Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 203 of 210
Found at i:59853392 original size:124 final size:124
Alignment explanation
Indices: 59853248--59853527 Score: 393
Period size: 124 Copynumber: 2.3 Consensus size: 124
59853238 TTTTTTCGAG
* ** ** *
59853248 TTGACGTATCTG-GTCAAATAGTGGGAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTGTAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
* *
59853312 GAAATCGTGGCCTCGTGGACGCGATTTCACTAC-AGTGGTCATGTAAGAAATAAATTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTCACTACAAGTGGTCATGTAAGAAATAAATTTTT
* *
59853371 TTGACGTTTTCTTAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
** * *
59853436 GAAATCGCGCCCTCGTGGACGCGATTTCGTTACAATTGGTCATGTAGGAAATAAATTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTCACTACAAGTGGTCATGTAAGAAATAAATTTTT
*
59853496 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTGTAAAATCGC
59853528 GCCCTCGTGG
Statistics
Matches: 137, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
123 6 0.04
124 100 0.73
125 31 0.23
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTCACTACAAGTGGTCATGTAAGAAATAAATTTTT
Found at i:59858197 original size:14 final size:15
Alignment explanation
Indices: 59858180--59858213 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
59858170 AATAAATATC
59858180 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
59858194 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
59858209 TAAAA
1 TAAAA
59858214 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:59858479 original size:22 final size:22
Alignment explanation
Indices: 59858453--59858501 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
59858443 AATTTGGGAG
59858453 TTTGAGAGAATTTTGGAAGGAA
1 TTTGAGAGAATTTTGGAAGGAA
*
59858475 TTTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTGGAAGGAA
*
59858497 ATTGA
1 TTTGA
59858502 TATTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.35
Consensus pattern (22 bp):
TTTGAGAGAATTTTGGAAGGAA
Found at i:59860894 original size:27 final size:26
Alignment explanation
Indices: 59860841--59860898 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
59860831 AGTACTGTTT
** *
59860841 TAACAAAGAAAAATATCAGAAGCAAC
1 TAACAAAGAAAAATAAAAGAAGAAAC
*
59860867 TAACCAAGAAAAATAAAAGAGAGAAAC
1 TAACAAAGAAAAATAAAAGA-AGAAAC
59860894 TAACA
1 TAACA
59860899 TGAACACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (26 bp):
TAACAAAGAAAAATAAAAGAAGAAAC
Found at i:59862543 original size:17 final size:17
Alignment explanation
Indices: 59862521--59862554 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59862511 ATATATTTTT
*
59862521 AATTAAATTTTTTTAAA
1 AATTAAATATTTTTAAA
*
59862538 AATTAACTATTTTTAAA
1 AATTAAATATTTTTAAA
59862555 CAAGAAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTAAATATTTTTAAA
Found at i:59865904 original size:18 final size:18
Alignment explanation
Indices: 59865859--59865904 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
59865849 TAAACCGACA
*
59865859 ATTAATTTTAAATTATTT
1 ATTAATTTTAAATAATTT
* *
59865877 ATGAATTTTTAATAATTT
1 ATTAATTTTAAATAATTT
59865895 ATTTAATTTT
1 A-TTAATTTT
59865905 GACTAGATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTAATTTTAAATAATTT
Found at i:59871503 original size:16 final size:16
Alignment explanation
Indices: 59871469--59871520 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
59871459 ATAGCATTAG
59871469 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
59871485 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* * *
59871501 TCATACCATATTCAAT
1 TCATGCAATACTCAAT
59871517 TCAT
1 TCAT
59871521 AAGTATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 5 0.17
16 21 0.72
17 3 0.10
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:59872758 original size:16 final size:15
Alignment explanation
Indices: 59872737--59872778 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
59872727 TTTGGTTTTT
59872737 TATTTCTTTTTATTTC
1 TATTTC-TTTTATTTC
59872753 TATTTCTTTTA-TT-
1 TATTTCTTTTATTTC
*
59872766 TATTTGTTTTATT
1 TATTTCTTTTATT
59872779 ATTATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.42
14 3 0.12
15 5 0.21
16 6 0.25
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.76
Consensus pattern (15 bp):
TATTTCTTTTATTTC
Found at i:59873474 original size:20 final size:20
Alignment explanation
Indices: 59873436--59873474 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
59873426 GGTCTTTGTA
* *
59873436 TTATCAAATTAGTCCATTTG
1 TTATCAAATGAGTCAATTTG
*
59873456 TTATCAAATGGGTCAATTT
1 TTATCAAATGAGTCAATTT
59873475 AGCCTCTACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
TTATCAAATGAGTCAATTTG
Found at i:59875829 original size:3 final size:3
Alignment explanation
Indices: 59875821--59875858 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
59875811 CTTGAAGCTC
59875821 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
59875859 GCCTAAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:59883773 original size:25 final size:25
Alignment explanation
Indices: 59883739--59883789 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
59883729 ATCGATTCAA
*
59883739 TCGATTTTTAACTCGGTTCAATCGT
1 TCGATTTTTAACTCGGTTAAATCGT
*
59883764 TCGATTTTTAACTTGGTTAAATCGT
1 TCGATTTTTAACTCGGTTAAATCGT
59883789 T
1 T
59883790 TTCAAGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (25 bp):
TCGATTTTTAACTCGGTTAAATCGT
Found at i:59885737 original size:47 final size:45
Alignment explanation
Indices: 59885678--59885790 Score: 120
Period size: 47 Copynumber: 2.4 Consensus size: 45
59885668 TAAGAAAAAG
** * *
59885678 CCTTTCTTCAAAGCCATTTCTTTTTTTTTTATCCTTTAAAAAGAAA-C
1 CCTTT-TTCAAAGCCATTTC-TTCCTCTTTACCCTTTAAAAA-AAACC
*
59885725 CCTTTTTCCAAAGTCATTTCTTCCTCTTTACCCTTTAAAAAAAATCC
1 CCTTTTT-CAAAGCCATTTCTTCCTCTTTACCCTTTAAAAAAAA-CC
59885772 CCTTTTTTCAAAGCCATTT
1 CC-TTTTTCAAAGCCATTT
59885791 TTTGCTTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
45 3 0.05
46 19 0.34
47 29 0.52
48 5 0.09
ACGTcount: A:0.27, C:0.26, G:0.04, T:0.44
Consensus pattern (45 bp):
CCTTTTTCAAAGCCATTTCTTCCTCTTTACCCTTTAAAAAAAACC
Found at i:59888273 original size:20 final size:21
Alignment explanation
Indices: 59888250--59888291 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
59888240 TTTTTTAGAT
*
59888250 AATTATGT-TTATTTTCTTTA
1 AATTAAGTGTTATTTTCTTTA
*
59888270 AATTAAGTGTTATTTTTTTTA
1 AATTAAGTGTTATTTTCTTTA
59888291 A
1 A
59888292 CTTCATGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (21 bp):
AATTAAGTGTTATTTTCTTTA
Found at i:59890226 original size:25 final size:25
Alignment explanation
Indices: 59890173--59890219 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
59890163 ATAATTGTAG
59890173 TGTATTTA-G-TATTATTTAT-ATGA
1 TGTATTTATGTTATTATTT-TCATGA
59890196 TGTATTTATGTTATTATTTTCATG
1 TGTATTTATGTTATTATTTTCATG
59890220 TGTTATTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 8 0.38
24 2 0.10
25 11 0.52
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.60
Consensus pattern (25 bp):
TGTATTTATGTTATTATTTTCATGA
Found at i:59890947 original size:16 final size:16
Alignment explanation
Indices: 59890922--59890960 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
59890912 ACGAATTTTC
59890922 TGTTTGGGCT-ATGGG
1 TGTTTGGGCTCATGGG
*
59890937 TTGTTTTGGCTCATGGG
1 -TGTTTGGGCTCATGGG
59890954 TGTTTGG
1 TGTTTGG
59890961 CATTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.05, C:0.08, G:0.41, T:0.46
Consensus pattern (16 bp):
TGTTTGGGCTCATGGG
Found at i:59895193 original size:16 final size:16
Alignment explanation
Indices: 59895172--59895207 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
59895162 ATCCTTTATC
*
59895172 ACTTGGTGTCAATACA
1 ACTTGGTGCCAATACA
*
59895188 ACTTGGTGCCAATATA
1 ACTTGGTGCCAATACA
59895204 ACTT
1 ACTT
59895208 TGTGAGACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (16 bp):
ACTTGGTGCCAATACA
Found at i:59895586 original size:15 final size:15
Alignment explanation
Indices: 59895566--59895604 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
59895556 GAATTATTTA
59895566 AAAATATTAAAAGA-T
1 AAAATATTAAAA-ATT
*
59895581 AAAATACTAAAAATT
1 AAAATATTAAAAATT
59895596 AAAATATTA
1 AAAATATTA
59895605 TTTTTACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATATTAAAAATT
Found at i:59900382 original size:4 final size:4
Alignment explanation
Indices: 59900373--59900404 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
59900363 GATTTTTAAG
59900373 ATTA ATTA ATTA ATTA ATTA ATTA ATT- ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
59900405 ATTGACGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:59901091 original size:9 final size:9
Alignment explanation
Indices: 59901072--59901105 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
59901062 TTATTAATTA
59901072 TTAAGTTCGG
1 TTAA-TTCGG
59901082 TTAATTCGG
1 TTAATTCGG
59901091 TTAATTCGG
1 TTAATTCGG
59901100 TTAATT
1 TTAATT
59901106 ACCCGATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (9 bp):
TTAATTCGG
Found at i:59901549 original size:16 final size:16
Alignment explanation
Indices: 59901528--59901560 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
59901518 TGCGACAATG
59901528 GGGTTTTAATTAGAAA
1 GGGTTTTAATTAGAAA
59901544 GGGTTTTAATTAGAAA
1 GGGTTTTAATTAGAAA
59901560 G
1 G
59901561 AGATTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (16 bp):
GGGTTTTAATTAGAAA
Found at i:59905646 original size:30 final size:30
Alignment explanation
Indices: 59905612--59905668 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
59905602 ATGTTACCAT
59905612 AAATACTTTTAATAACTAGAGCACAATAAC
1 AAATACTTTTAATAACTAGAGCACAATAAC
59905642 AAATACTTTTAATAACTAGAGCACAAT
1 AAATACTTTTAATAACTAGAGCACAAT
59905669 CAGTGTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (30 bp):
AAATACTTTTAATAACTAGAGCACAATAAC
Found at i:59907767 original size:12 final size:12
Alignment explanation
Indices: 59907750--59907792 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
59907740 AAATCACAAT
*
59907750 ATAATAATAACA
1 ATAATAACAACA
59907762 ATAATAACAACA
1 ATAATAACAACA
* *
59907774 ACAATAACCACA
1 ATAATAACAACA
59907786 ATAATAA
1 ATAATAA
59907793 TAAGTCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAATAACAACA
Found at i:59909262 original size:13 final size:14
Alignment explanation
Indices: 59909244--59909274 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
59909234 ACTTGGACTT
59909244 TTTTATTT-TTTAG
1 TTTTATTTATTTAG
59909257 TTTTATTTATTTAG
1 TTTTATTTATTTAG
59909271 TTTT
1 TTTT
59909275 GGGCCTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (14 bp):
TTTTATTTATTTAG
Found at i:59910182 original size:11 final size:11
Alignment explanation
Indices: 59910166--59910196 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
59910156 GAAGATCATG
59910166 CAAAGTGAGTT
1 CAAAGTGAGTT
59910177 CAAAGTGAGTT
1 CAAAGTGAGTT
*
59910188 CAAAATGAG
1 CAAAGTGAG
59910197 CATGGTAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (11 bp):
CAAAGTGAGTT
Found at i:59912708 original size:17 final size:17
Alignment explanation
Indices: 59912686--59912718 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
59912676 ATATTTTTTA
59912686 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
59912703 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
59912719 TATATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:59913776 original size:2 final size:2
Alignment explanation
Indices: 59913734--59913760 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59913724 TTAAAAAAAA
59913734 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
59913761 ATAATCGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59913965 original size:33 final size:33
Alignment explanation
Indices: 59913923--59914015 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
59913913 ATATAAACTT
59913923 AATTCCACAAATCATCCTTACAAATTATTCAAC
1 AATTCCACAAATCATCCTTACAAATTATTCAAC
*
59913956 AATTCCACAAATCATCCTCACAAATTATTCAAC
1 AATTCCACAAATCATCCTTACAAATTATTCAAC
*
59913989 AATTCCACAAATAATCCTTACAAATTA
1 AATTCCACAAATCATCCTTACAAATTA
59914016 ACAACCCGGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (33 bp):
AATTCCACAAATCATCCTTACAAATTATTCAAC
Found at i:59916365 original size:107 final size:107
Alignment explanation
Indices: 59916175--59916369 Score: 327
Period size: 107 Copynumber: 1.8 Consensus size: 107
59916165 CTTTTTTTTC
* * *
59916175 TTTTTTGCTTAAGAATATATTAAACCTTTTGATGGGAAGAGAGATGACAGCCAAGTACCCCACCC
1 TTTTTTGCTTAAGAATATATTAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
*
59916240 CGGTTACTCAGCCCAACATATTCCTAATTTATTATATTTATA
66 CAGTTACTCAGCCCAACATATTCCTAATTTATTATATTTATA
* *
59916282 TTTTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
1 TTTTTTGCTTAAGAATATATTAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
*
59916347 CAGTTACTCAGCCTAACATATTC
66 CAGTTACTCAGCCCAACATATTC
59916370 TTAAAAATTT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 81 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (107 bp):
TTTTTTGCTTAAGAATATATTAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
CAGTTACTCAGCCCAACATATTCCTAATTTATTATATTTATA
Found at i:59918746 original size:3 final size:3
Alignment explanation
Indices: 59918738--59918789 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
59918728 TAAAGTGATA
59918738 AAT AAT AAT -AT AAT AAT -AT AAT AAT -AT AAT -AT AAT AA- ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
59918779 AAT AAA AAT AA
1 AAT AAT AAT AA
59918790 AAATTGGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
2 9 0.22
3 31 0.76
4 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:59918752 original size:5 final size:5
Alignment explanation
Indices: 59918742--59918782 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
59918732 GTGATAAATA
59918742 ATAAT ATAAT A-ATAT AATAAT ATAAT ATAAT A-AAT ATAAT A
1 ATAAT ATAAT ATA-AT -ATAAT ATAAT ATAAT ATAAT ATAAT A
59918783 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 5 0.16
5 23 0.72
6 3 0.09
7 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:59918760 original size:16 final size:15
Alignment explanation
Indices: 59918735--59918789 Score: 71
Period size: 16 Copynumber: 3.7 Consensus size: 15
59918725 AATTAAAGTG
59918735 ATAAATAATAATATA
1 ATAAATAATAATATA
59918750 ATAATATAATAATATA
1 ATAA-ATAATAATATA
59918766 AT--ATAATAAATATA
1 ATAAATAAT-AATATA
59918780 ATAAA-AATAA
1 ATAAATAATAA
59918790 AAATTGGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.14
14 10 0.28
15 7 0.19
16 14 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAATAATAATATA
Found at i:59918774 original size:8 final size:8
Alignment explanation
Indices: 59918735--59918768 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
59918725 AATTAAAGTG
59918735 ATAA-ATA
1 ATAATATA
59918742 ATAATATA
1 ATAATATA
59918750 ATAATATA
1 ATAATATA
59918758 ATAATATA
1 ATAATATA
59918766 ATA
1 ATA
59918769 TAATAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 22 0.85
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAATATA
Found at i:59921112 original size:18 final size:17
Alignment explanation
Indices: 59921079--59921117 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
59921069 TTTTATAAAT
59921079 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
59921097 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
59921114 TGTG
1 TGTG
59921118 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:59921395 original size:23 final size:23
Alignment explanation
Indices: 59921343--59921395 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
59921333 AGTGTTATTG
*
59921343 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGATAGCTTCGGCTACAT
* * *
59921366 TTTAGTGATAGCTTTGGCTACAT
1 ATCAGTGATAGCTTCGGCTACAT
59921389 ATCAGTG
1 ATCAGTG
59921396 TGGCACTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (23 bp):
ATCAGTGATAGCTTCGGCTACAT
Found at i:59924297 original size:45 final size:45
Alignment explanation
Indices: 59924245--59924335 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
59924235 CTATTTCACA
*
59924245 TACTGGCCCATTTTATCTTTAAATTCACGCTTTTTTCCC-TAAATT
1 TACTGGCCCATTTTATCTTTAAATTCACAC-TTTTTCCCTTAAATT
59924290 TACTGGCCCATTTTATCTTTAAATTCACACTTTTTCCCTTAAATT
1 TACTGGCCCATTTTATCTTTAAATTCACACTTTTTCCCTTAAATT
59924335 T
1 T
59924336 CCTTTTACCT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 8 0.18
45 36 0.82
ACGTcount: A:0.23, C:0.24, G:0.05, T:0.47
Consensus pattern (45 bp):
TACTGGCCCATTTTATCTTTAAATTCACACTTTTTCCCTTAAATT
Found at i:59927556 original size:2 final size:2
Alignment explanation
Indices: 59927549--59927577 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59927539 ATTCCGATAA
59927549 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
59927578 ATAAAACAAC
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:59927904 original size:16 final size:17
Alignment explanation
Indices: 59927883--59927923 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
59927873 TAAAAGAATA
59927883 TTTTATTTA-T-ATAAAT
1 TTTTATTTATTAAT-AAT
*
59927899 TTTTATATATTAATAAT
1 TTTTATTTATTAATAAT
59927916 TTTTATTT
1 TTTTATTT
59927924 TCTAGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 8 0.38
17 11 0.52
18 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTTATTAATAAT
Found at i:59928854 original size:34 final size:34
Alignment explanation
Indices: 59928803--59928907 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 34
59928793 CTTAGTATAA
* * *
59928803 AAGGTGCCGCT-TATGCATTGAGAACCCTTAATTG
1 AAGGTGCCCCTAT-TGCATTGAAAATCCTTAATTG
* *
59928837 AAGGTGCCCCTATTGCATTGAAAATCCTTAACTA
1 AAGGTGCCCCTATTGCATTGAAAATCCTTAATTG
* *
59928871 AATGTGTCCCTGA-TGCATTGAAAATCCTTAATTG
1 AAGGTGCCCCT-ATTGCATTGAAAATCCTTAATTG
59928905 AAG
1 AAG
59928908 ATTGAAGAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 57 0.97
35 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (34 bp):
AAGGTGCCCCTATTGCATTGAAAATCCTTAATTG
Found at i:59929373 original size:10 final size:9
Alignment explanation
Indices: 59929342--59929401 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
59929332 TTTTTTTTTC
59929342 AAAAATCAA
1 AAAAATCAA
*
59929351 AGAAAATC-T
1 A-AAAATCAA
*
59929360 AAAAGTCAA
1 AAAAATCAA
59929369 AAAAATCATA
1 AAAAATCA-A
59929379 AAAAAT-AA
1 AAAAATCAA
*
59929387 AAAATGTCAA
1 AAAA-ATCAA
59929397 AAAAA
1 AAAAA
59929402 ACTTAAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
8 10 0.25
9 11 0.28
10 19 0.47
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (9 bp):
AAAAATCAA
Found at i:59929373 original size:17 final size:19
Alignment explanation
Indices: 59929342--59929382 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
59929332 TTTTTTTTTC
59929342 AAAAATCAAAGAAAATC-T
1 AAAAATCAAAGAAAATCAT
*
59929360 AAAAGTCAAA-AAAATCAT
1 AAAAATCAAAGAAAATCAT
59929378 AAAAA
1 AAAAA
59929383 ATAAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAATCAAAGAAAATCAT
Found at i:59929390 original size:27 final size:28
Alignment explanation
Indices: 59929342--59929401 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
59929332 TTTTTTTTTC
**
59929342 AAAAATCAAAGAAAATCTAAAA-GTCAA
1 AAAAATCAAAGAAAATAAAAAATGTCAA
59929369 AAAAATCATAA-AAAATAAAAAATGTCAA
1 AAAAATCA-AAGAAAATAAAAAATGTCAA
59929397 AAAAA
1 AAAAA
59929402 ACTTAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (28 bp):
AAAAATCAAAGAAAATAAAAAATGTCAA
Found at i:59929430 original size:3 final size:3
Alignment explanation
Indices: 59929422--59929482 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
59929412 TAAAAGTTAT
59929422 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59929470 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
59929483 AATTTTAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:59929521 original size:21 final size:22
Alignment explanation
Indices: 59929480--59929529 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
59929470 ATAATAATAA
59929480 TAAAATTTTAAAAAATATATTT
1 TAAAATTTTAAAAAATATATTT
*
59929502 TAAAATTTTAAAATAT-TATTT
1 TAAAATTTTAAAAAATATATTT
*
59929523 AAAAATT
1 TAAAATT
59929530 CAAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAAATTTTAAAAAATATATTT
Found at i:59930651 original size:14 final size:15
Alignment explanation
Indices: 59930623--59930672 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
59930613 GTTTTTATGG
59930623 TTTTGTAAATGAAATT
1 TTTTGTAAA-GAAATT
59930639 TTTTGTAAA-AAATT
1 TTTTGTAAAGAAATT
*
59930653 TAATTT-TCAAGAAATT
1 T--TTTGTAAAGAAATT
59930669 TTTT
1 TTTT
59930673 TACAACAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 9 0.30
15 3 0.10
16 18 0.60
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (15 bp):
TTTTGTAAAGAAATT
Found at i:59941801 original size:19 final size:19
Alignment explanation
Indices: 59941772--59941843 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
59941762 TTAAGTAATT
59941772 ATTTATATAATTTTTTTGTA
1 ATTT-TATAATTTTTTTGTA
*
59941792 ATTTTATAATTTTTTT-CA
1 ATTTTATAATTTTTTTGTA
**
59941810 ATTTT-TAATAATTTTGTA
1 ATTTTATAATTTTTTTGTA
*
59941828 ACTTCTTTTAATTTTT
1 A-TT-TTATAATTTTT
59941844 GTACTTTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.19
18 8 0.19
19 14 0.33
20 6 0.14
21 6 0.14
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTATAATTTTTTTGTA
Found at i:59941814 original size:28 final size:26
Alignment explanation
Indices: 59941783--59941859 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 26
59941773 TTTATATAAT
59941783 TTTTTTGTAATTTTATAATTTTTTTCAA
1 TTTTTTGTAATTTT-TAATTTTTTT-AA
** *
59941811 TTTTTAATAATTTTGTAACTTCTTTTAA
1 TTTTTTGTAATTTT-TAA-TTTTTTTAA
* *
59941839 -TTTTTGTACTTTTTCATTTTT
1 TTTTTTGTAATTTTTAATTTTT
59941860 AAAGATTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
25 4 0.10
26 2 0.05
27 10 0.26
28 17 0.44
29 6 0.15
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTTTGTAATTTTTAATTTTTTTAA
Found at i:59942331 original size:12 final size:12
Alignment explanation
Indices: 59942314--59942343 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
59942304 AAATTAAAAT
*
59942314 ATTTTTTTTTTA
1 ATTTTTTTTATA
59942326 ATTTTTTTTATA
1 ATTTTTTTTATA
59942338 ATTTTT
1 ATTTTT
59942344 AAATTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTTTTATA
Found at i:59949349 original size:16 final size:16
Alignment explanation
Indices: 59949317--59949346 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59949307 AAAATACTAA
59949317 AAATAATTTAATAAAT
1 AAATAATTTAATAAAT
59949333 AAAT-ATTTAATAAA
1 AAATAATTTAATAAA
59949347 ATACTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAATTTAATAAAT
Found at i:59950173 original size:73 final size:73
Alignment explanation
Indices: 59950087--59950232 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
59950077 AATCAAATGT
*
59950087 TGACCAAAGCATGAAAAATAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
1 TGACCAAAGCATGAAAAACAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
59950152 TATTTTAA
66 TATTTTAA
59950160 TGACCAAAGCATGAAAAACAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
1 TGACCAAAGCATGAAAAACAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
59950225 TATTTTAA
66 TATTTTAA
59950233 CCATTACCTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (73 bp):
TGACCAAAGCATGAAAAACAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
TATTTTAA
Found at i:59956448 original size:30 final size:30
Alignment explanation
Indices: 59956414--59956475 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
59956404 TTAAATTATA
*
59956414 AACCTTCTAAAAATAGAAAATTTATAATTT
1 AACCTTCTAAAAATAGAAAATTTATAAGTT
* * * *
59956444 AACCTTTTAAAACTAGTAAATTTTTAAGTT
1 AACCTTCTAAAAATAGAAAATTTATAAGTT
59956474 AA
1 AA
59956476 TACAATAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.39
Consensus pattern (30 bp):
AACCTTCTAAAAATAGAAAATTTATAAGTT
Found at i:59960836 original size:2 final size:2
Alignment explanation
Indices: 59960829--59960886 Score: 107
Period size: 2 Copynumber: 28.5 Consensus size: 2
59960819 TACTTATAAT
59960829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59960871 TA TA TA TA TA TGA TA T
1 TA TA TA TA TA T-A TA T
59960887 GTTTGGAAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 53 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59962411 original size:23 final size:23
Alignment explanation
Indices: 59962384--59962437 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
59962374 GTTGGGGTCA
59962384 TTGGGCCTTTAAGG-TTT-TCAATT
1 TTGGGCCTTT-AGGATTTGT-AATT
* *
59962407 TTGGGTCTTTTGGATTTGTAATT
1 TTGGGCCTTTAGGATTTGTAATT
59962430 TTGGGCCT
1 TTGGGCCT
59962438 GCAATTTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 23 0.88
24 1 0.04
ACGTcount: A:0.13, C:0.11, G:0.26, T:0.50
Consensus pattern (23 bp):
TTGGGCCTTTAGGATTTGTAATT
Found at i:59965423 original size:44 final size:44
Alignment explanation
Indices: 59965373--59965461 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
59965363 TGTCGGATAT
59965373 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
1 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
59965417 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
1 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
59965461 T
1 T
59965462 AGAAACTCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (44 bp):
TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
Found at i:59966077 original size:29 final size:29
Alignment explanation
Indices: 59966044--59966102 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
59966034 ATTTATTTTG
* *
59966044 TTTTGTTATTTAAATCATTGTTGATATCC
1 TTTTGTTATTTAAATAATTATTGATATCC
* *
59966073 TTTTGTTATTTGAATAATTATTGTTATCC
1 TTTTGTTATTTAAATAATTATTGATATCC
59966102 T
1 T
59966103 ATTCAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (29 bp):
TTTTGTTATTTAAATAATTATTGATATCC
Found at i:59969645 original size:12 final size:12
Alignment explanation
Indices: 59969628--59969664 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
59969618 ATTATATTTT
59969628 TATAAAAAATTA
1 TATAAAAAATTA
*
59969640 TATAAAAAATAA
1 TATAAAAAATTA
59969652 TATTAAAAAATTA
1 TA-TAAAAAATTA
59969665 ATTCGAGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TATAAAAAATTA
Found at i:59970057 original size:41 final size:41
Alignment explanation
Indices: 59970000--59970085 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
59969990 AAATAATAAA
59970000 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
1 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
59970041 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
1 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
59970082 ATAA
1 ATAA
59970086 ATGCATTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (41 bp):
ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
Found at i:59976909 original size:24 final size:24
Alignment explanation
Indices: 59976877--59976925 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
59976867 AGAACATCCT
* *
59976877 AAAAGTTAAGTGATAAAATGAAAA
1 AAAAATTAAGTAATAAAATGAAAA
* *
59976901 AAAAATTAAGTAATCAAATTAAAA
1 AAAAATTAAGTAATAAAATGAAAA
59976925 A
1 A
59976926 CGTCCTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.22
Consensus pattern (24 bp):
AAAAATTAAGTAATAAAATGAAAA
Found at i:59977051 original size:34 final size:36
Alignment explanation
Indices: 59976985--59977055 Score: 119
Period size: 34 Copynumber: 2.0 Consensus size: 36
59976975 ACATCATTAG
59976985 TTTATCTAAATTGATAACACTACTAATTATTTTCGT
1 TTTATCTAAATTGATAACACTACTAATTATTTTCGT
*
59977021 TTTATCTAAATTGAT-A-ACTATTAATTATTTTCGT
1 TTTATCTAAATTGATAACACTACTAATTATTTTCGT
59977055 T
1 T
59977056 AAACTGATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 18 0.53
35 1 0.03
36 15 0.44
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (36 bp):
TTTATCTAAATTGATAACACTACTAATTATTTTCGT
Found at i:59983567 original size:17 final size:19
Alignment explanation
Indices: 59983547--59983591 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
59983537 TTTTCTTTCA
59983547 AAAATATTTA-TTT-AAAT
1 AAAATATTTATTTTAAAAT
*
59983564 AAAATACTTATTTTAAAAT
1 AAAATATTTATTTTAAAAT
*
59983583 AATATATTT
1 AAAATATTT
59983592 TAAGATACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 3 0.13
19 11 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATTTATTTTAAAAT
Found at i:59983582 original size:14 final size:14
Alignment explanation
Indices: 59983563--59983602 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
59983553 TTTATTTAAA
59983563 TAAAATACTTATTT
1 TAAAATACTTATTT
*
59983577 TAAAATAATATATTT
1 TAAAATACT-TATTT
*
59983592 TAAGATACTTA
1 TAAAATACTTA
59983603 AATCTTGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TAAAATACTTATTT
Found at i:59985686 original size:17 final size:18
Alignment explanation
Indices: 59985647--59985693 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
59985637 ATAAAAAATT
59985647 AAAATTAA-AAAATATCAA
1 AAAATTAATAAAATA-CAA
59985665 AAAATTAATAAAATA-AA
1 AAAATTAATAAAATACAA
* *
59985682 TAAATAAATAAA
1 AAAATTAATAAA
59985694 TTATAGTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 12 0.46
18 8 0.31
19 6 0.23
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATTAATAAAATACAA
Found at i:59985687 original size:13 final size:13
Alignment explanation
Indices: 59985632--59985694 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
59985622 TAATAATATT
59985632 ATAAAATAAA-AA
1 ATAAAATAAATAA
59985644 ATTAAAATTAAA-AA
1 A-TAAAA-TAAATAA
*
59985658 ATATCAAA-AAATTA
1 ATA--AAATAAATAA
59985672 ATAAAATAAATAA
1 ATAAAATAAATAA
59985685 AT-AAATAAAT
1 ATAAAATAAAT
59985695 TATAGTAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
12 12 0.28
13 17 0.40
14 11 0.26
15 3 0.07
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAAAATAAATAA
Found at i:59988551 original size:19 final size:20
Alignment explanation
Indices: 59988521--59988558 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
59988511 TTAAGCTTTT
59988521 TATTTTTAATATAATTAAAA
1 TATTTTTAATATAATTAAAA
*
59988541 TATTTTT-ATATTATTAAA
1 TATTTTTAATATAATTAAA
59988559 TTACTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTTAATATAATTAAAA
Found at i:59997173 original size:10 final size:9
Alignment explanation
Indices: 59997145--59997178 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
59997135 CTATTTAAAT
59997145 TAAAAATTA
1 TAAAAATTA
59997154 TAAAAATTA
1 TAAAAATTA
*
59997163 TAAAATTTTA
1 TAAAA-ATTA
59997173 TAAAAA
1 TAAAAA
59997179 ATAGAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:60000090 original size:7 final size:7
Alignment explanation
Indices: 60000078--60000109 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
60000068 AAAGTATTTT
60000078 AAAATTA
1 AAAATTA
60000085 AAAATTA
1 AAAATTA
*
60000092 AAAAATA
1 AAAATTA
60000099 AAAATTA
1 AAAATTA
60000106 AAAA
1 AAAA
60000110 ATATATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAATTA
Found at i:60000100 original size:14 final size:14
Alignment explanation
Indices: 60000078--60000112 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
60000068 AAAGTATTTT
*
60000078 AAAATTAAAAATTA
1 AAAAATAAAAATTA
60000092 AAAAATAAAAATTA
1 AAAAATAAAAATTA
60000106 AAAAATA
1 AAAAATA
60000113 TATATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATAAAAATTA
Found at i:60000553 original size:28 final size:28
Alignment explanation
Indices: 60000514--60000579 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
60000504 ATAAAAATTA
60000514 ACCAAAATATTA-TAAGTTTTTT-TTATTT
1 ACCAAAATATTACT--GTTTTTTATTATTT
*
60000542 ACCAAAATATTACTTTTTTTTATTATTT
1 ACCAAAATATTACTGTTTTTTATTATTT
*
60000570 ACGAAAATAT
1 ACCAAAATAT
60000580 ACCAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 6 0.18
28 27 0.79
29 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (28 bp):
ACCAAAATATTACTGTTTTTTATTATTT
Found at i:60001066 original size:18 final size:19
Alignment explanation
Indices: 60001026--60001092 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 19
60001016 CTATTCTCAT
* *
60001026 TTAAATTAAACTAGAAGTTA
1 TTAAATGAAAATAG-AGTTA
* *
60001046 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
60001064 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
60001083 TTAAAT-AAAA
1 TTAAATGAAAA
60001093 AAATGAGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 19 0.49
19 9 0.23
20 11 0.28
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.36
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:60001100 original size:20 final size:19
Alignment explanation
Indices: 60001061--60001101 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
60001051 TGAGAATAGT
* *
60001061 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
60001080 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
60001100 TT
1 TT
60001102 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:60001468 original size:37 final size:37
Alignment explanation
Indices: 60001426--60001496 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
60001416 AGTATTACTT
60001426 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
60001463 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
60001497 AAAAAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:60001501 original size:19 final size:19
Alignment explanation
Indices: 60001432--60001500 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
60001422 ACTTAATAGT
60001432 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
60001451 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
60001469 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
60001488 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
60001501 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:60001662 original size:27 final size:27
Alignment explanation
Indices: 60001575--60001653 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 27
60001565 AATTTTAGTC
*
60001575 CTTTGGCACCATTGGTGCCGCCAATCA
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
60001602 CTTTGGCACCATTGGTGCCACCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
60001629 CTTTGGCA-CATTTGGTGCCGCCAAT
1 CTTTGGCACCA-TTGGTGCCGCCAAT
60001654 GTGATTGGCC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
26 2 0.04
27 46 0.96
ACGTcount: A:0.18, C:0.32, G:0.22, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:60001977 original size:30 final size:32
Alignment explanation
Indices: 60001943--60002003 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
60001933 CACTTTTTAA
60001943 ACAAT-TTTA-ATGATTTTCAATTTTTAAAAG
1 ACAATATTTATATGATTTTCAATTTTTAAAAG
** *
60001973 ACAATATTTATATTTTTTTGAATTTTTAAAA
1 ACAATATTTATATGATTTTCAATTTTTAAAA
60002004 ATTTAAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.19
31 4 0.15
32 17 0.65
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (32 bp):
ACAATATTTATATGATTTTCAATTTTTAAAAG
Found at i:60002218 original size:14 final size:14
Alignment explanation
Indices: 60002183--60002223 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
60002173 AAATAAGTCG
60002183 TTATACCTTTAAAA
1 TTATACCTTTAAAA
60002197 TTAT---TTTAAAA
1 TTATACCTTTAAAA
60002208 TTATACCTTTAAAA
1 TTATACCTTTAAAA
60002222 TT
1 TT
60002224 TAATCACAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 11 0.46
14 13 0.54
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (14 bp):
TTATACCTTTAAAA
Found at i:60005838 original size:6 final size:6
Alignment explanation
Indices: 60005827--60005858 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
60005817 CACTGGATGT
60005827 GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GC
1 GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GC
60005859 AGAAGATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.34, G:0.19, T:0.00
Consensus pattern (6 bp):
GCCAAA
Found at i:60029935 original size:20 final size:20
Alignment explanation
Indices: 60029910--60029957 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
60029900 GTTTATTTTT
60029910 AAATAATT-TTCTAAAAAATA
1 AAATAATTATT-TAAAAAATA
60029930 AAATAATTATTTAAAAAATA
1 AAATAATTATTTAAAAAATA
60029950 ATAATAAT
1 A-AATAAT
60029958 AAACAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATAATTATTTAAAAAATA
Found at i:60031981 original size:20 final size:21
Alignment explanation
Indices: 60031956--60032011 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
60031946 AAAACCTTTT
*
60031956 TTTTTAATTTTTTTTA-CTAA
1 TTTTTAATATTTTTTAGCTAA
*
60031976 TTTTTAGA-ATTTTATAGCTAA
1 TTTTTA-ATATTTTTTAGCTAA
*
60031997 TTTTT-ATGTTTTTTA
1 TTTTTAATATTTTTTA
60032012 ATTATCAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 1 0.03
20 18 0.62
21 10 0.34
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTTTAATATTTTTTAGCTAA
Found at i:60034808 original size:2 final size:2
Alignment explanation
Indices: 60034801--60034853 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
60034791 AATTCGTGTT
*
60034801 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60034843 TA TA TA TA TA T
1 TA TA TA TA TA T
60034854 GTTACACTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:60038261 original size:15 final size:15
Alignment explanation
Indices: 60038241--60038292 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
60038231 TATGTTTTAT
60038241 ATATTATTTTATATC
1 ATATTATTTTATATC
60038256 ATATTATTTTATATC
1 ATATTATTTTATATC
* * *
60038271 ATATTGTATTATATT
1 ATATTATTTTATATC
60038286 ATATTAT
1 ATATTAT
60038293 ATTAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (15 bp):
ATATTATTTTATATC
Found at i:60038280 original size:5 final size:5
Alignment explanation
Indices: 60038240--60038296 Score: 69
Period size: 5 Copynumber: 11.4 Consensus size: 5
60038230 TTATGTTTTA
* * * * *
60038240 TATAT TATTT TATAT CATAT TATTT TATAT CATAT TGTAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
60038290 TATAT TA
1 TATAT TA
60038297 AATAAACTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:60038521 original size:22 final size:22
Alignment explanation
Indices: 60038483--60038529 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
60038473 ATAAAAAGAC
60038483 AAAGAAACAAGAGAAGA-ACAGA
1 AAAGAAACAAGAGAAGAGAC-GA
60038505 AAAGAAAC-AGAGAAAGAGACGA
1 AAAGAAACAAGAG-AAGAGACGA
60038527 AAA
1 AAA
60038530 CAGGGGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 17 0.74
23 2 0.09
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAGAAACAAGAGAAGAGACGA
Found at i:60039635 original size:23 final size:19
Alignment explanation
Indices: 60039608--60039690 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 19
60039598 GGCTTTACTG
60039608 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCAC-TT-TGTGTCGT
60039629 ACATCAGGCACTTTGTGTCGT
1 --ATCAGGCACTTTGTGTCGT
**
60039650 ATCAGGCACCACGTGTGTCGT
1 ATCAGGCA-C-TTTGTGTCGT
* *
60039671 TTCTGGCACTTATGTGTCGT
1 ATCAGGCACTT-TGTGTCGT
60039691 TTTGGGCACA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 8 0.16
20 10 0.20
21 22 0.43
22 2 0.04
23 9 0.18
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (19 bp):
ATCAGGCACTTTGTGTCGT
Found at i:60048999 original size:2 final size:2
Alignment explanation
Indices: 60048992--60049018 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60048982 TAAAGTTAGC
60048992 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
60049019 GTAGAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60053053 original size:55 final size:55
Alignment explanation
Indices: 60052969--60053078 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
60052959 GTATGAGGGA
60052969 CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
1 CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
60053024 CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
1 CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
60053079 ACACTACAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (55 bp):
CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
Found at i:60056134 original size:3 final size:3
Alignment explanation
Indices: 60056075--60056119 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
60056065 GGTTATTATT
60056075 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
60056120 ACTGAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:60057125 original size:20 final size:21
Alignment explanation
Indices: 60057092--60057133 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
60057082 CTAATTCAAC
*
60057092 TCAAGAATTATCAAATTAAAT
1 TCAAGAATTATCAAATAAAAT
*
60057113 TCAA-AATTTTCAAATAAAAT
1 TCAAGAATTATCAAATAAAAT
60057133 T
1 T
60057134 GGAATAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (21 bp):
TCAAGAATTATCAAATAAAAT
Found at i:60057954 original size:34 final size:35
Alignment explanation
Indices: 60057899--60057965 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
60057889 CAAACACCAG
*
60057899 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
60057934 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
60057966 TATTTTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:60060030 original size:20 final size:19
Alignment explanation
Indices: 60059992--60060031 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
60059982 AAAATTCATA
*
60059992 AAAATAAAAAAATATATTT
1 AAAATAAAAAAATAGATTT
*
60060011 AAAATTAAAAAATAAGATTT
1 AAAATAAAAAAAT-AGATTT
60060031 A
1 A
60060032 GTCAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAATAAAAAAATAGATTT
Found at i:60065958 original size:33 final size:33
Alignment explanation
Indices: 60065921--60065987 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
60065911 GCTCTTTTAG
60065921 AGTTCACATCTTTTTAAGTAATTTTGAATCACT
1 AGTTCACATCTTTTTAAGTAATTTTGAATCACT
* **
60065954 AGTTCATATCTTTTTGGGTAATTTTGAATCACT
1 AGTTCACATCTTTTTAAGTAATTTTGAATCACT
60065987 A
1 A
60065988 AGTCGTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (33 bp):
AGTTCACATCTTTTTAAGTAATTTTGAATCACT
Found at i:60066513 original size:21 final size:21
Alignment explanation
Indices: 60066487--60066542 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
60066477 AACAGCGGTG
*
60066487 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
60066508 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
60066529 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
60066543 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:60078748 original size:18 final size:17
Alignment explanation
Indices: 60078706--60078757 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
60078696 CGATTATGTC
60078706 AAATTTAAGTATCAAGA
1 AAATTTAAGTATCAAGA
*
60078723 AATGTTTAAGTATCAA-A
1 AA-ATTTAAGTATCAAGA
60078740 TTAAATTTAA-TATCAAGA
1 --AAATTTAAGTATCAAGA
60078758 TAAGGGGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 9 0.31
18 18 0.62
19 2 0.07
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.35
Consensus pattern (17 bp):
AAATTTAAGTATCAAGA
Found at i:60082382 original size:28 final size:28
Alignment explanation
Indices: 60082347--60082403 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
60082337 GAACTACCCT
60082347 ATATACAAGATAACAAAATGATATACCA
1 ATATACAAGATAACAAAATGATATACCA
60082375 ATATACAAGATAACAAAATGATATACCA
1 ATATACAAGATAACAAAATGATATACCA
60082403 A
1 A
60082404 AAGTATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.58, C:0.14, G:0.07, T:0.21
Consensus pattern (28 bp):
ATATACAAGATAACAAAATGATATACCA
Found at i:60085365 original size:16 final size:16
Alignment explanation
Indices: 60085344--60085377 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
60085334 GTTTTTATGT
* *
60085344 TATAAATTATATAATA
1 TATAAATAACATAATA
60085360 TATAAATAACATAATA
1 TATAAATAACATAATA
60085376 TA
1 TA
60085378 ATGTATTATA
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:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAAATAACATAATA
Found at i:60089734 original size:18 final size:18
Alignment explanation
Indices: 60089707--60089769 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
60089697 GTGCACTAGT
* *
60089707 CACACATGCACTTTGTGC
1 CACACGTGCACTTAGTGC
*
60089725 AACACGTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
*
60089743 CACA-TTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
60089760 CACACGTGCA
1 CACACGTGCA
60089770 ACTCATACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 16 0.42
18 22 0.58
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (18 bp):
CACACGTGCACTTAGTGC
Found at i:60089753 original size:17 final size:16
Alignment explanation
Indices: 60089709--60089763 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
60089699 GCACTAGTCA
*
60089709 CACATGCACTTTGTGC
1 CACATGCACTTAGTGC
*
60089725 AACACGTGCACTTAGTGC
1 --CACATGCACTTAGTGC
60089743 CACATTGCACTTAGTGC
1 CACA-TGCACTTAGTGC
60089760 CACA
1 CACA
60089764 CGTGCAACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 3 0.09
17 16 0.48
18 14 0.42
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (16 bp):
CACATGCACTTAGTGC
Found at i:60089754 original size:35 final size:33
Alignment explanation
Indices: 60089697--60089769 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 33
60089687 CTTTGGAGAA
*
60089697 GTGCACTAGTCACACATGCACTTTGTGCAACAC
1 GTGCACTAGTCACACATGCACTTAGTGCAACAC
*
60089730 GTGCACTTAGTGC-CACATTGCACTTAGTGCCACAC
1 GTGCAC-TAGT-CACACA-TGCACTTAGTGCAACAC
60089765 GTGCA
1 GTGCA
60089770 ACTCATACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 6 0.17
34 8 0.23
35 21 0.60
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (33 bp):
GTGCACTAGTCACACATGCACTTAGTGCAACAC
Found at i:60089858 original size:18 final size:18
Alignment explanation
Indices: 60089802--60089863 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
60089792 GAAGTGCAGT
*
60089802 CACACGTGCAGTTAGTGC
1 CACACGTGCACTTAGTGC
60089820 CACATC-T-CACTT-GTGC
1 CACA-CGTGCACTTAGTGC
*
60089836 AACACGTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
60089854 CACACGTGCA
1 CACACGTGCA
60089864 ACTCATCTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 1 0.03
16 8 0.22
17 9 0.24
18 18 0.49
19 1 0.03
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (18 bp):
CACACGTGCACTTAGTGC
Found at i:60089929 original size:18 final size:18
Alignment explanation
Indices: 60089906--60090002 Score: 112
Period size: 18 Copynumber: 5.6 Consensus size: 18
60089896 GAAGTGAAGT
*
60089906 CACACGTGCAGTTAGTGC
1 CACACGTGCACTTAGTGC
60089924 CACACGTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
*
60089942 CATATC-T-CACTT-GTGC
1 CACA-CGTGCACTTAGTGC
* *
60089958 AACACGTGCACTTAGTGT
1 CACACGTGCACTTAGTGC
*
60089976 CACA-TTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
60089993 CACACGTGCA
1 CACACGTGCA
60090003 ACTCATCTCA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
15 1 0.02
16 7 0.11
17 25 0.38
18 31 0.48
19 1 0.02
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.26
Consensus pattern (18 bp):
CACACGTGCACTTAGTGC
Found at i:60089954 original size:70 final size:70
Alignment explanation
Indices: 60089837--60090066 Score: 249
Period size: 70 Copynumber: 3.3 Consensus size: 70
60089827 CACTTGTGCA
60089837 ACACGTGCACTTAGTGCCACACGTGCAACTCATCTCACCTCATACTTGTAATCTTTGGTGAAGTG
1 ACACGTGCACTTAGTGCCACACGTGCAACTCATCTCACCTCATACTTGTAATCTTTGGTGAAGTG
60089902 AAGTC
66 AAGTC
* * ** **
60089907 ACACGTGCAGTTAGTGCCACACGTGC-ACTTAGTGC-CATATC-TCACTTGTGCAA-C--ACGTG
1 ACACGTGCACTTAGTGCCACACGTGCAACTCA-T-CTCACCTCAT-ACTTGT--AATCTTTGGTG
* * * *
60089966 CACTTAGTGTC
61 AAGTGA-AGTC
*
60089977 ACA-TTGCACTTAGTGCCACACGTGCAACTCATCTCACCTCATACTTGTAATCTTTGGTGAAGTG
1 ACACGTGCACTTAGTGCCACACGTGCAACTCATCTCACCTCATACTTGTAATCTTTGGTGAAGTG
*
60090041 CAGTC
66 AAGTC
60090046 ACACGTGCACTTAGTGCCACA
1 ACACGTGCACTTAGTGCCACA
60090067 TTTCACTTGT
Statistics
Matches: 124, Mismatches: 23, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
67 2 0.02
68 2 0.02
69 48 0.39
70 68 0.55
71 2 0.02
72 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (70 bp):
ACACGTGCACTTAGTGCCACACGTGCAACTCATCTCACCTCATACTTGTAATCTTTGGTGAAGTG
AAGTC
Found at i:60089968 original size:34 final size:35
Alignment explanation
Indices: 60089912--60090002 Score: 123
Period size: 34 Copynumber: 2.6 Consensus size: 35
60089902 AAGTCACACG
* *
60089912 TGCAGTTAGTGCCACACGTGCACTTAGTGCCATAT
1 TGCACTTAGTGCCACACGTGCACTTAGTGCCACAT
* *
60089947 CT-CACTT-GTGCAACACGTGCACTTAGTGTCACAT
1 -TGCACTTAGTGCCACACGTGCACTTAGTGCCACAT
60089981 TGCACTTAGTGCCACACGTGCA
1 TGCACTTAGTGCCACACGTGCA
60090003 ACTCATCTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.02
34 29 0.60
35 17 0.35
36 1 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (35 bp):
TGCACTTAGTGCCACACGTGCACTTAGTGCCACAT
Found at i:60090078 original size:121 final size:121
Alignment explanation
Indices: 60089771--60090187 Score: 510
Period size: 121 Copynumber: 3.4 Consensus size: 121
60089761 ACACGTGCAA
*
60089771 CTCATACTTGTAATCTTTGGTGAAGTGCAGTCACACGTGCAGTTAGTGCCACATCTCACTTGTGC
1 CTCATACTTGTAATCTTTGGTGAAGTGCAGTCACACGTGCACTTAGTGCCACATCTCACTTGTGC
* * * * *
60089836 AACACGTGCACTTAGTGCCACACGTGCAACTCA-T-CTCAC-C-T-CATACT--TGTAAT
66 AACACGTGCACTTAGTGCCACA-TTGC-ACTTAGTGC-CACACGTGCA-ACTCATCTCAC
* ** * **** * * *
60089889 CT-TTGGTGAAGTGAAGTCACACGTGCAGT-TAGTGCCACACGTGCACTTAGTGCCATATCTCAC
1 CTCATACT--TGT-AA-TCTTTGGTGAAGTGCAGT--CACACGTGCACTTAGTGCCACATCTCAC
*
60089952 TTGTGCAACACGTGCACTTAGTGTCACATTGCACTTAGTGCCACACGTGCAACTCATCTCAC
60 TTGTGCAACACGTGCACTTAGTGCCACATTGCACTTAGTGCCACACGTGCAACTCATCTCAC
*
60090014 CTCATACTTGTAATCTTTGGTGAAGTGCAGTCACACGTGCACTTAGTGCCACATTTCACTTGTGC
1 CTCATACTTGTAATCTTTGGTGAAGTGCAGTCACACGTGCACTTAGTGCCACATCTCACTTGTGC
60090079 AACACGTGCACTTAGTGCCACATTGCACTTAGTGCCACACGTGCAACTCATCTCAC
66 AACACGTGCACTTAGTGCCACATTGCACTTAGTGCCACACGTGCAACTCATCTCAC
60090135 CTCATACTTGTAATCTTTGGTGAAGTGCAGTCACACGTGCACTTAGTGCCACA
1 CTCATACTTGTAATCTTTGGTGAAGTGCAGTCACACGTGCACTTAGTGCCACA
60090188 AGTGCACTTA
Statistics
Matches: 253, Mismatches: 31, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
117 2 0.01
118 2 0.01
119 2 0.01
120 9 0.04
121 155 0.61
122 63 0.25
123 9 0.04
124 4 0.02
125 5 0.02
126 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (121 bp):
CTCATACTTGTAATCTTTGGTGAAGTGCAGTCACACGTGCACTTAGTGCCACATCTCACTTGTGC
AACACGTGCACTTAGTGCCACATTGCACTTAGTGCCACACGTGCAACTCATCTCAC
Found at i:60090084 original size:34 final size:35
Alignment explanation
Indices: 60090046--60090123 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 35
60090036 AAGTGCAGTC
*
60090046 ACACGTGCACTTAGTGCCACATTTCACTT-GTGCA
1 ACACGTGCACTTAGTGCCACATTGCACTTAGTGCA
*
60090080 ACACGTGCACTTAGTGCCACATTGCACTTAGTGCC
1 ACACGTGCACTTAGTGCCACATTGCACTTAGTGCA
60090115 ACACGTGCA
1 ACACGTGCA
60090124 ACTCATCTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 28 0.68
35 13 0.32
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (35 bp):
ACACGTGCACTTAGTGCCACATTGCACTTAGTGCA
Found at i:60090090 original size:17 final size:18
Alignment explanation
Indices: 60090045--60090123 Score: 101
Period size: 17 Copynumber: 4.6 Consensus size: 18
60090035 GAAGTGCAGT
60090045 CACACGTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
* *
60090063 CACA-TTTCACTT-GTGC
1 CACACGTGCACTTAGTGC
*
60090079 AACACGTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
*
60090097 CACA-TTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
60090114 CACACGTGCA
1 CACACGTGCA
60090124 ACTCATCTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
16 7 0.14
17 28 0.56
18 15 0.30
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (18 bp):
CACACGTGCACTTAGTGC
Found at i:60090210 original size:18 final size:18
Alignment explanation
Indices: 60090166--60090211 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
60090156 GAAGTGCAGT
60090166 CACACGTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
*
60090184 CACAAGTGCACTTAGTGC
1 CACACGTGCACTTAGTGC
*
60090202 CTCACGTGCA
1 CACACGTGCA
60090212 ACTCATCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.22
Consensus pattern (18 bp):
CACACGTGCACTTAGTGC
Found at i:60090228 original size:88 final size:87
Alignment explanation
Indices: 60090080--60090253 Score: 312
Period size: 88 Copynumber: 2.0 Consensus size: 87
60090070 CACTTGTGCA
*
60090080 ACACGTGCACTTAGTGCCACATTGCACTTAGTGCCACACGTGCAACTCATCTCACCTCATACTTG
1 ACACGTGCACTTAGTGCCACAGTGCACTTAGTGCCACACGTGCAACTCATCTCACCTCATACTTG
*
60090145 TAATCTTTGGTGAAGTGCAGTC
66 TAATCTTCGGTGAAGTGCAGTC
*
60090167 ACACGTGCACTTAGTGCCACAAGTGCACTTAGTGCCTCACGTGCAACTCATCTCACCTCATACTT
1 ACACGTGCACTTAGTGCCAC-AGTGCACTTAGTGCCACACGTGCAACTCATCTCACCTCATACTT
60090232 GTAATCTTCGGTGAAGTGCAGT
65 GTAATCTTCGGTGAAGTGCAGT
60090254 TTGGGGAGGG
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
87 20 0.24
88 63 0.76
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (87 bp):
ACACGTGCACTTAGTGCCACAGTGCACTTAGTGCCACACGTGCAACTCATCTCACCTCATACTTG
TAATCTTCGGTGAAGTGCAGTC
Found at i:60091311 original size:6 final size:6
Alignment explanation
Indices: 60091302--60091339 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
60091292 TCTCTTTAAC
*
60091302 GTTGGT GTTGGT GTTGGT GTTGGT GATGGT GTTGGT GT
1 GTTGGT GTTGGT GTTGGT GTTGGT GTTGGT GTTGGT GT
60091340 GATGTGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (6 bp):
GTTGGT
Found at i:60105564 original size:18 final size:18
Alignment explanation
Indices: 60105541--60105589 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
60105531 ATAAATACCA
60105541 AAAAAATATTTTAAAAAT
1 AAAAAATATTTTAAAAAT
60105559 AAAAAATATTTT-AAAAT
1 AAAAAATATTTTAAAAAT
*
60105576 AAAATATATATTTA
1 AAAAAATAT-TTTA
60105590 TTATATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAAATATTTTAAAAAT
Found at i:60108467 original size:3 final size:3
Alignment explanation
Indices: 60108459--60108486 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
60108449 TCTGCAGTTT
60108459 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
60108487 GACATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:60108536 original size:4 final size:4
Alignment explanation
Indices: 60108527--60108570 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
60108517 CAAAAATCTT
60108527 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
60108571 AATGAATGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:60116989 original size:18 final size:17
Alignment explanation
Indices: 60116945--60116989 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
60116935 TAATTGAGAA
60116945 AAAATAATTATT-ATTTT
1 AAAATAA-TATTAATTTT
60116962 -AAAT-ATATTAATTTAT
1 AAAATAATATTAATTT-T
60116978 AAAATAATATTA
1 AAAATAATATTA
60116990 GATAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.17
15 5 0.21
16 5 0.21
17 4 0.17
18 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATAATATTAATTTT
Found at i:60117108 original size:92 final size:93
Alignment explanation
Indices: 60116993--60117191 Score: 357
Period size: 92 Copynumber: 2.2 Consensus size: 93
60116983 AATATTAGAT
*
60116993 AATAT-TTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTTTATATT
1 AATATATTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
60117057 TAATTGAG-AAAAATAATTATTATTTTA
66 TAATTGAGAAAAAATAATTATTATTTTA
* *
60117084 AATATATTAGTTTATAAAATAATATGTTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
1 AATATATTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
60117149 TAATTGAGAAAAAATAATTATTATTTTA
66 TAATTGAGAAAAAATAATTATTATTTTA
60117177 AATATATTAATTTAT
1 AATATATTAATTTAT
60117192 TTTTAATATT
Statistics
Matches: 102, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
91 5 0.05
92 64 0.63
93 33 0.32
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (93 bp):
AATATATTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
TAATTGAGAAAAAATAATTATTATTTTA
Found at i:60117130 original size:214 final size:214
Alignment explanation
Indices: 60116896--60117322 Score: 766
Period size: 214 Copynumber: 2.0 Consensus size: 214
60116886 GTGTTTTTAA
60116896 TTAATTATTAATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAATTATTATTT
1 TTAATTATTAATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAATTATTATTT
* *
60116961 TAAATATATTAATTTATAAAATAATATTAGATAATATTTAATTTATAAAATAATATATTAATTAT
66 TAAATATATTAATTTAT-AAATAATATTAGATAAGATTCAATTTATAAAATAATATATTAATTAT
* *
60117026 TAATGATCGAAGCACTTAATTTTTTTATATTTAATTGAG-AAAAATAATTATTATTTTAAATATA
130 TAATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAAATATTATTTTAAATATA
*
60117090 TTAGTTTATAAAATAATATG
195 TTAATTTATAAAATAATATG
60117110 TTAATTATTAATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAATTATTATTT
1 TTAATTATTAATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAATTATTATTT
***
60117175 TAAATATATTAATTTATTTTTAATATTAGATAAGATTCAATTTATAAAATAATATATTAATTATT
66 TAAATATATTAATTTATAAATAATATTAGATAAGATTCAATTTATAAAATAATATATTAATTATT
60117240 AATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAAATATTATTTTAAATATAT
131 AATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAAATATTATTTTAAATATAT
60117305 TAATTTATAAAATAATAT
196 TAATTTATAAAATAATAT
60117323 TAGATAATAT
Statistics
Matches: 204, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
213 80 0.39
214 124 0.61
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (214 bp):
TTAATTATTAATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAATTATTATTT
TAAATATATTAATTTATAAATAATATTAGATAAGATTCAATTTATAAAATAATATATTAATTATT
AATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAAATATTATTTTAAATATAT
TAATTTATAAAATAATATG
Found at i:60117318 original size:29 final size:29
Alignment explanation
Indices: 60117285--60117608 Score: 102
Period size: 29 Copynumber: 10.8 Consensus size: 29
60117275 GAGAAAAAAT
*
60117285 AAATATTATTTTAAATATATTAATTTATA
1 AAATAATATTTTAAATATATTAATTTATA
**
60117314 AAATAATATTAGATAATAT-TTAATTTATA
1 AAATAATATTTTA-AATATATTAATTTATA
* *
60117343 AAATAATATATT-AAT-TATTAA-TGATCGA
1 AAATAATATTTTAAATATATTAATTTAT--A
** * * *
60117371 AGCGCTTAATCTTTTAAA-AT-TTAATTGAGAAA
1 A---AATAATATTTTAAATATATTAATT--TATA
60117403 AAATAAATATTATTTTAAATATATTAATTTATA
1 AAAT--A-A-TATTTTAAATATATTAATTTATA
* **
60117436 AAATAACATTAGATAATAT-TTAATTTATA
1 AAATAATATTTTA-AATATATTAATTTATA
* *
60117465 AAATAATATATT-AAT-TATTAA-TGATCGA
1 AAATAATATTTTAAATATATTAATTTAT--A
** * * *
60117493 AGCGCTTAATCTTTTAAA-AT-TTAATTGAGAAA
1 A---AATAATATTTTAAATATATTAATT--TATA
60117525 AAATAAATATTATTTTAAATATATTAATTTATA
1 AAAT--A-A-TATTTTAAATATATTAATTTATA
* **
60117558 AAATAACATTAGATAATAT-TTAATTTATA
1 AAATAATATTTTA-AATATATTAATTTATA
*
60117587 AAATAATATATT-AAT-TATTAAT
1 AAATAATATTTTAAATATATTAAT
60117609 GATCGAAGCG
Statistics
Matches: 215, Mismatches: 42, Indels: 78
0.64 0.13 0.23
Matches are distributed among these distances:
26 9 0.04
27 22 0.10
28 4 0.02
29 75 0.35
30 17 0.08
31 26 0.12
32 14 0.07
33 28 0.13
34 8 0.04
35 12 0.06
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
AAATAATATTTTAAATATATTAATTTATA
Found at i:60117324 original size:18 final size:17
Alignment explanation
Indices: 60117280--60117324 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
60117270 TAATTGAGAA
60117280 AAAATAAATATT-ATTTT
1 AAAAT-AATATTAATTTT
60117297 -AAAT-ATATTAATTTAT
1 AAAATAATATTAATTT-T
60117313 AAAATAATATTA
1 AAAATAATATTA
60117325 GATAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 5 0.21
15 4 0.17
16 5 0.21
17 4 0.17
18 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATAATATTAATTTT
Found at i:60117730 original size:122 final size:122
Alignment explanation
Indices: 60117084--60117695 Score: 1046
Period size: 122 Copynumber: 5.0 Consensus size: 122
60117074 TATTATTTTA
* * * * *
60117084 AATATATTAGTTTATAAAATAATATGTTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
1 AATAT-TTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATT
* ***
60117149 TAATTGAGAAAAAATAATTATTATTTTAAATATATTAATTTAT-TTTTAATATTAGAT
65 TAATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
* * * * *
60117206 AAGATTCAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTTAATATTT
1 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATTT
60117271 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
66 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
60117328 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATTT
1 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATTT
*
60117393 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAACATTAGAT
66 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
60117450 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATTT
1 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATTT
*
60117515 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAACATTAGAT
66 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
60117572 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATTT
1 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATTT
* *
60117637 AATTGAGAAAAAATAATTATTATTTTAAATATTTTAATTTATAAAATAATATTAGAT
66 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
60117694 AA
1 AA
60117696 GAAATTGGGG
Statistics
Matches: 472, Mismatches: 17, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
121 98 0.21
122 374 0.79
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (122 bp):
AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATTT
AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
Found at i:60118469 original size:21 final size:21
Alignment explanation
Indices: 60118423--60118485 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
60118413 CCTGATCAGT
* *
60118423 AAACGACACATAA-GTGTCTG
1 AAACGACACACAAGGTGCCTG
*
60118443 AAACGACACACGAGGTGCCTG
1 AAACGACACACAAGGTGCCTG
* *
60118464 ATACGACACATAAGGTGCCTG
1 AAACGACACACAAGGTGCCTG
60118485 A
1 A
60118486 GATACAATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 11 0.31
21 25 0.69
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (21 bp):
AAACGACACACAAGGTGCCTG
Found at i:60118532 original size:23 final size:22
Alignment explanation
Indices: 60118457--60118531 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 22
60118447 GACACACGAG
* *
60118457 GTGCCTGA-TACGACACATAAG
1 GTGCCTGAGTACAACACATAAA
*
60118478 GTGCCTGAGATACAATACATAAA
1 GTGCCTGAG-TACAACACATAAA
**
60118501 GTGTTTGATGTACAACACATAAA
1 GTGCCTGA-GTACAACACATAAA
60118524 GTGCCTGA
1 GTGCCTGA
60118532 TTGGCCAAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 8 0.19
23 34 0.79
24 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (22 bp):
GTGCCTGAGTACAACACATAAA
Found at i:60118894 original size:16 final size:17
Alignment explanation
Indices: 60118873--60118904 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
60118863 TAAGAATAAT
60118873 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
60118889 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
60118905 GCTTGCCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:60119980 original size:18 final size:19
Alignment explanation
Indices: 60119936--60119973 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
60119926 CTATTTGATT
60119936 TAATTTATAATATAATATCA
1 TAATTT-TAATATAATATCA
60119956 TAATTTTAAT-TAATATCA
1 TAATTTTAATATAATATCA
60119974 AGATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATTTTAATATAATATCA
Found at i:60119981 original size:19 final size:20
Alignment explanation
Indices: 60119936--60119982 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
60119926 CTATTTGATT
*
60119936 TAATTTATAATATAATATCA
1 TAATTTTTAATATAATATCA
60119956 TAA-TTTTAAT-TAATATCA
1 TAATTTTTAATATAATATCA
60119974 -AGATTTTTA
1 TA-ATTTTTA
60119983 TGAAGTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 9 0.38
19 11 0.46
20 3 0.12
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
TAATTTTTAATATAATATCA
Done.