Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 52 of 93
Found at i:19925951 original size:14 final size:14
Alignment explanation
Indices: 19925932--19925962 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19925922 GAGTTTATAC
19925932 TCATGTTTTCAACT
1 TCATGTTTTCAACT
*
19925946 TCATGTTTTCAGCT
1 TCATGTTTTCAACT
19925960 TCA
1 TCA
19925963 AGGGTGGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (14 bp):
TCATGTTTTCAACT
Found at i:19926492 original size:21 final size:20
Alignment explanation
Indices: 19926442--19926493 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
19926432 TTACAACAAT
* *
19926442 TATATTGATACATTCTGGAA
1 TATATTGATACATGCAGGAA
* *
19926462 TGTATCGATACATGCAAGGAA
1 TATATTGATACATGC-AGGAA
19926483 TATATTGATAC
1 TATATTGATAC
19926494 CTTTGAGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (20 bp):
TATATTGATACATGCAGGAA
Found at i:19927291 original size:80 final size:78
Alignment explanation
Indices: 19927118--19927438 Score: 341
Period size: 80 Copynumber: 4.1 Consensus size: 78
19927108 TAATATTTCA
* * * * *
19927118 ATAAATCATT-ATCATGCTTAGCCTATAGTGTATATAACTATCTCATCATATACATCTCAT--AA
1 ATAAATCATTCA-CATGCTTAGCC-ATATTGTATATGACTATCTCAACACATACATCTCATGGCA
*
19927180 T-C--TCATAGACCTC
64 TACATTTATA-ACCTC
* *
19927193 ATAAATCACTCACATGCTTAGTCCATATTGTATATGACTCTCTCAACACATACATCTCATGGCAT
1 ATAAATCATTCACATGCTTAG-CCATATTGTATATGACTATCTCAACACATACATCTCATGGCAT
19927258 ACATTTGATAACCTC
65 ACATTT-ATAACCTC
*
19927273 ATAAATCATTCACATGCTTAGCTCATAGTGTATATGACTATCTCAACACATACATCTCATGGCAT
1 ATAAATCATTCACATGCTTAGC-CATATTGTATATGACTATCTCAACACATACATCTCATGGCAT
* *
19927338 GCGTTTCATAACCTC
65 ACATTT-ATAACCTC
* * * * *
19927353 ATAAATCATTCACATGCCTAGCCCATATAGTACATGA-TATGCTTAACACATGCATCTCATGGCA
1 ATAAATCATTCACATGCTTAG-CCATATTGTATATGACTAT-CTCAACACATACATCTCATGGCA
*
19927417 TACATGTTATAATCTC
64 TACAT-TTATAACCTC
*
19927433 TTAAAT
1 ATAAAT
19927439 GGAACTCACG
Statistics
Matches: 210, Mismatches: 24, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
75 49 0.23
76 3 0.01
77 2 0.01
78 1 0.00
79 4 0.02
80 145 0.69
81 6 0.03
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.33
Consensus pattern (78 bp):
ATAAATCATTCACATGCTTAGCCATATTGTATATGACTATCTCAACACATACATCTCATGGCATA
CATTTATAACCTC
Found at i:19927313 original size:155 final size:157
Alignment explanation
Indices: 19927118--19927438 Score: 395
Period size: 160 Copynumber: 2.0 Consensus size: 157
19927108 TAATATTTCA
* *
19927118 ATAAATCATTATCATGCTTAGCCTATAGTGTATATAACTATCTCATCATATACATCTCAT-AAT-
1 ATAAATCATTATCATGCTTAGCCTATAGTGTATATAACTATCTCAACACATACATCTCATGAATG
* * * * *
19927181 C-TCATAGACCTCATAAATCACTCACATGCTTAGTCCATATTGTATATGACTCT-CTCAACACAT
66 CTTCATA-ACCTCATAAATCACTCACATGCCTAGCCCATATAGTACATGA-TATGCTCAACACAT
19927244 ACATCTCATGGCATACAT-TTGATAACCTC
129 ACATCTCATGGCATACATGTT-ATAACCTC
* *
19927273 ATAAATCATTCA-CATGCTTAG-CTCATAGTGTATATGACTATCTCAACACATACATCTCATGGC
1 ATAAATCATT-ATCATGCTTAGCCT-ATAGTGTATATAACTATCTCAACACATACATCTCAT-GA
* *
19927336 ATGCGTTTCATAACCTCATAAATCATTCACATGCCTAGCCCATATAGTACATGATATGCTTAACA
63 ATGC--TTCATAACCTCATAAATCACTCACATGCCTAGCCCATATAGTACATGATATGCTCAACA
* *
19927401 CATGCATCTCATGGCATACATGTTATAATCTC
126 CATACATCTCATGGCATACATGTTATAACCTC
*
19927433 TTAAAT
1 ATAAAT
19927439 GGAACTCACG
Statistics
Matches: 142, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
154 2 0.01
155 52 0.37
156 1 0.01
157 2 0.01
158 1 0.01
159 2 0.01
160 75 0.53
161 7 0.05
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.33
Consensus pattern (157 bp):
ATAAATCATTATCATGCTTAGCCTATAGTGTATATAACTATCTCAACACATACATCTCATGAATG
CTTCATAACCTCATAAATCACTCACATGCCTAGCCCATATAGTACATGATATGCTCAACACATAC
ATCTCATGGCATACATGTTATAACCTC
Found at i:19929914 original size:21 final size:22
Alignment explanation
Indices: 19929865--19929954 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 22
19929855 GAATGACGTT
19929865 ACTAG-TTCTTAGGCATTGCATCG
1 ACTAGCTT-TTAGGCATTGCAT-G
* *
19929888 -CAAG-TTTTAGGCATTGCAAG
1 ACTAGCTTTTAGGCATTGCATG
* * *
19929908 ACTAGTTTTTAAGCATTACATG
1 ACTAGCTTTTAGGCATTGCATG
* *
19929930 ATTGGCTTTTAGGCATTGCATG
1 ACTAGCTTTTAGGCATTGCATG
19929952 ACT
1 ACT
19929955 TAATCATTGC
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.02
21 15 0.28
22 37 0.70
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (22 bp):
ACTAGCTTTTAGGCATTGCATG
Found at i:19929993 original size:82 final size:81
Alignment explanation
Indices: 19929892--19930043 Score: 216
Period size: 82 Copynumber: 1.9 Consensus size: 81
19929882 GCATCGCAAG
* *
19929892 TTTTAGGCATTGCAAGACTAGTTTTTAAG-CATTACATGATTGGCTTTTAGGCATTGCATGACTT
1 TTTTAAGCATTGCAAGACTAGTTTTT-AGTCATTACATGACTGG-TTTTAGGCATTGCATGACTT
*
19929956 AATCATTGCGTCTCTGAT
64 AAGCATTGCGTCTCTGAT
** **
19929974 TTTTAAGCATTGCGTGACTAGTTTTTAGTCATTACATGACTGGTTTTAGGCATTGTGTGACTTAA
1 TTTTAAGCATTGCAAGACTAGTTTTTAGTCATTACATGACTGGTTTTAGGCATTGCATGACTTAA
19930039 GCATT
66 GCATT
19930044 ACGTGACTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 26 0.42
82 36 0.58
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (81 bp):
TTTTAAGCATTGCAAGACTAGTTTTTAGTCATTACATGACTGGTTTTAGGCATTGCATGACTTAA
GCATTGCGTCTCTGAT
Found at i:19929998 original size:22 final size:21
Alignment explanation
Indices: 19929954--19930035 Score: 58
Period size: 22 Copynumber: 3.8 Consensus size: 21
19929944 ATTGCATGAC
* **
19929954 TTAATCATTGCGTCTCTGATTT
1 TTAAGCATTGCGTGACTG-TTT
19929976 TTAAGCATTGCGTGACTAGTTT
1 TTAAGCATTGCGTGACT-GTTT
* * *
19929998 TT-AGTCATTACATGACTGGTT
1 TTAAG-CATTGCGTGACTGTTT
* *
19930019 TTAGGCATTGTGTGACT
1 TTAAGCATTGCGTGACT
19930036 TAAGCATTAC
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
21 16 0.34
22 30 0.64
23 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (21 bp):
TTAAGCATTGCGTGACTGTTT
Found at i:19930095 original size:81 final size:82
Alignment explanation
Indices: 19929911--19930087 Score: 205
Period size: 81 Copynumber: 2.2 Consensus size: 82
19929901 TTGCAAGACT
* * * * * *
19929911 AGTTTTTAAGCATTACATGATTGGCTTTTAGGCATTGCATGACTTAATCATTGCGTCTCTGATTT
1 AGTTTTTAGGCATTACATGACTGGCTTTTAGGCATTGCATGACTTAAGCATTACGTCACTGAGTT
* *
19929976 TTAAGCATTGCGTGACT
66 GTAAGCATTGCGTGACA
* ** *
19929993 AGTTTTTAGTCATTACATGACTGG-TTTTAGGCATTGTGTGACTTAAGCATTACGTGACTGAGTT
1 AGTTTTTAGGCATTACATGACTGGCTTTTAGGCATTGCATGACTTAAGCATTACGTCACTGAGTT
* *
19930057 GTAGGCATTGTGTGA-A
66 GTAAGCATTGCGTGACA
19930073 AGGTTTTTAGGCATT
1 A-GTTTTTAGGCATT
19930088 GCGTGACTTA
Statistics
Matches: 79, Mismatches: 15, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
80 1 0.01
81 57 0.72
82 21 0.27
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (82 bp):
AGTTTTTAGGCATTACATGACTGGCTTTTAGGCATTGCATGACTTAAGCATTACGTCACTGAGTT
GTAAGCATTGCGTGACA
Found at i:19930100 original size:16 final size:16
Alignment explanation
Indices: 19930079--19930111 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19930069 TGAAAGGTTT
*
19930079 TTAGGCATTGCGTGAC
1 TTAGGCATTGCGAGAC
19930095 TTAGGCATTGCGAGAC
1 TTAGGCATTGCGAGAC
19930111 T
1 T
19930112 ATCGTTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (16 bp):
TTAGGCATTGCGAGAC
Found at i:19930125 original size:38 final size:38
Alignment explanation
Indices: 19930078--19930220 Score: 103
Period size: 38 Copynumber: 3.7 Consensus size: 38
19930068 GTGAAAGGTT
* *
19930078 TTTAGGCATTGCGTGACTTAGGCATTGCGAGACTATCG
1 TTTAAGCATTGCGTGACTTAGGCATTGCGAGACTATCC
* ** ** *
19930116 TTTAAGCATTGCATGACTTAATCATTGC-ATGTTTGAT-T
1 TTTAAGCATTGCGTGACTTAGGCATTGCGA-GACT-ATCC
* * **
19930154 TTTAGAGCATTGTGTGACTTAGGCGTTATGAGACTA-CC
1 TTTA-AGCATTGCGTGACTTAGGCATTGCGAGACTATCC
* *
19930192 TTTGAAGCATTGTGTGACTTAGTCATTGC
1 TTT-AAGCATTGCGTGACTTAGGCATTGC
19930221 ATGTTTAATT
Statistics
Matches: 78, Mismatches: 21, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
37 1 0.01
38 54 0.69
39 22 0.28
40 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (38 bp):
TTTAAGCATTGCGTGACTTAGGCATTGCGAGACTATCC
Found at i:19930187 original size:77 final size:76
Alignment explanation
Indices: 19930076--19930256 Score: 247
Period size: 77 Copynumber: 2.4 Consensus size: 76
19930066 GTGTGAAAGG
* * *
19930076 TTTTTAGGCATTGCGTGACTTAGGCATTGCGAGACTATCGTTT-AAGCATTGCATGACTTAATCA
1 TTTTTAGGCATTGTGTGACTTAGGCATTACGAGACTA-CCTTTGAAGCATTGCATGACTTAATCA
*
19930140 TTGCATGTTTGA
65 TTGCATGTTTAA
* * ** *
19930152 TTTTTAGAGCATTGTGTGACTTAGGCGTTATGAGACTACCTTTGAAGCATTGTGTGACTTAGTCA
1 TTTTTAG-GCATTGTGTGACTTAGGCATTACGAGACTACCTTTGAAGCATTGCATGACTTAATCA
19930217 TTGCATGTTTAA
65 TTGCATGTTTAA
*
19930229 TTTTTAGGAATTGTGTGACTTAGGCATT
1 TTTTTAGGCATTGTGTGACTTAGGCATT
19930257 GCATGATTGG
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
76 30 0.33
77 62 0.67
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (76 bp):
TTTTTAGGCATTGTGTGACTTAGGCATTACGAGACTACCTTTGAAGCATTGCATGACTTAATCAT
TGCATGTTTAA
Found at i:19930242 original size:38 final size:38
Alignment explanation
Indices: 19930200--19930284 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 38
19930190 CCTTTGAAGC
* *
19930200 ATTGTGTGACTTAGTCATTGCATGTTTAATTTTTAGGA
1 ATTGTGTGACTTAGGCATTGCATGATTAATTTTTAGGA
** *
19930238 ATTGTGTGACTTAGGCATTGCATGATTGGTTTTTAGGC
1 ATTGTGTGACTTAGGCATTGCATGATTAATTTTTAGGA
*
19930276 ATTCTGTGA
1 ATTGTGTGA
19930285 ATAAAGCATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.25, T:0.45
Consensus pattern (38 bp):
ATTGTGTGACTTAGGCATTGCATGATTAATTTTTAGGA
Found at i:19930294 original size:38 final size:38
Alignment explanation
Indices: 19930215--19930295 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
19930205 GTGACTTAGT
* * * * *
19930215 CATTGCATGTTTAATTTTTAGGAATTGTGTGACTTAGG
1 CATTGCATGATTAATTTTTAGGAATTCTGTGAATAAAG
** *
19930253 CATTGCATGATTGGTTTTTAGGCATTCTGTGAATAAAG
1 CATTGCATGATTAATTTTTAGGAATTCTGTGAATAAAG
19930291 CATTG
1 CATTG
19930296 TGTGACTGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (38 bp):
CATTGCATGATTAATTTTTAGGAATTCTGTGAATAAAG
Found at i:19930353 original size:22 final size:22
Alignment explanation
Indices: 19930288--19930354 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
19930278 TCTGTGAATA
* * *
19930288 AAGCATTGTGTGACTGGGTTGT
1 AAGCATTGCGTGACTGGATTTT
* * *
19930310 AAGCATTGCGTAACTAGTTTTT
1 AAGCATTGCGTGACTGGATTTT
19930332 AAGCATTGCGTGACTGGATTTT
1 AAGCATTGCGTGACTGGATTTT
19930354 A
1 A
19930355 GGCACATTGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (22 bp):
AAGCATTGCGTGACTGGATTTT
Found at i:19934549 original size:46 final size:46
Alignment explanation
Indices: 19934481--19934569 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 46
19934471 CTCTGCAGCT
* * *
19934481 TCATTTTCCACCCATTTTTTCTCAACTTTCACACCCTT-CAAACTCA
1 TCATTCTCCACCCATTTCTTCTCAACTCTCACA-CCTTGCAAACTCA
19934527 TCATTCTCCACCCATTTCTTCTCAACTCTCACACCTTGCAAAC
1 TCATTCTCCACCCATTTCTTCTCAACTCTCACACCTTGCAAAC
19934570 CCACTCAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 4 0.10
46 35 0.90
ACGTcount: A:0.24, C:0.39, G:0.01, T:0.36
Consensus pattern (46 bp):
TCATTCTCCACCCATTTCTTCTCAACTCTCACACCTTGCAAACTCA
Found at i:19935854 original size:34 final size:34
Alignment explanation
Indices: 19935816--19935883 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
19935806 TCACCAAGCT
* *
19935816 TTTACAATGGCTTTTCACAGGCTCAGCCAAAACC
1 TTTACAATAGCTTTTCACAGGCTCAACCAAAACC
* * *
19935850 TTTACACTAGTTTTTCACAGGCTCAACTAAAACC
1 TTTACAATAGCTTTTCACAGGCTCAACCAAAACC
19935884 CAAAGTGGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (34 bp):
TTTACAATAGCTTTTCACAGGCTCAACCAAAACC
Found at i:19947066 original size:28 final size:28
Alignment explanation
Indices: 19946929--19947102 Score: 197
Period size: 29 Copynumber: 6.0 Consensus size: 28
19946919 TGATAGCTTT
19946929 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
19946957 AACATGTTTGGTCTTAATTTAGATAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
19946986 AATATGTTTGTCTTAATTTAGGACAAGAAA
1 AACATGTTTGTCTTAATTTA-GACAAG-AA
* *
19947016 AATATTTTTTGTCTT-ATTCTAGACAAGAA
1 AACA-TGTTTGTCTTAATT-TAGACAAGAA
*
19947045 AACATGTTTGTCTCAATTTAGACAAGATAA
1 AACATGTTTGTCTTAATTTAGACAAG--AA
* * *
19947075 AATATTTTTGTCTTAATTAAAGACAAGA
1 AACATGTTTGTCTTAATT-TAGACAAGA
19947103 GTTGTCTTAA
Statistics
Matches: 126, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
28 36 0.29
29 40 0.32
30 32 0.25
31 18 0.14
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:19947099 original size:59 final size:57
Alignment explanation
Indices: 19946929--19947102 Score: 226
Period size: 59 Copynumber: 3.0 Consensus size: 57
19946919 TGATAGCTTT
* * *
19946929 AACATGTTTGTCTTAATTTAGACAAGAAAACAT-GTTTGGTCTTAATTTAGATAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAA-ATATTTTTGTCTTAATTTAGACAAGAA
*
19946986 AATATGTTTGTCTTAATTTAGGACAAGAAAAATATTTTTTGTCTT-ATTCTAGACAAGAA
1 AACATGTTTGTCTTAATTTA-GACAAGAAAAATA-TTTTTGTCTTAATT-TAGACAAGAA
* *
19947045 AACATGTTTGTCTCAATTTAGACAAGATAAAATATTTTTGTCTTAATTAAAGACAAGA
1 AACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTGTCTTAATT-TAGACAAGA
19947103 GTTGTCTTAA
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
57 21 0.20
58 30 0.29
59 52 0.50
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (57 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTGTCTTAATTTAGACAAGAA
Found at i:19947586 original size:55 final size:54
Alignment explanation
Indices: 19947502--19947610 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 54
19947492 AGTTTCAACC
19947502 ATCACTTCTCTCCTCCTCCTCCAAACTTTGTTGTATCTTTCTTCCTTTTTCCCA
1 ATCACTTCTCTCCTCCTCCTCCAAACTTTGTTGTATCTTTCTTCCTTTTTCCCA
19947556 NATCACTTCTCTCCTCCTCCTCCAAACTTTGTTGTATCTTTCTTCCTTTTTCCCA
1 -ATCACTTCTCTCCTCCTCCTCCAAACTTTGTTGTATCTTTCTTCCTTTTTCCCA
19947611 TTCTTGGCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.13, C:0.37, G:0.04, T:0.46
Consensus pattern (54 bp):
ATCACTTCTCTCCTCCTCCTCCAAACTTTGTTGTATCTTTCTTCCTTTTTCCCA
Found at i:19956329 original size:23 final size:23
Alignment explanation
Indices: 19956303--19956356 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
19956293 ACCAATCATG
19956303 CAATGCCTTATCAACCAGTCAAA
1 CAATGCCTTATCAACCAGTCAAA
* *
19956326 CAATGCCCTATCAACCAGTCACA
1 CAATGCCTTATCAACCAGTCAAA
19956349 CAATGCCT
1 CAATGCCT
19956357 AAAAACCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.35, G:0.09, T:0.20
Consensus pattern (23 bp):
CAATGCCTTATCAACCAGTCAAA
Found at i:19956390 original size:23 final size:22
Alignment explanation
Indices: 19956344--19956473 Score: 82
Period size: 23 Copynumber: 5.8 Consensus size: 22
19956334 TATCAACCAG
* *
19956344 TCACACAATGCCTAAAAACCAA
1 TCACGCAATGCCTAAAAACTAA
19956366 TCACGCAATGCCTTAAAAACTAA
1 TCACGCAATGCC-TAAAAACTAA
* * *
19956389 TCATGGAATGCTTAAAAACCT-A
1 TCACGCAATGCCTAAAAA-CTAA
* * * * *
19956411 TCATGTAATGCCCTGAAAACCAG
1 TCACGCAATG-CCTAAAAACTAA
* ** *
19956434 TCATGCAATGCCCTATCAACTAG
1 TCACGCAATG-CCTAAAAACTAA
*
19956457 TCACACAATGCCTAAAA
1 TCACGCAATGCCTAAAA
19956474 CCAGTCACAC
Statistics
Matches: 85, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
22 33 0.39
23 52 0.61
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.22
Consensus pattern (22 bp):
TCACGCAATGCCTAAAAACTAA
Found at i:19956399 original size:45 final size:45
Alignment explanation
Indices: 19956290--19956445 Score: 132
Period size: 45 Copynumber: 3.4 Consensus size: 45
19956280 ATAATGACTT
** * **
19956290 AAAACCAATCATGCAATGCCTTATCAACCAGTCAAACAATGCCCTA
1 AAAACCAATCATGCAATGCC-TAAAAACCAATCACGCAATGCCCTA
** * ** *
19956336 TCAACCAGTCACACAATGCCTAAAAACCAATCACGCAATGCCTTA
1 AAAACCAATCATGCAATGCCTAAAAACCAATCACGCAATGCCCTA
* * * * * * *
19956381 AAAACTAATCATGGAATGCTTAAAAACCTATCATGTAATGCCCTG
1 AAAACCAATCATGCAATGCCTAAAAACCAATCACGCAATGCCCTA
*
19956426 AAAACCAGTCATGCAATGCC
1 AAAACCAATCATGCAATGCC
19956446 CTATCAACTA
Statistics
Matches: 82, Mismatches: 28, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
45 67 0.82
46 15 0.18
ACGTcount: A:0.40, C:0.28, G:0.11, T:0.21
Consensus pattern (45 bp):
AAAACCAATCATGCAATGCCTAAAAACCAATCACGCAATGCCCTA
Found at i:19956495 original size:43 final size:45
Alignment explanation
Indices: 19956290--19956502 Score: 116
Period size: 45 Copynumber: 4.7 Consensus size: 45
19956280 ATAATGACTT
* * *
19956290 AAAACCAATCATGCAATGCCTTATCAACCAGTCAAACAATGCCCT-
1 AAAACCAGTCA-GCAATGCCCTATCAACCAGTCACACAATGCCCTG
* * ** * * * *
19956335 ATCAACCAGTCACACAATG-CCTAAAAACCAATCACGCAATGCCTTA
1 A-AAACCAGTCA-GCAATGCCCTATCAACCAGTCACACAATGCCCTG
* * * * ** ***
19956381 AAAACTAATCATGGAATG-CTTAAAAACCTA-TCATGTAATGCCCTG
1 AAAACCAGTCA-GCAATGCCCTATCAACC-AGTCACACAATGCCCTG
*
19956426 AAAACCAGTCATGCAATGCCCTATCAACTAGTCACACAATG-CCT-
1 AAAACCAGTCA-GCAATGCCCTATCAACCAGTCACACAATGCCCTG
*
19956470 AAAACCAGTCA-CACATGCCTTATCAACCAGTCA
1 AAAACCAGTCAGCA-ATGCCCTATCAACCAGTCA
19956503 TGCATGCCTT
Statistics
Matches: 128, Mismatches: 34, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
42 2 0.02
43 17 0.13
44 11 0.09
45 70 0.55
46 28 0.22
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (45 bp):
AAAACCAGTCAGCAATGCCCTATCAACCAGTCACACAATGCCCTG
Found at i:19956500 original size:22 final size:22
Alignment explanation
Indices: 19956428--19956518 Score: 89
Period size: 22 Copynumber: 4.1 Consensus size: 22
19956418 ATGCCCTGAA
*
19956428 AACCAGTCATGCA-ATGCCCTATC
1 AACCAGTCA--CACATGCCTTATC
* *
19956451 AACTAGTCACACAATGCC-TA-A
1 AACCAGTCACAC-ATGCCTTATC
19956472 AACCAGTCACACATGCCTTATC
1 AACCAGTCACACATGCCTTATC
**
19956494 AACCAGTCATGCATGCCTTATC
1 AACCAGTCACACATGCCTTATC
19956516 AAC
1 AAC
19956519 ATTCGACCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
20 5 0.09
21 15 0.26
22 25 0.43
23 13 0.22
ACGTcount: A:0.34, C:0.33, G:0.11, T:0.22
Consensus pattern (22 bp):
AACCAGTCACACATGCCTTATC
Found at i:19958775 original size:2 final size:2
Alignment explanation
Indices: 19958768--19958803 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19958758 AGATATTCAA
19958768 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
19958804 TCAACAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19959828 original size:31 final size:30
Alignment explanation
Indices: 19959793--19959852 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
19959783 GTTGGAAGGA
* * *
19959793 TCAAATTGTAAAGGATGAAAAGTTTCGAGGG
1 TCAAATGGTAAAGAAGGAAAAGTTT-GAGGG
*
19959824 TCAAATGGTAAATAAGGAAAAGTTTGAGG
1 TCAAATGGTAAAGAAGGAAAAGTTTGAGG
19959853 ACTTATGTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (30 bp):
TCAAATGGTAAAGAAGGAAAAGTTTGAGGG
Found at i:19960199 original size:31 final size:31
Alignment explanation
Indices: 19960161--19960233 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
19960151 AGTGAAGCTT
19960161 GTGCATGAAATGTGATTAGAGGAATAAGGTG
1 GTGCATGAAATGTGATTAGAGGAATAAGGTG
19960192 GTGCATGAAATGTGATTAGAGGAATAAGGTG
1 GTGCATGAAATGTGATTAGAGGAATAAGGTG
19960223 GTGCATGAAAT
1 GTGCATGAAAT
19960234 AAAGAATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.26
Consensus pattern (31 bp):
GTGCATGAAATGTGATTAGAGGAATAAGGTG
Found at i:19960464 original size:27 final size:28
Alignment explanation
Indices: 19960417--19960469 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
19960407 GCTTGGAAAA
* *
19960417 AATCGCACCTTTGAGAGAAAAGAAAGAG
1 AATCGCACCTTTGAAAGAAAAAAAAGAG
19960445 AATCG-ACC-TTGAAAGCAAAAAAAAG
1 AATCGCACCTTTGAAAG-AAAAAAAAG
19960470 GAAGAAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 6 0.27
27 11 0.50
28 5 0.23
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (28 bp):
AATCGCACCTTTGAAAGAAAAAAAAGAG
Found at i:19960496 original size:21 final size:21
Alignment explanation
Indices: 19960472--19960512 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19960462 AAAAAAAGGA
19960472 AGAAAGGAGAAAAAAGAAAAG
1 AGAAAGGAGAAAAAAGAAAAG
* *
19960493 AGAAAGGAGGAAGAAGAAAA
1 AGAAAGGAGAAAAAAGAAAA
19960513 AGGCTTGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (21 bp):
AGAAAGGAGAAAAAAGAAAAG
Found at i:19961481 original size:13 final size:13
Alignment explanation
Indices: 19961463--19961487 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19961453 GCTTTGTATT
19961463 TATATATGTAAAC
1 TATATATGTAAAC
19961476 TATATATGTAAA
1 TATATATGTAAA
19961488 GGGTTTTAAA
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:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
TATATATGTAAAC
Found at i:19963898 original size:61 final size:62
Alignment explanation
Indices: 19963823--19963994 Score: 240
Period size: 61 Copynumber: 2.8 Consensus size: 62
19963813 ACCCCATTTG
* **
19963823 CACTGTTCTCGCTGCAGCCAAATTGATTTTTACTGCAACGAGAAACTTT-T-TGCTTGGGAAT
1 CACTGTTCTCGCTGCAGCCAAATTGATTTTCACTGCAGTGAGAAACTTTCTAT-CTTGGGAAT
* *
19963884 CACTGTTCTCGCTGCAGCCAAATTGATTTTCGCTGCAGTGAGAAACTTTCTATCTTGGGAGT
1 CACTGTTCTCGCTGCAGCCAAATTGATTTTCACTGCAGTGAGAAACTTTCTATCTTGGGAAT
* * *
19963946 CACTATTCTCGTTGCAAGCCAAATTGATTCTCACTGCAGTGAGAAACTT
1 CACTGTTCTCGCTGC-AGCCAAATTGATTTTCACTGCAGTGAGAAACTT
19963995 GCTTACTTCG
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
61 45 0.45
62 22 0.22
63 32 0.32
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (62 bp):
CACTGTTCTCGCTGCAGCCAAATTGATTTTCACTGCAGTGAGAAACTTTCTATCTTGGGAAT
Found at i:19964812 original size:25 final size:25
Alignment explanation
Indices: 19964753--19964812 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
19964743 TCTGTGATAT
* *
19964753 ATATACATGGCAAGGTCACAAGATG
1 ATATACGTGGCAAGGCCACAAGATG
* *
19964778 ATATACGTGGCCAGGCCACAAGTTG
1 ATATACGTGGCAAGGCCACAAGATG
*
19964803 ATATATGTGG
1 ATATACGTGG
19964813 TTACGACCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (25 bp):
ATATACGTGGCAAGGCCACAAGATG
Found at i:19968566 original size:5 final size:5
Alignment explanation
Indices: 19968551--19968597 Score: 69
Period size: 5 Copynumber: 9.4 Consensus size: 5
19968541 AGAAAGAAAG
*
19968551 AAGAA ATGAA AAGAA AAGAA AAGAA AAGAA AAGAA CAAG-A AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA -AAGAA AAGAA AA
19968598 ATGGCATGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 3 0.08
5 32 0.84
6 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:19970789 original size:11 final size:11
Alignment explanation
Indices: 19970773--19970813 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
19970763 CAGAGCTTTG
19970773 GGTTTAAAGTT
1 GGTTTAAAGTT
19970784 GGTTTAAAGTT
1 GGTTTAAAGTT
*
19970795 GTTTTAAAGTT
1 GGTTTAAAGTT
*
19970806 GTTTTAAA
1 GGTTTAAA
19970814 ATTTACAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (11 bp):
GGTTTAAAGTT
Found at i:19975410 original size:34 final size:34
Alignment explanation
Indices: 19975349--19975457 Score: 125
Period size: 34 Copynumber: 3.2 Consensus size: 34
19975339 TTCTTTTGGT
*
19975349 TGCTGATTTTTGGAGGGAAAATAGAGCAGCTTAGC
1 TGCTGATTTTTGGA-AGAAAATAGAGCAGCTTAGC
19975384 TGCTGATTTTTGAGAAG-AAATAGAGCAGCTTAGC
1 TGCTGATTTTTG-GAAGAAAATAGAGCAGCTTAGC
* **
19975418 TGCCGA-TTTT-GAAGTCAATATGAGCAGCCTTAGC
1 TGCTGATTTTTGGAAGAAAATA-GAGCAG-CTTAGC
19975452 TGCTGA
1 TGCTGA
19975458 AAAATTATGG
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
31 4 0.06
32 4 0.06
33 10 0.15
34 33 0.50
35 13 0.20
36 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (34 bp):
TGCTGATTTTTGGAAGAAAATAGAGCAGCTTAGC
Found at i:19975608 original size:5 final size:5
Alignment explanation
Indices: 19975586--19975640 Score: 73
Period size: 5 Copynumber: 11.6 Consensus size: 5
19975576 ACGATGGAAG
19975586 AAAG- AAAG- AAAG- AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA ACAAG-
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA
19975633 AAAGA AAA
1 AAAGA AAA
19975641 ATGGCATGAC
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
4 15 0.31
5 30 0.62
6 3 0.06
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:19975686 original size:26 final size:26
Alignment explanation
Indices: 19975627--19975690 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
19975617 AAAAGAAAAG
*
19975627 AACAAGAAAGAAAAATGGCATGACTC
1 AACAAGAAAGAAAAATGGCATGACCC
*
19975653 AACAAGAAAGAAAAATGGGCATGGCCC
1 AACAAGAAAGAAAAAT-GGCATGACCC
*
19975680 AA-TAGAAAGAA
1 AACAAGAAAGAA
19975691 GTTGAGGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 24 0.71
27 10 0.29
ACGTcount: A:0.55, C:0.14, G:0.22, T:0.09
Consensus pattern (26 bp):
AACAAGAAAGAAAAATGGCATGACCC
Found at i:19978401 original size:24 final size:24
Alignment explanation
Indices: 19978358--19978418 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
19978348 TCATTTATTT
19978358 TTATTTCCTATTGAGCCATGCCCAC
1 TTATTT-CTATTGAGCCATGCCCAC
* * *
19978383 TTATTTCTATTGGGTCATGCCCAT
1 TTATTTCTATTGAGCCATGCCCAC
19978407 TTATTTTCTATT
1 TTA-TTTCTATT
19978419 TCTTTTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (24 bp):
TTATTTCTATTGAGCCATGCCCAC
Found at i:19978445 original size:10 final size:10
Alignment explanation
Indices: 19978417--19978452 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
19978407 TTATTTTCTA
19978417 TTTC-TTTTC
1 TTTCTTTTTC
19978426 TTTTCTTTTTC
1 -TTTCTTTTTC
19978437 TTTCTTTTTC
1 TTTCTTTTTC
19978447 TTTCTT
1 TTTCTT
19978453 CCACGTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:19978445 original size:16 final size:16
Alignment explanation
Indices: 19978410--19978449 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
19978400 TGCCCATTTA
*
19978410 TTTTCTATTTCTTTTC
1 TTTTCTTTTTCTTTTC
19978426 TTTTCTTTTTC-TTTC
1 TTTTCTTTTTCTTTTC
19978441 TTTTTCTTT
1 -TTTTCTTT
19978450 CTTCCACGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:19982056 original size:13 final size:13
Alignment explanation
Indices: 19982038--19982062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19982028 TTCCAGAAAA
19982038 TTTATAAAATCAT
1 TTTATAAAATCAT
19982051 TTTATAAAATCA
1 TTTATAAAATCA
19982063 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:20021917 original size:13 final size:13
Alignment explanation
Indices: 20021899--20021923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20021889 AAAGAAATTG
20021899 TGATTTTATAAAA
1 TGATTTTATAAAA
20021912 TGATTTTATAAA
1 TGATTTTATAAA
20021924 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:20023145 original size:15 final size:15
Alignment explanation
Indices: 20023121--20023166 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
20023111 AGATCAGAGA
*
20023121 TTTT-GATTTTGAAG
1 TTTTGGATTTTAAAG
20023135 TTTTGGATTTTAAAG
1 TTTTGGATTTTAAAG
20023150 TTTTAGG-TTTTAAAG
1 TTTT-GGATTTTAAAG
20023165 TT
1 TT
20023167 GTTTTAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 4 0.14
15 23 0.79
16 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.57
Consensus pattern (15 bp):
TTTTGGATTTTAAAG
Found at i:20023226 original size:14 final size:15
Alignment explanation
Indices: 20023201--20023233 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
20023191 TGCGTGGCGC
20023201 AAGTTAAGTTAAGTT
1 AAGTTAAGTTAAGTT
20023216 AAGTT-AGTTAAGTT
1 AAGTTAAGTTAAGTT
20023230 AAGT
1 AAGT
20023234 CAGGTTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (15 bp):
AAGTTAAGTTAAGTT
Found at i:20023240 original size:19 final size:19
Alignment explanation
Indices: 20023202--20023241 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20023192 GCGTGGCGCA
*
20023202 AGTTAAGTTAAGTTAAGTT
1 AGTTAAGTTAAGTCAAGTT
*
20023221 AGTTAAGTTAAGTCAGGTT
1 AGTTAAGTTAAGTCAAGTT
20023240 AG
1 AG
20023242 GTAGAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (19 bp):
AGTTAAGTTAAGTCAAGTT
Found at i:20023243 original size:5 final size:5
Alignment explanation
Indices: 20023201--20023233 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
20023191 TGCGTGGCGC
20023201 AAGTT AAGTT AAGTT AAGTT -AGTT AAGTT AAGT
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGT
20023234 CAGGTTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (5 bp):
AAGTT
Found at i:20029667 original size:5 final size:5
Alignment explanation
Indices: 20029660--20029699 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
20029650 CTATTCAATC
* *
20029660 TAACC TAACT TAACT TAACT TAACT TATCT TAACT TAACT
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT
20029700 GGACTTGGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (5 bp):
TAACT
Found at i:20029765 original size:15 final size:15
Alignment explanation
Indices: 20029745--20029791 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
20029735 TAAAAGAACC
20029745 TTAAAATCAAAAACT
1 TTAAAATCAAAAACT
* *
20029760 TTAAAATCCAAAGCT
1 TTAAAATCAAAAACT
* *
20029775 TTAAAACCAAAATCT
1 TTAAAATCAAAAACT
20029790 TT
1 TT
20029792 GATCTTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (15 bp):
TTAAAATCAAAAACT
Found at i:20031187 original size:13 final size:13
Alignment explanation
Indices: 20031169--20031193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20031159 TTTCAGAAAA
20031169 TTTATAAAATCAT
1 TTTATAAAATCAT
20031182 TTTATAAAATCA
1 TTTATAAAATCA
20031194 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:20033742 original size:27 final size:28
Alignment explanation
Indices: 20033712--20033764 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
20033702 TGTTCTGGTG
20033712 GTGG-AAAATTACAATTTTACCCCTAGA
1 GTGGCAAAATTACAATTTTACCCCTAGA
*
20033739 GTGGCAAAATTACCATTTTACCCCTA
1 GTGGCAAAATTACAATTTTACCCCTA
20033765 TACTCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (28 bp):
GTGGCAAAATTACAATTTTACCCCTAGA
Found at i:20033831 original size:19 final size:19
Alignment explanation
Indices: 20033807--20033844 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20033797 ACTTCTAAAC
20033807 CTCAAACCATACTCCAATA
1 CTCAAACCATACTCCAATA
* *
20033826 CTCAAATCATACTCTAATA
1 CTCAAACCATACTCCAATA
20033845 AGTCAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAACCATACTCCAATA
Found at i:20052769 original size:22 final size:22
Alignment explanation
Indices: 20052726--20052769 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20052716 TTTAAAACAA
* *
20052726 CTTTAAAACTAAAAACTTTGAT
1 CTTTAAAACCAAAAACTCTGAT
*
20052748 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
20052770 ACCAATCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:20055320 original size:28 final size:27
Alignment explanation
Indices: 20055269--20055321 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
20055259 TGTCCTGGTG
*
20055269 GTGGAAAATTACAATTTTGCCCCTAGA
1 GTGGAAAATTACAATTTTACCCCTAGA
* *
20055296 GTGGCAAAATTACCATTTTATCCCTA
1 GTGG-AAAATTACAATTTTACCCCTA
20055322 TACTCCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (27 bp):
GTGGAAAATTACAATTTTACCCCTAGA
Found at i:20077294 original size:20 final size:20
Alignment explanation
Indices: 20077249--20077286 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
20077239 TTTTGGCCCC
20077249 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
20077269 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
20077287 AGATTTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:20094544 original size:20 final size:20
Alignment explanation
Indices: 20094519--20094556 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
20094509 TTACAATTAA
20094519 GCCTTAATAAAACAAAACAT
1 GCCTTAATAAAACAAAACAT
20094539 GCCTTAATAAAACAAAAC
1 GCCTTAATAAAACAAAAC
20094557 CTATCTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.18
Consensus pattern (20 bp):
GCCTTAATAAAACAAAACAT
Found at i:20098003 original size:13 final size:13
Alignment explanation
Indices: 20097985--20098009 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20097975 TTTCAGAAAA
20097985 TTTATAAAATCAT
1 TTTATAAAATCAT
20097998 TTTATAAAATCA
1 TTTATAAAATCA
20098010 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:20102176 original size:28 final size:28
Alignment explanation
Indices: 20102144--20102208 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
20102134 TAACTTACCA
*
20102144 TTGGGCTTTTTTCATTTCTTTATGACCT
1 TTGGGCCTTTTTCATTTCTTTATGACCT
20102172 TTGGGCCTTTTTCATTTCTTTATGACCT
1 TTGGGCCTTTTTCATTTCTTTATGACCT
20102200 TTGGGCCTT
1 TTGGGCCTT
20102209 CTCCGTGGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.09, C:0.20, G:0.17, T:0.54
Consensus pattern (28 bp):
TTGGGCCTTTTTCATTTCTTTATGACCT
Found at i:20102266 original size:32 final size:32
Alignment explanation
Indices: 20102228--20102293 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
20102218 GTTCTCCATT
* *
20102228 TTTCCTATTTGGGCTAAGCCCGTTTATTTT-TA
1 TTTCCTA-TTGGGCCAAGCCCATTTATTTTCTA
*
20102260 TTTCCTATTGGGCCATGCCCATTTATTTTCTA
1 TTTCCTATTGGGCCAAGCCCATTTATTTTCTA
20102292 TT
1 TT
20102294 GGGCCATGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.15, C:0.21, G:0.14, T:0.50
Consensus pattern (32 bp):
TTTCCTATTGGGCCAAGCCCATTTATTTTCTA
Found at i:20102285 original size:31 final size:30
Alignment explanation
Indices: 20102226--20102317 Score: 104
Period size: 25 Copynumber: 3.2 Consensus size: 30
20102216 GGGTTCTCCA
* * *
20102226 TTTTTCCTATTTGGGCTAAGCCCGTTTATTT
1 TTTTTCCTA-TTGGGCCATGCCCATTTATTT
20102257 TTATTTCCTATTGGGCCATGCCCATTTA---
1 TT-TTTCCTATTGGGCCATGCCCATTTATTT
20102285 -TTTT-CTATTGGGCCATGCCCATTTATTT
1 TTTTTCCTATTGGGCCATGCCCATTTATTT
20102313 TTTTT
1 TTTTT
20102318 TTCTTTTCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
25 21 0.40
26 3 0.06
27 1 0.02
29 4 0.08
31 17 0.32
32 7 0.13
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.51
Consensus pattern (30 bp):
TTTTTCCTATTGGGCCATGCCCATTTATTT
Found at i:20102314 original size:26 final size:25
Alignment explanation
Indices: 20102256--20102313 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
20102246 CCCGTTTATT
*
20102256 TTTATTTCCTATTGGGCCATGCCCA
1 TTTATTTTCTATTGGGCCATGCCCA
20102281 TTTATTTTCTATTGGGCCATGCCCA
1 TTTATTTTCTATTGGGCCATGCCCA
20102306 TTTATTTT
1 TTTATTTT
20102314 TTTTTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (25 bp):
TTTATTTTCTATTGGGCCATGCCCA
Found at i:20102329 original size:10 final size:9
Alignment explanation
Indices: 20102312--20102346 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
20102302 CCCATTTATT
20102312 TTTTTTTTC
1 TTTTTTTTC
20102321 TTTTCTTTTC
1 TTTT-TTTTC
20102331 TTTTTCTTTC
1 TTTTT-TTTC
20102341 TTTTTT
1 TTTTTT
20102347 CTCTCTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:20102334 original size:16 final size:15
Alignment explanation
Indices: 20102310--20102344 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
20102300 TGCCCATTTA
*
20102310 TTTTTTTTTTCTTTTC
1 TTTTCTTTTTC-TTTC
20102326 TTTTCTTTTTCTTTC
1 TTTTCTTTTTCTTTC
20102341 TTTT
1 TTTT
20102345 TTCTCTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTCTTTTTCTTTC
Found at i:20102526 original size:34 final size:34
Alignment explanation
Indices: 20102481--20102555 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
20102471 AATGCTGTCC
* *
20102481 AATTTTCCTGCACAAATTGGTAGCAAACAGCTCT
1 AATTTTCCTGCACAAATTGGTAACAAACAGCTCA
*
20102515 AATTTTTCTGCACAAATTGGTAACAAACAGCTCA
1 AATTTTCCTGCACAAATTGGTAACAAACAGCTCA
20102549 AATTTTC
1 AATTTTC
20102556 AACAGCCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (34 bp):
AATTTTCCTGCACAAATTGGTAACAAACAGCTCA
Found at i:20102667 original size:25 final size:25
Alignment explanation
Indices: 20102620--20102667 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
20102610 AAAAATCAGC
* *
20102620 TTTCTTACCTCAAAATTTTCAGCTT
1 TTTCTTACCTCAAAAATTGCAGCTT
20102645 TTTCTT-CCTCCAAAAATTGCAGC
1 TTTCTTACCT-CAAAAATTGCAGC
20102668 AAAAAGCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.42
Consensus pattern (25 bp):
TTTCTTACCTCAAAAATTGCAGCTT
Found at i:20103217 original size:21 final size:21
Alignment explanation
Indices: 20103192--20103231 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
20103182 TTTGTTCACC
*
20103192 TATATTTATAT-TA-TTATTA
1 TATATATATATATATTTATTA
20103211 TATATATATATATATTTATTA
1 TATATATATATATATTTATTA
20103232 ACTTCAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATATATATATATTTATTA
Found at i:20112100 original size:77 final size:77
Alignment explanation
Indices: 20111975--20112139 Score: 219
Period size: 77 Copynumber: 2.1 Consensus size: 77
20111965 AAATGCCATC
* * *
20111975 TATTTTAATTTTGGGTGATTCATAAAAAATATAAAATTTTTTCCTACTTTAAAAGTAATTGC-TA
1 TATTTTAATTTTGGGTGATTCATAAAAAATATAAAACTGTTTCCTACTTTAAAAGAAATT-CATA
*
20112039 AAATTAATAATAGA
65 AAATTAAGAATA-A
* *
20112053 -ATTTTAATTTTGGGTGATTCATAAAGAATA-AGAAACTGTTTCTTACTTTAAAAGAAATTCATA
1 TATTTTAATTTTGGGTGATTCATAAAAAATATA-AAACTGTTTCCTACTTTAAAAGAAATTCATA
*
20112116 AAATTAAGGATAA
65 AAATTAAGAATAA
20112129 TATTTTAATTT
1 TATTTTAATTT
20112140 GAGAAATTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
76 3 0.04
77 74 0.96
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (77 bp):
TATTTTAATTTTGGGTGATTCATAAAAAATATAAAACTGTTTCCTACTTTAAAAGAAATTCATAA
AATTAAGAATAA
Found at i:20113271 original size:22 final size:21
Alignment explanation
Indices: 20113243--20113285 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
20113233 ATCCGCCCAT
20113243 GAAAGAAAAGTAA-AGAGAAAAG
1 GAAAGAAAA-TAATAGA-AAAAG
20113265 GAAAGAAAATAATAGAAAAAG
1 GAAAGAAAATAATAGAAAAAG
20113286 AATGACTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (21 bp):
GAAAGAAAATAATAGAAAAAG
Found at i:20114903 original size:25 final size:25
Alignment explanation
Indices: 20114859--20114916 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
20114849 GCCACAGTCT
20114859 ATGATAATACATGGCAAGGCCACAAG
1 ATGAT-ATACATGGCAAGGCCACAAG
* *
20114885 ATGATATACGTGGCTAGGCCACAAG
1 ATGATATACATGGCAAGGCCACAAG
20114910 -TGATATA
1 ATGATATA
20114917 TGCAGTTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.23
25 18 0.60
26 5 0.17
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (25 bp):
ATGATATACATGGCAAGGCCACAAG
Found at i:20116117 original size:15 final size:15
Alignment explanation
Indices: 20116092--20116134 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
20116082 AAAAGAAGTT
20116092 TTAATAATGGAAAGAA
1 TTAA-AATGGAAAGAA
**
20116108 TTAAAATGGAAAGTC
1 TTAAAATGGAAAGAA
*
20116123 TTAAAAAGGAAA
1 TTAAAATGGAAA
20116135 ATTTTATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23
Consensus pattern (15 bp):
TTAAAATGGAAAGAA
Found at i:20117783 original size:17 final size:16
Alignment explanation
Indices: 20117761--20117816 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
20117751 AATTGAATTA
20117761 TAATTTTATTAATTAAT
1 TAATTTTA-TAATTAAT
*
20117778 TAATTTAATGAATTATAT
1 TAATTTTAT-AATTA-AT
*
20117796 TCAATTTTA-AATTAAC
1 T-AATTTTATAATTAAT
20117812 TAATT
1 TAATT
20117817 CAATTCCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 17 0.52
18 3 0.09
19 6 0.18
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TAATTTTATAATTAAT
Found at i:20123461 original size:16 final size:15
Alignment explanation
Indices: 20123440--20123482 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
20123430 TAGGTAAAAA
*
20123440 AAGAAAGGAAAAGGG
1 AAGAAAGGAAAAGAG
*
20123455 CAAGAAAAGAAAAAGAG
1 -AAG-AAAGGAAAAGAG
20123472 AAGAAAGGAAA
1 AAGAAAGGAAA
20123483 GAGTTGTCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 6 0.26
17 10 0.43
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGAAAGGAAAAGAG
Found at i:20127827 original size:31 final size:31
Alignment explanation
Indices: 20127789--20127850 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
20127779 TAGGTAGCCA
* *
20127789 ACTAGTTGATATTAAGAAATCTTAGAACATT
1 ACTAGTTGATATTAAGAAATCTAAAAACATT
*
20127820 ACTAGTTGGTATTAAGAAATCTAAAAACATT
1 ACTAGTTGATATTAAGAAATCTAAAAACATT
20127851 CTTTTATAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (31 bp):
ACTAGTTGATATTAAGAAATCTAAAAACATT
Found at i:20129324 original size:2 final size:2
Alignment explanation
Indices: 20129317--20129342 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20129307 TATAACTAAG
20129317 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
20129343 TTATAGAAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20143062 original size:2 final size:2
Alignment explanation
Indices: 20143055--20143101 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
20143045 AAACATAAGA
20143055 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
20143097 AT AT A
1 AT AT A
20143102 AACAATTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20146389 original size:28 final size:28
Alignment explanation
Indices: 20146358--20146446 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
20146348 ATAAAGCGAT
*
20146358 AACCCATGGTTTTAATAGGTTCACCACA
1 AACCCATGGTTTTAATAGGATCACCACA
* * * *
20146386 AA-CCATAGTTTT--TCCGAGCTCATCACA
1 AACCCATGGTTTTAAT-AG-GATCACCACA
* *
20146413 AACTCATGGTTTTAATGGGATCACCACA
1 AACCCATGGTTTTAATAGGATCACCACA
20146441 AACCCA
1 AACCCA
20146447 CACACTAACT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 19 0.41
28 23 0.50
29 1 0.02
30 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (28 bp):
AACCCATGGTTTTAATAGGATCACCACA
Found at i:20146391 original size:27 final size:27
Alignment explanation
Indices: 20146361--20146444 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
20146351 AAGCGATAAC
*
20146361 CCATGGTTTTAATAGGTTCACCACAAA
1 CCATGGTTTTAATAGGATCACCACAAA
* * * *
20146388 CCATAGTTTT--TCCGAGCTCATCACAAA
1 CCATGGTTTTAAT-AG-GATCACCACAAA
*
20146415 CTCATGGTTTTAATGGGATCACCACAAA
1 C-CATGGTTTTAATAGGATCACCACAAA
20146443 CC
1 CC
20146445 CACACACTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 21 0.48
28 19 0.43
29 1 0.02
30 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (27 bp):
CCATGGTTTTAATAGGATCACCACAAA
Found at i:20150167 original size:33 final size:33
Alignment explanation
Indices: 20150130--20150195 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
20150120 AGGAATCAAT
20150130 TGTGAAATAATCAATTAAGCACAATCATAAAAC
1 TGTGAAATAATCAATTAAGCACAATCATAAAAC
20150163 TGTGAAATAATCAATTAAGCACAATCATAAAAC
1 TGTGAAATAATCAATTAAGCACAATCATAAAAC
20150196 ATATTCCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (33 bp):
TGTGAAATAATCAATTAAGCACAATCATAAAAC
Found at i:20166242 original size:43 final size:43
Alignment explanation
Indices: 20166194--20166308 Score: 169
Period size: 43 Copynumber: 2.7 Consensus size: 43
20166184 CAGCTCATGT
* * *
20166194 GCACTCCCTACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
1 GCACTCCCTACTCGCACATAGCCGGGTCAACATCGACTTATGC
* * *
20166237 GCACTCCCTACTCGCATATAGCCGGATCAACATCGACTTATGT
1 GCACTCCCTACTCGCACATAGCCGGGTCAACATCGACTTATGC
20166280 GCACTCCC-ACTCGCACATAGCCGGGTCAA
1 GCACTCCCTACTCGCACATAGCCGGGTCAA
20166309 TATCATCATA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 19 0.30
43 45 0.70
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.22
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAGCCGGGTCAACATCGACTTATGC
Found at i:20167407 original size:23 final size:25
Alignment explanation
Indices: 20167380--20167425 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
20167370 TCATCATTTT
*
20167380 TATTTCCTTC-TTCATTT-TACCCA
1 TATTTCCATCATTCATTTATACCCA
*
20167403 TATTTTCATCATTCATTTATACC
1 TATTTCCATCATTCATTTATACC
20167426 TTAGGCCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 7 0.37
25 4 0.21
ACGTcount: A:0.22, C:0.26, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTCCATCATTCATTTATACCCA
Found at i:20169273 original size:42 final size:42
Alignment explanation
Indices: 20169209--20169350 Score: 212
Period size: 42 Copynumber: 3.4 Consensus size: 42
20169199 ACGGCTTATG
* *
20169209 CGCATATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACT
1 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
* * * *
20169251 CACACATAGCCGGGTTAGCAACGACTTATGTGCACTCTTACT
1 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
* *
20169293 CGCACATAGCCAGGTCAGCAACTGCTTATGTGCACTCCTACT
1 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
20169335 CGCACATAGCCGGGTC
1 CGCACATAGCCGGGTC
20169351 CAAATCAACA
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (42 bp):
CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
Found at i:20173835 original size:58 final size:58
Alignment explanation
Indices: 20173771--20173882 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
20173761 TATCTTTGCA
* *
20173771 TGCATAACATTTATTAAATCACATAAAATAAATCAATCACATGCATATTACTTTACAT
1 TGCATAACATTTATTAAATCACATAAAATAAATCAATCACATGCAAACTACTTTACAT
** * *
20173829 TGCATAACATTTATTAAATTGCATATAATAAATCTATCACATGCAAACTACTTT
1 TGCATAACATTTATTAAATCACATAAAATAAATCAATCACATGCAAACTACTTT
20173883 GGATGATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (58 bp):
TGCATAACATTTATTAAATCACATAAAATAAATCAATCACATGCAAACTACTTTACAT
Found at i:20175254 original size:33 final size:34
Alignment explanation
Indices: 20175216--20175296 Score: 85
Period size: 36 Copynumber: 2.4 Consensus size: 34
20175206 TGTTGTTTTG
*
20175216 GCTGCTAATTTTTGGAAGG-AAA-AGTGCAGCTTA
1 GCTGCTAATTTTTGG-AGGAAAATAGAGCAGCTTA
* *
20175249 GCTGCTGATTTTTTTGAGGATAAATAGAGCAGCTTA
1 GCTGCT-AATTTTTGGAGGA-AAATAGAGCAGCTTA
*
20175285 GCTGCTGATTTT
1 GCTGCTAATTTT
20175297 GAAGCCAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 9 0.23
34 7 0.18
35 7 0.18
36 16 0.41
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (34 bp):
GCTGCTAATTTTTGGAGGAAAATAGAGCAGCTTA
Found at i:20175478 original size:5 final size:5
Alignment explanation
Indices: 20175464--20175504 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
20175454 AGAAAGGGAG
20175464 AAAG- AAAGA AAAGA AAAGA AAAGA ACAAG- AAAGA AAA-A AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA AAAGA AAAGA AAA
20175505 ATGGGCATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 11 0.32
5 20 0.59
6 3 0.09
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:20175524 original size:27 final size:27
Alignment explanation
Indices: 20175494--20175546 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
20175484 AAGAACAAGA
20175494 AAGAAAAAAAAATGGGCATGACCCAAC
1 AAGAAAAAAAAATGGGCATGACCCAAC
* * *
20175521 AAGAAAGAAACATGGGCATGGCCCAA
1 AAGAAAAAAAAATGGGCATGACCCAA
20175547 TAGAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.51, C:0.19, G:0.23, T:0.08
Consensus pattern (27 bp):
AAGAAAAAAAAATGGGCATGACCCAAC
Found at i:20184767 original size:19 final size:19
Alignment explanation
Indices: 20184743--20184780 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20184733 ACTTCTTAAC
20184743 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
20184762 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
20184781 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:20189120 original size:189 final size:190
Alignment explanation
Indices: 20188854--20189233 Score: 638
Period size: 190 Copynumber: 2.0 Consensus size: 190
20188844 ACACTTTCAA
* * * *
20188854 TTTAATTCAAATTGCAAACTTTTGTGTGTGACCCATTAGATTCCTATCATGTTGGCAATGGAATT
1 TTTAATCCAAATTGCAAACTTTTGTGTGTGACACATTAGATTCCTAACATGTTGGCAATGAAATT
* *
20188919 GATTTGTAATATTATTAATTAATTAA-TTAAATGAATCATATTCAATTTTAAATAAACTAATTCA
66 GAATTATAATATTATTAATTAATTAATTTAAATGAATCATATTCAATTTTAAATAAACTAATTCA
* * *
20188983 ATTCCATAGACCCTGATTGGCATCTAGCAATGCATCATGGCCACCCAATTGTTAGGAGAG
131 ATTCCATAGACCATGATTGGCATCTAGCAATGCATCATGGCCACCCAATTATTAAGAGAG
*
20189043 NTTTAATCCAAATTGC-AACTTTTGTGTGTGACACATTAGGTTCCTAACATGTTGGCAATGAAAT
1 -TTTAATCCAAATTGCAAACTTTTGTGTGTGACACATTAGATTCCTAACATGTTGGCAATGAAAT
*
20189107 TGAATTATAATATTATTAATTAATTAATTTAAATGAATCATATTCAATTTTAAATTAACTAATTC
65 TGAATTATAATATTATTAATTAATTAATTTAAATGAATCATATTCAATTTTAAATAAACTAATTC
20189172 AATTCCATAGACCATGATTGGCATCTAGCAATGCATCATGGCCACCCAATTATTAAGAGAG
130 AATTCCATAGACCATGATTGGCATCTAGCAATGCATCATGGCCACCCAATTATTAAGAGAG
20189233 T
1 T
20189234 CAAAGGATTC
Statistics
Matches: 178, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
189 70 0.39
190 108 0.61
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (190 bp):
TTTAATCCAAATTGCAAACTTTTGTGTGTGACACATTAGATTCCTAACATGTTGGCAATGAAATT
GAATTATAATATTATTAATTAATTAATTTAAATGAATCATATTCAATTTTAAATAAACTAATTCA
ATTCCATAGACCATGATTGGCATCTAGCAATGCATCATGGCCACCCAATTATTAAGAGAG
Found at i:20201600 original size:20 final size:21
Alignment explanation
Indices: 20201575--20201614 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20201565 CTTTTCCAAG
*
20201575 AATGTATCGATACAT-TTGCT
1 AATGTATCAATACATCTTGCT
20201595 AATGTATCAATACATCTTGC
1 AATGTATCAATACATCTTGC
20201615 CCAAATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
AATGTATCAATACATCTTGCT
Found at i:20202055 original size:27 final size:27
Alignment explanation
Indices: 20202022--20202082 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
20202012 ATGTGCCAAA
*
20202022 CACATGCATAATAATATTTTGAGCCTT
1 CACATGCACAATAATATTTTGAGCCTT
*
20202049 CTCATGCACAATAATATTTTGAGCCTT
1 CACATGCACAATAATATTTTGAGCCTT
20202076 CACATGC
1 CACATGC
20202083 TTATATATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (27 bp):
CACATGCACAATAATATTTTGAGCCTT
Found at i:20204557 original size:43 final size:42
Alignment explanation
Indices: 20204509--20204631 Score: 160
Period size: 43 Copynumber: 2.9 Consensus size: 42
20204499 ATTATGTGAT
* *
20204509 GATGATGACCTCGCTATGTGCAAGTAGGGAGTGCACATGAGCC
1 GATGATGA-CTCGATATGTGCGAGTAGGGAGTGCACATGAGCC
* *
20204552 GATGATGACTCTGTTATGTGCGAGTAGGGAGTGCACATGAGCT
1 GATGATGACTC-GATATGTGCGAGTAGGGAGTGCACATGAGCC
* *
20204595 GATGATG--TTGAAATGTGCGAGTAGGGAGTGCACATGA
1 GATGATGACTCGATATGTGCGAGTAGGGAGTGCACATGA
20204632 TGATGAATGA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
40 26 0.36
41 1 0.01
42 3 0.04
43 43 0.59
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (42 bp):
GATGATGACTCGATATGTGCGAGTAGGGAGTGCACATGAGCC
Found at i:20212227 original size:14 final size:14
Alignment explanation
Indices: 20212208--20212250 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
20212198 TATATGCATG
*
20212208 TATATATGTATACA
1 TATATATATATACA
*
20212222 TATATACATATACA
1 TATATATATATACA
*
20212236 TATACATATATACA
1 TATATATATATACA
20212250 T
1 T
20212251 GCATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (14 bp):
TATATATATATACA
Found at i:20213750 original size:49 final size:49
Alignment explanation
Indices: 20213696--20213848 Score: 171
Period size: 49 Copynumber: 3.1 Consensus size: 49
20213686 ATGTTCCGTC
*** * * * *
20213696 CGTGGATGGTTTTGGATGATGCTATGATGCGAGATATATATATTCCTTT
1 CGTGGATGGTTCCAGATGATGATATGATGTGAGATATGTATATTCCATT
* * *
20213745 CGTGGATGGTTCCAGACGATGATTTGATGTGAGATATGTATATTCCGTT
1 CGTGGATGGTTCCAGATGATGATATGATGTGAGATATGTATATTCCATT
** * * *
20213794 CGTAAATGATTCCAGATGATGATATGATGTGAGATATGTATGTGCCATT
1 CGTGGATGGTTCCAGATGATGATATGATGTGAGATATGTATATTCCATT
20213843 CGTGGA
1 CGTGGA
20213849 GGATTTTTGG
Statistics
Matches: 85, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 85 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (49 bp):
CGTGGATGGTTCCAGATGATGATATGATGTGAGATATGTATATTCCATT
Found at i:20216854 original size:10 final size:11
Alignment explanation
Indices: 20216836--20216872 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
20216826 GTGGCTGAAA
20216836 TTGATGATATT
1 TTGATGATATT
20216847 TT-ATGATATT
1 TTGATGATATT
*
20216857 TTGGTGATA-T
1 TTGATGATATT
20216867 TTGATG
1 TTGATG
20216873 TTTGGTGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (11 bp):
TTGATGATATT
Found at i:20222705 original size:27 final size:27
Alignment explanation
Indices: 20222675--20222746 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
20222665 GGATCAAGTG
* *
20222675 ATAACCCATGGTTTTAATGGGTTCACC
1 ATAACCCATGGTTTTAATGAGCTCACC
* **
20222702 ATAAATCCATGGTTTTTTTGAGCTCACC
1 AT-AACCCATGGTTTTAATGAGCTCACC
*
20222730 ACAATCCCATGGTTTTA
1 ATAA-CCCATGGTTTTA
20222747 GCATAATCAC
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 4 0.11
28 31 0.89
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (27 bp):
ATAACCCATGGTTTTAATGAGCTCACC
Found at i:20222756 original size:28 final size:28
Alignment explanation
Indices: 20222725--20222795 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
20222715 TTTTTTGAGC
* * *
20222725 TCACCACAATCCCATGGTTTTAGCATAA
1 TCACCACAAACCCATGGTTTTAACAGAA
20222753 TCACCACAAACCCATGGTTTTAACAGAA
1 TCACCACAAACCCATGGTTTTAACAGAA
20222781 TCACCACAAACCCAT
1 TCACCACAAACCCAT
20222796 ATACTAACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.37, C:0.32, G:0.08, T:0.23
Consensus pattern (28 bp):
TCACCACAAACCCATGGTTTTAACAGAA
Found at i:20226680 original size:58 final size:57
Alignment explanation
Indices: 20226609--20226717 Score: 173
Period size: 58 Copynumber: 1.9 Consensus size: 57
20226599 AAGTAGTTTT
20226609 CATGTGATAGATTTATCTTATGCAATTTAATAAATGCTATGCAATACAAAATAGTAAG
1 CATGTGATAGATTTATCTTATGCAATTTAATAAATGCTATG-AATACAAAATAGTAAG
* * * *
20226667 CATGTGATTGATTTATTTTATGCGATTTAATAAATGCTATGAATGCAAAAT
1 CATGTGATAGATTTATCTTATGCAATTTAATAAATGCTATGAATACAAAAT
20226718 GAGACCTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 9 0.19
58 38 0.81
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.38
Consensus pattern (57 bp):
CATGTGATAGATTTATCTTATGCAATTTAATAAATGCTATGAATACAAAATAGTAAG
Found at i:20233343 original size:38 final size:38
Alignment explanation
Indices: 20233185--20233343 Score: 221
Period size: 38 Copynumber: 4.2 Consensus size: 38
20233175 ATAGCCAGAG
*
20233185 TCATCATGTACATCCCCCCACATCGTGCACAA-CTAATA
1 TCATCATGTGCATCCCCCCACATCGTGCACAAGC-AATA
* **
20233223 CCATTGTGTGCATCCCCCCACATCGTGCACAAGCAATA
1 TCATCATGTGCATCCCCCCACATCGTGCACAAGCAATA
* * * *
20233261 TCATCGTGTGTATCCCCCCACATCGTGCACAAGAAATT
1 TCATCATGTGCATCCCCCCACATCGTGCACAAGCAATA
*
20233299 TTATCATGTGCATCCCCCCACATCGTGCACAAGCAATA
1 TCATCATGTGCATCCCCCCACATCGTGCACAAGCAATA
20233337 TCATCAT
1 TCATCAT
20233344 CCACACACCC
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 104 0.99
39 1 0.01
ACGTcount: A:0.28, C:0.35, G:0.13, T:0.25
Consensus pattern (38 bp):
TCATCATGTGCATCCCCCCACATCGTGCACAAGCAATA
Found at i:20233451 original size:2 final size:2
Alignment explanation
Indices: 20233444--20233472 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20233434 AATGTACAAC
20233444 AT 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 AT A
20233473 CCAACATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20235796 original size:15 final size:15
Alignment explanation
Indices: 20235776--20235814 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20235766 TTGAAATAAA
*
20235776 ACTTTCCTTTTTAAG
1 ACTTTCCATTTTAAG
*
20235791 ACTTTCCATTTTAAT
1 ACTTTCCATTTTAAG
*
20235806 TCTTTCCAT
1 ACTTTCCAT
20235815 AATTAAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.54
Consensus pattern (15 bp):
ACTTTCCATTTTAAG
Found at i:20236100 original size:69 final size:70
Alignment explanation
Indices: 20236027--20236213 Score: 223
Period size: 80 Copynumber: 2.5 Consensus size: 70
20236017 ATCACATAAC
* ** *
20236027 TTTAGGAATTTCTTTTAAAGTAGGAAACTATTTCCTATGAATTTCC-CAAATTAAAATACTATCC
1 TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTATGAATCACCTAAAATTAAAATACTATCC
20236091 TTAAT
66 TTAAT
20236096 TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTATTTTTTTTTATGAATCACCTAAAATTAA
1 TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCC----------TATGAATCACCTAAAATTAA
*
20236161 AATTCTATCCTTAAT
56 AATACTATCCTTAAT
*
20236176 TTTAGGAATTGCTTTTAAAGTAGGAAACAATTTCCTAT
1 TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTAT
20236214 TTTTTATGGA
Statistics
Matches: 101, Mismatches: 6, Indels: 21
0.79 0.05 0.16
Matches are distributed among these distances:
69 34 0.34
70 3 0.03
79 9 0.09
80 55 0.54
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (70 bp):
TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTATGAATCACCTAAAATTAAAATACTATCC
TTAAT
Found at i:20240427 original size:58 final size:57
Alignment explanation
Indices: 20240337--20240451 Score: 203
Period size: 58 Copynumber: 2.0 Consensus size: 57
20240327 CACCCGGCTC
20240337 ATGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCGTGTGCATCCCCCCACA
1 ATGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCGTGTGCATCCCCCCACA
* *
20240394 NATGTACATCCCCTCACATCGTGCACATAGCCGGCACCATCGTGTGCATCCCTCCACA
1 -ATGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCGTGTGCATCCCCCCACA
20240452 TTGTGCGCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (57 bp):
ATGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCGTGTGCATCCCCCCACA
Found at i:20246455 original size:35 final size:36
Alignment explanation
Indices: 20246348--20246498 Score: 189
Period size: 36 Copynumber: 4.2 Consensus size: 36
20246338 TTTATACCCT
*
20246348 CTTTTTCATGGGATCAAGCAATAACCCTTACACTTG
1 CTTTTTAATGGGATCAAGCAATAACCCTTACACTTG
20246384 -TGTTTTAATGGGATCAAGCAATAACCCTTACACTTG
1 CT-TTTTAATGGGATCAAGCAATAACCCTTACACTTG
* * *
20246420 CTTTTTAAAGGGATCAAACAATAA-CCTTATACTTG
1 CTTTTTAATGGGATCAAGCAATAACCCTTACACTTG
* * ** **
20246455 CTTTTTCAGGGGATCAAGTGATAACCCTTACACCAG
1 CTTTTTAATGGGATCAAGCAATAACCCTTACACTTG
20246491 CTTTTTAA
1 CTTTTTAA
20246499 CAAGATCAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
35 30 0.30
36 68 0.69
37 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (36 bp):
CTTTTTAATGGGATCAAGCAATAACCCTTACACTTG
Found at i:20246479 original size:71 final size:72
Alignment explanation
Indices: 20246348--20246498 Score: 189
Period size: 71 Copynumber: 2.1 Consensus size: 72
20246338 TTTATACCCT
* * * *
20246348 CTTTTTCATGGGATCAAGCAATAACCCTTACACTTGTGTTTTAATGGGATCAAGCAATAACCCTT
1 CTTTTTAAAGGGATCAAACAATAACCCTTACACTTGTGTTTTAAGGGGATCAAGCAATAACCCTT
**
20246413 ACACTTG
66 ACACCAG
* * **
20246420 CTTTTTAAAGGGATCAAACAATAA-CCTTATACTTGCT-TTTTCAGGGGATCAAGTGATAACCCT
1 CTTTTTAAAGGGATCAAACAATAACCCTTACACTTG-TGTTTTAAGGGGATCAAGCAATAACCCT
20246483 TACACCAG
65 TACACCAG
20246491 CTTTTTAA
1 CTTTTTAA
20246499 CAAGATCAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
71 46 0.68
72 22 0.32
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (72 bp):
CTTTTTAAAGGGATCAAACAATAACCCTTACACTTGTGTTTTAAGGGGATCAAGCAATAACCCTT
ACACCAG
Found at i:20246903 original size:35 final size:35
Alignment explanation
Indices: 20246864--20247040 Score: 124
Period size: 35 Copynumber: 5.2 Consensus size: 35
20246854 CCAAGCTTAG
*
20246864 CCAAAACCTTTCACAATGGTTTTT-ACCAGGATCAA
1 CCAAAACCTTTCACAATGGTTTTTCA-AAGGATCAA
*
20246899 CCAAAACC---CA-AAGTGGTTTTTCAAAGGCTCAA
1 CCAAAACCTTTCACAA-TGGTTTTTCAAAGGATCAA
* * *
20246931 CCACAACCTTTCACAATGG-TTTTCAACGGCCTCAA
1 CCAAAACCTTTCACAATGGTTTTTCAAAGG-ATCAA
* *
20246966 CCAAAACC---CA-AAGTGGTTTTTCAGAGGCTCAA
1 CCAAAACCTTTCACAA-TGGTTTTTCAAAGGATCAA
* * * **
20246998 CCATAACC-TACAACAGTGGTTTTTCACGGGATCAA
1 CCAAAACCTTTC-ACAATGGTTTTTCAAAGGATCAA
20247033 CCAAAACC
1 CCAAAACC
20247041 CAACAACTAA
Statistics
Matches: 116, Mismatches: 13, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
31 4 0.03
32 41 0.35
33 9 0.08
34 10 0.09
35 49 0.42
36 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (35 bp):
CCAAAACCTTTCACAATGGTTTTTCAAAGGATCAA
Found at i:20246931 original size:32 final size:32
Alignment explanation
Indices: 20246895--20247043 Score: 149
Period size: 35 Copynumber: 4.5 Consensus size: 32
20246885 TTTACCAGGA
20246895 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* *
20246927 TCAACCACAACCTTTCACAA-TGG-TTTTCAACGGCC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGG-C
*
20246962 TCAACCAAAACCCAAAGTGGTTTTTCAGAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* ** *
20246994 TCAACCATAACCTACAACAGTGGTTTTTCACGGGA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCAAAGGC
20247029 TCAACCAAAACCCAA
1 TCAACCAAAACCCAA
20247044 CAACTAAATT
Statistics
Matches: 97, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
31 2 0.02
32 28 0.29
33 11 0.11
34 12 0.12
35 42 0.43
36 2 0.02
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:20246952 original size:67 final size:66
Alignment explanation
Indices: 20246868--20247043 Score: 237
Period size: 67 Copynumber: 2.6 Consensus size: 66
20246858 GCTTAGCCAA
20246868 AACCTTTCACAATGGTTTTTACCAGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTACC-GGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
20246933 AC
65 AC
* * * *
20246935 AACCTTTCACAATGGTTTTCAACGGCCTCAACCAAAACCCAAAGTGGTTTTTCAGAGGCTCAACC
1 AACCTTTCACAATGGTTTTTACCGG-ATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
*
20247000 AT
65 AC
* * *
20247002 AACC-TACAACAGTGGTTTTTCACGGGATCAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTT-ACCGGATCAACCAAAACCCAA
20247044 CAACTAAATT
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
66 4 0.04
67 88 0.93
68 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (66 bp):
AACCTTTCACAATGGTTTTTACCGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCA
C
Found at i:20249625 original size:20 final size:20
Alignment explanation
Indices: 20249597--20249635 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20249587 CTTCAAGCAC
* *
20249597 TATTCTCAATTATCATCAAG
1 TATTATCAATCATCATCAAG
20249617 TATTATCAATCATCATCAA
1 TATTATCAATCATCATCAA
20249636 ACATTCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (20 bp):
TATTATCAATCATCATCAAG
Found at i:20254513 original size:67 final size:67
Alignment explanation
Indices: 20254405--20254580 Score: 257
Period size: 67 Copynumber: 2.6 Consensus size: 67
20254395 GCTTAGCCAA
* *
20254405 AACCTTTCGCAATGGTTTTT-ATCGGGATCAATCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
20254469 CAC
65 CAC
* *
20254472 AACCTTTCACAATGATTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
*
20254537 AT
66 AC
* *
20254539 AACC-TACAATAATGGTTTTTCACGGGATCAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACCCAA
20254581 CAACTAAATT
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
66 2 0.02
67 95 0.97
68 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:20254532 original size:32 final size:32
Alignment explanation
Indices: 20254432--20254580 Score: 138
Period size: 35 Copynumber: 4.5 Consensus size: 32
20254422 TTTATCGGGA
*
20254432 TCAATCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * **
20254464 TCAACCACAACCTTTCACAA-TGATTTTTCACGGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
20254499 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * ** *
20254531 TCAACCATAACCTACAATAATGGTTTTTCACGGGA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCAAAGGC
20254566 TCAACCAAAACCCAA
1 TCAACCAAAACCCAA
20254581 CAACTAAATT
Statistics
Matches: 94, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
31 2 0.02
32 35 0.37
33 3 0.03
34 3 0.03
35 49 0.52
36 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:20257237 original size:26 final size:26
Alignment explanation
Indices: 20257208--20257265 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
20257198 GCTTAGGTTA
20257208 GAAGCTCACCGTGTAAATGCTTGGTG
1 GAAGCTCACCGTGTAAATGCTTGGTG
*
20257234 GAAGCTCACCTTGTAAATGCTTGGTG
1 GAAGCTCACCGTGTAAATGCTTGGTG
20257260 GAAGCT
1 GAAGCT
20257266 GTTAACTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (26 bp):
GAAGCTCACCGTGTAAATGCTTGGTG
Found at i:20264336 original size:45 final size:45
Alignment explanation
Indices: 20264285--20264383 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
20264275 TATGCTGAAC
*
20264285 AAGAAGAATAG-GGAAAGGAAAAGTCAA-AAACCATAGAAGAAAATG
1 AAGAAGAA-AGAGGAAAGGAAAAAT-AAGAAACCATAGAAGAAAATG
* * *
20264330 AAGAAGAAAGAGGAATGGAAAAATAAGCAACCATAGAAGAGAATG
1 AAGAAGAAAGAGGAAAGGAAAAATAAGAAACCATAGAAGAAAATG
*
20264375 AGGAAGAAA
1 AAGAAGAAA
20264384 AAGAAATAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.60, C:0.06, G:0.26, T:0.08
Consensus pattern (45 bp):
AAGAAGAAAGAGGAAAGGAAAAATAAGAAACCATAGAAGAAAATG
Found at i:20271176 original size:38 final size:40
Alignment explanation
Indices: 20271134--20271236 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 40
20271124 ATAGTGCCCG
*
20271134 TGTGCACGATGTGGGGGGATGTACACGAT-G-GCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGC-CGGATA
* * *
20271172 TGTGCAGGATGTGGGGGGATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
*
20271212 TGTGCACGATGTGGAGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
20271237 TGAGCCGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 27 0.49
39 4 0.07
40 24 0.44
ACGTcount: A:0.20, C:0.16, G:0.42, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
Found at i:20273149 original size:22 final size:21
Alignment explanation
Indices: 20273115--20273159 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
20273105 ATGTGCCCCT
20273115 AAGATGGGAGATATATGATTGA
1 AAGATGGGAGATATATGA-TGA
** *
20273137 AAGATGGTTGATATTTGATGA
1 AAGATGGGAGATATATGATGA
20273158 AA
1 AA
20273160 TAGTTCAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (21 bp):
AAGATGGGAGATATATGATGA
Found at i:20274474 original size:16 final size:16
Alignment explanation
Indices: 20274453--20274483 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20274443 TAAAATCTTT
*
20274453 AAACAAAGAACTAAAG
1 AAACAAAGAAATAAAG
20274469 AAACAAAGAAATAAA
1 AAACAAAGAAATAAA
20274484 ATGAGAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.10, T:0.06
Consensus pattern (16 bp):
AAACAAAGAAATAAAG
Found at i:20276995 original size:31 final size:30
Alignment explanation
Indices: 20276956--20277015 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
20276946 GCATCAATTT
20276956 ATTTGTCAATGATAGGATATTATGAATTAA
1 ATTTGTCAATGATAGGATATTATGAATTAA
* *
20276986 ATTTGGTCAATGATAGTATGTTATGAATTA
1 ATTT-GTCAATGATAGGATATTATGAATTA
20277016 TACAGAGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (30 bp):
ATTTGTCAATGATAGGATATTATGAATTAA
Found at i:20283088 original size:36 final size:36
Alignment explanation
Indices: 20283041--20283252 Score: 151
Period size: 36 Copynumber: 5.7 Consensus size: 36
20283031 TAACCGTGCA
* * *
20283041 TGTGCGGTGTGGGAGTGCACATGACGGTGCTAGTAG
1 TGTGCGGTGTGGGAGTGCACATGATGATGATAGTAG
** **
20283077 TGTGCGGTGTGGGAAAGCACATGCCGATGATA-TATG
1 TGTGCGGTGTGGGAGTGCACATGATGATGATAGTA-G
* * * *
20283113 CCATGTGCGATGTGGGAGAGCACGTGATGATGATATATGTTG
1 ---TGTGCGGTGTGGGAGTGCACATGATGATG--ATA-GTAG
* *
20283155 TGTGCAGTGTGGGAGTGCACATGAT-AGTGATGGTGAG
1 TGTGCGGTGTGGGAGTGCACATGATGA-TGATAGT-AG
* * * *
20283192 -GTACGGTGTGGGAATGCACCTGATGATGATATTGTAA
1 TGTGCGGTGTGGGAGTGCACATGATGATGATA--GTAG
20283229 TGTGCGGTGTGGGAGTGCACATGA
1 TGTGCGGTGTGGGAGTGCACATGA
20283253 GCCGGGGGAG
Statistics
Matches: 136, Mismatches: 26, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
35 2 0.01
36 54 0.40
37 5 0.04
38 23 0.17
39 47 0.35
41 3 0.02
42 1 0.01
43 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.39, T:0.27
Consensus pattern (36 bp):
TGTGCGGTGTGGGAGTGCACATGATGATGATAGTAG
Found at i:20283159 original size:39 final size:39
Alignment explanation
Indices: 20283076--20283179 Score: 111
Period size: 39 Copynumber: 2.7 Consensus size: 39
20283066 GGTGCTAGTA
* * **
20283076 GTGTGCGGTGTGGGAAAGCACATGCCGATGATATATGCC
1 GTGTGCGATGTGGGAGAGCACATGATGATGATATATGCC
* * **
20283115 ATGTGCGATGTGGGAGAGCACGTGATGATGATATATGTT
1 GTGTGCGATGTGGGAGAGCACATGATGATGATATATGCC
*
20283154 GTGTGC-AGTGTGGGAGTGCACATGAT
1 GTGTGCGA-TGTGGGAGAGCACATGAT
20283180 AGTGATGGTG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 1 0.02
39 52 0.98
ACGTcount: A:0.23, C:0.12, G:0.38, T:0.27
Consensus pattern (39 bp):
GTGTGCGATGTGGGAGAGCACATGATGATGATATATGCC
Found at i:20283199 original size:114 final size:113
Alignment explanation
Indices: 20283041--20283248 Score: 265
Period size: 114 Copynumber: 1.8 Consensus size: 113
20283031 TAACCGTGCA
* * * * *
20283041 TGTGCGGTGTGGGAGTGCACATGACGGTGCTAGTAGTGTGCGGTGTGGGAAAGCACATGCCGATG
1 TGTGCAGTGTGGGAGTGCACATGACAGTGATAGTAGTGTACGGTGTGGGAAAGCACATGACGATG
*
20283106 ATATATGCCATGTGCGATGTGGGAGAGCACGTGATGATGATATATGTTG
66 ATAT-TGCAATGTGCGATGTGGGAGAGCACGTGATGATGATATATGTTG
* * * * *
20283155 TGTGCAGTGTGGGAGTGCACATGATAGTGATGGTGAG-GTACGGTGTGGGAATGCACCTGATGAT
1 TGTGCAGTGTGGGAGTGCACATGACAGTGATAGT-AGTGTACGGTGTGGGAAAGCACATGACGAT
* * *
20283219 GATATTGTAATGTGCGGTGTGGGAGTGCAC
65 GATATTGCAATGTGCGATGTGGGAGAGCAC
20283249 ATGAGCCGGG
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
113 21 0.27
114 56 0.71
115 2 0.03
ACGTcount: A:0.22, C:0.12, G:0.39, T:0.27
Consensus pattern (113 bp):
TGTGCAGTGTGGGAGTGCACATGACAGTGATAGTAGTGTACGGTGTGGGAAAGCACATGACGATG
ATATTGCAATGTGCGATGTGGGAGAGCACGTGATGATGATATATGTTG
Found at i:20287018 original size:36 final size:36
Alignment explanation
Indices: 20286907--20287025 Score: 152
Period size: 36 Copynumber: 3.3 Consensus size: 36
20286897 TGTGGTGCGA
* * *
20286907 GAGTGTACATGATGATATT--GCCATGTGTGGTGTGG
1 GAGTGCACATGATGAT-TTCAGCTATGTGCGGTGTGG
* * *
20286942 GAGTACACATGACGATATCAGCTATGTGCGGTGTGG
1 GAGTGCACATGATGATTTCAGCTATGTGCGGTGTGG
20286978 GAGTGCACATGATGATTTCAGCTATGTGCGGTGTGG
1 GAGTGCACATGATGATTTCAGCTATGTGCGGTGTGG
*
20287014 GAGTGCATATGA
1 GAGTGCACATGA
20287026 GCTGGTGAGC
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
34 1 0.01
35 13 0.18
36 58 0.81
ACGTcount: A:0.23, C:0.13, G:0.35, T:0.29
Consensus pattern (36 bp):
GAGTGCACATGATGATTTCAGCTATGTGCGGTGTGG
Found at i:20304865 original size:28 final size:28
Alignment explanation
Indices: 20304767--20304886 Score: 114
Period size: 28 Copynumber: 4.3 Consensus size: 28
20304757 AAGTCATTGT
* * * *
20304767 ATGGGTTTGTGGTGATCCTGATAAAACC
1 ATGGGTTTCTGGTGAGCCCGAAAAAACC
* * * *
20304795 ATGAGTTTTTGGTGAGCTCAAAAAAACC
1 ATGGGTTTCTGGTGAGCCCGAAAAAACC
*
20304823 ATGGGTTTGTGGTGAGCCCGAAAAAACC
1 ATGGGTTTCTGGTGAGCCCGAAAAAACC
* * * **
20304851 ATGGGTTTCTAGTGAACCTGTTAAAACC
1 ATGGGTTTCTGGTGAGCCCGAAAAAACC
20304879 ATGGGTTT
1 ATGGGTTT
20304887 ATCACTTGAT
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
ATGGGTTTCTGGTGAGCCCGAAAAAACC
Found at i:20308318 original size:4 final size:4
Alignment explanation
Indices: 20308302--20308360 Score: 50
Period size: 4 Copynumber: 14.2 Consensus size: 4
20308292 TTTCTCTCTT
* *
20308302 TTTC TTCC TTTC TTTC TTTCC TTTCC TTTC TTT- TTTC -TTC TTTC TATCC
1 TTTC TTTC TTTC TTTC TTT-C TTT-C TTTC TTTC TTTC TTTC TTTC T-TTC
20308351 TTTCC TTTC T
1 TTT-C TTTC T
20308361 CTTTTCTTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
3 6 0.13
4 24 0.52
5 16 0.35
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Done.