Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006374.1 Hibiscus syriacus cultivar Beakdansim tig00015335_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 750659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:11672 original size:24 final size:24
Alignment explanation
Indices: 11644--11690 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
11634 TCGATTTCAC
*
11644 TTTTTTCTTTTATTTCTTGCTTTGA
1 TTTTGTCTTTTATTT-TTGCTTTGA
*
11669 TTTTGTCTTTTCTTTTTGCTTT
1 TTTTGTCTTTTATTTTTGCTTT
11691 CTTTCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.04, C:0.13, G:0.09, T:0.74
Consensus pattern (24 bp):
TTTTGTCTTTTATTTTTGCTTTGA
Found at i:22773 original size:26 final size:26
Alignment explanation
Indices: 22717--22771 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
22707 TTAATTATCC
*
22717 TAAATATTTAATTTAAATTAATTAAA
1 TAAATATTTAATTTAAATTAAATAAA
*
22743 TAAATATTTAA-TTAATTTGAAAT-AA
1 TAAATATTTAATTTAAATT-AAATAAA
22768 TAAA
1 TAAA
22772 ATCCCTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAATATTTAATTTAAATTAAATAAA
Found at i:37455 original size:3 final size:3
Alignment explanation
Indices: 37447--37592 Score: 267
Period size: 3 Copynumber: 48.3 Consensus size: 3
37437 ATAAACAATT
37447 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
37495 GGA GGA GGGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGGA GGA GGA
1 GGA GGA -GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA -GGA GGA GGA
37542 GGA GGA GGA -GA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
37589 GGA G
1 GGA G
37593 ACACATGGGG
Statistics
Matches: 140, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.01
3 132 0.94
4 6 0.04
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:38313 original size:24 final size:24
Alignment explanation
Indices: 38286--38342 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
38276 CCGTTAACAT
* *
38286 TTAACGAAACTGCTTACATGGTAA
1 TTAACGAAACTACTTACATGGCAA
*
38310 TTAACGAAACTACTTACGTGGCAA
1 TTAACGAAACTACTTACATGGCAA
38334 TTAACGAAA
1 TTAACGAAA
38343 TTGGTATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (24 bp):
TTAACGAAACTACTTACATGGCAA
Found at i:38707 original size:27 final size:27
Alignment explanation
Indices: 38677--38730 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
38667 ATATTTAAAA
* * *
38677 TTTAAAATAACTTTATTATTTTTATAT
1 TTTAAAATAAATTCAATATTTTTATAT
*
38704 TTTAAACTAAATTCAATATTTTTATAT
1 TTTAAAATAAATTCAATATTTTTATAT
38731 GGATTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTAAAATAAATTCAATATTTTTATAT
Found at i:46099 original size:20 final size:21
Alignment explanation
Indices: 46068--46106 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
46058 ACTCGTCCGA
46068 GTTAACCCGTTGACTTTGATT
1 GTTAACCCGTTGACTTTGATT
46089 GTTAA-CCGTTGACTTTGA
1 GTTAACCCGTTGACTTTGA
46107 CCCAAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (21 bp):
GTTAACCCGTTGACTTTGATT
Found at i:47241 original size:18 final size:18
Alignment explanation
Indices: 47218--47259 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
47208 TGACCTAGAA
* *
47218 ATAAGTGATTGTTTTTGG
1 ATAAGTGATTGTTGTAGG
47236 ATAAGTGATTGTTGTAGG
1 ATAAGTGATTGTTGTAGG
47254 ATAAGT
1 ATAAGT
47260 TTTGGAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (18 bp):
ATAAGTGATTGTTGTAGG
Found at i:50706 original size:2 final size:2
Alignment explanation
Indices: 50699--50741 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
50689 TTTTCACTTC
50699 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
50741 T
1 T
50742 TTATTTATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60362 original size:30 final size:29
Alignment explanation
Indices: 60305--60388 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 29
60295 GATTTATTTA
*
60305 GTGACCAAATTATAATTTGGTAAAGTTTG
1 GTGACCAAATTATAATTTGGAAAAGTTTG
60334 GTGACCAAATTATAAACTTT-GAAAAGTTTAG
1 GTGACCAAATTAT-AA-TTTGGAAAAGTTT-G
* * *
60365 G-GACTAAAATGTAATTTTGGAAAA
1 GTGACCAAATTATAA-TTTGGAAAA
60389 TTACAAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 18 0.39
30 23 0.50
31 5 0.11
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (29 bp):
GTGACCAAATTATAATTTGGAAAAGTTTG
Found at i:61595 original size:24 final size:24
Alignment explanation
Indices: 61563--61608 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
61553 GCATAATATG
61563 GTACATAGATGCTTTATACATCGT
1 GTACATAGATGCTTTATACATCGT
*
61587 GTACATAGATGTTTTATACATC
1 GTACATAGATGCTTTATACATC
61609 ATCTGGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (24 bp):
GTACATAGATGCTTTATACATCGT
Found at i:63839 original size:20 final size:20
Alignment explanation
Indices: 63814--63860 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
63804 GACTTGTTTT
63814 GAAAATTTTGAAATGTTCAA
1 GAAAATTTTGAAATGTTCAA
63834 GAAAATTTTGAAATGTTCAA
1 GAAAATTTTGAAATGTTCAA
63854 GAAAATT
1 GAAAATT
63861 CAATTTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (20 bp):
GAAAATTTTGAAATGTTCAA
Found at i:72968 original size:24 final size:24
Alignment explanation
Indices: 72936--73003 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
72926 TACCACATTG
72936 ATGTTATATTCCTGTGAATTACTT
1 ATGTTATATTCCTGTGAATTACTT
**
72960 ATGTTATATTCCCATGAATTACTT
1 ATGTTATATTCCTGTGAATTACTT
*
72984 ATGTTATATTCTTGTGAATT
1 ATGTTATATTCCTGTGAATT
73004 TGTATGTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (24 bp):
ATGTTATATTCCTGTGAATTACTT
Found at i:74686 original size:26 final size:25
Alignment explanation
Indices: 74657--74733 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
74647 AGAACTTGTT
* *
74657 GAAAAGGAAGAGGAGAAAGGAGAAGG
1 GAAAACGAAGAGGAGAAAGGAGAA-A
* **
74683 GAAACCGAAGACGGA-AAAAAAGAAA
1 GAAAACGAAGA-GGAGAAAGGAGAAA
* *
74708 GAAAATGAAGAGGGGAAAGGAGAAA
1 GAAAACGAAGAGGAGAAAGGAGAAA
74733 G
1 G
74734 GACGCCGTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
24 2 0.05
25 18 0.46
26 16 0.41
27 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.38, T:0.01
Consensus pattern (25 bp):
GAAAACGAAGAGGAGAAAGGAGAAA
Found at i:76375 original size:2 final size:2
Alignment explanation
Indices: 76368--76414 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
76358 TCAATCTACA
76368 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76410 AT AT A
1 AT AT A
76415 ATTTATGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76659 original size:85 final size:85
Alignment explanation
Indices: 76432--76651 Score: 307
Period size: 85 Copynumber: 2.6 Consensus size: 85
76422 AAATAAAATC
** * * * * * *
76432 ATGACACATGAATGTGTGTCATCTT-TTTTAATGATGTGTGCTTTAATGACACGCAATGTAATTC
1 ATGACACACAAATGTGTGTCATCTTCATTT-ATGACGAGGGCTTCAATGACACGCAATGTAAGTC
76496 ATACATGCGTATCATAAATTT
65 ATACATGCGTATCATAAATTT
* * *
76517 ATGACACACAAATGTGTGTCAACTTCATTTATGACGAGGTCTTCAATGACAAGCAATGTAAGTCA
1 ATGACACACAAATGTGTGTCATCTTCATTTATGACGAGGGCTTCAATGACACGCAATGTAAGTCA
*
76582 TACATGCGTGTCATAAATTT
66 TACATGCGTATCATAAATTT
*
76602 ATGACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGAC
1 ATGACACACAAATGTGTGTCATCTTCATTTATGACGAGGGCTTCAATGAC
76652 GCTCAATGCG
Statistics
Matches: 119, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
85 116 0.97
86 3 0.03
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (85 bp):
ATGACACACAAATGTGTGTCATCTTCATTTATGACGAGGGCTTCAATGACACGCAATGTAAGTCA
TACATGCGTATCATAAATTT
Found at i:86710 original size:16 final size:17
Alignment explanation
Indices: 86689--86721 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
86679 CGTCGAAAAC
86689 ATAAAATATGA-TTTTT
1 ATAAAATATGACTTTTT
*
86705 ATAAAATTTGACTTTTT
1 ATAAAATATGACTTTTT
86722 GGTTAAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (17 bp):
ATAAAATATGACTTTTT
Found at i:109067 original size:20 final size:20
Alignment explanation
Indices: 109042--109313 Score: 124
Period size: 20 Copynumber: 13.4 Consensus size: 20
109032 GATTTTCCAG
*
109042 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
109062 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
109082 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
109102 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
109123 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
109143 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* *
109164 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* * *
109184 AATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
109204 AATCGCAATGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
** * * *
109224 AATTACAACGAGAATATGTA
1 AATCGCAACGCGAATACGAA
* * * * *
109244 TATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
109264 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
109285 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
109305 AATCGCAAC
1 AATCGCAAC
109314 ATAATTTTTA
Statistics
Matches: 192, Mismatches: 45, Indels: 30
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.02
20 136 0.71
21 53 0.28
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:109134 original size:41 final size:41
Alignment explanation
Indices: 109103--109313 Score: 282
Period size: 41 Copynumber: 5.2 Consensus size: 41
109093 GATTCTGACT
** *
109103 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
*
109144 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCTGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* * * *
109185 ATCGCAATGAGAATACGT-AAATCGCAATGCGTATCTGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
** * * * *
109225 ATTACAACGAGAATATGT-ATATCGCAATGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
109265 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
109306 ATCGCAAC
1 ATCGCAAC
109314 ATAATTTTTA
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 69 0.46
41 81 0.54
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:109935 original size:21 final size:21
Alignment explanation
Indices: 109874--109952 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
109864 TTCTAAACTT
109874 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
109894 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
109914 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
109935 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
109953 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:109975 original size:19 final size:19
Alignment explanation
Indices: 109874--109995 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 19
109864 TTCTAAACTT
**
109874 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
109894 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
109914 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
109935 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
109949 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
* **
109968 AAAATCGCAACGTGAAACC
1 AAAATCGCAACGCGAAATG
109987 AAAATCGCA
1 AAAATCGCA
109996 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 25 0.30
20 28 0.34
21 13 0.16
22 1 0.01
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:110013 original size:19 final size:19
Alignment explanation
Indices: 109991--110055 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
109981 GAAACCAAAA
*
109991 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
110010 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
110024 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
110043 TCGCGTTGCGATT
1 TCGCGTTGCGATT
110056 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 10 0.27
16 2 0.05
17 3 0.08
19 22 0.59
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:110038 original size:33 final size:33
Alignment explanation
Indices: 109996--110088 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
109986 CAAAATCGCA
109996 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
110029 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
110062 TTGCGATAGTCATTTCCGCGTTACGAT
1 TTGCGATTTTCATTT-CGCGTTGCGAT
110089 AGTCATTCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 44 0.81
34 10 0.19
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:110105 original size:20 final size:20
Alignment explanation
Indices: 110053--110108 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
110043 TCGCGTTGCG
*
110053 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTACGATAGTC
*
110073 ATT-TCCGCGTTACGATAGTC
1 ATTCT-CTCGTTACGATAGTC
*
110093 ATTCTCTCATTACGAT
1 ATTCTCTCGTTACGAT
110109 TTTCATTTCA
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:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTACGATAGTC
Found at i:110990 original size:21 final size:21
Alignment explanation
Indices: 110970--111007 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 21
110960 TCTATATAAT
*
110970 ATTTTCAA-AATTA-TAATTA
1 ATTTTTAACAATTACTAATTA
110989 ATTTTTAACAATTACTAAT
1 ATTTTTAACAATTACTAAT
111008 GTTTGTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 5 0.31
21 4 0.25
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTTAACAATTACTAATTA
Found at i:111330 original size:22 final size:22
Alignment explanation
Indices: 111305--111348 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
111295 GCTTGCCACT
111305 GATTGGTGGCAAGCTAGTCAGC
1 GATTGGTGGCAAGCTAGTCAGC
111327 GATTGGTGGCAAGCTAGTCAGC
1 GATTGGTGGCAAGCTAGTCAGC
111349 ATTTTTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (22 bp):
GATTGGTGGCAAGCTAGTCAGC
Found at i:111994 original size:94 final size:94
Alignment explanation
Indices: 111833--112213 Score: 622
Period size: 94 Copynumber: 4.1 Consensus size: 94
111823 TTAGATTGCT
* * *
111833 AAGTAAATTTATTCGGTTTCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAG
1 AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
111898 TATTTGTCTTTTGTTTTGTCTTTTGGTTG-
66 TATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
111927 AAGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
1 AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
*
111992 TATTTGTCTTTGTTTTATCTTTTGGTTGA
66 TATTTGTCTTTGTTTTGTCTTTTGGTTGA
*
112021 AAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
1 AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
112086 TATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 TATTTGTCTTTGTTTTGTCTTTTGGTTGA
* * * * *
112115 AAGTAAATTTGTTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAT
1 AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
* *
112180 TATTTTTCTTTGTTCTGTCTTTTGGTTG-
66 TATTTGTCTTTGTTTTGTCTTTTGGTTGA
112208 AAGTAA
1 AAGTAA
112214 TGCAATCCAT
Statistics
Matches: 272, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 25 0.09
94 247 0.91
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.48
Consensus pattern (94 bp):
AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
TATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:112339 original size:14 final size:14
Alignment explanation
Indices: 112322--112373 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
112312 AAATGAATTA
112322 CAACGAGAGAATCG
1 CAACGAGAGAATCG
112336 CAACGAGAAATGAAAATCG
1 CAACGAG--A-G--AATCG
*
112355 CTACGAGAGAATCG
1 CAACGAGAGAATCG
112369 CAACG
1 CAACG
112374 CAAAATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 16 0.52
16 2 0.06
17 2 0.06
19 11 0.35
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (14 bp):
CAACGAGAGAATCG
Found at i:112355 original size:19 final size:19
Alignment explanation
Indices: 112331--112390 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
112321 ACAACGAGAG
112331 AATCGCAACGAGAAATGAA
1 AATCGCAACGAGAAATGAA
*
112350 AATCGCTACGAG--A-G--
1 AATCGCAACGAGAAATGAA
112364 AATCGCAACGCA-AAATGAA
1 AATCGCAACG-AGAAATGAA
112383 AATCGCAA
1 AATCGCAA
112391 TGCGAAACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
19 19 0.58
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (19 bp):
AATCGCAACGAGAAATGAA
Found at i:112366 original size:33 final size:33
Alignment explanation
Indices: 112301--112388 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
112291 AAAAATGACT
** *
112301 ATCGCAACGCAAAATG--AATTACAACGAGAGA
1 ATCGCAACGCAAAATGAAAATCGCTACGAGAGA
112332 ATCGCAACG-AGAAATGAAAATCGCTACGAGAGA
1 ATCGCAACGCA-AAATGAAAATCGCTACGAGAGA
112365 ATCGCAACGCAAAATGAAAATCGC
1 ATCGCAACGCAAAATGAAAATCGC
112389 AATGCGAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
30 1 0.02
31 14 0.28
33 34 0.68
34 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCAAAATGAAAATCGCTACGAGAGA
Found at i:112490 original size:20 final size:20
Alignment explanation
Indices: 112465--112547 Score: 130
Period size: 20 Copynumber: 4.2 Consensus size: 20
112455 CTCTCGTTGT
**
112465 GATAGTCAAATTCGCATTGC
1 GATAGTCATTTTCGCATTGC
112485 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
112505 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
* *
112525 AATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
112545 GAT
1 GAT
112548 TTTAGGTTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:113128 original size:42 final size:42
Alignment explanation
Indices: 113056--113138 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
113046 CCTCCCCTAT
113056 CGTTCAAGAGGACCCTATCATCCCTAAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGACCCTATCATCCCTAAAGAGGT-CCCTCCCAC
* ** *
113098 CGTTCAAGAGG-CCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGACC-CTATCATCCCTAAAGAGGTCCCTCCCA
113139 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 2 0.06
42 31 0.89
43 2 0.06
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGACCCTATCATCCCTAAAGAGGTCCCTCCCAC
Found at i:114508 original size:14 final size:14
Alignment explanation
Indices: 114489--114524 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
114479 ATTGTTTAAT
114489 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
114503 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
114517 TGATTTGT
1 TGATTTGT
114525 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:114714 original size:34 final size:33
Alignment explanation
Indices: 114626--114721 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
114616 AAAACATACT
* **
114626 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
114660 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
114693 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
114722 CGAAACTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:114717 original size:20 final size:19
Alignment explanation
Indices: 114659--114726 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
114649 GCAACGAGAG
114659 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
114678 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
114692 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
114712 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
114727 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:114793 original size:33 final size:34
Alignment explanation
Indices: 114736--114831 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
114726 ACTAATTTCG
114736 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
114770 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
114803 CGTTGCGATAGTCATTTTCACGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
114832 AGTCAATTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:114828 original size:20 final size:20
Alignment explanation
Indices: 114803--114896 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
114793 GCGATTCTCT
* *
114803 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTCCG
*
114823 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
114843 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
114863 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
114883 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
114897 AATGAATGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 63 0.97
21 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:117340 original size:24 final size:24
Alignment explanation
Indices: 117306--117359 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
117296 CTGAAAAATC
117306 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
117330 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
117354 ATCAAA
1 ATCAAA
117360 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:117373 original size:24 final size:24
Alignment explanation
Indices: 117306--117373 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
117296 CTGAAAAATC
* * *
117306 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
117330 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
117354 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
117374 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:118234 original size:20 final size:20
Alignment explanation
Indices: 118219--118270 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
118209 GTCAGAATCT
118219 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACAGATTCG
*
118239 CATTGCGATTTAC-GTATTCG
1 CGTTGCGATTTACAG-ATTCG
118259 CGTTGCGATTTA
1 CGTTGCGATTTA
118271 GGAAAATAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACAGATTCG
Found at i:118382 original size:20 final size:20
Alignment explanation
Indices: 118359--118435 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
118349 TACCCGAGAT
118359 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
** *
118379 CGCGTTGTAATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
118399 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
118420 TGCGTTGCGATTTACG
1 CGCGTTGCGATTTACG
118436 TATTCTCATT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 31 0.66
21 16 0.34
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:118418 original size:41 final size:40
Alignment explanation
Indices: 118361--118450 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 40
118351 CCCGAGATCG
* *
118361 CGTTGCGATTTACGGATACGCGTTGTAATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCAA-TTTACGTATTCT
* *
118402 CGTTGCGATTTACGGATATGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCAATTTACGTATTCT
*
118442 CATTGCGAT
1 CGTTGCGAT
118451 AGACAGAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 19 0.43
41 25 0.57
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCAATTTACGTATTCT
Found at i:118447 original size:20 final size:19
Alignment explanation
Indices: 118390--118450 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
118380 GCGTTGTAAT
118390 TTTACGTATTGTCGTTGCGA
1 TTTACGTATT-TCGTTGCGA
* *
118410 TTTACGGATATGCGTTGCGA
1 TTTACGTAT-TTCGTTGCGA
*
118430 TTTACGTATTCTCATTGCGA
1 TTTACGTATT-TCGTTGCGA
118450 T
1 T
118451 AGACAGAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (19 bp):
TTTACGTATTTCGTTGCGA
Found at i:118485 original size:20 final size:20
Alignment explanation
Indices: 118462--118511 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
118452 GACAGAATCA
*
118462 CGTTGCGATTTAT-ATGTTCG
1 CGTTGCGATTT-TCATATTCG
118482 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATATTCG
118502 CGTTGCGATT
1 CGTTGCGATT
118512 CTGGAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCG
Found at i:118610 original size:20 final size:19
Alignment explanation
Indices: 118561--118614 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
118551 ATTCTTCATA
118561 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
118580 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
118601 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
118615 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:118866 original size:19 final size:19
Alignment explanation
Indices: 118844--118886 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
118834 AATGGGCTTG
*
118844 ATTTATAAAATGAACTAGT
1 ATTTATAAAATGAACTAAT
**
118863 ATTTATTTAATGAACTAAT
1 ATTTATAAAATGAACTAAT
118882 ATTTA
1 ATTTA
118887 ACACTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (19 bp):
ATTTATAAAATGAACTAAT
Found at i:119729 original size:43 final size:42
Alignment explanation
Indices: 119666--119766 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 42
119656 AGTAGTGGTG
* *
119666 ATGATCCAACTCCTTTTGTGAATAATCAATA-ACAAGGTTGTTGC
1 ATGATCCAACTCCTTATGTGAATAATCAAGAGA-AAGGTT-TT-C
119710 -TGATCCAACTCCTTATGTGAATAATCAAGAGAAAGGTTTTC
1 ATGATCCAACTCCTTATGTGAATAATCAAGAGAAAGGTTTTC
119751 ATTGATCCAACTCCTT
1 A-TGATCCAACTCCTT
119767 CCATTAAGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
41 1 0.02
42 2 0.04
43 48 0.92
44 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (42 bp):
ATGATCCAACTCCTTATGTGAATAATCAAGAGAAAGGTTTTC
Found at i:120522 original size:6 final size:6
Alignment explanation
Indices: 120513--120559 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
120503 TTTTTTATAT
*
120513 TTTTTC TTTTTC TTTTAT- TTTTCC TTTTTCC TTTTTCC TTTTTC TTT
1 TTTTTC TTTTTC TTTT-TC TTTTTC TTTTT-C TTTTT-C TTTTTC TTT
120560 GCAATTGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 22 0.61
7 14 0.39
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:120533 original size:18 final size:19
Alignment explanation
Indices: 120510--120547 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
120500 TTATTTTTTA
*
120510 TATTTTTTCTTTTT-CTTT
1 TATTTTTCCTTTTTCCTTT
120528 TATTTTTCCTTTTTCCTTT
1 TATTTTTCCTTTTTCCTTT
120547 T
1 T
120548 TCCTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (19 bp):
TATTTTTCCTTTTTCCTTT
Found at i:120540 original size:7 final size:7
Alignment explanation
Indices: 120530--120556 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
120520 TTTTCTTTTA
120530 TTTTTCC
1 TTTTTCC
120537 TTTTTCC
1 TTTTTCC
120544 TTTTTCC
1 TTTTTCC
120551 TTTTTC
1 TTTTTC
120557 TTTGCAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCC
Found at i:121238 original size:9 final size:9
Alignment explanation
Indices: 121224--121256 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
121214 TCTTTCTATA
121224 TTTTTTTCC
1 TTTTTTTCC
*
121233 TTTTTTT-T
1 TTTTTTTCC
121241 TTTTTTTCC
1 TTTTTTTCC
121250 TTTTTTT
1 TTTTTTT
121257 AATTCTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:121254 original size:17 final size:17
Alignment explanation
Indices: 121224--121256 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
121214 TCTTTCTATA
121224 TTTTTTTCCTTTTTTTT
1 TTTTTTTCCTTTTTTTT
121241 TTTTTTTCCTTTTTTT
1 TTTTTTTCCTTTTTTT
121257 AATTCTTTAA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTCCTTTTTTTT
Found at i:140361 original size:81 final size:80
Alignment explanation
Indices: 140221--140876 Score: 857
Period size: 81 Copynumber: 8.1 Consensus size: 80
140211 CTATTCCAAA
* * * * * *
140221 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGTAGAAATGTGTTAATGATGCCTGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
140286 CGGTTAAATACAGTTG
66 CGGTTAAATAC-GTTG
* * *
140302 AGTAAAAGATTAATGGCCTAGCTGTGCATTTAAG-AGAAATGTGTCAATTATTCCAGTTAGATGA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTT-GGCAGAAAGGTGTCAATTATGCCAGTTAGATGA
*
140366 ATGGTTAAATACCGTTG
65 ACGGTTAAATA-CGTTG
* * *
140383 AGTAAAAGATTAATGGCCTAGTTGTGCATTCGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
**
140448 CAATTAAATACTGTTG
66 CGGTTAAATAC-GTTG
140464 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
140529 CAGTTAAATACCATTG
66 CGGTTAAATA-CGTTG
* * *
140545 AGT-AAAGAGTAATGGCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATTATGTCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
140609 TGGTTAAATATCGTTG
66 CGGTTAAATA-CGTTG
* * * *
140625 AGAAAAAGAGTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
140690 CGGTTAAATACCGTTG
66 CGGTTAAATA-CGTTG
* * * *
140706 AATAAAAGATTAATGGCCTAGCTATGCATTTGGTAAAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
140771 CGGTTAAATATCGTTG
66 CGGTTAAATA-CGTTG
* * ** ** * *
140787 TGTAAAAGAGTAATGGCCTAGCTGTGCATTTGATAGAAAAATGTCAATTATGCAAGTTAGACGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
140852 AGGTTAAATTCGTTTG
66 CGGTTAAATACG-TTG
*
140868 GGTAAAAGA
1 AGTAAAAGA
140877 ATAAAGGAAT
Statistics
Matches: 511, Mismatches: 57, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
80 76 0.15
81 432 0.85
82 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (80 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
CGGTTAAATACGTTG
Found at i:140834 original size:323 final size:323
Alignment explanation
Indices: 140225--140860 Score: 893
Period size: 323 Copynumber: 2.0 Consensus size: 323
140215 TCCAAAAGTA
* * * * * * *
140225 AAAGATTAATGGCCTAGTTGTGCATTTGGTAGAAATGTGTTAATGATGCCTGTTAGATGAACGGT
1 AAAGAGTAATGGCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATGATGCCAGTTAGATGAACGGT
* * * *
140290 TAAATACAGTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTAAGAGAAATGTGTCAATTATTC
66 TAAATACAGTTGAGAAAAAGAGTAATGGCCTAGCTGTGCATTTAAGAGAAAGGTGTCAATTATGC
* * * * *
140355 CAGTTAGATGAATGGTTAAATACCGTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTCGGCAGA
131 CAGTTAGATGAACGGTTAAATACCGTTGAATAAAAGATTAATGGCCTAGCTATGCATTCGGCAAA
*
140420 AAGGTGTCAATCATGCCAGTTAGATGAACAATTAAATACTGTTGAGTAAAAGATTAATGGCCTAG
196 AAGGTGTCAATCATGCCAGTTAGATGAACAATTAAATACTGTTGAGTAAAAGAGTAATGGCCTAG
* ** * *
140485 CTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACA-GTTAAATACCATTGAGT
261 CTGTGCATTTGACAGAAAAATGTCAATTATGCAAGTTAGACGAA-AGGTTAAATACCATTGAGT
* * *
140548 AAAGAGTAATGGCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATTATGTCAGTTAGATGAATGGT
1 AAAGAGTAATGGCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATGATGCCAGTTAGATGAACGGT
* *
140613 TAAATATC-GTTGAGAAAAAGAGTAATGGCCTAGTTGTGCATTT-GGCAGAAAGGTGTCAATTAT
66 TAAATA-CAGTTGAGAAAAAGAGTAATGGCCTAGCTGTGCATTTAAG-AGAAAGGTGTCAATTAT
* * *
140676 GCTAGTTAGATGAACGGTTAAATACCGTTGAATAAAAGATTAATGGCCTAGCTATGCATTTGGTA
129 GCCAGTTAGATGAACGGTTAAATACCGTTGAATAAAAGATTAATGGCCTAGCTATGCATTCGGCA
* ** *
140741 AAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-TCGTTGTGTAAAAGAGTAATGGCC
194 AAAAGGTGTCAATCATGCCAGTTAGATGAACAATTAAATACT-GTTGAGTAAAAGAGTAATGGCC
*
140805 TAGCTGTGCATTTGATAGAAAAATGTCAATTATGCAAGTTAGACGAAAGGTTAAAT
258 TAGCTGTGCATTTGACAGAAAAATGTCAATTATGCAAGTTAGACGAAAGGTTAAAT
140861 TCGTTTGGGT
Statistics
Matches: 274, Mismatches: 35, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
322 3 0.01
323 270 0.99
324 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (323 bp):
AAAGAGTAATGGCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATGATGCCAGTTAGATGAACGGT
TAAATACAGTTGAGAAAAAGAGTAATGGCCTAGCTGTGCATTTAAGAGAAAGGTGTCAATTATGC
CAGTTAGATGAACGGTTAAATACCGTTGAATAAAAGATTAATGGCCTAGCTATGCATTCGGCAAA
AAGGTGTCAATCATGCCAGTTAGATGAACAATTAAATACTGTTGAGTAAAAGAGTAATGGCCTAG
CTGTGCATTTGACAGAAAAATGTCAATTATGCAAGTTAGACGAAAGGTTAAATACCATTGAGT
Found at i:140970 original size:45 final size:45
Alignment explanation
Indices: 140920--141037 Score: 191
Period size: 45 Copynumber: 2.6 Consensus size: 45
140910 GTACATAAGT
140920 GGCATGAAAGGATGCCATAAATGAAATGTATAACAATGTATAAAA
1 GGCATGAAAGGATGCCATAAATGAAATGTATAACAATGTATAAAA
* *
140965 GGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATAAAA
1 GGCATGAAAGGATGCCATAAATGAAATGTATAACAATGTATAAAA
* * *
141010 GGCATGAAAGGGTGACATAATTGAAATG
1 GGCATGAAAGGATGCCATAAATGAAATG
141038 CATATGGGTA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.23
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAAATGAAATGTATAACAATGTATAAAA
Found at i:141073 original size:90 final size:90
Alignment explanation
Indices: 140966--141166 Score: 262
Period size: 90 Copynumber: 2.2 Consensus size: 90
140956 TGTATAAAAG
* * *
140966 GCATGAAAGGATGCCATAAATGAAATGTATAAT-AGTGTATAAAAGGCATGAAAGGGTGACATAA
1 GCATGAAAGGATGCCATAAATGAAATGCAT-ATGAGTGCATAAAAGGCATGAAAGGATGACATAA
141030 TTGAAATGCATATGGGTACATTATC-
65 TTGAAATGCATATGGGTACATTATCA
* * * ** *
141055 GACATGAAAGGATGCCATAACTGAAATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAA
1 G-CATGAAAGGATGCCATAAATGAAATGCATATGAGTGCATAAAAGGCATGAAAGGATGACATAA
*
141120 TTGAAATGCATATGGGTGCATTATCA
65 TTGAAATGCATATGGGTACATTATCA
* *
141146 GTATGAAAGAATGCCATAAAT
1 GCATGAAAGGATGCCATAAAT
141167 AATGCTCTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
89 3 0.03
90 92 0.96
91 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (90 bp):
GCATGAAAGGATGCCATAAATGAAATGCATATGAGTGCATAAAAGGCATGAAAGGATGACATAAT
TGAAATGCATATGGGTACATTATCA
Found at i:141152 original size:45 final size:44
Alignment explanation
Indices: 140966--141164 Score: 220
Period size: 45 Copynumber: 4.4 Consensus size: 44
140956 TGTATAAAAG
* * * * * **
140966 GCATGAAAGGATGCCATAAATGAAATGTATAAT-AGTGTATAAAAG
1 GCATGAAAGGATGCCATAATTGAAATGCAT-ATGGGTGCAT-TATC
* * *
141011 GCATGAAAGGGTGACATAATTGAAATGCATATGGGTACATTATC
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*
141055 GACATGAAAGGATGCCATAACTGAAATGCATATGGGTGCATTATC
1 G-CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*
141100 GGCATGAAAGGATGTCATAATTGAAATGCATATGGGTGCATTATC
1 -GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
141145 AGTATGAAAGAATGCCATAA
1 -GCATGAAAGGATGCCATAA
141165 ATAATGCTCT
Statistics
Matches: 131, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
44 4 0.03
45 126 0.96
46 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (44 bp):
GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
Found at i:144607 original size:20 final size:20
Alignment explanation
Indices: 144565--144616 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
144555 GATTCAAGTG
*
144565 GTATCGATACCAAGAGGGGA
1 GTATCGATACCAAGAGGAGA
* * *
144585 GTATCGATACTATGAGGATA
1 GTATCGATACCAAGAGGAGA
*
144605 GTATCAATACCA
1 GTATCGATACCA
144617 TTGTTGATAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (20 bp):
GTATCGATACCAAGAGGAGA
Found at i:146463 original size:79 final size:79
Alignment explanation
Indices: 146332--146858 Score: 772
Period size: 79 Copynumber: 6.7 Consensus size: 79
146322 GGTACTGTGT
* * * *
146332 GTGCATTATTGGCATGAAAGGATGACATAGATGAAATGCATATGAGTTCATTATCAGCATAAAAA
1 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAA
146397 AATAATGCATATGG
66 AATAATGCATATGG
* * * *
146411 GTGCATTATTGGCATGAACA-TATGTCATAGCTGAAATGCATATCGGTGCATTATCGGCATAAAA
1 GTGCATTATTGGCATGAA-AGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAA
*
146475 GAATAATGCATATGG
65 AAATAATGCATATGG
*
146490 ATGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCAT-AAAA
1 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAA
146554 AATAATGCATATGG
66 AATAATGCATATGG
* *
146568 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATAGGTGCATTATCAACA-AAAAA
1 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAA
*
146632 TAATAATGCATATAG
66 -AATAATGCATATGG
* * * * *
146647 GTACATTATTGGCATGAAAGGATGTCATAGCTGAAATACATATAGGTGCATTATCAACATAAAAA
1 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAA
146712 AATAATGCATATGG
66 AATAATGCATATGG
* * * *
146726 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGAATATGGGTACATTATCAGTATAAAAG
1 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAA
**
146791 AATAATGTTTATGG
66 AATAATGCATATGG
** *
146805 GTGCATTATTGGCATGAAAGGATGTTAAAGCTGAAATGCATATGGGTGCATTAT
1 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
146859 TGGCATGACA
Statistics
Matches: 405, Mismatches: 38, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
78 78 0.19
79 321 0.79
80 6 0.01
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (79 bp):
GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAA
AATAATGCATATGG
Found at i:146608 original size:45 final size:44
Alignment explanation
Indices: 146557--146903 Score: 189
Period size: 45 Copynumber: 8.5 Consensus size: 44
146547 CATAAAAAAT
146557 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATG-CATAGCTGA
* ** * *
146602 AATGCATATAGGTGCATTA-T--CAACAAA--A--AATA-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCATAGCTGA
* *
146636 AATGCATATAGGTACATTATTGGCATGAAAGGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATG-CATAGCTGA
* * *** *
146681 AATACATATAGGTGCATTATCAACAT-AAA--A---A-A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCATAGCTGA
146715 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATG-CATAGCTGA
* * ** *
146760 AATGAATATGGGTACATTATCAGTAT-AAA--A-G-A-A--T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCATAGCTGA
** * *
146794 AATGTTTATGGGTGCATTATTGGCATGAAAGGATGTTAAAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATG-CATAGCTGA
* * *
146839 AATGCATATGGGTGCATTATTGGCATGACATGATGCCA-ACGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATG-CATA-GCTGA
*
146884 AATGCATATGGGTACATTAT
1 AATGCATATGGGTGCATTAT
146904 CAACCTAAAA
Statistics
Matches: 227, Mismatches: 41, Indels: 68
0.68 0.12 0.20
Matches are distributed among these distances:
34 59 0.26
35 7 0.03
36 3 0.01
37 11 0.05
38 3 0.01
39 2 0.01
40 2 0.01
41 3 0.01
42 11 0.05
43 3 0.01
44 8 0.04
45 115 0.51
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCATAGCTGA
Found at i:146745 original size:236 final size:236
Alignment explanation
Indices: 146332--146858 Score: 799
Period size: 236 Copynumber: 2.2 Consensus size: 236
146322 GGTACTGTGT
* * *
146332 GTGCATTATTGGCATGAAAGGATGACATAGATGAAATGCATATGAGTTCATTATCAGCATAAAAA
1 GTGCATTATTGGCATGAAAGGATGACATAGCTGAAATGCATATG-GTGCATTATCAACATAAAAA
* * * * *
146397 AATAATGCATATGGGTGCATTATTGGCATGAACATATGTCATAGCTGAAATGCATATCGGTGCAT
65 AATAATGCATATAGGTACATTATTGGCATGAACAGATGTCATAGCTGAAATACATATAGGTGCAT
** *
146462 TATCGGCATAAAAGAATAATGCATATGGATGCATTATTGGCATGAAAGGATGCCATAGCTGAAAT
130 TATCAACATAAAAAAATAATGCATATGGATGCATTATTGGCATGAAAGGATGCCATAGCTGAAAT
* *
146527 GCATATGGGTGCATTATCAGCATAAAA-AATAATGCATATGG
195 GAATATGGGTACATTATCAGCATAAAAGAATAATGCATATGG
*
146568 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATAGGTGCATTATCAACA-AAAAA
1 GTGCATTATTGGCATGAAAGGATGACATAGCTGAAATGCATAT-GGTGCATTATCAACATAAAAA
146632 TAATAATGCATATAGGTACATTATTGGCATGAA-AGGATGTCATAGCTGAAATACATATAGGTGC
65 -AATAATGCATATAGGTACATTATTGGCATGAACA-GATGTCATAGCTGAAATACATATAGGTGC
*
146696 ATTATCAACATAAAAAAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAA
128 ATTATCAACATAAAAAAATAATGCATATGGATGCATTATTGGCATGAAAGGATGCCATAGCTGAA
* **
146761 ATGAATATGGGTACATTATCAGTATAAAAGAATAATGTTTATGG
193 ATGAATATGGGTACATTATCAGCATAAAAGAATAATGCATATGG
** *
146805 GTGCATTATTGGCATGAAAGGATGTTAAAGCTGAAATGCATATGGGTGCATTAT
1 GTGCATTATTGGCATGAAAGGATGACATAGCTGAAATGCATAT-GGTGCATTAT
146859 TGGCATGACA
Statistics
Matches: 265, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
235 6 0.02
236 196 0.74
237 63 0.24
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (236 bp):
GTGCATTATTGGCATGAAAGGATGACATAGCTGAAATGCATATGGTGCATTATCAACATAAAAAA
ATAATGCATATAGGTACATTATTGGCATGAACAGATGTCATAGCTGAAATACATATAGGTGCATT
ATCAACATAAAAAAATAATGCATATGGATGCATTATTGGCATGAAAGGATGCCATAGCTGAAATG
AATATGGGTACATTATCAGCATAAAAGAATAATGCATATGG
Found at i:151578 original size:20 final size:20
Alignment explanation
Indices: 151529--151584 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
151519 TACCGAAAGG
* *
151529 GGGTATCGATACCATAGTAT
1 GGGTATCGATACCATAGCAA
*
151549 GGTAGTATCGATACCATGGCAA
1 GG--GTATCGATACCATAGCAA
151571 GGGTATCGATACCA
1 GGGTATCGATACCA
151585 GGTAACATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCATAGCAA
Found at i:152182 original size:45 final size:44
Alignment explanation
Indices: 152131--152240 Score: 166
Period size: 45 Copynumber: 2.5 Consensus size: 44
152121 ATAAAAGAAT
*
152131 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATG-CATAGATGA
* *
152176 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTTA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATG-CATAGATGA
*
152221 AATTCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
152241 CAATAAAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCATAGATGA
Found at i:152261 original size:79 final size:79
Alignment explanation
Indices: 152176--152570 Score: 569
Period size: 79 Copynumber: 5.0 Consensus size: 79
152166 TCATAGCTGA
* *
152176 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTTAAATTCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
* * *
152241 CAATAAAAAAGATT
66 CAACATAAAAGAAT
* *
152255 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGATGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
*
152320 CAGCATAAAAGAAT
66 CAACATAAAAGAAT
* *
152334 AATGCATATAGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
152399 CAACATAAAAGAAT
66 CAACATAAAAGAAT
*** * ** *
152413 AATGCATATAAATGCATTATTAGCATGAAATAATGTCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
*
152478 CAGCATAAAAGAAT
66 CAACATAAAAGAAT
* *
152492 AATGCATATGGGTTCATTATTGGCATGACAA-GATGCCA-ATGTTGAAATGCATATGGGTGCATT
1 AATGCATATGGGTGCATTATTGGCATGA-AAGGATGCCATA-GCTGAAATGCATATGGGTGCATT
*
152555 ATCAACCTAAAAGAAT
64 ATCAACATAAAAGAAT
152571 GCTATAATTT
Statistics
Matches: 285, Mismatches: 29, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
78 1 0.00
79 282 0.99
80 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
CAACATAAAAGAAT
Found at i:152286 original size:124 final size:124
Alignment explanation
Indices: 152066--152319 Score: 420
Period size: 124 Copynumber: 2.0 Consensus size: 124
152056 ACTGTGTGTT
* * *
152066 CATTATTGTCATGAAAGGATGCCATAGCTAAAATGCATATGGGTGCATTATCAGCATAAAAGAAT
1 CATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATGGGTGCATTATCAACAAAAAAGAAT
*
152131 AATGCATATGGGTGCATTATTGGCATGAAAGGATG-TCATAGCTGAAATGCATATGGGTG
66 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCT-ATAGATGAAATGCATATGGGTG
* * * *
152190 CATTATTGGCATGAAAGGATGCCATAGCTTAAATTCATATGGGTGCATTATCAATAAAAAAGATT
1 CATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATGGGTGCATTATCAACAAAAAAGAAT
152255 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGATGAAATGCATATGGGTG
66 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGATGAAATGCATATGGGTG
152314 CATTAT
1 CATTAT
152320 CAGCATAAAA
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
124 120 0.99
125 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (124 bp):
CATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATGGGTGCATTATCAACAAAAAAGAAT
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGATGAAATGCATATGGGTG
Found at i:152338 original size:34 final size:34
Alignment explanation
Indices: 152300--152421 Score: 109
Period size: 34 Copynumber: 3.3 Consensus size: 34
152290 CTATAGATGA
152300 AATGCATATGGGTGCATTATCAGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCAGCATAAAAGAAT
* **
152334 AATGCATATAGGTGCATTATTGGCATGAAAGAATGCCATAGCT
1 AATGCATATGGGTGCATTATCAGCAT--AA-AA-G--A-A--T
*
152377 GAAATGCATATGGGTGCATTATCAACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCAGCATAAAAGAAT
152413 AATGCATAT
1 AATGCATAT
152422 AAATGCATTA
Statistics
Matches: 70, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
34 32 0.46
36 3 0.04
37 2 0.03
38 2 0.03
39 1 0.01
40 1 0.01
41 2 0.03
42 2 0.03
43 3 0.04
45 22 0.31
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCAGCATAAAAGAAT
Found at i:152385 original size:45 final size:44
Alignment explanation
Indices: 152334--152491 Score: 138
Period size: 45 Copynumber: 3.8 Consensus size: 44
152324 ATAAAAGAAT
**
152334 AATGCATATAGGTGCATTATTGGCATGAAAGAATGCCATAGCTGA
1 AATGCATATAGGTGCATTATCAGCATGAAAGAATG-CATAGCTGA
* *
152379 AATGCATATGGGTGCATTATCAACAT--AA-AA-G-A-A--T--
1 AATGCATATAGGTGCATTATCAGCATGAAAGAATGCATAGCTGA
** * *
152413 AATGCATATAAATGCATTATTAGCATGAAATAATGTCATAGCTGA
1 AATGCATATAGGTGCATTATCAGCATGAAAGAATG-CATAGCTGA
* *
152458 AATGCATATGGGTGCATTATCAGCATAAAAGAAT
1 AATGCATATAGGTGCATTATCAGCATGAAAGAAT
152492 AATGCATATG
Statistics
Matches: 87, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
34 21 0.24
36 3 0.03
37 2 0.02
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 2 0.02
43 3 0.03
45 50 0.57
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (44 bp):
AATGCATATAGGTGCATTATCAGCATGAAAGAATGCATAGCTGA
Found at i:152464 original size:203 final size:199
Alignment explanation
Indices: 152066--152477 Score: 517
Period size: 203 Copynumber: 2.0 Consensus size: 199
152056 ACTGTGTGTT
* *
152066 CATTATTGTCATGAAAGGATGCCATAGCTAAAATGCATATGGGTGCATTATCAGCATAAAAGAAT
1 CATTATTGGCATGAAAGGATGCCATAGATAAAATGCATATGGGTGCATTATCAGCATAAAAGAAT
* * *
152131 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
66 AATGCATATAGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGGTGCATTAT
*** * * * * * *
152196 TGGCATGAAAGGATGCCATAGCTTAAATTCATATGGGTGCATTATCAATAAAAAAGATTAATGCA
131 CAACATAAAAGAAT-CAATAGCTTAAATGCATAT--GTGCATGA-CAATAAAAAAGATAAATGCA
152261 TATGGGTG
192 TATGGGTG
* *
152269 CATTATTGGCATGAAAGGATGCTATAGATGAAATGCATATGGGTGCATTATCAGCATAAAAGAAT
1 CATTATTGGCATGAAAGGATGCCATAGATAAAATGCATATGGGTGCATTATCAGCATAAAAGAAT
152334 AATGCATATAGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGGTGCATTAT
66 AATGCATATAGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGGTGCATTAT
* * *
152399 CAACATAAAAGAAT-AAT-GCATATAAATGCATTAT-TAGCATGA-AATAATGTCATAGCTGAAA
131 CAACATAAAAGAATCAATAGC-T-TAAATGCA-TATGT-GCATGACAATAA---AAAAGAT-AAA
152460 TGCATATGGGTG
188 TGCATATGGGTG
152472 CATTAT
1 CATTAT
152478 CAGCATAAAA
Statistics
Matches: 182, Mismatches: 19, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
199 5 0.03
200 3 0.02
201 8 0.04
202 11 0.06
203 155 0.85
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (199 bp):
CATTATTGGCATGAAAGGATGCCATAGATAAAATGCATATGGGTGCATTATCAGCATAAAAGAAT
AATGCATATAGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGGTGCATTAT
CAACATAAAAGAATCAATAGCTTAAATGCATATGTGCATGACAATAAAAAAGATAAATGCATATG
GGTG
Found at i:154168 original size:81 final size:81
Alignment explanation
Indices: 154029--154659 Score: 832
Period size: 81 Copynumber: 7.8 Consensus size: 81
154019 CTATTCCAAA
* * * * *
154029 AGTAAAAGATTAAAGGCTTAGCTGTGCTTTTGGCAGAAAGGTGTAAATTATGCAAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
154094 CGGTTAAATATCGTTG
66 TGGTTAAATACCGTTG
* * * **
154110 AGTAAAATATTAATGGCCTAGCTGTGCATTTGGCAGAAAGATGTTAATTACACCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
154175 CGGTTAAATACCGTTG
66 TGGTTAAATACCGTTG
* * *
154191 AGTAAAAGATTAATGGTCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGTCAGTTATATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
154256 TAGTTAAATACTGTTG
66 TGGTTAAATACCGTTG
* *
154272 AATAAAAGATTAATGGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* * *
154337 CGGTTAAATATCGTTA
66 TGGTTAAATACCGTTG
* * *
154353 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATACTAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
154418 TAGTTAAATACCGTTG
66 TGGTTAAATACCGTTG
* * * * * *
154434 AGTACAAGATTAATGGCCTAGGTGTGCATTTAGTAGAGAGGTGTCAATTATGCTAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
154499 TAGTTAAATACCGTTG
66 TGGTTAAATACCGTTG
* * * *
154515 AGTAAAAGACTAATGGCGTAGCTGTGCATTTGGCAGAAAGGTGTTAATTATGCCAGTTAAATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
154580 TGGTTAAATATCGTTG
66 TGGTTAAATACCGTTG
* * ** * * * *
154596 AGTAAAAGAGTAATGGAC-AATTGTGCATTTGACAGAAAAGTGTCAATTATGCAATTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
154660 AGTCTAATTG
Statistics
Matches: 480, Mismatches: 70, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
80 38 0.08
81 442 0.92
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
TGGTTAAATACCGTTG
Found at i:154778 original size:45 final size:44
Alignment explanation
Indices: 154728--154935 Score: 238
Period size: 45 Copynumber: 4.6 Consensus size: 44
154718 GTACATAACT
* *
154728 GGCATGAAAGGATGACATGAATGAAATGTATAATAGTTTATAAAA
1 GGCATGAAAGGATGCCAT-AATGAAATGTATAATAGTGTATAAAA
* *
154773 GGCATGAAAGGATGCCACAAATGAAATGTATAATAATGTATAAAA
1 GGCATGAAAGGATGCCA-TAATGAAATGTATAATAGTGTATAAAA
* *
154818 TGCATGAAAGGATGCCATCAATGATATGTATAATAGTGTATAAAA
1 GGCATGAAAGGATGCCAT-AATGAAATGTATAATAGTGTATAAAA
* * * * * **
154863 GGCATGAAAGGGTGCCATAATTGAAATGCAT-ATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAA-TGAAATGTATAAT-AGTGTATAAAA
154908 GGCATGAAAGGATGCCATAATTGAAATG
1 GGCATGAAAGGATGCCATAA-TGAAATG
154936 CATATGGGTG
Statistics
Matches: 141, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
44 4 0.03
45 137 0.97
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.25
Consensus pattern (44 bp):
GGCATGAAAGGATGCCATAATGAAATGTATAATAGTGTATAAAA
Found at i:154899 original size:24 final size:24
Alignment explanation
Indices: 154872--154946 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
154862 AGGCATGAAA
154872 GGGTGCCATAATTGAAATGCATAT
1 GGGTGCCATAATTGAAATGCATAT
* * ** *
154896 GGGTG-CATTATCGGCATG-A-AA
1 GGGTGCCATAATTGAAATGCATAT
*
154917 GGATGCCATAATTGAAATGCATAT
1 GGGTGCCATAATTGAAATGCATAT
154941 GGGTGC
1 GGGTGC
154947 ATTATCAGCA
Statistics
Matches: 36, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
21 5 0.14
22 10 0.28
23 10 0.28
24 11 0.31
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (24 bp):
GGGTGCCATAATTGAAATGCATAT
Found at i:154936 original size:45 final size:45
Alignment explanation
Indices: 154863--154972 Score: 202
Period size: 45 Copynumber: 2.4 Consensus size: 45
154853 GTGTATAAAA
*
154863 GGCATGAAAGGGTGCCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
154908 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*
154953 AGCATGAAAGGATGCCATAA
1 GGCATGAAAGGATGCCATAA
154973 ATAATGCTCT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.25
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
Found at i:176088 original size:4 final size:4
Alignment explanation
Indices: 176079--176233 Score: 310
Period size: 4 Copynumber: 38.8 Consensus size: 4
176069 CGTTATTTAA
176079 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
176127 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
176175 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
176223 ATAC ATAC ATA
1 ATAC ATAC ATA
176234 TATATATATA
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 151 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:184067 original size:31 final size:31
Alignment explanation
Indices: 184032--184127 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
184022 ACGCCCTAAG
*
184032 GGAATACCTTGGGGCCTTAGAGCCTACCCAA
1 GGAATACCTTGGGGCCTAAGAGCCTACCCAA
184063 GGAATACCTTGGGGCCTCAA-AGCCTACCCAA
1 GGAATACCTTGGGGCCT-AAGAGCCTACCCAA
* ** *
184094 GGGAACATATTGGGGCCTAAGAACCTACCCAA
1 -GGAATACCTTGGGGCCTAAGAGCCTACCCAA
184126 GG
1 GG
184128 GTCACCTTAG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
31 32 0.56
32 25 0.44
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (31 bp):
GGAATACCTTGGGGCCTAAGAGCCTACCCAA
Found at i:187687 original size:16 final size:16
Alignment explanation
Indices: 187666--187697 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
187656 TCTTCCACCA
187666 ATGTTAGAATGAAAAT
1 ATGTTAGAATGAAAAT
*
187682 ATGTTAGAATGCAAAT
1 ATGTTAGAATGAAAAT
187698 GAGCTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGAAAAT
Found at i:189804 original size:5 final size:5
Alignment explanation
Indices: 189794--189847 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
189784 GAACTTCTCA
* *
189794 TTTTC TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TTCT- TTTTC TCTTC
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC TTTTC TTTTC TTTTC
189844 TTTT
1 TTTT
189848 TGCACTCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
4 3 0.07
5 35 0.83
6 4 0.10
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:189817 original size:8 final size:8
Alignment explanation
Indices: 189796--189836 Score: 64
Period size: 8 Copynumber: 4.9 Consensus size: 8
189786 ACTTCTCATT
189796 TTCTTTTC
1 TTCTTTTC
189804 TTTTCTTTTC
1 --TTCTTTTC
189814 TTCTTTTC
1 TTCTTTTC
189822 TTCTTTTC
1 TTCTTTTC
189830 TTCTTTT
1 TTCTTTT
189837 TCTCTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 23 0.74
10 8 0.26
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTCTTTTC
Found at i:189827 original size:16 final size:17
Alignment explanation
Indices: 189796--189847 Score: 70
Period size: 16 Copynumber: 2.9 Consensus size: 17
189786 ACTTCTCATT
189796 TTCTTTTCTTTTCTTTTC
1 TTCTTTTC-TTTCTTTTC
189814 TTCTTTTC-TTCTTTTC
1 TTCTTTTCTTTCTTTTC
189830 TTCTTTTTCTCTTCTTTT
1 TTC-TTTTCT-TTCTTTT
189848 TGCACTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 11 0.35
17 5 0.16
18 8 0.26
19 7 0.23
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTTTTCTTTCTTTTC
Found at i:191288 original size:16 final size:16
Alignment explanation
Indices: 191267--191298 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
191257 TCTTCCACCA
191267 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
191283 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
191299 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:200029 original size:14 final size:14
Alignment explanation
Indices: 200010--200038 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
200000 ATTATCTTTT
200010 AAAATAATTTTAAA
1 AAAATAATTTTAAA
200024 AAAATAATTTTAAA
1 AAAATAATTTTAAA
200038 A
1 A
200039 GAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATAATTTTAAA
Found at i:201909 original size:19 final size:20
Alignment explanation
Indices: 201882--201923 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
201872 AAAACTAATG
* *
201882 AATTTAAAATATAAGGTTTT
1 AATTAAAAATATAAGATTTT
201902 AATTAAAAAATATAAGATTTT
1 AATT-AAAAATATAAGATTTT
201923 A
1 A
201924 TTTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATTAAAAATATAAGATTTT
Found at i:204662 original size:6 final size:6
Alignment explanation
Indices: 204651--204738 Score: 52
Period size: 6 Copynumber: 13.5 Consensus size: 6
204641 TTTTGTTTTG
* * * *
204651 TTTTCT TTTTCT CCTTTTCC TTTTCC TTTTCC TTTTCT TTCCTT-T TCTTTCC
1 TTTTCT TTTTCT --TTTTCT TTTTCT TTTTCT TTTTCT TT--TTCT T-TTTCT
*
204703 TTTTCTT TTTTAT TTTTCTT TTGTTCT TTTTCT TTT
1 TTTTC-T TTTTCT TTTTC-T TT-TTCT TTTTCT TTT
204739 CCCTTTGTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
6 43 0.64
7 13 0.19
8 11 0.16
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.75
Consensus pattern (6 bp):
TTTTCT
Found at i:204681 original size:26 final size:24
Alignment explanation
Indices: 204651--204712 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 24
204641 TTTTGTTTTG
204651 TTTTCTTTTTCTCCTTTTCCTTTTCC
1 TTTTCTTTTTCTCCTTTT-C-TTTCC
*
204677 TTTTCCTTTTCTTTCCTTTTCTTTCC
1 TTTT-CTTTT-TCTCCTTTTCTTTCC
204703 TTTTCTTTTT
1 TTTTCTTTTT
204713 TATTTTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.03
25 5 0.15
26 13 0.39
27 6 0.18
28 8 0.24
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTCTTTTTCTCCTTTTCTTTCC
Found at i:204711 original size:5 final size:5
Alignment explanation
Indices: 204637--204739 Score: 70
Period size: 5 Copynumber: 20.8 Consensus size: 5
204627 TACATTGGTA
* * * *
204637 TTTCT TTTGT TTTGT TTTCT TTT-T CTCCT TTTCCT TTTCCT TTTCCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT-CT TTT-CT TTT-CT
* * * * *
204684 TTTCT TTCCT TTTCT TTCCT TTTCT TTT-T TAT-T TTTCT TTTGT TCT-T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
204731 TTTCT TTTC
1 TTTCT TTTC
204740 CCTTTGTAAC
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
4 11 0.14
5 51 0.65
6 17 0.22
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTCT
Found at i:204734 original size:14 final size:13
Alignment explanation
Indices: 204703--204738 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
204693 TTTTCTTTCC
204703 TTTTCTTTTTTAT
1 TTTTCTTTTTTAT
*
204716 TTTTCTTTTGTTCT
1 TTTTCTTTT-TTAT
204730 TTTTCTTTT
1 TTTTCTTTT
204739 CCCTTTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTTAT
Found at i:224325 original size:24 final size:24
Alignment explanation
Indices: 224297--224343 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
224287 TCGATTTCAC
*
224297 TTTTTTCTTTTATTTCTTGCTTTGA
1 TTTTGTCTTTTATTT-TTGCTTTGA
*
224322 TTTTGTCTTTTCTTTTTGCTTT
1 TTTTGTCTTTTATTTTTGCTTT
224344 CTTTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.04, C:0.13, G:0.09, T:0.74
Consensus pattern (24 bp):
TTTTGTCTTTTATTTTTGCTTTGA
Found at i:235443 original size:26 final size:26
Alignment explanation
Indices: 235387--235441 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
235377 TTAATTATCC
*
235387 TAAATATTTAATTTAAATTAATTAAA
1 TAAATATTTAATTTAAATTAAATAAA
*
235413 TAAATATTTAA-TTAATTTGAAAT-AA
1 TAAATATTTAATTTAAATT-AAATAAA
235438 TAAA
1 TAAA
235442 ATCCCTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAATATTTAATTTAAATTAAATAAA
Found at i:252193 original size:54 final size:54
Alignment explanation
Indices: 252147--252932 Score: 991
Period size: 54 Copynumber: 14.6 Consensus size: 54
252137 ATCAACTCAT
** * **
252147 GATGAATTATGTGAATTGCACACTTAGTATCGAAACGGTTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * **
252201 GATGAATTCCGTGAAATGTACACTTAGTGCCGAAACAGTTATTCATCCATGTAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * *
252255 GATGAATTCCATGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACGTAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * * *
252309 GATGAATTCAGTGAAATGCACACTTAGTACCGAAATGGTTATTCATCCATATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* *
252363 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAGTTATTCATCCACGTAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * * *
252417 GATGAATTCCGTGAAATGAACACTTAGTGCCAAAATGGTTATTCATCCACGTAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * * * *
252471 GATGATTTTCGTGAAATG-AGCACTTAGTGCTGAAACAGTTATTCATACACATAG
1 GATGAATTCCGTGAAATGCA-CACTTAGTGCCGAAACGGTTATTCATCCACATAG
** * * ** * **
252525 GATGAATT-ATTGAAATACACACTTCGTATCGAAATGGTTATTCATCCATGTAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * * *
252578 GATGAATTCCGTGAAATGTACACTTAGTGTCGAAACGATTATTCATCCACGTAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * *
252632 GATGAAGTCCGTAAAATGCACACTTAGTACCGAAACGGTTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * * **
252686 GATGAATTTCGTGAAATGCACACTTAGTGCCGAAACAGTTATTCAACCATGTAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * *
252740 GATGAATTCCGTGAAATGCACACTTAGTGGCGAAATGATTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * * *
252794 GATGAATTCCTTGAAATGCACTCTTAGTGCCAAAACGGTTATTCATCCACGTAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
** * * * *
252848 GATGAATTATGTGAAACGCACACTTAGTGCCGAAAAGATTATTCATCAACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
*
252902 GATGAATTTCGTGAAATGCACACTTAGTGCC
1 GATGAATTCCGTGAAATGCACACTTAGTGCC
252933 TATTTAGTAA
Statistics
Matches: 625, Mismatches: 104, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
53 40 0.06
54 585 0.94
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (54 bp):
GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
Found at i:258931 original size:35 final size:35
Alignment explanation
Indices: 258892--258962 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
258882 TGAAAAACTT
258892 TATATGGTTGCTAAAAATTTATAGGATCCCCTCTA
1 TATATGGTTGCTAAAAATTTATAGGATCCCCTCTA
258927 TATATGGTTGCTAAAAATTTATAGGATCCCCTCTA
1 TATATGGTTGCTAAAAATTTATAGGATCCCCTCTA
258962 T
1 T
258963 GGAATTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (35 bp):
TATATGGTTGCTAAAAATTTATAGGATCCCCTCTA
Found at i:265454 original size:34 final size:35
Alignment explanation
Indices: 265413--265495 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
265403 AAAATATATA
* *
265413 ATATCTGTAAATATCTGATAACT-ATAATCATCAG
1 ATATCTGTAAATATCTGAAAACTGAAAATCATCAG
* * *
265447 ATATCTGTAAATATCTTAAAATTGAAAATCATCTG
1 ATATCTGTAAATATCTGAAAACTGAAAATCATCAG
*
265482 ATAACTGTAAATAT
1 ATATCTGTAAATAT
265496 TTAGAATTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 20 0.48
35 22 0.52
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (35 bp):
ATATCTGTAAATATCTGAAAACTGAAAATCATCAG
Found at i:265490 original size:35 final size:34
Alignment explanation
Indices: 265438--265503 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
265428 TGATAACTAT
*
265438 AATCATCAGATATCTGTAAATATCTTAAAATTGAA
1 AATCATCAGATAACTGTAAATAT-TTAAAATTGAA
* *
265473 AATCATCTGATAACTGTAAATATTTAGAATT
1 AATCATCAGATAACTGTAAATATTTAAAATT
265504 CATCATCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 7 0.25
35 21 0.75
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (34 bp):
AATCATCAGATAACTGTAAATATTTAAAATTGAA
Found at i:272428 original size:17 final size:17
Alignment explanation
Indices: 272406--272462 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
272396 GATAACTGTA
272406 AAATATCTGATATATGT
1 AAATATCTGATATATGT
*
272423 AAATATCTAATA-AT-T
1 AAATATCTGATATATGT
*
272438 ATAATTATCTGATATCTGT
1 A-AA-TATCTGATATATGT
272457 AAATAT
1 AAATAT
272463 ATGAAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 2 0.06
16 4 0.12
17 22 0.67
18 3 0.09
19 2 0.06
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (17 bp):
AAATATCTGATATATGT
Found at i:281881 original size:49 final size:49
Alignment explanation
Indices: 281828--281925 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
281818 AACCTTTATC
281828 TTTAATTTCTGACATCTGAACATAATCAGAATCATCATACTTTAGTAAA
1 TTTAATTTCTGACATCTGAACATAATCAGAATCATCATACTTTAGTAAA
281877 TTTAATTTCTGACATCTGAACATAATCAGAATCATCATACTTTAGTAAA
1 TTTAATTTCTGACATCTGAACATAATCAGAATCATCATACTTTAGTAAA
281926 GAGTAACTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (49 bp):
TTTAATTTCTGACATCTGAACATAATCAGAATCATCATACTTTAGTAAA
Found at i:282329 original size:21 final size:22
Alignment explanation
Indices: 282303--282344 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
282293 TAATAGTAAC
*
282303 GGTATCGGTA-CACTGTAGCAG
1 GGTATCGATACCACTGTAGCAG
*
282324 GGTATCGATACCCCTGTAGCA
1 GGTATCGATACCACTGTAGCA
282345 TTCTGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (22 bp):
GGTATCGATACCACTGTAGCAG
Found at i:282777 original size:45 final size:45
Alignment explanation
Indices: 282713--282932 Score: 363
Period size: 45 Copynumber: 4.9 Consensus size: 45
282703 AATTTCTTAT
282713 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
282758 CAATATACTTACCATTTATTCCATAATCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
282803 CAATATACTTACCATTTATTCCATAAGCTCGTAAGTTTA-TTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
282847 CAATATACTTACCATTTATTCCTTAAGCTCGTAATCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
282892 CAATATACTTGCCA-TTATTCCATAATCTCGTAAGCCTATTT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
282933 GCATGCTTAC
Statistics
Matches: 163, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
44 64 0.39
45 99 0.61
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.41
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:282888 original size:89 final size:90
Alignment explanation
Indices: 282713--282932 Score: 363
Period size: 89 Copynumber: 2.5 Consensus size: 90
282703 AATTTCTTAT
282713 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATT
*
282778 CCATAATCTCGTAAGCTTATTTTAC
66 CCATAAGCTCGTAAGCTTATTTTAC
*
282803 CAATATACTTACCATTTATTCCATAAGCTCGTAAGTTTA-TTTACCAATATACTTACCATTTATT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATT
* *
282867 CCTTAAGCTCGTAATCTTATTTTAC
66 CCATAAGCTCGTAAGCTTATTTTAC
* * *
282892 CAATATACTTGCCA-TTATTCCATAATCTCGTAAGCCTATTT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
282933 GCATGCTTAC
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
88 21 0.17
89 62 0.51
90 38 0.31
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.41
Consensus pattern (90 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATT
CCATAAGCTCGTAAGCTTATTTTAC
Found at i:283081 original size:40 final size:40
Alignment explanation
Indices: 283037--283194 Score: 262
Period size: 40 Copynumber: 4.0 Consensus size: 40
283027 ACCGTAGTGC
*
283037 TACACATACGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
283077 TACACATAAGGTCGTGCCCATCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
283117 TACACATAAGGTCATGCCCACCACATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
283157 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGT
283195 CTTATAAACC
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 108 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:303888 original size:11 final size:11
Alignment explanation
Indices: 303872--303910 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
303862 GAAATTGACT
*
303872 AAGAAAGGAGG
1 AAGAAAGGAAG
*
303883 AAGAAAGGATG
1 AAGAAAGGAAG
*
303894 AAGAAAGTAAG
1 AAGAAAGGAAG
303905 AAGAAA
1 AAGAAA
303911 ATAAGGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (11 bp):
AAGAAAGGAAG
Found at i:331035 original size:17 final size:17
Alignment explanation
Indices: 331013--331113 Score: 69
Period size: 17 Copynumber: 5.9 Consensus size: 17
331003 AATTATGAGT
331013 TAGTTTAATAAAT-ATAC
1 TAGTTTAATAAATGA-AC
* *
331030 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
331047 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
331064 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
* ** *
331082 TAGATGCATAAATGAAA
1 TAGTTTAATAAATGAAC
* *
331099 TAGCTTACTAAATGA
1 TAGTTTAATAAATGA
331114 TCTAAATATG
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
17 49 0.77
18 15 0.23
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:331078 original size:18 final size:18
Alignment explanation
Indices: 331040--331083 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
331030 TAGTTTGATG
*
331040 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
331057 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
331074 CAATGAACTA
1 -AATGAACTA
331084 GATGCATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:335975 original size:23 final size:24
Alignment explanation
Indices: 335940--335998 Score: 102
Period size: 23 Copynumber: 2.5 Consensus size: 24
335930 TTAAAAGAAA
*
335940 AGAAAAGAAAAGTTTCTGATTTTG
1 AGAAAAGAAAAGTGTCTGATTTTG
335964 AGAAAA-AAAAGTGTCTGATTTTG
1 AGAAAAGAAAAGTGTCTGATTTTG
335987 AGAAAAGAAAAG
1 AGAAAAGAAAAG
335999 ATGAAGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 22 0.67
24 11 0.33
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.25
Consensus pattern (24 bp):
AGAAAAGAAAAGTGTCTGATTTTG
Found at i:348233 original size:21 final size:19
Alignment explanation
Indices: 348200--348240 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
348190 TGCATCAAGG
*
348200 TCTTTGTGGAAGCCATGAAA
1 TCTTTGTCGAAGCCAT-AAA
348220 TCTTTCGTCGAAGCCATAAA
1 TCTTT-GTCGAAGCCATAAA
348240 T
1 T
348241 TCCTACAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (19 bp):
TCTTTGTCGAAGCCATAAA
Found at i:355797 original size:17 final size:17
Alignment explanation
Indices: 355775--355813 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
355765 TGAATAATTT
355775 TAGTTCATTCATCAAAC
1 TAGTTCATTCATCAAAC
*
355792 TAGTTCATTCATCAAGC
1 TAGTTCATTCATCAAAC
355809 TAGTT
1 TAGTT
355814 AATTTATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (17 bp):
TAGTTCATTCATCAAAC
Found at i:359492 original size:17 final size:17
Alignment explanation
Indices: 359448--359508 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
359438 ATTCATGCAT
359448 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
* *
359465 GTTAATTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
359483 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
359500 CTAGTTCAT
1 CTAGTTCAT
359509 ATATTAGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 24 0.67
18 12 0.33
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:370720 original size:40 final size:40
Alignment explanation
Indices: 370641--370720 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
370631 ATAGGAGTCA
* * *
370641 AATATTGCACCGCAGTACTGAGGTCGAGCTTTTCTCACCT
1 AATAATGCACCGCAGTACTGAGGTCGAGCTTTACCCACCT
* *
370681 AATAATGCACCGTAGTGA-TGAGGTCGGGCTTTACCCACCT
1 AATAATGCACCGCAGT-ACTGAGGTCGAGCTTTACCCACCT
370721 TGTACATCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
AATAATGCACCGCAGTACTGAGGTCGAGCTTTACCCACCT
Found at i:385335 original size:17 final size:17
Alignment explanation
Indices: 385315--385356 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
385305 TTTGATGAAC
385315 GAACTAGTTTAATT-AAT
1 GAACTAGTTT-ATTCAAT
*
385332 GAACTAACTTTATTCAAT
1 GAACT-AGTTTATTCAAT
385350 GAACTAG
1 GAACTAG
385357 ATTCTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
GAACTAGTTTATTCAAT
Found at i:390382 original size:17 final size:17
Alignment explanation
Indices: 390346--390414 Score: 57
Period size: 17 Copynumber: 4.0 Consensus size: 17
390336 TAATAGTTAC
* * *
390346 TTTAATAAATAAACTCG
1 TTTAATGAATGAACTAG
*
390363 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
* *
390380 TTTAATTAATGAACTAAC
1 TTTAATGAATGAACT-AG
* *
390398 TTTATTCAATGAACTAG
1 TTTAATGAATGAACTAG
390415 ATTCTTTAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
17 27 0.66
18 14 0.34
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:390408 original size:18 final size:18
Alignment explanation
Indices: 390370--390413 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
390360 TCGTTTGATG
*
390370 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
390387 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
390404 CAATGAACTA
1 -AATGAACTA
390414 GATTCTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:395460 original size:17 final size:17
Alignment explanation
Indices: 395440--395481 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
395430 TTTGATGAAC
395440 GAACTAGTTTAATT-AAT
1 GAACTAGTTT-ATTCAAT
*
395457 GAACTAACTTTATTCAAT
1 GAACT-AGTTTATTCAAT
395475 GAACTAG
1 GAACTAG
395482 ATTCTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
GAACTAGTTTATTCAAT
Found at i:397903 original size:14 final size:13
Alignment explanation
Indices: 397874--397910 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
397864 CCTCTTTAAA
397874 ATTTTC-TTTTTT
1 ATTTTCTTTTTTT
397886 -TTTTCTTTTTTT
1 ATTTTCTTTTTTT
397898 CATTTTCTTTTTT
1 -ATTTTCTTTTTT
397911 CACTAACCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.23
12 6 0.27
14 11 0.50
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTCTTTTTTT
Found at i:399413 original size:17 final size:17
Alignment explanation
Indices: 399366--399418 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
399356 AATTAAGAGT
*
399366 TAGTTTAATAAATAAAC
1 TAGTTTAATAAATGAAC
* *
399383 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
399400 TAGTTTAAGT-AATGAAC
1 TAGTTTAA-TAAATGAAC
399417 TA
1 TA
399419 ACTTTATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 30 0.97
18 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:407443 original size:17 final size:17
Alignment explanation
Indices: 407423--407462 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
407413 TTTAGGGAAG
* *
407423 TAGTTTATTAATTAAAC
1 TAGTTCATTAATCAAAC
*
407440 TAGTTCATTCATCAAAC
1 TAGTTCATTAATCAAAC
407457 TAGTTC
1 TAGTTC
407463 GTTTATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:409032 original size:14 final size:15
Alignment explanation
Indices: 409013--409041 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
409003 GGAGTGTTTG
409013 GTGAGGTT-TTTTTT
1 GTGAGGTTATTTTTT
409027 GTGAGGTTATTTTTT
1 GTGAGGTTATTTTTT
409042 TATTACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (15 bp):
GTGAGGTTATTTTTT
Found at i:413476 original size:17 final size:17
Alignment explanation
Indices: 413456--413504 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
413446 GCAGGGAAGT
413456 AGTTCATTAATTAAACA
1 AGTTCATTAATTAAACA
* * *
413473 AGTTCATTCATCAAACT
1 AGTTCATTAATTAAACA
*
413490 AGTTCATTTATTAAA
1 AGTTCATTAATTAAA
413505 TTAACTCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (17 bp):
AGTTCATTAATTAAACA
Found at i:414484 original size:16 final size:16
Alignment explanation
Indices: 414463--414507 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
414453 TAGAGGGCCA
414463 CAATCCATTTTCTTTT
1 CAATCCATTTTCTTTT
*
414479 CAATCCATCTTCTTTT
1 CAATCCATTTTCTTTT
414495 CAATCCATCTTTC
1 CAATCCAT-TTTC
414508 ATATTCCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49
Consensus pattern (16 bp):
CAATCCATTTTCTTTT
Found at i:417915 original size:24 final size:23
Alignment explanation
Indices: 417887--417973 Score: 120
Period size: 24 Copynumber: 3.7 Consensus size: 23
417877 ATTCAAATCG
417887 AGTATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* *
417910 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCATATCAGAATCCAGGTC
*
417934 AATATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
*
417957 AGGTATCATAACAGAAT
1 A-GTATCATATCAGAAT
417974 TCAAATTTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
23 21 0.38
24 34 0.62
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAGGTC
Found at i:419130 original size:18 final size:18
Alignment explanation
Indices: 419109--419144 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
419099 TTACCATCTG
*
419109 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
419127 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
419145 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:420459 original size:8 final size:8
Alignment explanation
Indices: 420429--420510 Score: 61
Period size: 8 Copynumber: 10.6 Consensus size: 8
420419 GGTCAACAAT
420429 GGTCAACG
1 GGTCAACG
420437 CCGGTCAAC-
1 --GGTCAACG
420446 GGTCAACG
1 GGTCAACG
420454 GGTCAACG
1 GGTCAACG
420462 GGT---CG
1 GGTCAACG
420467 GGTCAACG
1 GGTCAACG
420475 GGT---CG
1 GGTCAACG
*
420480 GGTAAACG
1 GGTCAACG
*
420488 GGTCAGGTCG
1 GGTCA--ACG
420498 GGTCAACG
1 GGTCAACG
420506 GGTCA
1 GGTCA
420511 GGTAAACGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
5 10 0.17
7 7 0.12
8 29 0.48
10 14 0.23
ACGTcount: A:0.21, C:0.24, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:420459 original size:15 final size:16
Alignment explanation
Indices: 420429--420462 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
420419 GGTCAACAAT
420429 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
420446 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
420461 GG
1 GG
420463 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:420470 original size:13 final size:13
Alignment explanation
Indices: 420452--420527 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
420442 CAACGGTCAA
420452 CGGGTCAACGGGT
1 CGGGTCAACGGGT
420465 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
420478 CGGGTAAACGGGTCAGGT
1 CGGGTCAAC--G---GGT
420496 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* *
420509 CAGGTAAACGGGT
1 CGGGTCAACGGGT
420522 CGGGTC
1 CGGGTC
420528 GGGTCAATGG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 39 0.75
15 1 0.02
16 1 0.02
18 11 0.21
ACGTcount: A:0.18, C:0.21, G:0.45, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:420496 original size:18 final size:18
Alignment explanation
Indices: 420475--420549 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 18
420465 CGGGTCAACG
420475 GGTCGGGTAAACGGGTCA
1 GGTCGGGTAAACGGGTCA
*
420493 GGTCGGGTCAACGGGTCA
1 GGTCGGGTAAACGGGTCA
*
420511 -----GGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCA
* * *
420524 GGTCGGGTCAATGGGTCG
1 GGTCGGGTAAACGGGTCA
420542 GGTCGGGT
1 GGTCGGGT
420550 TGTGACCGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
13 11 0.23
18 36 0.77
ACGTcount: A:0.16, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCA
Done.