Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008065.1 Hibiscus syriacus cultivar Beakdansim tig00110562_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: 676718
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
File 2 of 3
Found at i:296967 original size:7 final size:7
Alignment explanation
Indices: 296954--296991 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
296944 GTCAAAGAAA
296954 GTCAACG
1 GTCAACG
*
296961 ATCAACG
1 GTCAACG
296968 GTCAACG
1 GTCAACG
296975 GTCAACG
1 GTCAACG
296982 GTCAACG
1 GTCAACG
296989 GTC
1 GTC
296992 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:296998 original size:5 final size:5
Alignment explanation
Indices: 296988--297045 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
296978 AACGGTCAAC
* *
296988 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
297037 GGTCG GGTC
1 GGTCG GGTC
297046 AGACCGATCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:297009 original size:22 final size:22
Alignment explanation
Indices: 296981--297045 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
296971 AACGGTCAAC
296981 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
297003 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
297025 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
297046 AGACCGATCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:297068 original size:19 final size:19
Alignment explanation
Indices: 297044--297082 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
297034 TCGGGTCGGG
*
297044 TCAGACCGATCAACCCGGT
1 TCAGACCGATCAAACCGGT
*
297063 TCAGACCGGTCAAACCGGT
1 TCAGACCGATCAAACCGGT
297082 T
1 T
297083 TGAACCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.18
Consensus pattern (19 bp):
TCAGACCGATCAAACCGGT
Found at i:297081 original size:9 final size:9
Alignment explanation
Indices: 297042--297140 Score: 54
Period size: 9 Copynumber: 10.3 Consensus size: 9
297032 GGTCGGGTCG
*
297042 GGTCAGACC
1 GGTCAAACC
* *
297051 GATCAACCC
1 GGTCAAACC
*
297060 GGTTCAGACC
1 GG-TCAAACC
297070 GGTCAAACC
1 GGTCAAACC
**
297079 GGTTTGAACC
1 GG-TCAAACC
*
297089 GGTTGAAACC
1 GG-TCAAACC
*
297099 GATCAAACC
1 GGTCAAACC
297108 GGTCAGAACC
1 GGTCA-AACC
*
297118 GGTTGAAAACC
1 GG-T-CAAACC
*
297129 GGTTAAACC
1 GGTCAAACC
297138 GGT
1 GGT
297141 TTCCAGCAGC
Statistics
Matches: 69, Mismatches: 16, Indels: 10
0.73 0.17 0.11
Matches are distributed among these distances:
9 33 0.48
10 28 0.41
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:297099 original size:29 final size:29
Alignment explanation
Indices: 297058--297142 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
297048 ACCGATCAAC
* *
297058 CCGGTTCAGACCGGTCAAACCGGTTTGAA
1 CCGGTTGAAACCGGTCAAACCGGTTTGAA
* **
297087 CCGGTTGAAACCGATCAAACCGGTCAGAA
1 CCGGTTGAAACCGGTCAAACCGGTTTGAA
*
297116 CCGGTTGAAAACCGGTTAAACCGGTTT
1 CCGGTTG-AAACCGGTCAAACCGGTTT
297143 CCAGCAGCCA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 31 0.67
30 15 0.33
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (29 bp):
CCGGTTGAAACCGGTCAAACCGGTTTGAA
Found at i:297139 original size:20 final size:21
Alignment explanation
Indices: 297103--297141 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
297093 GAAACCGATC
297103 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
297124 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
297142 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:297141 original size:9 final size:9
Alignment explanation
Indices: 297067--297141 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 9
297057 CCCGGTTCAG
*
297067 ACCGGTCAA
1 ACCGGTTAA
*
297076 ACCGGTTTGA
1 ACCGG-TTAA
297086 ACCGGTTGAA
1 ACCGGTT-AA
* *
297096 ACCGATCAA
1 ACCGGTTAA
*
297105 ACCGGTCAGA
1 ACCGGTTA-A
297115 ACCGGTTGAAA
1 ACCGGTT--AA
297126 ACCGGTTAA
1 ACCGGTTAA
297135 ACCGGTT
1 ACCGGTT
297142 TCCAGCAGCC
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
9 25 0.46
10 20 0.37
11 8 0.15
12 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:298177 original size:182 final size:181
Alignment explanation
Indices: 297863--298375 Score: 803
Period size: 182 Copynumber: 2.8 Consensus size: 181
297853 GTTGTTATAT
* * * *
297863 TTTATTATAAGTATCGAAACTTTTGAAATTTAAAAGAGAATAAGTTATAGCATTAATAAAGTGTC
1 TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGTCAATAAAGTGTC
* * * * **
297928 GATACTTTATAAATATGTATCGATCCAAAACAATAAAACAGGTAAAACTATGACAAAACCGGTCT
66 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-TAGTCT
* *
297993 CGAAATGACAAAATCGGTAAAGCA-CTATCGGATATGTTGAAAGTGTCGATAC
130 CGAAATGACAAAACCGGTAAAG-AGCTACCGGATATGTTGAAAGTGTCGATAC
* *
298045 TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGCCAATAAAGTGTC
1 TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGTCAATAAAGTGTC
*
298110 GATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAATTAGTCT
66 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-TAGTCT
*
298175 CGAAATGACAAAACCGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATAC
130 CGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATAC
* *
298227 TTTATTATAAGTATTGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTC
1 TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGTCAATAAAGTGTC
* *
298292 GATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAATCGATCT
66 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATAG-TCT
298357 CGAAATGACAAAACCGGTA
130 CGAAATGACAAAACCGGTA
298376 GTAAAAAAGT
Statistics
Matches: 304, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
181 3 0.01
182 301 0.99
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (181 bp):
TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGTCAATAAAGTGTC
GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATAGTCTC
GAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATAC
Found at i:301556 original size:2 final size:2
Alignment explanation
Indices: 301549--301575 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
301539 GAGTATTTTA
301549 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
301576 GGTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:304315 original size:20 final size:20
Alignment explanation
Indices: 304278--304317 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
304268 TTGTAACTCC
* * *
304278 CTCATATTTTTTAGAATTAT
1 CTCATATTATTAACAATTAT
304298 CTCATATTATTAACAATTAT
1 CTCATATTATTAACAATTAT
304318 ATTGAGTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (20 bp):
CTCATATTATTAACAATTAT
Found at i:304650 original size:2 final size:2
Alignment explanation
Indices: 304643--304732 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
304633 ATAAGAACCT
304643 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
304685 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
304727 TA TA TA
1 TA TA TA
304733 AAAAAACATA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:307759 original size:21 final size:21
Alignment explanation
Indices: 307735--307788 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
307725 AAATGACCGG
307735 TTTGACCGGTTTTGCTCTTGT
1 TTTGACCGGTTTTGCTCTTGT
307756 TTTGACCGGTTTTGCTCTTGT
1 TTTGACCGGTTTTGCTCTTGT
307777 TTTGACCGGTTT
1 TTTGACCGGTTT
307789 GACCGATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.06, C:0.19, G:0.24, T:0.52
Consensus pattern (21 bp):
TTTGACCGGTTTTGCTCTTGT
Found at i:310114 original size:24 final size:24
Alignment explanation
Indices: 310087--310202 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
310077 TTCGATTTGA
310087 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
310111 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
310135 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
310159 ATTCTGATCTGTTACTTGACCT-A
1 ATTCTGATCTGATACTTGACATGG
*
310182 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
310203 CTGATTTATT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.02
24 80 0.96
25 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:312977 original size:20 final size:20
Alignment explanation
Indices: 312952--313161 Score: 104
Period size: 20 Copynumber: 10.4 Consensus size: 20
312942 GATTTTCCAG
312952 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATATGAA
*
312972 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
312992 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATATGAA
* ** * **
313012 TATCGCAACAAGTATCCGTAA
1 AATCGCAACGCGAATATG-AA
* * *
313033 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGAA
*
313053 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATATG-AA
* * ** *
313074 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
* *
313094 AATCGCAACGAGAATA-CATA
1 AATCGCAACGCGAATATGA-A
* *
313114 AATCGCAATGC-ATATATGTA
1 AATCGCAACGCGA-ATATGAA
* * *
313134 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
313154 AATCGCAA
1 AATCGCAA
313162 TGTGTATCCG
Statistics
Matches: 142, Mismatches: 38, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.01
20 108 0.76
21 32 0.23
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATATGAA
Found at i:313039 original size:21 final size:20
Alignment explanation
Indices: 313013--313204 Score: 145
Period size: 20 Copynumber: 9.4 Consensus size: 20
313003 GATTCTGACT
*
313013 ATCGCAACAAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
313034 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGTATCCGTAA
** *
313054 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
313075 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
313095 ATCGCAACGAGAATACATAA
1 ATCGCAACGAGTATCCGTAA
* **
313115 ATCGCAATGCA-TATATGTAA
1 ATCGCAACG-AGTATCCGTAA
* *
313135 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
313155 ATCGCAATGTGTATCCGTGA
1 ATCGCAACGAGTATCCGTAA
*
313175 ATCGCAACGACG-ATACGTAAA
1 ATCGCAACGA-GTATCCGT-AA
313196 ATCGCAACG
1 ATCGCAACG
313205 CGATTTTTAA
Statistics
Matches: 132, Mismatches: 34, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
19 1 0.01
20 89 0.67
21 42 0.32
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:313058 original size:41 final size:41
Alignment explanation
Indices: 312952--313206 Score: 245
Period size: 40 Copynumber: 6.3 Consensus size: 41
312942 GATTTTCCAG
* * * * *
312952 AATCGCAACGCGAATATGAAAATCGCAACGCG-A-ACATATA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA-A
* * * *
312992 AATCGCAACGCG-ATTCTG-ACTATCGCAACAAGTATCCGTAA
1 AATCGCAACGCGTA-TCTGTA-AATCGCAACGAGAATACGTAA
*
313033 AATCGCAACGCGTATCTGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
* * *
313074 AATCGTAACGCGTATCCGTAAATCGCAACGAGAATACAT-A
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
* * *
313114 AATCGCAATGCATATATGTAAATCGCAACGAGAATACGT-A
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
* * * *
313154 AATCGCAATGTGTATCCGTGAATCGCAACGACG-ATACGTAA
1 AATCGCAACGCGTATCTGTAAATCGCAACGA-GAATACGTAA
313195 AATCGCAACGCG
1 AATCGCAACGCG
313207 ATTTTTAAAG
Statistics
Matches: 179, Mismatches: 28, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
39 2 0.01
40 91 0.51
41 81 0.45
42 5 0.03
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
Found at i:313117 original size:81 final size:81
Alignment explanation
Indices: 312952--313206 Score: 243
Period size: 81 Copynumber: 3.1 Consensus size: 81
312942 GATTTTCCAG
* * * ** * *
312952 AATCGCAACGCGAATATGAAAATCGCAACG-CGAACATATAAATCGCAACGCG-ATTC-TGACTA
1 AATCGCAACGCGTATATGTAAATCGCAACGAC-AATACGTAAATCGCAACGCGTATCCGT-A-AA
* * *
313014 TCGCAAC-AAGTATCCGTAA
63 TCGCAACGACG-ATACATAA
* *
313033 AATCGCAACGCGTATCTGTAAATCGCAACGACAATACGTAAAATCGTAACGCGTATCCGTAAATC
1 AATCGCAACGCGTATATGTAAATCGCAACGACAATACGT-AAATCGCAACGCGTATCCGTAAATC
313098 GCAACGA-GAATACAT-A
65 GCAACGACG-ATACATAA
* * * * * *
313114 AATCGCAATGCATATATGTAAATCGCAACGAGAATACGTAAATCGCAATGTGTATCCGTGAATCG
1 AATCGCAACGCGTATATGTAAATCGCAACGACAATACGTAAATCGCAACGCGTATCCGTAAATCG
*
313179 CAACGACGATACGTAA
66 CAACGACGATACATAA
313195 AATCGCAACGCG
1 AATCGCAACGCG
313207 ATTTTTAAAG
Statistics
Matches: 144, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
80 33 0.23
81 79 0.55
82 26 0.18
83 5 0.03
84 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (81 bp):
AATCGCAACGCGTATATGTAAATCGCAACGACAATACGTAAATCGCAACGCGTATCCGTAAATCG
CAACGACGATACATAA
Found at i:313825 original size:21 final size:20
Alignment explanation
Indices: 313764--313839 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
313754 TTCTAAACTT
313764 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
313784 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
313804 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
313825 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
313840 TAATCGCAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 30 0.61
21 19 0.39
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:313934 original size:19 final size:19
Alignment explanation
Indices: 313867--313934 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
313857 CAAAATCGCA
313867 TTGCGATTTTCATTT-TGCG
1 TTGCGATTTTCATTTCT-CG
313886 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
*
313900 TTGTGATTTTCATTTCTCG
1 TTGCGATTTTCATTTCTCG
313919 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
313935 AACCAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
14 8 0.20
15 1 0.02
16 3 0.07
17 3 0.07
19 26 0.63
ACGTcount: A:0.10, C:0.19, G:0.18, T:0.53
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:314055 original size:25 final size:26
Alignment explanation
Indices: 314001--314055 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
313991 TTATGTTTAT
*
314001 TGTTTTTGGTATATCTTCACTGTGTA
1 TGTTTTTGGTATATCTTAACTGTGTA
314027 -GTTTTTGGTATATC-TAACT-TGGTA
1 TGTTTTTGGTATATCTTAACTGT-GTA
314051 TGTTT
1 TGTTT
314056 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 1 0.04
24 7 0.27
25 18 0.69
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (26 bp):
TGTTTTTGGTATATCTTAACTGTGTA
Found at i:315786 original size:94 final size:94
Alignment explanation
Indices: 315625--316004 Score: 656
Period size: 94 Copynumber: 4.1 Consensus size: 94
315615 TAGATTGCTT
* *
315625 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
315690 ATTTGTCTTTTTTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
315719 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
315784 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
315813 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
315878 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
315907 AGTAAATTTGTTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
315972 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
316000 AGTAA
1 AGTAA
316005 TGCAATCTAT
Statistics
Matches: 276, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 25 0.09
94 251 0.91
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:316167 original size:19 final size:19
Alignment explanation
Indices: 316121--316158 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
316111 ATCGCAACGA
316121 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
316140 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
316159 TATAATCGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.32, G:0.16, T:0.05
Consensus pattern (19 bp):
CAAAATCGCAACGCGAAAC
Found at i:316186 original size:19 final size:20
Alignment explanation
Indices: 316164--316218 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
316154 GAAACTATAA
316164 TCGCGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTTCATTT
**
316183 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA-TTT
*
316204 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
316219 AAGTTCCAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
21 14 0.48
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:318107 original size:14 final size:14
Alignment explanation
Indices: 318087--318123 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
318077 GATTGTTTAA
318087 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
318100 TATGATTTGTAAAAG
1 T-TGATTTGTAAAAG
318115 TTGATTTGT
1 TTGATTTGT
318124 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:318346 original size:20 final size:19
Alignment explanation
Indices: 318300--318372 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
318290 GCGAAACTCT
*
318300 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
318319 CATTGCGATAGTCATTTCCG
1 CGTTGCGATATTCATTT-CG
318339 CGTTGCGATATTCATATTCG
1 CGTTGCGATATTCAT-TTCG
*
318359 CGTTGCGATTTTCA
1 CGTTGCGATATTCA
318373 CGTTGTGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.30
20 30 0.65
21 2 0.04
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:318382 original size:14 final size:14
Alignment explanation
Indices: 318359--318419 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
318349 TTCATATTCG
318359 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
*
318373 CGTTGTGATTTTCA
1 CGTTGCGATTTTCA
* *
318387 TTTCGCATTGCGATTCTCT
1 ---CG--TTGCGATTTTCA
318406 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
318420 TTTCGCATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
14 23 0.64
16 2 0.06
17 2 0.06
19 9 0.25
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:318398 original size:33 final size:33
Alignment explanation
Indices: 318300--318433 Score: 151
Period size: 33 Copynumber: 3.8 Consensus size: 33
318290 GCGAAACTCT
*
318300 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCG--A-T--TTT-CA
* *
318339 CGTTGCGATATTCATATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTTTCA
* * *
318373 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTCA
318406 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
318434 AGACATTAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
33 42 0.49
34 14 0.16
35 3 0.04
37 1 0.01
38 1 0.01
39 14 0.16
40 10 0.12
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTCA
Found at i:321003 original size:24 final size:24
Alignment explanation
Indices: 320952--321003 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
320942 ATCTGAGTAT
** *
320952 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
320976 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
321000 TGAC
1 TGAC
321004 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:321923 original size:20 final size:20
Alignment explanation
Indices: 321898--322058 Score: 148
Period size: 20 Copynumber: 8.0 Consensus size: 20
321888 GCAATGCGAA
321898 TACGTATTCGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
*
321918 TACGTATTCTCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
*
321938 TACAG-ATACGCGTTGCGATT
1 TAC-GTATTCGCGTTGCGATT
* *
321958 TACGTATTCTCGTTACGATT
1 TACGTATTCGCGTTGCGATT
* *
321978 TACGGATACGCGTTGCGATTT
1 TACGTATTCGCGTTGCGA-TT
* * * *
321999 TACGGATACTCGTTGCGATAG
1 TACGTATTCGCGTTGCGAT-T
*
322020 T-CAG-AATCGCGTTGCGATT
1 TAC-GTATTCGCGTTGCGATT
* *
322039 TTCATATTCGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
322059 CTGGAAAATC
Statistics
Matches: 116, Mismatches: 18, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
19 2 0.02
20 92 0.79
21 22 0.19
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
TACGTATTCGCGTTGCGATT
Found at i:321956 original size:40 final size:40
Alignment explanation
Indices: 321906--322058 Score: 193
Period size: 40 Copynumber: 3.8 Consensus size: 40
321896 AATACGTATT
321906 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATA
* *
321946 CGCGTTGCGATTTACGTATTCTCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATA
* * *
321986 CGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-A
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGAT-TTACAGATA
* * *
322026 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 -CGCGTTGCGATTTACGTATTCTCGTTGCGATT
322059 CTGGAAAATC
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
40 65 0.67
41 31 0.32
42 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (40 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATA
Found at i:321979 original size:60 final size:61
Alignment explanation
Indices: 321898--322017 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 61
321888 GCAATGCGAA
* * * *
321898 TACGTATTCGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACAGATACGCGTTGCGATT
1 TACGTATTCGCGTTACGATTTACGGATACGCGTTGCGATTTTACAGATACGCGTTGCGATT
* * *
321958 TACGTATTCTCGTTACGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 TACGTATTCGCGTTACGATTTACGGATACGCGTTGCGATTTTACAGATACGCGTTGCGAT
322018 AGTCAGAATC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
60 33 0.63
61 19 0.37
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (61 bp):
TACGTATTCGCGTTACGATTTACGGATACGCGTTGCGATTTTACAGATACGCGTTGCGATT
Found at i:322047 original size:81 final size:80
Alignment explanation
Indices: 321906--322058 Score: 202
Period size: 81 Copynumber: 1.9 Consensus size: 80
321896 AATACGTATT
* * * * *
321906 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGT
1 CGCGTTGCGATTTACGGATACTCGTTGCGATGTACAGATACGCGTTGCGATTTACATATTCGCGT
321971 TACGATTTACGGATA
66 TACGATTTACGGATA
*
321986 CGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTTCATATTCG
1 CGCGTTGCGA-TTTACGGATACTCGTTGCGAT-GTACAGATA-CGCGTTGCGATTTACATATTCG
*
322049 CGTTGCGATT
63 CGTTACGATT
322059 CTGGAAAATC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
80 11 0.17
81 51 0.81
82 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (80 bp):
CGCGTTGCGATTTACGGATACTCGTTGCGATGTACAGATACGCGTTGCGATTTACATATTCGCGT
TACGATTTACGGATA
Found at i:323572 original size:173 final size:173
Alignment explanation
Indices: 323119--323632 Score: 728
Period size: 173 Copynumber: 3.0 Consensus size: 173
323109 TTTATCATCT
* * * * *
323119 TGCTACCTTTTCATCTTTATTTTATTTATGTTTTATTCAATGTT-TTTCGACCATTGGGTTACAG
1 TGCTACCTATTCATCTTTATTTTA-TT-TGTGTTATTGAATGTTATTTTGACCATTGGGTTACAA
** * ** * *
323183 TGATGATTTTTTGGGATCAGTGGAAGGCATTTGTTGAATGTTTGATGAAACTTTCGACCATTGTG
64 TGATGAGGTTTTGGAATCAGTGGAAGGCATTCATTGAATGCTTGATGAAACTTTTGACCATTGTG
* * * *
323248 TCGGTCCTGAGCGGTTAGCTGAGCAACTTAGTGACTTAATTGTCA
129 TCGATCCTGAGCGGTTACCTGAGCAACCTAGTGACTTAATTGCCA
* * * *
323293 TGCTACCTATTCATCTTT-TTTTATTCGTGTTGTAGAATGTTATTTTGAACATTGGGTTACAATG
1 TGCTACCTATTCATCTTTATTTTATTTGTGTTATTGAATGTTATTTTGACCATTGGGTTACAATG
323357 ATGAGGTTTTGGAATCAGTGGAAGGCATTCATTGAATGCTTGATGAAACTTTTGACTC-TTGTGT
66 ATGAGGTTTTGGAATCAGTGGAAGGCATTCATTGAATGCTTGATGAAACTTTTGAC-CATTGTGT
*
323421 CGATCCTGAGCGGTTACCTGAGCAACCTAGTGAATTAATTGCCA
130 CGATCCTGAGCGGTTACCTGAGCAACCTAGTGACTTAATTGCCA
* *
323465 TGCTACATATTCATCTTTATTTTATTTGTGTTATTGAATGTTATTTTGACCATTGGGTTGCAATG
1 TGCTACCTATTCATCTTTATTTTATTTGTGTTATTGAATGTTATTTTGACCATTGGGTTACAATG
* ** * *
323530 ACGAGGTTTCAGAATCAGTGGAAGGCATTCATTGAATGCTTGATGAAACTTTTTACCATTGTGTT
66 ATGAGGTTTTGGAATCAGTGGAAGGCATTCATTGAATGCTTGATGAAACTTTTGACCATTGTGTC
323595 GATCCTGAGCGGTTACCTGAGCAACCTAGTGACTTAAT
131 GATCCTGAGCGGTTACCTGAGCAACCTAGTGACTTAAT
323633 CATCTTGCTG
Statistics
Matches: 303, Mismatches: 33, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
171 11 0.04
172 133 0.44
173 142 0.47
174 17 0.06
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (173 bp):
TGCTACCTATTCATCTTTATTTTATTTGTGTTATTGAATGTTATTTTGACCATTGGGTTACAATG
ATGAGGTTTTGGAATCAGTGGAAGGCATTCATTGAATGCTTGATGAAACTTTTGACCATTGTGTC
GATCCTGAGCGGTTACCTGAGCAACCTAGTGACTTAATTGCCA
Found at i:327475 original size:12 final size:12
Alignment explanation
Indices: 327458--327486 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
327448 TTCATCATCT
327458 AAAACTTTATTA
1 AAAACTTTATTA
327470 AAAACTTTATTA
1 AAAACTTTATTA
327482 AAAAC
1 AAAAC
327487 AAATCTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAACTTTATTA
Found at i:329081 original size:2 final size:2
Alignment explanation
Indices: 329076--329108 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
329066 ATTTAAGTAC
329076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
329109 TTCTATTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:329140 original size:20 final size:21
Alignment explanation
Indices: 329102--329142 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
329092 TATATATATA
329102 TATATATTTCTATTCATTTTC
1 TATATATTTCTATTCATTTTC
329123 TATATA-TTCTTATT-ATTTTC
1 TATATATTTC-TATTCATTTTC
329143 GTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (21 bp):
TATATATTTCTATTCATTTTC
Found at i:329254 original size:18 final size:17
Alignment explanation
Indices: 329207--329254 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
329197 TTTTCTTTAT
*
329207 TATTTTAATTATTATGTA
1 TATTTT-ATTATTATATA
*
329225 TATTGTTTTTATTATCATA
1 TATT-TTATTATTAT-ATA
329244 TATTTTATTAT
1 TATTTTATTAT
329255 CTTTTTCCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (17 bp):
TATTTTATTATTATATA
Found at i:341223 original size:24 final size:25
Alignment explanation
Indices: 341198--341245 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
341188 TCAATAGTAA
341198 TTAAATATTATTTCAT-TTTTTAAAT
1 TTAAATATT-TTTCATATTTTTAAAT
* *
341223 TTAATTATTTTTTATATTTTTAA
1 TTAAATATTTTTCATATTTTTAA
341246 TCTATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTAAATATTTTTCATATTTTTAAAT
Found at i:341234 original size:17 final size:18
Alignment explanation
Indices: 341198--341241 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
341188 TCAATAGTAA
*
341198 TTAAATATTATTTCATTTT
1 TTAAAT-TTAATTCATTTT
341217 TTAAATTTAATT-ATTTT
1 TTAAATTTAATTCATTTT
*
341234 TTATATTT
1 TTAAATTT
341242 TTAATCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TTAAATTTAATTCATTTT
Found at i:341791 original size:2 final size:2
Alignment explanation
Indices: 341728--341776 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
341718 AATAAAAAAT
341728 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
341770 TA TA TA T
1 TA TA TA T
341777 TGATTTAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:342645 original size:34 final size:34
Alignment explanation
Indices: 342599--342676 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
342589 TTTGATTCAA
* *
342599 TTTGATTCTTAATCTTTTCATATTTATTTTTAGT
1 TTTGATTTTTAATCTTTTCATATTTACTTTTAGT
342633 TTTGATTTTTAATCTTTTCATATTTACTTTTAGT
1 TTTGATTTTTAATCTTTTCATATTTACTTTTAGT
342667 TTTGATTTTT
1 TTTGATTTTT
342677 TTTCTATTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (34 bp):
TTTGATTTTTAATCTTTTCATATTTACTTTTAGT
Found at i:348775 original size:20 final size:20
Alignment explanation
Indices: 348750--348787 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
348740 AGAAAGATGT
348750 AAAAAATATATATAATGTCA
1 AAAAAATATATATAATGTCA
* *
348770 AAAAAATGTATTTAATGT
1 AAAAAATATATATAATGT
348788 TTAATTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (20 bp):
AAAAAATATATATAATGTCA
Found at i:352234 original size:2 final size:2
Alignment explanation
Indices: 352229--352262 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
352219 AATAGGCTTA
352229 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
352263 TAAACTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:357336 original size:64 final size:64
Alignment explanation
Indices: 357264--357415 Score: 304
Period size: 64 Copynumber: 2.4 Consensus size: 64
357254 TCTGGAGGGA
357264 ATACAAAACAAAAAATGTTCAAATACTTTTAACTATTTAATAATAGGTACTTATATTCTTGTAT
1 ATACAAAACAAAAAATGTTCAAATACTTTTAACTATTTAATAATAGGTACTTATATTCTTGTAT
357328 ATACAAAACAAAAAATGTTCAAATACTTTTAACTATTTAATAATAGGTACTTATATTCTTGTAT
1 ATACAAAACAAAAAATGTTCAAATACTTTTAACTATTTAATAATAGGTACTTATATTCTTGTAT
357392 ATACAAAACAAAAAATGTTCAAAT
1 ATACAAAACAAAAAATGTTCAAAT
357416 GGATTTGGGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 88 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (64 bp):
ATACAAAACAAAAAATGTTCAAATACTTTTAACTATTTAATAATAGGTACTTATATTCTTGTAT
Found at i:361876 original size:24 final size:24
Alignment explanation
Indices: 361822--361878 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
361812 CGTGTATTGA
* *
361822 CTTGTTTGTCGACTCACTTATCAG
1 CTTGTTTATCGACTCACTTATAAG
* *
361846 -TTCGTTTATCGACTTATTTATAAG
1 CTT-GTTTATCGACTCACTTATAAG
361870 CTTGTTTAT
1 CTTGTTTAT
361879 TCGGTGCTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 23 0.85
25 2 0.07
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (24 bp):
CTTGTTTATCGACTCACTTATAAG
Found at i:366080 original size:32 final size:33
Alignment explanation
Indices: 366034--366096 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
366024 TTTGTTTTAT
* * *
366034 GTTATTTTTCAGTTCGTGTTACTTTCAATTCAA
1 GTTAATTTTCAGTTCGGGTTAATTTCAATTCAA
366067 GTTAATTTT-AGTTCGGGTTAATTTCAATTC
1 GTTAATTTTCAGTTCGGGTTAATTTCAATTC
366097 GGTTTGCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.22, C:0.13, G:0.14, T:0.51
Consensus pattern (33 bp):
GTTAATTTTCAGTTCGGGTTAATTTCAATTCAA
Found at i:366097 original size:16 final size:16
Alignment explanation
Indices: 366040--366098 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
366030 TTATGTTATT
* * *
366040 TTTCAGTTCGTGTTAC
1 TTTCAATTCGGGTTAA
**
366056 TTTCAATTCAAGTTAA
1 TTTCAATTCGGGTTAA
* *
366072 TTTTAGTTCGGGTTAA
1 TTTCAATTCGGGTTAA
366088 TTTCAATTCGG
1 TTTCAATTCGG
366099 TTTGCTTTCG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (16 bp):
TTTCAATTCGGGTTAA
Found at i:367633 original size:157 final size:158
Alignment explanation
Indices: 367347--367648 Score: 579
Period size: 157 Copynumber: 1.9 Consensus size: 158
367337 TTTCACCTCC
* *
367347 TAAAATTTTATAAGTTCGTCTCCTCTTTAAAATTTTATAAGTTCACCCTCTCTAACATAAAATCA
1 TAAAATTTTATAAGTTCGTATCCCCTTTAAAATTTTATAAGTTCACCCTCTCTAACATAAAATCA
367412 TGCGTTCGTCCCTGGTTGTCGACTGCCAGTATTCTTTATTATCTTTTTATTTTCTTATATTACAT
66 TGCGTTCGTCCCTGGTTGTCGACTGCCAGTATTCTTTATTATCTTTTTATTTTCTTATATTACAT
367477 CTTTATTT-TTTTTTATTTTCAATCTCT
131 CTTTATTTCTTTTTTATTTTCAATCTCT
367504 TAAAATTTTATAAGTTCGTATCCCCTTTAAAATTTTATAAGTTCACCCTCTCTAACATAAAATCA
1 TAAAATTTTATAAGTTCGTATCCCCTTTAAAATTTTATAAGTTCACCCTCTCTAACATAAAATCA
367569 TGCGTTCGTCCCTGGTTGTCGACTGCCAGTATTCTTTATTATCTTTTTATTTTCTTATATTACAT
66 TGCGTTCGTCCCTGGTTGTCGACTGCCAGTATTCTTTATTATCTTTTTATTTTCTTATATTACAT
367634 CTTTATTTCTTTTTT
131 CTTTATTTCTTTTTT
367649 TTTAATTTTC
Statistics
Matches: 142, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
157 136 0.96
158 6 0.04
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (158 bp):
TAAAATTTTATAAGTTCGTATCCCCTTTAAAATTTTATAAGTTCACCCTCTCTAACATAAAATCA
TGCGTTCGTCCCTGGTTGTCGACTGCCAGTATTCTTTATTATCTTTTTATTTTCTTATATTACAT
CTTTATTTCTTTTTTATTTTCAATCTCT
Found at i:368550 original size:20 final size:20
Alignment explanation
Indices: 368509--368550 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
368499 TATATAAAAA
**
368509 TATTTACAATTTATATGTTT
1 TATTTACAATTTATATAATT
368529 TATTTA-AATTATATATAATT
1 TATTTACAATT-TATATAATT
368549 TA
1 TA
368551 AAGAGAGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTACAATTTATATAATT
Found at i:369971 original size:90 final size:88
Alignment explanation
Indices: 369813--369985 Score: 208
Period size: 90 Copynumber: 1.9 Consensus size: 88
369803 GGTCTTTCTA
* * * * *
369813 AATTACTCTAAATATGACCGTGTGAACCACCTTAGATTTGTATGAACTAACATAGTATACAAAAA
1 AATTACTCTAAATATGACAGTGCGAACCACCTTACATTTGTATCAACAAACATAGTATACAAAAA
369878 ATTAACATATATTATACACATTTTT
66 ATTAAC--ATATTATACACATTTTT
* *
369903 AATTACTCTACATATGGCAGTGCGAA-CAGCCTTACATTTGTATCAACAAACAT-GTTATA-AAT
1 AATTACTCTAAATATGACAGTGCGAACCA-CCTTACATTTGTATCAACAAACATAG-TATACAA-
*
369965 ATAATTAACATATTATACACA
63 AAAATTAACATATTATACACA
369986 CAAATCAACA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
88 12 0.17
89 5 0.07
90 55 0.76
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (88 bp):
AATTACTCTAAATATGACAGTGCGAACCACCTTACATTTGTATCAACAAACATAGTATACAAAAA
ATTAACATATTATACACATTTTT
Found at i:374940 original size:18 final size:18
Alignment explanation
Indices: 374913--374947 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
374903 GATGCAATGC
374913 CTTAACACATTCCTCTAG
1 CTTAACACATTCCTCTAG
*
374931 CTTAATACATTCCTCTA
1 CTTAACACATTCCTCTA
374948 AATCAGAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.31, G:0.03, T:0.37
Consensus pattern (18 bp):
CTTAACACATTCCTCTAG
Found at i:377263 original size:19 final size:16
Alignment explanation
Indices: 377229--377259 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
377219 TACAAAATCT
377229 AATAATCCATAATATA
1 AATAATCCATAATATA
*
377245 AATAATCCATTATAT
1 AATAATCCATAATAT
377260 TATATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATCCATAATATA
Found at i:393405 original size:142 final size:142
Alignment explanation
Indices: 393146--393430 Score: 516
Period size: 142 Copynumber: 2.0 Consensus size: 142
393136 AATGCTACAA
*
393146 CCTTTTCCAGATTGGATCCATAGACTGTAATACTTGTCATATTTTCTTGTTGCCTGAGTACGCTA
1 CCTTTTCCAGATTGGATCCATAGACTGTAATACTTGTCATATTTTCTTGTTGCCTGAGTACGCCA
*
393211 TGGTCTCTCAAACCCAAATGCTTAAACGGTTGAATTTATAAACATGCCTTCTTCTTCCTCTAATT
66 TGGTCTCTCAAACCCAAATACTTAAACGGTTGAATTTATAAACATGCCTTCTTCTTCCTCTAATT
393276 TTATAAAGCAAT
131 TTATAAAGCAAT
* *
393288 CCTTTTCCAGATTGGATCCATAGACTGTAATACTTGTCATCTTTTCTTGTTGCCTTAGTACGCCA
1 CCTTTTCCAGATTGGATCCATAGACTGTAATACTTGTCATATTTTCTTGTTGCCTGAGTACGCCA
**
393353 TGGTCTCTCAAACCCAAATACTTAAACGGTTGAATTTATAAACATGTTTTCTTCTTCCTCTAATT
66 TGGTCTCTCAAACCCAAATACTTAAACGGTTGAATTTATAAACATGCCTTCTTCTTCCTCTAATT
393418 TTATAAAGCAAT
131 TTATAAAGCAAT
393430 C
1 C
393431 TAACATAGGG
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 137 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (142 bp):
CCTTTTCCAGATTGGATCCATAGACTGTAATACTTGTCATATTTTCTTGTTGCCTGAGTACGCCA
TGGTCTCTCAAACCCAAATACTTAAACGGTTGAATTTATAAACATGCCTTCTTCTTCCTCTAATT
TTATAAAGCAAT
Found at i:400878 original size:14 final size:15
Alignment explanation
Indices: 400859--400887 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
400849 TACATGATCT
400859 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
400873 GCATAAAACATAAGA
1 GCATAAAACATAAGA
400888 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:400927 original size:23 final size:22
Alignment explanation
Indices: 400888--400930 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
400878 AAACATAAGA
400888 TATATGATATGGTATATATGAT
1 TATATGATATGGTATATATGAT
400910 TATATGCATAT-GTGATATATG
1 TATATG-ATATGGT-ATATATG
400931 CTATGAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (22 bp):
TATATGATATGGTATATATGAT
Found at i:408301 original size:218 final size:217
Alignment explanation
Indices: 407923--408357 Score: 852
Period size: 218 Copynumber: 2.0 Consensus size: 217
407913 ACAAACCTTT
*
407923 AGTTTGAAGTGTGGTTATAACAAGTTTCCCGCTAAAAGTTGAGCTCCAAAAACAGCAAAAAAGGA
1 AGTTTGAAGTGTGGTTATAACAAGTTTCCCGCTAAAAGTTGAGCTCCAAAAACAGCAAAAAAGAA
407988 ATTCCCTGTTGAAAACAAAGGATCACTAGCTAGCTTCTTCTTCTTCGCCATACCTCACAGTCGCA
66 ATTCCCTGTTGAAAACAAAGGATCACTAGCTAGCTTCTTCTTCTTCGCCATACCTCACAGTCGCA
408053 TAATGGCCAAACTCCAATACTCCAATCTCCCCTTCAAACTAATCGCATCTTTCTCATTTATTTTT
131 TAATGGCCAAACTCCAATACTCCAATCT-CCCTTCAAACTAATCGCATCTTTCTCATTTATTTTT
408118 TTTTAATTTTATTTTATTATTAC
195 TTTTAATTTTATTTTATTATTAC
408141 AGTTTGAAGTGTGGTTATAACAAGTTTCCCGCTAAAAGTTGAGCTCCAAAAACAGCAAAAAAGAA
1 AGTTTGAAGTGTGGTTATAACAAGTTTCCCGCTAAAAGTTGAGCTCCAAAAACAGCAAAAAAGAA
408206 ATTCCCTGTTGAAAACAAAGGATCACTAGCTAGCTTCTTCTTCTTCGCCATACCTCACAGTCGCA
66 ATTCCCTGTTGAAAACAAAGGATCACTAGCTAGCTTCTTCTTCTTCGCCATACCTCACAGTCGCA
408271 TAATGGCCAAACTCCAATACTCCAATCTCCCTTCAAACTAATCGCATCTTTCTCATTTATTTTTT
131 TAATGGCCAAACTCCAATACTCCAATCTCCCTTCAAACTAATCGCATCTTTCTCATTTATTTTTT
408336 TTTAATTTTATTTTATTATTAC
196 TTTAATTTTATTTTATTATTAC
408358 CGTAATGCGA
Statistics
Matches: 216, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
217 59 0.27
218 157 0.73
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (217 bp):
AGTTTGAAGTGTGGTTATAACAAGTTTCCCGCTAAAAGTTGAGCTCCAAAAACAGCAAAAAAGAA
ATTCCCTGTTGAAAACAAAGGATCACTAGCTAGCTTCTTCTTCTTCGCCATACCTCACAGTCGCA
TAATGGCCAAACTCCAATACTCCAATCTCCCTTCAAACTAATCGCATCTTTCTCATTTATTTTTT
TTTAATTTTATTTTATTATTAC
Found at i:415046 original size:27 final size:27
Alignment explanation
Indices: 415014--415107 Score: 188
Period size: 27 Copynumber: 3.5 Consensus size: 27
415004 CCTTTTAAAT
415014 AATGTATATATATTTTTTGAAAAATAA
1 AATGTATATATATTTTTTGAAAAATAA
415041 AATGTATATATATTTTTTGAAAAATAA
1 AATGTATATATATTTTTTGAAAAATAA
415068 AATGTATATATATTTTTTGAAAAATAA
1 AATGTATATATATTTTTTGAAAAATAA
415095 AATGTATATATAT
1 AATGTATATATAT
415108 ATATATATAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (27 bp):
AATGTATATATATTTTTTGAAAAATAA
Found at i:421637 original size:34 final size:34
Alignment explanation
Indices: 421479--421674 Score: 129
Period size: 35 Copynumber: 5.6 Consensus size: 34
421469 ATATAAAAAC
421479 ATTTTCAAAACTATATAT-TATATAGTTTTCAAAAATG
1 ATTTT-AAAACTATATATAT-TATA-TTTTC-AAAATG
* *
421516 ATTTAAAAAATAT-TATA-TA-AGTTTTCCAAAATG
1 ATTTTAAAACTATATATATTATA-TTTT-CAAAATG
* *
421549 TTTTGTTAAAACTATATATTATATAAATTTTCCCAAAATG
1 -ATT-TTAAAACTATATA-TAT-TATATTTT--CAAAATG
* *
421589 TTTTTAAAA-AATATATATTATATTTTCAAAATG
1 ATTTTAAAACTATATATATTATATTTTCAAAATG
* * *
421622 ATTTCAAAACTATATACTA-CATAATTTCCAAAATG
1 ATTTTAAAACTATATA-TATTAT-ATTTTCAAAATG
421657 -TTTTAAAACT-TATATATT
1 ATTTTAAAACTATATATATT
421675 GTATATAAGT
Statistics
Matches: 131, Mismatches: 14, Indels: 32
0.74 0.08 0.18
Matches are distributed among these distances:
32 2 0.02
33 30 0.23
34 21 0.16
35 31 0.24
36 12 0.09
37 11 0.08
38 6 0.05
39 9 0.07
40 9 0.07
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (34 bp):
ATTTTAAAACTATATATATTATATTTTCAAAATG
Found at i:423772 original size:54 final size:53
Alignment explanation
Indices: 423613--423789 Score: 192
Period size: 54 Copynumber: 3.3 Consensus size: 53
423603 TGATAGATGG
* * * *
423613 CGTGTCCACGCCTTAACTGAAGACTTCTTATGCGATAGCTCAGTATGAATAAGT
1 CGTGCCCACACCTTAACTGAAGACTTCTTCTG-GATAGCTCAGGATGAATAAGT
* * * * *
423667 CGTGCCCACGCCTTAACTGAAGACTTTTTCTGCAGCAGCTCAGGATGAATAAGC
1 CGTGCCCACACCTTAACTGAAGACTTCTTCTGGA-TAGCTCAGGATGAATAAGT
* * * *
423721 CGTGCCCACACCTTAACTAAAGACTTCTTCTGTGATAGGTCGGGATAAATAAGT
1 CGTGCCCACACCTTAACTGAAGACTTCTTCTG-GATAGCTCAGGATGAATAAGT
* *
423775 CTTGCCCACATCTTA
1 CGTGCCCACACCTTA
423790 TACGGGAGCC
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
53 1 0.01
54 101 0.98
55 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (53 bp):
CGTGCCCACACCTTAACTGAAGACTTCTTCTGGATAGCTCAGGATGAATAAGT
Found at i:435685 original size:22 final size:23
Alignment explanation
Indices: 435660--435704 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
435650 TAATATTGAT
435660 TTGAATATTGATGAAAA-CTGAG
1 TTGAATATTGATGAAAACCTGAG
435682 TTGAATATTGATGAAAACCTGAG
1 TTGAATATTGATGAAAACCTGAG
435705 ATATAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (23 bp):
TTGAATATTGATGAAAACCTGAG
Found at i:441942 original size:36 final size:37
Alignment explanation
Indices: 441854--441944 Score: 166
Period size: 37 Copynumber: 2.5 Consensus size: 37
441844 TTTTGGTGAG
441854 TTTAACGAGCAACGAGTCAAGTTGATGAACTAATCTT
1 TTTAACGAGCAACGAGTCAAGTTGATGAACTAATCTT
*
441891 TTTAACGAGCAACGAGTCAAGTTGATGAACTAATTTT
1 TTTAACGAGCAACGAGTCAAGTTGATGAACTAATCTT
441928 TTTAACGAGC-ACGAGTC
1 TTTAACGAGCAACGAGTC
441945 GAGCAAAACC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 7 0.13
37 46 0.87
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (37 bp):
TTTAACGAGCAACGAGTCAAGTTGATGAACTAATCTT
Found at i:444789 original size:16 final size:15
Alignment explanation
Indices: 444746--444792 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 15
444736 TACAACATTT
*
444746 TATATAAAAATTTAA
1 TATATAAAATTTTAA
444761 TATATAATTAATTTGTAA
1 TATATAA--AATTT-TAA
444779 TATATAAAATTTTA
1 TATATAAAATTTTA
444793 CACATGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 9 0.32
16 5 0.18
17 4 0.14
18 10 0.36
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TATATAAAATTTTAA
Found at i:455064 original size:19 final size:17
Alignment explanation
Indices: 455040--455086 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 17
455030 ATGTTAAGCC
455040 GAATTAAATTATTATAAAT
1 GAATTAAATT-TTA-AAAT
455059 GAATTAAAATTTTAAAAT
1 GAATT-AAATTTTAAAAT
455077 GTAATTAAAT
1 G-AATTAAAT
455087 AGATTTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 9 0.35
19 12 0.46
20 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (17 bp):
GAATTAAATTTTAAAAT
Found at i:457877 original size:26 final size:26
Alignment explanation
Indices: 457832--457897 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 26
457822 TCTTAAAATT
*
457832 TTAAAATTATTATATATATT-TTTATCCTC
1 TTAAAATT-TTATATAT-TTGTCTAT--TC
457861 TTAAAATTTTATATATTTGTCTATTC
1 TTAAAATTTTATATATTTGTCTATTC
457887 TTAAAATTTTA
1 TTAAAATTTTA
457898 AAAATTCATC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 13 0.37
27 2 0.06
28 12 0.34
29 8 0.23
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.56
Consensus pattern (26 bp):
TTAAAATTTTATATATTTGTCTATTC
Found at i:458591 original size:24 final size:24
Alignment explanation
Indices: 458530--458581 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
458520 AAAAAATAAT
458530 AAAAGAATAATTAAATGGAAAGTG
1 AAAAGAATAATTAAATGGAAAGTG
*
458554 AAAAGAATAATTAAGTGGAAAGTG
1 AAAAGAATAATTAAATGGAAAGTG
458578 AAAA
1 AAAA
458582 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.21, T:0.19
Consensus pattern (24 bp):
AAAAGAATAATTAAATGGAAAGTG
Found at i:459404 original size:16 final size:17
Alignment explanation
Indices: 459374--459406 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
459364 TAAATCAAAG
459374 ATGTATTTTTGTAGGAA
1 ATGTATTTTTGTAGGAA
*
459391 ATGT-TTTTTTTAGGAA
1 ATGTATTTTTGTAGGAA
459407 GCATCTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (17 bp):
ATGTATTTTTGTAGGAA
Found at i:462287 original size:26 final size:26
Alignment explanation
Indices: 462257--462308 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
462247 CTTTCCTGTT
*
462257 TGGCCCATCTCTCGCTGAATTTTCTG
1 TGGCCAATCTCTCGCTGAATTTTCTG
* *
462283 TGGCCAATTTCTCGCTGAGTTTTCTG
1 TGGCCAATCTCTCGCTGAATTTTCTG
462309 AGGCTTGTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.27, G:0.21, T:0.40
Consensus pattern (26 bp):
TGGCCAATCTCTCGCTGAATTTTCTG
Found at i:479036 original size:243 final size:244
Alignment explanation
Indices: 478602--479092 Score: 876
Period size: 243 Copynumber: 2.0 Consensus size: 244
478592 AGATAAAAGG
* *
478602 TAGCATATGATTCCAAAAATACTCGTGTAGCTAAAACAAGTTCACTGATTAGAAGAAATGAATAA
1 TAGCATATGATTCCAAAAACACTCGTGTAGCTAAAACAAGTTCACTGATCAGAAGAAATGAATAA
478667 ATAAAGTTCAATCTTCGAATTCTTCAAAACCCTTTGAAGTAATAGTTAAACAAATGGAATCATCA
66 ATAAAGTTCAATCTTCGAATTCTTCAAAACCCTTTGAAGTAATAGTTAAACAAATGGAATCATCA
**
478732 CTAGGACCAATTCACTATAGAGATCTAGATCATAAATTCACTACAAGAAGATTTGCATGTTTTCG
131 CTAGGACCAATTCACTATAGAGATCTAGATCATAAATTCACTACAAGAAGATTCACATGTTTTCG
*
478797 ACTCTAATAGCAATCACCGTGAATCACCATGGGAACCTCTTTTTTCTGC
196 ACTCTAATAGCAATCACCATGAATCACCATGGGAACCTCTTTTTTCTGC
* *
478846 TAGCATATGATTCCAAAAACACTCGTGTAGCTAAAA-AAGTTCACTGATCAGGAGAAATGACTAA
1 TAGCATATGATTCCAAAAACACTCGTGTAGCTAAAACAAGTTCACTGATCAGAAGAAATGAATAA
478910 ATAAAGTTCAATCTTCGAATTCTTCAAAACCCTTTGAAGTAATAGTTAAACAAATGGAATCATCA
66 ATAAAGTTCAATCTTCGAATTCTTCAAAACCCTTTGAAGTAATAGTTAAACAAATGGAATCATCA
* * *
478975 CTAGGGCCAATTCACTATAGAGATCTAGCTTATAAATTCACTACAAGAAGATTCACATGTTTTCG
131 CTAGGACCAATTCACTATAGAGATCTAGATCATAAATTCACTACAAGAAGATTCACATGTTTTCG
*
479040 ACTCTAATAGCAATCATCATGAATCACCATGGGAACCTCTTTTTTCTGC
196 ACTCTAATAGCAATCACCATGAATCACCATGGGAACCTCTTTTTTCTGC
479089 TAGC
1 TAGC
479093 TGCTGGAATT
Statistics
Matches: 236, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
243 201 0.85
244 35 0.15
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.29
Consensus pattern (244 bp):
TAGCATATGATTCCAAAAACACTCGTGTAGCTAAAACAAGTTCACTGATCAGAAGAAATGAATAA
ATAAAGTTCAATCTTCGAATTCTTCAAAACCCTTTGAAGTAATAGTTAAACAAATGGAATCATCA
CTAGGACCAATTCACTATAGAGATCTAGATCATAAATTCACTACAAGAAGATTCACATGTTTTCG
ACTCTAATAGCAATCACCATGAATCACCATGGGAACCTCTTTTTTCTGC
Found at i:487388 original size:60 final size:60
Alignment explanation
Indices: 487286--487400 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
487276 GAACATATGA
* * *
487286 ATAATTGAGTGATCATTTTATGACTTTTAATAGATAGAAGACTCAATAAAGTAACGACCT
1 ATAATTGAATGATCATTTTATAACTTTTAATAGATAGAAGACTCAACAAAGTAACGACCT
* *
487346 ATAATTGAATGATCATTTTGTAACTTTTAATA-ATCA-AGAGACTTAACAAAGTAAC
1 ATAATTGAATGATCATTTTATAACTTTTAATAGAT-AGA-AGACTCAACAAAGTAAC
487401 ATTATATAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.06
60 45 0.94
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (60 bp):
ATAATTGAATGATCATTTTATAACTTTTAATAGATAGAAGACTCAACAAAGTAACGACCT
Found at i:489564 original size:45 final size:45
Alignment explanation
Indices: 489513--489605 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
489503 TATTAAACAT
*
489513 CATCCATAGATATTCCTATCTTCATGCTAATCATTAAAATGATTG
1 CATCCATAGATATTCCTATCTTCATGCTAATCATTAAAATGAGTG
*
489558 CATCCATAGATATTCCTATCTTCATGCTTATCATTAAAATGAGTG
1 CATCCATAGATATTCCTATCTTCATGCTAATCATTAAAATGAGTG
489603 CAT
1 CAT
489606 GATATGCATC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (45 bp):
CATCCATAGATATTCCTATCTTCATGCTAATCATTAAAATGAGTG
Found at i:499182 original size:10 final size:10
Alignment explanation
Indices: 499153--499202 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
499143 GCTGCTGGAA
499153 AACCGGTTTG
1 AACCGGTTTG
*
499163 -ACCAGTTTTG
1 AACC-GGTTTG
499173 AACCGGTTTG
1 AACCGGTTTG
*
499183 -ACCGGTTCG
1 AACCGGTTTG
499192 AACCGGTTTG
1 AACCGGTTTG
499202 A
1 A
499203 CCCGACCCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 11 0.33
10 19 0.58
11 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:499196 original size:19 final size:20
Alignment explanation
Indices: 499153--499204 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
499143 GCTGCTGGAA
* *
499153 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACCAGGTTCG
499173 AACCGGTTTGACC-GGTTCG
1 AACCGGTTTGACCAGGTTCG
499192 AACCGGTTTGACC
1 AACCGGTTTGACC
499205 CGACCCGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (20 bp):
AACCGGTTTGACCAGGTTCG
Found at i:499221 original size:17 final size:17
Alignment explanation
Indices: 499199--499255 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
499189 TCGAACCGGT
*
499199 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACCG
499216 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
499233 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
499250 TTGACC
1 TTGACC
499256 GTGACCGTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.16
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:499255 original size:7 final size:7
Alignment explanation
Indices: 499245--499280 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
499235 GACCCGACCC
499245 GACCGTT
1 GACCGTT
499252 GACCG-T
1 GACCGTT
499258 GACCGTT
1 GACCGTT
499265 GACCG-T
1 GACCGTT
499271 GACCGTT
1 GACCGTT
499278 GAC
1 GAC
499281 TTTCTTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (7 bp):
GACCGTT
Found at i:499263 original size:13 final size:13
Alignment explanation
Indices: 499245--499280 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
499235 GACCCGACCC
499245 GACCGTTGACCGT
1 GACCGTTGACCGT
499258 GACCGTTGACCGT
1 GACCGTTGACCGT
499271 GACCGTTGAC
1 GACCGTTGAC
499281 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:500218 original size:63 final size:63
Alignment explanation
Indices: 500150--500273 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
500140 CTAATGTGAC
* * * *
500150 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
500213 TCTTAGGTAGGCCCTACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCTACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
500274 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 1 0.02
63 51 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCTACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:500227 original size:32 final size:31
Alignment explanation
Indices: 500150--500234 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
500140 CTAATGTGAC
* *
500150 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
500181 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
*
500213 TCTTAGGTAGGCCCTACGGCCC
1 TCTTAGGTAGGCCCTGCGGCCC
500235 CGAAATCTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 24 0.55
32 20 0.45
ACGTcount: A:0.14, C:0.29, G:0.31, T:0.26
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:503311 original size:13 final size:15
Alignment explanation
Indices: 503280--503315 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
503270 AACCCACATA
503280 ATAAATATAGATATT
1 ATAAATATAGATATT
503295 -TAAA-ATAGA-ATT
1 ATAAATATAGATATT
503307 ATAAATATA
1 ATAAATATA
503316 AATTGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.16
13 9 0.47
14 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (15 bp):
ATAAATATAGATATT
Found at i:506830 original size:27 final size:27
Alignment explanation
Indices: 506800--506860 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
506790 ACTAATAATA
506800 GTTGCATAATGCATAATAATGGTTCAT
1 GTTGCATAATGCATAATAATGGTTCAT
506827 GTTGCATAATGCATAATAATGGTTCAT
1 GTTGCATAATGCATAATAATGGTTCAT
*
506854 GATGCAT
1 GTTGCAT
506861 TGTAAGTTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (27 bp):
GTTGCATAATGCATAATAATGGTTCAT
Found at i:507598 original size:18 final size:16
Alignment explanation
Indices: 507577--507607 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
507567 GCTTCTAATT
507577 TTTTTTGAGTTCAAGC
1 TTTTTTGAGTTCAAGC
507593 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
507608 TTTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:508956 original size:14 final size:14
Alignment explanation
Indices: 508934--508967 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
508924 GGAAGACAGA
*
508934 CAAGTAAATCGGTG
1 CAAGAAAATCGGTG
508948 CAAGAAAATCGGTG
1 CAAGAAAATCGGTG
508962 CAAGAA
1 CAAGAA
508968 CAAATGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (14 bp):
CAAGAAAATCGGTG
Found at i:512864 original size:20 final size:21
Alignment explanation
Indices: 512827--512868 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
512817 GTCATGCAAC
512827 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
512848 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
512868 T
1 T
512869 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:513978 original size:24 final size:24
Alignment explanation
Indices: 513951--513999 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
513941 TAACACCTAT
513951 ACTTGCATTCTTAATTTAAGAATG
1 ACTTGCATTCTTAATTTAAGAATG
513975 ACTTGCATTCTTAATTTAAGAATG
1 ACTTGCATTCTTAATTTAAGAATG
513999 A
1 A
514000 AATAAACGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (24 bp):
ACTTGCATTCTTAATTTAAGAATG
Found at i:527690 original size:11 final size:11
Alignment explanation
Indices: 527674--527749 Score: 80
Period size: 11 Copynumber: 6.9 Consensus size: 11
527664 TTCAAAAAGA
527674 AGAATTATTAT
1 AGAATTATTAT
*
527685 AGAATTGTTAT
1 AGAATTATTAT
* * *
527696 ACAATTGTTGT
1 AGAATTATTAT
*
527707 AGAATTATTGT
1 AGAATTATTAT
* *
527718 AGAGTTGTTAT
1 AGAATTATTAT
*
527729 AGAATTATTGT
1 AGAATTATTAT
527740 AGAATTATTA
1 AGAATTATTA
527750 ATAACAGAGC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 53 1.00
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (11 bp):
AGAATTATTAT
Found at i:527701 original size:22 final size:22
Alignment explanation
Indices: 527674--527749 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
527664 TTCAAAAAGA
* *
527674 AGAATTATTATAGAATTGTTAT
1 AGAATTATTATAGAATTATTGT
* * *
527696 ACAATTGTTGTAGAATTATTGT
1 AGAATTATTATAGAATTATTGT
* *
527718 AGAGTTGTTATAGAATTATTGT
1 AGAATTATTATAGAATTATTGT
527740 AGAATTATTA
1 AGAATTATTA
527750 ATAACAGAGC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (22 bp):
AGAATTATTATAGAATTATTGT
Found at i:527711 original size:33 final size:33
Alignment explanation
Indices: 527674--527749 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
527664 TTCAAAAAGA
*
527674 AGAATTATTATAGAATTGTTATACAATTGTTGT
1 AGAATTATTATAGAATTGTTATACAATTATTGT
* * *
527707 AGAATTATTGTAGAGTTGTTATAGAATTATTGT
1 AGAATTATTATAGAATTGTTATACAATTATTGT
527740 AGAATTATTA
1 AGAATTATTA
527750 ATAACAGAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (33 bp):
AGAATTATTATAGAATTGTTATACAATTATTGT
Found at i:530707 original size:19 final size:19
Alignment explanation
Indices: 530683--530722 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
530673 TGGCTGACGA
530683 TTTAGCTAAAAGTGCAAGC
1 TTTAGCTAAAAGTGCAAGC
530702 TTTAGCTAAAAGTGCAAGC
1 TTTAGCTAAAAGTGCAAGC
530721 TT
1 TT
530723 CAATCTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (19 bp):
TTTAGCTAAAAGTGCAAGC
Found at i:531440 original size:36 final size:36
Alignment explanation
Indices: 531399--531506 Score: 191
Period size: 35 Copynumber: 3.0 Consensus size: 36
531389 ATATTTCAAC
*
531399 AAACATCTACCAAACTTTGAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
531435 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
531470 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
531507 TTGGTTGCCA
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
35 35 0.51
36 25 0.36
37 9 0.13
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:536069 original size:21 final size:21
Alignment explanation
Indices: 536045--536104 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
536035 TCAAAGAAAT
536045 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
*
536066 ATTT-TCAAA----G-AAA-C
1 ATTTACCAAACTTTGAAAACC
*
536080 ATTTACCAAACTTTGAAAACG
1 ATTTACCAAACTTTGAAAACC
536101 ATTT
1 ATTT
536105 TTCAAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 14
0.63 0.07 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.24
16 1 0.03
19 1 0.03
20 7 0.24
21 8 0.28
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (21 bp):
ATTTACCAAACTTTGAAAACC
Found at i:536078 original size:35 final size:36
Alignment explanation
Indices: 536004--536110 Score: 171
Period size: 35 Copynumber: 3.0 Consensus size: 36
535994 ATATTTCAAC
*
536004 AAACATCTACCAAACTTTGAAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCATTTTTCAAAG
*
536041 AAATATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
*
536076 AAACATTTACCAAACTTTGAAAACGATTTTTCAAA
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAA
536111 ATTGGTTGCC
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 33 0.51
36 15 0.23
37 17 0.26
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:536472 original size:21 final size:21
Alignment explanation
Indices: 536440--536489 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
536430 GATTTACATA
*
536440 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
536461 TTTGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
536482 TTCGCGTT
1 TTCGCGTT
536490 TCAAATCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:536565 original size:21 final size:20
Alignment explanation
Indices: 536527--536565 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
536517 TCGAAGTTCG
* *
536527 CGTTGCGATTATTTCAAATT
1 CGTTACGATTATTCCAAATT
536547 CGTTACGATTTATTCCAAA
1 CGTTACGA-TTATTCCAAA
536566 AAGATAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (20 bp):
CGTTACGATTATTCCAAATT
Found at i:536615 original size:6 final size:6
Alignment explanation
Indices: 536604--536628 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
536594 GACACGTATT
536604 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
536629 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:537443 original size:42 final size:42
Alignment explanation
Indices: 537384--537540 Score: 237
Period size: 42 Copynumber: 3.7 Consensus size: 42
537374 TGCGATTTTG
*
537384 GACTATCGCAACGAACTTGGAATAAATCGTAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
537426 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
537468 GACTATCGCAACGCGAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* *
537512 GGCTATCGCAACGAATTTGG-A-AAATCGCA
1 GACTATCGCAACGAACTTGGAATAAATCGCA
537541 TTGCGATAGT
Statistics
Matches: 108, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
40 8 0.07
41 1 0.01
42 60 0.56
44 39 0.36
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:537521 original size:21 final size:21
Alignment explanation
Indices: 537384--537524 Score: 112
Period size: 21 Copynumber: 6.6 Consensus size: 21
537374 TGCGATTTTG
*
537384 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTC
* *
537403 GAATAAATCGTAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
*
537426 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTC
*
537445 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
*
537468 GACTATCGCAACGCGAA-TTT
1 GACTATCGCAACGCGAACTTC
*
537488 GAAATAAATCGCAACGCGAACTTC
1 G-ACT--ATCGCAACGCGAACTTC
*
537512 GGCTATCGCAACG
1 GACTATCGCAACG
537525 AATTTGGAAA
Statistics
Matches: 96, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
19 13 0.14
20 3 0.03
21 43 0.45
23 34 0.35
24 3 0.03
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTC
Found at i:537532 original size:86 final size:82
Alignment explanation
Indices: 537384--537540 Score: 233
Period size: 86 Copynumber: 1.9 Consensus size: 82
537374 TGCGATTTTG
* *
537384 GACTATCGCAACGAACTTGGAATAAATCGTAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG-A-
537449 AAATCGCAACGCGAACTTC
64 AAATCGCAACGCGAACTTC
* * *
537468 GACTATCGCAACGCGAATTTGAAATAAATCGCAACGCGAACTTCGGCTATCGCAACGAATTTGGA
1 GACTATCGCAA--CGAACTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
537533 AAATCGCA
64 AAATCGCA
537541 TTGCGATAGT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
84 19 0.29
85 1 0.02
86 46 0.70
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (82 bp):
GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAA
ATCGCAACGCGAACTTC
Found at i:537565 original size:21 final size:21
Alignment explanation
Indices: 537536--537588 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
537526 ATTTGGAAAA
*
537536 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
537557 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
537578 TCGCGTTGCGA
1 TCGCGTTGCGA
537589 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:543478 original size:18 final size:19
Alignment explanation
Indices: 543449--543491 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
543439 TAGCTATTTA
* *
543449 ATTTTTTGGTTTATTTTTT
1 ATTTTTTGGTTTAGTTATT
543468 ATTTTTT-GTTTAGTTATT
1 ATTTTTTGGTTTAGTTATT
543486 ATTTTT
1 ATTTTT
543492 ATAGCTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (19 bp):
ATTTTTTGGTTTAGTTATT
Found at i:543540 original size:74 final size:76
Alignment explanation
Indices: 543383--543542 Score: 184
Period size: 74 Copynumber: 2.1 Consensus size: 76
543373 TTTTTTTGTA
* * *
543383 GTATTTTTATATTTCCTGTTTAGTTATTATTATGTATAGTCATTATATGGCTTATTTAGCTATTT
1 GTATTTTTTTATTTCCTGTTTAGTTATTATTATGTATAGTCATTATATGACTTACTTAGCTATTT
*
543448 AATTTTTTGGT
66 AATTCTTTGGT
* ** * * * *
543459 TTA-TTTTTTATTTTTTGTTTAGTTATTATT-TTTATAG-CTGTTATATGACTTGCTTAGTTATT
1 GTATTTTTTTATTTCCTGTTTAGTTATTATTATGTATAGTC-ATTATATGACTTACTTAGCTATT
543521 TAA-TCTTTGGT
65 TAATTCTTTGGT
543532 GTATTTTTTTA
1 GTATTTTTTTA
543543 AAAAATTTAT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
73 10 0.14
74 34 0.49
75 24 0.34
76 2 0.03
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.61
Consensus pattern (76 bp):
GTATTTTTTTATTTCCTGTTTAGTTATTATTATGTATAGTCATTATATGACTTACTTAGCTATTT
AATTCTTTGGT
Found at i:543623 original size:16 final size:16
Alignment explanation
Indices: 543587--543628 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
543577 TATGTTTAGC
543587 ATTTT-TTTGTTTAATT
1 ATTTTATTT-TTTAATT
*
543603 A-TTTATTTTTTAGTT
1 ATTTTATTTTTTAATT
543618 ATTTTATTTTT
1 ATTTTATTTTT
543629 ATTAAAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (16 bp):
ATTTTATTTTTTAATT
Found at i:545209 original size:33 final size:33
Alignment explanation
Indices: 545114--545211 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
545104 AGAAACTGTG
* * *
545114 AAACCTGCGGCAAAAACTGAGCCA-AAGACAGCT
1 AAACCTGCAGCAGAAACTGAG-CAGAAGACGGCT
*
545147 AAACCTGCAGCAGAAACCGAGCAGAAGACGGCT
1 AAACCTGCAGCAGAAACTGAGCAGAAGACGGCT
*
545180 AAACCTGCAGCAGAAACTGAGAAGAAGACGGC
1 AAACCTGCAGCAGAAACTGAGCAGAAGACGGC
545212 AGAGAAGGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 2 0.03
33 56 0.97
ACGTcount: A:0.42, C:0.26, G:0.26, T:0.07
Consensus pattern (33 bp):
AAACCTGCAGCAGAAACTGAGCAGAAGACGGCT
Found at i:553690 original size:17 final size:16
Alignment explanation
Indices: 553664--553697 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
553654 AAAAAAAAGT
553664 ATATAAATCTTGGTTA
1 ATATAAATCTTGGTTA
553680 ATATGAAATCTTGGTTA
1 ATAT-AAATCTTGGTTA
553697 A
1 A
553698 CTCAATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (16 bp):
ATATAAATCTTGGTTA
Found at i:557879 original size:8 final size:8
Alignment explanation
Indices: 557866--557906 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
557856 CTCATTTTCA
557866 GAGAATTT
1 GAGAATTT
557874 GAGAATTT
1 GAGAATTT
*
557882 -AGAGTTT
1 GAGAATTT
*
557889 GGGAATTT
1 GAGAATTT
557897 GAGAATTT
1 GAGAATTT
557905 GA
1 GA
557907 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:558334 original size:126 final size:126
Alignment explanation
Indices: 557974--558705 Score: 1353
Period size: 126 Copynumber: 5.8 Consensus size: 126
557964 CTATAATCGA
*
557974 TTCACTATTCACATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATA--T
558039 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
64 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
558102 TTCACTATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
558166 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
558227 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
558292 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
558353 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
558418 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
558479 TTCACTATTCACATGAAGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
558542 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
558603 TTCACTATTCACATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATA--T
*
558668 TATCATTGCCCTATTATGTCACTCAAGTCCCTCGGGGA
64 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
558706 ATAACTTAAA
Statistics
Matches: 594, Mismatches: 5, Indels: 10
0.98 0.01 0.02
Matches are distributed among these distances:
124 119 0.20
125 103 0.17
126 274 0.46
127 28 0.05
128 70 0.12
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:559185 original size:34 final size:34
Alignment explanation
Indices: 559092--559189 Score: 121
Period size: 34 Copynumber: 3.0 Consensus size: 34
559082 AAATTTAATG
*
559092 TTAAATTTCGAATACTATAATTTATA-TTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
559125 TT-AATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
559157 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
559190 AACATTTATC
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
31 14 0.26
32 12 0.23
33 7 0.13
34 20 0.38
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:559738 original size:21 final size:21
Alignment explanation
Indices: 559714--559793 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
559704 ATAAAACCCT
*
559714 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
559735 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
559756 GCGGGCTAGGAATGTAACCCT-
1 GCGGGCTAGGAATGTAA-CCTG
*
559777 GCGGGCTCGGAATGTAA
1 GCGGGCTAGGAATGTAA
559794 ACATGCGGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
21 53 0.95
22 3 0.05
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.19
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:559829 original size:21 final size:21
Alignment explanation
Indices: 559805--559852 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
559795 CATGCGGAGA
*
559805 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
559826 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
559847 GGGCAT
1 TGGCAT
559853 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:564494 original size:20 final size:20
Alignment explanation
Indices: 564452--564510 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
564442 TATGAACTTC
*
564452 TATTTATATATATATATCAATAT
1 TATTTATA-ATATAT-T-TATAT
564475 TATTTATAATATATTTATAT
1 TATTTATAATATATTTATAT
**
564495 TATAAATAATAT-TTTA
1 TATTTATAATATATTTA
564511 GTTTTAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.12
20 14 0.42
21 1 0.03
22 6 0.18
23 8 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTATAATATATTTATAT
Found at i:566090 original size:142 final size:144
Alignment explanation
Indices: 565896--566174 Score: 499
Period size: 142 Copynumber: 2.0 Consensus size: 144
565886 AGTTATAGTG
565896 TTATATATATTATAATTATAATAACATGTATAATAGTACGAACCAAGCGACTTCAGTGGTTAAAG
1 TTATATATATTATAATTATAATAACATGTATAATAGTACGAACCAAGCGACTTCAGTGGTTAAAG
*
565961 GGATGATAGTTATTATTAAAGGTCTTGAGTTCGAGTAGCTGTAACTATAAGGTTTTTGAGCGTTC
66 GGATGATAGTTATTATTAAAGGTCTTGAGTTCGAGTAGCTGTAACTATAAGGTATTTGAGCGTTC
566026 ATTGTTATATTATA
131 ATTGTTATATTATA
566040 TTATAT-TA-TATAATTATAATAACATGTATAATAGTACGAACCAAGCGACTTCAGTGGTTAAAG
1 TTATATATATTATAATTATAATAACATGTATAATAGTACGAACCAAGCGACTTCAGTGGTTAAAG
* * * *
566103 GGATGGTAGTTATTCTTAAAGGTCTTGGGTTCGAGTAGTTGTAACTATAAGGTATTTGAGCGTTC
66 GGATGATAGTTATTATTAAAGGTCTTGAGTTCGAGTAGCTGTAACTATAAGGTATTTGAGCGTTC
566168 ATTGTTA
131 ATTGTTA
566175 AATAATTGAG
Statistics
Matches: 130, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
142 122 0.94
143 2 0.02
144 6 0.05
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (144 bp):
TTATATATATTATAATTATAATAACATGTATAATAGTACGAACCAAGCGACTTCAGTGGTTAAAG
GGATGATAGTTATTATTAAAGGTCTTGAGTTCGAGTAGCTGTAACTATAAGGTATTTGAGCGTTC
ATTGTTATATTATA
Found at i:569732 original size:31 final size:31
Alignment explanation
Indices: 569697--569764 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
569687 TTGCAATACA
569697 GTCCCCCAACATTTAATCCGTTTGCAACATG
1 GTCCCCCAACATTTAATCCGTTTGCAACATG
* * *
569728 GTCCCTCAACATTTAGTCCGTTTGCAATATG
1 GTCCCCCAACATTTAATCCGTTTGCAACATG
569759 GTCCCC
1 GTCCCC
569765 AATGTAACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.32, G:0.15, T:0.31
Consensus pattern (31 bp):
GTCCCCCAACATTTAATCCGTTTGCAACATG
Found at i:575249 original size:20 final size:21
Alignment explanation
Indices: 575193--575249 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
575183 TACACCACTC
575193 AATTTTTTTAATTTACTCTCT
1 AATTTTTTTAATTTACTCTCT
* * * *
575214 TA-TTTTTCACTGTACTCT-T
1 AATTTTTTTAATTTACTCTCT
575233 AATTTTTTTAATTTACT
1 AATTTTTTTAATTTACT
575250 TACTAAATTT
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.23, C:0.14, G:0.02, T:0.61
Consensus pattern (21 bp):
AATTTTTTTAATTTACTCTCT
Found at i:575392 original size:24 final size:24
Alignment explanation
Indices: 575356--575406 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
575346 ATGTATTTTT
* * * * *
575356 ATTAATATTTAATTATAATATATA
1 ATTAAAATATAATAATAAAATAAA
575380 ATTAAAATATAATAATAAAATAAA
1 ATTAAAATATAATAATAAAATAAA
575404 ATT
1 ATT
575407 CTTAAATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTAAAATATAATAATAAAATAAA
Found at i:575398 original size:13 final size:13
Alignment explanation
Indices: 575359--575401 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
575349 TATTTTTATT
* *
575359 AATATTTAATTAT
1 AATATATAATTAA
575372 AATATATAATTAA
1 AATATATAATTAA
575385 AATATAATAA-TAA
1 AATAT-ATAATTAA
575398 AATA
1 AATA
575402 AAATTCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATATAATTAA
Found at i:575981 original size:30 final size:29
Alignment explanation
Indices: 575924--576331 Score: 219
Period size: 31 Copynumber: 13.7 Consensus size: 29
575914 AAATATATGT
* *
575924 TAAAAATA-TTTTTAAATTAAGATAAAAA
1 TAAAAATATTTTTTAAGTTAAAATAAAAA
575952 TAAAAATATTTTTTGAAGTTAAAATAAAAA
1 TAAAAATATTTTTT-AAGTTAAAATAAAAA
* ** *
575982 TAAAAAATACATTTTTTTTA-TTAAGCTAAGATGAT
1 T-AAAAAT--A-TTTTTTAAGTTAAAATAA-A--AA
*
576017 TAAAACAT-TTTTTTAAGTTAAAAT-AAGA
1 TAAAA-ATATTTTTTAAGTTAAAATAAAAA
** *
576045 TTTAAAT-TTTTTTAAGTTAAAAT-AAGA
1 TAAAAATATTTTTTAAGTTAAAATAAAAA
* * * *
576072 TTAAAACATTTTTTAAGTTAATATATAAA
1 TAAAAATATTTTTTAAGTTAAAATAAAAA
** * *
576101 TAAAAACATATTTAATAATTTAAAATAAGAA
1 T-AAAA-ATATTTTTTAAGTTAAAATAAAAA
* *
576132 TAAAATATATTTTTTAAAGTTAAAATGATAA
1 TAAAA-ATATTTTTT-AAGTTAAAATAAAAA
* * *
576163 TAAAAATATATTTTTAAAAGTTAAGAT-GACA
1 TAAAAATAT-TTTTT--AAGTTAAAATAAAAA
* * *
576194 T-AAAATATATATTTAAATT--AATAAGAA
1 TAAAAATAT-TTTTTAAGTTAAAATAAAAA
** *
576221 T-AAAATATATTTTTAAACTAAAATAATAA
1 TAAAAATAT-TTTTTAAGTTAAAATAAAAA
* ** * *
576250 T-AAAATATATTTTTAATTTAATTTGATAA
1 TAAAAATAT-TTTTTAAGTTAAAATAAAAA
*
576279 TAAAAATATATTTAATAAGTTAAAATAAAAA
1 TAAAAATAT-TTT-TTAAGTTAAAATAAAAA
576310 TAAAATATATTTTTTAAGTTAA
1 TAAAA-ATATTTTTTAAGTTAA
576332 GATACATAAA
Statistics
Matches: 299, Mismatches: 57, Indels: 46
0.74 0.14 0.11
Matches are distributed among these distances:
26 2 0.01
27 45 0.15
28 30 0.10
29 40 0.13
30 64 0.21
31 75 0.25
32 26 0.09
33 3 0.01
34 10 0.03
35 4 0.01
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (29 bp):
TAAAAATATTTTTTAAGTTAAAATAAAAA
Found at i:576053 original size:27 final size:27
Alignment explanation
Indices: 576014--576092 Score: 113
Period size: 27 Copynumber: 2.8 Consensus size: 27
576004 AAGCTAAGAT
576014 GATTAAAACATTTTTTTAAGTTAAAATAA
1 GATT-AAA-ATTTTTTTAAGTTAAAATAA
*
576043 GATTTAAATTTTTTTAAGTTAAAATAA
1 GATTAAAATTTTTTTAAGTTAAAATAA
*
576070 GATTAAAACATTTTTTAAGTTAA
1 GATTAAAA-TTTTTTTAAGTTAA
576093 TATATAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.59
28 15 0.33
29 4 0.09
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (27 bp):
GATTAAAATTTTTTTAAGTTAAAATAA
Found at i:576174 original size:32 final size:30
Alignment explanation
Indices: 576052--576331 Score: 195
Period size: 30 Copynumber: 9.4 Consensus size: 30
576042 AGATTTAAAT
* *
576052 TTTTTTAAGTTAAAAT-A-AGATTAAA-ACA
1 TTTTTTAAGTTAAAATGATA-ATAAAATATA
* *
576080 TTTTTTAAGTTAATAT-ATAAATAAAAACATA
1 TTTTTTAAGTTAAAATGAT-AAT-AAAATATA
** * * *
576111 TTTAATAATTTAAAATAAGAATAAAATATA
1 TTTTTTAAGTTAAAATGATAATAAAATATA
576141 TTTTTTAAAGTTAAAATGATAATAAAAATATA
1 TTTTTT-AAGTTAAAATGATAAT-AAAATATA
* * *
576173 TTTTTAAAAGTTAAGATGA-CATAAAATATA
1 TTTTT-TAAGTTAAAATGATAATAAAATATA
* *
576203 -TATTTAAATTAATAA-G--AATAAAATATA
1 TTTTTTAAGTTAA-AATGATAATAAAATATA
** *
576230 -TTTTTAAACTAAAATAATAATAAAATATA
1 TTTTTTAAGTTAAAATGATAATAAAATATA
* **
576259 -TTTTTAATTTAATTTGATAATAAAAATATA
1 TTTTTTAAGTTAAAATGATAAT-AAAATATA
** * *
576289 TTTAATAAGTTAAAATAAAAATAAAATATA
1 TTTTTTAAGTTAAAATGATAATAAAATATA
576319 TTTTTTAAGTTAA
1 TTTTTTAAGTTAA
576332 GATACATAAA
Statistics
Matches: 199, Mismatches: 39, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
26 2 0.01
27 20 0.10
28 23 0.12
29 33 0.17
30 50 0.25
31 46 0.23
32 25 0.13
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (30 bp):
TTTTTTAAGTTAAAATGATAATAAAATATA
Found at i:576226 original size:89 final size:90
Alignment explanation
Indices: 576050--576340 Score: 305
Period size: 89 Copynumber: 3.3 Consensus size: 90
576040 TAAGATTTAA
* * * * * *
576050 ATTTTTTTAAGTTAAAATAAGATTAAAACAT-TTTTTAAGTTAATAT-ATAAATAAAAACATATT
1 ATTTTTTAAAGTTAAAATAATAATAAAATATATTTTTAAGTTAAGATGAT-AATAAAAATATATT
*
576113 TAATAATTTAAAATAAGAATAAAATAT
65 TAATAAGTT-AAATAAGAATAAAATAT
* *
576140 ATTTTTTAAAGTTAAAATGATAATAAAAATATATTTTTAAAAGTTAAGATGA-CATAAAATATAT
1 ATTTTTTAAAGTTAAAATAATAAT-AAAATATATTTTT--AAGTTAAGATGATAATAAAA-ATAT
576204 ATTT-A-AA-TT-AATAAGAATAAAATAT
62 ATTTAATAAGTTAAATAAGAATAAAATAT
* * **
576229 A-TTTTTAAA-CTAAAATAATAATAAAATATATTTTTAATTTAATTTGATAATAAAAATATATTT
1 ATTTTTTAAAGTTAAAATAATAATAAAATATATTTTTAAGTTAAGATGATAATAAAAATATATTT
*
576292 AATAAGTTAAAATAAAAATAAAATAT
66 AATAAGTT-AAATAAGAATAAAATAT
*
576318 ATTTTTT-AAGTTAAGATACATAA
1 ATTTTTTAAAGTTAAAATA-ATAA
576341 AATATTCTAT
Statistics
Matches: 169, Mismatches: 17, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
84 17 0.10
85 7 0.04
86 15 0.09
87 13 0.08
88 8 0.05
89 35 0.21
90 31 0.18
91 12 0.07
92 7 0.04
93 7 0.04
94 16 0.09
95 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (90 bp):
ATTTTTTAAAGTTAAAATAATAATAAAATATATTTTTAAGTTAAGATGATAATAAAAATATATTT
AATAAGTTAAATAAGAATAAAATAT
Found at i:576304 original size:178 final size:178
Alignment explanation
Indices: 575924--576331 Score: 449
Period size: 178 Copynumber: 2.3 Consensus size: 178
575914 AAATATATGT
*
575924 TAAAAATAT-TTT--TAAATTAAGATAAAAATAAAA-ATATTTTTTGAAGTTAAAATAAAAATAA
1 TAAAAATATATTTAATAAATTAAAATAAAAATAAAATATATTTTTT-AAGTTAAAATAAAAATAA
* * * * * * * *
575985 AAAATACATTTTTTTTATTAAGCTAAGATGATTAAAACATTTTTTTAAGTTAAAATAAGATTTAA
65 AAAATA-ATTATTTTTATAAAGCTAAGATGAATAAAACATATATTTAAATT-AAATAAGAATAAA
** *
576050 ATTTTTTTAAGTTAAAATAAGATTAAAACATTTTTTAAGTTAATATATAAA
128 ATTTTTTTAAACTAAAATAAGAATAAAACATTTTTTAAGTTAATATATAAA
* * * * *
576101 TAAAAACATATTTAATAATTTAAAATAAGAATAAAATATATTTTTTAAAGTTAAAATGATAAT-A
1 TAAAAATATATTTAATAAATTAAAATAAAAATAAAATATATTTTTT-AAGTTAAAATAAAAATAA
* *
576165 AAAAT-A-TATTTTTA-AAAGTTAAGATGACATAAAATATATATTTAAATT-AATAAGAATAAAA
65 AAAATAATTATTTTTATAAAGCTAAGATGA-ATAAAACATATATTTAAATTAAATAAGAATAAAA
* * * *
576226 TATATTTTTAAACTAAAATAATAATAAAATATATTTTTAATTTAATTTGAT-AA
129 T-T-TTTTTAAACTAAAATAAGAATAAAACAT-TTTTTAAGTTAATAT-ATAAA
*
576279 TAAAAATATATTTAATAAGTTAAAATAAAAATAAAATATATTTTTTAAGTTAA
1 TAAAAATATATTTAATAAATTAAAATAAAAATAAAATATATTTTTTAAGTTAA
576332 GATACATAAA
Statistics
Matches: 195, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
175 12 0.06
176 12 0.06
177 60 0.31
178 62 0.32
179 2 0.01
180 24 0.12
181 23 0.12
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (178 bp):
TAAAAATATATTTAATAAATTAAAATAAAAATAAAATATATTTTTTAAGTTAAAATAAAAATAAA
AAATAATTATTTTTATAAAGCTAAGATGAATAAAACATATATTTAAATTAAATAAGAATAAAATT
TTTTTAAACTAAAATAAGAATAAAACATTTTTTAAGTTAATATATAAA
Found at i:576683 original size:44 final size:46
Alignment explanation
Indices: 576633--576725 Score: 154
Period size: 46 Copynumber: 2.1 Consensus size: 46
576623 TCTTTTTTAA
576633 CCAAGAATTATGTTTT-AGC-TTCTTCCCAAAACCCCATTTCCACT
1 CCAAGAATTATGTTTTGAGCATTCTTCCCAAAACCCCATTTCCACT
* *
576677 CCAAGAATTTTGTTTTGAGCATTCTTCCCAAAACCCCATTTTCACT
1 CCAAGAATTATGTTTTGAGCATTCTTCCCAAAACCCCATTTCCACT
576723 CCA
1 CCA
576726 TACTTCTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 15 0.33
45 3 0.07
46 27 0.60
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.34
Consensus pattern (46 bp):
CCAAGAATTATGTTTTGAGCATTCTTCCCAAAACCCCATTTCCACT
Done.