Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 4 of 106
Found at i:1573059 original size:19 final size:20
Alignment explanation
Indices: 1573035--1573074 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1573025 CATGGTGTTC
1573035 TTTTCTT-TTCTTTT-CTTTT
1 TTTTCTTCTT-TTTTCCTTTT
1573054 TTTTCTTCTTTTTTCCTTTT
1 TTTTCTTCTTTTTTCCTTTT
1573074 T
1 T
1573075 AAGTTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTCTTCTTTTTTCCTTTT
Found at i:1579704 original size:51 final size:51
Alignment explanation
Indices: 1579644--1579745 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
1579634 CAAGGAAAGT
*
1579644 TACAACGGATGGTCTTCTGACATGGCAAGGAGTCTCATTGTTAGCATCCTC
1 TACAACGGATGGTCTTCTGACATGGCAAGGAGTCTCATTGTTACCATCCTC
1579695 TACAACGGATGGTCTTCTGACATGGCAAGGAGTCTCATTGTTACCATCCTC
1 TACAACGGATGGTCTTCTGACATGGCAAGGAGTCTCATTGTTACCATCCTC
1579746 CCCCTTTTGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (51 bp):
TACAACGGATGGTCTTCTGACATGGCAAGGAGTCTCATTGTTACCATCCTC
Found at i:1591629 original size:16 final size:18
Alignment explanation
Indices: 1591603--1591637 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1591593 ATGAAAATAT
1591603 AAACAAAAAAAGAA-AAA
1 AAACAAAAAAAGAAGAAA
1591620 AAAC-AAAAAAGAAGAAA
1 AAACAAAAAAAGAAGAAA
1591637 A
1 A
1591638 TGGGAGAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.86, C:0.06, G:0.09, T:0.00
Consensus pattern (18 bp):
AAACAAAAAAAGAAGAAA
Found at i:1592319 original size:2 final size:2
Alignment explanation
Indices: 1592312--1592377 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1592302 GGCAAAGCAA
1592312 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1592354 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
1592378 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1593937 original size:17 final size:15
Alignment explanation
Indices: 1593917--1593961 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 15
1593907 TTGCTTACGA
1593917 AAAAATATAATAATAAT
1 AAAAATATAA-AA-AAT
1593934 AAAAATATAAAAAAT
1 AAAAATATAAAAAAT
1593949 ATAAAATATAAAA
1 A-AAAATATAAAA
1593962 TTTTTGTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 10 0.37
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATATAAAAAAT
Found at i:1603526 original size:26 final size:24
Alignment explanation
Indices: 1603471--1603519 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
1603461 ATTACAAAGC
1603471 AAAAAAAATCATGTTATATATTAG
1 AAAAAAAATCATGTTATATATTAG
1603495 AAAAAAAATCATGCTT-TATATTAG
1 AAAAAAAATCATG-TTATATATTAG
1603519 A
1 A
1603520 GTCAAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (24 bp):
AAAAAAAATCATGTTATATATTAG
Found at i:1603985 original size:17 final size:16
Alignment explanation
Indices: 1603957--1603999 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
1603947 TTAAAAAATA
1603957 AAAATT-ATAATTTAT
1 AAAATTAATAATTTAT
* *
1603972 ATAATATAATAATTTTT
1 AAAAT-TAATAATTTAT
1603989 AAAATTAATAA
1 AAAATTAATAA
1604000 AAGATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 7 0.30
17 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATTAATAATTTAT
Found at i:1616632 original size:15 final size:15
Alignment explanation
Indices: 1616611--1616656 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1616601 TCACCACCGC
1616611 CGTCGTCATCGTCAT
1 CGTCGTCATCGTCAT
* *
1616626 C-TACGTCATCTTCGT
1 CGT-CGTCATCGTCAT
1616641 CGTCGTCATCGTCAT
1 CGTCGTCATCGTCAT
1616656 C
1 C
1616657 ACCGCCGCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.13, C:0.35, G:0.17, T:0.35
Consensus pattern (15 bp):
CGTCGTCATCGTCAT
Found at i:1616669 original size:30 final size:30
Alignment explanation
Indices: 1616611--1616669 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1616601 TCACCACCGC
* *
1616611 CGTCGTCATCGTCATCTACGTCATCTTCGT
1 CGTCGTCATCGTCATCTACGCCACCTTCGT
*
1616641 CGTCGTCATCGTCATC-ACCGCCGCCTTCG
1 CGTCGTCATCGTCATCTA-CGCCACCTTCG
1616670 AAGCTTCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.12, C:0.39, G:0.19, T:0.31
Consensus pattern (30 bp):
CGTCGTCATCGTCATCTACGCCACCTTCGT
Found at i:1622745 original size:3 final size:3
Alignment explanation
Indices: 1622737--1622763 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1622727 CCAGATATCA
1622737 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1622764 GTTCGATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1635945 original size:26 final size:26
Alignment explanation
Indices: 1635909--1636097 Score: 216
Period size: 26 Copynumber: 7.3 Consensus size: 26
1635899 TTAGGTATTA
*
1635909 CGTGACTAGTTTTTGATAAGACATTG
1 CGTGACTAGTTTCTGATAAGACATTG
**
1635935 CGTGACTAGTTTCTGATAAGGTATTG
1 CGTGACTAGTTTCTGATAAGACATTG
* **
1635961 CGTGACTTGTTTCTGATAAGGTATTG
1 CGTGACTAGTTTCTGATAAGACATTG
* * *
1635987 TGTGACTAATTTTTGATAAGACATTG
1 CGTGACTAGTTTCTGATAAGACATTG
* *
1636013 TGTGACTAGTTTTTGATAAGACATTG
1 CGTGACTAGTTTCTGATAAGACATTG
* *
1636039 CGTGACTAATTTCTGATAAAACATTG
1 CGTGACTAGTTTCTGATAAGACATTG
* * * * *
1636065 CTTGACTAATTTCTAATAAGGCATTA
1 CGTGACTAGTTTCTGATAAGACATTG
1636091 CGTGACT
1 CGTGACT
1636098 TGTTAGTAAG
Statistics
Matches: 142, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 142 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (26 bp):
CGTGACTAGTTTCTGATAAGACATTG
Found at i:1636111 original size:23 final size:23
Alignment explanation
Indices: 1636081--1636129 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1636071 TAATTTCTAA
1636081 TAAGGCATTACGTGACTTGTTAG
1 TAAGGCATTACGTGACTTGTTAG
*
1636104 TAAGGCATTACGTGACTTGTTTG
1 TAAGGCATTACGTGACTTGTTAG
1636127 TAA
1 TAA
1636130 AGTATTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (23 bp):
TAAGGCATTACGTGACTTGTTAG
Found at i:1656409 original size:3 final size:3
Alignment explanation
Indices: 1656401--1656447 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
1656391 AGTTTCTCCA
* * * *
1656401 TCT TCT TCT TCT TCT TCT TTT TCC TCC TCT TCT TCT CCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1656448 CACTGCTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:1663791 original size:2 final size:2
Alignment explanation
Indices: 1663784--1663816 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1663774 TTTAGTGCAA
*
1663784 AT AT AT AT AC 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 A
1663817 GCAATGGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1685342 original size:30 final size:30
Alignment explanation
Indices: 1685306--1685374 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
1685296 CGATGCAAAT
* *
1685306 ATGATGCCTGCGGGATACAGTGCTCCCGAC
1 ATGATGCCTGAGGGATACAGTGCTCCCAAC
*
1685336 ATGATGCCTGAGGGATTCAGTGCTCCCAAC
1 ATGATGCCTGAGGGATACAGTGCTCCCAAC
1685366 ATGATGCCT
1 ATGATGCCT
1685375 CCTCCTCCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.23
Consensus pattern (30 bp):
ATGATGCCTGAGGGATACAGTGCTCCCAAC
Found at i:1692056 original size:23 final size:23
Alignment explanation
Indices: 1692029--1692085 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1692019 AAGGTTTAAG
*
1692029 AACGACAAAGGTAGAAAAGGGAA
1 AACGACAAAGGTAGAAAAAGGAA
*
1692052 AACGACAAAGGTAGAAAAAGTAA
1 AACGACAAAGGTAGAAAAAGGAA
1692075 AACGACAAAGG
1 AACGACAAAGG
1692086 ATTAGCATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.58, C:0.11, G:0.26, T:0.05
Consensus pattern (23 bp):
AACGACAAAGGTAGAAAAAGGAA
Found at i:1695454 original size:16 final size:16
Alignment explanation
Indices: 1695433--1695468 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1695423 TCATATCCAT
1695433 TCAAAGAAAAATAATA
1 TCAAAGAAAAATAATA
1695449 TCAAAGAAAAATAATA
1 TCAAAGAAAAATAATA
1695465 TCAA
1 TCAA
1695469 GTAGAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.19
Consensus pattern (16 bp):
TCAAAGAAAAATAATA
Found at i:1700608 original size:33 final size:33
Alignment explanation
Indices: 1700552--1700691 Score: 199
Period size: 33 Copynumber: 4.2 Consensus size: 33
1700542 TTGCTCTTCT
* * **
1700552 TCTTCTTCATGTTTACTCACTTCTTCCTGCTCC
1 TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
*
1700585 TCTTCTTCGTGTTTGCTTGCTTCTTCCGGCTCC
1 TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
* *
1700618 TCTTCCTCGTGTTTGCTTGCTTCTTCCAGCTCC
1 TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
* *
1700651 TCTTCTTCGTGTTTGCTTGCTCCTTCTTGCTCC
1 TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
1700684 TCTTCTTC
1 TCTTCTTC
1700692 AAGCCTCGTA
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 96 1.00
ACGTcount: A:0.03, C:0.35, G:0.13, T:0.49
Consensus pattern (33 bp):
TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
Found at i:1703876 original size:12 final size:12
Alignment explanation
Indices: 1703859--1703884 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1703849 GTCACACATC
1703859 CACATGGCAATA
1 CACATGGCAATA
1703871 CACATGGCAATA
1 CACATGGCAATA
1703883 CA
1 CA
1703885 TTGATAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (12 bp):
CACATGGCAATA
Found at i:1718146 original size:21 final size:22
Alignment explanation
Indices: 1718103--1718151 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1718093 CTTCATCTGT
**
1718103 TGTTAATTTGTTTTAAATTAAA
1 TGTTAATTTGTTTTAAAAAAAA
*
1718125 TGTTCATTT-TTTTAAAAAAAA
1 TGTTAATTTGTTTTAAAAAAAA
1718146 T-TTAAT
1 TGTTAAT
1718152 ATGATATCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 8 0.35
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (22 bp):
TGTTAATTTGTTTTAAAAAAAA
Found at i:1721609 original size:2 final size:2
Alignment explanation
Indices: 1721602--1721671 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
1721592 CAGCCATGGC
1721602 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1721644 AT AT AT NT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1721672 TAATTTATGC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1722933 original size:4 final size:4
Alignment explanation
Indices: 1722924--1722953 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1722914 AGCTCAAGAA
1722924 AAAT AAAT -AAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1722954 ACAGGTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1741048 original size:13 final size:13
Alignment explanation
Indices: 1741032--1741059 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1741022 AAAATAATAC
1741032 TATAAATAGTATT
1 TATAAATAGTATT
1741045 TATAAATAGTATT
1 TATAAATAGTATT
1741058 TA
1 TA
1741060 GTAACTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
TATAAATAGTATT
Found at i:1741637 original size:122 final size:120
Alignment explanation
Indices: 1741362--1741770 Score: 303
Period size: 123 Copynumber: 3.4 Consensus size: 120
1741352 TATAATAATT
* * * * * * * * *
1741362 TTTTTAATTATCAACATATTAA-AGATATATATTTTACCATGTGATTTATGTTTCTTCTAAACTT
1 TTTTTAATTATCAATAGATTAACA-ATATATATTTCACTATGTGATATATGCTTATACTAAACAT
* ** * ** * *
1741426 ATAATTAAGGTTTAGTAATTAATGTTCAGAATTTAAAATTTAAAGTACAATATTCGTCA
65 ATAATTAAAGTTTAACATTTAAAATTTAG---TTAAGATTTAAAGTACAATATTCGTCA
* ** ** *
1741485 TTTTTAGTTATCAATTTATTAACGAA-ATATATTTCACTATGTGATATATGCTTATTTTAAATAT
1 TTTTTAATTATCAATAGATTAAC-AATATATATTTCACTATGTGATATATGCTTATACTAAACAT
* * * *
1741549 ATAATTAAATTTTAATATTTAAAATTTAAGCTTAAGATTTAAAGTACAATCTTCGTTA
65 ATAATTAAAGTTTAACATTTAAAATTT-AG-TTAAGATTTAAAGTACAATATTCGTCA
* * * * * *
1741607 TTTTTAATTATCAATAGATT-A-TATATATATATGATTACGTGATATATGCTTCTACTAAACATA
1 TTTTTAATTATCAATAGATTAACAATATATATTTCACTATGTGATATATGCTTATACTAAACATA
** * * * **
1741670 TAATTAGGGTTTAACATTTAATATTTAG----GATTTAAAGTACGATGTTTATCA
66 TAATTAAAGTTTAACATTTAAAATTTAGTTAAGATTTAAAGTACAATATTCGTCA
* * *
1741721 TTTTTAATTGTCAATAGATTAAGAATATATATTTCACTTTGTGATTATAT
1 TTTTTAATTATCAATAGATTAACAATATATATTTCACTATGTGA-TATAT
1741771 ATTTTTTTTA
Statistics
Matches: 228, Mismatches: 51, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
114 37 0.16
115 1 0.00
116 15 0.07
117 5 0.02
119 3 0.01
120 52 0.23
121 1 0.00
122 41 0.18
123 69 0.30
124 3 0.01
125 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (120 bp):
TTTTTAATTATCAATAGATTAACAATATATATTTCACTATGTGATATATGCTTATACTAAACATA
TAATTAAAGTTTAACATTTAAAATTTAGTTAAGATTTAAAGTACAATATTCGTCA
Found at i:1760248 original size:18 final size:21
Alignment explanation
Indices: 1760212--1760255 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1760202 CATTATATAT
1760212 TTTTTAAAAAAGTTAAATT-A
1 TTTTTAAAAAAGTTAAATTAA
*
1760232 TTTTT-AAAAA-TTTAATTAA
1 TTTTTAAAAAAGTTAAATTAA
1760251 TTTTT
1 TTTTT
1760256 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 11 0.50
20 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTTAAAAAAGTTAAATTAA
Found at i:1773563 original size:17 final size:18
Alignment explanation
Indices: 1773532--1773573 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1773522 ATCAACTACC
1773532 ATATAAAATAAAAA-TAA
1 ATATAAAATAAAAATTAA
**
1773549 ATATAAAATTCAAATTAA
1 ATATAAAATAAAAATTAA
1773567 A-ATAAAA
1 ATATAAAA
1773574 ATTTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
ATATAAAATAAAAATTAA
Found at i:1773751 original size:29 final size:29
Alignment explanation
Indices: 1773697--1773764 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
1773687 AAAGAAAATT
1773697 AAAATTTAAAAAAAATAAATAAAAAA-AGA
1 AAAATTTAAAAAAAATAAATAAAAAATA-A
* * *
1773726 AAAATTTAAAAATAGAT-ATTATAAAATAA
1 AAAATTTAAAAA-AAATAAATAAAAAATAA
1773755 AAAATATTAA
1 AAAAT-TTAA
1773765 TTTTATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 25 0.76
30 8 0.24
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (29 bp):
AAAATTTAAAAAAAATAAATAAAAAATAA
Found at i:1773776 original size:22 final size:22
Alignment explanation
Indices: 1773743--1773849 Score: 76
Period size: 22 Copynumber: 4.9 Consensus size: 22
1773733 AAAAATAGAT
*
1773743 ATTATA-AAATAAAAAATATTA
1 ATTATATATATAAAAAATATTA
*
1773764 ATTTTATATATAAAAAATAATT-
1 ATTATATATATAAAAAAT-ATTA
* * * * *
1773786 ATTAGAGATAATTAAATATTTTA
1 ATTATATAT-ATAAAAAATATTA
* *
1773809 ANTATA-AAATAAATAAATATTA
1 ATTATATATATAAA-AAATATTA
*
1773831 ATTTTATATATAAAAAATA
1 ATTATATATATAAAAAATA
1773850 ACTATTAGAG
Statistics
Matches: 63, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
21 9 0.14
22 34 0.54
23 20 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTATATATATAAAAAATATTA
Found at i:1773838 original size:67 final size:65
Alignment explanation
Indices: 1773745--1773901 Score: 242
Period size: 67 Copynumber: 2.3 Consensus size: 65
1773735 AAATAGATAT
*
1773745 TATAAAATAAAAAATATTAATTTTATATATAAAAAATAATTATTAGAGATAATTAAATATTTTAA
1 TATAAAATAAAAAATATTAATTTTATATATAAAAAATAACTATTAGAGATAATTAAATATTTTAA
1773810 NTATAAAATAAATAAATATTAATTTTATATATAAAAAATAACTATTAGAGATAATTAAATATTTT
1 -TATAAAATAAA-AAATATTAATTTTATATATAAAAAATAACTATTAGAGATAATTAAATATTTT
1773875 AA
64 AA
1773877 TTGATTAAAAATAAAAAATAATTAA
1 -T-A-T-AAAATAAAAAAT-ATTAA
1773902 AAAAAAACTA
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
66 11 0.13
67 54 0.64
68 1 0.01
69 5 0.06
70 13 0.15
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (65 bp):
TATAAAATAAAAAATATTAATTTTATATATAAAAAATAACTATTAGAGATAATTAAATATTTTAA
Found at i:1775833 original size:17 final size:17
Alignment explanation
Indices: 1775799--1775832 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1775789 ACAAATCTAA
1775799 TGCTCCCATGAATTTTT
1 TGCTCCCATGAATTTTT
*
1775816 TGCTCCCTTG-ATTTTT
1 TGCTCCCATGAATTTTT
1775832 T
1 T
1775833 TTTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.53
Consensus pattern (17 bp):
TGCTCCCATGAATTTTT
Found at i:1782673 original size:13 final size:13
Alignment explanation
Indices: 1782644--1782692 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1782634 AAAATAAAAA
1782644 ATATTAT-ATGAT
1 ATATTATCATGAT
*
1782656 AATATTATCATAAT
1 -ATATTATCATGAT
* *
1782670 ATATTAACATGTT
1 ATATTATCATGAT
1782683 ATATTATCAT
1 ATATTATCAT
1782693 TTATTATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (13 bp):
ATATTATCATGAT
Found at i:1782736 original size:27 final size:26
Alignment explanation
Indices: 1782703--1782772 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 26
1782693 TTATTATAAT
*
1782703 ATATTAATTTATCATAAAAACGTGATC
1 ATATTAATTTATCATAAAAACATG-TC
* * *
1782730 ATATTAATATATCATGACAACATGTC
1 ATATTAATTTATCATAAAAACATGTC
1782756 ATATT-ATATTATCATAA
1 ATATTAAT-TTATCATAA
1782773 CACATCAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 2 0.06
26 14 0.39
27 20 0.56
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (26 bp):
ATATTAATTTATCATAAAAACATGTC
Found at i:1785622 original size:15 final size:15
Alignment explanation
Indices: 1785583--1785624 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1785573 AGCATTCACG
*
1785583 ATTGAATTTGCAAGACA
1 ATTGAA-TTGC-AGAAA
1785600 ATTG-ATTGCAGAAA
1 ATTGAATTGCAGAAA
1785614 ATTGAATTGCA
1 ATTGAATTGCA
1785625 CCACGGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 8 0.35
15 10 0.43
16 1 0.04
17 4 0.17
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (15 bp):
ATTGAATTGCAGAAA
Found at i:1798054 original size:17 final size:16
Alignment explanation
Indices: 1798015--1798054 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 16
1798005 TATTTTTATA
1798015 ATTTTAGTTAATAAAAT
1 ATTTTA-TTAATAAAAT
1798032 -TTTTATTAATAAAATT
1 ATTTTATTAATAAAA-T
1798048 ATTTTAT
1 ATTTTAT
1798055 GATTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 6 0.29
17 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTTTATTAATAAAAT
Found at i:1798100 original size:22 final size:21
Alignment explanation
Indices: 1798058--1798100 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1798048 ATTTTATGAT
*
1798058 TTAATTTATAAATTAAAATTA
1 TTAATTTATAAATGAAAATTA
* *
1798079 TTAATTTGATAAGTGAAGATTA
1 TTAATTT-ATAAATGAAAATTA
1798101 AACACATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (21 bp):
TTAATTTATAAATGAAAATTA
Found at i:1798186 original size:9 final size:9
Alignment explanation
Indices: 1798162--1798201 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
1798152 CTTTTATATA
*
1798162 ATTAAATAT
1 ATTAAATTT
1798171 A-TAAATTT
1 ATTAAATTT
*
1798179 ATTAAATTA
1 ATTAAATTT
1798188 ATTAAATTT
1 ATTAAATTT
1798197 ATTAA
1 ATTAA
1798202 TTTTTTAGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATTAAATTT
Found at i:1807983 original size:33 final size:33
Alignment explanation
Indices: 1807946--1808010 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1807936 GTATCACATC
1807946 ATCATCAATTATAATAT-ATTAACATGTCATATA
1 ATCATCAATTATAATATGA-TAACATGTCATATA
*
1807979 ATCATCAATTATAATATGATAGCATGTCATAT
1 ATCATCAATTATAATATGATAACATGTCATAT
1808011 CAACGTCACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.38
Consensus pattern (33 bp):
ATCATCAATTATAATATGATAACATGTCATATA
Found at i:1809753 original size:20 final size:20
Alignment explanation
Indices: 1809708--1809746 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1809698 ATCTTATTAA
1809708 AAAATAAAAATAAAAATTTG
1 AAAATAAAAATAAAAATTTG
*
1809728 AAAATAAATATAAAAATTT
1 AAAATAAAAATAAAAATTT
1809747 TTGAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAATAAAAATAAAAATTTG
Found at i:1816116 original size:2 final size:2
Alignment explanation
Indices: 1816103--1816160 Score: 75
Period size: 2 Copynumber: 29.5 Consensus size: 2
1816093 TTGTCTTAAC
*
1816103 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1816143 GNA TA TA TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA T
1816161 TAAGATTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.94
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1824686 original size:14 final size:13
Alignment explanation
Indices: 1824639--1824682 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1824629 ACGATTTGAT
*
1824639 AATAATAATAATAA
1 AATAAAAATAA-AA
*
1824653 ACTAAAAATCAAAA
1 AATAAAAAT-AAAA
1824667 AATAAAAATAAAA
1 AATAAAAATAAAA
1824680 AAT
1 AAT
1824683 TAAATACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 7 0.27
14 17 0.65
15 2 0.08
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAAATAAAA
Found at i:1825067 original size:33 final size:31
Alignment explanation
Indices: 1825030--1825156 Score: 93
Period size: 33 Copynumber: 4.0 Consensus size: 31
1825020 TTAAATAAAT
* *
1825030 ATTAATAATATTATTAATATGTTATTATATTAA
1 ATTAAT-ATATTATTAATAT-TAATTATAATAA
* *
1825063 ATTAATATATCATGTTATTATTAATTATAATAA
1 ATTAATATAT--TATTAATATTAATTATAATAA
*
1825096 ATTAATATATTATTTAAGA-TATATT-TAATAA
1 ATTAATATATTA-TTAATATTA-ATTATAATAA
*
1825127 A--AA-ATATTAATTAAAATTAATTATTAATAA
1 ATTAATATATT-ATTAATATTAATTA-TAATAA
1825157 TAAAATTTAT
Statistics
Matches: 78, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
28 13 0.17
29 5 0.06
30 6 0.08
31 10 0.13
32 11 0.14
33 26 0.33
34 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (31 bp):
ATTAATATATTATTAATATTAATTATAATAA
Found at i:1827754 original size:2 final size:2
Alignment explanation
Indices: 1827742--1827771 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
1827732 CAAAGAGGTC
1827742 AG AG TAG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG -AG AG AG AG AG AG AG AG AG AG AG AG A
1827772 AAATGTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:1827950 original size:75 final size:75
Alignment explanation
Indices: 1827751--1828445 Score: 843
Period size: 75 Copynumber: 9.5 Consensus size: 75
1827741 CAGAGTAGAG
* * *
1827751 AGAG-AGAGAGAGAGAGAGAGAAA-ATGTTGAGACAG-GACACGGTGTGAGAGAAAGAGAGGGGT
1 AGAGTAGAGAGAGAAAGAGA-AAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAGGGGT
*
1827813 GC-AATGAGGTA
65 GCGAA-GAGGTC
* *
1827824 AGAGTAGAGAGAGAAAGAG--AAGATATTGAGACGGAGACAAGTTGTGAGAGAAAGAGAGCGGG-
1 AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAG-GGGT
*
1827886 GCGAAGAGGCC
65 GCGAAGAGGTC
* ** *
1827897 AGAATAGAGAGAGAAAGAGAAAAGGCGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGGGGGGTG
1 AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAGGGGTG
* *
1827962 CCAAGAGGTA
66 CGAAGAGGTC
*
1827972 AGAGTGGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGA-GGGTG
1 AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAGGGGTG
* *
1828036 CCAAGAGGTA
66 CGAAGAGGTC
* * *
1828046 AGAGTAGAGAGAAAAAGACAAAAGATGTTGAGACGGAGACAAGGTGTGAGTG--AGAGAGGGGTG
1 AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAGGGGTG
1828109 CGAAGAGGTC
66 CGAAGAGGTC
* ** *
1828119 AGCA-TAGAAAGAGAAAGAGAAAAGGCGTTGAGACGGAGACAAGGTGTGAGAGAAAGA-TGGGGT
1 AG-AGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAGGGGT
* * *
1828182 GCAAAGAAGTA
65 GCGAAGAGGTC
* * * *
1828193 AGAGTAGAGAGAGAAAGCGAAAAGGTGTTGAGACGGAGACAAGGTGTGAGAGCAAGAGAGGGATG
1 AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAGGGGTG
*
1828258 CGAAGACGTC
66 CGAAGAGGTC
* *
1828268 AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACCGAGATAAGGTGTGAGAGAAAGAGAGGGGTG
1 AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAGGGGTG
* *
1828333 CAAAGACGTC
66 CGAAGAGGTC
* * * *
1828343 AGACTAGAGAGAGAAATAGAAAAGATGTTGAGAC----A-AA-GTGTTAGAGAAATAGAGGGGTG
1 AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAGGGGTG
1828402 C-AAGGAGGTC
66 CGAA-GAGGTC
* *
1828412 CGAGTAGAGAGAGAAAGAGAAAAGATATTGAGAC
1 AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGAC
1828446 AAAGAGAGAG
Statistics
Matches: 545, Mismatches: 62, Indels: 34
0.85 0.10 0.05
Matches are distributed among these distances:
68 2 0.00
69 56 0.10
70 2 0.00
71 3 0.01
72 15 0.03
73 107 0.20
74 149 0.27
75 211 0.39
ACGTcount: A:0.42, C:0.07, G:0.40, T:0.11
Consensus pattern (75 bp):
AGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGAGGGGTG
CGAAGAGGTC
Found at i:1828114 original size:222 final size:222
Alignment explanation
Indices: 1827714--1828445 Score: 912
Period size: 222 Copynumber: 3.3 Consensus size: 222
1827704 AGACAGACGA
*
1827714 GAGAGAAAGAGAGGGGTGCAAAGAGGTCAGAGTAGAGAGAGAGAGAGAGAGAGAGAGAAAATGTT
1 GAGAGAAAGAGAGGGGTGCAAAGAGGTAAGAGTAGAGAGAGA-A-AGAGA-A-A-AG---ATGTT
* *
1827779 GAGACAG-GACACGGTGTGAGAGAAAGAGAGGGGTG-CAATGAGGTAAGAGTAGAGAGAGAAAG-
58 GAGACGGAGACAAGGTGTGAGAGAAAGAGA-GGGTGCCAA-GAGGTAAGAGTAGAGAGAGAAAGA
* * * *
1827841 AGAAGATATTGAGACGGAGACAAGTTGTGAGAGAAAGAGAGCGGG-GCGAAGAGGCCAGAATAGA
121 AAAAGATGTTGAGACGGAGACAAGGTGTGAGAG-AAGAGAG-GGGTGCGAAGAGGTCAGAATAGA
1827905 GAGAGAAAGAGAAAAGGCGTTGAGACGGAGACAAGGTGT
184 GAGAGAAAGAGAAAAGGCGTTGAGACGGAGACAAGGTGT
* * *
1827944 GAGAGAAAGAGGGGGGTGCCAAGAGGTAAGAGTGGAGAGAGAAAGAGAAAAGATGTTGAGACGGA
1 GAGAGAAAGAGAGGGGTGCAAAGAGGTAAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGA
*
1828009 GACAAGGTGTGAGAGAAAGAGAGGGTGCCAAGAGGTAAGAGTAGAGAGAAAAAGACAAAAGATGT
66 GACAAGGTGTGAGAGAAAGAGAGGGTGCCAAGAGGTAAGAGTAGAGAGAGAAAGA-AAAAGATGT
* * *
1828074 TGAGACGGAGACAAGGTGTGAGTG-AGAGAGGGGTGCGAAGAGGTCAGCATAGAAAGAGAAAGAG
130 TGAGACGGAGACAAGGTGTGAGAGAAGAGAGGGGTGCGAAGAGGTCAGAATAGAGAGAGAAAGAG
1828138 AAAAGGCGTTGAGACGGAGACAAGGTGT
195 AAAAGGCGTTGAGACGGAGACAAGGTGT
* * * *
1828166 GAGAGAAAGA-TGGGGTGCAAAGAAGTAAGAGTAGAGAGAGAAAGCGAAAAGGTGTTGAGACGGA
1 GAGAGAAAGAGAGGGGTGCAAAGAGGTAAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGA
* * * *
1828230 GACAAGGTGTGAGAGCAAGAGAGGGATGCGAAGACGTCAGAGTAGAGAGAGAAAGAGAAAAGATG
66 GACAAGGTGTGAGAGAAAGAGAGGG-TGCCAAGAGGTAAGAGTAGAGAGAGAAAGA-AAAAGATG
* * * * * *
1828295 TTGAGACCGAGATAAGGTGTGAGAGAAAGAGAGGGGTGCAAAGACGTCAGACTAGAGAGAGAAAT
129 TTGAGACGGAGACAAGGTGTGAGAG-AAGAGAGGGGTGCGAAGAGGTCAGAATAGAGAGAGAAAG
**
1828360 AGAAAAGATGTTGAGAC----A-AA-GTGT
193 AGAAAAGGCGTTGAGACGGAGACAAGGTGT
* * * ** *
1828384 TAGAGAAATAGAGGGGTGCAAGGAGGTCCGAGTAGAGAGAGAAAGAGAAAAGATATTGAGAC
1 GAGAGAAAGAGAGGGGTGCAAAGAGGTAAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGAC
1828446 AAAGAGAGAG
Statistics
Matches: 446, Mismatches: 47, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
218 12 0.03
219 45 0.10
220 1 0.00
221 75 0.17
222 165 0.37
223 24 0.05
224 76 0.17
225 2 0.00
226 1 0.00
227 1 0.00
228 5 0.01
229 1 0.00
230 38 0.09
ACGTcount: A:0.42, C:0.07, G:0.40, T:0.11
Consensus pattern (222 bp):
GAGAGAAAGAGAGGGGTGCAAAGAGGTAAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGA
GACAAGGTGTGAGAGAAAGAGAGGGTGCCAAGAGGTAAGAGTAGAGAGAGAAAGAAAAAGATGTT
GAGACGGAGACAAGGTGTGAGAGAAGAGAGGGGTGCGAAGAGGTCAGAATAGAGAGAGAAAGAGA
AAAGGCGTTGAGACGGAGACAAGGTGT
Found at i:1828166 original size:147 final size:148
Alignment explanation
Indices: 1827751--1828445 Score: 794
Period size: 147 Copynumber: 4.7 Consensus size: 148
1827741 CAGAGTAGAG
* * * *
1827751 AGAG-AGAGAGAGAGAGAGAGAAA-ATGTTGAGACAG-GACACGGTGTGAGAGAAAGAGAGGGGT
1 AGAGTAGAGAGAGAAAGACA-AAAGATGTTGAGACGGAGACAAGGTGTGAGAG-AAGAGAGGGGT
* *
1827813 GC-AATGAGGTAAGAGTAGAGAGAGAAAGAG--AAGATATTGAGACGGAGACAAGTTGTGAGAGA
64 GCGAA-GAGGTAAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGA
* * **
1827875 AAGAGAGCGGGGCGAAGAGGCC
128 AAGAGAG-GGTGCAAAGAGGTA
* * ** *
1827897 AGAATAGAGAGAGAAAGAGAAAAGGCGTTGAGACGGAGACAAGGTGTGAGAGAAAGAGGGGGGTG
1 AGAGTAGAGAGAGAAAGACAAAAGATGTTGAGACGGAGACAAGGTGTGAGAG-AAGAGAGGGGTG
* *
1827962 CCAAGAGGTAAGAGTGGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAA
65 CGAAGAGGTAAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAA
*
1828027 GAGAGGGTGCCAAGAGGTA
130 GAGAGGGTGCAAAGAGGTA
* *
1828046 AGAGTAGAGAGAAAAAGACAAAAGATGTTGAGACGGAGACAAGGTGTGAGTG-AGAGAGGGGTGC
1 AGAGTAGAGAGAGAAAGACAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAGAGAGGGGTGC
* * **
1828110 GAAGAGGTCAGCA-TAGAAAGAGAAAGAGAAAAGGCGTTGAGACGGAGACAAGGTGTGAGAGAAA
66 GAAGAGGTAAG-AGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAA
*
1828174 GATG-GGGTGCAAAGAAGTA
130 GA-GAGGGTGCAAAGAGGTA
* *
1828193 AGAGTAGAGAGAGAAAG-CGAAAAGGTGTTGAGACGGAGACAAGGTGTGAGAGCAAGAGAGGGAT
1 AGAGTAGAGAGAGAAAGAC-AAAAGATGTTGAGACGGAGACAAGGTGTGAGAG-AAGAGAGGGGT
* * * *
1828257 GCGAAGACGTCAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACCGAGATAAGGTGTGAGAGAA
64 GCGAAGAGGTAAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAA
* *
1828322 AGAGAGGGGTGCAAAGACGTC
129 AGAGA-GGGTGCAAAGAGGTA
* * * * *
1828343 AGACTAGAGAGAGAAATAGAAAAGATGTTGAGAC----A-AA-GTGTTAGAGAAATAGAGGGGTG
1 AGAGTAGAGAGAGAAAGACAAAAGATGTTGAGACGGAGACAAGGTGTGAGAG-AAGAGAGGGGTG
** *
1828402 C-AAGGAGGTCCGAGTAGAGAGAGAAAGAGAAAAGATATTGAGAC
65 CGAA-GAGGTAAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGAC
1828446 AAAGAGAGAG
Statistics
Matches: 481, Mismatches: 52, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
143 2 0.00
144 56 0.12
145 2 0.00
146 8 0.02
147 152 0.32
148 55 0.11
149 127 0.26
150 79 0.16
ACGTcount: A:0.42, C:0.07, G:0.40, T:0.11
Consensus pattern (148 bp):
AGAGTAGAGAGAGAAAGACAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAGAGAGGGGTGC
GAAGAGGTAAGAGTAGAGAGAGAAAGAGAAAAGATGTTGAGACGGAGACAAGGTGTGAGAGAAAG
AGAGGGTGCAAAGAGGTA
Found at i:1828453 original size:31 final size:33
Alignment explanation
Indices: 1828417--1828488 Score: 103
Period size: 31 Copynumber: 2.2 Consensus size: 33
1828407 AGGTCCGAGT
* *
1828417 AGAGAGAGAAAGAGAAAAGATATTGA-GACAA-
1 AGAGAGAGAAACAGAAAAGATACTGAGGACAAG
*
1828448 AGAGAGAGAAACAGAAAAGATGCTGAGGACAAG
1 AGAGAGAGAAACAGAAAAGATACTGAGGACAAG
1828481 AGAGAGAG
1 AGAGAGAG
1828489 GAAGTGGAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 23 0.64
32 5 0.14
33 8 0.22
ACGTcount: A:0.54, C:0.06, G:0.33, T:0.07
Consensus pattern (33 bp):
AGAGAGAGAAACAGAAAAGATACTGAGGACAAG
Found at i:1839857 original size:14 final size:14
Alignment explanation
Indices: 1839838--1839926 Score: 67
Period size: 14 Copynumber: 6.4 Consensus size: 14
1839828 TTTTAGATTC
1839838 ATAAAATATAATAT
1 ATAAAATATAATAT
1839852 ATAAAATATAA-AT
1 ATAAAATATAATAT
* **
1839865 AATTAAATACGATAT
1 -ATAAAATATAATAT
* *
1839880 ATAAAATTTTAT-T
1 ATAAAATATAATAT
1839893 ATAAAATATAA-AT
1 ATAAAATATAATAT
* * *
1839906 AATTAAATATTATAA
1 -ATAAAATATAATAT
1839921 ATAAAA
1 ATAAAA
1839927 AAATATAACT
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
13 13 0.23
14 41 0.72
15 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (14 bp):
ATAAAATATAATAT
Found at i:1839930 original size:17 final size:17
Alignment explanation
Indices: 1839899--1839932 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1839889 TATTATAAAA
**
1839899 TATAAATAATTAAATAT
1 TATAAATAAAAAAATAT
1839916 TATAAATAAAAAAATAT
1 TATAAATAAAAAAATAT
1839933 AACTTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TATAAATAAAAAAATAT
Found at i:1840172 original size:14 final size:15
Alignment explanation
Indices: 1840141--1840174 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1840131 TTTTGTGAAG
*
1840141 TTATTTTATTATTTA
1 TTATTTTATTATTAA
1840156 TTATTTTA-TATTAA
1 TTATTTTATTATTAA
1840170 TTATT
1 TTATT
1840175 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTTATTATTAA
Found at i:1843992 original size:22 final size:23
Alignment explanation
Indices: 1843964--1844015 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
1843954 AAAAAAGAAA
1843964 AATAATTTCAAAATTTGAACTT-
1 AATAATTTCAAAATTTGAACTTC
* *
1843986 AATAATTTCAAATTTTGGACTTC
1 AATAATTTCAAAATTTGAACTTC
1844009 AA-AATTT
1 AATAATTT
1844016 AGATTAGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (23 bp):
AATAATTTCAAAATTTGAACTTC
Found at i:1844217 original size:2 final size:2
Alignment explanation
Indices: 1844210--1844266 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1844200 ATCATATTTT
1844210 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1844250 TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1844267 AAATCTGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 49 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1844230 original size:15 final size:15
Alignment explanation
Indices: 1844209--1844266 Score: 98
Period size: 15 Copynumber: 3.7 Consensus size: 15
1844199 TATCATATTT
1844209 TTATATATATTATATA
1 TTATATATA-TATATA
1844225 TATATATATATATATA
1 T-TATATATATATATA
1844241 TTATATATATATATA
1 TTATATATATATATA
1844256 TTATATATATA
1 TTATATATATA
1844267 AAATCTGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 25 0.61
16 8 0.20
17 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:1849959 original size:15 final size:15
Alignment explanation
Indices: 1849932--1849964 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1849922 CAATAAACTT
1849932 AAAATCAAAAAATAA
1 AAAATCAAAAAATAA
1849947 AAAAT-AAATAAATAA
1 AAAATCAAA-AAATAA
1849962 AAA
1 AAA
1849965 CTAAGTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAATCAAAAAATAA
Found at i:1855691 original size:234 final size:235
Alignment explanation
Indices: 1855281--1855750 Score: 757
Period size: 234 Copynumber: 2.0 Consensus size: 235
1855271 AAATCACGGA
1855281 CAGAACAAAAATTACAGAAAGGAAAACGAAAATCCGACTTCTTTTTCGAAAAATCAAGTTTACTA
1 CAGAACAAAAATTACAGAAAGGAAAACGAAAATCCGACTTCTTTTTCGAAAAATCAAGTTTACTA
* * * * *
1855346 TTAAGAGAAAATGAAAGAAAAATAAAAGCACCAACAAGAAGAAAGCAGATCTGAACTTTAAATAA
66 TAAAAAGAAAATGAAAGAAAAATAAAAGCACCAACAAAAAAAAAGCAGATCTAAACTTTAAATAA
* *
1855411 AAATTTTGCAGAAAAAAAACCCACCATATTAAAAGAATCACCACCAACAGACCAGATCTGAAATT
131 AAATTTTCCAGAAAAAAAACCCACCATATTAAAAGAATCACCACCAACAAACCAGATCTGAAATT
* *
1855476 TTTTGTTGTAAAAACTCTATATTTGAGATTTTCAGCCTTT
196 TTTTGTTGTAAAAACTATAAATTTGAGATTTTCAGCCTTT
1855516 CAGAACAAAAATTACAGAAAGG-AAACAGAAAATCCGACTTC-TTTTCGAAAAATCAAGTTTACT
1 CAGAACAAAAATTACAGAAAGGAAAAC-GAAAATCCGACTTCTTTTTCGAAAAATCAAGTTTACT
*
1855579 ATAAAAAGAAAATGAAAGAAAAATAAAAGCACCAGCAAAAAAAAATGCAGATCTAAACTTTAAAT
65 ATAAAAAGAAAATGAAAGAAAAATAAAAGCACCAACAAAAAAAAA-GCAGATCTAAACTTTAAAT
* * * **
1855644 TAAAA-TTTCCAGAAAAATAACCCACCATATTAAAAGAATCACCACCAACAAATCAGATCTGTGA
129 AAAAATTTTCCAGAAAAAAAACCCACCATATTAAAAGAATCACCACCAACAAACCAGATCTGAAA
*
1855708 TTTTTTGTTGTAAAAACTATAAATTTGAGATTTTCAGGCTTT
194 TTTTTTGTTGTAAAAACTATAAATTTGAGATTTTCAGCCTTT
1855750 C
1 C
1855751 TTTTTCCTTG
Statistics
Matches: 217, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
234 159 0.73
235 58 0.27
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (235 bp):
CAGAACAAAAATTACAGAAAGGAAAACGAAAATCCGACTTCTTTTTCGAAAAATCAAGTTTACTA
TAAAAAGAAAATGAAAGAAAAATAAAAGCACCAACAAAAAAAAAGCAGATCTAAACTTTAAATAA
AAATTTTCCAGAAAAAAAACCCACCATATTAAAAGAATCACCACCAACAAACCAGATCTGAAATT
TTTTGTTGTAAAAACTATAAATTTGAGATTTTCAGCCTTT
Found at i:1855987 original size:44 final size:45
Alignment explanation
Indices: 1855895--1855993 Score: 173
Period size: 45 Copynumber: 2.2 Consensus size: 45
1855885 ACGACGGTAT
1855895 CGGCAGAAGGAAGGCTAGGGGTTTTCAGAAAAGAGAGCACACAGG
1 CGGCAGAAGGAAGGCTAGGGGTTTTCAGAAAAGAGAGCACACAGG
* *
1855940 CGGCAGAAGGAAGGCTAGGGGTTTTCAG-AAAGAGAGGATACAGG
1 CGGCAGAAGGAAGGCTAGGGGTTTTCAGAAAAGAGAGCACACAGG
1855984 CGGCAGAAGG
1 CGGCAGAAGG
1855994 CAGAGGAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
44 24 0.46
45 28 0.54
ACGTcount: A:0.34, C:0.14, G:0.40, T:0.11
Consensus pattern (45 bp):
CGGCAGAAGGAAGGCTAGGGGTTTTCAGAAAAGAGAGCACACAGG
Found at i:1868787 original size:400 final size:400
Alignment explanation
Indices: 1868038--1868810 Score: 1375
Period size: 400 Copynumber: 1.9 Consensus size: 400
1868028 ATAGATACAC
*
1868038 TTATTAATAAGTTAAATATTTAAGCACAAAAGATTTATGGTGTAAAAAATTATATATAAATATTT
1 TTATTAATAAGTCAAATATTTAAGCACAAAAGATTTATGGTGTAAAAAATTATATATAAATATTT
*
1868103 TCATACTCGATTATTTGATTATAAAATGTGTACATTAATTTATCTTCTCCGTAAAAATTAAATTT
66 TCATACTCGATTATTTGATTATAAAATATGTACATTAATTTATCTTCTCCGTAAAAATTAAATTT
* *
1868168 AAATTCTCCTTTTATAAAAAAAATTGAAAAAAATTTTATATCTAAAGTCAAATTTAGATGACTAA
131 AAATTCTCCTTTTATAAAAAAAATTGAAAAAAATTTCATATCTAAAATCAAATTTAGATGACTAA
1868233 CTTGCATTGTATTCGAATAAAATAATATAAAAAATTAAATAATTTTTTTCTATTTTTAATAGCAT
196 CTTGCATTGTATTCGAATAAAATAATATAAAAAATTAAATAATTTTTTTCTATTTTTAATAGCAT
** *
1868298 AAAAATTTGAAATTAATTTGATTTAGGTTTTAACTTAAACTGAACTCAAATAAGCAAAATAGTTT
261 AAAAAAATAAAATTAATTTGATTTAGGTTTTAACTTAAACTGAACTCAAATAAGCAAAATAGTTT
* *
1868363 GATTTAGTTACAACTTTTACAATTTACAAATATCCATTCTCTTGGAATAAGTCAAATAATCGAGT
326 GATTTAGTTACAACTTTCACAATTTACAAATATCCATTATCTTGGAATAAGTCAAATAATCGAGT
1868428 ATGAAAATAT
391 ATGAAAATAT
1868438 TTATTAATAAGTCAAATATTTAAGCACAAAAGATTTATGGTGTAAAAAATTATATATAAATATTT
1 TTATTAATAAGTCAAATATTTAAGCACAAAAGATTTATGGTGTAAAAAATTATATATAAATATTT
*
1868503 TCATACTCGATTATTTGATTATAAAATATGTACATTAATTTATCTTCTCCGTAAAAATTAAGTTT
66 TCATACTCGATTATTTGATTATAAAATATGTACATTAATTTATCTTCTCCGTAAAAATTAAATTT
* *
1868568 GAATTCTCTTTTTATAAAAAAAATTGAAAAAAATTTCATATCTAAAATCAAATTTAGATGACTAA
131 AAATTCTCCTTTTATAAAAAAAATTGAAAAAAATTTCATATCTAAAATCAAATTTAGATGACTAA
* * *
1868633 CTTGCATTGTGTTTGAATAAAATAATATAAAAAATTAAATAATTTTTTTCTATTTTTAATAGTAT
196 CTTGCATTGTATTCGAATAAAATAATATAAAAAATTAAATAATTTTTTTCTATTTTTAATAGCAT
* * *
1868698 AAAAAAATAAAATTAATTTGATTTAGTTTTTAACTTGAACTGAACTTAAATAAGCAAAATAGTTT
261 AAAAAAATAAAATTAATTTGATTTAGGTTTTAACTTAAACTGAACTCAAATAAGCAAAATAGTTT
*
1868763 GATTTAGTTATAACTTTCACAATTTACAAATATCCATTATCTTGGAAT
326 GATTTAGTTACAACTTTCACAATTTACAAATATCCATTATCTTGGAAT
1868811 TATTTAACCC
Statistics
Matches: 354, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
400 354 1.00
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (400 bp):
TTATTAATAAGTCAAATATTTAAGCACAAAAGATTTATGGTGTAAAAAATTATATATAAATATTT
TCATACTCGATTATTTGATTATAAAATATGTACATTAATTTATCTTCTCCGTAAAAATTAAATTT
AAATTCTCCTTTTATAAAAAAAATTGAAAAAAATTTCATATCTAAAATCAAATTTAGATGACTAA
CTTGCATTGTATTCGAATAAAATAATATAAAAAATTAAATAATTTTTTTCTATTTTTAATAGCAT
AAAAAAATAAAATTAATTTGATTTAGGTTTTAACTTAAACTGAACTCAAATAAGCAAAATAGTTT
GATTTAGTTACAACTTTCACAATTTACAAATATCCATTATCTTGGAATAAGTCAAATAATCGAGT
ATGAAAATAT
Found at i:1882966 original size:15 final size:16
Alignment explanation
Indices: 1882942--1882975 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1882932 TAATCATATA
1882942 ATATTATAAATT-TAT
1 ATATTATAAATTGTAT
*
1882957 ATATTTTAAATTGTAT
1 ATATTATAAATTGTAT
1882973 ATA
1 ATA
1882976 AATTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATTATAAATTGTAT
Found at i:1883810 original size:22 final size:22
Alignment explanation
Indices: 1883793--1883835 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1883783 CGAATTGTAT
1883793 CATT-ACAATATCATAATTTAA
1 CATTGACAATATCATAATTTAA
*
1883814 CATTGATAATATCATAATTTAA
1 CATTGACAATATCATAATTTAA
1883836 TTGTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (22 bp):
CATTGACAATATCATAATTTAA
Found at i:1883960 original size:18 final size:19
Alignment explanation
Indices: 1883926--1883961 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1883916 TTGTATACTC
*
1883926 TTTTATATGAATTTTTTAT
1 TTTTATATGAATATTTTAT
1883945 TTTTATAT-AATATTTTA
1 TTTTATATGAATATTTTA
1883962 AAAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTATATGAATATTTTAT
Found at i:1883990 original size:10 final size:10
Alignment explanation
Indices: 1883958--1884000 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1883948 TATATAATAT
*
1883958 TTTAAAAAAA
1 TTTAAATAAA
*
1883968 TTTTAAAT-TA
1 -TTTAAATAAA
1883978 TTTAAATAAA
1 TTTAAATAAA
1883988 TTTAAATAAA
1 TTTAAATAAA
1883998 TTT
1 TTT
1884001 TTATTATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 7 0.25
10 15 0.54
11 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:1884000 original size:20 final size:20
Alignment explanation
Indices: 1883953--1883996 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1883943 ATTTTTATAT
*
1883953 AATATTTTAAAAAAATTTTA
1 AATAATTTAAAAAAATTTTA
* *
1883973 AATTATTTAAATAAA-TTTA
1 AATAATTTAAAAAAATTTTA
1883992 AATAA
1 AATAA
1883997 ATTTTTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATAATTTAAAAAAATTTTA
Found at i:1884007 original size:29 final size:31
Alignment explanation
Indices: 1883938--1884007 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
1883928 TTATATGAAT
*
1883938 TTTTTATT-TTTATATAATATTTTAAAAAAA
1 TTTTTATTATTTAAATAATATTTTAAAAAAA
* *
1883968 TTTTAAATTATTTAAATAA-A-TTTAAATAAA
1 TTTT-TATTATTTAAATAATATTTTAAAAAAA
1883998 TTTTTATTAT
1 TTTTTATTAT
1884008 GTTCAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 5 0.15
30 17 0.50
31 4 0.12
32 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TTTTTATTATTTAAATAATATTTTAAAAAAA
Found at i:1885185 original size:26 final size:26
Alignment explanation
Indices: 1885135--1885185 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1885125 AACATTTGTT
*
1885135 TGTTTATTTGGCTGTCATATGTCATA
1 TGTTTATTTGGCTGTCATATATCATA
* *
1885161 TGTTTATTTGGCTGTCTTTTATCAT
1 TGTTTATTTGGCTGTCATATATCAT
1885186 GTGTGGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.55
Consensus pattern (26 bp):
TGTTTATTTGGCTGTCATATATCATA
Found at i:1885891 original size:15 final size:15
Alignment explanation
Indices: 1885836--1885892 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 15
1885826 TGCTTGGTTC
*
1885836 ATTAGAAAAAATAAA
1 ATTAAAAAAAATAAA
* *
1885851 ATGAGAATAAAATAATA
1 ATTA-AAAAAAATAA-A
*
1885868 ATTTCAAAAAAATAAA
1 A-TTAAAAAAAATAAA
1885884 ATTAAAAAA
1 ATTAAAAAA
1885893 TAATTATTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
15 10 0.31
16 10 0.31
17 11 0.34
18 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (15 bp):
ATTAAAAAAAATAAA
Found at i:1886263 original size:46 final size:46
Alignment explanation
Indices: 1886207--1886357 Score: 144
Period size: 46 Copynumber: 3.5 Consensus size: 46
1886197 AAAAATATAT
* *
1886207 TTTTATTATAATTTAACAATATTTTGTATTAGAAGATAATTAAACC
1 TTTTATTATAATTAAATAATATTTTGTATTAGAAGATAATTAAACC
** * *
1886253 TTTTATTATAATTAAATAATATTTAATATTA-AA-A-GA-CAAA--
1 TTTTATTATAATTAAATAATATTTTGTATTAGAAGATAATTAAACC
* * *
1886293 ----A-TANAATTTAATAATATTTTGCATTAGAAGATAATTAAACC
1 TTTTATTATAATTAAATAATATTTTGTATTAGAAGATAATTAAACC
1886334 TTTTATTATAATTAAATAATATTT
1 TTTTATTATAATTAAATAATATTT
1886358 AATATTAAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
35 20 0.25
36 3 0.04
37 1 0.01
38 1 0.01
39 3 0.04
42 3 0.04
43 1 0.01
44 1 0.01
45 3 0.04
46 43 0.54
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (46 bp):
TTTTATTATAATTAAATAATATTTTGTATTAGAAGATAATTAAACC
Found at i:1886351 original size:81 final size:79
Alignment explanation
Indices: 1886216--1886375 Score: 284
Period size: 81 Copynumber: 2.0 Consensus size: 79
1886206 TTTTTATTAT
*
1886216 AATTTAACAATATTTTGTATTAGAAGATAATTAAACCTTTTATTATAATTAAATAATATTTAATA
1 AATTTAACAATATTTTGCATTAGAAGATAATTAAACCTTTTATTATAATTAAATAATATTTAATA
1886281 TTAAAAGACAAAATA
66 TTAAAAGA-AAAATA
*
1886296 NAATTTAATAATATTTTGCATTAGAAGATAATTAAACCTTTTATTATAATTAAATAATATTTAAT
1 -AATTTAACAATATTTTGCATTAGAAGATAATTAAACCTTTTATTATAATTAAATAATATTTAAT
1886361 ATTAAAAGAAAAATA
65 ATTAAAAGAAAAATA
1886376 TATTCTTCAT
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
80 6 0.08
81 71 0.92
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.40
Consensus pattern (79 bp):
AATTTAACAATATTTTGCATTAGAAGATAATTAAACCTTTTATTATAATTAAATAATATTTAATA
TTAAAAGAAAAATA
Found at i:1886451 original size:45 final size:45
Alignment explanation
Indices: 1886385--1886502 Score: 152
Period size: 44 Copynumber: 2.6 Consensus size: 45
1886375 ATATTCTTCA
* *
1886385 TTAAATTTAAATAATACTAAATAATATTCTTTATTACATTTATTATA-
1 TTAAA-TT-AATAATATTAAATAATATT-TTTATGACATTTATTATAG
*
1886432 TTCAAA-TAATAATATTAAATAATATTTTTATGATATTTATTATAG
1 TT-AAATTAATAATATTAAATAATATTTTTATGACATTTATTATAG
1886477 TTAAATTAAT-ATATTAAATAATATTT
1 TTAAATTAATAATATTAAATAATATTT
1886503 AAATATTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
44 35 0.54
45 24 0.37
46 1 0.02
47 2 0.03
48 3 0.05
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (45 bp):
TTAAATTAATAATATTAAATAATATTTTTATGACATTTATTATAG
Found at i:1886513 original size:10 final size:11
Alignment explanation
Indices: 1886429--1886507 Score: 54
Period size: 11 Copynumber: 7.0 Consensus size: 11
1886419 TACATTTATT
*
1886429 ATATTCAAATA
1 ATATTTAAATA
1886440 ATAATATTAAATA
1 AT-AT-TTAAATA
** *
1886453 ATATTTTTATG
1 ATATTTAAATA
*
1886464 ATATTT--ATT
1 ATATTTAAATA
*
1886473 ATAGTTAAATTA
1 ATATTTAAA-TA
1886485 ATATATTAAATA
1 ATAT-TTAAATA
1886497 ATATTTAAATA
1 ATATTTAAATA
1886508 TTTTTATTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 7 0.13
11 20 0.37
12 14 0.26
13 13 0.24
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (11 bp):
ATATTTAAATA
Found at i:1887437 original size:17 final size:17
Alignment explanation
Indices: 1887415--1887447 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1887405 ACGTGGTTGA
1887415 GAGAAAAATTCAAAACT
1 GAGAAAAATTCAAAACT
1887432 GAGAAAAATTCAAAAC
1 GAGAAAAATTCAAAAC
1887448 CGCCAGCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.15
Consensus pattern (17 bp):
GAGAAAAATTCAAAACT
Found at i:1896329 original size:12 final size:12
Alignment explanation
Indices: 1896312--1896336 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1896302 GCGATTTCAT
1896312 AAAAACATACCA
1 AAAAACATACCA
1896324 AAAAACATACCA
1 AAAAACATACCA
1896336 A
1 A
1896337 TGAAGTGGGC
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAACATACCA
Found at i:1904517 original size:57 final size:56
Alignment explanation
Indices: 1904422--1904537 Score: 160
Period size: 57 Copynumber: 2.1 Consensus size: 56
1904412 AAGTTAGCCA
* * * * *
1904422 TAAATTTTGTGGCACTAGTATGACCATGAAGGGATACTATCATTGTACGGAGAGGT
1 TAAATTTCGTGGCACTAGCATGACAATGAAGGGATACTATCAGTGTACCGAGAGGT
* *
1904478 TAAATTTCGTGGTCACTAGCATGACAATGGAGGGGTACTATCAGTGTACCGAGAGGT
1 TAAATTTCGTGG-CACTAGCATGACAATGAAGGGATACTATCAGTGTACCGAGAGGT
1904535 TAA
1 TAA
1904538 GTACTATCAG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
56 11 0.21
57 41 0.79
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (56 bp):
TAAATTTCGTGGCACTAGCATGACAATGAAGGGATACTATCAGTGTACCGAGAGGT
Found at i:1904541 original size:26 final size:26
Alignment explanation
Indices: 1904512--1904565 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1904502 CAATGGAGGG
1904512 GTACTATCAGTGTACCGAGAGGTTAA
1 GTACTATCAGTGTACCGAGAGGTTAA
1904538 GTACTATCAGTGTACCGAGAGGTTAA
1 GTACTATCAGTGTACCGAGAGGTTAA
1904564 GT
1 GT
1904566 CTTGTCGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (26 bp):
GTACTATCAGTGTACCGAGAGGTTAA
Found at i:1913495 original size:12 final size:12
Alignment explanation
Indices: 1913478--1913502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1913468 TGGCTTTGAA
1913478 TGGTAGTTAAGT
1 TGGTAGTTAAGT
1913490 TGGTAGTTAAGT
1 TGGTAGTTAAGT
1913502 T
1 T
1913503 TATAAGAAAA
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:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (12 bp):
TGGTAGTTAAGT
Found at i:1914535 original size:66 final size:65
Alignment explanation
Indices: 1914324--1914540 Score: 242
Period size: 64 Copynumber: 3.3 Consensus size: 65
1914314 TTATTTTGAC
* *
1914324 TATTATTCACAAC-ATCATTGTTAATCTCCAACTTGTCTGGAA-ACATTTCTTTTTTTGTTTTGA
1 TATTATTCACAACAATCATTGTTAATCTCAAACTTGTC---AAGACA-TT-TTTTTTTATTTTGA
1914387 GTGAT
61 GTGAT
* * * * * * *
1914392 TATTATTCACAACAATTATTGCTAATCTCAAAATTATCAA-AAATATTTTTTTATTTTGAGTAAT
1 TATTATTCACAACAATCATTGTTAATCTCAAACTTGTCAAGACATTTTTTTTTATTTTGAGTGAT
* * * *
1914456 TATTATTCACAACAATCATTATTAATCTCGAACTCGTCAAGACCATTTTTTTTTATTTTGAATGA
1 TATTATTCACAACAATCATTGTTAATCTCAAACTTGTCAAGA-CATTTTTTTTTATTTTGAGTGA
1914521 T
65 T
1914522 TATTATTCACAACAATCAT
1 TATTATTCACAACAATCAT
1914541 CACTAATTAT
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
64 50 0.40
65 2 0.02
66 42 0.33
68 13 0.10
69 19 0.15
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (65 bp):
TATTATTCACAACAATCATTGTTAATCTCAAACTTGTCAAGACATTTTTTTTTATTTTGAGTGAT
Found at i:1916204 original size:102 final size:102
Alignment explanation
Indices: 1916028--1916236 Score: 346
Period size: 102 Copynumber: 2.0 Consensus size: 102
1916018 CTTTGGATTC
* * * * **
1916028 TCAGACTGATGTAGTTCACTGTCGTGCTTTCCTTGATCTACTTCCTCTTGGAGCTGGGAGACTTG
1 TCAGACTGATGAAGTACACTGTCGTGCTTTCCTTGATCTACTTCATCTTGAAGCTGCAAGACTTG
1916093 AGTTCTATCTGCCAGGTTTTTTCTGGATAATTCATCT
66 AGTTCTATCTGCCAGGTTTTTTCTGGATAATTCATCT
*
1916130 TCAGACTGATGAAGTACACTGTCGTGCTTTCCTTGATTTACTTCATCTTGAAGCTGCAAGACTTG
1 TCAGACTGATGAAGTACACTGTCGTGCTTTCCTTGATCTACTTCATCTTGAAGCTGCAAGACTTG
*
1916195 AGTTCTATCTGCCAGGTTTTTTCTTGATAATTCATCT
66 AGTTCTATCTGCCAGGTTTTTTCTGGATAATTCATCT
1916232 TCAGA
1 TCAGA
1916237 TGAGGTTGAC
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (102 bp):
TCAGACTGATGAAGTACACTGTCGTGCTTTCCTTGATCTACTTCATCTTGAAGCTGCAAGACTTG
AGTTCTATCTGCCAGGTTTTTTCTGGATAATTCATCT
Found at i:1947291 original size:28 final size:28
Alignment explanation
Indices: 1947258--1947311 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1947248 TAATATCGAA
1947258 AATAAAAAATAAAAAATTAATTAAATAT
1 AATAAAAAATAAAAAATTAATTAAATAT
* *
1947286 AATAAAAAATAAAAATTTATTTAAAT
1 AATAAAAAATAAAAAATTAATTAAAT
1947312 TTATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAAAAAATAAAAAATTAATTAAATAT
Found at i:1953840 original size:71 final size:70
Alignment explanation
Indices: 1953724--1953859 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 70
1953714 ATCAACTCGG
* * *
1953724 CTTAAAATGATATTAATCTATCCTTACCTATTCTGGGGCTTGACTTCATCAAATTTCTTTCTGGA
1 CTTAAAATGATATTAATCTATCCTTACCTATCCTGGGGCTTGACTTCAAC-AATTTCTTTCAGGA
1953789 ATGGCT
65 ATGGCT
* * ** *
1953795 CTTAAAGTGATGTTAATCTATTGTTACTTATCCTGGGGCTTGACTTCAACAATTTCTTTCAGGAA
1 CTTAAAATGATATTAATCTATCCTTACCTATCCTGGGGCTTGACTTCAACAATTTCTTTCAGGAA
1953860 AATGTTTGAT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
70 14 0.25
71 43 0.75
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (70 bp):
CTTAAAATGATATTAATCTATCCTTACCTATCCTGGGGCTTGACTTCAACAATTTCTTTCAGGAA
TGGCT
Found at i:1956570 original size:77 final size:78
Alignment explanation
Indices: 1956428--1956586 Score: 284
Period size: 77 Copynumber: 2.1 Consensus size: 78
1956418 AGAAGCCTGC
*
1956428 AGCAGGCTCTCCATAGTTAAATGAAATCACTTTTTGAGACTTTATATCTGCACATTTGATGAGTA
1 AGCAGGCTCTCCATAGTTAAATGAAATCACTTTTTGACACTTTATATCTGCACATTTGATGAGTA
1956493 TAAGCTTCCACAT
66 TAAGCTTCCACAT
* *
1956506 AGCAGGCTCTCCTTAGTTAAATGAAATCAC-TTTTGACACTTTATATTTGCACATTTGATGAGTA
1 AGCAGGCTCTCCATAGTTAAATGAAATCACTTTTTGACACTTTATATCTGCACATTTGATGAGTA
1956570 TAAGCTTCCACAT
66 TAAGCTTCCACAT
1956583 AGCA
1 AGCA
1956587 CTATTCCGCA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 49 0.63
78 29 0.37
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (78 bp):
AGCAGGCTCTCCATAGTTAAATGAAATCACTTTTTGACACTTTATATCTGCACATTTGATGAGTA
TAAGCTTCCACAT
Found at i:1964638 original size:81 final size:81
Alignment explanation
Indices: 1964544--1964711 Score: 196
Period size: 81 Copynumber: 2.1 Consensus size: 81
1964534 TCTCATGAAT
* * *
1964544 TATATACCATTTTCTCTTTTAAGTTGATCGATACAAATATAATCC-GAAATTACTCTAATC-TTA
1 TATATACCATTTTCTCTTTTAAGTTAATCGATACAAACAAAATCCTG-AATTACTCT-ATCTTTA
* * *
1964607 GTTTTTCATGATTTTATA
64 ATTTTTCATAATTATATA
** ** * *
1964625 TATATACTGTTTTCTCTTTTACTTTAATTGATATAAACAAAATCCTGAATTACTCTATCTTTAAT
1 TATATACCATTTTCTCTTTTAAGTTAATCGATACAAACAAAATCCTGAATTACTCTATCTTTAAT
1964690 TTTTCATAATTATATA
66 TTTTCATAATTATATA
1964706 TATATA
1 TATATA
1964712 TGTATATATA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
80 3 0.04
81 69 0.95
82 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (81 bp):
TATATACCATTTTCTCTTTTAAGTTAATCGATACAAACAAAATCCTGAATTACTCTATCTTTAAT
TTTTCATAATTATATA
Found at i:1967865 original size:2 final size:2
Alignment explanation
Indices: 1967858--1967882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1967848 TGTGTCTCTT
1967858 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1967883 TTTTTGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1983750 original size:19 final size:20
Alignment explanation
Indices: 1983717--1983756 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
1983707 TGAATAAAGA
1983717 AACAAAGAGAGCTTACAGTT
1 AACAAAGAGAGCTTACAGTT
1983737 AACAAAGA-AGCTTACAGTT
1 AACAAAGAGAGCTTACAGTT
1983756 A
1 A
1983757 TGATTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.20
Consensus pattern (20 bp):
AACAAAGAGAGCTTACAGTT
Found at i:1985187 original size:38 final size:38
Alignment explanation
Indices: 1985136--1985211 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
1985126 TGTCGTTATA
*
1985136 CAAAAATAAAAAGGACAATGGCATGTTCTTGATTCCTT
1 CAAAAATAAAAAGGACAATGGCATGTTCTTGATACCTT
*
1985174 CAAAAATAAAAAGGGCAATGGCATGTTCTTGATACCTT
1 CAAAAATAAAAAGGACAATGGCATGTTCTTGATACCTT
1985212 TTGTATGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (38 bp):
CAAAAATAAAAAGGACAATGGCATGTTCTTGATACCTT
Found at i:1987757 original size:50 final size:50
Alignment explanation
Indices: 1987698--1987792 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 50
1987688 AACACAATTT
* * *
1987698 TGTTTAACTATTTATACGTTACTATGTATTATTTTTACCATAACAAAGTC
1 TGTTTAACTATTTATACATTACTATATATTAGTTTTACCATAACAAAGTC
* * *
1987748 TGTTTAACTATTTATCCATTATTGTATATTAGTTTTACCATAACA
1 TGTTTAACTATTTATACATTACTATATATTAGTTTTACCATAACA
1987793 TAATCTATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (50 bp):
TGTTTAACTATTTATACATTACTATATATTAGTTTTACCATAACAAAGTC
Found at i:1996931 original size:4 final size:4
Alignment explanation
Indices: 1996922--1996987 Score: 75
Period size: 4 Copynumber: 16.2 Consensus size: 4
1996912 CGTTTTTCTT
1996922 TTTC TTTC TTTC TTTC TTTCC TTTCC TTTC --TC TTTC -TTC TTTC TTTCAC
1 TTTC TTTC TTTC TTTC TTT-C TTT-C TTTC TTTC TTTC TTTC TTTC TTT--C
1996971 TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC T
1996988 CTCCTAGCCA
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.04
3 3 0.05
4 38 0.68
5 9 0.16
6 4 0.07
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:1996961 original size:27 final size:28
Alignment explanation
Indices: 1996916--1996987 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
1996906 CCTTTTCGTT
*
1996916 TTTCTTTTTCTTTCTTTCTTTCTTTC-C
1 TTTCTTTCTCTTTCTTTCTTTCTTTCAC
1996943 TTTCCTTTCTCTTTC-TTCTTTCTTTCAC
1 TTT-CTTTCTCTTTCTTTCTTTCTTTCAC
1996971 TTTC-TT-TCTTTCTTTCT
1 TTTCTTTCTCTTTCTTTCT
1996988 CTCCTAGCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 6 0.15
26 6 0.15
27 15 0.37
28 14 0.34
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTCTTTCTCTTTCTTTCTTTCTTTCAC
Found at i:1997050 original size:11 final size:11
Alignment explanation
Indices: 1997034--1997058 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1997024 AAAAAAAAAA
1997034 ATTATTTATTT
1 ATTATTTATTT
1997045 ATTATTTATTT
1 ATTATTTATTT
1997056 ATT
1 ATT
1997059 TTTTTAGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTATTTATTT
Found at i:2000453 original size:2 final size:2
Alignment explanation
Indices: 2000446--2000479 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2000436 CAAGTAAGCA
2000446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2000480 TCACTCCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2001592 original size:31 final size:32
Alignment explanation
Indices: 2001557--2001642 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 32
2001547 TGTATGATAT
* *
2001557 ATTTTTGTTTAATTTAGTTTTTATA-TTATTA
1 ATTTTTATTTAATTTAATTTTTATATTTATTA
*
2001588 ATTTTTATTTAATTTAATTTTTATATTTCTTA
1 ATTTTTATTTAATTTAATTTTTATATTTATTA
* *
2001620 A-TTTTATTCAATTTAATCTTTAT
1 ATTTTTATTTAATTTAATTTTTAT
2001643 GACGTTATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
31 43 0.88
32 6 0.12
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.66
Consensus pattern (32 bp):
ATTTTTATTTAATTTAATTTTTATATTTATTA
Found at i:2001593 original size:16 final size:15
Alignment explanation
Indices: 2001574--2001624 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
2001564 TTTAATTTAG
2001574 TTTTTATATTATTAA
1 TTTTTATATTATTAA
2001589 TTTTTAT-TTAATTTAA
1 TTTTTATATT-A-TTAA
*
2001605 TTTTTATATTTCTTAA
1 TTTTTATA-TTATTAA
2001621 TTTT
1 TTTT
2001625 ATTCAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 2 0.06
15 8 0.26
16 19 0.61
18 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTATATTATTAA
Found at i:2021858 original size:40 final size:41
Alignment explanation
Indices: 2021803--2021911 Score: 139
Period size: 40 Copynumber: 2.6 Consensus size: 41
2021793 TCTAACGACT
*
2021803 AATCCTCAATTACGTAGTTAGAGACTAACCA-CCAACATCC
1 AATCCTAAATTACGTAGTTAGAGACTAACCACCCAACATCC
*
2021843 AATCCTGAATTACGTAGTTAGAGACTAACCACTGCCCCAACATCC
1 AATCCTAAATTACGTAGTTAGAGACTAACCA----CCCAACATCC
* *
2021888 AACCCTAAATTACGTGGTTAGAGA
1 AATCCTAAATTACGTAGTTAGAGA
2021912 AGAAAAAGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
40 30 0.50
45 30 0.50
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.23
Consensus pattern (41 bp):
AATCCTAAATTACGTAGTTAGAGACTAACCACCCAACATCC
Found at i:2021899 original size:45 final size:40
Alignment explanation
Indices: 2021810--2021911 Score: 132
Period size: 45 Copynumber: 2.4 Consensus size: 40
2021800 ACTAATCCTC
* *
2021810 AATTACGTAGTTAGAGACTAACCACCAACATCCAATCCTG
1 AATTACGTAGTTAGAGACTAACCACCAACATCCAACCCTA
2021850 AATTACGTAGTTAGAGACTAACCACTGCCCCAACATCCAACCCTA
1 AATTACGTAGTTAGAGACTAACCA-----CCAACATCCAACCCTA
*
2021895 AATTACGTGGTTAGAGA
1 AATTACGTAGTTAGAGA
2021912 AGAAAAAGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
40 24 0.44
45 30 0.56
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (40 bp):
AATTACGTAGTTAGAGACTAACCACCAACATCCAACCCTA
Found at i:2024190 original size:26 final size:26
Alignment explanation
Indices: 2024161--2024210 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2024151 TCATATATTA
*
2024161 TTAATAAATGAAATATTAT-TATTTTG
1 TTAATAAATCAAAT-TTATATATTTTG
2024187 TTAATAAATCAAATTTATATATTT
1 TTAATAAATCAAATTTATATATTT
2024211 ATAAAGTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (26 bp):
TTAATAAATCAAATTTATATATTTTG
Found at i:2025312 original size:2 final size:2
Alignment explanation
Indices: 2025305--2025329 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2025295 TGTTTTTATT
2025305 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 T
2025330 GTGTGTGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2026755 original size:129 final size:130
Alignment explanation
Indices: 2026620--2026876 Score: 372
Period size: 129 Copynumber: 2.0 Consensus size: 130
2026610 TTAAGCGTAT
**
2026620 TCATATAAATAAAGTTTATTATAAGATATAGTAATATTTATATATAAATTAAATATATGTATATA
1 TCATATAAATAAAGACTATTATAAGATATAGTAATATTTATATATAAATTAAATATATGTATATA
* * *
2026685 TATTACATTA-TTAAATATATATAAAATTAATGATACAAATTATATATTAAAATGTTTTATATAA
66 TAATACATGACTTAAATATATATAAAATTAATGACACAAATTATATATTAAAATGTTTTATATAA
* *
2026749 TCATATAAATAAAGACTATTATAAGTTATAGTAATATTTATGTATAAATTAAATATATGTATATA
1 TCATATAAATAAAGACTATTATAAGATATAGTAATATTTATATATAAATTAAATATATGTATATA
* * * * * * * *
2026814 TAATATATGACTTTATTATATATATAATTAATGACATAATTTATATGTTATAATGTTTTATAT
66 TAATACATGACTTAAATATATATAAAATTAATGACACAAATTATATATTAAAATGTTTTATAT
2026877 CAAAGTTTGT
Statistics
Matches: 112, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
129 68 0.61
130 44 0.39
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (130 bp):
TCATATAAATAAAGACTATTATAAGATATAGTAATATTTATATATAAATTAAATATATGTATATA
TAATACATGACTTAAATATATATAAAATTAATGACACAAATTATATATTAAAATGTTTTATATAA
Found at i:2026821 original size:17 final size:18
Alignment explanation
Indices: 2026775--2026821 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2026765 TATTATAAGT
*
2026775 TATAGTAATATTTATGTA
1 TATAGTAATATATATGTA
* *
2026793 TAAATTAA-ATATATGTA
1 TATAGTAATATATATGTA
2026810 TATA-TAATATAT
1 TATAGTAATATAT
2026822 GACTTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TATAGTAATATATATGTA
Found at i:2042551 original size:2 final size:2
Alignment explanation
Indices: 2042544--2042573 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2042534 AATCTTCATT
2042544 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2042574 TTTAAGCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2045985 original size:73 final size:73
Alignment explanation
Indices: 2045866--2046008 Score: 286
Period size: 73 Copynumber: 2.0 Consensus size: 73
2045856 GTCAGAAGTT
2045866 ATGTATCAGATAGATTTTATCAGCTTCATTGCCTTGTCAGGTTTATGTTGGCTCAGGATTGATTC
1 ATGTATCAGATAGATTTTATCAGCTTCATTGCCTTGTCAGGTTTATGTTGGCTCAGGATTGATTC
2045931 AACCCTTG
66 AACCCTTG
2045939 ATGTATCAGATAGATTTTATCAGCTTCATTGCCTTGTCAGGTTTATGTTGGCTCAGGATTGATTC
1 ATGTATCAGATAGATTTTATCAGCTTCATTGCCTTGTCAGGTTTATGTTGGCTCAGGATTGATTC
2046004 AACCC
66 AACCC
2046009 CAATCAAGGT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (73 bp):
ATGTATCAGATAGATTTTATCAGCTTCATTGCCTTGTCAGGTTTATGTTGGCTCAGGATTGATTC
AACCCTTG
Found at i:2048185 original size:16 final size:15
Alignment explanation
Indices: 2048164--2048228 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 15
2048154 GATGAATATT
2048164 AATATTTAATTTAAAA
1 AATATTTAA-TTAAAA
*
2048180 AATATTTAA--AATATT
1 AATATTTAATTAA-A-A
2048195 AATATTTAATTAAAA
1 AATATTTAATTAAAA
*
2048210 AA-ATTTAACT-AAA
1 AATATTTAATTAAAA
2048223 AATATT
1 AATATT
2048229 AATGTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
13 7 0.17
14 11 0.27
15 11 0.27
16 10 0.24
17 2 0.05
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATTTAATTAAAA
Found at i:2048193 original size:31 final size:29
Alignment explanation
Indices: 2048158--2048217 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 29
2048148 AAATTCGATG
2048158 AATATTAATATTTAATTTAAAAAATATTTAA
1 AATATTAATATTTAA-TTAAAAAA-ATTTAA
2048189 AATATTAATATTTAATTAAAAAAATTTAA
1 AATATTAATATTTAATTAAAAAAATTTAA
2048218 CTAAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 6 0.21
30 8 0.28
31 15 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AATATTAATATTTAATTAAAAAAATTTAA
Found at i:2056533 original size:24 final size:24
Alignment explanation
Indices: 2056501--2056549 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2056491 ATCCTGAGAA
2056501 TAGGGCCACCGGAAGAGAGGTAAT
1 TAGGGCCACCGGAAGAGAGGTAAT
2056525 TAGGGCCACCGGAAGAGAGGTAAT
1 TAGGGCCACCGGAAGAGAGGTAAT
2056549 T
1 T
2056550 TCATAGCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.37, T:0.14
Consensus pattern (24 bp):
TAGGGCCACCGGAAGAGAGGTAAT
Found at i:2069966 original size:20 final size:20
Alignment explanation
Indices: 2069929--2069966 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2069919 TATACAGTAT
*
2069929 CACCAACTAAATGCATAATG
1 CACCAACCAAATGCATAATG
2069949 CACCAACCACAATG-ATAA
1 CACCAACCA-AATGCATAA
2069967 CTGTGGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.47, C:0.29, G:0.08, T:0.16
Consensus pattern (20 bp):
CACCAACCAAATGCATAATG
Found at i:2070032 original size:192 final size:195
Alignment explanation
Indices: 2069690--2070070 Score: 552
Period size: 192 Copynumber: 2.0 Consensus size: 195
2069680 CTAGCAACGA
* * * ** * *
2069690 TTATCAGTGCTGTTGCATCCGGGCTAGTTTTTTATGTAGTATCACCAATTAATGTAGAATCATAA
1 TTATCAATGCTGTTGCACCCGGGCTAGTCTTTTATACAGTATCACCAACTAATATAG-A-CATAA
** * *
2069755 TGCACCAATGACGATGATAACTGTGGATAACATAGAGAATTGATCTCAAAAGACAGATACATCAC
64 TGCACCAACCACAATGATAACTGTGGATAACATAGAGAATAGATCTCAAAAGACAGATACATCAC
2069820 TCAAGTAAATACAATGGCATTCATTTATGGAGTTATTCACTACTAATCTCTTACCATATGCCATA
129 TCAAGTAAATACAATGGCATTCATTTATGGAGTTATTCACTACTAATCTCTTACCATATGCCATA
2069885 GG
194 GG
2069887 TTATCAATGCTGTTGCACCCGGGCTAGTCTTTTATACAGTATCACCAACTAA-AT-G-CATAATG
1 TTATCAATGCTGTTGCACCCGGGCTAGTCTTTTATACAGTATCACCAACTAATATAGACATAATG
** *
2069949 CACCAACCACAATGATAACTGTGGATAACATAGAGAATAGATCTCAAAAGGGAGATGCATCACTC
66 CACCAACCACAATGATAACTGTGGATAACATAGAGAATAGATCTCAAAAGACAGATACATCACTC
* ** * *
2070014 AAGTAAATGCTTTGGCATTCATTTATGGAGTTATTCAGTACTAATCTTTTACCATAT
131 AAGTAAATACAATGGCATTCATTTATGGAGTTATTCACTACTAATCTCTTACCATAT
2070071 AGTTCTACAT
Statistics
Matches: 165, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
192 117 0.71
195 1 0.01
196 1 0.01
197 46 0.28
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (195 bp):
TTATCAATGCTGTTGCACCCGGGCTAGTCTTTTATACAGTATCACCAACTAATATAGACATAATG
CACCAACCACAATGATAACTGTGGATAACATAGAGAATAGATCTCAAAAGACAGATACATCACTC
AAGTAAATACAATGGCATTCATTTATGGAGTTATTCACTACTAATCTCTTACCATATGCCATAGG
Found at i:2086403 original size:43 final size:43
Alignment explanation
Indices: 2086342--2086440 Score: 189
Period size: 43 Copynumber: 2.3 Consensus size: 43
2086332 ATAAAGGCTT
2086342 TAATTGTTTGATAATGCCTCCACCTCATTGTTAGAGATAGACC
1 TAATTGTTTGATAATGCCTCCACCTCATTGTTAGAGATAGACC
2086385 TAATTGTTTGATAATGCCTCCACCTCATTGTTAGAGATAGACC
1 TAATTGTTTGATAATGCCTCCACCTCATTGTTAGAGATAGACC
*
2086428 TAGTTGTTTGATA
1 TAATTGTTTGATA
2086441 TTTTATATTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (43 bp):
TAATTGTTTGATAATGCCTCCACCTCATTGTTAGAGATAGACC
Found at i:2086414 original size:24 final size:24
Alignment explanation
Indices: 2086344--2086416 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
2086334 AAAGGCTTTA
2086344 ATTGTTTGATAATGCCTCCACCTC
1 ATTGTTTGATAATGCCTCCACCTC
* * *
2086368 ATTGTTAGA-GATAG-----ACCTA
1 ATTGTTTGATAAT-GCCTCCACCTC
2086387 ATTGTTTGATAATGCCTCCACCTC
1 ATTGTTTGATAATGCCTCCACCTC
2086411 ATTGTT
1 ATTGTT
2086417 AGAGATAGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 13 0.36
20 2 0.06
23 2 0.06
24 19 0.53
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (24 bp):
ATTGTTTGATAATGCCTCCACCTC
Found at i:2087992 original size:2 final size:2
Alignment explanation
Indices: 2087985--2088019 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2087975 TACGTTCTAT
2087985 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2088020 ATGTTGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2091755 original size:28 final size:30
Alignment explanation
Indices: 2091707--2091765 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
2091697 CCGAGGTTAG
2091707 ATATGATATAAACATTCATTTT-T-TATTC
1 ATATGATATAAACATTCATTTTATGTATTC
* *
2091735 ATATGATA-AAATATTTTATTTTATGTATTC
1 ATATGATATAAACA-TTCATTTTATGTATTC
2091765 A
1 A
2091766 ATATATTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 15 0.58
29 1 0.04
30 6 0.23
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (30 bp):
ATATGATATAAACATTCATTTTATGTATTC
Found at i:2092559 original size:6 final size:6
Alignment explanation
Indices: 2092548--2092573 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2092538 CAGTCAGTTC
2092548 GACCTT GACCTT GACCTT GACCTT GA
1 GACCTT GACCTT GACCTT GACCTT GA
2092574 TCTGCATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (6 bp):
GACCTT
Found at i:2112119 original size:22 final size:19
Alignment explanation
Indices: 2112077--2112121 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
2112067 TCTGAAATGG
*
2112077 GTTTTCTTTTTTTATTGAT
1 GTTTTCTTGTTTTATTGAT
2112096 GTTTTCTTGGTTTTAGTTGTAT
1 GTTTTCTT-GTTTTA-TTG-AT
2112118 GTTT
1 GTTT
2112122 GGTATGGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 5 0.23
21 3 0.14
22 6 0.27
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.69
Consensus pattern (19 bp):
GTTTTCTTGTTTTATTGAT
Found at i:2116243 original size:2 final size:2
Alignment explanation
Indices: 2116231--2116264 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2116221 TTAACCTAAC
2116231 TA TA TA T- 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 TA T
2116265 GATTGTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2127016 original size:40 final size:40
Alignment explanation
Indices: 2126972--2127052 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
2126962 TACATAATTA
2126972 TGCCCCAAATATTTTGCAAAATATGCTAAAATATTTCTAT
1 TGCCCCAAATATTTTGCAAAATATGCTAAAATATTTCTAT
2127012 TGCCCCAAATATTTTGCAAAATATGCTAAAATATTTCTAT
1 TGCCCCAAATATTTTGCAAAATATGCTAAAATATTTCTAT
2127052 T
1 T
2127053 ACCATTTACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (40 bp):
TGCCCCAAATATTTTGCAAAATATGCTAAAATATTTCTAT
Found at i:2131296 original size:18 final size:17
Alignment explanation
Indices: 2131273--2131323 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
2131263 TTTCTATAAG
2131273 AAATTAAAATTTTAACAT
1 AAATTAAAATTTTAA-AT
2131291 AAATTAAAATATTT-AAT
1 AAATTAAAAT-TTTAAAT
2131308 AGAATTAACAATTTTA
1 A-AATTAA-AATTTTA
2131324 TTGAATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.10
18 20 0.69
19 6 0.21
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATTAAAATTTTAAAT
Found at i:2141650 original size:9 final size:10
Alignment explanation
Indices: 2141627--2141651 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2141617 TTTCTTTCTC
2141627 TTTTTAATTA
1 TTTTTAATTA
2141637 TTTTTAATTA
1 TTTTTAATTA
2141647 TTTTT
1 TTTTT
2141652 TATATTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTAATTA
Found at i:2142858 original size:2 final size:2
Alignment explanation
Indices: 2142851--2142888 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2142841 GTTACGTGTG
2142851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2142889 TTTAATCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2143364 original size:3 final size:3
Alignment explanation
Indices: 2143356--2143386 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2143346 CTTGCCCATT
2143356 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2143387 AGTAGCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2147493 original size:2 final size:2
Alignment explanation
Indices: 2147486--2147592 Score: 105
Period size: 2 Copynumber: 55.5 Consensus size: 2
2147476 GCATTCTGAC
2147486 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* ** ** **
2147528 A- AG A- AG AG AG -G AG AN NN NN NN AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
2147567 AG AG AG AG A- AG AA AG AG AG GG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2147593 CATATACTGC
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
1 4 0.04
2 89 0.96
ACGTcount: A:0.49, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2147698 original size:6 final size:6
Alignment explanation
Indices: 2147689--2147738 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
2147679 AGATGCTAAA
* * * * *
2147689 GAAGAA GAAGAG GAAGAG GAGGAG GAGGAA GAAGAG GAAGTG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
2147737 GA
1 GA
2147739 GGAGAAGGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (6 bp):
GAAGAG
Found at i:2147716 original size:15 final size:15
Alignment explanation
Indices: 2147698--2147747 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2147688 AGAAGAAGAA
2147698 GAGGAAGAGGAGGAG
1 GAGGAAGAGGAGGAG
* *
2147713 GAGGAAGAAGAGGAA
1 GAGGAAGAGGAGGAG
*
2147728 GTGGAAGAGGAGGAG
1 GAGGAAGAGGAGGAG
*
2147743 AAGGA
1 GAGGA
2147748 TGTGGAAGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.54, T:0.02
Consensus pattern (15 bp):
GAGGAAGAGGAGGAG
Found at i:2147724 original size:24 final size:24
Alignment explanation
Indices: 2147692--2147745 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
2147682 TGCTAAAGAA
*
2147692 GAAGAAGAGGAAGAGGAGGAGGAG
1 GAAGAAGAGGAAGAGGAAGAGGAG
*
2147716 GAAGAAGAGGAAGTGGAAGAGGAG
1 GAAGAAGAGGAAGAGGAAGAGGAG
2147740 G-AGAAG
1 GAAGAAG
2147746 GATGTGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.46, C:0.00, G:0.52, T:0.02
Consensus pattern (24 bp):
GAAGAAGAGGAAGAGGAAGAGGAG
Found at i:2153405 original size:13 final size:13
Alignment explanation
Indices: 2153387--2153413 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2153377 GTTAATTCCC
2153387 GTTAATGGTATTT
1 GTTAATGGTATTT
2153400 GTTAATGGTATTT
1 GTTAATGGTATTT
2153413 G
1 G
2153414 AATGTGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (13 bp):
GTTAATGGTATTT
Found at i:2153887 original size:2 final size:2
Alignment explanation
Indices: 2153882--2153970 Score: 83
Period size: 2 Copynumber: 44.5 Consensus size: 2
2153872 TTTTAGATGT
2153882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* ** * * * *
2153923 GT- TNN NN GA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2153966 TA TA T
1 TA TA T
2153971 TTTGGTTAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.03
2 72 0.96
3 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Done.