Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 43
Found at i:10148 original size:14 final size:14
Alignment explanation
Indices: 10124--10179 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
10114 TGGTTTTTTA
10124 AAAATTGAATTATGG
1 AAAA-TGAATTATGG
10139 AAAATGAATTATTGG
1 AAAATGAATTA-TGG
** *
10154 AATTTGAATTGTGG
1 AAAATGAATTATGG
10168 AAAATGAATTAT
1 AAAATGAATTAT
10180 ATTTTTGGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 19 0.56
15 15 0.44
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.36
Consensus pattern (14 bp):
AAAATGAATTATGG
Found at i:10444 original size:12 final size:12
Alignment explanation
Indices: 10408--10445 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10398 ATTTATTTAT
10408 TATTAA-ATAAA
1 TATTAATATAAA
*
10419 TATTAATAAAAA
1 TATTAATATAAA
*
10431 TATTAATATTAA
1 TATTAATATAAA
10443 TAT
1 TAT
10446 ATTTTATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATTAATATAAA
Found at i:10554 original size:23 final size:23
Alignment explanation
Indices: 10510--10581 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
10500 AGTATTATAT
* * *
10510 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAATATATTTATTAA
*
10533 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAATATATTTATTAA
*
10556 AATATTATTAAAT-TATTTATTAA
1 TATATT-TTAAATATATTTATTAA
10579 TAT
1 TAT
10582 TAAATATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 35 0.85
24 6 0.15
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
TATATTTTAAATATATTTATTAA
Found at i:10648 original size:27 final size:27
Alignment explanation
Indices: 10587--10648 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
10577 AATATTAAAT
*
10587 ATATAAATAATATTATTCATTATTAATA
1 ATAT-AATAATATTATTCATAATTAATA
*
10615 ATTTAATAATATTATTTCGA-AATTAATA
1 ATATAATAATATTA-TTC-ATAATTAATA
10643 A-ATAAT
1 ATATAAT
10649 CTAAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 14 0.48
28 14 0.48
29 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
ATATAATAATATTATTCATAATTAATA
Found at i:10956 original size:39 final size:42
Alignment explanation
Indices: 10900--10987 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 42
10890 TTCCTCCAAC
* *
10900 CAAACACTGAAACATA-TTT-CGGAAAACGAATTACGT-AAA
1 CAAACACTGAAAAATATTTTCCGAAAAACGAATTACGTGAAA
*
10939 CAAACAC-GAGAAAATATTTTCCGAAAAATGAATTACGTGAAA
1 CAAACACTGA-AAAATATTTTCCGAAAAACGAATTACGTGAAA
10981 CAAACAC
1 CAAACAC
10988 ATGATTTCGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 2 0.05
39 12 0.29
40 3 0.07
41 15 0.36
42 10 0.24
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (42 bp):
CAAACACTGAAAAATATTTTCCGAAAAACGAATTACGTGAAA
Found at i:11185 original size:3 final size:3
Alignment explanation
Indices: 11177--11203 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11167 TAATTAATTA
11177 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
11204 GTTAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12853 original size:22 final size:22
Alignment explanation
Indices: 12828--12895 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
12818 TTCATTTCAA
12828 TTTAGTTATTCATTTTTTCCTT
1 TTTAGTTATTCATTTTTTCCTT
*
12850 TTTAATT-TTAGCATTTTTT--TAT
1 TTTAGTTATT--CATTTTTTCCT-T
12872 TTTAGTTATTCATTTTTTCCTT
1 TTTAGTTATTCATTTTTTCCTT
12894 TT
1 TT
12896 ATTTTTAGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
21 11 0.29
22 16 0.42
23 11 0.29
ACGTcount: A:0.16, C:0.10, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTAGTTATTCATTTTTTCCTT
Found at i:12858 original size:43 final size:43
Alignment explanation
Indices: 12810--12895 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 43
12800 TTAATCCATC
12810 AATTTTA-ATTCATTTCAATTTAGTTATTCATTTTTTCCTTTTT
1 AATTTTACATT-ATTTCAATTTAGTTATTCATTTTTTCCTTTTT
* * *
12853 AATTTTAGCATTTTTTTATTTTAGTTATTCATTTTTTCCTTTT
1 AATTTTA-CATTATTTCAATTTAGTTATTCATTTTTTCCTTTT
12896 ATTTTTAGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 7 0.18
44 28 0.74
45 3 0.08
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.65
Consensus pattern (43 bp):
AATTTTACATTATTTCAATTTAGTTATTCATTTTTTCCTTTTT
Found at i:12895 original size:21 final size:21
Alignment explanation
Indices: 12828--12896 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
12818 TTCATTTCAA
12828 TTTAGTTATTCATTTTTTCCTT
1 TTTAGTTATTCATTTTTTCC-T
* **
12850 TTTAATT-TTAGCATTTTTTTAT
1 TTTAGTTATT--CATTTTTTCCT
12872 TTTAGTTATTCATTTTTTCCT
1 TTTAGTTATTCATTTTTTCCT
12893 TTTA
1 TTTA
12897 TTTTTAGTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
21 15 0.39
22 13 0.34
23 10 0.26
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTAGTTATTCATTTTTTCCT
Found at i:12896 original size:43 final size:45
Alignment explanation
Indices: 12828--12917 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 45
12818 TTCATTTCAA
12828 TTTAGTTATTCATTTTTTCCTTTTTAATTTTAGCAT-TTTTTTAT
1 TTTAGTTATTCATTTTTTCCTTTTTAATTTTAGCATATTTTTTAT
* **
12872 TTTAGTTATTCATTTTTTCC-TTTTATTTTTAGTGTATTTTTTAT
1 TTTAGTTATTCATTTTTTCCTTTTTAATTTTAGCATATTTTTTAT
12916 TT
1 TT
12918 ATTTGTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 12 0.29
44 30 0.71
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.70
Consensus pattern (45 bp):
TTTAGTTATTCATTTTTTCCTTTTTAATTTTAGCATATTTTTTAT
Found at i:12915 original size:18 final size:17
Alignment explanation
Indices: 12892--12939 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
12882 CATTTTTTCC
12892 TTTTATTTTTAGTGTATT
1 TTTTATTTTTA-TGTATT
*
12910 TTTTATTTATT-TGTTTT
1 TTTTATTT-TTATGTATT
12927 TTCTTATTTTTAT
1 TT-TTATTTTTAT
12940 TTTATTACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 9 0.35
18 15 0.58
19 2 0.08
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTATTTTTATGTATT
Found at i:17427 original size:21 final size:21
Alignment explanation
Indices: 17403--17442 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17393 ATGTTTATAG
17403 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
17424 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
17443 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:20513 original size:20 final size:20
Alignment explanation
Indices: 20488--20542 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
20478 TTGTAGCCTT
*
20488 GGTGCATGGATGCACAGCAG
1 GGTGCATCGATGCACAGCAG
20508 GGTGCATCGATGCACAGCAG
1 GGTGCATCGATGCACAGCAG
20528 GGTGCATCGATGCAC
1 GGTGCATCGATGCAC
20543 TAATTGCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (20 bp):
GGTGCATCGATGCACAGCAG
Found at i:20611 original size:23 final size:23
Alignment explanation
Indices: 20581--20642 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
20571 TGCACTACAT
*
20581 GGTGCATCGATGCACTAGTGGTA
1 GGTGCATCGATGCACTAGTGGCA
*
20604 GGTGCATCAATGCACTAGTGGCA
1 GGTGCATCGATGCACTAGTGGCA
*
20627 GGTGCATGGATGCACT
1 GGTGCATCGATGCACT
20643 TTGACACCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (23 bp):
GGTGCATCGATGCACTAGTGGCA
Found at i:21813 original size:249 final size:249
Alignment explanation
Indices: 21532--21992 Score: 685
Period size: 249 Copynumber: 1.9 Consensus size: 249
21522 CCCAGTTTCA
* **
21532 TTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAGC-A-ACATTCATTGGATTT
1 TTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATACAAGC-TTGGATTT
* * * * *
21595 CAACTTCACGACGAATGATATCCAATTCCACGGCTCAACTTCACAACAAAGGGGCCATCCATAGT
65 CAACTTCACGACAAAGGATATCCAAGT-CAAGGCTCAACTTCACAACAAAGGGGCCATCCACAGT
*
21660 TTCAACTTCATGACGAAGGGAATCATGCAT-ACAAGCAACATCCATCTCTAGATTAGATTTCAAC
129 TTCAACTTCACGACGAAGGGAATCATGC-TCACAAGCAACATCCATCTCTAGATTAGATTTCAAC
21724 TTCACGACGAAGGATATCCAGCTCAAAGAATGAGTGTATGTCAATAAACTTTCAAGT
193 TTCACGACGAAGGATATCCAGCTCAAAGAATGAGTGTATGTCAATAAACTTTCAAGT
*
21781 TTCAGAGCCAATTTCAACTTCACGGTGAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTC
1 TTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTC
* * * *
21846 AACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGTCATCCACGGTTT
66 AACTTCACGACAAAGGATATCCAAGTCAAGGCTCAACTTCACAACAAAGGGGCCATCCACAGTTT
* * * ** *
21911 CAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTGATCTTTAGATTAGATTTCAACTTC
131 CAACTTCACGACGAAGGGAATCATGCTCACAAGCAACATCCATCTCTAGATTAGATTTCAACTTC
*
21976 ATGACGAAGGATATCCA
196 ACGACGAAGGATATCCA
21993 ATTCAAGGCT
Statistics
Matches: 188, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
248 1 0.01
249 151 0.80
250 32 0.17
251 4 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (249 bp):
TTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTC
AACTTCACGACAAAGGATATCCAAGTCAAGGCTCAACTTCACAACAAAGGGGCCATCCACAGTTT
CAACTTCACGACGAAGGGAATCATGCTCACAAGCAACATCCATCTCTAGATTAGATTTCAACTTC
ACGACGAAGGATATCCAGCTCAAAGAATGAGTGTATGTCAATAAACTTTCAAGT
Found at i:22006 original size:124 final size:124
Alignment explanation
Indices: 21837--22293 Score: 743
Period size: 124 Copynumber: 3.7 Consensus size: 124
21827 CAATACAAGC
* * * *
21837 TTGGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
*
21902 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTGATCTTTAGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAGA
* * *
21961 TTAGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* *
22026 CCACGGTTTCAACTTCACGACGAAGGGAATCGTTCTCACCAGTAACATTCATATTTAGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAGA
* *
22085 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCATAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
*
22150 CCACGGTTTCAACTTCACGACGAAGGGAATTGTGCTCACCAGTAACATTCATCTTTAGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAGA
* * * * *
22209 TTGGATTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGGTCCCT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
*
22274 CCACGATTTCAACTTCACGA
66 CCACGGTTTCAACTTCACGA
22294 TGAACGATAT
Statistics
Matches: 307, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 307 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAGA
Found at i:22049 original size:66 final size:65
Alignment explanation
Indices: 21966--22175 Score: 176
Period size: 66 Copynumber: 3.3 Consensus size: 65
21956 TTAGATTAGA
*
21966 TTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCATCCACG
1 TTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA-AATGAAGGGGCCATCCACG
22031 G
65 G
** * **
22032 TTTCAACTTCACGACGAAGGGA-AT-CGTTCTCACCA-G-T-AACATTCATATTTA---G--AT-
1 TTTCAACTTCACGACGAA-GGATATCCAAT-TCA--AGGCTCAAC-TTCAAATGAAGGGGCCATC
*
22086 --TGG
61 CACGG
* *
22089 ATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCATAACGAAGGGGCCATCCAC
1 -TTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA-AATGAAGGGGCCATCCAC
22154 GG
64 GG
22156 TTTCAACTTCACGACGAAGG
1 TTTCAACTTCACGACGAAGG
22176 GAATTGTGCT
Statistics
Matches: 108, Mismatches: 16, Indels: 40
0.66 0.10 0.24
Matches are distributed among these distances:
56 1 0.01
57 6 0.06
58 27 0.25
59 7 0.06
60 2 0.02
62 2 0.02
64 2 0.02
65 8 0.07
66 46 0.43
67 6 0.06
68 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (65 bp):
TTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCAAATGAAGGGGCCATCCACGG
Found at i:22515 original size:83 final size:83
Alignment explanation
Indices: 22363--22588 Score: 271
Period size: 84 Copynumber: 2.7 Consensus size: 83
22353 GATATCGTGT
* * *
22363 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTAT-TTTCCAACAAAAGACCTTTGAGTTCGACT
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGATATCTAT-C-A-AAAAGACCTTCGAGTTCGACT
*
22427 ACACTCAACTCCAAGGCA-CA
63 ACACTCAACTCAAAGGCACCA
* * * * * *
22447 TCATTTACATCATATCTCAAGGCTAGAAGGGTTATCTATCAATAAAGACCTTCGAGTTCGACTCC
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGATATCTATCAA-AAAGACCTTCGAGTTCGACTAC
*
22512 ACTCAGCTCAAAGGCACCA
65 ACTCAACTCAAAGGCACCA
* *
22531 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGATATCTGTC--AAAGACCTTCGAGTTCGA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGATATCTATCAAAAAGACCTTCGAGTTCGA
22589 TTCCTTTCAG
Statistics
Matches: 123, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
81 18 0.15
82 1 0.01
83 35 0.28
84 67 0.54
85 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (83 bp):
TCATTTGCAACATAGCTCAAGGCAAGAAGGGATATCTATCAAAAAGACCTTCGAGTTCGACTACA
CTCAACTCAAAGGCACCA
Found at i:22787 original size:35 final size:35
Alignment explanation
Indices: 22740--22817 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
22730 ACCTACGATT
*
22740 TTGACTTCACGAAGAAGAATATCGTACCCAATGGA
1 TTGACTTAACGAAGAAGAATATCGTACCCAATGGA
22775 TTGACTTAACGAAGAAGAATATCGTACCCAATGGA
1 TTGACTTAACGAAGAAGAATATCGTACCCAATGGA
22810 TTGACTTA
1 TTGACTTA
22818 GTGTCACAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGACTTAACGAAGAAGAATATCGTACCCAATGGA
Found at i:22987 original size:4 final size:4
Alignment explanation
Indices: 22978--23002 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
22968 TATCATATGA
22978 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
23003 ATTATTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:24737 original size:27 final size:28
Alignment explanation
Indices: 24707--24760 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
24697 TTCCTTTTTA
24707 ATTTTTGCATTTTTATTTTAGT-TATTC
1 ATTTTTGCATTTTTATTTTAGTGTATTC
* *
24734 ATTTTTTCCTTTTTATTTTAGTGTATT
1 ATTTTTGCATTTTTATTTTAGTGTATT
24761 TTTAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (28 bp):
ATTTTTGCATTTTTATTTTAGTGTATTC
Found at i:24762 original size:43 final size:44
Alignment explanation
Indices: 24680--24769 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 44
24670 TTTATTTCAA
24680 TTTAGTTATTCATTTTTTTCCTTTTTAATTTTTGCATTTTT-AT
1 TTTAGTTATTCATTTTTTTCCTTTTTAATTTTTGCATTTTTAAT
*
24723 TTTAGTTATTCA-TTTTTTCCTTTTT-ATTTTAGTGTATTTTTAAT
1 TTTAGTTATTCATTTTTTTCCTTTTTAATTTT--TGCATTTTTAAT
24767 TTT
1 TTT
24770 TTTGTTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
41 5 0.12
42 13 0.30
43 20 0.47
44 5 0.12
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.70
Consensus pattern (44 bp):
TTTAGTTATTCATTTTTTTCCTTTTTAATTTTTGCATTTTTAAT
Found at i:30456 original size:15 final size:15
Alignment explanation
Indices: 30438--30467 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30428 CCACGGTGCT
*
30438 CCCGGAATCCTGCGC
1 CCCGGAATCATGCGC
30453 CCCGGAATCATGCGC
1 CCCGGAATCATGCGC
30468 GATTGTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.43, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCATGCGC
Found at i:38617 original size:73 final size:72
Alignment explanation
Indices: 38540--38763 Score: 163
Period size: 73 Copynumber: 3.0 Consensus size: 72
38530 ATAAGAATGC
*
38540 ATATTAAATCAAACAAATCAAAGTTTAAATTAAGGAAACAAGTGGGGAAACAAATACTATAATAA
1 ATATTAAATCAAAC-AATCAAAGTTTAAATTAAGGAAACAAGTGGGGAAACAAATAATATAATAA
*
38605 TTCTATAT
65 TTCCATAT
* * * *
38613 ATATTACTAATAGCTAAAC-ACCAAATGTAGCTTAAATT-AGGAAA-AA-TGGAGAAACCAATAT
1 ATATTA--AAT--C-AAACAATCAAA-GT---TTAAATTAAGGAAACAAGTGGGGAAACAAATAA
38674 TATAATAATTCCATAT
57 TATAATAATTCCATAT
** * * * *
38690 ATTAAAAAAGT-AAACCA-CTATAGCTTAAATTAAGGAAACATGTGGGGAAACAAATAATATAAT
1 A-TATTAAA-TCAAACAATC-AAAGTTTAAATTAAGGAAACAAGTGGGGAAACAAATAATATAAT
* *
38753 GACTCCATAT
63 AATTCCATAT
38763 A
1 A
38764 ACCACTATAG
Statistics
Matches: 120, Mismatches: 15, Indels: 32
0.72 0.09 0.19
Matches are distributed among these distances:
70 7 0.06
71 6 0.05
72 1 0.01
73 39 0.32
74 3 0.03
75 3 0.03
76 7 0.06
77 32 0.27
78 9 0.08
79 6 0.05
80 7 0.06
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (72 bp):
ATATTAAATCAAACAATCAAAGTTTAAATTAAGGAAACAAGTGGGGAAACAAATAATATAATAAT
TCCATAT
Found at i:38767 original size:61 final size:61
Alignment explanation
Indices: 38702--38824 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
38692 TAAAAAAGTA
** *
38702 AACCACTATAGCTTAAATTAAGGAAACATGTGGGGAAACAAATAATATAATGACTCCATAT
1 AACCACTATAGCTTAAATTAAGGAAACACATGGGAAAACAAATAATATAATGACTCCATAT
* * * *
38763 AACCACTATAGCTTAAATTAAGGATACACATGGGAAAACAAATATTATAATGATTTCATAT
1 AACCACTATAGCTTAAATTAAGGAAACACATGGGAAAACAAATAATATAATGACTCCATAT
38824 A
1 A
38825 TTATATATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (61 bp):
AACCACTATAGCTTAAATTAAGGAAACACATGGGAAAACAAATAATATAATGACTCCATAT
Found at i:39408 original size:2 final size:2
Alignment explanation
Indices: 39401--39466 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
39391 TGGTTTTGAG
39401 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39443 GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
39467 ATAGAGATCC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40172 original size:26 final size:24
Alignment explanation
Indices: 40140--40204 Score: 94
Period size: 26 Copynumber: 2.6 Consensus size: 24
40130 GTGGCTGTTC
40140 TGGTCCAAGCGGTGGTGGCTATCGAG
1 TGGTCCAAGCGGTGGTGGC-AT-GAG
*
40166 TGGTCCAAGCGGCGGTGGCATGAG
1 TGGTCCAAGCGGTGGTGGCATGAG
*
40190 TGGTCCAAGTGGTGG
1 TGGTCCAAGCGGTGG
40205 CGGTTGTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 16 0.44
25 2 0.06
26 18 0.50
ACGTcount: A:0.15, C:0.18, G:0.45, T:0.22
Consensus pattern (24 bp):
TGGTCCAAGCGGTGGTGGCATGAG
Found at i:40194 original size:50 final size:50
Alignment explanation
Indices: 40101--40204 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
40091 GCTGGCAGCA
* * *
40101 GTGGTGGTTATTGAGTGATCCAAGAGGCGGTGGCTGTTCTGGTCCAAGCG
1 GTGGTGGCTATCGAGTGATCCAAGAGGCGGTGGCTGTACTGGTCCAAGCG
* * * *
40151 GTGGTGGCTATCGAGTGGTCCAAGCGGCGGTGGCATG-AGTGGTCCAAGTG
1 GTGGTGGCTATCGAGTGATCCAAGAGGCGGTGGC-TGTACTGGTCCAAGCG
40201 GTGG
1 GTGG
40205 CGGTTGTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
50 44 0.96
51 2 0.04
ACGTcount: A:0.15, C:0.16, G:0.43, T:0.25
Consensus pattern (50 bp):
GTGGTGGCTATCGAGTGATCCAAGAGGCGGTGGCTGTACTGGTCCAAGCG
Found at i:40195 original size:24 final size:24
Alignment explanation
Indices: 40112--40198 Score: 95
Period size: 24 Copynumber: 3.5 Consensus size: 24
40102 TGGTGGTTAT
* *
40112 TGAGTGATCCAAGAGGCGGTGGC-
1 TGAGTGGTCCAAGCGGCGGTGGCA
** *
40135 TGTTCTGGTCCAAGCGGTGGTGGCTA
1 TG-AGTGGTCCAAGCGGCGGTGGC-A
40161 TCGAGTGGTCCAAGCGGCGGTGGCA
1 T-GAGTGGTCCAAGCGGCGGTGGCA
40186 TGAGTGGTCCAAG
1 TGAGTGGTCCAAG
40199 TGGTGGCGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.04
24 28 0.54
25 2 0.04
26 19 0.37
27 1 0.02
ACGTcount: A:0.17, C:0.20, G:0.41, T:0.22
Consensus pattern (24 bp):
TGAGTGGTCCAAGCGGCGGTGGCA
Found at i:40434 original size:15 final size:16
Alignment explanation
Indices: 40411--40440 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40401 AAAATAAAAT
40411 ATAATTATAAATAATA
1 ATAATTATAAATAATA
40427 ATAA-TATAAATAAT
1 ATAATTATAAATAAT
40441 GACAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATTATAAATAATA
Found at i:40912 original size:115 final size:115
Alignment explanation
Indices: 40705--41021 Score: 449
Period size: 115 Copynumber: 2.8 Consensus size: 115
40695 GAATTGAGGC
** * * *
40705 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAAGAAGAGACCTTTTCTGCTTA
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAG-AGAGACATGTTCCGCTTA
* * * * * *
40770 CTCTGAAGGAAATATCAGAT-ATGAAGGAGTTTGA-TCCATTGAATCGGGGA
65 CACTGAAGGGAATATCAGATCTTAAAGGAGTTCGATTCC-TTGAATCAGGGA
* *
40820 AGACTTGTTCCACTTACTATGAAGGGAATATCAAATCTTGGGAAAGAGATACATGTTCCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACATGTTCCGCTTAC
* *
40885 ACTGAAGGGAATATCAAATCTTAAAGGAGTTCGATTCCTTGAATCAGGGC
66 ACTGAAGGGAATATCAGATCTTAAAGGAGTTCGATTCCTTGAATCAGGGA
*
40935 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACATGTTTCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACATGTTCCGCTTAC
*
41000 ACTAAAGGGAATATCAGATCTT
66 ACTGAAGGGAATATCAGATCTT
41022 GGGAAAGAGA
Statistics
Matches: 180, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
114 31 0.17
115 146 0.81
116 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (115 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACATGTTCCGCTTAC
ACTGAAGGGAATATCAGATCTTAAAGGAGTTCGATTCCTTGAATCAGGGA
Found at i:41021 original size:48 final size:48
Alignment explanation
Indices: 40935--41069 Score: 207
Period size: 48 Copynumber: 2.8 Consensus size: 48
40925 GAATCAGGGC
* * *
40935 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAG
1 AGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGGAAAGAG
* * *
40983 AGACATGTTTCGCTTACACTAAAGGGAATATCAGATCTTGGGAAAGAG
1 AGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGGAAAGAG
*
41031 AGACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTT
1 AGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTT
41070 ACAGGAGTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (48 bp):
AGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGGAAAGAG
Found at i:41023 original size:163 final size:163
Alignment explanation
Indices: 40841--41196 Score: 595
Period size: 163 Copynumber: 2.2 Consensus size: 163
40831 ACTTACTATG
* *
40841 AAGGGAATATCAAATCTTGGGAAAGAGATACATGTTCCGCTTACACTGAAGGGAATATCAAATCT
1 AAGGGAATATCAGATCTTGGGAAAGAGAGACATGTTCCGCTTACACTGAAGGGAATATCAAATCT
*
40906 TAAAGGAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAAT
66 TAAAGGAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAAT
*
40971 CTTGGGAAAGAGAGACATGTTTCGCTTACACTA
131 CTTGGGAAAGAGAGACATGTTCCGCTTACACTA
* * *
41004 AAGGGAATATCAGATCTTGGGAAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCT
1 AAGGGAATATCAGATCTTGGGAAAGAGAGACATGTTCCGCTTACACTGAAGGGAATATCAAATCT
* * *
41069 TACAGGAGTTTGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCACAT
66 TAAAGGAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAAT
* *
41134 CTTGGGAAAGAGAGACATGTTCCGCTTACTCTG
131 CTTGGGAAAGAGAGACATGTTCCGCTTACACTA
*
41167 AAGGGAATATCAGATATTGGGAAAGAGAGA
1 AAGGGAATATCAGATCTTGGGAAAGAGAGA
41197 GACCTTATCT
Statistics
Matches: 180, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
163 180 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (163 bp):
AAGGGAATATCAGATCTTGGGAAAGAGAGACATGTTCCGCTTACACTGAAGGGAATATCAAATCT
TAAAGGAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTAAAGGGAATATCAAAT
CTTGGGAAAGAGAGACATGTTCCGCTTACACTA
Found at i:41174 original size:48 final size:50
Alignment explanation
Indices: 41098--41234 Score: 181
Period size: 48 Copynumber: 2.8 Consensus size: 50
41088 GAATCAGGGC
* * *
41098 AGACTTGTTCCACTTACTCTAAAGGGAATATCACATCTTGGG-AA-AGAG
1 AGACATGTTCCGCTTACTCTAAAGGGAATATCAGATCTTGGGAAAGAGAG
* *
41146 AGACATGTTCCGCTTACTCTGAAGGGAATATCAGATATTGGGAAAGAGAG
1 AGACATGTTCCGCTTACTCTAAAGGGAATATCAGATCTTGGGAAAGAGAG
* *
41196 AGACCT-TATCTGCTTACTCTAAAGGGAATATCAGATCTT
1 AGACATGT-TCCGCTTACTCTAAAGGGAATATCAGATCTT
41235 ACAAGAGTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
48 37 0.48
49 3 0.04
50 37 0.48
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (50 bp):
AGACATGTTCCGCTTACTCTAAAGGGAATATCAGATCTTGGGAAAGAGAG
Found at i:41241 original size:48 final size:48
Alignment explanation
Indices: 41098--41234 Score: 152
Period size: 50 Copynumber: 2.8 Consensus size: 48
41088 GAATCAGGGC
* * * *
41098 AGACTTGTTCCACTTACTCTAAAGGGAATATCACATCTTGGGAA-AGAG
1 AGACATGTTCCGCTTACTCTAAAGGGAATATCAGATCTT-GAAAGAGAG
* *
41146 AGACATGTTCCGCTTACTCTGAAGGGAATATCAGATATTGGGAAAGAGAG
1 AGACATGTTCCGCTTACTCTAAAGGGAATATCAGATCTT--GAAAGAGAG
* *
41196 AGACCT-TATCTGCTTACTCTAAAGGGAATATCAGATCTT
1 AGACATGT-TCCGCTTACTCTAAAGGGAATATCAGATCTT
41235 ACAAGAGTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
48 34 0.45
49 5 0.07
50 37 0.49
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (48 bp):
AGACATGTTCCGCTTACTCTAAAGGGAATATCAGATCTTGAAAGAGAG
Found at i:44061 original size:20 final size:22
Alignment explanation
Indices: 44019--44061 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
44009 TTTACGCATG
44019 TTTTTATTTAAGTATGCTTTAAT
1 TTTTTATTT-AGTATGCTTTAAT
44042 TTTTTATTT-GTATG-TTTAAT
1 TTTTTATTTAGTATGCTTTAAT
44062 CTTAGGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
23 9 0.45
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.65
Consensus pattern (22 bp):
TTTTTATTTAGTATGCTTTAAT
Found at i:44847 original size:195 final size:195
Alignment explanation
Indices: 44515--44905 Score: 737
Period size: 195 Copynumber: 2.0 Consensus size: 195
44505 TGATGTTGAG
44515 TTTGATTAATGTGATTAGCATGTATATATTATATCCTTAAATGTTATTTTCAACTTTAGGTAAAT
1 TTTGATTAATGTGATTAGCATGTATATATTATATCCTTAAATGTTATTTTCAACTTTAGGTAAAT
* *
44580 AATATTAGTATTATTTGTAGTTATTAATTAATTTAGCGTAAAAAAATATTGATTACATGTTAATA
66 AATACTAGTATTATTTGTAGTTATTAATTAATTTAGAGTAAAAAAATATTGATTACATGTTAATA
44645 TAATTTTAATAAGTTTTTTCAGGGTATAGTTATATGTATATTTTAGACTAAAATATTTTTTCGAA
131 TAATTTTAATAAGTTTTTTCAGGGTATAGTTATATGTATATTTTAGACTAAAATATTTTTTCGAA
44710 TTTGATTAATGTGATTAGCATGTATATATTATATCCTTAAATGTTATTTTCAACTTTAGGTAAAT
1 TTTGATTAATGTGATTAGCATGTATATATTATATCCTTAAATGTTATTTTCAACTTTAGGTAAAT
*
44775 AATACTAGTATTATTTGTAGTTATTAATTGATTTAGAGTAAAAAAATATTGATTACATGTTAATA
66 AATACTAGTATTATTTGTAGTTATTAATTAATTTAGAGTAAAAAAATATTGATTACATGTTAATA
* *
44840 TAATTTTAATAATTTTTTTTAGGGTATAGTTATATGTATATTTTAGACTAAAATATTTTTTCGAA
131 TAATTTTAATAAGTTTTTTCAGGGTATAGTTATATGTATATTTTAGACTAAAATATTTTTTCGAA
44905 T
1 T
44906 GTTTGACATT
Statistics
Matches: 191, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
195 191 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (195 bp):
TTTGATTAATGTGATTAGCATGTATATATTATATCCTTAAATGTTATTTTCAACTTTAGGTAAAT
AATACTAGTATTATTTGTAGTTATTAATTAATTTAGAGTAAAAAAATATTGATTACATGTTAATA
TAATTTTAATAAGTTTTTTCAGGGTATAGTTATATGTATATTTTAGACTAAAATATTTTTTCGAA
Found at i:48995 original size:12 final size:13
Alignment explanation
Indices: 48973--49001 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
48963 TTTATACTTG
48973 CATTTAGCATTTA
1 CATTTAGCATTTA
48986 CATTTA-CATTTA
1 CATTTAGCATTTA
48998 CATT
1 CATT
49002 GCATGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.48
Consensus pattern (13 bp):
CATTTAGCATTTA
Found at i:51108 original size:2 final size:2
Alignment explanation
Indices: 51101--51147 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
51091 TCCGCATACA
*
51101 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51143 AT AT A
1 AT AT A
51148 CAATAAAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52669 original size:16 final size:18
Alignment explanation
Indices: 52644--52677 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
52634 AATGGGATAG
52644 AAATGTATGAAG-AGTGA
1 AAATGTATGAAGCAGTGA
52661 AAATG-ATGAAGCAGTGA
1 AAATGTATGAAGCAGTGA
52678 CAGTGCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.03, G:0.29, T:0.21
Consensus pattern (18 bp):
AAATGTATGAAGCAGTGA
Found at i:53550 original size:36 final size:36
Alignment explanation
Indices: 53498--53641 Score: 130
Period size: 36 Copynumber: 4.0 Consensus size: 36
53488 TGAGACTGGG
* * *
53498 GCAAGTCAATATTAAGCCTTCACTGAAGAGTAGAGAA
1 GCAA-TCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
* * *
53535 GCAATCAATCTTAAGCCTTCACCAAAGAGAATTGAA
1 GCAATCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
* * * * *
53571 GC-A-CCATCCTAAGCCTTAACCGGAGAATAGTGAA
1 GCAATCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
* * * *
53605 GCAAACCATCTTAAGCCTTCACAGAAAAGTAGTGAA
1 GCAATCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
53641 G
1 G
53642 AAAATCCATC
Statistics
Matches: 85, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
34 25 0.29
35 2 0.02
36 54 0.64
37 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (36 bp):
GCAATCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
Found at i:53820 original size:116 final size:116
Alignment explanation
Indices: 53598--53893 Score: 427
Period size: 116 Copynumber: 2.6 Consensus size: 116
53588 AACCGGAGAA
* * * * * *
53598 TAGTGAAGCAAA-CCATCTTAAGCCTTCACAGAAAAGTAGTGAAGAAAATCCATCAGTAAGCATT
1 TAGTGAAGCAAATCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATTCATCAATAAGCCTT
* * *
53662 CCGAGCATGATGATTAAGTCCTCCGGGTAATCTTAAACCTTCACTAAATAG
66 CCGAGCATGATGATTAAGTCCTCCGGGCAATCTTAAACCTTCACCAAAGAG
** *
53713 TAGTGAAGCAAATTTAT-TATAAGCCTTCACGGAAGAGTAGTGAAGCAAATTCATCAATAAGCCT
1 TAGTGAAGCAAATCAATCT-TAAGCCTTCACAGAAGAGTAGTGAAGCAAATTCATCAATAAGCCT
* *
53777 TCCGAGCATGATGATTAAGTCCTCCGGGCCATCTTAAACCTTCACCGAAGAG
65 TCCGAGCATGATGATTAAGTCCTCCGGGCAATCTTAAACCTTCACCAAAGAG
*
53829 TAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTCATC-ATAAGCCTT
1 TAGTGAAGCAAATCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATTCATCAATAAGCCTT
53893 C
66 C
53894 ACGGAAGAGT
Statistics
Matches: 162, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
115 23 0.14
116 138 0.85
117 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (116 bp):
TAGTGAAGCAAATCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATTCATCAATAAGCCTT
CCGAGCATGATGATTAAGTCCTCCGGGCAATCTTAAACCTTCACCAAAGAG
Found at i:53848 original size:37 final size:37
Alignment explanation
Indices: 53807--54152 Score: 223
Period size: 37 Copynumber: 9.1 Consensus size: 37
53797 CCTCCGGGCC
*
53807 ATCTTAAACCTTCACCGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
*
53844 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTC-
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA-TCA
* * *
53881 ATCATAAGCCTTCACGGAAGAGTAGTGAAACAAATTC-
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA-TCA
* * * * *** **** *
53918 ATCAGTAAGCCTTCCGAGCATGATGATTAAGT-CCTCCGGGCC
1 ATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTGAAGCAAATCA
*
53960 ATCTTAAACCTTCACCGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
* *
53997 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
* * * * *** **** *
54034 ATCAGTAAGCCTTCCGAGCATGATGATTTAGT-CCTCCGGGCC
1 ATC-TTAAGCCTT-C-A-C-CGAAGA-GTAGTGAAGCAAATCA
* *
54076 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGTAAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAG-CAAATCA
54114 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
54151 AT
1 AT
54153 TTCAAGTCTC
Statistics
Matches: 232, Mismatches: 60, Indels: 34
0.71 0.18 0.10
Matches are distributed among these distances:
36 7 0.03
37 124 0.53
38 50 0.22
39 4 0.02
40 4 0.02
41 18 0.08
42 18 0.08
43 7 0.03
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
Found at i:53879 original size:153 final size:153
Alignment explanation
Indices: 53690--54047 Score: 626
Period size: 153 Copynumber: 2.3 Consensus size: 153
53680 TCCTCCGGGT
* * * *
53690 AATCTTAAACCTTCACTAAATAGTAGTGAAGCAAATTTATTATAAGCCTTCACGGAAGAGTAGTG
1 AATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAATTCATCATAAGCCTTCACGGAAGAGTAGTG
*
53755 AAGCAAATTCATCAATAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCCATCTTAAACCTTC
66 AAACAAATTCATCAATAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCCATCTTAAACCTTC
53820 ACCGAAGAGTAGTGAAGCAAATC
131 ACCGAAGAGTAGTGAAGCAAATC
*
53843 AATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTCATCATAAGCCTTCACGGAAGAGTAGTG
1 AATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAATTCATCATAAGCCTTCACGGAAGAGTAGTG
*
53908 AAACAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCCATCTTAAACCTTC
66 AAACAAATTCATCAATAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCCATCTTAAACCTTC
53973 ACCGAAGAGTAGTGAAGCAAATC
131 ACCGAAGAGTAGTGAAGCAAATC
* *
53996 AATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTC
1 AATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAATTCATCA-TAAGCCTTC
54048 CGAGCATGAT
Statistics
Matches: 194, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
153 185 0.95
154 9 0.05
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (153 bp):
AATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAATTCATCATAAGCCTTCACGGAAGAGTAGTG
AAACAAATTCATCAATAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCCATCTTAAACCTTC
ACCGAAGAGTAGTGAAGCAAATC
Found at i:53964 original size:116 final size:116
Alignment explanation
Indices: 53844--54149 Score: 497
Period size: 116 Copynumber: 2.6 Consensus size: 116
53834 AAGCAAATCA
* * *
53844 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTC-ATCATAAGCCTTCACGGAAGAGTAGTG
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA-TCAATCTTAAGCCTTCACCGAAGAGTAGTG
* *
53908 AAACAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
65 AAGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* *
53960 ATCTTAAACCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAGAGTAGTGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
*
54025 AGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATTTAGTCCTCCGGGCC
66 AGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
* *
54076 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGTAAAATCAATCTTAAGCCTTCACCGAAGAGTAGTG
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAG-CAAATCAATCTTAAGCCTTCACCGAAGAGTAGTG
54141 AAGCAAATC
65 AAGCAAATC
54150 AATTTCAAGT
Statistics
Matches: 176, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
115 2 0.01
116 133 0.76
117 41 0.23
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (116 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
AGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGGCC
Found at i:54099 original size:269 final size:269
Alignment explanation
Indices: 53542--54149 Score: 886
Period size: 269 Copynumber: 2.3 Consensus size: 269
53532 GAAGCAATCA
* * * * * * *
53542 ATCTTAAGCCTTCACCAAAGAGAATTGAAGC--A-CCATCCTAAGCCTTAACCGGAGAATAGTGA
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
*
53604 AGCAAA-CCATCTTAAGCCTTCACAGAAAAGTAGTGAAGAAAATCCATCAGTAAGCATTCCGAGC
66 AGCAAATCCATCATAAGCCTTCACAGAAAAGTAGTGAAGAAAATCCATCAGTAAGCATTCCGAGC
* * * **
53668 ATGATGATTAAGTCCTCCGGGTAATCTTAAACCTTCACTAAATAGTAGTGAAGCAAATTTATTAT
131 ATGATGATTAAGTCCTCCGGGCAATCTTAAACCTTCACCAAAGAGTAGTGAAGCAAATCAATTAT
** *
53733 AAGCCTTCACGGAAGAGTAGTGAAGCAAATTCATCAATAAGCCTTCCGAGCATGATGATTAAGTC
196 AAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAATAAGCCTTCCGAGCATGATGATTAAGTC
53798 CTCCGGGCC
261 CTCCGGGCC
* * *
53807 ATCTTAAACCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
* * * * *
53872 AGCAAATTCATCATAAGCCTTCACGGAAGAGTAGTGAA-ACAAATTCATCAGTAAGCCTTCCGAG
66 AGCAAATCCATCATAAGCCTTCACAGAAAAGTAGTGAAGA-AAATCCATCAGTAAGCATTCCGAG
* *
53936 CATGATGATTAAGTCCTCCGGGCCATCTTAAACCTTCACCGAAGAGTAGTGAAGCAAATCAATCT
130 CATGATGATTAAGTCCTCCGGGCAATCTTAAACCTTCACCAAAGAGTAGTGAAGCAAATCAAT-T
* *
54001 -TAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATTTAG
194 ATAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAATAAGCCTTCCGAGCATGATGATTAAG
54065 TCCTCCGGGCC
259 TCCTCCGGGCC
*
54076 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGTAAAATCAATCTTAAGCCTTCACCGAAGAGTAGTG
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAG-CAAATCAATCTTAAGCCTTCACCGAAGAGTAGTG
54141 AAGCAAATC
65 AAGCAAATC
54150 AATTTCAAGT
Statistics
Matches: 303, Mismatches: 33, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
265 27 0.09
267 1 0.00
268 31 0.10
269 203 0.67
270 41 0.14
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (269 bp):
ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
AGCAAATCCATCATAAGCCTTCACAGAAAAGTAGTGAAGAAAATCCATCAGTAAGCATTCCGAGC
ATGATGATTAAGTCCTCCGGGCAATCTTAAACCTTCACCAAAGAGTAGTGAAGCAAATCAATTAT
AAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAATAAGCCTTCCGAGCATGATGATTAAGTC
CTCCGGGCC
Found at i:54122 original size:38 final size:37
Alignment explanation
Indices: 54076--54152 Score: 127
Period size: 38 Copynumber: 2.1 Consensus size: 37
54066 CCTCCGGGCC
54076 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGTAAAATCA
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAG-AAAATCA
* *
54114 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGAAAATCA
54151 AT
1 AT
54153 TTCAAGTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
37 8 0.22
38 29 0.78
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCAAAGAGTAGTGAAGAAAATCA
Found at i:55481 original size:20 final size:22
Alignment explanation
Indices: 55439--55481 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
55429 TTTACGCATG
55439 TTTTTATTTAAGTATGCTTTAAT
1 TTTTTATTT-AGTATGCTTTAAT
55462 TTTTTATTT-GTATG-TTTAAT
1 TTTTTATTTAGTATGCTTTAAT
55482 CTTAGGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
23 9 0.45
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.65
Consensus pattern (22 bp):
TTTTTATTTAGTATGCTTTAAT
Found at i:55687 original size:22 final size:19
Alignment explanation
Indices: 55662--55711 Score: 50
Period size: 22 Copynumber: 2.6 Consensus size: 19
55652 TGATATTTTA
55662 TATATTATTTAATAGTTATAAT
1 TATATTATTT-AT-GTT-TAAT
*
55684 TATAGTATTT-TGTTTAAT
1 TATATTATTTATGTTTAAT
55702 TA-ATTATTTA
1 TATATTATTTA
55712 CATGCAAGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.24
18 6 0.24
19 3 0.12
20 1 0.04
22 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TATATTATTTATGTTTAAT
Found at i:68238 original size:150 final size:145
Alignment explanation
Indices: 68066--68342 Score: 355
Period size: 150 Copynumber: 1.9 Consensus size: 145
68056 CAAATCAAAG
* * *
68066 CTTAAATTAAGGAAACAAGTGGGGAAACAAATACTATAATAATTCTATATATATTATTAATAACT
1 CTTAAATTAAGGAAACAAGTGGGGAAACAAATAATATAATAA--CTACATATATTA--AAAAACT
*
68131 AAACACCAAAC-ATAGCTTAAATTAAGG-A-AAGT-GGAGAAACCAATATTATAATAATTCCATA
62 -AA-ACC--ACTATAGCTTAAATTAAGGAACAAGTGGGA-AAACAAATATTATAATAATTCCATA
68192 TATTAAAAAAGTAAACCATTATAA
122 TATTAAAAAAGTAAACCATTATAA
* * *
68216 CTTAAATTAAGGAAACATGTGGGGAAACAAATAATATAATGACTCCATATATTAAAAAACTAAAC
1 CTTAAATTAAGGAAACAAGTGGGGAAACAAATAATATAATAACTACATATATTAAAAAACTAAAC
* *
68281 CACTATAGCTTAAATTAAGGACACAAGTGGGAAAACAAATATTATAATGATTTCATATATTA
66 CACTATAGCTTAAATTAAGGA-ACAAGTGGGAAAACAAATATTATAATAATTCCATATATTA
68343 TGTTTTTTTT
Statistics
Matches: 113, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
142 2 0.02
143 16 0.14
144 3 0.03
145 3 0.03
146 37 0.33
147 3 0.03
148 10 0.09
150 39 0.35
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.28
Consensus pattern (145 bp):
CTTAAATTAAGGAAACAAGTGGGGAAACAAATAATATAATAACTACATATATTAAAAAACTAAAC
CACTATAGCTTAAATTAAGGAACAAGTGGGAAAACAAATATTATAATAATTCCATATATTAAAAA
AGTAAACCATTATAA
Found at i:68329 original size:73 final size:73
Alignment explanation
Indices: 68064--68342 Score: 280
Period size: 73 Copynumber: 3.8 Consensus size: 73
68054 AACAAATCAA
* * ** *
68064 AGCTTAAATTAAGGAAACAAGTGGGGAAACAAATACTATAATAATTCTATATATATTATTAATAA
1 AGCTTAAATTAAGGAAACAAGTGGGAAAACAAATATTATAATAA--CTCCATATATTA--AAAAA
68129 CTAAACACCAAAC-AT
62 CT-AA-ACC--ACTAT
* * *
68144 AGCTTAAATTAAGG--A-AAGT-GGAGAAACCAATATTATAATAATTCCATATATTAAAAAAGTA
1 AGCTTAAATTAAGGAAACAAGTGGGA-AAACAAATATTATAATAACTCCATATATTAAAAAACTA
*
68205 AACCATTAT
65 AACCACTAT
* * * * *
68214 AACTTAAATTAAGGAAACATGTGGGGAAACAAATAATATAATGACTCCATATATTAAAAAACTAA
1 AGCTTAAATTAAGGAAACAAGTGGGAAAACAAATATTATAATAACTCCATATATTAAAAAACTAA
68279 ACCACTAT
66 ACCACTAT
* * * *
68287 AGCTTAAATTAAGGACACAAGTGGGAAAACAAATATTATAATGATTTCATATATTA
1 AGCTTAAATTAAGGAAACAAGTGGGAAAACAAATATTATAATAACTCCATATATTA
68343 TGTTTTTTTT
Statistics
Matches: 168, Mismatches: 25, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
69 1 0.01
70 15 0.09
71 3 0.02
72 3 0.02
73 98 0.58
74 2 0.01
75 9 0.05
76 2 0.01
77 20 0.12
78 1 0.01
80 14 0.08
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (73 bp):
AGCTTAAATTAAGGAAACAAGTGGGAAAACAAATATTATAATAACTCCATATATTAAAAAACTAA
ACCACTAT
Found at i:68928 original size:2 final size:2
Alignment explanation
Indices: 68921--68950 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
68911 GTTTTGAGGA
68921 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
68951 TATATATCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:69616 original size:26 final size:26
Alignment explanation
Indices: 69584--69679 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 26
69574 TGGTAGCAGT
*
69584 GGTGGCTATTGAGTGGTCCAAGAGGC
1 GGTGGCTATTGAGTGGTCCAAGCGGC
* * *
69610 GGTGGCTGTT--CTGGTCCAAGCGGT
1 GGTGGCTATTGAGTGGTCCAAGCGGC
*
69634 GGTGGCTGTTGAGTGGTCCAAGCGGC
1 GGTGGCTATTGAGTGGTCCAAGCGGC
*
69660 GGTGGC-A-TGAGTGGTTCAAG
1 GGTGGCTATTGAGTGGTCCAAG
69680 TGGTTGCGAC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
24 33 0.55
26 27 0.45
ACGTcount: A:0.15, C:0.17, G:0.44, T:0.25
Consensus pattern (26 bp):
GGTGGCTATTGAGTGGTCCAAGCGGC
Found at i:69693 original size:50 final size:50
Alignment explanation
Indices: 69592--69693 Score: 116
Period size: 50 Copynumber: 2.0 Consensus size: 50
69582 GTGGTGGCTA
* * *
69592 TTGAGTGGTCCAAGAGGCGGTGGCTGTTCTGGTCCAAGCGGTGGTGGCTG
1 TTGAGTGGTCCAAGAGGCGGTGGCTGTACTGGTCCAAGCGGTGGCGACTG
* * * * *
69642 TTGAGTGGTCCAAGCGGCGGTGGCATG-AGTGGTTCAAGTGGTTGCGACTG
1 TTGAGTGGTCCAAGAGGCGGTGGC-TGTACTGGTCCAAGCGGTGGCGACTG
69692 TT
1 TT
69694 CTGGAAACCC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 41 0.95
51 2 0.05
ACGTcount: A:0.14, C:0.17, G:0.42, T:0.27
Consensus pattern (50 bp):
TTGAGTGGTCCAAGAGGCGGTGGCTGTACTGGTCCAAGCGGTGGCGACTG
Found at i:83099 original size:18 final size:18
Alignment explanation
Indices: 83068--83140 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
83058 ACTGAATATT
*
83068 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
* *
83086 TATCCCCAAGGACCACTAA
1 TGTCCCGAAGGACCACT-A
* *
83105 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
83124 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
83141 CCTTAAGAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 29 0.66
19 2 0.05
20 13 0.30
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:83892 original size:19 final size:19
Alignment explanation
Indices: 83870--83914 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
83860 AGGTGCATTG
*
83870 ATGCACTCCTCATGCATCA
1 ATGCACTCCTAATGCATCA
*
83889 ATGCACTCCTAATGCATCG
1 ATGCACTCCTAATGCATCA
83908 ATGCACT
1 ATGCACT
83915 AATTGCATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (19 bp):
ATGCACTCCTAATGCATCA
Found at i:83967 original size:21 final size:21
Alignment explanation
Indices: 83938--83980 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
83928 GTTCAATGTT
*
83938 TTGATTGTGCATCGATACACA
1 TTGAATGTGCATCGATACACA
*
83959 TTGAATGTGCATCGATGCACA
1 TTGAATGTGCATCGATACACA
83980 T
1 T
83981 AACCCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
TTGAATGTGCATCGATACACA
Found at i:89825 original size:18 final size:18
Alignment explanation
Indices: 89764--89827 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
89754 AATATTTGTC
* *
89764 CCGAAGGACCACTATATC
1 CCGAAGGACCACTATGTT
89782 CCGAAGG---ACT-TGATT
1 CCGAAGGACCACTATG-TT
* *
89797 CCGGAGAACCACTATGTT
1 CCGAAGGACCACTATGTT
89815 CCGAAGGACCACT
1 CCGAAGGACCACT
89828 GTATATGTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
18 23 0.66
19 2 0.06
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (18 bp):
CCGAAGGACCACTATGTT
Found at i:90092 original size:23 final size:21
Alignment explanation
Indices: 90037--90093 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 21
90027 TATATTTCTC
90037 ATCACTTTTCATATAAACATGT
1 ATCAC-TTTCATATAAACATGT
*
90059 ATTTCAC-TTCATATACCACATGT
1 A--TCACTTTCATATA-AACATGT
90082 GATCACTTTCAT
1 -ATCACTTTCAT
90094 TATTTCACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
22 13 0.45
23 11 0.38
24 5 0.17
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (21 bp):
ATCACTTTCATATAAACATGT
Found at i:98035 original size:14 final size:15
Alignment explanation
Indices: 98016--98044 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
98006 AAAGTTATAA
98016 TTATATA-AAAATAT
1 TTATATATAAAATAT
98030 TTATATATAAAATAT
1 TTATATATAAAATAT
98045 AAATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTATATATAAAATAT
Found at i:98340 original size:3 final size:3
Alignment explanation
Indices: 98334--98392 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
98324 TATTTTTATA
* * * *
98334 AAT AAT AA- AAT AAT AAT AAT GA- AAT AAT AATT AAA AAA AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
98378 AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT A
98393 TTGCAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:98348 original size:11 final size:11
Alignment explanation
Indices: 98333--98392 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
98323 TTATTTTTAT
98333 AAATAATAA-A
1 AAATAATAATA
*
98343 ATAATAATAATG
1 A-AATAATAATA
98355 AAATAATAATTA
1 AAATAATAA-TA
*
98367 AAA-AA-AAAA
1 AAATAATAATA
98376 ATAATAATAATA
1 A-AATAATAATA
98388 AAATA
1 AAATA
98393 TTGCAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 2 0.05
10 5 0.12
11 24 0.60
12 9 0.22
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (11 bp):
AAATAATAATA
Found at i:98390 original size:19 final size:19
Alignment explanation
Indices: 98337--98390 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
98327 TTTTATAAAT
**
98337 AATAA-AATAATAATAATGA
1 AATAATAATAATAA-AAAAA
98356 AATAATAATTAA-AAAAAAA
1 AATAATAA-TAATAAAAAAA
98375 AATAATAATAATAAAA
1 AATAATAATAATAAAA
98391 TATTGCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 3 0.10
19 20 0.67
20 4 0.13
21 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AATAATAATAATAAAAAAA
Found at i:98424 original size:42 final size:41
Alignment explanation
Indices: 98333--98416 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
98323 TTATTTTTAT
98333 AAATAATAAAATAATAATAATGAAATAATAATTAAAAAAAA
1 AAATAATAAAATAATAATAATGAAATAATAATTAAAAAAAA
* * *
98374 AAATAATAATAATAA-AATATTGCAAATAATGATTAAAATAAA
1 AAATAATAA-AATAATAATAATG-AAATAATAATTAAAAAAAA
98416 A
1 A
98417 GGAAATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 15 0.39
42 23 0.61
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (41 bp):
AAATAATAAAATAATAATAATGAAATAATAATTAAAAAAAA
Found at i:100225 original size:75 final size:76
Alignment explanation
Indices: 99882--100533 Score: 972
Period size: 73 Copynumber: 8.8 Consensus size: 76
99872 AGGCTTTAAG
* * * * *
99882 ATCAAAAAGCTCCCGAAGACTTTTTGAAAACATCATGCACTGTAGGTCTTACAGGTGACCCAGA-
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
* *
99946 GGTTT--TAAG
66 GGTTTGAAAAC
*
99955 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGTAGGACTTACAGATGACCCTGA-
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
* *
100019 GGTTT--TAAG
66 GGTTTGAAAAC
* * * * *
100028 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACAACATGAAATGTAGGTCTTACAGATGACCCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
100093 GGTTTGAAAAC
66 GGTTTGAAAAC
100104 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
100169 GGTTTGAAAAC
66 GGTTTGAAAAC
* *
100180 ATC-AAAAGCTACCGAAGGCTTTTTGGAAACATCATTCACTGTAGGACTTACAGATGACCCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
100244 GGTTTTGAAAAC
66 GG-TTTGAAAAC
* * *
100256 ATCAAAAAGCTCCCGAAGGCTTTTAGGAAACATCATGCACTGCAGGACTTACAGATGACCATGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
100321 GGTTTGAAAAC
66 GGTTTGAAAAC
* *
100332 ATCAAAAAGCT-CCGAAGGCTTTTTGGAAACATCATGCAC-GCAGGAGTTACAGATGA-CCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
100394 GGTTTGAAAAC
66 GGTTTGAAAAC
* *
100405 TTCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGA-CCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
100469 GGTTTGAAAAC
66 GGTTTGAAAAC
*
100480 ATC-AAAAGCTCCCGAAGGCTTTTT-GAAACATCATGCA-TGCAGGACTTACAGATG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
100534 TGGGAAATAG
Statistics
Matches: 541, Mismatches: 31, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
72 17 0.03
73 165 0.30
74 70 0.13
75 123 0.23
76 108 0.20
77 58 0.11
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (76 bp):
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAG
GGTTTGAAAAC
Found at i:100561 original size:149 final size:152
Alignment explanation
Indices: 99882--100533 Score: 922
Period size: 149 Copynumber: 4.4 Consensus size: 152
99872 AGGCTTTAAG
* * * * * *
99882 ATCAAAAAGCTCCCGAAGACTTTTTGAAAACATCATGCACTGTAGGTCTTACAGGTGACCCAGA-
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCA-TGCAGGACTTACAGATGACCCTGAG
* * * *
99946 GGTTT---TAAGATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGTAGGACTTACA
65 GGTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
* *
100008 GATGACCCTGA-GGTTT--TAAG
130 GATGACCCTGAGGGTTTGAAAAC
* * * * *
100028 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACAACATGAAATGTAGGTCTTACAGATGACCCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG-CATGCAGGACTTACAGATGACCCTGAG
*
100093 GGTTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACA
65 GGTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
100157 GATGACCCTGAGGGTTTGAAAAC
130 GATGACCCTGAGGGTTTGAAAAC
* * *
100180 ATC-AAAAGCTACCGAAGGCTTTTTGGAAACATCATTCACTGTAGGACTTACAGATGACCCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCA-TGCAGGACTTACAGATGACCCTGAG
*
100244 GGTTTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTAGGAAACATCATGCACTGCAGGACTTAC
65 GG-TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTAC
*
100308 AGATGACCATGAGGGTTTGAAAAC
129 AGATGACCCTGAGGGTTTGAAAAC
* *
100332 ATCAAAAAGCT-CCGAAGGCTTTTTGGAAACATCATGCACGCAGGAGTTACAGATGA-CCTGAGG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATGCAGGACTTACAGATGACCCTGAGG
*
100395 GTTTG-AAAACTTCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
66 GTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
100459 ATGA-CCTGAGGGTTTGAAAAC
131 ATGACCCTGAGGGTTTGAAAAC
100480 ATC-AAAAGCTCCCGAAGGCTTTTT-GAAACATCATGCATGCAGGACTTACAGATG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATGCAGGACTTACAGATG
100534 TGGGAAATAG
Statistics
Matches: 467, Mismatches: 28, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
146 57 0.12
147 41 0.09
148 32 0.07
149 130 0.28
150 14 0.03
151 70 0.15
152 116 0.25
153 7 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (152 bp):
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATGCAGGACTTACAGATGACCCTGAGG
GTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
ATGACCCTGAGGGTTTGAAAAC
Found at i:100678 original size:178 final size:179
Alignment explanation
Indices: 100477--100818 Score: 561
Period size: 179 Copynumber: 1.9 Consensus size: 179
100467 AGGGTTTGAA
*
100477 AACATCAAAAGCTCCCGAAGGCTTTTTGAAACATCATGCA-TGCAGGACTTACAGATGTGGGAAA
1 AACATCAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAA
100541 TAGTTTACTAAGTAAAAAAAAACTAAGGAAATCG-TT-TT-CTTTTCAA-AATTTCATTTTTAGA
66 TAGTTTACTAAGT--AAAAAAACTAAGGAAATCGTTTCTTACTTTTCAACAATTTCA-TTTTAGA
100602 AAAGA-TGAATGAGAAACTATGAAAATCGTTTTCTCATATTTTTCAAAGTAAC
128 AAAGATTGAATGAGAAACTATGAAAATCG-TTTCTCATATTTTTCAAAGTAAC
100654 AACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAA
1 AACATC-AAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAA
*
100719 ATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTCTTACTTTTCAACAATTTCATTTTATAAA
65 ATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTCTTACTTTTCAACAATTTCATTTTAGAAA
* *
100784 AGATTGGATGAGAAACTATGGAAATCGTTTCTCAT
130 AGATTGAATGAGAAACTATGAAAATCGTTTCTCAT
100819 TATGTTTTTG
Statistics
Matches: 154, Mismatches: 4, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
177 25 0.16
178 35 0.23
179 39 0.25
180 27 0.18
181 28 0.18
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (179 bp):
AACATCAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAA
TAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTCTTACTTTTCAACAATTTCATTTTAGAAAA
GATTGAATGAGAAACTATGAAAATCGTTTCTCATATTTTTCAAAGTAAC
Found at i:101407 original size:22 final size:22
Alignment explanation
Indices: 101382--101434 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
101372 TAAAGCTTTA
101382 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
*
101404 ATCTTTAAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
101426 ATCTTTGAA
1 ATCTTTGAA
101435 GAGTGATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:103230 original size:189 final size:191
Alignment explanation
Indices: 102898--103277 Score: 728
Period size: 189 Copynumber: 2.0 Consensus size: 191
102888 GGGCCTTCGA
102898 AATGCCCCACATGGATCATCTTTGTCTGAAATGGGCTTTCGAGATGCCCTAATATTCTGCTTCTG
1 AATGCCCCACATGGATCATCTTTGTCTGAAATGGGCTTTCGAGATGCCCTAATATTCTGCTTCTG
102963 ATTCACTCTCAATGTCTGTTTGACTGAAATGTCACGATCCCCACGAGGTCCAATTTTGACAATAC
66 ATTCACTCTCAATGTC-GTTTGACTGAAATGTCACGATCCCCACGAGGTCCAATTTTGACAATAC
103028 ACTGTTATAGGTACTTGTGGCTTTATTCGTGCCCCAAATCTATTCATTCTGAATACTCTTTG
130 ACTGTTATAGGTACTTGTGGCTTTATTCGTGCCCCAAATCTATTCATTCTGAATACTCTTTG
*
103090 AATGCCCCACATGGATCATCTTTGTCTGAAATGGGCTTTCGAGATGCTCTAATATTCTGCTT-TG
1 AATGCCCCACATGGATCATCTTTGTCTGAAATGGGCTTTCGAGATGCCCTAATATTCTGCTTCTG
103154 ATTCACTCTCAATGTC-TTTGACTGAAATGTCACGATCCCCACGAGGTCCAATTTTGACAATACA
66 ATTCACTCTCAATGTCGTTTGACTGAAATGTCACGATCCCCACGAGGTCCAATTTTGACAATACA
103218 CTGTTATAGGTACTTGTGGCTTTATTCGTGCCCCAAATCTATTCATTCTGAATACTCTTT
131 CTGTTATAGGTACTTGTGGCTTTATTCGTGCCCCAAATCTATTCATTCTGAATACTCTTT
103278 TCCTGGTGTC
Statistics
Matches: 187, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
189 108 0.58
191 18 0.10
192 61 0.33
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.36
Consensus pattern (191 bp):
AATGCCCCACATGGATCATCTTTGTCTGAAATGGGCTTTCGAGATGCCCTAATATTCTGCTTCTG
ATTCACTCTCAATGTCGTTTGACTGAAATGTCACGATCCCCACGAGGTCCAATTTTGACAATACA
CTGTTATAGGTACTTGTGGCTTTATTCGTGCCCCAAATCTATTCATTCTGAATACTCTTTG
Found at i:109057 original size:43 final size:44
Alignment explanation
Indices: 108993--109075 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 44
108983 CGGTACATCA
* * * *
108993 AACAAAACTCTTATATGTAGGGGACAAATTTCAGTCCTAACTTC
1 AACAAAACTCTTACATATAGGGAACAAATTTCACTCCTAACTTC
* *
109037 AACAAAACT-TTACATATAGGGAATAACTTTCACTCCTAA
1 AACAAAACTCTTACATATAGGGAACAAATTTCACTCCTAA
109076 TTTCTCTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 24 0.73
44 9 0.27
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (44 bp):
AACAAAACTCTTACATATAGGGAACAAATTTCACTCCTAACTTC
Found at i:111953 original size:2 final size:2
Alignment explanation
Indices: 111946--112012 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
111936 TCAATCTACA
111946 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
111988 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 A
112013 ATTAAGAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112190 original size:13 final size:13
Alignment explanation
Indices: 112174--112231 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
112164 GCTCAATGAA
112174 TGTCATAAATGCG
1 TGTCATAAATGCG
**
112187 TGTCATAAATATG
1 TGTCATAAATGCG
*
112200 TGTCATAAATGTG
1 TGTCATAAATGCG
*
112213 TGTCATATATGCG
1 TGTCATAAATGCG
*
112226 CGTCAT
1 TGTCAT
112232 CTAAAATTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (13 bp):
TGTCATAAATGCG
Found at i:117845 original size:13 final size:13
Alignment explanation
Indices: 117818--117880 Score: 60
Period size: 14 Copynumber: 4.9 Consensus size: 13
117808 CCTGTAACCA
* *
117818 AAATTATATTTAT
1 AAATTATAATAAT
117831 AAATTATAATAAT
1 AAATTATAATAAT
117844 -AA-TA-AATAAT
1 AAATTATAATAAT
117854 AAAATTATAATAAT
1 -AAATTATAATAAT
*
117868 ATATTTATAATAA
1 A-AATTATAATAA
117881 AACTCGGACG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
10 6 0.14
11 2 0.05
12 4 0.10
13 14 0.33
14 16 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTATAATAAT
Found at i:117860 original size:24 final size:25
Alignment explanation
Indices: 117831--117882 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
117821 TTATATTTAT
117831 AAATTATAATAATA-ATAAATAATA
1 AAATTATAATAATATATAAATAATA
**
117855 AAATTATAATAATATATTTATAATA
1 AAATTATAATAATATATAAATAATA
117880 AAA
1 AAA
117883 CTCGGACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AAATTATAATAATATATAAATAATA
Found at i:122370 original size:49 final size:49
Alignment explanation
Indices: 122296--122399 Score: 192
Period size: 49 Copynumber: 2.1 Consensus size: 49
122286 TTGAAAATAC
122296 TACTCCCCCTTACTTTAACACTACTCCTCTTTAAAACGCTTTTAACATT
1 TACTCCCCCTTACTTTAACACTACTCCTCTTTAAAACGCTTTTAACATT
*
122345 TACTCCCCCTTACTTTAACATTACTCCTCTTTAAAACGCTTTTAACATT
1 TACTCCCCCTTACTTTAACACTACTCCTCTTTAAAACGCTTTTAACATT
122394 T-CTCCC
1 TACTCCC
122400 TTTTTTTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 5 0.09
49 49 0.91
ACGTcount: A:0.25, C:0.34, G:0.02, T:0.39
Consensus pattern (49 bp):
TACTCCCCCTTACTTTAACACTACTCCTCTTTAAAACGCTTTTAACATT
Found at i:124698 original size:20 final size:20
Alignment explanation
Indices: 124644--124700 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
124634 AACCCCAGGG
*
124644 GGGTATCGATTCCC-CTAGG
1 GGGTATCGATTCCCTCTAGA
* * *
124663 GGGAATCGGTTTCCTCATA-A
1 GGGTATCGATTCCCTC-TAGA
124683 GGGTATCGATTCCCTCTA
1 GGGTATCGATTCCCTCTA
124701 CACCAAAATG
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 13 0.45
20 14 0.48
21 2 0.07
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (20 bp):
GGGTATCGATTCCCTCTAGA
Found at i:128554 original size:22 final size:21
Alignment explanation
Indices: 128512--128551 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
128502 GAGTTTATTT
*
128512 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
128533 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
128552 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:140506 original size:13 final size:13
Alignment explanation
Indices: 140479--140540 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
140469 CATGTAACCA
* *
140479 AAATTATATTTAT
1 AAATTATAATAAT
140492 AAATTATAATAAT
1 AAATTATAATAAT
*
140505 -AA-TA-AATAAA
1 AAATTATAATAAT
140515 AAATTATAATAAT
1 AAATTATAATAAT
*
140528 ATATTTATAATAA
1 A-AATTATAATAA
140541 AACTCTGATG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
10 5 0.12
11 4 0.10
12 4 0.10
13 17 0.43
14 10 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTATAATAAT
Found at i:143938 original size:23 final size:23
Alignment explanation
Indices: 143897--143944 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
143887 GGCCCAACCT
**
143897 GACCCGAACTGTTAACCTGACCC
1 GACCCGAACCATTAACCTGACCC
* *
143920 GACCCGAACCATTAGCCTGCCCC
1 GACCCGAACCATTAACCTGACCC
143943 GA
1 GA
143945 ACTGTTTGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.42, G:0.19, T:0.15
Consensus pattern (23 bp):
GACCCGAACCATTAACCTGACCC
Found at i:144541 original size:12 final size:12
Alignment explanation
Indices: 144526--144558 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
144516 TGTATAAACT
*
144526 ACTTGATTTGAA
1 ACTTGATTCGAA
144538 ACTTGATTCGAA
1 ACTTGATTCGAA
144550 ACTTGATTC
1 ACTTGATTC
144559 CTGATTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (12 bp):
ACTTGATTCGAA
Found at i:144983 original size:10 final size:10
Alignment explanation
Indices: 144968--145000 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
144958 TGCACAACAT
*
144968 TTTAGTTGTA
1 TTTAGTTGCA
144978 TTTAGTTGCA
1 TTTAGTTGCA
144988 -TTAGTTGCA
1 TTTAGTTGCA
144997 TTTA
1 TTTA
145001 AGTTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.55
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:147916 original size:19 final size:20
Alignment explanation
Indices: 147877--147916 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
147867 TAACTTTTAA
* *
147877 TGAATTTTAGTATTTTATAT
1 TGAATTTTAGAATTATATAT
147897 TGAATTTTA-AATTATATAT
1 TGAATTTTAGAATTATATAT
147916 T
1 T
147917 CGATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
TGAATTTTAGAATTATATAT
Found at i:149475 original size:19 final size:20
Alignment explanation
Indices: 149451--149498 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
149441 AACGATTTTC
*
149451 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
149470 TTTTGAAAACCAATATGAAA
1 TTTTGAAAACAAAAATGAAA
149490 TTTTGAAAA
1 TTTTGAAAA
149499 ATGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:149607 original size:14 final size:14
Alignment explanation
Indices: 149588--149614 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
149578 AACAAAAGAA
149588 AAATAATTCATTTT
1 AAATAATTCATTTT
149602 AAATAATTCATTT
1 AAATAATTCATTT
149615 AGTTTAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATAATTCATTTT
Found at i:150736 original size:19 final size:20
Alignment explanation
Indices: 150697--150736 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
150687 TAGGTGTTAA
*
150697 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
150717 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
150736 T
1 T
150737 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:165360 original size:21 final size:21
Alignment explanation
Indices: 165328--165410 Score: 53
Period size: 21 Copynumber: 3.9 Consensus size: 21
165318 TCTTAATTTG
165328 CCCGAACT-ACCATATAATTGT
1 CCCGAA-TGACCATATAATTGT
* * *
165349 CCCGAATGACCAGATAGGTTTGG
1 CCCGAATGACCATATA--ATTGT
* * * *
165372 ACCGAGTG-CCACATATTTGT
1 CCCGAATGACCATATAATTGT
*
165392 CCCGAAGGACCATATAATT
1 CCCGAATGACCATATAATT
165411 ATCCTGAAGG
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
20 10 0.22
21 21 0.46
22 6 0.13
23 9 0.20
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
CCCGAATGACCATATAATTGT
Found at i:165586 original size:21 final size:20
Alignment explanation
Indices: 165562--165612 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
165552 CATAGAGTTT
165562 GTTCACATTCACTTATTCAAA
1 GTTCACATTCACTTATTC-AA
*
165583 GTTCACATTCACTTGTTCAA
1 GTTCACATTCACTTATTCAA
165603 GATTCACATT
1 G-TTCACATT
165613 TCCTTATGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (20 bp):
GTTCACATTCACTTATTCAA
Found at i:166040 original size:19 final size:21
Alignment explanation
Indices: 165990--166041 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
165980 CTACCCCCAA
*
165990 GTACCGATACTTCCTTTCAAGG
1 GTACCGATACCTCC-TTCAAGG
* *
166012 GTATCAATACCTCC-TCAA-G
1 GTACCGATACCTCCTTCAAGG
166031 GTACCGATACC
1 GTACCGATACC
166042 AAAATAGCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 10 0.40
20 4 0.16
22 11 0.44
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (21 bp):
GTACCGATACCTCCTTCAAGG
Found at i:166141 original size:42 final size:42
Alignment explanation
Indices: 166091--166194 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 42
166081 GATACCACCC
166091 CTGGTATCGATACTACCCTTACAGCATCGATACCCAT-CACAA
1 CTGGTATCGATACTACCCTTACAGCATCGATACCC-TCCACAA
* * *
166133 CTGGTATCGATACTACCCTCACAGTATCGATACCCTCCTCAA
1 CTGGTATCGATACTACCCTTACAGCATCGATACCCTCCACAA
166175 -TAGGTATCGATACTACCCTT
1 CT-GGTATCGATACTACCCTT
166195 GGAAAATACT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
41 2 0.04
42 54 0.96
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.27
Consensus pattern (42 bp):
CTGGTATCGATACTACCCTTACAGCATCGATACCCTCCACAA
Found at i:166161 original size:20 final size:21
Alignment explanation
Indices: 166093--166193 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 21
166083 TACCACCCCT
*
166093 GGTATCGATACTACCCTTACA
1 GGTATCGATACTACCCTCACA
* *
166114 -GCATCGATAC--CCATCACAA
1 GGTATCGATACTACCCTCAC-A
166133 CTGGTATCGATACTACCCTCACA
1 --GGTATCGATACTACCCTCACA
* *
166156 -GTATCGATAC-CCTCCTCAATA
1 GGTATCGATACTAC-CCTC-ACA
166177 GGTATCGATACTACCCT
1 GGTATCGATACTACCCT
166194 TGGAAAATAC
Statistics
Matches: 62, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
18 5 0.08
19 2 0.03
20 23 0.37
21 2 0.03
22 22 0.35
23 2 0.03
24 6 0.10
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.26
Consensus pattern (21 bp):
GGTATCGATACTACCCTCACA
Found at i:167125 original size:498 final size:498
Alignment explanation
Indices: 166188--167187 Score: 1874
Period size: 498 Copynumber: 2.0 Consensus size: 498
166178 GTATCGATAC
*
166188 TACCCTTGGAAAATACTCATATTTAACCCATGAAGTATTGGTATTATTCTAACGGTACCGATAAT
1 TACCCTTGGAAAATACTCATATTTAACCCATGAAGTATTGGTACTATTCTAACGGTACCGATAAT
166253 CAAAGCCCAAAATGGTCATTTTCACTTCGAAAATCAACCCAAAAACTTCCCAAATCTCTTATATT
66 CAAAGCCCAAAATGGTCATTTTCACTTCGAAAATCAACCCAAAAACTTCCCAAATCTCTTATATT
*
166318 CATCACCCTCAAGCTTTAAAACTCACCCTTATACCTCCACACCAATTAGTATTCATTTACTACTC
131 CATCACCCTCAAGCTTTAAAACTCACCCCTATACCTCCACACCAATTAGTATTCATTTACTACTC
166383 TTAATTATCCAAATTCCCGTTTTAATACTTGAATCTTAAAATCATACCAAAGTTTCAAACATGTT
196 TTAATTATCCAAATTCCCGTTTTAATACTTGAATCTTAAAATCATACCAAAGTTTCAAACATGTT
* *
166448 CTTAACCAATTCCAACACCCCTGACTCTTAAGTTAGATCATTGACAAGTCAAATATCTCAACAAA
261 CTTAACCAAATCCAACACCCCTAACTCTTAAGTTAGATCATTGACAAGTCAAATATCTCAACAAA
** *
166513 ACTTCAAAAACTGTTTCATATAAAAATTTCATTTCAAAACCCATTTTATAAATTCATCTCTAATA
326 ACTTCAAAAACTACTCCATATAAAAATTTCATTTCAAAACCCATTTTATAAATTCATCTCTAATA
* *
166578 CACTCATCTTGTTGTTTTAATCATGTATAAGCTTTCCTTAAGCTTATATAACACTCCTAGTTCCA
391 CACTCATCTTGTTGTTTTAATCATATATAAGCTTTCCTTAAGCTTATATAACACCCCTAGTTCCA
166643 CTACCAAACCAAATATTAAAGGAAACCACAAAATTCATATTCT
456 CTACCAAACCAAATATTAAAGGAAACCACAAAATTCATATTCT
*
166686 TACCCTTGGAAAATACTCATATTTAACCCATGAAGTATTGGTACTATTCTAACGGTACCGATACT
1 TACCCTTGGAAAATACTCATATTTAACCCATGAAGTATTGGTACTATTCTAACGGTACCGATAAT
*
166751 CGAAGCCCAAAATGGTCATTTTCACTTCGAAAATCAACCCAAAAACTTCCCAAATCTCTTATATT
66 CAAAGCCCAAAATGGTCATTTTCACTTCGAAAATCAACCCAAAAACTTCCCAAATCTCTTATATT
*
166816 CATCACCCTCAAGCTTTAAAACTCACCCCTATACTTCCACACCAATTAGTATTCATTTACTACTC
131 CATCACCCTCAAGCTTTAAAACTCACCCCTATACCTCCACACCAATTAGTATTCATTTACTACTC
166881 TTAATTATCCAAATTCCCGTTTTAATACTTGAATCTTAAAATCATACCAAAGTTTCAAACATGTT
196 TTAATTATCCAAATTCCCGTTTTAATACTTGAATCTTAAAATCATACCAAAGTTTCAAACATGTT
*
166946 CTTAATCAAATCCAACACCCCTAACTCTTAAGTTAGATCATTGACAAGTCAAATATCTCAACAAA
261 CTTAACCAAATCCAACACCCCTAACTCTTAAGTTAGATCATTGACAAGTCAAATATCTCAACAAA
167011 ACTTCAAAAACTACTCCATATAAAAATTTCATTTCAAAACCCATTTTATAAATTCATCTCTAATA
326 ACTTCAAAAACTACTCCATATAAAAATTTCATTTCAAAACCCATTTTATAAATTCATCTCTAATA
*
167076 CACTCATCTTGTTGTTTTAATCCTATATAAGCTTTCCTTAAGCTTATATAACACCCCTAGTTCCA
391 CACTCATCTTGTTGTTTTAATCATATATAAGCTTTCCTTAAGCTTATATAACACCCCTAGTTCCA
167141 CTACCAAACCAAATATTAAAGGAAACCACAAAATTCATATTCT
456 CTACCAAACCAAATATTAAAGGAAACCACAAAATTCATATTCT
167184 TACC
1 TACC
167188 TTGTGGATGG
Statistics
Matches: 488, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
498 488 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (498 bp):
TACCCTTGGAAAATACTCATATTTAACCCATGAAGTATTGGTACTATTCTAACGGTACCGATAAT
CAAAGCCCAAAATGGTCATTTTCACTTCGAAAATCAACCCAAAAACTTCCCAAATCTCTTATATT
CATCACCCTCAAGCTTTAAAACTCACCCCTATACCTCCACACCAATTAGTATTCATTTACTACTC
TTAATTATCCAAATTCCCGTTTTAATACTTGAATCTTAAAATCATACCAAAGTTTCAAACATGTT
CTTAACCAAATCCAACACCCCTAACTCTTAAGTTAGATCATTGACAAGTCAAATATCTCAACAAA
ACTTCAAAAACTACTCCATATAAAAATTTCATTTCAAAACCCATTTTATAAATTCATCTCTAATA
CACTCATCTTGTTGTTTTAATCATATATAAGCTTTCCTTAAGCTTATATAACACCCCTAGTTCCA
CTACCAAACCAAATATTAAAGGAAACCACAAAATTCATATTCT
Found at i:173947 original size:21 final size:20
Alignment explanation
Indices: 173908--173958 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
173898 CATAAAGTTT
*
173908 GTTCACGTTCACATATTCAAA
1 GTTCACATTCACATATTC-AA
* *
173929 GTTCACATTCACTTGTTCAA
1 GTTCACATTCACATATTCAA
173949 GATTCACATT
1 G-TTCACATT
173959 TCCTTATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (20 bp):
GTTCACATTCACATATTCAA
Found at i:174467 original size:20 final size:20
Alignment explanation
Indices: 174442--174514 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
174432 CCATCCCTTG
*
174442 GTATCGATACTACCCTTACA
1 GTATCGATACTACCCTAACA
* * *
174462 GTATCGATACCCATCATAACTA
1 GTATCGATA-CTACCCTAAC-A
*
174484 GTATCGATACTACCCTCACA
1 GTATCGATACTACCCTAACA
*
174504 GTGTCGATACT
1 GTATCGATACT
174515 CTCCTCAACG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 20 0.48
21 12 0.29
22 10 0.24
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.29
Consensus pattern (20 bp):
GTATCGATACTACCCTAACA
Found at i:174530 original size:42 final size:42
Alignment explanation
Indices: 174441--174534 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
174431 ACCATCCCTT
* *
174441 GGTATCGATACTACCCTTACAGTATCGATACCCATCATAACT
1 GGTATCGATACTACCCTCACAGTATCGATACCCATCATAACG
* * * *
174483 AGTATCGATACTACCCTCACAGTGTCGATACTC-TCCTCAACG
1 GGTATCGATACTACCCTCACAGTATCGATACCCATCAT-AACG
174525 GGTATCGATA
1 GGTATCGATA
174535 TTTCCCTTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 3 0.07
42 41 0.93
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (42 bp):
GGTATCGATACTACCCTCACAGTATCGATACCCATCATAACG
Found at i:178548 original size:32 final size:32
Alignment explanation
Indices: 178511--178581 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
178501 AAATACAACT
*
178511 ATATGCTCCTAAATACATCTAAATAATCCTAC
1 ATATGCCCCTAAATACATCTAAATAATCCTAC
* *
178543 ATATGCCCCTAAATGCATCTAAATGATCCTAC
1 ATATGCCCCTAAATACATCTAAATAATCCTAC
178575 ATATGCC
1 ATATGCC
178582 ATAAGATGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (32 bp):
ATATGCCCCTAAATACATCTAAATAATCCTAC
Found at i:181730 original size:14 final size:14
Alignment explanation
Indices: 181711--181737 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
181701 CTTTCCAAGA
181711 CGAGTTTTATCTTC
1 CGAGTTTTATCTTC
181725 CGAGTTTTATCTT
1 CGAGTTTTATCTT
181738 GCAAGTCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.52
Consensus pattern (14 bp):
CGAGTTTTATCTTC
Found at i:201758 original size:21 final size:21
Alignment explanation
Indices: 201732--201775 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
201722 GTATCAAGGT
*
201732 CTTTGTGGAAGCCATGAAATC
1 CTTTGTCGAAGCCATGAAATC
* *
201753 CTTTGTCGAGGCCATGAATTC
1 CTTTGTCGAAGCCATGAAATC
201774 CT
1 CT
201776 GCAATGATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (21 bp):
CTTTGTCGAAGCCATGAAATC
Found at i:204877 original size:24 final size:24
Alignment explanation
Indices: 204842--204890 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
204832 AGTCTTCCAG
* *
204842 ATGATGTGTAAAACATCTATATAC
1 ATGATGTATAAAACATATATATAC
*
204866 ATGATGTATAAAACATATATGTAC
1 ATGATGTATAAAACATATATATAC
204890 A
1 A
204891 ATGTCATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATATATATAC
Found at i:213451 original size:21 final size:22
Alignment explanation
Indices: 213398--213453 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 22
213388 TAATTATTAA
213398 AATATTTAA-AATATATTTATT
1 AATATTTAATAATATATTTATT
213419 AATATTTCTAATAATAT-TTT-TT
1 AATA-TT-TAATAATATATTTATT
213441 AATATTATAATAA
1 AATATT-TAATAA
213454 ATAATCAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 12 0.39
22 8 0.26
23 6 0.19
24 5 0.16
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTAATAATATATTTATT
Found at i:213456 original size:22 final size:21
Alignment explanation
Indices: 213398--213456 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
213388 TAATTATTAA
213398 AATATTTAA-AATATATTTATT
1 AATATTTAATAA-ATATTTATT
*
213419 AATATTTCTAAT-AATATTTTTT
1 AATA-TT-TAATAAATATTTATT
213441 AATATTATAATAAATA
1 AATATT-TAATAAATA
213457 ATCAATTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 10 0.31
22 18 0.56
23 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTTAATAAATATTTATT
Found at i:213653 original size:23 final size:24
Alignment explanation
Indices: 213627--213672 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
213617 AATAATATTT
213627 TAATAAAGA-TATTTAAAATATAC
1 TAATAAAGATTATTTAAAATATAC
* * *
213650 TAATTAATATTTTTTAAAATATA
1 TAATAAAGATTATTTAAAATATA
213673 ATATGACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATAAAGATTATTTAAAATATAC
Found at i:213728 original size:32 final size:33
Alignment explanation
Indices: 213708--213778 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 33
213698 AATTAATTTA
213708 TAATATTTTTATTTCAATAAAATATATCAATAC
1 TAATATTTTTATTTCAATAAAATATATCAATAC
* *
213741 TAATATTTTTA-TT-AATAAAAT-TAT-AAAAA
1 TAATATTTTTATTTCAATAAAATATATCAATAC
213770 TAATATTTT
1 TAATATTTT
213779 AATAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 12 0.33
30 3 0.08
31 8 0.22
32 2 0.06
33 11 0.31
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (33 bp):
TAATATTTTTATTTCAATAAAATATATCAATAC
Found at i:213785 original size:14 final size:14
Alignment explanation
Indices: 213717--213786 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
213707 ATAATATTTT
*
213717 TATTTCAATAA-AA
1 TATTTTAATAATAA
* * *
213730 TATATCAATACTAA
1 TATTTTAATAATAA
*
213744 TATTTTTATTAATAA
1 TA-TTTTAATAATAA
* * *
213759 AATTATAAAAATAA
1 TATTTTAATAATAA
213773 TATTTTAATAATAA
1 TATTTTAATAATAA
213787 ATAAATTATT
Statistics
Matches: 42, Mismatches: 13, Indels: 3
0.72 0.22 0.05
Matches are distributed among these distances:
13 9 0.21
14 24 0.57
15 9 0.21
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:213801 original size:28 final size:29
Alignment explanation
Indices: 213770--213828 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
213760 ATTATAAAAA
*
213770 TAATATTTTAATAATAAATAA-ATTAT-TT
1 TAATATTTTAAAAAT-AATAATATTATGTT
213798 TAATATTTTAAAAATAATAATATTATGTT
1 TAATATTTTAAAAATAATAATATTATGTT
213827 TA
1 TA
213829 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.18
28 19 0.68
29 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TAATATTTTAAAAATAATAATATTATGTT
Found at i:222712 original size:32 final size:31
Alignment explanation
Indices: 222638--222714 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
222628 AAACATATCA
* *
222638 ATCTGATATTAACCTGACTCAAAAATCAACTG
1 ATCTGATATTGA-CTGACTCAAAAACCAACTG
* * * *
222670 ATATGGTATTGACTGGACTCGAAAACCAATTG
1 ATCTGATATTGACT-GACTCAAAAACCAACTG
222702 ATCTGATATTGAC
1 ATCTGATATTGAC
222715 CAGACCCGAC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
31 2 0.06
32 34 0.94
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (31 bp):
ATCTGATATTGACTGACTCAAAAACCAACTG
Found at i:222783 original size:44 final size:44
Alignment explanation
Indices: 222718--222815 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 44
222708 TATTGACCAG
* *
222718 ACCCGACCCGAAAACCAACCGATCTAAGTTTTACCCTGTCCGAT
1 ACCCGACCCGAAAACCAACCGATATAAGTTTTACCCTGCCCGAT
* * *
222762 ATCCGACCCGAAAACCAACCGATATGAGTTTTACCTTGCCCGAT
1 ACCCGACCCGAAAACCAACCGATATAAGTTTTACCCTGCCCGAT
222806 ACCCGACCCG
1 ACCCGACCCG
222816 TTATGACTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.29, C:0.37, G:0.15, T:0.19
Consensus pattern (44 bp):
ACCCGACCCGAAAACCAACCGATATAAGTTTTACCCTGCCCGAT
Found at i:223872 original size:21 final size:21
Alignment explanation
Indices: 223843--223882 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
223833 CCATCATCAT
223843 CGTCAGCCACCATCACCCATC
1 CGTCAGCCACCATCACCCATC
* *
223864 CGTCGGCCACCATTACCCA
1 CGTCAGCCACCATCACCCA
223883 CCCACCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.50, G:0.12, T:0.15
Consensus pattern (21 bp):
CGTCAGCCACCATCACCCATC
Found at i:223932 original size:7 final size:7
Alignment explanation
Indices: 223920--223952 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
223910 CGTGGATTGT
223920 AATTTGA
1 AATTTGA
223927 AATTTGA
1 AATTTGA
223934 AATTTGA
1 AATTTGA
223941 AATTTGCA
1 AATTTG-A
223949 AATT
1 AATT
223953 GTTTAGCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (7 bp):
AATTTGA
Found at i:225726 original size:23 final size:23
Alignment explanation
Indices: 225700--225743 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
225690 TATCATATGT
*
225700 TATCATTTATTTGCATGATTTGA
1 TATCATTCATTTGCATGATTTGA
225723 TATCATTCATTTGCATGATTT
1 TATCATTCATTTGCATGATTT
225744 TACTTGTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (23 bp):
TATCATTCATTTGCATGATTTGA
Found at i:230194 original size:17 final size:17
Alignment explanation
Indices: 230172--230210 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
230162 AACGGTCAAC
230172 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
230189 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
230206 GGTCA
1 GGTCA
230211 GACCGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:230199 original size:7 final size:7
Alignment explanation
Indices: 230152--230182 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
230142 GTCAAAGAAA
230152 GTCAACG
1 GTCAACG
230159 GTCAACG
1 GTCAACG
230166 GTCAACG
1 GTCAACG
230173 GTCAACG
1 GTCAACG
230180 GTC
1 GTC
230183 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:230230 original size:19 final size:19
Alignment explanation
Indices: 230208--230305 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
230198 TCGGGTCGGG
230208 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
230227 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
230246 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
230265 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
230285 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
230305 T
1 T
230306 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:230236 original size:10 final size:9
Alignment explanation
Indices: 230206--230304 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
230196 GGTCGGGTCG
*
230206 GGTCAGACC
1 GGTCAAACC
230215 GGTCAAACC
1 GGTCAAACC
*
230224 GGTTCAGACC
1 GG-TCAAACC
230234 GGTCAAACC
1 GGTCAAACC
*
230243 GGTTCGAACC
1 GG-TCAAACC
*
230253 GGTTGAAACC
1 GG-TCAAACC
230263 GGTCAAACC
1 GGTCAAACC
230272 GGTCAGAACC
1 GGTCA-AACC
*
230282 GGTTGAAAACC
1 GG-T-CAAACC
*
230293 GGTTAAACC
1 GGTCAAACC
230302 GGT
1 GGT
230305 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:230263 original size:29 final size:28
Alignment explanation
Indices: 230207--230304 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
230197 GTCGGGTCGG
* * *
230207 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
230235 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
230264 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
230294 GTTAAACCGGT
1 GTCAAACCGGT
230305 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 11 0.18
29 34 0.56
30 16 0.26
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:231095 original size:12 final size:12
Alignment explanation
Indices: 231078--231103 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
231068 TGCATATTTA
231078 ATTATCACTGTT
1 ATTATCACTGTT
231090 ATTATCACTGTT
1 ATTATCACTGTT
231102 AT
1 AT
231104 GGAACTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTATCACTGTT
Found at i:232314 original size:56 final size:56
Alignment explanation
Indices: 232245--232377 Score: 178
Period size: 56 Copynumber: 2.4 Consensus size: 56
232235 GATGTATGTA
*
232245 TTTATTGTAATTTATAAAAAAAATATTCTTTATTATAATTTATAAAAAAATTTGT-C
1 TTTATTGTAATTTATAAAAAAAATAGTCTTTATTATAATTTAT-AAAAAATTTGTCC
* ** * **
232301 TTTATTGTAATTTATACAAAATTTGGTCTTTATTATAATTTATAAAAGTTTTGTCC
1 TTTATTGTAATTTATAAAAAAAATAGTCTTTATTATAATTTATAAAAAATTTGTCC
*
232357 TTTATTGAAATTTATAAAAAA
1 TTTATTGTAATTTATAAAAAA
232378 GTTCTATCCT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
55 9 0.13
56 58 0.87
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.49
Consensus pattern (56 bp):
TTTATTGTAATTTATAAAAAAAATAGTCTTTATTATAATTTATAAAAAATTTGTCC
Found at i:232353 original size:28 final size:26
Alignment explanation
Indices: 232245--232428 Score: 131
Period size: 28 Copynumber: 6.6 Consensus size: 26
232235 GATGTATGTA
* *
232245 TTTATTGTAATTTATAAAAAAAATAT-TC
1 TTTATTATAATTTAT---AAAAATTTGTC
232273 TTTATTATAATTTATAAAAAAATTTGTC
1 TTTATTATAATTTAT--AAAAATTTGTC
*
232301 TTTATTGTAATTTATACAAAATTTGGTC
1 TTTATTATAATTTATA-AAAATTT-GTC
*
232329 TTTATTATAATTTATAAAAGTTTTGTCC
1 TTTATTATAATTTATAAAA-ATTTGT-C
*
232357 TTTATTGA-AATTTATAAAAAAGTTCTATCC
1 TTTATT-ATAATTTAT-AAAAA-TT-TGT-C
* * *
232387 TTTATTATATTTTTTAAAAATTAAG-C
1 TTTATTATAATTTATAAAAATT-TGTC
232413 TATTATTATAATTTAT
1 T-TTATTATAATTTAT
232429 TATTATTATT
Statistics
Matches: 131, Mismatches: 14, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
26 3 0.02
27 33 0.25
28 67 0.51
29 13 0.10
30 15 0.11
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (26 bp):
TTTATTATAATTTATAAAAATTTGTC
Found at i:232405 original size:30 final size:30
Alignment explanation
Indices: 232339--232406 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
232329 TTTATTATAA
* * *
232339 TTTATAAAAGTTTTGTCCTTTATTGAAATT
1 TTTAAAAAAGTTCTATCCTTTATTGAAATT
* *
232369 TATAAAAAAGTTCTATCCTTTATT-ATATT
1 TTTAAAAAAGTTCTATCCTTTATTGAAATT
*
232398 TTTTAAAAA
1 TTTAAAAAA
232407 TTAAGCTATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.50
Consensus pattern (30 bp):
TTTAAAAAAGTTCTATCCTTTATTGAAATT
Found at i:235722 original size:17 final size:17
Alignment explanation
Indices: 235702--235735 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
235692 TGTTTATACG
235702 TGTAAAAATTTTAAGTT
1 TGTAAAAATTTTAAGTT
235719 TGTAAAAATTTTAAGTT
1 TGTAAAAATTTTAAGTT
235736 GCATAAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
TGTAAAAATTTTAAGTT
Found at i:236313 original size:18 final size:19
Alignment explanation
Indices: 236290--236328 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
236280 TTTAAATAAT
236290 AATAAAAACGATTAAA-TA
1 AATAAAAACGATTAAAGTA
* *
236308 AATAAAAGCTATTAAAGTA
1 AATAAAAACGATTAAAGTA
236327 AA
1 AA
236329 AATAAGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (19 bp):
AATAAAAACGATTAAAGTA
Done.