Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008925.1 Hibiscus syriacus cultivar Beakdansim tig00112230_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: 2702387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1222468 original size:20 final size:20
Alignment explanation
Indices: 1222439--1222598 Score: 151
Period size: 20 Copynumber: 7.7 Consensus size: 20
1222429 GGTGTTTGAT
*
1222439 TGCATAGATGCACTACATGG
1 TGCATGGATGCACTACATGG
*
1222459 TGCATCGATGCACTACATGG
1 TGCATGGATGCACTACATGG
*
1222479 TGCATCGATGCACTACATGG
1 TGCATGGATGCACTACATGG
*
1222499 TGCATCGATGCACTAGTGCA-GG
1 TGCATGGATGCACTA---CATGG
* * **
1222521 TGTATGGAAGCACTAGTGTAGG
1 TGCATGGATGCACTA-CAT-GG
* *
1222543 TGCATGGATGCACTGCAGGG
1 TGCATGGATGCACTACATGG
*
1222563 ATGCATGGATGCACTGCATGGG
1 -TGCATGGATGCACTACAT-GG
1222585 TGCATGGATGCACT
1 TGCATGGATGCACT
1222599 TTCACACCCT
Statistics
Matches: 120, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
20 57 0.47
21 31 0.26
22 30 0.25
23 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (20 bp):
TGCATGGATGCACTACATGG
Found at i:1222533 original size:22 final size:22
Alignment explanation
Indices: 1222497--1222556 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1222487 TGCACTACAT
* *
1222497 GGTGCATCGATGCACTAGTGCA
1 GGTGCATGGAAGCACTAGTGCA
* *
1222519 GGTGTATGGAAGCACTAGTGTA
1 GGTGCATGGAAGCACTAGTGCA
*
1222541 GGTGCATGGATGCACT
1 GGTGCATGGAAGCACT
1222557 GCAGGGATGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (22 bp):
GGTGCATGGAAGCACTAGTGCA
Found at i:1222699 original size:29 final size:29
Alignment explanation
Indices: 1222678--1222735 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1222668 AAACTTTGAA
1222678 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
1222707 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1222736 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1222725 original size:30 final size:30
Alignment explanation
Indices: 1222678--1222737 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1222668 AAACTTTGAA
1222678 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1222707 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1222738 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1223521 original size:29 final size:30
Alignment explanation
Indices: 1223453--1223511 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1223443 AATTTAAGGC
1223453 AAAATGTTTTTGGACTTGAATTGAATTTAT
1 AAAATGTTTTTGGACTTGAATTGAATTTAT
*
1223483 AAAATATTTTTGGACTT-AATTGAATTTAT
1 AAAATGTTTTTGGACTTGAATTGAATTTAT
1223512 TCAAAGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAT
Found at i:1223616 original size:21 final size:21
Alignment explanation
Indices: 1223590--1223643 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1223580 AGGGTGTCAA
1223590 AGTGCATCCATGCAT-CCTTGC
1 AGTGCATCCATGCATACC-TGC
1223611 AGTGCATCCATGCATACCTGC
1 AGTGCATCCATGCATACCTGC
*
1223632 AATGCATCCATG
1 AGTGCATCCATG
1223644 TAGTGCATCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATACCTGC
Found at i:1223700 original size:13 final size:13
Alignment explanation
Indices: 1223599--1223700 Score: 56
Period size: 13 Copynumber: 8.0 Consensus size: 13
1223589 AAGTGCATCC
*
1223599 ATGCATCCTTGCA
1 ATGCATCCATGCA
*
1223612 GTGCATCCATGC-
1 ATGCATCCATGCA
1223624 AT--A-CC-TGCA
1 ATGCATCCATGCA
*
1223633 ATGCATCCATGTA
1 ATGCATCCATGCA
*
1223646 GTGCATCCATGCA
1 ATGCATCCATGCA
* *
1223659 CCTGCA-CTAATGCA
1 -ATGCATC-CATGCA
1223673 TCGATGCAT-CATGCA
1 ---ATGCATCCATGCA
1223688 ATGCATCCATGCA
1 ATGCATCCATGCA
1223701 CTCAAACATC
Statistics
Matches: 67, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
8 3 0.04
9 4 0.06
10 1 0.01
11 1 0.01
12 9 0.13
13 31 0.46
14 9 0.13
15 5 0.07
16 4 0.06
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (13 bp):
ATGCATCCATGCA
Found at i:1223746 original size:54 final size:54
Alignment explanation
Indices: 1223669--1223812 Score: 254
Period size: 54 Copynumber: 2.7 Consensus size: 54
1223659 CCTGCACTAA
* *
1223669 TGCATCGATGCATCATGCAATGCATCCATGCACTCAAACATCTAATGTACTTAG
1 TGCATCGATGCATCCTGCCATGCATCCATGCACTCAAACATCTAATGTACTTAG
*
1223723 TGCATTGATGCATCCTGCCATGCATCCATGCACTCAAACATCTAATGTACTTAG
1 TGCATCGATGCATCCTGCCATGCATCCATGCACTCAAACATCTAATGTACTTAG
1223777 TGCATCGATGCATCCTGCCATGCATCCATGCA-TCAA
1 TGCATCGATGCATCCTGCCATGCATCCATGCACTCAA
1223813 GGCTGCAACG
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 4 0.05
54 82 0.95
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (54 bp):
TGCATCGATGCATCCTGCCATGCATCCATGCACTCAAACATCTAATGTACTTAG
Found at i:1227061 original size:29 final size:29
Alignment explanation
Indices: 1227029--1227087 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
1227019 CAATTTAAGG
*
1227029 AAAAA-TGTTTTTGGACTTGAATTGAATTT
1 AAAAATTGTTTTTGGACAT-AATTGAATTT
*
1227058 AAAAATTTTTTTTGGACATAATTGAATTT
1 AAAAATTGTTTTTGGACATAATTGAATTT
1227087 A
1 A
1227088 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (29 bp):
AAAAATTGTTTTTGGACATAATTGAATTT
Found at i:1230033 original size:29 final size:29
Alignment explanation
Indices: 1230001--1230071 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
1229991 GTAACACTCT
*
1230001 ATAGTCAAATGATCATTTTATAACTTTTA
1 ATAGTCAAAGGATCATTTTATAACTTTTA
*
1230030 ATAGTCAAAGGATCATTTTATAATTTTTA
1 ATAGTCAAAGGATCATTTTATAACTTTTA
* *
1230059 ATAATAAAAGGAT
1 ATAGTCAAAGGAT
1230072 TTAATAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (29 bp):
ATAGTCAAAGGATCATTTTATAACTTTTA
Found at i:1230774 original size:20 final size:19
Alignment explanation
Indices: 1230749--1230802 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1230739 GCGAAATAAA
1230749 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
1230769 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
1230789 AATCGCAACGCGAT
1 AATCGCAACGCGAT
1230803 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:1230864 original size:21 final size:21
Alignment explanation
Indices: 1230749--1230864 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
1230739 GCGAAATAAA
*
1230749 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
1230769 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* **
1230789 AATCGCAACGCGATTATGAAG
1 AATCGCAACGCGATTTTCCAG
* * ** *
1230810 AATCACAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
* **
1230830 AATTAGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
1230852 AATCGCAACGCGA
1 AATCGCAACGCGA
1230865 ATATGAAAAT
Statistics
Matches: 66, Mismatches: 26, Indels: 7
0.67 0.26 0.07
Matches are distributed among these distances:
19 1 0.02
20 25 0.38
21 38 0.58
22 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:1230958 original size:41 final size:40
Alignment explanation
Indices: 1230852--1231061 Score: 217
Period size: 40 Copynumber: 5.2 Consensus size: 40
1230842 GATTTTCCAG
* ** * * * **
1230852 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * *
1230892 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT-A
* *
1230933 AATCGCAACGTGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
1230974 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * *
1231014 AATCGCAACGCATATCTGTAAATCACAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1231054 AATCGCAA
1 AATCGCAA
1231062 TGCGAATACG
Statistics
Matches: 144, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.02
40 70 0.49
41 66 0.46
42 4 0.03
43 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:1231072 original size:20 final size:20
Alignment explanation
Indices: 1230852--1231073 Score: 175
Period size: 20 Copynumber: 11.0 Consensus size: 20
1230842 GATTTTCCAG
* *
1230852 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
1230872 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
1230892 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
1230911 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* * *
1230933 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGTA
1230953 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
1230974 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
1230994 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
1231014 AATCGCAACGC--ATATCTGTA
1 AATCGCAACGCGAATA-C-GTA
* *
1231034 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
1231054 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
1231074 TTCGCATTGC
Statistics
Matches: 165, Mismatches: 26, Indels: 22
0.77 0.12 0.10
Matches are distributed among these distances:
18 4 0.02
19 3 0.02
20 116 0.70
21 37 0.22
22 5 0.03
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:1231091 original size:20 final size:20
Alignment explanation
Indices: 1231068--1231158 Score: 148
Period size: 20 Copynumber: 4.5 Consensus size: 20
1231058 GCAATGCGAA
* *
1231068 TACGTATTCGCATTGCGATT
1 TACGTAATCGCGTTGCGATT
1231088 TACGTAATCGCGTTGCGATT
1 TACGTAATCGCGTTGCGATT
1231108 TACGTAATCGCGTTGCGATT
1 TACGTAATCGCGTTGCGATT
1231128 TACGTAATCGCGTTGCGATT
1 TACGTAATCGCGTTGCGATT
1231148 TA-GTAAATCGC
1 TACGT-AATCGC
1231159 AACGAGATTC
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 2 0.03
20 66 0.97
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
TACGTAATCGCGTTGCGATT
Found at i:1231092 original size:40 final size:40
Alignment explanation
Indices: 1231048--1231138 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
1231038 ACAACGAGAA
*
1231048 TACGTAAATCGCAATGCGA-ATACGTATTCGCATTGCGATT
1 TACGT-AATCGCAATGCGATATACGTAATCGCATTGCGATT
** * *
1231088 TACGTAATCGCGTTGCGATTTACGTAATCGCGTTGCGATT
1 TACGTAATCGCAATGCGATATACGTAATCGCATTGCGATT
1231128 TACGTAATCGC
1 TACGTAATCGC
1231139 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
39 11 0.24
40 34 0.76
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (40 bp):
TACGTAATCGCAATGCGATATACGTAATCGCATTGCGATT
Found at i:1232073 original size:24 final size:24
Alignment explanation
Indices: 1232022--1232075 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1232012 GTATTCGAAA
*
1232022 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1232046 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1232070 TTTGAT
1 TTTGAT
1232076 GATTTTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1234639 original size:33 final size:33
Alignment explanation
Indices: 1234593--1234759 Score: 190
Period size: 33 Copynumber: 4.8 Consensus size: 33
1234583 CTTAATGTCT
1234593 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1234626 ATCACAATGCGAAATGAAAATCGCAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
1234659 ATCGTAACGCGAATATGAATATCGCAACGCGGAAATGA
1 ATCGCAATGCGAA-ATGAAAATCGCAA--C-GAGA-GA
*
1234697 CTATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1234732 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1234760 CGAATTTAGT
Statistics
Matches: 110, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
33 66 0.60
34 12 0.11
35 2 0.02
36 4 0.04
37 3 0.03
38 1 0.01
39 11 0.10
40 11 0.10
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1234677 original size:20 final size:19
Alignment explanation
Indices: 1234593--1234763 Score: 111
Period size: 19 Copynumber: 9.7 Consensus size: 19
1234583 CTTAATGTCT
*
1234593 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1234612 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
* *
1234626 ATCACAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1234645 ATCGCAA--CG---TGAAA
1 ATCGCAACGCGAAATGAAA
* *
1234659 ATCGTAACGCGAATATGAAT
1 ATCGCAACGCGAA-ATGAAA
**
1234679 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGAAA
*
1234699 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
1234718 ATCACAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
1234732 ATCGCAAAGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1234751 ATCGCAACGCGAA
1 ATCGCAACGCGAA
1234764 TTTAGTTTCG
Statistics
Matches: 119, Mismatches: 16, Indels: 34
0.70 0.09 0.20
Matches are distributed among these distances:
14 29 0.24
15 2 0.02
16 6 0.05
17 6 0.05
18 2 0.02
19 44 0.37
20 27 0.23
21 3 0.03
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1234814 original size:19 final size:19
Alignment explanation
Indices: 1234790--1234848 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1234780 AATTTTGTCG
1234790 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1234809 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1234823 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1234842 TTGCGAT
1 TTGCGAT
1234849 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1234824 original size:33 final size:33
Alignment explanation
Indices: 1234769--1234848 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
1234759 GCGAATTTAG
* * * *
1234769 TTTCGCGTTGCAATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1234802 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1234835 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1234849 AGTCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:1234856 original size:19 final size:17
Alignment explanation
Indices: 1234798--1234848 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1234788 CGTTGCGATT
1234798 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
1234815 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
1234829 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
1234848 T
1 T
1234849 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:1236413 original size:42 final size:40
Alignment explanation
Indices: 1236328--1236451 Score: 97
Period size: 42 Copynumber: 3.0 Consensus size: 40
1236318 GTGAATCGGG
* * * *
1236328 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGAAGTGGC
1 CTCTTGAAAGGTGGGAGGGGA-CTC-TCGAGGATGAAGGGGC
1236369 CTCTTGAAAGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAAAGGTGGGAGGGGACTCTCGAGG-ATGA-AGGGGC
* * * * * *
1236411 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGGGG
1 CTCTTGAAAGGTGGGAGGGGACTCTCGA-GGATGA-AGGGG
1236452 AGTCGGGCTT
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
40 4 0.06
41 22 0.32
42 40 0.59
43 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (40 bp):
CTCTTGAAAGGTGGGAGGGGACTCTCGAGGATGAAGGGGC
Found at i:1236888 original size:19 final size:19
Alignment explanation
Indices: 1236848--1236918 Score: 88
Period size: 19 Copynumber: 3.6 Consensus size: 19
1236838 TCTGGAACTT
*
1236848 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
1236869 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
1236888 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
1236907 AAAATCGAAACG
1 AAAATCGCAACG
1236919 AGGGAATCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
19 33 0.75
21 11 0.25
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1236954 original size:19 final size:18
Alignment explanation
Indices: 1236932--1237064 Score: 80
Period size: 19 Copynumber: 7.2 Consensus size: 18
1236922 GAATCGCAAC
*
1236932 GCGATTATAGTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
*
1236951 GCGATTTTGGTTTCGCGTT
1 GCGATTTT-ATTTCGCGTT
*
1236970 ACGA-TTT-TTT--CGTT
1 GCGATTTTATTTCGCGTT
1236984 GCGATTTTCATTTCGCGTT
1 GCGATTTT-ATTTCGCGTT
* *
1237003 GTGA-TTCATTTCGCGTT
1 GCGATTTTATTTCGCGTT
*
1237020 GCGATAGTCATT-TTTCACGTT
1 GCGAT--T--TTATTTCGCGTT
*
1237041 GCGATTTTAAGTTTCGTGTT
1 GCGATTTT-A-TTTCGCGTT
1237061 GCGA
1 GCGA
1237065 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
14 7 0.08
15 3 0.03
16 3 0.03
17 18 0.20
18 5 0.06
19 27 0.30
20 12 0.13
21 13 0.15
22 1 0.01
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.46
Consensus pattern (18 bp):
GCGATTTTATTTCGCGTT
Found at i:1237258 original size:94 final size:94
Alignment explanation
Indices: 1237112--1237491 Score: 640
Period size: 94 Copynumber: 4.1 Consensus size: 94
1237102 ATGGATTGCA
* * *
1237112 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTCCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1237176 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1237205 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1237270 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1237299 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATCACTAACTTCACAGTGTTAAAGAATACACAG
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAAT-ACTAACTTCACAGTGTTAAAGAATACACAG
* *
1237363 TTTAGCAGAATTGGCAGCAACTGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
*
1237393 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
1237457 TTTAGCAGTATTGACAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1237487 TTACT
1 TTACT
1237492 AAGCAATCTA
Statistics
Matches: 273, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
93 26 0.10
94 244 0.89
95 3 0.01
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1239220 original size:20 final size:20
Alignment explanation
Indices: 1239197--1239248 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1239187 ATGAAAATCG
1239197 CAACGAGAGAATGACTATCA
1 CAACGAGAGAATGACTATCA
* *
1239217 CAACGCG-GAAATGACTATCG
1 CAACGAGAG-AATGACTATCA
1239237 CAACGAGAGAAT
1 CAACGAGAGAAT
1239249 CGCAACGCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.13
Consensus pattern (20 bp):
CAACGAGAGAATGACTATCA
Found at i:1239263 original size:33 final size:33
Alignment explanation
Indices: 1239184--1239307 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
1239174 TCTTTTGGTT
*
1239184 GAAATGAAAATCGCAACGAGAGAATGACTATCACAACGC
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAACGC
**
1239223 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1239257 GAAATGAAAATCGCAACGAGAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1239290 GAAATTAAAATCGCAACG
1 GAAATGAAAATCGCAACG
1239308 CGAAATGAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
33 47 0.61
34 9 0.12
36 2 0.03
37 1 0.01
38 3 0.04
40 15 0.19
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1239270 original size:19 final size:19
Alignment explanation
Indices: 1239184--1239329 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
1239174 TCTTTTGGTT
*
1239184 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
1239203 GAGAATGACTATCACAACGC
1 GA-AATGAAAATCGCAACGC
**
1239223 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1239241 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1239257 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
1239274 G--A-GAGAATCGTAACGC
1 GAAATGAAAATCGCAACGC
*
1239290 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1239309 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1239328 GA
1 GA
1239330 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 18 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 42 0.42
20 26 0.26
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1239396 original size:20 final size:20
Alignment explanation
Indices: 1239336--1239413 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
1239326 GCGATTTTGG
1239336 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
* **
1239356 TTCTC-TCGTTACGATAGTCAT
1 TT-TCGT-GTTGCGATTTTCAT
1239377 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
1239397 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
1239414 AAGTTTAGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 32 0.67
21 16 0.33
ACGTcount: A:0.13, C:0.17, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:1240007 original size:20 final size:19
Alignment explanation
Indices: 1239972--1240165 Score: 145
Period size: 20 Copynumber: 9.6 Consensus size: 19
1239962 TTTAAAAATC
*
1239972 GCGTTGCGATTTTACGTATT
1 GCGTTGCGA-TTTACGGATT
*
1239992 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGAT-T
* *
1240013 GCATTGCGATTTATGGATAT
1 GCGTTGCGATTTACGGAT-T
* *
1240033 GCATTGCGATTTACGTATT
1 GCGTTGCGATTTACGGATT
* * * *
1240052 CTCGTTACGATTTACAGATAC
1 -GCGTTGCGATTTACGGAT-T
*
1240073 GCGTTGCGATTTACGTATT
1 GCGTTGCGATTTACGGATT
* *
1240092 CTCGTTGCGATTTACGGATAC
1 -GCGTTGCGATTTACGGAT-T
* *
1240113 ACGTTGCGATTTTACGTATT
1 GCGTTGCGA-TTTACGGATT
*
1240133 GTCGTTGCGATTTATGGATAT
1 G-CGTTGCGATTTACGGAT-T
1240154 GCGTTGCGATTT
1 GCGTTGCGATTT
1240166 TAAGGATACT
Statistics
Matches: 138, Mismatches: 27, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.01
20 110 0.80
21 27 0.20
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGTTGCGATTTACGGATT
Found at i:1240072 original size:60 final size:59
Alignment explanation
Indices: 1239972--1240205 Score: 220
Period size: 60 Copynumber: 3.8 Consensus size: 59
1239962 TTTAAAAATC
* *
1239972 GCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATTGCGATTTATGGATAT
1 GCGTTGCGA-TTTACGTATTCTCGTTGCGATTTAC-GATACGCGTTGCGATTTATGGATAT
* * * *
1240033 GCATTGCGATTTACGTATTCTCGTTACGATTTACAGATACGCGTTGCGATTTACGTAT-T
1 GCGTTGCGATTTACGTATTCTCGTTGCGATTTAC-GATACGCGTTGCGATTTATGGATAT
* * * * *
1240092 CTCGTTGCGATTTACGGATACACGTTGCGATTTTACG-TATTGTCGTTGCGATTTATGGATAT
1 -GCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGATA-CG-CGTTGCGATTTATGGATAT
* * * * *
1240154 GCGTTGCGATTTTAAGGATACTCGTTGTGATTTTACGGATACTCGTTGCGAT
1 GCGTTGCGA-TTTACGTATTCTCGTTGCGA-TTTAC-GATACGCGTTGCGAT
1240206 AGTCAGAATC
Statistics
Matches: 143, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
59 3 0.02
60 68 0.48
61 36 0.25
62 33 0.23
63 1 0.01
64 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.39
Consensus pattern (59 bp):
GCGTTGCGATTTACGTATTCTCGTTGCGATTTACGATACGCGTTGCGATTTATGGATAT
Found at i:1240139 original size:41 final size:41
Alignment explanation
Indices: 1239994--1240205 Score: 232
Period size: 40 Copynumber: 5.2 Consensus size: 41
1239984 TACGTATTGT
* * * * * *
1239994 CGTTGCGA-TTTACGGATACGCATTGCGATTTATGGATATG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* * *
1240034 CATTGCGA-TTTACGTATTCTCGTTACGATTTACAGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
*
1240074 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACA
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* * *
1240114 CGTTGCGATTTTACGTATTGTCGTTGCGATTTATGGATATG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* * * * *
1240155 CGTTGCGATTTTAAGGATACTCGTTGTGATTTTACGGATACT
1 CGTTGCGATTTTACGTATTCTCGTTGCGA-TTTACGGATACG
1240197 CGTTGCGAT
1 CGTTGCGAT
1240206 AGTCAGAATC
Statistics
Matches: 145, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
40 75 0.52
41 52 0.36
42 18 0.12
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:1240220 original size:62 final size:61
Alignment explanation
Indices: 1239994--1240227 Score: 169
Period size: 62 Copynumber: 3.8 Consensus size: 61
1239984 TACGTATTGT
* * * * * * * *
1239994 CGTTGCGA-TTTACGGATACGCATTGCGATTTATGGATATGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTTACGGATACTCGTTGCGA-TTATAGATATGCGTTGCGATTTTAAGGATACA
* * * * *
1240054 CGTTACGA-TTTACAGATACGCGTTGCGATT-TACG-TATTCTCGTTGCGA-TTTACGGATACA
1 CGTTGCGATTTTACGGATACTCGTTGCGATTATA-GATA-T-GCGTTGCGATTTTAAGGATACA
* ** * *
1240114 CGTTGCGATTTTACGTATTGTCGTTGCGATTTATGGATATGCGTTGCGATTTTAAGGATACT
1 CGTTGCGATTTTACGGATACTCGTTGCGA-TTATAGATATGCGTTGCGATTTTAAGGATACA
*
1240176 CGTTGTGATTTTACGGATACTCGTTGCGA-TAGTCAGA-ATCGCGTTGCGATTT
1 CGTTGCGATTTTACGGATACTCGTTGCGATTA-T-AGATAT-GCGTTGCGATTT
1240228 ATATGTTCGC
Statistics
Matches: 139, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
58 3 0.02
59 4 0.03
60 50 0.36
61 26 0.19
62 53 0.38
63 3 0.02
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (61 bp):
CGTTGCGATTTTACGGATACTCGTTGCGATTATAGATATGCGTTGCGATTTTAAGGATACA
Found at i:1240237 original size:20 final size:20
Alignment explanation
Indices: 1240214--1240266 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1240204 ATAGTCAGAA
1240214 TCGCGTTGCGATTT-ATATGT
1 TCGCGTTGCGATTTCATAT-T
1240234 TCGCGTTGCGATTTTCATATT
1 TCGCGTTGCGA-TTTCATATT
1240255 T-GCGTTGCGATT
1 TCGCGTTGCGATT
1240267 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.06
20 20 0.65
21 5 0.16
22 4 0.13
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTCATATT
Found at i:1244502 original size:20 final size:19
Alignment explanation
Indices: 1244477--1244517 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1244467 TGATTTAAGC
* *
1244477 ATTTAAATTTTATTTAACAA
1 ATTTAAATGTAATTTAA-AA
1244497 ATTTAAATGTAATTTAAAA
1 ATTTAAATGTAATTTAAAA
1244516 AT
1 AT
1244518 CATACATCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTTAAATGTAATTTAAAA
Found at i:1244659 original size:12 final size:12
Alignment explanation
Indices: 1244642--1244666 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1244632 TATTTTCAAT
1244642 TAAAGAGTAAAA
1 TAAAGAGTAAAA
1244654 TAAAGAGTAAAA
1 TAAAGAGTAAAA
1244666 T
1 T
1244667 TAAATTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (12 bp):
TAAAGAGTAAAA
Found at i:1247645 original size:17 final size:20
Alignment explanation
Indices: 1247610--1247649 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
1247600 ATTTAATTAA
1247610 TTTTTATTTGTTTATAATAT
1 TTTTTATTTGTTTATAATAT
1247630 TTTTTA-TT-TTTA-AATAT
1 TTTTTATTTGTTTATAATAT
1247647 TTT
1 TTT
1247650 AGATGGCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 2 0.10
20 6 0.30
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTATTTGTTTATAATAT
Found at i:1247769 original size:10 final size:10
Alignment explanation
Indices: 1247754--1247783 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1247744 GATATACGAT
1247754 TTTTTTTTTA
1 TTTTTTTTTA
1247764 TTTTTTTTTA
1 TTTTTTTTTA
1247774 TTTTTTTTTA
1 TTTTTTTTTA
1247784 AATTTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:1249703 original size:15 final size:15
Alignment explanation
Indices: 1249683--1249757 Score: 78
Period size: 15 Copynumber: 5.0 Consensus size: 15
1249673 GATTTTAGTA
*
1249683 ATATGTGAATATGAT
1 ATATGTGAATATGTT
1249698 ATATGTGAATATGTT
1 ATATGTGAATATGTT
* * * *
1249713 CTATATGAAAATGGT
1 ATATGTGAATATGTT
*
1249728 ATATGTTAATATGTT
1 ATATGTGAATATGTT
* *
1249743 CTACGTGAATATGTT
1 ATATGTGAATATGTT
1249758 TTAATATGAA
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.43
Consensus pattern (15 bp):
ATATGTGAATATGTT
Found at i:1249731 original size:30 final size:30
Alignment explanation
Indices: 1249688--1249745 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1249678 TAGTAATATG
*
1249688 TGAATATGATATATGTGAATATGTTCTATA
1 TGAAAATGATATATGTGAATATGTTCTATA
* *
1249718 TGAAAATGGTATATGTTAATATGTTCTA
1 TGAAAATGATATATGTGAATATGTTCTA
1249746 CGTGAATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.43
Consensus pattern (30 bp):
TGAAAATGATATATGTGAATATGTTCTATA
Found at i:1249930 original size:24 final size:24
Alignment explanation
Indices: 1249874--1249943 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
1249864 TCGAGGGTTA
* *
1249874 TACGCCGGTCATTCAGGA-TAATTC
1 TACG-CGGTCATTCGGGACAAATTC
* *
1249898 TATGTGGTCATTCGGGACAAATTC
1 TACGCGGTCATTCGGGACAAATTC
*
1249922 TACGCGGTCCA-CCGGGACAAAT
1 TACGCGGT-CATTCGGGACAAAT
1249944 CTTTGTGGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 11 0.30
24 24 0.65
25 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (24 bp):
TACGCGGTCATTCGGGACAAATTC
Found at i:1256184 original size:22 final size:22
Alignment explanation
Indices: 1256158--1256210 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
1256148 ACTAAAGTAG
1256158 GTATTGGTACCATAGAAGAGAA
1 GTATTGGTACCATAGAAGAGAA
1256180 GTATTGGTACCATAGAAGAGAA
1 GTATTGGTACCATAGAAGAGAA
1256202 GTATTGGTA
1 GTATTGGTA
1256211 ATGTGGGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (22 bp):
GTATTGGTACCATAGAAGAGAA
Found at i:1256548 original size:23 final size:22
Alignment explanation
Indices: 1256508--1256550 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1256498 TTCTATCGAA
*
1256508 AATATTTTTATTTATTTTATGC
1 AATATTTTTATATATTTTATGC
*
1256530 AATATTTTTATGATGTTTTAT
1 AATATTTTTAT-ATATTTTAT
1256551 ATAAATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (22 bp):
AATATTTTTATATATTTTATGC
Found at i:1256609 original size:15 final size:15
Alignment explanation
Indices: 1256589--1256660 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
1256579 TATTTTAGTA
*
1256589 ATATGTGAATATGAT
1 ATATGTGAATATGTT
1256604 ATATGTGAATATGTT
1 ATATGTGAATATGTT
* *
1256619 CTATGTGATTATGTT
1 ATATGTGAATATGTT
* *
1256634 CTACGTGAATATGTT
1 ATATGTGAATATGTT
*
1256649 TTAATGTGAATA
1 AT-ATGTGAATA
1256661 AATGATACTT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 41 0.84
16 8 0.16
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.44
Consensus pattern (15 bp):
ATATGTGAATATGTT
Found at i:1256841 original size:23 final size:24
Alignment explanation
Indices: 1256783--1256841 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1256773 CCTTCAAGAT
*
1256783 AATTCTATGTGGTTATTCGGGACA
1 AATTCTATGTGGTGATTCGGGACA
* *
1256807 AATTCTACGTGGTGCTTCGGGACA
1 AATTCTATGTGGTGATTCGGGACA
1256831 AA-TCTATGTGG
1 AATTCTATGTGG
1256842 CACTTTGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 8 0.26
24 23 0.74
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (24 bp):
AATTCTATGTGGTGATTCGGGACA
Found at i:1256860 original size:24 final size:24
Alignment explanation
Indices: 1256839--1256909 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
1256829 CAAATCTATG
*
1256839 TGGCACTTTGGTGCATATTCTACA
1 TGGCACTTCGGTGCATATTCTACA
1256863 TGGCACTTCGGTGCATATTCTACA
1 TGGCACTTCGGTGCATATTCTACA
*
1256887 TGGCACTTCGGTGCAAATTCTAC
1 TGGCACTTCGGTGCATATTCTAC
1256910 GCGGCAGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (24 bp):
TGGCACTTCGGTGCATATTCTACA
Found at i:1256915 original size:24 final size:24
Alignment explanation
Indices: 1256805--1256915 Score: 118
Period size: 24 Copynumber: 4.7 Consensus size: 24
1256795 TTATTCGGGA
**
1256805 CAAATTCTACGTGGTGCTTCGG-G
1 CAAATTCTACGTGGCACTTCGGTG
* *
1256828 ACAAA-TCTATGTGGCACTTTGGTG
1 -CAAATTCTACGTGGCACTTCGGTG
* *
1256852 CATATTCTACATGGCACTTCGGTG
1 CAAATTCTACGTGGCACTTCGGTG
* *
1256876 CATATTCTACATGGCACTTCGGTG
1 CAAATTCTACGTGGCACTTCGGTG
*
1256900 CAAATTCTACGCGGCA
1 CAAATTCTACGTGGCA
1256916 GTTTTGACTG
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.22
24 58 0.78
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (24 bp):
CAAATTCTACGTGGCACTTCGGTG
Found at i:1272268 original size:3 final size:3
Alignment explanation
Indices: 1272262--1272294 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1272252 AAAAAAATTA
1272262 ATT ATT ATT ATT -TT ATT ATT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
1272295 TTTTACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1272281 original size:14 final size:13
Alignment explanation
Indices: 1272258--1272294 Score: 60
Period size: 11 Copynumber: 3.0 Consensus size: 13
1272248 GTTTAAAAAA
1272258 ATTAATTATTATT
1 ATTAATTATTATT
1272271 ATT--TTATTATT
1 ATTAATTATTATT
1272282 ATTAATTATTATT
1 ATTAATTATTATT
1272295 TTTTACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTAATTATTATT
Found at i:1275313 original size:22 final size:22
Alignment explanation
Indices: 1275284--1275339 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
1275274 AATGGGGCCT
1275284 CAGTATCGATACTATCACCCT-G
1 CAGTATCGATACT-TCACCCTGG
* *
1275306 TAGTATCGATAC-TCTCCCTGG
1 CAGTATCGATACTTCACCCTGG
1275327 CAGTATCGATACT
1 CAGTATCGATACT
1275340 CCCTGCCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.21
21 12 0.41
22 11 0.38
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (22 bp):
CAGTATCGATACTTCACCCTGG
Found at i:1278268 original size:22 final size:20
Alignment explanation
Indices: 1278225--1278269 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
1278215 TGTTTTTTTT
* *
1278225 TTGTTCTCTGTTTTTGCTGG
1 TTGTTCTCTCTTTTTGCAGG
1278245 TTGTTCCTCTCTTCTTTGCAGG
1 TTGTT-CTCTCTT-TTTGCAGG
1278267 TTG
1 TTG
1278270 GGTGATGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.02, C:0.20, G:0.22, T:0.56
Consensus pattern (20 bp):
TTGTTCTCTCTTTTTGCAGG
Found at i:1278607 original size:3 final size:3
Alignment explanation
Indices: 1278601--1278664 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
1278591 TATATTTTTT
*
1278601 TAA TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA -TAA
*
1278647 TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1278665 ATAAATAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 46 0.85
4 6 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1280126 original size:20 final size:20
Alignment explanation
Indices: 1280101--1280160 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
1280091 TATTTTGCCT
1280101 TTGTTCATCTAATATCAATA
1 TTGTTCATCTAATATCAATA
1280121 TTGTTCATCTAATATCAATA
1 TTGTTCATCTAATATCAATA
*
1280141 TTGTTTATCTAATATCAATA
1 TTGTTCATCTAATATCAATA
1280161 CTATAACCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (20 bp):
TTGTTCATCTAATATCAATA
Found at i:1280479 original size:17 final size:18
Alignment explanation
Indices: 1280439--1280485 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
1280429 TGTCACTATC
1280439 AATTAACTATTTCGTCAT
1 AATTAACTATTTCGTCAT
* *
1280457 TA-TAAC-ATTTTGTCAT
1 AATTAACTATTTCGTCAT
1280473 AATTAACTTATTT
1 AATTAAC-TATTT
1280486 TAACATCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
16 10 0.43
17 8 0.35
18 1 0.04
19 4 0.17
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (18 bp):
AATTAACTATTTCGTCAT
Found at i:1280639 original size:20 final size:21
Alignment explanation
Indices: 1280616--1280658 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1280606 AAATATTTAT
1280616 TTTTATCACAA-AAAATTAAA
1 TTTTATCACAATAAAATTAAA
* * *
1280636 TTTTGTCGCAATTAAATTAAA
1 TTTTATCACAATAAAATTAAA
1280657 TT
1 TT
1280659 ATAACATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (21 bp):
TTTTATCACAATAAAATTAAA
Found at i:1283291 original size:20 final size:20
Alignment explanation
Indices: 1283266--1283313 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1283256 TCTAAATCAT
*
1283266 TTTTCAAAATTTC-ATTTTGC
1 TTTTCAAAA-TCCAATTTTGC
1283286 TTTTCAAAATCCAATTTTGC
1 TTTTCAAAATCCAATTTTGC
1283306 -TTTCAAAA
1 TTTTCAAAA
1283314 GATAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATCCAATTTTGC
Found at i:1285128 original size:21 final size:22
Alignment explanation
Indices: 1285102--1285144 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1285092 CCAGTACATG
1285102 GAGTAT-TGGTAC-TCCTTTAAT
1 GAGTATCT-GTACTTCCTTTAAT
1285123 GAGTATCTGTACTTCCTTTAAT
1 GAGTATCTGTACTTCCTTTAAT
1285145 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.44
Consensus pattern (22 bp):
GAGTATCTGTACTTCCTTTAAT
Found at i:1286322 original size:17 final size:17
Alignment explanation
Indices: 1286288--1286323 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1286278 TCATTTTTTA
*
1286288 TTATAAATGAATTGTTT
1 TTATAAATGAATTCTTT
*
1286305 TTATAAATGATTTCTTT
1 TTATAAATGAATTCTTT
1286322 TT
1 TT
1286324 CTTTTGTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (17 bp):
TTATAAATGAATTCTTT
Found at i:1291032 original size:21 final size:20
Alignment explanation
Indices: 1291007--1291077 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 20
1290997 CACAAATAAG
*
1291007 TATTTAAAATATATTAATTTT
1 TATTTAAAATA-ATTATTTTT
1291028 TATTTAAGTACATAAATTATTTTT
1 TATTTAA--A-AT-AATTATTTTT
* *
1291052 TATTTAAGATAATCATTTTT
1 TATTTAAAATAATTATTTTT
1291072 TATTTA
1 TATTTA
1291078 TGAACTGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
20 15 0.35
21 9 0.21
23 1 0.02
24 17 0.40
25 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
TATTTAAAATAATTATTTTT
Found at i:1291739 original size:35 final size:35
Alignment explanation
Indices: 1291691--1291760 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1291681 CATGTACTAA
1291691 AACTCTCTAATAGTCTCTAAATGAATTCAATGACT
1 AACTCTCTAATAGTCTCTAAATGAATTCAATGACT
* *
1291726 AACTCTCTCATAGTCTCTGAATGAATTCAATGACT
1 AACTCTCTAATAGTCTCTAAATGAATTCAATGACT
1291761 TCTACGGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (35 bp):
AACTCTCTAATAGTCTCTAAATGAATTCAATGACT
Found at i:1296214 original size:26 final size:26
Alignment explanation
Indices: 1296184--1296256 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
1296174 AATTTGGTGC
*
1296184 CAAAAAATGG-AAGGAAACATTTGCGA
1 CAAAAAATGGTAA-CAAACATTTGCGA
** *
1296210 CAAAATTTGGTAACAAACATTTGTGA
1 CAAAAAATGGTAACAAACATTTGCGA
1296236 C-AAAAATGAGTAACAAA-ATTT
1 CAAAAAATG-GTAACAAACATTT
1296257 ATTTTTTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 9 0.23
26 28 0.72
27 2 0.05
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.23
Consensus pattern (26 bp):
CAAAAAATGGTAACAAACATTTGCGA
Found at i:1296238 original size:13 final size:13
Alignment explanation
Indices: 1296198--1296239 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1296188 AAATGGAAGG
*
1296198 AAACATTTGCGAC
1 AAACATTTGTGAC
*
1296211 AAA-ATTTGGTAAC
1 AAACATTT-GTGAC
1296224 AAACATTTGTGAC
1 AAACATTTGTGAC
1296237 AAA
1 AAA
1296240 AATGAGTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 4 0.17
13 16 0.67
14 4 0.17
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.26
Consensus pattern (13 bp):
AAACATTTGTGAC
Found at i:1299447 original size:2 final size:2
Alignment explanation
Indices: 1299440--1299479 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1299430 GCTTGTGTTC
1299440 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
1299480 GCGTATGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1300705 original size:25 final size:25
Alignment explanation
Indices: 1300676--1300725 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
1300666 AAAGAAAGAA
1300676 AGAATAGAA-AGAAGGGTTTGAGAGC
1 AGAATA-AAGAGAAGGGTTTGAGAGC
*
1300701 AGAATAAAGGAGATGGGTTTGAGAG
1 AGAATAAA-GAGAAGGGTTTGAGAG
1300726 GTAAAACGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 2 0.09
25 6 0.27
26 14 0.64
ACGTcount: A:0.42, C:0.02, G:0.38, T:0.18
Consensus pattern (25 bp):
AGAATAAAGAGAAGGGTTTGAGAGC
Found at i:1302688 original size:20 final size:20
Alignment explanation
Indices: 1302659--1302698 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1302649 ATAAGTTACT
*
1302659 TATATTTTAATGTAAG-GTAA
1 TATATATTAAT-TAAGCGTAA
1302679 TATATATTAATTAAGCGTAA
1 TATATATTAATTAAGCGTAA
1302699 CTTACTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (20 bp):
TATATATTAATTAAGCGTAA
Found at i:1303223 original size:14 final size:15
Alignment explanation
Indices: 1303200--1303238 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
1303190 CCTTTTTATT
1303200 AAAATAAAATAAATA
1 AAAATAAAATAAATA
1303215 AAAAT-AAATAAATA
1 AAAATAAAATAAATA
*
1303229 AAAACAAAAT
1 AAAATAAAAT
1303239 TTGATGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAATA
Found at i:1305356 original size:18 final size:18
Alignment explanation
Indices: 1305333--1305408 Score: 107
Period size: 18 Copynumber: 4.1 Consensus size: 18
1305323 CACTGAAATT
1305333 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1305351 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1305369 TGTCCCGTAGGACTACTGTA
1 TGTCCCGAAGGACCAC--TA
1305389 TTGTCCCGAAGGACCACTA
1 -TGTCCCGAAGGACCACTA
1305408 T
1 T
1305409 AACCCTCGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
18 33 0.65
19 2 0.04
20 2 0.04
21 14 0.27
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1305909 original size:2 final size:2
Alignment explanation
Indices: 1305902--1305960 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1305892 CATAGCTTGT
1305902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1305944 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1305961 TCTCATAACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1311428 original size:16 final size:17
Alignment explanation
Indices: 1311407--1311439 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1311397 ATACCATGCA
*
1311407 TTTCAT-TTTTTTCATT
1 TTTCATGTTTTTACATT
1311423 TTTCATGTTTTTACATT
1 TTTCATGTTTTTACATT
1311440 CACATTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTCATGTTTTTACATT
Found at i:1319559 original size:115 final size:115
Alignment explanation
Indices: 1319349--1319566 Score: 294
Period size: 115 Copynumber: 1.9 Consensus size: 115
1319339 ATTGAACTCG
* **
1319349 AAAGCGACACAATTCACAAGAGTAGATTTCAACTTCACAATGAAGGACATTCAATTCAAAGCTCA
1 AAAGCGACACAATTCACAAGAGTAGATTCCAACTTCACAACAAAGGACATTCAATTCAAAGCTCA
* *
1319414 ACTTCACAACGAATGAGTCATCTACAATTTCAACTTCAAATATTAATCTC
66 ACTTCACAACGAATGAGCCACCTACAATTTCAACTTCAAATATTAATCTC
** * * *
1319464 AAAGCGATTCAATTTACAAGATTGGATTCCAACTTCACAACAAAGGACA-TCTAATTCAAAGCTC
1 AAAGCGACACAATTCACAAGAGTAGATTCCAACTTCACAACAAAGGACATTC-AATTCAAAGCTC
* * * *
1319528 GACTTTACAACGAATGAGCCACCTACGATTTCGACTTCA
65 AACTTCACAACGAATGAGCCACCTACAATTTCAACTTCA
1319567 CAACAAAGGA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
114 2 0.02
115 86 0.98
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (115 bp):
AAAGCGACACAATTCACAAGAGTAGATTCCAACTTCACAACAAAGGACATTCAATTCAAAGCTCA
ACTTCACAACGAATGAGCCACCTACAATTTCAACTTCAAATATTAATCTC
Found at i:1322351 original size:179 final size:179
Alignment explanation
Indices: 1322031--1322371 Score: 504
Period size: 179 Copynumber: 1.9 Consensus size: 179
1322021 TGGTTGCGAC
* * * *
1322031 AGTTATAGTTACAAAACATGTCATTCTATAACTTTTGTTTATGCGTCAAAAATTGGAGGAAAACA
1 AGTTATAGTTACAAAACATGTCACTCTATAACTTTTGTTTATGCGCCAAAAATTAGAAGAAAACA
* * * *
1322096 TTATGACTATATATTTTGTCACTACAATTAAAATATATAACTACAAACATAATTTGTTACCAAAA
66 TTATGACTATACATTTTGTCACTACAATTAAAATATATAACTACAAACAAAACTTGTCACCAAAA
* *
1322161 ATTTAAATCTCAATATTTGTTGTGATAATTTTCAGTAACAATAATTATA
131 AATTAAATCTCAATATTTGTTGTGACAATTTTCAGTAACAATAATTATA
* *
1322210 AGTTATAGTTACAAAACATGTCACTCTATAACTTTTGTTTTTGCGCCAAAAATTAGAAGAAAAGA
1 AGTTATAGTTACAAAACATGTCACTCTATAACTTTTGTTTATGCGCCAAAAATTAGAAGAAAACA
* * *
1322275 TTTGTGACTATACATTTTGTCACTATAATTAAAATATATAACTACAAACAAAACTTGTCA-TAAA
66 -TTATGACTATACATTTTGTCACTACAATTAAAATATATAACTACAAACAAAACTTGTCACCAAA
* * *
1322339 AAATTGAATCTCATTATTTGTTTTGACAATTTT
130 AAATTAAATCTCAATATTTGTTGTGACAATTTT
1322372 TTCTTGTCAT
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
179 90 0.63
180 53 0.37
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (179 bp):
AGTTATAGTTACAAAACATGTCACTCTATAACTTTTGTTTATGCGCCAAAAATTAGAAGAAAACA
TTATGACTATACATTTTGTCACTACAATTAAAATATATAACTACAAACAAAACTTGTCACCAAAA
AATTAAATCTCAATATTTGTTGTGACAATTTTCAGTAACAATAATTATA
Found at i:1322433 original size:180 final size:179
Alignment explanation
Indices: 1322033--1322462 Score: 465
Period size: 179 Copynumber: 2.4 Consensus size: 179
1322023 GTTGCGACAG
* * * * * *
1322033 TTATAGTTACAAAACATGTCATTCTATAACTTTTGTTTATGCGTCAAAAATTGGAGGAAAACA-T
1 TTATAGTTACAAAACATGTCACTATATAACATATGTTTTTGCGCCAAAAATTGGAGGAAAACATT
* * * * *
1322097 TATGACTATATATTTTGTCACTACAATTAAAATATATAACTACAAACATAATTTGTTACCAAAAA
66 TGTGACTATACATTTTGTCACTACAATTAAAATATATAACTACAAACAAAACTTGTCACCAAAAA
* * *
1322162 TTTAAATCTCAATATTTGTTGTGATAATTTTCAGTAACAATAATTATAAG
131 ATTAAATCTCAATATTTGTTGTGACAATTTTCAGT-ACAATAATTATAAC
* * * * * *
1322212 TTATAGTTACAAAACATGTCACTCTATAACTTTTGTTTTTGCGCCAAAAATTAGAAGAAAAGATT
1 TTATAGTTACAAAACATGTCACTATATAACATATGTTTTTGCGCCAAAAATTGGAGGAAAACATT
* *
1322277 TGTGACTATACATTTTGTCACTATAATTAAAATATATAACTACAAACAAAACTTGTCA-TAAAAA
66 TGTGACTATACATTTTGTCACTACAATTAAAATATATAACTACAAACAAAACTTGTCACCAAAAA
* * * *
1322341 ATTGAATCTCATTATTTGTTTTGACAATTTTTTCTTGT-C-ATAATTACTAAAC
131 ATTAAATCTCAATATTTGTTGTGACAA--TTTTC-AGTACAATAATTA-T-AAC
* *** ** * *
1322393 TTATAGTTACACAGTTTGTCACTATATGTCATAT-TTTTTGCGCAAAAAAATGGAGGAAAACATT
1 TTATAGTTACAAAACATGTCACTATATAACATATGTTTTTGCGCCAAAAATTGGAGGAAAACATT
1322457 TGTGAC
66 TGTGAC
1322463 AAAAAATAGT
Statistics
Matches: 211, Mismatches: 34, Indels: 11
0.82 0.13 0.04
Matches are distributed among these distances:
179 91 0.43
180 86 0.41
181 32 0.15
182 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (179 bp):
TTATAGTTACAAAACATGTCACTATATAACATATGTTTTTGCGCCAAAAATTGGAGGAAAACATT
TGTGACTATACATTTTGTCACTACAATTAAAATATATAACTACAAACAAAACTTGTCACCAAAAA
ATTAAATCTCAATATTTGTTGTGACAATTTTCAGTACAATAATTATAAC
Found at i:1326053 original size:16 final size:16
Alignment explanation
Indices: 1326032--1326064 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1326022 TAAAAAATAA
1326032 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1326048 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1326064 A
1 A
1326065 AATTTTTTTT
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1326145 original size:10 final size:10
Alignment explanation
Indices: 1326130--1326204 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1326120 CATTTAATAA
1326130 ATAAACGAAC
1 ATAAACGAAC
1326140 ATAAACGAAC
1 ATAAACGAAC
1326150 ----ACGAAC
1 ATAAACGAAC
1326156 ATAAACGAAC
1 ATAAACGAAC
** *
1326166 ACGAAC-ATAA
1 ATAAACGA-AC
1326176 ATGAACACGAAC
1 AT-AA-ACGAAC
1326188 ATAAACGAAC
1 ATAAACGAAC
1326198 ATAAACG
1 ATAAACG
1326205 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1326155 original size:16 final size:16
Alignment explanation
Indices: 1326134--1326198 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1326124 TAATAAATAA
1326134 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1326150 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1326166 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1326182 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1326198 A
1 A
1326199 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1326964 original size:14 final size:14
Alignment explanation
Indices: 1326947--1327002 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1326937 AATGAACATA
*
1326947 AACGAACATAATCG
1 AACGAACATAACCG
1326961 AACGAACAT-A---
1 AACGAACATAACCG
*
1326971 AACGAACATAACCA
1 AACGAACATAACCG
1326985 AACGAACATAACCG
1 AACGAACATAACCG
1326999 AACG
1 AACG
1327003 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1326967 original size:24 final size:24
Alignment explanation
Indices: 1326927--1327001 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
1326917 GATTGTGTTA
*
1326927 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1326951 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
1326975 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
1326999 AAC
1 AAC
1327002 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1336772 original size:19 final size:19
Alignment explanation
Indices: 1336748--1336798 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1336738 AATTTAATTT
1336748 GTGTATCGATACATAGATA
1 GTGTATCGATACATAGATA
*
1336767 GTGTATCGATACATAGGTA
1 GTGTATCGATACATAGATA
1336786 GTGTATCGATACA
1 GTGTATCGATACA
1336799 CATGTTAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (19 bp):
GTGTATCGATACATAGATA
Found at i:1337549 original size:20 final size:20
Alignment explanation
Indices: 1337521--1337575 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1337511 GAGGGTTCAT
*
1337521 AGGTCCTTCGGGACATACAG
1 AGGTCCTTCGAGACATACAG
* *
1337541 AGGTTCTTCGAGACATACAT
1 AGGTCCTTCGAGACATACAG
1337561 AGGTCCTTCGAGACA
1 AGGTCCTTCGAGACA
1337576 AATTTCACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (20 bp):
AGGTCCTTCGAGACATACAG
Found at i:1340165 original size:3 final size:3
Alignment explanation
Indices: 1340157--1340227 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
1340147 AAGTTCAAAT
1340157 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1340204 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1340228 AAACTCGATA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1348323 original size:13 final size:13
Alignment explanation
Indices: 1348305--1348330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1348295 AATTAACTGC
1348305 AAGTAGTATATGA
1 AAGTAGTATATGA
1348318 AAGTAGTATATGA
1 AAGTAGTATATGA
1348331 TATCAGAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
AAGTAGTATATGA
Found at i:1350697 original size:25 final size:25
Alignment explanation
Indices: 1350645--1350697 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1350635 ATTCAAACTT
* * *
1350645 AAAATATAAAAATAATTAGATATTA
1 AAAATATAAAAATAATGAGAAATAA
1350670 AAAATATATAAAATAATGA-AAATAA
1 AAAATATA-AAAATAATGAGAAATAA
1350695 AAA
1 AAA
1350698 TTAAATTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (25 bp):
AAAATATAAAAATAATGAGAAATAA
Found at i:1351128 original size:13 final size:12
Alignment explanation
Indices: 1351109--1351133 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1351099 ATCTTAAATG
1351109 ATTTTTTTGATT
1 ATTTTTTTGATT
1351121 ATTTTTTTGATT
1 ATTTTTTTGATT
1351133 A
1 A
1351134 ATTATTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (12 bp):
ATTTTTTTGATT
Found at i:1352175 original size:43 final size:44
Alignment explanation
Indices: 1352128--1352215 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
1352118 CTAATTATTC
* *
1352128 TGTATTTAATGGC-ATTTCTTGCCAAAAATGCTACTAATTCTCT
1 TGTATTTAATGACTATTTCTTGCCAAAAACGCTACTAATTCTCT
* * * **
1352171 TGTATTTAGTGACTTTTTTTTGCCAAAAACGCTGTTAATTCTCT
1 TGTATTTAATGACTATTTCTTGCCAAAAACGCTACTAATTCTCT
1352215 T
1 T
1352216 ATCTTTAGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 11 0.30
44 26 0.70
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (44 bp):
TGTATTTAATGACTATTTCTTGCCAAAAACGCTACTAATTCTCT
Found at i:1352296 original size:42 final size:42
Alignment explanation
Indices: 1352161--1352318 Score: 154
Period size: 42 Copynumber: 3.7 Consensus size: 42
1352151 AAAAATGCTA
* * * * * *
1352161 CTAATTCTCTTGTATTTAGTGACTTTTTTTTGCCAAAAACGCTG
1 CTAATTCTCTTGTCTTTAGTGGC--GTTTTTGCCACAAACACCG
* * ** *
1352205 TTAATTCTCTTATCTTTAGTGGCGTGCCTTGCTACAAACACCG
1 CTAATTCTCTTGTCTTTAGTGGCGT-TTTTGCCACAAACACCG
* *
1352248 CTAATTCTTTTGTCTTTAGTGGGGTTTTTGCCACAAACACCG
1 CTAATTCTCTTGTCTTTAGTGGCGTTTTTGCCACAAACACCG
* *
1352290 CTAATTCTCTTGTATTTAGTGGCATTTTT
1 CTAATTCTCTTGTCTTTAGTGGCGTTTTT
1352319 TGTATAAAAC
Statistics
Matches: 91, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
42 40 0.44
43 32 0.35
44 19 0.21
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (42 bp):
CTAATTCTCTTGTCTTTAGTGGCGTTTTTGCCACAAACACCG
Found at i:1365658 original size:26 final size:26
Alignment explanation
Indices: 1365622--1365684 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
1365612 GAGAAAGATT
1365622 TGAAATACATTCGAAGCATCGACACA
1 TGAAATACATTCGAAGCATCGACACA
1365648 TGAAATACATTCGAAGCATCGACACA
1 TGAAATACATTCGAAGCATCGACACA
1365674 TGAAATACATT
1 TGAAATACATT
1365685 ATGAATCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (26 bp):
TGAAATACATTCGAAGCATCGACACA
Found at i:1367726 original size:32 final size:32
Alignment explanation
Indices: 1367685--1367751 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
1367675 TCTAGGGTTT
*
1367685 AGTACCCTTAGAAATTCCCTAAATACCCTTGA
1 AGTACCCTTAGAAATTCCCTAAATACCCTTAA
1367717 AGTACCCTTAGAAATTCCCTAAATACCCTTAA
1 AGTACCCTTAGAAATTCCCTAAATACCCTTAA
1367749 AGT
1 AGT
1367752 TAAACCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.28
Consensus pattern (32 bp):
AGTACCCTTAGAAATTCCCTAAATACCCTTAA
Found at i:1377487 original size:23 final size:25
Alignment explanation
Indices: 1377465--1377518 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
1377455 GTGCTAATAA
*
1377465 ACATAAGGTCGTGCCCACCATAATAC
1 ACATAAGGTCGAGCCCACCAT-ATAC
*
1377491 ACATAAGGTCGAGCCCACCATATTC
1 ACATAAGGTCGAGCCCACCATATAC
1377516 ACA
1 ACA
1377519 CTATATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (25 bp):
ACATAAGGTCGAGCCCACCATATAC
Found at i:1377494 original size:26 final size:26
Alignment explanation
Indices: 1377459--1377512 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
1377449 ACTGAAGTGC
*
1377459 TAATAAACATAAGGTCGTGCCCACCA
1 TAATAAACATAAGGTCGAGCCCACCA
*
1377485 TAATACACATAAGGTCGAGCCCACCA
1 TAATAAACATAAGGTCGAGCCCACCA
1377511 TA
1 TA
1377513 TTCACACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.19
Consensus pattern (26 bp):
TAATAAACATAAGGTCGAGCCCACCA
Found at i:1384237 original size:19 final size:20
Alignment explanation
Indices: 1384213--1384253 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1384203 GTTGAAAATG
*
1384213 ATTTGA-TTTCAAAAGCAAA
1 ATTTGATTTTAAAAAGCAAA
1384232 ATTTGATTTTAAAAAGCAAA
1 ATTTGATTTTAAAAAGCAAA
1384252 AT
1 AT
1384254 GAAACTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (20 bp):
ATTTGATTTTAAAAAGCAAA
Found at i:1386541 original size:27 final size:27
Alignment explanation
Indices: 1386502--1386560 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
1386492 CTATTGTGGC
*
1386502 ATACTAAGCACCTAGAGACAAATTCAG
1 ATACTAAGAACCTAGAGACAAATTCAG
*
1386529 ATACTAAGAACCTATAGACAAATTCAG
1 ATACTAAGAACCTAGAGACAAATTCAG
1386556 ATACT
1 ATACT
1386561 TCCCTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (27 bp):
ATACTAAGAACCTAGAGACAAATTCAG
Found at i:1387555 original size:29 final size:29
Alignment explanation
Indices: 1387513--1387572 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1387503 TTGGGGGTTA
1387513 ACTTCGATGTTGTCTGCTGCTACAACGTG
1 ACTTCGATGTTGTCTGCTGCTACAACGTG
1387542 ACTTCGATGTTGTCTGCTGCTACAACGTG
1 ACTTCGATGTTGTCTGCTGCTACAACGTG
1387571 AC
1 AC
1387573 CCAAAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.33
Consensus pattern (29 bp):
ACTTCGATGTTGTCTGCTGCTACAACGTG
Found at i:1390838 original size:24 final size:24
Alignment explanation
Indices: 1390776--1390841 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
1390766 GTATCTGCTT
* * *
1390776 TCACTGTACGGATAGGTTCTTCGG
1 TCACTGTACGGACATGTTCTGCGG
1390800 TCACTGTACGGACATGTTCTGCGG
1 TCACTGTACGGACATGTTCTGCGG
*
1390824 TCACTGTACGAACATGTT
1 TCACTGTACGGACATGTT
1390842 TATAGGCTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.32
Consensus pattern (24 bp):
TCACTGTACGGACATGTTCTGCGG
Found at i:1399351 original size:11 final size:10
Alignment explanation
Indices: 1399336--1399383 Score: 73
Period size: 10 Copynumber: 5.0 Consensus size: 10
1399326 GAGATGGGGT
1399336 TGGGGGAGGG
1 TGGGGGAGGG
1399346 TGGGGGAGGG
1 TGGGGGAGGG
1399356 TGGGGGAGGG
1 TGGGGGAGGG
*
1399366 TGGGAGA-GG
1 TGGGGGAGGG
1399375 -GGGGGAGGG
1 TGGGGGAGGG
1399384 GGAGAGGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
8 5 0.14
9 4 0.11
10 26 0.74
ACGTcount: A:0.12, C:0.00, G:0.79, T:0.08
Consensus pattern (10 bp):
TGGGGGAGGG
Found at i:1399386 original size:6 final size:6
Alignment explanation
Indices: 1399367--1399404 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1399357 GGGGGAGGGT
*
1399367 GGGAGA GGG-G- GGGAGG GGGAGA GGGAGA GGGAGA GGGA
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGA
1399405 ATTATACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
4 3 0.10
5 2 0.07
6 24 0.83
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:1400115 original size:6 final size:6
Alignment explanation
Indices: 1400083--1400223 Score: 108
Period size: 6 Copynumber: 23.0 Consensus size: 6
1400073 GATAGAGATT
* * * * **
1400083 GAGGGA GAGAGGAA GAGGGA GA--TA GAGGGA GAGAGT GTGGGA GAAAGA
1 GAGGGA GAG-GG-A GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA
* * *
1400131 GAAGGA GAGGGA G-GGGA GAGGGA GAGGGA GATGGA GAGGGA GGGGGA
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA
* *
1400178 GGGGGA GGGGGA GAGGGA GAGAGAGA GAGGGA GGGAGGGA GAGGGA
1 GAGGGA GAGGGA GAGGGA GAG-G-GA GAGGGA --GAGGGA GAGGGA
1400224 ATGCTACAAT
Statistics
Matches: 110, Mismatches: 16, Indels: 18
0.76 0.11 0.12
Matches are distributed among these distances:
4 3 0.03
5 5 0.05
6 81 0.74
7 6 0.05
8 15 0.14
ACGTcount: A:0.34, C:0.00, G:0.63, T:0.03
Consensus pattern (6 bp):
GAGGGA
Found at i:1401085 original size:45 final size:45
Alignment explanation
Indices: 1401030--1401183 Score: 177
Period size: 45 Copynumber: 3.4 Consensus size: 45
1401020 TAATCCAAGG
*
1401030 CTTTTGATTATTGGGTTGTCAAAAGTAAAATCAAAGGATTAATTC
1 CTTTTGATTATTGGGTTGTCAAAAGTAAAATCAAAGGATTAGTTC
* * * *
1401075 CTCTTGATTATTGTGTTGTCAAAAGTAAAAGCAAAGGATTGGTT-
1 CTTTTGATTATTGGGTTGTCAAAAGTAAAATCAAAGGATTAGTTC
* * * * *
1401119 CTTTTCGATTATTAGATTG-CAAAAAATTAAAATAAAATGATTAGTTC
1 CTTTT-GATTATTGGGTTGTC--AAAAGTAAAATCAAAGGATTAGTTC
1401166 CTTTTGATTATTGGGTTG
1 CTTTTGATTATTGGGTTG
1401184 GTAAAATTAA
Statistics
Matches: 89, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
44 5 0.06
45 49 0.55
46 30 0.34
47 5 0.06
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGTCAAAAGTAAAATCAAAGGATTAGTTC
Found at i:1401458 original size:58 final size:56
Alignment explanation
Indices: 1401341--1401661 Score: 169
Period size: 58 Copynumber: 5.6 Consensus size: 56
1401331 AATCTTGCGT
*
1401341 TGATTCTAGTTTTTTAAGAAAAAAAATTGTTAAATTTATTTCCTTAAGAAGCTTAAA
1 TGATTCTA-ATTTTTAAGAAAAAAAATTGTTAAATTTATTTCCTTAAGAAGCTTAAA
* ** * * * *
1401398 TGATTTTAACTTTTTAAGAAAAATATTTTGTTAAATTTGTTTCTTTGAA-AATCTTTAA
1 TGATTCTAA-TTTTTAAGAAAAA-AAATTGTTAAATTTATTTCCTT-AAGAAGCTTAAA
* * * * * * ** *
1401456 TGATTCTAATTTTGAAAGGAAAATAAATTGTCAAATTTATTTTCTTGAGAAACGTGGAT
1 TGATTCTAATTTT-TAA-GAAAAAAAATTGTTAAATTTATTTCCTTAAGAAGC-TTAAA
* * * * *
1401515 TG-TTCT-ATCTTTTAA-AAAGAAGTAAATTATTAAATTTATTTTCTTGATAATCTTAAA
1 TGATTCTAAT-TTTTAAGAAA-AA--AAATTGTTAAATTTATTTCCTTAAGAAGCTTAAA
* * * * *
1401572 TTATTAT-ATTTTATAA-AATTTAATAAATTGTTAAATTTATTTTCTTGAG-AGTCTTAAA
1 TGATTCTAATTTT-TAAGAA---AAAAAATTGTTAAATTTATTTCCTTAAGAAG-CTTAAA
*
1401630 TGATTCT-A-TTTT--GTAAAAAAATTGTTAAATTT
1 TGATTCTAATTTTTAAGAAAAAAAATTGTTAAATTT
1401662 TTTTTCTCGA
Statistics
Matches: 205, Mismatches: 41, Indels: 41
0.71 0.14 0.14
Matches are distributed among these distances:
52 16 0.08
55 4 0.02
56 2 0.01
57 39 0.19
58 131 0.64
59 11 0.05
60 1 0.00
61 1 0.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.47
Consensus pattern (56 bp):
TGATTCTAATTTTTAAGAAAAAAAATTGTTAAATTTATTTCCTTAAGAAGCTTAAA
Found at i:1401923 original size:39 final size:38
Alignment explanation
Indices: 1401827--1401998 Score: 150
Period size: 39 Copynumber: 4.4 Consensus size: 38
1401817 TTTTGATTTG
* * **
1401827 TGAAAGGAAATAAATCATTGGATTTATTTTTCCAATTTCG
1 TGAAAGGAAATAAATCATTGAATTTA-TTTT-CTATTTTA
* *
1401867 TAAAAGGAAATAAATCATTGAATTTATTTTACTTTTTTA
1 TGAAAGGAAATAAATCATTGAATTTATTTT-CTATTTTA
* * * *
1401906 TGAAAGGAGATAAATCATTCAGTTTATTTTCATGTTTTA
1 TGAAAGGAAATAAATCATTGAATTTATTTTC-TATTTTA
***
1401945 TGAAAGGAAATAAATTGGTGAA-TTATTTTTCCTATTTTA
1 TGAAAGGAAATAAATCATTGAATTTA-TTTT-CTATTTTA
*
1401984 -AAAAGGAAATAAATC
1 TGAAAGGAAATAAATC
1401999 GATAATTTTT
Statistics
Matches: 108, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
38 17 0.16
39 66 0.61
40 25 0.23
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (38 bp):
TGAAAGGAAATAAATCATTGAATTTATTTTCTATTTTA
Found at i:1402131 original size:39 final size:39
Alignment explanation
Indices: 1402040--1402216 Score: 110
Period size: 39 Copynumber: 4.5 Consensus size: 39
1402030 TGACTATGAC
* ** * *
1402040 TTGTAAAAGAAAATAAATCATTGAATTTATTTTTATATT
1 TTGTAAAAGGAAATAAATCATTGAATTTAGATTCATAGT
* *
1402079 TTG-AAAATTGAAATAAATCATAT-AATTTAGATTCCTAGT
1 TTGTAAAA-GGAAATAAATCAT-TGAATTTAGATTCATAGT
** ** * *
1402118 TTGTAAAAGGAAATAAATTGTT-AGATTTATTTTCCTATT
1 TTGTAAAAGGAAATAAATCATTGA-ATTTAGATTCATAGT
* ** * *
1402157 TTGTAAAGAAAAGAAATAAATTGTTGGATTTAG-TTCATATT
1 TTGT--A-AAAGGAAATAAATCATTGAATTTAGATTCATAGT
1402198 TTGTAAAAGGAAATAAATC
1 TTGTAAAAGGAAATAAATC
1402217 GAAACAAATA
Statistics
Matches: 111, Mismatches: 19, Indels: 17
0.76 0.13 0.12
Matches are distributed among these distances:
38 18 0.16
39 55 0.50
40 5 0.05
41 12 0.11
42 21 0.19
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (39 bp):
TTGTAAAAGGAAATAAATCATTGAATTTAGATTCATAGT
Found at i:1402187 original size:42 final size:39
Alignment explanation
Indices: 1402110--1402318 Score: 150
Period size: 39 Copynumber: 5.1 Consensus size: 39
1402100 ATAATTTAGA
* * *
1402110 TTCCTAGTTTGTAAAAGGAAATAAATTGTTAGATTTATT
1 TTCCTATTTTGTAAAAAGAAATAAATTGTTGGATTTATT
*
1402149 TTCCTATTTTGTAAAGAAAAGAAATAAATTGTTGGATTTA-G
1 TTCCTATTTTGT--A-AAAAGAAATAAATTGTTGGATTTATT
* * * **
1402190 TTCATATTTTGTAAAAGGAAATAAATCGAAACAAATAATCTAATTTATT
1 TTCCTATTTTGTAAAAAGAAATAAATTG-------T--T-GGATTTATT
*
1402239 TTCCTGTTTTGTAAAAAGAAATAAATTGTTGGATTTATT
1 TTCCTATTTTGTAAAAAGAAATAAATTGTTGGATTTATT
** * * **
1402278 TTTTTGTTTTGTAAAAGGAAATAAATCATTGGATTTATT
1 TTCCTATTTTGTAAAAAGAAATAAATTGTTGGATTTATT
1402317 TT
1 TT
1402319 ATGGGAATCT
Statistics
Matches: 135, Mismatches: 21, Indels: 28
0.73 0.11 0.15
Matches are distributed among these distances:
38 13 0.10
39 55 0.41
40 1 0.01
41 12 0.09
42 23 0.17
45 1 0.01
47 1 0.01
48 5 0.04
49 24 0.18
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (39 bp):
TTCCTATTTTGTAAAAAGAAATAAATTGTTGGATTTATT
Found at i:1404246 original size:24 final size:24
Alignment explanation
Indices: 1404214--1404269 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1404204 CTATTCTTTC
1404214 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
1404238 GCTTCAATTGAGCTCATATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
1404262 GCTTCAAT
1 GCTTCAAT
1404270 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:1408670 original size:14 final size:14
Alignment explanation
Indices: 1408651--1408677 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1408641 AAATAATTAA
1408651 AATAATATATTTAG
1 AATAATATATTTAG
1408665 AATAATATATTTA
1 AATAATATATTTA
1408678 TTATATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
AATAATATATTTAG
Found at i:1408749 original size:21 final size:20
Alignment explanation
Indices: 1408693--1408754 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
1408683 TTTAAACTGT
1408693 TAAATTAATATATTTT-ATAA
1 TAAA-TAATATATTTTAATAA
** *
1408713 TAGTTTATAT-TTTTAATAA
1 TAAATAATATATTTTAATAA
1408732 TGAAATAATATATTTTAATAA
1 T-AAATAATATATTTTAATAA
1408753 TA
1 TA
1408755 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 4 0.12
19 10 0.30
20 9 0.27
21 10 0.30
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TAAATAATATATTTTAATAA
Found at i:1408762 original size:21 final size:22
Alignment explanation
Indices: 1408718--1408762 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1408708 TATAATAGTT
*
1408718 TATATTTTTAATAATGAAATAA
1 TATATTTTTAATAATGAAAAAA
1408740 TATA-TTTTAATAAT-ATAAAAA
1 TATATTTTTAATAATGA-AAAAA
1408761 TA
1 TA
1408763 AAAATTCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 16 0.76
22 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATTTTTAATAATGAAAAAA
Found at i:1409168 original size:42 final size:42
Alignment explanation
Indices: 1409074--1409193 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 42
1409064 ATTATGTGTA
* * *
1409074 TGGAGTCAGAGCTAGAGTGGAGCGGGGAGGTGAAGAACCTTC
1 TGGAGTCGGAGCTAGAGTGGAGCAGGGAGGTGAAGAACCGTC
* * * **
1409116 TGGAGTCGGAGCTAGAGTGGAGCATGGTGTTGAAGAGTCGTC
1 TGGAGTCGGAGCTAGAGTGGAGCAGGGAGGTGAAGAACCGTC
*
1409158 TAGGAG-CGGAGCT-GTAATGGAGC-GAGGAGGTGAAGA
1 T-GGAGTCGGAGCTAG-AGTGGAGCAG-GGAGGTGAAGA
1409194 GACATCGGGA
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.02
42 58 0.92
43 4 0.06
ACGTcount: A:0.26, C:0.12, G:0.44, T:0.18
Consensus pattern (42 bp):
TGGAGTCGGAGCTAGAGTGGAGCAGGGAGGTGAAGAACCGTC
Found at i:1409818 original size:51 final size:51
Alignment explanation
Indices: 1409763--1409897 Score: 164
Period size: 51 Copynumber: 2.6 Consensus size: 51
1409753 ACTATAATGT
*
1409763 TGTAAGTATGTGTTAAGTGCTACACCTTTTTGTTTTACTT-ACTCACACCGA
1 TGTAAGTATGTGTTAAGTGCTACACTTTTTTGTTTTA-TTCACTCACACCGA
* * ** * * *
1409814 TGTAACTATGTGTTAAGTGTTTTACTTTTTTGTTTTATTCATTTACACCGT
1 TGTAAGTATGTGTTAAGTGCTACACTTTTTTGTTTTATTCACTCACACCGA
* *
1409865 TGTAAGTATATGTTCAGTGCTACACTTTTTTGT
1 TGTAAGTATGTGTTAAGTGCTACACTTTTTTGT
1409898 AGTATTAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
50 2 0.03
51 67 0.97
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.48
Consensus pattern (51 bp):
TGTAAGTATGTGTTAAGTGCTACACTTTTTTGTTTTATTCACTCACACCGA
Found at i:1411855 original size:64 final size:64
Alignment explanation
Indices: 1411802--1411964 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 64
1411792 CGGTGCACCA
* * *
1411802 AGTGTGCATTGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCTTGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
1411866 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
1411931 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
1411965 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 38 0.46
65 45 0.54
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:1411936 original size:19 final size:19
Alignment explanation
Indices: 1411912--1411962 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1411902 GAAAATATTC
1411912 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1411931 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1411950 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1411963 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1412663 original size:8 final size:8
Alignment explanation
Indices: 1412610--1412663 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
1412600 AAATTAAGTT
1412610 CAAACATC
1 CAAACATC
*
1412618 CAAGCATC
1 CAAACATC
*
1412626 CAAGCATC
1 CAAACATC
*
1412634 CAAATATC
1 CAAACATC
*
1412642 CAAACAAATA
1 CAAAC--ATC
1412652 CAAACATC
1 CAAACATC
1412660 CAAA
1 CAAA
1412664 TCAAAAAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
8 31 0.82
10 7 0.18
ACGTcount: A:0.52, C:0.31, G:0.04, T:0.13
Consensus pattern (8 bp):
CAAACATC
Found at i:1418454 original size:22 final size:21
Alignment explanation
Indices: 1418412--1418451 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1418402 GAGTTTGTTT
*
1418412 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1418433 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1418452 ACAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1426222 original size:22 final size:23
Alignment explanation
Indices: 1426192--1426235 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1426182 TTTATTTATT
1426192 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
1426215 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
1426236 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:1426251 original size:31 final size:32
Alignment explanation
Indices: 1426184--1426264 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 32
1426174 AAATATTATT
1426184 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTTATTAATATTTATAATAATATAA
*
1426215 TATTATATTT-TTAATA-TTAT-ATAAAATAA
1 TATTATATTTATTAATATTTATAATAATATAA
*
1426244 TCAATTATATTATAATAATAT
1 T--ATTATATT-TATTAATAT
1426265 AAGATATTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 9 0.21
30 4 0.10
31 18 0.43
32 6 0.14
33 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTATATTTATTAATATTTATAATAATATAA
Found at i:1426309 original size:52 final size:52
Alignment explanation
Indices: 1426200--1426309 Score: 120
Period size: 52 Copynumber: 2.1 Consensus size: 52
1426190 TTTATTAATA
* *
1426200 TTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTAT
1 TTTATAATAATATAATATTACATTTTTAATATTATAAAAAATAATCAATTAT
* *
1426252 ATTATAATAATATAAGATATTACATTTTT-AT-TT-TAAAATATATAAT-AATTTT
1 TTTATAATAATAT-A-ATATTACATTTTTAATATTATAAAA-A-ATAATCAATTAT
1426304 TTTATA
1 TTTATA
1426310 TATTTAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
51 4 0.08
52 25 0.51
53 8 0.16
54 12 0.24
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (52 bp):
TTTATAATAATATAATATTACATTTTTAATATTATAAAAAATAATCAATTAT
Found at i:1426314 original size:30 final size:32
Alignment explanation
Indices: 1426280--1426351 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 32
1426270 ATTACATTTT
*
1426280 TATTTTAAAATATAT-AATAAT-TTTTTTATA
1 TATTTTAAAATATATGAATAATATTATTTATA
1426310 TA-TTT--AATA-ATGAATAATATTATTTATA
1 TATTTTAAAATATATGAATAATATTATTTATA
*
1426338 TATTTAAATAATAT
1 TATTTTAA-AATAT
1426352 TTTAATAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
26 2 0.06
27 10 0.30
28 10 0.30
29 5 0.15
30 2 0.06
32 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (32 bp):
TATTTTAAAATATATGAATAATATTATTTATA
Found at i:1426344 original size:28 final size:28
Alignment explanation
Indices: 1426287--1426349 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
1426277 TTTTATTTTA
*
1426287 AAATATAT-AATAATTTTTTTATATATTT
1 AAATA-ATGAATAATTTATTTATATATTT
1426315 -AATAATGAATAATATTATTTATATATTT
1 AAATAATGAATAAT-TTATTTATATATTT
1426343 AAATAAT
1 AAATAAT
1426350 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 2 0.06
27 10 0.32
28 13 0.42
29 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
AAATAATGAATAATTTATTTATATATTT
Found at i:1426380 original size:23 final size:22
Alignment explanation
Indices: 1426354--1426397 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1426344 AATAATATTT
1426354 TAATAAAGATATTTAAAATATAC
1 TAATAAAGAT-TTTAAAATATAC
* **
1426377 TAATTAATCTTTTAAAATATA
1 TAATAAAGATTTTAAAATATA
1426398 ATATAATACT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
TAATAAAGATTTTAAAATATAC
Found at i:1426530 original size:30 final size:27
Alignment explanation
Indices: 1426487--1426541 Score: 65
Period size: 30 Copynumber: 1.9 Consensus size: 27
1426477 TTTATTAATA
1426487 AAATTATAAAAATAATATTTAATAATAAAT
1 AAATTATAAAAAT-AT-TTTAA-AATAAAT
**
1426517 AAATTATTTAAATATTTTAAAATAA
1 AAATTATAAAAATATTTTAAAATAA
1426542 CAATATTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 5 0.22
29 2 0.09
30 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATTATAAAAATATTTTAAAATAAAT
Found at i:1426761 original size:14 final size:15
Alignment explanation
Indices: 1426742--1426784 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
1426732 TCTAGAAATG
1426742 TAATTCATTTTCCA-
1 TAATTCATTTTCCAT
**
1426756 TAATTCAAATTCCAT
1 TAATTCATTTTCCAT
1426771 TAATTCATTTTCCA
1 TAATTCATTTTCCA
1426785 GATCCAGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTCATTTTCCAT
Done.