Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 109 of 240
Found at i:33795947 original size:12 final size:12
Alignment explanation
Indices: 33795930--33795955 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33795920 GTAAGAAATG
33795930 ATTCATTTGAAA
1 ATTCATTTGAAA
33795942 ATTCATTTGAAA
1 ATTCATTTGAAA
33795954 AT
1 AT
33795956 GAAAATTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTCATTTGAAA
Found at i:33802087 original size:17 final size:17
Alignment explanation
Indices: 33802061--33802093 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33802051 AATTATGTGC
33802061 ATATAATAAATTTAAAA
1 ATATAATAAATTTAAAA
*
33802078 ATATACTAAATTTAAA
1 ATATAATAAATTTAAA
33802094 CTGTACGAAC
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:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAATAAATTTAAAA
Found at i:33812174 original size:22 final size:23
Alignment explanation
Indices: 33812149--33812208 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
33812139 TGGACTGAAT
33812149 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
33812171 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
33812193 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
33812209 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:33812176 original size:4 final size:4
Alignment explanation
Indices: 33812158--33812191 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
33812148 TATAAAAATT
33812158 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
33812192 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:33818684 original size:22 final size:23
Alignment explanation
Indices: 33818659--33818718 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
33818649 TGGACTGAAT
33818659 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
33818681 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
33818703 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
33818719 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:33818686 original size:4 final size:4
Alignment explanation
Indices: 33818668--33818701 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
33818658 TATAAAAATT
33818668 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
33818702 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:33826427 original size:12 final size:12
Alignment explanation
Indices: 33826393--33826424 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
33826383 TAGAGCTTCG
33826393 AAAGCTCAATTT
1 AAAGCTCAATTT
33826405 AAAGCTCAATTT
1 AAAGCTCAATTT
33826417 -AAGCTCAA
1 AAAGCTCAA
33826425 ATTGAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (12 bp):
AAAGCTCAATTT
Found at i:33833761 original size:26 final size:26
Alignment explanation
Indices: 33833732--33833812 Score: 162
Period size: 26 Copynumber: 3.1 Consensus size: 26
33833722 AACACACCAA
33833732 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
33833758 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
33833784 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
33833810 TAT
1 TAT
33833813 ACTTCCTCTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:33833995 original size:27 final size:27
Alignment explanation
Indices: 33833976--33834198 Score: 290
Period size: 27 Copynumber: 8.3 Consensus size: 27
33833966 GGGTATAACA
33833976 ATCATTTTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
33834003 ACCATTTTACCCTATGGGGGTATCTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
33834030 ATCATTTTACCCTATGGGGGTA--TCG
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
33834055 CAGTCATTTTATCCTATGAGGGTATTTCG
1 -A-TCATTTTACCCTATGGGGGTATTTCG
*
33834084 GTCATTTTACCCTATGGGGGTATTTC-
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
33834110 AGTCATTTTACCTTATTGGGGTATTTCG
1 A-TCATTTTACCCTATGGGGGTATTTCG
* * *
33834138 GTCATTTTACCCTATAGGGGTATCTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
**
33834165 ATCATTTTACCCTATAAGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
33834192 ATCATTT
1 ATCATTT
33834199 ATTGACCTCT
Statistics
Matches: 172, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
25 3 0.02
26 1 0.01
27 165 0.96
29 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (27 bp):
ATCATTTTACCCTATGGGGGTATTTCG
Found at i:33836377 original size:16 final size:18
Alignment explanation
Indices: 33836356--33836394 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
33836346 TTATTGTGTA
*
33836356 TAAAATAAA-ATAT-TCT
1 TAAAATAAATAAATGTCT
33836372 TAAAATAAATAAATGTCT
1 TAAAATAAATAAATGTCT
33836390 TAAAA
1 TAAAA
33836395 GTAATACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 3 0.15
18 8 0.40
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (18 bp):
TAAAATAAATAAATGTCT
Found at i:33842151 original size:19 final size:19
Alignment explanation
Indices: 33842124--33842160 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33842114 TGTATTGTGT
*
33842124 TGCTGTTAAATTAAATTAG
1 TGCTATTAAATTAAATTAG
*
33842143 TGCTATTAAATTACATTA
1 TGCTATTAAATTAAATTA
33842161 TGTTGGATTA
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:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (19 bp):
TGCTATTAAATTAAATTAG
Found at i:33842190 original size:19 final size:20
Alignment explanation
Indices: 33842147--33842183 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
33842137 AATTAGTGCT
33842147 ATTAAATTACATTATGTTGG
1 ATTAAATTACATTATGTTGG
33842167 ATT-AATTACATTATGTT
1 ATTAAATTACATTATGTT
33842184 TTCTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (20 bp):
ATTAAATTACATTATGTTGG
Found at i:33847207 original size:25 final size:25
Alignment explanation
Indices: 33847179--33847267 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 25
33847169 TAACCCACAT
33847179 CTCGTATGAGCATATCGATTTACAA
1 CTCGTATGAGCATATCGATTTACAA
* * * *
33847204 CTCGTAAGAGCATACCAATTTACAG
1 CTCGTATGAGCATATCGATTTACAA
* *
33847229 CTCG-AGTGAGCATATAGATTCACAA
1 CTCGTA-TGAGCATATCGATTTACAA
33847254 CTCGTATGAGCATA
1 CTCGTATGAGCATA
33847268 CATGTACAGG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 1 0.02
25 50 0.96
26 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (25 bp):
CTCGTATGAGCATATCGATTTACAA
Found at i:33852023 original size:13 final size:13
Alignment explanation
Indices: 33852005--33852029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33851995 TTCGTTAGTT
33852005 TTTATTTATTTTA
1 TTTATTTATTTTA
33852018 TTTATTTATTTT
1 TTTATTTATTTT
33852030 GATTAATATT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:33852286 original size:20 final size:21
Alignment explanation
Indices: 33852252--33852300 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
33852242 ACTTCTTCTT
* *
33852252 TTTTCTTATTTTTAT-TTTTA
1 TTTTCTTATTATTATATTTCA
*
33852272 TTTTCTTCTTATTATATTTCA
1 TTTTCTTATTATTATATTTCA
33852293 TATTTCTT
1 T-TTTCTT
33852301 GTCGTAGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.54
21 5 0.21
22 6 0.25
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTCTTATTATTATATTTCA
Found at i:33858407 original size:12 final size:12
Alignment explanation
Indices: 33858390--33858419 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33858380 CCCCACACGC
*
33858390 CCATGTGCTAGG
1 CCATGTGCTAGA
33858402 CCATGTGCTAGA
1 CCATGTGCTAGA
33858414 CCATGT
1 CCATGT
33858420 AACTAACTGA
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:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (12 bp):
CCATGTGCTAGA
Found at i:33860251 original size:18 final size:18
Alignment explanation
Indices: 33860228--33860266 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
33860218 ACCTTCCCAA
*
33860228 TAACATTCACTAATACCT
1 TAACATCCACTAATACCT
33860246 TAACATCCACTAATACCT
1 TAACATCCACTAATACCT
33860264 TAA
1 TAA
33860267 GTCCATTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (18 bp):
TAACATCCACTAATACCT
Found at i:33863825 original size:27 final size:26
Alignment explanation
Indices: 33863787--33863862 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 26
33863777 TTTGGATAAA
*
33863787 AATTAACCGAATTACCCAAATTAACCG
1 AATT-ACCGAATTAACCAAATTAACCG
* *
33863814 AATTACCTGAATTAACCGAATTAATCG
1 AATTACC-GAATTAACCAAATTAACCG
*
33863841 AATTACCCGAATTAACCGAATT
1 AATTA-CCGAATTAACCAAATT
33863863 GAATCACTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
27 39 0.89
28 2 0.05
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.26
Consensus pattern (26 bp):
AATTACCGAATTAACCAAATTAACCG
Found at i:33863843 original size:18 final size:18
Alignment explanation
Indices: 33863787--33863862 Score: 100
Period size: 18 Copynumber: 4.2 Consensus size: 18
33863777 TTTGGATAAA
* *
33863787 AATTAACCGAATTACCCA
1 AATTAACCGAATTAACCG
33863805 AATTAACCGAATT-ACCTG
1 AATTAACCGAATTAACC-G
*
33863823 AATTAACCGAATTAATCG
1 AATTAACCGAATTAACCG
*
33863841 AATTACCCGAATTAACCG
1 AATTAACCGAATTAACCG
33863859 AATT
1 AATT
33863863 GAATCACTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
17 2 0.04
18 47 0.92
19 2 0.04
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.26
Consensus pattern (18 bp):
AATTAACCGAATTAACCG
Found at i:33866704 original size:56 final size:55
Alignment explanation
Indices: 33866635--33866913 Score: 244
Period size: 56 Copynumber: 5.0 Consensus size: 55
33866625 ATAGCATAAT
* * * * * * *
33866635 AATGCTTACTTTGAGACACTGAAGCAACACTTTAATTTAATTTAGTACAACAT-AA
1 AATGCTCAATTTGAAACACTAAAACAGCACTTTAATTCAATTTAG-ACAACATGAA
* * * *
33866690 TAATACTCAATTTGAAACA-TTAAACAGCAGC-TTAATTTAATTTAAGACAGCATGAA
1 -AATGCTCAATTTGAAACACTAAAACAGCA-CTTTAATTCAATTT-AGACAACATGAA
* *
33866746 AATGCTCAATTT-AATACACTAAAATAGCAACTTTAATTCAATTTATGACAGCATGAA
1 AATGCTCAATTTGAA-ACACTAAAACAGC-ACTTTAATTCAATTTA-GACAACATGAA
* * *
33866803 AATGCTTAATTTGAAACACTAAAACAGCAGC-TTAATTCAATTTAAGATAATATGAA
1 AATGCTCAATTTGAAACACTAAAACAGCA-CTTTAATTCAATTT-AGACAACATGAA
* * * *
33866859 AATGCTCAATTTGAGACACTCAAACAACAACTTTAATTCAATTTATGACAGCATG
1 AATGCTCAATTTGAAACACTAAAACAGC-ACTTTAATTCAATTTA-GACAACATG
33866914 CAAACAGTAA
Statistics
Matches: 185, Mismatches: 24, Indels: 27
0.78 0.10 0.11
Matches are distributed among these distances:
54 2 0.01
55 39 0.21
56 75 0.41
57 67 0.36
58 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (55 bp):
AATGCTCAATTTGAAACACTAAAACAGCACTTTAATTCAATTTAGACAACATGAA
Found at i:33866789 original size:57 final size:57
Alignment explanation
Indices: 33866663--33866913 Score: 280
Period size: 57 Copynumber: 4.5 Consensus size: 57
33866653 CTGAAGCAAC
* * * *
33866663 ACTTTAATTTAATTT-AGTACAACAT-AATAATACTCAATTTGAAACA-TTAAACAGCA
1 ACTTTAATTCAATTTAAG-ACAGCATGAA-AATGCTCAATTTGAAACACTAAAACAGCA
* * *
33866719 GC-TTAATTTAATTTAAGACAGCATGAAAATGCTCAATTT-AATACACTAAAATAGCA
1 ACTTTAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAA-ACACTAAAACAGCA
* *
33866775 ACTTTAATTCAATTTATGACAGCATGAAAATGCTTAATTTGAAACACTAAAACAGCA
1 ACTTTAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAACAGCA
* * ** * * *
33866832 GC-TTAATTCAATTTAAGATAATATGAAAATGCTCAATTTGAGACACTCAAACAACA
1 ACTTTAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAACAGCA
*
33866888 ACTTTAATTCAATTTATGACAGCATG
1 ACTTTAATTCAATTTAAGACAGCATG
33866914 CAAACAGTAA
Statistics
Matches: 164, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
54 2 0.01
55 32 0.20
56 61 0.37
57 67 0.41
58 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (57 bp):
ACTTTAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACTAAAACAGCA
Found at i:33866858 original size:113 final size:113
Alignment explanation
Indices: 33866648--33866913 Score: 342
Period size: 113 Copynumber: 2.4 Consensus size: 113
33866638 GCTTACTTTG
* * * *
33866648 AGACACTGAAGCAAC-ACTTTAATTTAATTTA-GTACAACAT-AATAATACTCAATTTGAAACAT
1 AGACACTAAAACAACAACTTTAATTCAATTTATG-ACAGCATGAATAATACTCAATTTGAAACAT
* * *
33866710 TAAACAGCAGCTTAATTTAATTTAAGACAGCATGAAAATGCTCAATTTA
65 AAAACAGCAGCTTAATTCAATTTAAGACAACATGAAAATGCTCAATTTA
* * * * *
33866759 ATACACTAAAATAGCAACTTTAATTCAATTTATGACAGCATGAA-AATGCTTAATTTGAAACACT
1 AGACACTAAAACAACAACTTTAATTCAATTTATGACAGCATGAATAATACTCAATTTGAAACA-T
* * *
33866823 AAAACAGCAGCTTAATTCAATTTAAGATAATATGAAAATGCTCAATTTG
65 AAAACAGCAGCTTAATTCAATTTAAGACAACATGAAAATGCTCAATTTA
*
33866872 AGACACTCAAACAACAACTTTAATTCAATTTATGACAGCATG
1 AGACACTAAAACAACAACTTTAATTCAATTTATGACAGCATG
33866914 CAAACAGTAA
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
111 10 0.08
112 37 0.28
113 85 0.64
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (113 bp):
AGACACTAAAACAACAACTTTAATTCAATTTATGACAGCATGAATAATACTCAATTTGAAACATA
AAACAGCAGCTTAATTCAATTTAAGACAACATGAAAATGCTCAATTTA
Found at i:33877657 original size:43 final size:44
Alignment explanation
Indices: 33877550--33877667 Score: 118
Period size: 43 Copynumber: 2.7 Consensus size: 44
33877540 CTCGTACAAC
* *** *
33877550 GCCAACGTCCTAGACGTGGTCTTACA-TGTAATCACTAATCGAT
1 GCCAACATCCTAGACGTGGTCTTACACAAAAATCACAAATCGAT
* *
33877593 GCC-ACTATCCCAAACAG-GGTCTTACACAAAAAT-ACAAATCGAT
1 GCCAAC-ATCCTAGAC-GTGGTCTTACACAAAAATCACAAATCGAT
*
33877636 GCCAACATCCTAGACGTGGTCTTACACGAAAA
1 GCCAACATCCTAGACGTGGTCTTACACAAAAA
33877668 CACTTATCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
42 3 0.05
43 51 0.85
44 6 0.10
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (44 bp):
GCCAACATCCTAGACGTGGTCTTACACAAAAATCACAAATCGAT
Found at i:33879063 original size:27 final size:27
Alignment explanation
Indices: 33879032--33879251 Score: 248
Period size: 27 Copynumber: 8.1 Consensus size: 27
33879022 AAAGGTTGTT
* *
33879032 AAATTACCAAAATACCTTTGAAGGGTA
1 AAATTACCAAAATACCCTCGAAGGGTA
* *
33879059 AAATTACCGAAATACCCTCAAAGGGTA
1 AAATTACCAAAATACCCTCGAAGGGTA
* *** *
33879086 AATTTATTGAAATACCCTCGATGGGTA
1 AAATTACCAAAATACCCTCGAAGGGTA
*
33879113 AAATTACCAAAATACCCTCGATGGGTA
1 AAATTACCAAAATACCCTCGAAGGGTA
33879140 AAATTACCAAAATACCCTCGAAGGGTA
1 AAATTACCAAAATACCCTCGAAGGGTA
*
33879167 AAATTATCAAAATACCCTC-AATGGGTA
1 AAATTACCAAAATACCCTCGAA-GGGTA
* *
33879194 AAATTACTAAAATA-CCTCCGATGGGTA
1 AAATTACCAAAATACCCT-CGAAGGGTA
* * *
33879221 AAATTATCGAAATACCC-CTATAGGGTA
1 AAATTACCAAAATACCCTCGA-AGGGTA
33879248 AAAT
1 AAAT
33879252 GACCGTTATA
Statistics
Matches: 165, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
26 7 0.04
27 155 0.94
28 3 0.02
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.25
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGAAGGGTA
Found at i:33879167 original size:81 final size:81
Alignment explanation
Indices: 33879032--33879251 Score: 300
Period size: 81 Copynumber: 2.7 Consensus size: 81
33879022 AAAGGTTGTT
* * * * **
33879032 AAATTACCAAAATACCTTTGAAGGGTAAAATTACCGAAATACCCTCAAAGGGTAAATTTATTGAA
1 AAATTACCAAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTATCAAA
*
33879097 ATACCCTCGATGGGTA
66 ATACCCTCAATGGGTA
* *
33879113 AAATTACCAAAATACCCTCGATGGGTAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCAAA
1 AAATTACCAAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTATCAAA
33879178 ATACCCTCAATGGGTA
66 ATACCCTCAATGGGTA
* * *
33879194 AAATTACTAAAATA-CCTCCGATGGGTAAAATTATCGAAATACCC-CTATAGGGTAAAAT
1 AAATTACCAAAATACCCT-CGATGGGTAAAATTACCGAAATACCCTC-AAAGGGTAAAAT
33879252 GACCGTTATA
Statistics
Matches: 123, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 4 0.03
81 119 0.97
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.25
Consensus pattern (81 bp):
AAATTACCAAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTATCAAA
ATACCCTCAATGGGTA
Found at i:33884413 original size:5 final size:5
Alignment explanation
Indices: 33884403--33884428 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33884393 TGAGTATTCG
33884403 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
33884429 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:33885220 original size:30 final size:31
Alignment explanation
Indices: 33885181--33885240 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
33885171 GGAGGTGGGA
*
33885181 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
33885212 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
33885241 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:33885534 original size:9 final size:9
Alignment explanation
Indices: 33885517--33885547 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33885507 TCGAGTTGAT
33885517 TCGAATAAC
1 TCGAATAAC
*
33885526 TCGATTAAC
1 TCGAATAAC
33885535 TCGAATAAC
1 TCGAATAAC
33885544 TCGA
1 TCGA
33885548 TTCGTTTAAC
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:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:33894003 original size:14 final size:14
Alignment explanation
Indices: 33893984--33894018 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
33893974 CTGGGATGGT
33893984 TTTTATTTATCTTA
1 TTTTATTTATCTTA
33893998 TTTTATTTATCTTA
1 TTTTATTTATCTTA
33894012 TTTTATT
1 TTTTATT
33894019 GTTTGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATTTATCTTA
Found at i:33896374 original size:18 final size:18
Alignment explanation
Indices: 33896351--33896390 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
33896341 AATTTTTTAA
33896351 AATTGTAACTTAAAT-TCT
1 AATTGT-ACTTAAATGTCT
*
33896369 AATTGTTCTTAAATGTCT
1 AATTGTACTTAAATGTCT
33896387 AATT
1 AATT
33896391 ATCACAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (18 bp):
AATTGTACTTAAATGTCT
Found at i:33896619 original size:44 final size:44
Alignment explanation
Indices: 33896565--33896648 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
33896555 ATAAAATAAA
* *
33896565 AGTTGCGATAACTATACATTTAAAAATAATTATAATTTAATATC
1 AGTTGCGATAACTACACATTTAAAAATAATTAGAATTTAATATC
* *
33896609 AGTTGTGATAATTACACATTTAAAAATAATTAGAATTTAA
1 AGTTGCGATAACTACACATTTAAAAATAATTAGAATTTAA
33896649 ATTACAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.38
Consensus pattern (44 bp):
AGTTGCGATAACTACACATTTAAAAATAATTAGAATTTAATATC
Found at i:33896648 original size:17 final size:18
Alignment explanation
Indices: 33896616--33896649 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33896606 ATCAGTTGTG
33896616 ATAATTACACATTTAAAA
1 ATAATTACACATTTAAAA
*
33896634 ATAATTAGA-ATTTAAA
1 ATAATTACACATTTAAA
33896650 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAATTACACATTTAAAA
Found at i:33907291 original size:25 final size:23
Alignment explanation
Indices: 33907256--33907341 Score: 100
Period size: 25 Copynumber: 3.5 Consensus size: 23
33907246 ATATATACAA
33907256 AATATATAAATGTTTTCAAAAAATAT
1 AATA-ATAAAT-TTTT-AAAAAATAT
* *
33907282 AATAATAAATTTATAAAATATAT
1 AATAATAAATTTTTAAAAAATAT
*
33907305 AAAAATAAATATTTTTAAAAAATAT
1 AATAAT-AA-ATTTTTAAAAAATAT
33907330 AATAATAAATTT
1 AATAATAAATTT
33907342 AAATTTTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
23 17 0.33
24 7 0.13
25 24 0.46
26 4 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (23 bp):
AATAATAAATTTTTAAAAAATAT
Found at i:33907325 original size:48 final size:52
Alignment explanation
Indices: 33907239--33907344 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 52
33907229 TTTAAAAATT
33907239 TTTAAAAATATATACAAAATATATAAATGTTTTCAAAAAATATAATAATAAA
1 TTTAAAAATATATACAAAATATATAAATGTTTTCAAAAAATATAATAATAAA
*
33907291 TTTATAAAATATATA-AAAATA-A-ATAT-TTTT-AAAAAATATAATAATAAA
1 TTTA-AAAATATATACAAAATATATAAATGTTTTCAAAAAATATAATAATAAA
33907339 TTTAAA
1 TTTAAA
33907345 TTTTATATTG
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
47 2 0.04
48 22 0.42
49 4 0.08
50 3 0.06
51 1 0.02
52 10 0.19
53 10 0.19
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (52 bp):
TTTAAAAATATATACAAAATATATAAATGTTTTCAAAAAATATAATAATAAA
Found at i:33909872 original size:27 final size:24
Alignment explanation
Indices: 33909829--33909881 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
33909819 CAAGTTTGAG
*
33909829 TTTATAAAGTTTGTTTGTAATTATT
1 TTTATAAACTTTGTTTGT-ATTATT
*
33909854 TTTATATAACTTTGTTTTGTTTTATT
1 TTTATA-AACTTTG-TTTGTATTATT
33909880 TT
1 TT
33909882 ATTTTGATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
26 13 0.54
27 5 0.21
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (24 bp):
TTTATAAACTTTGTTTGTATTATT
Found at i:33913518 original size:21 final size:21
Alignment explanation
Indices: 33913493--33913535 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
33913483 ACATGAACCA
33913493 AATTTAA-TGTTAAGTGTGAAC
1 AATTTAATTGTT-AGTGTGAAC
33913514 AATTTAATTGTTAGTGTGAAC
1 AATTTAATTGTTAGTGTGAAC
33913535 A
1 A
33913536 CATCTAGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (21 bp):
AATTTAATTGTTAGTGTGAAC
Found at i:33914969 original size:20 final size:22
Alignment explanation
Indices: 33914941--33914980 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
33914931 TGGAAAATTA
33914941 TTTTAAGAA-TA-AATTCTATT
1 TTTTAAGAATTACAATTCTATT
*
33914961 TTTTGAGAATTACAATTCTA
1 TTTTAAGAATTACAATTCTA
33914981 CCGGTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
TTTTAAGAATTACAATTCTATT
Found at i:33915615 original size:36 final size:36
Alignment explanation
Indices: 33915575--33915645 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
33915565 ATCAAGGGCT
*
33915575 ACAATTAAAAGTTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
33915611 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
33915646 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:33915616 original size:19 final size:19
Alignment explanation
Indices: 33915592--33915645 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
33915582 AAAGTTGTAT
33915592 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
33915611 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
33915628 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
33915646 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:33915633 original size:17 final size:17
Alignment explanation
Indices: 33915574--33915637 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
33915564 CATCAAGGGC
* *
33915574 TACAATTAAAAGTTGTA
1 TACAATTAGAAGCTGTA
*
33915591 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
33915610 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
33915627 TACAATTAGAA
1 TACAATTAGAA
33915638 CTCTAAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 2 0.05
17 21 0.57
19 11 0.30
20 3 0.08
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:33924834 original size:21 final size:22
Alignment explanation
Indices: 33924792--33924833 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
33924782 TAGTATACAC
*
33924792 TGGTTGAACCAAGTTAAAAAAT
1 TGGTTGAACCAAGCTAAAAAAT
*
33924814 TGGTTGAACCGAGCTAAAAA
1 TGGTTGAACCAAGCTAAAAA
33924834 TCAATTGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (22 bp):
TGGTTGAACCAAGCTAAAAAAT
Found at i:33934617 original size:15 final size:15
Alignment explanation
Indices: 33934597--33934664 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
33934587 ATACTACAAA
33934597 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
33934612 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
33934629 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
*
33934646 ATA-TTAATATTAA-
1 ATATTTATTATTAAT
33934659 ATATTT
1 ATATTT
33934665 TCAATAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.25
15 12 0.27
16 1 0.02
17 7 0.16
18 1 0.02
19 9 0.20
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:33934708 original size:15 final size:16
Alignment explanation
Indices: 33934688--33934718 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33934678 AATAATATCA
33934688 TTTAAAA-TTATTATT
1 TTTAAAATTTATTATT
33934703 TTTAAAATTTATTATT
1 TTTAAAATTTATTATT
33934719 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTTATTATT
Found at i:33934779 original size:22 final size:22
Alignment explanation
Indices: 33934745--33934786 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33934735 ATTAAATAAC
33934745 TTATTAAAATAATAAATTATAT
1 TTATTAAAATAATAAATTATAT
* * *
33934767 TTATTATATTAATAATTTAT
1 TTATTAAAATAATAAATTAT
33934787 TATATGAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTAAAATAATAAATTATAT
Found at i:33934798 original size:19 final size:16
Alignment explanation
Indices: 33934765--33934799 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
33934755 AATAAATTAT
33934765 ATTTATTATATTAATA
1 ATTTATTATATTAATA
*
33934781 ATTTATTATATGAATA
1 ATTTATTATATTAATA
33934797 ATT
1 ATT
33934800 ATAAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTATTATATTAATA
Found at i:33934871 original size:10 final size:9
Alignment explanation
Indices: 33934842--33934867 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
33934832 TAAAAAATAT
33934842 AATATTTTA
1 AATATTTTA
33934851 AATATTTTA
1 AATATTTTA
33934860 AATATTTT
1 AATATTTT
33934868 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:33943649 original size:22 final size:20
Alignment explanation
Indices: 33943606--33943660 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
33943596 GGGGCGTGGC
*
33943606 AAATACATATAAAAATTCTTAA
1 AAAT-CATA-AAAAAATCTTAA
*
33943628 AAACTTATAAAAAAATCATTAA
1 AAA-TCATAAAAAAATC-TTAA
33943650 AAATCATAAAA
1 AAATCATAAAA
33943661 TATTATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 14 0.50
22 13 0.46
23 1 0.04
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATCATAAAAAAATCTTAA
Found at i:33943736 original size:9 final size:9
Alignment explanation
Indices: 33943724--33943864 Score: 140
Period size: 10 Copynumber: 14.6 Consensus size: 9
33943714 AAATCATAAA
33943724 AAAAATTAT
1 AAAAATTAT
33943733 AAAAACTTAT
1 AAAAA-TTAT
*
33943743 AAAGATTAT
1 AAAAATTAT
33943752 AAAAATTTAT
1 AAAAA-TTAT
*
33943762 AAAATATATTT
1 AAAA-AT-TAT
33943773 AAAATATTAT
1 AAAA-ATTAT
33943783 AAAAACTTAT
1 AAAAA-TTAT
33943793 AAAAATTCAT
1 AAAAATT-AT
33943803 AAAAATTAT
1 AAAAATTAT
33943812 AACAAATTAT
1 AA-AAATTAT
33943822 AAAAAAATTAT
1 --AAAAATTAT
*
33943833 AAAAAATAT
1 AAAAATTAT
33943842 -AAAATTATT
1 AAAAATTA-T
*
33943851 AAAACTTAT
1 AAAAATTAT
33943860 AAAAA
1 AAAAA
33943865 AATTCATATA
Statistics
Matches: 113, Mismatches: 8, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
8 6 0.05
9 34 0.30
10 54 0.48
11 17 0.15
12 2 0.02
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:33943782 original size:50 final size:47
Alignment explanation
Indices: 33943708--33943864 Score: 174
Period size: 50 Copynumber: 3.2 Consensus size: 47
33943698 TGAGATAAAC
*
33943708 TTATAAAAATCATAAAAAAAATTATAAAAACTTATAAAGATTATAAAAA
1 TTATAAAAATTAT-AAAAAAATTATAAAAACTTATAAA-ATTATAAAAA
* *
33943757 TT-TATAAAATATATTTAAAATATTATAAAAACTTATAAAAATTCATAAAAA
1 TTATA-AAAAT-TA-TAAAAAAATTATAAAAACTTAT-AAAATT-ATAAAAA
* *
33943808 TTATAACAAATTATAAAAAAATTATAAAAA-ATATAAAATTATTAAAAC
1 TTATAA-AAATTATAAAAAAATTATAAAAACTTATAAAATTA-TAAAAA
33943856 TTATAAAAA
1 TTATAAAAA
33943865 AATTCATATA
Statistics
Matches: 93, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
47 4 0.04
48 19 0.20
49 10 0.11
50 38 0.41
51 16 0.17
52 6 0.06
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (47 bp):
TTATAAAAATTATAAAAAAATTATAAAAACTTATAAAATTATAAAAA
Found at i:33944405 original size:10 final size:10
Alignment explanation
Indices: 33944392--33944417 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
33944382 AATTTAAATA
33944392 TTTTTATAAG
1 TTTTTATAAG
33944402 TTTTTATAAG
1 TTTTTATAAG
33944412 TTTTTA
1 TTTTTA
33944418 AGAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (10 bp):
TTTTTATAAG
Found at i:33944407 original size:20 final size:19
Alignment explanation
Indices: 33944384--33944543 Score: 80
Period size: 20 Copynumber: 8.2 Consensus size: 19
33944374 TTTATATCAA
33944384 TTTAAATATTTTTATAAGTT
1 TTTAAATATTTTTATAA-TT
* *
33944404 TTTATAAGT-TTTTAAGAATT
1 TTTA-AA-TATTTTTATAATT
* * *
33944424 TTT-ATTTTTTTTATAAAAT
1 TTTAAATATTTTTAT-AATT
33944443 TTTAAATATGTTTTATTAATT
1 TTTAAATAT-TTTTA-TAATT
* *
33944464 TTATAAAAATTATTATAATT
1 TT-TAAATATTTTTATAATT
*
33944484 TATT--ATATTTTTATAA-G
1 T-TTAAATATTTTTATAATT
* *
33944501 TTTATATCAATTTTA-AATT
1 TTTAAAT-ATTTTTATAATT
* *
33944520 TTTAAATAAATTTTATAAAT
1 TTTAAAT-ATTTTTATAATT
33944540 TTTA
1 TTTA
33944544 TAATTTTAAT
Statistics
Matches: 107, Mismatches: 19, Indels: 28
0.69 0.12 0.18
Matches are distributed among these distances:
16 2 0.02
17 2 0.02
18 20 0.19
19 25 0.23
20 26 0.24
21 24 0.22
22 8 0.07
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTAAATATTTTTATAATT
Found at i:33944418 original size:30 final size:29
Alignment explanation
Indices: 33944384--33944499 Score: 87
Period size: 30 Copynumber: 3.9 Consensus size: 29
33944374 TTTATATCAA
**
33944384 TTTAAATATTTTTATAAGTTTTTATAAGTT
1 TTTAAATATTTTTAT-AGTTTTTATAAAAT
**
33944414 TTTAAGA-ATTTTTATTTTTTTTATAAAAT
1 TTTAA-ATATTTTTATAGTTTTTATAAAAT
*
33944443 TTTAAATATGTTTTATTA-ATTTTATAAAAAT
1 TTTAAATAT-TTTTA-TAGTTTTTAT-AAAAT
*
33944474 TATTATAAT-TTATTATA-TTTTTATAA
1 T-TTA-AATATTTTTATAGTTTTTATAA
33944500 GTTTATATCA
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
28 1 0.01
29 19 0.27
30 32 0.45
31 12 0.17
32 4 0.06
33 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTAAATATTTTTATAGTTTTTATAAAAT
Found at i:33944445 original size:29 final size:30
Alignment explanation
Indices: 33944384--33944471 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
33944374 TTTATATCAA
* **
33944384 TTTAAATAT-TTTTATAAGTTTTTATAAGTT
1 TTTAAATATGTTTTATTA-TTTTTATAAAAT
*
33944414 TTTAAGA-AT-TTTTATTTTTTTTATAAAAT
1 TTTAA-ATATGTTTTATTATTTTTATAAAAT
*
33944443 TTTAAATATGTTTTATTAATTTTATAAAA
1 TTTAAATATGTTTTATTATTTTTATAAAA
33944472 ATTATTATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.02
29 17 0.35
30 30 0.61
31 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTAAATATGTTTTATTATTTTTATAAAAT
Found at i:33944551 original size:28 final size:28
Alignment explanation
Indices: 33944453--33944552 Score: 82
Period size: 28 Copynumber: 3.5 Consensus size: 28
33944443 TTTAAATATG
*
33944453 TTTTATTAATTTTATAA-AAATTATTATAAT
1 TTTTA-TAATTTTA-AATAAATT-TTATAAA
* * *
33944483 TTATTAT-ATTTT-TATAAGTTTATATCAA
1 TT-TTATAATTTTAAATAAATTT-TATAAA
33944511 TTTTA-AATTTTTAAATAAATTTTATAAA
1 TTTTATAA-TTTTAAATAAATTTTATAAA
33944539 TTTTATAATTTTAA
1 TTTTATAATTTTAA
33944553 TGTTTTGTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
27 6 0.11
28 30 0.54
29 14 0.25
30 3 0.05
31 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
TTTTATAATTTTAAATAAATTTTATAAA
Found at i:33954763 original size:10 final size:10
Alignment explanation
Indices: 33954748--33954778 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
33954738 AAAGACATGG
33954748 TTGCCAATGT
1 TTGCCAATGT
33954758 TTGCCAATGT
1 TTGCCAATGT
33954768 TTGCCAATGT
1 TTGCCAATGT
33954778 T
1 T
33954779 ACTACCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (10 bp):
TTGCCAATGT
Found at i:33960021 original size:12 final size:14
Alignment explanation
Indices: 33959990--33960025 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
33959980 ATGATATAAA
33959990 ATAAAAATAATTTC
1 ATAAAAATAATTTC
33960004 ATAAAAA-AATTT-
1 ATAAAAATAATTTC
33960016 AT-AAAATAAT
1 ATAAAAATAAT
33960026 ATGAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.19
12 5 0.24
13 5 0.24
14 7 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAAATAATTTC
Found at i:33961996 original size:32 final size:31
Alignment explanation
Indices: 33961951--33962046 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
33961941 CTTAGATAAT
33961951 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
33961982 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
33962014 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
33962045 TT
1 TT
33962047 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:33962622 original size:10 final size:9
Alignment explanation
Indices: 33962602--33962680 Score: 67
Period size: 8 Copynumber: 8.7 Consensus size: 9
33962592 TAAAAAACCA
*
33962602 AAAAAAAGC
1 AAAAAAGGC
33962611 AAAAAAGCGC
1 AAAAAAG-GC
33962621 AAAAAAAGGC
1 -AAAAAAGGC
33962631 -AAAAA-GC
1 AAAAAAGGC
33962638 AAAAAAGCGC
1 AAAAAAG-GC
*
33962648 AAAAAAAAG-
1 -AAAAAAGGC
33962657 AAAAAA-GC
1 AAAAAAGGC
33962665 AAAAAAGCGC
1 AAAAAAG-GC
33962675 AAAAAA
1 AAAAAA
33962681 AAAGTTGCCT
Statistics
Matches: 59, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
7 3 0.05
8 22 0.37
9 6 0.10
10 15 0.25
11 13 0.22
ACGTcount: A:0.72, C:0.13, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAGGC
Found at i:33962634 original size:27 final size:27
Alignment explanation
Indices: 33962603--33962682 Score: 142
Period size: 27 Copynumber: 3.0 Consensus size: 27
33962593 AAAAAACCAA
*
33962603 AAAAAAGCAAAAAAGCGCAAAAAAAGG
1 AAAAAAGCAAAAAAGCGCAAAAAAAAG
*
33962630 CAAAAAGCAAAAAAGCGCAAAAAAAAG
1 AAAAAAGCAAAAAAGCGCAAAAAAAAG
33962657 AAAAAAGCAAAAAAGCGCAAAAAAAA
1 AAAAAAGCAAAAAAGCGCAAAAAAAA
33962683 AGTTGCCTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.72, C:0.12, G:0.15, T:0.00
Consensus pattern (27 bp):
AAAAAAGCAAAAAAGCGCAAAAAAAAG
Found at i:33965762 original size:32 final size:31
Alignment explanation
Indices: 33965717--33965812 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
33965707 CTTAGATAAT
33965717 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
33965748 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
33965780 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
33965811 TT
1 TT
33965813 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:33981944 original size:48 final size:49
Alignment explanation
Indices: 33981878--33981974 Score: 153
Period size: 48 Copynumber: 2.0 Consensus size: 49
33981868 CATAAAAAGG
*
33981878 AGAGAAGACCAAGGTGAAAA-CCTTCAAAGGGCGCTTTGAGTCCAAAAAA
1 AGAGAAGACCAAGGTGAAAACCCTT-AAAGGGCCCTTTGAGTCCAAAAAA
*
33981927 AGAG-AGACCAATGTGAAAACCCTTAAAGGGCCCTTTGAGTCCAAAAAA
1 AGAGAAGACCAAGGTGAAAACCCTTAAAGGGCCCTTTGAGTCCAAAAAA
33981975 TGAAAAATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 37 0.82
49 8 0.18
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (49 bp):
AGAGAAGACCAAGGTGAAAACCCTTAAAGGGCCCTTTGAGTCCAAAAAA
Found at i:33987218 original size:11 final size:11
Alignment explanation
Indices: 33987204--33987234 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
33987194 GTTTTTTGCT
33987204 TTAGTTTTCTC
1 TTAGTTTTCTC
33987215 TTAGTTTTCTC
1 TTAGTTTTCTC
33987226 TTAGGTTTT
1 TTA-GTTTT
33987235 TTTCCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.10, C:0.13, G:0.13, T:0.65
Consensus pattern (11 bp):
TTAGTTTTCTC
Found at i:33991420 original size:15 final size:15
Alignment explanation
Indices: 33991400--33991429 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33991390 GGCTTGGCCG
33991400 AACTTGGGCATGATC
1 AACTTGGGCATGATC
*
33991415 AACTTGGGCTTGATC
1 AACTTGGGCATGATC
33991430 CCAAAGTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (15 bp):
AACTTGGGCATGATC
Found at i:33995682 original size:86 final size:86
Alignment explanation
Indices: 33995576--33995745 Score: 295
Period size: 86 Copynumber: 2.0 Consensus size: 86
33995566 TATAGAATTG
* * *
33995576 CCCCAAGCCTAACTTAGCAAAGTTGAAACTATCAACCTTGCCACATGTGAGGCCAGCCAAGGGAG
1 CCCCAAGCCTAAATTAGCAAAGTCGAAACTATCAAACTTGCCACATGTGAGGCCAGCCAAGGGAG
33995641 GGCTCTTTGGCTGATAATTTT
66 GGCTCTTTGGCTGATAATTTT
*
33995662 CCCCAAGCCTAAATTAGCAAAGTCGAAACTATCAAACTTGCCACATGTGAGGCTAGCCAAGGGAG
1 CCCCAAGCCTAAATTAGCAAAGTCGAAACTATCAAACTTGCCACATGTGAGGCCAGCCAAGGGAG
*
33995727 GGCTCTTTTGCTGATAATT
66 GGCTCTTTGGCTGATAATT
33995746 ATTTCTATTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (86 bp):
CCCCAAGCCTAAATTAGCAAAGTCGAAACTATCAAACTTGCCACATGTGAGGCCAGCCAAGGGAG
GGCTCTTTGGCTGATAATTTT
Found at i:34001619 original size:12 final size:12
Alignment explanation
Indices: 34001602--34001627 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34001592 ATCAAAGGCA
34001602 TACTTGAGAACG
1 TACTTGAGAACG
34001614 TACTTGAGAACG
1 TACTTGAGAACG
34001626 TA
1 TA
34001628 GTTTGCCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (12 bp):
TACTTGAGAACG
Found at i:34003900 original size:15 final size:16
Alignment explanation
Indices: 34003870--34003901 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34003860 ACTTTAGGGA
34003870 CAAAAATGTAATTTTT
1 CAAAAATGTAATTTTT
*
34003886 CAAAAATGTGATTTTT
1 CAAAAATGTAATTTTT
34003902 GGACTAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
CAAAAATGTAATTTTT
Found at i:34004250 original size:26 final size:26
Alignment explanation
Indices: 34004221--34004301 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
34004211 TTCGATCACG
34004221 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
*
34004247 TGTGTA-T-CGGATAGTG-ATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
34004272 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
34004298 TGTG
1 TGTG
34004302 AACCAGTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
24 1 0.02
25 19 0.43
26 23 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:34004300 original size:51 final size:51
Alignment explanation
Indices: 34004107--34004301 Score: 204
Period size: 51 Copynumber: 3.9 Consensus size: 51
34004097 TGAAACTGAA
* * * *
34004107 AGTGAT-GGTCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGA-
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTA-CGGAT
* * * **
34004157 A-TTATAGGTCGCATGTGTAGTACAATGTGCAGGCTACTATGCATACTGGAT
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTAC-GGAT
* * *
34004208 AGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGAT
1 AG-TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTA-CGGAT
34004259 AGTGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
34004302 AACCAGTATC
Statistics
Matches: 119, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
49 4 0.03
50 36 0.30
51 76 0.64
52 2 0.02
53 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACGGAT
Found at i:34004546 original size:16 final size:16
Alignment explanation
Indices: 34004525--34004556 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34004515 TGATTGAAAG
*
34004525 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
34004541 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
34004557 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:34006164 original size:21 final size:21
Alignment explanation
Indices: 34006138--34006179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34006128 TGGATGAAAT
34006138 TTTATAACGTGT-TTTAATATG
1 TTTATAA-GTGTATTTAATATG
*
34006159 TTTATAAGTGTATTTATTATG
1 TTTATAAGTGTATTTAATATG
34006180 GTAATGCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTATAAGTGTATTTAATATG
Found at i:34014432 original size:16 final size:17
Alignment explanation
Indices: 34014413--34014445 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34014403 CAATTTGGGC
34014413 CGAG-AGGCCACACGGG
1 CGAGTAGGCCACACGGG
*
34014429 CGAGTGGGCCACACGGG
1 CGAGTAGGCCACACGGG
34014446 TAGACCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.21, C:0.30, G:0.45, T:0.03
Consensus pattern (17 bp):
CGAGTAGGCCACACGGG
Found at i:34021350 original size:29 final size:28
Alignment explanation
Indices: 34021314--34021391 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
34021304 TCATGAGATT
34021314 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
34021344 -GCACTAAGTGTGTGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
34021371 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
34021392 GATTATTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
29 33 0.80
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:34021666 original size:173 final size:174
Alignment explanation
Indices: 34021344--34021670 Score: 620
Period size: 173 Copynumber: 1.9 Consensus size: 174
34021334 AAATTGTACA
34021344 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
34021409 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGAGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
34021474 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
34021518 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
34021583 TGT-AGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGAGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
34021647 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
34021671 ACCTTGAGTT
Statistics
Matches: 150, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
173 82 0.55
174 68 0.45
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGAGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:34029489 original size:29 final size:28
Alignment explanation
Indices: 34029453--34029530 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
34029443 TCATGAGATT
34029453 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
34029483 -GCACTAAGTGTGTGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
34029510 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
34029531 GATTATTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
29 33 0.80
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:34029748 original size:174 final size:174
Alignment explanation
Indices: 34029483--34029810 Score: 638
Period size: 174 Copynumber: 1.9 Consensus size: 174
34029473 AAATTGTACA
34029483 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
34029548 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
34029613 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
34029657 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
34029722 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
34029787 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
34029811 ACCTTGAGTT
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 152 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:34035148 original size:50 final size:49
Alignment explanation
Indices: 34035055--34035200 Score: 141
Period size: 50 Copynumber: 2.9 Consensus size: 49
34035045 TTTCTTGTAC
* * * * * * **
34035055 TGCCAATGTCATATCCCAGATATGGTATTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATAACCAAGACATGGTCTTACAGGGGACCTCTCATA-CGG
** *
34035105 TGCTC-ATGCCATGTCCAAGACATGGTCTTACGGGGGACCTCTCATCACGG
1 TGC-CAATGCCATAACCAAGACATGGTCTTACAGGGGACCTCTCAT-ACGG
* *
34035155 TGCCAATGCCATAACCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAATGCCATAACCAAGACATGGTCTTACAGGGGACCTCTCATA
34035201 ATCTCAATGA
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
49 2 0.03
50 75 0.95
51 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (49 bp):
TGCCAATGCCATAACCAAGACATGGTCTTACAGGGGACCTCTCATACGG
Found at i:34041982 original size:19 final size:19
Alignment explanation
Indices: 34041960--34041997 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
34041950 TCAATCATCC
34041960 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
34041979 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
34041998 ACTATTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:34051058 original size:22 final size:22
Alignment explanation
Indices: 34051033--34051089 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 22
34051023 TTATAAGTAT
*
34051033 TGTGATATATGCTTAAATGTTA
1 TGTGATATATGCTTAAATGTAA
*
34051055 TGTGAT-TAT-C-T--GTGTAA
1 TGTGATATATGCTTAAATGTAA
34051072 TGTGATATATGCTTAAAT
1 TGTGATATATGCTTAAAT
34051090 TTTAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
17 10 0.37
18 3 0.11
19 2 0.07
20 2 0.07
21 3 0.11
22 7 0.26
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (22 bp):
TGTGATATATGCTTAAATGTAA
Found at i:34051110 original size:39 final size:39
Alignment explanation
Indices: 34051033--34051110 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
34051023 TTATAAGTAT
* **
34051033 TGTGATATATGCTTAAATGTTATGTGATTATCTGTGTAA
1 TGTGATATATGCTTAAATGTTATGTAATTATCCATGTAA
* *
34051072 TGTGATATATGCTTAAATTTTAATTTAATTA-CCATGTAA
1 TGTGATATATGCTTAAATGTT-ATGTAATTATCCATGTAA
34051111 ATGAACTAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 26 0.79
40 7 0.21
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (39 bp):
TGTGATATATGCTTAAATGTTATGTAATTATCCATGTAA
Found at i:34058608 original size:71 final size:71
Alignment explanation
Indices: 34058510--34058646 Score: 204
Period size: 71 Copynumber: 1.9 Consensus size: 71
34058500 AAAGTATAGG
* * *
34058510 TAGAAGTGCAAGGGATGCTGAACTTTGGCTACTAACTTTACTTGTTTCAGTAGAAATCCTCAAAG
1 TAGAAGTGCAAGGGATGCTGAAATTTGGCTACTAACTTGACTTGCTTCAGTAGAAATCCTCAAAG
34058575 TATCAA
66 TATCAA
* * *
34058581 TAGAAGTGC-AGGAGATGCTGAAATTTGGCTACTGACTTGACTTGCTTCGGTAGAAGTCCTCAAA
1 TAGAAGTGCAAGG-GATGCTGAAATTTGGCTACTAACTTGACTTGCTTCAGTAGAAATCCTCAAA
34058645 GT
65 GT
34058647 TTCGATAGTA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 3 0.05
71 56 0.95
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (71 bp):
TAGAAGTGCAAGGGATGCTGAAATTTGGCTACTAACTTGACTTGCTTCAGTAGAAATCCTCAAAG
TATCAA
Found at i:34059854 original size:51 final size:50
Alignment explanation
Indices: 34059799--34059933 Score: 173
Period size: 51 Copynumber: 2.7 Consensus size: 50
34059789 AAAGTGATGG
*
34059799 TCACGTGTGTAGTACTATGTGCAAGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA-CTAT-GA
* * * * *
34059850 TCACGTGTGTAGCACTATGTGCAGGCTACTACGTGTATCGGATACTGATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATACT-ATGA
*
34059901 TCACTTGTGTAGTACTATGTGCAGGCTACTATG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATG
34059934 TGAACCGGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
50 2 0.03
51 70 0.96
52 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATACTATGA
Found at i:34060180 original size:16 final size:16
Alignment explanation
Indices: 34060159--34060190 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34060149 TGATTGAAAG
*
34060159 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
34060175 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
34060191 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:34062285 original size:20 final size:20
Alignment explanation
Indices: 34062260--34062305 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
34062250 AATTTTTAAT
34062260 ATACTTTTTGTTATATCAAA
1 ATACTTTTTGTTATATCAAA
34062280 ATACTTTTTGTTATATCAAA
1 ATACTTTTTGTTATATCAAA
34062300 ATACTT
1 ATACTT
34062306 GAAAAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (20 bp):
ATACTTTTTGTTATATCAAA
Found at i:34064811 original size:30 final size:30
Alignment explanation
Indices: 34064775--34064838 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
34064765 CGGTTGGAAG
* *
34064775 TTGGCAGTGAAGACGGAAACATACTTCAAT
1 TTGGCAGCGAAGACGGAAACATACTTCAAA
34064805 TTGGCAGCGAAGACGGAAACATACTTCAAA
1 TTGGCAGCGAAGACGGAAACATACTTCAAA
34064835 TTGG
1 TTGG
34064839 TTAAGCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (30 bp):
TTGGCAGCGAAGACGGAAACATACTTCAAA
Found at i:34073011 original size:11 final size:13
Alignment explanation
Indices: 34072995--34073028 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
34072985 AATTTTACGG
34072995 AAAAATTTCG-T-
1 AAAAATTTCGTTC
34073006 AAAAATTTCGTTC
1 AAAAATTTCGTTC
34073019 AAAAATTTCG
1 AAAAATTTCG
34073029 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:34074173 original size:76 final size:76
Alignment explanation
Indices: 34074084--34074267 Score: 291
Period size: 76 Copynumber: 2.4 Consensus size: 76
34074074 GAGTACATTG
**
34074084 AATATGAA-GGGGTTGCTAAGTGCTGATTCCCCGA-CTCATTGGTGGTTGTTAAGTGCTAATTCC
1 AATATGAAGGGGGTTGCTAAGTGCTGATTCCCCGATC-CATTGGTGGTTACTAAGTGCTAATTCC
34074147 ACCGTATCTTTA
65 ACCGTATCTTTA
* * *
34074159 AATATAAAGGGGGTTGCTAAGTGCTGATTCCCCGATCCATTGGTGGTTACTAAGTGTTGATTCCA
1 AATATGAAGGGGGTTGCTAAGTGCTGATTCCCCGATCCATTGGTGGTTACTAAGTGCTAATTCCA
34074224 CCGTATCTTTA
66 CCGTATCTTTA
*
34074235 AATGTGAAGGGGGTTGCTAAGTGCTGATTCCCC
1 AATATGAAGGGGGTTGCTAAGTGCTGATTCCCC
34074268 CAAGGGGTTG
Statistics
Matches: 100, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
75 7 0.07
76 92 0.92
77 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (76 bp):
AATATGAAGGGGGTTGCTAAGTGCTGATTCCCCGATCCATTGGTGGTTACTAAGTGCTAATTCCA
CCGTATCTTTA
Found at i:34074180 original size:43 final size:41
Alignment explanation
Indices: 34074127--34074265 Score: 132
Period size: 43 Copynumber: 3.5 Consensus size: 41
34074117 ACTCATTGGT
* *
34074127 GGTTGTTAAGTGCTAATTCCACCGTATCTTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAAT-T-AAGGG
* *
34074170 GGTTGCTAAGTGCTGATTCC-CCG-ATC----CATT--GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATTAAGGG
* *
34074203 GGTTACTAAGTGTTGATTCCACCGTATCTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAAT-T-AAGGG
34074246 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
34074266 CCCAAGGGGT
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
33 20 0.26
34 3 0.04
35 3 0.04
36 1 0.01
37 2 0.03
39 2 0.03
40 1 0.01
41 3 0.04
42 3 0.04
43 38 0.50
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATTAAGGG
Found at i:34074290 original size:103 final size:103
Alignment explanation
Indices: 34074168--34074370 Score: 345
Period size: 103 Copynumber: 2.0 Consensus size: 103
34074158 AAATATAAAG
*
34074168 GGGGTTGCTAAGTGCTGATTCCCCG-ATCCATTGGTGGTTACTAAGTGTTGATTCCACCGTATCT
1 GGGGTTGCTAAGTGCTGATTCCCCGAAT-CATTGGTGGTTACTAAGTGTTGATTCCACCATATCT
* *
34074232 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
65 TTAAATGTGAAAGGGGTTGCTAAATGCTGATTCCCCCAA
*
34074271 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCATATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTACTAAGTGTTGATTCCACCATATCTT
*
34074336 TGAATGTGAAAGGGGTTGCTAAATGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAATGCTGATTCCCC
34074371 GAATCACTAG
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 92 0.98
104 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.33
Consensus pattern (103 bp):
GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTACTAAGTGTTGATTCCACCATATCTT
TAAATGTGAAAGGGGTTGCTAAATGCTGATTCCCCCAA
Found at i:34074315 original size:33 final size:33
Alignment explanation
Indices: 34074246--34074406 Score: 102
Period size: 33 Copynumber: 4.7 Consensus size: 33
34074236 ATGTGAAGGG
*
34074246 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
34074273 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
34074306 GGTTGCTAAGTGTTGATTCCACC-ATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGA-ATC-----AT-TG---GT
* * *
34074349 GGTTGCTAAATGCTGATTCCCCGAATCACTAGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
34074382 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
34074407 TAACAGTTAA
Statistics
Matches: 105, Mismatches: 10, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
27 22 0.21
31 2 0.02
32 2 0.02
33 39 0.37
34 9 0.09
36 1 0.01
37 1 0.01
39 2 0.02
40 2 0.02
42 5 0.05
43 20 0.19
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:34077568 original size:50 final size:50
Alignment explanation
Indices: 34077513--34077622 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 50
34077503 CATCAGAGTA
* * * *
34077513 TCGGTAGAAGTGCAGGGGATGTTGAACTTTGGTTACTGACTTGACTTGTT
1 TCGGTAGAAGTGCAAGAGATGTTGAACTTTGGCTACTAACTTGACTTGTT
* *
34077563 TCGGTAGAAGTGTAAGAGATGTTGAACTTTGGCTACTAACTTGGCTTGTT
1 TCGGTAGAAGTGCAAGAGATGTTGAACTTTGGCTACTAACTTGACTTGTT
*
34077613 TTGGTAGAAG
1 TCGGTAGAAG
34077623 CCATCAAGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.35
Consensus pattern (50 bp):
TCGGTAGAAGTGCAAGAGATGTTGAACTTTGGCTACTAACTTGACTTGTT
Found at i:34078776 original size:24 final size:23
Alignment explanation
Indices: 34078745--34078791 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
34078735 TTATTTATGT
*
34078745 ATAAAATTAAAACCAAATTTTAA
1 ATAAAATTAAAACCAAATATTAA
34078768 ATAATAATTAAAACCAAATATTAA
1 ATAA-AATTAAAACCAAATATTAA
34078792 TTGACGCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAAAATTAAAACCAAATATTAA
Found at i:34079705 original size:16 final size:17
Alignment explanation
Indices: 34079686--34079718 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34079676 TAATTGTTAC
34079686 TTATT-TAAATAATTTT
1 TTATTATAAATAATTTT
*
34079702 TTATTATTAATAATTTT
1 TTATTATAAATAATTTT
34079719 ATAATAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATAAATAATTTT
Found at i:34079728 original size:18 final size:18
Alignment explanation
Indices: 34079693--34079741 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
34079683 TACTTATTTA
* *
34079693 AATAATTTT-TTATTATT
1 AATAATTTTATAATAATT
34079710 AATAATTTTATAATAATT
1 AATAATTTTATAATAATT
* *
34079728 AGTATTTTTATAAT
1 AATAATTTTATAAT
34079742 TTAAAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AATAATTTTATAATAATT
Found at i:34090694 original size:14 final size:15
Alignment explanation
Indices: 34090683--34090712 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34090673 GTTGGAGGTG
34090683 TGTCG-ATGGAGGAA
1 TGTCGAATGGAGGAA
34090697 TGTCGAATGGAGGAA
1 TGTCGAATGGAGGAA
34090712 T
1 T
34090713 TCCGTAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.30, C:0.07, G:0.40, T:0.23
Consensus pattern (15 bp):
TGTCGAATGGAGGAA
Found at i:34102861 original size:29 final size:29
Alignment explanation
Indices: 34102826--34102884 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
34102816 TTAGTAGAGA
*
34102826 GAAAATTATATTTTAA-CTCTAAAAATTAT
1 GAAAATT-TAATTTAACCTCTAAAAATTAT
*
34102855 GAAAATTTAATTTAATCCTTTAAAAATTAT
1 GAAAATTTAATTTAA-CCTCTAAAAATTAT
34102885 AAAGATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.27
29 7 0.27
30 12 0.46
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (29 bp):
GAAAATTTAATTTAACCTCTAAAAATTAT
Found at i:34104322 original size:29 final size:30
Alignment explanation
Indices: 34104289--34104357 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
34104279 TAGTAATTGT
*
34104289 AAAATTATACTTTAAT-TTCAAAAAATATA
1 AAAATTATAATTTAATCTTCAAAAAATATA
* *
34104318 AAAATT-TAATTTAATCCTTTAAAAATTATA
1 AAAATTATAATTTAAT-CTTCAAAAAATATA
34104348 AAAATTATAA
1 AAAATTATAA
34104358 AGATATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.24
29 6 0.18
30 17 0.50
31 3 0.09
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (30 bp):
AAAATTATAATTTAATCTTCAAAAAATATA
Found at i:34104350 original size:8 final size:8
Alignment explanation
Indices: 34104339--34104388 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
34104329 TAATCCTTTA
34104339 AAAATTAT
1 AAAATTAT
34104347 AAAAATTAT
1 -AAAATTAT
34104356 AAAGA-TAT
1 AAA-ATTAT
34104364 -AAATTATT
1 AAAATTA-T
*
34104372 AAAATGAT
1 AAAATTAT
34104380 AAAATTAT
1 AAAATTAT
34104388 A
1 A
34104389 TTTTTACTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
6 1 0.03
7 4 0.11
8 16 0.46
9 14 0.40
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:34104372 original size:18 final size:17
Alignment explanation
Indices: 34104339--34104387 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
34104329 TAATCCTTTA
*
34104339 AAAATTATAAAA--ATT
1 AAAATGATAAAATTATT
34104354 ATAAA-GATATAAATTATT
1 A-AAATGATA-AAATTATT
34104372 AAAATGATAAAATTAT
1 AAAATGATAAAATTAT
34104388 ATTTTTACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 4 0.14
16 6 0.21
17 10 0.36
18 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (17 bp):
AAAATGATAAAATTATT
Found at i:34104388 original size:24 final size:24
Alignment explanation
Indices: 34104340--34104388 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
34104330 AATCCTTTAA
* *
34104340 AAATTATAAAAATTATAAAGATAT
1 AAATTATAAAAATGATAAAAATAT
* *
34104364 AAATTATTAAAATGATAAAATTAT
1 AAATTATAAAAATGATAAAAATAT
34104388 A
1 A
34104389 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATTATAAAAATGATAAAAATAT
Found at i:34110656 original size:699 final size:695
Alignment explanation
Indices: 34108802--34111037 Score: 3362
Period size: 697 Copynumber: 3.2 Consensus size: 695
34108792 GTGCACACTA
* * * * * * *
34108802 TGTTTCACAGGCCTTAACATTTTATAAAATCTCTATTTTTCTTTCTAGTTTAAACTTTTATTTGA
1 TGTTTCACAGGCCTCAACGTTTCATAAAATCCCTATTCTTCCTTCTAATTTAAACTTTTATTTGA
* * *
34108867 TTTTTATTTTGATTATTTTTTCGTATTTGATAAATTAAATATAAACTATTCTATTCTTACTTTAT
66 TTTTAATTTTGATT-GTTTTTCGTATTTGATAAATTAAATATAAACTATTCTATTCTTATTTTAT
* *
34108932 ATGTGTTTATTTATATTTAATTTATTTTGTTCTCT-AACT-TATTGTCTAACAATATTAAGACAG
130 ATGTGTTTATTTATATTTAATTTATTTTGTT-TCTAAAGTGTTTTGTCTAACAATATTAAGACAG
* *
34108995 ATCCTTGTTATTTTTGCAATTCTCTAATCTGAGACAAACGAAACACCAAGGCGAATAG--AAAAA
194 ATCCTTGTTATTTTTGCAATTCTCTAATCAGAGACAAACGAAACACCAAGGCGAAAAGAAAAAAA
* * * *
34109058 AATTATTTTTAAAATAAATTTTTTAAAAAAAAGTGGAAAAAATTTGTTTCGAGATTTATTCTCGC
259 AATCATTTTTAAAAT-AATTTTTT-TAAAAAAGTGGATAAAATCTGTTTCGAGATTTATTCTCGC
* * * * * *
34109123 CGTTCAACGGATTTTATTCCAATTTTAATTTTATTTTAGCCTAACACGAATTTCTTTTTGGATCT
322 CGTTCAAC-GATTTTATTCCAATTTTGATTTTATTTTTGCCCAACACGAATTTATTTTTGGCTCC
* * * * *
34109188 TTAATGACATATTTTGTAGTTATTTCCAAATTTTCCACCATTCTACATGCCTATAAAAGGCTATA
386 TTAATGGCAGATTTTGTGGTTATTTCTAAATTTTCCACCATCCTACATGCCTATAAAAGGCTATA
*
34109253 TTTTCTGTAGGATTAAACCAACACTCTGATATTTTTCTTATACTGAAATTCTGTTGCTCTCAAAA
451 TTTTCTGTAGGATTAAACCAACACTCTGATATTTTTCTTATACCGAAATTCTGTTGCTCTCAAAA
* *
34109318 TTCTTCCTTTTCCTCTTCGTATTTTTCAAATTTTTCGGTGATAGAAAAAGGCAAAATTCGTTCGT
516 TTCTTCCTTTTCCTCTTCGTATTTTTCAAACTTTTCGGTGATAGAAAAAGGCAAAGTTCGTTCGT
* * *
34109383 TGATCATTGTAGAGGTGCTACTACTTTGATCACTGTTGTTGTAGTATCCTGGGAGACATTCAACC
581 TGATCGTTGTAGAGGTGCTACTACTTTGATCACTGTTGTT-TTGTATCCTGGGAGACATTCGACC
*
34109448 AACGTTTCTCCAAGTACTGTAGGAGC-AGTCGAATCTGTCTTAAGGAAATTG
645 AACGTTTCTCCAAGTACCGTAGGAGCGA-TCGAATCTGTCTTAAGGAAATTG
* * * *
34109499 TGTTTCACAAGCCTCAACGTTTCGTAAAATCCCTA---TTCCTCCTAATATAAACTTTTATTTGA
1 TGTTTCACAGGCCTCAACGTTTCATAAAATCCCTATTCTTCCTTCTAATTTAAACTTTTATTTGA
*
34109561 TTTTAATTTTGATTATTTTTACGTATTTGATAAATTAAATATAAACTATTCTATTCTTATTTTAT
66 TTTTAATTTTGATTGTTTTT-CGTATTTGATAAATTAAATATAAACTATTCTATTCTTATTTTAT
** * *
34109626 ATGTGTTTATTTATATTTAATTTATTTTGTCCGCTAACGTGCTTTGTCTAACAATATTAAGACAG
130 ATGTGTTTATTTATATTTAATTTATTTTGT-TTCTAAAGTGTTTTGTCTAACAATATTAAGACAG
* *
34109691 ATCCTTGTTATTTTTTGCAATTCTCTAATCAAAGACAAACGAAACACTAAGGCGAAAAGAAAAAA
194 ATCCTTGTTA-TTTTTGCAATTCTCTAATCAGAGACAAACGAAACACCAAGGCGAAAAGAAAAAA
* * ***
34109756 AAATCATTTTTAAAATAATTTTTTTAAAAAAGTGGATAAAATCTGTTTTGAGATTTATTCCCATT
258 AAATCATTTTTAAAATAATTTTTTTAAAAAAGTGGATAAAATCTGTTTCGAGATTTATTCTCGCC
* *
34109821 ATTCAACGAATTTTATTCCAATTTTGATTTTATTTTTGCCCAATACGAATTTATTTTTGGCTCCT
323 GTTCAACG-ATTTTATTCCAATTTTGATTTTATTTTTGCCCAACACGAATTTATTTTTGGCTCCT
*
34109886 TAATGGCAGATTTTGTGGTTATTTCTAAATTTTCCACCATCCTTCATGCCTATAAAAGGCTATAT
387 TAATGGCAGATTTTGTGGTTATTTCTAAATTTTCCACCATCCTACATGCCTATAAAAGGCTATAT
* *
34109951 TTTCTGTAGGATTAAACCAACACTCTGATATTTTTCTTATACCAAAATTCTGTAGCTCTCAAAAT
452 TTTCTGTAGGATTAAACCAACACTCTGATATTTTTCTTATACCGAAATTCTGTTGCTCTCAAAAT
* * *
34110016 TCTTCCATTTCCTCTTCGTATTTTTCAAACTTTTCGGTGATAGAAAAAGGCAAAGTTTGTTCGTC
517 TCTTCCTTTTCCTCTTCGTATTTTTCAAACTTTTCGGTGATAGAAAAAGGCAAAGTTCGTTCGTT
** *
34110081 GATCGTTGTAGAGGTGCTACTACTTTGGCCACTGTTGTTATTGTATCCTGAGAGACATTCGACCA
582 GATCGTTGTAGAGGTGCTACTACTTTGATCACTGTTGTT-TTGTATCCTGGGAGACATTCGACCA
34110146 ACGTTTCTCCAAGTACCGTAGGAGCGATCGAATCTGTCTTAAGGAAATTG
646 ACGTTTCTCCAAGTACCGTAGGAGCGATCGAATCTGTCTTAAGGAAATTG
* * *
34110196 TGTTTCATAGGCCTCAATGTTTCATAAAATCTCTATTCTTCCTTCTAATTTAAACTTTTATTTGA
1 TGTTTCACAGGCCTCAACGTTTCATAAAATCCCTATTCTTCCTTCTAATTTAAACTTTTATTTGA
* * *
34110261 TTTTAATTTTGATTGTTTTTCATATTTTATAAATTAAATATAAACTATTCTATTCTTATTTTATG
66 TTTTAATTTTGATTGTTTTTCGTATTTGATAAATTAAATATAAACTATTCTATTCTTATTTTATA
* * *
34110326 TGTGTTTATTTATATTTAATTTATTTTGTTTACTAAAGTGTTTTGTTTAACAATCTTAAGACAAA
131 TGTGTTTATTTATATTTAATTTATTTTGTTT-CTAAAGTGTTTTGTCTAACAATATTAAGACAGA
* * *
34110391 TCCTTATTATTTTTGCAATTCTCTAATCCGAGACGAACGAAACACCAAGGCGAAAAGAAAAAAAA
195 TCCTTGTTATTTTTGCAATTCTCTAATCAGAGACAAACGAAACACCAAGGCGAAAAGAAAAAAAA
* *
34110456 CATCATTTTTAAAATAATTTTTTTAAAAAAGTGGGTAAAATCTATTTCGAGATTTATTCTCGCCG
260 -ATCATTTTTAAAATAATTTTTTTAAAAAAGTGGATAAAATCTGTTTCGAGATTTATTCTCGCCG
* *
34110521 TTCAGCAGATTTTATTCCAATTTTGATTTTATTTTTGCCCAACACGAATTTATTTTTGTCTCCTT
324 TTCAAC-GATTTTATTCCAATTTTGATTTTATTTTTGCCCAACACGAATTTATTTTTGGCTCCTT
*
34110586 AATGGCAGATTTTGTGGTTATTTCTAAATTTTCCACCATCCTACATGCCTATAAAAGGCTATGTT
388 AATGGCAGATTTTGTGGTTATTTCTAAATTTTCCACCATCCTACATGCCTATAAAAGGCTATATT
*
34110651 TTCTGTAGGATTAAACCAACACTCTGATATTTTTCTTATACCGAAATTCTGTTGCTCTCAAAATA
453 TTCTGTAGGATTAAACCAACACTCTGATATTTTTCTTATACCGAAATTCTGTTGCTCTCAAAATT
* * * *
34110716 CTTCCTTTTCGTCTTCGTATTTTTCAAACTTTCCGGTGATAG--AAAGACAAAGTTCGTCCGTTG
518 CTTCCTTTTCCTCTTCGTATTTTTCAAACTTTTCGGTGATAGAAAAAGGCAAAGTTCGTTCGTTG
* ** *
34110779 ATTGTTGTAGAGGTGCTACTACTTTGATCACTGTTG--TTGTATTTTGGGAGACATTCGACTAAC
583 ATCGTTGTAGAGGTGCTACTACTTTGATCACTGTTGTTTTGTATCCTGGGAGACATTCGACCAAC
* * * * *
34110842 ATTTCTCCAAGTACCATAGGAACGGTCGAATCTGTCTTAAGGAAACTG
648 GTTTCTCCAAGTACCGTAGGAGCGATCGAATCTGTCTTAAGGAAATTG
* *
34110890 TGTTTCACAGGCCTTAACGTTTCGTAAAATCCCTATTCTTCCTTCTAATTTAAACTTTTATTTGA
1 TGTTTCACAGGCCTCAACGTTTCATAAAATCCCTATTCTTCCTTCTAATTTAAACTTTTATTTGA
*
34110955 TTTTAATTTTGATTGTTTTTTCGTATTTGATAAATTAAATATAAACTATTTTATTCTTATTTTAT
66 TTTTAATTTTGATTG-TTTTTCGTATTTGATAAATTAAATATAAACTATTCTATTCTTATTTTAT
*
34111020 ATGTATTTATTTATATTT
130 ATGTGTTTATTTATATTT
34111038 CCAGATTATC
Statistics
Matches: 1393, Mismatches: 130, Indels: 34
0.89 0.08 0.02
Matches are distributed among these distances:
693 5 0.00
694 252 0.18
695 64 0.05
696 33 0.02
697 527 0.38
698 61 0.04
699 406 0.29
700 45 0.03
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (695 bp):
TGTTTCACAGGCCTCAACGTTTCATAAAATCCCTATTCTTCCTTCTAATTTAAACTTTTATTTGA
TTTTAATTTTGATTGTTTTTCGTATTTGATAAATTAAATATAAACTATTCTATTCTTATTTTATA
TGTGTTTATTTATATTTAATTTATTTTGTTTCTAAAGTGTTTTGTCTAACAATATTAAGACAGAT
CCTTGTTATTTTTGCAATTCTCTAATCAGAGACAAACGAAACACCAAGGCGAAAAGAAAAAAAAA
TCATTTTTAAAATAATTTTTTTAAAAAAGTGGATAAAATCTGTTTCGAGATTTATTCTCGCCGTT
CAACGATTTTATTCCAATTTTGATTTTATTTTTGCCCAACACGAATTTATTTTTGGCTCCTTAAT
GGCAGATTTTGTGGTTATTTCTAAATTTTCCACCATCCTACATGCCTATAAAAGGCTATATTTTC
TGTAGGATTAAACCAACACTCTGATATTTTTCTTATACCGAAATTCTGTTGCTCTCAAAATTCTT
CCTTTTCCTCTTCGTATTTTTCAAACTTTTCGGTGATAGAAAAAGGCAAAGTTCGTTCGTTGATC
GTTGTAGAGGTGCTACTACTTTGATCACTGTTGTTTTGTATCCTGGGAGACATTCGACCAACGTT
TCTCCAAGTACCGTAGGAGCGATCGAATCTGTCTTAAGGAAATTG
Found at i:34111189 original size:18 final size:17
Alignment explanation
Indices: 34111147--34111198 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
34111137 AAATAATTTA
34111147 AAACTT-AAATTTTGA-
1 AAACTTAAAATTTTGAG
*
34111162 AAACTTAAAAATTTGGAG
1 AAACTT-AAAATTTTGAG
*
34111180 AAATTTAAAATTTTGAG
1 AAACTTAAAATTTTGAG
34111197 AA
1 AA
34111199 TCGAGTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 6 0.19
17 20 0.65
18 5 0.16
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.35
Consensus pattern (17 bp):
AAACTTAAAATTTTGAG
Found at i:34122626 original size:13 final size:12
Alignment explanation
Indices: 34122603--34122630 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34122593 AAAAGAAACA
34122603 AAAATTATTTTT
1 AAAATTATTTTT
34122615 AAAATTATTTTT
1 AAAATTATTTTT
34122627 AAAA
1 AAAA
34122631 AAAAGTAATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AAAATTATTTTT
Found at i:34122883 original size:689 final size:679
Alignment explanation
Indices: 34121259--34122732 Score: 1578
Period size: 687 Copynumber: 2.1 Consensus size: 679
34121249 AAACGTGGAT
* *
34121259 AAAATCTGTTTCGAGATTTATTC-CAC-CGTTCAAC-GAATTTTATTCCAATTTTGATTTTATTT
1 AAAATCTGTTTCGGGATTTATTCTCGCGCGTTCAACAG-ATTTTATTCCAATTTTGATTTTATTT
* * * * *** * * * ** * *
34121321 TAGCCCA-ACACGAATTTATTTTTGGCTCATTAATGGTATATTTTGAAGTTATTTCCAAATTTTC
65 TA--CCAGA-AAGGAGTT-GTTTTAAATC-TAAAT-GAAAATTTTGTGGTTATATCCAAATATTC
* * * * * * * **
34121385 CACCATCCTACATGCCTATAAAGGTTGTGTTTTCTATAA-GATTAAA-CCAACACTCTGATATTT
124 CACCATCCTACATGACTATAAAAGTTGT-ATTTCCAAAACGA-GAAAGCAAACACT-TGATATAA
* * * * * * * * * **
34121448 TTCTTATACCAAAATTTTGTTGCTTTCAAAATTCTTCCTTTTCCTCTTCGTATTTTTCAAACTTT
186 ATCTTATACCGAAATTCTATAGCTATC-AAATTCTT-CTATTCATATTAATATTTTTCAAACTTT
* * *
34121513 TCTGTGATAAAAAAAGGCAAAGTTCGTTCGTTGATCGTTGTAGAGGTGTTACTACTTTGATCACT
249 CCGGTGATAAAAAAAGGCAAAGTTCGTTCGTTGATCGTTGTAGAGGTGCTACTACTTTGATCACT
** * *
34121578 GTTGTTGTGTATCCTAAAAGACATTTGACCAATGTTTCTCCAAGTACCTTAGGAGTGGTCGAATC
314 GTTGTTGTGTATCCTAAAAGACATTCAACCAACGTTTCTCCAAGTACCGTAGGAGTGGTCGAATC
*
34121643 TGTCTTAAGGAAACTGTGTTTCACATGCCTCAACGTTTCGTAAAATCCCTATTCATCCTTCTAAT
379 TGTCTTAAGGAAACTGTGTTTCACAGGCCTCAACGTTTCGTAAAATCCCTATTCATCCTTCTAAT
* * * * *
34121708 TTAAACTTTTATTTGATTTTAATTTTCATTGTTTTCGTATTTATAAATTAAAACAAACTATTCTA
444 TTAAAATTTTATTTCATTTTAATTTTCATTGTTTTCGTATTGATAAATTAAAACAAACGATTATA
* * *
34121773 TTTTATTTATATGTGTTTATTTATATTTAATTTATTTTGTTCGCTAACGTGTTTTGTCTAATAAT
509 TTTTATTTATATGTGTTTATTTATATTTAATTTATTTTGTTCACTAACATGTTTTGTCTAACAAT
* *
34121838 CTTAAGATAGATCCCTGTTATTTTGCAATTCTCTAAGTCGAGACAACGAAACACCAAGGCGAAAG
574 CTTAAGATAGATCCCTATTATTTTGCAATTCTCTAAGTCGAGACAACGAAACACCAAGGCAAAAG
*** *
34121903 AAAAAAAATCTTTTTTAAAATATTTTTTTTAAAAGTGGATA
639 AAAAAAAATCTTTTTTAAAATATTTTTAAAAAAAGTGAATA
* **
34121944 AAAATCTGTTTTGGGATTTATTCTCGCGCGTTCAATGGATTTTATTCCAATTTTGATTTTATTTT
1 AAAATCTGTTTCGGGATTTATTCTCGCGCGTTCAACAGATTTTATTCCAATTTTGATTTTATTTT
* * * * * * * * *
34122009 AGCCCAGTACGGATTTGTTTTGACTCCTTAATGGCAAATTTTGTGGTTATTTCCAAATTTTCCAC
66 A--CCAGAAAGGAGTTGTTTTAAAT-CTAAAT-GAAAATTTTGTGGTTATATCCAAATATTCCAC
* * * *** * ** ***
34122074 CATCCTACATGCCTATAAAAGGTTGTGTTTTCTGTAGGATTAAGCAAACACTTTGATATTTTTCT
127 CATCCTACATGACTATAAAA-GTTGTATTTCCAAAACGAGAAAGCAAACAC-TTGATATAAATCT
* * * * **
34122139 TATACCGAAATTCTATAGCTCTCAAATTCTTCCTTTTCCTCTTCGTATTTTTCAAACTTTCCCGG
190 TATACCGAAATTCTATAGCTATCAAATTCTT-CTATTCATATTAATATTTTTCAAACTTT-CCGG
* * *
34122204 TGATAGAAAAAGGCAAAGTTCGTTCGTTGATCGTTGTAGAGGTGCTCCTACTTTGATTACTGTTG
253 TGATAAAAAAAGGCAAAGTTCGTTCGTTGATCGTTGTAGAGGTGCTACTACTTTGATCACTGTTG
*** *
34122269 TTGTTGTATCCTGGGAGACATTCAACCAACGTTTCTCCAAGTACCGTAGGAGTGGTTGAATCTGT
318 TTG-TGTATCCTAAAAGACATTCAACCAACGTTTCTCCAAGTACCGTAGGAGTGGTCGAATCTGT
*
34122334 CTTAAGGAAACTGTGTTTCAACAGGCCTCAACGTTTCGTAAAATCCCTATTCTTCCTTCTAATTT
382 CTTAAGGAAACTGTGTTTC-ACAGGCCTCAACGTTTCGTAAAATCCCTATTCATCCTTCTAATTT
* * *
34122399 AAAATTTTATTTCATTTTAATTTT-ATTTTTTTTGTATTCGATAAATTAAAAATAAACGATTATA
446 AAAATTTTATTTCATTTTAATTTTCATTGTTTTCGTATT-GATAAATT-AAAACAAACGATTATA
*
34122463 TTCTTATTTTATATGTGTTTATTTATATTTAATTTATTTTGTTCACTAATATGTTTTGTCTAACA
509 TT-TTA-TTTATATGTGTTTATTTATATTTAATTTATTTTGTTCACTAACATGTTTTGTCTAACA
* * * * *
34122528 ATTTTAAGATAGATCCTTATTATTTTTGCAATTTTCTAATTCGAGACAAATGAAACACCAAGGCA
572 ATCTTAAGATAGATCCCTATTA-TTTTGCAATTCTCTAAGTCGAGAC-AACGAAACACCAAGGC-
34122593 AAAAGAAACAAAAAT-TATTTTTAAAATTATTTTTAAAAAAAAGT-AAT-
634 AAAAGAAA-AAAAATCT-TTTTTAAAA-TATTTTT-AAAAAAAGTGAATA
34122640 AAAATCTGTTTCGGGATTTATTCTCGC-CGTTCAACAGATTTTATTCCAATTTTGATTTTA-TTT
1 AAAATCTGTTTCGGGATTTATTCTCGCGCGTTCAACAGATTTTATTCCAATTTTGATTTTATTTT
*
34122703 -CCA-AAATGAGTT-TTTTAAAT-TAAAT-AAAAT
66 ACCAGAAAGGAGTTGTTTTAAATCTAAATGAAAAT
34122733 CTACTTAGGG
Statistics
Matches: 690, Mismatches: 76, Indels: 46
0.85 0.09 0.06
Matches are distributed among these distances:
685 25 0.04
686 106 0.15
687 161 0.23
688 86 0.12
689 78 0.11
690 20 0.03
691 6 0.01
692 73 0.11
693 22 0.03
694 18 0.03
695 39 0.06
696 41 0.06
697 9 0.01
698 6 0.01
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (679 bp):
AAAATCTGTTTCGGGATTTATTCTCGCGCGTTCAACAGATTTTATTCCAATTTTGATTTTATTTT
ACCAGAAAGGAGTTGTTTTAAATCTAAATGAAAATTTTGTGGTTATATCCAAATATTCCACCATC
CTACATGACTATAAAAGTTGTATTTCCAAAACGAGAAAGCAAACACTTGATATAAATCTTATACC
GAAATTCTATAGCTATCAAATTCTTCTATTCATATTAATATTTTTCAAACTTTCCGGTGATAAAA
AAAGGCAAAGTTCGTTCGTTGATCGTTGTAGAGGTGCTACTACTTTGATCACTGTTGTTGTGTAT
CCTAAAAGACATTCAACCAACGTTTCTCCAAGTACCGTAGGAGTGGTCGAATCTGTCTTAAGGAA
ACTGTGTTTCACAGGCCTCAACGTTTCGTAAAATCCCTATTCATCCTTCTAATTTAAAATTTTAT
TTCATTTTAATTTTCATTGTTTTCGTATTGATAAATTAAAACAAACGATTATATTTTATTTATAT
GTGTTTATTTATATTTAATTTATTTTGTTCACTAACATGTTTTGTCTAACAATCTTAAGATAGAT
CCCTATTATTTTGCAATTCTCTAAGTCGAGACAACGAAACACCAAGGCAAAAGAAAAAAAATCTT
TTTTAAAATATTTTTAAAAAAAGTGAATA
Found at i:34123955 original size:16 final size:15
Alignment explanation
Indices: 34123920--34123955 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
34123910 TTTTATCCAC
34123920 TTTTTAAAAAAAATT
1 TTTTTAAAAAAAATT
*
34123935 ATTTTAAAAAAAGATT
1 TTTTTAAAAAAA-ATT
34123951 TTTTT
1 TTTTT
34123956 TCTTTTCGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTTTTAAAAAAAATT
Found at i:34143332 original size:16 final size:16
Alignment explanation
Indices: 34143308--34143347 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
34143298 AGATTGTAAC
*
34143308 ACCCCAAAATCTCGAA
1 ACCCAAAAATCTCGAA
34143324 ACCCAAAAATCTCGAA
1 ACCCAAAAATCTCGAA
*
34143340 ATCCAAAA
1 ACCCAAAA
34143348 CTTTTTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.33, G:0.05, T:0.12
Consensus pattern (16 bp):
ACCCAAAAATCTCGAA
Found at i:34144748 original size:24 final size:25
Alignment explanation
Indices: 34144721--34144772 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
34144711 GCCTAGCCTC
*
34144721 TTTTAAT-AACTGGGGCGAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
**
34144745 TTTTGGTAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
34144770 TTT
1 TTT
34144773 CGCACTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:34144875 original size:21 final size:21
Alignment explanation
Indices: 34144822--34144862 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
34144812 AATGAGTATA
*
34144822 TCATAGCATATCATGTGCATC
1 TCATAACATATCATGTGCATC
34144843 TCATAACATATCATGTGCAT
1 TCATAACATATCATGTGCAT
34144863 ACCATGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (21 bp):
TCATAACATATCATGTGCATC
Found at i:34146742 original size:19 final size:20
Alignment explanation
Indices: 34146718--34146755 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
34146708 CACAACCCAA
34146718 TACCAAATT-TTAAAAATTC
1 TACCAAATTCTTAAAAATTC
*
34146737 TACCAAATTCTTGAAAATT
1 TACCAAATTCTTAAAAATT
34146756 ACGAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.37
Consensus pattern (20 bp):
TACCAAATTCTTAAAAATTC
Found at i:34152909 original size:21 final size:22
Alignment explanation
Indices: 34152885--34152942 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
34152875 AATGAGTATA
34152885 TCATAGCATATCATGTGCAT-C
1 TCATAGCATATCATGTGCATAC
*
34152906 TCATAACATATCATGTGCATAC
1 TCATAGCATATCATGTGCATAC
34152928 -CAT-GTCATATCATGT
1 TCATAG-CATATCATGT
34152943 ATTGCAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATAGCATATCATGTGCATAC
Found at i:34153024 original size:26 final size:27
Alignment explanation
Indices: 34152979--34153029 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
34152969 ATAATTAAAC
*
34152979 CCTAGGGGGAATAATGGTCATTTTTTT
1 CCTAGGGGGAATAATAGTCATTTTTTT
*
34153006 CCTAGGGGTAA-AATAGTCATTTTT
1 CCTAGGGGGAATAATAGTCATTTTT
34153030 CATATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (27 bp):
CCTAGGGGGAATAATAGTCATTTTTTT
Found at i:34154824 original size:19 final size:20
Alignment explanation
Indices: 34154800--34154837 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
34154790 CACAACCTAA
34154800 TACCAAATT-TTAAAAATTC
1 TACCAAATTCTTAAAAATTC
*
34154819 TACCAAATTCTTGAAAATT
1 TACCAAATTCTTAAAAATT
34154838 TTGAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.37
Consensus pattern (20 bp):
TACCAAATTCTTAAAAATTC
Found at i:34155861 original size:29 final size:29
Alignment explanation
Indices: 34155819--34155920 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 29
34155809 TGAATATGAC
*
34155819 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
34155848 TGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* * **
34155877 TGGGCCTAATAGGCCATATGAATAAGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
34155905 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
34155921 AATACAGGTA
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 15 0.24
29 47 0.76
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:34155926 original size:57 final size:58
Alignment explanation
Indices: 34155819--34155929 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
34155809 TGAATATGAC
* ** *
34155819 TGGGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAACAGGCCATATAAATAAGATTTGGGCCTAATGGGCCAAATACAGGTGATT
* * *
34155877 TGGGCCTAATAGGCCATATGAATAAGA-TTGGGCTTAATGGGCCAAATACAGGT
1 TGGGCCTAACAGGCCATATAAATAAGATTTGGGCCTAATGGGCCAAATACAGGT
34155930 ATGTGAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 24 0.52
58 22 0.48
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (58 bp):
TGGGCCTAACAGGCCATATAAATAAGATTTGGGCCTAATGGGCCAAATACAGGTGATT
Found at i:34164201 original size:24 final size:24
Alignment explanation
Indices: 34164157--34164204 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
34164147 TAATTCAATC
*
34164157 TAACCATATTAAGCACACATATAT
1 TAACCATATTAAACACACATATAT
*
34164181 TAACCATATTATAAC-CTCATATAT
1 TAACCATATTA-AACACACATATAT
34164205 ATATATTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (24 bp):
TAACCATATTAAACACACATATAT
Found at i:34181987 original size:30 final size:29
Alignment explanation
Indices: 34181944--34182029 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
34181934 ACCGGGTTTG
* *
34181944 AGCTAAGCTGAGCTAAGCTTTAGC-CCTTA
1 AGCTAAGTTGAGCTAAGATTTAGCTCC-TA
*
34181973 AGCTAAAGTTGAGCTGAGATTATA-CTCCTA
1 AGCT-AAGTTGAGCTAAGATT-TAGCTCCTA
*
34182003 AGCTGAAGTTGAGCTAAGGTTTAGCTC
1 AGCT-AAGTTGAGCTAAGATTTAGCTC
34182030 GAGCTGAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 6 0.13
30 37 0.79
31 4 0.09
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (29 bp):
AGCTAAGTTGAGCTAAGATTTAGCTCCTA
Found at i:34186187 original size:21 final size:22
Alignment explanation
Indices: 34186139--34186188 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
34186129 TATTAAAGAG
**
34186139 TGTTGTGATTGCATCTGACTCT
1 TGTTGTGGGTGCATCTGACTCT
*
34186161 TG-TGTGGGTGCATCTGGCT-T
1 TGTTGTGGGTGCATCTGACTCT
34186181 TGTTGTGG
1 TGTTGTGG
34186189 TTGTATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 19 0.79
22 2 0.08
ACGTcount: A:0.08, C:0.14, G:0.34, T:0.44
Consensus pattern (22 bp):
TGTTGTGGGTGCATCTGACTCT
Found at i:34189668 original size:47 final size:47
Alignment explanation
Indices: 34189617--34189788 Score: 222
Period size: 47 Copynumber: 3.7 Consensus size: 47
34189607 TTAGGATTCT
* * *
34189617 ATGTGATGGATGTGAACA-TGCATATATGAGAAAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGAAAAGGCCTAATGGCCG
*
34189664 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGAAAAGGCCTAATGGCCG
* * *
34189711 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC-AAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGAAAAGGCCTAA-TGGCCG
* * *
34189758 ACGTGATGGATGTGAAAGTGTATAAATGTGA
1 ATGTGATGAATGTGAAAGTGTATATATGTGA
34189789 TAAGTCCCGA
Statistics
Matches: 113, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
46 3 0.03
47 110 0.97
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGAAAAGGCCTAATGGCCG
Found at i:34189961 original size:37 final size:37
Alignment explanation
Indices: 34189911--34190063 Score: 252
Period size: 37 Copynumber: 4.1 Consensus size: 37
34189901 CCGAGCTCTA
*
34189911 AAGACCCGATGACTACGTGTGGGGATTTTGTCCAGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
*
34189948 AAGACCCAATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
34189985 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
* * * *
34190022 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
34190059 AAGAC
1 AAGAC
34190064 TTCGTAATAA
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 109 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
Found at i:34192972 original size:47 final size:48
Alignment explanation
Indices: 34192860--34193125 Score: 227
Period size: 47 Copynumber: 5.7 Consensus size: 48
34192850 GTTATTGTGG
* * * *
34192860 GCTAGTGAAAGA-CATGTCTGGGACAT-GCATCAGCCA-C-ATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCATCGA-GATGATA
* * * *
34192906 GCCAGTGTAAGACCGTGTCTGGGATATGGCATCGGCATTGAGATGA-A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGATA
* * *
34192953 TGCTAGTGTAAGA-CATGTCTGGGACGT-GCATCGGCCTCGAGA-GGTAA
1 -GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGAT-A
* *
34193000 GCCAGTGTAAGA-CATGTCTAGGACAT-GCATCGGC-TACGAGATGATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-CGAGATGATA
34193046 G-TCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-GAGAT-ATGA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGAT-A
* * *
34193093 GCTAGTGTAAGACCGTGTCTGGGATATGTCATC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC
34193126 AGCACTTTAC
Statistics
Matches: 182, Mismatches: 23, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
45 2 0.01
46 72 0.40
47 77 0.42
48 29 0.16
49 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGATA
Found at i:34195905 original size:29 final size:29
Alignment explanation
Indices: 34195842--34195909 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
34195832 TAATCAACCG
34195842 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
34195871 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
34195900 CGCACACTTA
1 CGCACACTTA
34195910 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Done.