Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 34 of 51
Found at i:6850988 original size:26 final size:25
Alignment explanation
Indices: 6850927--6850988 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
6850917 TTAATGAATA
6850927 TTTAATTCAGAATAATTAAAGAAGAT
1 TTTAATT-AGAATAATTAAAGAAGAT
* * * *
6850953 CTGATTTTAGAATAATTAAAATAAGAT
1 TTTA-ATTAGAATAATT-AAAGAAGAT
6850980 TTTAATTAG
1 TTTAATTAG
6850989 TTCAGAATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (25 bp):
TTTAATTAGAATAATTAAAGAAGAT
Found at i:6853298 original size:13 final size:13
Alignment explanation
Indices: 6853280--6853311 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
6853270 GATTTTCTTG
6853280 TTGAAAATCATTT
1 TTGAAAATCATTT
6853293 TTG-AAATCATTT
1 TTGAAAATCATTT
6853305 TTGAAAA
1 TTGAAAA
6853312 ATTACCCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTGAAAATCATTT
Found at i:6855156 original size:20 final size:19
Alignment explanation
Indices: 6855119--6855160 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
6855109 AGTTTTCACG
6855119 AAAACAACATAATTAAATCA
1 AAAACAACATAATTAAAT-A
*
6855139 AAAACAACA-ATTTAAAATA
1 AAAACAACATAATT-AAATA
6855158 AAA
1 AAA
6855161 TCATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAACAACATAATTAAATA
Found at i:6859903 original size:18 final size:18
Alignment explanation
Indices: 6859880--6859919 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6859870 TCCAACATTT
*
6859880 TTCTTTTTCTCCTTCTCC
1 TTCTTTGTCTCCTTCTCC
* *
6859898 TTCTTTGTCTCGTTCTTC
1 TTCTTTGTCTCCTTCTCC
6859916 TTCT
1 TTCT
6859920 CGGTGTCTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.05, T:0.62
Consensus pattern (18 bp):
TTCTTTGTCTCCTTCTCC
Found at i:6860728 original size:71 final size:72
Alignment explanation
Indices: 6860649--6860791 Score: 227
Period size: 71 Copynumber: 2.0 Consensus size: 72
6860639 TTTGATACCA
* * *
6860649 ATTGTTGAGTTAATCGATTGATGAATCGACCAAGAGG-GGGTGAATTGGCAATAAAA-TTTTCGG
1 ATTGTTGAGTTAATCAATCGATGAATCGACCAAGAGGAGGCTGAATTGGCAATAAAAGTTTT-GG
6860712 TGGAAGCT
65 TGGAAGCT
*
6860720 ATTGTTGAGTTAATCAATCGATGAATCGACCAAGAGGAGGCTGAATTGGTAATAAAAGTTTTGGT
1 ATTGTTGAGTTAATCAATCGATGAATCGACCAAGAGGAGGCTGAATTGGCAATAAAAGTTTTGGT
6860785 GGAAGCT
66 GGAAGCT
6860792 TTTGCAGAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
71 35 0.53
72 27 0.41
73 4 0.06
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (72 bp):
ATTGTTGAGTTAATCAATCGATGAATCGACCAAGAGGAGGCTGAATTGGCAATAAAAGTTTTGGT
GGAAGCT
Found at i:6862059 original size:20 final size:20
Alignment explanation
Indices: 6862021--6862061 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
6862011 TTGACCAAAG
*
6862021 GATCGATCCCATTGAAAAAA
1 GATCGATCCCATTCAAAAAA
6862041 GATCGATCCC-TTCACAAAAA
1 GATCGATCCCATTCA-AAAAA
6862061 G
1 G
6862062 GATTGATCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (20 bp):
GATCGATCCCATTCAAAAAA
Found at i:6870368 original size:24 final size:24
Alignment explanation
Indices: 6870329--6870377 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
6870319 ATTGAAGTGT
*
6870329 AAATAAATAAATTAAATATACTAA
1 AAATAAATAAATTAAAAATACTAA
*
6870353 AAATAAATGAAA-TAAAAATGCTAA
1 AAATAAAT-AAATTAAAAATACTAA
6870377 A
1 A
6870378 GTTTAGGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (24 bp):
AAATAAATAAATTAAAAATACTAA
Found at i:6873915 original size:18 final size:18
Alignment explanation
Indices: 6873892--6873929 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6873882 TTCATGCATC
6873892 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGT
*
6873910 TAGTTCATTGAATAATGT
1 TAGTTCATTGAATAAAGT
6873928 TA
1 TA
6873930 TTTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (18 bp):
TAGTTCATTGAATAAAGT
Found at i:6874897 original size:17 final size:17
Alignment explanation
Indices: 6874875--6874946 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
6874865 AATTAAGAGT
6874875 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
6874892 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
6874909 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
6874926 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
6874944 TAG
1 TAG
6874947 ATGCATGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 32 0.70
18 14 0.30
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:6879804 original size:31 final size:30
Alignment explanation
Indices: 6879766--6879862 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 30
6879756 TTTAAAAAAT
6879766 AATTTAGAATGTTAATGTGAAATAATTTAAG
1 AATTTAGAATGTTAA-GTGAAATAATTTAAG
* * *
6879797 AATTTAGAATGTTACGGTGACAA-AAATTATG
1 AATTTAGAATGTTA-AGTGA-AATAATTTAAG
* * *
6879828 AAATTAGAATATTAGAGTGAAATAATTTGAG
1 AATTTAGAATGTTA-AGTGAAATAATTTAAG
6879859 AATT
1 AATT
6879863 ATGAAAAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
30 2 0.04
31 48 0.92
32 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (30 bp):
AATTTAGAATGTTAAGTGAAATAATTTAAG
Found at i:6880821 original size:24 final size:24
Alignment explanation
Indices: 6880789--6880853 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
6880779 GAACAAATGA
* *
6880789 AAAATCATAAATGCAATATAAAAAT
1 AAAA-CATAAATACAACATAAAAAT
* *
6880814 AAAGCATAAATACAACATAAAATT
1 AAAACATAAATACAACATAAAAAT
6880838 AAAACATAAATA-AACA
1 AAAACATAAATACAACA
6880854 ATTAACGACT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 4 0.11
24 28 0.80
25 3 0.09
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (24 bp):
AAAACATAAATACAACATAAAAAT
Found at i:6881621 original size:22 final size:22
Alignment explanation
Indices: 6881596--6881642 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
6881586 TATATTATTT
*
6881596 AAATTATTTATGTTTATGTGTA
1 AAATTATTTACGTTTATGTGTA
6881618 AAATTATTTACGTTTATGTGTA
1 AAATTATTTACGTTTATGTGTA
6881640 AAA
1 AAA
6881643 AAATTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
AAATTATTTACGTTTATGTGTA
Found at i:6881648 original size:22 final size:22
Alignment explanation
Indices: 6881601--6881648 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
6881591 TATTTAAATT
* **
6881601 ATTTATGTTTATGTGTAAAATT
1 ATTTACGTTTATGTGTAAAAAA
6881623 ATTTACGTTTATGTGTAAAAAA
1 ATTTACGTTTATGTGTAAAAAA
6881645 ATTT
1 ATTT
6881649 TGTTATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTTACGTTTATGTGTAAAAAA
Found at i:6885058 original size:31 final size:31
Alignment explanation
Indices: 6884997--6885086 Score: 126
Period size: 31 Copynumber: 2.8 Consensus size: 31
6884987 AATGGTAATA
*
6884997 AACAAAATTAACAAAATAAATAAACAAAAAAGTCC
1 AACAAAATTAACAAAATAAAT----TAAAAAGTCC
6885032 AACAAAATTAACAAAATAAATTAAAAAGTCC
1 AACAAAATTAACAAAATAAATTAAAAAGTCC
*
6885063 AACCAAATTAACAAAATAAATTAA
1 AACAAAATTAACAAAATAAATTAA
6885087 GTATTAAATG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
31 32 0.60
35 21 0.40
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.18
Consensus pattern (31 bp):
AACAAAATTAACAAAATAAATTAAAAAGTCC
Found at i:6886284 original size:64 final size:66
Alignment explanation
Indices: 6886214--6886359 Score: 208
Period size: 64 Copynumber: 2.2 Consensus size: 66
6886204 TGGACCCTTA
*
6886214 GTGCATCGATGCATCAAGTGCATTCAATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGG-C
1 GTGCATCGATGCATCAAGTGCATTCAATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGGAC
6886276 TG
65 TG
* * * *
6886278 GTGCATCGATGCATCAATTGCATTCAATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAGTGCATTCAATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGACT
6886343 G
66 G
*
6886344 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
6886360 CTTTGATAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
64 28 0.38
65 25 0.34
66 20 0.27
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (66 bp):
GTGCATCGATGCATCAAGTGCATTCAATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGACT
G
Found at i:6887036 original size:14 final size:15
Alignment explanation
Indices: 6887017--6887046 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6887007 TTCAAACATT
6887017 AAACAATCCA-AAAC
1 AAACAATCCAGAAAC
6887031 AAACAATCCAGAAAC
1 AAACAATCCAGAAAC
6887046 A
1 A
6887047 TCAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.63, C:0.27, G:0.03, T:0.07
Consensus pattern (15 bp):
AAACAATCCAGAAAC
Found at i:6888997 original size:23 final size:23
Alignment explanation
Indices: 6888971--6889029 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
6888961 TACATGGCCT
6888971 TGTGCATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
* * * *
6888994 TGTGCATCGGTTCACCTTCATGG
1 TGTGCATCGATGCACATTCAAGG
6889017 TGT--ATCGATGCAC
1 TGTGCATCGATGCAC
6889030 TGTTAGGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 8 0.27
23 22 0.73
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (23 bp):
TGTGCATCGATGCACATTCAAGG
Found at i:6892516 original size:13 final size:14
Alignment explanation
Indices: 6892498--6892535 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
6892488 CAAAACCAAT
6892498 AGCAAGCAACGA-G
1 AGCAAGCAACGACG
6892511 AGCAAGCAACGACG
1 AGCAAGCAACGACG
*
6892525 ACCAA-CAACGA
1 AGCAAGCAACGA
6892536 AAAGAAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.47, C:0.29, G:0.24, T:0.00
Consensus pattern (14 bp):
AGCAAGCAACGACG
Found at i:6898654 original size:2 final size:2
Alignment explanation
Indices: 6898647--6898673 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6898637 ATTTATCCTT
6898647 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 T
6898674 CCTTTGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6898980 original size:24 final size:27
Alignment explanation
Indices: 6898953--6899004 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 27
6898943 TATTAGACTC
6898953 ATCTAGCAAAG-AA-G-AAAAAGAAAA
1 ATCTAGCAAAGAAAGGAAAAAAGAAAA
6898977 ATCTAGCAAAGAAAGGAAAAAAGAAAA
1 ATCTAGCAAAGAAAGGAAAAAAGAAAA
6899004 A
1 A
6899005 AGAGGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 11 0.44
25 2 0.08
26 1 0.04
27 11 0.44
ACGTcount: A:0.67, C:0.08, G:0.17, T:0.08
Consensus pattern (27 bp):
ATCTAGCAAAGAAAGGAAAAAAGAAAA
Found at i:6899006 original size:19 final size:19
Alignment explanation
Indices: 6898984--6899078 Score: 87
Period size: 19 Copynumber: 5.2 Consensus size: 19
6898974 AAAATCTAGC
6898984 AAAGAAAGGAAAAAAGAAA
1 AAAGAAAGGAAAAAAGAAA
6899003 AAAG--AGGAAAAAAG-AA
1 AAAGAAAGGAAAAAAGAAA
*
6899019 AAA-AAAGGAAAGAAATAGAA
1 AAAGAAAGGAAA-AAAGA-AA
6899039 AAAGAAA--AAGAAAAGAAA
1 AAAGAAAGGAA-AAAAGAAA
*
6899057 AACAGAAAAG-AAAAAGAAA
1 AA-AGAAAGGAAAAAAGAAA
6899076 AAA
1 AAA
6899079 ATTGAATCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 21
0.74 0.02 0.24
Matches are distributed among these distances:
16 5 0.08
17 16 0.25
18 8 0.12
19 25 0.39
20 7 0.11
21 3 0.05
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (19 bp):
AAAGAAAGGAAAAAAGAAA
Found at i:6899020 original size:6 final size:6
Alignment explanation
Indices: 6899011--6899077 Score: 73
Period size: 6 Copynumber: 10.8 Consensus size: 6
6899001 AAAAAGAGGA
* * *
6899011 AAAAAG AAAAAA AAGGAAAG AAATAG AAAAAG AAAAAG -AAAAG AAAAAC
1 AAAAAG AAAAAG AA--AAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
6899060 AGAAAAG AAAAAG AAAAA
1 A-AAAAG AAAAAG AAAAA
6899078 AATTGAATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 5 0.10
6 36 0.71
7 5 0.10
8 5 0.10
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:6899065 original size:13 final size:12
Alignment explanation
Indices: 6898995--6899076 Score: 63
Period size: 12 Copynumber: 7.3 Consensus size: 12
6898985 AAGAAAGGAA
6898995 AAAAGAAAAAAG
1 AAAAGAAAAAAG
*
6899007 --AGGAAAAAAG
1 AAAAGAAAAAAG
6899017 --AA-AAAAAAG
1 AAAAGAAAAAAG
* *
6899026 GAAAG-AAATAG
1 AAAAGAAAAAAG
6899037 AAAA-AGAAAAAG
1 AAAAGA-AAAAAG
6899049 AAAAGAAAAACAG
1 AAAAGAAAAA-AG
6899062 AAAAG-AAAAAG
1 AAAAGAAAAAAG
6899073 AAAA
1 AAAA
6899077 AAATTGAATC
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
9 7 0.12
10 10 0.17
11 16 0.28
12 17 0.29
13 8 0.14
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:6903685 original size:50 final size:54
Alignment explanation
Indices: 6903505--6903710 Score: 253
Period size: 54 Copynumber: 3.9 Consensus size: 54
6903495 AGAAATCTTG
* * * * *
6903505 GCAGAAGCCATAGAAAAGGATGAATGTGTTGTCAAACGCTTTACGAACGTCTGA
1 GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
6903559 GCAGAAACCACA-AGAAAGAATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAACCACAGA-AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* * *
6903613 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC-ATC-TC-GA
1 GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* *
6903664 -CAGAAACCATAGGAAAA-GATGAATGTATTGTCAAATGTTTTACGAAC
1 GCAGAAACCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
6903711 CAGTGATTAT
Statistics
Matches: 133, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
50 33 0.25
51 9 0.07
52 2 0.02
53 3 0.02
54 85 0.64
55 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (54 bp):
GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
Found at i:6904106 original size:22 final size:22
Alignment explanation
Indices: 6904077--6904131 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
6904067 ATCTACACTC
6904077 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
6904099 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
6904121 TTCAAAGATGA
1 TTCAAAGATGA
6904132 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:6904830 original size:40 final size:40
Alignment explanation
Indices: 6904775--6904875 Score: 193
Period size: 40 Copynumber: 2.5 Consensus size: 40
6904765 TTACCAGGTC
6904775 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
6904815 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
*
6904855 AAGTTCATAATGAGAAGAACT
1 GAGTTCATAATGAGAAGAACT
6904876 TGTTCAATTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.46, C:0.10, G:0.26, T:0.19
Consensus pattern (40 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:6904841 original size:153 final size:153
Alignment explanation
Indices: 6904662--6904988 Score: 582
Period size: 153 Copynumber: 2.1 Consensus size: 153
6904652 TTTTGAGGTA
6904662 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
6904727 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAG
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTAGAGTTCATAATGAGAAG
*
6904792 AACTCATCTGAAGAAGGAAGAAG
131 AACTCATCTGAAGAAAGAAGAAG
6904815 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* **
6904880 CAATTTTTCGCTTGAATTCATCATTCGATGGATCAACATTGTCAGGTAGAGTTCATAATGAGAAG
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTAGAGTTCATAATGAGAAG
*
6904945 AACTCATCTGAAGAAAGAAGAAT
131 AACTCATCTGAAGAAAGAAGAAG
* *
6904968 AAGTTCATAATAAGAAGAACT
1 GAGTTCATAATGAGAAGAACT
6904989 TGTTAAACCT
Statistics
Matches: 166, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
153 166 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (153 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTAGAGTTCATAATGAGAAG
AACTCATCTGAAGAAAGAAGAAG
Found at i:6904933 original size:113 final size:119
Alignment explanation
Indices: 6904815--6905619 Score: 757
Period size: 123 Copynumber: 6.7 Consensus size: 119
6904805 AAGGAAGAAG
6904815 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
6904880 CAA-TTTT-TCG-CT-TGAAT-TC-ATCAT-TCGAT-GGATCAACATTGT-CAG-GTA
66 CAACTTTTCTCGACTCT--ATCCCAAGCATATAGATAGCATCAACATT-TCCAGAG-A
* * *
6904928 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAATAAGTTCATAATAAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
6904993 AAACCTTTTGCTCGACTCTATCCCAGAAGGATATAGATCAGCATCAACATTTCCAGAGA
66 CAA-CTTTT-CTCGACTCTATCCC--AAGCATATAGAT-AGCATCAACATTTCCAGAGA
* *
6905052 AAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
6905116 CAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAACATTTCCAGAGA
66 CAA-CTTTT-CTCGACTCTATC-C-CAAGCATATAGAT-AGCATCAACATTTCCAGAGA
* * *
6905175 CAGCTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
6905239 AAACCTTTTGCTCGACTCTATCCCAGAAGGATATAGATCAGCATCAACATTTCCAGAGA
66 CAA-CTTTT-CTCGACTCTATCCC--AAGCATATAGAT-AGCATCAACATTTCCAGAGA
* *
6905298 AAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
6905362 CAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGATCAACATC-ACATTTCCAGAGA
66 CAA-CTTTT-CTCGACTCTATC-C-CAAGCATATAGAT-AGCATCAACATTTCCAGAGA
* * *
6905420 CAG--C-TCATGAGAAGAAACTCATCTG-AG-AGGAAGAAAAAGTTCATAATGAGAAGAACTTGT
1 GAGTTCATAATGAGAAG-AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * ** *
6905480 TCAACCTTTTGCTTGATTCTATCACATA--AGGTAGATCAACATCAAC-TTTCCCAGA-A
65 TCAA-CTTTT-CTCGACTCTATCCCA-AGCATATAGAT-AGCATCAACATTT-CCAGAGA
* * *
6905536 GAAGTTCATAATGAAAAGAACTCATCT---GAA-GAAGAAGAAGTTCGTAATGAGAAGAACTTAT
1 G-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
6905597 TCAACATTTGGT-TCGACTCTATC
65 TCAAC-TTT--TCTCGACTCTATC
6905620 GTAGAAGGAT
Statistics
Matches: 608, Mismatches: 51, Indels: 62
0.84 0.07 0.09
Matches are distributed among these distances:
113 64 0.11
115 4 0.01
116 19 0.03
117 60 0.10
118 5 0.01
119 76 0.12
120 19 0.03
121 3 0.00
122 20 0.03
123 292 0.48
124 45 0.07
125 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (119 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTCTCGACTCTATCCCAAGCATATAGATAGCATCAACATTTCCAGAGA
Found at i:6905131 original size:123 final size:123
Alignment explanation
Indices: 6904929--6905644 Score: 1017
Period size: 123 Copynumber: 5.9 Consensus size: 123
6904919 TGTCAGGTAG
* * * *
6904929 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAATAAGTTCATAATAAGAAGAACTTGTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
6904994 AACCTTTTGCTCGACTCTATCCCAGAAGGATATAGATCAGCATCAACATTTCCAGAGAA
65 AACCTTTTGCTCGACTCTATCGCAGAAGGATATAGATCAACATCAACATTTCCAGAGAA
*
6905053 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
6905118 ACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCAACATTTCCAGAGAC
66 ACCTTTTGCTCGACTCTATCGCAGAAGGATATAGATCAACATCAACATTTCCAGAGAA
* * *
6905176 AGCTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
6905241 ACCTTTTGCTCGACTCTATCCCAGAAGGATATAGATCAGCATCAACATTTCCAGAGAA
66 ACCTTTTGCTCGACTCTATCGCAGAAGGATATAGATCAACATCAACATTTCCAGAGAA
*
6905299 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
6905364 ACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGATCAACATC-ACATTTCCAGAGAC
66 ACCTTTTGCTCGACTCTATCGCAGAAGGATATAGATCAACATCAACATTTCCAGAGAA
* *
6905421 AG--C-TCATGAGAAGAAACTCATCTG-AGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAG-AACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
6905482 AACCTTTTGCTTGATTCTATCACATAAGG---TAGATCAACATCAAC-TTTCCCAGA-AGA
65 AACCTTTTGCTCGACTCTATCGCAGAAGGATATAGATCAACATCAACATTT-CCAGAGA-A
* * *
6905538 AGTTCATAATGAAAAGAACTCATCTG-A-A-GAAGAAGAAGTTCGTAATGAGAAGAACTTATTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * *
6905600 ACATTTGGTTCGACTCTATCGTAGAAGGATATAGAGCAACATCAA
66 ACCTTTTGCTCGACTCTATCGCAGAAGGATATAGATCAACATCAA
6905645 TGTTCAACCT
Statistics
Matches: 535, Mismatches: 47, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
116 16 0.03
117 60 0.11
118 1 0.00
119 82 0.15
120 32 0.06
122 15 0.03
123 300 0.56
124 29 0.05
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (123 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTCGACTCTATCGCAGAAGGATATAGATCAACATCAACATTTCCAGAGAA
Found at i:6906141 original size:13 final size:14
Alignment explanation
Indices: 6906121--6906161 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
6906111 CACCAAAACC
6906121 ACGAGCAAGCAACG
1 ACGAGCAAGCAACG
6906135 A-GAGCAAGCAACG
1 ACGAGCAAGCAACG
*
6906148 ACGACCAA-CAACG
1 ACGAGCAAGCAACG
6906161 A
1 A
6906162 AAAGAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.46, C:0.29, G:0.24, T:0.00
Consensus pattern (14 bp):
ACGAGCAAGCAACG
Found at i:6907427 original size:22 final size:22
Alignment explanation
Indices: 6907374--6907428 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
6907364 CTCTTTTCTG
6907374 ATATTTTTGA-A-TAAATAAAT
1 ATATTTTTGATATTAAATAAAT
**
6907394 ATATTACT-ATATTAAAATAAA-
1 ATATTTTTGATATT-AAATAAAT
6907415 ATATTTTTGATATT
1 ATATTTTTGATATT
6907429 TATTTATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 1 0.04
20 7 0.26
21 7 0.26
22 12 0.44
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
ATATTTTTGATATTAAATAAAT
Found at i:6908834 original size:117 final size:117
Alignment explanation
Indices: 6908615--6908835 Score: 277
Period size: 117 Copynumber: 1.9 Consensus size: 117
6908605 TTTTAAATCA
* *
6908615 AAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGAGTTT
1 AAATTTTCTTTTTCAATACTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTTT
* *
6908680 ATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTTTTTAATTTG
66 ATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTTTTTAATTTG
* * * *
6908732 AAATTTTCTTTTTCAA-AGTTTTCAAATTTTAGTTTTGAAAGCTCTAACTCCTTTTTCAACA-TT
1 AAATTTTCTTTTTCAATA-CTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTT
* * * **
6908795 TCATTTTGCTTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
65 T-ATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
6908836 ATCATTTTTA
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 4 0.05
117 80 0.91
118 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (117 bp):
AAATTTTCTTTTTCAATACTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTTT
ATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTTTTTAATTTG
Found at i:6910174 original size:65 final size:65
Alignment explanation
Indices: 6910037--6910196 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
6910027 TGCACTAAGA
* * *
6910037 GTGCATCGATTCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCAATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGGTTG
* * * *
6910101 GTGGATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCAATGCATGGT-
6910165 T-
64 TG
* * *
6910166 GTGCATCGACGCATGAAATGCATTTGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
6910197 CAATTTAATT
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 26 0.32
65 52 0.63
66 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGGTTG
Found at i:6912297 original size:30 final size:29
Alignment explanation
Indices: 6912257--6912320 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
6912247 ATTAACGGCC
*
6912257 GGTGGTTTGATTGAA-TCAATTAAATAGTTG
1 GGTGGCTTGATT-AATTCAATTAAA-AGTTG
* *
6912287 GGTGGCTTGATTAATTCAATTGAAAGTTT
1 GGTGGCTTGATTAATTCAATTAAAAGTTG
6912316 GGTGG
1 GGTGG
6912321 TTATATTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.39
Consensus pattern (29 bp):
GGTGGCTTGATTAATTCAATTAAAAGTTG
Found at i:6913109 original size:19 final size:19
Alignment explanation
Indices: 6913080--6913124 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
6913070 TTTTTTTATC
*
6913080 TAAAT-AAATAAAAATTAAA
1 TAAATAAAAT-AAAATAAAA
6913099 T-AATAAAATAAAATAAAA
1 TAAATAAAATAAAATAAAA
6913117 TAAATAAA
1 TAAATAAA
6913125 CTACTGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAATAAAATAAAATAAAA
Found at i:6913850 original size:29 final size:28
Alignment explanation
Indices: 6913793--6913850 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
6913783 AACAAAATCT
** *
6913793 TTCAATTCTCTCCTTTTTTTCCTCTTTG
1 TTCAATTCTCTCCTTTTTGCCCTATTTG
6913821 TTCAA-TCTCTCTCTTTTTGCCCTATGTTG
1 TTCAATTCTCTC-CTTTTTGCCCTAT-TTG
6913850 T
1 T
6913851 GGGGTTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 6 0.24
28 15 0.60
29 4 0.16
ACGTcount: A:0.09, C:0.28, G:0.07, T:0.57
Consensus pattern (28 bp):
TTCAATTCTCTCCTTTTTGCCCTATTTG
Found at i:6914995 original size:146 final size:143
Alignment explanation
Indices: 6914639--6915164 Score: 535
Period size: 146 Copynumber: 3.7 Consensus size: 143
6914629 GATCTGTCGT
* * * *
6914639 CGTCCACCGTCCGATCGTCCT-ACTTTTTTAATATGTTGTTTGTGTTGACATCGCACAACTTTTC
1 CGTCCACCGTCCGATCGTCTTGA--TTTTTAGTATGTTGTTCGTGTTGACATCGCACAACTTTTG
** * * * *
6914703 ACCGTTCGGAACGTTGATCGGAGAACCCGATCGCTGACAAGAGGCCTAAAACCGTCCGGATTTGT
64 ACCGTTCGGAATATTGATCGGAGATCCCGATCGCCGACCAGAGGCCAAAAACCGTCCGGATTTGT
*
6914768 TTTCTCTGA-T---C
129 TTTCTCCGATTCCCC
* * *
6914779 CG-ACACCGTCCGATCGTCTTGATTGTTTAGTATGTTGTTCGTGTTGATATCGCGCAACTTTTGA
1 CGTCCACCGTCCGATCGTCTTGATT-TTTAGTATGTTGTTCGTGTTGACATCGCACAACTTTTGA
** * *** *
6914843 ATGTTCGGAATATTGATCGGAGTTTTTGATCGCCGACCGGAGGCCAAAAACCGTCCGGATTTGTT
65 CCGTTCGGAATATTGATCGGAGATCCCGATCGCCGACCAGAGGCCAAAAACCGTCCGGATTTGTT
6914908 TTCTCCGATTCGCCAC
130 TTCTCCGATTC-CC-C
* *
6914924 CGTCCACCGTCCAATCGTCTTGATTTTTCAGTATGTTGTTCGTGTTGACATCGCACAACTTTTTA
1 CGTCCACCGTCCGATCGTCTTGATTTTT-AGTATGTTGTTCGTGTTGACATCGCACAACTTTTGA
* * *** * *
6914989 CCGTTCGGAATATTGATCGGAGGTCCCGATCGTCGACCAGAGGCCAAAAAATTTTCGGTTTTGTT
65 CCGTTCGGAATATTGATCGGAGATCCCGATCGCCGACCAGAGGCCAAAAACCGTCCGGATTTGTT
*
6915054 TTCTCCGATCCACCGC
130 TTCTCCGATTC-CC-C
* ** * * * * * *
6915070 CATCCACCGT-CGATCGTCCTAAATTTTTAGTATGTTGTTCTTGCTGGCCTTGCGCAACTTTTGA
1 CGTCCACCGTCCGATCGT-CTTGATTTTTAGTATGTTGTTCGTGTTGACATCGCACAACTTTTGA
* * *
6915134 CCGTTCAGAATATTGATCGGAAATCTCGATC
65 CCGTTCGGAATATTGATCGGAGATCCCGATC
6915165 ACCGGCGAGA
Statistics
Matches: 318, Mismatches: 57, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
138 2 0.01
139 109 0.34
140 4 0.01
145 68 0.21
146 135 0.42
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (143 bp):
CGTCCACCGTCCGATCGTCTTGATTTTTAGTATGTTGTTCGTGTTGACATCGCACAACTTTTGAC
CGTTCGGAATATTGATCGGAGATCCCGATCGCCGACCAGAGGCCAAAAACCGTCCGGATTTGTTT
TCTCCGATTCCCC
Found at i:6924121 original size:24 final size:24
Alignment explanation
Indices: 6924089--6924153 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
6924079 GAACAAATGA
* *
6924089 AAAATCATAAATGCAATATAAAAAT
1 AAAA-CATAAATACAACATAAAAAT
*
6924114 AAAGCATAAATACAACATAAAAAT
1 AAAACATAAATACAACATAAAAAT
6924138 AAAACATAAATA-AACA
1 AAAACATAAATACAACA
6924154 GTTAACGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 4 0.11
24 29 0.81
25 3 0.08
ACGTcount: A:0.68, C:0.11, G:0.03, T:0.18
Consensus pattern (24 bp):
AAAACATAAATACAACATAAAAAT
Found at i:6925259 original size:21 final size:22
Alignment explanation
Indices: 6925233--6925278 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
6925223 TGCAATTTTT
6925233 TTAAAAAAATCATT-ATATATA
1 TTAAAAAAATCATTAATATATA
* *
6925254 TTAAAAAATTCATTAATATGTA
1 TTAAAAAAATCATTAATATATA
6925276 TTA
1 TTA
6925279 CAAATTTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAAAAAAATCATTAATATATA
Found at i:6925272 original size:22 final size:22
Alignment explanation
Indices: 6925233--6925292 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
6925223 TGCAATTTTT
*
6925233 TTAAAAAAATCATT-ATATATA
1 TTAAAAAATTCATTAATATATA
*
6925254 TTAAAAAATTCATTAATATGTA
1 TTAAAAAATTCATTAATATATA
* *
6925276 TTACAAATTTCCATTAA
1 TTAAAAAATT-CATTAA
6925293 ATTTTCTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.39
22 14 0.42
23 6 0.18
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAAAAATTCATTAATATATA
Found at i:6925348 original size:30 final size:29
Alignment explanation
Indices: 6925299--6925360 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
6925289 TTAAATTTTC
* *
6925299 TTTTTAAAACAATTCATCAAATTATATAT
1 TTTTTAAAAAAAATCATCAAATTATATAT
6925328 TTTTTAAAAAAAAATCATCAAATTATATAT
1 TTTTT-AAAAAAAATCATCAAATTATATAT
6925358 TTT
1 TTT
6925361 AAAAATTCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTTTAAAAAAAATCATCAAATTATATAT
Found at i:6925439 original size:29 final size:29
Alignment explanation
Indices: 6925377--6925458 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 29
6925367 TCCGTAAAGT
*
6925377 TTATTTTTTAATATTTCA-TAAAAAAATA
1 TTATTTTTTAAAATTTCACTAAAAAAATA
* *
6925405 TATATTTTTGTAAAATTTCACTAAACATA-A
1 T-TATTTTT-TAAAATTTCACTAAAAAAATA
6925435 TTA-TTTTTAAAGATTTCACTAAAA
1 TTATTTTTTAAA-ATTTCACTAAAA
6925459 TACCAACATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 4 0.09
28 16 0.35
29 9 0.20
30 11 0.24
31 6 0.13
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (29 bp):
TTATTTTTTAAAATTTCACTAAAAAAATA
Found at i:6926226 original size:17 final size:16
Alignment explanation
Indices: 6926197--6926261 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 16
6926187 TTACAATTAA
*
6926197 TTTAAATAATAATTTG
1 TTTAAAAAATAATTTG
6926213 TTTAAACAAATAATTTG
1 TTTAAA-AAATAATTTG
*
6926230 TTGTAAGGAAAATAATTTA
1 TT-TAA--AAAATAATTTG
6926249 TTTAAATAAATAA
1 TTTAAA-AAATAA
6926262 AGGTTGGTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 7 0.17
17 17 0.40
18 6 0.14
19 11 0.26
20 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.42
Consensus pattern (16 bp):
TTTAAAAAATAATTTG
Found at i:6926300 original size:16 final size:16
Alignment explanation
Indices: 6926281--6926316 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6926271 CGATTAACGG
6926281 TTAAAAAATAATTTAT
1 TTAAAAAATAATTTAT
* *
6926297 TTAAAAAATATTTTTT
1 TTAAAAAATAATTTAT
6926313 TTAA
1 TTAA
6926317 TTTTCAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAAAATAATTTAT
Found at i:6926326 original size:66 final size:68
Alignment explanation
Indices: 6926256--6926391 Score: 168
Period size: 66 Copynumber: 2.0 Consensus size: 68
6926246 TTATTTAAAT
* * **
6926256 AAATAAAGGTTGGTTCGATTAACGGTT-AAAAAATAATTTATTTAAA-AAATATTTTTTTTAATT
1 AAATAAAGGTTAGTTCGATTAACGGTTAAAAAAATAATTTATTTAAATAAATAATTAGTTTAATT
6926319 TTC
66 TTC
** *
6926322 AAATAAATTTTAGTTCGATTAATGGTTAAAGAAAAAATAATTTATTTAAATAAATAATTAGTTTA
1 AAATAAAGGTTAGTTCGATTAACGGTT--A-AAAAAATAATTTATTTAAATAAATAATTAGTTTA
6926387 ATTTT
63 ATTTT
6926392 TTATCATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
66 23 0.40
70 19 0.33
71 16 0.28
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (68 bp):
AAATAAAGGTTAGTTCGATTAACGGTTAAAAAAATAATTTATTTAAATAAATAATTAGTTTAATT
TTC
Found at i:6928475 original size:14 final size:15
Alignment explanation
Indices: 6928452--6928490 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
6928442 TTATTTATCT
6928452 AAATAAATAAAAATA
1 AAATAAATAAAAATA
*
6928467 ATA-AAAT-AAAATA
1 AAATAAATAAAAATA
6928480 AAATAAATAAA
1 AAATAAATAAA
6928491 CTACTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
13 8 0.40
14 8 0.40
15 4 0.20
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAAATAAAAATA
Found at i:6928483 original size:18 final size:19
Alignment explanation
Indices: 6928452--6928490 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
6928442 TTATTTATCT
6928452 AAATAAATAAAAAT-AATA
1 AAATAAATAAAAATAAATA
6928470 AAATAAA-ATAAAATAAATA
1 AAATAAATA-AAAATAAATA
6928489 AA
1 AA
6928491 CTACTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 12 0.63
19 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
AAATAAATAAAAATAAATA
Found at i:6929943 original size:5 final size:5
Alignment explanation
Indices: 6929933--6929962 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
6929923 CGATGTTACG
*
6929933 GGGGA GGGGA GGGGA GGGGA AGGGA GGGGA
1 GGGGA GGGGA GGGGA GGGGA GGGGA GGGGA
6929963 AAAAGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (5 bp):
GGGGA
Found at i:6930133 original size:19 final size:19
Alignment explanation
Indices: 6930111--6930147 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6930101 GTAATCAAGA
6930111 TAATGATTTATAATTGAGG
1 TAATGATTTATAATTGAGG
6930130 TAATGATTTATAATTGAG
1 TAATGATTTATAATTGAG
6930148 AAGTAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (19 bp):
TAATGATTTATAATTGAGG
Found at i:6939549 original size:21 final size:21
Alignment explanation
Indices: 6939520--6939597 Score: 79
Period size: 23 Copynumber: 3.6 Consensus size: 21
6939510 CATGGGAGGT
6939520 ATCGATTCCC-TCAAGGAGGGA
1 ATCGATTCCCTTCAAGG-GGGA
*
6939541 ATCGGTTCCCATTCAAAGGGGGA
1 ATCGATTCCC-TTC-AAGGGGGA
*
6939564 ATC-AGTTCCCCTTCAAGGGGGT
1 ATCGA-TT-CCCTTCAAGGGGGA
6939586 ATCGATTCCCTT
1 ATCGATTCCCTT
6939598 TGCACTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
21 14 0.29
22 12 0.25
23 15 0.31
24 7 0.15
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (21 bp):
ATCGATTCCCTTCAAGGGGGA
Found at i:6950881 original size:34 final size:32
Alignment explanation
Indices: 6950843--6950992 Score: 107
Period size: 34 Copynumber: 4.6 Consensus size: 32
6950833 ACTCAAATCA
*
6950843 AATATCTTTTAATATTCAAATTTAAACATATAAT
1 AATATCTTTTAATATTCAAATTTAAA-AGAT-AT
*
6950877 AATATCTTTTAAT-TTAAAATATTCAAAAGATAT
1 AATATCTTTTAATATTCAAAT-TT-AAAAGATAT
* *
6950910 AGATATCTTTTTATATTCAAAATTAAATAGATAT
1 A-ATATCTTTTAATATTCAAATTTAAA-AGATAT
*
6950944 --TA--TTTTAAT-TTGAAATATTCAAAAGGATAT
1 AATATCTTTTAATATTCAAAT-TT-AAAA-GATAT
*
6950974 AATTATC-TTTAATAATCAA
1 AA-TATCTTTTAATATTCAA
6950993 TGTCAAAAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
28 5 0.05
29 9 0.10
30 8 0.09
31 2 0.02
33 14 0.15
34 43 0.47
35 11 0.12
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (32 bp):
AATATCTTTTAATATTCAAATTTAAAAGATAT
Found at i:6953901 original size:34 final size:33
Alignment explanation
Indices: 6953852--6953956 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 33
6953842 AGATTTACTT
6953852 AGATAA-AATATCTTTTAATATTCAAATTTAAA
1 AGATAATAATATCTTTTAATATTCAAATTTAAA
* *
6953884 CAGATAATAATATCTTTTAAT-TTGAAATATTCAA
1 -AGATAATAATATCTTTTAATATTCAAAT-TTAAA
* * *
6953918 AGAT-ATAGATATCTTTCACTATTCAAAATTAAA
1 AGATAATA-ATATCTTTTAATATTCAAATTTAAA
6953951 TAGATA
1 -AGATA
6953957 TTATTTTAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
32 3 0.05
33 30 0.51
34 26 0.44
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (33 bp):
AGATAATAATATCTTTTAATATTCAAATTTAAA
Found at i:6954277 original size:17 final size:17
Alignment explanation
Indices: 6954242--6954289 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
6954232 AAAGAATCAG
* * *
6954242 TAAAAGAAACAATACAA
1 TAAAAGAAATAGTATAA
*
6954259 TAATAGAAATAGTATAA
1 TAAAAGAAATAGTATAA
6954276 TAAAAGAAATAGTA
1 TAAAAGAAATAGTA
6954290 AAGTGAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.21
Consensus pattern (17 bp):
TAAAAGAAATAGTATAA
Found at i:6958796 original size:36 final size:35
Alignment explanation
Indices: 6958749--6958817 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
6958739 TTGGTTTTCC
*
6958749 GGAAAATGAATTATTGAAATTTGAATTACTGGAACT
1 GGAAAATGAATTACTGAAATTTGAATT-CTGGAACT
*
6958785 GGAAAATGAATTACTGGAATTTGAATTCTGGAA
1 GGAAAATGAATTACTGAAATTTGAATTCTGGAA
6958818 AATGAATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (35 bp):
GGAAAATGAATTACTGAAATTTGAATTCTGGAACT
Found at i:6958823 original size:14 final size:15
Alignment explanation
Indices: 6958782--6958827 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
6958772 AATTACTGGA
6958782 ACTGGAAAATGAATT
1 ACTGGAAAATGAATT
**
6958797 ACTGGAATTTGAATT
1 ACTGGAAAATGAATT
6958812 -CTGGAAAATGAATT
1 ACTGGAAAATGAATT
6958826 AC
1 AC
6958828 ATTTCTGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:6959082 original size:49 final size:50
Alignment explanation
Indices: 6958985--6959083 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
6958975 TACAAATATT
*
6958985 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
6959035 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
6959084 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:6959128 original size:32 final size:30
Alignment explanation
Indices: 6959062--6959130 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
6959052 ATTTATTATT
*
6959062 AAATATT-ATTTTTATAATTTTATTAATAA
1 AAATATTAATTTTTATAATTTTATAAATAA
*
6959091 AAATATTAATTTTTGTATATTTTAGTGAAAT-A
1 AAATATTAATTTTTATA-ATTTTA-T-AAATAA
6959123 AAATATTA
1 AAATATTA
6959131 TAAATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.21
30 8 0.24
31 6 0.18
32 10 0.29
33 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
AAATATTAATTTTTATAATTTTATAAATAA
Found at i:6959221 original size:23 final size:23
Alignment explanation
Indices: 6959172--6959234 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
6959162 TTGTTATATT
* **
6959172 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
6959195 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
6959218 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
6959235 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:6959262 original size:19 final size:20
Alignment explanation
Indices: 6959210--6959262 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
6959200 TTAAATATCT
6959210 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
6959229 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
6959250 TTATTAAATATAT
1 TTATTAAATATAT
6959263 AAAAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:6959274 original size:28 final size:27
Alignment explanation
Indices: 6959219--6959283 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
6959209 TTTATTAAAA
*
6959219 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAAAAATATTAT
6959247 TCATTATTAAATATATAAAAAA-ATTTAT
1 T-ATTATTAAATATATAAAAAATA-TTAT
6959275 TATATATTA
1 TAT-TATTA
6959284 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 26 0.79
29 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:6959309 original size:31 final size:32
Alignment explanation
Indices: 6959219--6959316 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 32
6959209 TTTATTAAAA
*
6959219 TATTATTTAAATATAT--AAATA-ATATTAT-T
1 TATTA-TTAAATATATAAAAAAATATATTATAT
* *
6959248 CATTATTAAATATATAAAAAAATTTATTATA-
1 TATTATTAAATATATAAAAAAATATATTATAT
*
6959279 TATTATTAAA-ATA-AAAATATAATATCTTATAT
1 TATTATTAAATATATAAAA-A-AATATATTATAT
6959311 TATTAT
1 TATTAT
6959317 AATATAATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 10 0.18
29 8 0.14
30 8 0.14
31 24 0.43
32 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (32 bp):
TATTATTAAATATATAAAAAAATATATTATAT
Found at i:6959361 original size:22 final size:23
Alignment explanation
Indices: 6959336--6959379 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
6959326 GATTATTTTA
6959336 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
6959358 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
6959380 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:6959385 original size:4 final size:4
Alignment explanation
Indices: 6959376--6959400 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6959366 TATAAATATT
6959376 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
6959401 TATTTTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:6959594 original size:43 final size:42
Alignment explanation
Indices: 6959513--6959629 Score: 207
Period size: 43 Copynumber: 2.8 Consensus size: 42
6959503 ATTACATTCT
*
6959513 GGAAAACCAATTACGTGAAACAAACACGGGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
*
6959555 GGAAAATGAATTACGTGAAACCAAACACGGGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAA-CAAACACGGGAAAACATTTTCC
6959598 GGAAAACGAATTACGTGAAACAAACACGGGAA
1 GGAAAACGAATTACGTGAAACAAACACGGGAA
6959630 TTCGGGGAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
42 30 0.42
43 41 0.58
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (42 bp):
GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
Found at i:6963651 original size:21 final size:17
Alignment explanation
Indices: 6963607--6963641 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6963597 GTATAAAGAG
6963607 AATGTTTGATTTGGCAA
1 AATGTTTGATTTGGCAA
6963624 AATGTTTGATTTGGCAA
1 AATGTTTGATTTGGCAA
6963641 A
1 A
6963642 GTGTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (17 bp):
AATGTTTGATTTGGCAA
Found at i:6968187 original size:9 final size:10
Alignment explanation
Indices: 6968161--6968186 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6968151 TCAACCAAAG
6968161 GGAAAAATAA
1 GGAAAAATAA
6968171 GGAAAAATAA
1 GGAAAAATAA
6968181 GGAAAA
1 GGAAAA
6968187 TTATAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (10 bp):
GGAAAAATAA
Found at i:6969525 original size:17 final size:17
Alignment explanation
Indices: 6969490--6969537 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
6969480 AAAGAATCAT
* * *
6969490 TAAAAGAAACAATACAA
1 TAAAAGAAATAGTATAA
*
6969507 TAAGAGAAATAGTATAA
1 TAAAAGAAATAGTATAA
6969524 TAAAAGAAATAGTA
1 TAAAAGAAATAGTA
6969538 AGGTGAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (17 bp):
TAAAAGAAATAGTATAA
Found at i:6976143 original size:68 final size:68
Alignment explanation
Indices: 6976034--6976238 Score: 383
Period size: 68 Copynumber: 3.0 Consensus size: 68
6976024 ATGTGTTCAT
6976034 TTGATAAGCTAATAGAATTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCGACCTAAATTGG
1 TTGATAAGCTAATAGAATTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCGACCTAAATTGG
6976099 TAA
66 TAA
**
6976102 TTGATAAGCTAACGGAATTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCGACCTAAATTGG
1 TTGATAAGCTAATAGAATTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCGACCTAAATTGG
6976167 TAA
66 TAA
*
6976170 TTGATAAGCTAATAGAATTAATGAATAAGCTAAGGATGCAAATTAGTGAAATCGACCTAAATTGG
1 TTGATAAGCTAATAGAATTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCGACCTAAATTGG
6976235 TAA
66 TAA
6976238 T
1 T
6976239 ATGAATTGTT
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 132 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.28
Consensus pattern (68 bp):
TTGATAAGCTAATAGAATTAGTGAATAAGCTAAGGATGCAAATTAGTGAAATCGACCTAAATTGG
TAA
Found at i:6978850 original size:12 final size:12
Alignment explanation
Indices: 6978833--6978858 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6978823 TAAGTCTCAA
6978833 AATTTCAAAGCT
1 AATTTCAAAGCT
6978845 AATTTCAAAGCT
1 AATTTCAAAGCT
6978857 AA
1 AA
6978859 ACATTTTTCA
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
AATTTCAAAGCT
Found at i:6981657 original size:35 final size:36
Alignment explanation
Indices: 6981617--6981695 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 36
6981607 ACATGGCATC
* *
6981617 GAATGTTCCACACCTATGGTGCAATCACAAGGCACT
1 GAATGTGCCACACCTACGGTGCAATCACAAGGCACT
*
6981653 -AATGTGCCACATCTACGGTGCAATCACAAGGCACT
1 GAATGTGCCACACCTACGGTGCAATCACAAGGCACT
6981688 GAATGTGC
1 GAATGTGC
6981696 AATACGATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 32 0.82
36 7 0.18
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (36 bp):
GAATGTGCCACACCTACGGTGCAATCACAAGGCACT
Found at i:6982015 original size:17 final size:17
Alignment explanation
Indices: 6981980--6982024 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
6981970 AAAGAATCAG
6981980 TAAAAGGAAA-AGTACAA
1 TAAAA-GAAATAGTACAA
* *
6981997 TAAGAGAAATAGTATAA
1 TAAAAGAAATAGTACAA
6982014 TAAAAGAAATA
1 TAAAAGAAATA
6982025 AGAAGGTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.64, C:0.02, G:0.16, T:0.18
Consensus pattern (17 bp):
TAAAAGAAATAGTACAA
Found at i:6990288 original size:33 final size:33
Alignment explanation
Indices: 6990209--6990312 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
6990199 ATACAATCTG
* *
6990209 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
6990245 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
6990278 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
6990311 TC
1 TC
6990313 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:6990755 original size:14 final size:15
Alignment explanation
Indices: 6990721--6990767 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
6990711 AATTTGGAGT
6990721 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
6990736 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
6990750 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
6990767 G
1 G
6990768 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:6994320 original size:33 final size:33
Alignment explanation
Indices: 6994241--6994344 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
6994231 ATACAATCTG
* *
6994241 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
6994277 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
6994310 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
6994343 TC
1 TC
6994345 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:6999741 original size:29 final size:30
Alignment explanation
Indices: 6999686--6999742 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
6999676 GCTTAGAAGA
* *
6999686 AAAATGAGAAAAAAAAAAAATATAAAAATG
1 AAAATGAGAAAAAAAAAAAAGAAAAAAATG
* *
6999716 AAAA-GAGAAAGAAAAGAAAGAAAAAAA
1 AAAATGAGAAAAAAAAAAAAGAAAAAAA
6999743 ATTGAAAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (30 bp):
AAAATGAGAAAAAAAAAAAAGAAAAAAATG
Found at i:7001094 original size:114 final size:114
Alignment explanation
Indices: 7000962--7001273 Score: 353
Period size: 114 Copynumber: 2.7 Consensus size: 114
7000952 AAGAAGATGT
* * * *
7000962 ATCAACATTTCAACATAGTTCATAATTAGAAGAACTCATTCAAAATAAGGGCGAAGAAGTTCATA
1 ATCAACAATTCAACATAGTTCATAATAAGAAGAACTCATTCAAAATAAGGGAGAAAAAGTTCATA
* * * *
7001027 TATGAGAGTTTGTTTAACCTTTGCTCAAAACTATAACAGAAATAGATAG
66 TAGGAGAGCTTGTTCAACATTTGCTCAAAACTATAACAGAAATAGATAG
* *
7001076 ATCAACAATTCGATATAGTTCATAATAAGAAGAACTCATTCAAAATAAGGGAGAAAAAGTTCATA
1 ATCAACAATTCAACATAGTTCATAATAAGAAGAACTCATTCAAAATAAGGGAGAAAAAGTTCATA
* * *
7001141 TAGGAGAGCTTGTTCAACATTTGCTCAAATCCATCACAG-AATGAGAT-G
66 TAGGAGAGCTTGTTCAACATTTGCTCAAAACTATAACAGAAAT-AGATAG
* * * * * * * *
7001189 AATCAACATTTCAACAGACTTCATAA-AGAAAAGAACTCATTC-AAATGAGTGAAAAAAAGTTAA
1 -ATCAACAATTCAACATAGTTCATAATA-AGAAGAACTCATTCAAAATAAGGGAGAAAAAGTTCA
* * *
7001252 TATAGAAGAGCCTGTTCGACAT
64 TATAGGAGAGCTTGTTCAACAT
7001274 GGACTCATCC
Statistics
Matches: 169, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
113 41 0.24
114 128 0.76
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (114 bp):
ATCAACAATTCAACATAGTTCATAATAAGAAGAACTCATTCAAAATAAGGGAGAAAAAGTTCATA
TAGGAGAGCTTGTTCAACATTTGCTCAAAACTATAACAGAAATAGATAG
Found at i:7001310 original size:111 final size:113
Alignment explanation
Indices: 7000943--7001323 Score: 267
Period size: 114 Copynumber: 3.4 Consensus size: 113
7000933 CTTGTTTCAC
* * * * ** *
7000943 CCATCACAGAA-GAAGATGTATCAACATTTCAACATAGTTCATAATTAGAAGAACTCATTCAAAA
1 CCATCACAAAATG-AGATGAATCAACATTTCAACAGAATTCATAAAGAAAAGAACTCATTCAAAA
** * * ** * * * *
7001007 TAAGGGCGAAGAAGTTCATATATG-AGAGTTTGTTTAACCTTTGCTCAAAA
65 TAAGGGAAAAAAAGTTAATATA-GAAGAGCCTGTTCAACATTGGCTC-AAT
* * * * * * * *
7001057 CTATAACAGAAAT-AGAT-AGATCAACAATTCGATATAGTTCATAATA-AGAAGAACTCATTCAA
1 CCATCACA-AAATGAGATGA-ATCAACATTTCAACAGAATTCATAA-AGAAAAGAACTCATTCAA
* * * * *
7001119 AATAAGGGAGAAAAAGTTCATATAGGAGAGCTTGTTCAACATTTGCTCAAAT
63 AATAAGGGAAAAAAAGTTAATATAGAAGAGCCTGTTCAACATTGGCTC-AAT
* *
7001171 CCATCACAGAATGAGATGAATCAACATTTCAACAGACTTCATAAAGAAAAGAACTCATTC-AAAT
1 CCATCACAAAATGAGATGAATCAACATTTCAACAGAATTCATAAAGAAAAGAACTCATTCAAAAT
* * *
7001235 GAGTGAAAAAAAGTTAATATAGAAGAGCCTGTTCGACA-TGGACTC-AT
66 AAGGGAAAAAAAGTTAATATAGAAGAGCCTGTTCAACATTGG-CTCAAT
* * * *
7001282 CCATCATGAAAAT-ATATGGATCAACATTTTAACAGAATTCAT
1 CCATCA-CAAAATGAGATGAATCAACATTTCAACAGAATTCAT
7001324 CATGACGAAA
Statistics
Matches: 220, Mismatches: 37, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
111 33 0.15
112 6 0.03
113 43 0.20
114 135 0.61
115 3 0.01
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (113 bp):
CCATCACAAAATGAGATGAATCAACATTTCAACAGAATTCATAAAGAAAAGAACTCATTCAAAAT
AAGGGAAAAAAAGTTAATATAGAAGAGCCTGTTCAACATTGGCTCAAT
Found at i:7002004 original size:14 final size:14
Alignment explanation
Indices: 7001987--7002015 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
7001977 TAATCCCTGT
7001987 AAATAATTCCCTAC
1 AAATAATTCCCTAC
7002001 AAATAATTCCCTAC
1 AAATAATTCCCTAC
7002015 A
1 A
7002016 TAGAAATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAATTCCCTAC
Found at i:7004396 original size:30 final size:25
Alignment explanation
Indices: 7004320--7004379 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
7004310 TTTTCTTTAG
*
7004320 TTTTG-CCGTATATTTCTTTTAATT
1 TTTTGACCTTATATTTCTTTTAATT
7004344 TTTTGACCTTATATTTCTTTTAATT
1 TTTTGACCTTATATTTCTTTTAATT
7004369 TTTTGACCTTA
1 TTTTGACCTTA
7004380 CCTAAATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 5 0.15
25 29 0.85
ACGTcount: A:0.18, C:0.13, G:0.07, T:0.62
Consensus pattern (25 bp):
TTTTGACCTTATATTTCTTTTAATT
Found at i:7013735 original size:19 final size:19
Alignment explanation
Indices: 7013707--7013753 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
7013697 CTGAGATCGA
* *
7013707 AGTGGCTCAGACCATTCAC
1 AGTGGTTCAGACAATTCAC
7013726 AGTGGTTCAGACAATTCAC
1 AGTGGTTCAGACAATTCAC
7013745 AGTGGTTCA
1 AGTGGTTCA
7013754 AATATTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (19 bp):
AGTGGTTCAGACAATTCAC
Found at i:7018508 original size:23 final size:24
Alignment explanation
Indices: 7018459--7018514 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
7018449 CATAAGGAAT
*
7018459 GTGCCACAAGAGTAAAACAAAAGC
1 GTGCCACAAGAGCAAAACAAAAGC
7018483 GTGCCACAAGAGCAAAGA-AAAA-C
1 GTGCCACAAGAGCAAA-ACAAAAGC
*
7018506 GTGTCACAA
1 GTGCCACAA
7018515 AGACATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.31
24 19 0.66
25 1 0.03
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.09
Consensus pattern (24 bp):
GTGCCACAAGAGCAAAACAAAAGC
Found at i:7020643 original size:10 final size:11
Alignment explanation
Indices: 7020624--7020652 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
7020614 GAGAAACATT
7020624 AGATTTTTTTA
1 AGATTTTTTTA
7020635 AGATTTTTTTA
1 AGATTTTTTTA
7020646 AGATTTT
1 AGATTTT
7020653 CGAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (11 bp):
AGATTTTTTTA
Found at i:7023053 original size:21 final size:21
Alignment explanation
Indices: 7023029--7023076 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
7023019 CAAGGTATCG
7023029 ATACCCTATGCAGGGGTACCA
1 ATACCCTATGCAGGGGTACCA
*
7023050 ATACCCTATGCAGGGGTACCG
1 ATACCCTATGCAGGGGTACCA
7023071 ATACCC
1 ATACCC
7023077 CCAACACTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (21 bp):
ATACCCTATGCAGGGGTACCA
Found at i:7026706 original size:46 final size:45
Alignment explanation
Indices: 7026637--7026880 Score: 310
Period size: 46 Copynumber: 5.4 Consensus size: 45
7026627 ACCAATATGA
* * *
7026637 ATTTCAATTATTGCATCCTTTCATGCCTTTTATACGCTATTGTAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACGCTATTATAC
* ** *
7026682 ATTTCATTTATGGCTTTTTTTTCATGCCTTTTATACACTATTATAC
1 ATTTCATTTATGGC-ATCCTTTCATGCCTTTTATACGCTATTATAC
* * *
7026728 ATTTCATTTATGGTATCCTTTCAAGCCATTTATACGCTATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACGCTATTATAC
* * * *
7026773 ATTTAATTTATGGCATCATTTCATGCCCTTTTATACACTATTATAT
1 ATTTCATTTATGGCATCCTTTCATG-CCTTTTATACGCTATTATAC
*
7026819 ATTTCATTTATGAG-ATCCTTTCATTCCCTTTTATACGCTATTATAC
1 ATTTCATTTATG-GCATCCTTTCA-TGCCTTTTATACGCTATTATAC
7026865 ATTTCATTTATGGCAT
1 ATTTCATTTATGGCAT
7026881 ACGTTATGCA
Statistics
Matches: 168, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
45 59 0.35
46 107 0.64
47 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTTATACGCTATTATAC
Found at i:7026762 original size:91 final size:90
Alignment explanation
Indices: 7026637--7026880 Score: 337
Period size: 91 Copynumber: 2.7 Consensus size: 90
7026627 ACCAATATGA
* * * * **
7026637 ATTTCAATTATTGCATCCTTTCATGCCTTTTATACGCTATTGTACATTTCATTTATGGCTTTTTT
1 ATTTCATTTA-TGGATCCTTTCATGCCTTTTATACGCTATTATACATTTCATTTATGGC-ATCAT
7026702 TTCATG-CCTTTTATACACTATTATAC
64 TTCATGCCCTTTTATACACTATTATAC
* * *
7026728 ATTTCATTTATGGTATCCTTTCAAGCCATTTATACGCTATTATACATTTAATTTATGGCATCATT
1 ATTTCATTTATGG-ATCCTTTCATGCCTTTTATACGCTATTATACATTTCATTTATGGCATCATT
*
7026793 TCATGCCCTTTTATACACTATTATAT
65 TCATGCCCTTTTATACACTATTATAC
*
7026819 ATTTCATTTATGAGATCCTTTCATTCCCTTTTATACGCTATTATACATTTCATTTATGGCAT
1 ATTTCATTTATG-GATCCTTTCA-TGCCTTTTATACGCTATTATACATTTCATTTATGGCAT
7026881 ACGTTATGCA
Statistics
Matches: 135, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
90 10 0.07
91 90 0.67
92 35 0.26
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (90 bp):
ATTTCATTTATGGATCCTTTCATGCCTTTTATACGCTATTATACATTTCATTTATGGCATCATTT
CATGCCCTTTTATACACTATTATAC
Found at i:7027022 original size:81 final size:81
Alignment explanation
Indices: 7026908--7027061 Score: 227
Period size: 81 Copynumber: 1.9 Consensus size: 81
7026898 ATATCTAGTC
* * *
7026908 TTTTACTCAAAAGCATTTAACCTTTAATCTAACTGACATGATTGACACCTTTTTGTCAAATGCAC
1 TTTTACTCAAAAGCATTAAACCTTTAATCTAACTGACATAATTGACACCTTTCTGTCAAATGCAC
7026973 AGCTAGGCCATTAATA
66 AGCTAGGCCATTAATA
* * * * *
7026989 TTTTACTCAAAGGTATTAAACCTTTCATTTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
1 TTTTACTCAAAAGCATTAAACCTTTAATCTAACTGACATAATTGACACCTTTCTGTCAAATGCAC
*
7027054 TGCTAGGC
66 AGCTAGGC
7027062 TTCAAAGGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (81 bp):
TTTTACTCAAAAGCATTAAACCTTTAATCTAACTGACATAATTGACACCTTTCTGTCAAATGCAC
AGCTAGGCCATTAATA
Found at i:7027106 original size:68 final size:68
Alignment explanation
Indices: 7026994--7027468 Score: 700
Period size: 68 Copynumber: 7.0 Consensus size: 68
7026984 TAATATTTTA
* * * * *
7026994 CTCAAAGGTATTAAACCTTTCATTTAACTGGCATAATTGACACCTTTCTGTCAAATGCACTGCTA
1 CTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
7027059 GGC
66 GGC
* * * *
7027062 TTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGTCACCTTTCTATCAAATGCACAACTA
1 CTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
7027127 GGC
66 GGC
* *
7027130 CTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATAGACACCTTTCTATCAAATGCACAGCTA
1 CTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
7027195 GGC
66 GGC
* *
7027198 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTA
1 CTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
7027263 GGC
66 GGC
* * * *
7027266 CTCAAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAATACACAACTA
1 CTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
7027331 GGC
66 GGC
* * * * * *
7027334 CTCAAAGGCATTTAACCTTTCATCGAACTAGCATAATTGACACCTTTCTCTCAAATGCACAACTG
1 CTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
7027399 GGC
66 GGC
* ** *
7027402 CTCAAAGGCACTTAGCCTTTCATCTAACT-GCATAATTGACATTTTTCTGTCAAATGCATAGCTA
1 CTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
7027466 GGC
66 GGC
7027469 AATTCATCTT
Statistics
Matches: 369, Mismatches: 38, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
67 32 0.09
68 337 0.91
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (68 bp):
CTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
GGC
Found at i:7027901 original size:56 final size:57
Alignment explanation
Indices: 7027676--7027893 Score: 339
Period size: 57 Copynumber: 3.8 Consensus size: 57
7027666 TAAAGTTCTT
* * * *
7027676 ATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTCTTGCACCCGAAGTCCCC
1 ATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
7027733 ATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * * *
7027790 ATATGAAAATTAATAAACAAATTATAAATTTCTTTACTTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
7027847 AT-CGGAAATTCATAAACAAATTATGAATTTCTTAACTTTATGCACAC
1 ATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACAC
7027894 TCAGTGCCAT
Statistics
Matches: 147, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
56 39 0.27
57 108 0.73
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (57 bp):
ATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:7036505 original size:33 final size:32
Alignment explanation
Indices: 7036468--7036556 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 32
7036458 ATTGATATAA
7036468 CACTTCATTTCAAAAAAAATATCAGTGATACAT
1 CACTTCATTTCAAAAAAAA-ATCAGTGATACAT
*
7036501 CACTTCATTTCAAAAAACAATCAGTGATACAT
1 CACTTCATTTCAAAAAAAAATCAGTGATACAT
*
7036533 CACTTCATTTCAGAAAAAACATCA
1 CACTTCATTTCA-AAAAAAAATCA
7036557 TTTTCTCATA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 25 0.48
33 27 0.52
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (32 bp):
CACTTCATTTCAAAAAAAAATCAGTGATACAT
Found at i:7036524 original size:32 final size:33
Alignment explanation
Indices: 7036468--7036556 Score: 144
Period size: 32 Copynumber: 2.7 Consensus size: 33
7036458 ATTGATATAA
7036468 CACTTCATTTCAAAAAAAATATCAGTGATACAT
1 CACTTCATTTCAAAAAAAATATCAGTGATACAT
*
7036501 CACTTCATTTCAAAAAACA-ATCAGTGATACAT
1 CACTTCATTTCAAAAAAAATATCAGTGATACAT
* *
7036533 CACTTCATTTCAGAAAAAACATCA
1 CACTTCATTTCAAAAAAAATATCA
7036557 TTTTCTCATA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 30 0.58
33 22 0.42
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (33 bp):
CACTTCATTTCAAAAAAAATATCAGTGATACAT
Found at i:7047590 original size:12 final size:12
Alignment explanation
Indices: 7047561--7047595 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
7047551 ATATTATGGT
*
7047561 TTTTCAAACATTG
1 TTTTCAAA-ATAG
7047574 TTTTCAAAATAG
1 TTTTCAAAATAG
7047586 TTTTCAAAAT
1 TTTTCAAAAT
7047596 TTTCCCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (12 bp):
TTTTCAAAATAG
Found at i:7047647 original size:13 final size:13
Alignment explanation
Indices: 7047629--7047662 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
7047619 AGAACCTTGA
7047629 ATATTGAGGACTC
1 ATATTGAGGACTC
7047642 ATATTGAGGACTC
1 ATATTGAGGACTC
7047655 ATATTGAG
1 ATATTGAG
7047663 TTTTGGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (13 bp):
ATATTGAGGACTC
Found at i:7049327 original size:13 final size:13
Alignment explanation
Indices: 7049305--7049338 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
7049295 AGGGGGAGTA
*
7049305 ATTTTCAAAATTG
1 ATTTTCAAAAATG
7049318 A-TTTCAAAAATG
1 ATTTTCAAAAATG
7049330 ATTTTCAAA
1 ATTTTCAAA
7049339 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:7051490 original size:17 final size:17
Alignment explanation
Indices: 7051468--7051528 Score: 122
Period size: 17 Copynumber: 3.6 Consensus size: 17
7051458 CAATTTTGTT
7051468 ATTAAAATTCTATTACA
1 ATTAAAATTCTATTACA
7051485 ATTAAAATTCTATTACA
1 ATTAAAATTCTATTACA
7051502 ATTAAAATTCTATTACA
1 ATTAAAATTCTATTACA
7051519 ATTAAAATTC
1 ATTAAAATTC
7051529 GTTTTAACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAAATTCTATTACA
Found at i:7054733 original size:27 final size:25
Alignment explanation
Indices: 7054690--7054775 Score: 122
Period size: 24 Copynumber: 3.4 Consensus size: 25
7054680 AAATTGAACG
*
7054690 ACCGGTTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
7054714 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT--AACCGGATAAAAA
*
7054741 ACCGG-TTTTTTATCCGGATAAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
7054765 ACCGGTTTTTT
1 ACCGGTTTTTT
7054776 AAAAAAACCG
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
24 29 0.52
25 5 0.09
26 6 0.11
27 16 0.29
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATAAAAA
Found at i:7054782 original size:17 final size:17
Alignment explanation
Indices: 7054760--7054794 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
7054750 TTATCCGGAT
7054760 AAAAAACCGGTTTTTTA
1 AAAAAACCGGTTTTTTA
7054777 AAAAAACCGGTTTTTTA
1 AAAAAACCGGTTTTTTA
7054794 A
1 A
7054795 CCGAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (17 bp):
AAAAAACCGGTTTTTTA
Found at i:7054791 original size:41 final size:40
Alignment explanation
Indices: 7054736--7054833 Score: 126
Period size: 40 Copynumber: 2.4 Consensus size: 40
7054726 CAAACCGGAT
*
7054736 AAAAAACCGGTTTTTTATCCGGATAAAAAACC-GGTTTTTTA
1 AAAAAACCGGTTTTTTAACC-GA-AAAAAACCAGGTTTTTTA
* * *
7054777 AAAAAACCGGTTTTTTAACCGAAAAAATCCAGTTTTTTTT
1 AAAAAACCGGTTTTTTAACCGAAAAAAACCAGGTTTTTTA
*
7054817 TAAAAACCGGTTTTTTA
1 AAAAAACCGGTTTTTTA
7054834 CAAACCGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
39 7 0.14
40 25 0.49
41 19 0.37
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (40 bp):
AAAAAACCGGTTTTTTAACCGAAAAAAACCAGGTTTTTTA
Found at i:7055646 original size:6 final size:6
Alignment explanation
Indices: 7055635--7055661 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7055625 TTTTAATGTG
7055635 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
7055662 ACAAAGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:7059301 original size:8 final size:9
Alignment explanation
Indices: 7059288--7059320 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
7059278 TTAGGAATCA
7059288 ATTATA-AT
1 ATTATATAT
7059296 ATTATATAT
1 ATTATATAT
7059305 ATATATATAT
1 AT-TATATAT
7059315 ATTATA
1 ATTATA
7059321 GTTAATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 8 0.35
10 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTATATAT
Found at i:7059973 original size:14 final size:14
Alignment explanation
Indices: 7059948--7059999 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
7059938 TAAAATATAA
7059948 TAATATTTTTATTTT
1 TAATA-TTTTATTTT
7059963 TAATATTTTATTTT
1 TAATATTTTATTTT
* * *
7059977 TGATATATTATCTT
1 TAATATTTTATTTT
7059991 TAATTATTT
1 TAA-TATTT
7060000 AATAAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 22 0.71
15 9 0.29
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
TAATATTTTATTTT
Found at i:7060809 original size:25 final size:23
Alignment explanation
Indices: 7060783--7060830 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
7060773 TATTTTAATA
*
7060783 TATATATATTTTTAAATAAAATT
1 TATATATATTTTTTAATAAAATT
*
7060806 TATATATATTTTTTTATAAAATT
1 TATATATATTTTTTAATAAAATT
7060829 TA
1 TA
7060831 AAAGGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATATATATTTTTTAATAAAATT
Found at i:7066930 original size:67 final size:69
Alignment explanation
Indices: 7066802--7066930 Score: 174
Period size: 67 Copynumber: 1.9 Consensus size: 69
7066792 ATTATGTCCT
** **
7066802 AATTTCAATTTAATTTAATAAATTAATTTATCCAATCAAATTGTGACACATTTCACATTTTGTAT
1 AATTTCAATTTAATTTAATAAATT-ATTTATCCAATCAAAAGGTGACACACGTCACATTTTGTAT
7066867 AATGC
65 AATGC
*
7066872 AATTT-AA-TTAATTTAATAAATT-TTTAATCCAATCAAAAGGTGACACACGTCACCTTTTG
1 AATTTCAATTTAATTTAATAAATTATTT-ATCCAATCAAAAGGTGACACACGTCACATTTTG
7066931 AATTAAAGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
66 3 0.06
67 28 0.53
68 15 0.28
69 2 0.04
70 5 0.09
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (69 bp):
AATTTCAATTTAATTTAATAAATTATTTATCCAATCAAAAGGTGACACACGTCACATTTTGTATA
ATGC
Found at i:7071136 original size:23 final size:23
Alignment explanation
Indices: 7071110--7071154 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
7071100 AAATGTAATT
7071110 TATATTAA-TAATAATTATAATAA
1 TATA-TAATTAATAATTATAATAA
* *
7071133 TATATAATTAATATTTTTAATA
1 TATATAATTAATAATTATAATA
7071155 TTTTTCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATAATTAATAATTATAATAA
Found at i:7071556 original size:116 final size:116
Alignment explanation
Indices: 7071337--7071631 Score: 414
Period size: 116 Copynumber: 2.5 Consensus size: 116
7071327 CTCGAGATTG
* *
7071337 ATTTGCTTCACTACTCTTTGGTGAAGGCTTAAAATTGATTTTGCTTCACTACTCTTTGGTGAAGA
1 ATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGA-TTTGCTTCACTACTCTTCGGTGAAGA
* * * *
7071402 CTTAAGATGGCCCGGACGACTTAATCATCATGCTCGGAAGGCTTACTGATGA
65 CTTAAAATGGCCAGGACGACTTAATCATCATACTCGGAAGGCTTACTAATGA
* **
7071454 ATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTAGTCTTCGGTGAAGGT
1 ATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGAC
* *
7071519 TTAAAATGGTCAGGAGGACTTAATCATCATACTCGGAAGGCTTACTAATGA
66 TTAAAATGGCCAGGACGACTTAATCATCATACTCGGAAGGCTTACTAATGA
* * * *
7071570 ATTTTCTTTACTACTCTTCT-GTGAAGGCTTATGA-TGAATTTGCTTCACTACTCTTCAGTGAA
1 ATTTGCTTCACTACTCTT-TGGTGAAGGCTTAAGATTG-ATTTGCTTCACTACTCTTCGGTGAA
7071632 AGCTTAAGAT
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
115 2 0.01
116 120 0.75
117 38 0.24
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (116 bp):
ATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGAC
TTAAAATGGCCAGGACGACTTAATCATCATACTCGGAAGGCTTACTAATGA
Found at i:7071651 original size:36 final size:36
Alignment explanation
Indices: 7071335--7071891 Score: 351
Period size: 36 Copynumber: 15.0 Consensus size: 36
7071325 AACTCGAGAT
* *
7071335 TGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAAA
1 TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
* *
7071371 TTGATTTTGCTTCACTACTCTTTGGTGAAGACTTAAGA
1 -TGA-TTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
**** ** * * * *
7071409 TGGCCCG-GACGACTTAATCATCATGCTCGGAAGGCTTACTGA
1 TGATTTGCTTC-AC-TACTCTTC--GGT--GAAGGCTTA-AGA
*
7071451 TGAATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGA
1 TG-ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
* * *
7071488 TTGATTTGCTTCACTAGTCTTCGGTGAAGGTTTAAAA
1 -TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
* ** ****
7071525 TGGTCAGGAGGACTTAATCATCATACTC-G-GAAGGCTTACTA-A
1 TGATTTGCTTCAC-T-A-C-TC-T--TCGGTGAAGGCTTA--AGA
* * * *
7071567 TGAATTTTCTTTACTACTCTTCTGTGAAGGCTTATGA
1 TG-ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
* *
7071604 TGAATTTGCTTCACTACTCTTCAGTGAAAGCTTAAGA
1 TG-ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
* *
7071641 TGATTTGCTTCACTACTCTCCGGTGAAGGCTTCAGA
1 TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
* * * * *
7071677 TGGTTTGCTTCACTATTCTCCGGTGAAGGATTAGGA
1 TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
* *
7071713 TGGTTTGCTTCACTACT-TTCCGGTGAAGGCTTAGGA
1 TGATTTGCTTCACTACTCTT-CGGTGAAGGCTTAAGA
* * *
7071749 T-AGTTTGCTTCACTACTCTCCAGTGAAGGCTTCAGA
1 TGA-TTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
* * *
7071785 TTG-TTTGCTTCACTATTCTCCGGTGAAGGCTTAGGA
1 -TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
* * * *
7071821 TG--GTGCTTCACTCCTCTTTGGTGAAGGGTTAAGA
1 TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
*
7071855 TTGA-TTGCTTCACTACTCTTCAGTGAAGGCTTAAGA
1 -TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
7071891 T
1 T
7071892 TGACTTGCCC
Statistics
Matches: 404, Mismatches: 85, Indels: 64
0.73 0.15 0.12
Matches are distributed among these distances:
34 25 0.06
35 7 0.02
36 187 0.46
37 81 0.20
38 53 0.13
39 4 0.01
40 5 0.01
41 18 0.04
42 14 0.03
43 9 0.02
44 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (36 bp):
TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA
Found at i:7071797 original size:108 final size:107
Alignment explanation
Indices: 7071590--7071893 Score: 416
Period size: 108 Copynumber: 2.8 Consensus size: 107
7071580 CTACTCTTCT
* * * *
7071590 GTGAAGGCTTATGATGAATTTGCTTCACTACTCTTCAGTGAAAGCTTAAGATGATTTGCTTCACT
1 GTGAAGGCTTAGGATG-GTTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-TTTGCTTCACT
* *
7071655 ACTCTCCGGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCCG
64 ACTCTCCAGTGAAGGCTTCAGATTGTTTGCTTCACTATTCTCCG
* *
7071699 GTGAAGGATTAGGATGGTTTGCTTCACTACT-TTCCGGTGAAGGCTTAGGATAGTTTGCTTCACT
1 GTGAAGGCTTAGGATGGTTTGCTTCACTACTCTT-CGGTGAAGGCTTAAGAT-GTTTGCTTCACT
7071763 ACTCTCCAGTGAAGGCTTCAGATTGTTTGCTTCACTATTCTCCG
64 ACTCTCCAGTGAAGGCTTCAGATTGTTTGCTTCACTATTCTCCG
* * * *
7071807 GTGAAGGCTTAGGATGG--TGCTTCACTCCTCTTTGGTGAAGGGTTAAGATTGATTGCTTCACTA
1 GTGAAGGCTTAGGATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA-TGTTTGCTTCACTA
* *
7071870 CTCTTCAGTGAAGGCTTAAGATTG
65 CTCTCCAGTGAAGGCTTCAGATTG
7071894 ACTTGCCCCA
Statistics
Matches: 175, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
106 58 0.33
107 5 0.03
108 97 0.55
109 15 0.09
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (107 bp):
GTGAAGGCTTAGGATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGTTTGCTTCACTAC
TCTCCAGTGAAGGCTTCAGATTGTTTGCTTCACTATTCTCCG
Found at i:7072744 original size:16 final size:18
Alignment explanation
Indices: 7072717--7072751 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
7072707 ACCTCCACTG
7072717 TCACTACTTCAT-CATTT
1 TCACTACTTCATACATTT
7072734 TCACT-CTTCATACATTT
1 TCACTACTTCATACATTT
7072751 T
1 T
7072752 TATCCCATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTACTTCATACATTT
Found at i:7073869 original size:2 final size:2
Alignment explanation
Indices: 7073864--7073919 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
7073854 GTATACACAC
7073864 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
7073906 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
7073920 TGTTGGGTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7078292 original size:55 final size:55
Alignment explanation
Indices: 7078199--7078336 Score: 188
Period size: 55 Copynumber: 2.5 Consensus size: 55
7078189 TAACTTCAAA
* * * *
7078199 CTTCATTCATCGGATGTCTTTCTTCATGGATCGATCTTCAATCAGTTTCAGATTT
1 CTTCATTCATCGGATGTCCTTCTTCATGAATCGATCTTCAATCAGGTTCAAATTT
* *
7078254 CTTCATTCATCGGATATCCATCTTCATGAATC-ATTCTTCAATCAGGTTCAAATTT
1 CTTCATTCATCGGATGTCCTTCTTCATGAATCGA-TCTTCAATCAGGTTCAAATTT
* *
7078309 CTTCATTCATAGTATGTCCTTCTTCATG
1 CTTCATTCATCGGATGTCCTTCTTCATG
7078337 GATCCCTTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 1 0.01
55 71 0.99
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (55 bp):
CTTCATTCATCGGATGTCCTTCTTCATGAATCGATCTTCAATCAGGTTCAAATTT
Found at i:7079631 original size:17 final size:19
Alignment explanation
Indices: 7079609--7079648 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
7079599 AAACGCTGTC
7079609 ATTTTAAAT-AAA-AATAA
1 ATTTTAAATAAAACAATAA
*
7079626 ATTTTAATTAAAACAATAA
1 ATTTTAAATAAAACAATAA
7079645 ATTT
1 ATTT
7079649 ATGTCCGCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 3 0.15
19 9 0.45
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTTTAAATAAAACAATAA
Found at i:7093600 original size:15 final size:14
Alignment explanation
Indices: 7093570--7093603 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7093560 TTTTGGGGAT
7093570 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
*
7093584 AAAATGAAAACAAAG
1 AAAAAGAAAA-AAAG
7093599 AAAAA
1 AAAAA
7093604 CGGTGCGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:7097138 original size:17 final size:17
Alignment explanation
Indices: 7097116--7097154 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
7097106 TGATGTCAGA
7097116 AAGGAAGTTATTACTAC
1 AAGGAAGTTATTACTAC
7097133 AAGGAAGTTATTACTAC
1 AAGGAAGTTATTACTAC
7097150 AAGGA
1 AAGGA
7097155 TGTCAGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (17 bp):
AAGGAAGTTATTACTAC
Found at i:7103513 original size:19 final size:19
Alignment explanation
Indices: 7103477--7103514 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
7103467 CAAAATAATC
*
7103477 CAATTTCACATTCTAACAT
1 CAATTTCACACTCTAACAT
7103496 CAATTTCAACACTC-AACAT
1 CAATTTC-ACACTCTAACAT
7103515 TGATTTCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (19 bp):
CAATTTCACACTCTAACAT
Found at i:7108514 original size:59 final size:59
Alignment explanation
Indices: 7108422--7108661 Score: 376
Period size: 59 Copynumber: 4.1 Consensus size: 59
7108412 CTAACCCGAG
* * * *
7108422 TATGACACATAAGGTCATGCCCACCATCTGCACTAGTTATACTGTAGTGCAGTCTCGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCTCGAA
*
7108481 TATGACACATAAGGTTGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCTCGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCTCGAA
* *
7108540 TATGACACATAAGGTCGTGCCCACCATATACACTAGTTATACTTTAGTACAA--TCGAATA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCTCG-A-A
*
7108599 TATGACACATAAGGTCGTGTCCACCATATGCACTAGTTATACTTTAGTGCAATCTCGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCTCGAA
7108658 TATG
1 TATG
7108662 TAACCTACTA
Statistics
Matches: 166, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
57 3 0.02
58 1 0.01
59 158 0.95
60 1 0.01
61 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCTCGAA
Found at i:7110440 original size:293 final size:291
Alignment explanation
Indices: 7109911--7110440 Score: 746
Period size: 293 Copynumber: 1.8 Consensus size: 291
7109901 ATGTCACAAT
7109911 ATAATTGTTAAACATAAAACTTTAAAATTGACCATTCAAGCCCCTTTTTTATCCAAATTTCACAT
1 ATAATTGTTAAACATAAAACTTTAAAATTGACCATTCAAGCCCCTTTTTTATCCAAATTTCACAT
* * * * *
7109976 AACATTTTCACTTAAGCTCCCAACTTTTCCATATTTGTGATTTAAGCTTCAACTTTTACCAACTT
66 AACATTTTCACTTAAACTCCCAACTTTTCCATATTTGCGATTTAAACCTAAACTTTTACCAACTT
* * *
7110041 CCCAAAATAATCAAATTTCACATTATAACATCAATTTCAACACTCAAACATTAATTTCCAGAACA
131 CCCAAAATAATCAAATTTCAAATTATAACATCAATTTCAACACGCAAAAATTAATTTCCA-AACA
* * ** * * *
7110106 TTACTTAACTTTTTTTAATTACTAATTAGGTCCCCTAACTTTCATAAAATTAAACAATGATCCCC
195 TTACTCAAATTTTAATAATTACTAAATA-GACCCATAACTTTCATAAAATTAAACAATGATCCCC
7110171 AAATTTTTCTAAGACTTGGGGAATACTTCCTAC
259 AAATTTTTCTAAGACTTGGGGAATACTTCCTAC
* * * *
7110204 ATAATTGTTAACCATAAAACTTTAGAATTTACCATTCAAATCCCC-TTTTTATCCAAATTTCACA
1 ATAATTGTTAAACATAAAACTTTAAAATTGACCATTC-AAGCCCCTTTTTTATCCAAATTTCACA
7110268 TAACATTTTCACTTAAACTCCCAACTTTTCCATATTTGCGATTTAAACCTAAACTTTTACCAACT
65 TAACATTTTCACTTAAACTCCCAACTTTTCCATATTTGCGATTTAAACCTAAACTTTTACCAACT
** *
7110333 TCTTAAAATAATTC-AATTTCAAATTCTAACATCAATTTCAACACGCAAAAATTAATTTCC-AAC
130 TCCCAAAATAA-TCAAATTTCAAATTATAACATCAATTTCAACACGCAAAAATTAATTTCCAAAC
7110396 ATAGTACCTCAAATATTTAATAATTAC-ACAATA-ACCCATAACTTT
194 AT--TA-CTCAAAT-TTTAATAATTACTA-AATAGACCCATAACTTT
7110441 TTCTGTAATT
Statistics
Matches: 208, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
291 5 0.02
293 176 0.85
294 14 0.07
295 13 0.06
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.36
Consensus pattern (291 bp):
ATAATTGTTAAACATAAAACTTTAAAATTGACCATTCAAGCCCCTTTTTTATCCAAATTTCACAT
AACATTTTCACTTAAACTCCCAACTTTTCCATATTTGCGATTTAAACCTAAACTTTTACCAACTT
CCCAAAATAATCAAATTTCAAATTATAACATCAATTTCAACACGCAAAAATTAATTTCCAAACAT
TACTCAAATTTTAATAATTACTAAATAGACCCATAACTTTCATAAAATTAAACAATGATCCCCAA
ATTTTTCTAAGACTTGGGGAATACTTCCTAC
Found at i:7111604 original size:391 final size:391
Alignment explanation
Indices: 7110934--7111684 Score: 1245
Period size: 391 Copynumber: 1.9 Consensus size: 391
7110924 TCATCGAATA
*
7110934 GAACAATTTTCTATTTCACGTCTTAATCAAAAAAACCTAATAAATTGGCTTAAAATAAAAATAAA
1 GAACAATTTTCTATTTCACATCTTAATCAAAAAAACCTAATAAATTGGCTTAAAATAAAAATAAA
* *
7110999 AATTCTCTTACCTAGGGTATGAAGTCCACAAAATGGAGGAGAAATATGACATGTTTTCATGAAAT
66 AATTCTCTTACCTAGGGTATGAAGTCCACAAAATGGAGGAGAAAGATGACAAGTTTTCATGAAAT
7111064 TTTAGTTAATTTCATGTTAATTTATCATGTATTTAAGCTTAAATGAATATAAAATTCATTTAATG
131 TTTAGTTAATTTCATGTTAATTTATCATGTATTTAAGCTTAAATGAATATAAAATTCATTTAATG
* * *
7111129 AGAAATGACAATTGTACCATTAATGAAACGTGATAATTACATCTATACCAATCCACATAACCCTT
196 AGAAATAAAAATTGTACCATTAATGAAACGTAATAATTACATCTATACCAATCCACATAACCCTT
* *
7111194 ATCATCTTTATAAAGTCAAATACGAACAAAATATTTTACCCTTTTCCAATATAACCAAGCAATTT
261 ACCATCTCTATAAAGTCAAATACGAACAAAATATTTTACCCTTTTCCAATATAACCAAGCAATTT
* *
7111259 TCCAAAACTTACAATCTTGCCACTTTGATCCAACGAAATGGAGGCCAAGAAAACCCTAATAAATT
326 TCCAAAAATTACAATATTGCCACTTTGATCCAACGAAATGGAGGCCAAGAAAACCCTAATAAATT
7111324 T
391 T
* * *
7111325 GAACAATTTTCTATTTCATATCTTAATC-GAAAAACCTAATAAATTGGTTTAAAATGAAAAATAA
1 GAACAATTTTCTATTTCACATCTTAATCAAAAAAACCTAATAAATTGGCTTAAAAT-AAAAATAA
** *
7111389 AAATTCTCTTACCTAGGGTATGAAGTCCATGAAATGGAGGAGAAAGATGACCAAGTTTTCTTGAA
65 AAATTCTCTTACCTAGGGTATGAAGTCCACAAAATGGAGGAGAAAGATGA-CAAGTTTTCATGAA
* *
7111454 ATTTTAGTTAATTTCATGTTACTTTTTCATGTATTTAAGCTTAAATGAATATAAAATTCATTTAA
129 ATTTTAGTTAATTTCATGTTAATTTATCATGTATTTAAGCTTAAATGAATATAAAATTCATTTAA
* *
7111519 TGAGAAATAAAAATTTTACCATTAATGAAACTTAATAATTACAT-TATACCAATCCACATAACCC
194 TGAGAAATAAAAATTGTACCATTAATGAAACGTAATAATTACATCTATACCAATCCACATAACCC
* * *
7111583 TTACCATCTCTATATAGTCAAATATGAACAAAATATTTTACCCTTTTCTAATATAACCAAGCAAT
259 TTACCATCTCTATAAAGTCAAATACGAACAAAATATTTTACCCTTTTCCAATATAACCAAGCAAT
* *
7111648 TTTCCAAAAATTAGAATATTGCGACTTTGATCCAACG
324 TTTCCAAAAATTACAATATTGCCACTTTGATCCAACG
7111685 GTCCAAATTA
Statistics
Matches: 333, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
390 25 0.08
391 194 0.58
392 114 0.34
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34
Consensus pattern (391 bp):
GAACAATTTTCTATTTCACATCTTAATCAAAAAAACCTAATAAATTGGCTTAAAATAAAAATAAA
AATTCTCTTACCTAGGGTATGAAGTCCACAAAATGGAGGAGAAAGATGACAAGTTTTCATGAAAT
TTTAGTTAATTTCATGTTAATTTATCATGTATTTAAGCTTAAATGAATATAAAATTCATTTAATG
AGAAATAAAAATTGTACCATTAATGAAACGTAATAATTACATCTATACCAATCCACATAACCCTT
ACCATCTCTATAAAGTCAAATACGAACAAAATATTTTACCCTTTTCCAATATAACCAAGCAATTT
TCCAAAAATTACAATATTGCCACTTTGATCCAACGAAATGGAGGCCAAGAAAACCCTAATAAATT
T
Found at i:7116020 original size:115 final size:116
Alignment explanation
Indices: 7115839--7116135 Score: 472
Period size: 116 Copynumber: 2.6 Consensus size: 116
7115829 CCAATGAGGG
*
7115839 GTTCATAATGAGAAGAACTCATCCAACAAGGAAAAAGAAGTTCATAATGAGAAGAAATTGTCCAA
1 GTTCATAATGAGAAGAACTCATCCAACAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTCCAA
* * *
7115904 CCTTTGCTCGATT-CATCACA-AAGAAGTTGGATCATCATTTCCATATCAGA
66 CC-TTGCTCAATTCCATCACAGAAGAAGTTGGATCAGCATTTCCAGATCAGA
* *
7115954 GTTCATAATGAGAAGAACTCATCCAACAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCCAACAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTCCAA
*
7116019 CCTTGCTCAATTCCATCACAGAAGGAGTTGGATCAGCATTTCCAGATCAGA
66 CCTTGCTCAATTCCATCACAGAAGAAGTTGGATCAGCATTTCCAGATCAGA
* * * *
7116070 GTTCATAATGAGAAGAAATTATCCAACAAGGAAAAAGAAGTTCATAATGAAAAGAACTTATCCAA
1 GTTCATAATGAGAAGAACTCATCCAACAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTCCAA
7116135 C
66 C
7116136 AATGAAAAAG
Statistics
Matches: 167, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
114 9 0.05
115 71 0.43
116 87 0.52
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (116 bp):
GTTCATAATGAGAAGAACTCATCCAACAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTCCAA
CCTTGCTCAATTCCATCACAGAAGAAGTTGGATCAGCATTTCCAGATCAGA
Found at i:7116112 original size:39 final size:39
Alignment explanation
Indices: 7116069--7116164 Score: 156
Period size: 39 Copynumber: 2.5 Consensus size: 39
7116059 TCCAGATCAG
7116069 AGTTCATAATGAGAAGAAATTATCCAACAAGGAAAAAGA
1 AGTTCATAATGAGAAGAAATTATCCAACAAGGAAAAAGA
* * *
7116108 AGTTCATAATGAAAAGAACTTATCCAACAATGAAAAAGA
1 AGTTCATAATGAGAAGAAATTATCCAACAAGGAAAAAGA
*
7116147 AGTTCATAATAAGAAGAA
1 AGTTCATAATGAGAAGAA
7116165 CATTTTCAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.20
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAAATTATCCAACAAGGAAAAAGA
Found at i:7116147 original size:22 final size:21
Alignment explanation
Indices: 7116086--7116147 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
7116076 AATGAGAAGA
*
7116086 AATTATCCAACAAGGAAAAAG
1 AATTATCCAACAATGAAAAAG
* *
7116107 AAGT-T-C-ATAATG-AAAAG
1 AATTATCCAACAATGAAAAAG
7116124 AACTTATCCAACAATGAAAAAG
1 AA-TTATCCAACAATGAAAAAG
7116146 AA
1 AA
7116148 GTTCATAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
17 7 0.23
18 5 0.16
19 2 0.06
20 2 0.06
21 8 0.26
22 7 0.23
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.18
Consensus pattern (21 bp):
AATTATCCAACAATGAAAAAG
Found at i:7118027 original size:46 final size:47
Alignment explanation
Indices: 7117913--7118005 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
7117903 AGTTAAAATG
* *
7117913 CTAACACTACTAACCGCTAACTCCTAACTTTGATTTTATTTTTATTT
1 CTAACACCACTAACCGCTAACTACTAACTTTGATTTTATTTTTATTT
* *
7117960 CTAACACCACTAACCTCTAACTACTAACTTTTATTTTA-TTTTATTT
1 CTAACACCACTAACCGCTAACTACTAACTTTGATTTTATTTTTATTT
7118006 TTTATGCCAC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 8 0.19
47 34 0.81
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (47 bp):
CTAACACCACTAACCGCTAACTACTAACTTTGATTTTATTTTTATTT
Done.