Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 19
Found at i:1471985 original size:3 final size:3
Alignment explanation
Indices: 1471977--1472018 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1471967 CCACCGTTGC
1471977 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1472019 TGGACATGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:1472066 original size:21 final size:21
Alignment explanation
Indices: 1472040--1472080 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1472030 CCAAAGCCTC
1472040 CTACAAATACACCCACCGTTG
1 CTACAAATACACCCACCGTTG
1472061 CTACAAATACACCCACCGTT
1 CTACAAATACACCCACCGTT
1472081 CTTCTTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.07, T:0.20
Consensus pattern (21 bp):
CTACAAATACACCCACCGTTG
Found at i:1472087 original size:3 final size:3
Alignment explanation
Indices: 1472079--1472941 Score: 1561
Period size: 3 Copynumber: 294.0 Consensus size: 3
1472069 ACACCCACCG
1472079 TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472125 TTC TTC TT- TT- TTC TTC TTC TTC TTC TTC TTC TCTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC
1472169 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472215 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472263 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472311 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472359 -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472406 TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472453 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472500 TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472546 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472593 TTC TTC -TC TTC TTC TTC TTC TTTC TTC -TC TT- TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC
1472636 -TC TTC TTC TTC TTC TT- TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472681 -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472728 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472775 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472822 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472870 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1472918 TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC
1472942 AACTTCAACT
Statistics
Matches: 839, Mismatches: 0, Indels: 42
0.95 0.00 0.05
Matches are distributed among these distances:
2 42 0.05
3 791 0.94
4 6 0.01
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1472125 original size:106 final size:106
Alignment explanation
Indices: 1471912--1472121 Score: 390
Period size: 106 Copynumber: 2.0 Consensus size: 106
1471902 TGGGGATCCA
*
1471912 TTGGACATGATTCCAAAGCCTCCTACAAATACACCCACTGTTGCTACAAATACACCCACCGTTGC
1 TTGGACATGATTCCAAAGCCTCCTACAAATACACCCACCGTTGCTACAAATACACCCACCGTTGC
1471977 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
66 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
1472018 TTGGACATGATTCCAAAGCCTCCTACAAATACACCCACCGTTGCTACAAATACACCCACCGTT--
1 TTGGACATGATTCCAAAGCCTCCTACAAATACACCCACCGTTGCTACAAATACACCCACCGTTGC
1472081 CTTCTTCTTCTTCTTCTTCTT-TTCTTCTTCTTCTTCTTCT
66 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
1472121 T
1 T
1472122 CTTTTCTTCT
Statistics
Matches: 103, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
103 20 0.19
104 21 0.20
106 62 0.60
ACGTcount: A:0.19, C:0.34, G:0.07, T:0.40
Consensus pattern (106 bp):
TTGGACATGATTCCAAAGCCTCCTACAAATACACCCACCGTTGCTACAAATACACCCACCGTTGC
CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
Found at i:1473800 original size:9 final size:10
Alignment explanation
Indices: 1473767--1473812 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1473757 ATAACTGGAA
1473767 AACCGGTTT-
1 AACCGGTTTG
*
1473776 AACCAGTTTTG
1 AACC-GGTTTG
1473787 AACCGGTTTG
1 AACCGGTTTG
*
1473797 -ACCGGTCTG
1 AACCGGTTTG
1473806 AACCGGT
1 AACCGGT
1473813 CCGACCCGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 12 0.39
10 15 0.48
11 4 0.13
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:1473904 original size:29 final size:29
Alignment explanation
Indices: 1473843--1474022 Score: 136
Period size: 29 Copynumber: 6.3 Consensus size: 29
1473833 ACCGTTGACC
* * * ** *
1473843 GGTGATATTCTGGGAATTAATTTGATTTT
1 GGTGCTATTTTGGGAATTAATTCGAAATG
1473872 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
* ** *
1473901 GGTGCTATTTTGGTAATTTTTTTCAAAAT-
1 GGTGCTATTTTGGGAA-TTAATTCGAAATG
* *
1473930 --TGATATTCTT-GTAATTAATTCGAAA-G
1 GGTGCTATT-TTGGGAATTAATTCGAAATG
* * *
1473956 GATGCTATTTTGGGAATTAATTCAAAAAG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
* * **
1473985 GGTGCTATTTTGGTAATTAATTTGAAAAA
1 GGTGCTATTTTGGGAATTAATTCGAAATG
1474014 GGTGCTATT
1 GGTGCTATT
1474023 GTGGTTATTA
Statistics
Matches: 122, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
26 8 0.07
27 12 0.10
28 21 0.17
29 72 0.59
30 9 0.07
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATG
Found at i:1474027 original size:29 final size:29
Alignment explanation
Indices: 1473872--1474052 Score: 142
Period size: 29 Copynumber: 6.3 Consensus size: 29
1473862 ATTTGATTTT
* * **
1473872 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGTAATTAATTTGAAAAA
* **
1473901 GGTGCTATTTTGGTAATT-TTTTTCAAAA
1 GGTGCTATTTTGGTAATTAATTTGAAAAA
* * *
1473929 -TTGATATTCTT-GTAATTAATTCG--AAA
1 GGTGCTATT-TTGGTAATTAATTTGAAAAA
* *
1473955 GGATGCTATTTTGGGAATTAA-TTCAAAAA
1 GG-TGCTATTTTGGTAATTAATTTGAAAAA
1473984 GGGTGCTATTTTGGTAATTAATTTGAAAAA
1 -GGTGCTATTTTGGTAATTAATTTGAAAAA
* * *
1474014 GGTGCTATTGTGGTTATT-ATTTTAAAAA
1 GGTGCTATTTTGGTAATTAATTTGAAAAA
1474042 TGGTGCTATTT
1 -GGTGCTATTT
1474053 ATGTACCTCC
Statistics
Matches: 119, Mismatches: 23, Indels: 20
0.73 0.14 0.12
Matches are distributed among these distances:
26 3 0.03
27 15 0.13
28 30 0.25
29 62 0.52
30 9 0.08
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTTGAAAAA
Found at i:1474746 original size:117 final size:117
Alignment explanation
Indices: 1474540--1474766 Score: 332
Period size: 117 Copynumber: 1.9 Consensus size: 117
1474530 GAGTGGATGG
* * * ***
1474540 GGAACCTACACATTGTAGTGAGTGGAGTGACTGGATGGGGAAGTTATTACTGCAGACTCCTTTGC
1 GGAACCTACACATTGTAGTGAGTGAAGCGACTGGATGGAGAAGTTATTACTGCAGACTCCTCAAC
* *
1474605 TGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGA
66 TGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGAGTGTATGGTTCTGA
* *
1474657 GGAACCTACACATTGTAGTGA-TGAAAGCGACTGGATGGAGACGTTATTACTGCAGGCTCCTCAA
1 GGAACCTACACATTGTAGTGAGTG-AAGCGACTGGATGGAGAAGTTATTACTGCAGACTCCTCAA
1474721 CT-TCGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGAGTGTATG
65 CTGT-GTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGAGTGTATG
1474767 TTTCGGGAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
116 3 0.03
117 95 0.97
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (117 bp):
GGAACCTACACATTGTAGTGAGTGAAGCGACTGGATGGAGAAGTTATTACTGCAGACTCCTCAAC
TGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGAGTGTATGGTTCTGA
Found at i:1477022 original size:19 final size:19
Alignment explanation
Indices: 1477000--1477040 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1476990 AACATAATGG
*
1477000 AAATAAATATTAA-ATAAAA
1 AAAT-AATAATAAGATAAAA
1477019 AAATAATAATAAGATAAAA
1 AAATAATAATAAGATAAAA
1477038 AAA
1 AAA
1477041 ACAACATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AAATAATAATAAGATAAAA
Found at i:1477063 original size:5 final size:5
Alignment explanation
Indices: 1477000--1477077 Score: 63
Period size: 5 Copynumber: 15.6 Consensus size: 5
1476990 AACATAATGG
* * * *
1477000 AAATA AATATT AAAT- AAA-A AAATA ATAATA AGATA AAA-A AAACA ACATA
1 AAATA AA-ATA AAATA AAATA AAATA A-AATA AAATA AAATA AAATA AAATA
*
1477049 CAAATG AAATA AAATA AAATA AAATA AAA
1 -AAATA AAATA AAATA AAATA AAATA AAA
1477078 CACAACATGC
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
4 10 0.17
5 37 0.63
6 12 0.20
ACGTcount: A:0.74, C:0.04, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1478735 original size:3 final size:3
Alignment explanation
Indices: 1478727--1478772 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
1478717 ATTTATATAT
* * *
1478727 TAA TAA TAA AAA TAA TAA TAA TAG TAA TAA TAA TAGA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
1478773 ATAGAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:1479226 original size:134 final size:135
Alignment explanation
Indices: 1478980--1479319 Score: 481
Period size: 134 Copynumber: 2.5 Consensus size: 135
1478970 ACATAGCTCT
* * * *
1478980 TACGTGATGAGGAAATCTGGTCGAGGTATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCAT
1 TACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGTGATGAAGAGTTCATGGCCAT
* * *
1479045 CTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTAACACG
66 CTATAGGAAGGGTGATAACTCGGTTCCTACACGATAAGGACGGCTGGTTATCTAGGGGTAACACG
1479110 ACTCC
131 ACTCC
* * *
1479115 TACGCGATGAGGAGATCTGGTCGAGGGATGGCACGGCTCATACGTGATGAAGAGTT-ATGGTCAT
1 TACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGTGATGAAGAGTTCATGGCCAT
* * *
1479179 CTATAGGAAGGGTGATAACAT-GGTTCCTACATGATAAGGACGTCTGGTTATCTAGGGGTGACAC
66 CTATAGGAAGGGTGATAAC-TCGGTTCCTACACGATAAGGACGGCTGGTTATCTAGGGGTAACAC
*
1479243 GGCTCC
130 GACTCC
* *
1479249 TACGTGATGAAGAGATCTGGTC-AGGAGATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCT
1 TACGTGATGAGGAGATCTGGTCGAGG-GATGACACGGCTCATACGTGATGAAGAGTTCATGGCCA
*
1479312 TCTTTAGG
65 TCTATAGG
1479320 GATAATGATT
Statistics
Matches: 182, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
133 3 0.02
134 127 0.70
135 52 0.29
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (135 bp):
TACGTGATGAGGAGATCTGGTCGAGGGATGACACGGCTCATACGTGATGAAGAGTTCATGGCCAT
CTATAGGAAGGGTGATAACTCGGTTCCTACACGATAAGGACGGCTGGTTATCTAGGGGTAACACG
ACTCC
Found at i:1479629 original size:91 final size:89
Alignment explanation
Indices: 1479527--1479753 Score: 291
Period size: 91 Copynumber: 2.5 Consensus size: 89
1479517 GTTAACAGAC
*
1479527 ACAATCTCAAAGA-TTTTTCAAAAGGAACAGACTCAAAGATTTTTCTCAAGAAAATCTGTCTCAA
1 ACAAACTCAAAGATTTTTTCAAAAGGAACAGACTCAAAGATTTTT-TCAAG-AAAT-TGTCTCAA
* *
1479591 GAGAGACAAAACTTTGTTTCAAAAGAA
63 GAGAAACAAAACTTTGGTTCAAAAGAA
* *
1479618 ACAAACTCAAAGATTTTGGTTTCAAAA-GAA-ATGACTCAAAGATTTTTTCACGAAATTGTCTTA
1 ACAAACTCAAAGA-TTT--TTTCAAAAGGAACA-GACTCAAAGATTTTTTCAAGAAATTGTCTCA
1479681 AGAGAAACAAAACTTTGGTTCAAAAGAA
62 AGAGAAACAAAACTTTGGTTCAAAAGAA
* *
1479709 ACATACTCAAAGAATTTTTTCAAAAGAAACA-ACTCAAAGATTTTT
1 ACAAACTCAAAG-ATTTTTTCAAAAGGAACAGACTCAAAGATTTTT
1479754 GGTTTCAAAA
Statistics
Matches: 121, Mismatches: 7, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
89 22 0.18
90 2 0.02
91 59 0.49
92 5 0.04
93 7 0.06
94 18 0.15
95 8 0.07
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.28
Consensus pattern (89 bp):
ACAAACTCAAAGATTTTTTCAAAAGGAACAGACTCAAAGATTTTTTCAAGAAATTGTCTCAAGAG
AAACAAAACTTTGGTTCAAAAGAA
Found at i:1479773 original size:31 final size:29
Alignment explanation
Indices: 1479603--1479860 Score: 143
Period size: 30 Copynumber: 8.6 Consensus size: 29
1479593 GAGACAAAAC
1479603 TTTGTTTCAAAAGAAACAAACTCAAAGATT
1 TTTGTTTCAAAAGAAAC-AACTCAAAGATT
* **
1479633 TTGGTTTCAAAAGAAATGACTCAAAGATTT
1 TTTGTTTCAAAAGAAACAACTCAAAGA-TT
** * *
1479663 TTTCACGAAATTGTCTTAAGAGA-AA--CAAA-A-C
1 TTT---G---TT-TCAAAAGAAACAACTCAAAGATT
* *
1479694 TTTGGTTCAAAAGAAACATACTCAAAGA-A
1 TTTGTTTCAAAAGAAACA-ACTCAAAGATT
1479723 TTT-TTTCAAAAGAAACAACTCAAAGATT
1 TTTGTTTCAAAAGAAACAACTCAAAGATT
* * *
1479751 TTTGGTTTCAAAAAAAAACAACTCACAGACT
1 TTT-GTTTC-AAAAGAAACAACTCAAAGATT
*
1479782 TTTGTTTCAAGAGAAACAAACTCAAAGATAAGT
1 TTTGTTTCAAAAGAAAC-AACTCAAAGAT---T
** * *
1479815 TTTGTTTCAAGGGAAACAATCTCAAAGGTG
1 TTTGTTTCAAAAGAAACAA-CTCAAAGATT
* *
1479845 TTTGTTTTAAGAGAAA
1 TTTGTTTCAAAAGAAA
1479861 TTGTCTTAAA
Statistics
Matches: 178, Mismatches: 28, Indels: 44
0.71 0.11 0.18
Matches are distributed among these distances:
24 7 0.04
25 2 0.01
26 1 0.01
27 9 0.05
28 21 0.12
29 20 0.11
30 51 0.29
31 24 0.13
32 2 0.01
33 27 0.15
34 4 0.02
36 3 0.02
37 7 0.04
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAACTCAAAGATT
Found at i:1479932 original size:66 final size:67
Alignment explanation
Indices: 1479856--1480044 Score: 244
Period size: 64 Copynumber: 2.9 Consensus size: 67
1479846 TTGTTTTAAG
* * ** *
1479856 AGAAATTGTCTTAAAAGAGACAAACCTTTATTTTCATAA-AAACATACTTAAAGATTTTTCTTTA
1 AGAAACTGTCTCAAAAGAGACAAAATTTTATTTTCA-AAGAAACATACTCAAAGATTTTTCTTTA
1479920 AAA
65 AAA
* *
1479923 AG-AACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACATACTCAAAGA---TTCTTTAA
1 AGAAACTGTCTCAAAAGAGACAAAATTTTATTTTCAAAGAAACATACTCAAAGATTTTTCTTTAA
1479984 AA
66 AA
* * *
1479986 AGAAACTTTCTCAAAAAAGACAAAATTTTATTATCAAAGAAACATACTCAAAGATTTTT
1 AGAAACTGTCTCAAAAGAGACAAAATTTTATTTTCAAAGAAACATACTCAAAGATTTTT
1480045 TTTCATTTTG
Statistics
Matches: 105, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
63 12 0.11
64 46 0.44
65 2 0.02
66 41 0.39
67 4 0.04
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (67 bp):
AGAAACTGTCTCAAAAGAGACAAAATTTTATTTTCAAAGAAACATACTCAAAGATTTTTCTTTAA
AA
Found at i:1480053 original size:103 final size:102
Alignment explanation
Indices: 1479946--1480145 Score: 244
Period size: 105 Copynumber: 1.9 Consensus size: 102
1479936 AAGAGACAAA
* * *
1479946 ATTTTGTTTCCA-AAGAAACATACTCAAAGA-TTCTTTAAAAAGAAACTTTCTCAAAAAAGACAA
1 ATTTTGTTT-CAGAAGAAACAGACTCAAAGATTTCTTCAAAAAG-AACTGTCTCAAAAAAGACAA
1480009 AATTTTATTAT-CAAAGAAACATACTCAAAGATTTTTTTTC
64 AATTTTATT-TCCAAA-AAACATACTCAAAGATTTTTTTTC
* ** * *
1480049 ATTTTGTTTTAGGTGAAACAGACTCAAAGATTTTTCTTCAAAATGAACTGTCTCAAAAGAGACAA
1 ATTTTGTTTCAGAAGAAACAGACTCAAAGA--TTTCTTCAAAAAGAACTGTCTCAAAAAAGACAA
*
1480114 AATTTTGTTTCCAAAAAACATACTCAAAGATT
64 AATTTTATTTCCAAAAAACATACTCAAAGATT
1480146 CTTTCAAAAG
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
102 1 0.01
103 24 0.29
104 18 0.22
105 30 0.36
106 10 0.12
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (102 bp):
ATTTTGTTTCAGAAGAAACAGACTCAAAGATTTCTTCAAAAAGAACTGTCTCAAAAAAGACAAAA
TTTTATTTCCAAAAAACATACTCAAAGATTTTTTTTC
Found at i:1480105 original size:169 final size:169
Alignment explanation
Indices: 1479895--1480316 Score: 629
Period size: 168 Copynumber: 2.5 Consensus size: 169
1479885 ATTTTCATAA
* * * *
1479895 AAACATACTTAAAGATTTTTCTTTAAAAAGAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAA
1 AAACAGACTCAAAGATTTTTCTTCAAAATGAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAA
1479960 GAAACATACTCAAAGATTCTTTAAAAAGAAACTTTCTCAAAAAAGACAAAATTTTATTATCAAAG
66 GAAACATACTCAAAGATTCTTTAAAAAGAAACTTTCTCAAAAAAGACAAAATTTTATTATCAAAG
*
1480025 AAACATACTCAAAGATTTTTTTTCATTTTGTTTTAGGTG
131 AAACATACTCAAAGATTTTTTTTCATTTTGTTTTAAGTG
1480064 AAACAGACTCAAAGATTTTTCTTCAAAATGAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAA
1 AAACAGACTCAAAGATTTTTCTTCAAAATGAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAA
* * *
1480129 -AAACATACTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAAAG
66 GAAACATACTCAAAGATTCTTTAAAAAGAAACTTTCTCAAAAAAGACAAAATTTTATTATCAAAG
*
1480193 AAACATACTCAAAGATTTTTTTTTATTTTGTTTTAAGTG
131 AAACATACTCAAAGATTTTTTTTCATTTTGTTTTAAGTG
* *** * * *
1480232 AAATAGACTCAAAGATTTTTCAAGAAAAT--A-TGTCTCAAGAGA-ATCAAAGTTTTGTTTCAAA
1 AAACAGACTCAAAGATTTTTCTTCAAAATGAACTGTCTCAAAAGAGA-CAAAATTTTGTTTCCAA
* * *
1480293 AGAAATAGACTCAAAGATCCTTTA
65 AGAAACATACTCAAAGATTCTTTA
1480317 TTTCAAAAGA
Statistics
Matches: 231, Mismatches: 20, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
164 1 0.00
165 27 0.12
166 19 0.08
168 123 0.53
169 61 0.26
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (169 bp):
AAACAGACTCAAAGATTTTTCTTCAAAATGAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAA
GAAACATACTCAAAGATTCTTTAAAAAGAAACTTTCTCAAAAAAGACAAAATTTTATTATCAAAG
AAACATACTCAAAGATTTTTTTTCATTTTGTTTTAAGTG
Found at i:1480170 original size:63 final size:65
Alignment explanation
Indices: 1480063--1480209 Score: 212
Period size: 63 Copynumber: 2.3 Consensus size: 65
1480053 TGTTTTAGGT
* *
1480063 GAAACAGACTCAAAGATTTTTCTTCAAAATGAACTGTCTCAAAAGAGACAAAATTTTGTT-TCCA
1 GAAACATACTCAAAGA-TTCTCTTCAAAATGAACTGTCTCAAAAGAGACAAAATTTTGTTAT-CA
1480127 AA
64 AA
*
1480129 -AAACATACTCAAAGATTCT-TTCAAAA-GAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAA
1 GAAACATACTCAAAGATTCTCTTCAAAATG-AACTGTCTCAAAAGAGACAAAATTTTGTTATCAA
1480191 A
65 A
1480192 GAAACATACTCAAAGATT
1 GAAACATACTCAAAGATT
1480210 TTTTTTTATT
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
62 1 0.01
63 39 0.52
64 21 0.28
65 14 0.19
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (65 bp):
GAAACATACTCAAAGATTCTCTTCAAAATGAACTGTCTCAAAAGAGACAAAATTTTGTTATCAAA
Found at i:1480418 original size:36 final size:36
Alignment explanation
Indices: 1480378--1480472 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 36
1480368 ATAATTTGGA
* * * *
1480378 AAATTTTCTCAAGTGAGACAATATTTGTTTTTAGAG
1 AAATTTTCTCAAGCGAGACAAAAATTGCTTTTAGAG
* * *
1480414 AAATTGTT-TCAAACAAGACAAAAAATTGCTTTTAGGG
1 AAATT-TTCTCAAGCGAGAC-AAAAATTGCTTTTAGAG
*
1480451 AAATTGTCTCAAGCGAGACAAA
1 AAATTTTCTCAAGCGAGACAAA
1480473 GCATGTTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
36 17 0.37
37 29 0.63
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (36 bp):
AAATTTTCTCAAGCGAGACAAAAATTGCTTTTAGAG
Found at i:1480741 original size:105 final size:102
Alignment explanation
Indices: 1480478--1480778 Score: 311
Period size: 106 Copynumber: 2.9 Consensus size: 102
1480468 ACAAAGCATG
* * *
1480478 TTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTA
1 TTTTTAAGAAAACGATCTCAAATGAGATAAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTA
**
1480543 CTCTCAAAGGAAAAATG-CATCAAATGAGACGAAATTTAT
66 --CTCAAAGGAAAAATGTC-TCAAACAAGACGAAATTTAT
** ** * * * *
1480582 TTTGAAAGAAATAATAATCTCAAATTAGATTAA-TTTTTTTCCAA-GTGAATCAAATTCGAAATT
1 TTTTTAAG-AA-AACGATCTCAAATGAGATAAACTTTGTTT--AATGTGAAACAAATTCGAAATT
* * * *
1480645 TGTACGTCAAAGGAAAAAATGTCTCAAGCAAGACGGAGTTTGTT
62 TGTAC-TCAAAGG-AAAAATGTCTCAAACAAGACGAAATTT-AT
*
1480689 TTTTTAAGAAAGCGATCTCAAATGAGATAAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTA
1 TTTTTAAGAAAACGATCTCAAATGAGATAAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTA
1480754 TTCTCAAAGGAAAAATGTCTCAAAC
66 --CTCAAAGGAAAAATGTCTCAAAC
1480779 GAGAAAGAAT
Statistics
Matches: 159, Mismatches: 26, Indels: 23
0.76 0.12 0.11
Matches are distributed among these distances:
104 8 0.05
105 67 0.42
106 73 0.46
107 11 0.07
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (102 bp):
TTTTTAAGAAAACGATCTCAAATGAGATAAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTA
CTCAAAGGAAAAATGTCTCAAACAAGACGAAATTTAT
Found at i:1484571 original size:31 final size:32
Alignment explanation
Indices: 1484510--1484571 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1484500 TGACAAAATA
1484510 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
*
1484542 ACACAAACAAAAGAGAA-AAATGAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
1484572 CATGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.60, C:0.10, G:0.16, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:1486335 original size:5 final size:5
Alignment explanation
Indices: 1486309--1486411 Score: 70
Period size: 5 Copynumber: 20.6 Consensus size: 5
1486299 AACATAATGG
* * * *
1486309 AAATA AATATT AAATAA AAATA AAATA AGATA AGATA AGATA AAAT- AAATA
1 AAATA AA-ATA AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * * *
1486360 GAA-A AAATA AAA-A AAACA ACATA CAAATG AAATA AAATA AAA-A AAACTA
1 AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAATA AAATA AAA-TA
1486409 AAA
1 AAA
1486412 CACAACATGC
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
4 15 0.19
5 49 0.62
6 15 0.19
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:1488601 original size:134 final size:134
Alignment explanation
Indices: 1488299--1488683 Score: 460
Period size: 135 Copynumber: 2.9 Consensus size: 134
1488289 ACGACACTGC
* * * * * * * *
1488299 TCCTACGCGATGAAGAG-GTCTGGTCATCTAAGGGTAACACAGCTCTTACATGATGAGGAAATCT
1 TCCTACGTGATG-AGGGCGTCTGGTTATCTAGGGGTGACACGGCTCCTACATGATGAGGAGATCT
* * *
1488363 GGTCGAGGGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAA
65 GGTTGA-GGATGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAA
*
1488428 CTCGGT
129 CACGGT
* ** **
1488434 TCCTAC-TCGATGAGGACAACTGGTTATCTAGGGGTGACACGGCTCCTACGCGATGAGGAGATCT
1 TCCTACGT-GATGAGGGCGTCTGGTTATCTAGGGGTGACACGGCTCCTACATGATGAGGAGATCT
*
1488498 GGTTGATGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGTCAT-TTATAGGAAGGGCGATA
65 GGTTGA-GGATGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTT-TAGGAAGGGCGATA
1488561 ACACGGT
128 ACACGGT
* *
1488568 TCCTACGTGATGAGGGCGTCTGGTTATCTAGGGGTGACACGGCTCCTA-TTGATGAAGAGATCTG
1 TCCTACGTGATGAGGGCGTCTGGTTATCTAGGGGTGACACGGCTCCTACATGATGAGGAGATCTG
* *
1488632 G-TCAGGAAATGACACGACTCATACGTGATGAAGAGTT-TTGGCCATCTTTAGG
66 GTTGAGG--ATGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGG
1488684 GATAACGATT
Statistics
Matches: 214, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
131 2 0.01
132 2 0.01
133 54 0.25
134 72 0.34
135 84 0.39
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (134 bp):
TCCTACGTGATGAGGGCGTCTGGTTATCTAGGGGTGACACGGCTCCTACATGATGAGGAGATCTG
GTTGAGGATGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACA
CGGT
Found at i:1488993 original size:91 final size:89
Alignment explanation
Indices: 1488896--1489117 Score: 263
Period size: 91 Copynumber: 2.4 Consensus size: 89
1488886 GAGACACAAT
*
1488896 CTCAAAGA-TTTTTCAAAAGGAACAGACTCAAAGATTTTTCTCAAGAAAAATTGTCTCAAGAGAG
1 CTCAAAGATTTTTTCAAAAGGAACAGACTCAAAGATTTTT-TCAAG--AAATTGTCTCAAGAGAA
* *
1488960 ACAAAACTTTGTTTCAAAATAAAAAAA
63 ACAAAACTTTGGTTCAAAAGAAAAAAA
* *
1488987 CTCAAAGATTTTGGTTTCAAAA-GAA-ATGACTCAAAGATTTTTTCACGAAATTGTCTTAAGAGA
1 CTCAAAGA-TTT--TTTCAAAAGGAACA-GACTCAAAGATTTTTTCAAGAAATTGTCTCAAGAGA
* * *
1489050 AACAAAACTTTGGTTCAGAAGAAACATA
62 AACAAAACTTTGGTTCAAAAGAAAAAAA
*
1489078 CTCAAAGAATTTTTTCAAAAGAAACA-ACTCAAAGATTTTT
1 CTCAAAG-ATTTTTTCAAAAGGAACAGACTCAAAGATTTTT
1489118 ATTTCAAAAG
Statistics
Matches: 114, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
89 22 0.19
90 2 0.02
91 56 0.49
92 1 0.01
93 7 0.06
94 18 0.16
95 8 0.07
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.29
Consensus pattern (89 bp):
CTCAAAGATTTTTTCAAAAGGAACAGACTCAAAGATTTTTTCAAGAAATTGTCTCAAGAGAAACA
AAACTTTGGTTCAAAAGAAAAAAA
Found at i:1489004 original size:30 final size:29
Alignment explanation
Indices: 1488970--1489027 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1488960 ACAAAACTTT
1488970 GTTTCAAAATAAAAAAACTCAAAGATTTTG
1 GTTTCAAAA-AAAAAAACTCAAAGATTTTG
* **
1489000 GTTTCAAAAGAAATGACTCAAAGATTTT
1 GTTTCAAAAAAAAAAACTCAAAGATTTT
1489028 TTCACGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (29 bp):
GTTTCAAAAAAAAAAACTCAAAGATTTTG
Found at i:1489131 original size:29 final size:29
Alignment explanation
Indices: 1489058--1489222 Score: 154
Period size: 29 Copynumber: 5.6 Consensus size: 29
1489048 GAAACAAAAC
* * *
1489058 TTTGGTTCAGAAGAAACATACTCAAAGA-A
1 TTTGTTTCAAAAGAAACA-ACTCAAAGATT
1489087 TTT-TTTCAAAAGAAACAACTCAAAGATT
1 TTTGTTTCAAAAGAAACAACTCAAAGATT
* * *
1489115 TTTATTTCAAAAGAAACAACTCACAGACT
1 TTTGTTTCAAAAGAAACAACTCAAAGATT
*
1489144 TTTGTTTCAAGAGAAACACACTCAAAGATAGGT
1 TTTGTTTCAAAAGAAACA-ACTCAAAGAT---T
** *
1489177 TTTGTTTCAAGGGAAACAATCTCAAAGATG
1 TTTGTTTCAAAAGAAACAA-CTCAAAGATT
* *
1489207 TTTGTTTTAAGAGAAA
1 TTTGTTTCAAAAGAAA
1489223 TTGTCTTAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.08
28 15 0.13
29 42 0.36
30 22 0.19
32 1 0.01
33 27 0.23
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAACTCAAAGATT
Found at i:1489222 original size:63 final size:58
Alignment explanation
Indices: 1489063--1489222 Score: 164
Period size: 63 Copynumber: 2.7 Consensus size: 58
1489053 AAAACTTTGG
* * *
1489063 TTCAGAAGAAACATACTCAAAGA-ATTT-TTTCAAAAGAAACAACTCAAAGATTTTTAT
1 TTCAAAAGAAACA-ACTCAAAGACTTTTGTTTCAAGAGAAACAACTCAAAGATTTTTAT
* *
1489120 TTCAAAAGAAACAACTCACAGACTTTTGTTTCAAGAGAAACACACTCAAAGATAGGTTTTGT
1 TTCAAAAGAAACAACTCAAAGACTTTTGTTTCAAGAGAAACA-ACTCAAAGAT---TTTTAT
** *
1489182 TTCAAGGGAAACAATCTCAAAGA-TGTTTGTTTTAAGAGAAA
1 TTCAAAAGAAACAA-CTCAAAGACT-TTTGTTTCAAGAGAAA
1489223 TTGTCTTAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
56 8 0.09
57 15 0.17
58 13 0.15
59 10 0.12
62 18 0.21
63 22 0.26
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (58 bp):
TTCAAAAGAAACAACTCAAAGACTTTTGTTTCAAGAGAAACAACTCAAAGATTTTTAT
Found at i:1489363 original size:64 final size:64
Alignment explanation
Indices: 1489224--1489409 Score: 173
Period size: 64 Copynumber: 2.9 Consensus size: 64
1489214 TAAGAGAAAT
* ** ** * * *
1489224 TGTCTTAAAAGAGACAAACCTTTGTTTTCATAA-AAACAGACTTAAAGATTTTTCTTCAAAAAGA
1 TGTCTCAAAAGAGACAAAATTTTGTTACCA-AAGAAACATACTCAAAGA-TTCT-TTCAAAAAGA
1489288 AC
63 AC
1489290 TGTCTCAAAAGAGACAAAAATGTTT-TT-CCAAAGAAACATACTCAAAGATTCTTTCAAAATA-A
1 TGTCTCAAAAGAGAC-AAAAT-TTTGTTACCAAAGAAACATACTCAAAGATTCTTTCAAAA-AGA
1489352 AC
63 AC
* * * * *
1489354 TTTCTCAAAATAGACAAAATTTTGTTATCAAAGAAACATACTCAAAGGTTTTTTCA
1 TGTCTCAAAAGAGACAAAATTTTGTTACCAAAGAAACATACTCAAAGATTCTTTCA
1489410 TTTTGTTTTA
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
62 3 0.03
63 7 0.07
64 49 0.48
65 6 0.06
66 29 0.28
67 5 0.05
68 3 0.03
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.31
Consensus pattern (64 bp):
TGTCTCAAAAGAGACAAAATTTTGTTACCAAAGAAACATACTCAAAGATTCTTTCAAAAAGAAC
Found at i:1489418 original size:103 final size:100
Alignment explanation
Indices: 1489320--1489511 Score: 244
Period size: 103 Copynumber: 1.9 Consensus size: 100
1489310 TGTTTTTCCA
* * *
1489320 AAGAAACATACTCAAAGATTCTTTC-AAAATAAACTTTCTCAAAATAGACAAAATTTTGTTAT-C
1 AAGAAACAGACTCAAAGATT-TTTCTAAAATAAACTGTCTCAAAAGAGACAAAATTTTGTT-TCC
* *
1489383 AAAGAAACATACTCAAAGGTTTTTTCATTTTGTTTTAG
64 AAA-AAACATACTCAAAGATTCTTTCATTTTGTTTTAG
** * *
1489421 GTGAAACAGACTCAAAGATTTTTCTTTAAAATGAAGTGTCTCAAAAGAGACAAAATTTTGTTTCC
1 AAGAAACAGACTCAAAGATTTTTC--TAAAATAAACTGTCTCAAAAGAGACAAAATTTTGTTTCC
1489486 AAAAAACATACTCAAAGATTCTTTCA
64 AAAAAACATACTCAAAGATTCTTTCA
1489512 AAAGAAACTT
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
100 4 0.05
101 17 0.22
102 22 0.28
103 35 0.45
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (100 bp):
AAGAAACAGACTCAAAGATTTTTCTAAAATAAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAA
AAAACATACTCAAAGATTCTTTCATTTTGTTTTAG
Found at i:1489547 original size:166 final size:168
Alignment explanation
Indices: 1489257--1489611 Score: 581
Period size: 167 Copynumber: 2.1 Consensus size: 168
1489247 GTTTTCATAA
*
1489257 AAACAGACTTAAAGATTTTTCTTCAAAAAGAACTGTCTCAAAAGAGACAAAAATGTTTTTCCAAA
1 AAACAGACTCAAAGATTTTTCTTCAAAAAGAACTGTCTCAAAAGAGACAAAAATGTTTTTCCAAA
* *
1489322 GAAACATACTCAAAGATTCTTTCAAAATAAACTTTCTCAAAATAGACAAAATTTTGTTATCAAAG
66 GAAACATACTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAAAG
*
1489387 AAACATACTCAAAG-GTTTTTTCATTTTGTTTTAGGTG
131 AAACATACTCAAAGAGTTTTTTCATTTTGTTTTAAGTG
* * * *
1489424 AAACAGACTCAAAGATTTTTCTTTAAAATGAAGTGTCTCAAAAGAGAC-AAAATTTTGTTTCCAA
1 AAACAGACTCAAAGATTTTTCTTCAAAAAGAACTGTCTCAAAAGAGACAAAAATGTT-TTTCCAA
1489488 A-AAACATACTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAAA
65 AGAAACATACTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAAA
* *
1489552 GAAACATACTCAAAGATTTTTTTTATTTTGTTTTAAGTG
130 GAAACATACTCAAAGAGTTTTTTCATTTTGTTTTAAGTG
*
1489591 AAATAGACTCAAAGATTTTTC
1 AAACAGACTCAAAGATTTTTC
1489612 AAGAAAATCT
Statistics
Matches: 175, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
166 83 0.47
167 92 0.53
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (168 bp):
AAACAGACTCAAAGATTTTTCTTCAAAAAGAACTGTCTCAAAAGAGACAAAAATGTTTTTCCAAA
GAAACATACTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAAAG
AAACATACTCAAAGAGTTTTTTCATTTTGTTTTAAGTG
Found at i:1489580 original size:38 final size:38
Alignment explanation
Indices: 1489538--1489610 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
1489528 AAGAGACAAA
*
1489538 ATTTTGTTATCAA-AGAAACATACTCAAAGATTTTTTTT
1 ATTTTGTT-TCAAGAGAAACAGACTCAAAGATTTTTTTT
* * *
1489576 ATTTTGTTTTAAGTGAAATAGACTCAAAGATTTTT
1 ATTTTGTTTCAAGAGAAACAGACTCAAAGATTTTT
1489611 CAAGAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 3 0.10
38 27 0.90
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (38 bp):
ATTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTTT
Found at i:1489777 original size:36 final size:35
Alignment explanation
Indices: 1489737--1489847 Score: 107
Period size: 37 Copynumber: 3.1 Consensus size: 35
1489727 ATAATTTGGA
* * *
1489737 AAATTTTCTCAAGTGAGACAATATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAA-AATTGTTTTTAGAG
* * * *
1489773 AAATTGTCTCAAACAAGACAAAAAATTGCTTTTAGGG
1 AAATTGTCTCAAGCGAGAC--AAAATTGTTTTTAGAG
*
1489810 AAATTGTCTCAAGCGAGACAAAGCTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAAA-ATTGTTTTTAGAG
1489845 AAA
1 AAA
1489848 ACGATCTCAA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
35 8 0.13
36 22 0.37
37 28 0.47
38 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (35 bp):
AAATTGTCTCAAGCGAGACAAAATTGTTTTTAGAG
Found at i:1490001 original size:107 final size:104
Alignment explanation
Indices: 1489843--1490141 Score: 361
Period size: 107 Copynumber: 2.8 Consensus size: 104
1489833 CTTGTTTTTG
* *
1489843 AGAAAACGATCTCAAGTGAGATTAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTACTCTCA
1 AGAAAACGATCTCAAATGAGATTAACTTTATTTAATGTGAAACAAATTCGAAATTTGTACTCTCA
* *
1489908 AAGGAAAAATGCCTCAAATGAGACGAAATTTATTTTGAA
66 AAGGAAAAATGTCTCAAACGAGACGAAATTTATTTTGAA
* * *
1489947 AGAAATAAC-AGTCTCAAATGAGATTAATTTTTTTTCCAA-GTGAATCAAATTCGAAATTTGTAC
1 AG-AA-AACGA-TCTCAAATGAGATTAACTTTATTT--AATGTGAAACAAATTCGAAATTTGTAC
* * * * * * **
1490010 -GTCAAAGGAAAAAATGTCTCAAGCAAGACGGAGTTTTTTTTTTA
61 TCTCAAAGG-AAAAATGTCTCAAACGAGACGAAATTTATTTTGAA
* * *
1490054 AGAAAGCGATCTCAAATGAGATCAACTTTATTTAATGTGAAACAAATTCGAAATTTGTATTCTCA
1 AGAAAACGATCTCAAATGAGATTAACTTTATTTAATGTGAAACAAATTCGAAATTTGTACTCTCA
1490119 AAGGAAAAATGTCTCAAACGAGA
66 AAGGAAAAATGTCTCAAACGAGA
1490142 AAGAATTTTG
Statistics
Matches: 163, Mismatches: 23, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
103 2 0.01
104 41 0.25
105 33 0.20
106 34 0.21
107 51 0.31
108 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (104 bp):
AGAAAACGATCTCAAATGAGATTAACTTTATTTAATGTGAAACAAATTCGAAATTTGTACTCTCA
AAGGAAAAATGTCTCAAACGAGACGAAATTTATTTTGAA
Found at i:1490471 original size:16 final size:16
Alignment explanation
Indices: 1490450--1490489 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1490440 CTCATGTAAT
**
1490450 ATGTATGTATGTGTTG
1 ATGTATGTATGAATTG
*
1490466 ATGTATATATGAATTG
1 ATGTATGTATGAATTG
1490482 ATGTATGT
1 ATGTATGT
1490490 TTTCTCAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (16 bp):
ATGTATGTATGAATTG
Found at i:1491807 original size:14 final size:14
Alignment explanation
Indices: 1491788--1491823 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1491778 TCTTTGTCAT
1491788 CTTTTTGTTCTTTG
1 CTTTTTGTTCTTTG
*
1491802 CTTTTTTTTCTTTG
1 CTTTTTGTTCTTTG
1491816 -TTTTTGTT
1 CTTTTTGTT
1491824 TTTTCCTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (14 bp):
CTTTTTGTTCTTTG
Found at i:1495686 original size:5 final size:5
Alignment explanation
Indices: 1495660--1495743 Score: 73
Period size: 5 Copynumber: 16.6 Consensus size: 5
1495650 AACATAATGG
* * *
1495660 AAATA AATATT AAATAA AAATA AAATA AAATA AGATA AGATA AAATA AAAT-
1 AAATA AA-ATA AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * *
1495711 AAA-A AAACA ACATA CAAATG AAATA AAATA AAA
1 AAATA AAATA AAATA -AAATA AAATA AAATA AAA
1495744 CCACAACATG
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
4 6 0.09
5 48 0.74
6 11 0.17
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1495708 original size:25 final size:24
Alignment explanation
Indices: 1495676--1495742 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
1495666 ATATTAAATA
* *
1495676 AAAATAAAATAAAATAAGATAAGAT
1 AAAATAAAATAAAATAA-ACAACAT
1495701 AAAATAAAATAAAA-AAACAACAT
1 AAAATAAAATAAAATAAACAACAT
*
1495724 ACAAATGAAATAAAATAAA
1 A-AAATAAAATAAAATAAA
1495743 ACCACAACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 6 0.16
24 14 0.38
25 17 0.46
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (24 bp):
AAAATAAAATAAAATAAACAACAT
Found at i:1498047 original size:3 final size:3
Alignment explanation
Indices: 1498039--1498103 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
1498029 AGTATCGTTC
1498039 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1498086 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
1498104 CCTTTTTCTC
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1510789 original size:43 final size:43
Alignment explanation
Indices: 1510742--1510854 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
1510732 CTGCAACATA
* *
1510742 TCAGGTTCTATATCGACTTTTTTTTTACAAACACCGCAACAGG
1 TCAGGTTCTATATCGACTTTTTTTATACAAACACCACAACAGG
* * *
1510785 TCAGGTTCTATAGTGGA-TTTTTTTATACAAACGCCACAACATG
1 TCAGGTTCTATA-TCGACTTTTTTTATACAAACACCACAACAGG
* *
1510828 TCAGGTTCTATAACGACTTTTTATATA
1 TCAGGTTCTATATCGACTTTTTTTATA
1510855 AACGCAGCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 55 0.92
44 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (43 bp):
TCAGGTTCTATATCGACTTTTTTTATACAAACACCACAACAGG
Found at i:1510849 original size:41 final size:41
Alignment explanation
Indices: 1510735--1510883 Score: 138
Period size: 43 Copynumber: 3.5 Consensus size: 41
1510725 ACAAATGCTG
* * * * *
1510735 CAACATATCAGGTTCTATATCGACTTTTTTTTTACAAACACCG
1 CAACATGTCAGGTTCTATAACGAC--TTTTTATACAAACGCCA
* ** *
1510778 CAACAGGTCAGGTTCTATAGTGGATTTTTTTATACAAACGCCA
1 CAACATGTCAGGTTCTATA-ACGA-CTTTTTATACAAACGCCA
*
1510821 CAACATGTCAGGTTCTATAACGACTTTTTATATAAACG-CA
1 CAACATGTCAGGTTCTATAACGACTTTTTATACAAACGCCA
* *
1510861 GCAACAAGTCAGGTTATATAACG
1 -CAACATGTCAGGTTCTATAACG
1510884 GCGATTTTTA
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
40 2 0.02
41 33 0.37
42 2 0.02
43 49 0.55
44 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (41 bp):
CAACATGTCAGGTTCTATAACGACTTTTTATACAAACGCCA
Found at i:1513624 original size:39 final size:39
Alignment explanation
Indices: 1513568--1513642 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
1513558 TTTACCATTT
*
1513568 AGAGGTAATAAATTGAGTTGATTGCCATTAGTGATAATC
1 AGAGGTAATAAACTGAGTTGATTGCCATTAGTGATAATC
*
1513607 AGAGGTAATAAACTGAGTTGATTGTCATTAGTGATA
1 AGAGGTAATAAACTGAGTTGATTGCCATTAGTGATA
1513643 CTGAACTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (39 bp):
AGAGGTAATAAACTGAGTTGATTGCCATTAGTGATAATC
Found at i:1514014 original size:53 final size:53
Alignment explanation
Indices: 1513941--1514042 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 53
1513931 ATCTACTAAT
* * *
1513941 ACTATATAAAACTTAATATAAGCATAAATTGAT-ATATTTAACCAAAAAAATTA
1 ACTATACAAAACTTAATATAAACATAAATGGATAAT-TTTAACCAAAAAAATTA
* * **
1513994 ACTATACAAAGCTTATTATAAATGTAAATGGATAATTTTAACCAAAAAA
1 ACTATACAAAACTTAATATAAACATAAATGGATAATTTTAACCAAAAAA
1514043 TTATCAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 39 0.95
54 2 0.05
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (53 bp):
ACTATACAAAACTTAATATAAACATAAATGGATAATTTTAACCAAAAAAATTA
Found at i:1517689 original size:39 final size:39
Alignment explanation
Indices: 1517638--1517735 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
1517628 AACGAAGAGA
* *
1517638 AAAATGGTGAATTAGGGATTGAGATGCGA-AGGAGAATTG
1 AAAATGGGGAATTAGGGATTGAGATGCGAGAGG-GAAATG
*
1517677 TAAAA-GGGGAATTAGGGATTGAGGTGCGAGAGGGAAATG
1 -AAAATGGGGAATTAGGGATTGAGATGCGAGAGGGAAATG
*
1517716 AAAATGGGAAATTAGGGATT
1 AAAATGGGGAATTAGGGATT
1517736 CTGGGAATTG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
38 4 0.08
39 41 0.79
40 7 0.13
ACGTcount: A:0.39, C:0.02, G:0.38, T:0.21
Consensus pattern (39 bp):
AAAATGGGGAATTAGGGATTGAGATGCGAGAGGGAAATG
Found at i:1518691 original size:19 final size:18
Alignment explanation
Indices: 1518659--1518716 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
1518649 TCATTGAAAA
*
1518659 AACCAAAAAACCGAACCG
1 AACCAAAAACCCGAACCG
1518677 AACCGAAAAACCCGAACCG
1 AACC-AAAAACCCGAACCG
1518696 TTAA--AAAAA-CCGAACCG
1 --AACCAAAAACCCGAACCG
1518713 AACC
1 AACC
1518717 GATAAAACCG
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
15 2 0.06
17 8 0.24
18 9 0.26
19 13 0.38
21 2 0.06
ACGTcount: A:0.52, C:0.33, G:0.12, T:0.03
Consensus pattern (18 bp):
AACCAAAAACCCGAACCG
Found at i:1522268 original size:31 final size:31
Alignment explanation
Indices: 1522230--1522379 Score: 266
Period size: 31 Copynumber: 4.8 Consensus size: 31
1522220 CGAGGGTTAT
1522230 CTATGTTCTTCGGGACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
1522261 CTATGTTCTTCGGGACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
1522292 CTATGTTCTTCGGGACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
1522323 CTATGTTCTTCGGGACATATGGACTGTTTAC
1 CTATGTTCTTCGGGACATATGGACTGTTTAC
* *
1522354 CTAGGTTCTTCGGAATC-TATGGACTG
1 CTATGTTCTTCGGGA-CATATGGACTG
1522380 GTCTTTTGGG
Statistics
Matches: 116, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
CTATGTTCTTCGGGACATATGGACTGTTTAC
Found at i:1525148 original size:39 final size:39
Alignment explanation
Indices: 1525096--1525194 Score: 121
Period size: 39 Copynumber: 2.5 Consensus size: 39
1525086 AAACGAAGAG
* *
1525096 AAAAATGGTGAATTAGGGATTGAGATGCGA-AGGAGAATT
1 AAAAATGGGGAATTAGGGATTGAGATGCGAGAGG-GAAAT
* *
1525135 GTAAAA-GGGGAATTAGGGATTGAGGTGCGAGAGGGAAAT
1 -AAAAATGGGGAATTAGGGATTGAGATGCGAGAGGGAAAT
*
1525174 AAAAATGGGAAATTAGGGATT
1 AAAAATGGGGAATTAGGGATT
1525195 CTGGGAATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 4 0.08
39 40 0.78
40 7 0.14
ACGTcount: A:0.40, C:0.02, G:0.36, T:0.21
Consensus pattern (39 bp):
AAAAATGGGGAATTAGGGATTGAGATGCGAGAGGGAAAT
Found at i:1528398 original size:16 final size:16
Alignment explanation
Indices: 1528377--1528409 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1528367 TGGACTTGAA
1528377 AGTATTCATTTTGTGT
1 AGTATTCATTTTGTGT
1528393 AGTATTCATTTTGTGT
1 AGTATTCATTTTGTGT
1528409 A
1 A
1528410 TTTAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.55
Consensus pattern (16 bp):
AGTATTCATTTTGTGT
Found at i:1535149 original size:8 final size:8
Alignment explanation
Indices: 1535136--1535176 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1535126 CTTATTTTTA
1535136 GAGAATTT
1 GAGAATTT
1535144 GAGAATTT
1 GAGAATTT
*
1535152 -AGAGTTT
1 GAGAATTT
*
1535159 GGGAATTT
1 GAGAATTT
1535167 GAGAATTT
1 GAGAATTT
1535175 GA
1 GA
1535177 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1535485 original size:128 final size:128
Alignment explanation
Indices: 1535257--1535589 Score: 569
Period size: 128 Copynumber: 2.6 Consensus size: 128
1535247 ACTATTCATA
*
1535257 TGAAGGCGCGTTCCCGGGGGCGCGCTTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * *
1535322 TTATGTCACTCATGTCCCTCATGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAATACATATTATGTCTCAGGGGACT
*
1535385 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
1535450 TTATGTCACTCATGTCCCTCGGGGATACTATTCATATCAATACATATTATGTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAATACATATTATGTCTCAGGGGACT
* *
1535513 TGAAGGCGCGTTCCCGGGGG-GTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1535577 TTATGTCACTCAT
66 TTATGTCACTCAT
1535590 TATCCTATTA
Statistics
Matches: 194, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
127 55 0.28
128 139 0.72
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAATACATATTATGTCTCAGGGGACT
Found at i:1535595 original size:20 final size:20
Alignment explanation
Indices: 1535566--1535609 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1535556 GAATATGTTA
*
1535566 TCATTGTCCTATTATGTCAC
1 TCATTATCCTATTATGTCAC
1535586 TCATTATCCTATTATGTCAC
1 TCATTATCCTATTATGTCAC
1535606 TCAT
1 TCAT
1535610 GTCCCTCGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (20 bp):
TCATTATCCTATTATGTCAC
Found at i:1536058 original size:34 final size:32
Alignment explanation
Indices: 1536019--1536122 Score: 113
Period size: 34 Copynumber: 3.2 Consensus size: 32
1536009 TAAGTTGAAA
*
1536019 TTTAATGTTAAATTTTGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATA-TATAATTTATAT
* *
1536053 TTTAATTTTAAATTTCGAATAATATTATTTTTATT
1 TTTAA-TTTAAATTTCGAAT-ATATAATTTATA-T
*
1536088 TTTAATTTAAATTTCG-A-ATATAATTTGTAT
1 TTTAATTTAAATTTCGAATATATAATTTATAT
1536118 TTTAA
1 TTTAA
1536123 AAACATTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
30 6 0.10
31 10 0.16
33 1 0.02
34 37 0.60
35 8 0.13
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (32 bp):
TTTAATTTAAATTTCGAATATATAATTTATAT
Found at i:1536660 original size:21 final size:20
Alignment explanation
Indices: 1536633--1536744 Score: 152
Period size: 21 Copynumber: 5.3 Consensus size: 20
1536623 GGTATAAAAC
*
1536633 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
1536653 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
1536674 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
1536695 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
1536716 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
1536737 CCCTGCGG
1 -CCTGCGG
1536745 AGATGGCATA
Statistics
Matches: 84, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
20 6 0.07
21 72 0.86
22 6 0.07
ACGTcount: A:0.20, C:0.26, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:1536693 original size:42 final size:42
Alignment explanation
Indices: 1536630--1536738 Score: 200
Period size: 42 Copynumber: 2.6 Consensus size: 42
1536620 TATGGTATAA
* *
1536630 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1536672 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1536714 AACCCTGCGGGCTCGGAATGTAACC
1 AACCCTGCGGGCTCGGAATGTAACC
1536739 CTGCGGAGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.22, C:0.26, G:0.34, T:0.18
Consensus pattern (42 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:1537915 original size:245 final size:243
Alignment explanation
Indices: 1537480--1537970 Score: 818
Period size: 245 Copynumber: 2.0 Consensus size: 243
1537470 TTCGAAAATT
1537480 ACCTCACAATAAGGGAATACGTATGGTCATTCACGATCGGGCATAAGAACGGCATACGGAACCAC
1 ACCTCACAATAAGGGAATACGTATGGTCATTCACGATCGGGCATAAGAACGGCATACGGAACCAC
1537545 GCCCATGATTGTAAGCATGGACGCCATCGATAGCAATTTTCTTATAATTCGTCACCCGACATATT
66 GCCCATGATTGTAAGCATGGAC-CCATCGATAGCAA-TTTCTTATAATTCGTCACCCGACATATT
1537610 TCTCTAAAGAGAAATGCCAAAACTGCAGCGCCCCCAACTATATCTTCCTTCATCAAATCGATCAG
129 TCTCTAAAGAGAAATGCCAAAACTGCAGCGCCCCCAACTATATCTTCCTTCATCAAATCGATCAG
1537675 ATGCCGCAACCACATACAATGCACCTGGTTGCGAGATTTGTCGGACATCA
194 ATGCCGCAACCACATACAATGCACCTGGTTGCGAGATTTGTCGGACATCA
1537725 ACCTCACAATAAGGGGAATACGTTATGG-CAATTCACGATCGGGCATAAGAA-GG-ATACGGAAC
1 ACCTCACAATAA-GGGAATACG-TATGGTC-ATTCACGATCGGGCATAAGAACGGCATACGGAAC
1537787 CACGCCCATGATTGTAGAAGCATGAGA-CCATCGATAGCAA-TT-TTATAATTCGTCACCCGAC-
63 CACGCCCATGATTGT--AAGCATG-GACCCATCGATAGCAATTTCTTATAATTCGTCACCCGACA
1537848 TATTTCTCTAAAGAGAAATGCCAAAACTGCAGCG-CCCCAACTATATCTTCCAGCTTCATCAAAA
125 TATTTCTCTAAAGAGAAATGCCAAAACTGCAGCGCCCCCAACTATATCTT-C--CTTCATC-AAA
1537912 TCGATCAGATGCCGCAACCACATACAATGCACCTGGTTGCGAGATTTGTCGGACATCA
186 TCGATCAGATGCCGCAACCACATACAATGCACCTGGTTGCGAGATTTGTCGGACATCA
1537970 A
1 A
1537971 TATTCTCCAA
Statistics
Matches: 236, Mismatches: 0, Indels: 20
0.92 0.00 0.08
Matches are distributed among these distances:
241 15 0.06
242 35 0.15
243 19 0.08
244 9 0.04
245 98 0.42
246 25 0.11
247 33 0.14
248 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (243 bp):
ACCTCACAATAAGGGAATACGTATGGTCATTCACGATCGGGCATAAGAACGGCATACGGAACCAC
GCCCATGATTGTAAGCATGGACCCATCGATAGCAATTTCTTATAATTCGTCACCCGACATATTTC
TCTAAAGAGAAATGCCAAAACTGCAGCGCCCCCAACTATATCTTCCTTCATCAAATCGATCAGAT
GCCGCAACCACATACAATGCACCTGGTTGCGAGATTTGTCGGACATCA
Found at i:1538364 original size:26 final size:27
Alignment explanation
Indices: 1538335--1538399 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
1538325 GTATCCTAAA
*
1538335 TAATATACATT-ATAAAAAATTAAAAT
1 TAATATAAATTCATAAAAAATTAAAAT
* * *
1538361 TAATATAAATTCATAATAACTTTAAAT
1 TAATATAAATTCATAAAAAATTAAAAT
*
1538388 TAAAAATAAATT
1 T-AATATAAATT
1538400 TAAATAGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 10 0.31
27 13 0.41
28 9 0.28
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (27 bp):
TAATATAAATTCATAAAAAATTAAAAT
Found at i:1538388 original size:17 final size:17
Alignment explanation
Indices: 1538351--1538404 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1538341 ACATTATAAA
* *
1538351 AAATT-AAAATTAATAT
1 AAATTAAAAATAAATTT
* * *
1538367 AAATTCATAATAACTTT
1 AAATTAAAAATAAATTT
1538384 AAATTAAAAATAAATTT
1 AAATTAAAAATAAATTT
1538401 AAAT
1 AAAT
1538405 AGTAACATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTAAAAATAAATTT
Found at i:1538601 original size:16 final size:15
Alignment explanation
Indices: 1538552--1538616 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
1538542 ATAATTCTAA
*
1538552 ATAAATAATAATTAT
1 ATAAATAATATTTAT
*
1538567 ATAAATATTATTT-T
1 ATAAATAATATTTAT
1538581 AATAAAATAATATTTAT
1 -AT-AAATAATATTTAT
* *
1538598 AT-AATTATATTAAT
1 ATAAATAATATTTAT
1538612 ATAAA
1 ATAAA
1538617 ATATAATAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 13 0.32
15 15 0.37
16 12 0.29
17 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAATAATATTTAT
Found at i:1538613 original size:14 final size:14
Alignment explanation
Indices: 1538559--1538615 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
1538549 TAAATAAATA
1538559 ATAATTATA-TAA-
1 ATAATTATATTAAT
*
1538571 AT-ATTATTTTAAT
1 ATAATTATATTAAT
* * *
1538584 AAAATAATATTTAT
1 ATAATTATATTAAT
1538598 ATAATTATATTAAT
1 ATAATTATATTAAT
1538612 ATAA
1 ATAA
1538616 AATATAATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 1 0.03
14 23 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATATTAAT
Found at i:1538977 original size:61 final size:60
Alignment explanation
Indices: 1538829--1538977 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
1538819 GGCATTTAAT
* * * * * *
1538829 GGAAGGCGCGTCCCCGGGGATGCGCCTTCCACACGTGGCAGCCGAGTCATCAGAATCCCG
1 GGAAAGCGCGTCCCCGGGGATGCGCCTTCAACACGTGGCAGCCAACTCAGCAAAATCCCG
* * *
1538889 GGAAGGCGCGTCCCCGGGGATGCGCCTTCAACACGTGGCATCCAACTCAGCGAAAAT-CTG
1 GGAAAGCGCGTCCCCGGGGATGCGCCTTCAACACGTGGCAGCCAACTCAGC-AAAATCCCG
* *
1538949 GGTAAAGCGCGTCCCCGAGGATACGCCTT
1 GG-AAAGCGCGTCCCCGGGGATGCGCCTT
1538978 TCGCCAGCTC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
60 50 0.65
61 27 0.35
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.15
Consensus pattern (60 bp):
GGAAAGCGCGTCCCCGGGGATGCGCCTTCAACACGTGGCAGCCAACTCAGCAAAATCCCG
Found at i:1542690 original size:18 final size:18
Alignment explanation
Indices: 1542667--1542715 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1542657 TATTTTATAT
1542667 ATATTAACTTAAATTCAC
1 ATATTAACTTAAATTCAC
* * *
1542685 ATATTAAGTTAATTTTAC
1 ATATTAACTTAAATTCAC
*
1542703 ATTTTAACATTAA
1 ATATTAAC-TTAA
1542716 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATATTAACTTAAATTCAC
Found at i:1542814 original size:31 final size:29
Alignment explanation
Indices: 1542737--1542870 Score: 151
Period size: 29 Copynumber: 4.5 Consensus size: 29
1542727 TCAACATATT
* * **
1542737 AAATATATTTTATTCTTTTCGTAACCTAA
1 AAATATATTTTATTCTTATCTTAAATTAA
* * *
1542766 AAATATAGTTTATTCTTATTTTAATTTTAA
1 AAATATATTTTATTCTTATCTTAA-ATTAA
*
1542796 AATATATATTTTAATCTTATCTTAAATTAA
1 AA-ATATATTTTATTCTTATCTTAAATTAA
*
1542826 AAATATAATTTATTCTTATCTTAAATTAA
1 AAATATATTTTATTCTTATCTTAAATTAA
1542855 ATATATATATTTTATT
1 A-A-ATATATTTTATT
1542871 ATGATAATAT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
29 46 0.52
30 12 0.14
31 30 0.34
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (29 bp):
AAATATATTTTATTCTTATCTTAAATTAA
Found at i:1542827 original size:60 final size:60
Alignment explanation
Indices: 1542739--1542868 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 60
1542729 AACATATTAA
* * * * * *
1542739 ATATATTTTATTCTTTTCGTAACCTAAAAATATAGTTTATTCTTATTTTAATTTTAAA-AT
1 ATATATTTTAATCTTATCGTAAACTAAAAATATAATTTATTCTTATCTTAA-ATTAAATAT
* *
1542799 ATATATTTTAATCTTATCTTAAATTAAAAATATAATTTATTCTTATCTTAAATTAAATAT
1 ATATATTTTAATCTTATCGTAAACTAAAAATATAATTTATTCTTATCTTAAATTAAATAT
1542859 ATATATTTTA
1 ATATATTTTA
1542869 TTATGATAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 5 0.08
60 56 0.92
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (60 bp):
ATATATTTTAATCTTATCGTAAACTAAAAATATAATTTATTCTTATCTTAAATTAAATAT
Found at i:1542961 original size:25 final size:24
Alignment explanation
Indices: 1542926--1543012 Score: 84
Period size: 25 Copynumber: 3.3 Consensus size: 24
1542916 TAGTTAAGAC
*
1542926 AAAATTAAAAATATATTTTTCTAGTT
1 AAAA-TAAAAATATATTTTT-AAGTT
1542952 AAAATAAAAATATATTTTTAAGTT
1 AAAATAAAAATATATTTTTAAGTT
*
1542976 AAGATAATAATAAAAGATATGTTTTAAGTT
1 -A-A-AAT-A-AAAATATAT-TTTTAAGTT
1543006 AAAATAA
1 AAAATAA
1543013 TAATTAATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
24 4 0.08
25 17 0.32
26 6 0.11
27 6 0.11
28 2 0.04
29 9 0.17
30 9 0.17
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (24 bp):
AAAATAAAAATATATTTTTAAGTT
Found at i:1542990 original size:30 final size:29
Alignment explanation
Indices: 1542877--1543180 Score: 199
Period size: 30 Copynumber: 10.3 Consensus size: 29
1542867 TATTATGATA
* * * *
1542877 ATATTTTAAATTTAAGATAAAAATATAAT
1 ATATTTTTAAGTTAAGATAAGAATAAAAT
* *
1542906 ATATTTTTTGTAGTTAAGACAA-AATTAAAAAT
1 ATA-TTTTT-AAGTTAAGATAAGAA-T-AAAAT
* *
1542938 ATATTTTT---CT-AGTTAA-AATAAAAAT
1 ATATTTTTAAGTTAAGATAAGAAT-AAAAT
* *
1542963 ATATTTTTAAGTTAAGATAATAATAAAAG
1 ATATTTTTAAGTTAAGATAAGAATAAAAT
* * * *
1542992 ATATGTTTTAAGTTAAAATAATAATTAATT
1 ATAT-TTTTAAGTTAAGATAAGAATAAAAT
* * * * *
1543022 ATATTTAATAATTTCAGGTAAGAATATAAT
1 ATATTT-TTAAGTTAAGATAAGAATAAAAT
* * *
1543052 ATATTTAATAATTTAAG-TAAAGAATATAAT
1 ATATTT-TTAAGTTAAGAT-AAGAATAAAAT
* **
1543082 TTATGTAATAAGTTAAGATAAGAATAAAAT
1 ATAT-TTTTAAGTTAAGATAAGAATAAAAT
**
1543112 ATATTTTTTAAGTTAAGATAAAGTCTAAAAT
1 ATA-TTTTTAAGTTAAGAT-AAGAATAAAAT
*
1543143 ATGTTTTTAAGTTAAGATAAGAATAAAAT
1 ATATTTTTAAGTTAAGATAAGAATAAAAT
1543172 ATATTTTTA
1 ATATTTTTA
1543181 GGTTGTACAA
Statistics
Matches: 221, Mismatches: 38, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
25 15 0.07
26 6 0.03
27 1 0.00
28 1 0.00
29 36 0.16
30 126 0.57
31 29 0.13
32 7 0.03
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (29 bp):
ATATTTTTAAGTTAAGATAAGAATAAAAT
Found at i:1543696 original size:2 final size:2
Alignment explanation
Indices: 1543689--1543715 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1543679 ATCTTAACCC
1543689 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1543716 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1547245 original size:8 final size:8
Alignment explanation
Indices: 1547232--1547296 Score: 53
Period size: 8 Copynumber: 8.4 Consensus size: 8
1547222 AAATCCATCA
1547232 AAATAAAT
1 AAATAAAT
1547240 AAATAAAT
1 AAATAAAT
* *
1547248 AAAT-TAG
1 AAATAAAT
*
1547255 AAACAAAT
1 AAATAAAT
* *
1547263 GAATACAT
1 AAATAAAT
**
1547271 AAATTTA-
1 AAATAAAT
1547278 AAATAAAT
1 AAATAAAT
1547286 AAATAAAT
1 AAATAAAT
1547294 AAA
1 AAA
1547297 AATTACCTCC
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
7 9 0.21
8 33 0.79
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (8 bp):
AAATAAAT
Found at i:1547267 original size:23 final size:23
Alignment explanation
Indices: 1547231--1547296 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1547221 TAAATCCATC
*
1547231 AAAATAAATAAATAAATAAA-TT
1 AAAACAAATAAATAAATAAATTT
* *
1547253 AGAAACAAATGAATACATAAATTT
1 A-AAACAAATAAATAAATAAATTT
*
1547277 AAAATAAATAAATAAATAAA
1 AAAACAAATAAATAAATAAA
1547297 AATTACCTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.03
23 32 0.89
24 3 0.08
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (23 bp):
AAAACAAATAAATAAATAAATTT
Found at i:1549448 original size:22 final size:22
Alignment explanation
Indices: 1549420--1549487 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
1549410 ACGAACATAA
1549420 ATGAACAATAACAAAAACGAAC
1 ATGAACAATAACAAAAACGAAC
* *
1549442 ATGAACAATAAAAAAAACGAAT
1 ATGAACAATAACAAAAACGAAC
* * * *
1549464 ACGAACAAAAACGAACACGAAC
1 ATGAACAATAACAAAAACGAAC
1549486 AT
1 AT
1549488 AAATGAATGC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.63, C:0.18, G:0.10, T:0.09
Consensus pattern (22 bp):
ATGAACAATAACAAAAACGAAC
Found at i:1549475 original size:16 final size:16
Alignment explanation
Indices: 1549454--1549507 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
1549444 GAACAATAAA
1549454 AAAAACGAATACGAAC
1 AAAAACGAATACGAAC
*
1549470 AAAAACGAACACGAAC
1 AAAAACGAATACGAAC
* * *
1549486 ATAAATGAATGCGAAC
1 AAAAACGAATACGAAC
*
1549502 ATAAAC
1 AAAAAC
1549508 ATTAGATACC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.59, C:0.19, G:0.13, T:0.09
Consensus pattern (16 bp):
AAAAACGAATACGAAC
Found at i:1549759 original size:12 final size:11
Alignment explanation
Indices: 1549728--1549771 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
1549718 AACTCGAGAC
*
1549728 TCAAGCTCAAT
1 TCAAGCTCGAT
*
1549739 TGAAGCTCGAT
1 TCAAGCTCGAT
1549750 TCAGAGCTCGAT
1 TCA-AGCTCGAT
1549762 TCAAGCTCGA
1 TCAAGCTCGA
1549772 CATTGCCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (11 bp):
TCAAGCTCGAT
Found at i:1549767 original size:23 final size:23
Alignment explanation
Indices: 1549705--1549772 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
1549695 AAAAAAATTA
*
1549705 AGAGCTCGATTAAAACTCGAGACTC
1 AGAGCTCGATTAAAGCTC--GACTC
* * *
1549730 A-AGCTCAATTGAAGCTCGATTC
1 AGAGCTCGATTAAAGCTCGACTC
*
1549752 AGAGCTCGATTCAAGCTCGAC
1 AGAGCTCGATTAAAGCTCGAC
1549773 ATTGCCCCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 5 0.14
23 16 0.46
24 13 0.37
25 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
AGAGCTCGATTAAAGCTCGACTC
Found at i:1550658 original size:14 final size:14
Alignment explanation
Indices: 1550641--1550671 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1550631 AATGAACATA
*
1550641 AACGAACATAATCG
1 AACGAACATAAACG
1550655 AACGAACATAAACG
1 AACGAACATAAACG
1550669 AAC
1 AAC
1550672 ACAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1550661 original size:24 final size:24
Alignment explanation
Indices: 1550634--1550682 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1550624 ATAAATGAAT
* *
1550634 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACACAACCGAAC
1550658 GAACATAAACGAACACAACCGAAC
1 GAACATAAACGAACACAACCGAAC
1550682 G
1 G
1550683 TTCACGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.24, G:0.14, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACACAACCGAAC
Found at i:1563835 original size:2 final size:2
Alignment explanation
Indices: 1563830--1563889 Score: 70
Period size: 2 Copynumber: 30.5 Consensus size: 2
1563820 TTTATATTAG
*
1563830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1563870 GAT AT AT AT TT TT AT AT AT A
1 -AT AT AT AT AT AT AT AT AT A
1563890 CTTTTATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
1 2 0.04
2 48 0.94
3 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
AT
Found at i:1564111 original size:21 final size:21
Alignment explanation
Indices: 1564067--1564112 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1564057 TCTACAATTA
*
1564067 TTATTTTCTTTATTTGTGTTT
1 TTATTTTCTTTATTTGTGTAT
*
1564088 TTATTTT-TTTATTTTTGATAT
1 TTATTTTCTTTATTTGTG-TAT
1564109 TTAT
1 TTAT
1564113 GTATTTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (21 bp):
TTATTTTCTTTATTTGTGTAT
Found at i:1569964 original size:35 final size:36
Alignment explanation
Indices: 1569899--1569973 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 36
1569889 CTCAAAATTG
1569899 ATATCTTTTAATAATAAAATTTAAACATATA-ATA-
1 ATATCTTTTAATAATAAAATTTAAACATATATATAT
* * *
1569933 ATATCTTTTTAAT-TTAAAATATTTAATATATATATAT
1 ATATC-TTTTAATAATAAAAT-TTAAACATATATATAT
1569970 ATAT
1 ATAT
1569974 ATATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 11 0.32
35 16 0.47
36 3 0.09
37 4 0.12
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (36 bp):
ATATCTTTTAATAATAAAATTTAAACATATATATAT
Found at i:1569965 original size:2 final size:2
Alignment explanation
Indices: 1569958--1569983 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1569948 AAAATATTTA
1569958 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
1569984 CTTTCACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1570646 original size:15 final size:16
Alignment explanation
Indices: 1570608--1570648 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1570598 ACAGAGCCTC
*
1570608 TGAATCATTCAACGTT
1 TGAATCATTCAACGCT
1570624 TGAATCATTCAACGCT
1 TGAATCATTCAACGCT
1570640 T-AATCATTC
1 TGAATCATTC
1570649 TGAAGTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAACGCT
Found at i:1572984 original size:25 final size:24
Alignment explanation
Indices: 1572956--1573018 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
1572946 TAAAAAAACT
1572956 AAAATGATTTTATTTGTTTGTCAAA
1 AAAAT-ATTTTATTTGTTTGTCAAA
1572981 AAAATATTTTATTTGTTTGTCAAA
1 AAAATATTTTATTTGTTTGTCAAA
1573005 AAAATATTTTATTT
1 AAAATATTTTATTT
1573019 TTACGCCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 33 0.87
25 5 0.13
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (24 bp):
AAAATATTTTATTTGTTTGTCAAA
Found at i:1576934 original size:15 final size:16
Alignment explanation
Indices: 1576914--1576943 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1576904 TCTTTTGATT
1576914 TTTAAAAT-TATTATA
1 TTTAAAATGTATTATA
1576929 TTTAAAATGTATTAT
1 TTTAAAATGTATTAT
1576944 TAGAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAAAATGTATTATA
Found at i:1577146 original size:14 final size:14
Alignment explanation
Indices: 1577127--1577155 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1577117 TGGGGTGGAC
1577127 GCAACATTTATGTT
1 GCAACATTTATGTT
1577141 GCAACATTTATGTT
1 GCAACATTTATGTT
1577155 G
1 G
1577156 AGGGTGAACT
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:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (14 bp):
GCAACATTTATGTT
Found at i:1579376 original size:16 final size:16
Alignment explanation
Indices: 1579346--1579392 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1579336 TAGATTATTT
*
1579346 ATTAACATTATTTTAAA
1 ATTAA-ATTAATTTAAA
1579363 ATTAAATTAATTTAAA
1 ATTAAATTAATTTAAA
*
1579379 TTTAAATTGAATTT
1 ATTAAATT-AATTT
1579393 TTTTCATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTAAATTAATTTAAA
Found at i:1587826 original size:31 final size:31
Alignment explanation
Indices: 1587788--1587864 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
1587778 TAATACGTGG
1587788 ATTAAGTTTTGGTCACTTACA-TTATCGTTTT
1 ATTAAGTTTTGGTCACTTA-AGTTATCGTTTT
1587819 ATTAAGTTTTGGTCACTTAAGTTATCGTTTT
1 ATTAAGTTTTGGTCACTTAAGTTATCGTTTT
1587850 ATTAAGTTTTGGTCA
1 ATTAAGTTTTGGTCA
1587865 TTTGGACGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 1 0.02
31 44 0.98
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (31 bp):
ATTAAGTTTTGGTCACTTAAGTTATCGTTTT
Found at i:1588929 original size:16 final size:16
Alignment explanation
Indices: 1588908--1588946 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
1588898 AAAGAAGGCA
1588908 AATGGAATAATGAAGC
1 AATGGAATAATGAAGC
1588924 AATGGAATAATGAAGC
1 AATGGAATAATGAAGC
1588940 AATGGAA
1 AATGGAA
1588947 CAGAGATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.18
Consensus pattern (16 bp):
AATGGAATAATGAAGC
Found at i:1589186 original size:31 final size:31
Alignment explanation
Indices: 1589151--1589258 Score: 189
Period size: 31 Copynumber: 3.5 Consensus size: 31
1589141 TTCAACGTCC
*
1589151 AAGTGACCAAAAATTAATAAAACGATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAACGT
1589182 AAGTGACCAAAACTTAATAAAACGATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAACGT
**
1589213 AAGTGACCAAAACTTAATAAAATAATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAACGT
1589244 AAGTGACCAAAACTT
1 AAGTGACCAAAACTT
1589259 TTTTTTTGAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACGATAACGT
Found at i:1589990 original size:50 final size:50
Alignment explanation
Indices: 1589930--1590030 Score: 132
Period size: 50 Copynumber: 2.0 Consensus size: 50
1589920 AAATTTAAAA
* *
1589930 TAAATTTATTATTTTCCATTT-TGAAAATAAATTCAATATTGTTTTCATAT
1 TAAATTTATTATTTTACATTTCT-AAAATAAATTCAACATTGTTTTCATAT
* * * *
1589980 TAAATTTATTATTTTATATTTCTAAATTAAATTCAGCATTTTTTTCATAT
1 TAAATTTATTATTTTACATTTCTAAAATAAATTCAACATTGTTTTCATAT
1590030 T
1 T
1590031 TATATTTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (50 bp):
TAAATTTATTATTTTACATTTCTAAAATAAATTCAACATTGTTTTCATAT
Found at i:1590768 original size:67 final size:67
Alignment explanation
Indices: 1590659--1590790 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
1590649 CGTAGTGATG
* * * *
1590659 TGACACATAAGGTCGTGCCCACCACCTGCACTAAGTGCCCTTATATACTATAGTGTTGAATCAAA
1 TGACACATAAGATCGTGCCCACCACCTGCACTAAGTGCCCTTACACACTATAGTGATGAATCAAA
1590724 TA
66 TA
* *
1590726 TGACACATAAGATCGTGCTCACCACCTGCACTAAGTGTCCTTACACACTATAGTGATGAATCAAA
1 TGACACATAAGATCGTGCCCACCACCTGCACTAAGTGCCCTTACACACTATAGTGATGAATCAAA
1590791 CCTGCAGCTG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (67 bp):
TGACACATAAGATCGTGCCCACCACCTGCACTAAGTGCCCTTACACACTATAGTGATGAATCAAA
TA
Found at i:1595983 original size:19 final size:19
Alignment explanation
Indices: 1595939--1596001 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1595929 TAAAATATTT
* *
1595939 TAAAAATAAATATAAAATTA
1 TAAAATTAAGTATAAAA-TA
1595959 TAAAATTAAGTATAAAATA
1 TAAAATTAAGTATAAAATA
* * * *
1595978 TTAAATTTAGTTTAAAATG
1 TAAAATTAAGTATAAAATA
1595997 TAAAA
1 TAAAA
1596002 ATAATAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 21 0.58
20 15 0.42
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TAAAATTAAGTATAAAATA
Found at i:1596651 original size:15 final size:15
Alignment explanation
Indices: 1596631--1596660 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1596621 ATTCGGATCG
1596631 GGTTCGGGTCATTTC
1 GGTTCGGGTCATTTC
*
1596646 GGTTCGGGTTATTTC
1 GGTTCGGGTCATTTC
1596661 AATTTAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTCGGGTCATTTC
Found at i:1597509 original size:14 final size:14
Alignment explanation
Indices: 1597490--1597517 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1597480 TAGTGTCCTG
1597490 TCATTAAAAACTTA
1 TCATTAAAAACTTA
1597504 TCATTAAAAACTTA
1 TCATTAAAAACTTA
1597518 ACACGTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
TCATTAAAAACTTA
Found at i:1602842 original size:52 final size:52
Alignment explanation
Indices: 1602786--1602891 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
1602776 GAGGCACATG
* * *
1602786 TGCTCATGTAGCGTTCTGGCCCGGAAAAGAAGTTAAATTAGGCTCCAATCAT
1 TGCTCATGCAGCGTTCTGACCCAGAAAAGAAGTTAAATTAGGCTCCAATCAT
* * *
1602838 TGCTCATGCAGCGTTCTGACCCAGAAAAGAAGTTGAATTCGGCTCCAGTCAT
1 TGCTCATGCAGCGTTCTGACCCAGAAAAGAAGTTAAATTAGGCTCCAATCAT
1602890 TG
1 TG
1602892 TAGAGTCGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (52 bp):
TGCTCATGCAGCGTTCTGACCCAGAAAAGAAGTTAAATTAGGCTCCAATCAT
Found at i:1613450 original size:13 final size:13
Alignment explanation
Indices: 1613432--1613490 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
1613422 TTTATATTTT
1613432 TTAAATTCATATC
1 TTAAATTCATATC
1613445 TTAAATTCATAT-
1 TTAAATTCATATC
**
1613457 TTTTATT--T-TC
1 TTAAATTCATATC
1613467 -TAAATTCATATC
1 TTAAATTCATATC
1613479 TTAAATTCATAT
1 TTAAATTCATAT
1613491 TTTTATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
9 5 0.14
10 1 0.03
11 1 0.03
12 7 0.19
13 23 0.62
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAAATTCATATC
Found at i:1613457 original size:34 final size:34
Alignment explanation
Indices: 1613412--1613511 Score: 155
Period size: 34 Copynumber: 2.9 Consensus size: 34
1613402 TATTTTAGTC
* *
1613412 TAAATTTATATTTATATTTTTTAAATTCATATCT
1 TAAATTCATATTTTTATTTTTTAAATTCATATCT
*
1613446 TAAATTCATATTTTTATTTTCTAAATTCATATCT
1 TAAATTCATATTTTTATTTTTTAAATTCATATCT
* *
1613480 TAAATTCATATTTTTATTTTTAAAATTTATAT
1 TAAATTCATATTTTTATTTTTTAAATTCATAT
1613512 ATTTTATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (34 bp):
TAAATTCATATTTTTATTTTTTAAATTCATATCT
Found at i:1613506 original size:21 final size:22
Alignment explanation
Indices: 1613481--1613522 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1613471 TTCATATCTT
1613481 AAATTCATAT-TTTTATTTTTA
1 AAATTCATATATTTTATTTTTA
*
1613502 AAATTTATATATTTTATTTTT
1 AAATTCATATATTTTATTTTT
1613523 TAATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
AAATTCATATATTTTATTTTTA
Found at i:1613735 original size:13 final size:12
Alignment explanation
Indices: 1613713--1613742 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1613703 TTAATATATT
1613713 AAAATTGTGATC
1 AAAATTGTGATC
1613725 AAAACTTGTGATC
1 AAAA-TTGTGATC
1613738 AAAAT
1 AAAAT
1613743 AAAACTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (12 bp):
AAAATTGTGATC
Found at i:1621100 original size:5 final size:5
Alignment explanation
Indices: 1621090--1621154 Score: 130
Period size: 5 Copynumber: 13.0 Consensus size: 5
1621080 AAACTTCTCC
1621090 GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT
1 GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT GTAAT
1621140 GTAAT GTAAT GTAAT
1 GTAAT GTAAT GTAAT
1621155 AAAATAATCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 60 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GTAAT
Found at i:1622370 original size:51 final size:52
Alignment explanation
Indices: 1622310--1622417 Score: 150
Period size: 51 Copynumber: 2.1 Consensus size: 52
1622300 ATCATCGCAT
*
1622310 AAGTATCAATATTTTAAATTT-TGATCTTTATATT-AA-CTTTTCAATTTTTAA
1 AAGTATCAATATTTTAAATTTCT-AT-TTTATATTCAACCTTTTCAATGTTTAA
* *
1622361 AAGTATCAATATTTTAACTTTCTATTTTATCTTCAACCTTTTCAATGTTTAA
1 AAGTATCAATATTTTAAATTTCTATTTTATATTCAACCTTTTCAATGTTTAA
1622413 AAGTA
1 AAGTA
1622418 ACGGTAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
50 7 0.14
51 24 0.47
52 20 0.39
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (52 bp):
AAGTATCAATATTTTAAATTTCTATTTTATATTCAACCTTTTCAATGTTTAA
Found at i:1623810 original size:14 final size:14
Alignment explanation
Indices: 1623791--1623818 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1623781 AAATAAGAAA
1623791 TTAATTAATATATT
1 TTAATTAATATATT
1623805 TTAATTAATATATT
1 TTAATTAATATATT
1623819 CTTCTTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAATTAATATATT
Found at i:1624954 original size:16 final size:16
Alignment explanation
Indices: 1624933--1624977 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1624923 AAGGTTTCAT
1624933 TTTTTATTTTAATAAA
1 TTTTTATTTTAATAAA
1624949 TTTTTATTTTCAA-AAA
1 TTTTTATTTT-AATAAA
*
1624965 TTATT-TTTTAATA
1 TTTTTATTTTAATA
1624978 TTAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.08
15 5 0.19
16 17 0.65
17 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTATTTTAATAAA
Found at i:1628106 original size:50 final size:51
Alignment explanation
Indices: 1628047--1628143 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
1628037 AGCATAATTT
* *
1628047 TTTAATAGAAATCT-AGAA-TATAAATAAATTGAGTTTAAACGAATAATATA
1 TTTAATAGAAATCTGA-AAGTATAAATAAATTGAATTTAAACAAATAATATA
*
1628097 TTTAATAGAAATCTGAAAGTATAAATAAATTGAATTTGAACAAATAA
1 TTTAATAGAAATCTGAAAGTATAAATAAATTGAATTTAAACAAATAA
1628144 GATGATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 16 0.38
51 26 0.62
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (51 bp):
TTTAATAGAAATCTGAAAGTATAAATAAATTGAATTTAAACAAATAATATA
Found at i:1631899 original size:3 final size:3
Alignment explanation
Indices: 1631891--1631949 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
1631881 GCCTGTAATG
* *
1631891 TAA TAA TAA TAA T-T TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1631937 T-A TAAA TAA TAA T
1 TAA T-AA TAA TAA T
1631950 CAAATGGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
2 5 0.10
3 42 0.86
4 2 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1631938 original size:26 final size:26
Alignment explanation
Indices: 1631891--1631949 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1631881 GCCTGTAATG
** *
1631891 TAATAATAATAATTTAATAATA-ATAA
1 TAATAATAATAATAAAACAATATA-AA
1631917 TAATAATAATAATAAAACAATATAAA
1 TAATAATAATAATAAAACAATATAAA
1631943 TAATAAT
1 TAATAAT
1631950 CAAATGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
TAATAATAATAATAAAACAATATAAA
Found at i:1632485 original size:18 final size:18
Alignment explanation
Indices: 1632425--1632485 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
1632415 GTTGAACAAG
1632425 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAAC-T
* **
1632444 CTTCTTCCTCTTTAT-ATAAG
1 -TTCTT-CTCATTATGA-ACT
1632464 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
1632482 TTCT
1 TTCT
1632486 CTGGAAAAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 12 0.38
19 6 0.19
20 6 0.19
21 8 0.25
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.52
Consensus pattern (18 bp):
TTCTTCTCATTATGAACT
Found at i:1632623 original size:114 final size:113
Alignment explanation
Indices: 1632396--1632732 Score: 394
Period size: 126 Copynumber: 2.9 Consensus size: 113
1632386 ATCTCATTCT
* *
1632396 GTGATAGAA-TCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTTA
1 GTGAT-GAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCA
* * * *
1632458 TATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAGCTGATCCATCAA
* *
1632507 GTGATGAATTCAAACAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCA
1 GTGATGAATTCAAACAAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCA
* *
1632572 GATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGCTGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACT-TACTCTGGAAAAGCTGATCCATCAA
*
1632621 GTGATGAATTCAAGTGATGAATTCGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTT
1 GTGATGAATTC---------A----AACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT
*
1632686 ATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
53 ATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAA
1632733 TGTTTTAAGA
Statistics
Matches: 192, Mismatches: 15, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
110 3 0.02
111 11 0.06
112 5 0.03
113 33 0.17
114 56 0.29
115 2 0.01
123 1 0.01
125 2 0.01
126 70 0.36
127 9 0.05
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAGCTGATCCATCAA
Found at i:1632635 original size:13 final size:13
Alignment explanation
Indices: 1632617--1632644 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1632607 TGCTGATCCA
1632617 TCAAGTGATGAAT
1 TCAAGTGATGAAT
1632630 TCAAGTGATGAAT
1 TCAAGTGATGAAT
1632643 TC
1 TC
1632645 GAACAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (13 bp):
TCAAGTGATGAAT
Found at i:1633545 original size:22 final size:22
Alignment explanation
Indices: 1633490--1633547 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
1633480 AATAAAGCTT
*
1633490 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1633512 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1633534 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
1633548 TGTAGATGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1646510 original size:21 final size:21
Alignment explanation
Indices: 1646484--1646546 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1646474 TTTTGGTGCA
*
1646484 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
1646505 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
1646526 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
1646547 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:1646554 original size:21 final size:21
Alignment explanation
Indices: 1646528--1646567 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1646518 CCCCCTTTGA
*
1646528 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1646549 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1646568 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1650841 original size:43 final size:43
Alignment explanation
Indices: 1650770--1650855 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
1650760 TCGTGCATCA
*
1650770 AACAAAACTTTACATATAGGGGACAACTTTCAGTCCTAACTTC
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* * * *
1650813 AACAAAATTTTACATATATGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
1650856 TCTAAAGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.31
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:1652845 original size:16 final size:17
Alignment explanation
Indices: 1652824--1652855 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1652814 ATCCTTTCTT
1652824 AATATTAA-AAAAAATA
1 AATATTAATAAAAAATA
1652840 AATATTAATAAAAAAT
1 AATATTAATAAAAAAT
1652856 TATCTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AATATTAATAAAAAATA
Found at i:1653005 original size:21 final size:21
Alignment explanation
Indices: 1652971--1653014 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1652961 GTCATTTCTT
1652971 AATATTGATTAAAT-ATATTAA
1 AATATTGATTAAATGAT-TTAA
1652992 AATA-TGATTAAAATGATTTAA
1 AATATTGATT-AAATGATTTAA
1653013 AA
1 AA
1653015 GTAATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 14 0.67
22 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
AATATTGATTAAATGATTTAA
Found at i:1653157 original size:28 final size:27
Alignment explanation
Indices: 1653126--1653202 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
1653116 AAATATACAT
1653126 ATAAAATTTAAAATATAAATAAACAAG-A
1 ATAAAATTTAAAAT-TAAATAAA-AAGTA
*
1653154 AT-AAATTTAACATTAAATATAAAAGTA
1 ATAAAATTTAAAATTAAATA-AAAAGTA
* * *
1653181 ATAAGACTTATAATTAAATAAA
1 ATAAAATTTAAAATTAAATAAA
1653203 GGTATTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
26 9 0.22
27 17 0.41
28 15 0.37
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (27 bp):
ATAAAATTTAAAATTAAATAAAAAGTA
Found at i:1654493 original size:3 final size:3
Alignment explanation
Indices: 1654485--1654534 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
1654475 GCCTGTAATG
* *
1654485 TAA TAA TAA TAA T-T TAA TAA TAA TAA TAA TAA -AA CAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
1654528 TAA TAA T
1 TAA TAA T
1654535 CAAATGGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
2 5 0.12
3 33 0.82
4 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1654502 original size:14 final size:14
Alignment explanation
Indices: 1654480--1654511 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1654470 TTTAGGCCTG
1654480 TAATGTAATAATAA
1 TAATGTAATAATAA
*
1654494 TAATTTAATAATAA
1 TAATGTAATAATAA
1654508 TAAT
1 TAAT
1654512 AATAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
TAATGTAATAATAA
Found at i:1654523 original size:17 final size:17
Alignment explanation
Indices: 1654486--1654533 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1654476 CCTGTAATGT
** *
1654486 AATAATAATAATTTAAT
1 AATAATAATAATAAAAC
1654503 AATAATAATAATAAAAC
1 AATAATAATAATAAAAC
1654520 AAT-ATAAATAATAA
1 AATAAT-AATAATAA
1654534 TCAAATGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 2 0.07
17 25 0.93
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAATAATAATAAAAC
Found at i:1654523 original size:20 final size:19
Alignment explanation
Indices: 1654485--1654534 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1654475 GCCTGTAATG
***
1654485 TAATAATAATAATTTAATAA
1 TAATAATAATAAAACAAT-A
1654505 TAATAATAATAAAACAATA
1 TAATAATAATAAAACAATA
1654524 TAAATAATAAT
1 T-AATAATAAT
1654535 CAAATGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATAATAATAAAACAATA
Found at i:1655681 original size:31 final size:32
Alignment explanation
Indices: 1655621--1655691 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
1655611 ACTTGAATAA
1655621 AAATTAATGGAGGGGCCAATATTTTCAAACCC
1 AAATTAATGGAGGGGCCAATATTTTCAAACCC
1655653 AAATTAATGGAGGGGCCAATA-TTTCAAACCC
1 AAATTAATGGAGGGGCCAATATTTTCAAACCC
1655684 AAATTAAT
1 AAATTAAT
1655692 ACAAGGACTC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
31 18 0.46
32 21 0.54
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (32 bp):
AAATTAATGGAGGGGCCAATATTTTCAAACCC
Found at i:1656928 original size:159 final size:157
Alignment explanation
Indices: 1656517--1656939 Score: 440
Period size: 159 Copynumber: 2.7 Consensus size: 157
1656507 TCTGATTTCA
* * * * * * *
1656517 TTATTTCTTCAATTTC-TCCTTCATTTTAATTCTATTTTTTTACTAAATTTGAACCACATGCTCC
1 TTATTTCTTCAA-TTCGTCATTTATTTGAAGTC-AATTTTTCACCAAATTTGAACCACATGCTCC
* * * *
1656581 CAAACCATATTAGAATA-CAAGTGTACTTTCAATTTTATTTTTGATAACAAAATTTTTATTTTTC
64 TAAACCATAATAGAATACCTA-TGTACTTTCAATTTTATTTTTCATAACAAAATTTTTATTTTTC
* *
1656645 AATTTAGACCTTCAATTTTTCATAATTTCC
128 AATTTAGACATTCAATTTTTCATAATCTCC
** * * *
1656675 TTATTTCTTCAATTCGTCATTTATTTGAAGTCAGCTTTTCATCAAATCTGAGCCACATGCTCCTA
1 TTATTTCTTCAATTCGTCATTTATTTGAAGTCAATTTTTCACCAAATTTGAACCACATGCTCCTA
* * * * * * * *
1656740 AATCATAGTAGAGTACATATGCACTTTCAATTCTTCTTTTTCATAATAAATTTTTTTATTTTTCA
66 AACCATAATAGAATACCTATGTACTTTCAATT-TTATTTTTCATAACAAA-ATTTTTATTTTTCA
* *
1656805 ATTTAGTCATTCAATTTTTTATAATCTCC
129 ATTTAGACATTCAATTTTTCATAATCTCC
* * * *
1656834 TTA-TTCGTTCAATTTGTGATTTATTTTAAGTCAATTTTTCACCAAATTTGAACCACATGCTCAT
1 TTATTTC-TTCAATTCGTCATTTATTTGAAGTCAATTTTTCACCAAATTTGAACCACATGCTCCT
* *
1656898 ATACCACAATAGAATACCTATGTAAC-TTCAATTATTATTTTT
65 AAACCATAATAGAATACCTATGT-ACTTTCAATT-TTATTTTT
1656940 TACTAAAGAT
Statistics
Matches: 215, Mismatches: 44, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
157 52 0.24
158 42 0.20
159 119 0.55
160 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (157 bp):
TTATTTCTTCAATTCGTCATTTATTTGAAGTCAATTTTTCACCAAATTTGAACCACATGCTCCTA
AACCATAATAGAATACCTATGTACTTTCAATTTTATTTTTCATAACAAAATTTTTATTTTTCAAT
TTAGACATTCAATTTTTCATAATCTCC
Found at i:1657799 original size:75 final size:75
Alignment explanation
Indices: 1657664--1657804 Score: 194
Period size: 75 Copynumber: 1.9 Consensus size: 75
1657654 ACGTGACCAT
* * * *
1657664 CTGAAATTCGAATTTTCTTCGATTAGTCACTTATTTTATTAATGGTATATATCCTGAAATTTTAT
1 CTGAAATTCAAATTTTCTTCGATTAGTCACATATTTTATTAATGGTATATACCCTCAAATTTTAT
1657729 TGTATCCACA
66 TGTATCCACA
* * * *
1657739 CTGAAATTTAAATTTTCTTCTATTAGTCACATATTTTATTGATGGT-TCTTACCCTCAAATTTTA
1 CTGAAATTCAAATTTTCTTCGATTAGTCACATATTTTATTAATGGTAT-ATACCCTCAAATTTTA
1657803 TT
65 TT
1657805 TATGCTCAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 1 0.02
75 56 0.98
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (75 bp):
CTGAAATTCAAATTTTCTTCGATTAGTCACATATTTTATTAATGGTATATACCCTCAAATTTTAT
TGTATCCACA
Found at i:1658438 original size:32 final size:32
Alignment explanation
Indices: 1658396--1658483 Score: 158
Period size: 32 Copynumber: 2.7 Consensus size: 32
1658386 AGACATTTCA
*
1658396 TTCAACAACATTAAAATGCTATTTAAACCAAG
1 TTCAATAACATTAAAATGCTATTTAAACCAAG
1658428 TTCAATAACATTAAAATGCTATTTAAACCAAG
1 TTCAATAACATTAAAATGCTATTTAAACCAAG
1658460 TTCAATAACATTAAAAATGCTATT
1 TTCAATAACATT-AAAATGCTATT
1658484 AATTTTTATC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 43 0.80
33 11 0.20
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.32
Consensus pattern (32 bp):
TTCAATAACATTAAAATGCTATTTAAACCAAG
Done.