Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 21 of 187
Found at i:6986242 original size:34 final size:34
Alignment explanation
Indices: 6986183--6986262 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
6986173 TGTGTTTTCA
* *
6986183 AAAAAAAATCTCGTGTTTCATAAATTTTCATTTTTT
1 AAAAAAAAT-T-GTGTTTCATAAATTCTCATGTTTT
* *
6986219 AAACAAAATTGTGTTTCCA-AAATTCTCGTGTTTT
1 AAAAAAAATTGTGTTT-CATAAATTCTCATGTTTT
6986253 AAAAAAAATT
1 AAAAAAAATT
6986263 CTCGTGTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
34 27 0.71
35 3 0.08
36 8 0.21
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (34 bp):
AAAAAAAATTGTGTTTCATAAATTCTCATGTTTT
Found at i:6986257 original size:17 final size:17
Alignment explanation
Indices: 6986112--6986274 Score: 69
Period size: 17 Copynumber: 9.1 Consensus size: 17
6986102 CATGTTTTCA
* *
6986112 AAAAATTCCCGTGTTTC
1 AAAAATTCTCGTGTTTT
*
6986129 AAAAATCCTCGTGTTTT
1 AAAAATTCTCGTGTTTT
* *
6986146 CAAAATTTTCGATGTTTT
1 AAAAATTCTCG-TGTTTT
* * *
6986164 GAAAATTTTTGTGTTTT
1 AAAAATTCTCGTGTTTT
* *
6986181 CAAAAAAAAATCTCGTGTTTC
1 ----AAAAATTCTCGTGTTTT
* * * *
6986202 ATAAATTTTCATTTTTT
1 AAAAATTCTCGTGTTTT
* *
6986219 AAACAAAAT-T-GTGTTTC
1 -AA-AAATTCTCGTGTTTT
*
6986236 CAAAATTCTCGTGTTTT
1 AAAAATTCTCGTGTTTT
6986253 AAAAAAAATTCTCGTGTTTT
1 ---AAAAATTCTCGTGTTTT
6986273 AA
1 AA
6986275 TCGGATCACG
Statistics
Matches: 106, Mismatches: 28, Indels: 24
0.67 0.18 0.15
Matches are distributed among these distances:
15 4 0.04
16 2 0.02
17 51 0.48
18 17 0.16
19 4 0.04
20 16 0.15
21 12 0.11
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTT
Found at i:6986262 original size:20 final size:20
Alignment explanation
Indices: 6986237--6986274 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6986227 TTGTGTTTCC
6986237 AAAATTCTCGTGTTTTAAAA
1 AAAATTCTCGTGTTTTAAAA
6986257 AAAATTCTCGTGTTTTAA
1 AAAATTCTCGTGTTTTAA
6986275 TCGGATCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (20 bp):
AAAATTCTCGTGTTTTAAAA
Found at i:6986753 original size:30 final size:31
Alignment explanation
Indices: 6986719--6986778 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
6986709 AAACCTTTTA
*
6986719 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
6986749 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
6986779 TCACACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:6986898 original size:17 final size:16
Alignment explanation
Indices: 6986864--6986894 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6986854 CCTATTTACT
*
6986864 TTCCCTAAAACTTTTA
1 TTCCCCAAAACTTTTA
6986880 TTCCCCAAAACTTTT
1 TTCCCCAAAACTTTT
6986895 TATTTTCCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (16 bp):
TTCCCCAAAACTTTTA
Found at i:6989634 original size:77 final size:75
Alignment explanation
Indices: 6989502--6989643 Score: 205
Period size: 77 Copynumber: 1.9 Consensus size: 75
6989492 GAATTGATCG
* * *
6989502 AAAAATCAACAAAAAAATAAAAACTATCAGAATACCAATTGACTACACAAACTCAGAACAAAAAA
1 AAAAATCAACAAAAAAATAAAAAATATCAGAATACCAATCGACCACACAAACTCAGAACAAAAAA
6989567 TAGAAACTCT
66 TAGAAACTCT
* *
6989577 AAAAATCAAC-AAAAAATAGAAACTAATATCAGAATACCAATCGGCCACACAATCTCAGAACAAA
1 AAAAATCAACAAAAAAATA-AAA--AATATCAGAATACCAATCGACCACACAAACTCAGAACAAA
6989641 AAA
63 AAA
6989644 AAAAATCTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
74 8 0.14
75 13 0.22
77 38 0.64
ACGTcount: A:0.59, C:0.20, G:0.06, T:0.15
Consensus pattern (75 bp):
AAAAATCAACAAAAAAATAAAAAATATCAGAATACCAATCGACCACACAAACTCAGAACAAAAAA
TAGAAACTCT
Found at i:6990926 original size:14 final size:14
Alignment explanation
Indices: 6990890--6990923 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6990880 TCATCATTTG
6990890 CCTATAACCAAAAC
1 CCTATAACCAAAAC
6990904 CCTATAACCAAAAC
1 CCTATAACCAAAAC
6990918 CC-ATAA
1 CCTATAA
6990924 ACCCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:6993373 original size:5 final size:5
Alignment explanation
Indices: 6993365--6993390 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6993355 ATTGATTTAA
6993365 AAATC AAATC AAATC AAATC AAATC A
1 AAATC AAATC AAATC AAATC AAATC A
6993391 GATGCTGTCC
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:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:6993525 original size:250 final size:245
Alignment explanation
Indices: 6993089--6993585 Score: 940
Period size: 250 Copynumber: 2.0 Consensus size: 245
6993079 AAAATCTGCC
6993089 ATTAAGGAACCAAAAAATCAAATTGATTTAAAAATCAAATCAAATCAAATCAGATGCTGTCCATA
1 ATTAAGGAACCAAAAAATCAAATTGATTTAAAAATCAAATCAAATCAAATCAGATGCTGTCCATA
6993154 TATAAGCAGATTATGTCTGTTGAGGATAAATAAATTCGTGTTGGACTTACCGTAGGCCCATTTTG
66 TATAAGCAGATTATGTCTGTTGAGGATAAATAAATTCGTGTTGGACTTACCGTAGGCCCATTTTG
6993219 GCCCGACCGGTTCGAACATTTCGTGTCGCCCACATCGTGCGGTGCCCCCCAATTTAAAAATCAAA
131 GCCCGACCGGTTCGAACATTTCGTGTCGCCCACATCGTGCGGTGCCCCCCAATTTAAAAATCAAA
6993284 TCAAATCAAATACTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAA
196 TCAAATCAAATACTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAA
6993334 ATTAAGGAACCAAAAAATCAAATTGATTTAAAAATCAAATCAAATCAAATCAAATCAGATGCTGT
1 ATTAAGGAACCAAAAAATCAAATTGATTT---AA--AAATCAAATCAAATCAAATCAGATGCTGT
6993399 CCATATATAAGCAGATTATGTCTGTTGAGGATAAATAAATTCGTGTTGGACTTACCGTAGGCCCA
61 CCATATATAAGCAGATTATGTCTGTTGAGGATAAATAAATTCGTGTTGGACTTACCGTAGGCCCA
6993464 TTTTGGCCCGACCGGTTCGAACATTTCGTGTCGCCCACATCGTGCGGTGCCCCCCAATTTAAAAA
126 TTTTGGCCCGACCGGTTCGAACATTTCGTGTCGCCCACATCGTGCGGTGCCCCCCAATTTAAAAA
*
6993529 TCAAATCAAATCAGATACTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAA
191 TCAAATCAAATCAAATACTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAA
6993584 AT
1 AT
6993586 AAATTCGTGT
Statistics
Matches: 246, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
245 29 0.12
248 2 0.01
250 215 0.87
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (245 bp):
ATTAAGGAACCAAAAAATCAAATTGATTTAAAAATCAAATCAAATCAAATCAGATGCTGTCCATA
TATAAGCAGATTATGTCTGTTGAGGATAAATAAATTCGTGTTGGACTTACCGTAGGCCCATTTTG
GCCCGACCGGTTCGAACATTTCGTGTCGCCCACATCGTGCGGTGCCCCCCAATTTAAAAATCAAA
TCAAATCAAATACTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAA
Found at i:6993649 original size:151 final size:151
Alignment explanation
Indices: 6993375--6993671 Score: 567
Period size: 151 Copynumber: 2.0 Consensus size: 151
6993365 AAATCAAATC
*
6993375 AAATCAAATCAAATCAGATGCTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAAATAAATT
1 AAATCAAATCAAATCAGATACTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAAATAAATT
*
6993440 CGTGTTGGACTTACCGTAGGCCCATTTTGGCCCGACCGGTTCGAACATTTCGTGTCGCCCACATC
66 CGTGTTGGACTTACCGTAGACCCATTTTGGCCCGACCGGTTCGAACATTTCGTGTCGCCCACATC
6993505 GTGCGGTGCCCCCCAATTTAA
131 GTGCGGTGCCCCCCAATTTAA
6993526 AAATCAAATCAAATCAGATACTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAAATAAATT
1 AAATCAAATCAAATCAGATACTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAAATAAATT
*
6993591 CGTGTTGGACTTACCGTAGACCCATTTTTGCCCGACCGGTTCGAACATTTCGTGTCGCCCACATC
66 CGTGTTGGACTTACCGTAGACCCATTTTGGCCCGACCGGTTCGAACATTTCGTGTCGCCCACATC
6993656 GTGCGGTGCCCCCCAA
131 GTGCGGTGCCCCCCAA
6993672 CCTCATTAGG
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 143 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (151 bp):
AAATCAAATCAAATCAGATACTGTCCATATATAAGCAGATTATGTCTGTTGAGGATAAATAAATT
CGTGTTGGACTTACCGTAGACCCATTTTGGCCCGACCGGTTCGAACATTTCGTGTCGCCCACATC
GTGCGGTGCCCCCCAATTTAA
Found at i:7001253 original size:111 final size:111
Alignment explanation
Indices: 7001111--7001343 Score: 448
Period size: 111 Copynumber: 2.1 Consensus size: 111
7001101 AAAGAAGCTT
7001111 CTTGAATATTCATAGATGTAGCTATTTGTTATCGATGGCACTAACATCTAAATAGCTAAATTTCT
1 CTTGAATATTCATAGATGTAGCTATTTGTTATCGATGGCACTAACATCTAAATAGCTAAATTTCT
7001176 ACTGCTTTTACAACCTATGGCATATCTTCTCAATCTTTTCTACTTG
66 ACTGCTTTTACAACCTATGGCATATCTTCTCAATCTTTTCTACTTG
7001222 CTTGAATATTCATAGATGTAGCTATTTGTTATCGATGGCACTAACATCTAAATAGCTAAATTTCT
1 CTTGAATATTCATAGATGTAGCTATTTGTTATCGATGGCACTAACATCTAAATAGCTAAATTTCT
*
7001287 ACTGCTTTTACAACCTATGGCATATCTTCTTAATCTTTTCTACTTG
66 ACTGCTTTTACAACCTATGGCATATCTTCTCAATCTTTTCTACTTG
7001333 CTTGAAATATT
1 CTTG-AATATT
7001344 TCCCTAGTAT
Statistics
Matches: 120, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
111 114 0.95
112 6 0.05
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (111 bp):
CTTGAATATTCATAGATGTAGCTATTTGTTATCGATGGCACTAACATCTAAATAGCTAAATTTCT
ACTGCTTTTACAACCTATGGCATATCTTCTCAATCTTTTCTACTTG
Found at i:7001878 original size:14 final size:14
Alignment explanation
Indices: 7001859--7001888 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
7001849 TTTAGATGTT
7001859 TAGTTTTTATTTTA
1 TAGTTTTTATTTTA
7001873 TAGTTTTTATTTTA
1 TAGTTTTTATTTTA
7001887 TA
1 TA
7001889 TCTTCTAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TAGTTTTTATTTTA
Found at i:7006375 original size:30 final size:31
Alignment explanation
Indices: 7006320--7006404 Score: 109
Period size: 30 Copynumber: 2.7 Consensus size: 31
7006310 TAATGTTATT
* ** *
7006320 TAATATTAAATTAAATTAAATATTTATCTTTA
1 TAATATTATATT-AATTTGATATTTATCTTGA
7006352 TAATATTAT-TTAATTTGATATTTATCTTGA
1 TAATATTATATTAATTTGATATTTATCTTGA
*
7006382 TAATATTTTATTAATTTGATATT
1 TAATATTATATTAATTTGATATT
7006405 AAGGTGATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
30 24 0.51
31 15 0.32
32 8 0.17
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (31 bp):
TAATATTATATTAATTTGATATTTATCTTGA
Found at i:7006413 original size:30 final size:31
Alignment explanation
Indices: 7006351--7006420 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
7006341 ATTTATCTTT
* * *
7006351 ATAATATTAT-TTAATTTGATATTTATCTTG
1 ATAATATTTTATTAATTTGATATTTAACGTG
*
7006381 ATAATATTTTATTAATTTGATA-TTAAGGTG
1 ATAATATTTTATTAATTTGATATTTAACGTG
7006411 ATAA-ATTTTA
1 ATAATATTTTA
7006421 ATCCTTGAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.17
30 18 0.51
31 11 0.31
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (31 bp):
ATAATATTTTATTAATTTGATATTTAACGTG
Found at i:7006966 original size:18 final size:18
Alignment explanation
Indices: 7006943--7006985 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
7006933 ACTCAATCCA
**
7006943 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
7006961 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
7006979 AACCCAA
1 AACCCAA
7006986 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:7007103 original size:9 final size:9
Alignment explanation
Indices: 7007089--7007119 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
7007079 GTAGTGATTC
7007089 AATTCGGTT
1 AATTCGGTT
*
7007098 AATTCGGGT
1 AATTCGGTT
7007107 AATTCGGTT
1 AATTCGGTT
7007116 AATT
1 AATT
7007120 TTTAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:7008752 original size:13 final size:13
Alignment explanation
Indices: 7008736--7008763 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7008726 TTAATTGGAA
7008736 AATTAATTTAGTT
1 AATTAATTTAGTT
7008749 AATTAATTTAGTT
1 AATTAATTTAGTT
7008762 AA
1 AA
7008764 AGTAATTAAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
AATTAATTTAGTT
Found at i:7011740 original size:47 final size:47
Alignment explanation
Indices: 7011645--7011751 Score: 126
Period size: 47 Copynumber: 2.3 Consensus size: 47
7011635 ATATATTTGC
* * *
7011645 GTTAAAAATGTGTATTCATCATATCATAATATATTTTTTTCGAGTGT
1 GTTAAAAATGTGTATTCATCATACCATAATAGATTTTTTTCGAATGT
* * * **
7011692 GTTAGAAAGGTGTACTT-ATCATACCTTAATAGATTTTTTTTTAATGT
1 GTTAAAAATGTGTA-TTCATCATACCATAATAGATTTTTTTCGAATGT
7011739 GTTAAAAATGTGT
1 GTTAAAAATGTGT
7011752 TTTTGAGAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
47 47 0.96
48 2 0.04
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (47 bp):
GTTAAAAATGTGTATTCATCATACCATAATAGATTTTTTTCGAATGT
Found at i:7013984 original size:9 final size:9
Alignment explanation
Indices: 7013972--7014005 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
7013962 TCAAAAATAA
7013972 AAAAATCAT
1 AAAAATCAT
7013981 AAAAATCAT
1 AAAAATCAT
*
7013990 -AAAATTAT
1 AAAAATCAT
7013998 AAAAATCA
1 AAAAATCA
7014006 GTTAAGGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATCAT
Found at i:7013986 original size:17 final size:17
Alignment explanation
Indices: 7013964--7014003 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
7013954 ATACAAATTC
7013964 AAAAATAAAAAAATCAT
1 AAAAATAAAAAAATCAT
* * *
7013981 AAAAATCATAAAATTAT
1 AAAAATAAAAAAATCAT
7013998 AAAAAT
1 AAAAAT
7014004 CAGTTAAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATAAAAAAATCAT
Found at i:7014004 original size:17 final size:17
Alignment explanation
Indices: 7013973--7014005 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7013963 CAAAAATAAA
7013973 AAAATCATAAAAATCAT
1 AAAATCATAAAAATCAT
*
7013990 AAAATTATAAAAATCA
1 AAAATCATAAAAATCA
7014006 GTTAAGGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATCATAAAAATCAT
Found at i:7024823 original size:8 final size:8
Alignment explanation
Indices: 7024789--7024822 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
7024779 AGGCTCTTAG
*
7024789 TAAACAAA
1 TAAAAAAA
7024797 TAAAAAAA
1 TAAAAAAA
7024805 TAAAAAAA
1 TAAAAAAA
*
7024813 TAGAAAAA
1 TAAAAAAA
7024821 TA
1 TA
7024823 GGGTCCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:7026085 original size:2 final size:2
Alignment explanation
Indices: 7026078--7026142 Score: 69
Period size: 2 Copynumber: 33.0 Consensus size: 2
7026068 TTTTATGATT
* * * ** *
7026078 TA TA TA TA TT TA T- TA CA TA TA TA TG TA CG TG 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
7026119 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
7026143 ATACTTTCTA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:7026309 original size:16 final size:16
Alignment explanation
Indices: 7026278--7026329 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
7026268 ATTATGCACT
*
7026278 TTTTTTTCTTTA--TA
1 TTTTTTTGTTTATTTA
7026292 TTTTTTTGTTTATTTA
1 TTTTTTTGTTTATTTA
* *
7026308 TTTGTTTGTTGATTTA
1 TTTTTTTGTTTATTTA
7026324 TGTTTT
1 T-TTTT
7026330 CGTATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 11 0.35
16 17 0.55
17 3 0.10
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.77
Consensus pattern (16 bp):
TTTTTTTGTTTATTTA
Found at i:7029567 original size:36 final size:36
Alignment explanation
Indices: 7029516--7029584 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
7029506 GTAGGTTCAC
7029516 TGACATATTGATTGGCCTTCCCACTAAAACTAGCAG
1 TGACATATTGATTGGCCTTCCCACTAAAACTAGCAG
*
7029552 TGACATATTGGTTGGCCTTCCCACTAAAACTAG
1 TGACATATTGATTGGCCTTCCCACTAAAACTAG
7029585 AGAAAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (36 bp):
TGACATATTGATTGGCCTTCCCACTAAAACTAGCAG
Found at i:7030877 original size:15 final size:16
Alignment explanation
Indices: 7030857--7030886 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7030847 TATTATTCCA
7030857 TATTTATATT-TATAT
1 TATTTATATTCTATAT
7030872 TATTTATATTCTATA
1 TATTTATATTCTATA
7030887 ATATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATATTCTATAT
Found at i:7034374 original size:43 final size:43
Alignment explanation
Indices: 7034310--7034400 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
7034300 CTTTGAGTTC
* * * *
7034310 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTCATTAAGAAAATGCATTATATCTTTT
* *
7034352 ATTACCAAGATTTACTTCATTAAGAAAATGCATTGTATGTTTT
1 ATTACCAAGATTTACTTCATTAAGAAAATGCATTATATCTTTT
7034395 ATTACC
1 ATTACC
7034401 TTGCAATGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 4 0.10
43 38 0.90
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTCATTAAGAAAATGCATTATATCTTTT
Found at i:7038916 original size:19 final size:18
Alignment explanation
Indices: 7038892--7038928 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
7038882 CCAAAATATT
7038892 GAATATGATTAAATAAAAA
1 GAATAT-ATTAAATAAAAA
*
7038911 GAATATTTTAAATAAAAA
1 GAATATATTAAATAAAAA
7038929 CAAAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (18 bp):
GAATATATTAAATAAAAA
Found at i:7044070 original size:18 final size:18
Alignment explanation
Indices: 7044030--7044076 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
7044020 ACTTAATTGG
*
7044030 AAAATTAATTTATCTAAT
1 AAAATTAATTTATCAAAT
*
7044048 TAAATTAATTTAAT-AAAT
1 AAAATTAATTT-ATCAAAT
*
7044066 AAAATTTATTT
1 AAAATTAATTT
7044077 TGGGAAATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATTAATTTATCAAAT
Found at i:7044379 original size:20 final size:20
Alignment explanation
Indices: 7044342--7044379 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7044332 ATAGTGGGAA
*
7044342 TTTATTTTCTAAGTATAAAT
1 TTTATTTTCTAAGAATAAAT
*
7044362 TTTATTTTCTAGGAATAA
1 TTTATTTTCTAAGAATAA
7044380 CAATTCTACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTATTTTCTAAGAATAAAT
Found at i:7056707 original size:11 final size:11
Alignment explanation
Indices: 7056687--7056752 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
7056677 TAAAAATTAA
7056687 AAAAAGTATTTT
1 AAAAA-TATTTT
7056699 AAAAATATTTT
1 AAAAATATTTT
7056710 --AAA-A--TT
1 AAAAATATTTT
*
7056716 AAAAA-AATTT
1 AAAAATATTTT
7056726 AAAAAGTATTTT
1 AAAAA-TATTTT
*
7056738 AAAAAAATTTT
1 AAAAATATTTT
7056749 AAAA
1 AAAA
7056753 TTTAAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
6 2 0.04
8 5 0.11
9 3 0.07
10 7 0.15
11 15 0.33
12 14 0.30
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:7056730 original size:39 final size:39
Alignment explanation
Indices: 7056654--7056782 Score: 159
Period size: 39 Copynumber: 3.1 Consensus size: 39
7056644 ATAAATACCA
*
7056654 AAAAATTATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTTT-AAAATT--AA-AAAAATT-TAAAAAGTATTTT
7056699 AAAAATATTTTAAAATTAAAAAAATTTAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAATTTAAAAAGTATTTT
* *
7056738 AAAAAAATTTTAAAATTTAAAAAATTTAATAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAATTT-A-AAAAGTATTTT
7056779 AAAA
1 AAAA
7056783 TTAAAAAATA
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
39 37 0.47
40 8 0.10
41 17 0.22
43 6 0.08
44 6 0.08
45 5 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (39 bp):
AAAAATATTTTAAAATTAAAAAAATTTAAAAAGTATTTT
Found at i:7056755 original size:30 final size:29
Alignment explanation
Indices: 7056719--7056791 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
7056709 TAAAATTAAA
7056719 AAAATTTAAAAAGTATTTTAA-AAAA-ATTTT
1 AAAATTTAAAAA--A-TTTAATAAAAGATTTT
7056749 AAAATTTAAAAAATTTAATAAAAGTATTTT
1 AAAATTTAAAAAATTTAATAAAAG-ATTTT
7056779 AAAA-TTAAAAAAT
1 AAAATTTAAAAAAT
7056792 AAAAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 5 0.12
28 5 0.12
29 9 0.22
30 21 0.52
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTTAAAAAATTTAATAAAAGATTTT
Found at i:7068619 original size:23 final size:23
Alignment explanation
Indices: 7068561--7068619 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
7068551 AAGAGAACAT
*
7068561 AAGTGCTAAATT-AGGAGCACCG
1 AAGTGCTAAATTCAAGAGCACCG
*
7068583 AAGTGC-AAGTTTCAAGAGCACCGG
1 AAGTGCTAA-ATTCAAGAGCACC-G
7068607 AA-TGCTAAATTCA
1 AAGTGCTAAATTCA
7068620 TGAACGCGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
21 2 0.07
22 8 0.27
23 15 0.50
24 5 0.17
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (23 bp):
AAGTGCTAAATTCAAGAGCACCG
Found at i:7076002 original size:12 final size:12
Alignment explanation
Indices: 7075985--7076023 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
7075975 GAAATAAGAG
7075985 GTGAAGAAGACA
1 GTGAAGAAGACA
*
7075997 GTGAAGAAGAAA
1 GTGAAGAAGACA
7076009 GATGAAGAAGACA
1 G-TGAAGAAGACA
7076022 GT
1 GT
7076024 ATGATGGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.51, C:0.05, G:0.33, T:0.10
Consensus pattern (12 bp):
GTGAAGAAGACA
Found at i:7086447 original size:60 final size:60
Alignment explanation
Indices: 7086348--7086460 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
7086338 ATTCACCTTC
*
7086348 AAAGAAAAATATTTAAATTTATTTAAAAAATCATAAAAAA-ATTACAAAATATTTAGAAAT
1 AAAGAAAAATATTTAAATTTATTTAAAAAATCAAAAAAAATATTA-AAAATATTTAGAAAT
* * *
7086408 AAAGAAAAA-ATTTATATTT-TTTATAAAATATTAAAAAAAATATTATAAATATT
1 AAAGAAAAATATTTAAATTTATTTA-AAAA-ATCAAAAAAAATATTAAAAATATT
7086461 ATAAATTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
58 4 0.09
59 13 0.28
60 25 0.54
61 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (60 bp):
AAAGAAAAATATTTAAATTTATTTAAAAAATCAAAAAAAATATTAAAAATATTTAGAAAT
Found at i:7090958 original size:21 final size:21
Alignment explanation
Indices: 7090925--7091005 Score: 94
Period size: 21 Copynumber: 3.7 Consensus size: 21
7090915 GGATATGATA
7090925 ATTTTTATAAATTTTTTTCAGG
1 ATTTTTAT-AATTTTTTTCAGG
*
7090947 ATTTTTATAATTTTCTTTTACA-A
1 ATTTTTATAA-TTT-TTTT-CAGG
7090970 ATTTTTATAATTTTTTT-AGG
1 ATTTTTATAATTTTTTTCAGG
7090990 ATATTTTATAATTTTT
1 AT-TTTTATAATTTTT
7091006 GCAATTTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 19 0.37
22 14 0.27
23 14 0.27
24 2 0.04
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (21 bp):
ATTTTTATAATTTTTTTCAGG
Found at i:7093135 original size:2 final size:2
Alignment explanation
Indices: 7093130--7093160 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7093120 AGAAACAGGA
7093130 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 A
7093161 AAAGGTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7098100 original size:18 final size:19
Alignment explanation
Indices: 7098074--7098110 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
7098064 AACTAAAACA
7098074 AATTCTAAAAAT-ATAAAAT
1 AATTCT-AAAATGATAAAAT
7098093 AATT-TAAAATGATAAAAT
1 AATTCTAAAATGATAAAAT
7098111 GAGTGATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AATTCTAAAATGATAAAAT
Found at i:7099586 original size:2 final size:2
Alignment explanation
Indices: 7099581--7099608 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7099571 ACACACACAC
7099581 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
7099609 TTAAATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7107865 original size:31 final size:30
Alignment explanation
Indices: 7107830--7107890 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
7107820 TGGAGGTGGG
* *
7107830 ATGGGAAGGGAATAAAAGTTTTAGGGGAAAA
1 ATGGG-AGAGAATAAAAATTTTAGGGGAAAA
* *
7107861 ATGGGAGAGAGTAAAAATTTTGGGGGAAAA
1 ATGGGAGAGAATAAAAATTTTAGGGGAAAA
7107891 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (30 bp):
ATGGGAGAGAATAAAAATTTTAGGGGAAAA
Found at i:7109220 original size:24 final size:24
Alignment explanation
Indices: 7109157--7109208 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
7109147 TTTCTAGAAG
* * *
7109157 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
7109181 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
7109205 ATTT
1 ATTT
7109209 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:7110463 original size:2 final size:2
Alignment explanation
Indices: 7110456--7110540 Score: 73
Period size: 2 Copynumber: 41.0 Consensus size: 2
7110446 ATACATTCGA
* *
7110456 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT -T CAT CAT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT -AT AT AT AT
* * * *
7110499 TT AA AT GAGT AC AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7110541 CCCAATTGCA
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
1 1 0.01
2 59 0.88
3 6 0.09
4 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7110899 original size:41 final size:41
Alignment explanation
Indices: 7110843--7110955 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 41
7110833 TGATTCAGTA
* * * *
7110843 CACCGGCTTTTAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
* * * * *
7110884 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTGGATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
* *
7110925 CACCGGCATCAAGCCTGCTAGACGTAAAGTC
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTC
7110956 TGTATTACAT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
Found at i:7110956 original size:41 final size:41
Alignment explanation
Indices: 7110883--7110962 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
7110873 CCGAAATGTA
* *
7110883 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGGATTATT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGGATTATT
*
7110924 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTA
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGGATTA
7110963 CATTCGATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (41 bp):
TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGGATTATT
Found at i:7115943 original size:50 final size:50
Alignment explanation
Indices: 7115836--7116017 Score: 150
Period size: 50 Copynumber: 3.5 Consensus size: 50
7115826 ATTTGGGTAA
* * * * *
7115836 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGTGACATGGCATGGGCA-C--CGAG---ATG
** ** *
7115892 AGAGGTTTCATGTAAGACCATGTCTAG-GACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCT-GTGACATGGCATGGGCACCGAGATG
** *
7115942 AGAGGTCCCCCGTAAGACCATGTCTGTGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGTGACATGGCATGGGCACCGAGATG
** *
7115992 AGAACTCCCATGTAAGACCATATCTG
1 AGAGGTCCCATGTAAGACCATGTCTG
7116018 GGATATGATA
Statistics
Matches: 104, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 64 0.62
53 3 0.03
55 1 0.01
56 34 0.33
57 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGTGACATGGCATGGGCACCGAGATG
Found at i:7116131 original size:49 final size:49
Alignment explanation
Indices: 7115997--7116118 Score: 244
Period size: 49 Copynumber: 2.5 Consensus size: 49
7115987 ATATGAGAAC
7115997 TCCCATGTAAGACCATATCTGGGATATGATATTGGCAGTACAAGAAACA
1 TCCCATGTAAGACCATATCTGGGATATGATATTGGCAGTACAAGAAACA
7116046 TCCCATGTAAGACCATATCTGGGATATGATATTGGCAGTACAAGAAACA
1 TCCCATGTAAGACCATATCTGGGATATGATATTGGCAGTACAAGAAACA
7116095 TCCCATGTAAGACCATATCTGGGA
1 TCCCATGTAAGACCATATCTGGGA
7116119 CATGGCTTTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 73 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (49 bp):
TCCCATGTAAGACCATATCTGGGATATGATATTGGCAGTACAAGAAACA
Found at i:7121515 original size:24 final size:24
Alignment explanation
Indices: 7121481--7121532 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
7121471 TGTTTAGAAG
* *
7121481 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
7121505 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
7121529 ATTT
1 ATTT
7121533 GACTTTGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:7122822 original size:17 final size:17
Alignment explanation
Indices: 7122800--7122836 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
7122790 TGTGAATTAT
*
7122800 AAAAATAAAATAAGATA
1 AAAAATAAAATAAAATA
*
7122817 AAAAATGAAATAAAATA
1 AAAAATAAAATAAAATA
7122834 AAA
1 AAA
7122837 TATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAAATAAAATAAAATA
Found at i:7123102 original size:3 final size:3
Alignment explanation
Indices: 7123082--7123192 Score: 70
Period size: 3 Copynumber: 37.3 Consensus size: 3
7123072 AAATAAAAAC
* * * * *
7123082 ATA ACA ATA ATA ACA ATA ATA TTA ATA ATA ATA CTA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
7123130 A-A GATA ATA AAA ACA ATA ATA ATA A-A AT- ATG ATA ATA CATTA A-A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA
*
7123174 ATA ATGA AGA A-A ATA ATA A
1 ATA AT-A ATA ATA ATA ATA A
7123193 AAATGGTAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
2 9 0.11
3 68 0.81
4 5 0.06
5 2 0.02
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:7124494 original size:24 final size:24
Alignment explanation
Indices: 7124460--7124511 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
7124450 TGTTTAGAAG
* *
7124460 ATTTAGTATTTATGAGTAAAATAT
1 ATTTAGCATTTATGAGCAAAATAT
* *
7124484 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCAAAATAT
7124508 ATTT
1 ATTT
7124512 GACTTTGGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCAAAATAT
Found at i:7130148 original size:20 final size:19
Alignment explanation
Indices: 7130123--7130162 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
7130113 GTGAGAAAAC
7130123 AACAACAA-AAATAGCAACAA
1 AACAACAAGAAA-AG-AACAA
7130143 AACAACAAGAAAAGAACAA
1 AACAACAAGAAAAGAACAA
7130162 A
1 A
7130163 TCTTTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 10 0.53
21 3 0.16
ACGTcount: A:0.72, C:0.17, G:0.07, T:0.03
Consensus pattern (19 bp):
AACAACAAGAAAAGAACAA
Found at i:7131472 original size:22 final size:23
Alignment explanation
Indices: 7131442--7131484 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
7131432 ACACCAAAAC
*
7131442 AGGCTTTTAGCGGC-CTTTTTTT
1 AGGCCTTTAGCGGCACTTTTTTT
7131464 AGGCCTTTAGCGGCACTTTTT
1 AGGCCTTTAGCGGCACTTTTT
7131485 AGCGCCGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (23 bp):
AGGCCTTTAGCGGCACTTTTTTT
Found at i:7131690 original size:43 final size:43
Alignment explanation
Indices: 7131643--7131787 Score: 177
Period size: 43 Copynumber: 3.4 Consensus size: 43
7131633 AGACTAAGAG
* * *
7131643 CTTTAGCAGCGTTTTTAATATAACCGCCGCTATAGAT-TGGTGT
1 CTTTAGCGGCGTTTTTAATATAAGCGCCGCTATAGATCAGG-GT
**
7131686 CTTTAGCGGCGTTTTTGTTGA-AAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTAAT-ATAAGCGCCGCTATAGATCAGGGT
* * *
7131729 CTTTAGCGGCGTTTTTTATATAAGCGCCGCTATAGATCATGGC
1 CTTTAGCGGCGTTTTTAATATAAGCGCCGCTATAGATCAGGGT
*
7131772 CTTTAGCGGCGCTTTT
1 CTTTAGCGGCGTTTTT
7131788 CCCAAAAACG
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
42 1 0.01
43 85 0.96
44 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTAATATAAGCGCCGCTATAGATCAGGGT
Found at i:7131800 original size:86 final size:86
Alignment explanation
Indices: 7131643--7131807 Score: 199
Period size: 86 Copynumber: 1.9 Consensus size: 86
7131633 AGACTAAGAG
* * ****
7131643 CTTTAGCAGCGTTTTTAATATAACCGCCGCTATAGATTGGTGTCTTTAGCGGCGTTTTTGTTGAA
1 CTTTAGCAGCGTTTTTAATATAACCGCCGCTATAGATTGGTGCCTTTAGCGGCGCTTTTCCCAAA
* *
7131708 AGCGCCGCTATAGATCAGGGT
66 AACGCCGCAATAGATCAGGGT
* * *
7131729 CTTTAGCGGCGTTTTTTATATAAGCGCCGCTATAGATCAT-G-GCCTTTAGCGGCGCTTTTCCCA
1 CTTTAGCAGCGTTTTTAATATAACCGCCGCTATAGAT--TGGTGCCTTTAGCGGCGCTTTTCCCA
7131792 AAAACGCCGCAATAGA
64 AAAACGCCGCAATAGA
7131808 CCCTGATCTA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 64 0.97
87 1 0.02
88 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (86 bp):
CTTTAGCAGCGTTTTTAATATAACCGCCGCTATAGATTGGTGCCTTTAGCGGCGCTTTTCCCAAA
AACGCCGCAATAGATCAGGGT
Found at i:7131941 original size:89 final size:89
Alignment explanation
Indices: 7131775--7131981 Score: 246
Period size: 89 Copynumber: 2.4 Consensus size: 89
7131765 TCATGGCCTT
* * * * * *
7131775 TAGCGGCGCTTTTCCCAAAAACGCCGC-AATAGAC-CCTGATC--TATAGCGGCGCTTATCCCAA
1 TAGCGGCGCTTATACCAAAAACGCCGCTAA-ATACTCTTTATCTATATAGCGGCGCTTAGCCCAA
*
7131836 AAACGCCGTAATAGACCCTGATCTA
65 AAACGCCGTAATAGACCCTAATCTA
* *
7131861 TAGCGGCGCTTAT-CCAGAAAACGCCGCTAAATACTCTTTATCTATATAGCGGCGCTTCGCGCAA
1 TAGCGGCGCTTATACCA-AAAACGCCGCTAAATACTCTTTATCTATATAGCGGCGCTTAGCCCAA
7131925 AAACGCCGCTAA-AGACCCTAATCTA
65 AAACGCCG-TAATAGACCCTAATCTA
* *
7131950 TAGCGGCGCTTTTACCAAAAATGCCGCTAAAT
1 TAGCGGCGCTTATACCAAAAACGCCGCTAAAT
7131982 TTGGCAGATT
Statistics
Matches: 104, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
85 3 0.03
86 25 0.24
87 7 0.07
89 63 0.61
90 6 0.06
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.22
Consensus pattern (89 bp):
TAGCGGCGCTTATACCAAAAACGCCGCTAAATACTCTTTATCTATATAGCGGCGCTTAGCCCAAA
AACGCCGTAATAGACCCTAATCTA
Found at i:7131979 original size:43 final size:43
Alignment explanation
Indices: 7131775--7131980 Score: 238
Period size: 43 Copynumber: 4.7 Consensus size: 43
7131765 TCATGGCCTT
7131775 TAGCGGCGCTTTTCCCAAAAACGCCGC-AATAGACCCTGATCTA
1 TAGCGGCGCTTTTCCCAAAAACGCCGCTAA-AGACCCTGATCTA
*
7131818 TAGCGGCGCTTATCCCAAAAACGCCG-TAATAGACCCTGATCTA
1 TAGCGGCGCTTTTCCCAAAAACGCCGCTAA-AGACCCTGATCTA
* * * *
7131861 TAGCGGCGCTTAT-CCAGAAAACGCCGCTAAATACTCTTTATCTATA
1 TAGCGGCGCTTTTCCCA-AAAACGCCGCTAAAGAC-CCTGATC--TA
** * *
7131907 TAGCGGCGCTTCGCGCAAAAACGCCGCTAAAGACCCTAATCTA
1 TAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCCTGATCTA
* *
7131950 TAGCGGCGCTTTTACCAAAAATGCCGCTAAA
1 TAGCGGCGCTTTTCCCAAAAACGCCGCTAAA
7131981 TTTGGCAGAT
Statistics
Matches: 141, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
42 3 0.02
43 94 0.67
44 8 0.06
45 5 0.04
46 29 0.21
47 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (43 bp):
TAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCCTGATCTA
Found at i:7132311 original size:21 final size:21
Alignment explanation
Indices: 7132285--7132396 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
7132275 TTTGACGCTG
7132285 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
7132306 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
7132327 CTCTGCTTCCCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* ** * *
7132348 CTGTTATTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
7132369 CTCTGCTTCTCTTGCTGCTGC
1 CTCTGCTTCCCTCGCTGCAGC
*
7132390 ATCTGCT
1 CTCTGCT
7132397 CTAAGCTGCT
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:7132443 original size:65 final size:66
Alignment explanation
Indices: 7132373--7132511 Score: 203
Period size: 65 Copynumber: 2.1 Consensus size: 66
7132363 TGCCGCCTCT
*
7132373 GCTTCTCTTGCTGCTGCATCTGCTCTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTTGAAC-
1 GCTTCTCTTGCTGCTACATCTGCTCTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTTGAACA
7132435 TCA
64 TCA
* * *
7132438 GCTTCTCTTGCTGCTACATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACATC
1 GCTTCTCTTGCTGCTACATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACATC
7132503 A
66 A
7132504 GCTTCTCT
1 GCTTCTCT
7132512 CGATGTTGCC
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
64 1 0.01
65 51 0.76
66 15 0.22
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (66 bp):
GCTTCTCTTGCTGCTACATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACATC
A
Found at i:7138126 original size:16 final size:16
Alignment explanation
Indices: 7138105--7138138 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
7138095 ATAGTTAAGC
7138105 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
7138121 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
7138137 TA
1 TA
7138139 CCCAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:7138170 original size:25 final size:25
Alignment explanation
Indices: 7138119--7138174 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
7138109 TAAGTTATGT
* *
7138119 ATTATGTAAGTTATTTATTACCCAA
1 ATTATGTAAGTTATGTATTACCAAA
* **
7138144 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATGTATTACCAAA
7138169 ATTATG
1 ATTATG
7138175 CTATGTAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTACCAAA
Found at i:7138188 original size:9 final size:9
Alignment explanation
Indices: 7138176--7138373 Score: 60
Period size: 9 Copynumber: 22.7 Consensus size: 9
7138166 AAAATTATGC
7138176 TATGTAAGT
1 TATGTAAGT
7138185 TATGTAAGT
1 TATGTAAGT
* **
7138194 CACATAAGT
1 TATGTAAGT
7138203 TATGTAAG-
1 TATGTAAGT
* * *
7138211 -AAGTTATT
1 TATGTAAGT
7138219 TATGTAAGT
1 TATGTAAGT
*
7138228 TAT-TTA-T
1 TATGTAAGT
* *
7138235 TATGAAAAT
1 TATGTAAGT
*
7138244 TAAGTAAGT
1 TATGTAAGT
*
7138253 TATGTAATT
1 TATGTAAGT
*
7138262 TACG-AA-T
1 TATGTAAGT
* **
7138269 AAT-TAAAAA
1 TATGT-AAGT
7138278 TATGTAAGT
1 TATGTAAGT
7138287 TATGTAAG-
1 TATGTAAGT
7138295 T-TGTAAGT
1 TATGTAAGT
*
7138303 TATGTATA-A
1 TATGTA-AGT
7138312 TAT-TAA-T
1 TATGTAAGT
**
7138319 TAACTAAGT
1 TATGTAAGT
* *
7138328 TATGTCATT
1 TATGTAAGT
*
7138337 TATGTATCATAT
1 TATGTA--A-GT
7138349 TAATGTAAGT
1 T-ATGTAAGT
*
7138359 TATGTAATT
1 TATGTAAGT
7138368 TATGTA
1 TATGTA
7138374 TATTAACTAA
Statistics
Matches: 134, Mismatches: 38, Indels: 34
0.65 0.18 0.17
Matches are distributed among these distances:
7 19 0.14
8 14 0.10
9 88 0.66
10 4 0.03
11 2 0.01
12 2 0.01
13 5 0.04
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.43
Consensus pattern (9 bp):
TATGTAAGT
Found at i:7138256 original size:34 final size:34
Alignment explanation
Indices: 7138218--7138296 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
7138208 AAGAAGTTAT
*** * *
7138218 TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
1 TTATGTAAGTTACGAATAATGAAAAATAAGTAAG
* * *
7138252 TTATGTAATTTACGAATAATTAAAAATATGTAAG
1 TTATGTAAGTTACGAATAATGAAAAATAAGTAAG
7138286 TTATGTAAGTT
1 TTATGTAAGTT
7138297 GTAAGTTATG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43
Consensus pattern (34 bp):
TTATGTAAGTTACGAATAATGAAAAATAAGTAAG
Found at i:7138340 original size:34 final size:31
Alignment explanation
Indices: 7138296--7138375 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
7138286 TTATGTAAGT
*
7138296 TGTAAGTTATGTATAATATTAATTAACTAAGTTA
1 TGTAATTTATGTATAATATTAA-T--CTAAGTTA
* * *
7138330 TGTCATTTATGTATCATATTAATGTAAGTTA
1 TGTAATTTATGTATAATATTAATCTAAGTTA
7138361 TGTAATTTATGTATA
1 TGTAATTTATGTATA
7138376 TTAACTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 20 0.50
33 1 0.03
34 19 0.47
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.47
Consensus pattern (31 bp):
TGTAATTTATGTATAATATTAATCTAAGTTA
Found at i:7138393 original size:31 final size:31
Alignment explanation
Indices: 7138311--7138394 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
7138301 GTTATGTATA
* *
7138311 ATATTAATTAACTAAGTTATGTCATTTATGT
1 ATATTAATTAATTAAGTTATGTAATTTATGT
7138342 ATCA-T-ATTAATGTAAGTTATGTAATTTATGT
1 AT-ATTAATTAAT-TAAGTTATGTAATTTATGT
* *
7138373 ATATTAACTAATTAATTTATGT
1 ATATTAATTAATTAAGTTATGT
7138395 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 6 0.13
31 33 0.73
32 6 0.13
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (31 bp):
ATATTAATTAATTAAGTTATGTAATTTATGT
Found at i:7138910 original size:24 final size:24
Alignment explanation
Indices: 7138878--7138930 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
7138868 AGTATTTTAT
7138878 AATATAATATTAATTTTAGATACA
1 AATATAATATTAATTTTAGATACA
*
7138902 AATATAATATTAATTTTAGTTACA
1 AATATAATATTAATTTTAGATACA
7138926 AATAT
1 AATAT
7138931 TATACAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
AATATAATATTAATTTTAGATACA
Found at i:7140423 original size:17 final size:17
Alignment explanation
Indices: 7140403--7140440 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
7140393 TTAAAGTTCA
7140403 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
* *
7140420 CAAGGAAGTAGAGGTTG
1 CAAGGAAGTAAAGGCTG
7140437 CAAG
1 CAAG
7140441 TTCCTAGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.37, T:0.13
Consensus pattern (17 bp):
CAAGGAAGTAAAGGCTG
Found at i:7140727 original size:33 final size:33
Alignment explanation
Indices: 7140680--7140747 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
7140670 ATATACATAT
*
7140680 ATTCATACCTAACACTAATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
*
7140713 ATTCATACCCAACACTCATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
7140746 AT
1 AT
7140748 AACATAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (33 bp):
ATTCATACCCAACACTAATCTCATTTAACTCGA
Found at i:7140988 original size:14 final size:15
Alignment explanation
Indices: 7140969--7141007 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
7140959 AATTGGGAAA
7140969 TTGGGGAAAAT-ACT
1 TTGGGGAAAATAACT
7140983 TTGGGGAAGAATAACT
1 TTGGGGAA-AATAACT
*
7140999 TGGGGGAAA
1 TTGGGGAAA
7141008 TTGGGGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 4 0.18
16 10 0.45
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (15 bp):
TTGGGGAAAATAACT
Found at i:7141012 original size:25 final size:22
Alignment explanation
Indices: 7140983--7141039 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
7140973 GGAAAATACT
*
7140983 TTGGGGAAGAATAACTTGGGGGAAA
1 TTGGGGAA-AAGAACTT--GGGAAA
*
7141008 TTGGGGGAAAAGAAGTTGGGAAA
1 TT-GGGGAAAAGAACTTGGGAAA
7141031 TTGGGGAAA
1 TTGGGGAAA
7141040 TGAAATCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
25 8 0.28
26 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.42, T:0.19
Consensus pattern (22 bp):
TTGGGGAAAAGAACTTGGGAAA
Found at i:7141052 original size:23 final size:23
Alignment explanation
Indices: 7141002--7141055 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
7140992 AATAACTTGG
* *
7141002 GGGAAATTGGGGGAAAAGAAGTT
1 GGGAAATTGGGGGAAAAGAAATC
*
7141025 GGGAAATT-GGGGAAATGAAATC
1 GGGAAATTGGGGGAAAAGAAATC
7141047 GTGGAAATT
1 G-GGAAATT
7141056 TGACTTGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.39, C:0.02, G:0.39, T:0.20
Consensus pattern (23 bp):
GGGAAATTGGGGGAAAAGAAATC
Found at i:7143188 original size:41 final size:41
Alignment explanation
Indices: 7143143--7143419 Score: 167
Period size: 42 Copynumber: 6.7 Consensus size: 41
7143133 TAATACATTC
* * * * *
7143143 GCGGCGCGTAGATACAAACGCAGCTGAATACAGGAGAATTA
1 GCGGCGCATAGATAAAAACGCAGCTAAAGACACGAGAATTA
* * * *
7143184 GCGGCGCATATATAAAAACGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCATAGATAAAAACGCAGCTAAAGACACGAGAATTA
*** * * * *
7143225 GCGGCGCATAGGCGAAAACGCCGCTATAGACCCAGAGTATTA
1 GCGGCGCATAGATAAAAACGCAGCTAAAGACAC-GAGAATTA
* ** * * *
7143267 GCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAGCATTA
1 GCGGCGCATAGATAAAAACGCAGCTAAAGACAC-GAGAATTA
* * ** * * *
7143309 CCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAGCATTA
1 GCGGCGCATAGATAAAAACGCAGCTAAAGACAC-GAGAATTA
* * ** * * * *
7143351 GCGGCACTTAGACGAAAACGCCGCTATAGACCCGAGCATTA
1 GCGGCGCATAGATAAAAACGCAGCTAAAGACACGAGAATTA
* * *
7143392 GCGGCGCTTAGACAAAAACGCCGCTAAA
1 GCGGCGCATAGATAAAAACGCAGCTAAA
7143420 TGTTTAAAAA
Statistics
Matches: 206, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 93 0.45
42 113 0.55
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.14
Consensus pattern (41 bp):
GCGGCGCATAGATAAAAACGCAGCTAAAGACACGAGAATTA
Found at i:7143283 original size:42 final size:41
Alignment explanation
Indices: 7143180--7143419 Score: 327
Period size: 42 Copynumber: 5.8 Consensus size: 41
7143170 ATACAGGAGA
* * **
7143180 ATTAGCGGCGCATATATAAAAACGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACCCGAGC
* * * *
7143221 ATTAGCGGCGCATAGGCGAAAACGCCGCTATAGACCCAGAGT
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACCC-GAGC
*
7143263 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGAC-CCGAGC
* *
7143305 ATTACCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGAC-CCGAGC
* *
7143347 ATTAGCGGCACTTAGACGAAAACGCCGCTATAGACCCGAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACCCGAGC
*
7143388 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAA
7143420 TGTTTAAAAA
Statistics
Matches: 178, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
41 66 0.37
42 111 0.62
43 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.15
Consensus pattern (41 bp):
ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACCCGAGC
Found at i:7143591 original size:40 final size:39
Alignment explanation
Indices: 7143468--7143594 Score: 112
Period size: 40 Copynumber: 3.2 Consensus size: 39
7143458 GGTTTTTTGT
* * *
7143468 GGCGCTTTATATAAAACGCCGTTAATTC-CTATTTTTAGC
1 GGCGCTTTA-GTAAAACGCCGCTAATGCTCTATTTTTAGC
** * **
7143507 GGCGCTTCCGTATAAACGCCGCTGATGCTCTACCTTTAGC
1 GGCGCTTTAGTA-AAACGCCGCTAATGCTCTATTTTTAGC
* * * *
7143547 GGCGCTTTGGCTAAATCGCCGCTAATGCTCTATTTTTTGT
1 GGCGCTTTAG-TAAAACGCCGCTAATGCTCTATTTTTAGC
7143587 GGCGCTTT
1 GGCGCTTT
7143595 TGTTCCAAAC
Statistics
Matches: 69, Mismatches: 16, Indels: 5
0.77 0.18 0.06
Matches are distributed among these distances:
38 2 0.03
39 19 0.28
40 46 0.67
41 2 0.03
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.35
Consensus pattern (39 bp):
GGCGCTTTAGTAAAACGCCGCTAATGCTCTATTTTTAGC
Found at i:7167720 original size:20 final size:19
Alignment explanation
Indices: 7167670--7167716 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
7167660 GTTGATCTGG
*
7167670 GAATTGATACAAACCGGTT
1 GAATTGATAAAAACCGGTT
*
7167689 GAATTGGATAAAAATCGGTT
1 GAATT-GATAAAAACCGGTT
7167709 GAATTGAT
1 GAATTGAT
7167717 TAAATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (19 bp):
GAATTGATAAAAACCGGTT
Found at i:7169474 original size:22 final size:22
Alignment explanation
Indices: 7169449--7169496 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
7169439 AAATAGTGGG
* *
7169449 AAAACAATAGGAAAACAACAAT
1 AAAACAATAGAAAAACAACAAC
*
7169471 AAAACAATAGAAAAATAACAAC
1 AAAACAATAGAAAAACAACAAC
7169493 AAAA
1 AAAA
7169497 TAAGAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.73, C:0.12, G:0.06, T:0.08
Consensus pattern (22 bp):
AAAACAATAGAAAAACAACAAC
Found at i:7173405 original size:27 final size:27
Alignment explanation
Indices: 7173375--7173436 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
7173365 AAAAGTTATT
*
7173375 TTTTTTAACTTTTAAAGGTTAAAAAAA
1 TTTTTTAACTTTTAAAGGTCAAAAAAA
* * *
7173402 TTTTATTAACTTTTAAGGGTCCAAAAAT
1 TTTT-TTAACTTTTAAAGGTCAAAAAAA
7173430 TTTTTTA
1 TTTTTTA
7173437 CCAACTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (27 bp):
TTTTTTAACTTTTAAAGGTCAAAAAAA
Found at i:7173427 original size:28 final size:27
Alignment explanation
Indices: 7173374--7173450 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 27
7173364 AAAAAGTTAT
* *
7173374 TTTTTTTAACTTTTAAAGGTTAAAAAAA
1 TTTTTTTAACTTTT-AAGGGTCAAAAAA
* *
7173402 TTTTATTAACTTTTAAGGGTCCAAAAA
1 TTTTTTTAACTTTTAAGGGTCAAAAAA
7173429 TTTTTTTACCAACTTTTAAGGG
1 TTTTTTT---AACTTTTAAGGG
7173451 ACTTAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 16 0.39
28 13 0.32
30 12 0.29
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.45
Consensus pattern (27 bp):
TTTTTTTAACTTTTAAGGGTCAAAAAA
Found at i:7173825 original size:47 final size:49
Alignment explanation
Indices: 7173717--7173837 Score: 147
Period size: 47 Copynumber: 2.5 Consensus size: 49
7173707 TTTTTTTCCG
* * * * *
7173717 TGAAAGGAAATAAAAAGTTTTTTTGAAGCCTGAAAATTTTAGGGTTTTCG
1 TGAAAGGAAATGAAAGGTTTTTTTGAAGCCTG-AAATTTTAGGATTATCC
** *
7173767 TGAAAACAAATGAAAGGTTTTTTT-AAGCCTG-AGTTTTAGGATTATCC
1 TGAAAGGAAATGAAAGGTTTTTTTGAAGCCTGAAATTTTAGGATTATCC
7173814 TGAAAGGAAATGAAAGGTTTTTTT
1 TGAAAGGAAATGAAAGGTTTTTTT
7173838 TCTTAGATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
47 34 0.56
49 7 0.11
50 20 0.33
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (49 bp):
TGAAAGGAAATGAAAGGTTTTTTTGAAGCCTGAAATTTTAGGATTATCC
Found at i:7182034 original size:22 final size:20
Alignment explanation
Indices: 7182009--7182049 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
7181999 ATAATTATTT
*
7182009 TAAATTTTTTATGATGTAAAAA
1 TAAATATTTTAT-AT-TAAAAA
7182031 TAAATATTTTATATTAAAA
1 TAAATATTTTATATTAAAA
7182050 TAGTGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TAAATATTTTATATTAAAAA
Found at i:7190406 original size:25 final size:24
Alignment explanation
Indices: 7190365--7190447 Score: 91
Period size: 25 Copynumber: 3.5 Consensus size: 24
7190355 GGATTAGACA
*
7190365 TAAAAC-TAGAATTAGACTTAAGTT
1 TAAAACTTAGGATTAGACTTAAG-T
7190389 TAAAACTTAGGATTAGACTTAAGT
1 TAAAACTTAGGATTAGACTTAAGT
* *
7190413 TAAGAGCTTAGGATTAGA-TTTAG-
1 TAA-AACTTAGGATTAGACTTAAGT
*
7190436 TCAAACTTAGGA
1 TAAAACTTAGGA
7190448 CTTAAAACTC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
22 8 0.15
23 2 0.04
24 14 0.27
25 28 0.54
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (24 bp):
TAAAACTTAGGATTAGACTTAAGT
Found at i:7191415 original size:16 final size:16
Alignment explanation
Indices: 7191394--7191432 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
7191384 GGGCCATGTC
7191394 TAGATTATATGATATT
1 TAGATTATATGATATT
7191410 TAGATTATATGATATT
1 TAGATTATATGATATT
7191426 TAGATTA
1 TAGATTA
7191433 CTAGGTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (16 bp):
TAGATTATATGATATT
Found at i:7196148 original size:11 final size:10
Alignment explanation
Indices: 7196125--7196154 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
7196115 TTCACTGGCA
7196125 TCTTTCTTTT
1 TCTTTCTTTT
7196135 TCTTTCTCTTT
1 TCTTTCT-TTT
7196146 TCTTTCTTT
1 TCTTTCTTT
7196155 GTGAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TCTTTCTTTT
Found at i:7199522 original size:3 final size:3
Alignment explanation
Indices: 7199514--7199544 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
7199504 ATATCAGTCA
7199514 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
7199545 GAACTTGCAT
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:7203489 original size:34 final size:35
Alignment explanation
Indices: 7203445--7203511 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
7203435 CAGTAAAATG
* * *
7203445 TTTTCCGTAAAATGA-TTTCTGGAAAATTTTTTAC
1 TTTTCCGTAAAATGACTTACTAGAAAATATTTTAC
*
7203479 TTTTCTGTAAAATGACTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTAGAAAATATTTT
7203512 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTAGAAAATATTTTAC
Found at i:7204889 original size:27 final size:27
Alignment explanation
Indices: 7204859--7204928 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
7204849 AATAATCAAT
*
7204859 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
7204886 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
7204914 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
7204929 CTAAAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:7207004 original size:13 final size:13
Alignment explanation
Indices: 7206986--7207011 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7206976 CCAGAAACTG
7206986 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
7206999 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
7207012 TACCCATTTG
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:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTTGCAGAAAAC
Found at i:7232989 original size:27 final size:26
Alignment explanation
Indices: 7232959--7233021 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 26
7232949 TTAAGTTTTT
**
7232959 TATTTTATTTTATTTATATATTTTTAA
1 TATTTTATAATATTTA-ATATTTTTAA
*
7232986 TATTTGATAATATTTAATATTTTTAA
1 TATTTTATAATATTTAATATTTTTAA
7233012 -ATTTT-TAATA
1 TATTTTATAATA
7233022 AATTTAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 5 0.16
25 4 0.12
26 10 0.31
27 13 0.41
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TATTTTATAATATTTAATATTTTTAA
Found at i:7233017 original size:8 final size:9
Alignment explanation
Indices: 7232971--7233021 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
7232961 TTTTATTTTA
7232971 TTTATATATT
1 TTTA-ATATT
7232981 TTTAATATT
1 TTTAATATT
*
7232990 TGATAATA--
1 T-TTAATATT
7232998 TTTAATATT
1 TTTAATATT
7233007 TTTAA-ATT
1 TTTAATATT
7233015 TTTAATA
1 TTTAATA
7233022 AATTTAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
7 5 0.14
8 9 0.26
9 12 0.34
10 9 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTAATATT
Found at i:7233018 original size:17 final size:17
Alignment explanation
Indices: 7232969--7233021 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
7232959 TATTTTATTT
7232969 TATTT-ATATATTTTTAA
1 TATTTGATA-ATTTTTAA
*
7232986 TATTTGATAATATTTAA
1 TATTTGATAATTTTTAA
*
7233003 TATTT-TTAAATTTTTAA
1 TATTTGAT-AATTTTTAA
7233020 TA
1 TA
7233022 AATTTAATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 27 0.87
18 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTTGATAATTTTTAA
Found at i:7233026 original size:26 final size:26
Alignment explanation
Indices: 7232969--7233029 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
7232959 TATTTTATTT
*
7232969 TATTTATATATTTTTAATATTTGATAA
1 TATTTA-ATATTTTTAATATTTAATAA
*
7232996 TATTTAATATTTTTAAATTTTTAATAA
1 TATTTAATATTTTT-AATATTTAATAA
7233023 -ATTTAAT
1 TATTTAAT
7233030 TCAAAAGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 15 0.48
27 16 0.52
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TATTTAATATTTTTAATATTTAATAA
Found at i:7249198 original size:2 final size:2
Alignment explanation
Indices: 7249191--7249217 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7249181 CAACATGTAT
7249191 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7249218 TAGAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7249287 original size:21 final size:24
Alignment explanation
Indices: 7249254--7249316 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 24
7249244 TAAGTTTTTG
*
7249254 AACATTT--GAATTTTTTATATAT
1 AACATTTGAGAATTTTTTATACAT
7249276 -AC-TTT-AGAATTTTTT-TACAT
1 AACATTTGAGAATTTTTTATACAT
*
7249296 AACATTTGATAATTTTTTATA
1 AACATTTGAGAATTTTTTATA
7249317 ATTTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 7 0.21
21 13 0.38
22 3 0.09
23 9 0.26
24 2 0.06
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (24 bp):
AACATTTGAGAATTTTTTATACAT
Found at i:7249311 original size:22 final size:21
Alignment explanation
Indices: 7249254--7249314 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
7249244 TAAGTTTTTG
*
7249254 AACATTTG-AATTTTTTATAT
1 AACATTTGAAATTTTTTACAT
*
7249274 ATAC-TTTAGAATTTTTTTACAT
1 A-ACATTT-GAAATTTTTTACAT
7249296 AACATTTGATAATTTTTTA
1 AACATTTGA-AATTTTTTA
7249315 TAATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
20 4 0.12
21 7 0.21
22 22 0.67
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (21 bp):
AACATTTGAAATTTTTTACAT
Found at i:7251324 original size:16 final size:16
Alignment explanation
Indices: 7251277--7251326 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
7251267 ACAAATCTTT
*
7251277 TATATT-TATAATATAA
1 TATATTATATAAT-TTA
*
7251293 TATATTAT-TACTTTTA
1 TATATTATATA-ATTTA
7251309 TATATTATATAATTTA
1 TATATTATATAATTTA
7251325 TA
1 TA
7251327 ACACAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 24 0.86
17 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTATATAATTTA
Found at i:7268795 original size:20 final size:20
Alignment explanation
Indices: 7268770--7268826 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
7268760 GATACAAGGT
*
7268770 AAGGTATTGATACTTTGT-A
1 AAGGTATTGATACTTTATGA
*
7268789 GAAGGTATCGATACTTTATGA
1 -AAGGTATTGATACTTTATGA
7268810 AAGGTATTGATATCTTT
1 AAGGTATTGATA-CTTT
7268827 TATTTTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (20 bp):
AAGGTATTGATACTTTATGA
Found at i:7269299 original size:33 final size:33
Alignment explanation
Indices: 7269259--7269324 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
7269249 AAATTTATAA
* *
7269259 AAAAAATTACAAAAATTATTAAATATTGTCATAC
1 AAAAATTTAC-AAAATAATTAAATATTGTCATAC
7269293 AAAAATTTACAAAATAATTAAATATTGTCATA
1 AAAAATTTACAAAATAATTAAATATTGTCATA
7269325 TCTCACGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 21 0.70
34 9 0.30
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (33 bp):
AAAAATTTACAAAATAATTAAATATTGTCATAC
Found at i:7273220 original size:30 final size:29
Alignment explanation
Indices: 7273150--7273220 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
7273140 TTTTCAAAAA
* *
7273150 TTAGAAATTTAGTTTTTGTACTTGTATTT
1 TTAGAAATTTAGTTTTTCTACTTGTAATT
* *
7273179 TTAGGAATTTAGTTTTTCTACTTTTTAAATT
1 TTAGAAATTTAGTTTTTCTAC-TTGT-AATT
7273210 TTA-AAATTTAG
1 TTAGAAATTTAG
7273221 GTTCAATTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 19 0.54
30 10 0.29
31 6 0.17
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.56
Consensus pattern (29 bp):
TTAGAAATTTAGTTTTTCTACTTGTAATT
Found at i:7275993 original size:26 final size:26
Alignment explanation
Indices: 7275948--7276020 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
7275938 TATTTTCTTG
* * *
7275948 AAATTTTACCAAGGGCAAAATCGTCA
1 AAATTTTACTAGGGGTAAAATCGTCA
*
7275974 AAATTTTACTAGGGGTAAAATTGTCA
1 AAATTTTACTAGGGGTAAAATCGTCA
* *
7276000 AACTTTTGCTAGGGGTAAAAT
1 AAATTTTACTAGGGGTAAAAT
7276021 AGGGATGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (26 bp):
AAATTTTACTAGGGGTAAAATCGTCA
Found at i:7278253 original size:24 final size:24
Alignment explanation
Indices: 7278215--7278269 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
7278205 TAAATGTTAT
*
7278215 CAACATCATCTTTCAATAC-AACAC
1 CAACATCATCATTCAAT-CTAACAC
* *
7278239 CAACATTATCATTCAATCTATCAC
1 CAACATCATCATTCAATCTAACAC
7278263 CAACATC
1 CAACATC
7278270 CCAATTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (24 bp):
CAACATCATCATTCAATCTAACAC
Found at i:7290929 original size:97 final size:96
Alignment explanation
Indices: 7290762--7290952 Score: 247
Period size: 97 Copynumber: 2.0 Consensus size: 96
7290752 ATTGCTTTGA
* * * * * * **
7290762 ACGTTATGAATATGCAAGCCAAAATCCAAACAACTTTTTTTTCCAATCTTTGACACTGACTGTCA
1 ACGTTACGAATATGCAAACCAAAATCCAAACAACCTTTTTCTACAATCTTTGACACTAACCCTCA
*
7290827 TATCAAATTGGATCTAAAGTATGTTCTTTCAC
66 GATCAAATTGGATCTAAAGTATGTT-TTTCAC
* * *
7290859 ACGTTACGAATATGCAAACCAAAATCTAAACAACCTTTTTCTACGATCTTTGTCACTAACCCTCA
1 ACGTTACGAATATGCAAACCAAAATCCAAACAACCTTTTTCTACAATCTTTGACACTAACCCTCA
* *
7290924 GATCAACTTGGATCTAATGTATGTTTTTC
66 GATCAAATTGGATCTAAAGTATGTTTTTC
7290953 TACTCATCAA
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
96 4 0.05
97 76 0.95
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (96 bp):
ACGTTACGAATATGCAAACCAAAATCCAAACAACCTTTTTCTACAATCTTTGACACTAACCCTCA
GATCAAATTGGATCTAAAGTATGTTTTTCAC
Found at i:7296577 original size:6 final size:6
Alignment explanation
Indices: 7296566--7296609 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
7296556 CCGATTGATA
* * * *
7296566 TAGGAG TAGGAG TAGGTG TAGGAA TAGGAG TATGAG TAGAAG TA
1 TAGGAG TAGGAG TAGGAG TAGGAG TAGGAG TAGGAG TAGGAG TA
7296610 AAAGTAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.41, T:0.23
Consensus pattern (6 bp):
TAGGAG
Found at i:7301140 original size:3 final size:3
Alignment explanation
Indices: 7301122--7301175 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
7301112 ACAGGGAAAA
* * * *
7301122 GAT GAT GAC GAG GAT GAT GAT GAT GAT GAT GAT GAT GAA GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
7301170 AAT GAT
1 GAT GAT
7301176 AACTAAATTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:7301991 original size:17 final size:17
Alignment explanation
Indices: 7301971--7302004 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
7301961 AATTGCTTTG
*
7301971 ATTTTTTAAATATTTTA
1 ATTTTTTAAATAATTTA
*
7301988 ATTTTTTTAATAATTTA
1 ATTTTTTAAATAATTTA
7302005 TTGAATTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTTAAATAATTTA
Found at i:7302189 original size:3 final size:3
Alignment explanation
Indices: 7302130--7302170 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
7302120 TTCTCATGAG
7302130 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
7302171 ACAGTGACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:7304301 original size:28 final size:29
Alignment explanation
Indices: 7304257--7304312 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
7304247 ATTTTCAACA
*
7304257 AATATAAAAATATTAAAAAATCTTAAAAG
1 AATATAAAAATATTAAAAAATCTAAAAAG
7304286 AATATAAAAA-ATTAAAAAATCTAAAAA
1 AATATAAAAATATTAAAAAATCTAAAAA
7304313 AAACACCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (29 bp):
AATATAAAAATATTAAAAAATCTAAAAAG
Found at i:7304313 original size:9 final size:8
Alignment explanation
Indices: 7304256--7304313 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 8
7304246 TATTTTCAAC
7304256 AAATATAAA
1 AAAT-TAAA
7304265 AATATTAAA
1 AA-ATTAAA
7304274 AAATCTTAAA
1 AAA--TTAAA
7304284 AGAATATAAA
1 A-AAT-TAAA
7304294 AAATTAAA
1 AAATTAAA
7304302 AAATCTAAA
1 AAAT-TAAA
7304311 AAA
1 AAA
7304314 AACACCCTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
8 9 0.21
9 19 0.44
10 13 0.30
11 2 0.05
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (8 bp):
AAATTAAA
Found at i:7306769 original size:13 final size:13
Alignment explanation
Indices: 7306681--7306772 Score: 73
Period size: 13 Copynumber: 6.9 Consensus size: 13
7306671 ATCCAATGTT
*
7306681 CCATTTCATATAT
1 CCATTTCATATAA
*
7306694 CTATTTCCATATAA
1 CCATTT-CATATAA
*
7306708 CCGA-GTCATATAA
1 CC-ATTTCATATAA
7306721 CCATTTCATAT-A
1 CCATTTCATATAA
*
7306733 TCATTTTTCATATAA
1 CCA--TTTCATATAA
*
7306748 CCGA-GTCATATAA
1 CC-ATTTCATATAA
7306761 CCATTTCATATA
1 CCATTTCATATA
7306773 TCATTTTTCA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
12 5 0.08
13 37 0.60
14 16 0.26
15 3 0.05
16 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (13 bp):
CCATTTCATATAA
Found at i:7306779 original size:40 final size:40
Alignment explanation
Indices: 7306681--7306786 Score: 187
Period size: 40 Copynumber: 2.6 Consensus size: 40
7306671 ATCCAATGTT
*
7306681 CCATTTCATATATC-TATTTCCATATAACCGAGTCATATAA
1 CCATTTCATATATCAT-TTTTCATATAACCGAGTCATATAA
7306721 CCATTTCATATATCATTTTTCATATAACCGAGTCATATAA
1 CCATTTCATATATCATTTTTCATATAACCGAGTCATATAA
7306761 CCATTTCATATATCATTTTTCATATA
1 CCATTTCATATATCATTTTTCATATA
7306787 TTATTTTTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
40 63 0.98
41 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (40 bp):
CCATTTCATATATCATTTTTCATATAACCGAGTCATATAA
Found at i:7306798 original size:16 final size:14
Alignment explanation
Indices: 7306764--7306794 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
7306754 CATATAACCA
7306764 TTTCATATATCATT
1 TTTCATATATCATT
*
7306778 TTTCATATATTATT
1 TTTCATATATCATT
7306792 TTT
1 TTT
7306795 TTCACCTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTCATATATCATT
Found at i:7317771 original size:22 final size:19
Alignment explanation
Indices: 7317746--7317794 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 19
7317736 GTATAAACAA
7317746 ATTAATTAATCTAATAATATAT
1 ATTAATTAAT-TAA-AAT-TAT
7317768 ATTAATTAATTAAAATTAT
1 ATTAATTAATTAAAATTAT
*
7317787 ATTTATTA
1 ATTAATTA
7317795 TCATCATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.38
20 3 0.12
21 3 0.12
22 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAATTAATTAAAATTAT
Found at i:7320082 original size:24 final size:26
Alignment explanation
Indices: 7320055--7320105 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
7320045 AAGAAATGAA
7320055 GAAAT-GAAAGA-AAG-AAAATTATAT
1 GAAATAGAAAGATAAGTAAAA-TATAT
*
7320079 GAAATAGAAGGATAAGTAAAATATAT
1 GAAATAGAAAGATAAGTAAAATATAT
7320105 G
1 G
7320106 TTCAAGAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.22
25 5 0.22
26 9 0.39
27 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.20, T:0.22
Consensus pattern (26 bp):
GAAATAGAAAGATAAGTAAAATATAT
Found at i:7323663 original size:3 final size:3
Alignment explanation
Indices: 7323655--7323710 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
7323645 ACTTGAATGG
7323655 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7323703 TAA TAA TA
1 TAA TAA TA
7323711 CTCAGGCCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:7324132 original size:2 final size:2
Alignment explanation
Indices: 7324125--7324165 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
7324115 AAAATCGATG
* *
7324125 AT AT AT AT AT AT AT AT AT AT AT GT AT GT 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 AT AT A
7324166 AAGGTGGCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7328094 original size:15 final size:16
Alignment explanation
Indices: 7328068--7328097 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7328058 TTCATTGAAG
7328068 TGTTTTTAAGTTAGTC
1 TGTTTTTAAGTTAGTC
7328084 TGTTTTT-AGTTAGT
1 TGTTTTTAAGTTAGT
7328098 GACACACCAT
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:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (16 bp):
TGTTTTTAAGTTAGTC
Found at i:7329199 original size:35 final size:36
Alignment explanation
Indices: 7329139--7329209 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
7329129 AAATAGTATT
*
7329139 GGTGTTGCGATACTCACTAGAAAAGGACTCAATTTC
1 GGTGTTGCGATACTCACTAAAAAAGGACTCAATTTC
*
7329175 GGTGTTGTGATAC-CACTAAAAAAGGACTCAATTTC
1 GGTGTTGCGATACTCACTAAAAAAGGACTCAATTTC
7329210 TTCACTTCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 21 0.64
36 12 0.36
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (36 bp):
GGTGTTGCGATACTCACTAAAAAAGGACTCAATTTC
Found at i:7331451 original size:21 final size:21
Alignment explanation
Indices: 7331410--7331452 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
7331400 ACCCCAAACT
* *
7331410 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
7331431 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
7331452 C
1 C
7331453 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:7331765 original size:17 final size:17
Alignment explanation
Indices: 7331726--7331771 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
7331716 ACTCCCCCTA
7331726 TTTACTTTCCCTC-AAACT
1 TTTA-TTTCCC-CAAAACT
7331744 TTTA-TTCCCCAAAACTT
1 TTTATTTCCCCAAAAC-T
7331761 TTTATTTCCCC
1 TTTATTTCCCC
7331772 CCTAAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 5 0.20
18 10 0.40
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTATTTCCCCAAAACT
Found at i:7335663 original size:18 final size:18
Alignment explanation
Indices: 7335628--7335665 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
7335618 TGAAAAGAAT
*
7335628 AAAAAGAAAAACGGTTCA
1 AAAAAGAAAAACGATTCA
7335646 AAAAAGAGAAAA-GATTCA
1 AAAAAGA-AAAACGATTCA
7335664 AA
1 AA
7335666 GGTTGCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.66, C:0.08, G:0.16, T:0.11
Consensus pattern (18 bp):
AAAAAGAAAAACGATTCA
Found at i:7336462 original size:15 final size:15
Alignment explanation
Indices: 7336444--7336473 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7336434 TTGTTTTAAA
7336444 TTTATATATTATTAT
1 TTTATATATTATTAT
7336459 TTTATATATTATTAT
1 TTTATATATTATTAT
7336474 CTATGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATATATTATTAT
Done.