Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008676.1 Hibiscus syriacus cultivar Beakdansim tig00111693_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: 957917
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 4
Found at i:8314 original size:6 final size:6
Alignment explanation
Indices: 8303--8331 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
8293 AACTTTTTAG
8303 TTTATT TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTAT
8332 AAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:8752 original size:14 final size:14
Alignment explanation
Indices: 8733--8774 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
8723 AGTCATTTTA
*
8733 ATTTTAATTTTAGC
1 ATTTTATTTTTAGC
*
8747 ATTTTATTCTTTAAC
1 ATTTTATT-TTTAGC
8762 ATTTTATTTTTAG
1 ATTTTATTTTTAG
8775 ACAAAAAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (14 bp):
ATTTTATTTTTAGC
Found at i:11548 original size:17 final size:18
Alignment explanation
Indices: 11526--11562 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11516 TCTTATGCAC
11526 ATCAATA-GT-TTTATCAG
1 ATCAATATGTCTTT-TCAG
11543 ATCAATATGTCTTTTCAG
1 ATCAATATGTCTTTTCAG
11561 AT
1 AT
11563 TTATTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
ATCAATATGTCTTTTCAG
Found at i:13366 original size:20 final size:20
Alignment explanation
Indices: 13324--13368 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
13314 GGCTTAAGAT
**
13324 TTTAATTTTAAATTTTATGA
1 TTTAATTTTAAATTTTAAAA
**
13344 TTTAATTTTGTATTTTAAAA
1 TTTAATTTTAAATTTTAAAA
13364 TTTAA
1 TTTAA
13369 AATTAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTAATTTTAAATTTTAAAA
Found at i:13407 original size:16 final size:17
Alignment explanation
Indices: 13374--13409 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13364 TTTAAAATTA
13374 AAATAAATTAATTGTAT
1 AAATAAATTAATTGTAT
*
13391 AAATAAATTTA-TGTAT
1 AAATAAATTAATTGTAT
13407 AAA
1 AAA
13410 AATAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
AAATAAATTAATTGTAT
Found at i:13922 original size:20 final size:21
Alignment explanation
Indices: 13876--13922 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
13866 TAGGGTTCAT
*
13876 GAGTTTAGGGTTTATAATGTA
1 GAGTTTAGGGTTTAAAATGTA
*
13897 -AGGTTTA-GGTTTAAAATTTA
1 GA-GTTTAGGGTTTAAAATGTA
13917 GAGTTT
1 GAGTTT
13923 GAAGTGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.45
Consensus pattern (21 bp):
GAGTTTAGGGTTTAAAATGTA
Found at i:14891 original size:8 final size:8
Alignment explanation
Indices: 14878--14903 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
14868 ACTTGATGTA
14878 ATTTGTTT
1 ATTTGTTT
14886 ATTTGTTT
1 ATTTGTTT
14894 ATTTGTTT
1 ATTTGTTT
14902 AT
1 AT
14904 ATATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (8 bp):
ATTTGTTT
Found at i:15058 original size:2 final size:2
Alignment explanation
Indices: 15051--15092 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
15041 TGTTTTAGAA
15051 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
15093 CCTCGTTCGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22071 original size:17 final size:17
Alignment explanation
Indices: 22049--22086 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
22039 TTTCAGGTAC
22049 TAAACTAAAACATAATA
1 TAAACTAAAACATAATA
* *
22066 TAAACTAAAATATAATT
1 TAAACTAAAACATAATA
22083 TAAA
1 TAAA
22087 TTTAAATCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAACTAAAACATAATA
Found at i:24130 original size:24 final size:24
Alignment explanation
Indices: 24102--24155 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
24092 GAACAAACTC
** *
24102 GTTTATAAGCTTGTTTATCAAATT
1 GTTTATAAGCTCATTTATCAAATA
* *
24126 GTTTATGAGCTCATTTATCGAATA
1 GTTTATAAGCTCATTTATCAAATA
24150 GTTTAT
1 GTTTAT
24156 TTATGTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (24 bp):
GTTTATAAGCTCATTTATCAAATA
Found at i:24498 original size:70 final size:70
Alignment explanation
Indices: 24387--24633 Score: 304
Period size: 70 Copynumber: 3.5 Consensus size: 70
24377 ACAACCTCAA
** * *
24387 AAATAAATAAACACAAACATGATATTAAAATTTTAAATGAACATGAACCGAACACGAACATTTTC
1 AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACATGAACCGAACACGAACA-TTTC
24452 AAAAAT
65 AAAAAT
* * * *
24458 AAATAAACGAACAC-AACACGATATTAAAAATTTAAATGAACACGAGA-CGAACACAAACACTTA
1 AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACATGA-ACCGAACACGAACATTTC
24521 AAAAAT
65 AAAAAT
* *
24527 AAATAAACGAACACAAACACGATATTAAAAATTTAAATAAACACT-AGCCGAACACGAACACTTT
1 AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACA-TGAACCGAACACGAACA-TTT
*
24591 -AAAAAA
64 CAAAAAT
* * *
24597 AAATAAACGAACACGAATACAATATTAAAAATTTAAA
1 AAATAAACGAACACAAACACGATATTAAAAATTTAAA
24634 CGAATACGAA
Statistics
Matches: 154, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
69 22 0.14
70 117 0.76
71 15 0.10
ACGTcount: A:0.57, C:0.16, G:0.07, T:0.19
Consensus pattern (70 bp):
AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACATGAACCGAACACGAACATTTCA
AAAAT
Found at i:24543 original size:140 final size:140
Alignment explanation
Indices: 24387--24642 Score: 372
Period size: 140 Copynumber: 1.8 Consensus size: 140
24377 ACAACCTCAA
* * * * *
24387 AAATAAATAAACACAAACATGATATTAAAATTTTAAATGAACA-TGAACCGAACACGAACATTTT
1 AAATAAACAAACACAAACACGATATTAAAAATTTAAATAAACACT-AACCGAACACGAACACTTT
* * *
24451 CAAAAATAAATAAACGAACAC-AACACGATATTAAAAATTTAAATGAACACGAGACGAACACAAA
65 -AAAAAAAAATAAACGAACACGAACACAATATTAAAAATTTAAACGAACACGAGACGAACACAAA
24515 CACTTAAAAAAT
129 CACTTAAAAAAT
* *
24527 AAATAAACGAACACAAACACGATATTAAAAATTTAAATAAACACTAGCCGAACACGAACACTTTA
1 AAATAAACAAACACAAACACGATATTAAAAATTTAAATAAACACTAACCGAACACGAACACTTTA
* *
24592 AAAAAAAATAAACGAACACGAATACAATATTAAAAATTTAAACGAATACGA
66 AAAAAAAATAAACGAACACGAACACAATATTAAAAATTTAAACGAACACGA
24643 ACATTATCTT
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
139 19 0.19
140 82 0.80
141 1 0.01
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.19
Consensus pattern (140 bp):
AAATAAACAAACACAAACACGATATTAAAAATTTAAATAAACACTAACCGAACACGAACACTTTA
AAAAAAAATAAACGAACACGAACACAATATTAAAAATTTAAACGAACACGAGACGAACACAAACA
CTTAAAAAAT
Found at i:28306 original size:151 final size:155
Alignment explanation
Indices: 27860--28325 Score: 759
Period size: 159 Copynumber: 3.0 Consensus size: 155
27850 CTCTTCAATT
27860 TGCGCA-TTGAGTCTCCTGTTACCACTATATCATCCACATAAACCAACATGTACAAATACTGCCC
1 TGCGCATTTGAGTCTCCTGTTACCACTATATCATCCACATAAACCAACATGTACAAATACTGCCC
27924 TCTAACACAACGAACAAATAAGAAGTATATGCCTTAGACTCCTT-AATCCTATTCG-ATAAAGCA
66 TCTAACACAACGAACAAATAAGAAGTATATGCCTTAGACTCCTTAAATCCTATTCGAATAAAGCA
27987 CTGTTTTAACTTGACATGCCAAC-C
131 CTGTTTTAACTTGACATGCCAACTC
* **
28011 TGAGGCCCCTATCTCAAAGTCTCCTGTTACCACTATATCATCCACATAAACCAACATGTACAAAT
1 T---G-CGC-AT-T-TGAGTCTCCTGTTACCACTATATCATCCACATAAACCAACATGTACAAAT
28076 ACTGCCCTCTAACACAACGAACAAATAAGAAGTATATGCCTTAGACTCCTTAAATCCTATTCGAA
59 ACTGCCCTCTAACACAACGAACAAATAAGAAGTATATGCCTTAGACTCCTTAAATCCTATTCGAA
28141 TAAAGCACTGTTTTAACTTGACATGCCAACTC
124 TAAAGCACTGTTTTAACTTGACATGCCAACTC
*
28173 TGCGCATTTGAGTCTCCTGTTACCACTATATCATCCACATAAACC-ACATGTACAAATACCGCCC
1 TGCGCATTTGAGTCTCCTGTTACCACTATATCATCCACATAAACCAACATGTACAAATACTGCCC
*
28237 TCT-A-ACAACGAAC-AATAAGAAGTATATGCCTTAGACTCCTTAAATCCTATTCGAATCAAGCA
66 TCTAACACAACGAACAAATAAGAAGTATATGCCTTAGACTCCTTAAATCCTATTCGAATAAAGCA
*
28299 CTATTTTAACTTGACATGCCAACTC
131 CTGTTTTAACTTGACATGCCAACTC
28324 TG
1 TG
28326 AGCCCCTATC
Statistics
Matches: 295, Mismatches: 9, Indels: 22
0.90 0.03 0.07
Matches are distributed among these distances:
151 75 0.25
152 9 0.03
153 1 0.00
154 22 0.07
155 37 0.13
156 2 0.01
157 2 0.01
158 3 0.01
159 100 0.34
160 11 0.04
161 31 0.11
162 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (155 bp):
TGCGCATTTGAGTCTCCTGTTACCACTATATCATCCACATAAACCAACATGTACAAATACTGCCC
TCTAACACAACGAACAAATAAGAAGTATATGCCTTAGACTCCTTAAATCCTATTCGAATAAAGCA
CTGTTTTAACTTGACATGCCAACTC
Found at i:30751 original size:16 final size:16
Alignment explanation
Indices: 30732--30774 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
30722 ACAGCTTTTA
30732 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
*
30748 AATCATTCAGTATTTG
1 AATCATTCAGCATTTG
30764 AATCATTCAGC
1 AATCATTCAGC
30775 GCTTAATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (16 bp):
AATCATTCAGCATTTG
Found at i:31170 original size:20 final size:20
Alignment explanation
Indices: 31086--31178 Score: 141
Period size: 20 Copynumber: 4.7 Consensus size: 20
31076 TTTTCCAAAT
31086 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
31106 TCCCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
31126 TCACAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
31146 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
* *
31166 GCGCAACGCGAAT
1 TCGCAATGCGAAT
31179 CTGACTATCG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:31193 original size:60 final size:61
Alignment explanation
Indices: 31046--31197 Score: 150
Period size: 60 Copynumber: 2.5 Consensus size: 61
31036 TTTCCAGATT
* * * * *
31046 CGCAATGCGATTCTGACTATCGCATTGCGATTTTCCAAATTCGCAATGCGAATACGTAAAT
1 CGCAATGCGAATCTGACTATCGCAATGCGATATACCAAATTCGCAATGCGAATACGTAAAG
* * * * *
31107 CCCAATGCGAATAC-GTA-AATCACAATGCGA-ATACGTAAA-TCGCAATGCGAATATGTAAAG
1 CGCAATGCGAAT-CTG-ACTATCGCAATGCGATATAC-CAAATTCGCAATGCGAATACGTAAAG
*
31167 CGCAACGCGAATCTGACTATCGCAATGCGAT
1 CGCAATGCGAATCTGACTATCGCAATGCGAT
31198 TTACATAGCG
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
59 2 0.03
60 43 0.61
61 24 0.34
62 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (61 bp):
CGCAATGCGAATCTGACTATCGCAATGCGATATACCAAATTCGCAATGCGAATACGTAAAG
Found at i:31430 original size:22 final size:22
Alignment explanation
Indices: 31369--31439 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
31359 CTCTAAGCCG
* *
31369 AATCTGTCCCCATCTCCAACGA
1 AATCAGTCCCCATCTCCGACGA
31391 AATCAGTCCCCATCTCCGACGA
1 AATCAGTCCCCATCTCCGACGA
* * **
31413 TATCAGTCTCCATCTCCGGTGA
1 AATCAGTCCCCATCTCCGACGA
31435 AATCA
1 AATCA
31440 TTCACGATCA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.24
Consensus pattern (22 bp):
AATCAGTCCCCATCTCCGACGA
Found at i:31848 original size:20 final size:20
Alignment explanation
Indices: 31777--31865 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
31767 AATTCTGTCA
31777 TTGCGATTTTCA-TTTCGCG
1 TTGCGATTTTCATTTTCGCG
** **
31796 TTGCGATAGTCAAATTCGCG
1 TTGCGATTTTCATTTTCGCG
* ** *
31816 TTGTGATAGTCATTTTCGTG
1 TTGCGATTTTCATTTTCGCG
*
31836 TTGCGATTTTCATTTTCGTG
1 TTGCGATTTTCATTTTCGCG
31856 TTGCGATTTT
1 TTGCGATTTT
31866 AAATTTCAGA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
19 10 0.17
20 49 0.83
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCGCG
Found at i:31872 original size:20 final size:20
Alignment explanation
Indices: 31829--31872 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
31819 TGATAGTCAT
* *
31829 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAA
31849 TTTCGTGTTGCGATTTTAAA
1 TTTCGTGTTGCGATTTTAAA
31869 TTTC
1 TTTC
31873 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAA
Found at i:34192 original size:103 final size:103
Alignment explanation
Indices: 34013--34226 Score: 347
Period size: 103 Copynumber: 2.1 Consensus size: 103
34003 TAATGTCCAT
* * *
34013 AAGGACCACATATCATTCCTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
34078 GACTTCACACATGTTCCAAATAATACATATATATTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
34116 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
34181 GACTTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
34219 AAAGACCA
1 AAGGACCA
34227 TAGACCCTCG
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:35426 original size:21 final size:21
Alignment explanation
Indices: 35402--35445 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
35392 ATTTTATTCG
*
35402 CTTGAAGGGGTATCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
*
35423 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
35444 CT
1 CT
35446 AGCCCAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:36622 original size:33 final size:33
Alignment explanation
Indices: 36565--36645 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
36555 ATAGTTTACT
** * * *
36565 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACAACAAA
*
36599 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
36632 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
36646 ATGACTATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:36657 original size:20 final size:20
Alignment explanation
Indices: 36632--36683 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
36622 CAACAACAAA
*
36632 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
36652 ATCGCAATACGAAAATGACT
1 ATCGCAATGCGAAAATGACT
36672 ATCGCAATGCGA
1 ATCGCAATGCGA
36684 TAGTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:37294 original size:42 final size:42
Alignment explanation
Indices: 37185--37295 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
37175 CCTGACTCAC
* * *
37185 CTGTCATCGTTTAAGAGGCCTC-CCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCTCTCCC-ACCGTTCAAGAGGCCA
* ** ** *
37227 CTATCATCCCTCAAGATCCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGCCTCTCCCACCGTTCAAGAGGCCA
* *
37269 CTGTCATCGTTGAAGAGGTCTCTCCCA
1 CTGTCATCGTTCAAGAGGCCTCTCCCA
37296 ATATTCTAGA
Statistics
Matches: 51, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
42 48 0.94
43 3 0.06
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGCCTCTCCCACCGTTCAAGAGGCCA
Found at i:38830 original size:20 final size:20
Alignment explanation
Indices: 38807--38845 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38797 TGTTGAATGC
38807 AAAATAGACTATCGCAACGCA
1 AAAAT-GACTATCGCAACGCA
38828 AAAATGACTATCGCAACG
1 AAAATGACTATCGCAACG
38846 AGAGAATCGC
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:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATGACTATCGCAACGCA
Found at i:38856 original size:14 final size:14
Alignment explanation
Indices: 38837--38890 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
38827 AAAAATGACT
38837 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
38851 ATCGCAATACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
38870 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
38884 ATCGCAA
1 ATCGCAA
38891 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 15 0.45
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.24
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:38905 original size:34 final size:34
Alignment explanation
Indices: 38817--38912 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
38807 AAAATAGACT
* * **
38817 ATCGCAACGCAAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
38851 ATCGCAATACG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
38884 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
38913 CGAAACTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:39011 original size:33 final size:33
Alignment explanation
Indices: 38927--39022 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
38917 ACTAAATTCG
* *
38927 CGTTGCGATTTTCATTTTCGAATTGTGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
*
38961 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
38994 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
39023 AGTCAATTCC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 31 0.57
34 23 0.43
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:39019 original size:20 final size:20
Alignment explanation
Indices: 38994--39088 Score: 156
Period size: 20 Copynumber: 4.8 Consensus size: 20
38984 GCGATTCTCT
*
38994 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
39014 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
39034 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
39054 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCA-ATTCCG
39074 CGTTGCGATAGTCAA
1 CGTTGCGATAGTCAA
39089 ATGAATATCT
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
19 1 0.01
20 67 0.94
21 3 0.04
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:41567 original size:24 final size:24
Alignment explanation
Indices: 41516--41567 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
41506 ATCCAAGTAT
** *
41516 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
41540 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
41564 TGAC
1 TGAC
41568 TAGTGCTCAC
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:42421 original size:20 final size:20
Alignment explanation
Indices: 42396--42459 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
42386 TTCAGTATTA
42396 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
*
42416 CGATAGTCAGAATCTCGTTG
1 CGATAGTCAGAATCGCGTTG
*
42436 CGATAGTCAGATTCGCGTTG
1 CGATAGTCAGAATCGCGTTG
42456 CGAT
1 CGAT
42460 TTATGTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
CGATAGTCAGAATCGCGTTG
Found at i:42469 original size:20 final size:20
Alignment explanation
Indices: 42446--42498 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
42436 CGATAGTCAG
* *
42446 ATTCGCGTTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
42466 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
42486 ATTCGCATTGCGA
1 ATTCGCATTGCGA
42499 ATTAGGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:42519 original size:21 final size:21
Alignment explanation
Indices: 42495--42540 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
42485 TATTCGCATT
42495 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
42516 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
42537 GCGA
1 GCGA
42541 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:42821 original size:2 final size:2
Alignment explanation
Indices: 42814--42847 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42804 TAATAATAGA
42814 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
42848 CTTAAAATTA
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:43665 original size:22 final size:21
Alignment explanation
Indices: 43637--43698 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 21
43627 TGAGAGGAAG
43637 AAGAAAATGAGATTTTTTTATA
1 AAGAAAATGAG-TTTTTTTATA
*
43659 AAGAAAATTTAGTTTTTTTATA
1 AAGAAAA-TGAGTTTTTTTATA
*
43681 AAGAAAATTTAGTTTTTT
1 AAGAAAA-TGAGTTTTTT
43699 ATACCATCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 35 0.92
23 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (21 bp):
AAGAAAATGAGTTTTTTTATA
Found at i:43701 original size:21 final size:22
Alignment explanation
Indices: 43649--43698 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
43639 GAAAATGAGA
43649 TTTTTTTATAAAGAAAATTTAG
1 TTTTTTTATAAAGAAAATTTAG
43671 TTTTTTTATAAAGAAAATTTAG
1 TTTTTTTATAAAGAAAATTTAG
43693 TTTTTT
1 TTTTTT
43699 ATACCATCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (22 bp):
TTTTTTTATAAAGAAAATTTAG
Found at i:44733 original size:23 final size:23
Alignment explanation
Indices: 44707--44765 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
44697 GTTCTTTCAT
44707 TTTGACATCAATATTGCTCTATG
1 TTTGACATCAATATTGCTCTATG
*
44730 TTTGACATCAATATTGTTCTATG
1 TTTGACATCAATATTGCTCTATG
44753 TTTGACATCAATA
1 TTTGACATCAATA
44766 CTAATGGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (23 bp):
TTTGACATCAATATTGCTCTATG
Found at i:51988 original size:29 final size:29
Alignment explanation
Indices: 51946--52032 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
51936 GTGTTGGCCG
*
51946 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCAGGCGACCTAC
51975 TAGGTCGCCATGCCTTCCAGGCGACCTAC
1 TAGGTCGCCATGCCTTCCAGGCGACCTAC
* * *
52004 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCAGGCGACCTAC
52033 AAGAGATTGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCAGGCGACCTAC
Found at i:52096 original size:20 final size:20
Alignment explanation
Indices: 52071--52108 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
52061 AACACGCTGG
52071 GCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAGA
52091 GCATCCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGA
52109 CCGAGGCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.37, G:0.29, T:0.11
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAGA
Found at i:52114 original size:14 final size:14
Alignment explanation
Indices: 52095--52127 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
52085 CCGAGAGCAT
52095 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
52109 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
52123 ACGAG
1 CCGAG
52128 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:52122 original size:10 final size:10
Alignment explanation
Indices: 52072--52108 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
52062 ACACGCTGGG
52072 CATCCGAGGC
1 CATCCGAGGC
52082 CATCCGAGAG-
1 CATCCGAG-GC
52092 CATCCGAGGC
1 CATCCGAGGC
52102 CATCCGA
1 CATCCGA
52109 CCGAGGCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 23 0.92
11 1 0.04
ACGTcount: A:0.24, C:0.38, G:0.27, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:52240 original size:33 final size:37
Alignment explanation
Indices: 52203--52271 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 37
52193 GTTGGGCATA
52203 CGAGGCCATCCG-A-GAGC-AT-CGAGGCCATCCGAC
1 CGAGGCCATCCGAACGAGCTATGCGAGGCCATCCGAC
*
52236 CGAGGCCATCCGAACGAGCTATGCGAGGGCATCCGA
1 CGAGGCCATCCGAACGAGCTATGCGAGGCCATCCGA
52272 GGGCAACAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 12 0.39
34 1 0.03
35 4 0.13
36 2 0.06
37 12 0.39
ACGTcount: A:0.25, C:0.33, G:0.32, T:0.10
Consensus pattern (37 bp):
CGAGGCCATCCGAACGAGCTATGCGAGGCCATCCGAC
Found at i:52241 original size:14 final size:14
Alignment explanation
Indices: 52222--52253 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
52212 CCGAGAGCAT
*
52222 CGAGGCCATCCGAC
1 CGAGGCCATCCGAA
52236 CGAGGCCATCCGAA
1 CGAGGCCATCCGAA
52250 CGAG
1 CGAG
52254 CTATGCGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.38, G:0.31, T:0.06
Consensus pattern (14 bp):
CGAGGCCATCCGAA
Found at i:52274 original size:126 final size:127
Alignment explanation
Indices: 52041--52293 Score: 472
Period size: 126 Copynumber: 2.0 Consensus size: 127
52031 ACAAGAGATT
*
52041 GCATGTGCCATGCACGTCCCAACACGCTGGGCATCCGAGGCCATCCGAGAGCATCCGAGGCCATC
1 GCATGTGCCATGCACGTCCCAACACGCTGGGCATACGAGGCCATCCGAGAGCATCCGAGGCCATC
*
52106 CGACCGAGGCCATCCGAACGAGCTATGCGAGGGCATCCGAGGGCAACCGAGCGAGCTATGCG
66 CGACCGAGGCCATCCGAACGAGCTATGCGAGGGCATCCGAGGGCAACAGAGCGAGCTATGCG
*
52168 GCATGTGCCATGCACGTCCCAACACGTTGGGCATACGAGGCCATCCGAGAGCAT-CGAGGCCATC
1 GCATGTGCCATGCACGTCCCAACACGCTGGGCATACGAGGCCATCCGAGAGCATCCGAGGCCATC
52232 CGACCGAGGCCATCCGAACGAGCTATGCGAGGGCATCCGAGGGCAACAGAGCGAGCTATGCG
66 CGACCGAGGCCATCCGAACGAGCTATGCGAGGGCATCCGAGGGCAACAGAGCGAGCTATGCG
52294 AGAGAATCCG
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
126 71 0.58
127 52 0.42
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.12
Consensus pattern (127 bp):
GCATGTGCCATGCACGTCCCAACACGCTGGGCATACGAGGCCATCCGAGAGCATCCGAGGCCATC
CGACCGAGGCCATCCGAACGAGCTATGCGAGGGCATCCGAGGGCAACAGAGCGAGCTATGCG
Found at i:52317 original size:33 final size:33
Alignment explanation
Indices: 52235--52319 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
52225 GGCCATCCGA
* * * * *
52235 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
*
52268 CCGAGGGCAACAGAGCGAGCTATGCGAGAGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
52301 CCGAGGG-AAGCCGAGCGAG
1 CCGAGGGCAA-CCGAGCGAG
52320 GGTAGGTCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 2 0.05
33 42 0.95
ACGTcount: A:0.28, C:0.26, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
Found at i:52480 original size:29 final size:29
Alignment explanation
Indices: 52437--52493 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
52427 GAGCAAGGGT
* *
52437 AGGTCGCCTGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGAAGTGCATGGCGACCTACA
52466 AGGTCGCCCGAAGTGCATGGCGACCTAC
1 AGGTCGCCCGAAGTGCATGGCGACCTAC
52494 GGCCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGAAGTGCATGGCGACCTACA
Found at i:55967 original size:15 final size:15
Alignment explanation
Indices: 55944--56024 Score: 108
Period size: 15 Copynumber: 5.4 Consensus size: 15
55934 CGCCCCGCAT
*
55944 CCGCACCGCATCCAC
1 CCGCCCCGCATCCAC
55959 CCGCCCCGCATCCAC
1 CCGCCCCGCATCCAC
* *
55974 CCGCCCTGCATCCGC
1 CCGCCCCGCATCCAC
*
55989 CCGCCCCGCATCCTC
1 CCGCCCCGCATCCAC
* *
56004 CCGCCCCACATCCGC
1 CCGCCCCGCATCCAC
56019 CCGCCC
1 CCGCCC
56025 AACTAAATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.11, C:0.65, G:0.15, T:0.09
Consensus pattern (15 bp):
CCGCCCCGCATCCAC
Found at i:55988 original size:26 final size:26
Alignment explanation
Indices: 55931--56001 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 26
55921 TTGAGACCTT
*
55931 ACCCGCCCCGCATCCGCACCGCATCC
1 ACCCGCCCCGCATCCACACCGCATCC
*
55957 ACCCGCCCCGCATCCACCCGCCCTGCATCC
1 ACCCGCCCCGCATCCA--C-ACC-GCATCC
*
55987 GCCCGCCCCGCATCC
1 ACCCGCCCCGCATCC
56002 TCCCGCCCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 15 0.39
28 1 0.03
29 2 0.05
30 20 0.53
ACGTcount: A:0.13, C:0.63, G:0.15, T:0.08
Consensus pattern (26 bp):
ACCCGCCCCGCATCCACACCGCATCC
Found at i:57169 original size:19 final size:19
Alignment explanation
Indices: 57145--57200 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
57135 GAACGTTGGA
57145 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
57164 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
57185 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
57201 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:57180 original size:11 final size:11
Alignment explanation
Indices: 57145--57193 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
57135 GAACGTTGGA
57145 AACCGGTTTTG
1 AACCGGTTTTG
57156 -ACCGG-TTT-
1 AACCGGTTTTG
57164 AACCGGTTTTG
1 AACCGGTTTTG
57175 AACCGGTTTTG
1 AACCGGTTTTG
57186 -ACCGGTTT
1 AACCGGTTT
57194 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:57196 original size:9 final size:10
Alignment explanation
Indices: 57146--57200 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
57136 AACGTTGGAA
57146 ACCGGTTTTG
1 ACCGGTTTTG
*
57156 ACCGG-TTTA
1 ACCGGTTTTG
57165 ACCGGTTTTG
1 ACCGGTTTTG
57175 AACCGGTTTTG
1 -ACCGGTTTTG
57186 ACCGG-TTTG
1 ACCGGTTTTG
57195 ACCGGT
1 ACCGGT
57201 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:57231 original size:13 final size:13
Alignment explanation
Indices: 57213--57267 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
57203 CGACCCGTTT
*
57213 ACCCGTTTACCCG
1 ACCCGTTGACCCG
57226 ACCCGTTGACCCGACCCG
1 ACCCGTTGA--C---CCG
57244 ACCCGTTGACCCG
1 ACCCGTTGACCCG
57257 ACCCGTTGACC
1 ACCCGTTGACC
57268 GTTGACCGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 22 0.61
15 1 0.03
16 1 0.03
18 12 0.33
ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:57244 original size:18 final size:18
Alignment explanation
Indices: 57221--57261 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
57211 TTACCCGTTT
57221 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
57239 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
57257 ACCCG
1 ACCCG
57262 TTGACCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:57335 original size:29 final size:29
Alignment explanation
Indices: 57275--57340 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
57265 ACCGTTGACC
*** *
57275 GTGCTATTCTGGGAATTAATTCGGTTTTG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
57304 GTGCTATTCTGGGAATTAATTCGAAATGG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
57333 GTGCTATT
1 GTGCTATT
57341 TCGGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (29 bp):
GTGCTATTCTGGGAATTAATTCGAAATGG
Found at i:64385 original size:19 final size:19
Alignment explanation
Indices: 64361--64416 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
64351 GAACGTTGGA
64361 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
64380 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
64401 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
64417 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:64396 original size:11 final size:11
Alignment explanation
Indices: 64361--64409 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
64351 GAACGTTGGA
64361 AACCGGTTTTG
1 AACCGGTTTTG
64372 -ACCGG-TTT-
1 AACCGGTTTTG
64380 AACCGGTTTTG
1 AACCGGTTTTG
64391 AACCGGTTTTG
1 AACCGGTTTTG
64402 -ACCGGTTT
1 AACCGGTTT
64410 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:64412 original size:9 final size:10
Alignment explanation
Indices: 64362--64416 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
64352 AACGTTGGAA
64362 ACCGGTTTTG
1 ACCGGTTTTG
*
64372 ACCGG-TTTA
1 ACCGGTTTTG
64381 ACCGGTTTTG
1 ACCGGTTTTG
64391 AACCGGTTTTG
1 -ACCGGTTTTG
64402 ACCGG-TTTG
1 ACCGGTTTTG
64411 ACCGGT
1 ACCGGT
64417 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:64460 original size:18 final size:18
Alignment explanation
Indices: 64437--64477 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
64427 TTACCCGTTT
64437 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
64455 ACCCGACCCGTTGACCTG
1 ACCCGACCCGTTGACCCG
64473 ACCCG
1 ACCCG
64478 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:64479 original size:13 final size:13
Alignment explanation
Indices: 64429--64459 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
64419 CGACCCGTTT
*
64429 ACCCGTTTACCCG
1 ACCCGTTGACCCG
64442 ACCCGTTGACCCG
1 ACCCGTTGACCCG
64455 ACCCG
1 ACCCG
64460 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:64480 original size:13 final size:13
Alignment explanation
Indices: 64454--64483 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
64444 CCGTTGACCC
64454 GACCCGACCCGTT
1 GACCCGACCCGTT
*
64467 GACCTGACCCGTT
1 GACCCGACCCGTT
64480 GACC
1 GACC
64484 GTTGACCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:68414 original size:23 final size:23
Alignment explanation
Indices: 68388--68431 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
68378 AAACGAATGT
*
68388 TAAACGAACATGTTCGTGAACGC
1 TAAACGAACATGTTCGCGAACGC
*
68411 TAAATGAACATGTTCGCGAAC
1 TAAACGAACATGTTCGCGAAC
68432 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (23 bp):
TAAACGAACATGTTCGCGAACGC
Found at i:68437 original size:23 final size:23
Alignment explanation
Indices: 68388--68438 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
68378 AAACGAATGT
* * **
68388 TAAACGAACATGTTCGTGAACGC
1 TAAATGAACATGTTCGCGAACAA
68411 TAAATGAACATGTTCGCGAACAA
1 TAAATGAACATGTTCGCGAACAA
68434 TAAAT
1 TAAAT
68439 AAATGAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (23 bp):
TAAATGAACATGTTCGCGAACAA
Found at i:69589 original size:12 final size:12
Alignment explanation
Indices: 69572--69638 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
69562 TTCTTAAACG
69572 AAAAATAAATTT
1 AAAAATAAATTT
69584 AAAAATAATATTAT
1 AAAAATAA-ATT-T
*
69598 TAAAATAAA--T
1 AAAAATAAATTT
* *
69608 AAATA-AAATCT
1 AAAAATAAATTT
*
69619 AAATATAAATTT
1 AAAAATAAATTT
*
69631 TAAAATAA
1 AAAAATAA
69639 CATTAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 3 0.07
10 4 0.09
11 6 0.14
12 19 0.43
13 4 0.09
14 8 0.18
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAATAAATTT
Found at i:69634 original size:33 final size:34
Alignment explanation
Indices: 69574--69638 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
69564 CTTAAACGAA
*
69574 AAATAAATTTAAAAATAATATTATTAAAATAAAT
1 AAATAAATCTAAAAATAATATTATTAAAATAAAT
*
69608 AAATAAAATCTAAATATAA-ATT-TTAAAATAA
1 AAAT-AAATCTAAAAATAATATTATTAAAATAA
69639 CATTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 9 0.32
34 7 0.25
35 12 0.43
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (34 bp):
AAATAAATCTAAAAATAATATTATTAAAATAAAT
Found at i:71331 original size:15 final size:16
Alignment explanation
Indices: 71311--71357 Score: 80
Period size: 15 Copynumber: 3.1 Consensus size: 16
71301 AATAGGAGAA
71311 AGAAAAAGGAAAAAAT
1 AGAAAAAGGAAAAAAT
71327 A-AAAAAGGAAAAAA-
1 AGAAAAAGGAAAAAAT
71341 AGAAAAAGGAAAAAAT
1 AGAAAAAGGAAAAAAT
71357 A
1 A
71358 TTTTATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.03
15 26 0.90
16 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (16 bp):
AGAAAAAGGAAAAAAT
Found at i:71354 original size:8 final size:8
Alignment explanation
Indices: 71313--71355 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
71303 TAGGAGAAAG
71313 AAAAAGGA
1 AAAAAGGA
*
71321 AAAAA-TA
1 AAAAAGGA
71328 AAAAAGGA
1 AAAAAGGA
*
71336 AAAAAAG-
1 AAAAAGGA
71343 AAAAAGGA
1 AAAAAGGA
71351 AAAAA
1 AAAAA
71356 TATTTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (8 bp):
AAAAAGGA
Found at i:73928 original size:20 final size:20
Alignment explanation
Indices: 73903--73952 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
73893 TTTTCCTAAT
73903 TCGCAATGCGAATACGTA-AA
1 TCGCAATGCGAATACG-ACAA
* *
73923 TCGCAACGCGAATACGACTA
1 TCGCAATGCGAATACGACAA
73943 TCGCAATGCG
1 TCGCAATGCG
73953 TATTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATACGACAA
Found at i:74126 original size:22 final size:22
Alignment explanation
Indices: 74101--74166 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
74091 GGCAACATCC
74101 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
74123 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
74145 GTCTCTATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
74167 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:74560 original size:20 final size:20
Alignment explanation
Indices: 74535--74582 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
74525 CGATTCTTGC
*
74535 GTTGCGATAGTCATTTTTGT
1 GTTGCGATAGTCATTTTCGT
*
74555 GTTGCGATATTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
74575 GTTGCGAT
1 GTTGCGAT
74583 TTAAAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.48
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:76530 original size:34 final size:34
Alignment explanation
Indices: 76483--76576 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 34
76473 ATAGTTTACT
* * *
76483 ATCACAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCACAATGCGAAAATGACTATCGCAACAACAAA
* **
76517 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCACAATGCGAAAATGACTATCGCAACAACAAA
* * *
76550 ATTACAACGTGAAAATGACTATCGCAA
1 ATCACAATGCGAAAATGACTATCGCAA
76577 TGCGAAAATG
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
33 24 0.51
34 23 0.49
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.16
Consensus pattern (34 bp):
ATCACAATGCGAAAATGACTATCGCAACAACAAA
Found at i:76701 original size:40 final size:40
Alignment explanation
Indices: 76643--76729 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
76633 GATTCTCTCG
*
76643 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCATTGCAATAGTCATTTTCGCA
* *
76683 TTGCGATAGT-AATTTTCGCGTTGCAATAGTCATTTTCGCA
1 TTGCGATAGTCAA-ATTCGCATTGCAATAGTCATTTTCGCA
76723 TTGCGAT
1 TTGCGAT
76730 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 2 0.05
40 41 0.95
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCGCATTGCAATAGTCATTTTCGCA
Found at i:76739 original size:20 final size:20
Alignment explanation
Indices: 76643--76729 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
76633 GATTCTCTCG
*
76643 TTGCGATAGTCAA-ATTCGCA
1 TTGCGATAGT-AATTTTCGCA
*
76663 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTAATTTTCGCA
*
76683 TTGCGATAGTAATTTTCGCG
1 TTGCGATAGTAATTTTCGCA
* *
76703 TTGCAATAGTCATTTTCGCA
1 TTGCGATAGTAATTTTCGCA
76723 TTGCGAT
1 TTGCGAT
76730 TTTAAGTTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 1 0.02
20 57 0.98
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTAATTTTCGCA
Found at i:77236 original size:21 final size:21
Alignment explanation
Indices: 77210--77266 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
77200 CTCACCTGTC
77210 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGGCCTCCCCT
77231 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGGCCTCCCCT
77252 ATCGTTCAAGAGGCC
1 ATCGTTCAAGAGGCC
77267 CCTATCATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCTCCCCT
Found at i:77320 original size:21 final size:21
Alignment explanation
Indices: 77209--77336 Score: 107
Period size: 21 Copynumber: 6.1 Consensus size: 21
77199 ACTCACCTGT
77209 CATCGTTCAAGAGGCCTCC-CC
1 CATCGTTCAAGAGGCC-CCTCC
*
77230 TATCGTTCAAGAGGCCTCC-CC
1 CATCGTTCAAGAGGCC-CCTCC
* **
77251 TATCGTTCAAGAGGCCCCTAT
1 CATCGTTCAAGAGGCCCCTCC
** *
77272 CATCCCTCAAGAGTCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * **
77293 CACCGTTCAAGAGGCCACTGT
1 CATCGTTCAAGAGGCCCCTCC
* *
77314 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
77335 CA
1 CA
77337 ACATTCTAGA
Statistics
Matches: 84, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
20 2 0.02
21 82 0.98
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:78739 original size:14 final size:14
Alignment explanation
Indices: 78720--78755 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
78710 ATTATTTAAT
78720 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
78734 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
78748 TGATTTGT
1 TGATTTGT
78756 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:78916 original size:34 final size:34
Alignment explanation
Indices: 78872--78967 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
78862 TCTAAATTCG
78872 CGTTGCGATTTTCATTTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCCCT
* *
78906 CGTTGAGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCCCT
** * *
78939 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
78968 AGTCAAATGA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCCCT
Found at i:81424 original size:24 final size:24
Alignment explanation
Indices: 81397--81443 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
81387 CAAAATCCGA
81397 GTATTGACCAAGATCAAATTTCGG
1 GTATTGACCAAGATCAAATTTCGG
81421 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAATTTCG
81444 AATACTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAATTTCGG
Found at i:81452 original size:24 final size:24
Alignment explanation
Indices: 81401--81452 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
81391 ATCCGAGTAT
** *
81401 TGACCAAGATCAAATTTCGGGTAT
1 TGACCAAGATCAAATTTCGAATAC
81425 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAATTTCGAATAC
81449 TGAC
1 TGAC
81453 TAGTACTCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAATTTCGAATAC
Found at i:82306 original size:20 final size:20
Alignment explanation
Indices: 82281--82347 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
82271 AAATTCAGTA
82281 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
82301 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
82321 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
82341 TTGCGAT
1 TTGCGAT
82348 TTACGTATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:82357 original size:20 final size:20
Alignment explanation
Indices: 82334--82393 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
82324 CGATAGTCAG
* *
82334 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTACGATTTACGT
82354 ATTCGCATTACGATTTACGT
1 ATTCGCATTACGATTTACGT
* *
82374 ATTTGCATTACAATTTACGT
1 ATTCGCATTACGATTTACGT
82394 GGTGAGGTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (20 bp):
ATTCGCATTACGATTTACGT
Found at i:82694 original size:20 final size:20
Alignment explanation
Indices: 82669--82845 Score: 175
Period size: 20 Copynumber: 9.5 Consensus size: 20
82659 AGAATAGTTT
82669 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
82689 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
82709 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
82725 A--ATCGCAATACG-AAATG
1 ACTATCGCAATGCGAAAATG
**
82742 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
82758 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
82776 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
82796 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
82816 ACTATCTTAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
82836 ACTATCGCAA
1 ACTATCGCAA
82846 CAAAAGAATC
Statistics
Matches: 135, Mismatches: 8, Indels: 28
0.79 0.05 0.16
Matches are distributed among these distances:
14 14 0.10
16 10 0.07
17 8 0.06
18 5 0.04
19 7 0.05
20 91 0.67
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:82772 original size:33 final size:33
Alignment explanation
Indices: 82692--82772 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
82682 GAAAATGACT
** * * *
82692 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACAACAAA
**
82726 ATCGCAATACGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
82759 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
82773 ATGACTATCG
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:82814 original size:40 final size:40
Alignment explanation
Indices: 82669--82883 Score: 175
Period size: 40 Copynumber: 5.9 Consensus size: 40
82659 AGAATAGTTT
*
82669 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* *
82709 ACTATCGCAA--CG-AGA-GA--ATCGCAATACG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
82742 AAAATCGCAA--C-AACAA--A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAA-AATGACTATCGCAATGCGAAAATG
82776 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
**
82816 ACTATCTTAATGCGAAAATGACTATCGCAA--C-AAAA-G
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
82852 A--ATCGCAATGCG-AAATGAAAATCGCATTGCGA
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGA
82884 TTCTCTCGTT
Statistics
Matches: 144, Mismatches: 18, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
33 37 0.26
34 32 0.22
35 1 0.01
36 8 0.06
37 8 0.06
38 4 0.03
40 54 0.38
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
Found at i:82944 original size:20 final size:20
Alignment explanation
Indices: 82890--82998 Score: 146
Period size: 20 Copynumber: 5.5 Consensus size: 20
82880 GCGATTCTCT
**
82890 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
82910 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
82930 CATTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
** *
82950 CGTTGTAATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
82970 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
82990 CGTTGCGAT
1 CGTTGCGAT
82999 TTTAAGTTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:83568 original size:21 final size:21
Alignment explanation
Indices: 83477--83575 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
83467 GACTCACCTG
*
83477 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
83499 T-ATAGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
83519 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
83540 TCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
83561 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
83576 TCCATCCCAA
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 3 0.05
21 56 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:84973 original size:14 final size:14
Alignment explanation
Indices: 84954--84989 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
84944 ATTGTTTAAT
84954 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
84968 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
84982 TGATTTGT
1 TGATTTGT
84990 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:85122 original size:20 final size:20
Alignment explanation
Indices: 85097--85190 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
85087 AATAGACTAT
85097 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
85117 CGTTGCGATAGTTAATTCCG
1 CGTTGCGATAGTCATTTCCG
85137 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
85157 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
85177 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
85191 AATGAATGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 65 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:87638 original size:24 final size:24
Alignment explanation
Indices: 87604--87657 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
87594 CTGAAAGATC
87604 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
87628 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
87652 ATCAAA
1 ATCAAA
87658 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:87671 original size:24 final size:24
Alignment explanation
Indices: 87604--87671 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
87594 CTGAAAGATC
* * *
87604 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
87628 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
87652 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
87672 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:88560 original size:20 final size:20
Alignment explanation
Indices: 88499--88565 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
88489 AAATTCAGTA
*
88499 TTGCGATAGTCAGAATCTCA
1 TTGCGATAGTCAGAATCTCG
*
88519 TTACGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
88539 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
88559 TTGCGAT
1 TTGCGAT
88566 TTACGTATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:88575 original size:20 final size:20
Alignment explanation
Indices: 88552--88604 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
88542 CGATAGTCAG
*
88552 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
88572 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
88592 ATTCGCATTGCGA
1 ATTCGCATTGCGA
88605 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:88625 original size:21 final size:21
Alignment explanation
Indices: 88601--88646 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
88591 TATTCGCATT
88601 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
88622 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
88643 GCGA
1 GCGA
88647 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:88849 original size:2 final size:2
Alignment explanation
Indices: 88842--88877 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
88832 CACTCTAAAT
88842 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
88878 ATACTCGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:90334 original size:2 final size:2
Alignment explanation
Indices: 90327--90376 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
90317 AATTGCTTGC
90327 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
90369 AT AT AT AT
1 AT AT AT AT
90377 TATGTTACAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94461 original size:18 final size:18
Alignment explanation
Indices: 94438--94474 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
94428 ATATAAGATC
94438 ACTCGATTCAAAAAAATT
1 ACTCGATTCAAAAAAATT
94456 ACTCGATTCAAAAAAATT
1 ACTCGATTCAAAAAAATT
94474 A
1 A
94475 ATTTGTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.27
Consensus pattern (18 bp):
ACTCGATTCAAAAAAATT
Found at i:96181 original size:22 final size:22
Alignment explanation
Indices: 96151--96197 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
96141 TCAAAACCTA
96151 AACTACCAT-CCATATTTAGGG
1 AACTACCATACCATATTTAGGG
*
96172 AACTAACCATACCATATTTCGGG
1 AACT-ACCATACCATATTTAGGG
96195 AAC
1 AAC
96198 AATAACGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 14 0.61
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (22 bp):
AACTACCATACCATATTTAGGG
Found at i:101146 original size:36 final size:36
Alignment explanation
Indices: 101093--101332 Score: 399
Period size: 36 Copynumber: 6.7 Consensus size: 36
101083 GTGCGCTACA
* * *
101093 TCCTTCTGTTCGACTTGAATCGGAAGTGCCAATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* *
101129 TCATTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
101165 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
**
101201 TCCTTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
101237 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* *
101273 TCATTCCATTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
101309 TCCTTCCGTTCGACTTGAATCGGA
1 TCCTTCCGTTCGACTTGAATCGGA
101333 CATGTAGATG
Statistics
Matches: 191, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 191 1.00
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.30
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
Found at i:104480 original size:2 final size:2
Alignment explanation
Indices: 104473--104505 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
104463 CTGCTGACTC
104473 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104506 TATTTTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:104919 original size:44 final size:43
Alignment explanation
Indices: 104839--104935 Score: 126
Period size: 44 Copynumber: 2.3 Consensus size: 43
104829 TATTAAAAAT
104839 AATAAT-TATATATATATATATAATATTAATAAATTTAAATTA
1 AATAATATATATATATATATATAATATTAATAAATTTAAATTA
* ** * *
104881 AATTAATATATATATATATATATATTATTTTTATATTTAATTTA
1 AA-TAATATATATATATATATATAATATTAATAAATTTAAATTA
104925 AAT-ATATATAT
1 AATAATATATAT
104936 CCGGCCCGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 10 0.21
43 5 0.10
44 33 0.69
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (43 bp):
AATAATATATATATATATATATAATATTAATAAATTTAAATTA
Found at i:109440 original size:17 final size:16
Alignment explanation
Indices: 109420--109462 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
109410 AATCTGGAGA
109420 AACTTTCTGAGAAGAAT
1 AACTTTCTGAG-AGAAT
109437 AACTTTCTG-GAGAAT
1 AACTTTCTGAGAGAAT
*
109452 ACCCTTTCTGA
1 A-ACTTTCTGA
109463 TGCTAATGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 8 0.35
17 9 0.39
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (16 bp):
AACTTTCTGAGAGAAT
Found at i:109450 original size:15 final size:15
Alignment explanation
Indices: 109412--109452 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
109402 CAACTGAGAA
109412 TCTGGAG-A-AACTT
1 TCTGGAGAATAACTT
109425 TCTGAGAAGAATAACTT
1 TCTG-G-AGAATAACTT
109442 TCTGGAGAATA
1 TCTGGAGAATA
109453 CCCTTTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.17
14 1 0.04
15 8 0.33
16 2 0.08
17 9 0.38
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (15 bp):
TCTGGAGAATAACTT
Found at i:115980 original size:2 final size:2
Alignment explanation
Indices: 115973--115997 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
115963 TAAATCTTTT
115973 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
115998 TATTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117679 original size:2 final size:2
Alignment explanation
Indices: 117672--117698 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
117662 AAGAAAATTG
117672 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 T
117699 GGGTGATCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:118639 original size:17 final size:18
Alignment explanation
Indices: 118605--118642 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
118595 ATATATTTAG
118605 AATTTTTTAATTATTAAT
1 AATTTTTTAATTATTAAT
*
118623 AATTTTTTTATTA-TAAT
1 AATTTTTTAATTATTAAT
118640 AAT
1 AAT
118643 ATAATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTTTAATTATTAAT
Found at i:130337 original size:22 final size:23
Alignment explanation
Indices: 130294--130344 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
130284 TTTTTTATAT
130294 GTTAAATAAAATAAAAAATTAAA
1 GTTAAATAAAATAAAAAATTAAA
**
130317 -TTAAATAAAGAT-AAATTTTAAA
1 GTTAAATAAA-ATAAAAAATTAAA
130339 GTTAAA
1 GTTAAA
130345 AATGTGAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (23 bp):
GTTAAATAAAATAAAAAATTAAA
Found at i:136354 original size:2 final size:2
Alignment explanation
Indices: 136347--136393 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
136337 TTATTACAAT
136347 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
136389 TA TA T
1 TA TA T
136394 TCTGGGTATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:152688 original size:6 final size:6
Alignment explanation
Indices: 152677--152702 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
152667 GTCGTTTACT
152677 CGTTTC CGTTTC CGTTTC CGTTTC CG
1 CGTTTC CGTTTC CGTTTC CGTTTC CG
152703 AAAGGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.19, T:0.46
Consensus pattern (6 bp):
CGTTTC
Found at i:163135 original size:4 final size:4
Alignment explanation
Indices: 163126--163157 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
163116 ATACATATTG
163126 TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC
163158 CATATGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:166160 original size:30 final size:30
Alignment explanation
Indices: 166126--166183 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
166116 ATACATGACG
166126 TATGAGAATAACACGA-CAAATATGACAACT
1 TATGAGAATAACAC-ACCAAATATGACAACT
166156 TATGAGAATAACACACCAAATATGACAA
1 TATGAGAATAACACACCAAATATGACAA
166184 GTTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (30 bp):
TATGAGAATAACACACCAAATATGACAACT
Found at i:166259 original size:2 final size:2
Alignment explanation
Indices: 166252--166310 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
166242 TTTTGATACG
166252 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
166294 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
166311 GATGTTCGCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:170577 original size:282 final size:284
Alignment explanation
Indices: 170029--170597 Score: 769
Period size: 282 Copynumber: 2.0 Consensus size: 284
170019 AAACTCTCTG
* * * *
170029 TAAGGATCAATTCAACTTGTGAGTGTTGAGGTATTGTTTCAATTTGGCCATTGGGTTTATTGATT
1 TAAGGATCAATTCAACTTGGGAGTGTTGAGGTATTGATTCAATTTGGCCATTGGATTTATTGAGT
*
170094 TTCTTCTCAAAATTCACCTGAAAAGTTGGGTTCAAGATCCATCATAAACTAAGACTGGATTCCCT
66 TTCTTCTCAAAATTCACCTGAAAAGTTGGGTTCAAGATCCATCATAAACTAAGACTGGACTCCCT
* * *
170159 ACTGTCTATCTGATGCGGGATACTTTTAGGGTTGATATCTCCTATGTCATCCTGTTGTCTTCACC
131 ACTGTCTATCTGATGCGGGA-ACTTTTAAGGTTGATATCTCCTATGGCATCCTGCTGTCTTCACC
* * * * *
170224 AGGAAGCCATTTTGTGGAGTCCTGCAACACTGATTACTATCCAAAGTGTTGTACTCCCCTTATCT
195 AGGAAGCCACTTTGTGGAGGCCTGCAACACTGATTACCATACAAAGTGTTGTACTCCACTTATCT
170289 GACCTGCAGAAGTTCATTGGACGCA
260 GACCTGCAGAAGTTCATTGGACGCA
* ** *
170314 TAAGGATCAATTGAACTTGGGAGT-TCTGATTTATTGATTCAATTTGTCCATTGGATTTCA-TGA
1 TAAGGATCAATTCAACTTGGGAGTGT-TGAGGTATTGATTCAATTTGGCCATTGGATTT-ATTGA
* *
170377 GTTTCTTCTCAAAATTCATCTGAAAAGTTGGGTTCAAGGTCCAT-A-AAA-TAAGACTGGACTCC
64 GTTTCTTCTCAAAATTCACCTGAAAAGTTGGGTTCAAGATCCATCATAAACTAAGACTGGACTCC
* *
170439 CTACTG-CGTATCTGATGTGGG-ACTGTTTAAGGTTGGA-GTCTCCTATGGCATACTCTGCTGTC
129 CTACTGTC-TATCTGATGCGGGAACT-TTTAAGGTT-GATATCTCCTATGGCAT-C-CTGCTGTC
*
170501 TTCACCAGGAAGCCACTTTGTGG-GGCCTGCAACACTGATTACCATACAAATTGTTGTACTCCAC
189 TTCACCAGGAAGCCACTTTGTGGAGGCCTGCAACACTGATTACCATACAAAGTGTTGTACTCCAC
* * * *
170565 TTATTTGACCTGCGGTAGTTCATTGGATGCA
254 TTATCTGACCTGCAGAAGTTCATTGGACGCA
170596 TA
1 TA
170598 TTAGGTTCAA
Statistics
Matches: 251, Mismatches: 26, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
280 3 0.01
281 21 0.08
282 99 0.39
283 32 0.13
284 2 0.01
285 93 0.37
286 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (284 bp):
TAAGGATCAATTCAACTTGGGAGTGTTGAGGTATTGATTCAATTTGGCCATTGGATTTATTGAGT
TTCTTCTCAAAATTCACCTGAAAAGTTGGGTTCAAGATCCATCATAAACTAAGACTGGACTCCCT
ACTGTCTATCTGATGCGGGAACTTTTAAGGTTGATATCTCCTATGGCATCCTGCTGTCTTCACCA
GGAAGCCACTTTGTGGAGGCCTGCAACACTGATTACCATACAAAGTGTTGTACTCCACTTATCTG
ACCTGCAGAAGTTCATTGGACGCA
Found at i:177787 original size:2 final size:2
Alignment explanation
Indices: 177782--177833 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
177772 AAAAATTGTT
177782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
177823 TA TA TA TA TA T
1 TA TA TA TA TA T
177834 TGATGTTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:179182 original size:21 final size:21
Alignment explanation
Indices: 179156--179202 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
179146 AGGAGTAGAA
179156 GCAGGAGCGCCAGTCCACGCC
1 GCAGGAGCGCCAGTCCACGCC
*
179177 GCAGGAGTGCCAGTCCACGCC
1 GCAGGAGCGCCAGTCCACGCC
*
179198 ACAGG
1 GCAGG
179203 CGTGACAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.34, T:0.06
Consensus pattern (21 bp):
GCAGGAGCGCCAGTCCACGCC
Found at i:181407 original size:17 final size:17
Alignment explanation
Indices: 181380--181418 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
181370 AATTTACAAT
181380 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
181396 TAATTATAAATAATATC
1 TAATTATAAATAATATC
181413 TAATTA
1 TAATTA
181419 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:181490 original size:11 final size:11
Alignment explanation
Indices: 181474--181498 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
181464 AATATTGATT
181474 TGGGTTTTAAA
1 TGGGTTTTAAA
181485 TGGGTTTTAAA
1 TGGGTTTTAAA
181496 TGG
1 TGG
181499 ATTGGGCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (11 bp):
TGGGTTTTAAA
Found at i:182062 original size:15 final size:14
Alignment explanation
Indices: 182031--182073 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
182021 ATTTTAAAAT
*
182031 TTAAATTTTTATAA
1 TTAAATTTATATAA
*
182045 TTATAATTTATATTA
1 TTA-AATTTATATAA
182060 TTAAATATTATATA
1 TTAAAT-TTATATA
182074 GAAAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAAATTTATATAA
Found at i:195414 original size:15 final size:15
Alignment explanation
Indices: 195359--195418 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
195349 ATTTAGTTAG
195359 TATGTATATATTTATT
1 TATGTATATATTT-TT
*
195375 TAT-TATTATTTTTTT
1 TATGTA-TATATTTTT
* *
195390 TATCTA-ATATTTTA
1 TATGTATATATTTTT
195404 TATGTATATATTTTT
1 TATGTATATATTTTT
195419 ATTTTACTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
14 11 0.31
15 14 0.39
16 11 0.31
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (15 bp):
TATGTATATATTTTT
Found at i:195418 original size:16 final size:16
Alignment explanation
Indices: 195359--195420 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 16
195349 ATTTAGTTAG
195359 TATGTATATATTTATT-
1 TATGTATATATTT-TTA
*
195375 TAT-TAT-TATTTTTTT
1 TATGTATATA-TTTTTA
*
195390 TATCTA-ATA-TTTTA
1 TATGTATATATTTTTA
195404 TATGTATATATTTTTA
1 TATGTATATATTTTTA
195420 T
1 T
195421 TTTACTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
14 13 0.34
15 12 0.32
16 13 0.34
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (16 bp):
TATGTATATATTTTTA
Found at i:195444 original size:38 final size:37
Alignment explanation
Indices: 195363--195452 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 37
195353 AGTTAGTATG
* * *
195363 TATATATTTATTTATTATTATTTTTTTTATCTAATAT
1 TATATATATATATATTATTATTTTCTTTATCTAATAT
* * *
195400 TTTATATGTATATATTTTTATTTTACTTTAT-TACATAT
1 TATATATATATATATTATTATTTT-CTTTATCTA-ATAT
195438 TATATATATATATAT
1 TATATATATATATAT
195453 ATATATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 22 0.50
38 22 0.50
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (37 bp):
TATATATATATATATTATTATTTTCTTTATCTAATAT
Found at i:195445 original size:2 final size:2
Alignment explanation
Indices: 195434--195470 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
195424 ACTTTATTAC
195434 AT AT -T 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
195471 CTACACACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.