (20 bp):
GTATTGATACCATGGTAAGG
Found at i:1643610 original size:95 final size:94
Alignment explanation
Indices: 1643459--1643718 Score: 260
Period size: 95 Copynumber: 2.8 Consensus size: 94
1643449 AATTTAATCA
* * * * * *
1643459 GTATCGGTACCGAAAAGGTAGTATTGATACCATGGTAAGGGTA-T-TGATACCATGGTAAGGGTA
1 GTATCGATACC-AGAAGGGAGTATAGATACCATAG-AAGAGTAGTATGATACCATGGTAAGGGTA
*
1643522 TTGATACTAGGT-AACATCGAACCTAATTTTG
64 TCGATACTA-GTCAACATCGAACCTAATTTTG
* * *
1643553 GTATCGATACCAGGAGGGGGTATTAG-TACCATAGAATAGTAGTATCGATACCATGGTAAGGGTA
1 GTATCGATACCAGAAGGGAGTA-TAGATACCATAGAAGAGTAGTAT-GATACCATGGTAAGGGTA
* * *
1643617 TCGATACTATTCCACATCGAATCTAATTTTG
64 TCGATACTAGTCAACATCGAACCTAATTTTG
* * * * *
1643648 GTATCGATACTAGAAGGGAGTATCGATACCATAGTAGGGTAGTAGTGATACCATGGT-AGGATAT
1 GTATCGATACCAGAAGGGAGTATAGATACCATAGAAGAGTAGTA-TGATACCATGGTAAGGGTAT
*
1643712 CAATACT
65 CGATACT
1643719 GAAGAACCAT
Statistics
Matches: 137, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
92 5 0.04
93 15 0.11
94 28 0.20
95 88 0.64
96 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (94 bp):
GTATCGATACCAGAAGGGAGTATAGATACCATAGAAGAGTAGTATGATACCATGGTAAGGGTATC
GATACTAGTCAACATCGAACCTAATTTTG
Found at i:1644018 original size:59 final size:59
Alignment explanation
Indices: 1643950--1644287 Score: 491
Period size: 59 Copynumber: 5.7 Consensus size: 59
1643940 ATGGCACTAA
* * * *
1643950 GTGTACTAAAATGTTATGAAATTCATACTAAGTGTATGAATTTTTGTATAGGGCACTTT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATAGGGCACTTC
* * * *
1644009 GTGTGCTAAAATGACAAGAAATTCATACTAAATGTGTGAATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATAGGGCACTTC
* * * *
1644068 GTGTGTTAAAATGATAAGAAATTCAAACTAAGTGTGTGAATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATAGGGCACTTC
* *
1644127 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTA-CATATTTCTGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGA-ATTTTTGTATAGGGCACTTC
* *
1644186 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGGCATCTT-
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATAGGGCA-CTTC
*
1644245 GTGTGCTAATATGATAAGAAATTCATACTAAGTGTATGAATTT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTT
1644288 CCATATGTGA
Statistics
Matches: 252, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
58 1 0.00
59 247 0.98
60 4 0.02
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.36
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATAGGGCACTTC
Found at i:1645910 original size:40 final size:40
Alignment explanation
Indices: 1645819--1645902 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
1645809 TAGTGTTTAT
* *
1645819 AGATGATATCCTGGTTTATTCAAAGTTAAAGGAGGATCAC
1 AGATGATATCTTGGTTTATTCAAAGTTAAAGGAGGACCAC
*
1645859 AGATGATATCTTGGTTTATTCCAAGTTAAAGGAGGACCAC
1 AGATGATATCTTGGTTTATTCAAAGTTAAAGGAGGACCAC
1645899 -GATG
1 AGATG
1645903 CTTATCTTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 4 0.10
40 37 0.90
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (40 bp):
AGATGATATCTTGGTTTATTCAAAGTTAAAGGAGGACCAC
Found at i:1647956 original size:94 final size:95
Alignment explanation
Indices: 1647857--1648036 Score: 247
Period size: 95 Copynumber: 1.9 Consensus size: 95
1647847 ATATCAGATA
* * * * *
1647857 ACATCGAACCTAATTTTGGTATCGATACCAGGA-GGGGTATCAATACCATGGAATAGTAGTATCG
1 ACATCGAACCTAATTTTGGTATAGATACCAGAAGGGGGTATCAATACAATAGAAGAGTAGTATCG
1647921 ATACCATGGT-GAGAGTATCGAAACCATACC
66 ATACCATGGTAG-GAGTATCGAAACCATACC
* * * * *
1647951 ACATCGAATCTAATTTTGGTATAGGTACCAGAAGGGGGTATCAATACAATAGTAGGGTAGTATTG
1 ACATCGAACCTAATTTTGGTATAGATACCAGAAGGGGGTATCAATACAATAGAAGAGTAGTATCG
1648016 ATACCATGGTAGGAGTATCGA
66 ATACCATGGTAGGAGTATCGA
1648037 TATTAAAGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
94 29 0.39
95 44 0.59
96 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (95 bp):
ACATCGAACCTAATTTTGGTATAGATACCAGAAGGGGGTATCAATACAATAGAAGAGTAGTATCG
ATACCATGGTAGGAGTATCGAAACCATACC
Found at i:1648440 original size:59 final size:59
Alignment explanation
Indices: 1648371--1648828 Score: 686
Period size: 59 Copynumber: 7.8 Consensus size: 59
1648361 ATGGCACTAA
* *
1648371 GTGTGTTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
*
1648430 GTGTGCTAAAATTATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * * *
1648489 GTGTGCTAAAATGATAAGACATTCATACTAAGTGTGTGAATTTTCATATAGGCCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
1648548 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTGTGAATTTCCATATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * *
1648607 GTGTGCTAAAATGATAAGAAATTCGTACTATGTGTGTGAATTTCCGTAAAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * *
1648666 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTAAGGATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * *
1648725 GTGTGCTAAAATGTTAAGAAATTCATACTCAGTGTATTAATTTTCGTATTA-GGCATCTT-
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTA-TAGGGCA-CTTC
*
1648784 GTGTACTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCC
1648829 ATATGTGAAA
Statistics
Matches: 364, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
59 359 0.99
60 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
Found at i:1650019 original size:59 final size:59
Alignment explanation
Indices: 1649544--1650004 Score: 615
Period size: 59 Copynumber: 7.8 Consensus size: 59
1649534 ATGACACTAA
*
1649544 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTC
* * * *
1649603 GTGTGCTAAAATTATAAGAAATTCATACTAACTGTGTGAATTT-TCGTATAGGGTACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCT-GTATAGGGCACTTC
* * * * *
1649662 ATGTGCTAAAATGATAAGAAATTCATAGTAAGTGTGTGAATTTCCGTATAGGGCACTTT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTC
* * *
1649721 GTGTGCTAAATTGATAAGAAATTCATACTAGGTGTGTGAATTTCTGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTC
* * * * *
1649780 GTGTGCTAAAAAGATAAGAATTTTATACTAAGTGTGTGAATTT-TCGTATAGGGAACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCT-GTATAGGGCACTTC
* * **
1649839 GTGTGCTAAAATGATAAGAAATTTATACTAAGTGTATGGATTTCCATATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTC
* * * * *
1649898 GTGTGCTAAAATGTTAAGAAATTTATACTAAGTGTATGAATTTCCGTATTGGCCACCTT-
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCA-CTTC
*
1649957 GTGTGCTAAAATGATAAGAAATT-ATACTAAGTTTATGAATTTCTGTAT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTAT
1650005 GTGAAATATA
Statistics
Matches: 358, Mismatches: 39, Indels: 11
0.88 0.10 0.03
Matches are distributed among these distances:
58 25 0.07
59 330 0.92
60 3 0.01
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTC
Found at i:1652398 original size:19 final size:19
Alignment explanation
Indices: 1652374--1652424 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1652364 CTTCTTGGTC
1652374 AAAGTCAACGGTCTGGGTA
1 AAAGTCAACGGTCTGGGTA
* * *
1652393 AAAGTCAATGGT-TTGGTC
1 AAAGTCAACGGTCTGGGTA
*
1652411 AAAGTTAACGGTCT
1 AAAGTCAACGGTCT
1652425 AACCGGTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (19 bp):
AAAGTCAACGGTCTGGGTA
Found at i:1655213 original size:246 final size:248
Alignment explanation
Indices: 1654749--1655239 Score: 851
Period size: 246 Copynumber: 2.0 Consensus size: 248
1654739 TAGCTGCTAC
1654749 GATGAGAGTCATCTTATCACAACTACTATCCTACACTCTAGATGAACTGAATCAAACATTCCATC
1 GATGAGAGTCATCTTATCACAACTAC-ATCCTACACTCTAGATGAACTGAATCAAACATTCCATC
* * *
1654814 CCTGAGCTAGTCAGGCAGAGTCATTCTATGACTACTTTCATTCACTCAAATACTACAATTGTCAT
65 CCTAAGCTAGTCAGGCAGAGTCATCCTATGACTACTTTCATTCACTCAAATACTACAACTGTCAT
* * *
1654879 TTATTGAAAGGGGTTTCCATGCAATGCTATAACAATGAGAAGTGTCCCTCAATAGTAATGTCGAA
130 TTATTGAAAGGGGTTTCCATGCAAAGCTATAACAAAGAGAAGTGTCCCTCAATAGTAATGTCAAA
*
1654944 GCATTTATTCACATATCAACACATTTACTAACATAAGGGAGTTTAATTTACTAT
195 GCATTTATTCACATATCAACACATTTACCAACATAAGGGAGTTTAATTTACTAT
*
1654998 GATGGGAGTCATCTTATCACAACTAC-T-CTACACTCTAGATGAACTGAATCAAACATTCCATCC
1 GATGAGAGTCATCTTATCACAACTACATCCTACACTCTAGATGAACTGAATCAAACATTCCATCC
* * *
1655061 CTAAGCTAGTCAGGTAGAGTCATCCTGTGACTACTTTCATTCACTCATATACTACAACTGTCATT
66 CTAAGCTAGTCAGGCAGAGTCATCCTATGACTACTTTCATTCACTCAAATACTACAACTGTCATT
*
1655126 TATTGAAAGGGGTTTCCATGCAAAGCTATAACAAAGAGGAGTGTCCCTCAATAGTAATGTCAAAG
131 TATTGAAAGGGGTTTCCATGCAAAGCTATAACAAAGAGAAGTGTCCCTCAATAGTAATGTCAAAG
1655191 CATTTATTCACATATCAACACATTTACCAACATAAGGGAGTTTAATTTA
196 CATTTATTCACATATCAACACATTTACCAACATAAGGGAGTTTAATTTA
1655240 AGAATTTATT
Statistics
Matches: 230, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
246 204 0.89
247 1 0.00
249 25 0.11
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (248 bp):
GATGAGAGTCATCTTATCACAACTACATCCTACACTCTAGATGAACTGAATCAAACATTCCATCC
CTAAGCTAGTCAGGCAGAGTCATCCTATGACTACTTTCATTCACTCAAATACTACAACTGTCATT
TATTGAAAGGGGTTTCCATGCAAAGCTATAACAAAGAGAAGTGTCCCTCAATAGTAATGTCAAAG
CATTTATTCACATATCAACACATTTACCAACATAAGGGAGTTTAATTTACTAT
Found at i:1677868 original size:9 final size:8
Alignment explanation
Indices: 1677846--1677870 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1677836 TAGGATGATT
1677846 TTAAAAAA
1 TTAAAAAA
1677854 TTAAAAAA
1 TTAAAAAA
1677862 TTAAAAAA
1 TTAAAAAA
1677870 T
1 T
1677871 AATAGTACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TTAAAAAA
Found at i:1685444 original size:53 final size:53
Alignment explanation
Indices: 1685380--1685486 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 53
1685370 TTTCCTGTAC
*** * * *
1685380 TTTCGAAACTATGTGTGCATTTATGGTATTCATAATGAGTTTTTGAATTACCA
1 TTTCGAAACTATGTGTGCACCCATGGTAATCATAATGAGGTTGTGAATTACCA
*
1685433 TTTCGACACTATGTGTGCACCCATGGTAATCATAATGAGGTTGTGAATTACCA
1 TTTCGAAACTATGTGTGCACCCATGGTAATCATAATGAGGTTGTGAATTACCA
1685486 T
1 T
1685487 ATAGTTACAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (53 bp):
TTTCGAAACTATGTGTGCACCCATGGTAATCATAATGAGGTTGTGAATTACCA
Found at i:1689144 original size:25 final size:24
Alignment explanation
Indices: 1689116--1689163 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1689106 CGAATTAATT
1689116 AAAAAAATCTTATTTTACTTATTCC
1 AAAAAAATCTTATTTTA-TTATTCC
* *
1689141 AAAAAACTTTTATTTTATTATTC
1 AAAAAAATCTTATTTTATTATTC
1689164 TAAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAAAAATCTTATTTTATTATTCC
Found at i:1726336 original size:24 final size:24
Alignment explanation
Indices: 1726304--1726364 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
1726294 TATTTTTTGT
1726304 GAAGGACCACATAGGTTTTGTCCC
1 GAAGGACCACATAGGTTTTGTCCC
1726328 GAAGGACCACATA-GTTTTGTCCC
1 GAAGGACCACATAGGTTTTGTCCC
1726351 -AGAGGACCACATAG
1 GA-AGGACCACATAG
1726365 AACCCTCGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
22 1 0.03
23 21 0.60
24 13 0.37
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (24 bp):
GAAGGACCACATAGGTTTTGTCCC
Found at i:1733198 original size:23 final size:24
Alignment explanation
Indices: 1733150--1733210 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
1733140 CCACATATTT
*
1733150 TCCCGAAGGACCATATAGGTTTTG
1 TCCCGAAGGACCACATAGGTTTTG
*
1733174 TCCCAAAGGACCACATA-GTTTTG
1 TCCCGAAGGACCACATAGGTTTTG
*
1733197 TCTCGAAGGACCAC
1 TCCCGAAGGACCAC
1733211 GTAGAACCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (24 bp):
TCCCGAAGGACCACATAGGTTTTG
Found at i:1754566 original size:21 final size:20
Alignment explanation
Indices: 1754520--1754569 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
1754510 GGGTCTACGT
* *
1754520 GGTCCTTCGGACATATATGT
1 GGTCCTTTGGACATATATGC
**
1754540 AATCCTTTGGAACATATATGC
1 GGTCCTTTGG-ACATATATGC
1754561 GGTCCTTTG
1 GGTCCTTTG
1754570 ACACACATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
GGTCCTTTGGACATATATGC
Found at i:1754677 original size:23 final size:23
Alignment explanation
Indices: 1754651--1754707 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1754641 TTTATATAGA
*
1754651 ACTTCGGT-CAATTTCTACGTGGC
1 ACTTCGGTGCAA-TTCTACATGGC
* *
1754674 ACTTTGGTGCAATTCTATATGGC
1 ACTTCGGTGCAATTCTACATGGC
*
1754697 CCTTCGGTGCA
1 ACTTCGGTGCA
1754708 TTTATACGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.35
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACATGGC
Found at i:1764088 original size:21 final size:21
Alignment explanation
Indices: 1764063--1764109 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1764053 CGTTGATGTG
1764063 CCACCACTAGCAACTCAAGTA
1 CCACCACTAGCAACTCAAGTA
1764084 CCACCACTAGCAACTCAAGTA
1 CCACCACTAGCAACTCAAGTA
1764105 CCACC
1 CCACC
1764110 TGTACCAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.43, G:0.09, T:0.13
Consensus pattern (21 bp):
CCACCACTAGCAACTCAAGTA
Found at i:1765538 original size:65 final size:65
Alignment explanation
Indices: 1765405--1765564 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
1765395 TGCACTAAGA
* *
1765405 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATACATGGCTG
1 GTGCATCGATGCATGAAATGCATTAGATGTTTTCAAAATAGCCAGAGTGCATCGATACATAGCTG
* * * *
1765469 GTGCATCGATGCATCAAATGCATTAAATGTTTTCATAAA-A-CTATGAGTGCATCGATGCATAG-
1 GTGCATCGATGCATGAAATGCATTAGATGTTTTCA-AAATAGCCA-GAGTGCATCGATACATAGC
*
1765531 TAT
64 T-G
1765534 GTGCATCGATGCATGAAATGCATTAGATGTT
1 GTGCATCGATGCATGAAATGCATTAGATGTT
1765565 CAATTTTATT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 29 0.35
65 51 0.61
66 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTAGATGTTTTCAAAATAGCCAGAGTGCATCGATACATAGCTG
Found at i:1765584 original size:65 final size:64
Alignment explanation
Indices: 1765386--1765593 Score: 176
Period size: 65 Copynumber: 3.2 Consensus size: 64
1765376 TGGACCCTTG
* * ** *
1765386 GTGCATCGGTGCACTAAG-AGTGCATCGATGCATGAAATGCATTCGATGTTTCAA-AATAGCCA-
1 GTGCATCGATGCA-T-AGTAGTGCATCGATGCATGAAATGCATTAGATG-TTCAATTTTAACCAT
1765448 GA
63 GA
* * * * * ** *
1765450 GTGCATCGATACATGGCTGGTGCATCGATGCATCAAATGCATTAAATGTTTTC-A-TAAAACTAT
1 GTGCATCGATGCATAG-TAGTGCATCGATGCATGAAATGCATTAGATG--TTCAATTTTAACCAT
1765513 GA
63 GA
*
1765515 GTGCATCGATGCATAGTATGTGCATCGATGCATGAAATGCATTAGATGTTCAATTTTATTCCATG
1 GTGCATCGATGCATAGTA-GTGCATCGATGCATGAAATGCATTAGATGTTCAATTTTA-ACCATG
1765580 -
64 A
1765580 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1765594 CACTTTGAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 44 0.38
65 63 0.54
66 4 0.03
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAGTAGTGCATCGATGCATGAAATGCATTAGATGTTCAATTTTAACCATGA
Found at i:1765956 original size:55 final size:56
Alignment explanation
Indices: 1765890--1766000 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
1765880 AAATTTTGAA
*
1765890 AAATTAAGTTTGAAATTACT-CCCTTTACTTTAACACTTCTCCCCTTTAAAACATT
1 AAATTAAGTTTGAAATTACTCCCCCTTACTTTAACACTTCTCCCCTTTAAAACATT
*
1765945 AAATTAAGTTTGAAATTACTCCCCCTTACTTTAACACTTCTCTCCTTTAAAACATT
1 AAATTAAGTTTGAAATTACTCCCCCTTACTTTAACACTTCTCCCCTTTAAAACATT
1766001 TTAACACTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 20 0.38
56 33 0.62
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (56 bp):
AAATTAAGTTTGAAATTACTCCCCCTTACTTTAACACTTCTCCCCTTTAAAACATT
Found at i:1774312 original size:65 final size:63
Alignment explanation
Indices: 1774118--1774321 Score: 188
Period size: 65 Copynumber: 3.2 Consensus size: 63
1774108 AGCACTAAGA
* * *
1774118 GTGCATCGATGCATGAAATGCATTCGATG-T-AAATAGCCA-GAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTAACCATGAGTGCATCGATGCATGGTTG
* * * * *
1774178 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAGTTCATCGATACATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG--TTCAAT-TAAC-CATGAGTGCATCGATGCATGGT
1774241 AT-
62 -TG
* *
1774243 GTGCATCGATGCATGAAATGAATTCGATGTTCAATTTATTCCATG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAAATGCATTCGATGTTCAA-TTA-ACCATGAGTGCATCGATGCATGG-TT
1774307 G
63 G
*
1774308 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
1774322 CATTTTGAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
60 28 0.25
63 5 0.04
64 19 0.17
65 61 0.54
66 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTCAATTAACCATGAGTGCATCGATGCATGGTTG
Found at i:1782670 original size:44 final size:44
Alignment explanation
Indices: 1782620--1782755 Score: 202
Period size: 44 Copynumber: 3.1 Consensus size: 44
1782610 CCATTACAAA
*
1782620 GGAAGTATCGGTATTGTACCTTGGGTACCGATACTATTTAATAG
1 GGAAGTATCGGTAATGTACCTTGGGTACCGATACTATTTAATAG
* *
1782664 GGAAGTATCGATACTGTACCTTGGGTACCGATACTATTTAATAG
1 GGAAGTATCGGTAATGTACCTTGGGTACCGATACTATTTAATAG
* * *
1782708 GGAAGTATCGGTAATGTATCC-TGGGTATCGATACTACTTAATAA
1 GGAAGTATCGGTAATGTA-CCTTGGGTACCGATACTATTTAATAG
1782752 GGAA
1 GGAA
1782756 AATGTGAATT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 82 0.98
45 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (44 bp):
GGAAGTATCGGTAATGTACCTTGGGTACCGATACTATTTAATAG
Found at i:1783287 original size:21 final size:21
Alignment explanation
Indices: 1783220--1783296 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1783210 CGTGGTCTAC
* *
1783220 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTTGGAACATATAT
**
1783241 GTAATCCTTTGGAACATATAT
1 GTGGTCCTTTGGAACATATAT
1783262 GTGGTCCTTTGAGACACATAT-T
1 GTGGTCCTTTG-GA-ACATATAT
1783284 -TGGTCCTTTGGAA
1 GTGGTCCTTTGGAA
1783297 TATGCTTATG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 36 0.75
22 3 0.06
23 6 0.12
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (21 bp):
GTGGTCCTTTGGAACATATAT
Found at i:1783418 original size:23 final size:23
Alignment explanation
Indices: 1783350--1783418 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1783340 ACATTTTATA
1783350 TGGCACTTCAGG-GCATTTCTACG
1 TGGCACTTC-GGTGCATTTCTACG
* * * *
1783373 CGACACTTTGGTGCAGTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
1783396 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
1783419 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1785403 original size:32 final size:32
Alignment explanation
Indices: 1785336--1785409 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1785326 TCTCATGATT
* * *
1785336 TACCCAAGGGAGCGCCTTGAGGCCTTAGAGTC
1 TACCTAAGGGAGCACCTTGAGGCCTTAGAGCC
* *
1785368 TACCTAAGGGAGTACCTT-AGGGCTTAAGAGCC
1 TACCTAAGGGAGCACCTTGAGGCCTT-AGAGCC
1785400 TACCTAAGGG
1 TACCTAAGGG
1785410 CCACCTTAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 6 0.17
32 30 0.83
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (32 bp):
TACCTAAGGGAGCACCTTGAGGCCTTAGAGCC
Found at i:1794679 original size:31 final size:32
Alignment explanation
Indices: 1794644--1794800 Score: 165
Period size: 32 Copynumber: 5.0 Consensus size: 32
1794634 CGAACCTAAT
* *
1794644 GGAATGCCTTGGGGCCTTAGAGCCTAACC-AA
1 GGAATACCTTGGGGCCTTAGAGCCTACCCAAA
* *
1794675 GGAATACCTTGGGGCCTTAGATCCTACCCAAG
1 GGAATACCTTGGGGCCTTAGAGCCTACCCAAA
* *
1794707 GGAGTACCTTGGGG-CTGAGAGCCTACCCAAA
1 GGAATACCTTGGGGCCTTAGAGCCTACCCAAA
* * * *
1794738 GGAATATCTCGTGGCCTCAGAGCCTACCCAAA
1 GGAATACCTTGGGGCCTTAGAGCCTACCCAAA
* * * * *
1794770 GGAATATCTCGTGGCCTCAAAGCCTACCCAA
1 GGAATACCTTGGGGCCTTAGAGCCTACCCAA
1794801 TGGTCATCAT
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
31 50 0.45
32 60 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (32 bp):
GGAATACCTTGGGGCCTTAGAGCCTACCCAAA
Found at i:1794740 original size:63 final size:63
Alignment explanation
Indices: 1794650--1794768 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
1794640 TAATGGAATG
* * * *
1794650 CCTTGGGGCCTTAGAGCCTAACCAAGGAATACCTTGGGGCCTTAGATCCTACCCAAGGGAGTA
1 CCTTGGGGCCTGAGAGCCTAACCAAGGAATACCTCGGGGCCTCAGAGCCTACCCAAGGGAGTA
* * *
1794713 CCTTGGGG-CTGAGAGCCTACCCAAAGGAATATCTCGTGGCCTCAGAGCCTACCCAA
1 CCTTGGGGCCTGAGAGCCTAACC-AAGGAATACCTCGGGGCCTCAGAGCCTACCCAA
1794769 AGGAATATCT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 12 0.25
63 36 0.75
ACGTcount: A:0.25, C:0.29, G:0.26, T:0.19
Consensus pattern (63 bp):
CCTTGGGGCCTGAGAGCCTAACCAAGGAATACCTCGGGGCCTCAGAGCCTACCCAAGGGAGTA
Found at i:1796958 original size:13 final size:13
Alignment explanation
Indices: 1796940--1796989 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
1796930 TGACTTTTTA
1796940 GTCAAAGTCAATG
1 GTCAAAGTCAATG
1796953 GTCAAAGTCAATG
1 GTCAAAGTCAATG
*
1796966 GTCAAAGCCAATG
1 GTCAAAGTCAATG
1796979 GTCAAAGTCAA
1 GTCAAAGTCAA
1796990 CCTTGGATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (13 bp):
GTCAAAGTCAATG
Found at i:1823957 original size:17 final size:19
Alignment explanation
Indices: 1823916--1823957 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1823906 GGATTGTAGC
1823916 TGTATCGGTACACTATCAAAG
1 TGTATCGGTACAC-ATC-AAG
1823937 TGTATCGGTACAC-TC-AG
1 TGTATCGGTACACATCAAG
1823954 TGTA
1 TGTA
1823958 AAATTGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
19 2 0.10
21 13 0.62
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (19 bp):
TGTATCGGTACACATCAAG
Found at i:1824324 original size:19 final size:20
Alignment explanation
Indices: 1824300--1824343 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1824290 TAATTTAATC
*
1824300 GAATATATAAT-TTAAAATT
1 GAATATAAAATCTTAAAATT
1824319 GAATATAAAATCTTAAAATT
1 GAATATAAAATCTTAAAATT
*
1824339 CAATA
1 GAATA
1824344 ATATTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
GAATATAAAATCTTAAAATT
Found at i:1824451 original size:13 final size:13
Alignment explanation
Indices: 1824435--1824470 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1824425 TAAGATTTCC
1824435 TTTTTGAAAATCA
1 TTTTTGAAAATCA
1824448 TTTTTG-AAATCA
1 TTTTTGAAAATCA
*
1824460 ATTTTGAAAAT
1 TTTTTGAAAAT
1824471 TTACTCCCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:1827492 original size:9 final size:9
Alignment explanation
Indices: 1827475--1827507 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1827465 AATAAAAATA
*
1827475 AATAGTATT
1 AATAATATT
1827484 AATAATATT
1 AATAATATT
1827493 AATAATA-T
1 AATAATATT
1827501 AATAATA
1 AATAATA
1827508 ATTATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (9 bp):
AATAATATT
Found at i:1827970 original size:73 final size:74
Alignment explanation
Indices: 1827690--1827993 Score: 310
Period size: 73 Copynumber: 4.1 Consensus size: 74
1827680 ATCATACTCG
* * * * *
1827690 AGATTGATTTGCTTCACCACTCTTC-GATGAAGGCCTAAAATGAATTTGCTTCACTACTCTTCAG
1 AGATTGATTTGCTTCACTACTCTTCAG-TGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCGG
1827754 TGAAGGCTTA
65 TGAAGGCTTA
** *** **** * *
1827764 CTATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGG-CCCGGAGGACTTAATCATCAT
1 AGATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTGCTTCAC-TACTCTTC--
*
1827828 GCTCGGAAGGC-TA
63 GGT--GAAGGCTTA
* ** *
1827841 ACTAATAAATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCG
1 A--GATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCG
1827906 GTGAAGGCTTA
64 GTGAAGGCTTA
*
1827917 AGATTGA-TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGT
1 AGATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGT
1827981 GAAGGCTTA
66 GAAGGCTTA
1827990 AGAT
1 AGAT
1827994 GGCCCGAAGG
Statistics
Matches: 183, Mismatches: 37, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
73 71 0.39
74 44 0.24
75 7 0.04
76 4 0.02
77 4 0.02
78 6 0.03
79 44 0.24
80 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (74 bp):
AGATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGT
GAAGGCTTA
Found at i:1827991 original size:37 final size:37
Alignment explanation
Indices: 1827690--1827995 Score: 285
Period size: 37 Copynumber: 8.2 Consensus size: 37
1827680 ATCATACTCG
* * * *
1827690 AGATTGATTTGCTTCACCACTCTTCGATGAAGGCCTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * *
1827727 AAATGAATTTGCTTCACTACTCTTCAGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
** * *
1827764 CTATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*** **** * * *
1827801 AGATGG-CCCGGAGGACTTAATCATCATGCTCGGAAGGC-TA
1 AGATGGATTTGCTTCAC-TACTCTTC--GGT--GAAGGCTTA
* ** *
1827841 ACTAATAAATTTGCTTCACTACTCTTCAGTGAAGGCTTA
1 A--GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*
1827880 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*
1827917 AGATTGA-TTGCTTCACTACTCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1827953 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1827990 AGATGG
1 AGATGG
1827996 CCCGAAGGAC
Statistics
Matches: 215, Mismatches: 44, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
36 38 0.18
37 146 0.68
38 6 0.03
39 4 0.02
40 4 0.02
41 6 0.03
42 8 0.04
43 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (37 bp):
AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
Found at i:1828061 original size:42 final size:40
Alignment explanation
Indices: 1827986--1828113 Score: 125
Period size: 42 Copynumber: 3.1 Consensus size: 40
1827976 TCGGTGAAGG
* * * * *
1827986 CTTA-AGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGG
1 CTTATAGAT-GCCTGAAGGATTTATCATCATGCTCGAAAGA
*
1828026 CTTATAGATGACCTAAAGGATTTAATCATCATGCTCGAAAGA
1 CTTATAGATG-CCTGAAGGATTT-ATCATCATGCTCGAAAGA
*
1828068 CTTACT-GATGTCTCGAAGGATTTCATCATCATGCTCGAAAGA
1 CTTA-TAGATGCCT-GAAGGATTT-ATCATCATGCTCGAAAGA
1828110 CTTA
1 CTTA
1828114 CTAATGGATT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
40 5 0.07
41 15 0.20
42 53 0.72
43 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (40 bp):
CTTATAGATGCCTGAAGGATTTATCATCATGCTCGAAAGA
Found at i:1828084 original size:20 final size:19
Alignment explanation
Indices: 1828054--1828115 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
1828044 GATTTAATCA
1828054 TCATGCTCGAAAGACTTAC
1 TCATGCTCGAAAGACTTAC
* * *
1828073 TGATGTCTCGAAGGATTTCATC
1 TCATG-CTCGAAAGACTT-A-C
1828095 ATCATGCTCGAAAGACTTAC
1 -TCATGCTCGAAAGACTTAC
1828115 T
1 T
1828116 AATGGATTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 5 0.15
20 11 0.33
21 2 0.06
22 11 0.33
23 4 0.12
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (19 bp):
TCATGCTCGAAAGACTTAC
Found at i:1828360 original size:42 final size:41
Alignment explanation
Indices: 1828258--1828364 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
1828248 ACCCAAAGGT
* * * *
1828258 CTTACGGATGGCCAGAAGGACTTATCATCTTGCTCGAAAGT
1 CTTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* * * * *
1828299 CTTACAGATGACTCTAAGGATTTAATCATCATGCTGGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGA
*
1828341 CTTACTGATGGCCCGAAGGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
1828365 CCAATTTTGG
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
41 18 0.35
42 33 0.65
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:1828504 original size:225 final size:225
Alignment explanation
Indices: 1828217--1828864 Score: 1021
Period size: 225 Copynumber: 2.9 Consensus size: 225
1828207 GATTTAATCA
** * * * *
1828217 TCATTTTTTTATAGACATGTAAAAACATCCTACCCAAAGGTCTTACGGATGGCCAGAAGGACTTA
1 TCATTTTTCAATAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTA
* * * * *
1828282 TCATCTTGCTCGAAAGTCTTACAGATGACTCT-AAGGATTTAATCATCATGCTGGAAAGACTTAC
66 TCATCTTGCTTGAAAGGCTTACAGATGAC-CTGAAGGGTTTAAACATCATGCTCGAAAGACTTAC
* *
1828346 TGATGGCCCGAAGGACTTACCAATTTTGGAAATAATTTACAAGGTAAGAAAACTTTCTTACTTTT
130 TAATGGCCCGAAGGACTTACCAATTTTGGAAATAATTTACAAGGTAAGAAATCTTTCTTACTTTT
1828411 CAAATCTTCAGATTTTAATGAGAAAACATTC
195 CAAATCTTCAGATTTTAATGAGAAAACATTC
* *
1828442 TCATTTTTCAATAGATATGTGAAAACATCCTGCCCAAAGATCTTATGGATGGCCCGAAGGACTTA
1 TCATTTTTCAATAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTA
*
1828507 TCATCTTGCTTGAAAGGCTTACAGATGGCCTGAAGGGTTTAAACATCATGCTCGAAAGACTTACT
66 TCATCTTGCTTGAAAGGCTTACAGATGACCTGAAGGGTTTAAACATCATGCTCGAAAGACTTACT
*
1828572 AATGGCCCGAAGGACTTACCAATTTTGGAAATAATTTACTAGGTAAGAAATCTTTCTTACTTTTC
131 AATGGCCCGAAGGACTTACCAATTTTGGAAATAATTTACAAGGTAAGAAATCTTTCTTACTTTTC
* *
1828637 AAATCTTCAGATTTTAATGAGAAATCTTTC
196 AAATCTTCAGATTTTAATGAGAAAACATTC
* * *
1828667 TCATTTTTCGATAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGACCCGAATGACTTA
1 TCATTTTTCAATAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTA
* *
1828732 TCATCTTGCTTGAAAGGCTTACAGATGACCTGAAGGGTTTAAGCATCATGCTCGAAAGACATACT
66 TCATCTTGCTTGAAAGGCTTACAGATGACCTGAAGGGTTTAAACATCATGCTCGAAAGACTTACT
* * *
1828797 AATGGCCCGAAGGACTTACTAATTTTGGAAATAGTTTACTCA-GTAAGAAATCTTTCTTACTTTT
131 AATGGCCCGAAGGACTTACCAATTTTGGAAATAATTTAC-AAGGTAAGAAATCTTTCTTACTTTT
1828861 CAAA
195 CAAA
1828865 AATTTCAAAT
Statistics
Matches: 391, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
224 2 0.01
225 388 0.99
226 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (225 bp):
TCATTTTTCAATAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTA
TCATCTTGCTTGAAAGGCTTACAGATGACCTGAAGGGTTTAAACATCATGCTCGAAAGACTTACT
AATGGCCCGAAGGACTTACCAATTTTGGAAATAATTTACAAGGTAAGAAATCTTTCTTACTTTTC
AAATCTTCAGATTTTAATGAGAAAACATTC
Found at i:1830353 original size:125 final size:125
Alignment explanation
Indices: 1830126--1830380 Score: 357
Period size: 125 Copynumber: 2.0 Consensus size: 125
1830116 CTAATGACGT
* * * *
1830126 AACATTATCGTATACTGGTACACACCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCGTTC
1 AACATTATCGTATACCGGTACACACCCTCAAAATGCCCCATCACCTCAAATTGAAAGGCTCATTC
* * * *
1830191 TTTATGCCTCCTTGGTCTGAATCTTATCAACTTAACATGATGTGGGTTTAGTCGTGCCCC
66 TTCATGCCTCCTTGGTCTAAATCTTATCAACTCAACATGATGTGGGTTCAGTCGTGCCCC
* *** *
1830251 AACATTATCTTATACCGGTACGGGCCCTCAAAATGCCTCATCACCTCAAATTGAAAGGCTCATTC
1 AACATTATCGTATACCGGTACACACCCTCAAAATGCCCCATCACCTCAAATTGAAAGGCTCATTC
* * * *
1830316 TTCATGCCTCCTTGGTTTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCT
66 TTCATGCCTCCTTGGTCTAAATCTTATCAACTCAACATGATGTGGGTTCAGTCGTGCCCC
1830376 AACAT
1 AACAT
1830381 ATCCTAACTT
Statistics
Matches: 113, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
125 113 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (125 bp):
AACATTATCGTATACCGGTACACACCCTCAAAATGCCCCATCACCTCAAATTGAAAGGCTCATTC
TTCATGCCTCCTTGGTCTAAATCTTATCAACTCAACATGATGTGGGTTCAGTCGTGCCCC
Found at i:1835425 original size:16 final size:16
Alignment explanation
Indices: 1835397--1835447 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1835387 GTAACAAAAT
1835397 AAAAAGAAATAAT-AG
1 AAAAAGAAATAATAAG
*
1835412 AAAAATAAATTAATAAG
1 AAAAAGAAA-TAATAAG
* *
1835429 AAAATGCAAAAAATAAG
1 AAAAAG-AAATAATAAG
1835446 AA
1 AA
1835448 TGCAATTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.28
16 4 0.14
17 14 0.48
18 3 0.10
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAAAGAAATAATAAG
Found at i:1837893 original size:2 final size:2
Alignment explanation
Indices: 1837886--1837911 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1837876 TCATTAATAA
1837886 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
1837912 GTAACAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1839477 original size:9 final size:9
Alignment explanation
Indices: 1839460--1839492 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1839450 AATAAAAATA
*
1839460 AATAGTATT
1 AATAATATT
1839469 AATAATATT
1 AATAATATT
1839478 AATAATA-T
1 AATAATATT
1839486 AATAATA
1 AATAATA
1839493 ATTATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (9 bp):
AATAATATT
Found at i:1840032 original size:17 final size:18
Alignment explanation
Indices: 1839999--1840048 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
1839989 GGAATGTTTC
1839999 TGAAGGAATTAGAATCTG
1 TGAAGGAATTAGAATCTG
1840017 TGAAGGAATT-GAATCTG
1 TGAAGGAATTAGAATCTG
* *
1840034 T-TAGGAATTGGAATC
1 TGAAGGAATTAGAATC
1840049 CAATTCCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.23
17 13 0.43
18 10 0.33
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (18 bp):
TGAAGGAATTAGAATCTG
Found at i:1840819 original size:244 final size:236
Alignment explanation
Indices: 1840454--1840889 Score: 606
Period size: 244 Copynumber: 1.8 Consensus size: 236
1840444 AATTAGAAAC
* *
1840454 CCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAAATA
1 CCGACCCGAAATAATAAAAAAA-TA--TTTATTCAATAAAAACAATGACTTAATTGAAAAAAATA
* * *
1840519 TATAGAGAGATGGGTATTATTGTATTTATTCCTAAATATATAACATAAAATTATATATTTTTTGG
63 TATAGAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAACATAAAATTATATA-TATTT--
*
1840584 GTCATGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCGACCAGAATATCACACTTA
125 -TCAGGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGA--C--CC-GAATATCACACTTA
1840649 AAAAAAACCGACCCGACCCGACCTGAATATATGAATTAGAAATCCGACCTGAT
184 AAAAAAACCGACCCGACCCGACCTGAATATATGAATTAGAAATCCGACCTGAT
* * *
1840702 CCGACCCGAAATATTAAAAAAA-A-TTATTCAATAAAAATAATGACTTAATTGAAAAAAATTTTA
1 CCGACCCGAAATAATAAAAAAATATTTATTCAATAAAAACAATGACTTAATTGAAAAAAA-TATA
* * ** *
1840765 TATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAGTTATATATATTTTCAGG
65 TAGAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAACATAAAATTATATATATTTTCAGG
*
1840830 TCGGGTATTTTTCACCCTAAACCCAAACTCGACCCGACCCGAATATCACACTTAAAAAAA
130 TCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCGAATATCACACTTAAAAAAA
1840890 CTAACCTGAC
Statistics
Matches: 172, Mismatches: 15, Indels: 15
0.85 0.07 0.07
Matches are distributed among these distances:
235 20 0.12
236 2 0.01
238 1 0.01
240 40 0.23
243 36 0.21
244 51 0.30
246 1 0.01
248 21 0.12
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (236 bp):
CCGACCCGAAATAATAAAAAAATATTTATTCAATAAAAACAATGACTTAATTGAAAAAAATATAT
AGAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAACATAAAATTATATATATTTTCAGGT
CGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCGAATATCACACTTAAAAAAAACCGAC
CCGACCCGACCTGAATATATGAATTAGAAATCCGACCTGAT
Found at i:1841509 original size:15 final size:15
Alignment explanation
Indices: 1841489--1841533 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
1841479 ATTTCTCTCT
1841489 CGTTATCTAAACCAA
1 CGTTATCTAAACCAA
1841504 CGTTATCTAAACCAA
1 CGTTATCTAAACCAA
*
1841519 CGTTATATAAACCAA
1 CGTTATCTAAACCAA
1841534 ATGTCCTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (15 bp):
CGTTATCTAAACCAA
Found at i:1842704 original size:13 final size:13
Alignment explanation
Indices: 1842686--1842710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1842676 ATAGCGAGGG
1842686 GGTATCGATACAT
1 GGTATCGATACAT
1842699 GGTATCGATACA
1 GGTATCGATACA
1842711 CTTTGCACAG
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:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (13 bp):
GGTATCGATACAT
Found at i:1847043 original size:18 final size:18
Alignment explanation
Indices: 1847002--1847044 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1846992 AACTCCAACG
*
1847002 TTCTTCTTTTTCTCCGTC
1 TTCTTCTTTGTCTCCGTC
*
1847020 TCCTTCTTTGTCT-CGTCC
1 TTCTTCTTTGTCTCCGT-C
1847038 TTCTTCT
1 TTCTTCT
1847045 CGAGGTCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.00, C:0.35, G:0.07, T:0.58
Consensus pattern (18 bp):
TTCTTCTTTGTCTCCGTC
Found at i:1847438 original size:31 final size:31
Alignment explanation
Indices: 1847403--1847469 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1847393 GGCAGCTGTA
* *
1847403 CAAGATGAAACTCTCCCGTATTTATCTGGTC
1 CAAGATGAAACTCTCCCGTATTCATCTAGTC
*
1847434 CAAGATGAAACTCTCTCGTATTCATCTAGTC
1 CAAGATGAAACTCTCCCGTATTCATCTAGTC
1847465 CAAGA
1 CAAGA
1847470 GCACAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (31 bp):
CAAGATGAAACTCTCCCGTATTCATCTAGTC
Found at i:1848498 original size:18 final size:19
Alignment explanation
Indices: 1848472--1848518 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1848462 TGGTAGAAGT
1848472 GTATCGGTACAACCTA-GG
1 GTATCGGTACAACCTAGGG
* *
1848490 GTATTGGTAC-ACGTAGGG
1 GTATCGGTACAACCTAGGG
1848508 GTATCGGTACA
1 GTATCGGTACA
1848519 CTAATTACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
GTATCGGTACAACCTAGGG
Found at i:1851964 original size:32 final size:32
Alignment explanation
Indices: 1851927--1852005 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
1851917 CCTAAGGTGA
* *
1851927 CCCTTGGGTAGGCTCTTAGGCCACAAGGTGCT
1 CCCTTGGGTAGGCTCTTAGGCCACAAGGTACC
* *
1851959 CCCTTGGATAGGCTCTTAGGCCCCAAGGTACC
1 CCCTTGGGTAGGCTCTTAGGCCACAAGGTACC
* *
1851991 CCCTTAGGTTGGCTC
1 CCCTTGGGTAGGCTC
1852006 CTATGCCTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.15, C:0.32, G:0.28, T:0.25
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTTAGGCCACAAGGTACC
Found at i:1852825 original size:23 final size:23
Alignment explanation
Indices: 1852799--1852851 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1852789 CAATCGTAAC
1852799 AGAAATAAA-AAAACAAATTAGGG
1 AGAAATAAATAAAACAAA-TAGGG
* *
1852822 AGAAATAAATATAAGAAATAGGG
1 AGAAATAAATAAAACAAATAGGG
1852845 -GAAATAA
1 AGAAATAA
1852852 GCAATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 7 0.26
23 14 0.52
24 6 0.22
ACGTcount: A:0.64, C:0.02, G:0.19, T:0.15
Consensus pattern (23 bp):
AGAAATAAATAAAACAAATAGGG
Found at i:1852890 original size:28 final size:28
Alignment explanation
Indices: 1852858--1852912 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1852848 ATAAGCAATA
1852858 AAAATCTAAAAAAATAAAGAA-TAAAAAC
1 AAAATCTAAAAAAATAAA-AATTAAAAAC
* *
1852886 AAAATTTAAGAAAATAAAAATTAAAAA
1 AAAATCTAAAAAAATAAAAATTAAAAA
1852913 ATGAACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (28 bp):
AAAATCTAAAAAAATAAAAATTAAAAAC
Found at i:1852945 original size:44 final size:44
Alignment explanation
Indices: 1852854--1852947 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 44
1852844 GGAAATAAGC
* * *
1852854 AATAAAAATCTAAAAAAATAAAGAATAAAAACAAAATTTAAGAA
1 AATAAAAATCTAAAAAAATAAACAAAAAAAACAAAAGTTAAGAA
* * *
1852898 AATAAAAAT-T-AAAAAATGAACAAAAAAAATAAAAGGTTGAGATA
1 AATAAAAATCTAAAAAAATAAACAAAAAAAACAAAA-GTTAAGA-A
1852942 AATAAA
1 AATAAA
1852948 GGTGAAGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 20 0.48
43 6 0.14
44 16 0.38
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.18
Consensus pattern (44 bp):
AATAAAAATCTAAAAAAATAAACAAAAAAAACAAAAGTTAAGAA
Found at i:1853467 original size:14 final size:16
Alignment explanation
Indices: 1853429--1853464 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1853419 ATCGATTGGA
1853429 AAAAATAAGACCAAAAG
1 AAAAATAAGA-CAAAAG
1853446 AAAAATAAGA-AAAAG
1 AAAAATAAGACAAAAG
1853461 AAAA
1 AAAA
1853465 TAACAGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
17 10 0.53
ACGTcount: A:0.78, C:0.06, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAATAAGACAAAAG
Found at i:1854511 original size:43 final size:43
Alignment explanation
Indices: 1854463--1854626 Score: 157
Period size: 43 Copynumber: 3.8 Consensus size: 43
1854453 AAGTTCTTTG
* *
1854463 GATGACTCCCTTTCGGGGGTTAAGCCAGGTGACACATTATTCA
1 GATGACTCCCCTTCGGGGGTTAAGCCAGGTGAAACATTATTCA
* ** * **
1854506 GATGACTCCCCTTCGTGGGTTAAGCCATATGAAACGTTATTTG
1 GATGACTCCCCTTCGGGGGTTAAGCCAGGTGAAACATTATTCA
* *** ** *
1854549 GATGACTCCCCTGCACTGGTTAAGTTAGGTGAAACATTCTTCA
1 GATGACTCCCCTTCGGGGGTTAAGCCAGGTGAAACATTATTCA
* * *
1854592 GATGACTCCCCTTCATGGGTTTAAGCCATGTGAAA
1 GATGACTCCCCTTC-GGGGGTTAAGCCAGGTGAAA
1854627 TTTCCTTTAC
Statistics
Matches: 92, Mismatches: 28, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
43 79 0.86
44 13 0.14
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (43 bp):
GATGACTCCCCTTCGGGGGTTAAGCCAGGTGAAACATTATTCA
Found at i:1854572 original size:86 final size:87
Alignment explanation
Indices: 1854448--1854626 Score: 234
Period size: 86 Copynumber: 2.1 Consensus size: 87
1854438 TTGAAGTCAG
* * * ** *
1854448 ATGAAAAGTTCTTTGGATGACTCCCTTTCGGGGGTTAAGCCAGGTGACACATTATTCAGATGACT
1 ATGAAAAGTTATTTGGATGACTCCCCTGCACGGGTTAAGCCAGGTGAAACATTATTCAGATGACT
*
1854513 CCCCTTCGTGGG-TTAAGCCAT
66 CCCCTTCATGGGTTTAAGCCAT
* * ** *
1854534 ATGAAACGTTATTTGGATGACTCCCCTGCACTGGTTAAGTTAGGTGAAACATTCTTCAGATGACT
1 ATGAAAAGTTATTTGGATGACTCCCCTGCACGGGTTAAGCCAGGTGAAACATTATTCAGATGACT
1854599 CCCCTTCATGGGTTTAAGCCAT
66 CCCCTTCATGGGTTTAAGCCAT
*
1854621 GTGAAA
1 ATGAAA
1854627 TTTCCTTTAC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
86 65 0.82
87 14 0.18
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (87 bp):
ATGAAAAGTTATTTGGATGACTCCCCTGCACGGGTTAAGCCAGGTGAAACATTATTCAGATGACT
CCCCTTCATGGGTTTAAGCCAT
Found at i:1864393 original size:2 final size:2
Alignment explanation
Indices: 1864381--1864411 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1864371 AATGAAGAGA
*
1864381 AT AT GT 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 A
1864412 ATTAGATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1864517 original size:32 final size:32
Alignment explanation
Indices: 1864476--1864540 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1864466 AATGAAATCG
1864476 ATATTATTGTGCGGCAGTGTTAGCGTTCCTTA
1 ATATTATTGTGCGGCAGTGTTAGCGTTCCTTA
*
1864508 ATATTATTGTGCGGCAGTGTTAGTGTTCCTTA
1 ATATTATTGTGCGGCAGTGTTAGCGTTCCTTA
1864540 A
1 A
1864541 ATCCGAGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.42
Consensus pattern (32 bp):
ATATTATTGTGCGGCAGTGTTAGCGTTCCTTA
Found at i:1865409 original size:17 final size:17
Alignment explanation
Indices: 1865387--1865421 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1865377 AAAATTATTT
*
1865387 TAAAATTTAGTTAATAA
1 TAAAATATAGTTAATAA
*
1865404 TAAAATATATTTAATAA
1 TAAAATATAGTTAATAA
1865421 T
1 T
1865422 TTAATGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAAATATAGTTAATAA
Found at i:1867753 original size:17 final size:17
Alignment explanation
Indices: 1867731--1867771 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1867721 GTATAATTCA
*
1867731 TTTAAA-AACGTATATAT
1 TTTAAATAAC-TAAATAT
1867748 TTTAAATAACTAAATAT
1 TTTAAATAACTAAATAT
1867765 TTTAAAT
1 TTTAAAT
1867772 TGGGTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (17 bp):
TTTAAATAACTAAATAT
Found at i:1870415 original size:21 final size:21
Alignment explanation
Indices: 1870378--1870417 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1870368 TACTGAGTTT
*
1870378 GTATATAAATAATTTTTTTGA
1 GTATATAAATAAATTTTTTGA
1870399 GTATAT-AATGAAATTTTTT
1 GTATATAAAT-AAATTTTTT
1870418 ACACTGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
GTATATAAATAAATTTTTTGA
Found at i:1871801 original size:48 final size:45
Alignment explanation
Indices: 1871595--1871867 Score: 327
Period size: 47 Copynumber: 5.9 Consensus size: 45
1871585 GATAGACTTG
*
1871595 TTTTTATTTATTTTGTTTCTTAATGTTTTTA-TTTAATTATGG-T
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTTAATTATGGAC
* * *
1871638 TTTTTGTTTATTTTGTTTCTTATTGTTTTTATTTAAAAATTATGGAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTT--TAATTATGGAC
* *
1871685 TTTTTATTTATTTTGTTTTTTAATGTTTTTA-TTTAATTATAGAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTTAATTATGGAC
* * *
1871729 TTTTTTATTTCTTTTATTTCTTAATGTTTTTATTATTAAATTATGGAA
1 -TTTTTATTTATTTTGTTTCTTAATGTTTTTATT-TT-AATTATGGAC
* *
1871777 TTTTTATTTATTTTTGTTTATTAATATTTTTATTATTTAATTATGGAC
1 TTTTTATTTA-TTTTGTTTCTTAATGTTTTTA-T-TTTAATTATGGAC
*
1871825 TTTTTATTTATTTTGTTTCTTAATATTTTTATTATTTAATTAT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTA-T-TTTAATTAT
1871868 TTGAATTATA
Statistics
Matches: 199, Mismatches: 20, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
43 29 0.15
44 11 0.06
45 28 0.14
46 11 0.06
47 71 0.36
48 45 0.23
49 3 0.02
50 1 0.01
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (45 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTTAATTATGGAC
Found at i:1871842 original size:140 final size:137
Alignment explanation
Indices: 1871586--1871857 Score: 370
Period size: 140 Copynumber: 2.0 Consensus size: 137
1871576 GATGACATCG
* * *
1871586 ATAGACTTGTTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGTTTTTTGTTTATTT
1 ATAGACTTGTTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGGATTTTTATTTATTT
* * * * *
1871651 TGTTTCTTATTGTTTTTATTTAAAAATTATGGACTTTTTATTTATTTTGTTTTTTAATGTTTTTA
66 TGTTTATTAATATTTTTATTTAAAAATTATGGACTTTTTATTTATTTTGTTTCTTAATATTTTTA
1871716 TTTAATT
131 TTTAATT
*
1871723 ATAGAC-T-TTTTTATTTCTTTTATTTCTTAATGTTTTTATTATTAAATTATGGAATTTTTATTT
1 ATAGACTTGTTTTTATTTATTTTATTTCTTAATGTTTTTA-T-TT-AATTATGG-ATTTTTATTT
**
1871786 ATTTTTGTTTATTAATATTTTTA-TTATTTAATTATGGACTTTTTATTTATTTTGTTTCTTAATA
62 A-TTTTGTTTATTAATATTTTTATTTA-AAAATTATGGACTTTTTATTTATTTTGTTTCTTAATA
1871850 TTTTTATT
125 TTTTTATT
1871858 ATTTAATTAT
Statistics
Matches: 118, Mismatches: 11, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
135 29 0.25
136 2 0.02
137 8 0.07
138 8 0.07
139 12 0.10
140 59 0.50
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.67
Consensus pattern (137 bp):
ATAGACTTGTTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGGATTTTTATTTATTT
TGTTTATTAATATTTTTATTTAAAAATTATGGACTTTTTATTTATTTTGTTTCTTAATATTTTTA
TTTAATT
Found at i:1874991 original size:16 final size:16
Alignment explanation
Indices: 1874970--1875004 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1874960 CAAATAATTA
1874970 AATATAA-AATAAAAAT
1 AATATAATAA-AAAAAT
1874986 AATATAATAAAAAAAT
1 AATATAATAAAAAAAT
1875002 AAT
1 AAT
1875005 TTTTCCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATATAATAAAAAAAT
Found at i:1879783 original size:3 final size:3
Alignment explanation
Indices: 1879766--1879798 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1879756 TTTTTCTTCC
1879766 TCA TCA CTC- TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA -TCA TCA TCA TCA TCA TCA TCA TCA TCA
1879799 CCAATAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1886226 original size:14 final size:15
Alignment explanation
Indices: 1886196--1886226 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1886186 GAATATTTTA
1886196 TATCAAAATTATATT
1 TATCAAAATTATATT
1886211 TATCAAAATT-TATT
1 TATCAAAATTATATT
1886225 TA
1 TA
1886227 ATAATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TATCAAAATTATATT
Found at i:1887637 original size:10 final size:10
Alignment explanation
Indices: 1887618--1887655 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1887608 ATCATACCAT
1887618 ATTCTCTCAA
1 ATTCTCTCAA
*
1887628 ATTCTATCAA
1 ATTCTCTCAA
1887638 ATTCTCTCAA
1 ATTCTCTCAA
*
1887648 ATACTCTC
1 ATTCTCTC
1887656 TCTGTTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTCTCTCAA
Found at i:1887898 original size:45 final size:48
Alignment explanation
Indices: 1887835--1887957 Score: 139
Period size: 53 Copynumber: 2.6 Consensus size: 48
1887825 AATATTTTAT
1887835 GAATT-ATTTGTAATAA-T-TTG-TTTAATGCATGATTATTAGATTAA
1 GAATTAATTTGTAATAATTATTGTTTTAATGCATGATTATTAGATTAA
1887879 GAATTAATTTGTAATAATTTATTGATTTATTTAATGCATGATTATTAGATTAA
1 GAATTAATTTGTAATAA-TTATTG---T-TTTAATGCATGATTATTAGATTAA
* * *
1887932 AAATTAATTTGT-GTAATTATTATTTT
1 GAATTAATTTGTAATAATTATTGTTTT
1887958 TTAGGAGAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 15
0.79 0.04 0.18
Matches are distributed among these distances:
44 5 0.07
45 11 0.16
47 4 0.06
48 4 0.06
51 5 0.07
52 3 0.04
53 35 0.52
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (48 bp):
GAATTAATTTGTAATAATTATTGTTTTAATGCATGATTATTAGATTAA
Found at i:1887939 original size:26 final size:26
Alignment explanation
Indices: 1887856--1887939 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
1887846 AATAATTTGT
*
1887856 TTAATGCATGATTATTAGATTAAGAA
1 TTAATGCATGATTATTAGATTAAAAA
* * * *
1887882 TTAATTTGTAATAATTTATT-GATT--TAT
1 TTAA--TG-CATGA-TTATTAGATTAAAAA
1887909 TTAATGCATGATTATTAGATTAAAAA
1 TTAATGCATGATTATTAGATTAAAAA
1887935 TTAAT
1 TTAAT
1887940 TTGTGTAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
23 5 0.12
24 7 0.16
25 2 0.05
26 10 0.23
27 5 0.12
28 2 0.05
29 7 0.16
30 5 0.12
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.46
Consensus pattern (26 bp):
TTAATGCATGATTATTAGATTAAAAA
Found at i:1889487 original size:18 final size:18
Alignment explanation
Indices: 1889446--1889490 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1889436 CACAGCAGCC
*
1889446 ACCGCAGCCATTTATGAT
1 ACCGCAGCCATATATGAT
*
1889464 GCCGCAGCCATATATGAT
1 ACCGCAGCCATATATGAT
*
1889482 ATCGCAGCC
1 ACCGCAGCC
1889491 TTTCCATTAC
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:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (18 bp):
ACCGCAGCCATATATGAT
Found at i:1890032 original size:26 final size:24
Alignment explanation
Indices: 1889961--1890032 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
1889951 TTATATTTGT
1889961 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
1889986 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
1890008 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
1890033 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:1893444 original size:12 final size:13
Alignment explanation
Indices: 1893427--1893455 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1893417 TATAATAAAA
1893427 AAAATTTATAAC-
1 AAAATTTATAACG
1893439 AAAATTTATAACG
1 AAAATTTATAACG
1893452 AAAA
1 AAAA
1893456 ATCGCACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAATTTATAACG
Found at i:1894270 original size:21 final size:21
Alignment explanation
Indices: 1894246--1894303 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1894236 ATTTAAAAGT
1894246 TAAAAAATATAAAAAAAATAC
1 TAAAAAATATAAAAAAAATAC
* *
1894267 TAAAAAATA-AAAATTAAATTGC
1 TAAAAAATATAAAA--AAAATAC
1894289 T-AAAAATATAAAAAA
1 TAAAAAATATAAAAAA
1894304 TATATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAAAATATAAAAAAAATAC
Done.