Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 58 of 335
Found at i:20418113 original size:131 final size:130
Alignment explanation
Indices: 20417881--20418484 Score: 810
Period size: 131 Copynumber: 4.6 Consensus size: 130
20417871 TAAATTCAAC
* * * *
20417881 CTGTTACCCTACTGGTTAGGGGTTAAGATTTGTAAAT-TTTAGCCTGTTACCCTACTGCTTAGGG
1 CTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGG
* * * **
20417945 TTTAAGGTTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTTAT
66 GTTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGAT
*
20418010 CTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCAGCCAGTTACCCTACTGCTTAGGG
1 CTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGG
*
20418075 GTTTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTGA
66 G-TTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGA
20418140 T
130 T
*
20418141 CTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTACTTAGGG
1 CTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGG
* *
20418206 GTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCTTAAGGGGTTAAAGCCCATCATCTTCGAT
66 GTTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGAT
* * *
20418271 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTC-GATCTGTTTCCCTACTGCTTAG
1 CTGTTTCCCTACTGCTTA-GGGGTTAAGATCTGTAAATCTTCAG-CCTGTTACCCTACTGCTTAG
* * * *** * * *
20418333 GGAGATAA-GATCTG-CAATTCGG-TCTGTTACCCTACCAATTA-GGGGTTTAAGACCCTTCGTC
64 GG-GTTAAGGCT-TGTAAATTCGGCT-TGTTACCCTACTGCTTAGGGGGTTAAAG-CCCATCATC
20418394 TTCGAT
125 TTCGAT
* *
20418400 CTGTTTCCCTACTACTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTATTGCTTAGG
1 CTGTTTCCCTACTGCTTA-GGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
*
20418465 GGCTTAAGGCTTGTGAATTC
65 GG-TTAAGGCTTGTAAATTC
20418485 ACTGATTCTA
Statistics
Matches: 425, Mismatches: 36, Indels: 25
0.87 0.07 0.05
Matches are distributed among these distances:
128 11 0.03
129 125 0.29
130 113 0.27
131 168 0.40
132 8 0.02
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (130 bp):
CTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGG
GTTAAGGCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGAT
Found at i:20418292 original size:43 final size:44
Alignment explanation
Indices: 20417967--20418426 Score: 227
Period size: 44 Copynumber: 10.6 Consensus size: 44
20417957 AAATTCGGCT
* **
20417967 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCAT-CATTTTTTATC
1 TGTTACCCTACTGCTTA-GGGGTTAAAGCCCATACATCTTCGATC
* * ** * *
20418011 TGTTTCCCTACTGCTTAGGGGTT-AAGATCTGTAAATCTTC-AGCC
1 TGTTACCCTACTGCTTAGGGGTTAAAG-CCCATACATCTTCGA-TC
* * *** * *
20418055 AGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTA-A-ATTCG-GC
1 TGTTACCCTACTGCTTAGGGG-TTAAAGCCCATACATCTTCGATC
*
20418097 TTGTTACCCTACTGCTTAGGGGGTTAAAGCCCAT-CATCTTTGATC
1 -TGTTACCCTACTGCTTA-GGGGTTAAAGCCCATACATCTTCGATC
* * ** * *
20418142 TGTTTCCCTACTGCTTAGGGGTT-AAGATCTGTAAATCTTC-AGCC
1 TGTTACCCTACTGCTTAGGGGTTAAAG-CCCATACATCTTCGA-TC
* * *** * * *
20418186 TGTTACCCTACTACTTAGGGGTTAAGGCTTGTAAAT-TTGGCT-
1 TGTTACCCTACTGCTTAGGGGTTAAAGCCCATACATCTTCGATC
20418228 TGTTACCCTACTGCTTAAGGGGTTAAAGCCCAT-CATCTTCGATC
1 TGTTACCCTACTGCTT-AGGGGTTAAAGCCCATACATCTTCGATC
* ** *
20418272 TGTTTCCCTACTGCTTAGGGGGTT-AAGATC-TTCATCTTCGATC
1 TGTTACCCTACTGCTTA-GGGGTTAAAGCCCATACATCTTCGATC
* * ** * * *
20418315 TGTTTCCCTACTGCTTAGGGAGAT-AAGATC-TGCA-ATTCGGTC
1 TGTTACCCTACTGCTTAGGG-GTTAAAGCCCATACATCTTCGATC
*** * * *
20418357 TGTTACCCTACCAATTAGGGGTTTAAGACCC-TTCGTCTTCGATC
1 TGTTACCCTACTGCTTAGGGGTTAAAG-CCCATACATCTTCGATC
* *
20418401 TGTTTCCCTACTACTTAGGGGGTTAA
1 TGTTACCCTACTGCTTA-GGGGTTAA
20418427 GATCTGTAAA
Statistics
Matches: 322, Mismatches: 68, Indels: 51
0.73 0.15 0.12
Matches are distributed among these distances:
41 2 0.01
42 53 0.16
43 110 0.34
44 139 0.43
45 16 0.05
46 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (44 bp):
TGTTACCCTACTGCTTAGGGGTTAAAGCCCATACATCTTCGATC
Found at i:20418642 original size:66 final size:66
Alignment explanation
Indices: 20418536--20418662 Score: 236
Period size: 66 Copynumber: 1.9 Consensus size: 66
20418526 TCTATGCTTA
*
20418536 TGTCAAATGATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
20418601 G
66 G
*
20418602 TGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
20418663 TATATGAATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (66 bp):
TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
G
Found at i:20419862 original size:6 final size:6
Alignment explanation
Indices: 20419853--20419884 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
20419843 TTTTTTTTTA
20419853 CCTTTG CCTTTG CCTTTG CCTTTG CCTTTG CC
1 CCTTTG CCTTTG CCTTTG CCTTTG CCTTTG CC
20419885 ATATAACTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.38, G:0.16, T:0.47
Consensus pattern (6 bp):
CCTTTG
Found at i:20423794 original size:12 final size:12
Alignment explanation
Indices: 20423772--20423814 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
20423762 AATAAAAAAC
20423772 AATACTATATATA
1 AATA-TATATATA
20423785 AATATATATATA
1 AATATATATATA
* * *
20423797 TATATACATAAA
1 AATATATATATA
20423809 AATATA
1 AATATA
20423815 CACTAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (12 bp):
AATATATATATA
Found at i:20424050 original size:3 final size:3
Alignment explanation
Indices: 20424037--20424122 Score: 56
Period size: 3 Copynumber: 28.3 Consensus size: 3
20424027 GAGGACATAT
*
20424037 ATA AT- ATA ATA ATA A-G ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
20424081 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20424123 AACAAAGCTC
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
2 8 0.12
3 47 0.71
4 9 0.14
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:20424061 original size:12 final size:12
Alignment explanation
Indices: 20424037--20424119 Score: 64
Period size: 12 Copynumber: 6.8 Consensus size: 12
20424027 GAGGACATAT
20424037 ATAATAT-AATA
1 ATAATATAAATA
*
20424048 ATAAGATAAATA
1 ATAATATAAATA
20424060 ATAATATATACATGA
1 ATAATATA-A-AT-A
20424075 GA-AATA-ATAATA
1 -ATAATATA-AATA
20424087 ATAATATAAATA
1 ATAATATAAATA
* *
20424099 ATAGTAAAAATA
1 ATAATATAAATA
*
20424111 ATAAAATAA
1 ATAATATAA
20424120 TAAAACAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
11 7 0.12
12 36 0.62
13 4 0.07
14 5 0.09
15 5 0.09
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:20424081 original size:21 final size:18
Alignment explanation
Indices: 20424042--20424122 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 18
20424032 CATATATAAT
* *
20424042 ATAATAATAAGATAAATA
1 ATAATAATAATAGAAATA
20424060 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
20424081 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
* *
20424099 ATAGTAAAAATA-ATAA-A
1 ATAATAATAATAGA-AATA
20424116 ATAATAA
1 ATAATAA
20424123 AACAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
17 8 0.15
18 24 0.45
19 5 0.09
20 4 0.08
21 12 0.23
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.28
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:20424110 original size:27 final size:29
Alignment explanation
Indices: 20424056--20424121 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 29
20424046 TAATAAGATA
20424056 AATAATAATAT--ATACATGAGAAATAAT
1 AATAATAATATAAATACATGAGAAATAAT
*
20424083 AATAATAATATAAATA-ATAGTAAAAATAAT
1 AATAATAATATAAATACAT-G-AGAAATAAT
20424113 AA-AATAATA
1 AATAATAATA
20424122 AAACAAAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 11 0.32
28 2 0.06
29 11 0.32
30 10 0.29
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (29 bp):
AATAATAATATAAATACATGAGAAATAAT
Found at i:20424476 original size:22 final size:23
Alignment explanation
Indices: 20424450--20424500 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
20424440 TAACCTTCTT
20424450 TCCAAAAAAACAAAAAAA-CACC
1 TCCAAAAAAACAAAAAAACCACC
*
20424472 TCC-AAAAAACAAAAAAACCTCC
1 TCCAAAAAAACAAAAAAACCACC
20424494 TCCAAAA
1 TCCAAAA
20424501 CAAAGAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 14 0.54
22 9 0.35
23 3 0.12
ACGTcount: A:0.63, C:0.29, G:0.00, T:0.08
Consensus pattern (23 bp):
TCCAAAAAAACAAAAAAACCACC
Found at i:20424523 original size:23 final size:20
Alignment explanation
Indices: 20424456--20424523 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
20424446 TCTTTCCAAA
*
20424456 AAAACAAAAAAA-CACCTCC
1 AAAACAAAAAAACCTCCTCC
20424475 AAAAAACAAAAAAACCTCCTCC
1 --AAAACAAAAAAACCTCCTCC
*
20424497 AAAACAAAGAACAATCCTTCTCC
1 AAAACAAA-AA-AA-CCTCCTCC
20424520 AAAA
1 AAAA
20424524 AACCAAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.20
21 14 0.34
22 8 0.20
23 11 0.27
ACGTcount: A:0.59, C:0.29, G:0.01, T:0.10
Consensus pattern (20 bp):
AAAACAAAAAAACCTCCTCC
Found at i:20425220 original size:46 final size:46
Alignment explanation
Indices: 20425152--20425320 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 46
20425142 GTAACCCGCC
20425152 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGAG-CGTTCGCAT
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCAT
* *
20425197 CAATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 C-ATAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-GAC--GTTCGCAT
* * * * * *
20425247 C-TCA-CGAACTCGGACTCAACTCAATGAGTTTG-GACATTCGCAT
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCAT
20425290 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 -CATAAGTGAACTCGGACTCAACTCAACGAG
20425321 TTCGGATGCT
Statistics
Matches: 102, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 3 0.03
46 55 0.54
47 25 0.25
48 3 0.03
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCAT
Found at i:20425287 original size:93 final size:93
Alignment explanation
Indices: 20425159--20425329 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
20425149 GCCCATAAGT
*
20425159 GAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCAATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCAATAAGTGAACTCGGACTCAACTCAA
20425224 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * * *
20425252 GAACTCGGACTCAACTCAATGAGTTTG-GACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGAG-CATTCGCATCAATAAGTGAACTCGGACTCAACTCA
*
20425316 ACGAGTTCGGATGC
65 ACGAGCTCGGATGC
20425330 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 70 0.99
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCAATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:20439371 original size:25 final size:26
Alignment explanation
Indices: 20439319--20439371 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
20439309 ACTCAAATAA
*
20439319 TTTAATTAATTATTAAAATGATCCACTTT
1 TTTAATTAAATATTAAAATG---CACTTT
20439348 TTTAATTAAATATTAAAATG-ACTT
1 TTTAATTAAATATTAAAATGCACTT
20439372 GAAATCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
29 19 0.83
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTAATTAAATATTAAAATGCACTTT
Found at i:20439670 original size:13 final size:13
Alignment explanation
Indices: 20439647--20439694 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
20439637 TTGAGTTTTA
20439647 TATTT-TTTATTT
1 TATTTATTTATTT
*
20439659 TGTTTATTTATTT
1 TATTTATTTATTT
*
20439672 TATTTATTTTTTGT
1 TATTTATTTATT-T
*
20439686 TATTAATTT
1 TATTTATTT
20439695 TAAAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 4 0.13
13 17 0.57
14 9 0.30
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (13 bp):
TATTTATTTATTT
Found at i:20439792 original size:21 final size:20
Alignment explanation
Indices: 20439759--20439797 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
20439749 TTTAAATATT
*
20439759 ATTTTTAAATTATTTTTTAA
1 ATTTTGAAATTATTTTTTAA
20439779 ATTTTGAATATTATTTTTT
1 ATTTTGAA-ATTATTTTTT
20439798 TGAAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
ATTTTGAAATTATTTTTTAA
Found at i:20439856 original size:36 final size:34
Alignment explanation
Indices: 20439736--20439982 Score: 128
Period size: 34 Copynumber: 7.0 Consensus size: 34
20439726 TTATAATATA
*
20439736 TATTTTTTAAAATTTTAAATAT-TATTTTT-AAAT
1 TATTTTTT-AAATTTTAAAAATATATTTTTGAAAT
* * * *
20439769 TATTTTTTAAATTTTGAATATTATTTTTTTGAAAA
1 TATTTTTTAAATTTT-AAAAATATATTTTTGAAAT
* * *
20439804 TATGTCTTATATATTTTAAAAATATGTTTTTGAAAT
1 TAT-T-TTTTAAATTTTAAAAATATATTTTTGAAAT
* *
20439840 TAATTTTTCTAAATTTTAAATTTTAAATATATTTTTAAAAA
1 T-ATTTTT-TAAATTTT-AA----AAATATATTTTTGAAAT
* * * ** *
20439881 TATATTTTTAAA--TAAAATAAAATAATTTCAAAAA
1 TAT-TTTTTAAATTTTAAA-AATATATTTTTGAAAT
* * *
20439915 TATACTTTTAAATTTGAAATATATATTTTTGAAAT
1 TAT-TTTTTAAATTTTAAAAATATATTTTTGAAAT
* *
20439950 TATTTTTTAAAATATTAAATAT-TATTTTT-AAAT
1 TATTTTTT-AAATTTTAAAAATATATTTTTGAAAT
20439983 ATTAAATATA
Statistics
Matches: 166, Mismatches: 31, Indels: 34
0.72 0.13 0.15
Matches are distributed among these distances:
32 7 0.04
33 16 0.10
34 41 0.25
35 32 0.19
36 29 0.17
37 15 0.09
38 1 0.01
40 6 0.04
41 19 0.11
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (34 bp):
TATTTTTTAAATTTTAAAAATATATTTTTGAAAT
Found at i:20439877 original size:12 final size:12
Alignment explanation
Indices: 20439860--20439894 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
20439850 AAATTTTAAA
20439860 TTTTAAATATAT
1 TTTTAAATATAT
20439872 TTTTAAAAATATAT
1 TTTT--AAATATAT
20439886 TTTTAAATA
1 TTTTAAATA
20439895 AAATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.43
14 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTTAAATATAT
Found at i:20439881 original size:14 final size:14
Alignment explanation
Indices: 20439864--20439892 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20439854 TTTAAATTTT
20439864 AAATATATTTTTAA
1 AAATATATTTTTAA
20439878 AAATATATTTTTAA
1 AAATATATTTTTAA
20439892 A
1 A
20439893 TAAAATAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATATTTTTAA
Found at i:20439928 original size:21 final size:22
Alignment explanation
Indices: 20439904--20439950 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
20439894 AAAATAAAAT
20439904 AATTTCAAAAATATACTTTT-A
1 AATTTCAAAAATATACTTTTGA
* * *
20439925 AATTTGAAATATATATTTTTGA
1 AATTTCAAAAATATACTTTTGA
20439947 AATT
1 AATT
20439951 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
AATTTCAAAAATATACTTTTGA
Found at i:20439956 original size:13 final size:15
Alignment explanation
Indices: 20439927--20439964 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
20439917 TACTTTTAAA
20439927 TTTGAAATATATATT
1 TTTGAAATATATATT
20439942 TTTGAAAT-TAT-TT
1 TTTGAAATATATATT
*
20439955 TTTAAAATAT
1 TTTGAAATAT
20439965 TAAATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.43
14 4 0.19
15 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (15 bp):
TTTGAAATATATATT
Found at i:20440010 original size:22 final size:21
Alignment explanation
Indices: 20439948--20440006 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 21
20439938 TATTTTTGAA
20439948 ATTATTTTTTAAAATATTAAAT
1 ATTA-TTTTTAAAATATTAAAT
20439970 ATTATTTTT-AAATATTAAAT
1 ATTATTTTTAAAATATTAAAT
20439990 A-TATTTTTAATAATATT
1 ATTATTTTTAA-AATATT
20440007 TAAACATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.20
20 13 0.37
21 11 0.31
22 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATTTTTAAAATATTAAAT
Found at i:20440036 original size:13 final size:12
Alignment explanation
Indices: 20440016--20440070 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 12
20440006 TTAAACATTT
20440016 AAAA-TTTTTAA
1 AAAATTTTTTAA
20440027 ATAAATTTTTTATA
1 A-AAATTTTTTA-A
20440041 AAAATTCTTTTAA
1 AAAATT-TTTTAA
*
20440054 AAATTTTTATTAA
1 AAAATTTT-TTAA
20440067 AAAA
1 AAAA
20440071 AAAAGTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 1 0.03
12 5 0.14
13 24 0.65
14 7 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
AAAATTTTTTAA
Found at i:20442495 original size:53 final size:53
Alignment explanation
Indices: 20442414--20442559 Score: 204
Period size: 53 Copynumber: 2.7 Consensus size: 53
20442404 CTTACACGGT
* *
20442414 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATATGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATATGGAATCACATTA
*
20442469 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATATGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATATGGAATCACATTA
** *
20442522 TCACATTGCACTGATGCCATAGCCCAGCTATGGTCTTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTA
20442560 AACGGGCGCA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 76 0.90
54 1 0.01
55 6 0.07
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATATGGAATCACATTA
Found at i:20450023 original size:24 final size:23
Alignment explanation
Indices: 20449996--20450044 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
20449986 ATTTGTAACA
20449996 ATTTATAT-ATTAATAATTTCATTT
1 ATTTATATCATTAA-AATTT-ATTT
*
20450020 ATTTATATCATTTAAATTTATTT
1 ATTTATATCATTAAAATTTATTT
20450043 AT
1 AT
20450045 ATAATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 13 0.57
25 4 0.17
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTTATATCATTAAAATTTATTT
Found at i:20450068 original size:22 final size:21
Alignment explanation
Indices: 20450040--20450080 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
20450030 TTTAAATTTA
20450040 TTTATATAATAATTATATTTTG
1 TTTATATAATAA-TATATTTTG
*
20450062 TTTATATATTAATATATTT
1 TTTATATAATAATATATTT
20450081 GTTGATCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTATATAATAATATATTTTG
Found at i:20450188 original size:24 final size:24
Alignment explanation
Indices: 20450161--20450209 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20450151 TTACCTGCAA
20450161 GTGTAATATTTTTATGTTATAATG
1 GTGTAATATTTTTATGTTATAATG
20450185 GTGTAATATTTTTATGTTATAATG
1 GTGTAATATTTTTATGTTATAATG
20450209 G
1 G
20450210 AATACAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (24 bp):
GTGTAATATTTTTATGTTATAATG
Found at i:20466923 original size:1 final size:1
Alignment explanation
Indices: 20466887--20466911 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20466877 CTTCTTAACT
20466887 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
20466912 GAGGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20468845 original size:10 final size:9
Alignment explanation
Indices: 20468832--20468856 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20468822 CTTTTATCTA
20468832 TTTTTTATT
1 TTTTTTATT
20468841 TTTTTTATT
1 TTTTTTATT
20468850 TTTTTTA
1 TTTTTTA
20468857 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:20469678 original size:2 final size:2
Alignment explanation
Indices: 20469666--20469697 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20469656 TACAACCAAA
*
20469666 AT AT GT 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
20469698 TTAAGTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20469806 original size:33 final size:33
Alignment explanation
Indices: 20469769--20469853 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 33
20469759 ACCATTAAAG
* *
20469769 TCTTATTTGTCAAGTATTATATTTCATCTGTCA
1 TCTTATTTGTCAAGTACTATATTTCATCTATCA
** * * *
20469802 TCTTATCGGTCAAGAACTATATTTTATTTATCA
1 TCTTATTTGTCAAGTACTATATTTCATCTATCA
* *
20469835 TCCTATTTGTCGAGTACTA
1 TCTTATTTGTCAAGTACTA
20469854 CTTGCCTAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (33 bp):
TCTTATTTGTCAAGTACTATATTTCATCTATCA
Found at i:20488108 original size:21 final size:21
Alignment explanation
Indices: 20488082--20488167 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
20488072 GGCTTTATCG
* *
20488082 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
20488103 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
20488124 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
* * * *
20488145 TTTAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
20488166 AT
1 AT
20488168 ACTGATCAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (21 bp):
ATCAGGCACCTCATGTGTCGT
Found at i:20489460 original size:18 final size:16
Alignment explanation
Indices: 20489420--20489462 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
20489410 TGTCGGATGA
*
20489420 GAGAATAAATGATACT
1 GAGAAGAAATGATACT
20489436 GATGAAGAAATGCATACT
1 GA-GAAGAAATG-ATACT
20489454 GGAGAAGAA
1 -GAGAAGAA
20489463 GAATCTTACG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 8 0.35
18 11 0.48
19 2 0.09
ACGTcount: A:0.49, C:0.07, G:0.26, T:0.19
Consensus pattern (16 bp):
GAGAAGAAATGATACT
Found at i:20495994 original size:21 final size:21
Alignment explanation
Indices: 20495968--20496053 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
20495958 GGCTTTATCG
* *
20495968 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
20495989 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
20496010 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
* * * *
20496031 TTTAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
20496052 AT
1 AT
20496054 ACTGATCAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (21 bp):
ATCAGGCACCTCATGTGTCGT
Found at i:20502061 original size:32 final size:32
Alignment explanation
Indices: 20502020--20502083 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
20502010 AATTCATACC
20502020 TTCTCATGTCTACTTGAGATAGTGCATATGTA
1 TTCTCATGTCTACTTGAGATAGTGCATATGTA
20502052 TTCTCATGTCTACTTGAGATAGTGCATATGTA
1 TTCTCATGTCTACTTGAGATAGTGCATATGTA
20502084 CAGGAAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (32 bp):
TTCTCATGTCTACTTGAGATAGTGCATATGTA
Found at i:20510393 original size:16 final size:16
Alignment explanation
Indices: 20510372--20510406 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
20510362 CCCATAAGAA
20510372 AAAAAAAAAAATCCTG
1 AAAAAAAAAAATCCTG
20510388 AAAAAAAAAAATCCTG
1 AAAAAAAAAAATCCTG
20510404 AAA
1 AAA
20510407 TGAAGTTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.71, C:0.11, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAAAAAAAAATCCTG
Found at i:20512911 original size:21 final size:21
Alignment explanation
Indices: 20512886--20512929 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20512876 GAGGGGATTA
20512886 AATAAGCAAATAAGTCAAAGT
1 AATAAGCAAATAAGTCAAAGT
20512907 AATAAGCAAATAAGTCAAAGT
1 AATAAGCAAATAAGTCAAAGT
20512928 AA
1 AA
20512930 GTGCCAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (21 bp):
AATAAGCAAATAAGTCAAAGT
Found at i:20512966 original size:22 final size:24
Alignment explanation
Indices: 20512938--20512984 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
20512928 AAGTGCCAAG
20512938 TGTGTGAT-AATAATA-AAATACA
1 TGTGTGATAAATAATATAAATACA
*
20512960 TGTGTGATAAATAATATACATACA
1 TGTGTGATAAATAATATAAATACA
20512984 T
1 T
20512985 TTGTAATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 7 0.32
24 7 0.32
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (24 bp):
TGTGTGATAAATAATATAAATACA
Found at i:20513385 original size:31 final size:32
Alignment explanation
Indices: 20513344--20513406 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
20513334 TTATTTATAA
*
20513344 AAGATATTTAT-TAATTAAATAT-TTATATTAT
1 AAGATATTTATGTAA-TAAATATATTAAATTAT
*
20513375 AAGATTTTTATGTAATAAATATATTAAATTAT
1 AAGATATTTATGTAATAAATATATTAAATTAT
20513407 GACAAGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
AAGATATTTATGTAATAAATATATTAAATTAT
Found at i:20513494 original size:2 final size:2
Alignment explanation
Indices: 20513483--20513518 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
20513473 TTAAGTTATC
20513483 AT AT -T AT AT 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 AT AT AT AT AT A
20513519 AAGTAAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20513553 original size:15 final size:16
Alignment explanation
Indices: 20513528--20513580 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 16
20513518 AAAGTAAAAC
20513528 AAAAGAAAAAGAAATG
1 AAAAGAAAAAGAAATG
*
20513544 AAAA-AAAAAGATA-G
1 AAAAGAAAAAGAAATG
*
20513558 AAAAGAAACAG-AATG
1 AAAAGAAAAAGAAATG
*
20513573 AAACGAAA
1 AAAAGAAA
20513581 CAGAGAGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 6 0.19
15 21 0.68
16 4 0.13
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAAGAAATG
Found at i:20514379 original size:45 final size:45
Alignment explanation
Indices: 20514329--20514439 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 45
20514319 CGACTACTGT
* * **
20514329 TACTGTTACCATTACTGTTGCCGATTTGGCACTTTGTGTGTCGAA
1 TACTGTTACTATTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
* * *
20514374 TACTGTTA-TATTTACCGTTATCGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTA-TTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
* *
20514419 TATTGTTACTGTTACTGTTAC
1 TACTGTTACTATTACTGTTAC
20514440 TGTTCAGAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
44 1 0.02
45 51 0.96
46 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (45 bp):
TACTGTTACTATTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
Found at i:20518195 original size:18 final size:18
Alignment explanation
Indices: 20517933--20518197 Score: 147
Period size: 18 Copynumber: 14.3 Consensus size: 18
20517923 AAATGTATAA
* *
20517933 AATAACTGATTATTTCTG
1 AATAACTGATTGTTACTG
* * *
20517951 AATAATTTACTGTTACTG
1 AATAACTGATTGTTACTG
* **
20517969 AATAATTGACCGTTACTG
1 AATAACTGATTGTTACTG
* *
20517987 GATAA-TAGACTGTTACTG
1 AATAACT-GATTGTTACTG
* *
20518005 AATAACTGAATATTACTG
1 AATAACTGATTGTTACTG
* **
20518023 AATAAATGATCATTACTG
1 AATAACTGATTGTTACTG
*
20518041 AATAACTGATTGTCACTG
1 AATAACTGATTGTTACTG
* *
20518059 AATAACTTAATTGCTACTG
1 AATAAC-TGATTGTTACTG
* *
20518078 AATATCTGATT-TTACTA
1 AATAACTGATTGTTACTG
* *
20518095 AATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
20518113 GATAACCAATCAATTGATCGATACTG
1 AATAA-C--T-GATTG-T---TACTG
* * *
20518139 AATAACTGGTTATTATTG
1 AATAACTGATTGTTACTG
* * *
20518157 AATAATTGATTGTTGCCG
1 AATAACTGATTGTTACTG
*
20518175 AATAACTGACTGTTACTG
1 AATAACTGATTGTTACTG
20518193 AATAA
1 AATAA
20518198 ATAATTGTTC
Statistics
Matches: 186, Mismatches: 49, Indels: 24
0.72 0.19 0.09
Matches are distributed among these distances:
17 13 0.07
18 139 0.75
19 15 0.08
21 2 0.01
22 5 0.03
23 2 0.01
25 1 0.01
26 9 0.05
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:20522151 original size:46 final size:46
Alignment explanation
Indices: 20522043--20522268 Score: 330
Period size: 46 Copynumber: 5.0 Consensus size: 46
20522033 TTTGACATGA
* * * * * * *
20522043 TGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*** **
20522088 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
20522134 TGCCATGGTATCTTTCAACCATGGT-TTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
20522179 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
20522225 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
20522269 AGAGCACACT
Statistics
Matches: 165, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
45 71 0.43
46 94 0.57
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:20522183 original size:91 final size:92
Alignment explanation
Indices: 20522043--20522268 Score: 330
Period size: 91 Copynumber: 2.5 Consensus size: 92
20522033 TTTGACATGA
* * * * * * *
20522043 TGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTC-TGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
***
20522107 CATGGTCTTGTTCATTTCATATCACAT
66 CATGGTCTTACACATTTCATATCACAT
20522134 TGCCATGGTATCTTTCAACCATGGT-TTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
**
20522198 CATGGTCTTACACATTTCATATCAGGT
66 CATGGTCTTACACATTTCATATCACAT
20522225 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
20522269 AGAGCACACT
Statistics
Matches: 121, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
90 10 0.08
91 93 0.77
92 18 0.15
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCACAT
Found at i:20522451 original size:59 final size:59
Alignment explanation
Indices: 20522359--20522480 Score: 235
Period size: 59 Copynumber: 2.1 Consensus size: 59
20522349 TATTGTCGGG
20522359 ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCAGA
1 ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCAGA
*
20522418 ATTACTAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCAGA
1 ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCAGA
20522477 ATTA
1 ATTA
20522481 ATCAGGCTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (59 bp):
ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCAGA
Found at i:20524502 original size:11 final size:11
Alignment explanation
Indices: 20524458--20524509 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
20524448 TATACTAAAT
20524458 AAATAATAATA
1 AAATAATAATA
*
20524469 TAATAATAAT-
1 AAATAATAATA
* *
20524479 AAATATCTCATA
1 AAATA-ATAATA
*
20524491 AAATATTAATA
1 AAATAATAATA
20524502 AAATAATA
1 AAATAATA
20524510 TTTATCTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
10 4 0.12
11 23 0.72
12 5 0.16
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:20538718 original size:46 final size:44
Alignment explanation
Indices: 20538614--20538721 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
20538604 TGTCTTTGAC
** * * *
20538614 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
20538658 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
20538704 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
20538722 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:20544848 original size:46 final size:44
Alignment explanation
Indices: 20544744--20544851 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
20544734 TGTCTTTGAC
** * * *
20544744 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
20544788 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
20544834 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
20544852 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:20547110 original size:46 final size:44
Alignment explanation
Indices: 20547051--20547165 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
20547041 ACAGGACAGA
* *
20547051 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
20547097 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
20547141 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
20547166 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:20547146 original size:44 final size:45
Alignment explanation
Indices: 20547051--20547184 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
20547041 ACAGGACAGA
* *
20547051 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
20547097 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
20547141 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20547185 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:20550377 original size:44 final size:45
Alignment explanation
Indices: 20550287--20550415 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
20550277 GACAGAACGA
*
20550287 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
20550333 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
20550377 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20550416 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:20570821 original size:33 final size:33
Alignment explanation
Indices: 20570753--20570824 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
20570743 TAGAAAAATT
* *
20570753 AATATTTTTTTATATTTAGATAAATTTGTGTAA
1 AATATTTTTTTATATTTACATAAATTTCTGTAA
*
20570786 AATATTTTTTTATTATTT-CATAGATTTCT-TAAA
1 AATATTTTTTTA-TATTTACATAAATTTCTGT-AA
20570819 AATATT
1 AATATT
20570825 CCATAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 1 0.03
33 28 0.82
34 5 0.15
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (33 bp):
AATATTTTTTTATATTTACATAAATTTCTGTAA
Found at i:20571222 original size:15 final size:16
Alignment explanation
Indices: 20571202--20571271 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 16
20571192 ACTATAAAAC
20571202 ATTTATTA-TGAATAT
1 ATTTATTATTGAATAT
*
20571217 ATTTATAATTGTAATAAAT
1 ATTTATTATTG-AAT--AT
*
20571236 ATTTATTATT-AAAAT
1 ATTTATTATTGAATAT
*
20571251 A-TTAATATTGAATATT
1 ATTTATTATTGAATA-T
20571267 ATTTA
1 ATTTA
20571272 AAATTATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
14 7 0.16
15 13 0.30
16 4 0.09
17 8 0.19
19 11 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (16 bp):
ATTTATTATTGAATAT
Found at i:20571282 original size:16 final size:17
Alignment explanation
Indices: 20571263--20571299 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
20571253 TAATATTGAA
20571263 TATTATTTAAAA-TTAT
1 TATTATTTAAAATTTAT
20571279 TATT-TTTAAAATTTAT
1 TATTATTTAAAATTTAT
20571295 TATTA
1 TATTA
20571300 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATTTAAAATTTAT
Found at i:20571468 original size:18 final size:21
Alignment explanation
Indices: 20571445--20571489 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
20571435 CAATATTTTA
20571445 AATATTT-TT-TTAAAATA-T
1 AATATTTATTATTAAAATATT
*
20571463 AATATTTATTATTAATATATT
1 AATATTTATTATTAAAATATT
20571484 AATATT
1 AATATT
20571490 AAGCTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
20 7 0.30
21 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATTTATTATTAAAATATT
Found at i:20571786 original size:39 final size:39
Alignment explanation
Indices: 20571732--20571808 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
20571722 AACACTTAAA
*
20571732 AAATTAAATTGTAGTTTTTAGTTTTTTATGTATATATAT
1 AAATTAAATTGTAGTTTTTAGTTTTTCATGTATATATAT
20571771 AAATTAAATTGTAGTTTTTAGTTTTTCATGTATATATA
1 AAATTAAATTGTAGTTTTTAGTTTTTCATGTATATATA
20571809 AAGAATGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.55
Consensus pattern (39 bp):
AAATTAAATTGTAGTTTTTAGTTTTTCATGTATATATAT
Found at i:20572144 original size:3 final size:3
Alignment explanation
Indices: 20572136--20572166 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20572126 ATTCCAAGAT
20572136 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
20572167 ATGACATGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:20583206 original size:13 final size:14
Alignment explanation
Indices: 20583188--20583223 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
20583178 CTAAATTTGT
20583188 AAAATTAAAATA-A
1 AAAATTAAAATATA
20583201 AAAATTAAAATATA
1 AAAATTAAAATATA
20583215 AAAA-TAAAA
1 AAAATTAAAA
20583224 CAAGAACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATTAAAATATA
Found at i:20589086 original size:47 final size:47
Alignment explanation
Indices: 20588977--20589087 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
20588967 CCGGGATAAG
* *
20588977 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
20589024 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
20589071 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
20589088 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:20591870 original size:4 final size:4
Alignment explanation
Indices: 20591861--20591889 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
20591851 CCCTTTTCTA
20591861 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
20591890 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:20597453 original size:29 final size:29
Alignment explanation
Indices: 20597412--20597489 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
20597402 TTTTAATAAG
* *
20597412 TAAATTTGA-CACTAAATTTTTATGTTAT
1 TAAATTTTACCACTAAATTTTAATGTTAT
* *
20597440 TAAATTTTACCACTAAACTTTAAATTTTAT
1 TAAATTTTACCACTAAA-TTTTAATGTTAT
* *
20597470 TAATTTTTGCCAC-AAATTTT
1 TAAATTTTACCACTAAATTTT
20597490 CATTTTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 11 0.27
29 10 0.24
30 20 0.49
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.49
Consensus pattern (29 bp):
TAAATTTTACCACTAAATTTTAATGTTAT
Found at i:20606787 original size:17 final size:17
Alignment explanation
Indices: 20606767--20606815 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
20606757 TTAAAATTAT
20606767 TAAAAAATTAAAAAAAA
1 TAAAAAATTAAAAAAAA
* *
20606784 TAAAAAATTCATAAAAA
1 TAAAAAATTAAAAAAAA
20606801 TAAAGAAATATAAAA
1 TAAA-AAAT-TAAAA
20606816 TACATATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 19 0.73
18 4 0.15
19 3 0.12
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
TAAAAAATTAAAAAAAA
Found at i:20606799 original size:27 final size:27
Alignment explanation
Indices: 20606769--20606828 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
20606759 AAAATTATTA
*
20606769 AAAAATTAAAAAAAATAAAAAATTCAT
1 AAAAATTAAAAAAAATAAAAAATACAT
* *
20606796 AAAAA-T-AAAGAAATATAAAATACAT
1 AAAAATTAAAAAAAATAAAAAATACAT
*
20606821 ATAAATTA
1 AAAAATTA
20606829 CCATACGAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
25 20 0.74
26 2 0.07
27 5 0.19
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (27 bp):
AAAAATTAAAAAAAATAAAAAATACAT
Found at i:20607286 original size:12 final size:12
Alignment explanation
Indices: 20607269--20607301 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20607259 TAAGATGGTG
20607269 AAATAAATAAAA
1 AAATAAATAAAA
20607281 AAATAAA-AAAA
1 AAATAAATAAAA
20607292 AAATACAATA
1 AAATA-AATA
20607302 GGTCTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.47
12 9 0.47
13 1 0.05
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAATAAAA
Found at i:20612988 original size:2 final size:2
Alignment explanation
Indices: 20612981--20613006 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20612971 CTCAGCAGGA
20612981 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
20613007 TTACACTAAG
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:20614766 original size:15 final size:15
Alignment explanation
Indices: 20614748--20614799 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
20614738 TACTACAAAA
20614748 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
20614763 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
20614782 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
20614797 ATT
1 ATT
20614800 ACTATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:20614927 original size:22 final size:21
Alignment explanation
Indices: 20614880--20614934 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
20614870 AATAAAATTA
*
20614880 AAATATTAAA-TA-ATTTATT
1 AAATAATAAATTATATTTATT
20614899 AAATAATAAATTATATTTATT
1 AAATAATAAATTATATTTATT
* *
20614920 ATATTAATAATTTAT
1 A-AATAATAAATTAT
20614935 TATATGACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 2 0.07
21 8 0.27
22 11 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAATAAATTATATTTATT
Found at i:20617965 original size:11 final size:11
Alignment explanation
Indices: 20617946--20617993 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
20617936 TAGCTATTTA
20617946 TAATAAAATAT
1 TAATAAAATAT
*
20617957 TAGTAAAATAT
1 TAATAAAATAT
* *
20617968 CTCATTAAAATAA
1 -T-AATAAAATAT
20617981 TAATAAAATAT
1 TAATAAAATAT
20617992 TA
1 TA
20617994 TTTATCAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 20 0.67
12 2 0.07
13 8 0.27
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:20624866 original size:19 final size:18
Alignment explanation
Indices: 20624842--20624879 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
20624832 TTTTATATTC
*
20624842 ATATTTTAAATTAATTTTT
1 ATATTTAAAATT-ATTTTT
20624861 ATATTTAAAATTATTTTT
1 ATATTTAAAATTATTTTT
20624879 A
1 A
20624880 ATTGAGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTAAAATTATTTTT
Found at i:20625636 original size:5 final size:5
Alignment explanation
Indices: 20625626--20625651 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20625616 TCTACTCCCC
20625626 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
20625652 TTCTTTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:20630629 original size:33 final size:33
Alignment explanation
Indices: 20630592--20630660 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
20630582 ATAGACATGG
20630592 TTTTTCTTGAAAAATTAAGAAATTAAAGGCTAT
1 TTTTTCTTGAAAAATTAAGAAATTAAAGGCTAT
*
20630625 TTTTTCTTGAAAAATTAAGAAATTAAGGGCTAT
1 TTTTTCTTGAAAAATTAAGAAATTAAAGGCTAT
20630658 TTT
1 TTT
20630661 AGACTGGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (33 bp):
TTTTTCTTGAAAAATTAAGAAATTAAAGGCTAT
Found at i:20634862 original size:10 final size:10
Alignment explanation
Indices: 20634849--20634874 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20634839 TTTACACATG
20634849 GTTACAGTTA
1 GTTACAGTTA
20634859 GTTACAGTTA
1 GTTACAGTTA
20634869 GTTACA
1 GTTACA
20634875 CGGTCTGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (10 bp):
GTTACAGTTA
Found at i:20635951 original size:47 final size:46
Alignment explanation
Indices: 20635832--20635964 Score: 194
Period size: 46 Copynumber: 2.9 Consensus size: 46
20635822 ATAATCTCAC
* * * *
20635832 CCATAATGAACTCGGAACGCAACTCAACAAGCTCGGGTGTTTGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTGCAT
* *
20635878 CCATAATGAACTCGGAACACAACTCAACGAGTTCAGATGCTTGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTGCAT
*
20635924 CCATAGGTGAACTCGGAACGCAACTCAACGAGTTCGGATGC
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTCGGATGC
20635965 CTCATAATTC
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
46 45 0.58
47 32 0.42
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTGCAT
Found at i:20639068 original size:16 final size:15
Alignment explanation
Indices: 20639043--20639076 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
20639033 ATTAGTGTTT
*
20639043 TTTATTTATTTATAAA
1 TTTATATATTT-TAAA
20639059 TTTATATATTTTAAA
1 TTTATATATTTTAAA
20639074 TTT
1 TTT
20639077 GGATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATATATTTTAAA
Found at i:20644951 original size:44 final size:44
Alignment explanation
Indices: 20644823--20644974 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 44
20644813 TATAACATGT
*
20644823 AAATTATTTTTTATAATA-AATTTTTTGGCCATAACTT-TAAAA-AAA
1 AAATTA-TTTTTATAATATAATTTTTTAG---TAACTTATAAAATAAA
* *
20644868 AAATTATGATTTAAATAATATACTTTTTTA-TAACTTTATAAAATACAA
1 AAATTAT--TTT-TATAATATAATTTTTTAGTAAC-TTATAAAATA-AA
*
20644916 AAATTATTTTTATAATATAATTTTTTAGT-ACTTATAATATAAGA
1 AAATTATTTTTATAATATAATTTTTTAGTAACTTATAAAATAA-A
* *
20644960 AATTTTTTTTTATAA
1 AAATTATTTTTATAA
20644975 CCATCTCAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
43 1 0.01
44 28 0.31
45 25 0.28
46 12 0.13
47 7 0.08
48 16 0.18
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (44 bp):
AAATTATTTTTATAATATAATTTTTTAGTAACTTATAAAATAAA
Found at i:20649835 original size:4 final size:4
Alignment explanation
Indices: 20649826--20649850 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20649816 TTAAACCTAA
20649826 AATC AATC AATC AATC AATC AATC A
1 AATC AATC AATC AATC AATC AATC A
20649851 GTCAGCTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
AATC
Found at i:20654476 original size:2 final size:2
Alignment explanation
Indices: 20654469--20654494 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20654459 AACGTTCACA
20654469 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
20654495 CCTGACATGC
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:20659647 original size:36 final size:36
Alignment explanation
Indices: 20659600--20659672 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
20659590 TGCAAACACT
20659600 AGAAATCTAGTTGCTCAAATGTAACATTAAGCTGAA
1 AGAAATCTAGTTGCTCAAATGTAACATTAAGCTGAA
20659636 AGAAATCTAGTTGCTCAAATGTAACATTAAGCTGAA
1 AGAAATCTAGTTGCTCAAATGTAACATTAAGCTGAA
20659672 A
1 A
20659673 CATCCATCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (36 bp):
AGAAATCTAGTTGCTCAAATGTAACATTAAGCTGAA
Found at i:20666718 original size:35 final size:36
Alignment explanation
Indices: 20666674--20666840 Score: 196
Period size: 35 Copynumber: 4.6 Consensus size: 36
20666664 TCCTCATTGA
** *
20666674 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTATGGGAT
* **
20666709 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTATGG----GAT
* *
20666749 AATACCATACCTACATTTCACAGCTCAGTA-CGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGGAT
20666784 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGGAT
*
20666819 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
20666841 CTTTGCCATG
Statistics
Matches: 115, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
35 86 0.75
39 3 0.03
40 26 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (36 bp):
AATACCATACCTACATTTCACAACTCAGTATGGGAT
Found at i:20666757 original size:75 final size:73
Alignment explanation
Indices: 20666669--20666840 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
20666659 GGTTTTCCTC
** * * * **
20666669 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTA-CGGATAATACCATACCTACATTTCACAAC
20666733 TCAGTATGG
65 TCAGTATGG
*
20666742 ATTTGATAATACCATACCTACATTTCACAGCTCAGTACGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTACGGATAATACCATACCTACATTTCACAA
20666807 CTCAGTATGG
64 CTCAGTATGG
20666817 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
20666841 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTACGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:20668253 original size:2 final size:2
Alignment explanation
Indices: 20668248--20668273 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20668238 TCTTCTTTTT
20668248 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
20668274 CTAACTATGT
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):
TA
Found at i:20675951 original size:13 final size:13
Alignment explanation
Indices: 20675933--20675960 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20675923 TACCGGTTGT
20675933 CTTAACCATTAAG
1 CTTAACCATTAAG
20675946 CTTAACCATTAAG
1 CTTAACCATTAAG
20675959 CT
1 CT
20675961 CATAATCTTC
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:0.25, G:0.07, T:0.32
Consensus pattern (13 bp):
CTTAACCATTAAG
Found at i:20677392 original size:5 final size:6
Alignment explanation
Indices: 20677376--20677415 Score: 50
Period size: 5 Copynumber: 7.0 Consensus size: 6
20677366 ACATTATGTA
20677376 CTTTTT CTTTTT CTTTTT CCTTTTT -TTTTT -TTTTT -TTTTT
1 CTTTTT CTTTTT CTTTTT -CTTTTT CTTTTT CTTTTT CTTTTT
20677416 TTTGAGAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 15 0.45
6 12 0.36
7 6 0.18
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
CTTTTT
Found at i:20677412 original size:19 final size:19
Alignment explanation
Indices: 20677376--20677410 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20677366 ACATTATGTA
20677376 CTTTTTCTTTTTCTTTTTC
1 CTTTTTCTTTTTCTTTTTC
20677395 CTTTTT-TTTTT-TTTTT
1 CTTTTTCTTTTTCTTTTT
20677411 TTTTTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (19 bp):
CTTTTTCTTTTTCTTTTTC
Found at i:20683198 original size:28 final size:29
Alignment explanation
Indices: 20683146--20683206 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
20683136 ATTTCTGTAT
*
20683146 ATTTTCAAAAAAATTGACTTATTTTTATA
1 ATTTTCAAAAAAATTGACTTATTTTGATA
*
20683175 ATTTTTAAAAAAATT-AGCTT-TTTTGATA
1 ATTTTCAAAAAAATTGA-CTTATTTTGATA
20683203 ATTT
1 ATTT
20683207 ATTCTCATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (29 bp):
ATTTTCAAAAAAATTGACTTATTTTGATA
Found at i:20683441 original size:15 final size:17
Alignment explanation
Indices: 20683421--20683452 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
20683411 ATATTTCATT
20683421 AATAAA-AAA-AGTAAA
1 AATAAATAAACAGTAAA
20683436 AATAAATAAACAGTAAA
1 AATAAATAAACAGTAAA
20683453 GATTTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (17 bp):
AATAAATAAACAGTAAA
Found at i:20683505 original size:26 final size:24
Alignment explanation
Indices: 20683457--20683503 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20683447 AGTAAAGATT
* *
20683457 TATATTATTAATTAAATAAAAATA
1 TATATTATAAATTAAAAAAAAATA
20683481 TATATTATAAATTATAAAAAAAA
1 TATATTATAAATTA-AAAAAAAA
20683504 ATGGTACTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TATATTATAAATTAAAAAAAAATA
Found at i:20685009 original size:15 final size:15
Alignment explanation
Indices: 20684989--20685026 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
20684979 TTTTCTATGG
20684989 TCTTCATCGCTTGTA
1 TCTTCATCGCTTGTA
20685004 TCTTCATCGCTTGTA
1 TCTTCATCGCTTGTA
20685019 TCTTCATC
1 TCTTCATC
20685027 ACTGGAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.29, G:0.11, T:0.47
Consensus pattern (15 bp):
TCTTCATCGCTTGTA
Found at i:20693401 original size:29 final size:27
Alignment explanation
Indices: 20693338--20693395 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 27
20693328 TTAAAATATT
20693338 ATAATTTTTATATTTTTAAATTTTTTAAA
1 ATAATTTTTATATTTTTAAA--TTTTAAA
20693367 ATAATTTTTATATATTTTAAA-TTTAAA
1 ATAATTTTTATAT-TTTTAAATTTTAAA
20693394 AT
1 AT
20693396 TTAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 8 0.29
29 13 0.46
30 7 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATAATTTTTATATTTTTAAATTTTAAA
Found at i:20695798 original size:19 final size:19
Alignment explanation
Indices: 20695765--20695803 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20695755 TATTAAAATA
* *
20695765 TTAATAACATAACAACTGC
1 TTAATAAAATAACAAATGC
*
20695784 TTAATAAAATGACAAATGC
1 TTAATAAAATAACAAATGC
20695803 T
1 T
20695804 ATATAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (19 bp):
TTAATAAAATAACAAATGC
Found at i:20696018 original size:7 final size:7
Alignment explanation
Indices: 20695996--20696030 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
20695986 TATAGAAACA
20695996 ATAT-AT
1 ATATGAT
20696002 ATAT-AT
1 ATATGAT
20696008 ATATGAT
1 ATATGAT
20696015 ATATGAT
1 ATATGAT
20696022 ATATGAT
1 ATATGAT
20696029 AT
1 AT
20696031 GCTTTTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 10 0.36
7 18 0.64
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (7 bp):
ATATGAT
Found at i:20700799 original size:15 final size:16
Alignment explanation
Indices: 20700779--20700813 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
20700769 AGGTTTTCCA
20700779 TTTTTTT-TTCTTTT-
1 TTTTTTTATTCTTTTG
20700793 TTTTTTTATTCTTTTG
1 TTTTTTTATTCTTTTG
20700809 TTTTT
1 TTTTT
20700814 CTGTCAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 7 0.37
16 5 0.26
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.89
Consensus pattern (16 bp):
TTTTTTTATTCTTTTG
Found at i:20701478 original size:28 final size:28
Alignment explanation
Indices: 20701447--20701502 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
20701437 TTAAGAATAT
20701447 TCTCTCCATTTATAGAGTTTAAATCGGA
1 TCTCTCCATTTATAGAGTTTAAATCGGA
20701475 TCTCTCCATTTATAGAGTTTAAATCGGA
1 TCTCTCCATTTATAGAGTTTAAATCGGA
20701503 AATCACACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (28 bp):
TCTCTCCATTTATAGAGTTTAAATCGGA
Found at i:20703996 original size:13 final size:14
Alignment explanation
Indices: 20703975--20704003 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20703965 TGAAAAATGG
20703975 ATTAGAAAATATTT
1 ATTAGAAAATATTT
20703989 ATTA-AAAATATTT
1 ATTAGAAAATATTT
20704002 AT
1 AT
20704004 GAAGTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:20704566 original size:31 final size:32
Alignment explanation
Indices: 20704517--20704578 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
20704507 ATATTAAATA
*
20704517 AGATATTTATTAATTAAATA-ATTATATTATG
1 AGATATTTATTAATTAAATATATTAAATTATG
*
20704548 AGATTTTTATGTAA-TAAATATATTAAATTAT
1 AGATATTTAT-TAATTAAATATATTAAATTAT
20704579 AAAAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (32 bp):
AGATATTTATTAATTAAATATATTAAATTATG
Found at i:20704882 original size:15 final size:15
Alignment explanation
Indices: 20704859--20704906 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
20704849 TATCAAATTT
20704859 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
20704874 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
20704889 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
20704903 ATAT
1 ATAT
20704907 AATATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:20706171 original size:53 final size:53
Alignment explanation
Indices: 20706101--20706293 Score: 298
Period size: 53 Copynumber: 3.6 Consensus size: 53
20706091 CACATATCAT
* * * * *
20706101 ACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATTAT
1 ACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAGTCATATTATCACATTAC
*
20706154 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTATCACATTGC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTATCACATTAC
*
20706207 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTATCACATTGC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTATCACATTAC
*
20706260 ACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGG
20706294 GCGCACTTAT
Statistics
Matches: 132, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
52 1 0.01
53 131 0.99
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (53 bp):
ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTATCACATTAC
Found at i:20708045 original size:23 final size:23
Alignment explanation
Indices: 20708017--20708065 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
20708007 TAATATTCCG
20708017 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
20708040 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
20708063 GGT
1 GGT
20708066 ATCTATCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.08, C:0.04, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:20708179 original size:18 final size:19
Alignment explanation
Indices: 20708158--20708198 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20708148 AATGAAATGA
20708158 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
20708176 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
20708195 GAAA
1 GAAA
20708199 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:20709505 original size:6 final size:6
Alignment explanation
Indices: 20709495--20709536 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
20709485 TATATATTTT
* *
20709495 TTTTAT TTTTAA TTAT-A TTTTAA TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
20709537 ATAATCAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:20709511 original size:23 final size:23
Alignment explanation
Indices: 20709487--20709531 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20709477 ATAATAAATA
*
20709487 TATATTTT--TTTTATTTTTAAT
1 TATATTTTAATTTTAATTTTAAT
20709508 TATATTTTAATTTTAATTTTAAT
1 TATATTTTAATTTTAATTTTAAT
20709531 T
1 T
20709532 TTAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
23 13 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TATATTTTAATTTTAATTTTAAT
Found at i:20709517 original size:11 final size:11
Alignment explanation
Indices: 20709487--20709559 Score: 51
Period size: 11 Copynumber: 6.7 Consensus size: 11
20709477 ATAATAAATA
**
20709487 TATATTTTTTT
1 TATATTTTAAT
20709498 TAT-TTTTAAT
1 TATATTTTAAT
20709508 TATATTTTAAT
1 TATATTTTAAT
*
20709519 TTTAATTTTAAT
1 TAT-ATTTTAAT
* * *
20709531 TTTAATATAAT
1 TATATTTTAAT
* *
20709542 CA-ATTTTTAT
1 TATATTTTAAT
20709552 TATATTTT
1 TATATTTT
20709560 TCAAATCGTG
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
10 14 0.29
11 23 0.48
12 11 0.23
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTTAAT
Found at i:20715477 original size:45 final size:45
Alignment explanation
Indices: 20715422--20715513 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
20715412 TGTTTTACAT
* **
20715422 AGGGTAGTAAATTAATTGTTATGTGGGGACGAATATTGTTAGCTG
1 AGGGTAGTAAATTAAGTGTTATGTACGGACGAATATTGTTAGCTG
* *
20715467 AGGGTGGTAAATTAAGTGTTATGTACTGACGAATATTGTTAGCTG
1 AGGGTAGTAAATTAAGTGTTATGTACGGACGAATATTGTTAGCTG
20715512 AG
1 AG
20715514 TCCGCACCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.35
Consensus pattern (45 bp):
AGGGTAGTAAATTAAGTGTTATGTACGGACGAATATTGTTAGCTG
Found at i:20715712 original size:31 final size:32
Alignment explanation
Indices: 20715667--20715727 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
20715657 CTTATCTTAG
* *
20715667 TTTAATTTTAATATTTGAGTTTTTT-TTTTAA
1 TTTAATTTTAATATTTAAATTTTTTCTTTTAA
20715698 TTTAATATTT-ATATTTAAATTTTTTCTTTT
1 TTTAAT-TTTAATATTTAAATTTTTTCTTTT
20715728 TGCCTTAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (32 bp):
TTTAATTTTAATATTTAAATTTTTTCTTTTAA
Found at i:20717584 original size:5 final size:5
Alignment explanation
Indices: 20717574--20717600 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20717564 GAAGTTTAAG
20717574 ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT AT
20717601 AGTGGGGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:20717861 original size:29 final size:31
Alignment explanation
Indices: 20717829--20717887 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
20717819 AAAATAAAGT
20717829 AATTAAACTCTTAAA-A-AT-AAAAATATAAA
1 AATTAAA-TCTTAAATATATGAAAAATATAAA
*
20717858 AATTAAATTTTAAATATATGAAAAATATAA
1 AATTAAATCTTAAATATATGAAAAATATAA
20717888 TAACATCTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
29 8 0.31
30 2 0.08
31 10 0.38
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (31 bp):
AATTAAATCTTAAATATATGAAAAATATAAA
Found at i:20721127 original size:37 final size:37
Alignment explanation
Indices: 20721077--20721149 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
20721067 AAAAAATTTC
20721077 TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAGT
1 TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAGT
20721114 TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAG
1 TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAG
20721150 CTGTACTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (37 bp):
TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAGT
Found at i:20721856 original size:15 final size:16
Alignment explanation
Indices: 20721828--20721857 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20721818 TTTTATTTGC
20721828 AAAGAAGAAGAATAAG
1 AAAGAAGAAGAATAAG
20721844 AAAGAAG-AGAATAA
1 AAAGAAGAAGAATAA
20721858 TTGTATGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (16 bp):
AAAGAAGAAGAATAAG
Found at i:20730789 original size:34 final size:37
Alignment explanation
Indices: 20730750--20730834 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 37
20730740 GTTGCTTATA
20730750 TTTAAAATTTTAATCAA-GAAAAAT-ATATAAA-ATT
1 TTTAAAATTTTAATCAATGAAAAATAATATAAATATT
* **
20730784 TTT-AAA-TATAA--AATTTAAAATAATATAAATATT
1 TTTAAAATTTTAATCAATGAAAAATAATATAAATATT
20730817 TTTAAAATTTTAATCAAT
1 TTTAAAATTTTAATCAAT
20730835 TATAAAAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
30 2 0.05
31 5 0.12
32 11 0.28
33 9 0.22
34 6 0.15
35 4 0.10
37 3 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (37 bp):
TTTAAAATTTTAATCAATGAAAAATAATATAAATATT
Found at i:20730792 original size:17 final size:17
Alignment explanation
Indices: 20730770--20730822 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
20730760 TAATCAAGAA
20730770 AAATATATAAAATTTTT
1 AAATATATAAAATTTTT
*
20730787 -AA-ATATAAAA-TTTA
1 AAATATATAAAATTTTT
20730801 AAATAATATAAATATTTTT
1 AAAT-ATATAAA-ATTTTT
20730820 AAA
1 AAA
20730823 ATTTTAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.10
15 10 0.34
16 2 0.07
17 7 0.24
18 1 0.03
19 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATATAAAATTTTT
Found at i:20739099 original size:13 final size:14
Alignment explanation
Indices: 20739067--20739104 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
20739057 AGTATTTGGG
* *
20739067 GTTCTAGGTTCGAT
1 GTTCAAGGTTTGAT
20739081 GTTCAAGGTTTGA-
1 GTTCAAGGTTTGAT
20739094 GTTCAAGGTTT
1 GTTCAAGGTTT
20739105 AAAAGTTCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (14 bp):
GTTCAAGGTTTGAT
Found at i:20739402 original size:24 final size:24
Alignment explanation
Indices: 20739316--20739409 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
20739306 TATATTATAT
*
20739316 AAATAGTATATAATTTAATAAATA
1 AAATATTATATAATTTAATAAATA
* *
20739340 AAA-ATTATTTAATTTAAATTAAAGGGA
1 AAATATTATATAATTT-AA-TAAA--TA
* *
20739367 AAATGGTAATATAATTTAATAAATA
1 AAAT-ATTATATAATTTAATAAATA
*
20739392 AAATTTTATATAATTTAA
1 AAATATTATATAATTTAA
20739410 ATTATTGACT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
23 10 0.18
24 17 0.31
25 9 0.16
27 8 0.15
28 2 0.04
29 9 0.16
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.39
Consensus pattern (24 bp):
AAATATTATATAATTTAATAAATA
Found at i:20747398 original size:30 final size:31
Alignment explanation
Indices: 20747338--20747398 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
20747328 TATTTTATTA
* *
20747338 CTAATTTTTTTTATTATTTTAAAGATATTTG
1 CTAATTTTTGTTATTATTTTAAAGACATTTG
* *
20747369 CTAA-TTTTGTTATTATTTTAGAGGCATTTG
1 CTAATTTTTGTTATTATTTTAAAGACATTTG
20747399 TGATAATACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.57
Consensus pattern (31 bp):
CTAATTTTTGTTATTATTTTAAAGACATTTG
Found at i:20754109 original size:20 final size:21
Alignment explanation
Indices: 20754086--20754133 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
20754076 TTCTTTTTAT
20754086 TTTTATTTATTTATT-TTTTC
1 TTTTATTTATTTATTATTTTC
*
20754106 TTTTA-TTATTTATTATTTTT
1 TTTTATTTATTTATTATTTTC
20754126 TTTTATTT
1 TTTTATTT
20754134 TATATTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 14 0.56
21 2 0.08
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTATTTATTTATTATTTTC
Found at i:20754117 original size:27 final size:25
Alignment explanation
Indices: 20754075--20754140 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
20754065 CAACCCAGTC
20754075 TTTCTTTTTATT-TTTATTTATTTATTT
1 TTTC-TTTTATTATTTA-TTATTT-TTT
20754102 TTTCTTTTATTATTTATTATTTTTT
1 TTTCTTTTATTATTTATTATTTTTT
*
20754127 TTTATTTTA-TATTT
1 TTTCTTTTATTATTT
20754141 CTCTTCTTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
24 5 0.14
25 11 0.30
26 13 0.35
27 8 0.22
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTCTTTTATTATTTATTATTTTTT
Found at i:20754139 original size:20 final size:21
Alignment explanation
Indices: 20754079--20754139 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
20754069 CCAGTCTTTC
20754079 TTTTTATTTTTA-TTTAT-TTA
1 TTTTT-TTTTTATTTTATATTA
20754099 TTTTTTCTTTTATTATT-TATTA
1 TTTTTT-TTTTATT-TTATATTA
20754121 -TTTTTTTTTATTTTATATT
1 TTTTTTTTTTATTTTATATT
20754140 TCTCTTCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.08
20 21 0.58
21 7 0.19
22 5 0.14
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTTTTATTTTATATTA
Found at i:20754311 original size:43 final size:42
Alignment explanation
Indices: 20754229--20754319 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
20754219 TCCATGCTGT
* **
20754229 CAAACAGTTCTATTCCAGCCCAGAATACCACATCCCTGCAGC
1 CAAACAGTCCTATTCCAGCCCAGAATACCACAAACCTGCAGC
* *
20754271 CAAACAGTCCTATTCCAGCCTTAGAAT-CCCCAAAACCTGCAGC
1 CAAACAGTCCTATTCCAGCC-CAGAATACCAC-AAACCTGCAGC
20754314 CAAACA
1 CAAACA
20754320 CCCCTTTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 22 0.52
43 20 0.48
ACGTcount: A:0.34, C:0.37, G:0.11, T:0.18
Consensus pattern (42 bp):
CAAACAGTCCTATTCCAGCCCAGAATACCACAAACCTGCAGC
Found at i:20755192 original size:118 final size:118
Alignment explanation
Indices: 20754984--20755214 Score: 390
Period size: 118 Copynumber: 2.0 Consensus size: 118
20754974 TGTTTTCCAT
* *
20754984 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
20755049 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
20755102 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
20755167 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
20755215 ACCGGAAATA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:20755347 original size:21 final size:21
Alignment explanation
Indices: 20755318--20755357 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20755308 TATTCCTAAG
*
20755318 TAAATAAATAATAAT-AAAATT
1 TAAAAAAATAA-AATCAAAATT
20755339 TAAAAAAATAAAATCAAAA
1 TAAAAAAATAAAATCAAAA
20755358 AATCAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAAAAATAAAATCAAAATT
Done.