Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 7 of 117
Found at i:1835459 original size:5 final size:5
Alignment explanation
Indices: 1835386--1835490 Score: 54
Period size: 5 Copynumber: 20.2 Consensus size: 5
1835376 AAAATAGAAT
* * *
1835386 AATAA AACAA AATAA AAGTGAA GAT-A AATAA ATAAAA AATAA AA-AA
1 AATAA AATAA AATAA AA-T-AA AATAA AATAA A-ATAA AATAA AATAA
* * *
1835432 AATAA AGA-AA AGTAA AACAAA AATAAA AATAA AATAA AGATAA AAGAA
1 AATAA A-ATAA AATAA AA-TAA AAT-AA AATAA AATAA A-ATAA AATAA
* *
1835480 TATTA AATAA A
1 AATAA AATAA A
1835491 CCTAATCTAA
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
4 7 0.09
5 43 0.58
6 21 0.28
7 3 0.04
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (5 bp):
AATAA
Found at i:1835459 original size:17 final size:17
Alignment explanation
Indices: 1835439--1835477 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1835429 AAAAATAAAG
1835439 AAAAGTAAAACAAAAAT
1 AAAAGTAAAACAAAAAT
* * *
1835456 AAAAATAAAATAAAGAT
1 AAAAGTAAAACAAAAAT
1835473 AAAAG
1 AAAAG
1835478 AATATTAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAAGTAAAACAAAAAT
Found at i:1835519 original size:10 final size:9
Alignment explanation
Indices: 1835499--1835557 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
1835489 AACCTAATCT
1835499 AAAAATTAA
1 AAAAATTAA
1835508 AAAAATTAA
1 AAAAATTAA
*
1835517 AAAAA-AAA
1 AAAAATTAA
*
1835525 AAATAAATAA
1 AAA-AATTAA
*
1835535 ACAAA-TAA
1 AAAAATTAA
*
1835543 ATAAATTCAA
1 AAAAATT-AA
1835553 AAAAA
1 AAAAA
1835558 AAAAATCTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
8 12 0.29
9 19 0.46
10 10 0.24
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAATTAA
Found at i:1835519 original size:16 final size:15
Alignment explanation
Indices: 1835506--1835563 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
1835496 TCTAAAAATT
1835506 AAAAAAATTAAAAAA
1 AAAAAAATTAAAAAA
1835521 AAAAAAATAAATAAACAAA
1 AAAAAAAT---TAAA-AAA
* *
1835540 TAAATAAATTCAAAAA
1 -AAAAAAATTAAAAAA
1835556 AAAAAAAT
1 AAAAAAAT
1835564 CTGAAGCGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
15 15 0.43
16 3 0.09
17 3 0.09
18 4 0.11
19 3 0.09
20 7 0.20
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAAATTAAAAAA
Found at i:1836033 original size:19 final size:19
Alignment explanation
Indices: 1836011--1836051 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1836001 ACTTGGCCGA
1836011 AATTTTCACCAAAAAATTC
1 AATTTTCACCAAAAAATTC
* *
1836030 AATTTTCATCGAAAAATTC
1 AATTTTCACCAAAAAATTC
1836049 AAT
1 AAT
1836052 CGAAATCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.34
Consensus pattern (19 bp):
AATTTTCACCAAAAAATTC
Found at i:1836563 original size:6 final size:5
Alignment explanation
Indices: 1836526--1836622 Score: 81
Period size: 5 Copynumber: 18.0 Consensus size: 5
1836516 TCAAGATAAA
*
1836526 AAAAT AATAAT AAAAG AAAA- AAATAT AAAAT AATAAT AAAAAT AAAACT
1 AAAAT AA-AAT AAAAT AAAAT AAA-AT AAAAT AA-AAT -AAAAT AAAA-T
*
1836575 AAAAT AGAAAT AAAAT AAAAATGT AAAAT ACAA- AAAAT AAAAT AAAAT
1 AAAAT A-AAAT AAAAT -AAAA--T AAAAT AAAAT AAAAT AAAAT AAAAT
1836623 GAAGAGAAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
4 6 0.08
5 37 0.47
6 28 0.36
7 6 0.08
8 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1836577 original size:23 final size:24
Alignment explanation
Indices: 1836526--1836622 Score: 74
Period size: 26 Copynumber: 3.9 Consensus size: 24
1836516 TCAAGATAAA
*
1836526 AAAATAATAATAAAAGAAAAAAATAT
1 AAAATAATAAT-AAA-AATAAAATAT
*
1836552 AAAATAATAATAAAAATAAAA-CT
1 AAAATAATAATAAAAATAAAATAT
*
1836575 AAAATAGA-AAT-AAAATAAAAATGT
1 AAAATA-ATAATAAAAAT-AAAATAT
* *
1836599 AAAATACAAAAAATAAAATAAAAT
1 AAAATA-ATAATA-AAAATAAAAT
1836623 GAAGAGAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
22 5 0.08
23 14 0.23
24 15 0.25
25 5 0.08
26 16 0.27
27 5 0.08
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (24 bp):
AAAATAATAATAAAAATAAAATAT
Found at i:1836889 original size:43 final size:43
Alignment explanation
Indices: 1836832--1836931 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
1836822 TTGATAAAAA
* ** * * *
1836832 CTCCTCTAGGCAGAGGTTCAATGACTTTGAGAAACATAAATGG
1 CTCCTCTAAGCAGAGGTTCAACAACTTTAAAAAAAATAAATGG
* * *
1836875 CTCCTCTAATCAGAGGTTTAACAACTTTAAAAAAAATAAATTG
1 CTCCTCTAAGCAGAGGTTCAACAACTTTAAAAAAAATAAATGG
1836918 CTCCTCTAAGCAGA
1 CTCCTCTAAGCAGA
1836932 AACACCACGA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (43 bp):
CTCCTCTAAGCAGAGGTTCAACAACTTTAAAAAAAATAAATGG
Found at i:1837052 original size:42 final size:42
Alignment explanation
Indices: 1836905--1837100 Score: 279
Period size: 41 Copynumber: 4.7 Consensus size: 42
1836895 ACAACTTTAA
* * **
1836905 AAAAAATAAATTGCTCCTCTAAGCAGAAACACCACGACTTTG
1 AAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
* * *
1836947 -AAAAGTAGATTGCTCCTCTAAATAGAGCCACCACGACTTTG
1 AAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
*
1836988 -AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGATTTTG
1 AAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
* *
1837029 AAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACGACTTTA
1 AAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
*
1837071 AAAAAGTAAATTGCTCTTCTAAACAGAGGC
1 AAAAAGTAAATTGCTCCTCTAAACAGAGGC
1837101 TTGCTCCTCT
Statistics
Matches: 138, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 72 0.52
42 66 0.48
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.23
Consensus pattern (42 bp):
AAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
Found at i:1837106 original size:20 final size:20
Alignment explanation
Indices: 1837081--1837120 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1837071 AAAAAGTAAA
*
1837081 TTGCTCTTCTAAACAGAGGC
1 TTGCTCCTCTAAACAGAGGC
1837101 TTGCTCCTCTAAACAGAGGC
1 TTGCTCCTCTAAACAGAGGC
1837121 ACCACGACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (20 bp):
TTGCTCCTCTAAACAGAGGC
Found at i:1838837 original size:19 final size:19
Alignment explanation
Indices: 1838815--1838871 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 19
1838805 TCAATTTGAA
1838815 TCTCTTTTTTTTTTCATTT
1 TCTCTTTTTTTTTTCATTT
* **
1838834 TCTCATTTTTTTTTCATCA
1 TCTCTTTTTTTTTTCATTT
1838853 TCT-TTTTTTTTTTCATTT
1 TCTCTTTTTTTTTTCATTT
1838871 T
1 T
1838872 TCATCTATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 13 0.41
19 19 0.59
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (19 bp):
TCTCTTTTTTTTTTCATTT
Found at i:1843030 original size:11 final size:10
Alignment explanation
Indices: 1842999--1843057 Score: 57
Period size: 11 Copynumber: 5.7 Consensus size: 10
1842989 AAGCGAAGAT
1842999 AAATAAATAAA
1 AAATAAA-AAA
*
1843010 AAAT-ATAAA
1 AAATAAAAAA
*
1843019 AAATAAAGAA
1 AAATAAAAAA
*
1843029 AAGTAAAACAA
1 AAATAAAA-AA
1843040 AAATAAAAATA
1 AAATAAAAA-A
1843051 AAATAAA
1 AAATAAA
1843058 GATAAAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 7 0.18
10 11 0.28
11 21 0.54
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (10 bp):
AAATAAAAAA
Found at i:1843047 original size:17 final size:17
Alignment explanation
Indices: 1843027--1843065 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1843017 AAAAATAAAG
1843027 AAAAGTAAAACAAAAAT
1 AAAAGTAAAACAAAAAT
* * *
1843044 AAAAATAAAATAAAGAT
1 AAAAGTAAAACAAAAAT
1843061 AAAAG
1 AAAAG
1843066 AATATTAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAAGTAAAACAAAAAT
Found at i:1843074 original size:28 final size:27
Alignment explanation
Indices: 1843005--1843074 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
1842995 AGATAAATAA
*
1843005 ATAAAAAATATAAAAAATAAAGAAAAG
1 ATAAAAAATATTAAAAATAAAGAAAAG
* *
1843032 -TAAAACAAAAATAAAAATAAA-ATAAAG
1 ATAAAA-AATATTAAAAATAAAGA-AAAG
1843059 ATAAAAGAATATTAAA
1 ATAAAA-AATATTAAA
1843075 TAAACCTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
26 6 0.18
27 16 0.47
28 12 0.35
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (27 bp):
ATAAAAAATATTAAAAATAAAGAAAAG
Found at i:1843892 original size:15 final size:14
Alignment explanation
Indices: 1843851--1843900 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
1843841 AATTTTCAGC
1843851 CAAATAAATAAAAA-
1 CAAATAAA-AAAAAT
1843865 -AAATAAAAAAAAT
1 CAAATAAAAAAAAT
*
1843878 CAAATGAAAATAAAT
1 CAAAT-AAAAAAAAT
*
1843893 CAGATAAA
1 CAAATAAA
1843901 CTAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 5 0.16
13 7 0.23
14 7 0.23
15 12 0.39
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.16
Consensus pattern (14 bp):
CAAATAAAAAAAAT
Found at i:1843917 original size:21 final size:21
Alignment explanation
Indices: 1843884--1843942 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
1843874 AAATCAAATG
*
1843884 AAAATAAATCAGATAAACTAAA
1 AAAATTAA-CAGATAAACTAAA
*
1843906 AAAATTAACAGATAAATTAAA
1 AAAATTAACAGATAAACTAAA
1843927 ATTAAA-TAACAGATAA
1 A--AAATTAACAGATAA
1843943 TACATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.39
22 17 0.52
23 3 0.09
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (21 bp):
AAAATTAACAGATAAACTAAA
Found at i:1844037 original size:61 final size:56
Alignment explanation
Indices: 1843972--1844128 Score: 145
Period size: 61 Copynumber: 2.6 Consensus size: 56
1843962 AAAAAAGAAG
* *
1843972 AAAAAAATAATAATAATAAAAATATATATATATATTAATAGATACATAAATACTCAAGAT
1 AAAAAAATAATAATAA-AAAAATATATATATATATTAATA-ATA-ATAAATAAT-AAAAT
* *
1844032 AAAAAAATAATAAAAGGAAAAAATATATA-ATAATAATAATAATAATAAATAATAAAAT
1 AAAAAAATAATAATA--AAAAAATATATATAT-ATATTAATAATAATAAATAATAAAAT
* *
1844090 AAATATAAAATAAAAATGTAAAATAATATATATATATAT
1 -AA-A-AAAATAATAA--TAAAAAAATATATATATATAT
1844129 ATAGACTTAC
Statistics
Matches: 80, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
58 4 0.05
59 10 0.12
60 20 0.25
61 42 0.52
62 3 0.04
63 1 0.01
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (56 bp):
AAAAAAATAATAATAAAAAAATATATATATATATTAATAATAATAAATAATAAAAT
Found at i:1844066 original size:3 final size:3
Alignment explanation
Indices: 1844053--1844091 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
1844043 AAAAGGAAAA
1844053 AAT ATAT AAT AAT AAT AAT AAT AAT AAAT AAT AA- AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
1844092 ATATAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 25 0.76
4 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1844075 original size:12 final size:12
Alignment explanation
Indices: 1844053--1844091 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
1844043 AAAAGGAAAA
1844053 AATATATAATAAT
1 AATA-ATAATAAT
1844066 AATAATAATAAT
1 AATAATAATAAT
1844078 AAATAATAA-AAT
1 -AATAATAATAAT
1844090 AA
1 AA
1844092 ATATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 11 0.44
13 12 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:1844094 original size:9 final size:8
Alignment explanation
Indices: 1844030--1844117 Score: 58
Period size: 8 Copynumber: 10.8 Consensus size: 8
1844020 AATACTCAAG
*
1844030 ATAAAAAA
1 ATAATAAA
1844038 ATAATAAA
1 ATAATAAA
*
1844046 AGGAA-AAA
1 A-TAATAAA
1844054 ATATATAATA
1 ATA-ATAA-A
1844064 ATAATAATA
1 ATAATAA-A
1844073 ATAAT-AA
1 ATAATAAA
1844080 ATAATAAA
1 ATAATAAA
*
1844088 ATAAATATA
1 AT-AATAAA
1844097 A-AATAAA
1 ATAATAAA
*
1844104 A-ATGTAAA
1 ATA-ATAAA
1844112 ATAATA
1 ATAATA
1844118 TATATATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
7 14 0.22
8 25 0.38
9 22 0.34
10 4 0.06
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (8 bp):
ATAATAAA
Found at i:1844100 original size:19 final size:20
Alignment explanation
Indices: 1844052--1844102 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1844042 TAAAAGGAAA
*
1844052 AAATATATAATAATAATAAT
1 AAATATAAAATAATAATAAT
1844072 -AATA-ATAAATAATAA-AAT
1 AAATATA-AAATAATAATAAT
1844090 AAATATAAAATAA
1 AAATATAAAATAA
1844103 AAATGTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.15
19 22 0.81
20 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATATAAAATAATAATAAT
Found at i:1849920 original size:21 final size:21
Alignment explanation
Indices: 1849892--1849949 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1849882 GAAAAAAAAT
*
1849892 AATTTTAAATATTAATATTTAA
1 AATTTTAAAT-TTAATATATAA
*
1849914 AA-TTTAAATTATAAAATATAA
1 AATTTTAAATT-TAATATATAA
1849935 AATTTTAAATTTAAT
1 AATTTTAAATTTAAT
1849950 TGTATGACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 20 0.65
22 10 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTAAATTTAATATATAA
Found at i:1849921 original size:7 final size:7
Alignment explanation
Indices: 1849892--1849948 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
1849882 GAAAAAAAAT
*
1849892 AATTTTA
1 AATTTAA
1849899 AATATTAA
1 AAT-TTAA
*
1849907 TATTTAA
1 AATTTAA
1849914 AATTT-A
1 AATTTAA
1849920 AATTATAA
1 AATT-TAA
*
1849928 AATATAA
1 AATTTAA
*
1849935 AATTTTA
1 AATTTAA
1849942 AATTTAA
1 AATTTAA
1849949 TTGTATGACT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
6 5 0.12
7 26 0.65
8 9 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATTTAA
Found at i:1856594 original size:20 final size:20
Alignment explanation
Indices: 1856557--1856594 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1856547 TTTTATAATA
*
1856557 TTTTATTTAAGATGAATTTT
1 TTTTATTTAAGATCAATTTT
1856577 TTTTATTTATA-ATCAATT
1 TTTTATTTA-AGATCAATT
1856595 AATTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTATTTAAGATCAATTTT
Found at i:1857178 original size:6 final size:6
Alignment explanation
Indices: 1857167--1857200 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1857157 AAAAAAAATC
1857167 AATTAA AATTAA AATTAA AATTAA AATTAA AATT
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATT
1857201 TATAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AATTAA
Found at i:1865535 original size:27 final size:27
Alignment explanation
Indices: 1865505--1865599 Score: 70
Period size: 27 Copynumber: 3.4 Consensus size: 27
1865495 TTTGTGCAAA
1865505 AAAAATTGATACTTTCAACTTTTTCTC
1 AAAAATTGATACTTTCAACTTTTTCTC
** *
1865532 AAAAA-T-ATTTTTTTGAAACTTTAATT-TC
1 AAAAATTGA-TACTTT-CAACTTT--TTCTC
*
1865560 GAGAAAAATTGATACTTTCAACTTTTCCTC
1 ---AAAAATTGATACTTTCAACTTTTTCTC
1865590 AAAAATTGAT
1 AAAAATTGAT
1865600 TTTTTTGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 20
0.65 0.09 0.26
Matches are distributed among these distances:
25 1 0.02
26 5 0.10
27 21 0.41
28 2 0.04
29 3 0.06
30 2 0.04
31 11 0.22
32 5 0.10
33 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (27 bp):
AAAAATTGATACTTTCAACTTTTTCTC
Found at i:1865610 original size:17 final size:17
Alignment explanation
Indices: 1865590--1865632 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1865580 ACTTTTCCTC
**
1865590 AAAAATTGATTTTTTTG
1 AAAAATTGATTTTTAAG
*
1865607 -AAAATTTATTTTTAAG
1 AAAAATTGATTTTTAAG
1865623 AAAAATTGAT
1 AAAAATTGAT
1865633 ACTTTCAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (17 bp):
AAAAATTGATTTTTAAG
Found at i:1865625 original size:60 final size:58
Alignment explanation
Indices: 1865505--1865722 Score: 312
Period size: 60 Copynumber: 3.7 Consensus size: 58
1865495 TTTGTGCAAA
* * * *
1865505 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTCAAG
*
1865563 AAAAATTGATACTTTCAACTTTTCCTCAAAAATTGATTTTTTTGAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAA-T-ATTTTTTTGAAAATTTATTTTCAAG
**
1865623 AAAAATTGATACTTTCAACTTTTTTTCAAAAATA-TTTTTTGAAAACTTTGATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAA-TTT-ATTTTCAAG
* *
1865682 AAAAATTGATATTTTCAACTTTTCCCCAAAAATATTTTTTT
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1865723 TTATTTTTAT
Statistics
Matches: 143, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
57 11 0.08
58 35 0.24
59 40 0.28
60 57 0.40
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTCAAG
Found at i:1865723 original size:118 final size:117
Alignment explanation
Indices: 1865505--1865722 Score: 350
Period size: 118 Copynumber: 1.9 Consensus size: 117
1865495 TTTGTGCAAA
*
1865505 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAACTTTAATTTCGAGAAAAATT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAACTTTAATTTCAAGAAAAATT
*
1865570 GATACTTTCAACTTTTCCTCAAAAATTGATTTTTTTGAAAATTTATTTTTAAG
66 GATACTTTCAACTTTTCCCCAAAAATT-ATTTTTTTGAAAATTTATTTTTAAG
* *
1865623 AAAAATTGATACTTTCAACTTTTTTTCAAAAATA-TTTTTTGAAAACTTTGATTTTCAAGAAAAA
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTG-AAACTTT-AATTTCAAGAAAAA
*
1865687 TTGATATTTTCAACTTTTCCCCAAAAA-TATTTTTTT
64 TTGATACTTTCAACTTTTCCCCAAAAATTATTTTTTT
1865723 TTATTTTTAT
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
117 15 0.16
118 41 0.44
119 37 0.40
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (117 bp):
AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAACTTTAATTTCAAGAAAAATT
GATACTTTCAACTTTTCCCCAAAAATTATTTTTTTGAAAATTTATTTTTAAG
Found at i:1865789 original size:11 final size:11
Alignment explanation
Indices: 1865773--1865909 Score: 70
Period size: 11 Copynumber: 12.0 Consensus size: 11
1865763 AAGTGAAGAT
1865773 AAATAAATAAA
1 AAATAAATAAA
1865784 AAATAAA-AAA
1 AAATAAATAAA
*
1865794 AAATAAA-GAA
1 AAATAAATAAA
*
1865804 AAGTAAA-ACAA
1 AAATAAATA-AA
1865815 AAATAAA-AATA
1 AAATAAATAA-A
1865826 AAATAAAGATAAA
1 AAAT-AA-ATAAA
* * *
1865839 AGATTATTAAA
1 AAATAAATAAA
*
1865850 TAAACCTAATCTAAA
1 -AAA--TAA-ATAAA
1865865 AAAT-AA-AAA
1 AAATAAATAAA
*
1865874 AAATAAAAAAAA
1 AAAT-AAATAAA
1865886 TAAATAAATAAA
1 -AAATAAATAAA
1865898 CAAATAAATAAA
1 -AAATAAATAAA
1865910 TTCAAAAAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 25
0.72 0.09 0.18
Matches are distributed among these distances:
9 7 0.07
10 19 0.19
11 28 0.28
12 26 0.26
13 9 0.09
14 7 0.07
15 4 0.04
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:1865799 original size:17 final size:17
Alignment explanation
Indices: 1865735--1865905 Score: 71
Period size: 17 Copynumber: 9.1 Consensus size: 17
1865725 ATTTTTATTT
*
1865735 AAAAAAATAGAATAATAA
1 AAAAAAATA-AAAAATAA
* *
1865753 AACAAAAT-AAAAGTGAA
1 AAAAAAATAAAAAAT-AA
1865770 GATAAATAAATAAAAAATAA
1 -A-AAA-AAATAAAAAATAA
1865790 AAAAAAATAAAGAAAAGTAA
1 AAAAAAAT-AA-AAAA-TAA
1865810 AACAAAAAT-AAAAATAA
1 AA-AAAAATAAAAAATAA
*
1865827 AATAAAGATAAAAGATTATTAA
1 AA-AAAAATAAAA-A--A-TAA
*
1865849 ATAAACCTAATCTAAAAAAT-A
1 A-AAA---AA-ATAAAAAATAA
1865870 AAAAAAATAAAAAA-AA
1 AAAAAAATAAAAAATAA
*
1865886 TAAATAAATAAACAAATAA
1 -AAAAAAATAAA-AAATAA
1865905 A
1 A
1865906 TAAATTCAAA
Statistics
Matches: 119, Mismatches: 11, Indels: 46
0.68 0.06 0.26
Matches are distributed among these distances:
16 12 0.10
17 28 0.24
18 24 0.20
19 11 0.09
20 14 0.12
21 14 0.12
22 7 0.06
23 2 0.02
25 2 0.02
26 5 0.04
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAAAATAAAAAATAA
Found at i:1865829 original size:5 final size:5
Alignment explanation
Indices: 1865748--1865839 Score: 53
Period size: 5 Copynumber: 17.4 Consensus size: 5
1865738 AAAATAGAAT
* * * *
1865748 AATAA AACAA AATAA AAGTGAA GAT-A AATAA ATAAAA AATAA AAAAA
1 AATAA AATAA AATAA AA-T-AA AATAA AATAA A-ATAA AATAA AATAA
* *
1865795 AATAA AGA-AA AGTAA AACAAA AATAAA AATAA AATAA AGATAA AA
1 AATAA A-ATAA AATAA AA-TAA AAT-AA AATAA AATAA A-ATAA AA
1865840 GATTATTAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
4 3 0.05
5 39 0.59
6 21 0.32
7 3 0.05
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (5 bp):
AATAA
Found at i:1865882 original size:16 final size:15
Alignment explanation
Indices: 1865861--1865925 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
1865851 AAACCTAATC
1865861 TAAAAAATAAAAAAAA
1 TAAAAAA-AAAAAAAA
1865877 TAAAAAAAATAAATAAA
1 TAAAAAAAA-AAA-AAA
* *
1865894 TAAACAAATAAATAAA
1 TAAA-AAAAAAAAAAA
**
1865910 TTCAAAAAAAAAAAA
1 TAAAAAAAAAAAAAA
1865925 T
1 T
1865926 CTAAAGTGGC
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
15 12 0.30
16 15 0.38
17 9 0.22
18 4 0.10
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAAAAAAAAAAA
Found at i:1866398 original size:19 final size:19
Alignment explanation
Indices: 1866376--1866412 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1866366 TGGCCAAAAT
*
1866376 TTTCACCGAAAAGTTCAAC
1 TTTCACCGAAAAATTCAAC
1866395 TTTCACCGAAAAATTCAA
1 TTTCACCGAAAAATTCAA
1866413 TCGAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (19 bp):
TTTCACCGAAAAATTCAAC
Found at i:1866869 original size:63 final size:60
Alignment explanation
Indices: 1866798--1866948 Score: 148
Period size: 63 Copynumber: 2.5 Consensus size: 60
1866788 TAAATAACAG
* *
1866798 ATAATACATAAATATTAACAG-GAAAAAAAAGAA-AAAAAAATAATAAAAATATATAAATATTA
1 ATAATACATAAATACTAA-AGAGAAAAAAAAGAATAAAAAAAGAA-AAAAATATATAAA-A-TA
* * * *
1866860 ATAGATACATAAATACTCAAGATAAAAAAAATAATAATAAAAGAAAAAAATATATAAAATA
1 ATA-ATACATAAATACTAAAGAGAAAAAAAAGAATAAAAAAAGAAAAAAATATATAAAATA
* * *
1866921 ATAATA-ATAAA-AATAAAAATAAAAAAAA
1 ATAATACATAAATACTAAAGAGAAAAAAAA
1866949 ATGTAAAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
58 14 0.18
59 5 0.06
60 3 0.04
61 5 0.06
62 6 0.08
63 36 0.47
64 8 0.10
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (60 bp):
ATAATACATAAATACTAAAGAGAAAAAAAAGAATAAAAAAAGAAAAAAATATATAAAATA
Found at i:1866901 original size:15 final size:15
Alignment explanation
Indices: 1866881--1866948 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
1866871 AATACTCAAG
1866881 ATAAAAAAAATAATA
1 ATAAAAAAAATAATA
*
1866896 ATAAAAGAAA-AA-A
1 ATAAAAAAAATAATA
* *
1866909 ATATATAAAATAATA
1 ATAAAAAAAATAATA
* *
1866924 ATAATAAAAATAAAA
1 ATAAAAAAAATAATA
1866939 ATAAAAAAAA
1 ATAAAAAAAA
1866949 ATGTAAAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
13 8 0.19
14 4 0.10
15 30 0.71
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.19
Consensus pattern (15 bp):
ATAAAAAAAATAATA
Found at i:1866927 original size:31 final size:30
Alignment explanation
Indices: 1866884--1866950 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
1866874 ACTCAAGATA
1866884 AAAAAAATAATAATAAAAGAAAAAAATATAT
1 AAAAAAATAATAATAAAA-AAAAAAATATAT
* *
1866915 AAAATAATAATAATAAAAATAAAAATA-A-
1 AAAAAAATAATAATAAAAAAAAAAATATAT
1866943 AAAAAAAT
1 AAAAAAAT
1866951 GTAAAATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 7 0.21
29 1 0.03
30 8 0.24
31 17 0.52
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.19
Consensus pattern (30 bp):
AAAAAAATAATAATAAAAAAAAAAATATAT
Found at i:1866943 original size:6 final size:6
Alignment explanation
Indices: 1866886--1866980 Score: 79
Period size: 6 Copynumber: 15.7 Consensus size: 6
1866876 TCAAGATAAA
* * * * *
1866886 AAAAAT AATAAT AAAAGAA AAAAAT ATATAA- AATAAT AATAAT AAAAAT
1 AAAAAT AAAAAT AAAA-AT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT
*
1866935 AAAAAT -AAAA- AAAAAT GTAAAAT ACAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT -AAAAAT A-AAAAT AAAAAT AAAAAT AAAA
1866981 TGAAGAGAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
5 12 0.16
6 43 0.58
7 19 0.26
ACGTcount: A:0.78, C:0.01, G:0.02, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:1867291 original size:42 final size:43
Alignment explanation
Indices: 1867197--1867315 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 43
1867187 TTTGATAAAA
* ** * *
1867197 GCTCCTCTAGGCAGAGGTTCAATGACTTTGAGAAACATAAATG
1 GCTCCTCTAAGCAGAGGTTCAACAACTTTGAAAAAAATAAATG
* * *
1867240 GCTCCTCTAATCAGAGGTTTAACAACTTT-AAAAAAATAAATT
1 GCTCCTCTAAGCAGAGGTTCAACAACTTTGAAAAAAATAAATG
* *
1867282 GCTCCTCTAAGCAGAGGCATC-ACGACTTTGAAAA
1 GCTCCTCTAAGCAGAGG-TTCAACAACTTTGAAAA
1867316 GTAGATTGCT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
42 33 0.53
43 29 0.47
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (43 bp):
GCTCCTCTAAGCAGAGGTTCAACAACTTTGAAAAAAATAAATG
Found at i:1867417 original size:42 final size:42
Alignment explanation
Indices: 1867264--1867465 Score: 257
Period size: 41 Copynumber: 4.9 Consensus size: 42
1867254 AGGTTTAACA
* * * * *
1867264 ACTTTAAAAAAATAAATTGCTCCTCTAAGCAGAGGCATCACG
1 ACTTTGAAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACG
* * *
1867306 ACTTTG-AAAAGTAGATTGCTCCTTTAAATAGAGCCACCACG
1 ACTTTGAAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACG
*
1867347 ACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 ACTTTGAAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACG
* *
1867388 ATTTTGAAAAAGTAAATTGCTCATTTAAACAGAGGCACCACG
1 ACTTTGAAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACG
* *
1867430 ACTTTAAAAAAGTAAATTGCT-CTTCTAAACAAAGGC
1 ACTTTGAAAAAGTAAATTGCTCCTT-TAAACAGAGGC
1867466 TTGCTCCTCT
Statistics
Matches: 139, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 72 0.52
42 67 0.48
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (42 bp):
ACTTTGAAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACG
Found at i:1867427 original size:83 final size:83
Alignment explanation
Indices: 1867264--1867465 Score: 289
Period size: 83 Copynumber: 2.4 Consensus size: 83
1867254 AGGTTTAACA
* * * * *
1867264 ACTTTAAAAAAATAAATTGCTCCTCTAAGCAGAGGCATCACGACTTTGAAAAGTAGATTGCTCCT
1 ACTTTAAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCAT
*
1867329 TTAAATAGAGCCACCACG
66 TTAAACAGAGCCACCACG
* *
1867347 ACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGATTTTGAAAAAGTAAATTGCTCA
1 ACTTTAAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTGCTCA
*
1867411 TTTAAACAGAGGCACCACG
65 TTTAAACAGAGCCACCACG
* *
1867430 ACTTTAAAAAAGTAAATTGCTCTTCTAAACAAAGGC
1 ACTTTAAAAAAGTAAATTGCTCCTCTAAACAGAGGC
1867466 TTGCTCCTCT
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
82 37 0.35
83 41 0.39
84 27 0.26
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (83 bp):
ACTTTAAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCAT
TTAAACAGAGCCACCACG
Found at i:1867471 original size:20 final size:20
Alignment explanation
Indices: 1867446--1867485 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1867436 AAAAAGTAAA
*
1867446 TTGCTCTTCTAAACAAAGGC
1 TTGCTCCTCTAAACAAAGGC
*
1867466 TTGCTCCTCTAAACAGAGGC
1 TTGCTCCTCTAAACAAAGGC
1867486 ACCACGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (20 bp):
TTGCTCCTCTAAACAAAGGC
Found at i:1867862 original size:43 final size:42
Alignment explanation
Indices: 1867804--1867885 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
1867794 TTTGGCAAAC
* *
1867804 TTGGAATTCATATCC-AAAAGTCTAAAGCTCTTCATTTGAATT
1 TTGGAATTCACATCCAAAAATTC-AAAGCTCTTCATTTGAATT
*
1867846 TTGGAAATTCACATCCAAAAATTCAAAGCTTTTCATTTGA
1 TTGG-AATTCACATCCAAAAATTCAAAGCTCTTCATTTGA
1867886 GTTCAAAGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 4 0.11
43 25 0.71
44 6 0.17
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (42 bp):
TTGGAATTCACATCCAAAAATTCAAAGCTCTTCATTTGAATT
Found at i:1869241 original size:14 final size:14
Alignment explanation
Indices: 1869213--1869245 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1869203 ATTTTTTTCT
1869213 TTTTTTTTTCATCA
1 TTTTTTTTTCATCA
1869227 TCTTTTTTTTC-TCA
1 T-TTTTTTTTCATCA
1869241 TTTTT
1 TTTTT
1869246 GATCTATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 5 0.28
15 9 0.50
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTCATCA
Found at i:1879479 original size:58 final size:58
Alignment explanation
Indices: 1879414--1879688 Score: 360
Period size: 58 Copynumber: 4.7 Consensus size: 58
1879404 TTGTGCAGGG
* * *
1879414 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTAAAACTTTATTTTCAAGA
* * *
1879472 AAAATTGATACTTTCAAC-TTTCCCTCAAAAATTGATTTTTTTAAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCC-CAAAAA-T-ATTTTTTTAAAACTTTATTTTCAAGA
* *
1879532 AAAATTGATACTTTCAA-TTTTTCTCCAAAAATATTTTTTGAAAACTTTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTC-CCAAAAATATTTTTTTAAAAC-TTTATTTTCAAGA
* * *
1879591 AAAATTGATACTTTCAAC-TTTTCCTCAAAAACT-CTTTTTTAAAATTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCC-CAAAAA-TATTTTTTTAAAACTTTATTTTCAAGA
1879649 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTT
1879689 TTATTTAAAG
Statistics
Matches: 189, Mismatches: 17, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
57 6 0.03
58 77 0.41
59 56 0.30
60 49 0.26
61 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTAAAACTTTATTTTCAAGA
Found at i:1879649 original size:117 final size:116
Alignment explanation
Indices: 1879414--1879687 Score: 426
Period size: 117 Copynumber: 2.3 Consensus size: 116
1879404 TTGTGCAGGG
*
1879414 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAACTTTAATTTCGAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATA-TTTTTTGAAACTTTAATTTCAAGAAAAATTG
* *
1879479 ATACTTTCAACTTTCCCTCAAAAATTGATTTTTTTAAAAATTTATTTTTAAGA
65 ATACTTTCAACTTTCCCTCAAAAACT-ACTTTTTTAAAAATTTATTTTTAAGA
* *
1879532 AAAATTGATACTTTCAA-TTTTTCTCCAAAAATATTTTTTGAAAACTTTTATTTTCAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTTC-CCAAAAATATTTTTTG-AAAC-TTTAATTTCAAGAAAAAT
* *
1879596 TGATACTTTCAACTTTTCCTCAAAAACT-CTTTTTTAAAATTTTATTTTTAAGA
63 TGATACTTTCAACTTTCCCTCAAAAACTACTTTTTTAAAAATTTATTTTTAAGA
1879649 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT
1879688 TTTATTTAAA
Statistics
Matches: 145, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
117 68 0.47
118 36 0.25
119 41 0.28
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (116 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAACTTTAATTTCAAGAAAAATTGA
TACTTTCAACTTTCCCTCAAAAACTACTTTTTTAAAAATTTATTTTTAAGA
Found at i:1879758 original size:21 final size:21
Alignment explanation
Indices: 1879734--1879860 Score: 60
Period size: 22 Copynumber: 5.8 Consensus size: 21
1879724 AAGCGAAGAT
1879734 AAATAAATAAAAAAATATAAA
1 AAATAAATAAAAAAATATAAA
* *
1879755 AAATAAAGAAAAGTAAA-ACAAA
1 AAATAAATAAAA--AAATATAAA
* *
1879777 AATAAAAATAAAATAAAGATAAA
1 AA-ATAAATAAAA-AAATATAAA
* * ** *
1879800 AGAAT-ATTAAATAAACCTAATC
1 A-AATAAATAAAAAAATATAA-A
* *
1879822 TAATAAATAAAAAAATAAAAA
1 AAATAAATAAAAAAATATAAA
* *
1879843 TAAATAACTAAATAAATA
1 -AAATAAATAAAAAAATA
1879861 AATAAATTCA
Statistics
Matches: 77, Mismatches: 21, Indels: 15
0.68 0.19 0.13
Matches are distributed among these distances:
21 20 0.26
22 39 0.51
23 17 0.22
24 1 0.01
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATAAATAAAAAAATATAAA
Found at i:1879760 original size:17 final size:18
Alignment explanation
Indices: 1879732--1879786 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
1879722 AAAAGCGAAG
*
1879732 ATAAATAAATAAAAAAAT
1 ATAAACAAATAAAAAAAT
1879750 ATAAA-AAATAAAGAAAAGT
1 ATAAACAAATAAA-AAAA-T
1879769 A-AAACAAA-AATAAAAAT
1 ATAAACAAATAA-AAAAAT
1879786 A
1 A
1879787 AAATAAAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.27
18 18 0.55
19 6 0.18
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (18 bp):
ATAAACAAATAAAAAAAT
Found at i:1879766 original size:11 final size:10
Alignment explanation
Indices: 1879742--1879793 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
1879732 ATAAATAAAT
1879742 AAAAAAAT-A
1 AAAAAAATAA
*
1879751 TAAAAAATAA
1 AAAAAAATAA
* *
1879761 AGAAAAGTAA
1 AAAAAAATAA
1879771 AACAAAAATAA
1 AA-AAAAATAA
1879782 AAATAAAATAA
1 AAA-AAAATAA
1879793 A
1 A
1879794 GATAAAAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 7 0.21
10 10 0.29
11 17 0.50
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:1879788 original size:17 final size:17
Alignment explanation
Indices: 1879744--1879800 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1879734 AAATAAATAA
*
1879744 AAAAATATAAAAAATAAAG
1 AAAAATA-AAAAAA-AAAT
* *
1879763 AAAAGTAAAACAAAAAT
1 AAAAATAAAAAAAAAAT
* *
1879780 AAAAATAAAATAAAGAT
1 AAAAATAAAAAAAAAAT
1879797 AAAA
1 AAAA
1879801 GAATATTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 21 0.66
18 5 0.16
19 6 0.19
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAAAAAAAT
Found at i:1879810 original size:28 final size:28
Alignment explanation
Indices: 1879740--1879810 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
1879730 AGATAAATAA
*
1879740 ATAAAAAAATATAAAAAATAAAGAAAAG
1 ATAAAAAAATATTAAAAATAAAGAAAAG
*
1879768 -TAAAACAAA-AATAAAAATAAA-ATAAAG
1 ATAAAA-AAATATTAAAAATAAAGA-AAAG
*
1879795 ATAAAAGAATATTAAA
1 ATAAAAAAATATTAAA
1879811 TAAACCTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
26 1 0.03
27 21 0.60
28 13 0.37
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (28 bp):
ATAAAAAAATATTAAAAATAAAGAAAAG
Found at i:1879830 original size:4 final size:4
Alignment explanation
Indices: 1879823--1879867 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1879813 AACCTAATCT
* *
1879823 AATA AATA AAAA AAT- AA-A AATA AATA ACTA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT
1879868 TCAAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 4 0.11
4 31 0.89
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:1880661 original size:21 final size:21
Alignment explanation
Indices: 1880628--1880686 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
1880618 AAATCAAATG
*
1880628 AAAATAAATCAGATAAACTAAA
1 AAAATTAA-CAGATAAACTAAA
*
1880650 AAAATTAACAGATAAATTAAA
1 AAAATTAACAGATAAACTAAA
1880671 ATTAAA-TAACAGATAA
1 A--AAATTAACAGATAA
1880687 TACATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.39
22 17 0.52
23 3 0.09
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (21 bp):
AAAATTAACAGATAAACTAAA
Found at i:1880787 original size:9 final size:9
Alignment explanation
Indices: 1880770--1880845 Score: 68
Period size: 9 Copynumber: 8.4 Consensus size: 9
1880760 AATACTCAAG
*
1880770 ATAAAAAAA
1 ATAATAAAA
1880779 ATAAT-AAA
1 ATAATAAAA
*
1880787 AGAA-AAAA
1 ATAATAAAA
*
1880795 ATATATAATA
1 ATA-ATAAAA
*
1880805 ATAATAATA
1 ATAATAAAA
1880814 ATAATAAATA
1 ATAATAAA-A
1880824 ATAA-AATAA
1 ATAATAA-AA
1880833 ATAATAAAA
1 ATAATAAAA
1880842 ATAA
1 ATAA
1880846 AAATGTAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
8 11 0.20
9 31 0.55
10 14 0.25
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (9 bp):
ATAATAAAA
Found at i:1880787 original size:12 final size:12
Alignment explanation
Indices: 1880770--1880842 Score: 65
Period size: 12 Copynumber: 5.6 Consensus size: 12
1880760 AATACTCAAG
1880770 ATAAAAAAAATA
1 ATAAAAAAAATA
*
1880782 ATAAAAGAAAAAA
1 ATAAAA-AAAATA
1880795 ATATATAATAATAATA
1 ATA-A-AA-AA-AATA
*
1880811 ATAATAATAAATA
1 ATAA-AAAAAATA
*
1880824 ATAAAATAAATA
1 ATAAAAAAAATA
1880836 ATAAAAA
1 ATAAAAA
1880843 TAAAAATGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
12 20 0.38
13 16 0.31
14 2 0.04
15 8 0.15
16 6 0.12
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.23
Consensus pattern (12 bp):
ATAAAAAAAATA
Found at i:1880794 original size:16 final size:17
Alignment explanation
Indices: 1880773--1880848 Score: 82
Period size: 19 Copynumber: 4.3 Consensus size: 17
1880763 ACTCAAGATA
*
1880773 AAAAAAATAATAA-AAG
1 AAAAAAATAATAATAAT
1880789 AAAAAAATATATAATAAT
1 AAAAAAATA-ATAATAAT
*
1880807 AATAATAATAATAAATAAT
1 AA-AAAAATAAT-AATAAT
*
1880826 AAAATAAATAATAAAAAT
1 AAAA-AAATAATAATAAT
1880844 AAAAA
1 AAAAA
1880849 TGTAAATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
16 9 0.18
17 5 0.10
18 17 0.33
19 20 0.39
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.22
Consensus pattern (17 bp):
AAAAAAATAATAATAAT
Found at i:1880805 original size:3 final size:3
Alignment explanation
Indices: 1880794--1880845 Score: 61
Period size: 3 Copynumber: 16.7 Consensus size: 3
1880784 AAAAGAAAAA
*
1880794 AAT ATAT AAT AAT AAT AAT AAT AAT AAAT AAT AA- AAT AAAT AAT AAA
1 AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT
1880841 AAT AA
1 AAT AA
1880846 AAATGTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 2 0.05
3 32 0.74
4 9 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1886647 original size:22 final size:21
Alignment explanation
Indices: 1886622--1886679 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1886612 GAAAAAAAAT
1886622 AATTTTAAATATTAATATTTAA
1 AATTTTAAAT-TTAATATTTAA
* *
1886644 AA-TTTAAATTATAAAATTTTA
1 AATTTTAAATT-TAATATTTAA
1886665 AATTTTAAATTTAAT
1 AATTTTAAATTTAAT
1886680 TGTATGACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 20 0.65
22 10 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTTAAATTTAATATTTAA
Found at i:1886650 original size:14 final size:13
Alignment explanation
Indices: 1886622--1886678 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 13
1886612 GAAAAAAAAT
*
1886622 AATTTTAAATATTA
1 AATTTAAAAT-TTA
1886636 ATATTTAAAATTTA
1 A-ATTTAAAATTTA
1886650 AATTATAAAATTTTA
1 AATT-TAAAA-TTTA
*
1886665 AATTTTAAATTTA
1 AATTTAAAATTTA
1886678 A
1 A
1886679 TTGTATGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
13 8 0.21
14 14 0.37
15 16 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATTTAAAATTTA
Found at i:1886852 original size:2 final size:2
Alignment explanation
Indices: 1886845--1886872 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1886835 ACAAAACAAC
1886845 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
1886873 CTAACAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1892716 original size:17 final size:17
Alignment explanation
Indices: 1892696--1892729 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1892686 TCAAATTGAA
* *
1892696 TTATATTTTTTATTGTT
1 TTATATATTTTAATGTT
1892713 TTATATATTTTAATGTT
1 TTATATATTTTAATGTT
1892730 ATAAAATAAA
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:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTATATATTTTAATGTT
Found at i:1893167 original size:20 final size:22
Alignment explanation
Indices: 1893126--1893176 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1893116 TCCGAAATTA
*
1893126 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATGTTTTAAAAT
1893148 ATAAAATATTA-GTTTT-AAAT
1 ATAAAATATTATGTTTTAAAAT
1893168 AT-AAATATT
1 ATAAAATATT
1893177 TAAAAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 7 0.25
20 6 0.21
21 4 0.14
22 11 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAAAATATTATGTTTTAAAAT
Found at i:1893218 original size:26 final size:26
Alignment explanation
Indices: 1893166--1893218 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1893156 TTAGTTTTAA
* *
1893166 ATATAAATATTTAAAAATATATCATT
1 ATATAAATATATAAAAATATATAATT
*
1893192 ATATAAATATATATAAATA-ATTAATT
1 ATATAAATATATAAAAATATA-TAATT
1893218 A
1 A
1893219 ATTAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATAAATATATAAAAATATATAATT
Found at i:1897207 original size:42 final size:41
Alignment explanation
Indices: 1897130--1897251 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 41
1897120 ATTTTGGATT
** * *
1897130 AAAAATTACTAAAATTATATTAAAGGTTATTAAAATT-GTA
1 AAAAATTACTAAAATTATATTAAAAATTATCAAAATTAATA
*
1897170 CAAAAACTTATTAAAATTATATTAAAAATTATCAAAATTAATAA
1 -AAAAA-TTACTAAAATTATATTAAAAATTATCAAAATTAAT-A
* ** *
1897214 AAAAATTACCAAAATTATAACAAAATTTATCAAAATTA
1 AAAAATTACTAAAATTATATTAAAAATTATCAAAATTA
1897252 TGTTAAAGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 5 0.07
42 56 0.82
43 6 0.09
44 1 0.01
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (41 bp):
AAAAATTACTAAAATTATATTAAAAATTATCAAAATTAATA
Found at i:1897265 original size:21 final size:21
Alignment explanation
Indices: 1897129--1897270 Score: 101
Period size: 21 Copynumber: 6.7 Consensus size: 21
1897119 TATTTTGGAT
*
1897129 TAAAAATTA-CTAAAATTATAT
1 TAAAAATTATC-AAAATTATAA
** * *
1897150 TAAAGGTTATTAAAATTGTACA
1 TAAAAATTATCAAAATTATA-A
* * *
1897172 -AAAACTTATTAAAATTATAT
1 TAAAAATTATCAAAATTATAA
1897192 TAAAAATTATCAAAATTAATAA
1 TAAAAATTATCAAAATT-ATAA
*
1897214 -AAAAATTACCAAAATTATAA
1 TAAAAATTATCAAAATTATAA
* * **
1897234 CAAAATTTATCAAAATTATGT
1 TAAAAATTATCAAAATTATAA
*
1897255 TAAAGATTATCCAAAA
1 TAAAAATTAT-CAAAA
1897271 AAAAAATCAA
Statistics
Matches: 95, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
20 4 0.04
21 83 0.87
22 8 0.08
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.34
Consensus pattern (21 bp):
TAAAAATTATCAAAATTATAA
Found at i:1897332 original size:21 final size:20
Alignment explanation
Indices: 1897317--1897397 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 20
1897307 GTATAAAATC
1897317 TTACCAAAATTATATAAAAA
1 TTACCAAAATTATATAAAAA
* *
1897337 ATA-CAAAAATATGATAAAAA
1 TTACCAAAATTAT-ATAAAAA
* *
1897357 TTACCAACATTATATCAAAAT
1 TTACCAAAATTATAT-AAAAA
* *
1897378 TTATCAAAATAATATAAAAA
1 TTACCAAAATTATATAAAAA
1897398 AATAAATTCT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
19 8 0.17
20 17 0.35
21 23 0.48
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.28
Consensus pattern (20 bp):
TTACCAAAATTATATAAAAA
Found at i:1897405 original size:27 final size:27
Alignment explanation
Indices: 1897374--1897425 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
1897364 CATTATATCA
1897374 AAATT-TATCAAAATAA-TATAAAAAAAT
1 AAATTCTAT-AAAA-AATTATAAAAAAAT
1897401 AAATTCTATAAAAAATTATAAAAAA
1 AAATTCTATAAAAAATTATAAAAAA
1897426 TATATCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 2 0.09
27 18 0.78
28 3 0.13
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (27 bp):
AAATTCTATAAAAAATTATAAAAAAAT
Found at i:1897501 original size:21 final size:21
Alignment explanation
Indices: 1897468--1897538 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
1897458 ACATTACACC
**
1897468 AAAATTACCAAAAATATG-ATA
1 AAAATTATAAAAAAT-TGTATA
*
1897489 AAAATTATAAAAAATTGTATC
1 AAAATTATAAAAAATTGTATA
* *
1897510 AAAATTATAAAAAACT-TATT
1 AAAATTATAAAAAATTGTATA
1897530 AAAATTATA
1 AAAATTATA
1897539 TTAAAGTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
20 14 0.32
21 30 0.68
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAATTATAAAAAATTGTATA
Found at i:1897540 original size:11 final size:11
Alignment explanation
Indices: 1897489--1897606 Score: 50
Period size: 10 Copynumber: 11.3 Consensus size: 11
1897479 AAATATGATA
*
1897489 AAAATTATA-A
1 AAAATTATATT
* *
1897499 AAAATTGTATC
1 AAAATTATATT
*
1897510 AAAATTATA-A
1 AAAATTATATT
*
1897520 AAAACT-TATT
1 AAAATTATATT
1897530 AAAATTATATT
1 AAAATTATATT
* *
1897541 AAAGTT-TATC
1 AAAATTATATT
* * *
1897551 AAAAGTACACT
1 AAAATTATATT
* **
1897562 AAAAGT-TCCT
1 AAAATTATATT
*
1897572 CAAATTATATT
1 AAAATTATATT
* *
1897583 AAAAGT-TATC
1 AAAATTATATT
1897593 AAAATTATATT
1 AAAATTATATT
1897604 AAA
1 AAA
1897607 GACTATCCAA
Statistics
Matches: 77, Mismatches: 25, Indels: 11
0.68 0.22 0.10
Matches are distributed among these distances:
9 2 0.03
10 39 0.51
11 36 0.47
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAATTATATT
Found at i:1897554 original size:21 final size:21
Alignment explanation
Indices: 1897489--1897607 Score: 93
Period size: 21 Copynumber: 5.7 Consensus size: 21
1897479 AAATATGATA
*
1897489 AAAATTATA-AAAAATTGTATC
1 AAAATTATATAAAAGTT-TATC
** *
1897510 AAAATTATA-AAAAACTTATT
1 AAAATTATATAAAAGTTTATC
*
1897530 AAAATTATATTAAAGTTTATC
1 AAAATTATATAAAAGTTTATC
* * **
1897551 AAAAGTACACTAAAAGTTCCTC
1 AAAATTATA-TAAAAGTTTATC
1897573 -AAATTATATTAAAAG-TTATC
1 AAAATTATA-TAAAAGTTTATC
*
1897593 AAAATTATATTAAAG
1 AAAATTATATAAAAG
1897608 ACTATCCAAA
Statistics
Matches: 78, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
20 20 0.26
21 49 0.63
22 9 0.12
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAATTATATAAAAGTTTATC
Found at i:1897613 original size:21 final size:22
Alignment explanation
Indices: 1897573--1897618 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1897563 AAAGTTCCTC
*
1897573 AAATTATATTAAAAGTTAT-CA
1 AAATTATATTAAAAGCTATCCA
1897594 AAATTATATT-AAAGACTATCCA
1 AAATTATATTAAAAG-CTATCCA
1897616 AAA
1 AAA
1897619 AAAAAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATTATATTAAAAGCTATCCA
Found at i:1897658 original size:21 final size:20
Alignment explanation
Indices: 1897629--1897742 Score: 86
Period size: 21 Copynumber: 5.5 Consensus size: 20
1897619 AAAAAAAAGT
*
1897629 TATAACAAAAGTTACCAAAA
1 TATATCAAAAGTTACCAAAA
**
1897649 TGATATCAAATCTTACCAAAA
1 T-ATATCAAAAGTTACCAAAA
* * ***
1897670 TTATATAAAAAATTGTAAAAA
1 -TATATCAAAAGTTACCAAAA
1897691 TATGAT-AAAAGTTACCAAAA
1 TAT-ATCAAAAGTTACCAAAA
* *
1897711 CTATATCAAAATTTATCAAAA
1 -TATATCAAAAGTTACCAAAA
1897732 TAATATCAAAA
1 T-ATATCAAAA
1897743 TAAATTCTAT
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
20 17 0.23
21 55 0.75
22 1 0.01
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.28
Consensus pattern (20 bp):
TATATCAAAAGTTACCAAAA
Found at i:1897738 original size:11 final size:11
Alignment explanation
Indices: 1897713--1897745 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1897703 TACCAAAACT
1897713 ATATCAAAAT-
1 ATATCAAAATA
*
1897723 TTATCAAAATA
1 ATATCAAAATA
1897734 ATATCAAAATA
1 ATATCAAAATA
1897745 A
1 A
1897746 ATTCTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (11 bp):
ATATCAAAATA
Found at i:1899368 original size:20 final size:20
Alignment explanation
Indices: 1899330--1899368 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1899320 TACTCACATA
*
1899330 TATATATATGTGTGCGTGTG
1 TATATATATGTGTACGTGTG
*
1899350 TATATATATGTGTATGTGT
1 TATATATATGTGTACGTGT
1899369 ACATGAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (20 bp):
TATATATATGTGTACGTGTG
Found at i:1900834 original size:60 final size:60
Alignment explanation
Indices: 1900741--1900860 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
1900731 AATCACTCGA
1900741 ACCCTCCTCCCACGTGCATACTCATGGGCTAGAACTTTGAATATTCCAAATCAAAGACCT
1 ACCCTCCTCCCACGTGCATACTCATGGGCTAGAACTTTGAATATTCCAAATCAAAGACCT
1900801 ACCCTCCTCCCACGTGCATACTCATGGGCTAGAACTTTGAATATTCCAAATCAAAGACCT
1 ACCCTCCTCCCACGTGCATACTCATGGGCTAGAACTTTGAATATTCCAAATCAAAGACCT
1900861 TCGAGAAGGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.30, C:0.32, G:0.13, T:0.25
Consensus pattern (60 bp):
ACCCTCCTCCCACGTGCATACTCATGGGCTAGAACTTTGAATATTCCAAATCAAAGACCT
Found at i:1904940 original size:10 final size:10
Alignment explanation
Indices: 1904927--1904958 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
1904917 TTTTTTTCTT
1904927 TTTTTACATA
1 TTTTTACATA
1904937 TTTTTA-ATA
1 TTTTTACATA
1904946 TTTTT-CATA
1 TTTTTACATA
1904955 TTTT
1 TTTT
1904959 GTATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTACATA
Found at i:1917408 original size:14 final size:14
Alignment explanation
Indices: 1917389--1917415 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1917379 TTTTCTCCTT
1917389 TGGAAATATATATG
1 TGGAAATATATATG
1917403 TGGAAATATATAT
1 TGGAAATATATAT
1917416 TAGTGTTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (14 bp):
TGGAAATATATATG
Found at i:1921616 original size:21 final size:21
Alignment explanation
Indices: 1921592--1921633 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1921582 TTAATTTATA
1921592 GGTTTAAAAAATACAAAAGTT
1 GGTTTAAAAAATACAAAAGTT
** *
1921613 GGTTTAATTACTACAAAAGTT
1 GGTTTAAAAAATACAAAAGTT
1921634 ATTTGCCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (21 bp):
GGTTTAAAAAATACAAAAGTT
Found at i:1926221 original size:29 final size:29
Alignment explanation
Indices: 1926179--1926242 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
1926169 TCTTTAATTA
1926179 GCATCAATAACAGTGGTTACTGCACGCGG
1 GCATCAATAACAGTGGTTACTGCACGCGG
1926208 GCATCAATAACAGTGGTTACTGCACGCGG
1 GCATCAATAACAGTGGTTACTGCACGCGG
*
1926237 GAATCA
1 GCATCA
1926243 TAAGCATGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (29 bp):
GCATCAATAACAGTGGTTACTGCACGCGG
Found at i:1937607 original size:13 final size:13
Alignment explanation
Indices: 1937589--1937614 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1937579 TTATGTCAAA
1937589 GTAAAATATACTT
1 GTAAAATATACTT
1937602 GTAAAATATACTT
1 GTAAAATATACTT
1937615 CAGAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
GTAAAATATACTT
Found at i:1941113 original size:202 final size:202
Alignment explanation
Indices: 1940779--1941265 Score: 674
Period size: 202 Copynumber: 2.4 Consensus size: 202
1940769 TTAAAGTGGG
* * * * * *
1940779 TTATCCCACATCTAATAAATTTTCAATATAC-TATAGTCTTATATTTAAATCAGGCCCCTCCACA
1 TTATCCCACATCTAATAAATCTTCAATAT-CTTGTAGTCTTATATTCAAGTTAAGCCCCTCCACA
** * * *
1940843 TGTTGTCAATTAGTTTTAAGTTTGATGCTTAACATGGTATGAGAACCAAAACTTTTTTTTCGTTG
65 TACTGTCAATTAATTTTAAATTTGATGCTTAACATGGTATCAGAACCAAAACTTTTTTTTCGTTG
* * *
1940908 CCCTTTCTTAATTTTTCACGTGGAAAGCTTTTTCCATTTTCACTTACACGTGAT-GGGGACTTGT
130 CCCTTTCTTAATTTGTCACGTGGAAAGCTTTTTCCATTTTCACTTACACGTAATAAGGG-CTTGT
1940972 TAAAGTAAA
194 TAAAGTAAA
*
1940981 TTATCCCATATCTAATAAATCTTCAATATCTTGTAGTCTTATATTCAAGTTAAGCCCCTCCACAT
1 TTATCCCACATCTAATAAATCTTCAATATCTTGTAGTCTTATATTCAAGTTAAGCCCCTCCACAT
* * * *
1941046 ACTGTCAATTAATTTTAAATTTGATGTTTAACTTGGTATCAGAGCCAGAACTTTTTTTTCGTTGC
66 ACTGTCAATTAATTTTAAATTTGATGCTTAACATGGTATCAGAACCAAAACTTTTTTTTCGTTGC
* *
1941111 CCTTTCTTAATTTGTCACGTGGAAAGCTTTTTTCATTTTCACTTATACGTAATAAGGGCTTGTTA
131 CCTTTCTTAATTTGTCACGTGGAAAGCTTTTTCCATTTTCACTTACACGTAATAAGGGCTTGTTA
*
1941176 AAGTAGA
196 AAGTAAA
* * * *
1941183 TTATCCCACATCTAATAAATCTTCAATAT-TCTGTAGTCTTATATTCAGGTTGAGCCCATCCACT
1 TTATCCCACATCTAATAAATCTTCAATATCT-TGTAGTCTTATATTCAAGTTAAGCCCCTCCACA
* *
1941247 TACTGCCAATTGATTTTAA
65 TACTGTCAATTAATTTTAA
1941266 GTTTAACATG
Statistics
Matches: 253, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
201 2 0.01
202 248 0.98
203 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (202 bp):
TTATCCCACATCTAATAAATCTTCAATATCTTGTAGTCTTATATTCAAGTTAAGCCCCTCCACAT
ACTGTCAATTAATTTTAAATTTGATGCTTAACATGGTATCAGAACCAAAACTTTTTTTTCGTTGC
CCTTTCTTAATTTGTCACGTGGAAAGCTTTTTCCATTTTCACTTACACGTAATAAGGGCTTGTTA
AAGTAAA
Found at i:1941338 original size:22 final size:22
Alignment explanation
Indices: 1941306--1941349 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1941296 TTTAAGTGTC
1941306 CCTTTTCTTAATTTGTCATGTG
1 CCTTTTCTTAATTTGTCATGTG
*
1941328 CCTTTTTTTAATTTGTCATGTG
1 CCTTTTCTTAATTTGTCATGTG
1941350 GAAGACTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (22 bp):
CCTTTTCTTAATTTGTCATGTG
Found at i:1943994 original size:28 final size:29
Alignment explanation
Indices: 1943929--1943983 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1943919 ATTGTCTCAC
* * *
1943929 AATAAAAAATATGAAATAAAAATTAATAT
1 AATACAAAATATAAAATAAAAATCAATAT
1943958 AATACAAAATATAAAAT-AAAATCAAT
1 AATACAAAATATAAAATAAAAATCAAT
1943984 TTAGTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (29 bp):
AATACAAAATATAAAATAAAAATCAATAT
Found at i:1945029 original size:20 final size:20
Alignment explanation
Indices: 1944991--1945042 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1944981 ACTCAAACTT
1944991 CAAATTGGGCCCCTTAAAC-C
1 CAAATTGGG-CCCTTAAACAC
1945011 CAAATTGGGCCCTTAAAACAC
1 CAAATTGGGCCCTT-AAACAC
*
1945032 CACA-TGGGCCC
1 CAAATTGGGCCC
1945043 AATCTCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.17
20 20 0.69
21 4 0.14
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (20 bp):
CAAATTGGGCCCTTAAACAC
Found at i:1945401 original size:3 final size:3
Alignment explanation
Indices: 1945393--1945448 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1945383 TAGTTTCTAA
1945393 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1945441 AAT AAT AA
1 AAT AAT AA
1945449 AAAGATATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1946873 original size:14 final size:14
Alignment explanation
Indices: 1946854--1946880 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1946844 TAATGGGGAA
1946854 AAAACAAAAAAAAG
1 AAAACAAAAAAAAG
1946868 AAAACAAAAAAAA
1 AAAACAAAAAAAA
1946881 AAGAAAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.07, G:0.04, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAAAAG
Found at i:1955213 original size:41 final size:41
Alignment explanation
Indices: 1955137--1955214 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
1955127 TCTTCATTTT
* * * * *
1955137 TTTTATTTTTTTTTATATTTTGTATTTTTTGATATTTGATA
1 TTTTAATTTTTTTGATATTTTATATTATATGATATTTGATA
1955178 TTTTAATTTTTTTGATATTTTATATATATAT-ATATTT
1 TTTTAATTTTTTTGATATTTTATAT-TATATGATATTT
1955215 TTTCTGGACA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 28 0.90
42 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (41 bp):
TTTTAATTTTTTTGATATTTTATATTATATGATATTTGATA
Found at i:1957600 original size:23 final size:21
Alignment explanation
Indices: 1957557--1957600 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
1957547 TGATATTTTA
*
1957557 TTAAAAATTTAATTTTAAAAT
1 TTAAAAAATTAATTTTAAAAT
1957578 TTAAAAACATTAATCTTTAAAAT
1 TTAAAAA-ATTAAT-TTTAAAAT
1957601 ATATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAAAAATTAATTTTAAAAT
Found at i:1963245 original size:17 final size:17
Alignment explanation
Indices: 1963204--1963246 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1963194 GGTCCAAAAT
*
1963204 CTTTTGCATTTCTAACC
1 CTTTTGCTTTTCTAACC
1963221 CTTTTGCTTTTCTAACC
1 CTTTTGCTTTTCTAACC
1963238 CTTTTGCTT
1 CTTTTGCTT
1963247 GTTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.12, C:0.28, G:0.07, T:0.53
Consensus pattern (17 bp):
CTTTTGCTTTTCTAACC
Found at i:1970321 original size:2 final size:2
Alignment explanation
Indices: 1970314--1970343 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1970304 AATTTCCATG
1970314 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
1970344 GTGTGTGTGT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1970348 original size:2 final size:2
Alignment explanation
Indices: 1970343--1970384 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1970333 TATATATATA
1970343 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1970385 ATATATCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1970561 original size:28 final size:28
Alignment explanation
Indices: 1970521--1970598 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
1970511 GAGAACGAAG
* *
1970521 TAGATGAGATTAATCTGTCTAATATAAC
1 TAGATGAGATTAATCTATCCAATATAAC
*
1970549 TAGATGAGATTAATCTATCCGATATAAC
1 TAGATGAGATTAATCTATCCAATATAAC
*
1970577 TAGATGAGATTAACCTCATCCA
1 TAGATGAGATTAATCT-ATCCA
1970599 TTTCGTGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 40 0.91
29 4 0.09
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (28 bp):
TAGATGAGATTAATCTATCCAATATAAC
Found at i:1975306 original size:15 final size:15
Alignment explanation
Indices: 1975286--1975318 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1975276 TAAATCATCA
1975286 TTATCAATCAAATCG
1 TTATCAATCAAATCG
*
1975301 TTATCATTCAAATCG
1 TTATCAATCAAATCG
1975316 TTA
1 TTA
1975319 GCTACGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
TTATCAATCAAATCG
Found at i:1977461 original size:121 final size:125
Alignment explanation
Indices: 1977209--1977462 Score: 288
Period size: 121 Copynumber: 2.1 Consensus size: 125
1977199 GATTTTAAGT
* * * * ** *
1977209 TTAACATGGTATCAGAGCCAAGATTTTTTTTTAAGTTTCCCTTTTCTTAATTTGTCATGTGGAAT
1 TTAACATGATATCAGAGCCAAGATTTTCTTTTAAGTTGCCCTTTTCCTAATTTGTCACATAGAAT
* * * *
1977274 ACTTTCATCCATCTTCGCCTACACCTGACAAATTAGGAATATGAGTATTTTTTTCAGTTGC
66 ACTTT-ATCCATCTTCGACTACACCTGACAAATTAGGAATAGGAGGATTTTTTTCAGTTGA
* * *
1977335 TTAACATGATATCAGAGCCAGGATTTTCTTTT-CGTTGCCC-TTTCCTAATTTTTCACATAGAA-
1 TTAACATGATATCAGAGCCAAGATTTTCTTTTAAGTTGCCCTTTTCCTAATTTGTCACATAGAAT
*
1977397 AGCTTT-TCCATCTTC-ACT-CACCGTGATAAATTAGGAA-AGGAAGGATTTTTTTCAGTTGA
66 A-CTTTATCCATCTTCGACTACACC-TGACAAATTAGGAATAGG-AGGATTTTTTTCAGTTGA
1977456 TTAACAT
1 TTAACAT
1977463 CATAGAATCA
Statistics
Matches: 110, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
120 6 0.05
121 38 0.35
122 9 0.08
123 1 0.01
124 21 0.19
125 6 0.05
126 29 0.26
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (125 bp):
TTAACATGATATCAGAGCCAAGATTTTCTTTTAAGTTGCCCTTTTCCTAATTTGTCACATAGAAT
ACTTTATCCATCTTCGACTACACCTGACAAATTAGGAATAGGAGGATTTTTTTCAGTTGA
Found at i:1979850 original size:14 final size:14
Alignment explanation
Indices: 1979818--1979869 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1979808 ATTGTCTCAC
*
1979818 AATAAAAAATATGA
1 AATAAAAAATATAA
1979832 AATAAAAAAT-TAA
1 AATAAAAAATATAA
1979845 ATATAATACAAAATATAA
1 A-AT-A-A-AAAATATAA
1979863 AATAAAA
1 AATAAAA
1979870 TCAATTTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
13 3 0.09
14 14 0.44
15 2 0.06
16 2 0.06
17 7 0.22
18 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (14 bp):
AATAAAAAATATAA
Found at i:1980121 original size:22 final size:22
Alignment explanation
Indices: 1980096--1980143 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1980086 ATAAAAAAAT
* *
1980096 TAAACAATATTCAAATATTTAA
1 TAAAAAATATTCAAATAATTAA
* *
1980118 TAAAAAATTTTCGAATAATTAA
1 TAAAAAATATTCAAATAATTAA
1980140 -AAAA
1 TAAAA
1980144 GAAACAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAAAAATATTCAAATAATTAA
Found at i:1980940 original size:20 final size:20
Alignment explanation
Indices: 1980882--1980938 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1980872 ACTCAAACTT
1980882 CAAATTGGGCCCCTTAAACC
1 CAAATTGGGCCCCTTAAACC
1980902 CAAATTGGGCCCCTTAAACC
1 CAAATTGGGCCCCTTAAACC
1980922 CAAATTGGG-CCCTTAAA
1 CAAATTGGGCCCCTTAAA
1980939 ACACCACATG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
CAAATTGGGCCCCTTAAACC
Found at i:1984994 original size:582 final size:581
Alignment explanation
Indices: 1983847--1985011 Score: 2188
Period size: 582 Copynumber: 2.0 Consensus size: 581
1983837 TTGGTATTCG
1983847 AAAATAATTTCCTTAATTTTTTATTTATTAGAAAAAAATTTTCATTCTCGAGAAAAATAAATTAA
1 AAAATAATTTCCTTAATTTTTTATTTATTAGAAAAAAATTTTCATTCTCGAGAAAAATAAATTAA
1983912 AACATTTTTATTGAAATAATTCTTAAAATGTTTCAGTACGTTGGTAACATTAGAAGAACTTTTTC
66 AACATTTTTATTGAAATAATTCTTAAAATGTTTCAGTACGTTGGTAACATTAGAAGAACTTTTTC
1983977 TCACCTAAAGATTTTTTAGGCATCGCTTTTCAGAATACCTTAGAATCTCATCCTCGGAGGCTCAA
131 TCACCTAAAGATTTTTTAGGCATCGCTTTTCAGAATACCTTAGAATCTCATCCTCGGAGGCTCAA
*
1984042 ATTTACTTTTCATAAAAAAATGTCATGCATGCAATTCAAAATGTTACCATATTGATGCACACATT
196 ATTTACTTTTCATAAAAAAATATCATGCATGCAATTCAAAATGTTACCATATTGATGCACACATT
1984107 TTATTCTCCTTTGTTAGAAATTTTATTAATTATTTTATTAATATTTATTTTTAATTAAAATTTTG
261 TTATTCTCCTTTGTTAGAAATTTTATTAATTATTTTATTAATATTTATTTTTAATTAAAATTTTG
*
1984172 AAGAAAAAGGAATTTAATTATATTACAAATTTTCTATAAATATTCAAATACACTGGTAATATTTT
326 AAGAAAAAAGAATTTAATTATATTACAAATTTTCTATAAATATTCAAATACACTGGTAATATTTT
*
1984237 ACAAAAAATCTTCTCACATAGGGATTTCTTAAAGCATCTCTACTCGGAATACTTTTAGAATCCTA
391 ACAAAAAATCTTCTCACATAGGGATTTCTTAAAGCATCTCTACTCGAAATACTTTTAGAATCCTA
1984302 TTATTGGATAAAATTTTCTTTCTTCTCATTTTTATTACTTATATTTTAATTTATTAATTAATTTT
456 TTATTGGATAAAATTTTCTTTCTTCTCATTTTTATTACTTATATTTTAATTTATTAATTAATTTT
1984367 ATTTATTACTATTTTATAAGAAAAAAAAAGAAAATTTTTATTGTATTAAAAATTTTTTATA
521 ATTTATTACTATTTTATAAGAAAAAAAAAGAAAATTTTTATTGTATTAAAAATTTTTTATA
*
1984428 AAAATAATTTCCTTAATTTTTTATTTATTAGAAAAAAATTTTTTATTCTCGAGAAAAATAAATTA
1 AAAATAATTTCCTTAATTTTTTATTTATTAGAAAAAAA-TTTTCATTCTCGAGAAAAATAAATTA
*
1984493 AAACATTTTTATTGAAATAATTCTTAAAATGTTTTAGTACGTTGGTAACATTAGAAGAACTTTTT
65 AAACATTTTTATTGAAATAATTCTTAAAATGTTTCAGTACGTTGGTAACATTAGAAGAACTTTTT
* *
1984558 CTCACCTAGAGATTTTTTAGGCATCGCTTTTCAGAATACCTTAGACTCTCATCCTCGGAGGCTCA
130 CTCACCTAAAGATTTTTTAGGCATCGCTTTTCAGAATACCTTAGAATCTCATCCTCGGAGGCTCA
*
1984623 AATTTACTTTTCATAAAAAAATATCATGCATGCAATTCAAAATGTTACCCTATTGATGCACACAT
195 AATTTACTTTTCATAAAAAAATATCATGCATGCAATTCAAAATGTTACCATATTGATGCACACAT
*
1984688 TTTATTCTCCTTTGTTAGAAGTTTTATTAATTATTTTATTAATATTTATTTTTAATTAAAATTTT
260 TTTATTCTCCTTTGTTAGAAATTTTATTAATTATTTTATTAATATTTATTTTTAATTAAAATTTT
*
1984753 GAAGAAAAAAGAATTTAATTATATTACAAATTTTTTATAAATATTCAAATACACTGGTAATATTT
325 GAAGAAAAAAGAATTTAATTATATTACAAATTTTCTATAAATATTCAAATACACTGGTAATATTT
* *
1984818 TACAAAAAATCTTCTCACATAGGGATTTCTTAAAGCATCTCTATTTGAAATACTTTTAGAATCCT
390 TACAAAAAATCTTCTCACATAGGGATTTCTTAAAGCATCTCTACTCGAAATACTTTTAGAATCCT
1984883 ATTATTGGATAAAATTTTCTTTCTTCTCATTTTTATTACTTATATTTTTAATTTATTAATTAATT
455 ATTATTGGATAAAATTTTCTTTCTTCTCATTTTTATTACTTATA-TTTTAATTTATTAATTAATT
*
1984948 TTATTTATTACTATTTTATAAG-AAAAAAAAGAAAATTTTTATTGTATTGAAAATTTTTTATA
519 TTATTTATTACTATTTTATAAGAAAAAAAAAGAAAATTTTTATTGTATTAAAAATTTTTTATA
1985010 AA
1 AA
1985012 TACTCCAATA
Statistics
Matches: 569, Mismatches: 13, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
581 38 0.07
582 489 0.86
583 42 0.07
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (581 bp):
AAAATAATTTCCTTAATTTTTTATTTATTAGAAAAAAATTTTCATTCTCGAGAAAAATAAATTAA
AACATTTTTATTGAAATAATTCTTAAAATGTTTCAGTACGTTGGTAACATTAGAAGAACTTTTTC
TCACCTAAAGATTTTTTAGGCATCGCTTTTCAGAATACCTTAGAATCTCATCCTCGGAGGCTCAA
ATTTACTTTTCATAAAAAAATATCATGCATGCAATTCAAAATGTTACCATATTGATGCACACATT
TTATTCTCCTTTGTTAGAAATTTTATTAATTATTTTATTAATATTTATTTTTAATTAAAATTTTG
AAGAAAAAAGAATTTAATTATATTACAAATTTTCTATAAATATTCAAATACACTGGTAATATTTT
ACAAAAAATCTTCTCACATAGGGATTTCTTAAAGCATCTCTACTCGAAATACTTTTAGAATCCTA
TTATTGGATAAAATTTTCTTTCTTCTCATTTTTATTACTTATATTTTAATTTATTAATTAATTTT
ATTTATTACTATTTTATAAGAAAAAAAAAGAAAATTTTTATTGTATTAAAAATTTTTTATA
Found at i:1992260 original size:41 final size:41
Alignment explanation
Indices: 1992184--1992261 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
1992174 CCTCATTTTT
* * * * *
1992184 TTTTATTTTTTTTTATATTTTGTATTTTTTGATATTTGATA
1 TTTTAATTTTTTTGATATTTTATATTATATGATATTTGATA
1992225 TTTTAATTTTTTTGATATTTTATATATATAT-ATATTT
1 TTTTAATTTTTTTGATATTTTATAT-TATATGATATTT
1992262 TGGACAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 28 0.90
42 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (41 bp):
TTTTAATTTTTTTGATATTTTATATTATATGATATTTGATA
Found at i:1998932 original size:17 final size:17
Alignment explanation
Indices: 1998910--1998949 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
1998900 AATAAATATC
1998910 TTAGCTATTCAGCTTCT
1 TTAGCTATTCAGCTTCT
1998927 TTAGCTATTCAGCTTCT
1 TTAGCTATTCAGCTTCT
1998944 TTAGCT
1 TTAGCT
1998950 GTTGCAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.23, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGCTATTCAGCTTCT
Found at i:2006193 original size:24 final size:23
Alignment explanation
Indices: 2006166--2006222 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
2006156 AAGATTAAAG
*
2006166 CCATGAGTT-GTAATGGTCGGTGGA
1 CCATGAGTTAGT--TGGTCGATGGA
2006190 CCATGAGTTACGTTGGTCGATGGA
1 CCATGAGTTA-GTTGGTCGATGGA
2006214 CCATGAGTT
1 CCATGAGTT
2006223 CTTGTGGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 28 0.93
26 2 0.07
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (23 bp):
CCATGAGTTAGTTGGTCGATGGA
Found at i:2006792 original size:17 final size:18
Alignment explanation
Indices: 2006767--2006804 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2006757 TGGAGGGGTC
2006767 GAGAGAATCCAAGT-TGT
1 GAGAGAATCCAAGTGTGT
* *
2006784 GAGATAATCGAAGTGTGT
1 GAGAGAATCCAAGTGTGT
2006802 GAG
1 GAG
2006805 TGCCACCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.34, C:0.08, G:0.34, T:0.24
Consensus pattern (18 bp):
GAGAGAATCCAAGTGTGT
Found at i:2013391 original size:17 final size:17
Alignment explanation
Indices: 2013369--2013402 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2013359 CCAGTTCTAG
*
2013369 AAGGGTTTACGGATGCT
1 AAGGGTTTACAGATGCT
2013386 AAGGGTTTACAGATGCT
1 AAGGGTTTACAGATGCT
2013403 GACATGGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.29
Consensus pattern (17 bp):
AAGGGTTTACAGATGCT
Found at i:2015145 original size:8 final size:8
Alignment explanation
Indices: 2015125--2015165 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2015115 TTATTTTTTT
2015125 TAAA-ATA
1 TAAATATA
*
2015132 TAAATATT
1 TAAATATA
2015140 TAAATATA
1 TAAATATA
*
2015148 TAATTATA
1 TAAATATA
2015156 TAAATATA
1 TAAATATA
2015164 TA
1 TA
2015166 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAATATA
Found at i:2015178 original size:26 final size:24
Alignment explanation
Indices: 2015129--2015179 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
2015119 TTTTTTTAAA
* *
2015129 ATATAAATATTTAAATATATAATT
1 ATATAAATATTTAAATAAAAAATT
2015153 ATATAAATATATATAAATAAAAAATT
1 ATATAAATAT-T-TAAATAAAAAATT
2015179 A
1 A
2015180 ATTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
26 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAAATATTTAAATAAAAAATT
Found at i:2015851 original size:22 final size:22
Alignment explanation
Indices: 2015826--2015870 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2015816 GCAGCTTATA
2015826 CCTTTCATTTCTCACTGAACCG
1 CCTTTCATTTCTCACTGAACCG
2015848 CCTTTCATTTCTCACTGAACCG
1 CCTTTCATTTCTCACTGAACCG
2015870 C
1 C
2015871 TTGGGACCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.38, G:0.09, T:0.36
Consensus pattern (22 bp):
CCTTTCATTTCTCACTGAACCG
Found at i:2021934 original size:202 final size:202
Alignment explanation
Indices: 2021584--2021994 Score: 617
Period size: 202 Copynumber: 2.0 Consensus size: 202
2021574 GCAAATCTTA
* * * **
2021584 TGTTAAAGTGGGTTATCCCACATCTAATAAATTTTTGATATACTATAGTCTTATATTTAAGTCAG
1 TGTTAAAGTAGATTATCCCACATCTAATAAATCTTCAATATACTATAGTCTTATATTTAAGTCAG
2021649 GCCCCTCCACATACTGTCAATTAGTTTTAAGTTTGATGCTTAACATGGTATCAGAACCAAAACTT
66 GCCCCTCCACATACTGTCAATTAGTTTTAAGTTTGATGCTTAACATGGTATCAGAACCAAAACTT
* * *
2021714 TCTTTTCGTTGCCCTTTCCTAATTTGTCACGTGGAAAGCTTTTTTCATTTTCACTTACACGTGAT
131 TCTTTCCATTGCCCTTTCCTAATTTGTCACGTGGAAAACTTTTTTCATTTTCACTTACACGTGAT
**
2021779 GGGGGCT
196 AAGGGCT
* ** *
2021786 TGTTAAAGTAGATTATCCCACATTTAATAAATCTTCAATATTTTATAGTCTTATATTTAAGT-TG
1 TGTTAAAGTAGATTATCCCACATCTAATAAATCTTCAATATACTATAGTCTTATATTTAAGTCAG
* * * *
2021850 AGCCCCTTCACATATTGTCAATTAGTTTTAAGTTTGATGCTTAACATGGTATCAGAGCCAGAACT
66 -GCCCCTCCACATACTGTCAATTAGTTTTAAGTTTGATGCTTAACATGGTATCAGAACCAAAACT
* *
2021915 TTCTTTCCATTGTCCTTTCCTAATTTGTCACGTGGAAAACTTTTTTCATTTTCACTTTCACGTGA
130 TTCTTTCCATTGCCCTTTCCTAATTTGTCACGTGGAAAACTTTTTTCATTTTCACTTACACGTGA
*
2021980 TAAGGTCT
195 TAAGGGCT
2021988 TGTTAAA
1 TGTTAAA
2021995 TTGATTTTAA
Statistics
Matches: 187, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
201 1 0.01
202 186 0.99
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (202 bp):
TGTTAAAGTAGATTATCCCACATCTAATAAATCTTCAATATACTATAGTCTTATATTTAAGTCAG
GCCCCTCCACATACTGTCAATTAGTTTTAAGTTTGATGCTTAACATGGTATCAGAACCAAAACTT
TCTTTCCATTGCCCTTTCCTAATTTGTCACGTGGAAAACTTTTTTCATTTTCACTTACACGTGAT
AAGGGCT
Found at i:2026162 original size:3 final size:3
Alignment explanation
Indices: 2026154--2026198 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2026144 ATTTCTAAAT
2026154 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2026199 AAGATATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2038538 original size:2 final size:2
Alignment explanation
Indices: 2038531--2038584 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
2038521 AAGATTAATG
* * * *
2038531 TA TA TA TA TA TA TA TA TA TA TA -A TA TA CA TT TA TA TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2038572 TA TA TA CA TA TA T
1 TA TA TA TA TA TA T
2038585 TGGGTAGACG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2046225 original size:13 final size:11
Alignment explanation
Indices: 2046209--2046286 Score: 59
Period size: 11 Copynumber: 6.6 Consensus size: 11
2046199 GATAAAAGAT
2046209 AATATTATTGAA
1 AATATTATT-AA
*
2046221 TAATATTACTGAA
1 -AATATTA-TTAA
2046234 ATAATATTATTAA
1 A--ATATTATTAA
*
2046247 AAT-TAATTTAA
1 AATATTA-TTAA
2046258 AATATTATTAA
1 AATATTATTAA
**
2046269 AATATTACAAA
1 AATATTATTAA
2046280 AATATTA
1 AATATTA
2046287 CTTATAAGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 2 0.04
11 29 0.54
12 3 0.06
13 13 0.24
14 7 0.13
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (11 bp):
AATATTATTAA
Found at i:2046249 original size:14 final size:14
Alignment explanation
Indices: 2046179--2046249 Score: 63
Period size: 14 Copynumber: 5.0 Consensus size: 14
2046169 GACCCTTTAA
*
2046179 AATATTACTAAAAT
1 AATATTATTAAAAT
* *
2046193 ATTATTGATAAAAGAT
1 AATATT-ATTAAA-AT
*
2046209 AATATTATT-GAAT
1 AATATTATTAAAAT
* *
2046222 AATATTACTGAAAT
1 AATATTATTAAAAT
2046236 AATATTATTAAAAT
1 AATATTATTAAAAT
2046250 TAATTTAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
13 10 0.23
14 21 0.48
15 6 0.14
16 7 0.16
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (14 bp):
AATATTATTAAAAT
Found at i:2046281 original size:22 final size:21
Alignment explanation
Indices: 2046209--2046305 Score: 70
Period size: 22 Copynumber: 4.2 Consensus size: 21
2046199 GATAAAAGAT
2046209 AATATTATTGAATAATATTACTGAAA
1 AATATTATT-AA-AATATTA---AAA
*
2046235 TAATATTATTAAAATTAATT-TAA
1 -AATATTATTAAAA-T-ATTAAAA
2046258 AATATTATTAAAATATTACAAA
1 AATATTATTAAAATATTA-AAA
* *
2046280 AATATTACTTATAAGATTAAAA
1 AATATTA-TTAAAATATTAAAA
2046302 AATA
1 AATA
2046306 AAAGAAAAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
20 3 0.05
21 1 0.02
22 29 0.48
23 11 0.18
25 2 0.03
26 3 0.05
27 12 0.20
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (21 bp):
AATATTATTAAAATATTAAAA
Found at i:2046303 original size:23 final size:22
Alignment explanation
Indices: 2046256--2046303 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2046246 AAATTAATTT
* *
2046256 AAAATATTATTAAAATATTACA
1 AAAATATTATTAAAAGATTAAA
*
2046278 AAAATATTACTTATAAGATTAAA
1 AAAATATTA-TTAAAAGATTAAA
2046301 AAA
1 AAA
2046304 TAAAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATTATTAAAAGATTAAA
Found at i:2046442 original size:20 final size:20
Alignment explanation
Indices: 2046401--2046441 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2046391 ACGATTTTTG
2046401 AATTATAATAAAATATTTAA
1 AATTATAATAAAATATTTAA
* *
2046421 AATTATATTTAAAT-TTTAA
1 AATTATAATAAAATATTTAA
2046440 AA
1 AA
2046442 ACTTTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTATAATAAAATATTTAA
Found at i:2046590 original size:28 final size:28
Alignment explanation
Indices: 2046538--2046620 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 28
2046528 AAAATTTATC
**
2046538 ATATTAAAAAATAATATATTA-ATTAATAA
1 ATATTAAAATTTAA-ATATTATATTAA-AA
*
2046567 A-ATTATAATTTAAATATTATATTAAAA
1 ATATTAAAATTTAAATATTATATTAAAA
* *
2046594 ATTTTAAAATTTAAATAATATATTAAA
1 ATATTAAAATTTAAATATTATATTAAA
2046621 TATTTTATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 9 0.20
28 36 0.78
29 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATTAAAATTTAAATATTATATTAAAA
Found at i:2046625 original size:28 final size:28
Alignment explanation
Indices: 2046573--2046627 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2046563 ATAAAATTAT
*
2046573 AATTTAAATATTATATTAAAAATTTTAA
1 AATTTAAATAATATATTAAAAATTTTAA
*
2046601 AATTTAAATAATATATTAAATATTTTA
1 AATTTAAATAATATATTAAAAATTTTA
2046628 TTATAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTTAAATAATATATTAAAAATTTTAA
Found at i:2055101 original size:18 final size:18
Alignment explanation
Indices: 2055062--2055102 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2055052 AATTAATTAA
* *
2055062 ATAATCAATTATTATATC
1 ATAATCAATTAATAAATC
*
2055080 ATAATCAATTAATAAATT
1 ATAATCAATTAATAAATC
2055098 ATAAT
1 ATAAT
2055103 ATAACTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATCAATTAATAAATC
Found at i:2057097 original size:18 final size:18
Alignment explanation
Indices: 2057074--2057108 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2057064 TTTAACATTT
*
2057074 AAATTGATTTAATATATC
1 AAATTGACTTAATATATC
*
2057092 AAATTGACTTGATATAT
1 AAATTGACTTAATATAT
2057109 ATAATATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (18 bp):
AAATTGACTTAATATATC
Found at i:2058399 original size:22 final size:22
Alignment explanation
Indices: 2058373--2058419 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2058363 TGTTAAATAC
*
2058373 TTATTTAAATATAAATTAAAAG
1 TTATTTAAATACAAATTAAAAG
* * *
2058395 TTATTTAGATACAATTTAAAGG
1 TTATTTAAATACAAATTAAAAG
2058417 TTA
1 TTA
2058420 AAAATTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (22 bp):
TTATTTAAATACAAATTAAAAG
Found at i:2059502 original size:74 final size:72
Alignment explanation
Indices: 2059374--2059528 Score: 220
Period size: 74 Copynumber: 2.1 Consensus size: 72
2059364 TTCTTGCTTT
* * * *
2059374 TCAAATCTTCTTATCTCTTGAATAATATCTAATCAATTCTATGAAATTTTTCAAACAAATGTTAT
1 TCAAATCTTCTTATCTCTTGAATAATATCTAATCAATTCTATAAAATATCTCAAACAAATCTTAT
2059439 ATCAAAATA
66 ATC-AAA-A
* * * *
2059448 TCAAATCTTCTTATCTTTTGAGTAATATCTAATCAATTTTTTAAAATATCTCAAACAAATCTTAT
1 TCAAATCTTCTTATCTCTTGAATAATATCTAATCAATTCTATAAAATATCTCAAACAAATCTTAT
2059513 ATCAAAA
66 ATCAAAA
2059520 TCAAATCTT
1 TCAAATCTT
2059529 TTGATTTAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 10 0.14
73 3 0.04
74 60 0.82
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.41
Consensus pattern (72 bp):
TCAAATCTTCTTATCTCTTGAATAATATCTAATCAATTCTATAAAATATCTCAAACAAATCTTAT
ATCAAAA
Done.