Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 64 of 82
Found at i:23001043 original size:2 final size:2
Alignment explanation
Indices: 23001036--23001060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23001026 AATCGTAATT
23001036 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
23001061 TTTTAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23005674 original size:12 final size:11
Alignment explanation
Indices: 23005635--23005673 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23005625 GTATATCTAG
*
23005635 AATTAGATGTA
1 AATTAGATTTA
*
23005646 AATTAGATTAA
1 AATTAGATTTA
23005657 AATTAAGATTTA
1 AATT-AGATTTA
23005669 AATTA
1 AATTA
23005674 AATATTATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (11 bp):
AATTAGATTTA
Found at i:23009284 original size:22 final size:22
Alignment explanation
Indices: 23009245--23009286 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
23009235 CACTGTGTCA
*
23009245 ACATAATCAATATCACATCATC
1 ACATAATCAATAGCACATCATC
23009267 ACATAATCAAT-GCGACATCA
1 ACATAATCAATAGC-ACATCA
23009287 ATAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (22 bp):
ACATAATCAATAGCACATCATC
Found at i:23010682 original size:84 final size:87
Alignment explanation
Indices: 23010545--23010717 Score: 255
Period size: 84 Copynumber: 2.0 Consensus size: 87
23010535 AATTGAACTT
* * *
23010545 TTCAATCGAAAACCATTAGATATATAACAATTAAAATTGCAAAGTAAATCAATTGA-ATTGATAA
1 TTCAATCGAAAACCATTAGATATAT-A-AATTAAAATTGAAAACTAAAACAATT-ACATTGATAA
23010609 ATATCAATAAGTAGATATATAATAA
63 ATATCAATAAGTAGATATATAATAA
*
23010634 TTCAATTG-AAACCATTAGATA-AT-AATTAAAATTGAAAACTAAAACAATTACATTGATAAATA
1 TTCAATCGAAAACCATTAGATATATAAATTAAAATTGAAAACTAAAACAATTACATTGATAAATA
23010696 TCAATAAGTAGATATATAATAA
66 TCAATAAGTAGATATATAATAA
23010718 GTATAATATT
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
83 1 0.01
84 56 0.71
87 2 0.03
88 13 0.16
89 7 0.09
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.31
Consensus pattern (87 bp):
TTCAATCGAAAACCATTAGATATATAAATTAAAATTGAAAACTAAAACAATTACATTGATAAATA
TCAATAAGTAGATATATAATAA
Found at i:23010797 original size:29 final size:29
Alignment explanation
Indices: 23010755--23010810 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
23010745 TGTTCAAAAA
23010755 ATTCAAATAAATTTTTAT-TCTTTTATTAT
1 ATTCAAATAAATTTTTATAT-TTTTATTAT
23010784 ATTC-AATAAAATTTTTATATTTTTATT
1 ATTCAAAT-AAATTTTTATATTTTTATT
23010811 TTAGATCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 3 0.12
29 21 0.84
30 1 0.04
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (29 bp):
ATTCAAATAAATTTTTATATTTTTATTAT
Found at i:23011917 original size:50 final size:50
Alignment explanation
Indices: 23011821--23011918 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 50
23011811 ACCATGTTTT
* * * * **
23011821 TAAAAATAATCCAGTCAACTAAAACTACCATGTCACTTGCTGCGTTAGTC
1 TAAAAATAAGCCAGTCAACTAAAAATACCATGTAACGTGCCCCGTTAGTC
*
23011871 TAAAAAT-AGCCACGTCAACTAAAAATATCATGTAACGTGCCCCGTTAG
1 TAAAAATAAGCCA-GTCAACTAAAAATACCATGTAACGTGCCCCGTTAG
23011919 CAGAAAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 4 0.10
50 36 0.90
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (50 bp):
TAAAAATAAGCCAGTCAACTAAAAATACCATGTAACGTGCCCCGTTAGTC
Found at i:23017740 original size:18 final size:18
Alignment explanation
Indices: 23017698--23017742 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
23017688 TCTTGACATA
* *
23017698 ATATTTAATAAATTTCAT
1 ATATTTATTAAAATTCAT
* *
23017716 ATTTTTATTAAAATTCTT
1 ATATTTATTAAAATTCAT
23017734 ATATTTATT
1 ATATTTATT
23017743 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTATTAAAATTCAT
Found at i:23017751 original size:24 final size:25
Alignment explanation
Indices: 23017715--23017781 Score: 64
Period size: 28 Copynumber: 2.6 Consensus size: 25
23017705 ATAAATTTCA
* *
23017715 TATTTTTATTAAAATTCTTATA-TT
1 TATTTTAAATAAAATTCTTATATTT
*
23017739 TATTTTAAATAAATAAGTTTTTATATTT
1 TATTTTAAAT-AA-AA-TTCTTATATTT
*
23017767 TATTTTAAATTAAAT
1 TATTTTAAATAAAAT
23017782 AAGTCTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
24 8 0.23
25 3 0.09
26 4 0.11
27 8 0.23
28 12 0.34
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (25 bp):
TATTTTAAATAAAATTCTTATATTT
Found at i:23017772 original size:28 final size:28
Alignment explanation
Indices: 23017732--23017791 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
23017722 ATTAAAATTC
*
23017732 TTATATTTATTTTAAA-TAAATAAGTTT
1 TTATATTTATTTTAAATTAAATAAGTCT
23017759 TTATATTTTATTTTAAATTAAATAAGTCT
1 TTATA-TTTATTTTAAATTAAATAAGTCT
23017788 TTAT
1 TTAT
23017792 GATTATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 5 0.17
28 11 0.37
29 14 0.47
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (28 bp):
TTATATTTATTTTAAATTAAATAAGTCT
Found at i:23018086 original size:26 final size:28
Alignment explanation
Indices: 23018053--23018116 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
23018043 ATAAAAATTT
*
23018053 ATTTAATTTAAA-ATAA-AAATACAT-AA
1 ATTTAATTTAAATATAATAAA-AAATAAA
23018079 ATTTAA-TTAAATATAATAAAAAATAAA
1 ATTTAATTTAAATATAATAAAAAATAAA
*
23018106 ATTTTATTTAA
1 ATTTAATTTAA
23018117 TTTTTTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 5 0.16
26 13 0.41
27 10 0.31
28 4 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTTAATTTAAATATAATAAAAAATAAA
Found at i:23022052 original size:2 final size:2
Alignment explanation
Indices: 23022045--23022069 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23022035 GAAAATTTAG
23022045 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
23022070 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23023138 original size:13 final size:13
Alignment explanation
Indices: 23023120--23023144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23023110 GGAAGATAAA
23023120 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
23023133 TTTTTCTTTTTT
1 TTTTTCTTTTTT
23023145 GGGTTATTTT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:23034185 original size:2 final size:2
Alignment explanation
Indices: 23034178--23034202 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23034168 TAACTAAATT
23034178 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
23034203 CCACCGAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23034242 original size:2 final size:2
Alignment explanation
Indices: 23034235--23034261 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23034225 TACTTAGNTT
23034235 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
23034262 CCACCGAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23043825 original size:21 final size:21
Alignment explanation
Indices: 23043783--23043828 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
23043773 CTATTTTATC
* * *
23043783 TATTAAGTTTTGGCGAGTACA
1 TATTAAGTTTTAGCAAGGACA
*
23043804 TATTAAGTTTTATCAAGGACA
1 TATTAAGTTTTAGCAAGGACA
23043825 TATT
1 TATT
23043829 GATGTTAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (21 bp):
TATTAAGTTTTAGCAAGGACA
Found at i:23048866 original size:15 final size:15
Alignment explanation
Indices: 23048844--23048882 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
23048834 TTAAATTGGC
23048844 TTTG-ATTAAAAAAA
1 TTTGAATTAAAAAAA
23048858 TTTGAATTAAAAAAA
1 TTTGAATTAAAAAAA
23048873 TTT-AATTAAA
1 TTTGAATTAAA
23048883 TGCATTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
TTTGAATTAAAAAAA
Found at i:23057869 original size:6 final size:6
Alignment explanation
Indices: 23057861--23057890 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
23057851 ATTTGTTCAT
*
23057861 TGGCAT TGGCAG TGGCAG TGGCAG TGGCAG
1 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG
23057891 ATGAAAGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.20
Consensus pattern (6 bp):
TGGCAG
Found at i:23070527 original size:2 final size:2
Alignment explanation
Indices: 23070516--23070565 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
23070506 ATAAGCATTC
23070516 AT AT -T AT AT AT AT AT A- AT -T AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23070554 A- AT -T AT AT AT AT
1 AT AT AT AT AT AT AT
23070566 TTCTTTCTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
1 6 0.14
2 36 0.86
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23070542 original size:23 final size:24
Alignment explanation
Indices: 23070516--23070566 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
23070506 ATAAGCATTC
23070516 ATATTATATAT-ATATAATTATAT
1 ATATTATATATAATATAATTATAT
23070539 ATA-TATATATAATATAATTATAT
1 ATATTATATATAATATAATTATAT
23070562 ATATT
1 ATATT
23070567 TCTTTCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.27
23 18 0.69
24 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATTATATATAATATAATTATAT
Found at i:23081888 original size:2 final size:2
Alignment explanation
Indices: 23081881--23081911 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23081871 TCATGTTGTT
23081881 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23081912 NTATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23083416 original size:19 final size:20
Alignment explanation
Indices: 23083387--23083473 Score: 87
Period size: 19 Copynumber: 4.5 Consensus size: 20
23083377 TTCATTCATC
*
23083387 ATTTT-TTTATTTTTTATTT
1 ATTTTATTTATTTTTAATTT
23083406 -TTTTATTTATTTTTAATTT
1 ATTTTATTTATTTTTAATTT
23083425 -TTTTGACTTT-TTTTTAATTAT
1 ATTTT-A-TTTATTTTTAATT-T
23083446 ATTTTA-TTATTATTT-ATTT
1 ATTTTATTTATT-TTTAATTT
23083465 ATTTTATTT
1 ATTTTATTT
23083474 TTTGAAATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
18 4 0.07
19 26 0.44
20 17 0.29
21 8 0.14
22 4 0.07
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.77
Consensus pattern (20 bp):
ATTTTATTTATTTTTAATTT
Found at i:23083424 original size:11 final size:10
Alignment explanation
Indices: 23083388--23083473 Score: 60
Period size: 10 Copynumber: 8.8 Consensus size: 10
23083378 TCATTCATCA
23083388 TTTT-TTTAT
1 TTTTATTTAT
23083397 TTTT-TATT-T
1 TTTTAT-TTAT
23083406 TTTTATTTAT
1 TTTTATTTAT
23083416 TTTTAATTT-T
1 TTTT-ATTTAT
*
23083426 TTTGACTTT-T
1 TTTTA-TTTAT
*
23083436 TTTTAATTAT
1 TTTTATTTAT
23083446 ATTTTA-TTAT
1 -TTTTATTTAT
23083456 TATTTATTTA-
1 T-TTTATTTAT
23083466 TTTTATTT
1 TTTTATTT
23083474 TTTGAAATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
9 23 0.35
10 30 0.46
11 12 0.18
ACGTcount: A:0.20, C:0.01, G:0.01, T:0.78
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:23083476 original size:26 final size:25
Alignment explanation
Indices: 23083387--23083476 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 25
23083377 TTCATTCATC
23083387 ATTT-TTTTATTTTTTATT-TTTTT
1 ATTTATTTTATTTTTTATTATTTTT
*
23083410 ATTTATTTTTAATTTTTT-TGACTTTTT
1 ATTTA-TTTT-ATTTTTTATTA-TTTTT
* *
23083437 -TTTA-ATTATATTTTATTATTATTT
1 ATTTATTTTATTTTTTATTATT-TTT
23083461 ATTTATTTTATTTTTT
1 ATTTATTTTATTTTTT
23083477 GAAATAAGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
23 12 0.23
24 7 0.13
25 9 0.17
26 19 0.37
27 5 0.10
ACGTcount: A:0.20, C:0.01, G:0.01, T:0.78
Consensus pattern (25 bp):
ATTTATTTTATTTTTTATTATTTTT
Found at i:23093259 original size:130 final size:130
Alignment explanation
Indices: 23093026--23093286 Score: 506
Period size: 130 Copynumber: 2.0 Consensus size: 130
23093016 GCTTTGCAAA
23093026 CAGCGTAACGTTGGCACAACCAGGGGCGGAGCCTCCTTATGCGATGGGAGGCCATGACCTTCTAA
1 CAGCGTAACGTTGGCACAACCAGGGGCGGAGCCTCCTTATGCGATGGGAGGCCATGACCTTCTAA
23093091 AATTTTTAAAATTTTTTTTCATAATATATAAAATTCTTAAA-TTTTTATATATTTTATTAATATC
66 AATTTTTAAAATTTTTTTTCATAATATATAAAATTCTTAAATTTTTTATATATTTTATTAATATC
23093155 NCAGCGTAACGTTGGCACAACCAGGGGCGGAGCCTCCTTATGCGATGGGAGGCCATGACCTTCTA
1 -CAGCGTAACGTTGGCACAACCAGGGGCGGAGCCTCCTTATGCGATGGGAGGCCATGACCTTCTA
23093220 AAATTTTTAAAATTTTTTTTCATAATATATAAAATTCTTAAATTTTTTATATATTTTATTAATAT
65 AAATTTTTAAAATTTTTTTTCATAATATATAAAATTCTTAAATTTTTTATATATTTTATTAATAT
23093285 C
130 C
23093286 C
1 C
23093287 TTTTTAAAAT
Statistics
Matches: 130, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
130 107 0.82
131 23 0.18
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (130 bp):
CAGCGTAACGTTGGCACAACCAGGGGCGGAGCCTCCTTATGCGATGGGAGGCCATGACCTTCTAA
AATTTTTAAAATTTTTTTTCATAATATATAAAATTCTTAAATTTTTTATATATTTTATTAATATC
Found at i:23093408 original size:18 final size:19
Alignment explanation
Indices: 23093361--23093409 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
23093351 TTGCTTAATT
23093361 TTAACTTTTTTTAATTTATA
1 TTAA-TTTTTTTAATTTATA
23093381 TT-ATTATTTTTAA-TTATA
1 TTAATT-TTTTTAATTTATA
23093399 TTAATTTTTTT
1 TTAATTTTTTT
23093410 TTTATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 14 0.52
19 11 0.41
20 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTAATTTTTTTAATTTATA
Found at i:23093409 original size:19 final size:20
Alignment explanation
Indices: 23093361--23093410 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
23093351 TTGCTTAATT
*
23093361 TTAACTTTTTTTAATTTATA
1 TTAATTTTTTTTAATTTATA
*
23093381 TT-ATTATTTTTAA-TTATA
1 TTAATTTTTTTTAATTTATA
23093399 TTAATTTTTTTT
1 TTAATTTTTTTT
23093411 TTATTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 7 0.27
19 17 0.65
20 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTAATTTTTTTTAATTTATA
Found at i:23101073 original size:18 final size:19
Alignment explanation
Indices: 23101025--23101075 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
23101015 TACAGAGAGT
*
23101025 AATTGCATAATTTAACATTT
1 AATT-CATAATTTAACATTG
* *
23101045 CATT-ATCATTTAA-ATTG
1 AATTCATAATTTAACATTG
23101062 AATTCATAATTTAA
1 AATTCATAATTTAA
23101076 TAATTGCCAC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
20 3 0.12
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (19 bp):
AATTCATAATTTAACATTG
Found at i:23108387 original size:21 final size:21
Alignment explanation
Indices: 23108361--23108411 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
23108351 GGAGTTTATT
23108361 GCATTTCCTTTAGGGTAAATA
1 GCATTTCCTTTAGGGTAAATA
23108382 GCATTTCCTTTAGGGTAAATA
1 GCATTTCCTTTAGGGTAAATA
*
23108403 GCATCTCCT
1 GCATTTCCT
23108412 CTTATAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (21 bp):
GCATTTCCTTTAGGGTAAATA
Found at i:23111588 original size:21 final size:22
Alignment explanation
Indices: 23111553--23111593 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
23111543 CATCCGAATC
23111553 CTCTCCATAAACCAATTTTGCA
1 CTCTCCATAAACCAATTTTGCA
*
23111575 CTCTCC-TCAACCAATTTTG
1 CTCTCCATAAACCAATTTTG
23111594 AGCTAATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.34, G:0.05, T:0.34
Consensus pattern (22 bp):
CTCTCCATAAACCAATTTTGCA
Found at i:23114769 original size:20 final size:20
Alignment explanation
Indices: 23114740--23114807 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 20
23114730 TTTGTTTTTA
*
23114740 TTTTTAATTTTTG-ATT-AT
1 TTTTTTATTTTTGAATTCAT
23114758 TTGTTTT-TATTTTGAATTCAT
1 TT-TTTTAT-TTTTGAATTCAT
* *
23114779 TTTTTTATTTTT--ATTTAC
1 TTTTTTATTTTTGAATTCAT
23114797 TTTTTTATTTT
1 TTTTTTATTTT
23114808 AAATTTACGA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
18 18 0.43
19 8 0.19
20 11 0.26
21 5 0.12
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTTTATTTTTGAATTCAT
Found at i:23114771 original size:19 final size:19
Alignment explanation
Indices: 23114761--23114812 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
23114751 TGATTATTTG
23114761 TTTTTATTTTGAATTCATT
1 TTTTTATTTTGAATTCATT
* * *
23114780 TTTTTATTTT-TATTTACT
1 TTTTTATTTTGAATTCATT
*
23114798 TTTTTATTTTAAATT
1 TTTTTATTTTGAATT
23114813 TACGAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTATTTTGAATTCATT
Found at i:23114813 original size:19 final size:18
Alignment explanation
Indices: 23114761--23114815 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
23114751 TGATTATTTG
* *
23114761 TTTTTATTTTGAATTCATT
1 TTTTTATTTT-AATTTACT
*
23114780 TTTTTATTTTTATTTACT
1 TTTTTATTTTAATTTACT
23114798 TTTTTATTTTAAATTTAC
1 TTTTTATTTT-AATTTAC
23114816 GAAACAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTTATTTTAATTTACT
Found at i:23124416 original size:94 final size:92
Alignment explanation
Indices: 23124255--23124439 Score: 352
Period size: 94 Copynumber: 2.0 Consensus size: 92
23124245 CTAGGTAAAG
23124255 GATTTGGATTAAGATTCCACCAGTATGATAAGAGAGTCTTAATGTCGAGTCATGATATTTCTAAT
1 GATTTGGATTAAGATTCCACCAGTATGATAAGAGAGTCTTAATGTCGAGTCATGATATTTCTAAT
23124320 CTTAAATAAATAAATAATATATTAATAA
66 CTTAAATAAATAAA-AATATATTAATAA
23124348 NGATTTGGATTAAGATTCCACCAGTATGATAAGAGAGTCTTAATGTCGAGTCATGATATTTCTAA
1 -GATTTGGATTAAGATTCCACCAGTATGATAAGAGAGTCTTAATGTCGAGTCATGATATTTCTAA
23124413 TCTTAAATAAATAAAAATATATTAATA
65 TCTTAAATAAATAAAAATATATTAATA
23124440 TAATTATTAA
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 12 0.13
94 79 0.87
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (92 bp):
GATTTGGATTAAGATTCCACCAGTATGATAAGAGAGTCTTAATGTCGAGTCATGATATTTCTAAT
CTTAAATAAATAAAAATATATTAATAA
Found at i:23124810 original size:12 final size:11
Alignment explanation
Indices: 23124787--23124823 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
23124777 AAATACTTAA
23124787 ATATAAAAAAT
1 ATATAAAAAAT
23124798 ATATAATAAAAT
1 ATATAA-AAAAT
23124810 ATAATAAAAAAT
1 AT-ATAAAAAAT
23124822 AT
1 AT
23124824 GGTTAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 14 0.58
13 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATATAAAAAAT
Found at i:23124813 original size:10 final size:10
Alignment explanation
Indices: 23124785--23124818 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
23124775 ATAAATACTT
*
23124785 AAATATAAAA
1 AAATATAATA
23124795 AATATATAATA
1 AA-ATATAATA
23124806 AAATATAATA
1 AAATATAATA
23124816 AAA
1 AAA
23124819 AATATGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAATATAATA
Found at i:23130184 original size:32 final size:32
Alignment explanation
Indices: 23130142--23130235 Score: 170
Period size: 32 Copynumber: 2.9 Consensus size: 32
23130132 GCAAAGAGGC
23130142 TTTCTCAAATGAATGCCATTTTAATGTCTCAT
1 TTTCTCAAATGAATGCCATTTTAATGTCTCAT
*
23130174 TTTCTTAAATGAATGCCATTTTAATGTCTCAT
1 TTTCTCAAATGAATGCCATTTTAATGTCTCAT
*
23130206 TTTCTCAAATGAATGCCGTTTTAATGTCTC
1 TTTCTCAAATGAATGCCATTTTAATGTCTC
23130236 CTTTCTTATA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.45
Consensus pattern (32 bp):
TTTCTCAAATGAATGCCATTTTAATGTCTCAT
Found at i:23132537 original size:34 final size:34
Alignment explanation
Indices: 23132490--23132554 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
23132480 AGTAAGAAGC
*
23132490 TTTGGCATGTAACATATGGTGCTGAAGCTTTGAT
1 TTTGGCATCTAACATATGGTGCTGAAGCTTTGAT
* * *
23132524 TTTGGCTTCTAACATTTGGTGTTGAAGCTTT
1 TTTGGCATCTAACATATGGTGCTGAAGCTTT
23132555 AGCCTTGACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.43
Consensus pattern (34 bp):
TTTGGCATCTAACATATGGTGCTGAAGCTTTGAT
Found at i:23133208 original size:26 final size:25
Alignment explanation
Indices: 23133124--23133210 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 25
23133114 TATGTTTACA
*
23133124 TGTAACAATATTTTTTTTCAAAATAGCG
1 TGTAACAATA--TTTTTT-AAAATAGTG
* * *
23133152 TGTATTAAAAT-TTTTTTAAACATAATA
1 TGTA--ACAATATTTTTTAAA-ATAGTG
23133179 TGTAACAATATTTTTTAAATATAGTG
1 TGTAACAATATTTTTTAAA-ATAGTG
23133205 TGTAAC
1 TGTAAC
23133211 TTGCTCTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
25 4 0.09
26 22 0.47
27 13 0.28
28 4 0.09
30 4 0.09
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (25 bp):
TGTAACAATATTTTTTAAAATAGTG
Found at i:23136275 original size:257 final size:256
Alignment explanation
Indices: 23135819--23136317 Score: 827
Period size: 257 Copynumber: 1.9 Consensus size: 256
23135809 AACTTGTCAA
* *
23135819 CAGTACTGCAACTACTGACTACAGGAAGATTTCTCGTTAAGCCACTTGCTAAATGCTTCATTACG
1 CAGTACTGCAACTACTGACTACAGGAAGATTTCTCGTTAAGCCACGTGCTAAATACTTCATTACG
* *
23135884 TGGTCGGAGGCTTCAGGCCTGGCAGCTGGCGGCTTGCCGAGTTCCGGTTTTCTGACTTTTTTCCT
66 TGGTCGGAGGCTTCAGGCCTGGCAGCTGGCGGCTTGCCGAGTTCCGCTTTTCTGACATTTTTCCT
* *
23135949 TTGTTTTCTGAACATTATGACTAACTTTTTAATTATTTGCTTGTTCGTTAATCTTAGGAGCTTTT
131 TTGTTTTCTGAACATTATGACTAACCTTTTAATTATTTGCTTGTTCGTTAATCTGAGGAGCTTTT
* * * *
23136014 GTTTACTAGCTCAAATGGCTTGGCCATTCAGGCAAGCAACTAGGAACATTCACCTCGTTTTG
196 GTTTAC-AGCCCAAATGGCTTAGCCATTCAGGCAACCAACGAGGAACATTCACCTCGTTTTG
* * *
23136076 CAGTACTGCAGCTACTGACTACAGGAAGATTTCTCTTTAAGGCACGTGCTAAATACTTCATTACG
1 CAGTACTGCAACTACTGACTACAGGAAGATTTCTCGTTAAGCCACGTGCTAAATACTTCATTACG
* * * * *
23136141 TGGTTGGAGGCTTCAGGCTTGGCCGTTGGCGGCTTGCCGAGTTCCGCTTTTCTGACATTTTTCTT
66 TGGTCGGAGGCTTCAGGCCTGGCAGCTGGCGGCTTGCCGAGTTCCGCTTTTCTGACATTTTTCCT
23136206 TTGTTTTCTGAACATTATGACTAACCTTTTAATTATTTGCTTGTTCGTTAATCTGAGGAGCTTTT
131 TTGTTTTCTGAACATTATGACTAACCTTTTAATTATTTGCTTGTTCGTTAATCTGAGGAGCTTTT
23136271 GTTTACAGCCCAAATGGCTTAGCCATTCAGGCAACCAACGAGGAACA
196 GTTTACAGCCCAAATGGCTTAGCCATTCAGGCAACCAACGAGGAACA
23136318 ACCATCATTC
Statistics
Matches: 224, Mismatches: 18, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
256 37 0.17
257 187 0.83
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (256 bp):
CAGTACTGCAACTACTGACTACAGGAAGATTTCTCGTTAAGCCACGTGCTAAATACTTCATTACG
TGGTCGGAGGCTTCAGGCCTGGCAGCTGGCGGCTTGCCGAGTTCCGCTTTTCTGACATTTTTCCT
TTGTTTTCTGAACATTATGACTAACCTTTTAATTATTTGCTTGTTCGTTAATCTGAGGAGCTTTT
GTTTACAGCCCAAATGGCTTAGCCATTCAGGCAACCAACGAGGAACATTCACCTCGTTTTG
Found at i:23137514 original size:106 final size:106
Alignment explanation
Indices: 23137323--23137535 Score: 246
Period size: 106 Copynumber: 2.0 Consensus size: 106
23137313 CTCTTTAATT
* * * * * * * *
23137323 TCAAGGGGCTCAGTTGTGTTATTCCAACATCTTCGCCATCCTTGTCTTATCTTTAAGGTGATGTT
1 TCAAGGAGCTCAGTTGTGTTACTCCAACATCTTCACCACCCTTGTCTCATCTCTAAGATGACGTT
* * *
23137388 TGATATTTTACAATATAATGTGATTACAAGTAATGTGTTTG
66 TGATATTTTACAATACAATGTGATAACAAGTAATGTGATTG
* * * *
23137429 TCAAGGAGTTCAGTTGTGTTACTCCAGCATCTTCACTACCCTTGTCTCATCTCTAAGATGGCGTT
1 TCAAGGAGCTCAGTTGTGTTACTCCAACATCTTCACCACCCTTGTCTCATCTCTAAGATGACGTT
* * * * *
23137494 TGGTATTTTATAATGCAATGTGATAATAGGTAATGTGATTG
66 TGATATTTTACAATACAATGTGATAACAAGTAATGTGATTG
23137535 T
1 T
23137536 AGAAAAAATA
Statistics
Matches: 87, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
106 87 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (106 bp):
TCAAGGAGCTCAGTTGTGTTACTCCAACATCTTCACCACCCTTGTCTCATCTCTAAGATGACGTT
TGATATTTTACAATACAATGTGATAACAAGTAATGTGATTG
Found at i:23137866 original size:31 final size:32
Alignment explanation
Indices: 23137811--23137874 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
23137801 TTTAATACAA
* * *
23137811 TTTCTTATATTATATATTATATTTTAATTTCTT
1 TTTCCTATATTATATA-TAAATTTTAATCTCTT
23137844 TTTCCTATATTATATA-AAATTTTAATCTCTT
1 TTTCCTATATTATATATAAATTTTAATCTCTT
23137875 ATATTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 13 0.46
33 15 0.54
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTCCTATATTATATATAAATTTTAATCTCTT
Found at i:23139576 original size:30 final size:30
Alignment explanation
Indices: 23139497--23139587 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 30
23139487 AAGTCATTAA
*
23139497 ATTTTTATTTTGAATTC-AATAAGTTTTTAT
1 ATTTTTATTTTGAA-TCAAATAAGTTCTTAT
*
23139527 ATTTTTATTTTGAACCAAATAAGTTCTTAT
1 ATTTTTATTTTGAATCAAATAAGTTCTTAT
* * * *
23139557 ATTTTTATTGTGAGTCAAATAAATCCTTAT
1 ATTTTTATTTTGAATCAAATAAGTTCTTAT
23139587 A
1 A
23139588 ACTAATTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.52
Consensus pattern (30 bp):
ATTTTTATTTTGAATCAAATAAGTTCTTAT
Found at i:23145646 original size:24 final size:24
Alignment explanation
Indices: 23145619--23145665 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
23145609 TTTTTTCTCC
*
23145619 AAGTTTACTGTTTATTTTCTTAAG
1 AAGTTTACTCTTTATTTTCTTAAG
*
23145643 AAGTTTGCTCTTTATTTTCTTAA
1 AAGTTTACTCTTTATTTTCTTAA
23145666 AAAGGTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (24 bp):
AAGTTTACTCTTTATTTTCTTAAG
Found at i:23150116 original size:23 final size:23
Alignment explanation
Indices: 23150086--23150131 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
23150076 TAGAATAACA
**
23150086 ATTTCTAATTCTATTAGGATAAG
1 ATTTCTAATTAAATTAGGATAAG
23150109 ATTTCTAATTAAATTAGGATAAG
1 ATTTCTAATTAAATTAGGATAAG
23150132 GTTATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (23 bp):
ATTTCTAATTAAATTAGGATAAG
Found at i:23153617 original size:23 final size:23
Alignment explanation
Indices: 23153591--23153659 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
23153581 TAGAATAACA
* *
23153591 ATTCATAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
23153614 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
23153637 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
23153660 GTTATTGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:23171767 original size:24 final size:23
Alignment explanation
Indices: 23171713--23171779 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 23
23171703 TTCCTGACAG
** *
23171713 ACACAATGGTCTATTTTTAATAA
1 ACACAATTATCTATTTTTAACAA
23171736 ACACAATTATCTATTTTTCAACAA
1 ACACAATTATCTATTTTT-AACAA
* * *
23171760 ATATAATTATTTATTTTTAA
1 ACACAATTATCTATTTTTAA
23171780 ACATAATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (23 bp):
ACACAATTATCTATTTTTAACAA
Found at i:23180658 original size:17 final size:17
Alignment explanation
Indices: 23180620--23180659 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
23180610 TAAAAAAAAA
*
23180620 AAAATATTATTTTTTGT
1 AAAATATTATTTTTTAT
*
23180637 CAAATATTATTTTTTAT
1 AAAATATTATTTTTTAT
23180654 AAAATA
1 AAAATA
23180660 CCTGTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
AAAATATTATTTTTTAT
Found at i:23183237 original size:20 final size:20
Alignment explanation
Indices: 23183200--23183238 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23183190 TTAAAACACA
*
23183200 TAAATAATAAAATTTAAATT
1 TAAATAATAAAATATAAATT
23183220 TAAATAATTAAAA-ATAAAT
1 TAAATAA-TAAAATATAAAT
23183239 ATCTGAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATAATAAAATATAAATT
Found at i:23183753 original size:350 final size:344
Alignment explanation
Indices: 23183250--23183945 Score: 889
Period size: 350 Copynumber: 2.0 Consensus size: 344
23183240 TCTGAAACAC
* *
23183250 AATTAATAACTTTATTAGTTATAATTTTTGTAATATTAACACAAAATAGAAGTAAATATATTTAT
1 AATTAATAACTTTATGAGTTATAATTTTTATAATATTAACACAAAATAGAAGTAAATATATTTAT
* * ** * *
23183315 ATTTAAAGTGTTTATATACTAAAAATATTTTAATATATATATATATAATAGTAATTATATTTCTT
66 ATTTAAAGTATTTATATACTAAAAATAATACAAGATATATATATATAATAATAATTATATTTCTT
* * * *
23183380 ATAAATGAACCCAATGTATATAAAGTACATATATTAAAAAATATTACAAGTCAATTAATAATCAT
131 ATAAATAAACCCAATATATATAAAATACATATATTAAAAAACATTACAAGTCAATTAATAATCAT
* * * * * * *
23183445 AATTTTATTAATTAATTTAATTAACTATA-TAAGTT-TATCCTTAATTATAAGAAATTTAAAAAA
196 AATTTCATGAATTAATTTAATTAACTATACGAAATTGT-T-ATTAATTACAAGAAATTAAAAAAA
* * *
23183508 TAACTAAGTTTCCA-AATTATTCTAATCTCACAACTTCCCTTTAGATTTATATGTTATAAGTTTA
259 TAACTAAGTTT-CAGAACTATTCTAACCTCACAACTTCCCTTTAGATTTATATATTATAAGTTTA
23183572 TATAAACAAATATATATATATTAT
323 TATAAACAAA-AT-TATATATTAT
* * *
23183596 AATTAATAATTTTATGAGTTATAATTTTTATAATGTTAATACAAAATAGAAAGTAAATATATTTA
1 AATTAATAACTTTATGAGTTATAATTTTTATAATATTAACACAAAATAG-AAGTAAATATATTTA
* *
23183661 TATTTAAAGTATTTATATA-TATATATAGATACACAGACTCATATATATATAATAATAATTATA-
65 TATTTAAAGTATTTATATACTAAAAATA-ATACA-AGA-T-ATATATATATAATAATAATTATAT
*** * *
23183724 TTCTTTATAAATAAATTGAATATATATAAAATATATATATTAAAAAACATTACAAGTTAATTAAT
126 TTC-TTATAAATAAACCCAATATATATAAAATACATATATTAAAAAACATTACAAGTCAATTAAT
* * *
23183789 AGTGATAATTTCATGAATTAATTTAATTAACTATACGAAATTGTTATTAATTACATGAAATTAAA
190 AATCATAATTTCATGAATTAATTTAATTAACTATACGAAATTGTTATTAATTACAAGAAATTAAA
* * * *
23183854 AAAATAACTACGTTTTAGAACTATTCTAACCTCACAACTTCTCTTTAGGTTTATATATTATAAGT
255 AAAATAACTAAGTTTCAGAACTATTCTAACCTCACAACTTCCCTTTAGATTTATATATTATAAGT
* *
23183919 TTATATAAATAAAGTTATATATTAT
320 TTATATAAACAAAATTATATATTAT
23183944 AA
1 AA
23183946 NNNNNNNNNN
Statistics
Matches: 300, Mismatches: 41, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
346 50 0.17
347 35 0.12
348 14 0.05
349 6 0.02
350 189 0.63
351 5 0.02
352 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (344 bp):
AATTAATAACTTTATGAGTTATAATTTTTATAATATTAACACAAAATAGAAGTAAATATATTTAT
ATTTAAAGTATTTATATACTAAAAATAATACAAGATATATATATATAATAATAATTATATTTCTT
ATAAATAAACCCAATATATATAAAATACATATATTAAAAAACATTACAAGTCAATTAATAATCAT
AATTTCATGAATTAATTTAATTAACTATACGAAATTGTTATTAATTACAAGAAATTAAAAAAATA
ACTAAGTTTCAGAACTATTCTAACCTCACAACTTCCCTTTAGATTTATATATTATAAGTTTATAT
AAACAAAATTATATATTAT
Found at i:23183922 original size:15 final size:15
Alignment explanation
Indices: 23183902--23183945 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
23183892 TTCTCTTTAG
23183902 GTTTATATATTATAA
1 GTTTATATATTATAA
*
23183917 GTTTATATA-AATAAA
1 GTTTATATATTAT-AA
23183932 G-TTATATATTATAA
1 GTTTATATATTATAA
23183946 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
GTTTATATATTATAA
Found at i:23184271 original size:2 final size:2
Alignment explanation
Indices: 23184266--23184306 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
23184256 GTTATAAATT
*
23184266 TA TA TA AA TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23184305 TA
1 TA
23184307 ATTAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23188662 original size:24 final size:23
Alignment explanation
Indices: 23188635--23188679 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
23188625 ATCTAGTTAG
23188635 ATTAGAATAACAATTCCTAATTCT
1 ATTAGAATAA-AATTCCTAATTCT
* *
23188659 ATTAGGATAAGATTCCTAATT
1 ATTAGAATAAAATTCCTAATT
23188680 AAATTAGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTAGAATAAAATTCCTAATTCT
Found at i:23188677 original size:23 final size:23
Alignment explanation
Indices: 23188647--23188692 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
23188637 TAGAATAACA
**
23188647 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTAAATTAGGATAAG
23188670 ATTCCTAATTAAATTAGGATAAG
1 ATTCCTAATTAAATTAGGATAAG
23188693 GTTATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (23 bp):
ATTCCTAATTAAATTAGGATAAG
Found at i:23192741 original size:13 final size:13
Alignment explanation
Indices: 23192723--23192749 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23192713 ATGGAACTAG
23192723 TTTTAATTTTTAA
1 TTTTAATTTTTAA
23192736 TTTTAATTTTTAA
1 TTTTAATTTTTAA
23192749 T
1 T
23192750 ATGCCTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:23194184 original size:13 final size:13
Alignment explanation
Indices: 23194153--23194190 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
23194143 CTAGTATTCA
*
23194153 ATTTTCTAAAAT-
1 ATTTTATAAAATC
23194165 A-TTTATAAAATC
1 ATTTTATAAAATC
23194177 ATTTTATAAAATC
1 ATTTTATAAAATC
23194190 A
1 A
23194191 CAATTTCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 9 0.39
12 2 0.09
13 12 0.52
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTTATAAAATC
Found at i:23195440 original size:19 final size:19
Alignment explanation
Indices: 23195416--23195453 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
23195406 ACTTCTAAAT
23195416 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
23195435 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
23195454 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:23225237 original size:26 final size:26
Alignment explanation
Indices: 23225207--23225270 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
23225197 TTTCATGATT
*
23225207 AAAAATATTTAAAAAC-ATAA-TATTC
1 AAAAAAATTTAAAAACTA-AATTATTC
*
23225232 AAAAAAATCTT-TAAACTAAATTATTC
1 AAAAAAAT-TTAAAAACTAAATTATTC
23225258 AAAAAAATTTAAA
1 AAAAAAATTTAAA
23225271 GAAGTCTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 15 0.47
26 17 0.53
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAAAATTTAAAAACTAAATTATTC
Found at i:23225353 original size:30 final size:30
Alignment explanation
Indices: 23225317--23225375 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
23225307 TTATAATTAT
*
23225317 ATTTTTATTTTAAATTGAATAAATTTTTAA
1 ATTTTTATTTTAAATTAAATAAATTTTTAA
* * *
23225347 ATTTTTATTTTGAGTTAAATAAGTTTTTA
1 ATTTTTATTTTAAATTAAATAAATTTTTA
23225376 TGACTAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (30 bp):
ATTTTTATTTTAAATTAAATAAATTTTTAA
Found at i:23225720 original size:20 final size:21
Alignment explanation
Indices: 23225695--23225733 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
23225685 AAAAAAATTA
23225695 TTTAAATTTT-TTTAAATAAT
1 TTTAAATTTTATTTAAATAAT
23225715 TTTAAATTTTATTTAAATA
1 TTTAAATTTTATTTAAATA
23225734 GTATATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAATTTTATTTAAATAAT
Found at i:23232053 original size:2 final size:2
Alignment explanation
Indices: 23232046--23232071 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23232036 TATTGTTTAT
23232046 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
23232072 AAGCAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23235466 original size:2 final size:2
Alignment explanation
Indices: 23235461--23235494 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
23235451 ATATATATAT
23235461 AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
23235495 AGCAAGAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23235502 original size:15 final size:15
Alignment explanation
Indices: 23235461--23235496 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
23235451 ATATATATAT
23235461 AGAG-AGAGAGAGAG
1 AGAGAAGAGAGAGAG
23235475 AGAGAAGAGAGAGAG
1 AGAGAAGAGAGAGAG
23235490 AGAGAAG
1 AGAGAAG
23235497 CAAGAGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (15 bp):
AGAGAAGAGAGAGAG
Found at i:23236891 original size:24 final size:24
Alignment explanation
Indices: 23236794--23236893 Score: 71
Period size: 24 Copynumber: 4.2 Consensus size: 24
23236784 AACAACTAGG
23236794 ATTAAATATTTATAAATTAATTAA
1 ATTAAATATTTATAAATTAATTAA
*** *
23236818 ATTTTTTGTTTATAAATTAATT--
1 ATTAAATATTTATAAATTAATTAA
** * * **
23236840 -TTATTTATTGAGTAAAATAAAAATA
1 ATTAAATATTTA-TAAATTAATTA-A
23236865 ATTAAATATTTATAAATTAATTAA
1 ATTAAATATTTATAAATTAATTAA
23236889 ATTAA
1 ATTAA
23236894 CTAATTTAAT
Statistics
Matches: 55, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
21 8 0.15
22 7 0.13
24 24 0.44
25 8 0.15
26 8 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
ATTAAATATTTATAAATTAATTAA
Found at i:23237847 original size:16 final size:17
Alignment explanation
Indices: 23237821--23237852 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
23237811 AAGTAAATTA
23237821 AAAATAAACAAAAAAAG
1 AAAATAAACAAAAAAAG
23237838 AAAA-AAACAAAAAAA
1 AAAATAAACAAAAAAA
23237853 AAAGAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAATAAACAAAAAAAG
Found at i:23237852 original size:19 final size:21
Alignment explanation
Indices: 23237820--23237862 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
23237810 AAAGTAAATT
*
23237820 AAAAATAAACAAAAAAAGA-A
1 AAAAACAAACAAAAAAAGAGA
23237840 AAAAACAAA-AAAAAAAGAGA
1 AAAAACAAACAAAAAAAGAGA
23237860 AAA
1 AAA
23237863 GGGGAAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.86, C:0.05, G:0.07, T:0.02
Consensus pattern (21 bp):
AAAAACAAACAAAAAAAGAGA
Found at i:23239933 original size:26 final size:25
Alignment explanation
Indices: 23239871--23239958 Score: 67
Period size: 26 Copynumber: 3.4 Consensus size: 25
23239861 AATATAGGAG
*
23239871 AATAA-AAAAATAAAAAATATGATAAT
1 AATAATAAAAATGAAAAATA--ATAAT
*
23239897 -ATGAA-ATAAAATG-AAAATAATAGTT
1 AAT-AATA-AAAATGAAAAATAATA-AT
23239922 AAATAATAAAAATGACAAAATAATAAT
1 -AATAATAAAAATGA-AAAATAATAAT
23239949 AATAATAAAA
1 AATAATAAAA
23239959 TAGATAATCG
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
24 3 0.06
25 3 0.06
26 27 0.53
27 9 0.18
28 9 0.18
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (25 bp):
AATAATAAAAATGAAAAATAATAAT
Found at i:23239958 original size:17 final size:17
Alignment explanation
Indices: 23239901--23239966 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
23239891 GATAATATGA
23239901 AATAAAATGAA-AATAAT
1 AATAAAAT-AATAATAAT
* * *
23239918 AGTTAAATAATAAAAAT
1 AATAAAATAATAATAAT
* *
23239935 GACAAAATAATAATAAT
1 AATAAAATAATAATAAT
23239952 AATAAAATAGATAAT
1 AATAAAATA-ATAAT
23239967 CGCATTAGCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
16 2 0.05
17 30 0.81
18 5 0.14
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26
Consensus pattern (17 bp):
AATAAAATAATAATAAT
Found at i:23248419 original size:84 final size:84
Alignment explanation
Indices: 23248275--23248440 Score: 314
Period size: 84 Copynumber: 2.0 Consensus size: 84
23248265 GTTAAATTTA
*
23248275 CTTAATAGCCAAAAGGGAGGAGTGATAGATTAGAATCCAATCCATGAATCTGGAGGCAACTCAAA
1 CTTAATAGCCAAAAGGGAGGAGTGATAGATTAGAATCCAATCCATGAATCTGGAGCCAACTCAAA
*
23248340 TAGCCTTTATTTATTTCCC
66 TAGCATTTATTTATTTCCC
23248359 CTTAATAGCCAAAAGGGAGGAGTGATAGATTAGAATCCAATCCATGAATCTGGAGCCAACTCAAA
1 CTTAATAGCCAAAAGGGAGGAGTGATAGATTAGAATCCAATCCATGAATCTGGAGCCAACTCAAA
23248424 TAGCATTTATTTATTTC
66 TAGCATTTATTTATTTC
23248441 TGAGTGATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (84 bp):
CTTAATAGCCAAAAGGGAGGAGTGATAGATTAGAATCCAATCCATGAATCTGGAGCCAACTCAAA
TAGCATTTATTTATTTCCC
Found at i:23249638 original size:13 final size:11
Alignment explanation
Indices: 23249608--23249642 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
23249598 AAGTTATTAA
23249608 AAAAAAAGCTT
1 AAAAAAAGCTT
23249619 AAAAAAAGCTCT
1 AAAAAAAGCT-T
23249631 AAATAAAAGCTT
1 AAA-AAAAGCTT
23249643 TCTTTTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.45
12 5 0.23
13 7 0.32
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (11 bp):
AAAAAAAGCTT
Found at i:23250572 original size:18 final size:20
Alignment explanation
Indices: 23250525--23250575 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
23250515 TTATCTGAGT
23250525 AATAATAAATATAACAAACG
1 AATAATAAATATAACAAACG
23250545 ATAATAATAAATATAACAAACG
1 --AATAATAAATATAACAAACG
23250567 -AT-ATAAATA
1 AATAATAAATA
23250576 ATTAATTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.24
19 2 0.07
22 20 0.69
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.24
Consensus pattern (20 bp):
AATAATAAATATAACAAACG
Found at i:23250576 original size:22 final size:22
Alignment explanation
Indices: 23250524--23250569 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
23250514 ATTATCTGAG
23250524 TAATAATAAATATAACAAACGA
1 TAATAATAAATATAACAAACGA
23250546 TAATAATAAATATAACAAACGA
1 TAATAATAAATATAACAAACGA
23250568 TA
1 TA
23250570 TAAATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (22 bp):
TAATAATAAATATAACAAACGA
Found at i:23250990 original size:14 final size:15
Alignment explanation
Indices: 23250965--23250993 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23250955 TAAATTTTTA
23250965 TAATTAATAATTAAT
1 TAATTAATAATTAAT
23250980 TAATT-ATAATTAAT
1 TAATTAATAATTAAT
23250994 CAAAATATCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTAATAATTAAT
Found at i:23252601 original size:2 final size:2
Alignment explanation
Indices: 23252594--23252627 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
23252584 CCCCTCCTTT
*
23252594 TC TC TC TC -C TC TC AC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
23252628 TCTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:23259479 original size:12 final size:12
Alignment explanation
Indices: 23259462--23259487 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23259452 GGGCTGATTG
23259462 CCTCTACCTCGA
1 CCTCTACCTCGA
23259474 CCTCTACCTCGA
1 CCTCTACCTCGA
23259486 CC
1 CC
23259488 AACCATAGTA
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:0.15, C:0.54, G:0.08, T:0.23
Consensus pattern (12 bp):
CCTCTACCTCGA
Found at i:23272145 original size:30 final size:30
Alignment explanation
Indices: 23272082--23272145 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
23272072 TGTTTGGGAC
* *
23272082 TGTGCTTGGAGGCGAGGTTGAGTTTGCTGT
1 TGTGCTTGGACGCGAGGTTGAGATTGCTGT
23272112 TGTGCTTGG-CGCTGAGGTTGAGATTG-TGAT
1 TGTGCTTGGACGC-GAGGTTGAGATTGCTG-T
23272142 TGTG
1 TGTG
23272146 GCTGGTGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.11, C:0.09, G:0.42, T:0.38
Consensus pattern (30 bp):
TGTGCTTGGACGCGAGGTTGAGATTGCTGT
Found at i:23272210 original size:108 final size:108
Alignment explanation
Indices: 23272034--23272264 Score: 453
Period size: 108 Copynumber: 2.1 Consensus size: 108
23272024 AGGTTGAAAA
23272034 TGTGGCTGGTGTTGAGGTTGTAAGAATGACTGAGTTTGTGTTTGGGACTGTGCTTGGAGGCGAGG
1 TGTGGCTGGTGTTGAGGTTGTAAGAATGACTGAGTTTGTGTTTGGGACTGTGCTTGGAGGCGAGG
23272099 TTGAGTTTGCTGTTGTGCTTGGCGCTGAGGTTGAGATTGTGAT
66 TTGAGTTTGCTGTTGTGCTTGGCGCTGAGGTTGAGATTGTGAT
23272142 TGTGGCTGGTGTTGAGGTTGTAAGAATGACTGAGTTTGTGTTTGGGACTGTGCTTGGAGGCGAGG
1 TGTGGCTGGTGTTGAGGTTGTAAGAATGACTGAGTTTGTGTTTGGGACTGTGCTTGGAGGCGAGG
23272207 TTGAGTTTGCTGTTGTGCTTGGCGCTGAGGTTGAGATTGTGAT
66 TTGAGTTTGCTGTTGTGCTTGGCGCTGAGGTTGAGATTGTGAT
*
23272250 TGTGGCTGGAGTTGA
1 TGTGGCTGGTGTTGA
23272265 ATTTGCGATG
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 122 1.00
ACGTcount: A:0.14, C:0.08, G:0.41, T:0.37
Consensus pattern (108 bp):
TGTGGCTGGTGTTGAGGTTGTAAGAATGACTGAGTTTGTGTTTGGGACTGTGCTTGGAGGCGAGG
TTGAGTTTGCTGTTGTGCTTGGCGCTGAGGTTGAGATTGTGAT
Found at i:23272253 original size:30 final size:30
Alignment explanation
Indices: 23272190--23272253 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
23272180 TGTTTGGGAC
* *
23272190 TGTGCTTGGAGGCGAGGTTGAGTTTGCTGT
1 TGTGCTTGGACGCGAGGTTGAGATTGCTGT
23272220 TGTGCTTGG-CGCTGAGGTTGAGATTG-TGAT
1 TGTGCTTGGACGC-GAGGTTGAGATTGCTG-T
23272250 TGTG
1 TGTG
23272254 GCTGGAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.11, C:0.09, G:0.42, T:0.38
Consensus pattern (30 bp):
TGTGCTTGGACGCGAGGTTGAGATTGCTGT
Found at i:23277544 original size:2 final size:2
Alignment explanation
Indices: 23277537--23277563 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23277527 ATAATTCTTA
23277537 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
23277564 CATACATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23279362 original size:2 final size:2
Alignment explanation
Indices: 23279355--23279404 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
23279345 TTTTATGAAC
23279355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
23279397 AT AC AT AT
1 AT AT AT AT
23279405 TTGAAGATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23279879 original size:16 final size:16
Alignment explanation
Indices: 23279858--23279896 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
23279848 AAATGTTTAC
23279858 GTGCAATGAATTACCT
1 GTGCAATGAATTACCT
23279874 GTGCAATGAATTACCT
1 GTGCAATGAATTACCT
23279890 GTGCAAT
1 GTGCAAT
23279897 TATGGTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (16 bp):
GTGCAATGAATTACCT
Found at i:23287501 original size:26 final size:27
Alignment explanation
Indices: 23287466--23287517 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
23287456 ATGTGTTTAA
*
23287466 TTAATTAGTACAAGGATTGAGTTAAAC
1 TTAATTAGTACAAAGATTGAGTTAAAC
* *
23287493 TTAA-TAGTATAAAGATTGCGTTAAA
1 TTAATTAGTACAAAGATTGAGTTAAA
23287518 ATTGAATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (27 bp):
TTAATTAGTACAAAGATTGAGTTAAAC
Found at i:23288011 original size:15 final size:14
Alignment explanation
Indices: 23287993--23288022 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
23287983 TGAGAGCGCC
23287993 AATAAAAATACAAAA
1 AATAAAAATA-AAAA
23288008 AATAAAAATAAAAA
1 AATAAAAATAAAAA
23288022 A
1 A
23288023 TTCAGAAAAT
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:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:23304159 original size:22 final size:22
Alignment explanation
Indices: 23304131--23304181 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
23304121 CTGATATTGA
23304131 TAAATTTTGAAAATAGAAAGAC
1 TAAATTTTGAAAATAGAAAGAC
23304153 TAAATTTTGAAAATAGAAAGAC
1 TAAATTTTGAAAATAGAAAGAC
*
23304175 TTAATTT
1 TAAATTT
23304182 ATGCAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (22 bp):
TAAATTTTGAAAATAGAAAGAC
Found at i:23323853 original size:10 final size:10
Alignment explanation
Indices: 23323838--23323862 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23323828 AATAATAATG
23323838 AAAAAATAGA
1 AAAAAATAGA
23323848 AAAAAATAGA
1 AAAAAATAGA
23323858 AAAAA
1 AAAAA
23323863 GAAAGGAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAATAGA
Found at i:23324539 original size:41 final size:39
Alignment explanation
Indices: 23324459--23324537 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
23324449 TGGGTGCGAC
23324459 GCCGGCGACGTCGGAGGGAATAGAGAGAAGGGAGAGAGA
1 GCCGGCGACGTCGGAGGGAATAGAGAGAAGGGAGAGAGA
* *
23324498 GCCGGCGACGTCGGAGTGAATAGAGAGAAGGGAAAGAGA
1 GCCGGCGACGTCGGAGGGAATAGAGAGAAGGGAGAGAGA
23324537 G
1 G
23324538 AGACGGCGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.47, T:0.06
Consensus pattern (39 bp):
GCCGGCGACGTCGGAGGGAATAGAGAGAAGGGAGAGAGA
Found at i:23328491 original size:35 final size:35
Alignment explanation
Indices: 23328420--23328493 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
23328410 AAACATGATA
* *
23328420 TAAAAATTAAACATGACTAAACATGCATAAATAGT
1 TAAAAATTAAACATGACGAAACATGCATAAACAGT
*
23328455 TAAAAATTAAACGTGACGAAACATGCAGT-AACAGT
1 TAAAAATTAAACATGACGAAACATGCA-TAAACAGT
23328490 TAAA
1 TAAA
23328494 TAATGTGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (35 bp):
TAAAAATTAAACATGACGAAACATGCATAAACAGT
Found at i:23334751 original size:14 final size:14
Alignment explanation
Indices: 23334728--23334771 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
23334718 TAGAAAGTAC
*
23334728 AAAAAA-AGAAAGG
1 AAAAAAGAGAAAAG
*
23334741 AAAAAAGAGAAAAA
1 AAAAAAGAGAAAAG
23334755 AAAAAAGA-AAAAG
1 AAAAAAGAGAAAAG
23334768 AAAA
1 AAAA
23334772 GAGCAACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAGAGAAAAG
Found at i:23334756 original size:12 final size:12
Alignment explanation
Indices: 23334728--23334774 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
23334718 TAGAAAGTAC
23334728 AAAAAAAGA-AA
1 AAAAAAAGAGAA
*
23334739 GGAAAAAAGAGAA
1 -AAAAAAAGAGAA
*
23334752 AAAAAAAAAGAA
1 AAAAAAAGAGAA
23334764 AAAGAAAAGAG
1 AAA-AAAAGAG
23334775 CAACCCGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 21 0.72
13 8 0.28
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGAA
Found at i:23335592 original size:28 final size:29
Alignment explanation
Indices: 23335561--23335625 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
23335551 AGTTTCAATC
23335561 TTTTCTTCT-TTTTTGT-CTCTCTCTTTTT-
1 TTTTCTTCTATTTTT-TCCT-TCTCTTTTTA
*
23335589 TTTTCTTATATTTTTTCCTTCTCTTTTTA
1 TTTTCTTCTATTTTTTCCTTCTCTTTTTA
23335618 TTTT-TTCT
1 TTTTCTTCT
23335626 CCTCTTCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 21 0.66
29 11 0.34
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (29 bp):
TTTTCTTCTATTTTTTCCTTCTCTTTTTA
Found at i:23336306 original size:37 final size:37
Alignment explanation
Indices: 23336218--23336313 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 37
23336208 TGATTTTGTT
* *
23336218 TCTTTTTTTCTTTTTTTTTTTATATGTTTCTCTTATC
1 TCTTTTTTTCTTTTTTTTTTTATACGTCTCTCTTATC
* *
23336255 TCTTTTTTCCTCTTTTTCTTTATTTAT-CG-CTCTTTTTTC
1 TCTTTTTT--TCTTTTT-TTT-TTTATACGTCTCTCTTATC
23336294 TCTTTTTTTCTTTTTTTTTT
1 TCTTTTTTTCTTTTTTTTTT
23336314 CTCTTGTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
35 2 0.04
36 3 0.06
37 15 0.29
39 22 0.43
40 4 0.08
41 5 0.10
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (37 bp):
TCTTTTTTTCTTTTTTTTTTTATACGTCTCTCTTATC
Found at i:23336311 original size:21 final size:22
Alignment explanation
Indices: 23336287--23336327 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
23336277 TTTATCGCTC
23336287 TTTTTTCTCTT-TTTTTCTTTT
1 TTTTTTCTCTTGTTTTTCTTTT
23336308 TTTTTTCTCTTGTTTTTCTT
1 TTTTTTCTCTTGTTTTTCTT
23336328 CTTGCCTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (22 bp):
TTTTTTCTCTTGTTTTTCTTTT
Found at i:23336318 original size:30 final size:31
Alignment explanation
Indices: 23336253--23336327 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
23336243 GTTTCTCTTA
*
23336253 TCTCTTTTTTC-CTCTTTTTCTTTATTTATC
1 TCTCTTTTTTCTCTTTTTTTCTTTATTTATC
* * *
23336283 GCTCTTTTTTCTCTTTTTTTCTTT-TTTTTT
1 TCTCTTTTTTCTCTTTTTTTCTTTATTTATC
23336313 TCTCTTGTTTT-TCTT
1 TCTCTT-TTTTCTCTT
23336328 CTTGCCTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 23 0.61
31 15 0.39
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.75
Consensus pattern (31 bp):
TCTCTTTTTTCTCTTTTTTTCTTTATTTATC
Found at i:23336806 original size:18 final size:18
Alignment explanation
Indices: 23336760--23336807 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
23336750 ATATTTCATT
*
23336760 AATTATGTTTATGTAAAC
1 AATTATGTTTGTGTAAAC
* *
23336778 AATTATATTTGTTTAAA-
1 AATTATGTTTGTGTAAAC
23336795 AGATTATGTTTGT
1 A-ATTATGTTTGT
23336808 ACAAATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (18 bp):
AATTATGTTTGTGTAAAC
Found at i:23341298 original size:4 final size:4
Alignment explanation
Indices: 23341289--23341321 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
23341279 AAGTTGCAAT
*
23341289 GAAA GAAA GAAA GAAA GAAA GAGA -AAA GAAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA
23341322 GGCTTACGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 2 0.08
4 24 0.92
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:23342158 original size:17 final size:18
Alignment explanation
Indices: 23342136--23342169 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23342126 AATACATAAA
*
23342136 TATAAA-AAAAATAATTC
1 TATAAATAAAAACAATTC
23342153 TATAAATAAAAACAATT
1 TATAAATAAAAACAATT
23342170 ATAAGTGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
TATAAATAAAAACAATTC
Found at i:23344749 original size:21 final size:22
Alignment explanation
Indices: 23344725--23344770 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
23344715 AATTGTAAAT
*
23344725 AACAATAAC-AATTTATAGGAA
1 AACAACAACTAATTTATAGGAA
*
23344746 AAC-ACAACTAATTTGTAGGAA
1 AACAACAACTAATTTATAGGAA
23344767 AACA
1 AACA
23344771 GTCAAGCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (22 bp):
AACAACAACTAATTTATAGGAA
Found at i:23345333 original size:23 final size:23
Alignment explanation
Indices: 23345285--23345336 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
23345275 AAAAATATGT
* ** *
23345285 TAAAAA-AAATTTATAATTTTTG
1 TAAAAAGAAAATTATAAAATTTC
23345307 TAAAAAGAAAATTATAAAATTTC
1 TAAAAAGAAAATTATAAAATTTC
23345330 TAAAAAG
1 TAAAAAG
23345337 CAGATACAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (23 bp):
TAAAAAGAAAATTATAAAATTTC
Found at i:23348894 original size:21 final size:20
Alignment explanation
Indices: 23348870--23348908 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
23348860 ATTAATATAA
23348870 TATTCAAAAAAGTTTCAAAAC
1 TATTCAAAAAA-TTTCAAAAC
*
23348891 TATTTAAAAAATTTCAAA
1 TATTCAAAAAATTTCAAA
23348909 TAAGTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (20 bp):
TATTCAAAAAATTTCAAAAC
Found at i:23348977 original size:30 final size:28
Alignment explanation
Indices: 23348904--23348977 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 28
23348894 TTAAAAAATT
*
23348904 TCAAATAAGTCTT-TATTCTTTTTTGCA
1 TCAAATAAGTCTTATATTCTTTTTTGAA
* *
23348931 TTAAATTAAGTTCTTATATTTTTATTTTGAA
1 TCAAA-TAAG-TCTTATATTCTT-TTTTGAA
23348962 TCAAATAAGTGCTTAT
1 TCAAATAAGT-CTTAT
23348978 GAATAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 4 0.11
28 4 0.11
29 5 0.13
30 15 0.39
31 10 0.26
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.51
Consensus pattern (28 bp):
TCAAATAAGTCTTATATTCTTTTTTGAA
Found at i:23349283 original size:24 final size:23
Alignment explanation
Indices: 23349256--23349300 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
23349246 ACTAAAAATA
*
23349256 TTTTAAATAACATATTTTTTTACG
1 TTTTAAAGAACAT-TTTTTTTACG
**
23349280 TTTTTTAGAACATTTTTTTTA
1 TTTTAAAGAACATTTTTTTTA
23349301 TCTAACTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTAAAGAACATTTTTTTTACG
Found at i:23350730 original size:23 final size:23
Alignment explanation
Indices: 23350697--23350758 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
23350687 GAATCATTTC
23350697 AAATATAATAAATAAAGAATTTT-A
1 AAATAT-ATAAATAAA-AATTTTAA
*
23350721 AAATATATAAAT-AAATTTTTAA
1 AAATATATAAATAAAAATTTTAA
23350743 AAATATATATAATAAA
1 AAATATATA-AATAAA
23350759 TAAATAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 5 0.15
22 12 0.35
23 9 0.26
24 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATATATAAATAAAAATTTTAA
Found at i:23350748 original size:22 final size:21
Alignment explanation
Indices: 23350697--23350759 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 21
23350687 GAATCATTTC
*
23350697 AAATATAATAAATAAAGAATTTTA
1 AAATAT-ATAAAT-AA-ATTTTTA
23350721 AAATATATAAATAAATTTTTAA
1 AAATATATAAATAAATTTTT-A
23350743 AAATATATATAATAAAT
1 AAATATATA-AATAAAT
23350760 AAATAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 5 0.14
22 12 0.33
23 13 0.36
24 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATATATAAATAAATTTTTA
Found at i:23350757 original size:27 final size:27
Alignment explanation
Indices: 23350723--23350775 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 27
23350713 GAATTTTAAA
23350723 ATATATAAATAAAT-TTTTAAAAATAT
1 ATATATAAATAAATATTTTAAAAATAT
23350749 ATATAATAAATAAATAATTTTAAAAAT
1 ATAT-ATAAATAAAT-ATTTTAAAAAT
23350776 TTTGAGAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 10 0.42
29 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATATATAAATAAATATTTTAAAAATAT
Found at i:23351114 original size:18 final size:18
Alignment explanation
Indices: 23351092--23351141 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
23351082 AATTTAAATA
23351092 AAATTTTATTTTTATTATT
1 AAATTTTATTTTT-TTATT
*
23351111 -AATTTTATTAATTTTATT
1 AAATTTTATT-TTTTTATT
23351129 AAATTTTTATTTT
1 AAA-TTTTATTTT
23351142 AAATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 14 0.54
19 5 0.19
20 7 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AAATTTTATTTTTTTATT
Found at i:23351118 original size:9 final size:9
Alignment explanation
Indices: 23351093--23351135 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
23351083 ATTTAAATAA
23351093 AATTTTATT
1 AATTTTATT
*
23351102 -TTTATTATT
1 AATT-TTATT
23351111 AATTTTATT
1 AATTTTATT
23351120 AATTTTATT
1 AATTTTATT
23351129 AAATTTT
1 -AATTTT
23351136 TATTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 2 0.07
9 19 0.66
10 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
AATTTTATT
Found at i:23352174 original size:16 final size:16
Alignment explanation
Indices: 23352155--23352197 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
23352145 TTTTTTCTCA
23352155 TTTCTCCTTTTTCCTT
1 TTTCTCCTTTTTCCTT
** *
23352171 TTTCTATTTTTTCTTT
1 TTTCTCCTTTTTCCTT
23352187 TTTC-CCTTTTT
1 TTTCTCCTTTTT
23352198 TTTTCTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTCCTTTTTCCTT
Found at i:23352212 original size:16 final size:16
Alignment explanation
Indices: 23352162--23352213 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
23352152 TCATTTCTCC
* * *
23352162 TTTTTCCTTTTTCTAT
1 TTTTTCTTTTTTTTTT
23352178 TTTTTCTTTTTTCCCTTTT
1 TTTTTCTTTTTT---TTTT
23352197 TTTTTCTTTTTTTTTT
1 TTTTTCTTTTTTTTTT
23352213 T
1 T
23352214 AAATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 16 0.53
19 14 0.47
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTT
Found at i:23352245 original size:22 final size:20
Alignment explanation
Indices: 23352177--23352237 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
23352167 CCTTTTTCTA
*
23352177 TTTTTTCTTTTTTC-CCTTT
1 TTTTTTCTTTTTTCTCTTTT
*
23352196 TTTTTTCTTTTTT-TTTTTAAAT
1 TTTTTTCTTTTTTCTCTTT---T
23352218 TTTTTTCTTTTTTCTCTTTT
1 TTTTTTCTTTTTTCTCTTTT
23352238 GTTATTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 15 0.44
20 1 0.03
22 14 0.41
23 4 0.12
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTTTCTCTTTT
Found at i:23352435 original size:24 final size:24
Alignment explanation
Indices: 23352401--23352464 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
23352391 TCACTATTCA
*
23352401 TTAATATAAAATAA-TAAGTGATATT
1 TTAAT-TAAAATAATTAAGTAAT-TT
*
23352426 TTAATTAAAATAATTAATTAATTT
1 TTAATTAAAATAATTAAGTAATTT
23352450 TTAATTATAAA-AATT
1 TTAATTA-AAATAATT
23352465 TATTTTGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 21 0.60
25 14 0.40
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
TTAATTAAAATAATTAAGTAATTT
Found at i:23355183 original size:23 final size:23
Alignment explanation
Indices: 23355157--23355270 Score: 95
Period size: 23 Copynumber: 4.9 Consensus size: 23
23355147 CAGAGCCGCT
23355157 AGATGTTACACACCATGGTTTCA
1 AGATGTTACACACCATGGTTTCA
* * *
23355180 AGATGTGACACACCATGTGGCTCCA
1 AGATGTTACACACCA--TGGTTTCA
*** *
23355205 AGATGTTACATGTCAAGGTTTCA
1 AGATGTTACACACCATGGTTTCA
* * *
23355228 AGATGTTACACGCCA-GAGTTACT
1 AGATGTTACACACCATG-GTTTCA
*
23355251 GGATGTTACACACCATGGTT
1 AGATGTTACACACCATGGTT
23355271 GCAGCAAGCT
Statistics
Matches: 71, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
22 1 0.01
23 52 0.73
24 1 0.01
25 17 0.24
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (23 bp):
AGATGTTACACACCATGGTTTCA
Found at i:23359953 original size:24 final size:23
Alignment explanation
Indices: 23359899--23359953 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
23359889 AAGAGAAATG
* *
23359899 AAAAAAATAAACAAATAATAATA
1 AAAAAAAGAAACAAATAAGAATA
23359922 AAACAAAAGAAA-AAATACAGAATA
1 AAA-AAAAGAAACAAATA-AGAATA
23359946 AATAAAAA
1 AA-AAAAA
23359954 AATTATTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 8 0.30
24 18 0.67
25 1 0.04
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.13
Consensus pattern (23 bp):
AAAAAAAGAAACAAATAAGAATA
Found at i:23360000 original size:27 final size:29
Alignment explanation
Indices: 23359944--23360003 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
23359934 AAATACAGAA
* *
23359944 TAAATAAAAAAATTATTTGTATTAATTAT
1 TAAATAAAAAAATTATTTGTATAAAGTAT
23359973 TAAAT-AAAAAATTATTT-TA-AAGAGTAT
1 TAAATAAAAAAATTATTTGTATAA-AGTAT
23360000 TAAA
1 TAAA
23360004 AATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 1 0.04
27 10 0.36
28 12 0.43
29 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (29 bp):
TAAATAAAAAAATTATTTGTATAAAGTAT
Found at i:23363823 original size:57 final size:56
Alignment explanation
Indices: 23363729--23363883 Score: 179
Period size: 57 Copynumber: 2.8 Consensus size: 56
23363719 AGTTGAATGT
* * * *
23363729 TTGTTTTCTTTGCACTGTCCATATGATATCCTGTAATTTGGTTATATGTTACGTGG-
1 TTGTTTTCTTTGCACT-TTCTTATGATATCCTATAATTTGGTTATATGTTACATGGA
* * * *
23363785 TTAGTTTTCTTTTCACTTTCTGTATGATGTCCTATAATTTGGTAATTTGTTACATGGA
1 TT-GTTTTCTTTGCACTTTCT-TATGATATCCTATAATTTGGTTATATGTTACATGGA
* *
23363843 TTG-TTTCTTTGCCCTTTCTTTTGATATCCTATAATTTGGTT
1 TTGTTTTCTTTGCACTTTCTTATGATATCCTATAATTTGGTT
23363884 CTAAGGCTTG
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
55 19 0.23
56 18 0.22
57 44 0.53
58 2 0.02
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.52
Consensus pattern (56 bp):
TTGTTTTCTTTGCACTTTCTTATGATATCCTATAATTTGGTTATATGTTACATGGA
Found at i:23373339 original size:15 final size:15
Alignment explanation
Indices: 23373321--23373354 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23373311 GAGAAGAGAG
23373321 ATATATACATATAAT
1 ATATATACATATAAT
* *
23373336 ATATATATATGTAAT
1 ATATATACATATAAT
23373351 ATAT
1 ATAT
23373355 TTATTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
ATATATACATATAAT
Found at i:23378284 original size:17 final size:18
Alignment explanation
Indices: 23378244--23378298 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
23378234 ACTGTAACTG
*
23378244 TTTGAATAAATATAATTA
1 TTTGAATAAACATAATTA
23378262 TTTGAATAAACAT-ATCT-
1 TTTGAATAAACATAAT-TA
* *
23378279 TTTGAACAATCATAATTA
1 TTTGAATAAACATAATTA
23378297 TT
1 TT
23378299 CAAAAGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (18 bp):
TTTGAATAAACATAATTA
Found at i:23389669 original size:25 final size:26
Alignment explanation
Indices: 23389630--23389706 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
23389620 ATTATTTAAA
* * * *
23389630 TATTTAATATCATTATTTATTTTTATT
1 TATTTAAAAT-ATTAGTAATTTATATT
*
23389657 T-TTTAGAATATTAGTAATTTATATT
1 TATTTAAAATATTAGTAATTTATATT
*
23389682 TCATTTAAAATATTAATAATTTATA
1 T-ATTTAAAATATTAGTAATTTATA
23389707 CTTAAAACAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 14 0.34
26 6 0.15
27 21 0.51
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (26 bp):
TATTTAAAATATTAGTAATTTATATT
Found at i:23389826 original size:23 final size:21
Alignment explanation
Indices: 23389777--23389835 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
23389767 AAATTTATAA
23389777 TTAAAATTT-TAATTTAA--TT
1 TTAAAATTTATAA-TTAATTTT
23389796 TTAAAATTTAATATATTAATTTT
1 TTAAAATTT-ATA-ATTAATTTT
*
23389819 TTATAATTTATAATTAA
1 TTAAAATTTATAATTAA
23389836 AAANNNNNNN
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 9 0.26
21 11 0.32
22 4 0.12
23 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAATTTATAATTAATTTT
Found at i:23391332 original size:16 final size:16
Alignment explanation
Indices: 23391313--23391361 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 16
23391303 TTAAATATAA
23391313 ATAAAATTTATTAATT
1 ATAAAATTTATTAATT
*
23391329 AT--AA-TTATTAATA
1 ATAAAATTTATTAATT
*
23391342 ATTAAATTTATTAATT
1 ATAAAATTTATTAATT
23391358 -TAAA
1 ATAAA
23391362 TATCAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
13 10 0.37
14 2 0.07
15 5 0.19
16 10 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAAATTTATTAATT
Found at i:23391436 original size:26 final size:25
Alignment explanation
Indices: 23391383--23391440 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
23391373 TAGTATAGTT
* * *
23391383 TAATTATTAATATTTTAATTAATTA
1 TAATTATTAATATTTAAAATAATAA
23391408 TAAATTATTAATATTTAAAAATAA-AA
1 T-AATTATTAATATTT-AAAATAATAA
23391434 TAATTAT
1 TAATTAT
23391441 ATATATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.25
26 16 0.57
27 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATTATTAATATTTAAAATAATAA
Found at i:23391439 original size:22 final size:22
Alignment explanation
Indices: 23391409--23391457 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
23391399 AATTAATTAT
* *
23391409 AAATTATTA-ATATTTAAAAATA
1 AAATAATTATATATATAAAAA-A
*
23391431 AAATAATTATATATATAATAAA
1 AAATAATTATATATATAAAAAA
23391453 AAATA
1 AAATA
23391458 TTTGTATCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATAATTATATATATAAAAAA
Done.