Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 13 of 130
Found at i:3661547 original size:16 final size:18
Alignment explanation
Indices: 3661526--3661561 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
3661516 TTTAGCTCTC
3661526 TTTTTT-CCTTTT-TTTT
1 TTTTTTGCCTTTTCTTTT
3661542 TTTTTTGCCTTTTCTTTT
1 TTTTTTGCCTTTTCTTTT
3661560 TT
1 TT
3661562 CGGGGAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 6 0.33
18 6 0.33
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTTGCCTTTTCTTTT
Found at i:3665717 original size:40 final size:40
Alignment explanation
Indices: 3665673--3665753 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3665663 TGCTAGCTAG
3665673 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
1 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
3665713 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
1 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
3665753 G
1 G
3665754 AACGTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (40 bp):
GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
Found at i:3665777 original size:2 final size:2
Alignment explanation
Indices: 3665770--3665794 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3665760 TTATAAGCAT
3665770 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 T
3665795 GCTAGTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3665914 original size:202 final size:202
Alignment explanation
Indices: 3665571--3666196 Score: 1238
Period size: 202 Copynumber: 3.1 Consensus size: 202
3665561 TTGAACTTAC
3665571 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
1 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
3665636 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
66 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
3665701 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
131 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
3665766 GCATTAT
196 GCATTAT
3665773 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
1 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
3665838 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
66 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
3665903 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
131 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
3665968 GCA-T-T
196 GCATTAT
3665973 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
1 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
3666038 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
66 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
3666103 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
131 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
3666168 GCATTAT
196 GCATTAT
3666175 ATATATATATATATATATATAT
1 ATATATATATATATATATATAT
3666197 ATATACACTC
Statistics
Matches: 422, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
200 199 0.47
201 2 0.00
202 221 0.52
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (202 bp):
ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
GCATTAT
Found at i:3665919 original size:40 final size:40
Alignment explanation
Indices: 3665875--3665955 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3665865 TGCTAGCTAG
3665875 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
1 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
3665915 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
1 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
3665955 G
1 G
3665956 AACGTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (40 bp):
GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
Found at i:3666115 original size:200 final size:200
Alignment explanation
Indices: 3665571--3666194 Score: 1230
Period size: 200 Copynumber: 3.1 Consensus size: 200
3665561 TTGAACTTAC
3665571 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
1 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
3665636 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
66 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
3665701 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
131 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
3665766 GCATTAT
196 GCA-T-T
3665773 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
1 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
3665838 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
66 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
3665903 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
131 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
3665968 GCATT
196 GCATT
3665973 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
1 ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
3666038 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
66 ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
3666103 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
131 GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
3666168 GCATT
196 GCATT
3666173 ATATATATATATATATATATAT
1 ATATATATATATATATATATAT
3666195 ATATATACAC
Statistics
Matches: 422, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
200 223 0.53
201 1 0.00
202 198 0.47
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (200 bp):
ATATATATATATATATATATATGCTAGTATTGGTCATACGTATATGATAGAGTGAAGTAAGCTTC
ACAAGCTCGTAAGTTCATGGAATGTTATGCTAGCTAGGGTGAAGTTGTAATAAAACTTCATATGA
GGTTTATGAAATGGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAATGAACGTTTTATAA
GCATT
Found at i:3666119 original size:40 final size:40
Alignment explanation
Indices: 3666075--3666155 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3666065 TGCTAGCTAG
3666075 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
1 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
3666115 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
1 GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
3666155 G
1 G
3666156 AACGTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (40 bp):
GGTGAAGTTGTAATAAAACTTCATATGAGGTTTATGAAAT
Found at i:3666179 original size:2 final size:2
Alignment explanation
Indices: 3666172--3666201 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3666162 TTATAAGCAT
3666172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3666202 CACTCACTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3670239 original size:50 final size:50
Alignment explanation
Indices: 3670169--3670323 Score: 184
Period size: 55 Copynumber: 3.0 Consensus size: 50
3670159 ACTTTAATAC
3670169 CTCATATCATAATTACAAAAATATCATTTTCTTAAATTGACTATTATGCT
1 CTCATATCATAATTACAAAAATATCATTTTCTTAAATTGACTATTATGCT
* * * * *
3670219 CTCATATCATAATTATAAAAATACTTATTTTCTTATAATTATTTACTATAATTCT
1 CTCATATCATAATTACAAAAATA-TCATTTTC-T-TAA--ATTGACTATTATGCT
* * *
3670274 CTCATATCATAATTACAGAAATATCCCTTCTCTTAAATTGACTATTATGC
1 CTCATATCATAATTACAAAAATAT-CATTTTCTTAAATTGACTATTATGC
3670324 ATTTACACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
50 22 0.26
51 18 0.21
52 1 0.01
53 6 0.07
54 2 0.02
55 37 0.43
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (50 bp):
CTCATATCATAATTACAAAAATATCATTTTCTTAAATTGACTATTATGCT
Found at i:3670278 original size:55 final size:54
Alignment explanation
Indices: 3670133--3670298 Score: 198
Period size: 55 Copynumber: 3.1 Consensus size: 54
3670123 CATAATTGTG
* * *
3670133 AAAATATCACTTTCTTATACTTATTTACTTTAATAC-CTCATATCATAATTACA
1 AAAATATCATTTTCTTATAATTATTTACTATAATACTCTCATATCATAATTACA
* * * *
3670186 AAAATATCATTTTC-T-TAA--ATTGACTATTATGCTCTCATATCATAATTATA
1 AAAATATCATTTTCTTATAATTATTTACTATAATACTCTCATATCATAATTACA
* *
3670236 AAAATACTTATTTTCTTATAATTATTTACTATAATTCTCTCATATCATAATTACA
1 AAAATA-TCATTTTCTTATAATTATTTACTATAATACTCTCATATCATAATTACA
*
3670291 GAAATATC
1 AAAATATC
3670299 CCTTCTCTTA
Statistics
Matches: 93, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
49 10 0.11
50 22 0.24
51 9 0.10
52 2 0.02
53 16 0.17
54 1 0.01
55 33 0.35
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.44
Consensus pattern (54 bp):
AAAATATCATTTTCTTATAATTATTTACTATAATACTCTCATATCATAATTACA
Found at i:3670337 original size:106 final size:103
Alignment explanation
Indices: 3670143--3670393 Score: 319
Period size: 106 Copynumber: 2.4 Consensus size: 103
3670133 AAAATATCAC
* * * *
3670143 TTTCTTATACTTATTTACTTTAATACCTCATATCATAATTACAAAAATATCATTTTCTTAAATTG
1 TTTCTTATAATTATTTACTATAATTCCTCATATCATAATTACAAAAATATCATTCTCTTAAATTG
*
3670208 ACTATTATGCTCTCATATCATAATTATAAAAATACTTAT
66 ACTATTATGCTCTCATATCATAATAATAAAAATACTT-T
* *
3670247 TTTCTTATAATTATTTACTATAATTCTCTCATATCATAATTACAGAAATATCCCTTCTCTTAAAT
1 TTTCTTATAATTATTTACTATAATTC-CTCATATCATAATTACAAAAATAT-CATTCTCTTAAAT
* * *
3670312 TGACTATTATGCAT-TTACA-CTATAATAATGAAAATACTTT
64 TGACTATTATGC-TCTCATATC-ATAATAATAAAAATACTTT
3670352 TTCTCTTATAATTATTTACTAT-ATTACCCTCATATCATAATT
1 TT-TCTTATAATTATTTACTATAATT--CCTCATATCATAATT
3670394 GTGAAAAAAC
Statistics
Matches: 130, Mismatches: 10, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
104 23 0.18
105 30 0.23
106 75 0.58
107 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.45
Consensus pattern (103 bp):
TTTCTTATAATTATTTACTATAATTCCTCATATCATAATTACAAAAATATCATTCTCTTAAATTG
ACTATTATGCTCTCATATCATAATAATAAAAATACTTT
Found at i:3678696 original size:8 final size:8
Alignment explanation
Indices: 3678679--3678713 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3678669 TTATAAGCGT
3678679 TATATAAA
1 TATATAAA
*
3678687 TATGTAAA
1 TATATAAA
3678695 TATATAAA
1 TATATAAA
*
3678703 TATATATA
1 TATATAAA
3678711 TAT
1 TAT
3678714 GGTAGACCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (8 bp):
TATATAAA
Found at i:3679452 original size:52 final size:51
Alignment explanation
Indices: 3679345--3679500 Score: 165
Period size: 52 Copynumber: 3.0 Consensus size: 51
3679335 TATAACCATA
* * * * *
3679345 CAAACTTG-CTCATTAAGAATCCTCT-CTTCTTAGAATTCTTTTCCTGTAAGT
1 CAAACTTGCCT-ATTAAGAATCCTTTCCCT-TTAGAATTCTTCTCTTGCAAGT
3679396 CAAACTTGCCTATTAAGAATCCATTTCCCTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-TTTCCCTTTAGAATTCTTCTCTTGCAAGT
* * * *
3679448 CAAACTTACCTATTAAGAATCTTCTTTCTC-TTAGAATTCTTCTTTTACAAGT
1 CAAACTTGCCTATTAAGAATC--CTTTCCCTTTAGAATTCTTCTCTTGCAAGT
3679500 C
1 C
3679501 TTCTTGTCCA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
51 19 0.21
52 64 0.70
53 7 0.08
54 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCTTTCCCTTTAGAATTCTTCTCTTGCAAGT
Found at i:3679553 original size:22 final size:22
Alignment explanation
Indices: 3679525--3679567 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3679515 GCAATATTTG
3679525 ACAAATC-CTAAACAAATCTCTA
1 ACAAATCTC-AAACAAATCTCTA
3679547 ACAAATCTCAAACAAATCTCT
1 ACAAATCTCAAACAAATCTCT
3679568 TATGAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (22 bp):
ACAAATCTCAAACAAATCTCTA
Found at i:3679565 original size:11 final size:11
Alignment explanation
Indices: 3679525--3679566 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
3679515 GCAATATTTG
3679525 ACAAATC-CTAA
1 ACAAATCTC-AA
*
3679536 ACAAATCTCTA
1 ACAAATCTCAA
3679547 ACAAATCTCAA
1 ACAAATCTCAA
3679558 ACAAATCTC
1 ACAAATCTC
3679567 TTATGAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 27 0.96
12 1 0.04
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:3679838 original size:25 final size:25
Alignment explanation
Indices: 3679810--3679857 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3679800 TCTTTTCATA
*
3679810 TCTCGAACCGTCAACTCTTCCCATG
1 TCTCGAACCATCAACTCTTCCCATG
**
3679835 TCTCGAACCATCGGCTCTTCCCA
1 TCTCGAACCATCAACTCTTCCCA
3679858 CATCTTGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.19, C:0.42, G:0.12, T:0.27
Consensus pattern (25 bp):
TCTCGAACCATCAACTCTTCCCATG
Found at i:3680541 original size:52 final size:51
Alignment explanation
Indices: 3680435--3680590 Score: 190
Period size: 52 Copynumber: 3.0 Consensus size: 51
3680425 TATAACCATA
* * * * *
3680435 CAAACTTG-CTCATTAAGAATCCTCTCTTCTTAGAATTCTTTTCCTGTAAGT
1 CAAACTTGCCT-ATTAAGAATCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
*
3680486 CAAACTTGCCTATTAAGAATCCATTTCCCCTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-TTTCCTCTTAGAATTCTTCTCTTGCAAGT
* *
3680538 CAAACTTACCTATTAAGAATCTTCTTT-CTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC--CTTTCCTCTTAGAATTCTTCTCTTGCAAGT
3680590 C
1 C
3680591 TTCTTGTCCA
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
51 19 0.21
52 69 0.75
53 3 0.03
54 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.40
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:3680631 original size:11 final size:11
Alignment explanation
Indices: 3680615--3680657 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
3680605 GCAATATCTG
3680615 ACAAATC-CTAA
1 ACAAATCTCT-A
3680626 ACAAATCTCTA
1 ACAAATCTCTA
*
3680637 ACAAATCTCAA
1 ACAAATCTCTA
*
3680648 ATAAATCTCT
1 ACAAATCTCT
3680658 TATGGGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 26 0.93
12 2 0.07
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:3680640 original size:22 final size:22
Alignment explanation
Indices: 3680615--3680657 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3680605 GCAATATCTG
3680615 ACAAATC-CTAAACAAATCTCTA
1 ACAAATCTC-AAACAAATCTCTA
*
3680637 ACAAATCTCAAATAAATCTCT
1 ACAAATCTCAAACAAATCTCT
3680658 TATGGGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (22 bp):
ACAAATCTCAAACAAATCTCTA
Found at i:3684141 original size:21 final size:21
Alignment explanation
Indices: 3684094--3684150 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
3684084 TTAACATGTA
* *
3684094 ATAATATCAAGAATAATAATT
1 ATAATAACAAAAATAATAATT
*
3684115 AAAATAACAAAAATAAT-ATAT
1 ATAATAACAAAAATAATAAT-T
*
3684136 ATAATATAAAAAAAT
1 ATAATA-ACAAAAAT
3684151 TTAAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAATAACAAAAATAATAATT
Found at i:3684937 original size:23 final size:23
Alignment explanation
Indices: 3684901--3684945 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3684891 TATTTATAGA
3684901 ATTTTTTGAGATTCAAATCTCAG
1 ATTTTTTGAGATTCAAATCTCAG
*
3684924 ATTTTTT-AGAATTCGAATCTCA
1 ATTTTTTGAG-ATTCAAATCTCA
3684946 TTTTTTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (23 bp):
ATTTTTTGAGATTCAAATCTCAG
Found at i:3684951 original size:23 final size:22
Alignment explanation
Indices: 3684902--3684951 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
3684892 ATTTATAGAA
3684902 TTTTTTGAGATTCAAATCTCAG
1 TTTTTTGAGATTCAAATCTCAG
*
3684924 ATTTTTT-AGAATTCGAATCTCA-
1 -TTTTTTGAG-ATTCAAATCTCAG
3684946 TTTTTT
1 TTTTTT
3684952 CAACCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 6 0.24
22 2 0.08
23 17 0.68
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTTTTGAGATTCAAATCTCAG
Found at i:3685095 original size:20 final size:22
Alignment explanation
Indices: 3685070--3685109 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3685060 TGAATCGGAT
3685070 AAGAAAG-AAG-AAGAAAAAAA
1 AAGAAAGAAAGAAAGAAAAAAA
3685090 AAGAAAGAAAGAAAGAAAAA
1 AAGAAAGAAAGAAAGAAAAA
3685110 TAAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (22 bp):
AAGAAAGAAAGAAAGAAAAAAA
Found at i:3685131 original size:9 final size:9
Alignment explanation
Indices: 3685111--3685169 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
3685101 AAAGAAAAAT
3685111 AAATAAATAA
1 AAAT-AATAA
*
3685121 AAATCATAA
1 AAATAATAA
3685130 AAATAATAA
1 AAATAATAA
3685139 TAATGATAATAA
1 -AA--ATAATAA
3685151 AAA-AAT-A
1 AAATAATAA
3685158 AAA-AATAA
1 AAATAATAA
3685166 AAAT
1 AAAT
3685170 GGTGTTTACA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
7 7 0.17
8 7 0.17
9 13 0.31
10 6 0.14
11 2 0.05
12 7 0.17
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (9 bp):
AAATAATAA
Found at i:3685147 original size:18 final size:19
Alignment explanation
Indices: 3685111--3685169 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
3685101 AAAGAAAAAT
3685111 AAATAAATAAAAATCATAA
1 AAATAAATAAAAATCATAA
* *
3685130 AAAT-AATAATAATGATAA
1 AAATAAATAAAAATCATAA
*
3685148 TAAAAAAATAAAAA--ATAA
1 -AAATAAATAAAAATCATAA
3685166 AAAT
1 AAAT
3685170 GGTGTTTACA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.09
18 16 0.48
19 7 0.21
20 7 0.21
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
AAATAAATAAAAATCATAA
Found at i:3685444 original size:99 final size:99
Alignment explanation
Indices: 3685340--3685524 Score: 268
Period size: 99 Copynumber: 1.9 Consensus size: 99
3685330 TCCTCTGAGC
* * *
3685340 AGAGGCTCAACAACTTTAAAAAAAT-TCATTTTAAAAAA-GCTCCTCTAAGTAAAGGCTCAATAA
1 AGAGGCTCAACAACTTT--AAAAATCTCATCTTAAAAAAGGCTCATCTAAGCAAAGGCTCAATAA
3685403 CTTT-AAAATCTCATCTTGAAAAAAAATCCTCTCAAT
64 CTTTAAAAATCT-ATCTTGAAAAAAAATCCTCTCAAT
* *
3685439 AGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAGGCTCATCTCAGCAGAGGCTCAATAACT
1 AGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAGGCTCATCTAAGCAAAGGCTCAATAACT
*
3685504 TTAAAAATCTATCTTTAAAAA
66 TTAAAAATCTATCTTGAAAAA
3685525 TTCATCTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
97 6 0.08
98 12 0.16
99 52 0.68
100 7 0.09
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (99 bp):
AGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAGGCTCATCTAAGCAAAGGCTCAATAACT
TTAAAAATCTATCTTGAAAAAAAATCCTCTCAAT
Found at i:3685445 original size:49 final size:50
Alignment explanation
Indices: 3685340--3685524 Score: 211
Period size: 50 Copynumber: 3.7 Consensus size: 50
3685330 TCCTCTGAGC
3685340 AGAGGCTCAACAACTTTAAAAAAAT-TCAT-TTTAAAAAAGCTCCTCT-AAGT
1 AGAGGCTCAACAACTTT--AAAAATCTCATCTTTAAAAAAGCTCCTCTCAA-T
* * * **
3685390 AAAGGCTCAATAACTTT-AAAATCTCATCTTGAAAAAAAATCCTCTCAAT
1 AGAGGCTCAACAACTTTAAAAATCTCATCTTTAAAAAAGCTCCTCTCAAT
* **
3685439 AGAGGCTCAACAACTTTAAAAATCTCATC-TTAAAAAAGGCTCATCTCAGC
1 AGAGGCTCAACAACTTTAAAAATCTCATCTTTAAAAAA-GCTCCTCTCAAT
*
3685489 AGAGGCTCAATAACTTTAAAAATCT-ATCTTTAAAAA
1 AGAGGCTCAACAACTTTAAAAATCTCATCTTTAAAAA
3685525 TTCATCTTAA
Statistics
Matches: 115, Mismatches: 14, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
47 5 0.04
48 4 0.03
49 40 0.35
50 66 0.57
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (50 bp):
AGAGGCTCAACAACTTTAAAAATCTCATCTTTAAAAAAGCTCCTCTCAAT
Found at i:3685530 original size:63 final size:64
Alignment explanation
Indices: 3685452--3685575 Score: 205
Period size: 63 Copynumber: 2.0 Consensus size: 64
3685442 GGCTCAACAA
* * * *
3685452 CTTTAAAAATCTCATCTTAAAAAAGGCTCATCTCAGCAGAGGCTCAATAACTTTAAAAATCTAT
1 CTTTAAAAATCTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAAATCTAT
3685516 CTTTAAAAAT-TCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAAATC
1 CTTTAAAAATCTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAAATC
3685576 CATATTGAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
63 46 0.82
64 10 0.18
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (64 bp):
CTTTAAAAATCTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAAATCTAT
Found at i:3685572 original size:49 final size:50
Alignment explanation
Indices: 3685516--3685876 Score: 416
Period size: 49 Copynumber: 7.4 Consensus size: 50
3685506 AAAAATCTAT
* *
3685516 CTTTAAAAAT-TCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
* * * *
3685565 CTTTAAAAATC-CATATTGAAAAAGGCTCTTCTCAGTAGAGACTCAACAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
* * *
3685614 CTTTAAAAAAT-TCATCTT-AAAAAAGCTCATATCAGCAGAGACTTAATAA
1 CTTT-AAAAATCTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
* * * *
3685663 CTTTAAAAATCTCATTTTGAAAAA-GCTCATTTCAGCAGAGGCTTAAC-A
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
* *
3685711 CTTTAAAAATCTTATCTTGAAAAA-GCTCATATCAGCAGATG-TTCAACAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATATCAGCAGA-GACTCAACAA
* * *
3685760 CTTTAAAAATCT-ATCTTGAAAAAGGCTCATCTCAACAGAGGCTCAACAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
* * * * * * *
3685809 CTTTAAAAATCTCATTTTGAAAAAGGCTCATCTTAGTAGAGGCTTAATAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
3685859 CTTTAAAAATCTCATCTT
1 CTTTAAAAATCTCATCTT
3685877 TTCTCGAAAT
Statistics
Matches: 270, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
48 59 0.22
49 147 0.54
50 64 0.24
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (50 bp):
CTTTAAAAATCTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
Found at i:3685759 original size:195 final size:196
Alignment explanation
Indices: 3685516--3685873 Score: 517
Period size: 195 Copynumber: 1.8 Consensus size: 196
3685506 AAAAATCTAT
3685516 CTTTAAAAATTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAAATCCATAT
1 CTTTAAAAATTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAAATCCATAT
* **
3685581 TGAAAAAGGCTCTTCTCAGTAGAGACTCAACAACTTTAAAAAAT-TCATCTT-AAAAAAGCTCAT
66 TGAAAAAGGCTCATCTCAACAGAGACTCAACAACTTT-AAAAATCTCATCTTGAAAAAAGCTCAT
3685644 ATCAGCAGAGACTTAATAACTTTAAAAATCTCATTTTGAAAAAGCTCATTTCAGCAGAGGCTTAA
130 ATCAGCAGAGACTTAATAACTTTAAAAATCTCATTTTGAAAAAGCTCATTTCAGCAGAGGCTTAA
3685709 CA
195 CA
* * * * *
3685711 CTTTAAAAATCTTATCTTGAAAAA-GCTCATATCAGCAGATG-TTCAACAACTTTAAAAATCTAT
1 CTTTAAAAAT-TCATCTTAAAAAAGGCTCATATCAGCA-AAGACTCAACAACTTTAAAAATCCAT
* * * *
3685774 CTTGAAAAAGGCTCATCTCAACAGAGGCTCAACAACTTTAAAAATCTCATTTTGAAAAAGGCTCA
64 ATTGAAAAAGGCTCATCTCAACAGAGACTCAACAACTTTAAAAATCTCATCTTGAAAAAAGCTCA
* * * *
3685839 TCTTAGTAGAGGCTTAATAACTTTAAAAATCTCAT
129 TATCAGCAGAGACTTAATAACTTTAAAAATCTCAT
3685874 CTTTTCTCGA
Statistics
Matches: 143, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
194 6 0.04
195 83 0.58
196 54 0.38
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.29
Consensus pattern (196 bp):
CTTTAAAAATTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAAATCCATAT
TGAAAAAGGCTCATCTCAACAGAGACTCAACAACTTTAAAAATCTCATCTTGAAAAAAGCTCATA
TCAGCAGAGACTTAATAACTTTAAAAATCTCATTTTGAAAAAGCTCATTTCAGCAGAGGCTTAAC
A
Found at i:3691289 original size:43 final size:43
Alignment explanation
Indices: 3691230--3691384 Score: 147
Period size: 43 Copynumber: 3.6 Consensus size: 43
3691220 TCAAAAAGCC
*
3691230 TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCCATA
1 TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCCTTA
* ** * *
3691273 TTTATTTTTTAAAGTTGTT-ATAACT-TTACTTAGAGGAGCTTTA
1 TTTATTTTTCAAAGTTGTTGA-GCCTCTGA-TTAGAGGAGCCTTA
* * **
3691316 TTTATTTCTT--AAGTTGTTGTGCCTCTGCTTAGAAAAGCCTTTA
1 TTTATTT-TTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCC-TTA
3691359 TTTACTTTTTCAAAGTTGTTGAGCCT
1 TTTA-TTTTTCAAAGTTGTTGAGCCT
3691385 TTATTTACTT
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
42 21 0.24
43 49 0.56
44 5 0.06
45 13 0.15
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (43 bp):
TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCCTTA
Found at i:3691414 original size:28 final size:29
Alignment explanation
Indices: 3691350--3691420 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
3691340 CTGCTTAGAA
* * **
3691350 AAGCCTTTATTTACTTTTTCAAAGTTGTT
1 AAGCCTTTATTTACTTTTCCAAAATCATT
*
3691379 GAGCCTTTATTTACTTTTCCAAAATCATT
1 AAGCCTTTATTTACTTTTCCAAAATCATT
* *
3691408 AAGCTTTTGTTTA
1 AAGCCTTTATTTA
3691421 AAGGAGCTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49
Consensus pattern (29 bp):
AAGCCTTTATTTACTTTTCCAAAATCATT
Found at i:3691702 original size:5 final size:5
Alignment explanation
Indices: 3691692--3691748 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
3691682 AAATTATTTA
*
3691692 TTATT TTA-T TTA-T TTATTT TTATTT TTATT TT-TT TAGATT TTATT
1 TTATT TTATT TTATT TTA-TT TTA-TT TTATT TTATT T-TATT TTATT
3691737 TTATT TTATT TT
1 TTATT TTATT TT
3691749 GATGATTATC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
4 11 0.24
5 22 0.48
6 13 0.28
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:3691706 original size:16 final size:16
Alignment explanation
Indices: 3691685--3691726 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3691675 TAAGCCTAAA
3691685 TTATTTATTATTT-TAT
1 TTATTTATT-TTTATAT
*
3691701 TTATTTATTTTTATTT
1 TTATTTATTTTTATAT
3691717 TTATTT-TTTT
1 TTATTTATTTT
3691727 AGATTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTATTTATTTTTATAT
Found at i:3691710 original size:20 final size:19
Alignment explanation
Indices: 3691685--3691747 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 19
3691675 TAAGCCTAAA
3691685 TTATTTATTATTTTATTTAT
1 TTATTT-TTATTTTATTTAT
*
3691705 TTATTTTTATTTTTATTTTT
1 TTATTTTTA-TTTTATTTAT
*
3691725 TTAGATTTTATTTTATTTTAT
1 TTA-TTTTTATTTTA-TTTAT
3691746 TT
1 TT
3691748 TGATGATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.08
20 23 0.62
21 11 0.30
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TTATTTTTATTTTATTTAT
Found at i:3692770 original size:8 final size:8
Alignment explanation
Indices: 3692757--3692783 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3692747 GAAATTTGGG
3692757 AAAAAATA
1 AAAAAATA
3692765 AAAAAATA
1 AAAAAATA
3692773 AAAAAATA
1 AAAAAATA
3692781 AAA
1 AAA
3692784 TATTTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:3698030 original size:26 final size:27
Alignment explanation
Indices: 3697962--3698034 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
3697952 TTAAGATGTT
*
3697962 AAATAATATTTTTTAAT-AAT-ATATAT
1 AAAT-ATATTTTTTAATAAATAATATAA
*** *
3697988 AAATATAGAATTAAATAAATAATA-AA
1 AAATATATTTTTTAATAAATAATATAA
3698014 AAATATATTTTTTAATAAATA
1 AAATATATTTTTTAATAAATA
3698035 GTAAGATCAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
25 8 0.22
26 25 0.69
27 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
AAATATATTTTTTAATAAATAATATAA
Found at i:3699808 original size:25 final size:23
Alignment explanation
Indices: 3699743--3699808 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 23
3699733 ATATTAAATC
* *
3699743 ATATCATATAAAAATTATCATGCAA
1 ATATCAT-TAATAA-TATCATCCAA
3699768 ATAT-ATT-ATAA-ATCATACCAA
1 ATATCATTAATAATATCAT-CCAA
3699789 ATATCATGTAATAATATCAT
1 ATATCAT-TAATAATATCAT
3699809 GCCTAGATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
20 5 0.15
21 7 0.21
22 5 0.15
23 2 0.06
24 6 0.18
25 9 0.26
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (23 bp):
ATATCATTAATAATATCATCCAA
Found at i:3699868 original size:17 final size:18
Alignment explanation
Indices: 3699847--3699938 Score: 75
Period size: 18 Copynumber: 5.1 Consensus size: 18
3699837 ATACATTAAT
3699847 TATCATGT-AATA-ATAA
1 TATCATGTAAATATATAA
*
3699863 TAATCAAGTAAATATATAA
1 T-ATCATGTAAATATATAA
*
3699882 TATCATATAAATATAT--
1 TATCATGTAAATATATAA
* *
3699898 TATCATGCAATAATATAAAA
1 TATCATG-TA-AATATATAA
*
3699918 TATCATATAAATATATCAA
1 TATCATGTAAATATAT-AA
3699937 TA
1 TA
3699939 ACTATTCATG
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.12
17 7 0.12
18 29 0.49
19 10 0.17
20 6 0.10
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (18 bp):
TATCATGTAAATATATAA
Found at i:3699886 original size:18 final size:18
Alignment explanation
Indices: 3699871--3699938 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
3699861 AATAATCAAG
3699871 TAAATATATAATATCATA
1 TAAATATATAATATCATA
*
3699889 TAAATATATTATCATGCA-A
1 TAAATATATAAT-AT-CATA
*
3699908 T-AATATAAAATATCATA
1 TAAATATATAATATCATA
3699925 TAAATATATCAATA
1 TAAATATAT-AATA
3699939 ACTATTCATG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
16 2 0.05
17 4 0.10
18 25 0.61
19 8 0.20
20 2 0.05
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (18 bp):
TAAATATATAATATCATA
Found at i:3699895 original size:16 final size:16
Alignment explanation
Indices: 3699876--3699932 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
3699866 TCAAGTAAAT
3699876 ATATAATATCATATAA
1 ATATAATATCATATAA
*
3699892 ATATATTATCATGCAATAA
1 ATATAATATCAT---ATAA
*
3699911 TATAAAATATCATATAA
1 -ATATAATATCATATAA
3699928 ATATA
1 ATATA
3699933 TCAATAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 15 0.45
17 4 0.12
19 4 0.12
20 10 0.30
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (16 bp):
ATATAATATCATATAA
Found at i:3702644 original size:6 final size:6
Alignment explanation
Indices: 3702633--3702694 Score: 60
Period size: 5 Copynumber: 10.7 Consensus size: 6
3702623 GTCTAATTGA
*
3702633 TTAAAT TTAAAT TT-AAT TTAAAAT TTAAAAT TT-AAT TTAAA- TTCAA-
1 TTAAAT TTAAAT TTAAAT TT-AAAT TT-AAAT TTAAAT TTAAAT TTAAAT
*
3702679 TTAAAT TTTAAT TTAA
1 TTAAAT TTAAAT TTAA
3702695 GATAAAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
5 18 0.38
6 18 0.38
7 12 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:3702665 original size:19 final size:18
Alignment explanation
Indices: 3702635--3702673 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
3702625 CTAATTGATT
3702635 AAATTTAAATTTAATTTA
1 AAATTTAAATTTAATTTA
3702653 AAATTTAAAATTTAATTTA
1 AAATTT-AAATTTAATTTA
3702672 AA
1 AA
3702674 TTCAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTTAAATTTAATTTA
Found at i:3702735 original size:46 final size:46
Alignment explanation
Indices: 3702629--3702755 Score: 127
Period size: 46 Copynumber: 2.7 Consensus size: 46
3702619 AGGAGTCTAA
* *
3702629 TTGATTAAATTTAAATTTAATTTAAAATTTAAA--ATTTAATTTAAAT
1 TTGATTAAATTT-AATTTAATATAAAAATTAAATTATTTAATTT-AAT
** *
3702675 TCAATTAAATTTTAATTTAAGATAAAAATTAAATTATTTAAATTT-AT
1 TTGATTAAA-TTTAATTTAATATAAAAATTAAATTATTT-AATTTAAT
*
3702722 TTGATTAAATTTAA-TTAATATATAAAAATAAATT
1 TTGATTAAATTTAATTTAATATA-AAAATTAAATT
3702756 TAATTTTTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
45 7 0.10
46 39 0.58
47 12 0.18
48 4 0.06
49 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (46 bp):
TTGATTAAATTTAATTTAATATAAAAATTAAATTATTTAATTTAAT
Found at i:3702843 original size:17 final size:17
Alignment explanation
Indices: 3702800--3702844 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3702790 TGTTTAAAAT
3702800 TAAATTTAAAATATTTTA
1 TAAA-TTAAAATATTTTA
*
3702818 TTAATTAAAATATTTTA
1 TAAATTAAAATATTTTA
3702835 -AAATATAAAA
1 TAAAT-TAAAA
3702845 ATTCAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 18 0.75
18 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTAAAATATTTTA
Found at i:3702889 original size:21 final size:21
Alignment explanation
Indices: 3702835--3702894 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
3702825 AAATATTTTA
*
3702835 AAATAT-AAAA-ATTC-AATT
1 AAATATAAAAATATTCAAATC
* *
3702853 AAATTTATAAACTATTCAAATC
1 AAATATA-AAAATATTCAAATC
*
3702875 AAATATAAAAATATTTAAAT
1 AAATATAAAAATATTCAAAT
3702895 TTGATTCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 5 0.16
20 3 0.09
21 15 0.47
22 9 0.28
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATAAAAATATTCAAATC
Found at i:3705082 original size:12 final size:13
Alignment explanation
Indices: 3705065--3705110 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
3705055 ACTTCAAATA
3705065 TTTTATTT-TTAT
1 TTTTATTTATTAT
3705077 TTTTATTTATT-T
1 TTTTATTTATTAT
*
3705089 ATTTATTTGATTAT
1 TTTTATTT-ATTAT
3705103 TTATTATT
1 TT-TTATT
3705111 CTTTAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 16 0.57
13 5 0.18
14 2 0.07
15 5 0.18
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTATTTATTAT
Found at i:3705087 original size:16 final size:18
Alignment explanation
Indices: 3705066--3705110 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
3705056 CTTCAAATAT
3705066 TTTATT-TTTATTT-TTA
1 TTTATTATTTATTTATTA
3705082 TTTATTTATTTATTTGATTA
1 TTTA-TTATTTATTT-ATTA
3705102 TTTATTATT
1 TTTATTATT
3705111 CTTTAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.16
17 2 0.08
18 7 0.28
19 5 0.20
20 7 0.28
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTATTATTTATTTATTA
Found at i:3705146 original size:16 final size:16
Alignment explanation
Indices: 3705115--3705148 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3705105 ATTATTCTTT
**
3705115 AAATATATTTTTATAA
1 AAATATATTTAAATAA
3705131 AAATATATTTAAATAA
1 AAATATATTTAAATAA
3705147 AA
1 AA
3705149 GCTTTACCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATATATTTAAATAA
Found at i:3711894 original size:18 final size:19
Alignment explanation
Indices: 3711853--3711903 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
3711843 TTATTAAAAC
*
3711853 ATAAATAATTAAATTGGTAAT
1 ATAAATAA--AAATTAGTAAT
*
3711874 ATAAA-AAAAATTAGTATT
1 ATAAATAAAAATTAGTAAT
3711892 ATAAATAAAAAT
1 ATAAATAAAAAT
3711904 AATAATCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 14 0.52
19 6 0.22
20 2 0.07
21 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
ATAAATAAAAATTAGTAAT
Found at i:3713301 original size:21 final size:20
Alignment explanation
Indices: 3713277--3713344 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
3713267 ATGAATAAGT
3713277 ATAAAAAAATATTATTGCAA
1 ATAAAAAAATATTATTGCAA
* *
3713297 CAT-AAATAATATTTTTGGCAA
1 -ATAAAAAAATATTATT-GCAA
*
3713318 TATAAAAAAATTATTATTACAA
1 -ATAAAAAAA-TATTATTGCAA
3713340 ATAAA
1 ATAAA
3713345 TAATAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.29
21 13 0.34
22 8 0.21
23 6 0.16
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (20 bp):
ATAAAAAAATATTATTGCAA
Found at i:3713309 original size:20 final size:19
Alignment explanation
Indices: 3713284--3713349 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 19
3713274 AGTATAAAAA
3713284 AATATTATTGCAACATAAAT
1 AATATTATTGCAA-ATAAAT
* *
3713304 AATATTTTTGGCAATATAAAAA
1 AATATTATT-GCAA-AT-AAAT
*
3713326 AATTATTATTACAAATAAAT
1 AA-TATTATTGCAAATAAAT
3713346 AATA
1 AATA
3713350 ATTTTAAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 13 0.35
21 8 0.22
22 8 0.22
23 6 0.16
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (19 bp):
AATATTATTGCAAATAAAT
Found at i:3713367 original size:18 final size:20
Alignment explanation
Indices: 3713322--3713368 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
3713312 TGGCAATATA
*
3713322 AAAAAATTATTATTACAAAT
1 AAAAAATAATTATTACAAAT
* *
3713342 AAATAATAATT-TTA-AACT
1 AAAAAATAATTATTACAAAT
3713360 AAAAAATAA
1 AAAAAATAA
3713369 GTGTTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 11 0.48
19 3 0.13
20 9 0.39
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAATAATTATTACAAAT
Found at i:3713805 original size:15 final size:16
Alignment explanation
Indices: 3713776--3713805 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3713766 ATTAGTATTA
3713776 TAAATAAAAATAATTC
1 TAAATAAAAATAATTC
3713792 TAAATAAAAA-AATT
1 TAAATAAAAATAATT
3713806 AAGTGTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAATAAAAATAATTC
Found at i:3713974 original size:939 final size:932
Alignment explanation
Indices: 3712226--3714001 Score: 2048
Period size: 939 Copynumber: 1.9 Consensus size: 932
3712216 TATAAAAAGG
* * * * * *
3712226 TAAGAATAGTTGTAAAATTGGTGTCACTTGACTTAAAATATATTAGAATTGTCGTAACACCTTGA
1 TAAGAATAGTTGTAAAATTAGTATCACTTGACATAAAATAGATTAGAAGTGTCATAACACCTTGA
* * * * * * *
3712291 CAAAGAGTTATAATAAATTTAAACGTAATAAAAAATAAGAATAAGTGTAAAAAATATATTGTTAT
66 AAAAAAATTATAATAAATTTAAACATAATAAAAAATAAGAATAAGTATAAAAAATATATTATTAC
* *
3712356 AACATAAATAATATTTTTGGCAATGTAAAAAAATTATTATTACAAATAATTAATAATTCTAAACA
131 AACATAAATAATATTTTTGGCAATATAAAAAAATTATTATTACAAATAAATAATAATTCTAAACA
*
3712421 AAAAAAAGTGTTAGTATAAAAAAAATGTGAGAGTAATCATAAAATTAGTATTATTTAGAGTAAAA
196 AAAAAAAGTGTTAATATAAAAAAAATGTGAGAGTAATCATAAAATTAGTATTATTTAGAGTAAAA
* ** *
3712486 TGATTAAAAGTATTGTAACACCTTTAAAAAAAAAAAAGTAGTAATAGTTTTAAACAAAATGAAAG
261 TAATTAAAAGTATCATAACACCTTT---AAAAAAAAAGTAGTAATAATTTTAAACAAAATGAAAG
* * * * * *
3712551 GTAACAACAAGCATAAAAAGATGTTACTAGAAGATAAATAATTAAATTAGCAATACAAAAGAACT
323 ATAACAACAAGAAAAAAAAAATGTTACTAGAACATAAATAATTAAATTAGCAATACAAAAAAACT
* * ** *
3712616 ATTATTACAAATAAGAAATAATTTTAAATAAAAAGTTAAGAGTTAATGTAAAATGGTGAGAATTA
388 ATTATTACAAATAAAAAATAATTTT--ATAAAAAGATAAGAGTTAACATAAAATGGTGAGAATAA
* * * * ** *
3712681 TCGTAAAATTGATATTATTTAACGTAAAATAGTTAGAAATATCGTTCCACTTTAAGAAAATTTTG
451 TCATAAAATTGATATTATTTAACGTAAAATAGTTAGAAATATCGTTACACCTTAAAAAAAAATTA
* * ** *
3712746 CAATAATTCTAAACGGAATAAAAATAATAATAAATGTAAAAATATATTATTGAAACGTAATAAAT
516 CAATAATTCTAAACGGAATAAAAATAACAACAAACATAAAAAGATATTATTGAAACGTAATAAAT
* * *
3712811 TAGTAACATGAAAAAAATTAGTAGTATAAATAAAAAATAATAATTCAATTAAAAAATAAGTGTTA
581 TAGTAACATAAAAAAAATTAGTAGTATAAATAAAAAATAAT-ATTAAATAAAAAAATAAGTGTTA
** * ** *
3712876 ACTTAAAAATGTGAAAATAATCGTAAAATTGATATCGTTCGGCATAAAATATATTAGAACTGTCG
645 AAGTAAAAA---GAAAATAATCATAAAATTGATATAATTCGGCATAAAATATATTAGAACTGTCA
* * * *
3712941 TAATACTTTAAGAAAAACTTATGATTATTCTAAATATAATAAAAGATAAGAATAAGCGTAAAAGA
707 TAATACTTTAAGAAAAACTTATAATTATTCTAAATATAATAAAAGATAACAACAAGCATAAAAGA
* * * *
3713006 TTTTATTGTAGCATAAATATAAGTTGACAATATAAAAAATTATTATTATAAATAAAAGTAATTCT
772 TTTTATTATAACATAAATATAAATTGACAACATAAAAAATTATTATTATAAATAAAAGTAATTCT
3713071 AAAAAAAAAAATGCATGTTAGCATAAAAAAGTGTTATAATTGAAATTTTGGAATCATTCAATGTA
837 AAAAAAAAAAATGCATGTTAGCATAAAAAAGTGTTATAATTGAAATTTTGGAATCATTCAATGTA
3713136 AAATATGTTACAATGTCATAACATAAAATTA
902 AAATATGTTACAATGTCATAACATAAAATTA
* * * * *
3713167 TAAGAATAGTTGTAAAATTAGTATCATTTGGCATAAATTGGATTATAAGTGTCATAACACCTT-A
1 TAAGAATAGTTGTAAAATTAGTATCACTTGACATAAAATAGATTAGAAGTGTCATAACACCTTGA
* * * * * *
3713231 AAAAAAATTGTGATAATTTTAAACATAATAAAAAGTATGAATAAGTATAAAAAA-ATATTATTGC
66 AAAAAAATTATAATAAATTTAAACATAATAAAAAATAAGAATAAGTATAAAAAATATATTATTAC
*
3713295 AACATAAATAATATTTTTGGCAATATAAAAAAATTATTATTACAAATAAATAATAATTTTAAACT
131 AACATAAATAATATTTTTGGCAATATAAAAAAATTATTATTACAAATAAATAATAATTCTAAAC-
** ** * * *
3713360 AAAAAATAAGTGTTAATATAAAAAAGGTG-GA-AGTAATTGTAACATT-GATATTATTTGGCGTA
195 AAAAAA-AAGTGTTAATATAAAAAAAATGTGAGAGTAATCATAAAATTAG-TATTATTTAGAGTA
* * * *
3713422 AAATAATTAAACGTATCATAACACCTTT-AAGAAAAAGTTA-TGATAATTTTAAACATAATGAAA
258 AAATAATTAAAAGTATCATAACACCTTTAAAAAAAAAG-TAGTAATAATTTTAAACAAAATGAAA
* * * * *
3713485 TATAACAACAAGTGTAAAAAAAAAAAT-TTATTATAACATAAATAATTAACTT-GATAATGTA-A
322 GATAACAACAA--G--AAAAAAAAAATGTTACTAGAACATAAATAATTAAATTAG-CAA--TACA
* *
3713547 AAAAATTATTATTATTATAAATAAAAAATAATTTT-TAAAAA-ATAAGAGTTAACATAAAATGGT
380 AAAAA--ACTATTATTACAAATAAAAAATAATTTTATAAAAAGATAAGAGTTAACATAAAATGGT
* * * *
3713610 GAGAATAATCATAAAATTGATATTATTTTATGTAAAATAGTTTGAAATATTGTTACACCTTAACA
443 GAGAATAATCATAAAATTGATATTATTTAACGTAAAATAGTTAGAAATATCGTTACACCTTAA-A
* * * *
3713675 AAAAAATTATAATAATTTTAAACGTAATGAAAAGTAACAACAAACATAAAAAGATATTATTGAAA
507 AAAAAATTACAATAATTCTAAACGGAAT-AAAAATAACAACAAACATAAAAAGATATTATTGAAA
* *
3713740 CTTAATAAATTTA-TAACATAAAAAAAATTAGTATTATAAAT-AAAAATAAT-TCTAAATAAAAA
571 CGTAATAAA-TTAGTAACATAAAAAAAATTAGTAGTATAAATAAAAAATAATAT-TAAATAAAAA
* * * * **
3713802 AATTAAGTGTTAAAGTAAAAA-AAAATGATCATTAAATTGGTATAATTTGGTGTAAAATACGT-T
634 AA-TAAGTGTTAAAGTAAAAAGAAAATAATCATAAAATTGATATAATTCGGCATAAAATA--TAT
* * *
3713865 TA-AAGTGTTATAATAC-TTAA-AATAAAGTTGTGATAATTAATTCTAAATATAATAAAATG-TA
696 TAGAACTGTCATAATACTTTAAGAA-AAA-CT-T-ATAATT-ATTCTAAATATAATAAAA-GATA
* * *
3713926 ACAACAAGTATAATAA-ATTTTATTATAACGTAAATAATTAAATTGACAACATAAAATATTATTA
755 ACAACAAGCATAA-AAGATTTTATTATAACATAAAT-A-TAAATTGACAACATAAAAAATTATTA
3713990 TTATAAATAAAA
817 TTATAAATAAAA
3714002 AATAATTTTA
Statistics
Matches: 694, Mismatches: 112, Indels: 60
0.80 0.13 0.07
Matches are distributed among these distances:
932 2 0.00
933 7 0.01
934 41 0.06
935 41 0.06
936 9 0.01
937 131 0.19
938 81 0.12
939 228 0.33
940 58 0.08
941 96 0.14
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.32
Consensus pattern (932 bp):
TAAGAATAGTTGTAAAATTAGTATCACTTGACATAAAATAGATTAGAAGTGTCATAACACCTTGA
AAAAAAATTATAATAAATTTAAACATAATAAAAAATAAGAATAAGTATAAAAAATATATTATTAC
AACATAAATAATATTTTTGGCAATATAAAAAAATTATTATTACAAATAAATAATAATTCTAAACA
AAAAAAAGTGTTAATATAAAAAAAATGTGAGAGTAATCATAAAATTAGTATTATTTAGAGTAAAA
TAATTAAAAGTATCATAACACCTTTAAAAAAAAAGTAGTAATAATTTTAAACAAAATGAAAGATA
ACAACAAGAAAAAAAAAATGTTACTAGAACATAAATAATTAAATTAGCAATACAAAAAAACTATT
ATTACAAATAAAAAATAATTTTATAAAAAGATAAGAGTTAACATAAAATGGTGAGAATAATCATA
AAATTGATATTATTTAACGTAAAATAGTTAGAAATATCGTTACACCTTAAAAAAAAATTACAATA
ATTCTAAACGGAATAAAAATAACAACAAACATAAAAAGATATTATTGAAACGTAATAAATTAGTA
ACATAAAAAAAATTAGTAGTATAAATAAAAAATAATATTAAATAAAAAAATAAGTGTTAAAGTAA
AAAGAAAATAATCATAAAATTGATATAATTCGGCATAAAATATATTAGAACTGTCATAATACTTT
AAGAAAAACTTATAATTATTCTAAATATAATAAAAGATAACAACAAGCATAAAAGATTTTATTAT
AACATAAATATAAATTGACAACATAAAAAATTATTATTATAAATAAAAGTAATTCTAAAAAAAAA
AATGCATGTTAGCATAAAAAAGTGTTATAATTGAAATTTTGGAATCATTCAATGTAAAATATGTT
ACAATGTCATAACATAAAATTA
Found at i:3715070 original size:10 final size:10
Alignment explanation
Indices: 3715025--3715072 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
3715015 GTTATATTAT
* *
3715025 TATTATAATT
1 TATTATGATA
3715035 TATTATGATA
1 TATTATGATA
* *
3715045 TATCATGAGA
1 TATTATGATA
3715055 TATTATGATA
1 TATTATGATA
*
3715065 TCTTATGA
1 TATTATGA
3715073 CCTTAGAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (10 bp):
TATTATGATA
Found at i:3720037 original size:24 final size:24
Alignment explanation
Indices: 3720010--3720057 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3720000 AATTAATTAC
* * *
3720010 ATTAAATATTATTCATTAAATAAA
1 ATTAAAAAATATTCAATAAATAAA
*
3720034 ATTAAAAAATATTTAATAAATAAA
1 ATTAAAAAATATTCAATAAATAAA
3720058 TACAATTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATTAAAAAATATTCAATAAATAAA
Found at i:3720868 original size:216 final size:215
Alignment explanation
Indices: 3720338--3720868 Score: 521
Period size: 216 Copynumber: 2.4 Consensus size: 215
3720328 AAATTAATTC
* * *
3720338 TAAAACAATAAATAAGTGTTAACATAAAAATATAAGAATAATCATAAAATTAATATCATTTAACG
1 TAAACCAAAAAATAAGTGTTAACATAAAAA-ATAAGAATAATCATAAAATT-ATAT-TTTTAACG
* * * *
3720403 TAAAATAAGTTAAAAGTATCATAACACCCTAACAAAGAGTTGTAATAATTATAAACGTAATAAAA
63 TAAAAT-AGTTAAAAGTATCGTAATACCTTAACAAAGAATTGTAATAATTATAAACGTAATAAAA
*** **
3720468 AGTAATAACAAGTATAAAAAGATATTATTGTAACAAAAATAATTAAATTGGTAATATAAAAGAAA
127 AGTAAT-A-AAGTATAAAAAGATATTATAAAAACAAAAATAATTAAATTAATAATATAAAAGAAA
* *
3720533 TATTATTACAAATAAAAAAATAATTT
190 TAGTATTACAAATAAAAAAATAATCT
* ** * * *
3720559 TAAACCAAAATATAAAAGTTAATATAAAAAAGTAAGAATAATCATAAAATTAGTATTATTTGACA
1 TAAACCAAAAAATAAGTGTTAACATAAAAAA-TAAGAATAATCATAAAATTA-TATT-TTTAACG
* * * * * * * *
3720624 TAAAATAGTTACAAGTATTGTTATACCTTAATAAA-ACATTGTGATAATTCTAAATGTAATGAAA
63 TAAAATAGTTAAAAGTATCGTAATACCTTAACAAAGA-ATTGTAATAATTATAAACGTAATAAAA
* * *
3720688 AGTAAT-AAGTGTAAAAA-ATATTATAAAAACATAAATAATTAATTTAATAATATAAAA-AAATT
127 AGTAATAAAGTATAAAAAGATATTATAAAAACAAAAATAATTAAATTAATAATATAAAAGAAA-T
**
3720750 AGTATTATTAATAAAAATAATAATCT
191 AGTATTACAAATAAAAA-AATAATCT
* * * * * *
3720776 TACACCAAAAAATATGTGTTAACGTAAAAAGATAAAAATAATCATAAAATTGATATTTTTTATGT
1 TAAACCAAAAAATAAGTGTTAACATAAAAA-ATAAGAATAATCATAAAATT-ATATTTTTAACGT
* * * *
3720841 AAAATGGTTAGACGTGTCGTAATACCTT
64 AAAATAGTTAAAAGTATCGTAATACCTT
3720869 TAAAAAAAAG
Statistics
Matches: 252, Mismatches: 50, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
215 3 0.01
216 75 0.30
217 62 0.25
218 2 0.01
219 1 0.00
220 52 0.21
221 57 0.23
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.31
Consensus pattern (215 bp):
TAAACCAAAAAATAAGTGTTAACATAAAAAATAAGAATAATCATAAAATTATATTTTTAACGTAA
AATAGTTAAAAGTATCGTAATACCTTAACAAAGAATTGTAATAATTATAAACGTAATAAAAAGTA
ATAAAGTATAAAAAGATATTATAAAAACAAAAATAATTAAATTAATAATATAAAAGAAATAGTAT
TACAAATAAAAAAATAATCT
Found at i:3721471 original size:225 final size:219
Alignment explanation
Indices: 3721135--3721640 Score: 511
Period size: 225 Copynumber: 2.3 Consensus size: 219
3721125 ACATATTGAC
* * * * * * *
3721135 AAAAAGTTATAATAAATTTAAACGTAATAAAAAATAAGAACAAGTGTAAAACATATGTTGTTATA
1 AAAAAGTTATAATAATTTTAAACATAAT-AAAAGTAACAACAAGTGTAAAA-AGATATTATTATA
** * * **
3721200 ACATAAATAATATTTTTGACAAAGTAAAAGAATTATTATTACAAATAATTAATAATTCTAAACCA
64 ACATAAATAATAAATTAGACAAAGTAAAAGAACTATTATTACAAATAAGAAATAATT-TAAACCA
* * *
3721265 AAAAAATAAGTGTTAGTATAAAAAAAAGGTGA-AAGTAATCATAAAATT-AGTATTATTTGACGT
128 AAAAAATAAGAGTTA--AT-AAAAAAAGGTGAGAA-TAATCATAAAATTGA-TATTATTTAACAT
* *
3721328 AAAATGGTTA-AAAGAATTATAACACCTTTAAGA
188 AAAATAGTTAGAAA-AATCATAACACCTTTAA-A
* *
3721361 AAAAAGTTATAATATTTTTAAACATAATAAAGGGTAACAACAAGTGTAAAAAGATATTATTATAA
1 AAAAAGTTATAATAATTTTAAACATAATAAA-AGTAACAACAAGTGTAAAAAGATATTATTATAA
* * **
3721426 TATAAATAATTAAATTAG-CAACA-TAAAAGAACTATTATTACAAATAAGAAATAATTTTAAGTA
65 CATAAATAA-TAAATTAGACAA-AGTAAAAGAACTATTATTACAAATAAGAAATAATTTAAACCA
* * * * *
3721489 AAAAATTAAGAGTTAATATAAAACGGTGAGAATTATCGTAAAATTGATATTATTTAACATAAAAT
128 AAAAAATAAGAGTTAATAAAAAAAGGTGAGAATAATCATAAAATTGATATTATTTAACATAAAAT
* * * *
3721554 AGTTAGAAATATCGTTACACTTTTAAA
193 AGTTAGAAAAATCATAACACCTTTAAA
* * * *
3721581 AAAAA-TTGTAATAATTCTAAACATAATGAAAAGTAACAACAAATGTAAAAAGTTATTATT
1 AAAAAGTTATAATAATTTTAAACATAAT-AAAAGTAACAACAAGTGTAAAAAGATATTATT
3721641 GAAATGTAAT
Statistics
Matches: 234, Mismatches: 39, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
219 45 0.19
220 9 0.04
221 53 0.23
222 8 0.03
224 17 0.07
225 55 0.24
226 47 0.20
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (219 bp):
AAAAAGTTATAATAATTTTAAACATAATAAAAGTAACAACAAGTGTAAAAAGATATTATTATAAC
ATAAATAATAAATTAGACAAAGTAAAAGAACTATTATTACAAATAAGAAATAATTTAAACCAAAA
AAATAAGAGTTAATAAAAAAAGGTGAGAATAATCATAAAATTGATATTATTTAACATAAAATAGT
TAGAAAAATCATAACACCTTTAAA
Found at i:3721760 original size:214 final size:220
Alignment explanation
Indices: 3721349--3721774 Score: 469
Period size: 214 Copynumber: 2.0 Consensus size: 220
3721339 AAGAATTATA
* * * *
3721349 ACACCTTTAAGAAAAAAGTTATAATATTTTTAAACATAATAAAGGGTAACAACAAGTGTAAAAAG
1 ACACCTTTAAGAAAAAAGTTATAATAATTCTAAACATAATAAAGAGTAACAACAAATGTAAAAAG
* * *
3721414 ATATTATTATAATATAAATAATTAAATTAGCAACATAAAAGAACTATTATTACAAATAAGAAATA
66 ATATTATTAGAATAT-AATAATTAAATTAGCAACATAAAAGAACTAGTATTACAAATAAAAAATA
* * * * * *
3721479 ATTTTAAGTAAAAAATTAAGAGTTAATATAAAACGGTGAGAATTATCGTAAAATTGATATTATTT
130 ATTTCAAGTAAAAAATTAAGAGTTAATATAAAAAGATGAGAATAATCATAAAATTGATATCATTT
3721544 AACAT-AAAATAGTTAGAAATATCGTT
195 AACATAAAAATA-TTAGAAATATCGTT
* *
3721570 ACACTTTTAA-AAAAAA-TTGTAATAATTCTAAACATAATGAAA-AGTAACAACAAATGTAAAAA
1 ACACCTTTAAGAAAAAAGTTATAATAATTCTAAACATAAT-AAAGAGTAACAACAAATGTAAAAA
* * * * * * *
3721632 GTTATTATT-GAA-AT-GTAA-TAAATTAGTAGCATAAAA-AATTGGTATTATAAATAAAAAATA
65 GATATTATTAGAATATAATAATTAAATTAGCAACATAAAAGAACTAGTATTACAAATAAAAAATA
* * * * *
3721692 ATAATTCAA-TCAAAAAA-TAAGTGTTAATGTAAAAATATGAGAATAATTATAAAATTGGTATCA
130 AT--TTCAAGT-AAAAAATTAAGAGTTAATATAAAAAGATGAGAATAATCATAAAATTGATATCA
*
3721755 TTTAACGTAAAAATATTAGA
192 TTTAACATAAAAATATTAGA
3721775 TGTGTCAAAA
Statistics
Matches: 172, Mismatches: 28, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
213 21 0.12
214 65 0.38
215 19 0.11
217 2 0.01
218 2 0.01
219 45 0.26
220 9 0.05
221 9 0.05
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (220 bp):
ACACCTTTAAGAAAAAAGTTATAATAATTCTAAACATAATAAAGAGTAACAACAAATGTAAAAAG
ATATTATTAGAATATAATAATTAAATTAGCAACATAAAAGAACTAGTATTACAAATAAAAAATAA
TTTCAAGTAAAAAATTAAGAGTTAATATAAAAAGATGAGAATAATCATAAAATTGATATCATTTA
ACATAAAAATATTAGAAATATCGTT
Found at i:3722168 original size:22 final size:21
Alignment explanation
Indices: 3722142--3722193 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
3722132 TTATTGTAAC
* * *
3722142 ATAAATAATTTTTTTTTGCAA
1 ATAAATAATTTATTATTACAA
*
3722163 TATAAAAAATTTATTATTACAA
1 -ATAAATAATTTATTATTACAA
3722185 ATAAATAAT
1 ATAAATAAT
3722194 AATTCTAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAAATAATTTATTATTACAA
Found at i:3727541 original size:25 final size:25
Alignment explanation
Indices: 3727486--3727614 Score: 64
Period size: 28 Copynumber: 5.0 Consensus size: 25
3727476 CACATCTTTC
* * * *
3727486 AGCAAACCACTCAGAAATACCATTC
1 AGCAAAACATTCAAAAATACCATTT
* *
3727511 ATCAAAACATTCAAAAATACTATTT
1 AGCAAAACATTCAAAAATACCATTT
* *
3727536 AGC-AAACTATTC-AACATACGATTT
1 AGCAAAAC-ATTCAAAAATACCATTT
* * * *
3727560 AGCATACCAATATCATACAATACCATTC
1 AGCAAAAC-AT-TCA-AAAATACCATTT
*
3727588 AGCAAAACAATATCACATAATACCATT
1 AGCAAAAC-AT-TCA-AAAATACCATT
3727615 CGACAAAATA
Statistics
Matches: 79, Mismatches: 20, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
24 17 0.22
25 29 0.37
26 2 0.03
28 31 0.39
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.25
Consensus pattern (25 bp):
AGCAAAACATTCAAAAATACCATTT
Found at i:3727598 original size:28 final size:27
Alignment explanation
Indices: 3727501--3727630 Score: 92
Period size: 28 Copynumber: 4.9 Consensus size: 27
3727491 ACCACTCAGA
* *
3727501 AATACCATTCATCAAAAC-AT-TCAAA
1 AATACCATTCAGCAAAACAATATCAAC
* * *
3727526 AATACTATTTAGC-AAACTAT-TCAAC
1 AATACCATTCAGCAAAACAATATCAAC
* * * *
3727551 -ATACGATTTAGCATACCAATATCATAC
1 AATACCATTCAGCAAAACAATATCA-AC
*
3727578 AATACCATTCAGCAAAACAATATCACAT
1 AATACCATTCAGCAAAACAATATCA-AC
*
3727606 AATACCATTC-GACAAAATAATATCA
1 AATACCATTCAG-CAAAACAATATCA
3727631 CATAACAAGG
Statistics
Matches: 84, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
24 15 0.18
25 20 0.24
26 3 0.04
27 3 0.04
28 43 0.51
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (27 bp):
AATACCATTCAGCAAAACAATATCAAC
Found at i:3727631 original size:28 final size:28
Alignment explanation
Indices: 3727567--3727635 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
3727557 TTTAGCATAC
* *
3727567 CAATATCATACAATACCATTCAGCAAAA
1 CAATATCACATAATACCATTCAGCAAAA
3727595 CAATATCACATAATACCATTC-GACAAAA
1 CAATATCACATAATACCATTCAG-CAAAA
*
3727623 TAATATCACATAA
1 CAATATCACATAA
3727636 CAAGGTTCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (28 bp):
CAATATCACATAATACCATTCAGCAAAA
Found at i:3727649 original size:28 final size:28
Alignment explanation
Indices: 3727583--3727649 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
3727573 CATACAATAC
* *
3727583 CATTCAGCAAAACAATATCACATAATAC
1 CATTCAGCAAAACAATATCACATAACAA
*
3727611 CATTC-GACAAAATAATATCACATAACAA
1 CATTCAG-CAAAACAATATCACATAACAA
**
3727639 GGTTCAGCAAA
1 CATTCAGCAAA
3727650 TCACATTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.03
28 30 0.94
29 1 0.03
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.21
Consensus pattern (28 bp):
CATTCAGCAAAACAATATCACATAACAA
Found at i:3728474 original size:186 final size:186
Alignment explanation
Indices: 3728131--3728572 Score: 536
Period size: 186 Copynumber: 2.4 Consensus size: 186
3728121 CGCCTTTGAT
* *
3728131 AATTTTGAA-AAAAAAAT-TTGAAGGCA-TT-TTCAATAAACAACCGCCTTCAATAATTATGTAC
1 AATTTT-AAGAAAAAATTATTGAAGGCATTTGTTC--TAAAAAACCGCCTTCAATAATTATGTAC
* * * * *
3728192 AAAAATTAAAAAAAATTAGGGAAGGCATTTCTCTAGAATAAACGCTTTCACTAACCATCTCAAAA
63 ATAAATTAGAAAAAATTAGGGAAGGCATTTCTCAAGAATAAACACATTCACTAACCATCTCAAAA
* * *
3728257 TTTGAGTTATGGAATGTTGAAGACGTTTTTCACTAGAAGACG-CTTTTAATAATCTCAAA
128 TTTGAGTTATGAAATATTGAAGACATTTTTCACTAGAAGACGTC-TTTAATAATCTCAAA
* * * * *
3728316 AATTTTAAGAGAAACTTATTGAAGGCATTTGTTCTCAAGAAA-CGCCTTTAATAATTATGTACTT
1 AATTTTAAGAAAAAATTATTGAAGGCATTTGTTCT-AAAAAACCGCCTTCAATAATTATGTACAT
** ** ** *
3728380 AAATTAGAAGCAATTATTGAAGGTGTTTTTCAAGAATAAACACATTCACTAACCATCTCAAAATT
65 AAATTAGAAAAAATTAGGGAAGGCATTTCTCAAGAATAAACACATTCACTAACCATCTCAAAATT
* * *
3728445 TGAGTTGTGAAATATTGAAGGCATTTTTCACTGGAAGACGTCTTTAATAATCTCAAA
130 TGAGTTATGAAATATTGAAGACATTTTTCACTAGAAGACGTCTTTAATAATCTCAAA
* * * *
3728502 AATTTTAAGAAAAAATTATTGAAGGCGTTTGTTCTAAAAAACCACCTTCAATAATTATGCACGTA
1 AATTTTAAGAAAAAATTATTGAAGGCATTTGTTCTAAAAAACCGCCTTCAATAATTATGTACATA
3728567 AATTAG
66 AATTAG
3728573 TAATCTAAAA
Statistics
Matches: 217, Mismatches: 33, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
184 2 0.01
185 16 0.07
186 189 0.87
187 7 0.03
188 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (186 bp):
AATTTTAAGAAAAAATTATTGAAGGCATTTGTTCTAAAAAACCGCCTTCAATAATTATGTACATA
AATTAGAAAAAATTAGGGAAGGCATTTCTCAAGAATAAACACATTCACTAACCATCTCAAAATTT
GAGTTATGAAATATTGAAGACATTTTTCACTAGAAGACGTCTTTAATAATCTCAAA
Found at i:3728966 original size:186 final size:185
Alignment explanation
Indices: 3728735--3729419 Score: 767
Period size: 186 Copynumber: 3.7 Consensus size: 185
3728725 TATTTCGCTA
** * *
3728735 GAATAAACGCCTTCACTAACCGTCTCAAAATTTGAGTTATGAAATATTAAATGCGTTTTTCACTG
1 GAATAAATACCTT-ACTAACCGTCTCAAAATTTGAGTTATGAAATATTAAAGGCATTTTTCACTG
* *
3728800 GAAGAAGCCTTTAATAATCTCAAAAATTTTTAA-AAAAAATTATTGAAGCTGTTTGTTCTCAAAA
65 AAAGACGCCTTTAATAATCTCAAAAATTTTTAAGAAAAAATTATTGAAGC-GTTTGTTCTCAAAA
* * *
3728864 AATACCTTTAATAATTATGTACGTAAATTAGAAGAAATTAGTGATGACGTTTTTCTC
129 AATACCTTTAATAATTATGCACGTAAATTAGAAGAAATTAGTGAAGACATTTTTCTC
* * * * *
3728921 GAATAAATACCTTATTTAACCGTCTCAAAATTTAAGTTGTGAAATATTGAAGACATTTTTCACTG
1 GAATAAATACCTTA-CTAACCGTCTCAAAATTTGAGTTATGAAATATTAAAGGCATTTTTCACTG
* * *
3728986 AAAGATGCCTTTAATAATCCCAAAAA-TTTTAAGAAAAAATTATTGAAGGTGTTTGTTCTC-AAA
65 AAAGACGCCTTTAATAATCTCAAAAATTTTTAAGAAAAAATTATTGAA-GCGTTTGTTCTCAAAA
* * *
3729049 AA-ACGCTTTCAATAATTATGCACATAAATTAGAA-AGAATTAGTGAAGATATTTTTCTA
129 AATAC-CTTT-AATAATTATGCACGTAAATTAGAAGA-AATTAGTGAAGACATTTTTCTC
** * * * * *
3729107 GAATAAACGCCTTCACTAACCATCTCAAAATTTGAGTTATAAAATATTGAAGGTATTTTTCATTG
1 GAATAAATACCTT-ACTAACCGTCTCAAAATTTGAGTTATGAAATATTAAAGGCATTTTTCACTG
* * * * * *
3729172 AAAGACGTCTTTAATAATCTCTAAATTTTTTTA-AAAAAATTATTAAAAGCGTTTGTTCTTAAAA
65 AAAGACGCCTTTAATAATCTCAAAAATTTTTAAGAAAAAATTATT-GAAGCGTTTGTTCTCAAAA
* * * * *
3729236 AATATCTTCAATAATTATGCATGTAAATTAGAATG-AATGAGTGAAGGCATTTTTCTAC
129 AATACCTTTAATAATTATGCACGTAAATTAGAA-GAAATTAGTGAAGACATTTTTCT-C
* * * * * *
3729294 -AATAAGTACCTCCACTAACTGTCTCAAAATTTGAGTTGTGAAATATTAAAGGCGTTTTTCATTG
1 GAATAAATACCT-TACTAACCGTCTCAAAATTTGAGTTATGAAATATTAAAGGCATTTTTCACTG
* * *
3729358 AAAGACGCCTTTAATAAT-TCAAAAAATTTTAAGAGAAAATTATTGAAGGCGTTTGTTTTCAA
65 AAAGACGCCTTTAATAATCTCAAAAATTTTTAAGAAAAAATTATTGAA-GCGTTTGTTCTCAA
3729420 GATATGCCTT
Statistics
Matches: 416, Mismatches: 66, Indels: 34
0.81 0.13 0.07
Matches are distributed among these distances:
184 2 0.00
185 29 0.07
186 367 0.88
187 17 0.04
188 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (185 bp):
GAATAAATACCTTACTAACCGTCTCAAAATTTGAGTTATGAAATATTAAAGGCATTTTTCACTGA
AAGACGCCTTTAATAATCTCAAAAATTTTTAAGAAAAAATTATTGAAGCGTTTGTTCTCAAAAAA
TACCTTTAATAATTATGCACGTAAATTAGAAGAAATTAGTGAAGACATTTTTCTC
Found at i:3729168 original size:372 final size:372
Alignment explanation
Indices: 3728702--3729419 Score: 985
Period size: 372 Copynumber: 1.9 Consensus size: 372
3728692 TTACGTATAA
* * *
3728702 AAATTAAAAATAATTAGTGAAGGTATTTCGCTAGAATAAACGCCTTCACTAACCGTCTCAAAATT
1 AAATTAAAAAGAATTAGTGAAGATATTTCGCTAGAATAAACGCCTTCACTAACCATCTCAAAATT
* * * *
3728767 TGAGTTATGAAATATTAAATGCGTTTTTCACTGGAAGAAGCCTTTAATAATCTCAAAAATTTTTA
66 TGAGTTATAAAATATTAAAGGCATTTTTCACTGAAAGAAGCCTTTAATAATCTCAAAAATTTTTA
* * *
3728832 AAAAAAATTATT-GAAGCTGTTTGTTCTCAAAAAATACCTTTAATAATTATGTACGTAAATTAGA
131 AAAAAAATTATTAAAAGC-GTTTGTTCTCAAAAAATACCTTCAATAATTATGCACGTAAATTAGA
* * * * *
3728896 A-GAAATTAGTGATGACGTTTTTCT-CGAATAAATACCT-TATTTAACCGTCTCAAAATTTAAGT
195 ATG-AATGAGTGAAGACATTTTTCTAC-AATAAATACCTCCA-CTAACCGTCTCAAAATTTAAGT
* * *
3728958 TGTGAAATATTGAAGACATTTTTCACTGAAAGATGCCTTTAATAATCCCAAAAATTTTAAGAAAA
257 TGTGAAATATTAAAGACATTTTTCACTGAAAGACGCCTTTAATAATCCAAAAAATTTTAAGAAAA
*
3729023 AATTATTGAAGGTGTTTGTTCTCAAAAAACGCTTTCAATAATTATGCACAT
322 AATTATTGAAGGCGTTTGTTCTCAAAAAACGCTTTCAATAATTATGCACAT
* **
3729074 AAATTAGAAAGAATTAGTGAAGATATTTTTCTAGAATAAACGCCTTCACTAACCATCTCAAAATT
1 AAATTAAAAAGAATTAGTGAAGATATTTCGCTAGAATAAACGCCTTCACTAACCATCTCAAAATT
* * * * * * * *
3729139 TGAGTTATAAAATATTGAAGGTATTTTTCATTGAAAGACGTCTTTAATAATCTCTAAATTTTTTT
66 TGAGTTATAAAATATTAAAGGCATTTTTCACTGAAAGAAGCCTTTAATAATCTCAAAAATTTTTA
* * *
3729204 AAAAAAATTATTAAAAGCGTTTGTTCTTAAAAAATATCTTCAATAATTATGCATGTAAATTAGAA
131 AAAAAAATTATTAAAAGCGTTTGTTCTCAAAAAATACCTTCAATAATTATGCACGTAAATTAGAA
* * * *
3729269 TGAATGAGTGAAGGCATTTTTCTACAATAAGTACCTCCACTAACTGTCTCAAAATTTGAGTTGTG
196 TGAATGAGTGAAGACATTTTTCTACAATAAATACCTCCACTAACCGTCTCAAAATTTAAGTTGTG
* * * * *
3729334 AAATATTAAAGGCGTTTTTCATTGAAAGACGCCTTTAATAATTCAAAAAATTTTAAGAGAAAATT
261 AAATATTAAAGACATTTTTCACTGAAAGACGCCTTTAATAATCCAAAAAATTTTAAGAAAAAATT
*
3729399 ATTGAAGGCGTTTGTTTTCAA
326 ATTGAAGGCGTTTGTTCTCAA
3729420 GATATGCCTT
Statistics
Matches: 299, Mismatches: 43, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
372 292 0.98
373 7 0.02
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (372 bp):
AAATTAAAAAGAATTAGTGAAGATATTTCGCTAGAATAAACGCCTTCACTAACCATCTCAAAATT
TGAGTTATAAAATATTAAAGGCATTTTTCACTGAAAGAAGCCTTTAATAATCTCAAAAATTTTTA
AAAAAAATTATTAAAAGCGTTTGTTCTCAAAAAATACCTTCAATAATTATGCACGTAAATTAGAA
TGAATGAGTGAAGACATTTTTCTACAATAAATACCTCCACTAACCGTCTCAAAATTTAAGTTGTG
AAATATTAAAGACATTTTTCACTGAAAGACGCCTTTAATAATCCAAAAAATTTTAAGAAAAAATT
ATTGAAGGCGTTTGTTCTCAAAAAACGCTTTCAATAATTATGCACAT
Found at i:3735913 original size:35 final size:34
Alignment explanation
Indices: 3735834--3735913 Score: 81
Period size: 35 Copynumber: 2.3 Consensus size: 34
3735824 AGAAACTGTG
* * *
3735834 CTAAATTATCGGTATTTTTTTGAAACAAATGCCA
1 CTAAATTAACGATATTTTTTTGAAACAAATACCA
* * *
3735868 CCAAAGTAACGATATTTTTTTTGATAA-AAATATCA
1 CTAAATTAACGATA-TTTTTTTGA-AACAAATACCA
3735903 CTAAATTAACG
1 CTAAATTAACG
3735914 GCGTATCAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
34 10 0.28
35 24 0.67
36 2 0.06
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (34 bp):
CTAAATTAACGATATTTTTTTGAAACAAATACCA
Found at i:3735989 original size:34 final size:34
Alignment explanation
Indices: 3735925--3736048 Score: 115
Period size: 34 Copynumber: 3.7 Consensus size: 34
3735915 CGTATCAAAA
** ** *
3735925 ATACAAATGTCGCTAATATAGCAACGTTTTTCAT
1 ATACAAATGTCGCTAATATAGTGATATTTTTCAG
* *
3735959 ATACAAATGTCGCTAATATAATGATATTTTTTAG
1 ATACAAATGTCGCTAATATAGTGATATTTTTCAG
** * *
3735993 ATACAAATGTCATTAAAATAGTGATATTTTTTAG
1 ATACAAATGTCGCTAATATAGTGATATTTTTCAG
* * *
3736027 ATATAAACGT-GCTAATGTAGTG
1 ATACAAATGTCGCTAATATAGTG
3736049 GTGTTTTATA
Statistics
Matches: 73, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
33 8 0.11
34 65 0.89
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (34 bp):
ATACAAATGTCGCTAATATAGTGATATTTTTCAG
Found at i:3736193 original size:23 final size:23
Alignment explanation
Indices: 3736150--3736193 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3736140 TAACGTTTAT
* *
3736150 AAATGTTACTAAATATAAAAAAA
1 AAATGTCACTAAAAATAAAAAAA
*
3736173 AAATGTCACTAAAAATCAAAA
1 AAATGTCACTAAAAATAAAAA
3736194 CCCTTGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.09, G:0.05, T:0.23
Consensus pattern (23 bp):
AAATGTCACTAAAAATAAAAAAA
Found at i:3738048 original size:42 final size:43
Alignment explanation
Indices: 3737972--3738054 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
3737962 TAAGGAGCCA
*
3737972 ATTTCCTATTTTAAAATTGTTTAACTTTAGTATAGAAGAGTCC
1 ATTTCCTAATTTAAAATTGTTTAACTTTAGTATAGAAGAGTCC
* * *
3738015 ATTTCTTAATTTAAATTTGTTTATCTTT-GTATAGAAGAGT
1 ATTTCCTAATTTAAAATTGTTTAACTTTAGTATAGAAGAGT
3738055 TTAGTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 12 0.33
43 24 0.67
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (43 bp):
ATTTCCTAATTTAAAATTGTTTAACTTTAGTATAGAAGAGTCC
Found at i:3738891 original size:21 final size:22
Alignment explanation
Indices: 3738856--3738897 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
3738846 AGGTTTTTTT
3738856 TATTTTATTTTTATTTATTTAAC
1 TATTTTA-TTTTATTTATTTAAC
3738879 TATTTTA-TTTATTTATTTA
1 TATTTTATTTTATTTATTTA
3738898 TTTGATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TATTTTATTTTATTTATTTAAC
Found at i:3739074 original size:107 final size:107
Alignment explanation
Indices: 3738944--3739142 Score: 253
Period size: 110 Copynumber: 1.9 Consensus size: 107
3738934 AAACATATTT
* *
3738944 AAATAAAAACATTACTAATAGATTGGA-AGGTAATCATTTT-TTTT-AAAT-AAGATTTTACTAA
1 AAATAAAAACATTACTAACAGATTGGAGAGGTAAT-ATTTTATTTTAAAATAAAG-TTTTACCAA
*
3739005 CATATCGAAAAACCTTATAACTTTTTTTATTTAAAAAAAAAATAA
64 CATATCGAAAAACCTTATAA-TTTCTTTATTTAAAAAAAAAATAA
* *
3739050 AAATAAAAAGCTTTACTAACAGATTGGAGAGTTAATATTTTATTTTCAAAATAAAGTTTTACCAA
1 AAATAAAAA-CATTACTAACAGATTGGAGAGGTAATATTTTATTTT-AAAATAAAGTTTTACCAA
* * *
3739115 CATATTGGAAAGCCTTATAATTTCTTTA
64 CATATCGAAAAACCTTATAATTTCTTTA
3739143 AAAAAATCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
106 9 0.11
107 21 0.27
108 10 0.13
109 7 0.09
110 29 0.37
111 3 0.04
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (107 bp):
AAATAAAAACATTACTAACAGATTGGAGAGGTAATATTTTATTTTAAAATAAAGTTTTACCAACA
TATCGAAAAACCTTATAATTTCTTTATTTAAAAAAAAAATAA
Found at i:3740676 original size:93 final size:92
Alignment explanation
Indices: 3740518--3740711 Score: 327
Period size: 93 Copynumber: 2.1 Consensus size: 92
3740508 ATTATATTTG
* *
3740518 ATAATTTTTAAAAATAAATATATATGTAAATATACATATGTAGTAATATCAACGTCTTTTTTATA
1 ATAATTTTTAAAAATAAATATATATGTAAATATACATATATAGTAACATCAACGTCTTTTTTATA
3740583 TAATTAATTTAGGAAAATTGATATCTT
66 TAATTAATTTAGGAAAATTGATATCTT
*
3740610 ATAATTTTTCAAATAA-ATATATATATGTAAATATACATATATAGTAACATCAACGTCTTTTTTA
1 ATAATTTTT-AAA-AATAAATATATATGTAAATATACATATATAGTAACATCAACGTCTTTTTTA
*
3740674 TATAATTAATTTAGGGAAATTGATATCTT
64 TATAATTAATTTAGGAAAATTGATATCTT
3740703 ATAATTTTT
1 ATAATTTTT
3740712 TTTTAATATT
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
92 9 0.09
93 85 0.89
94 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (92 bp):
ATAATTTTTAAAAATAAATATATATGTAAATATACATATATAGTAACATCAACGTCTTTTTTATA
TAATTAATTTAGGAAAATTGATATCTT
Found at i:3744086 original size:64 final size:64
Alignment explanation
Indices: 3744012--3744230 Score: 330
Period size: 64 Copynumber: 3.4 Consensus size: 64
3744002 TTGCTTATGA
* * * * *
3744012 ATGCATGATGATATTGATAAACGATTATCCTTTAATGATTAAGAAAATGACATCCACTCACTAT
1 ATGCATGATGATACTGACAAACGATTATCATTTGATGATTAAGAAAATGACATCCATTCACTAT
* *
3744076 ATGCATGATGATACTGACAACCGGTTATCATTTGATGATTAAGAAAATGACATCCATTCACTAT
1 ATGCATGATGATACTGACAAACGATTATCATTTGATGATTAAGAAAATGACATCCATTCACTAT
* *
3744140 ATGCATGATGATACTGACAACCGGTTATCATTTGATGATTAAGAAAATGACATCCATTCACTAT
1 ATGCATGATGATACTGACAAACGATTATCATTTGATGATTAAGAAAATGACATCCATTCACTAT
* * *
3744204 ATGCATGATGATCCTGATAAAAGATTA
1 ATGCATGATGATACTGACAAACGATTA
3744231 CCATGTTTTG
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 143 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (64 bp):
ATGCATGATGATACTGACAAACGATTATCATTTGATGATTAAGAAAATGACATCCATTCACTAT
Found at i:3744094 original size:31 final size:31
Alignment explanation
Indices: 3744059--3744158 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 31
3744049 ATTAAGAAAA
3744059 TGACATCCACTCACTATATGCATGATGATAC
1 TGACATCCACTCACTATATGCATGATGATAC
* ** * * * *
3744090 TGACAACCGGTTA-TCATTTG-ATGATTAAGAAAA
1 TGACATCCACTCACT-ATATGCATGA-T--GATAC
*
3744123 TGACATCCATTCACTATATGCATGATGATAC
1 TGACATCCACTCACTATATGCATGATGATAC
3744154 TGACA
1 TGACA
3744159 ACCGGTTATC
Statistics
Matches: 49, Mismatches: 14, Indels: 12
0.65 0.19 0.16
Matches are distributed among these distances:
30 5 0.10
31 22 0.45
33 17 0.35
34 5 0.10
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (31 bp):
TGACATCCACTCACTATATGCATGATGATAC
Found at i:3744127 original size:33 final size:33
Alignment explanation
Indices: 3744090--3744191 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 33
3744080 ATGATGATAC
3744090 TGACAACCGGTTATCATTTGATGATTAAGAAAA
1 TGACAACCGGTTATCATTTGATGATTAAGAAAA
* * * * *
3744123 TGACATCC-ATTCA-CTATATGCATGA-T--GATAC
1 TGACAACCGGTT-ATC-ATTTG-ATGATTAAGAAAA
3744154 TGACAACCGGTTATCATTTGATGATTAAGAAAA
1 TGACAACCGGTTATCATTTGATGATTAAGAAAA
3744187 TGACA
1 TGACA
3744192 TCCATTCACT
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
30 4 0.08
31 16 0.31
32 6 0.12
33 21 0.41
34 4 0.08
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (33 bp):
TGACAACCGGTTATCATTTGATGATTAAGAAAA
Found at i:3758301 original size:2 final size:2
Alignment explanation
Indices: 3758294--3758324 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3758284 CAGATAGGGA
3758294 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3758325 ATCTTGCTTC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3762009 original size:2 final size:2
Alignment explanation
Indices: 3762002--3762033 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3761992 TGAAATCCCC
*
3762002 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3762034 TGAAAAATTA
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:3764496 original size:12 final size:12
Alignment explanation
Indices: 3764479--3764507 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3764469 AAAATTACTC
3764479 TCCTTCCCAAGT
1 TCCTTCCCAAGT
3764491 TCCTTCCCAAGT
1 TCCTTCCCAAGT
3764503 TCCTT
1 TCCTT
3764508 TAGTGGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.41, G:0.07, T:0.38
Consensus pattern (12 bp):
TCCTTCCCAAGT
Found at i:3765437 original size:15 final size:16
Alignment explanation
Indices: 3765411--3765441 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3765401 AAATATATTC
3765411 ATATATTAATAAATTT
1 ATATATTAATAAATTT
3765427 ATATA-TAATAAATTT
1 ATATATTAATAAATTT
3765442 TTTTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATTAATAAATTT
Found at i:3765920 original size:19 final size:17
Alignment explanation
Indices: 3765878--3765920 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
3765868 AAATAACTCT
*
3765878 CATTTACTCTAAATTTC
1 CATTTACTCTAAATTAC
3765895 CATTTACTCTAATTATTAC
1 CATTTACTCTAA--ATTAC
*
3765914 TATTTAC
1 CATTTAC
3765921 ACCACTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 12 0.55
19 10 0.45
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.49
Consensus pattern (17 bp):
CATTTACTCTAAATTAC
Found at i:3766775 original size:127 final size:130
Alignment explanation
Indices: 3766568--3766823 Score: 353
Period size: 129 Copynumber: 2.0 Consensus size: 130
3766558 TTATAACTTA
* *
3766568 TATAATTATTTTTTTTAAGACTTATATATTTTAATATAATAAAATAAGTAAATTATATATTGAAT
1 TATAATTATTTTTTTTAAGACTTATATATTTTAATATAATAAAATAAGTAAATTACATATTGAAA
*
3766633 ATTTTTATGTCATTTTCATCAAAT-AAAAAAAAAACTT-AACTGTAATTTATTGAGTCCAAATAT
66 ATTTTTATGTCATTTTCATCAAATCAAAAAAAAAACTTAAACTATAATTTATTGAGTCCAAATAT
* * * *
3766696 TATAATTATTTTTTATTTAA-ATTTATATATTTTAATATAATTAATTAA-TTAATTACATATT-A
1 TATAATTA-TTTTT-TTTAAGACTTATATATTTTAATATAATAAAATAAGTAAATTACATATTGA
* * *
3766758 AAATTTTTATG-CAATTTTCATCAAATCTAAAAGAAAACTTAAACTATAATTTATTGAGTTCAAA
64 AAATTTTTATGTC-ATTTTCATCAAATCAAAAAAAAAACTTAAACTATAATTTATTGAGTCCAAA
3766822 TA
128 TA
3766824 ATTTCTAAAT
Statistics
Matches: 113, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
126 1 0.01
127 24 0.21
128 30 0.27
129 53 0.47
130 5 0.04
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (130 bp):
TATAATTATTTTTTTTAAGACTTATATATTTTAATATAATAAAATAAGTAAATTACATATTGAAA
ATTTTTATGTCATTTTCATCAAATCAAAAAAAAAACTTAAACTATAATTTATTGAGTCCAAATAT
Found at i:3766867 original size:129 final size:128
Alignment explanation
Indices: 3766589--3766868 Score: 273
Period size: 129 Copynumber: 2.2 Consensus size: 128
3766579 TTTTTAAGAC
* * * * * * *
3766589 TTATATATTTTAATATAATAAAATAAGTAAATTATATATTGAATATTTTTATGTCATTTTCATCA
1 TTATATATTTCAATAAAATTAATTAA-TTAATTACATATTGAAAATTTTTATGTCATTTTCATCA
* * *** * *
3766654 AATAAAAAAAAAACTTAACTGTAATTTATTGAGTCCAAATATTATAATTATTTTTTATTTAAAT
65 AATAAAAAAAAAACTTAACTATAATTTATTGAGTCCAAATATTATAAATAGAATATATATAAAT
* *
3766718 TTATATATTTTAATATAATTAATTAATTAATTACATATT-AAAATTTTTATG-CAATTTTCATCA
1 TTATATATTTCAATAAAATTAATTAATTAATTACATATTGAAAATTTTTATGTC-ATTTTCATCA
* * * *
3766781 AATCTAAAAGAAAACTTAAACTATAATTTATTGAGTTCAAATAATTTCTAAATAGAATATA-ATA
65 AAT-AAAAAAAAAACTT-AACTATAATTTATTGAGTCCAAAT-A-TTATAAATAGAATATATATA
3766845 ATAT
126 A-AT
*
3766849 TTTTA-ATTTCAA-AAAATTAA
1 TTATATATTTCAATAAAATTAA
3766869 AAATTTTGTT
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
126 1 0.01
127 24 0.19
128 22 0.17
129 53 0.42
130 10 0.08
131 16 0.13
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (128 bp):
TTATATATTTCAATAAAATTAATTAATTAATTACATATTGAAAATTTTTATGTCATTTTCATCAA
ATAAAAAAAAAACTTAACTATAATTTATTGAGTCCAAATATTATAAATAGAATATATATAAAT
Found at i:3767703 original size:22 final size:21
Alignment explanation
Indices: 3767673--3767713 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3767663 AATCAACTCT
3767673 TTTATAATTATAATTTTAATA
1 TTTATAATTATAATTTTAATA
*
3767694 TTTATTAATTATATTTTTAA
1 TTTA-TAATTATAATTTTAA
3767714 AAAAATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTATAATTATAATTTTAATA
Found at i:3774027 original size:2 final size:2
Alignment explanation
Indices: 3774020--3774047 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3774010 ATTTTAAATG
3774020 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
3774048 TCATAAGAGG
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:3779570 original size:10 final size:10
Alignment explanation
Indices: 3779555--3779581 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3779545 GATGCGATTT
3779555 TAAAATTAAA
1 TAAAATTAAA
3779565 TAAAATTAAA
1 TAAAATTAAA
3779575 TAAAATT
1 TAAAATT
3779582 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAATTAAA
Found at i:3782032 original size:2 final size:2
Alignment explanation
Indices: 3782025--3782053 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3782015 TGACATATGA
3782025 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 A
3782054 AAGAAGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3787873 original size:54 final size:54
Alignment explanation
Indices: 3787803--3787912 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
3787793 ATGGTAACAT
* *
3787803 AATATAAAAATGATATGAATAAAGAATATAAAAATAACATAATTTAAAATTTTA
1 AATATAAAAATGATATGAATAAAAAATACAAAAATAACATAATTTAAAATTTTA
* * * * *
3787857 AATATAAAAATTATATGAATAAAAAATACAGAGATAACATGATTTAAATTTTTA
1 AATATAAAAATGATATGAATAAAAAATACAAAAATAACATAATTTAAAATTTTA
3787911 AA
1 AA
3787913 AAAATCATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (54 bp):
AATATAAAAATGATATGAATAAAAAATACAAAAATAACATAATTTAAAATTTTA
Found at i:3790590 original size:24 final size:24
Alignment explanation
Indices: 3790559--3790616 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3790549 GAAATTAAAA
* * *
3790559 ATTATAATTAATGTAAGGTTAATC
1 ATTATAATGAATATAAGATTAATC
* *
3790583 ATTGTAATGAATATAAGATTAATT
1 ATTATAATGAATATAAGATTAATC
3790607 ATTATAATGA
1 ATTATAATGA
3790617 CGAGATTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (24 bp):
ATTATAATGAATATAAGATTAATC
Found at i:3793276 original size:25 final size:27
Alignment explanation
Indices: 3793225--3793277 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
3793215 ATTATAATTA
* *
3793225 AAATATAAATAAATAATCTCAAATTTT
1 AAATATAAATAAAAAAACTCAAATTTT
*
3793252 AAATA-AAATAAAAAAACT-AATTTTT
1 AAATATAAATAAAAAAACTCAAATTTT
3793277 A
1 A
3793278 CACTTTCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (27 bp):
AAATATAAATAAAAAAACTCAAATTTT
Found at i:3794191 original size:25 final size:26
Alignment explanation
Indices: 3794163--3794241 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 26
3794153 AAGTGATATC
3794163 AGAGCTGAAGGTTCGAA-ACGT-GAGA
1 AGAGCTGAAGGTTCGAAGACGTGGA-A
* * *
3794188 AGAGTTGAAGATTC-AAGATGTGGAA
1 AGAGCTGAAGGTTCGAAGACGTGGAA
* * *
3794213 AGAGCTGATGGTTCG-AGACATGGGA
1 AGAGCTGAAGGTTCGAAGACGTGGAA
3794238 AGAG
1 AGAG
3794242 TTGATAGTTC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
24 2 0.05
25 38 0.90
26 2 0.05
ACGTcount: A:0.35, C:0.09, G:0.37, T:0.19
Consensus pattern (26 bp):
AGAGCTGAAGGTTCGAAGACGTGGAA
Found at i:3794240 original size:50 final size:50
Alignment explanation
Indices: 3794163--3794288 Score: 132
Period size: 50 Copynumber: 2.6 Consensus size: 50
3794153 AAGTGATATC
* * * *
3794163 AGAGCTGAAGGTTCGAAACGTGAGAAGAGTTGA-AGATTCAAGATGTGGAA
1 AGAGCTGATGGTTCGAGACATGAGAAGAGTTGATAG-TTCAAGATATGGAA
* * *
3794213 AGAGCTGATGGTTCGAGACATGGGAAGAGTTGATAGTTCGAGATATGGGA
1 AGAGCTGATGGTTCGAGACATGAGAAGAGTTGATAGTTCAAGATATGGAA
* * *
3794263 AGCGC--ATGGTTTGAGACATGTGAAGA
1 AGAGCTGATGGTTCGAGACATGAGAAGA
3794289 AGTAAGTCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
48 19 0.29
50 44 0.68
51 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.36, T:0.22
Consensus pattern (50 bp):
AGAGCTGATGGTTCGAGACATGAGAAGAGTTGATAGTTCAAGATATGGAA
Found at i:3794246 original size:25 final size:25
Alignment explanation
Indices: 3794212--3794264 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
3794202 AAGATGTGGA
*
3794212 AAGAGCTGATGGTTCGAGACATGGG
1 AAGAGCTGATAGTTCGAGACATGGG
* *
3794237 AAGAGTTGATAGTTCGAGATATGGG
1 AAGAGCTGATAGTTCGAGACATGGG
3794262 AAG
1 AAG
3794265 CGCATGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.38, T:0.23
Consensus pattern (25 bp):
AAGAGCTGATAGTTCGAGACATGGG
Found at i:3795319 original size:19 final size:21
Alignment explanation
Indices: 3795274--3795319 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
3795264 GACTCGACTC
3795274 AAAAT-ATTATTATATTAATA
1 AAAATAATTATTATATTAATA
*
3795294 AATAATAATT-TTAT-TTAATT
1 AA-AATAATTATTATATTAATA
3795314 AAAATA
1 AAAATA
3795320 TTAACATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 9 0.39
21 7 0.30
22 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATAATTATTATATTAATA
Found at i:3795431 original size:28 final size:28
Alignment explanation
Indices: 3795377--3795431 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3795367 AAATATTTTA
* **
3795377 ATATTTCAATAATAAATAGTATTATATT
1 ATATTTCAATAATAAATAATAACATATT
*
3795405 ATATTTTAATAATAAATAATAACATAT
1 ATATTTCAATAATAAATAATAACATAT
3795432 ATAATAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (28 bp):
ATATTTCAATAATAAATAATAACATATT
Found at i:3795659 original size:21 final size:21
Alignment explanation
Indices: 3795620--3795694 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
3795610 TGTTATGATT
*
3795620 TAAT-AATATATAT-TTTTAA
1 TAATAAATATAAATATTTTAA
3795639 T-ATAAAATATAAATATTTTAA
1 TAAT-AAATATAAATATTTTAA
* *
3795660 TAATAAATATTACTATTTTAA
1 TAATAAATATAAATATTTTAA
* *
3795681 CAAT-AATAAAAATA
1 TAATAAATATAAATA
3795695 GTATATTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 15 0.33
21 25 0.56
22 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATAAATATAAATATTTTAA
Found at i:3795685 original size:24 final size:24
Alignment explanation
Indices: 3795658--3795713 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3795648 TAAATATTTT
*
3795658 AATAATAAATATTACTAT-TTTAAC
1 AATAATAAA-AATACTATATTTAAC
* *
3795682 AATAATAAAAATAGTATATTTAAG
1 AATAATAAAAATACTATATTTAAC
3795706 AATAATAA
1 AATAATAA
3795714 TACTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (24 bp):
AATAATAAAAATACTATATTTAAC
Found at i:3795715 original size:21 final size:20
Alignment explanation
Indices: 3795652--3795724 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 20
3795642 AAAATATAAA
* *
3795652 TATTTTAATAATAAATATTAC
1 TATTTTAAGAATAAA-AATAC
* *
3795673 TATTTTAACAATAATAAAAATAG
1 TATTTT---AAGAATAAAAATAC
*
3795696 TATATTTAAGAATAATAATAC
1 TAT-TTTAAGAATAAAAATAC
3795717 TATTTTAA
1 TATTTTAA
3795725 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 5 0.12
21 20 0.47
23 6 0.14
24 12 0.28
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (20 bp):
TATTTTAAGAATAAAAATAC
Found at i:3795735 original size:44 final size:42
Alignment explanation
Indices: 3795655--3795764 Score: 100
Period size: 43 Copynumber: 2.6 Consensus size: 42
3795645 ATATAAATAT
* *
3795655 TTTAATAATAAATATTACTATTTTAACAATAATAAAAATAGTATA
1 TTTAAGAAT-AATAATACTATTTTAACAATAAT-AAAATAGTA-A
** *
3795700 TTTAAGAATAATAATACTATTTTAA-ATATTTTAAAATATTAA
1 TTTAAGAATAATAATACTATTTTAACA-ATAATAAAATAGTAA
*
3795742 TATAAAGAATAATAA-A-TATTTTA
1 T-TTAAGAATAATAATACTATTTTA
3795765 TTTTAAGTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
41 7 0.12
42 3 0.05
43 21 0.37
44 18 0.32
45 8 0.14
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (42 bp):
TTTAAGAATAATAATACTATTTTAACAATAATAAAATAGTAA
Found at i:3799317 original size:74 final size:74
Alignment explanation
Indices: 3799239--3799390 Score: 297
Period size: 74 Copynumber: 2.1 Consensus size: 74
3799229 TTAATTAAAC
3799239 GAATTCAAATAATTTAATTTTTATTTCAAATTAATTTTAAATTAAAAAAATAAAATTTAAATAAA
1 GAATTCAAATAATTTAATTTTTATTTCAAATTAATTTTAAATTAAAAAAATAAAATTTAAATAAA
3799304 TTCAAATCA
66 TTCAAATCA
3799313 GAATTCAAATAATTTAATTTTTATTTCAAATTAATTTTAAATTAAAAAAATAAAATTTAAATAAA
1 GAATTCAAATAATTTAATTTTTATTTCAAATTAATTTTAAATTAAAAAAATAAAATTTAAATAAA
3799378 TTCAAATCA
66 TTCAAATCA
3799387 -AATT
1 GAATT
3799391 TTAAACGTAA
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 4 0.05
74 74 0.95
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (74 bp):
GAATTCAAATAATTTAATTTTTATTTCAAATTAATTTTAAATTAAAAAAATAAAATTTAAATAAA
TTCAAATCA
Found at i:3799448 original size:74 final size:74
Alignment explanation
Indices: 3799239--3799427 Score: 222
Period size: 74 Copynumber: 2.6 Consensus size: 74
3799229 TTAATTAAAC
** * ** *
3799239 GAATTCAAATAATTTAATTTTTATTTCAAATTAATTTTAAATTAAAAAAATAAAATTTAAATAAA
1 GAATTCAAATAACGTAAATTTTAAATCAAATTAAATTTAAATTAAAAAAATAAAATTTAAATAAA
3799304 TTCAAATCA
66 TTCAAATCA
** * ** *
3799313 GAATTCAAATAATTTAATTTTTATTTCAAATTAATTTTAAATTAAAAAAATAAAATTTAAATAAA
1 GAATTCAAATAACGTAAATTTTAAATCAAATTAAATTTAAATTAAAAAAATAAAATTTAAATAAA
3799378 TTCAAATCA
66 TTCAAATCA
**
3799387 -AATT-TTA-AACGTAAATTTTAAATCAAATTCAAATTTAAATT
1 GAATTCAAATAACGTAAATTTTAAATCAAATT-AAATTTAAATT
3799428 TAATATTATA
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
71 17 0.16
72 11 0.10
73 4 0.04
74 74 0.70
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (74 bp):
GAATTCAAATAACGTAAATTTTAAATCAAATTAAATTTAAATTAAAAAAATAAAATTTAAATAAA
TTCAAATCA
Found at i:3799708 original size:3 final size:3
Alignment explanation
Indices: 3799700--3799734 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3799690 TTTAAGAATT
3799700 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3799735 TTTCAATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3800301 original size:22 final size:21
Alignment explanation
Indices: 3800276--3800316 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3800266 ATTTAATAAA
*
3800276 TTTAAAATTTTTTTTCAAAAGT
1 TTTAAAA-TTTTATTCAAAAGT
*
3800298 TTTAATATTTTATTCAAAA
1 TTTAAAATTTTATTCAAAA
3800317 AGTATCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTAAAATTTTATTCAAAAGT
Found at i:3802297 original size:9 final size:9
Alignment explanation
Indices: 3802283--3802316 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
3802273 TTTATATATA
3802283 AGCAAACGG
1 AGCAAACGG
3802292 AGCAAACGG
1 AGCAAACGG
3802301 AGCAAACGG
1 AGCAAACGG
3802310 AGCAAAC
1 AGCAAAC
3802317 AGAAGAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.47, C:0.24, G:0.29, T:0.00
Consensus pattern (9 bp):
AGCAAACGG
Found at i:3812977 original size:3 final size:3
Alignment explanation
Indices: 3812969--3812998 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3812959 GAAGTGACAT
*
3812969 AAG AAG AAG AAG AAG AAG AAG AAG AGG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3812999 GAGGCGCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3816118 original size:2 final size:2
Alignment explanation
Indices: 3816113--3816141 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3816103 AAAAAAAAAA
3816113 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 A
3816142 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3827442 original size:14 final size:14
Alignment explanation
Indices: 3827411--3827450 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3827401 TCGAAATTCG
3827411 ATTTAAATTTAATTAA
1 ATTTAAATTT--TTAA
*
3827427 ATTTTAATTTTTAA
1 ATTTAAATTTTTAA
3827441 ATTTAAATTT
1 ATTTAAATTT
3827451 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTTTAA
Found at i:3828546 original size:17 final size:16
Alignment explanation
Indices: 3828520--3828553 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3828510 ATCGAGATAT
3828520 AAAAATTAAAATATTA
1 AAAAATTAAAATATTA
*
3828536 AAAATATTAAAATTTTA
1 AAAA-ATTAAAATATTA
3828553 A
1 A
3828554 TTTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATTAAAATATTA
Found at i:3833691 original size:18 final size:17
Alignment explanation
Indices: 3833668--3833714 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
3833658 TGATTTTTTT
3833668 TTTTTTGTTATTTATGCC
1 TTTTTTGTTATTT-TGCC
* *
3833686 TTTTTTCTTATTTTGCT
1 TTTTTTGTTATTTTGCC
3833703 TTCTTTTGTTAT
1 TT-TTTTGTTAT
3833715 CACAGAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.09, C:0.11, G:0.09, T:0.72
Consensus pattern (17 bp):
TTTTTTGTTATTTTGCC
Found at i:3840897 original size:114 final size:117
Alignment explanation
Indices: 3840681--3840926 Score: 421
Period size: 114 Copynumber: 2.1 Consensus size: 117
3840671 ATTCTCAACC
* *
3840681 CAAACAAAC--ACAAACCCAAACTCTTGTGCACTCTTTCAACATAACCAAACACATACCCATATG
1 CAAACAAACATACACACCCAAACCCTTGTGCACTCTTTCAACATAACCAAACACATACCCATATG
*
3840744 CTCCCATACATCATACCTATGTGGACCCTCTCAATCTCCTCTAGTCCACTCA
66 CTCCCATACATCATAACTATGTGGACCCTCTCAATCTCCTCTAGTCCACTCA
3840796 CAAACAAACATACACACCCAAACCCTTGTGCACTCTTTCAACATAACC-AA-AC-TACCCATATG
1 CAAACAAACATACACACCCAAACCCTTGTGCACTCTTTCAACATAACCAAACACATACCCATATG
*
3840858 CTCCCATACATCATAACTATGTGGACCTTCTCAATCTCCTCTAGTCCACTCA
66 CTCCCATACATCATAACTATGTGGACCCTCTCAATCTCCTCTAGTCCACTCA
3840910 CAAACAAACATACACAC
1 CAAACAAACATACACAC
3840927 ATACACACTC
Statistics
Matches: 125, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
114 77 0.62
115 11 0.09
116 2 0.02
117 35 0.28
ACGTcount: A:0.35, C:0.36, G:0.06, T:0.23
Consensus pattern (117 bp):
CAAACAAACATACACACCCAAACCCTTGTGCACTCTTTCAACATAACCAAACACATACCCATATG
CTCCCATACATCATAACTATGTGGACCCTCTCAATCTCCTCTAGTCCACTCA
Found at i:3841611 original size:23 final size:24
Alignment explanation
Indices: 3841584--3841638 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
3841574 TAATTTTATA
3841584 AAATTTT-ATAATTTTTCAAAAAT
1 AAATTTTCATAATTTTTCAAAAAT
**
3841607 AAATTTTCATAATTTTTTGAAAAT
1 AAATTTTCATAATTTTTCAAAAAT
3841631 AAATTTTC
1 AAATTTTC
3841639 GAAAACCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATTTTCATAATTTTTCAAAAAT
Found at i:3848113 original size:18 final size:18
Alignment explanation
Indices: 3848086--3848122 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3848076 TGCAGATGTT
*
3848086 GAGGAGTACGAGGAAGAG
1 GAGGAATACGAGGAAGAG
*
3848104 GAGGAATACGGGGAAGAG
1 GAGGAATACGAGGAAGAG
3848122 G
1 G
3848123 CTTAAAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.51, T:0.05
Consensus pattern (18 bp):
GAGGAATACGAGGAAGAG
Found at i:3852444 original size:13 final size:13
Alignment explanation
Indices: 3852426--3852455 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3852416 ACTTTTTTTT
3852426 TAAATTATAAATA
1 TAAATTATAAATA
*
3852439 TAAATTATAATTA
1 TAAATTATAAATA
3852452 TAAA
1 TAAA
3852456 AAAATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATTATAAATA
Found at i:3852464 original size:19 final size:19
Alignment explanation
Indices: 3852428--3852466 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3852418 TTTTTTTTTA
*
3852428 AATTATAAATATAAATTAT
1 AATTATAAATAAAAATTAT
3852447 AATTATAAA-AAAATATTAT
1 AATTATAAATAAAA-ATTAT
3852466 A
1 A
3852467 TTGTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTATAAATAAAAATTAT
Found at i:3853747 original size:3 final size:3
Alignment explanation
Indices: 3853741--3853774 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3853731 AGGTTTCCTT
3853741 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3853775 CATGAAACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3869319 original size:16 final size:16
Alignment explanation
Indices: 3869294--3869325 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3869284 ACTCACCTGA
3869294 TTGTTATAGTCAGTGT
1 TTGTTATAGTCAGTGT
*
3869310 TTGTTGTAGTCAGTGT
1 TTGTTATAGTCAGTGT
3869326 CATTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (16 bp):
TTGTTATAGTCAGTGT
Found at i:3869602 original size:26 final size:25
Alignment explanation
Indices: 3869555--3869604 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
3869545 ATTAATTAAA
3869555 ATTAATATATTTTGATTAAAAAACAT
1 ATTAATATATTTT-ATTAAAAAACAT
3869581 ATTAATATATATTT-TTATAAAAAC
1 ATTAATATAT-TTTATTA-AAAAAC
3869605 TTATCTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 3 0.14
26 16 0.73
27 3 0.14
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTAATATATTTTATTAAAAAACAT
Found at i:3872437 original size:23 final size:22
Alignment explanation
Indices: 3872408--3872489 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
3872398 TAACTTATTT
3872408 TAATAAAAATTATATTTATATA
1 TAATAAAAATTATATTTATATA
*
3872430 TAAT-TAAATTATAATTTATAT-
1 TAATAAAAATTAT-ATTTATATA
* *
3872451 TAAAAAAAACTTATATCTA-ATA
1 TAATAAAAA-TTATATTTATATA
* *
3872473 TATATATATATTATATT
1 TA-ATAAAAATTATATT
3872490 ACAGAATACA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
21 12 0.26
22 27 0.57
23 8 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATAAAAATTATATTTATATA
Done.