Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 81 of 208
Found at i:23676191 original size:18 final size:18
Alignment explanation
Indices: 23676155--23676193 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23676145 GAAAAAGTTA
*
23676155 TTAGGCTAAAAAATGAGC
1 TTAGGCTAAAAAATAAGC
23676173 TTAGG-TAAAAAATTAAGC
1 TTAGGCTAAAAAA-TAAGC
23676191 TTA
1 TTA
23676194 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (18 bp):
TTAGGCTAAAAAATAAGC
Found at i:23679688 original size:26 final size:26
Alignment explanation
Indices: 23679659--23679724 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
23679649 TCAATAATGC
* *
23679659 TCACACGAGTTGTGAAATAGGCCTAT
1 TCACACGAGCTGTGAAATAAGCCTAT
* *
23679685 TCACACGAGCTGTGGAATAAGCCTAC
1 TCACACGAGCTGTGAAATAAGCCTAT
* *
23679711 TCATACCAGCTGTG
1 TCACACGAGCTGTG
23679725 GGTCGGAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (26 bp):
TCACACGAGCTGTGAAATAAGCCTAT
Found at i:23694703 original size:22 final size:22
Alignment explanation
Indices: 23694678--23694720 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
23694668 CTCATGGCTA
23694678 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
23694700 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
23694721 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:23694850 original size:16 final size:16
Alignment explanation
Indices: 23694829--23694889 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
23694819 GGTTTCACTA
23694829 GATTAGAGGTGTATTG
1 GATTAGAGGTGTATTG
*
23694845 GATTAGAGGTGTAATG
1 GATTAGAGGTGTATTG
23694861 GATTAGAGGTGTATTG
1 GATTAGAGGTGTATTG
*
23694877 GAATAGAGGTGTA
1 GATTAGAGGTGTA
23694890 ATAGCAAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.33
Consensus pattern (16 bp):
GATTAGAGGTGTATTG
Found at i:23694870 original size:32 final size:32
Alignment explanation
Indices: 23694829--23694891 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
23694819 GGTTTCACTA
*
23694829 GATTAGAGGTGTATTGGATTAGAGGTGTAATG
1 GATTAGAGGTGTATTGGAATAGAGGTGTAATG
23694861 GATTAGAGGTGTATTGGAATAGAGGTGTAAT
1 GATTAGAGGTGTATTGGAATAGAGGTGTAAT
23694892 AGCAAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (32 bp):
GATTAGAGGTGTATTGGAATAGAGGTGTAATG
Found at i:23695146 original size:18 final size:17
Alignment explanation
Indices: 23695125--23695159 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23695115 TTATTATTAA
*
23695125 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
23695143 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
23695160 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:23695331 original size:47 final size:46
Alignment explanation
Indices: 23695262--23695430 Score: 154
Period size: 47 Copynumber: 3.7 Consensus size: 46
23695252 TTAATTAAAA
*
23695262 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * *
23695309 TATATGAATTTGTATAATTTAAAATAATTAT--TATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
23695354 TA-AT-AATGATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
23695400 TATATGAATTTATATAATTTAAAATAATTAT
1 TATATGAATTTATATAATTTAAAATAATTAT
23695431 TATTAAATAA
Statistics
Matches: 97, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
43 3 0.03
44 22 0.23
45 9 0.09
46 9 0.09
47 47 0.48
48 7 0.07
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:23700905 original size:18 final size:20
Alignment explanation
Indices: 23700878--23700916 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
23700868 TTTTTTACTA
23700878 AAAAATATAAAT-AAATTAT
1 AAAAATATAAATAAAATTAT
23700897 AAAAA-ATAAATAAAATTAT
1 AAAAATATAAATAAAATTAT
23700916 A
1 A
23700917 TTGAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATATAAATAAAATTAT
Found at i:23701047 original size:20 final size:20
Alignment explanation
Indices: 23701002--23701048 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
23700992 ATGAAAATTC
* *
23701002 TAAAAACTTTTAATAAATTA
1 TAAAAACTTTTAAAAAATAA
*
23701022 TGAAAA-TTTTATAAAAATAA
1 TAAAAACTTTTA-AAAAATAA
23701042 TAAAAAC
1 TAAAAAC
23701049 ACATATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAAAACTTTTAAAAAATAA
Found at i:23701080 original size:22 final size:22
Alignment explanation
Indices: 23701024--23701080 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
23701014 ATAAATTATG
*
23701024 AAAATTTTATAAAAATAATAAA
1 AAAATTATATAAAAATAATAAA
*
23701046 AACACA-TAT-TAAAAATATTAAA
1 AA-A-ATTATATAAAAATAATAAA
23701068 AAAATTATATAAA
1 AAAATTATATAAA
23701081 CTTACAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 20 0.69
23 3 0.10
24 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAATTATATAAAAATAATAAA
Found at i:23701590 original size:21 final size:21
Alignment explanation
Indices: 23701561--23701604 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23701551 GAAATAATAC
*
23701561 ATATGTATATATAT-GTTGAGT
1 ATATATATATATATAG-TGAGT
23701582 ATATATATATATATAGTGAGT
1 ATATATATATATATAGTGAGT
23701603 AT
1 AT
23701605 TTGGTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (21 bp):
ATATATATATATATAGTGAGT
Found at i:23706536 original size:27 final size:28
Alignment explanation
Indices: 23706481--23706588 Score: 110
Period size: 28 Copynumber: 3.9 Consensus size: 28
23706471 ATCACTATTC
* * ** *
23706481 TTGGTAGATACCCTCATTGATAATACTT
1 TTGGCAGATACCCTTATTGATCTTGCTT
*
23706509 TT-GCATATACCCTTATTGATCTTGCTT
1 TTGGCAGATACCCTTATTGATCTTGCTT
* * *
23706536 TTGGCGGATACCCTTACTAATCTTGCTT
1 TTGGCAGATACCCTTATTGATCTTGCTT
**
23706564 TTGGCAGATACCCTTAACGATCTTG
1 TTGGCAGATACCCTTATTGATCTTG
23706589 ATAAATTGAA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
27 21 0.32
28 44 0.68
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (28 bp):
TTGGCAGATACCCTTATTGATCTTGCTT
Found at i:23707166 original size:24 final size:24
Alignment explanation
Indices: 23707130--23707180 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
23707120 AGAATTTCGA
*
23707130 AAAGGCCATATCA-AGATACGCCAT
1 AAAGGCCAAATCAGAG-TACGCCAT
23707154 AAAGGCCAAATCAGAGTACGCCAT
1 AAAGGCCAAATCAGAGTACGCCAT
23707178 AAA
1 AAA
23707181 AGCTAGCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.14
Consensus pattern (24 bp):
AAAGGCCAAATCAGAGTACGCCAT
Found at i:23710030 original size:61 final size:61
Alignment explanation
Indices: 23709942--23710104 Score: 220
Period size: 61 Copynumber: 2.7 Consensus size: 61
23709932 TTAACAAAGG
* * * * *
23709942 TTGCCATGAAGGCTTACCCT-TCCAGAGTTCTGCCACAAAGGCGTTCCTTTACATTTAGTAC
1 TTGCCATAAAGGCTT-TCCTGTCTAGAGTTTTGCCACAAAGGCGTTCCTTTACATTTAATAC
* * *
23710003 TTGCCATAAAGGCTTTCCTGTCTAGAGTTTTGGCACAAAGGTGTTGCTTTACATTTAATAC
1 TTGCCATAAAGGCTTTCCTGTCTAGAGTTTTGCCACAAAGGCGTTCCTTTACATTTAATAC
* *
23710064 TCGCCATAAAGGCTTTCTTGTCTAGAGTTTTGCCACAAAGG
1 TTGCCATAAAGGCTTTCCTGTCTAGAGTTTTGCCACAAAGG
23710105 TATTCTTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 3 0.03
61 87 0.97
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (61 bp):
TTGCCATAAAGGCTTTCCTGTCTAGAGTTTTGCCACAAAGGCGTTCCTTTACATTTAATAC
Found at i:23710105 original size:61 final size:61
Alignment explanation
Indices: 23709965--23710116 Score: 223
Period size: 61 Copynumber: 2.5 Consensus size: 61
23709955 TTACCCTTCC
* * * *
23709965 AGAGTTCTGCCACAAAGGCGTTCCTTTACATTTAGTACTTGCCATAAAGGCTTTCCTGTCT
1 AGAGTTTTGCCACAAAGGTGTTCCTTTACATTTAATACTCGCCATAAAGGCTTTCCTGTCT
* * *
23710026 AGAGTTTTGGCACAAAGGTGTTGCTTTACATTTAATACTCGCCATAAAGGCTTTCTTGTCT
1 AGAGTTTTGCCACAAAGGTGTTCCTTTACATTTAATACTCGCCATAAAGGCTTTCCTGTCT
* *
23710087 AGAGTTTTGCCACAAAGGTATTCTTTTACA
1 AGAGTTTTGCCACAAAGGTGTTCCTTTACA
23710117 GTCAGTAACA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 80 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (61 bp):
AGAGTTTTGCCACAAAGGTGTTCCTTTACATTTAATACTCGCCATAAAGGCTTTCCTGTCT
Found at i:23710804 original size:28 final size:28
Alignment explanation
Indices: 23710756--23710888 Score: 149
Period size: 28 Copynumber: 4.8 Consensus size: 28
23710746 AAAACTATTC
* *
23710756 TTGGCAGATACCTTTATTGATCATACTT
1 TTGGCAGATACCCTTACTGATCATACTT
* *
23710784 TTGGCGGATACCCTTACTGATCAAACTT
1 TTGGCAGATACCCTTACTGATCATACTT
* * *
23710812 TTGACAGATACCCTTACTGATCTTGCTT
1 TTGGCAGATACCCTTACTGATCATACTT
* * * * *
23710840 TTGGTAGATGCCCTTATTGATCTTGCTT
1 TTGGCAGATACCCTTACTGATCATACTT
*
23710868 TTGGCGGATACCCTTACTGAT
1 TTGGCAGATACCCTTACTGAT
23710889 ATTAATAAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 88 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (28 bp):
TTGGCAGATACCCTTACTGATCATACTT
Found at i:23711404 original size:42 final size:43
Alignment explanation
Indices: 23711345--23711437 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 43
23711335 TTTATAGAGC
* *
23711345 ATGCCACAAAGGCCATATCAGAAT-ACCATAGAGGCTAACAAA
1 ATGCCACAAAGGCCATATCAAAATAACCATAAAGGCTAACAAA
* *
23711387 ATGCCATAAAGGCCATATCAAAATACACCATAAAGGCTAGCAAA
1 ATGCCACAAAGGCCATATCAAAATA-ACCATAAAGGCTAACAAA
23711431 ATGCCAC
1 ATGCCAC
23711438 CCAAGAGCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 22 0.50
44 22 0.50
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (43 bp):
ATGCCACAAAGGCCATATCAAAATAACCATAAAGGCTAACAAA
Found at i:23711430 original size:22 final size:20
Alignment explanation
Indices: 23711366--23711432 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 20
23711356 GCCATATCAG
*
23711366 AATACCATAGAGGCTAACAA
1 AATACCATAAAGGCTAACAA
* *
23711386 AATGCCATAAAGGCCATATCAA
1 AATACCATAAAGG-C-TAACAA
*
23711408 AATACACCATAAAGGCTAGCAA
1 AAT--ACCATAAAGGCTAACAA
23711430 AAT
1 AAT
23711433 GCCACCCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 11 0.29
21 1 0.03
22 16 0.42
23 1 0.03
24 9 0.24
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.16
Consensus pattern (20 bp):
AATACCATAAAGGCTAACAA
Found at i:23717137 original size:18 final size:18
Alignment explanation
Indices: 23717092--23717140 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
23717082 CTTTTAAAAA
23717092 TATATCGATACCTATTGAAT
1 TATATCGATACCTATT--AT
*
23717112 TTTATCGATACCATATT-T
1 TATATCGATACC-TATTAT
23717130 TATATCGATAC
1 TATATCGATAC
23717141 TAGTTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 11 0.42
20 11 0.42
21 4 0.15
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (18 bp):
TATATCGATACCTATTAT
Found at i:23720515 original size:50 final size:50
Alignment explanation
Indices: 23720394--23720627 Score: 271
Period size: 50 Copynumber: 4.7 Consensus size: 50
23720384 CATATCGGTT
* * *
23720394 CCGATGCCATGTCCTAGACATGGTCTTACACTAGCACTCATC--TC-GAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCTCAGTCTGTG
* * * * * * *
23720441 TCGATGCCACGTCCCATATATGGTCTTACAC-CG-ACTCTTCTCTGTCCGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTC--CTCAGTCTGTG
* **
23720491 CCAATGTTATGTCCCAGACATGGTCTTACACTAGCACTCCTCAGTCTGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCTCAGTCTGTG
* *
23720541 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCACTCCTCGGTCTGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCTCAGTCTGTG
*
23720591 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
23720628 ACTTATTGCC
Statistics
Matches: 155, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
45 4 0.03
46 1 0.01
47 28 0.18
49 2 0.01
50 115 0.74
51 1 0.01
52 4 0.03
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.27
Consensus pattern (50 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCTCAGTCTGTG
Found at i:23723502 original size:23 final size:24
Alignment explanation
Indices: 23723476--23723527 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
23723466 ATTTCAAATG
* *
23723476 TTTTGACTTTGTTTTTGAGTCAC-
1 TTTTGACTTTGCTTTTGAGTAACA
*
23723499 TTTTCACTTTGCTTTTGAGTAACA
1 TTTTGACTTTGCTTTTGAGTAACA
23723523 TTTTG
1 TTTTG
23723528 CTACACCTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (24 bp):
TTTTGACTTTGCTTTTGAGTAACA
Found at i:23730776 original size:64 final size:62
Alignment explanation
Indices: 23730659--23730778 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 62
23730649 CTTACCATAA
* *
23730659 ATCCTTTTCAATAAACCTTTTCATATGTTAACCTTTTTAAGGAAACAACCTTTTCATTTGAT
1 ATCCGTTTCAATAAACCTTTTCATATGTTAACCTTTTCAAGGAAACAACCTTTTCATTTGAT
* * *
23730721 ATCCGTTTCGAATATAACCTTTTCATATGTTAA-CTCTTTCAGGGTAACAATCTTTTCA
1 ATCCGTTTC-AATA-AACCTTTTCATATGTTAACCT-TTTCAAGGAAACAACCTTTTCA
23730779 ACCTTTTCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 8 0.16
63 6 0.12
64 36 0.72
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.42
Consensus pattern (62 bp):
ATCCGTTTCAATAAACCTTTTCATATGTTAACCTTTTCAAGGAAACAACCTTTTCATTTGAT
Found at i:23733132 original size:20 final size:20
Alignment explanation
Indices: 23733091--23733175 Score: 82
Period size: 20 Copynumber: 4.3 Consensus size: 20
23733081 AGGCACGATT
* **
23733091 GTGCAATCAGAGGTGCCGAA
1 GTGCAAACAGAGGCACCGAA
* *
23733111 GTGCAAACAGAGACACCCAA
1 GTGCAAACAGAGGCACCGAA
* *
23733131 GTG-TAATAGAGGCACCGAA
1 GTGCAAACAGAGGCACCGAA
* *
23733150 GTGTAAACAGAGGCATCGAA
1 GTGCAAACAGAGGCACCGAA
23733170 GTGCAA
1 GTGCAA
23733176 TCTCCTACAA
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
19 15 0.29
20 36 0.71
ACGTcount: A:0.38, C:0.20, G:0.29, T:0.13
Consensus pattern (20 bp):
GTGCAAACAGAGGCACCGAA
Found at i:23733146 original size:19 final size:19
Alignment explanation
Indices: 23733119--23733155 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23733109 AAGTGCAAAC
23733119 AGAGACACCCAAGTGTAAT
1 AGAGACACCCAAGTGTAAT
* *
23733138 AGAGGCACCGAAGTGTAA
1 AGAGACACCCAAGTGTAA
23733156 ACAGAGGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.14
Consensus pattern (19 bp):
AGAGACACCCAAGTGTAAT
Found at i:23739210 original size:20 final size:20
Alignment explanation
Indices: 23739185--23739290 Score: 90
Period size: 20 Copynumber: 5.3 Consensus size: 20
23739175 GATGAGTAAT
*
23739185 AGAGGCACCGAAGTTCAAAC
1 AGAGGCACCGAAGTGCAAAC
* * **
23739205 AGAGGC-GCGATTGTGCAGTC
1 AGAGGCACCGA-AGTGCAAAC
* *
23739225 AGAGGTACCGAAGTGCAAAT
1 AGAGGCACCGAAGTGCAAAC
* * *
23739245 AAAGACACCGAAGTG-TAAC
1 AGAGGCACCGAAGTGCAAAC
*
23739264 AGAGGCACCGAAATGCAAAC
1 AGAGGCACCGAAGTGCAAAC
23739284 AGAGGCA
1 AGAGGCA
23739291 TGAAAGTGCA
Statistics
Matches: 63, Mismatches: 20, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
19 17 0.27
20 43 0.68
21 3 0.05
ACGTcount: A:0.39, C:0.21, G:0.29, T:0.11
Consensus pattern (20 bp):
AGAGGCACCGAAGTGCAAAC
Found at i:23741630 original size:60 final size:60
Alignment explanation
Indices: 23741557--23741677 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
23741547 GTTGTAGGTG
23741557 AATAATTAGATGAATGAAATAAATTTTAGGAAAAATGATTGAGTATAGACCGAGATAATT
1 AATAATTAGATGAATGAAATAAATTTTAGGAAAAATGATTGAGTATAGACCGAGATAATT
*
23741617 AATAATTAGATGAATGAAATAAATTTTAGGAAAAATGATTGAGTCTAGACCGAGATAATT
1 AATAATTAGATGAATGAAATAAATTTTAGGAAAAATGATTGAGTATAGACCGAGATAATT
23741677 A
1 A
23741678 GGTTTTGAGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.48, C:0.04, G:0.18, T:0.30
Consensus pattern (60 bp):
AATAATTAGATGAATGAAATAAATTTTAGGAAAAATGATTGAGTATAGACCGAGATAATT
Found at i:23746005 original size:24 final size:25
Alignment explanation
Indices: 23745978--23746026 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
23745968 ATAAAAATTC
23745978 AATATA-TATTT-TTATTAAATATAA
1 AATATAGTATTTCTT-TTAAATATAA
23746002 AATATAGTTATTTCTTTTAAATATA
1 AATATAG-TATTTCTTTTAAATATA
23746027 TAATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
26 14 0.64
27 2 0.09
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
AATATAGTATTTCTTTTAAATATAA
Found at i:23748949 original size:27 final size:27
Alignment explanation
Indices: 23748919--23748977 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
23748909 AAATGAATTC
*
23748919 CTTTTAGAGTTTGCCAAAAAGGCTATT
1 CTTTCAGAGTTTGCCAAAAAGGCTATT
* *
23748946 CTTTCAGAGTTTTCCACAAAGGCTATT
1 CTTTCAGAGTTTGCCAAAAAGGCTATT
23748973 CTTTC
1 CTTTC
23748978 CTTACATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (27 bp):
CTTTCAGAGTTTGCCAAAAAGGCTATT
Found at i:23755386 original size:21 final size:21
Alignment explanation
Indices: 23755360--23755402 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
23755350 GATGGTTGTT
*
23755360 ATATACTTATAACAACACTTG
1 ATATACTTATAAAAACACTTG
* *
23755381 ATATACTTTTAAAAACATTTG
1 ATATACTTATAAAAACACTTG
23755402 A
1 A
23755403 GATTTAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (21 bp):
ATATACTTATAAAAACACTTG
Found at i:23757219 original size:29 final size:29
Alignment explanation
Indices: 23757180--23757237 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
23757170 ATTGAAGGCA
23757180 ACATTTTTCAGACAGCAATGACCAAAAAC
1 ACATTTTTCAGACAGCAATGACCAAAAAC
23757209 ACATTTTTCAGACAGCAATGACCAAAAAC
1 ACATTTTTCAGACAGCAATGACCAAAAAC
23757238 TGTGAGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (29 bp):
ACATTTTTCAGACAGCAATGACCAAAAAC
Found at i:23771468 original size:25 final size:24
Alignment explanation
Indices: 23771440--23771510 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 24
23771430 TTAACAATCC
23771440 CATTATTTAGCTCTTATGAGCATCG
1 CATTATTT-GCTCTTATGAGCATCG
* * * *
23771465 CATTATATGACTCTCATGAGCTTCT
1 CATTATTTG-CTCTTATGAGCATCG
23771490 CGA-TATTTCGCTCTTATGAGC
1 C-ATTATTT-GCTCTTATGAGC
23771511 TTCCCGATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.03
25 34 0.92
26 2 0.05
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (24 bp):
CATTATTTGCTCTTATGAGCATCG
Found at i:23771527 original size:25 final size:26
Alignment explanation
Indices: 23771449--23771562 Score: 78
Period size: 25 Copynumber: 4.5 Consensus size: 26
23771439 CCATTATTTA
* *
23771449 GCTCTTATGAGCATCGC-ATTATATG
1 GCTCTTATGAGCTTCCCGATTATATG
* * * * *
23771474 ACTCTCATGAGCTTCTCGA-TATTTC
1 GCTCTTATGAGCTTCCCGATTATATG
23771499 GCTCTTATGAGCTTCCCGATTA-ATG
1 GCTCTTATGAGCTTCCCGATTATATG
**
23771524 GCTCTCT-TGAGCTTTTTCG-TT-TATG
1 GCTCT-TATGAGC-TTCCCGATTATATG
*
23771549 GCTCGTATGAGCTT
1 GCTCTTATGAGCTT
23771563 TTCGATAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
24 3 0.04
25 58 0.84
26 8 0.12
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (26 bp):
GCTCTTATGAGCTTCCCGATTATATG
Found at i:23771529 original size:50 final size:50
Alignment explanation
Indices: 23771443--23771537 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
23771433 ACAATCCCAT
*
23771443 TATTTAGCTCTTATGAGCATCGCATTATATGACTCTCATGAGCTTCTCGA
1 TATTTAGCTCTTATGAGCATCCCATTATATGACTCTCATGAGCTTCTCGA
* * * *
23771493 TATTTCGCTCTTATGAGCTTCCCGATTA-ATGGCTCTCTTGAGCTT
1 TATTTAGCTCTTATGAGCATCCC-ATTATATGACTCTCATGAGCTT
23771538 TTTCGTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 35 0.90
51 4 0.10
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (50 bp):
TATTTAGCTCTTATGAGCATCCCATTATATGACTCTCATGAGCTTCTCGA
Found at i:23771575 original size:25 final size:23
Alignment explanation
Indices: 23771475--23771576 Score: 60
Period size: 25 Copynumber: 4.1 Consensus size: 23
23771465 CATTATATGA
* *
23771475 CTCTCATGAGCTTCTCGATATTTCG
1 CTCT-ATGAGCTTCTCGATA-ATGG
*
23771500 CTCTTATGAGCTTCCCGATTAATGG
1 CTC-TATGAGCTTCTCGA-TAATGG
* * * *
23771525 CTCTCTTGAGCTTTTTCGTTTATGG
1 CTCT-ATGAGC-TTCTCGATAATGG
*
23771550 CTCGTATGAGCTTTTCGATAATTGG
1 CTC-TATGAGCTTCTCGATAA-TGG
23771575 CT
1 CT
23771577 TGCAAGAGCT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
24 9 0.15
25 43 0.72
26 8 0.13
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (23 bp):
CTCTATGAGCTTCTCGATAATGG
Found at i:23783703 original size:21 final size:21
Alignment explanation
Indices: 23783679--23783723 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
23783669 GAAATAATTC
*
23783679 CCACCCA-ATCCAACCAATACA
1 CCACCCATA-CCAACCAACACA
*
23783700 CCACCCGTACCAACCAACACA
1 CCACCCATACCAACCAACACA
23783721 CCA
1 CCA
23783724 TGTGGGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.40, C:0.51, G:0.02, T:0.07
Consensus pattern (21 bp):
CCACCCATACCAACCAACACA
Found at i:23784492 original size:27 final size:27
Alignment explanation
Indices: 23784087--23784491 Score: 423
Period size: 27 Copynumber: 15.0 Consensus size: 27
23784077 GGGCATAACA
* *
23784087 GTCATTTTACACCCATAGGGGTATTTCG
1 GTCATTTTAC-CCTATGGGGGTATTTCG
* * *
23784115 GTCATTTTCCCCTTTAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * * *
23784142 ATTATTCTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
23784169 GTTATTCTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * **
23784196 CTCATTCTACCCTATGAGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
23784223 GTCATTTTACCCTATTGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
23784250 GTTATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
23784277 ATTATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
23784304 GTCATTTTACCCTATTGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
23784331 GTCATGTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
23784358 GTCATTTTACCCTACGAGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* ** *
23784385 ATCATTTTACCCTGCGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
23784412 GTCATTTTACCTTACGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
** *
23784439 GTCATTTTACCCTATAAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
23784466 GTCATTTTATCCTATGGGGGTATTTC
1 GTCATTTTACCCTATGGGGGTATTTC
23784492 ATGTTAGAGT
Statistics
Matches: 321, Mismatches: 56, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
27 312 0.97
28 9 0.03
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:23786656 original size:12 final size:12
Alignment explanation
Indices: 23786639--23786680 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
23786629 ATCCCAATAT
23786639 TCTCTCCTCAAA
1 TCTCTCCTCAAA
*
23786651 TCTCTCC-AAATA
1 TCTCTCCTCAA-A
23786663 TCTCTCCTCAAA
1 TCTCTCCTCAAA
23786675 TCTCTC
1 TCTCTC
23786681 TATGACCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (12 bp):
TCTCTCCTCAAA
Found at i:23786659 original size:24 final size:24
Alignment explanation
Indices: 23786634--23786680 Score: 85
Period size: 24 Copynumber: 1.9 Consensus size: 24
23786624 CCCAAATCCC
23786634 AATATTCTCTCCTCAAATCTCTCCA
1 AATA-TCTCTCCTCAAATCTCTCCA
23786659 AATATCTCTCCTCAAATCTCTC
1 AATATCTCTCCTCAAATCTCTC
23786681 TATGACCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (24 bp):
AATATCTCTCCTCAAATCTCTCCA
Found at i:23786668 original size:14 final size:14
Alignment explanation
Indices: 23786634--23786681 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
23786624 CCCAAATCCC
23786634 AATATTCTCTCCTC-
1 AATA-TCTCTCCTCA
23786648 AA-ATCTCT-C-CA
1 AATATCTCTCCTCA
23786659 AATATCTCTCCTCA
1 AATATCTCTCCTCA
*
23786673 AATCTCTCT
1 AATATCTCT
23786682 ATGACCAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
10 1 0.03
11 3 0.10
12 11 0.38
13 2 0.07
14 12 0.41
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATCTCTCCTCA
Found at i:23787782 original size:21 final size:21
Alignment explanation
Indices: 23787758--23787799 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
23787748 GAAGTTAAAA
23787758 TGTTTTAATTTCACA-TTAATT
1 TGTTTTAATTTC-CATTTAATT
23787779 TGTTTTAATTTCCATTTAATT
1 TGTTTTAATTTCCATTTAATT
23787800 ACAAAATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.60
Consensus pattern (21 bp):
TGTTTTAATTTCCATTTAATT
Found at i:23793410 original size:21 final size:21
Alignment explanation
Indices: 23793371--23793410 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
23793361 ATTATATAAA
*
23793371 TTAAAAATTACAATTATTTTT
1 TTAAAAATTACAATGATTTTT
* *
23793392 TTAAAATTTATAATGATTT
1 TTAAAAATTACAATGATTT
23793411 ATCAAATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAAAAATTACAATGATTTTT
Found at i:23794141 original size:8 final size:8
Alignment explanation
Indices: 23794113--23794147 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
23794103 ATATATACTA
23794113 AATAAAAT
1 AATAAAAT
23794121 AATAATAACT
1 AATAA-AA-T
23794131 AATAAAAT
1 AATAAAAT
23794139 AATAAAAT
1 AATAAAAT
23794147 A
1 A
23794148 TCATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.60
9 4 0.16
10 6 0.24
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (8 bp):
AATAAAAT
Found at i:23794739 original size:16 final size:17
Alignment explanation
Indices: 23794714--23794747 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
23794704 TCAAAAAACG
23794714 AAACACCTAAAAATAAC
1 AAACACCTAAAAATAAC
23794731 AAACA-CTAAAAATAAC
1 AAACACCTAAAAATAAC
23794747 A
1 A
23794748 GTCATAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.68, C:0.21, G:0.00, T:0.12
Consensus pattern (17 bp):
AAACACCTAAAAATAAC
Found at i:23800214 original size:17 final size:17
Alignment explanation
Indices: 23800192--23800225 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23800182 TTAAAAAACC
23800192 CTTCTTGAAATTTCAAA
1 CTTCTTGAAATTTCAAA
**
23800209 CTTCTTGCCATTTCAAA
1 CTTCTTGAAATTTCAAA
23800226 TTTGTACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (17 bp):
CTTCTTGAAATTTCAAA
Found at i:23800814 original size:45 final size:46
Alignment explanation
Indices: 23800739--23800825 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
23800729 AAAAGTGTAG
* * *
23800739 TGTGGGCCTTAGCCCATTACAATATTAGAATCAGAAATAGAATAGA
1 TGTGGGCCTAAGCCCAATACAATATCAGAATCAGAAATAGAATAGA
*
23800785 TGTGGGCCTAAG-CCAATACAATGA-CAGAATCAGTAATAGAA
1 TGTGGGCCTAAGCCCAATACAAT-ATCAGAATCAGAAATAGAA
23800826 ATGCAACAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 24 0.67
46 12 0.33
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (46 bp):
TGTGGGCCTAAGCCCAATACAATATCAGAATCAGAAATAGAATAGA
Found at i:23801094 original size:32 final size:32
Alignment explanation
Indices: 23801041--23801211 Score: 213
Period size: 32 Copynumber: 5.4 Consensus size: 32
23801031 AAATGGCTAC
*
23801041 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
* * *
23801072 AAGCCATCAGTAACAGTGATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
* *
23801104 CAA-TCATCAGTAACGGTAATATGATTGGCACA
1 -AAGCCATCAGTAACAGTAATATGATTGGCACA
* *
23801136 AAGCCATCAGTTAC-GATAATATGATCGGCACA
1 AAGCCATCAGTAACAG-TAATATGATTGGCACA
* *
23801168 AAGCCATCAGTAACGGTAATATGATTGGCAAA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
23801200 AAGCCATCAGTA
1 AAGCCATCAGTA
23801212 GCATCACAGC
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
31 13 0.11
32 104 0.87
33 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATTGGCACA
Found at i:23801158 original size:64 final size:64
Alignment explanation
Indices: 23801041--23801211 Score: 240
Period size: 64 Copynumber: 2.7 Consensus size: 64
23801031 AAATGGCTAC
* * *
23801041 AAGCCATAAGT-ACAGTAATATGATTGGCACAAAGCCATCAGTAACAGTGATATGATCGACACA
1 AAGCCATCAGTAACGGTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACA
* * *
23801104 CAA-TCATCAGTAACGGTAATATGATTGGCACAAAGCCATCAGTTAC-GATAATATGATCGGCAC
1 -AAGCCATCAGTAACGGTAATATGATTGGCACAAAGCCATCAGTAACAG-TAATATGATCGACAC
23801167 A
64 A
*
23801168 AAGCCATCAGTAACGGTAATATGATTGGCAAAAAGCCATCAGTA
1 AAGCCATCAGTAACGGTAATATGATTGGCACAAAGCCATCAGTA
23801212 GCATCACAGC
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
63 9 0.09
64 86 0.91
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (64 bp):
AAGCCATCAGTAACGGTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACA
Found at i:23801284 original size:27 final size:26
Alignment explanation
Indices: 23801249--23801318 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
23801239 TATCGCCGCA
* *
23801249 AAGCTACCAGTAATAGT-ATATGTGGCC
1 AAGCCACCAGTAACAGTGAT-TGTGG-C
*
23801276 AAGCCACCAGTAACAGTGATTGTGGT
1 AAGCCACCAGTAACAGTGATTGTGGC
23801302 AGAGCCACCAGT-ACAGT
1 A-AGCCACCAGTAACAGT
23801319 ACTTCCTCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 6 0.16
27 30 0.79
28 2 0.05
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (26 bp):
AAGCCACCAGTAACAGTGATTGTGGC
Found at i:23801467 original size:24 final size:24
Alignment explanation
Indices: 23801383--23801464 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
23801373 CCATGCTCAG
23801383 AATCAGTCATATAAATCACAGACA
1 AATCAGTCATATAAATCACAGACA
** * *
23801407 AATCAGTCATACCATTCACAAACA
1 AATCAGTCATATAAATCACAGACA
*
23801431 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATATAAATCACAGACA
*
23801455 AATCAATCAT
1 AATCAGTCAT
23801465 TTACACTCGA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (24 bp):
AATCAGTCATATAAATCACAGACA
Found at i:23801555 original size:27 final size:27
Alignment explanation
Indices: 23801518--23802004 Score: 371
Period size: 27 Copynumber: 18.1 Consensus size: 27
23801508 TTACAGTAAC
*
23801518 TTTACCTTATAGGGGTATTTTGGTCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
* * ** *
23801545 TTAACCCTATAGAGGTATTACGATCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
* * *
23801572 TTTACCCTATGGGGGTATTTCGATCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
* *
23801599 TTTACCCTATTGGGGTATTTTTGTCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
* *
23801626 TTTATCCTATGGGGGTATTTTGGTCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
* * ***
23801653 TTTATCCTATGGGGGTATTTCACTCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
* *
23801680 TTTACCTTATAGGGGTATTTTGGCCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
* *
23801707 TCTACCCTAT-GAGGGTATTTCT-ATCAT
1 TTTACCCTATAG-GGGTATTT-TGGTCAT
** * **
23801734 TTTACATTATAAGGGTATTTCAGTCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
*
23801761 TTTACCTTATTA-GGGTATTTTGGTCAT
1 TTTACCCTA-TAGGGGTATTTTGGTCAT
* * *
23801788 TTTACCCTATGGGGGTATTCTAGTCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
* * *
23801815 TTTACCTTATAAGGGTATTTCGGTCAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
** *
23801842 TTTACCCTAT-GGTGGTATTACGGTTAT
1 TTTACCCTATAGG-GGTATTTTGGTCAT
* *
23801869 TCTACCCTAT-GAGGGTATTTCGGTCAT
1 TTTACCCTATAG-GGGTATTTTGGTCAT
* * *
23801896 TCTACCCTATGGGGGTATTTTGGTAAT
1 TTTACCCTATAGGGGTATTTTGGTCAT
* * * *
23801923 TTTACCCT-TCGGGGGTATTTCGATAAT
1 TTTACCCTAT-AGGGGTATTTTGGTCAT
* ** *
23801950 TTTACCCT-TCGGAGGTATTTCAGTAAT
1 TTTACCCTATAGG-GGTATTTTGGTCAT
* *
23801977 TTTACCC-ATCGAGGG-ATTTCGGTCAT
1 TTTACCCTATAG-GGGTATTTTGGTCAT
23802003 TT
1 TT
23802005 AACAACCTTT
Statistics
Matches: 380, Mismatches: 67, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
26 17 0.04
27 357 0.94
28 6 0.02
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
TTTACCCTATAGGGGTATTTTGGTCAT
Found at i:23801925 original size:81 final size:81
Alignment explanation
Indices: 23801518--23802004 Score: 434
Period size: 81 Copynumber: 6.0 Consensus size: 81
23801508 TTACAGTAAC
* * * *
23801518 TTTACCTTATAGGGGTATTTTGGTCATT-TAACCCTAT-AGAGGTATTACGATCATTTTACCCTA
1 TTTACCCTATTGGGGTATTTTGGTCATTCT-ACCCTATGAG-GGTATTTCGGTCATTTTACCCTA
*
23801581 TGGGGGTATTTCGATCAT
64 TGGGGGTATTTCGGTCAT
* * * * * *
23801599 TTTACCCTATTGGGGTATTTTTGTCATTTTATCCTATGGGGGTATTTTGGTCATTTTATCCTATG
1 TTTACCCTATTGGGGTATTTTGGTCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTATG
**
23801664 GGGGTATTTCACTCAT
66 GGGGTATTTCGGTCAT
* * * ** ** *
23801680 TTTACCTTATAGGGGTATTTTGGCCATTCTACCCTATGAGGGTATTTCTATCATTTTACATTATA
1 TTTACCCTATTGGGGTATTTTGGTCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTATG
* *
23801745 AGGGTATTTCAGTCAT
66 GGGGTATTTCGGTCAT
* * * * * *
23801761 TTTACCTTATTAGGGTATTTTGGTCATTTTACCCTATGGGGGTA-TTCTAGTCATTTTACCTTAT
1 TTTACCCTATTGGGGTATTTTGGTCATTCTACCCTATGAGGGTATTTC-GGTCATTTTACCCTAT
**
23801825 AAGGGTATTTCGGTCAT
65 GGGGGTATTTCGGTCAT
** * *
23801842 TTTACCCTA-TGGTGGTATTACGGTTATTCTACCCTATGAGGGTATTTCGGTCATTCTACCCTAT
1 TTTACCCTATTGG-GGTATTTTGGTCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTAT
* *
23801906 GGGGGTATTTTGGTAAT
65 GGGGGTATTTCGGTCAT
* * * * * * *
23801923 TTTACCCT-TCGGGGGTATTTCGATAATTTTACCCT-TCG-GAGGTATTTCAGTAATTTTACCC-
1 TTTACCCTAT-TGGGGTATTTTGGTCATTCTACCCTAT-GAG-GGTATTTCGGTCATTTTACCCT
*
23801984 ATCGAGGG-ATTTCGGTCAT
63 AT-GGGGGTATTTCGGTCAT
23802003 TT
1 TT
23802005 AACAACCTTT
Statistics
Matches: 335, Mismatches: 61, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
80 20 0.06
81 308 0.92
82 7 0.02
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (81 bp):
TTTACCCTATTGGGGTATTTTGGTCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTATG
GGGGTATTTCGGTCAT
Found at i:23801939 original size:54 final size:54
Alignment explanation
Indices: 23801518--23802004 Score: 464
Period size: 54 Copynumber: 9.0 Consensus size: 54
23801508 TTACAGTAAC
* * * * *
23801518 TTTACCTTATAGGGGTATTTTGGTCATTTAACCCTAT-AGAGGTATTACGATCAT
1 TTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGAG-GGTATTTCGGTCAT
* * **
23801572 TTTACCCTATGGGGGTATTTCGATCATTTTACCCTATTG-GGGTATTTTTGTCAT
1 TTTACCCTATGGGGGTATTTTGGTCATTTTACCCTA-TGAGGGTATTTCGGTCAT
* * * **
23801626 TTTATCCTATGGGGGTATTTTGGTCATTTTATCCTATGGGGGTATTTCACTCAT
1 TTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTCGGTCAT
* * * * **
23801680 TTTACCTTATAGGGGTATTTTGGCCATTCTACCCTATGAGGGTATTTCTATCAT
1 TTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTCGGTCAT
** ** ** * * *
23801734 TTTACATTATAAGGGTATTTCAGTCATTTTACCTTATTAGGGTATTTTGGTCAT
1 TTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTCGGTCAT
* * * *
23801788 TTTACCCTATGGGGGTATTCTAGTCATTTTACCTTATAAGGGTATTTCGGTCAT
1 TTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTCGGTCAT
* ** * *
23801842 TTTACCCTATGGTGGTATTACGGTTATTCTACCCTATGAGGGTATTTCGGTCAT
1 TTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTCGGTCAT
* * * * *
23801896 TCTACCCTATGGGGGTATTTTGGTAATTTTACCCT-TCGGGGGTATTTCGATAAT
1 TTTACCCTATGGGGGTATTTTGGTCATTTTACCCTAT-GAGGGTATTTCGGTCAT
* ** *
23801950 TTTACCCT-TCGGAGGTATTTCAGTAATTTTACCC-ATCGAGGG-ATTTCGGTCAT
1 TTTACCCTAT-GGGGGTATTTTGGTCATTTTACCCTAT-GAGGGTATTTCGGTCAT
23802003 TT
1 TT
23802005 AACAACCTTT
Statistics
Matches: 359, Mismatches: 68, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
53 15 0.04
54 342 0.95
55 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (54 bp):
TTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTCGGTCAT
Found at i:23802760 original size:4 final size:4
Alignment explanation
Indices: 23802751--23802806 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
23802741 TATTGTTAGT
* * * *
23802751 TTTA TTTA TTTA TTT- GTTA TTAA CTTA TTTA TTTA TTT- GTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
23802798 TTTA TTTA T
1 TTTA TTTA T
23802807 GCTTTGTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
3 4 0.10
4 34 0.83
5 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:23802814 original size:23 final size:20
Alignment explanation
Indices: 23802743--23802806 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 20
23802733 CATTTTATTA
23802743 TTGTTAGTTTTATTTATTTAT
1 TTGTTA-TTTTATTTATTTAT
23802764 TTGTTATTAACTTATTTATTTAT
1 TTGTTATT---TTATTTATTTAT
23802787 TTGTTATTTTATTTATTTAT
1 TTGTTATTTTATTTATTTAT
23802807 GCTTTGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
20 14 0.35
21 6 0.15
23 20 0.50
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (20 bp):
TTGTTATTTTATTTATTTAT
Found at i:23804551 original size:18 final size:17
Alignment explanation
Indices: 23804524--23804557 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
23804514 ATTTGTTCTT
23804524 TTTATTTTATGTTTATG
1 TTTATTTTATGTTTATG
*
23804541 TTTATTGTTATTTTTAT
1 TTTATT-TTATGTTTAT
23804558 TAATTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTATTTTATGTTTATG
Found at i:23805525 original size:19 final size:19
Alignment explanation
Indices: 23805501--23805537 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
23805491 TAGATAGAAA
23805501 AAAAGAAAAAAAATATATC
1 AAAAGAAAAAAAATATATC
23805520 AAAAGAAAAAAAATATAT
1 AAAAGAAAAAAAATATAT
23805538 TGATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAGAAAAAAAATATATC
Found at i:23816296 original size:23 final size:23
Alignment explanation
Indices: 23816270--23816316 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
23816260 AAAAGATGCA
23816270 AATTTTGATCACTACATAATCTG
1 AATTTTGATCACTACATAATCTG
23816293 AATTTTGATCACTACATAATCTG
1 AATTTTGATCACTACATAATCTG
23816316 A
1 A
23816317 GTGATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (23 bp):
AATTTTGATCACTACATAATCTG
Found at i:23817392 original size:25 final size:25
Alignment explanation
Indices: 23817347--23817448 Score: 145
Period size: 25 Copynumber: 4.1 Consensus size: 25
23817337 CATTAAGGAT
* *
23817347 TACCGATT-GCAACTCGTGAGAGCT
1 TACCGATTCTCAACTCGTGAGAGCA
*
23817371 TACCGATTCTCAGCTCGTGAGAGCA
1 TACCGATTCTCAACTCGTGAGAGCA
*
23817396 TACCGATTCTCAGCTCGTGAGAGCA
1 TACCGATTCTCAACTCGTGAGAGCA
23817421 TACCGATTCTCAACTCGT-ATGAGCA
1 TACCGATTCTCAACTCGTGA-GAGCA
23817446 TAC
1 TAC
23817449 ATGTACAAGA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
24 9 0.12
25 63 0.88
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (25 bp):
TACCGATTCTCAACTCGTGAGAGCA
Found at i:23818102 original size:20 final size:20
Alignment explanation
Indices: 23818059--23818100 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
23818049 TAATGAGAGT
23818059 AAATGAAATAGAAAATAATG
1 AAATGAAATAGAAAATAATG
23818079 AAATGCAAAT-GAAAATAA-G
1 AAATG-AAATAGAAAATAATG
23818098 AAA
1 AAA
23818101 ATTTGAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.17
Consensus pattern (20 bp):
AAATGAAATAGAAAATAATG
Found at i:23819757 original size:30 final size:31
Alignment explanation
Indices: 23819722--23819779 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
23819712 TTACATACTC
* **
23819722 AAAATTTGAGGGATTAA-AGTGTAAATACGA
1 AAAATTTGAAGGACCAATAGTGTAAATACGA
23819752 AAAATTTGAAGGACCAATAGTGTAAATA
1 AAAATTTGAAGGACCAATAGTGTAAATA
23819780 TTTTAAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (31 bp):
AAAATTTGAAGGACCAATAGTGTAAATACGA
Found at i:23840302 original size:35 final size:35
Alignment explanation
Indices: 23840263--23840345 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 35
23840253 ATGGGCATAT
23840263 CCTTGGCCGTGTGGAT-TCTGGACACA-CGGATGTGC
1 CCTTGGCCGTGTGGATCT-TGGACACATCGGAT-TGC
* * * * *
23840298 CCTTGGTCGTTTGGATCTTGGACACATGGGCTTGT
1 CCTTGGCCGTGTGGATCTTGGACACATCGGATTGC
23840333 CCTTGGCCGTGTG
1 CCTTGGCCGTGTG
23840346 AGTCCTAGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
35 35 0.90
36 4 0.10
ACGTcount: A:0.11, C:0.24, G:0.34, T:0.31
Consensus pattern (35 bp):
CCTTGGCCGTGTGGATCTTGGACACATCGGATTGC
Found at i:23841329 original size:13 final size:13
Alignment explanation
Indices: 23841311--23841335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23841301 TAGTGTTTTG
23841311 TTTTCTATTATTC
1 TTTTCTATTATTC
23841324 TTTTCTATTATT
1 TTTTCTATTATT
23841336 TTCTTGCTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTCTATTATTC
Found at i:23851975 original size:11 final size:11
Alignment explanation
Indices: 23851959--23851985 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
23851949 AGGTGTGGGA
23851959 TTTAACTTAAT
1 TTTAACTTAAT
23851970 TTTAACTTAAT
1 TTTAACTTAAT
23851981 TTTAA
1 TTTAA
23851986 TATTACCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAACTTAAT
Found at i:23858005 original size:30 final size:30
Alignment explanation
Indices: 23857969--23858083 Score: 151
Period size: 30 Copynumber: 3.9 Consensus size: 30
23857959 GTGTGCTAAA
*
23857969 CGATGGTCGAAACCATCCCTTTTCCTTAAT
1 CGATGGTCGAAACCATCCCTTTTCATTAAT
* * *
23857999 CGATGGT-AAAACCATCCATCTTCATTAAT
1 CGATGGTCGAAACCATCCCTTTTCATTAAT
** *
23858028 TAATGGTCGAAATCATCCCTTTTCATTAAT
1 CGATGGTCGAAACCATCCCTTTTCATTAAT
*
23858058 TGATGGTCGAAACCATCCCTTTTCAT
1 CGATGGTCGAAACCATCCCTTTTCAT
23858084 AGATGCTCAT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 23 0.32
30 49 0.68
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (30 bp):
CGATGGTCGAAACCATCCCTTTTCATTAAT
Found at i:23861599 original size:32 final size:32
Alignment explanation
Indices: 23861532--23861778 Score: 162
Period size: 32 Copynumber: 7.7 Consensus size: 32
23861522 TATAGTAATG
* * * * *
23861532 TGATTGGCACAAAGCTATCAATAACAGTGATA
1 TGATCGGCACAAAGCCATCAGTAACAGTAACA
* *
23861564 TGATTGGCACACAA-CCATCAGTAACGGTAACA
1 TGATCGGCACA-AAGCCATCAGTAACAGTAACA
** ** * *
23861596 TGATCAACACAAAGCCATCAGTGGCAGTGATA
1 TGATCGGCACAAAGCCATCAGTAACAGTAACA
** *
23861628 TGATCGAAACACAA-CCATCAGTAATAGTGAA-A
1 TGATCGGCACA-AAGCCATCAGTAACAGT-AACA
* * * *
23861660 TGATCGACACACAGCCATCAGTAACGGTAATA
1 TGATCGGCACAAAGCCATCAGTAACAGTAACA
* * **
23861692 TAATCGGTACAAAGCCATCAGTAATGGT-ACTA
1 TGATCGGCACAAAGCCATCAGTAACAGTAAC-A
* *
23861724 TGATCGGCACAAAGCCATCAATAACTGT-ACTA
1 TGATCGGCACAAAGCCATCAGTAACAGTAAC-A
* *
23861756 TGATAGGCACAAAGCCAGCAGTA
1 TGATCGGCACAAAGCCATCAGTA
23861779 GCATCGCAGC
Statistics
Matches: 171, Mismatches: 37, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
31 6 0.04
32 160 0.94
33 5 0.03
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (32 bp):
TGATCGGCACAAAGCCATCAGTAACAGTAACA
Found at i:23861759 original size:96 final size:96
Alignment explanation
Indices: 23861532--23861778 Score: 232
Period size: 96 Copynumber: 2.6 Consensus size: 96
23861522 TATAGTAATG
* * * * *
23861532 TGATTGGCACAAAGCTATCAATAACAGTGATATGATTGGCACACAACCATCAGTAACGGTAACAT
1 TGATCGGCACAAAGCCATCAATAACTGTGATATGATAGGCACACAGCCATCAGTAACGGTAACAT
* **
23861597 GATCAACACAAAGCCATCAGTGGCAGTGATA
66 AATCAACACAAAGCCATCAGTAACAGTGATA
** * * * * *
23861628 TGATCGAAACACAA-CCATCAGTAA-TAGTGAAATGATCGACACACAGCCATCAGTAACGGTAAT
1 TGATCGGCACA-AAGCCATCAATAACT-GTGATATGATAGGCACACAGCCATCAGTAACGGTAAC
*** **
23861691 ATAATCGGTACAAAGCCATCAGTAATGGT-ACTA
64 ATAATCAACACAAAGCCATCAGTAACAGTGA-TA
* *
23861724 TGATCGGCACAAAGCCATCAATAACTGT-ACTATGATAGGCACAAAGCCAGCAGTA
1 TGATCGGCACAAAGCCATCAATAACTGTGA-TATGATAGGCACACAGCCATCAGTA
23861779 GCATCGCAGC
Statistics
Matches: 118, Mismatches: 27, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
95 4 0.03
96 111 0.94
97 3 0.03
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (96 bp):
TGATCGGCACAAAGCCATCAATAACTGTGATATGATAGGCACACAGCCATCAGTAACGGTAACAT
AATCAACACAAAGCCATCAGTAACAGTGATA
Found at i:23861772 original size:64 final size:64
Alignment explanation
Indices: 23861539--23861766 Score: 221
Period size: 64 Copynumber: 3.6 Consensus size: 64
23861529 ATGTGATTGG
* * * *
23861539 CACAAAGCTATCAATAACAGTGATATGATTGGCACACAACCATCAGTAACGGTAACATGATCAA
1 CACAAAGCCATCAATAACAGTGATATGATCGGCACACAACCATCAGTAATGGTAACATGATCGA
* ** ** *
23861603 CACAAAGCCATCAGTGGCAGTGATATGATCGAAACACAACCATCAGTAATAGTGAA-ATGATCGA
1 CACAAAGCCATCAATAACAGTGATATGATCGGCACACAACCATCAGTAATGGT-AACATGATCGA
* * * * * *
23861667 CACACAGCCATCAGTAACGGTAATATAATCGGTACA-AAGCCATCAGTAATGGT-ACTATGATCG
1 CACAAAGCCATCAATAACAGTGATATGATCGGCACACAA-CCATCAGTAATGGTAAC-ATGATCG
*
23861730 G
64 A
* *
23861731 CACAAAGCCATCAATAACTGT-ACTATGATAGGCACA
1 CACAAAGCCATCAATAACAGTGA-TATGATCGGCACA
23861767 AAGCCAGCAG
Statistics
Matches: 133, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 127 0.95
65 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (64 bp):
CACAAAGCCATCAATAACAGTGATATGATCGGCACACAACCATCAGTAATGGTAACATGATCGA
Found at i:23861800 original size:26 final size:26
Alignment explanation
Indices: 23861769--23861825 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
23861759 TAGGCACAAA
**
23861769 GCCAGCAGTAGCATCGCAGCAAAGCT
1 GCCAGCAACAGCATCGCAGCAAAGCT
*
23861795 GCCAGCAACAGTATCGCAGCAAAGCT
1 GCCAGCAACAGCATCGCAGCAAAGCT
23861821 GCCAG
1 GCCAG
23861826 TAATAGTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.26, T:0.11
Consensus pattern (26 bp):
GCCAGCAACAGCATCGCAGCAAAGCT
Found at i:23861854 original size:27 final size:27
Alignment explanation
Indices: 23861822--23861881 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
23861812 AGCAAAGCTG
*
23861822 CCAGTAATAGTAGA-TGTGGCCA-AGCCA
1 CCAGTAACAGT-GATTGTGG-CAGAGCCA
*
23861849 CTAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
23861876 CCAGTA
1 CCAGTA
23861882 CAATACTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:23862021 original size:23 final size:23
Alignment explanation
Indices: 23861950--23862036 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
23861940 CCATGCTCAG
* *
23861950 AATCAGTCATTCAAATCACAGACA
1 AATCAGTCATT-TAACCACAGACA
** *
23861974 AATCAGTCATACCAACTACAGACA
1 AATCAGTCAT-TTAACCACAGACA
*
23861998 AATTAGTCATTTAACCACAGACA
1 AATCAGTCATTTAACCACAGACA
* *
23862021 AAACAATCATTTAACC
1 AATCAGTCATTTAACC
23862037 TCGAGAGGCA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
23 23 0.45
24 28 0.55
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (23 bp):
AATCAGTCATTTAACCACAGACA
Found at i:23862107 original size:27 final size:27
Alignment explanation
Indices: 23862072--23862522 Score: 510
Period size: 27 Copynumber: 16.7 Consensus size: 27
23862062 CCACCAGGGC
* *
23862072 ATTACGGTCATTGTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
23862099 ATTACGGTCATTTTAACCTACAGGGGG
1 ATTACGGTCATTTTACCCTACAGGGGT
*
23862126 ATTACGGTCATTTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
23862153 ATTACGGTCATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
23862180 ATTACGATCATTTTACCCTACACGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
23862207 CTTACAGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
23862234 ATTACAGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
23862261 ATTACGATCATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * * **
23862288 ACTACGATCATTTTACTCGACAGGGAC
1 ATTACGGTCATTTTACCCTACAGGGGT
23862315 ATTACGGTCA-TTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
23862341 ATTACGATCATTTTACCTTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
23862368 ATTACGGTCATTTTAGCCTACAGGGGGT
1 ATTACGGTCATTTTACCCTACA-GGGGT
*
23862396 ATTACGGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
23862423 ATTACGATCATTTTACCTTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
**
23862450 ATTACGGTCATTTTACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** * **
23862477 ATTTTGGT-ATTCTACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** *
23862503 ATTTTGGTCGTTTTACCCTA
1 ATTACGGTCATTTTACCCTA
23862523 TGGGGCCATT
Statistics
Matches: 362, Mismatches: 59, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
26 46 0.13
27 291 0.80
28 25 0.07
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:23862495 original size:26 final size:27
Alignment explanation
Indices: 23862446--23862527 Score: 112
Period size: 26 Copynumber: 3.1 Consensus size: 27
23862436 TACCTTACAA
** *
23862446 GGGTATTACGGTCATTTTACCCTATGG
1 GGGTATTTTGGTCATTCTACCCTATGG
23862473 GGGTATTTTGGT-ATTCTACCCTATGG
1 GGGTATTTTGGTCATTCTACCCTATGG
* *
23862499 GGGTATTTTGGTCGTTTTACCCTATGG
1 GGGTATTTTGGTCATTCTACCCTATGG
23862526 GG
1 GG
23862528 CCATTTCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
26 25 0.51
27 24 0.49
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTCATTCTACCCTATGG
Found at i:23862523 original size:27 final size:27
Alignment explanation
Indices: 23862077--23862656 Score: 191
Period size: 27 Copynumber: 21.5 Consensus size: 27
23862067 AGGGCATTAC
* * **
23862077 GGTCATTGTACCCTATAGGGGTATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* * **
23862104 GGTCATTTTAACCTACAGGGGG-ATTAC
1 GGTCATTTTACCCTA-TGGGGGTATTTT
*** **
23862131 GGTCATTTTACCCTACAAGGGTATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* * **
23862158 GGTCATTTTACCCTATAGGGGCATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* *** * **
23862185 GATCATTTTACCCTACACGGGTCTTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* ** * **
23862212 AGTCATTTTACCCTACAGGGGCATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* * **
23862239 AGTCATTTTACCCTATAGGGGTATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* * * * **
23862266 GATCATTTTACCCTATAGGGGCACTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* * * ** ** **
23862293 GATCATTTTACTCGACAGGGACATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
** **
23862320 GGTCA-TTTACCCTACAGGGGTATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* * ** * **
23862346 GATCATTTTACCTTACAGGGGCATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* * **
23862373 GGTCATTTTAGCCTACAGGGGGTATTAC
1 GGTCATTTTACCCTA-TGGGGGTATTTT
** * **
23862401 GGTCATTTTACCCTACAGGGGCATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
* * *** **
23862428 GATCATTTTACCTTACAAGGGTATTAC
1 GGTCATTTTACCCTATGGGGGTATTTT
23862455 GGTCATTTTACCCTATGGGGGTATTTT
1 GGTCATTTTACCCTATGGGGGTATTTT
*
23862482 GGT-ATTCTACCCTATGGGGGTATTTT
1 GGTCATTTTACCCTATGGGGGTATTTT
* ** *
23862508 GGTCGTTTTACCCTATGGGGCCATTTC
1 GGTCATTTTACCCTATGGGGGTATTTT
** *** * *
23862535 AATCATTTTACCC-ATCAAAGTTATTTG
1 GGTCATTTTACCCTAT-GGGGGTATTTT
***
23862562 GGTCATTTTACCC-AT-CAAGTATATTT
1 GGTCATTTTACCCTATGGGGGTAT-TTT
* * * *
23862588 CGATCATTTTACCCTTTGAGGGTATTTC
1 -GGTCATTTTACCCTATGGGGGTATTTT
* * *
23862616 GGTCATTTTATCCTTTGAGGGTATTTT
1 GGTCATTTTACCCTATGGGGGTATTTT
23862643 GGTCATTTTACCCT
1 GGTCATTTTACCCT
23862657 TCGAGGGTAT
Statistics
Matches: 451, Mismatches: 92, Indels: 20
0.80 0.16 0.04
Matches are distributed among these distances:
25 4 0.01
26 53 0.12
27 360 0.80
28 30 0.07
29 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (27 bp):
GGTCATTTTACCCTATGGGGGTATTTT
Found at i:23867006 original size:50 final size:50
Alignment explanation
Indices: 23866931--23867165 Score: 206
Period size: 50 Copynumber: 4.7 Consensus size: 50
23866921 GTAAAGAGAT
*
23866931 CCCATGTAAGACCATGCCTGGGACATGGCGTTGGCACCAAGATGAGAGGC
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGC
* * * *
23866981 CCCATGTAAGACGATGTTTGGGACATGGCGTTGGCACTAAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGC
* * * * * * *
23867031 CTC-TCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGA-AC
1 CCCAT-GTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGC
* * * * * ** * * ***
23867080 TCCCATGTAAGACCATATCTAGGATATGACATTGGCA-GTACATGAAACAT
1 -CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGC
*
23867130 CCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
23867166 TGTTATTATC
Statistics
Matches: 150, Mismatches: 31, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
49 38 0.25
50 111 0.74
51 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGC
Found at i:23868726 original size:24 final size:25
Alignment explanation
Indices: 23868690--23868737 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
23868680 CCAAATCCCA
*
23868690 AAATATTCTCTCCTCCAA-TCTCTCC
1 AAATATTCCCTCCT-CAATTCTCTCC
23868715 AAATA-TCCCTCCTCAATTCTCTC
1 AAATATTCCCTCCTCAATTCTCTC
23868738 TATGACTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.25, C:0.40, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATATTCCCTCCTCAATTCTCTCC
Found at i:23880504 original size:100 final size:100
Alignment explanation
Indices: 23880331--23880555 Score: 423
Period size: 100 Copynumber: 2.2 Consensus size: 100
23880321 ACCACTAAAT
*
23880331 TGGCACAGCATATTGTCTGATGCATATTGTCTGGTTTCCATTCAAACTAGGTTGCCTCAATATCT
1 TGGCACAGCATATTGTCTGATGCATATTGTCTGGTTTCAATTCAAACTAGGTTGCCTCAATATCT
23880396 GGCTTTCTAATTCCTAGGTTTAACTCACTGAAAAG
66 GGCTTTCTAATTCCTAGGTTTAACTCACTGAAAAG
*
23880431 TGGCACAGCATATTGTCTGATGCATATTGTCTGGTTTCAATTCAAACTAGGTTGCCTCATTATCT
1 TGGCACAGCATATTGTCTGATGCATATTGTCTGGTTTCAATTCAAACTAGGTTGCCTCAATATCT
*
23880496 GGCTTTCTAATTCCTGGGTTTAACTCACTGAAAAG
66 GGCTTTCTAATTCCTAGGTTTAACTCACTGAAAAG
23880531 TGGCACAGCATATTGTCTGATGCAT
1 TGGCACAGCATATTGTCTGATGCAT
23880556 CGATCCCTAT
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 122 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (100 bp):
TGGCACAGCATATTGTCTGATGCATATTGTCTGGTTTCAATTCAAACTAGGTTGCCTCAATATCT
GGCTTTCTAATTCCTAGGTTTAACTCACTGAAAAG
Found at i:23884931 original size:33 final size:33
Alignment explanation
Indices: 23884894--23884967 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
23884884 AAGAGATAAT
*
23884894 GATGCTTGAGGGATGATTAAAGAATGATTGTGG
1 GATGCTTGAGGGACGATTAAAGAATGATTGTGG
*
23884927 GATGCTTAAGGGACGATTAAAGAATGATTGTGG
1 GATGCTTGAGGGACGATTAAAGAATGATTGTGG
23884960 GATGCTTG
1 GATGCTTG
23884968 TGGAATGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (33 bp):
GATGCTTGAGGGACGATTAAAGAATGATTGTGG
Found at i:23893133 original size:419 final size:419
Alignment explanation
Indices: 23892347--23893157 Score: 1026
Period size: 419 Copynumber: 1.9 Consensus size: 419
23892337 GAAAGAGGGT
* * *
23892347 CGAAAAAACCCTAGAACTTGTGCACACTAACGTTTGTGGCCCCATAAGCGTTAGTGAAAAAGGTG
1 CGAAAAAACCCTACAACTTGTGCACACTAACGTATGTGGCCCCATAAGCGCTAGTGAAAAAGGTG
* * *
23892412 GTTATGAGTATTATGTAACCTTTATTGATGAATATTCTAGATATGGGTATGTATACCAGATTCAC
66 GTTACGAGTATTATGTAACCTTTATTGATGAATATTCTAGATATGGCTATGTATACCAGATGCAC
* * **
23892477 CTCAAGAGTGAAAGATTTGATAAATTCAAAGAGTTTCGTGTAGCAGTGGAGAAACAACTAGGTTT
131 CTCAAAAGTGAAAGATTTGATAAATTCAAAGAGTTTCGTGCAAAAGTGGAGAAACAACTAGGTTT
* * * * *
23892542 ACCCATAAAGGCACTTTGCTTTGATTGAGGTTGGGAATATTTATCTTGTAAGTTCTTAAGGTATC
196 ACCCAGAAAAGAACTTCGCTTTGATCGAGGTTGGGAATATTTATCTTGTAAGTTCTTAAGGTATC
* * * *
23892607 TAATAGAGAATAGGATTCTATCCCAGCTAATCACGCCAGCCACTCCATAATAGAATGGCGTGGGA
261 TAATAAAGAATAAGATTATATCCCAGCTAATCACGCCAGCCACTCCATAACAGAATGGCGTGGGA
* * *
23892672 AAGACAAGAAATCAAACGTTGTTAGACATGGTACGCTCGATGTTAAGTTATTCGAAGCT-CTCAA
326 AAGACAACAAATCAAACATTGTTAGACATAGTACGCTCGATGTTAAGTTATTCGAAGCTGC-CAA
23892736 TCTTCCACAATATGAAAAAGGAACAGGGGC
390 TCTTCCACAATATGAAAAAGGAACAGGGGC
* * ** * * ** *
23892766 CGAAAAACCCCTACAACTTGTGCACATTGGCGTATGTGGCCCCATGAGTGCTAGTTCAAGAGGTG
1 CGAAAAAACCCTACAACTTGTGCACACTAACGTATGTGGCCCCATAAGCGCTAGTGAAAAAGGTG
* * *
23892831 GTTACGAGTATTATGTAACCTTTATTGATGACTATTCCT-GATATAGGCT-TGTATACCTGGTGC
66 GTTACGAGTATTATGTAACCTTTATTGATGAATATT-CTAGATAT-GGCTATGTATACCAGATGC
**
23892894 A-CTGCAAAAGTGAAATCTTTGATAAATTCAAAGAGTTTCGTGCAAAAGTGGAGAAACAACTAGG
129 ACCT-CAAAAGTGAAAGATTTGATAAATTCAAAGAGTTTCGTGCAAAAGTGGAGAAACAACTAGG
* * *
23892958 TTTACCCAGAAAAGAACTTCGGTCTT-ATCGAGG-TGGAGAATATTTATC-TGATGAGTTCTTAG
193 TTTACCCAGAAAAGAACTTCGCT-TTGATCGAGGTTGG-GAATATTTATCTTG-TAAGTTCTTAA
* * * * * * *
23893020 GGTA-CTTCATAAAGAATAAGATTATATCCTAGTTAATCACGTCGGGCACTCCATAACATAATGG
255 GGTATC-TAATAAAGAATAAGATTATATCCCAGCTAATCACGCCAGCCACTCCATAACAGAATGG
* * * * * *
23893084 TGTGGTAGAGAGAACAAATCAAACATTGTTAGACATAGTACGTTCGATGTTAAGTTATTTGAAGC
319 CGTGGGAAAGACAACAAATCAAACATTGTTAGACATAGTACGCTCGATGTTAAGTTATTCGAAGC
23893149 TGCCAATCT
384 TGCCAATCT
23893158 CTTTTTGGAA
Statistics
Matches: 332, Mismatches: 52, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
418 8 0.02
419 316 0.95
420 8 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (419 bp):
CGAAAAAACCCTACAACTTGTGCACACTAACGTATGTGGCCCCATAAGCGCTAGTGAAAAAGGTG
GTTACGAGTATTATGTAACCTTTATTGATGAATATTCTAGATATGGCTATGTATACCAGATGCAC
CTCAAAAGTGAAAGATTTGATAAATTCAAAGAGTTTCGTGCAAAAGTGGAGAAACAACTAGGTTT
ACCCAGAAAAGAACTTCGCTTTGATCGAGGTTGGGAATATTTATCTTGTAAGTTCTTAAGGTATC
TAATAAAGAATAAGATTATATCCCAGCTAATCACGCCAGCCACTCCATAACAGAATGGCGTGGGA
AAGACAACAAATCAAACATTGTTAGACATAGTACGCTCGATGTTAAGTTATTCGAAGCTGCCAAT
CTTCCACAATATGAAAAAGGAACAGGGGC
Found at i:23911242 original size:26 final size:26
Alignment explanation
Indices: 23911213--23911262 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
23911203 AAATTTTCTC
*
23911213 AAAATTTTACTGGGGGTAAAATCGTT
1 AAAATTTTACCGGGGGTAAAATCGTT
23911239 AAAATTTTACCGGGGGTAAAATCG
1 AAAATTTTACCGGGGGTAAAATCG
23911263 AGATGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (26 bp):
AAAATTTTACCGGGGGTAAAATCGTT
Found at i:23912231 original size:3 final size:3
Alignment explanation
Indices: 23912223--23912258 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
23912213 AAAGAAAAGG
23912223 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23912259 TAGCTTAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23931364 original size:29 final size:29
Alignment explanation
Indices: 23931331--23931394 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
23931321 TAGAGTAAAT
* *
23931331 GGTAGACGAGAAAGGTGAAAACTTGACGG
1 GGTAGACAAAAAAGGTGAAAACTTGACGG
*
23931360 GGTAGACAAAAAAGGTGAAAGCTTGACGG
1 GGTAGACAAAAAAGGTGAAAACTTGACGG
*
23931389 AGTAGA
1 GGTAGA
23931395 AAGAAACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.41, C:0.09, G:0.36, T:0.14
Consensus pattern (29 bp):
GGTAGACAAAAAAGGTGAAAACTTGACGG
Found at i:23939575 original size:19 final size:20
Alignment explanation
Indices: 23939525--23939572 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
23939515 ATGAAGTAGG
23939525 TGAAAAAAACATGGCTTTGA
1 TGAAAAAAACATGGCTTTGA
23939545 TGAAAAAAACATGGCTTTGA
1 TGAAAAAAACATGGCTTTGA
23939565 TGGAAAAA
1 T-GAAAAA
23939573 CATTCCGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (20 bp):
TGAAAAAAACATGGCTTTGA
Found at i:23940924 original size:50 final size:50
Alignment explanation
Indices: 23940829--23940968 Score: 154
Period size: 50 Copynumber: 2.8 Consensus size: 50
23940819 AATTGAGATT
* * * * *
23940829 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATCGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATAGGCACCGAG
** * * * *
23940879 ATGAGAGGTCCCCCGTAAGACCATGTCTAGGATGTGGCATAGGCACTGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATAGGCACCGAG
** *
23940929 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCAT
23940969 TTGCAGTACA
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATAGGCACCGAG
Found at i:23941231 original size:4 final size:4
Alignment explanation
Indices: 23941222--23941264 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
23941212 ATGAGTTATT
* * * *
23941222 TAAG TAAG TAAG TAAG TAAG TAAA CAAG TAAT TGAG TAAG TAA
1 TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAA
23941265 AGAAGCGAGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.02, G:0.21, T:0.26
Consensus pattern (4 bp):
TAAG
Found at i:23947644 original size:50 final size:50
Alignment explanation
Indices: 23947589--23947728 Score: 122
Period size: 50 Copynumber: 2.8 Consensus size: 50
23947579 CATAGAGATT
* * *
23947589 ATGAGAGTTCCTATGTAAGACCATG-GCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGCTCCTATGTAAGACCATGTG-TGGGACATGGCATGGGCACCGAG
* *** * * *
23947639 ATGAGAGGTCCCCCGTAAGAACATGTGTGGGACATGGCATGGGCACTGAT
1 ATGAGAGCTCCTATGTAAGACCATGTGTGGGACATGGCATGGGCACCGAG
* * * *
23947689 ATGAGAACT-CTCATGTAAGACCATATTTGGGATATGGCAT
1 ATGAGAGCTCCT-ATGTAAGACCATGTGTGGGACATGGCAT
23947729 TGGTAGTACA
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
49 1 0.01
50 68 0.97
51 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (50 bp):
ATGAGAGCTCCTATGTAAGACCATGTGTGGGACATGGCATGGGCACCGAG
Found at i:23947999 original size:12 final size:12
Alignment explanation
Indices: 23947982--23948009 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
23947972 ATGAGTTATT
23947982 TAAGTAAACAAG
1 TAAGTAAACAAG
23947994 TAAGTAAACAAG
1 TAAGTAAACAAG
23948006 TAAG
1 TAAG
23948010 GGAGTAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (12 bp):
TAAGTAAACAAG
Found at i:23962773 original size:27 final size:27
Alignment explanation
Indices: 23962754--23962806 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
23962744 TTGGTGAAAT
*
23962754 ATGTTTGCAGATGTGTTTTGGCGAACA
1 ATGTTTGCAGATGTATTTTGGCGAACA
23962781 ATGTTTGCAGATGTATTTTGGCGAAC
1 ATGTTTGCAGATGTATTTTGGCGAAC
23962807 TAAATTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (27 bp):
ATGTTTGCAGATGTATTTTGGCGAACA
Found at i:23980759 original size:6 final size:6
Alignment explanation
Indices: 23980748--23980784 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
23980738 AGTTGTAAAG
23980748 TTTTAT TTTTAT TTTTAT TTTTATT TATTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTA-T T-TTTAT TTTTA
23980785 CTTAGTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 21 0.72
7 4 0.14
8 4 0.14
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:23987236 original size:18 final size:19
Alignment explanation
Indices: 23987213--23987261 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
23987203 GTTGTAAAGT
*
23987213 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
23987231 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
23987250 TTTAATTTTTAT
1 TTT-ATTTTTAT
23987262 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:23987241 original size:22 final size:22
Alignment explanation
Indices: 23987212--23987261 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
23987202 AGTTGTAAAG
* *
23987212 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
23987233 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
23987256 TTTTAT
1 TTTTAT
23987262 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:23992652 original size:13 final size:14
Alignment explanation
Indices: 23992627--23992655 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
23992617 GAAAAGATGG
23992627 TAATTATTAATATA
1 TAATTATTAATATA
23992641 TAATTA-TAATATA
1 TAATTATTAATATA
23992654 TA
1 TA
23992656 TTAATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATTATTAATATA
Found at i:23997902 original size:33 final size:35
Alignment explanation
Indices: 23997865--23997932 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
23997855 AAATTTTTGA
* *
23997865 CACTG-TACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGATACTGAAATGGCCTAAGGCCCAAGACTGT
* *
23997898 CACTGATACTGAAATGGCCTTAGGCCTAAGACTGT
1 CACTGATACTGAAATGGCCTAAGGCCCAAGACTGT
23997933 TCAACTGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (35 bp):
CACTGATACTGAAATGGCCTAAGGCCCAAGACTGT
Found at i:23998661 original size:25 final size:26
Alignment explanation
Indices: 23998632--23998689 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
23998622 CTGTAAGTGT
*
23998632 TCTGAAACTGATACATGCTATGATA-
1 TCTGAAACTGATACATGCTACGATAG
* *
23998657 TCTGAAACTGATATATGTTACGATAG
1 TCTGAAACTGATACATGCTACGATAG
23998683 TCTGAAA
1 TCTGAAA
23998690 GTACTGTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (26 bp):
TCTGAAACTGATACATGCTACGATAG
Found at i:24016403 original size:24 final size:24
Alignment explanation
Indices: 24016355--24016401 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
24016345 ACTGGTCATA
* *
24016355 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAAGAGGAATATTTG
24016379 GAGAGATTTGAAGAGAGAATATT
1 GAGAGATTTGAAGAG-GAATATT
24016402 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAAGAGGAATATTTG
Found at i:24017093 original size:27 final size:27
Alignment explanation
Indices: 24017031--24017370 Score: 385
Period size: 27 Copynumber: 12.6 Consensus size: 27
24017021 CCTCCAAAGG
* *
24017031 CCATAGGGTAGAATGATCGAAA-ACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * *
24017057 CTATAAGGTAAAATAACCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * * *
24017084 CCACAGGGTAAAATGAGCAAAATAACC
1 CCATAGGGTAAAATGACCGAAATACCC
* *
24017111 CCATAGGGTAAAATTAGCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
*
24017138 CCATAGGGTAAAATGAACGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * * *
24017165 CTAGAGGGTAAAATAAGCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * *
24017192 CCTTAGTGTAAAATGAGCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * *
24017219 CCATAAGGTAAACTGACCGAATTACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* *
24017246 CCACAGGGTAAAATGATCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * *
24017273 CCACAAGGTAAAATGACCGAACTACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* *
24017300 CCATAGGGTAGAATGATCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
*
24017327 CCATAAGGTAAAATGACCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* *
24017354 CCAAAAGGTAAAATGAC
1 CCATAGGGTAAAATGAC
24017371 TATTATACCC
Statistics
Matches: 263, Mismatches: 50, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
26 17 0.06
27 246 0.94
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (27 bp):
CCATAGGGTAAAATGACCGAAATACCC
Found at i:24019977 original size:27 final size:27
Alignment explanation
Indices: 24019939--24020170 Score: 288
Period size: 27 Copynumber: 8.6 Consensus size: 27
24019929 TAAGCCGAGT
* *
24019939 AATGACCAAAATACCCCCATAGGGTTA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
24019966 AATGACCGAAATACCCTCATAAGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * *
24019993 AATAACCGAAATACCCCTACAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
24020020 AATGACCGAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * *
24020047 AATGACTGAAATACTCCCATAGGGTAG
1 AATGACCGAAATACCCCCATAGGGTAA
* *
24020074 AATG-CTCAAAATACCCCCATAGGGTAG
1 AATGAC-CGAAATACCCCCATAGGGTAA
* * *
24020101 AATGACTGGAATAACCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
24020128 AATGACCGAAATA-CCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
**
24020154 AATGACCGTTATACCCC
1 AATGACCGAAATACCCC
24020171 TAAGAGATTA
Statistics
Matches: 175, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
26 25 0.14
27 149 0.85
28 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (27 bp):
AATGACCGAAATACCCCCATAGGGTAA
Found at i:24020614 original size:29 final size:29
Alignment explanation
Indices: 24020553--24020644 Score: 127
Period size: 28 Copynumber: 3.3 Consensus size: 29
24020543 TGTATTAGGT
* *
24020553 TAAGGCTCACACTGATAC-TGTATTGGGC
1 TAAGGCCCACACTGATACTTGAATTGGGC
*
24020581 TAAGGCCCACACTAATACTTGAATTGGGC
1 TAAGGCCCACACTGATACTTGAATTGGGC
*
24020610 TAAGGCCCACACTGCTA-TTGAATTGGG-
1 TAAGGCCCACACTGATACTTGAATTGGGC
24020637 TAAGGCCC
1 TAAGGCCC
24020645 TCATTGTACT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
27 8 0.14
28 26 0.45
29 24 0.41
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (29 bp):
TAAGGCCCACACTGATACTTGAATTGGGC
Found at i:24022143 original size:27 final size:27
Alignment explanation
Indices: 24022113--24022329 Score: 244
Period size: 27 Copynumber: 8.1 Consensus size: 27
24022103 TTACGCTGTT
* * *
24022113 ATGACCAAAATACCTCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
24022140 ATGACTGAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
24022167 ATGACTGAAATACCCCCATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
24022194 ATAACCGAAATA--CCC-TAGGGGTAAA
1 ATGACCGAAATACCCCCATA-GGGTAAA
*
24022219 ATGACCGAAGTA-CCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
24022245 ATAACCAAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
24022272 ATGACCGAAATACCCCAATTGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
24022299 ATGACTGAAACACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
24022326 ATGA
1 ATGA
24022330 TTGTTATACC
Statistics
Matches: 161, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
24 2 0.01
25 19 0.12
26 19 0.12
27 121 0.75
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:24022584 original size:27 final size:26
Alignment explanation
Indices: 24022553--24022604 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
24022543 CTGCTGGTGG
*
24022553 CTTTGCCACATATACTGTTACTGGTAA
1 CTTTGCCACA-ATACTATTACTGGTAA
* *
24022580 CTTTGCTACAATTCTATTACTGGTA
1 CTTTGCCACAATACTATTACTGGTA
24022605 GTTTTACTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (26 bp):
CTTTGCCACAATACTATTACTGGTAA
Found at i:24022774 original size:28 final size:28
Alignment explanation
Indices: 24022727--24022831 Score: 129
Period size: 28 Copynumber: 3.8 Consensus size: 28
24022717 ATTGTAATGT
* * *
24022727 TACTGTATTGGGCAAAGGCCCACACTAA
1 TACTGAATTGGGCTAAGGCCCACACTGA
* * * *
24022755 TACTGTATTGGTCTAGGGCCCATACTGA
1 TACTGAATTGGGCTAAGGCCCACACTGA
* *
24022783 TTCTGAATTGGGCTAAGGCCCACACTGT
1 TACTGAATTGGGCTAAGGCCCACACTGA
24022811 TACTGAATTGGGCTAAGGCCC
1 TACTGAATTGGGCTAAGGCCC
24022832 TCATTATACT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.27
Consensus pattern (28 bp):
TACTGAATTGGGCTAAGGCCCACACTGA
Found at i:24024210 original size:27 final size:27
Alignment explanation
Indices: 24024172--24024391 Score: 163
Period size: 27 Copynumber: 8.2 Consensus size: 27
24024162 TTACACTGTT
*
24024172 ATGACA-AAATACCTCCATGGGGTAAA
1 ATGACAGAAATACCTCCATAGGGTAAA
*** *
24024198 ATGACAGAAATACACT-CATACAATAGA
1 ATGACAGAAATAC-CTCCATAGGGTAAA
* *
24024225 ATGACTA-AAATACTTCTATAGGGTAAA
1 ATGAC-AGAAATACCTCCATAGGGTAAA
24024252 ATGATC-GAAATACCCTCACA-A-GGTAAA
1 ATGA-CAGAAATA-CCTC-CATAGGGTAAA
*
24024279 ATGACTGAAATACC-CCTATAGGGTAAA
1 ATGACAGAAATACCTCC-ATAGGGTAAA
* *
24024306 ATGACCA-AAATACCCCCATAGGGTAGA
1 ATGA-CAGAAATACCTCCATAGGGTAAA
* * *
24024333 ATGACCGAAATATCC-CAATTGGGTAAA
1 ATGACAGAAATA-CCTCCATAGGGTAAA
*
24024360 ATGACTGAAATACC-CCTATAGGGTAAA
1 ATGACAGAAATACCTCC-ATAGGGTAAA
24024387 ATGAC
1 ATGAC
24024392 TGTTATACCC
Statistics
Matches: 155, Mismatches: 22, Indels: 33
0.74 0.10 0.16
Matches are distributed among these distances:
24 1 0.01
25 2 0.01
26 15 0.10
27 123 0.79
28 13 0.08
29 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (27 bp):
ATGACAGAAATACCTCCATAGGGTAAA
Found at i:24024316 original size:81 final size:80
Alignment explanation
Indices: 24024224--24024391 Score: 230
Period size: 81 Copynumber: 2.1 Consensus size: 80
24024214 CATACAATAG
* ** * *
24024224 AATGACTAAAATACTTCTATAGGGTAAAATGATCGAAATACCCTCACA-AGGTAAAATGACTGAA
1 AATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCC-CA-ATAGGTAAAATGACTGAA
24024288 ATACCCCTATAGGGTAA
64 ATACCCCTATAGGGTAA
* * *
24024305 AATGACCAAAATACCCCCATAGGGTAGAATGACCGAAATATCCCAATTGGGTAAAATGACTGAAA
1 AATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCCAA-TAGGTAAAATGACTGAAA
24024370 TACCCCTATAGGGTAA
65 TACCCCTATAGGGTAA
24024386 AATGAC
1 AATGAC
24024392 TGTTATACCC
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 1 0.01
80 2 0.03
81 74 0.96
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.21
Consensus pattern (80 bp):
AATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCCAATAGGTAAAATGACTGAAAT
ACCCCTATAGGGTAA
Found at i:24024392 original size:27 final size:27
Alignment explanation
Indices: 24024224--24024403 Score: 193
Period size: 27 Copynumber: 6.7 Consensus size: 27
24024214 CATACAATAG
* **
24024224 AATGACTAAAATACTTCTATAGGGTAA
1 AATGACTGAAATACCCCTATAGGGTAA
* *
24024251 AATGA-TCGAAATA-CCCTCACAAGGTAA
1 AATGACT-GAAATACCCCT-ATAGGGTAA
24024278 AATGACTGAAATACCCCTATAGGGTAA
1 AATGACTGAAATACCCCTATAGGGTAA
** * *
24024305 AATGACCAAAATACCCCCATAGGGTAG
1 AATGACTGAAATACCCCTATAGGGTAA
* * * *
24024332 AATGACCGAAATATCCCAATTGGGTAA
1 AATGACTGAAATACCCCTATAGGGTAA
24024359 AATGACTGAAATACCCCTATAGGGTAA
1 AATGACTGAAATACCCCTATAGGGTAA
**
24024386 AATGACTGTTATACCCCT
1 AATGACTGAAATACCCCT
24024404 GGGATATGAA
Statistics
Matches: 127, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
26 3 0.02
27 119 0.94
28 5 0.04
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.23
Consensus pattern (27 bp):
AATGACTGAAATACCCCTATAGGGTAA
Found at i:24024832 original size:28 final size:28
Alignment explanation
Indices: 24024792--24024887 Score: 149
Period size: 28 Copynumber: 3.4 Consensus size: 28
24024782 ATGTTATTGT
*
24024792 ATTGGGCTTAGGCCCACACTGATACT-A
1 ATTGGGCTAAGGCCCACACTGATACTGA
24024819 TATTGGGCTAAGGCCCACACTGATACTGA
1 -ATTGGGCTAAGGCCCACACTGATACTGA
* *
24024848 ATTGGGCTAAAGCACACACTGATACTGA
1 ATTGGGCTAAGGCCCACACTGATACTGA
24024876 ATTGGGCTAAGG
1 ATTGGGCTAAGG
24024888 GCCTCATTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 62 0.98
29 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (28 bp):
ATTGGGCTAAGGCCCACACTGATACTGA
Found at i:24025968 original size:27 final size:27
Alignment explanation
Indices: 24025575--24025957 Score: 428
Period size: 27 Copynumber: 14.2 Consensus size: 27
24025565 TTTACACTGT
* ***
24025575 AATGACCAAAATACCTATATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
24025602 AATGACTGAAATACCCCCATAGGGTAG
1 AATGACCGAAATACCCCCATAGGGTAA
* * *
24025629 AATGACAGAAATACCTCCATAGGATAA
1 AATGACCGAAATACCCCCATAGGGTAA
24025656 AATGACCGAAATA-CCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
24025682 AATGACTGAAATACCCCTATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
** *
24025709 AATGACC-AAATTACCCTTATATGGTAA
1 AATGACCGAAA-TACCCCCATAGGGTAA
***
24025736 AATGAAAAAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * **
24025763 AATGAGCAAAATACCCGTATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * *
24025790 AATAAGCGAAATATCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* **
24025817 AATGATCGAAATACCCCCATAAAGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * *
24025844 AATTACCGAAATACCTCCATAGGATAA
1 AATGACCGAAATACCCCCATAGGGTAA
*
24025871 AATGACCGAAATACCCCCATAGGGTAG
1 AATGACCGAAATACCCCCATAGGGTAA
* * * *
24025898 AATGACCGAAGTGCCCCTATGGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
24025925 AATGACCGAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
24025952 AATGAC
1 AATGAC
24025958 TGTTATACCC
Statistics
Matches: 297, Mismatches: 56, Indels: 6
0.83 0.16 0.02
Matches are distributed among these distances:
26 26 0.09
27 268 0.90
28 3 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (27 bp):
AATGACCGAAATACCCCCATAGGGTAA
Found at i:24026373 original size:28 final size:28
Alignment explanation
Indices: 24026341--24026409 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
24026331 GTTACTGTAC
24026341 TGGGCTAAGGCCCACACTGATACT-ATAT
1 TGGGCTAAGGCCCACACTGATACTGA-AT
* **
24026369 TGGGCTAAGGCCCACAGTTTTACTGAAT
1 TGGGCTAAGGCCCACACTGATACTGAAT
24026397 TGGGCTAAGGCCC
1 TGGGCTAAGGCCC
24026410 TAATTGTACT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 36 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (28 bp):
TGGGCTAAGGCCCACACTGATACTGAAT
Found at i:24027101 original size:27 final size:26
Alignment explanation
Indices: 24027061--24027435 Score: 383
Period size: 27 Copynumber: 14.0 Consensus size: 26
24027051 GTTATGACCA
* * *
24027061 AAATACCTCTATAGGGTAAAATGGCTG
1 AAATACCCCCATAGGGTAAAATGAC-G
*
24027088 AAATACCCCCATAGGGTAGAATGACTG
1 AAATACCCCCATAGGGTAAAATGAC-G
* *
24027115 AAATA-CCCCATAAGATAAAATGAACG
1 AAATACCCCCATAGGGTAAAATG-ACG
24027141 AAATACCCCCATAGGGTAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGAC-G
* *
24027168 AAATACCCCTATAGGGTAAAATGACC
1 AAATACCCCCATAGGGTAAAATGACG
** * **
24027194 AAATTACCCTTATATGGTAAAATGAAAA
1 AAA-TACCCCCATAGGGTAAAATG-ACG
*
24027222 AAATACCCCCATAGGGTAAAATGAGCA
1 AAATACCCCCATAGGGTAAAATGA-CG
** *
24027249 AAATACCCGTATAGGGTAAAATAAGCG
1 AAATACCCCCATAGGGTAAAATGA-CG
*
24027276 AAATATCCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGA-CG
** *
24027303 AAATACCCCCATAAAGTAAAATTACCG
1 AAATACCCCCATAGGGTAAAATGA-CG
* *
24027330 AAATACCTCCATAGGATAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGA-CG
*
24027357 AAATACCCCCATAGGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGA-CG
* * *
24027384 AAGTACCCCTATGGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGA-CG
24027411 AAATACCCCCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
24027436 TGTTATACCC
Statistics
Matches: 294, Mismatches: 48, Indels: 13
0.83 0.14 0.04
Matches are distributed among these distances:
26 27 0.09
27 263 0.89
28 4 0.01
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.19
Consensus pattern (26 bp):
AAATACCCCCATAGGGTAAAATGACG
Found at i:24027447 original size:54 final size:54
Alignment explanation
Indices: 24027061--24027448 Score: 426
Period size: 54 Copynumber: 7.2 Consensus size: 54
24027051 GTTATGACCA
* * * *
24027061 AAATACCTCTATAGGGTAAAATGGCTGAAATACCCCCATAGGGTAGAATGACTG
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTG
* * *
24027115 AAATACCCC-ATAAGATAAAATGAACGAAATACCCCCATAGGGTAAAATGACTG
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTG
** * ***
24027168 AAATACCCCTATAGGGTAAAATGACC-AAATTACCCTTATATGGTAAAATGAAAA
1 AAATACCCCTATAGGGTAAAATGACCGAAA-TACCCCCATAGGGTAAAATGACTG
* * * ** *
24027222 AAATACCCCCATAGGGTAAAATGAGCAAAATACCCGTATAGGGTAAAATAAGC-G
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGA-CTG
* ** * *
24027276 AAATATCCCC-ATAGGGTAAAATGATCGAAATACCCCCATAAAGTAAAATTACCG
1 AAATA-CCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTG
* * *
24027330 AAATACCTCC-ATAGGATAAAATGACCGAAATACCCCCATAGGGTAGAATGACCG
1 AAATACC-CCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTG
* *
24027384 AAGTACCCCTATGGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTG
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTG
**
24027438 TTATACCCCTA
1 AAATACCCCTA
24027449 GGAGATGAAA
Statistics
Matches: 282, Mismatches: 44, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
53 55 0.20
54 220 0.78
55 7 0.02
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (54 bp):
AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTG
Found at i:24027827 original size:28 final size:28
Alignment explanation
Indices: 24027795--24027863 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
24027785 GTTACTGTAC
24027795 TGGGCTAAGGCCCACACTGATACT-ATAT
1 TGGGCTAAGGCCCACACTGATACTGA-AT
* **
24027823 TGGGCTAAGGCCCACAGTTTTACTGAAT
1 TGGGCTAAGGCCCACACTGATACTGAAT
24027851 TGGGCTAAGGCCC
1 TGGGCTAAGGCCC
24027864 TAATTGTACT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 36 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (28 bp):
TGGGCTAAGGCCCACACTGATACTGAAT
Found at i:24028673 original size:14 final size:14
Alignment explanation
Indices: 24028654--24028680 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24028644 CATTTCTTGG
24028654 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
24028668 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
24028681 ACTGGACCTC
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:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:24032762 original size:35 final size:35
Alignment explanation
Indices: 24032718--24032884 Score: 264
Period size: 35 Copynumber: 4.8 Consensus size: 35
24032708 TTCACTTGTC
* * *
24032718 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
24032753 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
24032788 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
24032823 -TTTCTTGCAGGGAATCTCTCATGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
24032857 TGTTGTTGCAGGGAATCTCTCCTGTTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCA
24032885 TGTATCATTT
Statistics
Matches: 121, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
34 31 0.26
35 90 0.74
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:24032848 original size:69 final size:70
Alignment explanation
Indices: 24032718--24032884 Score: 264
Period size: 69 Copynumber: 2.4 Consensus size: 70
24032708 TTCACTTGTC
* * * * * *
24032718 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACG
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTCTTGCAGGGAATCTCTCATGTTCACG
24032783 CATTA
66 CATTA
24032788 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA-TTTCTTGCAGGGAATCTCTCATGTTCACG
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTCTTGCAGGGAATCTCTCATGTTCACG
24032852 CATTA
66 CATTA
*
24032857 TGTTGTTGCAGGGAATCTCTCCTGTTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCA
24032885 TGTATCATTT
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
69 59 0.66
70 31 0.34
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (70 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTCTTGCAGGGAATCTCTCATGTTCACG
CATTA
Found at i:24035441 original size:21 final size:22
Alignment explanation
Indices: 24035411--24035455 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
24035401 GAACAAATTG
24035411 TTGATTCTATTTCTTTCTTG-AT
1 TTGATTCTA-TTCTTTCTTGTAT
*
24035433 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTCTTGTAT
24035454 TT
1 TT
24035456 CTCTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCTTTCTTGTAT
Found at i:24038734 original size:30 final size:30
Alignment explanation
Indices: 24038677--24038738 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
24038667 AGAACTCAGA
* *
24038677 AATATTTACAAAAAGAGGTATCTAATTTTT
1 AATATTTACAAAAAGAGGTACCAAATTTTT
24038707 AATATTTACAAAAAGA-GTAACCAAATTTTT
1 AATATTTACAAAAAGAGGT-ACCAAATTTTT
24038737 AA
1 AA
24038739 AAAGAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGTACCAAATTTTT
Found at i:24055264 original size:15 final size:15
Alignment explanation
Indices: 24055244--24055275 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
24055234 GCAAATTACC
*
24055244 TTTTGACCTTCTTGA
1 TTTTGACCATCTTGA
24055259 TTTTGACCATCTTGA
1 TTTTGACCATCTTGA
24055274 TT
1 TT
24055276 GTTACCCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTTGACCATCTTGA
Found at i:24060419 original size:33 final size:34
Alignment explanation
Indices: 24060372--24060436 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
24060362 GTGGTCAAGT
* *
24060372 AGTATCAGTCTGGG-CTTCAGCCCTATACAGTATC
1 AGTATCAGTCTGGGCCTT-AGCCCAAAACAGTATC
*
24060406 AGTA-CAGTGTGGGCCTTAGCCCAAAACAGTA
1 AGTATCAGTCTGGGCCTTAGCCCAAAACAGTA
24060437 ACAATGTGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (34 bp):
AGTATCAGTCTGGGCCTTAGCCCAAAACAGTATC
Found at i:24060445 original size:28 final size:27
Alignment explanation
Indices: 24060405--24060457 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
24060395 TATACAGTAT
* *
24060405 CAGTACAGTGTGGGCCTTAGCCCAAAA
1 CAGTACAATGTGGGCCTTAGACCAAAA
24060432 CAGTAACAATGTGGGCCTTAGACCAA
1 CAGT-ACAATGTGGGCCTTAGACCAA
24060458 TACTAGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGTACAATGTGGGCCTTAGACCAAAA
Found at i:24060875 original size:27 final size:27
Alignment explanation
Indices: 24060825--24060995 Score: 123
Period size: 27 Copynumber: 6.3 Consensus size: 27
24060815 GGGGTATAAT
*** *
24060825 AGTCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTCCAGGAGTATTTC
**
24060852 AGTCATTTTACCCTTTAGGAGTATTTC
1 AGTCATTTTACCCTCCAGGAGTATTTC
* * *
24060879 AGTCATTTAACCCTCCGGGGGTATTTC
1 AGTCATTTTACCCTCCAGGAGTATTTC
*
24060906 -GATCATTTTACCCTCCAGGAGGTATTTT
1 AG-TCATTTTACCCTCCAGGA-GTATTTC
* * * *
24060934 GGTCATCTTACCCTCTGATG-GTATTTC
1 AGTCATTTTACCCTC-CAGGAGTATTTC
* * *
24060961 -GATCATCTTACCCTCCGGGGGTATTTC
1 AG-TCATTTTACCCTCCAGGAGTATTTC
*
24060988 GGTCATTT
1 AGTCATTT
24060996 GCCCACGAAT
Statistics
Matches: 117, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
26 3 0.03
27 92 0.79
28 19 0.16
29 3 0.03
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (27 bp):
AGTCATTTTACCCTCCAGGAGTATTTC
Found at i:24060912 original size:54 final size:54
Alignment explanation
Indices: 24060825--24060995 Score: 186
Period size: 54 Copynumber: 3.1 Consensus size: 54
24060815 GGGGTATAAT
* **
24060825 AGTCATTTTACCCTATGGGGGTATTTC-AGTCATTTTACCCTTTAGGA-GTATTTC
1 AGTCA-TTTACCCTCTGGGGGTATTTCGA-TCATTTTACCCTCCAGGAGGTATTTC
* *
24060879 AGTCATTTAACCCTCCGGGGGTATTTCGATCATTTTACCCTCCAGGAGGTATTTT
1 AGTCATTT-ACCCTCTGGGGGTATTTCGATCATTTTACCCTCCAGGAGGTATTTC
* ** * *
24060934 GGTCATCTTACCCTCTGATGGTATTTCGATCATCTTACCCTCC-GGGGGTATTTC
1 AGTCAT-TTACCCTCTGGGGGTATTTCGATCATTTTACCCTCCAGGAGGTATTTC
*
24060988 GGTCATTT
1 AGTCATTT
24060996 GCCCACGAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
53 5 0.05
54 52 0.51
55 42 0.42
56 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (54 bp):
AGTCATTTACCCTCTGGGGGTATTTCGATCATTTTACCCTCCAGGAGGTATTTC
Found at i:24061561 original size:36 final size:36
Alignment explanation
Indices: 24061511--24061583 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
24061501 CCTCCTCGAG
24061511 GAAAACACTAAAACCGCAACAAGCAGCACATTGTGA
1 GAAAACACTAAAACCGCAACAAGCAGCACATTGTGA
*
24061547 GAAAACACTGAAACCGCAACAAGCAGCACATTGTGA
1 GAAAACACTAAAACCGCAACAAGCAGCACATTGTGA
24061583 G
1 G
24061584 GAAAGCATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.11
Consensus pattern (36 bp):
GAAAACACTAAAACCGCAACAAGCAGCACATTGTGA
Done.