Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 32 of 34
Found at i:5083257 original size:33 final size:32
Alignment explanation
Indices: 5083200--5083267 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
5083190 GTAGCTAAAT
**
5083200 TTGTATCAATACACACAATCTGTATCGATACA
1 TTGTATCAATACACACAAAATGTATCGATACA
*
5083232 TTGTATCGATACACCACAAAATGTATCGATACA
1 TTGTATCAATACA-CACAAAATGTATCGATACA
5083265 TTG
1 TTG
5083268 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.31
Consensus pattern (32 bp):
TTGTATCAATACACACAAAATGTATCGATACA
Found at i:5089578 original size:22 final size:21
Alignment explanation
Indices: 5089535--5089575 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5089525 CAAAATTCTT
5089535 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
5089557 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
5089576 ATCAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:5091830 original size:20 final size:20
Alignment explanation
Indices: 5091799--5091855 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
5091789 GTCAAAACCC
*
5091799 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
5091819 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
5091839 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
5091856 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:5091859 original size:13 final size:13
Alignment explanation
Indices: 5091841--5091882 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
5091831 ATACAGATTG
5091841 CATTGTATCGATA
1 CATTGTATCGATA
5091854 CATTGTATCGATA
1 CATTGTATCGATA
5091867 CATTGTATCGATA
1 CATTGTATCGATA
5091880 CAT
1 CAT
5091883 GACAAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:5091895 original size:20 final size:21
Alignment explanation
Indices: 5091870--5091922 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
5091860 ATCGATACAT
*
5091870 TGTATCGATACATGACAAA-A
1 TGTATCGATACATGAAAAAGA
*
5091890 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
5091911 TGTATCGATACA
1 TGTATCGATACA
5091923 GGTCATTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:5091992 original size:13 final size:13
Alignment explanation
Indices: 5091974--5091998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5091964 ACACACAATC
5091974 TGTATCGATACAT
1 TGTATCGATACAT
5091987 TGTATCGATACA
1 TGTATCGATACA
5091999 CTACAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5092016 original size:33 final size:32
Alignment explanation
Indices: 5091954--5092021 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
5091944 GTAGCTAAAT
**
5091954 TTGTATCAATACACACAATCTGTATCGATACA
1 TTGTATCAATACACACAAAATGTATCGATACA
*
5091986 TTGTATCGATACACTACAAAATGTATCGATACA
1 TTGTATCAATACAC-ACAAAATGTATCGATACA
5092019 TTG
1 TTG
5092022 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (32 bp):
TTGTATCAATACACACAAAATGTATCGATACA
Found at i:5097835 original size:52 final size:52
Alignment explanation
Indices: 5097757--5097885 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
5097747 CGAAATATGA
* *
5097757 AAATTTGCCTGCATGTATAGATACATTGAATAATGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
** * *
5097809 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATTGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
5097861 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
5097886 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
Found at i:5097898 original size:52 final size:51
Alignment explanation
Indices: 5097757--5097905 Score: 199
Period size: 52 Copynumber: 2.9 Consensus size: 51
5097747 CGAAATATGA
* *
5097757 AAATTTGCCTGCATGTATAGATACATTGAATAATGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAATGTATCGATACATCTGGGC
* * *
5097809 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATTGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACA-TTGATAATGTATCGATACATCTGGGC
** *
5097861 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AATGTATCGATACA
5097906 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAATGTATCGATACATCTGGGC
Found at i:5097912 original size:13 final size:13
Alignment explanation
Indices: 5097894--5097918 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5097884 CAAAGATCAG
5097894 TGTATCGATACAA
1 TGTATCGATACAA
5097907 TGTATCGATACA
1 TGTATCGATACA
5097919 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5097996 original size:33 final size:33
Alignment explanation
Indices: 5097959--5098025 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5097949 AGTAGCTTGA
5097959 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
5097992 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
5098025 A
1 A
5098026 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:5097999 original size:13 final size:13
Alignment explanation
Indices: 5097981--5098005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5097971 CAAAAAAATA
5097981 TGTATCGATACAT
1 TGTATCGATACAT
5097994 TGTATCGATACA
1 TGTATCGATACA
5098006 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5103428 original size:13 final size:13
Alignment explanation
Indices: 5103410--5103435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5103400 CAATTTTTTG
5103410 TGTATCGATACAT
1 TGTATCGATACAT
5103423 TGTATCGATACAT
1 TGTATCGATACAT
5103436 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5103520 original size:20 final size:20
Alignment explanation
Indices: 5103495--5103567 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
5103485 CATCCTTTTT
5103495 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
5103515 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
5103536 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
5103556 ATGTATCGATAC
1 ATGTATCGATAC
5103568 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:5103540 original size:21 final size:21
Alignment explanation
Indices: 5103474--5103550 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
5103464 CTGCCAAGAA
*
5103474 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
5103495 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
5103515 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
5103536 ATGTATCGATACATT
1 ATGTATCGATACATT
5103551 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:5103540 original size:41 final size:41
Alignment explanation
Indices: 5103474--5103567 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
5103464 CTGCCAAGAA
5103474 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
5103515 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
5103556 ATGTATCGATAC
1 ATGTATCGATAC
5103568 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:5108099 original size:15 final size:15
Alignment explanation
Indices: 5108079--5108109 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5108069 ATTTCGTTTG
*
5108079 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5108094 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5108109 G
1 G
5108110 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:5112189 original size:13 final size:13
Alignment explanation
Indices: 5112171--5112196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5112161 CAATTTTTTG
5112171 TGTATCGATACAT
1 TGTATCGATACAT
5112184 TGTATCGATACAT
1 TGTATCGATACAT
5112197 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5112281 original size:20 final size:20
Alignment explanation
Indices: 5112256--5112328 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
5112246 CATCCTTTTT
5112256 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
5112276 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
5112297 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
5112317 ATGTATCGATAC
1 ATGTATCGATAC
5112329 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:5112301 original size:21 final size:21
Alignment explanation
Indices: 5112235--5112311 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
5112225 CTGCCAAGAA
*
5112235 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
5112256 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
5112276 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
5112297 ATGTATCGATACATT
1 ATGTATCGATACATT
5112312 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:5112301 original size:41 final size:41
Alignment explanation
Indices: 5112235--5112328 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
5112225 CTGCCAAGAA
5112235 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
5112276 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
5112317 ATGTATCGATAC
1 ATGTATCGATAC
5112329 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:5115514 original size:13 final size:13
Alignment explanation
Indices: 5115496--5115520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5115486 TACATGGTAC
5115496 ATTGTATCGATAT
1 ATTGTATCGATAT
5115509 ATTGTATCGATA
1 ATTGTATCGATA
5115521 CATAGTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:5116609 original size:81 final size:81
Alignment explanation
Indices: 5116328--5116743 Score: 489
Period size: 81 Copynumber: 5.2 Consensus size: 81
5116318 ACATTAAAAA
** * * * * * * * *
5116328 GGGATACTCCAACCCCACCATTTTTAAAGAGATACTCTAATCTCGTCTTCACTTCCAAAAAATAT
1 GGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAACCCCATCTTTATTTCC-AAAAACAT
5116393 CGAATTTTTCATCTTTG
65 CGAATTTTTCATCTTTG
* * *
5116410 GGGATACTCCAACCCCACCATTTTC-AAGAGGATACTCTAACCCCATATTTATTACCAAAAACAT
1 GGGATACTCCAACCCCACCATTTTCGAAG-GGATACTCCAACCCCATCTTTATTTCCAAAAACAT
* * *
5116474 TGAATTTTCCATC-TTA
65 CGAATTTTTCATCTTTG
* * *
5116490 GGGATACTCCAACCCCACCATTTTTGAAGGGATGCTCCAACCCCGTCTTTATTTCCAAAAACATC
1 GGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAACCCCATCTTTATTTCCAAAAACATC
*
5116555 AAATTTTTCATCTTTG
66 GAATTTTTCATCTTTG
** * *
5116571 GGGATACTCCAACCCCACCATTACCGAGGGGATACTCCAAACCCATCTTTATTTCCAAAAACATC
1 GGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAACCCCATCTTTATTTCCAAAAACATC
* *
5116636 AAATTTTTCATCTTCG
66 GAATTTTTCATCTTTG
* * * *
5116652 GGGATACTCCAACCCCGCCATTTTCGAAAGGATACTCCAACCCCATTTTTA-TT-CAAAAACATT
1 GGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAACCCCATCTTTATTTCCAAAAACATC
* * *
5116715 GAGTTTTCCATTTTTG
66 GAATTTTTCATCTTTG
5116731 GGGATACTCCAAC
1 GGGATACTCCAAC
5116744 TCCATTTTTA
Statistics
Matches: 287, Mismatches: 44, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
79 33 0.11
80 68 0.24
81 143 0.50
82 43 0.15
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (81 bp):
GGGATACTCCAACCCCACCATTTTCGAAGGGATACTCCAACCCCATCTTTATTTCCAAAAACATC
GAATTTTTCATCTTTG
Found at i:5119258 original size:12 final size:13
Alignment explanation
Indices: 5119203--5119258 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 13
5119193 TATCAATTTT
5119203 TTTAATTATATTA
1 TTTAATTATATTA
*
5119216 TTGAAATTATTATTA
1 TT-TAATTA-TATTA
* *
5119231 TTTTAGTAT-TTA
1 TTTAATTATATTA
5119243 TTTAATTATATT-
1 TTTAATTATATTA
5119255 TTTA
1 TTTA
5119259 TGTTAGTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
12 14 0.41
13 5 0.15
14 8 0.24
15 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (13 bp):
TTTAATTATATTA
Found at i:5119315 original size:16 final size:19
Alignment explanation
Indices: 5119278--5119319 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
5119268 TTTTTAAAAA
5119278 ATTAATAAAAGATCATATT
1 ATTAATAAAAGATCATATT
*
5119297 ATTAATAAAAGATAATATT
1 ATTAATAAAAGATCATATT
5119316 ATTA
1 ATTA
5119320 CATTTATGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (19 bp):
ATTAATAAAAGATCATATT
Found at i:5119423 original size:28 final size:28
Alignment explanation
Indices: 5119366--5119425 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
5119356 TATAATTGTG
* * * *
5119366 TTAAAATATTTAATTTAATTTGTTTGAT
1 TTAAAATATTTAATCTAAGTTGTATCAT
5119394 TTAAAAT-TTTAATCTAAGTTGTAATCAT
1 TTAAAATATTTAATCTAAGTTGT-ATCAT
5119422 TTAA
1 TTAA
5119426 TTATTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (28 bp):
TTAAAATATTTAATCTAAGTTGTATCAT
Found at i:5119458 original size:39 final size:38
Alignment explanation
Indices: 5119393--5119583 Score: 123
Period size: 38 Copynumber: 5.4 Consensus size: 38
5119383 ATTTGTTTGA
* * *
5119393 TTTAAAATTTTAATCT-A-AGTTGTAATCATTTAATTATT
1 TTTAAAATTTAAAT-TAAGAGTTATAATCATCTAATTA-T
*
5119431 TTTTAAATTTAAATTAAGAGTTATAATCATCTAATTAT
1 TTTAAAATTTAAATTAAGAGTTATAATCATCTAATTAT
*
5119469 TTTAAAATTTAAATT----G-TA-AATGC--CTACTTAT
1 TTTAAAATTTAAATTAAGAGTTATAAT-CATCTAATTAT
* *
5119500 TTT-AAA--T---TT-A-AGTTCTAATCCTCTAATTAT
1 TTTAAAATTTAAATTAAGAGTTATAATCATCTAATTAT
* *
5119530 TTTAAAATTTTAATTTA-AGTTATAATCATCTAATTATT
1 TTTAAAATTTAAATTAAGAGTTATAATCATCTAATTA-T
*
5119568 TTTAAAATTTTAATTA
1 TTTAAAATTTAAATTA
5119584 TTTTAAATTG
Statistics
Matches: 125, Mismatches: 11, Indels: 34
0.74 0.06 0.20
Matches are distributed among these distances:
25 2 0.02
27 1 0.01
28 3 0.02
29 3 0.02
30 13 0.10
31 13 0.10
32 3 0.02
33 4 0.03
34 1 0.01
36 2 0.02
37 19 0.15
38 44 0.35
39 17 0.14
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (38 bp):
TTTAAAATTTAAATTAAGAGTTATAATCATCTAATTAT
Found at i:5119530 original size:30 final size:30
Alignment explanation
Indices: 5119438--5119535 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
5119428 ATTTTTTAAA
* *
5119438 TTTAAATTAAGAGTTATAATCATCTAATTAT
1 TTTAAATTTA-AGTTATAATCCTCTAATTAT
* * * *
5119469 TTTAAAATTTAAATTGTAAATGC-CTACTTAT
1 TTT-AAATTTAAGTTAT-AATCCTCTAATTAT
*
5119500 TTTAAATTTAAGTTCTAATCCTCTAATTAT
1 TTTAAATTTAAGTTATAATCCTCTAATTAT
5119530 TTTAAA
1 TTTAAA
5119536 ATTTTAATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
29 4 0.07
30 24 0.44
31 17 0.31
32 9 0.17
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (30 bp):
TTTAAATTTAAGTTATAATCCTCTAATTAT
Found at i:5119531 original size:100 final size:98
Alignment explanation
Indices: 5119399--5119582 Score: 262
Period size: 99 Copynumber: 1.9 Consensus size: 98
5119389 TTGATTTAAA
* * *
5119399 ATTTTAATCTAAGTTGTAATCATTTAATTATTTTTTAAATTTAAATTAAGAGTTATAATCATCTA
1 ATTTTAATCTAAGTTCTAATCATCTAATTA-TTTTAAAATTTAAATTAA-AGTTATAATCATCTA
5119464 ATTA-TTTTAAAATTTAAATTGTAAATGCCTACTT
64 ATTATTTTTAAAATTTAAATTGTAAATGCCTACTT
* * * *
5119498 ATTTTAAATTTAAGTTCTAATCCTCTAATTATTTTAAAATTTTAATTTAAGTTATAATCATCTAA
1 ATTTT-AATCTAAGTTCTAATCATCTAATTATTTTAAAATTTAAATTAAAGTTATAATCATCTAA
*
5119563 TTATTTTTAAAATTTTAATT
65 TTATTTTTAAAATTTAAATT
5119583 ATTTTAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
98 19 0.25
99 35 0.47
100 21 0.28
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (98 bp):
ATTTTAATCTAAGTTCTAATCATCTAATTATTTTAAAATTTAAATTAAAGTTATAATCATCTAAT
TATTTTTAAAATTTAAATTGTAAATGCCTACTT
Found at i:5119545 original size:37 final size:38
Alignment explanation
Indices: 5119498--5119582 Score: 136
Period size: 37 Copynumber: 2.2 Consensus size: 38
5119488 ATGCCTACTT
* *
5119498 ATTTTAAATTTAAGTTCTAATCCTCTAATTA-TTTTAAA
1 ATTTT-AATTTAAGTTATAATCATCTAATTATTTTTAAA
5119536 ATTTTAATTTAAGTTATAATCATCTAATTATTTTTAAA
1 ATTTTAATTTAAGTTATAATCATCTAATTATTTTTAAA
5119574 ATTTTAATT
1 ATTTTAATT
5119583 ATTTTAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 23 0.52
38 21 0.48
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (38 bp):
ATTTTAATTTAAGTTATAATCATCTAATTATTTTTAAA
Found at i:5119912 original size:20 final size:20
Alignment explanation
Indices: 5119889--5119959 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
5119879 AATAAATACC
5119889 AATATAATAATATAATTAAA
1 AATATAATAATATAATTAAA
*
5119909 AATAT--TAACATAA-TAATA
1 AATATAATAATATAATTAA-A
* *
5119927 AATCTAATAATATTATTAAA
1 AATATAATAATATAATTAAA
*
5119947 AAAATAATAATAT
1 AATATAATAATAT
5119960 TGTAATAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
17 3 0.07
18 12 0.29
20 23 0.56
21 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AATATAATAATATAATTAAA
Found at i:5119924 original size:29 final size:28
Alignment explanation
Indices: 5119892--5119959 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
5119882 AAATACCAAT
* *
5119892 ATAATAATATAATTAAAAATATTAACATA
1 ATAATAATATAA-TAAAAATATTAAAAAA
* * *
5119921 ATAATAAATCTAATAATATTATTAAAAAA
1 ATAAT-AATATAATAAAAATATTAAAAAA
5119950 ATAATAATAT
1 ATAATAATAT
5119960 TGTAATAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 4 0.12
29 22 0.69
30 6 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (28 bp):
ATAATAATATAATAAAAATATTAAAAAA
Found at i:5119938 original size:26 final size:26
Alignment explanation
Indices: 5119892--5119941 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5119882 AAATACCAAT
5119892 ATAATAATATAATTAAAAATATTAAC
1 ATAATAATATAATTAAAAATATTAAC
*
5119918 ATAATAATA-AATCTAATAATATTA
1 ATAATAATATAAT-TAAAAATATTA
5119942 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (26 bp):
ATAATAATATAATTAAAAATATTAAC
Found at i:5120188 original size:28 final size:28
Alignment explanation
Indices: 5120160--5120220 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
5120150 CGAATCAAAA
*
5120160 TAATAATATTTTGATAATTTATTTTAAAT
1 TAATAATA-TTTAATAATTTATTTTAAAT
** *
5120189 TAATTTTATTTAATAATTTATTTAAAAAT
1 TAATAATATTTAATAATTTATTT-TAAAT
5120218 TAA
1 TAA
5120221 AAACACTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TAATAATATTTAATAATTTATTTTAAAT
Found at i:5124018 original size:10 final size:10
Alignment explanation
Indices: 5124003--5124093 Score: 84
Period size: 10 Copynumber: 9.3 Consensus size: 10
5123993 TAAATGATAT
5124003 AATATATTTA
1 AATATATTTA
*
5124013 AATATAATT-
1 AATATATTTA
5124022 AATATATTTA
1 AATATATTTA
5124032 ATATATATTTA
1 A-ATATATTTA
* *
5124043 TATTTATTTTA
1 AATATA-TTTA
*
5124054 AAAAT-TTTA
1 AATATATTTA
5124063 AA-ATATTT-
1 AATATATTTA
5124071 AATA-ATTTA
1 AATATATTTA
5124080 TAATATATTTA
1 -AATATATTTA
5124091 AAT
1 AAT
5124094 TTTTTACACA
Statistics
Matches: 66, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
8 8 0.12
9 18 0.27
10 20 0.30
11 20 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AATATATTTA
Found at i:5124037 original size:9 final size:9
Alignment explanation
Indices: 5124002--5124091 Score: 59
Period size: 9 Copynumber: 10.3 Consensus size: 9
5123992 ATAAATGATA
5124002 TAATATATT
1 TAATATATT
*
5124011 TAAATATAAT
1 T-AATATATT
5124021 TAATATATT
1 TAATATATT
5124030 TAATATATAT
1 TAATATAT-T
5124040 T--TATATT
1 TAATATATT
5124047 T-AT-T-TT
1 TAATATATT
* *
5124053 AAAAAT-TT
1 TAATATATT
*
5124061 TAAAATATT
1 TAATATATT
5124070 TAATA-ATTT
1 TAATATA-TT
5124079 ATAATATATT
1 -TAATATATT
5124089 TAA
1 TAA
5124092 ATTTTTTACA
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
6 2 0.03
7 4 0.06
8 15 0.23
9 27 0.41
10 17 0.26
11 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TAATATATT
Found at i:5124090 original size:19 final size:20
Alignment explanation
Indices: 5124000--5124091 Score: 70
Period size: 19 Copynumber: 4.7 Consensus size: 20
5123990 TAATAAATGA
5124000 TATAATATATTT-A-AATAT
1 TATAATATATTTAATAATAT
*
5124018 AATTAATATATTTAATATATAT
1 TA-TAATATATTTAATA-ATAT
*
5124040 T-TATATTTATTTTAA-AA-AT
1 TATA-ATATA-TTTAATAATAT
* *
5124059 TTTAAAATATTTAATAAT-T
1 TATAATATATTTAATAATAT
5124078 TATAATATATTTAA
1 TATAATATATTTAA
5124092 ATTTTTTACA
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
18 6 0.10
19 31 0.53
20 6 0.10
21 6 0.10
22 9 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATAATATATTTAATAATAT
Found at i:5126602 original size:26 final size:28
Alignment explanation
Indices: 5126560--5126613 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
5126550 ATTTAATTTT
5126560 TTTAAAATTATATTTAAAAAATA-ATTA
1 TTTAAAATTATATTTAAAAAATATATTA
* *
5126587 TTTAAATTTATA-TTAAAATATATATTA
1 TTTAAAATTATATTTAAAAAATATATTA
5126614 AATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAAAATTATATTTAAAAAATATATTA
Found at i:5126613 original size:12 final size:12
Alignment explanation
Indices: 5126561--5126632 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
5126551 TTTAATTTTT
5126561 TTAAAAT-TATA
1 TTAAAATATATA
*
5126572 TTTAAAAAATAATTA
1 -TTAAAATAT-A-TA
* *
5126587 TTTAAATTTATA
1 TTAAAATATATA
5126599 TTAAAATATATA
1 TTAAAATATATA
*
5126611 TT-AAATATAAA
1 TTAAAATATATA
5126622 TATAAAATATA
1 T-TAAAATATA
5126633 AATACTTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
11 9 0.19
12 21 0.44
13 9 0.19
14 7 0.15
15 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAAAATATATA
Found at i:5126629 original size:13 final size:13
Alignment explanation
Indices: 5126600--5126636 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5126590 AAATTTATAT
5126600 TAAAATAT--ATA
1 TAAAATATAAATA
*
5126611 TTAAATATAAATA
1 TAAAATATAAATA
5126624 TAAAATATAAATA
1 TAAAATATAAATA
5126637 CTTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 7 0.32
13 15 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAAATATAAATA
Found at i:5130156 original size:22 final size:21
Alignment explanation
Indices: 5130104--5130158 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
5130094 TTTCAATATC
*
5130104 AATAAATGTTTTAGAGTTATG
1 AATAAATGTTTTAGAGTTATA
*
5130125 AATAAATGTTTTCGAGCTT-TA
1 AATAAATGTTTTAGAG-TTATA
5130146 AATCAAATGTTTT
1 AAT-AAATGTTTT
5130159 TAAGTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (21 bp):
AATAAATGTTTTAGAGTTATA
Found at i:5130315 original size:20 final size:20
Alignment explanation
Indices: 5130290--5130343 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
5130280 CTACTACTGT
*
5130290 TTGTATCGATACATGACA-CA
1 TTGTATCGATACATGA-AGAA
5130310 TTGTATCGATACATGAAGAA
1 TTGTATCGATACATGAAGAA
*
5130330 TTGTATCCATACAT
1 TTGTATCGATACAT
5130344 TGTCCCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGAAGAA
Found at i:5131632 original size:13 final size:13
Alignment explanation
Indices: 5131614--5131640 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5131604 ACATTATGCT
5131614 TTGTATCGATACA
1 TTGTATCGATACA
5131627 TTGTATCGATACA
1 TTGTATCGATACA
5131640 T
1 T
5131641 GATCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5131674 original size:20 final size:20
Alignment explanation
Indices: 5131625--5131680 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
5131615 TGTATCGATA
*
5131625 CATTGTATCGATACAT-GAT
1 CATTGTATCAATACATGGAT
*
5131644 CATTATATCAATACATGGA-
1 CATTGTATCAATACATGGAT
5131663 CAATTGTATCAATACATG
1 C-ATTGTATCAATACATG
5131681 AAACTTGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (20 bp):
CATTGTATCAATACATGGAT
Found at i:5131743 original size:13 final size:13
Alignment explanation
Indices: 5131725--5131755 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5131715 CGATACATGG
5131725 TACATTATATCGA
1 TACATTATATCGA
*
5131738 TACATTGTATCGA
1 TACATTATATCGA
5131751 TACAT
1 TACAT
5131756 GATAAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTATATCGA
Found at i:5131751 original size:33 final size:33
Alignment explanation
Indices: 5131709--5131777 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
5131699 CTACCACTGT
* *
5131709 TTGTATCGATACATGGTACATTATATCGATACA
1 TTGTATCGATACATGATAAATTATATCGATACA
*
5131742 TTGTATCGATACATGATAAATTGTATCGATACA
1 TTGTATCGATACATGATAAATTATATCGATACA
5131775 TTG
1 TTG
5131778 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATAAATTATATCGATACA
Found at i:5131759 original size:20 final size:20
Alignment explanation
Indices: 5131736--5131775 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5131726 ACATTATATC
*
5131736 GATACATTGTATCGATACAT
1 GATAAATTGTATCGATACAT
5131756 GATAAATTGTATCGATACAT
1 GATAAATTGTATCGATACAT
5131776 TGCTTGTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (20 bp):
GATAAATTGTATCGATACAT
Found at i:5133342 original size:9 final size:9
Alignment explanation
Indices: 5133325--5133358 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5133315 GTCAACCATC
5133325 AATGATGAT
1 AATGATGAT
5133334 GAA-GATGAT
1 -AATGATGAT
5133343 AATGATGAT
1 AATGATGAT
5133352 AATGATG
1 AATGATG
5133359 GTGACTCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (9 bp):
AATGATGAT
Found at i:5137904 original size:27 final size:27
Alignment explanation
Indices: 5137861--5137928 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
5137851 TACATTGAAG
5137861 AATGTATCGATACATCTAGAAAACCCA
1 AATGTATCGATACATCTAGAAAACCCA
* *
5137888 GATGTATCGATAGATCTAGAAAACCCA
1 AATGTATCGATACATCTAGAAAACCCA
5137915 AATGTATCGATACA
1 AATGTATCGATACA
5137929 ATATTCCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (27 bp):
AATGTATCGATACATCTAGAAAACCCA
Found at i:5140513 original size:20 final size:20
Alignment explanation
Indices: 5140488--5140539 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
5140478 CGATACATTA
5140488 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTG
5140508 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTG
5140528 TATCGATACATG
1 TATCGATACATG
5140540 AAATTGGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (20 bp):
TATCGATACATGGACAATTG
Found at i:5140602 original size:13 final size:13
Alignment explanation
Indices: 5140584--5140682 Score: 105
Period size: 13 Copynumber: 8.5 Consensus size: 13
5140574 TGATACATGG
5140584 TACATTGTATCGA
1 TACATTGTATCGA
5140597 TACATTGTATCGA
1 TACATTGTATCGA
5140610 TACA-TG----G-
1 TACATTGTATCGA
5140617 TACATTGTATCGA
1 TACATTGTATCGA
5140630 TACATTGTATCGA
1 TACATTGTATCGA
*
5140643 TACATTGGATCGA
1 TACATTGTATCGA
5140656 TACA-TG-AT-G-
1 TACATTGTATCGA
5140665 -A-ATTGTATCGA
1 TACATTGTATCGA
5140676 TACATTG
1 TACATTG
5140683 CTTGTAACGG
Statistics
Matches: 73, Mismatches: 1, Indels: 24
0.74 0.01 0.24
Matches are distributed among these distances:
7 5 0.07
8 6 0.08
9 2 0.03
10 2 0.03
11 2 0.03
12 6 0.08
13 50 0.68
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:5140612 original size:33 final size:33
Alignment explanation
Indices: 5140568--5140647 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
5140558 CTACCACTAT
*
5140568 TTGTATTGATACATGGTACATTGTATCGATACA
1 TTGTATCGATACATGGTACATTGTATCGATACA
5140601 TTGTATCGATACATGGTACATTGTATCGATACA
1 TTGTATCGATACATGGTACATTGTATCGATACA
5140634 TTGTATCGATACAT
1 TTGTATCGATACAT
5140648 TGGATCGATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGGTACATTGTATCGATACA
Found at i:5140620 original size:20 final size:20
Alignment explanation
Indices: 5140597--5140680 Score: 80
Period size: 20 Copynumber: 3.9 Consensus size: 20
5140587 ATTGTATCGA
5140597 TACATTGTATCGATACATGG
1 TACATTGTATCGATACATGG
5140617 TACATTGTATCGATACATTGTATCG
1 TACATTGTATCGATACA-TG----G
* *
5140642 ATACATTGGATCGATACATGA
1 -TACATTGTATCGATACATGG
5140663 TGA-ATTGTATCGATACAT
1 T-ACATTGTATCGATACAT
5140681 TGCTTGTAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
20 32 0.59
21 3 0.06
25 3 0.06
26 16 0.30
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (20 bp):
TACATTGTATCGATACATGG
Found at i:5140637 original size:46 final size:46
Alignment explanation
Indices: 5140584--5140682 Score: 164
Period size: 46 Copynumber: 2.2 Consensus size: 46
5140574 TGATACATGG
* *
5140584 TACATTGTATCGATACATTGTATCGATACATGGT-ACATTGTATCGA
1 TACATTGTATCGATACATTGGATCGATACATGATGA-ATTGTATCGA
5140630 TACATTGTATCGATACATTGGATCGATACATGATGAATTGTATCGA
1 TACATTGTATCGATACATTGGATCGATACATGATGAATTGTATCGA
5140676 TACATTG
1 TACATTG
5140683 CTTGTAACGG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
46 49 0.98
47 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (46 bp):
TACATTGTATCGATACATTGGATCGATACATGATGAATTGTATCGA
Found at i:5140750 original size:20 final size:20
Alignment explanation
Indices: 5140718--5140772 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
5140708 ATTTCAAATC
5140718 AATT-TATCGATACATTATG
1 AATTGTATCGATACATTATG
*
5140737 AATTGTATCAATACATTATG
1 AATTGTATCGATACATTATG
5140757 AATTGTATCGATACAT
1 AATTGTATCGATACAT
5140773 GGCTACGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (20 bp):
AATTGTATCGATACATTATG
Found at i:5141932 original size:13 final size:13
Alignment explanation
Indices: 5141914--5141944 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5141904 ATATTTCATC
5141914 ATGTATTGATACA
1 ATGTATTGATACA
5141927 ATGTATTGATACA
1 ATGTATTGATACA
*
5141940 TTGTA
1 ATGTA
5141945 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:5141932 original size:33 final size:33
Alignment explanation
Indices: 5141894--5141960 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
5141884 GTTACAAGCT
* * *
5141894 ATGTATCGATATATT-TCATCATGTATTGATACA
1 ATGTATCGATACATTGT-ACCATGTATCGATACA
*
5141927 ATGTATTGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
5141960 A
1 A
5141961 ATAGTGATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:5142036 original size:19 final size:20
Alignment explanation
Indices: 5141989--5142038 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5141979 CTGCCAGTTT
* *
5141989 CATGTATCAATACAATTGTC
1 CATGTATCGATACAATTGAC
* *
5142009 CAAGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAC
5142028 CATGTATCGAT
1 CATGTATCGAT
5142039 GCATTGTATC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAC
Found at i:5142834 original size:13 final size:13
Alignment explanation
Indices: 5142816--5142841 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5142806 TACAGCAAGT
5142816 ATGTATCGATACA
1 ATGTATCGATACA
5142829 ATGTATCGATACA
1 ATGTATCGATACA
5142842 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5145093 original size:21 final size:21
Alignment explanation
Indices: 5145060--5145104 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5145050 TTGCAAGTTG
*
5145060 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
5145082 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
5145102 AAA
1 AAA
5145105 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:5146928 original size:15 final size:15
Alignment explanation
Indices: 5146908--5146938 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5146898 TAAAAATGTC
*
5146908 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
5146923 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
5146938 C
1 C
5146939 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:5149036 original size:13 final size:13
Alignment explanation
Indices: 5149018--5149056 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
5149008 ACATTTTTCT
5149018 TTGTATCGATACA
1 TTGTATCGATACA
5149031 TTGTATCGATACA
1 TTGTATCGATACA
5149044 TTGTATCGATACA
1 TTGTATCGATACA
5149057 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5151630 original size:13 final size:13
Alignment explanation
Indices: 5151612--5151637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5151602 TACAGCAAGT
5151612 ATGTATCGATACA
1 ATGTATCGATACA
5151625 ATGTATCGATACA
1 ATGTATCGATACA
5151638 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5160705 original size:20 final size:20
Alignment explanation
Indices: 5160680--5160733 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
5160670 GTTACAAGCT
*
5160680 ATGTATCGATACATT-TCATC
1 ATGTATCGATACATTGT-ACC
*
5160700 ATGTATTGATACCATTGTACC
1 ATGTATCGATA-CATTGTACC
5160721 ATGTATCGATACA
1 ATGTATCGATACA
5160734 AATAGTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 16 0.55
22 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:5160807 original size:19 final size:20
Alignment explanation
Indices: 5160763--5160812 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
5160753 CTGCCAGTTT
*
5160763 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATC
*
5160783 CATGTATCGATACAATGA-G
1 CATGTATCGATACAATGATC
5160802 CATGTATCGAT
1 CATGTATCGAT
5160813 GCATTGTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATGATC
Found at i:5166457 original size:15 final size:16
Alignment explanation
Indices: 5166421--5166460 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
5166411 AATTGTATTT
*
5166421 GTTTGATACAAATTAG
1 GTTTGATACAAATAAG
*
5166437 GATTGATA-AAATAAG
1 GTTTGATACAAATAAG
5166452 GTTTGATAC
1 GTTTGATAC
5166461 TAACTTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (16 bp):
GTTTGATACAAATAAG
Found at i:5166580 original size:13 final size:13
Alignment explanation
Indices: 5166562--5166601 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
5166552 ACAATGTTCT
5166562 TTGTATCGATACA
1 TTGTATCGATACA
*
5166575 TTGTATTGATACA
1 TTGTATCGATACA
*
5166588 ATGTATCGATACA
1 TTGTATCGATACA
5166601 T
1 T
5166602 GGGTTACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5168123 original size:13 final size:13
Alignment explanation
Indices: 5168105--5168130 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5168095 CAATTTTTTG
5168105 TGTATCGATACAT
1 TGTATCGATACAT
5168118 TGTATCGATACAT
1 TGTATCGATACAT
5168131 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5168195 original size:21 final size:21
Alignment explanation
Indices: 5168169--5168244 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
5168159 CTGCCAAGAA
*
5168169 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
5168190 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
5168210 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
5168231 ATGTATCGATACAT
1 ATGTATCGATACAT
5168245 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:5168215 original size:20 final size:20
Alignment explanation
Indices: 5168190--5168262 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
5168180 CATCTTTTTT
5168190 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
5168210 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
5168231 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
5168251 ATGTATCGATAC
1 ATGTATCGATAC
5168263 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:5168226 original size:41 final size:41
Alignment explanation
Indices: 5168169--5168262 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
5168159 CTGCCAAGAA
*
5168169 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
5168210 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
5168251 ATGTATCGATAC
1 ATGTATCGATAC
5168263 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:5168869 original size:48 final size:48
Alignment explanation
Indices: 5168814--5168909 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
5168804 AAATTTTACG
*
5168814 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTTTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
5168862 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
5168910 TTATCTCCCC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:5170752 original size:13 final size:13
Alignment explanation
Indices: 5170734--5170772 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
5170724 ATAATCACCC
*
5170734 TGTATCGATACAG
1 TGTATCGATACAA
5170747 TGTATCGATACAA
1 TGTATCGATACAA
5170760 TGTATCGATACAA
1 TGTATCGATACAA
5170773 GGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5172871 original size:15 final size:15
Alignment explanation
Indices: 5172851--5172881 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5172841 ATTTCGTTTG
*
5172851 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5172866 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5172881 G
1 G
5172882 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:5174714 original size:21 final size:21
Alignment explanation
Indices: 5174685--5174729 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5174675 AAGTTTTCAT
*
5174685 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
5174705 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
5174727 TTT
1 TTT
5174730 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:5176379 original size:13 final size:13
Alignment explanation
Indices: 5176361--5176386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5176351 CAATTTTTTG
5176361 TGTATCGATACAT
1 TGTATCGATACAT
5176374 TGTATCGATACAT
1 TGTATCGATACAT
5176387 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5176451 original size:21 final size:21
Alignment explanation
Indices: 5176425--5176500 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
5176415 CTGCCAAGAA
*
5176425 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
5176446 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
5176466 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
5176487 ATGTATCGATACAT
1 ATGTATCGATACAT
5176501 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:5176471 original size:20 final size:20
Alignment explanation
Indices: 5176446--5176518 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
5176436 CATCTTTTTT
5176446 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
5176466 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
5176487 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
5176507 ATGTATCGATAC
1 ATGTATCGATAC
5176519 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:5176482 original size:41 final size:41
Alignment explanation
Indices: 5176425--5176518 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
5176415 CTGCCAAGAA
*
5176425 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
5176466 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
5176507 ATGTATCGATAC
1 ATGTATCGATAC
5176519 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:5178658 original size:13 final size:13
Alignment explanation
Indices: 5178640--5178664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5178630 CACGACACAT
5178640 TGTATCGATACAA
1 TGTATCGATACAA
5178653 TGTATCGATACA
1 TGTATCGATACA
5178665 TAAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5182239 original size:32 final size:33
Alignment explanation
Indices: 5182150--5182241 Score: 80
Period size: 32 Copynumber: 2.8 Consensus size: 33
5182140 AGAGTAACTT
* * *
5182150 TTTCAAAGCCCACGACTCTATGGCACCACATCC
1 TTTCAAAGCCCACAACTCTGTGGCATCACATCC
* * * * *
5182183 TTT-TAAGCCCACACAAATCGGTGGCATC-CTTTC
1 TTTCAAAG-CC-CACAACTCTGTGGCATCACATCC
5182216 TTTCAAAGCCCACAACTCTGTGGCAT
1 TTTCAAAGCCCACAACTCTGTGGCAT
5182242 TTTCCTTTTA
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
32 17 0.38
33 13 0.29
34 15 0.33
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (33 bp):
TTTCAAAGCCCACAACTCTGTGGCATCACATCC
Found at i:5191323 original size:42 final size:41
Alignment explanation
Indices: 5191256--5191448 Score: 118
Period size: 42 Copynumber: 4.6 Consensus size: 41
5191246 ATTGGTTTTA
* **
5191256 ACCCGAGAGACTTTTTTACATTTTGTCTGCCCATCAACTTTG
1 ACCCG-GAGACTTCTTTACCCTTTGTCTGCCCATCAACTTTG
* * *
5191298 ACCCGGTAGACTTCTTTTCCCTTTGTCT-ACCATTCAACTTTA
1 ACCCGG-AGACTTCTTTACCCTTTGTCTGCCCA-TCAACTTTG
*** * * * * ***
5191340 ATTTGAGAAACTTCTATATCCTTTGTTTGCCCATTGGCTTTG
1 ACCCG-GAGACTTCTTTACCCTTTGTCTGCCCATCAACTTTG
* * *** *
5191382 ACCCAGTAGACTTCTTTACCTTTTGTCTGCTTGTCGACTTTG
1 ACCC-GGAGACTTCTTTACCCTTTGTCTGCCCATCAACTTTG
*
5191424 ACCCTGGAGAATTCTTTACCCTTTG
1 ACCC-GGAGACTTCTTTACCCTTTG
5191449 CCTACCTCTT
Statistics
Matches: 109, Mismatches: 37, Indels: 10
0.70 0.24 0.06
Matches are distributed among these distances:
41 4 0.04
42 100 0.92
43 5 0.05
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.41
Consensus pattern (41 bp):
ACCCGGAGACTTCTTTACCCTTTGTCTGCCCATCAACTTTG
Found at i:5191406 original size:126 final size:125
Alignment explanation
Indices: 5191224--5191454 Score: 295
Period size: 126 Copynumber: 1.8 Consensus size: 125
5191214 TGCTTGAAAG
* * *
5191224 ACTTCTTTATCTTTGTCTACCCATTGGTTTTAACCCGAGAGACTTTTTTACATTTTGTCTGCCCA
1 ACTTCTATATCTTTGTCTACCCATTGGCTTTAACCCGAGAGACTTCTTTACATTTTGTCTGCCCA
* * *
5191289 TCAACTTTGACCC-GGTAGACTTCTTTTCCCTTTGTCTACCATTCAACTTTAATTTGAGAA
66 TCAACTTTGACCCTGG-AGAATTCTTTACCCTTTGCCTACCATTCAACTTTAATTTGAGAA
* * * * *
5191349 ACTTCTATATCCTTTGTTTGCCCATTGGCTTTGACCC-AGTAGACTTCTTTACCTTTTGTCTGCT
1 ACTTCTATAT-CTTTGTCTACCCATTGGCTTTAACCCGAG-AGACTTCTTTACATTTTGTCTGCC
** *
5191413 TGTCGACTTTGACCCTGGAGAATTCTTTACCCTTTGCCTACC
64 CATCAACTTTGACCCTGGAGAATTCTTTACCCTTTGCCTACC
5191455 TCTTGGCTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
125 11 0.12
126 76 0.85
127 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.42
Consensus pattern (125 bp):
ACTTCTATATCTTTGTCTACCCATTGGCTTTAACCCGAGAGACTTCTTTACATTTTGTCTGCCCA
TCAACTTTGACCCTGGAGAATTCTTTACCCTTTGCCTACCATTCAACTTTAATTTGAGAA
Found at i:5191505 original size:42 final size:42
Alignment explanation
Indices: 5191375--5191524 Score: 147
Period size: 42 Copynumber: 3.6 Consensus size: 42
5191365 TTTGCCCATT
* * * *
5191375 GGCTTTGACCCAGTAGACTTCTTTACCTTTTGTCTGCTTGTC
1 GGCTTTGACCCTGGAGATTTCTTTACCTTTTGTCTGCTTATC
* * * * * * * *
5191417 GACTTTGACCCTGGAGAATTCTTTACCCTTTGCCTACCTCTT
1 GGCTTTGACCCTGGAGATTTCTTTACCTTTTGTCTGCTTATC
* * *
5191459 GGCTTTGACCTTGGAGATTTCTTTACCTTTTGTTTGTTTATC
1 GGCTTTGACCCTGGAGATTTCTTTACCTTTTGTCTGCTTATC
* *
5191501 GGCTTTGACTCTAGAGATTTCTTT
1 GGCTTTGACCCTGGAGATTTCTTT
5191525 TGTCTGCACG
Statistics
Matches: 84, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (42 bp):
GGCTTTGACCCTGGAGATTTCTTTACCTTTTGTCTGCTTATC
Found at i:5191626 original size:83 final size:83
Alignment explanation
Indices: 5191521--5191774 Score: 203
Period size: 83 Copynumber: 3.1 Consensus size: 83
5191511 CTAGAGATTT
* * * *
5191521 CTTTTGTCTGCACGTC-AGTTTTGACCTAGGAGACTTTTTTATCTTTGTTTACTTGTCAGCTTTG
1 CTTTTGTCTGCCCATCGA-TTTTGACCTAGGAGACTTTTTTACCTTTGTTTACTCGTCAGCTTTG
*
5191585 ACCTTGGAGACTTTTTTAC
65 ACCTAGGAGACTTTTTTAC
* * * * *** * *
5191604 CTTTTTTCTGCCCATCGATTTTGACTTGGGAGA-TTTCTTCACCTTTGTCCGCCCGTCCGCTTTG
1 CTTTTGTCTGCCCATCGATTTTGACCTAGGAGACTTT-TTTACCTTTGTTTACTCGTCAGCTTTG
*
5191668 ACCTAGGAGACTTTTTTAT
65 ACCTAGGAGACTTTTTTAC
* *** * *
5191687 C-TTTGTGTGCTTGTCGGTTTTGACCTTA-GAGACTTTTTTACCTTTTGTTTA-TCGATCGGCTT
1 CTTTTGTCTGCCCATCGATTTTGACC-TAGGAGACTTTTTTACC-TTTGTTTACTCG-TCAGCTT
* * * *
5191749 TCACCTGGGAGACTTCTTCAC
63 TGACCTAGGAGACTTTTTTAC
5191770 CTTTT
1 CTTTT
5191775 ATCTCCCCCG
Statistics
Matches: 130, Mismatches: 34, Indels: 13
0.73 0.19 0.07
Matches are distributed among these distances:
82 31 0.24
83 95 0.73
84 4 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (83 bp):
CTTTTGTCTGCCCATCGATTTTGACCTAGGAGACTTTTTTACCTTTGTTTACTCGTCAGCTTTGA
CCTAGGAGACTTTTTTAC
Found at i:5191628 original size:42 final size:40
Alignment explanation
Indices: 5191523--5191731 Score: 161
Period size: 41 Copynumber: 5.1 Consensus size: 40
5191513 AGAGATTTCT
* * *
5191523 TTTGTCTGCACGTCAGTTTTGACCTAGGAGACTTTTTTATC
1 TTTGTCTGCCCGTC-GTTTTGACCTTGGAGACTTTTTTACC
* * ** *
5191564 TTTGTTTACTTGTCAGCTTTGACCTTGGAGACTTTTTTACC
1 TTTGTCTGCCCGTC-GTTTTGACCTTGGAGACTTTTTTACC
* * *
5191605 TTTTTTCTGCCCATCGATTTTGA-CTTGGGAGA-TTTCTTCACC
1 -TTTGTCTGCCCGTCG-TTTTGACCTT-GGAGACTTT-TTTACC
* * * *
5191647 TTTGTCCGCCCGTCCGCTTTGACCTAGGAGACTTTTTTATC
1 TTTGTCTGCCCGT-CGTTTTGACCTTGGAGACTTTTTTACC
* ** *
5191688 TTTGTGTGCTTGTCGGTTTTGACCTTAGAGACTTTTTTACC
1 TTTGTCTGCCCGTC-GTTTTGACCTTGGAGACTTTTTTACC
5191729 TTT
1 TTT
5191732 TGTTTATCGA
Statistics
Matches: 130, Mismatches: 30, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
40 1 0.01
41 99 0.76
42 30 0.23
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (40 bp):
TTTGTCTGCCCGTCGTTTTGACCTTGGAGACTTTTTTACC
Found at i:5191709 original size:124 final size:126
Alignment explanation
Indices: 5191533--5191806 Score: 356
Period size: 124 Copynumber: 2.2 Consensus size: 126
5191523 TTTGTCTGCA
* * *
5191533 CGTCAGTTTTGACCTAGGAGACTTTTTTATCTTTGTTTACTTGTCAGCTTTGACCTTGGAGACTT
1 CGTCAGCTTTGACCTAGGAGACTTTTTTATCTTTGTGTACTTGTCAGCTTTGACCTTAGAGACTT
* * * * * * *
5191598 TTTTACCTTTT-TTCTGCCCATCGATTTTGACTTGGGAGATTTCTTCACC-TTTGTC-CGCC
66 TTTTACCTTTTGTT-TACCCATCGACTTTCACCTGGGAGACTTCTTCACCTTTTATCTCCCC
* * * *
5191657 CGTCCGCTTTGACCTAGGAGACTTTTTTATCTTTGTGTGCTTGTCGGTTTTGACCTTAGAGACTT
1 CGTCAGCTTTGACCTAGGAGACTTTTTTATCTTTGTGTACTTGTCAGCTTTGACCTTAGAGACTT
* * *
5191722 TTTTACCTTTTGTTTATCGATCGGCTTTCACCTGGGAGACTTCTTCACCTTTTATCTCCCC
66 TTTTACCTTTTGTTTACCCATCGACTTTCACCTGGGAGACTTCTTCACCTTTTATCTCCCC
*
5191783 CGTCAGCTTTGAGCTAGGAGACTT
1 CGTCAGCTTTGACCTAGGAGACTT
5191807 ATTCTCATTC
Statistics
Matches: 128, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
124 96 0.75
125 7 0.05
126 25 0.20
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (126 bp):
CGTCAGCTTTGACCTAGGAGACTTTTTTATCTTTGTGTACTTGTCAGCTTTGACCTTAGAGACTT
TTTTACCTTTTGTTTACCCATCGACTTTCACCTGGGAGACTTCTTCACCTTTTATCTCCCC
Found at i:5191880 original size:42 final size:42
Alignment explanation
Indices: 5191834--5191950 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
5191824 TGCCCGTTAC
* * * *
5191834 CTTTGACTCGAGAGACTTCTTTATCCTTTGTCTGCTTATTGG
1 CTTTGACTCGAGAGACTTCTTCACCCTTTGTCTGCTCATCGG
* * * *
5191876 CTTTGACCTGGA-AAACTTCTTCACCCTTTGTCGGCTCGTCGG
1 CTTTGA-CTCGAGAGACTTCTTCACCCTTTGTCTGCTCATCGG
*
5191918 CTTTGAC-CTAGAAGACTTCTTCACCCTTTGTCT
1 CTTTGACTCGAG-AGACTTCTTCACCCTTTGTCT
5191951 ACCCGACCCG
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.02
41 1 0.02
42 54 0.90
43 4 0.07
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.39
Consensus pattern (42 bp):
CTTTGACTCGAGAGACTTCTTCACCCTTTGTCTGCTCATCGG
Found at i:5192548 original size:14 final size:14
Alignment explanation
Indices: 5192512--5192548 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5192502 CCTACTTAAT
5192512 ATAAAATAAT-TAA
1 ATAAAATAATATAA
*
5192525 ATAAAA-AATATAC
1 ATAAAATAATATAA
5192538 ATAAAATAATA
1 ATAAAATAATA
5192549 ATAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 14 0.67
14 4 0.19
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATAATATAA
Found at i:5192555 original size:14 final size:14
Alignment explanation
Indices: 5192508--5192555 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
5192498 TTGACCTACT
5192508 TAAT-ATAAAATAA
1 TAATAATAAAATAA
*
5192521 TTA-AATAAAA-AA
1 TAATAATAAAATAA
5192533 T-ATACATAAAATAA
1 TAATA-ATAAAATAA
5192547 TAATAATAA
1 TAATAATAA
5192556 TTAATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
11 1 0.03
12 4 0.14
13 14 0.48
14 7 0.24
15 3 0.10
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAATAAAATAA
Found at i:5193001 original size:27 final size:27
Alignment explanation
Indices: 5192971--5193045 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
5192961 TAGTAGTAAT
*
5192971 TGAAAGAAATG-AATCGGCTGCAGCAAA
1 TGAAAGAAATGAAAT-AGCTGCAGCAAA
5192998 TGAAAGAAATGAAATAGCTGCAGCAAA
1 TGAAAGAAATGAAATAGCTGCAGCAAA
* *
5193025 TAAAAAAAATAGACAATAGCT
1 TGAAAGAAAT-GA-AATAGCT
5193046 CAAAGGAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 30 0.71
28 5 0.12
29 7 0.17
ACGTcount: A:0.52, C:0.12, G:0.20, T:0.16
Consensus pattern (27 bp):
TGAAAGAAATGAAATAGCTGCAGCAAA
Found at i:5203094 original size:51 final size:53
Alignment explanation
Indices: 5203017--5203137 Score: 133
Period size: 51 Copynumber: 2.4 Consensus size: 53
5203007 CTGGATGTAT
* * ** *
5203017 TGAAGAATGTAT--AAATACATTGGGGTCAAAAACCTAGTTGTATCGATACAA
1 TGAAGAATGTATCGATATACATTGGGGTCAAAAACCAAACTGTATCAATACAA
* * *
5203068 TGAAGAATGTATCGATATA-ATT-GGGTCAAGACCCAAACTGTATCAATATAA
1 TGAAGAATGTATCGATATACATTGGGGTCAAAAACCAAACTGTATCAATACAA
*
5203119 TGAAAAATGTATCGATATA
1 TGAAGAATGTATCGATATA
5203138 TTTTCTTTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
51 52 0.88
52 3 0.05
53 4 0.07
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (53 bp):
TGAAGAATGTATCGATATACATTGGGGTCAAAAACCAAACTGTATCAATACAA
Found at i:5203243 original size:21 final size:20
Alignment explanation
Indices: 5203176--5203249 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
5203166 TGCATGGTCC
**
5203176 TGTATCGATACATTTCAAATA
1 TGTATCGATACA-TTCACTTA
*
5203197 TGTATCAATACATTCACTTA
1 TGTATCGATACATTCACTTA
5203217 TGTATCGATACATT-ACCTTA
1 TGTATCGATACATTCA-CTTA
5203237 TTGTATCGATACA
1 -TGTATCGATACA
5203250 AATTACTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 23 0.49
21 23 0.49
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:5218408 original size:20 final size:20
Alignment explanation
Indices: 5218383--5218437 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
5218373 AAAATGCCTG
*
5218383 AATGTATCGATACATTGAAA
1 AATGTATCGATACAATGAAA
* *
5218403 AATGTACCGATACAATGAAC
1 AATGTATCGATACAATGAAA
5218423 AATGTATCGATACAA
1 AATGTATCGATACAA
5218438 ATTGTGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:5223486 original size:52 final size:52
Alignment explanation
Indices: 5223338--5223466 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
5223328 CGAAATATGA
* *
5223338 AAATTTGCCTGCATGTATCGATACATTTCATAGTATATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
* *
5223390 AAATTTTCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGAC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
5223442 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
5223467 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
Found at i:5223579 original size:19 final size:18
Alignment explanation
Indices: 5223551--5223613 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
5223541 AGCGATACAT
*
5223551 TGTATTGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
5223570 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
5223583 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
5223602 TGTGTCGATACA
1 TGTATCGATACA
5223614 TTGTATCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
16 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:5223584 original size:32 final size:32
Alignment explanation
Indices: 5223538--5223636 Score: 135
Period size: 32 Copynumber: 3.1 Consensus size: 32
5223528 GCAGTAGCTT
* *
5223538 TGTAGCGATACATTGTATTGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
*
5223570 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
* * *
5223602 TGTGTCGATACATTGTATCAATACAACACGTTA
1 TGTATCGATACATTGTATCGATACAAAAC-TTA
5223635 TG
1 TG
5223637 CCATGATACA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 56 0.92
33 5 0.08
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAAAACTTA
Found at i:5223588 original size:13 final size:13
Alignment explanation
Indices: 5223570--5223594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5223560 ACAAAACTTA
5223570 TGTATCGATACAT
1 TGTATCGATACAT
5223583 TGTATCGATACA
1 TGTATCGATACA
5223595 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5227694 original size:13 final size:13
Alignment explanation
Indices: 5227676--5227701 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5227666 ACATAAGTTT
5227676 TGTATCGATACAA
1 TGTATCGATACAA
5227689 TGTATCGATACAA
1 TGTATCGATACAA
5227702 AATTACCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5227751 original size:20 final size:21
Alignment explanation
Indices: 5227726--5227783 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
5227716 CTGCCAAGGG
* *
5227726 AATGTATCGATACATTATTA-
1 AATGTATCAATACATTACTAC
*
5227746 AATGTATCAATACATGACTAC
1 AATGTATCAATACATTACTAC
5227767 AATTGTATCAATACATT
1 AA-TGTATCAATACATT
5227784 TTGGGTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 17 0.53
21 2 0.06
22 13 0.41
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (21 bp):
AATGTATCAATACATTACTAC
Found at i:5240357 original size:20 final size:20
Alignment explanation
Indices: 5240314--5240365 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
5240304 GTAGCCAAAC
*
5240314 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
5240334 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
5240353 TTGTATCGATACA
1 TTGTATCGATACA
5240366 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:5242599 original size:21 final size:21
Alignment explanation
Indices: 5242566--5242615 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5242556 TTGCAAGTTG
*
5242566 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
5242588 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
5242609 AAATAAA
1 AAATAAA
5242616 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:5246522 original size:13 final size:13
Alignment explanation
Indices: 5246504--5246541 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
5246494 CATTTTTCTT
5246504 TGTATCGATACAA
1 TGTATCGATACAA
*
5246517 TGTATCGATACAC
1 TGTATCGATACAA
5246530 TGTATCGATACA
1 TGTATCGATACA
5246542 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5246705 original size:20 final size:20
Alignment explanation
Indices: 5246662--5246707 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
5246652 AAATCTTTTG
5246662 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
5246683 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
5246703 CAAAA
1 CAAAA
5246708 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:5249092 original size:19 final size:18
Alignment explanation
Indices: 5249068--5249131 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 18
5249058 TAGCCAAACT
5249068 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAA-A
5249087 TGTATCGAT--AC---AA
1 TGTATCGATACACAAAAA
5249100 TGTATCGATACACAAAAAA
1 TGTATCGATACAC-AAAAA
5249119 TTGTATCGATACA
1 -TGTATCGATACA
5249132 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 11 0.29
20 12 0.32
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (18 bp):
TGTATCGATACACAAAAA
Found at i:5249104 original size:13 final size:13
Alignment explanation
Indices: 5249086--5249111 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5249076 TACACAAAAT
5249086 ATGTATCGATACA
1 ATGTATCGATACA
5249099 ATGTATCGATACA
1 ATGTATCGATACA
5249112 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5249109 original size:32 final size:33
Alignment explanation
Indices: 5249068--5249131 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
5249058 TAGCCAAACT
*
5249068 TGTATCGATACACAAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
5249100 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
5249132 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:5252376 original size:9 final size:9
Alignment explanation
Indices: 5252362--5252408 Score: 60
Period size: 9 Copynumber: 5.0 Consensus size: 9
5252352 CTTTACACCC
5252362 CAAAAAAAA
1 CAAAAAAAA
5252371 CAAAAAAAA
1 CAAAAAAAA
5252380 -ACAAAAAAA
1 CA-AAAAAAA
5252389 CAAAAAAAA
1 CAAAAAAAA
5252398 CCAAGAAAAAA
1 -CAA-AAAAAA
5252409 TAGCAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.03
9 23 0.68
10 4 0.12
11 6 0.18
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:5252378 original size:10 final size:10
Alignment explanation
Indices: 5252363--5252419 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
5252353 TTTACACCCC
5252363 AAAAAAAACA
1 AAAAAAAACA
5252373 AAAAAAAAC-
1 AAAAAAAACA
5252382 -AAAAAAACA
1 AAAAAAAACA
*
5252391 AAAAAAACCA
1 AAAAAAAACA
5252401 AGAAAAAATAGCA
1 A-AAAAAA-A-CA
5252414 AAAAAA
1 AAAAAA
5252420 CAGAAAGGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 8 0.20
10 18 0.45
11 6 0.15
12 5 0.12
13 3 0.08
ACGTcount: A:0.84, C:0.11, G:0.04, T:0.02
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:5252387 original size:18 final size:18
Alignment explanation
Indices: 5252364--5252407 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5252354 TTACACCCCA
5252364 AAAAAAACAAAAAAAAAC
1 AAAAAAACAAAAAAAAAC
*
5252382 AAAAAAACAAAAAAAACC
1 AAAAAAACAAAAAAAAAC
5252400 AAGAAAAA
1 AA-AAAAA
5252408 ATAGCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAAC
Found at i:5253786 original size:85 final size:85
Alignment explanation
Indices: 5253639--5254169 Score: 714
Period size: 85 Copynumber: 6.2 Consensus size: 85
5253629 ATGTTCATCC
* **
5253639 CTTTCAAAGCCCACAAGTCAGTGGCACTATTTTCAAAGCCCATGAGTCAGTGGCACCCTTTCAAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
5253704 GCCCACAAGTCAGTGGCACT
66 GCCCACAAGTCAGTGGCACT
* * *
5253724 CTTTCAAAGCCCACAAG-CTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAATGGAACCCTTTTCA
1 CTTTCAAAGCCCACAAGTC-AGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTCA
*
5253787 AAGCCCACAAGTCAGTGGCACC
64 AAGCCCACAAGTCAGTGGCACT
* *
5253809 CTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
5253874 GCCCACAAGTCAGTGGCACT
66 GCCCACAAGTCAGTGGCACT
* * * *
5253894 CTTTCAAAACCCACAAGTCAATGGCACT-ATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAA
5253958 AGCCCACAAGTCAGTGGCA-T
65 AGCCCACAAGTCAGTGGCACT
* *
5253978 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAA
1 -CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
* *
5254043 AGCCCACAAGTCAATGGCGC-
65 AGCCCACAAGTCAGTGGCACT
* * *
5254063 CATTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGCCCACAAG-CTAGTGGTAACTCTTTT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTC-AGTGG-CAC-CCTTT
*
5254127 CAAAGCCCACACGAGTCGGTGGCGACT
62 CAAAGCCCACA--AGTCAGTGGC-ACT
*
5254154 CTTTTTAAAGCCCACA
1 C-TTTCAAAGCCCACA
5254170 CAAGTTACTG
Statistics
Matches: 393, Mismatches: 37, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
84 52 0.13
85 252 0.64
86 51 0.13
87 15 0.04
89 8 0.02
90 1 0.00
91 14 0.04
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (85 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
GCCCACAAGTCAGTGGCACT
Found at i:5253812 original size:57 final size:57
Alignment explanation
Indices: 5253637--5254169 Score: 743
Period size: 57 Copynumber: 9.3 Consensus size: 57
5253627 GAATGTTCAT
* **
5253637 CCCTTTCAAAGCCCACAAGTCAGTGGCACTATTTTCAAAGCCCATGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
5253694 CCCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAG-CTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTC-AGTGGCA
* * *
5253750 CCCTTTCAAAGCCCACAAGTCAATGGAACCCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
5253807 CCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
5253864 CCCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAACCCACAAGTCAATGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
**
5253920 CTATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
5253977 TCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
5254034 TCCTTTCAAAGCCCACAAGTCAATGGCGC-CATTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
5254090 TTCTTTTCAAAGCCCACAAG-CTAGTGGTAACTCTTTTCAAAGCCCACACGAGTCGGTGGCGA
1 -CCCTTTCAAAGCCCACAAGTC-AGTGG-CACTCTTTTCAAAGCCCACA--AGTCAGTGGC-A
* *
5254152 CTCTTTTTAAAGCCCACA
1 C-CCTTTCAAAGCCCACA
5254170 CAAGTTACTG
Statistics
Matches: 429, Mismatches: 35, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
55 1 0.00
56 126 0.29
57 260 0.61
58 2 0.00
59 15 0.03
61 9 0.02
62 16 0.04
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (57 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:5254733 original size:20 final size:20
Alignment explanation
Indices: 5254710--5254786 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
5254700 AGGTACCCAG
5254710 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* *
5254730 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
5254750 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
5254770 ATATATCGATACATTCT
1 ATGTATCGATACATTCT
5254787 ATCATTTTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:5254765 original size:40 final size:40
Alignment explanation
Indices: 5254710--5254857 Score: 152
Period size: 40 Copynumber: 3.4 Consensus size: 40
5254700 AGGTACCCAG
5254710 ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
* * *
5254750 ATGTATCGATACATTCTTCAATATATCGATACATTCTATCATTTTA
1 ATGTATCGATACATTCTTCAATGTATCGATACA---TGT-A--TGA
* *
5254796 CCCAGGTGTATTGATACATTCTTCAATGTATTGATACATGTATGA
1 ---A--TGTATCGATACATTCTTCAATGTATCGATACATGTATGA
5254841 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
5254858 ATCTTTTTAC
Statistics
Matches: 88, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
40 47 0.53
42 1 0.01
43 2 0.02
44 1 0.01
45 2 0.02
46 2 0.02
47 1 0.01
48 2 0.02
49 1 0.01
51 29 0.33
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (40 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
Found at i:5254827 original size:20 final size:20
Alignment explanation
Indices: 5254802--5254857 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
5254792 TTTACCCAGG
5254802 TGTATTGATACATTCTTCAA
1 TGTATTGATACATTCTTCAA
* *
5254822 TGTATTGATACATGT-ATGAA
1 TGTATTGATACAT-TCTTCAA
*
5254842 TGTATCGATACATTCT
1 TGTATTGATACATTCT
5254858 ATCTTTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (20 bp):
TGTATTGATACATTCTTCAA
Found at i:5254848 original size:71 final size:71
Alignment explanation
Indices: 5254749--5254905 Score: 210
Period size: 71 Copynumber: 2.2 Consensus size: 71
5254739 TACATGTATG
* * * * *
5254749 AATGTATCGATACAT-TCTTCAATATATCGATACATTCTATCATTTTACCCAGG-TGTATTGATA
1 AATGTATCGATACATGT-ATGAATGTATCGATACATTCTATCATTTTACCC-GGATGCATCGATA
5254812 CATTCTTC
64 CATTCTTC
* *
5254820 AATGTATTGATACATGTATGAATGTATCGATACATTCTATCTTTTTACCCGGATGCATCGATACA
1 AATGTATCGATACATGTATGAATGTATCGATACATTCTATCATTTTACCCGGATGCATCGATACA
*
5254885 TTTTTC
66 TTCTTC
5254891 AATGTATCGATACAT
1 AATGTATCGATACAT
5254906 CTAGTTAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
70 2 0.03
71 72 0.96
72 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (71 bp):
AATGTATCGATACATGTATGAATGTATCGATACATTCTATCATTTTACCCGGATGCATCGATACA
TTCTTC
Found at i:5257182 original size:25 final size:26
Alignment explanation
Indices: 5257154--5257203 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
5257144 ATTATCATTG
5257154 CCGA-GGATACTCCAACCCCATTTCT
1 CCGAGGGATACTCCAACCCCATTTCT
5257179 CCGAGGGGATACTCCAACCCCATTT
1 CCGA-GGGATACTCCAACCCCATTT
5257204 TTCAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 4 0.17
27 19 0.83
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (26 bp):
CCGAGGGATACTCCAACCCCATTTCT
Found at i:5260705 original size:19 final size:20
Alignment explanation
Indices: 5260662--5260733 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
5260652 TGCTAGTTTC
* ** *
5260662 ATGTATTGATACAATTCACT
1 ATGTATCGATACAAAGCAAT
* *
5260682 ATGTATCGATACCAAG-AGT
1 ATGTATCGATACAAAGCAAT
*
5260701 ATGTATCGGTACAAAGCAAT
1 ATGTATCGATACAAAGCAAT
5260721 ATGTATCGATACA
1 ATGTATCGATACA
5260734 TCTGGGTGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 16 0.38
20 26 0.62
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAAT
Found at i:5260725 original size:20 final size:19
Alignment explanation
Indices: 5260681--5260733 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
5260671 TACAATTCAC
* *
5260681 TATGTATCGATACCAAGAG
1 TATGTATCGATACAAAGAA
*
5260700 TATGTATCGGTACAAAGCAA
1 TATGTATCGATACAAAG-AA
5260720 TATGTATCGATACA
1 TATGTATCGATACA
5260734 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (19 bp):
TATGTATCGATACAAAGAA
Found at i:5260855 original size:91 final size:91
Alignment explanation
Indices: 5260720--5260914 Score: 381
Period size: 91 Copynumber: 2.1 Consensus size: 91
5260710 TACAAAGCAA
5260720 TATGTATCGATACATCTGGGTGTGTATCGATACTTTTTAGGGTTTTGACCTTTGTAGCCTAAGTC
1 TATGTATCGATACATCTGGGTGTGTATCGATACTTTTTAGGGTTTTGACCTTTGTAGCCTAAGTC
5260785 AACCATTATGTATCGATACAAATACC
66 AACCATTATGTATCGATACAAATACC
5260811 TATGTATCGATACATCTGGGTGTGTATCGATACTTTTTAGGGTTTTGACCTTTGTAGCCTAAGTC
1 TATGTATCGATACATCTGGGTGTGTATCGATACTTTTTAGGGTTTTGACCTTTGTAGCCTAAGTC
*
5260876 AACCTTTATGTATCGATACAAATACC
66 AACCATTATGTATCGATACAAATACC
5260902 TATGTATCGATAC
1 TATGTATCGATAC
5260915 TTTCAATTAT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 103 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (91 bp):
TATGTATCGATACATCTGGGTGTGTATCGATACTTTTTAGGGTTTTGACCTTTGTAGCCTAAGTC
AACCATTATGTATCGATACAAATACC
Done.