Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 76 of 109
Found at i:24521662 original size:20 final size:20
Alignment explanation
Indices: 24521593--24521663 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 20
24521583 GTCATGTTTA
24521593 ATGTATGTATATTATATG-GT
1 ATGTATGTATATTA-ATGTGT
24521613 A--TAT-TACTATT-ATGTGT
1 ATGTATGTA-TATTAATGTGT
* *
24521630 ATG-ACTGTTTATTAATGTTT
1 ATGTA-TGTATATTAATGTGT
24521650 ATGTATGTATATTA
1 ATGTATGTATATTA
24521664 TGTATGCATG
Statistics
Matches: 40, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
16 3 0.08
17 5 0.12
18 8 0.20
19 5 0.12
20 18 0.45
21 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (20 bp):
ATGTATGTATATTAATGTGT
Found at i:24521907 original size:9 final size:9
Alignment explanation
Indices: 24521893--24521923 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
24521883 GTTAAACGAA
24521893 TCGAGTTAT
1 TCGAGTTAT
24521902 TCGAGTTAT
1 TCGAGTTAT
*
24521911 TCAAGTTAT
1 TCGAGTTAT
24521920 TCGA
1 TCGA
24521924 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:24521994 original size:9 final size:9
Alignment explanation
Indices: 24521977--24522013 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
24521967 TGAGTTTTCG
24521977 AATTCGAAT
1 AATTCGAAT
*
24521986 AACTCGAAT
1 AATTCGAAT
24521995 AATTCGAAT
1 AATTCGAAT
24522004 AATTCGAAT
1 AATTCGAAT
24522013 A
1 A
24522014 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:24524481 original size:50 final size:50
Alignment explanation
Indices: 24524352--24524547 Score: 239
Period size: 50 Copynumber: 3.9 Consensus size: 50
24524342 GATAACAACA
* * * ** * *
24524352 TGCCAAAGCCATGTCCTAGAGATGGTCTTACATGGGATGTTCTCATATCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
24524403 TGCCCATGCCATGTCCCATACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * *
24524453 TGCGAACGCCATGTTCCAGACATTGTCTTACATGGGACCTTTCGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
24524503 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
24524548 GATCTCAATA
Statistics
Matches: 121, Mismatches: 24, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 90 0.74
51 31 0.26
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:24532016 original size:51 final size:50
Alignment explanation
Indices: 24531937--24532168 Score: 189
Period size: 50 Copynumber: 4.8 Consensus size: 50
24531927 GATAACAACA
* * * **
24531937 TGCCAAAGCCATGTCCTAGAGATGGTCTTACATGGGATGTTCTCATATCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCAG
* * * * * *
24531988 TGCCCATGCCATGTCCCATACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* * *
24532038 TGCGAACGCCATGTTCCAGACATTGTCTTACATGGGA-C-CT--T-TC-G
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* * * * *
24532082 T-----CTCCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* *
24532127 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
24532169 TTACCCAAAT
Statistics
Matches: 145, Mismatches: 25, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
39 27 0.19
40 1 0.01
41 2 0.01
43 1 0.01
44 4 0.03
45 4 0.03
46 1 0.01
48 2 0.01
49 1 0.01
50 71 0.49
51 31 0.21
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
Found at i:24532105 original size:39 final size:39
Alignment explanation
Indices: 24532046--24532124 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
24532036 GGTGCGAACG
* * * *
24532046 CCATGTTCCAGACATTGTCTTACATGGGACCTTTCGTCT
1 CCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTCT
24532085 CCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTCT
1 CCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTCT
24532124 C
1 C
24532125 GGTGCCAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.19, C:0.32, G:0.18, T:0.32
Consensus pattern (39 bp):
CCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTCT
Found at i:24532147 original size:89 final size:89
Alignment explanation
Indices: 24531996--24532163 Score: 264
Period size: 89 Copynumber: 1.9 Consensus size: 89
24531986 AGTGCCCATG
* * * *
24531996 CCATGTCCCATACATGGTCTTACAGGGGACCTCTCATCTCGGTGCGAACGCCATGTTCCAGACAT
1 CCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
*
24532061 TGTCTTACATGGGACCTTTCGTCT
66 GGTCTTACATGGGACCTTTCGTCT
* * *
24532085 CCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTCTCGGTGCCAATGCCATGTCCCAGACAT
1 CCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
24532150 GGTCTTACATGGGA
66 GGTCTTACATGGGA
24532164 TCTCTTTACC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.27
Consensus pattern (89 bp):
CCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
GGTCTTACATGGGACCTTTCGTCT
Found at i:24536032 original size:24 final size:24
Alignment explanation
Indices: 24536005--24536050 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24535995 CTGCAGCAAC
* *
24536005 TCCTGCTCCACTAGCTCCTTCTGA
1 TCCTACTCCACCAGCTCCTTCTGA
*
24536029 TCCTACTTCACCAGCTCCTTCT
1 TCCTACTCCACCAGCTCCTTCT
24536051 AAAACTGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.43, G:0.09, T:0.35
Consensus pattern (24 bp):
TCCTACTCCACCAGCTCCTTCTGA
Found at i:24536625 original size:25 final size:29
Alignment explanation
Indices: 24536563--24536626 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
24536553 ATGGTTTAAG
* *
24536563 TAATGGTTGTATTTTGATGGACATTTTAT
1 TAATGTTTGTATTTTGATGGACATTATAT
24536592 TAATGTTTGTATTTTGAT-GA-ATTAT-T
1 TAATGTTTGTATTTTGATGGACATTATAT
24536618 TAAT-TTTGT
1 TAATGTTTGT
24536627 TTGTAATGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 5 0.15
26 5 0.15
27 4 0.12
28 2 0.06
29 17 0.52
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.56
Consensus pattern (29 bp):
TAATGTTTGTATTTTGATGGACATTATAT
Found at i:24536627 original size:29 final size:29
Alignment explanation
Indices: 24536557--24536631 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
24536547 TGATAGATGG
* * *
24536557 TTTAAGTAATGGTTGTATTTTGATGGACA
1 TTTAATTAATGTTTGTATTTTGATGAACA
* *
24536586 TTTTATTAATGTTTGTATTTTGATGAATTA
1 TTTAATTAATGTTTGTATTTTGATGAA-CA
*
24536616 TTTAATT-TTGTTTGTA
1 TTTAATTAATGTTTGTA
24536632 ATGGATGGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 31 0.82
30 7 0.18
ACGTcount: A:0.25, C:0.01, G:0.17, T:0.56
Consensus pattern (29 bp):
TTTAATTAATGTTTGTATTTTGATGAACA
Found at i:24536659 original size:14 final size:14
Alignment explanation
Indices: 24536640--24536666 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24536630 TAATGGATGG
24536640 TTCAATTTATGGAT
1 TTCAATTTATGGAT
24536654 TTCAATTTATGGA
1 TTCAATTTATGGA
24536667 AAAAAAATAT
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:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (14 bp):
TTCAATTTATGGAT
Found at i:24542760 original size:12 final size:12
Alignment explanation
Indices: 24542743--24542767 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24542733 GAGGCACCTA
24542743 TGCTTGAAAATG
1 TGCTTGAAAATG
24542755 TGCTTGAAAATG
1 TGCTTGAAAATG
24542767 T
1 T
24542768 ACCCAAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TGCTTGAAAATG
Found at i:24544304 original size:5 final size:5
Alignment explanation
Indices: 24544294--24544334 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
24544284 AATTTTGATA
*
24544294 AAATT AAATT AAATT AAATT -AATC AAATT -AATT AAAATT AA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT -AAATT AA
24544335 TATGATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 7 0.23
5 20 0.65
6 4 0.13
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:24544323 original size:19 final size:19
Alignment explanation
Indices: 24544299--24544335 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
24544289 TGATAAAATT
24544299 AAATTAAATT-AAATTAATC
1 AAATT-AATTAAAATTAATC
24544318 AAATTAATTAAAATTAAT
1 AAATTAATTAAAATTAAT
24544336 ATGATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTAATTAAAATTAATC
Found at i:24546037 original size:16 final size:17
Alignment explanation
Indices: 24546016--24546092 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 17
24546006 ACTAATATTC
24546016 TTAAAA-TATATATTTT
1 TTAAAACTATATATTTT
*
24546032 TTAAAACTGATATTTCTTTGTT
1 TTAAAACT-ATA--T-ATT-TT
* *
24546054 TTAAAACTAAATAATTT
1 TTAAAACTATATATTTT
24546071 TTAAAAC-ATATATTTAT
1 TTAAAACTATATATTT-T
24546088 TTAAA
1 TTAAA
24546093 TGTTATCTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
16 12 0.25
17 16 0.33
18 4 0.08
19 1 0.02
20 1 0.02
21 4 0.08
22 10 0.21
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (17 bp):
TTAAAACTATATATTTT
Found at i:24546595 original size:3 final size:3
Alignment explanation
Indices: 24546587--24546611 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24546577 GGGTAGAAAA
24546587 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
24546612 GTGGATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:24548774 original size:11 final size:11
Alignment explanation
Indices: 24548758--24548797 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
24548748 TGCTTTCTCC
24548758 CTATTTTGCTA
1 CTATTTTGCTA
*
24548769 CTATTTTACTA
1 CTATTTTGCTA
* *
24548780 TTATGTTGCTA
1 CTATTTTGCTA
24548791 CTATTTT
1 CTATTTT
24548798 TTTTATTGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:24548867 original size:30 final size:31
Alignment explanation
Indices: 24548833--24548895 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
24548823 ACTTATTTTA
*
24548833 TTGTTAA-TTTTGTTATTATTTTAAAGTCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGGCAT
*
24548863 TTGTTAATTTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGGCAT
24548894 TT
1 TT
24548896 TCTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAAAGGCAT
Found at i:24549323 original size:19 final size:20
Alignment explanation
Indices: 24549285--24549323 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
24549275 AAATAAATCA
*
24549285 AATTTTAAATGTAAGCAAAAG
1 AATTTCAAATGT-AGCAAAAG
24549306 AATTTCAAATGT-GCAAAA
1 AATTTCAAATGTAGCAAAA
24549324 AATACATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (20 bp):
AATTTCAAATGTAGCAAAAG
Found at i:24551973 original size:120 final size:120
Alignment explanation
Indices: 24551760--24552006 Score: 494
Period size: 120 Copynumber: 2.1 Consensus size: 120
24551750 AATTTACATG
24551760 TTAACCATACCAAACCACACATCAAACATGATAAGGCCATTTATATATCTACATAGCAAAATATA
1 TTAACCATACCAAACCACACATCAAACATGATAAGGCCATTTATATATCTACATAGCAAAATATA
24551825 CCAAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
66 CCAAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
24551880 TTAACCATACCAAACCACACATCAAACATGATAAGGCCATTTATATATCTACATAGCAAAATATA
1 TTAACCATACCAAACCACACATCAAACATGATAAGGCCATTTATATATCTACATAGCAAAATATA
24551945 CCAAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
66 CCAAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
24552000 TTAACCA
1 TTAACCA
24552007 AAATAACTAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 127 1.00
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.21
Consensus pattern (120 bp):
TTAACCATACCAAACCACACATCAAACATGATAAGGCCATTTATATATCTACATAGCAAAATATA
CCAAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
Found at i:24552060 original size:120 final size:118
Alignment explanation
Indices: 24551760--24552060 Score: 302
Period size: 120 Copynumber: 2.5 Consensus size: 118
24551750 AATTTACATG
* * * * * * * * *
24551760 TTAACCATACCAAACCACACATCAAACATGATAAGGCCATTTATATATCTACATAGCAAAATATA
1 TTAACCATACAAAACCACACATC--ACATGATAACGCAAATTAGATACCAAAATACCAAAATATA
24551825 CCAAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
64 CCAAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
* * * * * * * * *
24551880 TTAACCATACCAAACCACACATCAAACATGATAAGGCCATTTATATATCTACATAGCAAAATATA
1 TTAACCATACAAAACCACACATC--ACATGATAACGCAAATTAGATACCAAAATACCAAAATATA
24551945 CCAAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
64 CCAAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
* * * *
24552000 TTAACCA-A-AATAACTATACATGC-CATTATAACTCAAAATTAGATAACCAAAAGTACCAAAA
1 TTAACCATACAA-AACCACACAT-CACATGATAACGC-AAATTAGAT-ACCAAAA-TACCAAAA
24552061 GAGCAGATAG
Statistics
Matches: 163, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
117 8 0.05
118 7 0.04
119 13 0.08
120 135 0.83
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.21
Consensus pattern (118 bp):
TTAACCATACAAAACCACACATCACATGATAACGCAAATTAGATACCAAAATACCAAAATATACC
AAAACACAAGCCAAATCAAATGGCTAAAACATAATAAAACATGTAGGCTATCA
Found at i:24552518 original size:26 final size:26
Alignment explanation
Indices: 24552487--24552560 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 26
24552477 AGCTGTAAAT
*
24552487 GGTAAGCTCCTCCGAGCTAAAATAAC
1 GGTAAGCTCCTCAGAGCTAAAATAAC
* * *
24552513 GGTAAGCTCCTCTGACCT-AAATAAT
1 GGTAAGCTCCTCAGAGCTAAAATAAC
* *
24552538 GGTAAGCTCATAAGAGCTAAAAT
1 GGTAAGCTCCTCAGAGCTAAAAT
24552561 CGGTAACCCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 20 0.50
26 20 0.50
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (26 bp):
GGTAAGCTCCTCAGAGCTAAAATAAC
Found at i:24552541 original size:25 final size:26
Alignment explanation
Indices: 24552484--24552546 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
24552474 ACGAGCTGTA
*
24552484 AATGGTAAGCTCCTCCGAGCTAAAAT
1 AATGGTAAGCTCCTCCGACCTAAAAT
* *
24552510 AACGGTAAGCTCCTCTGACCT-AAAT
1 AATGGTAAGCTCCTCCGACCTAAAAT
24552535 AATGGTAAGCTC
1 AATGGTAAGCTC
24552547 ATAAGAGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 15 0.45
26 18 0.55
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (26 bp):
AATGGTAAGCTCCTCCGACCTAAAAT
Found at i:24556955 original size:26 final size:26
Alignment explanation
Indices: 24556908--24556961 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
24556898 CTGAATTTAG
* * *
24556908 AAAACACTATAGTTAGAACTTTTTGA
1 AAAAAACTATAGTTACAACTTTCTGA
**
24556934 AAAAAACTATAGTTACTTCTTTCTGA
1 AAAAAACTATAGTTACAACTTTCTGA
24556960 AA
1 AA
24556962 TTGTACTGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (26 bp):
AAAAAACTATAGTTACAACTTTCTGA
Found at i:24560389 original size:114 final size:114
Alignment explanation
Indices: 24560207--24560710 Score: 742
Period size: 114 Copynumber: 4.4 Consensus size: 114
24560197 CGTTTCCAGA
* * * * * * *
24560207 AAAGCGCCACAAAAA-ACCTAAGCCCAAGGACGCCATTTTCGGAGCTTTCGGGGATTTAGTGGCA
1 AAAGCACCGCAAAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCA
*
24560271 TTTCTAAGTAAGCGCCGCTAATGCTCAGGGATTTAGCGGCATTTTTGGG
66 TTTCTAAGTAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGG
* * *
24560320 AAAGCACCACAAAAATACCTAAGGCCAACGACGCTGTTTTCTGAGCTGTCGGGGATTTAGTGGCA
1 AAAGCACCGCAAAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCA
*
24560385 TTTCTAGGTAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGG
66 TTTCTAAGTAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGG
** *
24560434 AAAGCACCGCAAAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTTAGGGATTTAGTGGCG
1 AAAGCACCGCAAAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCA
* * * * *
24560499 CTTCTATGTAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTCTGGG
66 TTTCTAAGTAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGG
* * *
24560548 AAAGCACCGCAAAAATACCTAAGACCAACGACGCCGTTTTTTGAGCTGTCGGGGTTTTAGCGGCA
1 AAAGCACCGCAAAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCA
* *
24560613 TTT-TTAGAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGG
66 TTTCTAAG-TAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGG
**
24560662 AAAGCGTCGCAAAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGT
1 AAAGCACCGCAAAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGT
24560711 NNNNNNNNNN
Statistics
Matches: 353, Mismatches: 36, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
113 16 0.05
114 337 0.95
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (114 bp):
AAAGCACCGCAAAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCA
TTTCTAAGTAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGG
Found at i:24562531 original size:9 final size:8
Alignment explanation
Indices: 24562512--24562541 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
24562502 GGTTCAGTGT
24562512 AATTTGGG
1 AATTTGGG
24562520 AATTTGGGG
1 AATTT-GGG
24562529 AATTTGGG
1 AATTTGGG
24562537 AATTT
1 AATTT
24562542 TTGCGTGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (8 bp):
AATTTGGG
Found at i:24563596 original size:31 final size:30
Alignment explanation
Indices: 24563558--24563615 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
24563548 AAATTACAGT
*
24563558 ATATATTACATTACTTACATTACTTACTAAA
1 ATATATTACATTACTTAAATTA-TTACTAAA
24563589 ATATATTACATTACTTAAATTATTACT
1 ATATATTACATTACTTAAATTATTACT
24563616 TACCTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATATTACATTACTTAAATTATTACTAAA
Found at i:24563602 original size:18 final size:18
Alignment explanation
Indices: 24563576--24563666 Score: 89
Period size: 18 Copynumber: 4.9 Consensus size: 18
24563566 CATTACTTAC
24563576 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
*
24563593 ATTACATTACTTAAAT-T
1 ATTACATTACTAAAATAT
24563610 ATTAC-TTACCTAAAATTTAT
1 ATTACATTA-CTAAAA--TAT
*
24563630 AACTTACATTACTTAAATAT
1 -A-TTACATTACTAAAATAT
24563650 ATTACATTACTTAAAAT
1 ATTACATTAC-TAAAAT
24563667 TTATATATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
16 3 0.05
17 16 0.26
18 18 0.30
19 7 0.11
20 4 0.07
21 1 0.02
22 9 0.15
23 3 0.05
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:24563686 original size:43 final size:42
Alignment explanation
Indices: 24563589--24563691 Score: 158
Period size: 41 Copynumber: 2.5 Consensus size: 42
24563579 ACTTACTAAA
24563589 ATATATTACATTACTTAAAT-TATTACTTACCTAAAATTTAT
1 ATATATTACATTACTTAAATATATTACTTACCTAAAATTTAT
* *
24563630 A-A-CTTACATTACTTAAATATATTACATTACTTAAAATTTAT
1 ATATATTACATTACTTAAATATATTAC-TTACCTAAAATTTAT
24563671 ATATATTACATTACTTAAATA
1 ATATATTACATTACTTAAATA
24563692 AAAATTAGCT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
39 15 0.27
40 7 0.13
41 16 0.29
42 1 0.02
43 16 0.29
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.45
Consensus pattern (42 bp):
ATATATTACATTACTTAAATATATTACTTACCTAAAATTTAT
Found at i:24564684 original size:9 final size:9
Alignment explanation
Indices: 24564670--24564864 Score: 95
Period size: 9 Copynumber: 21.6 Consensus size: 9
24564660 NNNNNNNNNN
24564670 TACATAACT
1 TACATAACT
24564679 TACATAACT
1 TACATAACT
24564688 TAC--AACT
1 TACATAACT
24564695 TACATAACT
1 TACATAACT
***
24564704 TACATTTTTT
1 TACA-TAACT
*
24564714 TA-ATTA-T
1 TACATAACT
*
24564721 T-CATAAAT
1 TACATAACT
24564729 TACATAACT
1 TACATAACT
* *
24564738 TACTTTAATATT
1 TAC-AT-A-ACT
*
24564750 ATACATAAAT
1 -TACATAACT
24564760 TACATAA-T
1 TACATAACT
24564768 TA-ATTAA-T
1 TACA-TAACT
*
24564776 ATACATAAAT
1 -TACATAACT
24564786 TACATAACT
1 TACATAACT
*
24564795 TACATTAATATT
1 TACA-T-A-ACT
*
24564807 ATACATAAAT
1 -TACATAACT
24564817 TACATAACT
1 TACATAACT
**
24564826 TAGTTAA-T
1 TACATAACT
24564834 TA-ATAACT
1 TACATAACT
*
24564842 TACACAACT
1 TACATAACT
24564851 TACATAACT
1 TACATAACT
24564860 TACAT
1 TACAT
24564865 TTTTTTAATT
Statistics
Matches: 147, Mismatches: 19, Indels: 40
0.71 0.09 0.19
Matches are distributed among these distances:
7 16 0.11
8 17 0.12
9 85 0.58
10 12 0.08
11 4 0.03
12 6 0.04
13 7 0.05
ACGTcount: A:0.45, C:0.15, G:0.01, T:0.39
Consensus pattern (9 bp):
TACATAACT
Found at i:24564696 original size:16 final size:16
Alignment explanation
Indices: 24564675--24564707 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
24564665 NNNNNTACAT
24564675 AACTTACATAACTTAC
1 AACTTACATAACTTAC
24564691 AACTTACATAACTTAC
1 AACTTACATAACTTAC
24564707 A
1 A
24564708 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:24564757 original size:31 final size:31
Alignment explanation
Indices: 24564716--24564827 Score: 171
Period size: 31 Copynumber: 3.8 Consensus size: 31
24564706 CATTTTTTTA
* *
24564716 ATTATTCATAAATTACATAACTTACTTTAAT
1 ATTATACATAAATTACATAACTTACATTAAT
24564747 ATTATACATAAATTACATAA-TTA-ATT-A-
1 ATTATACATAAATTACATAACTTACATTAAT
24564774 A-TATACATAAATTACATAACTTACATTAAT
1 ATTATACATAAATTACATAACTTACATTAAT
24564804 ATTATACATAAATTACATAACTTA
1 ATTATACATAAATTACATAACTTA
24564828 GTTAATTAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
26 18 0.24
27 4 0.05
28 4 0.05
29 3 0.04
30 4 0.05
31 41 0.55
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTATACATAAATTACATAACTTACATTAAT
Found at i:24564781 original size:26 final size:27
Alignment explanation
Indices: 24564713--24564852 Score: 133
Period size: 31 Copynumber: 5.0 Consensus size: 27
24564703 TTACATTTTT
* *
24564713 TTAATTATTCATAAATTACATAACTTACT
1 TTAA-TATACATAAATTACATAACTTA-A
24564742 TTAATATTATACATAAATTACATAA-TTAA
1 TT-A-A-TATACATAAATTACATAACTTAA
24564771 TTAATATACATAAATTACATAACTTACA
1 TTAATATACATAAATTACATAACTTA-A
*
24564799 TTAATATTATACATAAATTACATAACTTAG
1 TT-A-A-TATACATAAATTACATAACTTAA
* *
24564829 TTAAT-TA-ATAACTTACACAACTTA
1 TTAATATACATAAATTACATAACTTA
24564853 CATAACTTAC
Statistics
Matches: 99, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
25 15 0.15
26 20 0.20
27 5 0.05
28 5 0.05
29 6 0.06
30 7 0.07
31 41 0.41
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (27 bp):
TTAATATACATAAATTACATAACTTAA
Found at i:24564791 original size:57 final size:58
Alignment explanation
Indices: 24564713--24564855 Score: 211
Period size: 57 Copynumber: 2.5 Consensus size: 58
24564703 TTACATTTTT
* *
24564713 TTAATTATTCATAAATTACATAACTTACTTTAATATTATACATAAATTACATAA-TTAA
1 TTAA-TATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAA
*
24564771 TTAATATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAG
1 TTAATATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAA
* *
24564829 TTAAT-TA-ATAACTTACACAACTTACAT
1 TTAATATACATAAATTACATAACTTACAT
24564856 AACTTACATT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
56 18 0.23
57 49 0.62
58 12 0.15
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.40
Consensus pattern (58 bp):
TTAATATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAA
Found at i:24571906 original size:19 final size:19
Alignment explanation
Indices: 24571882--24571918 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
24571872 GAATTCACTT
24571882 TTATTTATA-TCATTTAATA
1 TTATTT-TAGTCATTTAATA
24571901 TTATTTTAGTCATTTAAT
1 TTATTTTAGTCATTTAAT
24571919 TTGAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATTTTAGTCATTTAATA
Found at i:24571990 original size:24 final size:25
Alignment explanation
Indices: 24571962--24572010 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
24571952 AGTTTAAATC
24571962 TGGTAGCTTTTGA-TTGTTGTTGCA
1 TGGTAGCTTTTGATTTGTTGTTGCA
24571986 TGGTAGCTTTTGATTTGTTGTTGCA
1 TGGTAGCTTTTGATTTGTTGTTGCA
24572011 AGAGGGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.12, C:0.08, G:0.29, T:0.51
Consensus pattern (25 bp):
TGGTAGCTTTTGATTTGTTGTTGCA
Found at i:24572165 original size:43 final size:42
Alignment explanation
Indices: 24572126--24572304 Score: 211
Period size: 43 Copynumber: 4.2 Consensus size: 42
24572116 AATAAGCGTA
24572126 GCTAAAGAACACTA-CTTTTAGCGGCGTTTTTTTCCTAAGCGCC
1 GCTAAAGAACA-TATC-TTTAGCGGCGTTTTTTTCCTAAGCGCC
24572169 GCTAAAGAACATGATCTTTAGCGGCG-TTTTTTCCTAAGCGCC
1 GCTAAAGAACAT-ATCTTTAGCGGCGTTTTTTTCCTAAGCGCC
* * *
24572211 GCTAAAGAATATTATCTTTAGTGGCGTTTATTTT-CTTAGCGCC
1 GCTAAAGAACA-TATCTTTAGCGGCGTTT-TTTTCCTAAGCGCC
* * *
24572254 GCTAAAGAACATGTTCTTTAGCGGCATTTTTTTCTTTAAGCGCC
1 GCTAAAGAACAT-ATCTTTAGCGGCGTTTTTTTC-CTAAGCGCC
*
24572298 GCAAAAG
1 GCTAAAG
24572305 TTAGCAACAT
Statistics
Matches: 118, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
42 44 0.37
43 56 0.47
44 18 0.15
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
GCTAAAGAACATATCTTTAGCGGCGTTTTTTTCCTAAGCGCC
Found at i:24572237 original size:85 final size:87
Alignment explanation
Indices: 24572142--24572304 Score: 242
Period size: 85 Copynumber: 1.9 Consensus size: 87
24572132 GAACACTACT
24572142 TTTAGCGGCGTTT-TTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGC-GTTTTTTC-CT
1 TTTAGCGGCGTTTATTTT-CTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCAGTTTTTTCTCT
*
24572204 AAGCGCCGCTAAAGAATATTATC
65 AAGCGCCGCAAAAGAATATTATC
* * * * *
24572227 TTTAGTGGCGTTTATTTTCTTAGCGCCGCTAAAGAACATGTTCTTTAGCGGCATTTTTTTCTTTA
1 TTTAGCGGCGTTTATTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCAGTTTTTTCTCTA
24572292 AGCGCCGCAAAAG
66 AGCGCCGCAAAAG
24572305 TTAGCAACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
85 44 0.64
86 11 0.16
87 14 0.20
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (87 bp):
TTTAGCGGCGTTTATTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCAGTTTTTTCTCTA
AGCGCCGCAAAAGAATATTATC
Found at i:24583767 original size:22 final size:23
Alignment explanation
Indices: 24583729--24583773 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
24583719 ATAAATTTAT
24583729 TAAATATTAAAATAAAA-TAAAA
1 TAAATATTAAAATAAAATTAAAA
*
24583751 TAAATATTTTAAA-AAAATTAAAA
1 TAAATA-TTAAAATAAAATTAAAA
24583774 ATAATATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAATATTAAAATAAAATTAAAA
Found at i:24584457 original size:5 final size:5
Alignment explanation
Indices: 24584449--24584493 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
24584439 AAGAATAGAA
24584449 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
24584494 TAAACTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:24584798 original size:142 final size:143
Alignment explanation
Indices: 24584542--24584828 Score: 567
Period size: 142 Copynumber: 2.0 Consensus size: 143
24584532 TAATTCTTTC
24584542 TTCTCTTTTAATGCACATTTAAAAAATTTTGTTAGATAACTTTTCTATGCAATCCTCTTACCATT
1 TTCTCTTTTAATGCACATTTAAAAAATTTTGTTAGATAACTTTTCTATGCAATCCTCTTACCATT
24584607 TTTTTTACTCAACTTCTTCTCAGTATTTGGATTTTATGCTTATTTGGGGTTTTTTCAATTATAGA
66 TTTTTTACTCAACTTCTTCTCAGTATTTGGATTTTATGCTTATTTGGGGTTTTTTCAATTATAGA
24584672 TATT-ACCCAACA
131 TATTCACCCAACA
24584684 TTCTCTTTTAATGCACATTTAAAAAATTTTGTTAGATAACTTTTCTATGCAATCCTCTTACCATT
1 TTCTCTTTTAATGCACATTTAAAAAATTTTGTTAGATAACTTTTCTATGCAATCCTCTTACCATT
24584749 TTTTTTACTCAACTTCTTCTCAGTATTTGGATTTTATGCTTATTTGGGGTTTTTTCAATTATAGA
66 TTTTTTACTCAACTTCTTCTCAGTATTTGGATTTTATGCTTATTTGGGGTTTTTTCAATTATAGA
24584814 TATTCACCCAACA
131 TATTCACCCAACA
24584827 TT
1 TT
24584829 AATTATTTTA
Statistics
Matches: 144, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
142 134 0.93
143 10 0.07
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (143 bp):
TTCTCTTTTAATGCACATTTAAAAAATTTTGTTAGATAACTTTTCTATGCAATCCTCTTACCATT
TTTTTTACTCAACTTCTTCTCAGTATTTGGATTTTATGCTTATTTGGGGTTTTTTCAATTATAGA
TATTCACCCAACA
Found at i:24586621 original size:14 final size:13
Alignment explanation
Indices: 24586594--24586633 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
24586584 TATATATTTT
*
24586594 TAAAAAAATTATA
1 TAAAAAAATAATA
24586607 TAAAAATAATAATA
1 TAAAAA-AATAATA
*
24586621 TAAAAAATTAATA
1 TAAAAAAATAATA
24586634 CAGTCGGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAAAAAATAATA
Found at i:24594098 original size:127 final size:126
Alignment explanation
Indices: 24593840--24594236 Score: 640
Period size: 127 Copynumber: 3.2 Consensus size: 126
24593830 GCCCACGTGT
*
24593840 ACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAG-
1 ACGCGCTTTTGCTACAGTAGGTCTTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGT
* * * * * *
24593903 TATAAAAAACGCTTCAAGCAGGATGCT-TTATGAGAAGAATTTGTCAAATCGCACCCTCATGG
66 TA-AAAAAACGCTTCAAGCAGGATGCTATT-TGAGAAAAACTTGTGAAATTGCACCCTCGTAG
*
24593965 ATGCGCTTTTGCTACAGTAGGTCTTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGT
1 ACGCGCTTTTGCTACAGTAGGTCTTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAG-
*
24594030 TTAAAAAAAAGCTTCAAGCAGGATGCTATTTGAGAAAAACTTGTGAAATTGCACCCTCGTAG
65 TTAAAAAAACGCTTCAAGCAGGATGCTATTTGAGAAAAACTTGTGAAATTGCACCCTCGTAG
24594092 ACGCGCTTTTGCTACAGTAGGTCTTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAG-
1 ACGCGCTTTTGCTACAGTAGGTCTTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGT
* *
24594156 TATAAAAACGCTTCTAGCAGGATGCTATTTGAGAAAAACTTGTGAAATTGCACCCTCGTAG
66 TAAAAAAACGCTTCAAGCAGGATGCTATTTGAGAAAAACTTGTGAAATTGCACCCTCGTAG
24594217 ACGCGCTTTTGCTACAGTAG
1 ACGCGCTTTTGCTACAGTAG
24594237 CATGTTTGGG
Statistics
Matches: 255, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
125 101 0.40
126 38 0.15
127 112 0.44
128 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (126 bp):
ACGCGCTTTTGCTACAGTAGGTCTTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGT
TAAAAAAACGCTTCAAGCAGGATGCTATTTGAGAAAAACTTGTGAAATTGCACCCTCGTAG
Found at i:24599288 original size:7 final size:7
Alignment explanation
Indices: 24599278--24599309 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
24599268 TTATATACAT
24599278 AATACTA
1 AATACTA
24599285 AATACTA
1 AATACTA
24599292 AATACTA
1 AATACTA
24599299 AATACTA
1 AATACTA
24599306 AATA
1 AATA
24599310 TCAATCGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:24599516 original size:20 final size:20
Alignment explanation
Indices: 24599479--24599516 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
24599469 TTCATTTTTA
*
24599479 AAAATCTACATAATAATTGC
1 AAAATCTACATAAAAATTGC
24599499 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
24599517 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGC
Found at i:24600300 original size:11 final size:12
Alignment explanation
Indices: 24600284--24600346 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 12
24600274 TTAAATAAAC
24600284 TTAAGA-GAAAT
1 TTAAGAGGAAAT
24600295 TTAAGAGGAAA-
1 TTAAGAGGAAAT
* *
24600306 TTGAGAGCAAA-
1 TTAAGAGGAAAT
*
24600317 TTGAGAGGAAAT
1 TTAAGAGGAAAT
*
24600329 TT-AGAGGAGAT
1 TTAAGAGGAAAT
*
24600340 TTGAGAG
1 TTAAGAG
24600347 AGGATTAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
11 35 0.78
12 10 0.22
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (12 bp):
TTAAGAGGAAAT
Found at i:24611791 original size:23 final size:23
Alignment explanation
Indices: 24611705--24611792 Score: 67
Period size: 23 Copynumber: 3.8 Consensus size: 23
24611695 AGCCAATAAT
* *
24611705 GGGAAGCTTCAAAGAGCCATTAAC
1 GGGAAGCTTCGAAGAGCCA-TATC
*
24611729 GGGAAGC-TCTGAATAGCTC-TATC
1 GGGAAGCTTC-GAAGAGC-CATATC
24611752 GGGAAG-TTC-AAGCGAGCCATATC
1 GGGAAGCTTCGAA--GAGCCATATC
*
24611775 AGGAAGCTTCGAAGAGCC
1 GGGAAGCTTCGAAGAGCC
24611793 TTTAACGAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
21 2 0.04
22 1 0.02
23 30 0.59
24 15 0.29
25 3 0.06
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (23 bp):
GGGAAGCTTCGAAGAGCCATATC
Found at i:24611816 original size:25 final size:26
Alignment explanation
Indices: 24611786--24611843 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
24611776 GGAAGCTTCG
24611786 AAGAGCCTTTAA-CGAGAAGCTCACA
1 AAGAGCCTTTAATCGAGAAGCTCACA
*
24611811 AAGAGCCTTTAATCGGGAAGCTCACA
1 AAGAGCCTTTAATCGAGAAGCTCACA
24611837 AAGAGCC
1 AAGAGCC
24611844 ATATATCGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 12 0.39
26 19 0.61
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (26 bp):
AAGAGCCTTTAATCGAGAAGCTCACA
Found at i:24611860 original size:26 final size:26
Alignment explanation
Indices: 24611786--24611854 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
24611776 GGAAGCTTCG
* *
24611786 AAGAGCCTTTAA-CGAGAAGCTCACA
1 AAGAGCCTATAATCGGGAAGCTCACA
*
24611811 AAGAGCCTTTAATCGGGAAGCTCACA
1 AAGAGCCTATAATCGGGAAGCTCACA
24611837 AAGAGCC-ATATATCGGGA
1 AAGAGCCTATA-ATCGGGA
24611855 CACTCATAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
25 14 0.35
26 26 0.65
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
AAGAGCCTATAATCGGGAAGCTCACA
Found at i:24612599 original size:22 final size:22
Alignment explanation
Indices: 24612571--24612618 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
24612561 ATACATCGGG
24612571 ACCAAATCGAGATTAAATCAAA
1 ACCAAATCGAGATTAAATCAAA
*
24612593 ACCAAATTGAGATTAAATCAAA
1 ACCAAATCGAGATTAAATCAAA
24612615 ACCA
1 ACCA
24612619 TAAGAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.54, C:0.19, G:0.08, T:0.19
Consensus pattern (22 bp):
ACCAAATCGAGATTAAATCAAA
Found at i:24618607 original size:14 final size:14
Alignment explanation
Indices: 24618588--24618618 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
24618578 AGGGTCTTAC
24618588 ATGAATCAAATACG
1 ATGAATCAAATACG
24618602 ATGAATCAAATACG
1 ATGAATCAAATACG
24618616 ATG
1 ATG
24618619 CCAATGTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (14 bp):
ATGAATCAAATACG
Found at i:24618645 original size:55 final size:54
Alignment explanation
Indices: 24618552--24618659 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 54
24618542 AAACACATAT
*
24618552 ATCACATACAATGCCATATCCCAGACAGGGTCTTACATGAATCAAATACGATGA
1 ATCAAATACAATGCCATATCCCAGACAGGGTCTTACATGAATCAAATACGATGA
* * *
24618606 ATCAAATACGATGCCAATGTCCCAGACATGGTCTTACATGAATCAAATACGATG
1 ATCAAATACAATGCC-ATATCCCAGACAGGGTCTTACATGAATCAAATACGATG
24618660 CCAATGTCCC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 13 0.27
55 36 0.73
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (54 bp):
ATCAAATACAATGCCATATCCCAGACAGGGTCTTACATGAATCAAATACGATGA
Found at i:24618647 original size:41 final size:41
Alignment explanation
Indices: 24618602--24618684 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
24618592 ATCAAATACG
24618602 ATGAATCAAATACGATGCCAATGTCCCAGACATGGTCTTAC
1 ATGAATCAAATACGATGCCAATGTCCCAGACATGGTCTTAC
24618643 ATGAATCAAATACGATGCCAATGTCCCAGACATGGTCTTAC
1 ATGAATCAAATACGATGCCAATGTCCCAGACATGGTCTTAC
24618684 A
1 A
24618685 CGAAATCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
ATGAATCAAATACGATGCCAATGTCCCAGACATGGTCTTAC
Found at i:24624972 original size:26 final size:26
Alignment explanation
Indices: 24624910--24624981 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
24624900 AGTGAGTCAT
*
24624910 ATCGGGAAGCTC-CGGAGAGCCTTTA
1 ATCGGGAAGCTCACGAAGAGCCTTTA
*
24624935 A-CGGGAAGCTCACAAAGAGCCTTTA
1 ATCGGGAAGCTCACGAAGAGCCTTTA
24624960 ATCGGGAAGCTCACGAAGAGCC
1 ATCGGGAAGCTCACGAAGAGCC
24624982 ATATATTGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 10 0.24
25 13 0.31
26 19 0.45
ACGTcount: A:0.31, C:0.25, G:0.29, T:0.15
Consensus pattern (26 bp):
ATCGGGAAGCTCACGAAGAGCCTTTA
Found at i:24645121 original size:70 final size:67
Alignment explanation
Indices: 24645044--24645176 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 67
24645034 TCTAAATAAG
* * * *
24645044 AAAAGGCAAAACTACGTCGTTTTGATAAATATTTACCTTTTCTAAAGTTAAAAGTCAAAATCATT
1 AAAAGGCAAAACTACATCGTTTTGATAAATATTTACC-TAT-T-AAGTTAAAAGGCAAAACCATT
24645109 AAGTT
63 AAGTT
*
24645114 AAAAGGCAAAACTACATCGTTTTGATAAATGTTTACCTATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGCAAAACTACATCGTTTTGATAAATATTTACCTATTAAGTTAAAAGGCAAAACCATTA
24645177 TATTGTTTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
67 20 0.34
68 1 0.02
69 2 0.03
70 35 0.60
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.32
Consensus pattern (67 bp):
AAAAGGCAAAACTACATCGTTTTGATAAATATTTACCTATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:24646733 original size:20 final size:20
Alignment explanation
Indices: 24646686--24646759 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
24646676 TCGTAGGAGA
*
24646686 TTGCACTTCGGTGCCCCTGT
1 TTGCACTTCGGTGCCCCTAT
*
24646706 TTGTACTTCGGTGCCCCTAT
1 TTGCACTTCGGTGCCCCTAT
* * * *
24646726 TTACACTTTGGTGTCTCTAT
1 TTGCACTTCGGTGCCCCTAT
24646746 TTGCACTTCGGTGC
1 TTGCACTTCGGTGC
24646760 TAGCACTACA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.09, C:0.28, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCACTTCGGTGCCCCTAT
Found at i:24654123 original size:72 final size:71
Alignment explanation
Indices: 24653981--24654152 Score: 192
Period size: 72 Copynumber: 2.4 Consensus size: 71
24653971 TAAACATTAC
* * * * *
24653981 CGGCG-TTTTAGGTACAGCGCCACAAAAAACCTAGCGCAACGACGCCGTTTCAAGAGCATTTGGT
1 CGGCGTTTTTAAGTA-AGCGCCGCAAAAAACCTAGCCCAACGACACCGTTTCAAGAGCATTTGGG
24654045 GATTTAG
65 GATTTAG
* *
24654052 CGGCGTTTTTAAGTAAGCGCCGCTAAAAACCCTAAGCCCAACGACACCGTTTC-TGAG-ATTTTG
1 CGGCGTTTTTAAGTAAGCGCCGC-AAAAAACCT-AGCCCAACGACACCGTTTCAAGAGCA-TTTG
24654115 GGGATTTAG
63 GGGATTTAG
24654124 CGGCGTTTGTATAA--AAGCGCCGCAAAAAA
1 CGGCGTTT-T-TAAGTAAGCGCCGCAAAAAA
24654153 ACTAAGCGTA
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
71 18 0.21
72 48 0.55
73 18 0.21
74 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.23
Consensus pattern (71 bp):
CGGCGTTTTTAAGTAAGCGCCGCAAAAAACCTAGCCCAACGACACCGTTTCAAGAGCATTTGGGG
ATTTAG
Found at i:24655126 original size:39 final size:40
Alignment explanation
Indices: 24655072--24655148 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
24655062 AATAAAATTT
24655072 TTTAGGGGTTTTGCTTT-AGGGATT-AGGGAGATTTAGGAG
1 TTTAGGGGTTTTGCTTTAAGGG-TTAAGGGAGATTTAGGAG
*
24655111 TTTA-GGGTTTATGCTTTAAGGGTTAAGGGGGATTTAGG
1 TTTAGGGGTTT-TGCTTTAAGGGTTAAGGGAGATTTAGG
24655149 GTTATGGGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
38 6 0.18
39 12 0.35
40 16 0.47
ACGTcount: A:0.21, C:0.03, G:0.38, T:0.39
Consensus pattern (40 bp):
TTTAGGGGTTTTGCTTTAAGGGTTAAGGGAGATTTAGGAG
Found at i:24658038 original size:33 final size:31
Alignment explanation
Indices: 24657974--24658046 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 31
24657964 GGTTTTTGCA
* *
24657974 GCTAAGATGGTACCTTCTACTGGTTTTTGCT
1 GCTAAGATGGTACCTTCTACTGATTTCTGCT
*
24658005 GCTAAGATGGTACCGCTTCTATTGATTTCTGCT
1 GCTAAGATGGTA-C-CTTCTACTGATTTCTGCT
24658038 GCTAA-ATGG
1 GCTAAGATGG
24658047 GAAATAGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 12 0.32
32 5 0.14
33 20 0.54
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GCTAAGATGGTACCTTCTACTGATTTCTGCT
Found at i:24671104 original size:21 final size:21
Alignment explanation
Indices: 24671078--24671144 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
24671068 NNNNAACTTA
24671078 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCGGAAGCGAGGG
* *
24671099 AAGCAGCGGCGGCAA-TGAGGG
1 AAGCAGAGGCGG-AAGCGAGGG
* * * *
24671120 AAGCGGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGAAGCGAGGG
24671141 AAGC
1 AAGC
24671145 GGAGCAGAGC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 33 0.92
22 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.48, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCGGAAGCGAGGG
Found at i:24671384 original size:14 final size:14
Alignment explanation
Indices: 24671365--24671398 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
24671355 ATTGCTATTG
24671365 GTTGCTTTTGAATT
1 GTTGCTTTTGAATT
24671379 GTTGCTTTTGAATT
1 GTTGCTTTTGAATT
24671393 GTTGCT
1 GTTGCT
24671399 ACAGGAGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.56
Consensus pattern (14 bp):
GTTGCTTTTGAATT
Found at i:24676773 original size:42 final size:42
Alignment explanation
Indices: 24676734--24676998 Score: 273
Period size: 42 Copynumber: 6.3 Consensus size: 42
24676724 TATAGAAGAT
*
24676734 GGGACCGTTCCTACTCTCCTGATGATCGATACTACAGAAGGC
1 GGGACCGTTCCTACTCACCTGATGATCGATACTACAGAAGGC
* ** * * * * * * * * *
24676776 GTGATAGATCTTACACTCCCGAGGA-CTGTTACTACCGCAGGC
1 GGGACCGTTCCTACTCACCTGATGATC-GATACTACAGAAGGC
* * **
24676818 GGAACCGTTCCTACTCACCTGATGATGGATACTGTAGAAGGC
1 GGGACCGTTCCTACTCACCTGATGATCGATACTACAGAAGGC
* * *
24676860 GGGACCGTTCTTA-TGCACCTGATGATCGGTACTACAGAAGGT
1 GGGACCGTTCCTACT-CACCTGATGATCGATACTACAGAAGGC
* *
24676902 GGGATCGTTCCTACTCACCTGACGATCGATACTACAGAAGGC
1 GGGACCGTTCCTACTCACCTGATGATCGATACTACAGAAGGC
*
24676944 GGGACCGTTCCTACTCACCTGATGATCGATACTATAGAAGGC
1 GGGACCGTTCCTACTCACCTGATGATCGATACTACAGAAGGC
* *
24676986 GTGACCGGTCCTA
1 GGGACCGTTCCTA
24676999 TGATTCAGCT
Statistics
Matches: 175, Mismatches: 44, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
41 2 0.01
42 172 0.98
43 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (42 bp):
GGGACCGTTCCTACTCACCTGATGATCGATACTACAGAAGGC
Found at i:24677546 original size:29 final size:27
Alignment explanation
Indices: 24677493--24677559 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 27
24677483 AGCGTTCCGT
*
24677493 ATTAAGATCTTTTTGATTTGATGATTGGA
1 ATTAAGAT-TTTTTGATTTGATGA-TGAA
*
24677522 ATTAAGATTTTGTT-ATTTTATTGATGAA
1 ATTAAGATTTT-TTGATTTGA-TGATGAA
24677550 ATGTAAGATT
1 AT-TAAGATT
24677560 ACTTAATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.49
Consensus pattern (27 bp):
ATTAAGATTTTTTGATTTGATGATGAA
Found at i:24680196 original size:14 final size:15
Alignment explanation
Indices: 24680171--24680199 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
24680161 TTTACTTCAT
24680171 CAAAATTAATTTTTC
1 CAAAATTAATTTTTC
24680186 CAAAA-TAATTTTTC
1 CAAAATTAATTTTTC
24680200 AAGAAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (15 bp):
CAAAATTAATTTTTC
Found at i:24681322 original size:16 final size:16
Alignment explanation
Indices: 24681301--24681331 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24681291 CTATGCATGC
*
24681301 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
24681317 AAAATACAAAAGACA
1 AAAATACAAAAGACA
24681332 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:24693274 original size:27 final size:27
Alignment explanation
Indices: 24693211--24693289 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
24693201 TAATTTAGTT
*
24693211 GTGGTGCCTATCTGATAGGCGGCACTA
1 GTGGTGCCTATCTGATAGGTGGCACTA
*** *
24693238 GTGACCCCTATCTGATAGGTGGCACTG
1 GTGGTGCCTATCTGATAGGTGGCACTA
*
24693265 GTGGTGCCTATCTAATAGGTGGCAC
1 GTGGTGCCTATCTGATAGGTGGCAC
24693290 ACCTAGTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.27
Consensus pattern (27 bp):
GTGGTGCCTATCTGATAGGTGGCACTA
Found at i:24696403 original size:51 final size:51
Alignment explanation
Indices: 24696233--24696684 Score: 427
Period size: 51 Copynumber: 8.9 Consensus size: 51
24696223 ACTATTATCA
* * *
24696233 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AA-TTT
1 TTCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * *
24696282 TTACGGTTCACGTAATAGCCTTCACATAGTACTATACACGTGATC-AAGCTT
1 TT-CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * *
24696333 TACGATTCACGTAGTAGCCTTCACATAGTACTACATATGTGACTAAAGCTT
1 TTCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * * *
24696384 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATT
1 TTCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGC-TT
* *
24696434 TATCAATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
1 T-TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * ** * * * *
24696486 CTCGGTACATATTGTAGCCTTCACTTAGTACTACACATGTGACCATTA--TT
1 TTCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGCTT
* *
24696536 TATCGATTCACGTAGTAGCCTTCACACAATACTACACACGTGACCAAAGCTT
1 T-TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * * * * *
24696588 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTA--TT
1 TTCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGCTT
*
24696638 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
1 T-TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAA
24696685 CACTTTCACT
Statistics
Matches: 320, Mismatches: 70, Indels: 25
0.77 0.17 0.06
Matches are distributed among these distances:
49 4 0.01
50 83 0.26
51 225 0.70
52 6 0.02
53 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (51 bp):
TTCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
Found at i:24696477 original size:102 final size:102
Alignment explanation
Indices: 24696234--24696684 Score: 631
Period size: 102 Copynumber: 4.4 Consensus size: 102
24696224 CTATTATCAT
* * * * * * * *
24696234 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AA-TTTTTACGGTTCACGTAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATAG
* * * * *
24696297 TAGCCTTCACATAGTACTATACACGTGATCAAGC-TTTA
65 TAGCCTTCACTTAGTACTACACATGTGA-CCATCATTTA
* * * * *
24696335 -CGATTCACGTAGTAGCCTTCACATAGTACTACATATGTGACTAAAGCTTTTCGGTACACATAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
24696399 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * *
24696436 TCAATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACATATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
*
24696501 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* *
24696538 TCGATTCACGTAGTAGCCTTCACACAATACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
*
24696603 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
24696640 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
24696685 CACTTTCACT
Statistics
Matches: 319, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
100 40 0.13
101 40 0.13
102 239 0.75
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:24702660 original size:3 final size:3
Alignment explanation
Indices: 24702646--24702699 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
24702636 TTCTTTTTCC
* *
24702646 CTT CTC CTT CTT CTT CTT CTT CTT CTT -TT CTT CTC CTT C-T CTTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
*
24702690 CTT CTC CTT C
1 CTT CTT CTT C
24702700 ACTCACCGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 4 0.10
3 36 0.86
4 2 0.05
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:24702669 original size:29 final size:29
Alignment explanation
Indices: 24702636--24702699 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
24702626 TTATTATTAT
24702636 TTCTT-TTTCCCTTCTCCTTCT-TCTTCTTC
1 TTCTTCTTT-CCTTCTCCTTCTCT-TTCTTC
*
24702665 TTCTTCTTTTCTTCTCCTTCTCTTTCTTC
1 TTCTTCTTTCCTTCTCCTTCTCTTTCTTC
*
24702694 TCCTTC
1 TTCTTC
24702700 ACTCACCGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (29 bp):
TTCTTCTTTCCTTCTCCTTCTCTTTCTTC
Found at i:24703790 original size:32 final size:33
Alignment explanation
Indices: 24703754--24703817 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
24703744 ATGGCTTGAT
24703754 TTAAAATGAAAAATT-AAA-AAAAAA-TTAAAACG
1 TTAAAATG--AAATTAAAATAAAAAATTTAAAACG
24703786 TTAAAATGAAATTAAAATAAAAAATTTAAAAC
1 TTAAAATGAAATTAAAATAAAAAATTTAAAAC
24703818 AAAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 5 0.17
31 3 0.10
32 14 0.48
33 7 0.24
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (33 bp):
TTAAAATGAAATTAAAATAAAAAATTTAAAACG
Found at i:24703802 original size:25 final size:25
Alignment explanation
Indices: 24703774--24703826 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
24703764 AAATTAAAAA
* * **
24703774 AAAATTAAAACGTTAAAATGAAATT
1 AAAATAAAAAAGTTAAAACAAAATT
*
24703799 AAAATAAAAAATTTAAAACAAAATT
1 AAAATAAAAAAGTTAAAACAAAATT
24703824 AAA
1 AAA
24703827 TCATTAATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (25 bp):
AAAATAAAAAAGTTAAAACAAAATT
Found at i:24705124 original size:23 final size:22
Alignment explanation
Indices: 24705092--24705134 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
24705082 GAAATCTTAC
*
24705092 CCATCCAGCCTCTGCACTCCACT
1 CCATCCAGCC-CAGCACTCCACT
*
24705115 CCATCTAGCCCAGCACTCCA
1 CCATCCAGCCCAGCACTCCA
24705135 TGTGGGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.21, C:0.51, G:0.09, T:0.19
Consensus pattern (22 bp):
CCATCCAGCCCAGCACTCCACT
Found at i:24705354 original size:25 final size:26
Alignment explanation
Indices: 24705321--24705372 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
24705311 ACAATCATAC
*
24705321 ATAACATAAAACAT-ACAGTCATTTT
1 ATAACATAAAACATAACAGGCATTTT
**
24705346 ATAACATAAGGCATAACAGGCATTTT
1 ATAACATAAAACATAACAGGCATTTT
24705372 A
1 A
24705373 CCACGTGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (26 bp):
ATAACATAAAACATAACAGGCATTTT
Found at i:24709332 original size:31 final size:30
Alignment explanation
Indices: 24709294--24709363 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
24709284 CGGCTCAGTT
*
24709294 ACTAAAATGTTACAGCA-CACAAACATATGTG
1 ACTAAAATGTTA-A-CATCACAAACATAAGTG
**
24709325 ACTAAAATG-TAACATTTCAAACATAAGTG
1 ACTAAAATGTTAACATCACAAACATAAGTG
24709354 ACTAAAATGT
1 ACTAAAATGT
24709364 AACCTAAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 21 0.62
30 2 0.06
31 9 0.26
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (30 bp):
ACTAAAATGTTAACATCACAAACATAAGTG
Found at i:24709758 original size:19 final size:20
Alignment explanation
Indices: 24709730--24709768 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
24709720 AGAAACTGCA
24709730 GAATTAAC-TTTATAACATT
1 GAATTAACTTTTATAACATT
*
24709749 GAATTGACTTTTATAACATT
1 GAATTAACTTTTATAACATT
24709769 TTTTTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (20 bp):
GAATTAACTTTTATAACATT
Found at i:24709903 original size:22 final size:23
Alignment explanation
Indices: 24709876--24709923 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
24709866 TATTATTGTT
*
24709876 AATTAATTATAAATTTT-GATTA
1 AATTAATTATAAATTTTAAATTA
*
24709898 AATTAATTTTAAATTTTAAATTA
1 AATTAATTATAAATTTTAAATTA
24709921 AAT
1 AAT
24709924 ATTAATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AATTAATTATAAATTTTAAATTA
Found at i:24710384 original size:18 final size:18
Alignment explanation
Indices: 24710357--24710391 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24710347 CATAATTAAT
24710357 AAAAAATAAAA-TTATTC
1 AAAAAATAAAAGTTATTC
24710374 AAAATAATAAAAGTTATT
1 AAAA-AATAAAAGTTATT
24710392 TTGTACCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAAATAAAAGTTATTC
Found at i:24718343 original size:19 final size:18
Alignment explanation
Indices: 24718321--24718446 Score: 96
Period size: 19 Copynumber: 6.7 Consensus size: 18
24718311 TTTTGATGCA
24718321 TTTTATAATTTTTTATAAT
1 TTTTATAATTTTTTA-AAT
** *
24718340 TTTTATAACATTTTACACT
1 TTTTATAATTTTTTA-AAT
24718359 TTTT-TATATTTTTTACAAT
1 TTTTATA-ATTTTTTA-AAT
*
24718378 TTTTAT-ATTTTTTTAAT
1 TTTTATAATTTTTTAAAT
**
24718395 TTTTAATAA-AATTTAAAT
1 TTTT-ATAATTTTTTAAAT
24718413 ATTGTTATAATTTTATTAAAT
1 -TT-TTATAATTTT-TTAAAT
*
24718434 TTTAATAATTTTT
1 TTTTATAATTTTT
24718447 ATTGATGTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
17 7 0.08
18 18 0.21
19 48 0.56
20 6 0.07
21 6 0.07
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTTTAAAT
Found at i:24718352 original size:29 final size:28
Alignment explanation
Indices: 24718320--24718446 Score: 118
Period size: 29 Copynumber: 4.5 Consensus size: 28
24718310 TTTTTGATGC
24718320 ATTTTATAATTTTTTATAATTTTTATAA
1 ATTTTATAATTTTTTATAATTTTTATAA
* * * *
24718348 CATTTTACACTTTTTTATATTTTTTACAA
1 -ATTTTATAATTTTTTATAATTTTTATAA
*
24718377 TTTTTAT-ATTTTTT-TAATTTTTAATAA
1 ATTTTATAATTTTTTATAATTTTT-ATAA
* *
24718404 AATTTA-AATATTGTTATAA-TTTTATTAA
1 ATTTTATAAT-TTTTTATAATTTTTA-TAA
24718432 ATTTTAATAATTTTT
1 ATTTT-ATAATTTTT
24718447 ATTGATGTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
26 7 0.09
27 16 0.21
28 20 0.26
29 31 0.40
30 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (28 bp):
ATTTTATAATTTTTTATAATTTTTATAA
Found at i:24718447 original size:10 final size:9
Alignment explanation
Indices: 24718321--24718448 Score: 82
Period size: 9 Copynumber: 13.7 Consensus size: 9
24718311 TTTTGATGCA
24718321 TTTTATAATT
1 TTTTATAA-T
24718331 TTTTATAAT
1 TTTTATAAT
*
24718340 TTTTATAACA
1 TTTTATAA-T
* *
24718350 TTTTACACTT
1 TTTTATA-AT
*
24718360 TTTTATATT
1 TTTTATAAT
*
24718369 TTTTACAAT
1 TTTTATAAT
24718378 TTTTAT-AT
1 TTTTATAAT
*
24718386 TTTTTTAAT
1 TTTTATAAT
*
24718395 TTTTAATAAA
1 TTTT-ATAAT
*
24718405 ATTTA-AAT
1 TTTTATAAT
24718413 ATTGTTATAA-
1 -TT-TTATAAT
24718423 TTTTATTAAAT
1 TTTTA-T-AAT
*
24718434 TTTAATAAT
1 TTTTATAAT
24718443 TTTTAT
1 TTTTAT
24718449 TGATGTTTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 21
0.71 0.12 0.16
Matches are distributed among these distances:
8 12 0.13
9 42 0.46
10 32 0.35
11 6 0.07
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:24718696 original size:83 final size:83
Alignment explanation
Indices: 24718608--24718782 Score: 192
Period size: 86 Copynumber: 2.1 Consensus size: 83
24718598 TGAGTGAAAG
* * ** ***
24718608 AAAAAAAGCAATGGCTTAATT-TTTTTTTTAAGT-TTCAAGGTTTTTTTGATGCATTTTGGCGGT
1 AAAAAAAG-AA-GGCTTAATTGTTTTTTTAAAATCTTCAAGGCCTTTTTGATGCATTTTGAAAGT
*
24718671 TCAAGTACTCAATTAAGTGCAA
64 TCAAGTACCCAATTAAGTG--A
* * *
24718693 AAAAAAAGAAGGCTTAATTGGTTTTTTTAAAATCTTGAGGGCCTTTTTGATGTATTTTGAAAGTT
1 AAAAAAAGAAGGCTTAATT-GTTTTTTTAAAATCTTCAAGGCCTTTTTGATGCATTTTGAAAGTT
24718758 CAAGTACCCAATTAAGTGA
65 CAAGTACCCAATTAAGTGA
24718777 AAAAAA
1 AAAAAA
24718783 TAAAAACAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
83 9 0.12
84 9 0.12
85 18 0.24
86 40 0.53
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.38
Consensus pattern (83 bp):
AAAAAAAGAAGGCTTAATTGTTTTTTTAAAATCTTCAAGGCCTTTTTGATGCATTTTGAAAGTTC
AAGTACCCAATTAAGTGA
Found at i:24719213 original size:87 final size:84
Alignment explanation
Indices: 24718994--24719231 Score: 243
Period size: 86 Copynumber: 2.8 Consensus size: 84
24718984 ATTCTTTAAA
* * **
24718994 AAAAAAGAGCAATTAAG--TTTTTTTTGCACTCAATTGGGTATTTGAATTTTCAAAATATATCAA
1 AAAAAA-AGCAATTAAGCATTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAA
*
24719057 AAAGGCCTTAAAACTTTTTC
65 AAAGACCTTAAAACTTTTTC
* * * * *
24719077 AAATAAGAGCCATTAAGCCCATTTTTTTT-CACTCAATTAGGTGCTTGAACTTTCAAAATGCATA
1 AAA-AAAAGCAATTAAG--CATTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATC
*
24719141 AAAAAGA-CTCTCAAACTTTTTTTC
63 AAAAAGACCT-TAAAAC--TTTTTC
* *
24719165 AAAAAAAGCAATTAAGTCATTTTTTTTGCACTCAATTGGGCACTTGAACTGT-AAAAGTGCATCA
1 AAAAAAAGCAATTAAG-CATTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAA-TGCATCA
24719229 AAA
64 AAA
24719232 GAGTACTTTG
Statistics
Matches: 126, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
83 12 0.10
84 2 0.02
85 2 0.02
86 53 0.42
87 48 0.38
88 9 0.07
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (84 bp):
AAAAAAAGCAATTAAGCATTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAA
AAGACCTTAAAACTTTTTC
Found at i:24719351 original size:10 final size:10
Alignment explanation
Indices: 24719336--24719396 Score: 65
Period size: 10 Copynumber: 6.3 Consensus size: 10
24719326 GACATGTGGC
24719336 AAAAAATTAT
1 AAAAAATTAT
24719346 AAAAAA--AT
1 AAAAAATTAT
***
24719354 AAAAACCAAT
1 AAAAAATTAT
24719364 -AAAAATTAT
1 AAAAAATTAT
24719373 AAAAAATTAT
1 AAAAAATTAT
24719383 AAAAAAATTAT
1 -AAAAAATTAT
24719394 AAA
1 AAA
24719397 TTTTTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 7 0.16
9 6 0.14
10 20 0.47
11 10 0.23
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:24719352 original size:11 final size:11
Alignment explanation
Indices: 24719336--24719396 Score: 55
Period size: 11 Copynumber: 6.2 Consensus size: 11
24719326 GACATGTGGC
24719336 AAAAAATTATA
1 AAAAAATTATA
24719347 AAAAAA-TA-A
1 AAAAAATTATA
**
24719356 AAACCA--AT-
1 AAAAAATTATA
24719364 AAA-AATTAT-
1 AAAAAATTATA
24719373 AAAAAATTATA
1 AAAAAATTATA
24719384 AAAAAATTATA
1 AAAAAATTATA
24719395 AA
1 AA
24719397 TTTTTAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
7 1 0.02
8 4 0.10
9 10 0.24
10 8 0.19
11 19 0.45
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:24719485 original size:20 final size:18
Alignment explanation
Indices: 24719450--24719497 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
24719440 AAAAAAAATA
* *
24719450 TAATTATTTTACAATTTTT
1 TAATT-TTTTTCAAATTTT
24719469 TATATTTTTTTCAAATTTT
1 TA-ATTTTTTTCAAATTTT
24719488 TAATTTTTTT
1 TAATTTTTTT
24719498 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 15 0.58
20 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
TAATTTTTTTCAAATTTT
Found at i:24721520 original size:17 final size:15
Alignment explanation
Indices: 24721465--24721532 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
24721455 CTTCCGGAGT
*
24721465 AATAACTCTTGTTTAG
1 AATAACT-TTGTTCAG
**
24721481 AATAGTTATTGTTCAG
1 AATAACT-TTGTTCAG
*
24721497 AACAACTGTTGTTCGAG
1 AATAACT-TTGTTC-AG
*
24721514 AATAACTATGTTCAG
1 AATAACTTTGTTCAG
24721529 AATA
1 AATA
24721533 GAGTTTTAGT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
15 6 0.15
16 27 0.66
17 8 0.20
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (15 bp):
AATAACTTTGTTCAG
Found at i:24722992 original size:43 final size:43
Alignment explanation
Indices: 24722922--24723068 Score: 258
Period size: 43 Copynumber: 3.4 Consensus size: 43
24722912 TGTTCGACCT
*
24722922 TTATATTGAGAACAACTCACGTTTAGAATAAGTCAAAATAACCA
1 TTAT-TTGGGAACAACTCACGTTTAGAATAAGTCAAAATAACCA
24722966 TTATTTGGGAACAACTCACGTTTAGAATAAGTCAAAATAACCA
1 TTATTTGGGAACAACTCACGTTTAGAATAAGTCAAAATAACCA
* *
24723009 TTATTTGGGAACAACTTACGTTTAGAGTAAGTCAAAATAACCA
1 TTATTTGGGAACAACTCACGTTTAGAATAAGTCAAAATAACCA
24723052 TTATTTGGGAACAACTC
1 TTATTTGGGAACAACTC
24723069 TTATCCAAGG
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 95 0.96
44 4 0.04
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (43 bp):
TTATTTGGGAACAACTCACGTTTAGAATAAGTCAAAATAACCA
Found at i:24723622 original size:12 final size:12
Alignment explanation
Indices: 24723605--24723634 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24723595 ATTATTATAT
24723605 TTTATTTAATAA
1 TTTATTTAATAA
*
24723617 TTTATTTAGTAA
1 TTTATTTAATAA
24723629 TTTATT
1 TTTATT
24723635 AATTATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (12 bp):
TTTATTTAATAA
Found at i:24725548 original size:22 final size:22
Alignment explanation
Indices: 24725523--24725614 Score: 132
Period size: 22 Copynumber: 4.2 Consensus size: 22
24725513 AAATTCAATA
24725523 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
24725545 TCAA-TTCCTTTAAAAAATTCTC
1 TCAATTTCC-TTCAAAAATTCTC
* *
24725567 TCAATTCCCTTCAAAATTTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
24725589 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
24725611 TCAA
1 TCAA
24725615 ACTCTCAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
21 4 0.07
22 54 0.89
23 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:24728750 original size:138 final size:138
Alignment explanation
Indices: 24728496--24728753 Score: 383
Period size: 138 Copynumber: 1.9 Consensus size: 138
24728486 CTATTTGCTC
* * *
24728496 AGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTATAGCGAAATCGCGTCCACGAGGGCGC
1 AGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTATAGCGAAATCACGTCCACGAGGCCAC
* ** *
24728561 GATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAGCGATTTTATACTATTTGCTCAGTAAA
66 GATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGCGATTTCATACTATTTGCTCAGTAAA
24728626 AGTAAAAA
131 AGTAAAAA
* *
24728634 AGAAACGTCAAAAAAAAATTATTTCTTACATGACC-ACTGTAGCGAAATCACGTCCACGAGGCCA
1 AGAAACGTC-AAAAAAAATTATTTCCTACATGACCAACTATAGCGAAATCACGTCCACGAGGCCA
* * * *
24728698 CTATTTCACAATTTCTTCTTAAATAGCATCTTGGTAGAAGCGATTTCCTACTATTT
65 CGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGCGATTTCATACTATTT
24728754 AACCAGATAC
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
138 82 0.77
139 24 0.23
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (138 bp):
AGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTATAGCGAAATCACGTCCACGAGGCCAC
GATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGCGATTTCATACTATTTGCTCAGTAAA
AGTAAAAA
Found at i:24729821 original size:90 final size:90
Alignment explanation
Indices: 24729665--24729868 Score: 236
Period size: 90 Copynumber: 2.3 Consensus size: 90
24729655 NNNNNNNNNN
* * * * * *
24729665 AAAAACCAATTAAGCCCTTGA--TTTTTTTTGCACTCATTTAGGTACTTGAATTTTCAAAATGTA
1 AAAAAGCAATTAAGCCCCT-ACTTTTTTTTTGCACCCAATCAGGTACTTGAATTTTCAAAATGCA
* *
24729728 TCAAAAAGAC-CGTCAAACATTTTCAG
65 TCAAAAAAACTC-TCAAACATTTTCAA
*
24729754 AAAAAGCAATTAAGCCCCTACTTTTTTTTTGCACCCAATCGGGTACTTGAACTTTT-AAAATGCA
1 AAAAAGCAATTAAGCCCCTACTTTTTTTTTGCACCCAATCAGGTACTTGAA-TTTTCAAAATGCA
* *
24729818 TCAAAAAAACTCTCAAGCTTTTTCAA
65 TCAAAAAAACTCTCAAACATTTTCAA
* *
24729844 AAAAAGCAATTAAACCCCTGCTTTT
1 AAAAAGCAATTAAGCCCCTACTTTT
24729869 ATTAAAAATT
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
88 1 0.01
89 17 0.17
90 75 0.77
91 5 0.05
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (90 bp):
AAAAAGCAATTAAGCCCCTACTTTTTTTTTGCACCCAATCAGGTACTTGAATTTTCAAAATGCAT
CAAAAAAACTCTCAAACATTTTCAA
Found at i:24729987 original size:19 final size:19
Alignment explanation
Indices: 24729963--24730008 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
24729953 AAAAATTAGA
24729963 AAAAAAATTGTAAAATTGT
1 AAAAAAATTGTAAAATTGT
*
24729982 AAAAAAATTGTAAAATTTT
1 AAAAAAATTGTAAAATTGT
*
24730001 ATAAAAAT
1 AAAAAAAT
24730009 CATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAAAAATTGTAAAATTGT
Found at i:24730014 original size:19 final size:19
Alignment explanation
Indices: 24729973--24730025 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
24729963 AAAAAAATTG
* * **
24729973 TAAAATTGTAAAAAAATTG
1 TAAAATTTTATAAAAATCA
24729992 TAAAATTTTATAAAAATCA
1 TAAAATTTTATAAAAATCA
**
24730011 TAAAAAATTATAAAA
1 TAAAATTTTATAAAA
24730026 TGTATAGAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (19 bp):
TAAAATTTTATAAAAATCA
Found at i:24730015 original size:29 final size:29
Alignment explanation
Indices: 24729983--24730051 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
24729973 TAAAATTGTA
* *
24729983 AAAAAATTGTAAAATTTTATA-AAA-ATCAT
1 AAAAAATTATAAAA-TGTATAGAAATAT-AT
24730012 AAAAAATTATAAAATGTATAGAAATATAT
1 AAAAAATTATAAAATGTATAGAAATATAT
24730041 AAAAAA-TATAA
1 AAAAAATTATAA
24730052 CATTTTNNNN
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 10 0.28
29 24 0.67
30 2 0.06
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAAAATTATAAAATGTATAGAAATATAT
Found at i:24730025 original size:9 final size:9
Alignment explanation
Indices: 24729965--24730051 Score: 50
Period size: 10 Copynumber: 9.2 Consensus size: 9
24729955 AAATTAGAAA
*
24729965 AAAAATTGT
1 AAAAATTAT
* *
24729974 AAAATTGTAA
1 AAAAAT-TAT
*
24729984 AAAAATTGT
1 AAAAATTAT
*
24729993 AAAATTTTAT
1 AAAA-ATTAT
*
24730003 AAAAATCAT
1 AAAAATTAT
24730012 AAAAAATTAT
1 -AAAAATTAT
24730022 -AAAATGTAT
1 AAAAAT-TAT
*
24730031 AGAAATATAT
1 AAAAAT-TAT
*
24730041 AAAAAATAT
1 AAAAATTAT
24730050 AA
1 AA
24730052 CATTTTNNNN
Statistics
Matches: 58, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
8 5 0.09
9 21 0.36
10 32 0.55
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:24730192 original size:19 final size:19
Alignment explanation
Indices: 24730149--24730212 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
24730139 NNNNNNNNNN
* *
24730149 GTAAAAA-ATATAAAAACC
1 GTAAAAATATAAAAAAATC
*
24730167 GTAAAAAATATAAAAAAATT
1 GT-AAAAATATAAAAAAATC
* * *
24730187 GTAAAATTTTATAAAAATC
1 GTAAAAATATAAAAAAATC
24730206 GTAAAAA
1 GTAAAAA
24730213 AAATATAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 2 0.06
19 24 0.67
20 10 0.28
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.25
Consensus pattern (19 bp):
GTAAAAATATAAAAAAATC
Found at i:24730219 original size:20 final size:20
Alignment explanation
Indices: 24730151--24730222 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
24730141 NNNNNNNNGT
*
24730151 AAAAAATATAAAAACCGTAA
1 AAAAAATATAAAAATCGTAA
* * *
24730171 AAAATATAAAAAAATTGT-A
1 AAAAAATATAAAAATCGTAA
***
24730190 AAATTTTATAAAAATCGTAA
1 AAAAAATATAAAAATCGTAA
24730210 AAAAAATATAAAA
1 AAAAAATATAAAA
24730223 TATATGGAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 15 0.38
20 25 0.62
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAAAATATAAAAATCGTAA
Found at i:24730528 original size:27 final size:28
Alignment explanation
Indices: 24730493--24730564 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
24730483 TTATAAAAAA
*
24730493 TTCTAATTTTTAATAAATTTTAAT-TTT
1 TTCTAATTTTTAATAAAATTTAATATTT
*
24730520 TTC-ATATTTTTATTAAAATTTAATAATTT
1 TTCTA-ATTTTTAATAAAATTTAAT-ATTT
24730549 TTCTAATTTTTAATAA
1 TTCTAATTTTTAATAA
24730565 GAGCAGGGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
29 16 0.42
30 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (28 bp):
TTCTAATTTTTAATAAAATTTAATATTT
Found at i:24730547 original size:47 final size:48
Alignment explanation
Indices: 24730460--24730550 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 48
24730450 AAAATTTTAC
* *
24730460 AATTGTTAATTTTTTTATGATTTTTATAAAAAATTCTAATTTTTAATA
1 AATTGTTAATTTTTTCATGATTTTTATAAAAAATTATAATTTTTAATA
* *
24730508 AATT-TTAATTTTTTCAT-ATTTTTATTAAAATTTAATAATTTTT
1 AATTGTTAATTTTTTCATGATTTTTATAAAAAATT-ATAATTTTT
24730551 CTAATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 14 0.37
47 20 0.53
48 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (48 bp):
AATTGTTAATTTTTTCATGATTTTTATAAAAAATTATAATTTTTAATA
Found at i:24730560 original size:46 final size:46
Alignment explanation
Indices: 24730452--24730562 Score: 118
Period size: 46 Copynumber: 2.4 Consensus size: 46
24730442 ATTTTTATAA
* * * *
24730452 AATTTTAC-AATTGTTAATTTTTTTATGATTTTTATAAAAAATTCT
1 AATTTTTCTAATTTTTAATTTTTTCATGATTTTTATAAAAAATTAT
* * * *
24730497 AATTTTTAATAAATTTTAATTTTTTCAT-ATTTTTATTAAAATTTAAT
1 AATTTTT-CTAATTTTTAATTTTTTCATGATTTTTATAAAAAATT-AT
24730544 AATTTTTCTAATTTTTAAT
1 AATTTTTCTAATTTTTAAT
24730563 AAGAGCAGGG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
45 6 0.11
46 24 0.45
47 23 0.43
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (46 bp):
AATTTTTCTAATTTTTAATTTTTTCATGATTTTTATAAAAAATTAT
Found at i:24734982 original size:12 final size:11
Alignment explanation
Indices: 24734914--24735021 Score: 57
Period size: 11 Copynumber: 9.6 Consensus size: 11
24734904 TTTTATTTTT
24734914 TATTTTTAAAAA
1 TATTTTT-AAAA
24734926 TATTTTTAAAA
1 TATTTTTAAAA
*
24734937 TACTTTTT---T
1 TA-TTTTTAAAA
*
24734946 TATTTTT---T
1 TATTTTTAAAA
24734954 TATTTTTAAAA
1 TATTTTTAAAA
24734965 TATTTTTAAAA
1 TATTTTTAAAA
***
24734976 TACTTTTTTATTTTGT
1 TA--TTTTTA---AAA
24734992 TATTTTTAAAA
1 TATTTTTAAAA
24735003 TATTTTTAAAA
1 TATTTTTAAAA
24735014 TACTTTTT
1 TA-TTTTT
24735022 TTATTTTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
8 13 0.17
9 2 0.03
11 32 0.41
12 17 0.22
13 6 0.08
14 6 0.08
16 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:24734983 original size:38 final size:39
Alignment explanation
Indices: 24734902--24735031 Score: 228
Period size: 39 Copynumber: 3.4 Consensus size: 39
24734892 TAAATATATA
24734902 TTTTTTA-TTTTTTATTTTTAAAAATATTTTTAAAATACT
1 TTTTTTATTTTTTTATTTTT-AAAATATTTTTAAAATACT
24734941 TTTTTTATTTTTTTATTTTTAAAATATTTTTAAAATAC-
1 TTTTTTATTTTTTTATTTTTAAAATATTTTTAAAATACT
*
24734979 TTTTTTATTTTGTTATTTTTAAAATATTTTTAAAATACT
1 TTTTTTATTTTTTTATTTTTAAAATATTTTTAAAATACT
24735018 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
24735032 TTATTTTTGG
Statistics
Matches: 87, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
38 37 0.43
39 38 0.44
40 12 0.14
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (39 bp):
TTTTTTATTTTTTTATTTTTAAAATATTTTTAAAATACT
Found at i:24735078 original size:15 final size:16
Alignment explanation
Indices: 24735058--24735087 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24735048 TTTAAAAAAT
24735058 GGGTCGGGC-CGGGCC
1 GGGTCGGGCTCGGGCC
24735073 GGGTCGGGCTCGGGC
1 GGGTCGGGCTCGGGC
24735088 TTATGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.30, G:0.60, T:0.10
Consensus pattern (16 bp):
GGGTCGGGCTCGGGCC
Found at i:24742093 original size:153 final size:152
Alignment explanation
Indices: 24741816--24742107 Score: 478
Period size: 153 Copynumber: 1.9 Consensus size: 152
24741806 ATCTATGGTG
* * *
24741816 AAAATTGGTGGAGCCATAGAATTTGGCACCACCAACATCCCACATCAAAAAACCCAATAAAAAAT
1 AAAATTGGTAGAGCCAAAGAATTTGACACCACCAACATCCCACATCAAAAAACCCAATAAAAAAT
* *
24741881 TATTTTTTTGGTGGAGCCATGTAGAATGGCCTCACCTATATAAATACTAGAGAAATACTGCTATT
66 TATTTTTTTGGTGGAGCCATGTAGAATGGCCTCACCTATATAAAAACTAAAGAAATACTGCTATT
24741946 TTTAAAAAAATTATTTCAGGTA
131 TTTAAAAAAATTATTTCAGGTA
* * *
24741968 AAAATTGGTAGAGCCAAAGAGTTTGACACCACCAACATGCCACATCAAGAAACCCAATAAAAAAT
1 AAAATTGGTAGAGCCAAAGAATTTGACACCACCAACATCCCACATCAAAAAACCCAATAAAAAAT
*
24742033 T-TCTGTTTTTGGTGGAGCCATGTAGAATGGCGTCACCTATATAAAAACTAAAGAAATACTGCTA
66 TAT-T-TTTTTGGTGGAGCCATGTAGAATGGCCTCACCTATATAAAAACTAAAGAAATACTGCTA
24742097 TTTTTAAAAAA
129 TTTTTAAAAAA
24742108 TTGGAGAGCT
Statistics
Matches: 129, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
151 1 0.01
152 61 0.47
153 67 0.52
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (152 bp):
AAAATTGGTAGAGCCAAAGAATTTGACACCACCAACATCCCACATCAAAAAACCCAATAAAAAAT
TATTTTTTTGGTGGAGCCATGTAGAATGGCCTCACCTATATAAAAACTAAAGAAATACTGCTATT
TTTAAAAAAATTATTTCAGGTA
Found at i:24743295 original size:19 final size:19
Alignment explanation
Indices: 24743268--24743323 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
24743258 CTCCCAACAT
*
24743268 TAGTGTTTTTTTTTTATTA
1 TAGTTTTTTTTTTTTATTA
*
24743287 TAGTTTTTTTAAGTTTTATTA
1 TAGTTTTTTT--TTTTTATTA
* *
24743308 TAGTTATTATTTTTTA
1 TAGTTTTTTTTTTTTA
24743324 GTTTTTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 14 0.47
21 16 0.53
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (19 bp):
TAGTTTTTTTTTTTTATTA
Found at i:24743303 original size:10 final size:12
Alignment explanation
Indices: 24743278--24743318 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
24743268 TAGTGTTTTT
24743278 TTTTTATTATAG
1 TTTTTATTATAG
24743290 TTTTT-TTA-AG
1 TTTTTATTATAG
24743300 -TTTTATTATAG
1 TTTTTATTATAG
*
24743311 TTATTATT
1 TTTTTATT
24743319 TTTTAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
9 4 0.16
10 5 0.20
11 5 0.20
12 11 0.44
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (12 bp):
TTTTTATTATAG
Found at i:24750355 original size:9 final size:9
Alignment explanation
Indices: 24750320--24750540 Score: 50
Period size: 9 Copynumber: 23.3 Consensus size: 9
24750310 TGTAAAGCAT
24750320 ATTAT-AAA
1 ATTATAAAA
*
24750328 ATT-TAGAA
1 ATTATAAAA
24750336 ATTATAGAAAA
1 ATTAT--AAAA
24750347 ATTATAAAA
1 ATTATAAAA
*
24750356 ATGTAT-TAA
1 AT-TATAAAA
*
24750365 ATTCATGAAAT
1 ATT-AT-AAAA
*
24750376 GTTATAAAA
1 ATTATAAAA
*
24750385 TATTATTAATAT
1 -ATTA-TAA-AA
24750397 ATTATGAAAA
1 ATTAT-AAAA
24750407 A-TATAAAAGA
1 ATTAT-AAA-A
24750417 ATTATAAAA
1 ATTATAAAA
*
24750426 AATATAATTAA
1 ATTATAA--AA
**
24750437 A-TATTTGAA
1 ATTA-TAAAA
24750446 ATTGA-AGAAA
1 ATT-ATA-AAA
24750456 ATTTATTAAAA
1 A-TTA-TAAAA
*
24750467 AAT-TAAAA
1 ATTATAAAA
24750475 A-TAT-AAA
1 ATTATAAAA
*
24750482 AGTATAAAA
1 ATTATAAAA
* *
24750491 AATATTAAA
1 ATTATAAAA
*
24750500 ATGATAAAA
1 ATTATAAAA
24750509 A-TATAAAGTA
1 ATTATAAA--A
24750519 TATT-TAAAA
1 -ATTATAAAA
24750528 ATTATATAAA
1 ATTATA-AAA
24750538 ATT
1 ATT
24750541 TAATGATCCA
Statistics
Matches: 158, Mismatches: 23, Indels: 62
0.65 0.09 0.26
Matches are distributed among these distances:
7 6 0.04
8 27 0.17
9 52 0.33
10 31 0.20
11 39 0.25
12 3 0.02
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (9 bp):
ATTATAAAA
Found at i:24750374 original size:29 final size:28
Alignment explanation
Indices: 24750320--24750414 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 28
24750310 TGTAAAGCAT
*
24750320 ATTATAAAAT-TTA-GAAATTATAGAAAA
1 ATTATAAAATATTATTAAATTAT-GAAAA
*
24750347 ATTATAAAA-ATGTATTAAATTCATGAAAT
1 ATTATAAAATAT-TATTAAATT-ATGAAAA
*
24750376 GTTATAAAATATTATTAATATATTATGAAAA
1 ATTATAAAATATTATT-A-A-ATTATGAAAA
24750407 A-TATAAAA
1 ATTATAAAA
24750415 GAATTATAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
27 10 0.18
28 2 0.04
29 21 0.38
30 12 0.22
31 7 0.13
32 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (28 bp):
ATTATAAAATATTATTAAATTATGAAAA
Found at i:24750481 original size:8 final size:8
Alignment explanation
Indices: 24750464--24750515 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
24750454 AAATTTATTA
24750464 AAAAAT-T
1 AAAAATAT
24750471 AAAAATAT
1 AAAAATAT
*
24750479 AAAAGTAT
1 AAAAATAT
24750487 AAAAAATAT
1 -AAAAATAT
*
24750496 TAAAATGAT
1 AAAAAT-AT
24750505 AAAAATAT
1 AAAAATAT
24750513 AAA
1 AAA
24750516 GTATATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
7 6 0.16
8 18 0.47
9 14 0.37
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (8 bp):
AAAAATAT
Found at i:24750492 original size:26 final size:26
Alignment explanation
Indices: 24750463--24750515 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
24750453 AAAATTTATT
*
24750463 AAAAAATTAAAAAT-ATAAAAGTATAA
1 AAAAAATT-AAAATGATAAAAATATAA
*
24750489 AAAATATTAAAATGATAAAAATATAA
1 AAAAAATTAAAATGATAAAAATATAA
24750515 A
1 A
24750516 GTATATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAAAATTAAAATGATAAAAATATAA
Found at i:24750493 original size:17 final size:17
Alignment explanation
Indices: 24750471--24750520 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
24750461 TTAAAAAATT
24750471 AAAAATATAAAAGTATA
1 AAAAATATAAAAGTATA
24750488 AAAAATATTAAAA-TGAT-
1 AAAAATA-TAAAAGT-ATA
24750505 AAAAATAT-AAAGTATA
1 AAAAATATAAAAGTATA
24750521 TTTAAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.17
16 2 0.07
17 15 0.52
18 7 0.24
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAATATAAAAGTATA
Found at i:24763362 original size:28 final size:29
Alignment explanation
Indices: 24763314--24763372 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
24763304 TAGCTGTAGG
*
24763314 GTTAATTTTTCTACTTTTTTCTTGTTCTT
1 GTTAATTTTTCTACTATTTTCTTGTTCTT
*
24763343 GTTAATTTTTCTGC-ATTTTCTTGTTCTT
1 GTTAATTTTTCTACTATTTTCTTGTTCTT
24763371 GT
1 GT
24763373 CATTTGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.10, C:0.14, G:0.10, T:0.66
Consensus pattern (29 bp):
GTTAATTTTTCTACTATTTTCTTGTTCTT
Found at i:24765434 original size:19 final size:19
Alignment explanation
Indices: 24765364--24765434 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
24765354 AAAAAAACTT
**
24765364 TAAAAATATAAAATTACTA
1 TAAAAATATAAAATTTTTA
**
24765383 -AAAAA-ATAATTTTTTCTA
1 TAAAAATATAAAATTTT-TA
24765401 TAAAAATACATAAAATTTTTA
1 TAAAAAT--ATAAAATTTTTA
24765422 TAAAAATATAAAA
1 TAAAAATATAAAA
24765435 ATATGCCTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
17 6 0.15
18 7 0.17
19 11 0.27
21 9 0.22
22 8 0.20
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAAAATTTTTA
Found at i:24766780 original size:17 final size:17
Alignment explanation
Indices: 24766758--24766806 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
24766748 ACAAAATCAA
24766758 ATCTTATAAGATTACAT
1 ATCTTATAAGATTACAT
24766775 ATCTTATAAGATTACAT
1 ATCTTATAAGATTACAT
*
24766792 ATCTTCTAAGATTAC
1 ATCTTATAAGATTAC
24766807 TTTCCCTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (17 bp):
ATCTTATAAGATTACAT
Found at i:24768630 original size:22 final size:23
Alignment explanation
Indices: 24768593--24768637 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
24768583 ATAAGTCTTT
24768593 CTTATTCACAATTTTAAATAAAG
1 CTTATTCACAATTTTAAATAAAG
*
24768616 CTTATTTAC-ATTTTAAATAAAG
1 CTTATTCACAATTTTAAATAAAG
24768638 AATTTGTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (23 bp):
CTTATTCACAATTTTAAATAAAG
Found at i:24768686 original size:17 final size:17
Alignment explanation
Indices: 24768653--24768687 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24768643 GTGGTTTTTC
**
24768653 TATTTTGTTTCTTTATT
1 TATTTTGTTTCAATATT
24768670 TATTTTGTTTCAATATT
1 TATTTTGTTTCAATATT
24768687 T
1 T
24768688 TAGCTGCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (17 bp):
TATTTTGTTTCAATATT
Found at i:24778433 original size:17 final size:17
Alignment explanation
Indices: 24778411--24778470 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
24778401 AGAACTCGCA
24778411 GGTGAGCTCTCAAGTTT
1 GGTGAGCTCTCAAGTTT
* *
24778428 GGTGAGGT-TAAAGTCTT
1 GGTGAGCTCTCAAGT-TT
* *
24778445 TGTGAGCTCGCATA-TTT
1 GGTGAGCTCTCA-AGTTT
24778462 GGTGAGCTC
1 GGTGAGCTC
24778471 GCAATTCATA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 5 0.15
17 25 0.76
18 2 0.06
19 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.32, T:0.35
Consensus pattern (17 bp):
GGTGAGCTCTCAAGTTT
Found at i:24782124 original size:17 final size:17
Alignment explanation
Indices: 24782104--24782136 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
24782094 CTCGCAATGT
*
24782104 TAGTGAGCTCTCAGTTC
1 TAGTGAGCTCACAGTTC
24782121 TAGTGAGCTCACAGTT
1 TAGTGAGCTCACAGTT
24782137 TGCATGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (17 bp):
TAGTGAGCTCACAGTTC
Found at i:24784206 original size:246 final size:248
Alignment explanation
Indices: 24783770--24784507 Score: 960
Period size: 246 Copynumber: 2.9 Consensus size: 248
24783760 CAGTGTCATG
* * * * *
24783770 GTTGATAGATGTACCCTTTGTAGCGGTATTAACACCTAGGATGCCATCAATGGCCTTGAGATTAT
1 GTTGATAGATGTACCCTTTGTAGCGTTATCAACATCTGGGATGCTATCAATGGCCTTGAGATTAT
** * ** * *
24783835 CTTCCCCTGATGGTGATGCATCCATGATACCTTGTTGACGAGACATATTTTGTATTTGTTCACCA
66 CTTCCATTGATTGTGATGTGTCCATGATACCTTCTTGACGAGACATATTTTGTATCTGTTCACCA
* * * *
24783900 TTTTTTATGTTATTCAAGCTCTTAGCTTCTCCTGCTGAAGTTGATAAGCTAGCGTTGGCTTCAGC
131 TTTTTTATGTTATTCAAGCTGTTAGTTTCTCCTGCTGAAGTTGATAGGCTAGCATTGGCTTCAGC
* ** * *
24783965 TTCAGCTAAAATTTTGGACTTGTGTTCAGAATCTTCTGGTTTTGATGC-TT-T
196 TTCGGCTAATCTTTTGGATTTGTGTTCAGAATCTTCTGGCTTTGATGCTTTAT
* *
24784016 GTTGATAGATGTACCCTTTGTAGCGTTATCAACTTCTGGGATGCTATCAAGGGCCTTGAGATTAT
1 GTTGATAGATGTACCCTTTGTAGCGTTATCAACATCTGGGATGCTATCAATGGCCTTGAGATTAT
* * *
24784081 CTTCCATTGATTGTGACGTGTCCATGATACCTTCTTGACGAGACATATTTTGCATCTGTTGACCA
66 CTTCCATTGATTGTGATGTGTCCATGATACCTTCTTGACGAGACATATTTTGTATCTGTTCACCA
* * * *
24784146 TTTCTAATGTTATTCAAGCGGTTAGTTTCTCCTGCTGAAGTTGATAGGCTAGCATTGGCTTCAAC
131 TTTTTTATGTTATTCAAGCTGTTAGTTTCTCCTGCTGAAGTTGATAGGCTAGCATTGGCTTCAGC
* *
24784211 TTCGGCTAATCTTTTGGATTTGTGTTCAGAATCTTTTTGCTTTGATGCTTTCGCAGCAAT
196 TTCGGCTAATCTTTTGGATTTGTGTTCAGAATCTTCTGGCTTTGATGCTTT-------AT
*
24784271 GTCATGGTCGATAGATGTACCCTTTGTAGCATTATCAACATCTGGGATGCTATCAATGGCCTTGC
1 G---T--T-GATAGATGTACCCTTTGTAGCGTTATCAACATCTGGGATGCTATCAATGGCCTTG-
* *
24784336 A-ATTATCTTCCATTGATTGTGATGTGCCCATGATACCTTCTTGTCGAGACATATTTTGTATCTG
59 AGATTATCTTCCATTGATTGTGATGTGTCCATGATACCTTCTTGACGAGACATATTTTGTATCTG
**
24784400 TTCACCATTTTTTATGCAATTCAAGCTGTTAGTTTCTCCTGCTGAAGTTGATAGGCTAGCATTGG
124 TTCACCATTTTTTATGTTATTCAAGCTGTTAGTTTCTCCTGCTGAAGTTGATAGGCTAGCATTGG
** * *
24784465 CTTTGGCTTTGGCTAATCTTTTGGATTTATGTTCAGAATCTTC
189 CTTCAGCTTCGGCTAATCTTTTGGATTTGTGTTCAGAATCTTC
24784508 AACAGATCCT
Statistics
Matches: 425, Mismatches: 51, Indels: 17
0.86 0.10 0.03
Matches are distributed among these distances:
246 211 0.50
247 2 0.00
255 2 0.00
258 1 0.00
260 1 0.00
261 207 0.49
262 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (248 bp):
GTTGATAGATGTACCCTTTGTAGCGTTATCAACATCTGGGATGCTATCAATGGCCTTGAGATTAT
CTTCCATTGATTGTGATGTGTCCATGATACCTTCTTGACGAGACATATTTTGTATCTGTTCACCA
TTTTTTATGTTATTCAAGCTGTTAGTTTCTCCTGCTGAAGTTGATAGGCTAGCATTGGCTTCAGC
TTCGGCTAATCTTTTGGATTTGTGTTCAGAATCTTCTGGCTTTGATGCTTTAT
Done.