Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 65 of 172
Found at i:21284589 original size:48 final size:47
Alignment explanation
Indices: 21284471--21284985 Score: 426
Period size: 48 Copynumber: 10.7 Consensus size: 47
21284461 GGTAAGATGT
* * *
21284471 CGATGCCATG-TCCTAGACATGGTCTTACACTGGCTCTCATATATCG-GTGC
1 CGATGCCATGTTCC-AAACATGGTCTTACACTAGC-C-CACA-ATCGAG-GC
*
21284521 CGATACCATGTTCCAAACATGGTCTTACACTAGCCCACAAGTCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACAA-TCGAGGC
* * * * ** *
21284569 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTCTA-TATAAATGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGC--CCACAATCGAGGC
* * ** *
21284617 CGATGCCATGTTCCAAACATGGTCATACACTGGCTCTCGTATATCG-GTGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGC-C-CACA-ATCGAG-GC
* ** * * * *
21284667 TGATGCCATGTTCCGGACATGGTCTTACACTACCCCACATGTTGAGGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
*
21284715 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATGTCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
* * * * ** *
21284763 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
* * * * *
21284811 CGATGCCATATTCCAATCATGGTTTTACACTAGCCCACATGTTGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
* *
21284859 CCATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATGTCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
* * * * * ** *
21284907 TGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACA-ATCGAGGC
21284955 CGATGCCATGTTCCAAACATGGTCTTACACT
1 CGATGCCATGTTCCAAACATGGTCTTACACT
21284986 GGCTCACATA
Statistics
Matches: 379, Mismatches: 76, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
47 3 0.01
48 308 0.81
49 5 0.01
50 60 0.16
51 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACAATCGAGGC
Found at i:21284875 original size:144 final size:144
Alignment explanation
Indices: 21284471--21284994 Score: 681
Period size: 144 Copynumber: 3.6 Consensus size: 144
21284461 GGTAAGATGT
* * ** *
21284471 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATATCGGTGCCGATACCATGTTCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATA--AATGCCGATGCCATGTTCCA
* * * *
21284536 AACATGGTCTTACACTAGCCCACAAGTCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTA
64 AACATGGTCTTACACTAGCCCACATGTTGAGGCCGATGCCATGTTCCAAACATGGTCTTACACTA
* * * ** *
21284601 GCTTC-TATATAAATGC
129 GC-CCACATGTCGAGGC
* * * * *** ** *
21284617 CGATGCCATGTTCCAAACATGGTCATACACTGGCTCTCGTATATCGGTGTTGATGCCATGTTCCG
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC--ATATAAATGCCGATGCCATGTTCCA
* * *
21284682 GACATGGTCTTACACTACCCCACATGTTGAGGTCGATGCCATGTTCCAAACATGGTCTTACACTA
64 AACATGGTCTTACACTAGCCCACATGTTGAGGCCGATGCCATGTTCCAAACATGGTCTTACACTA
21284747 GCCCACATGTCGAGGC
129 GCCCACATGTCGAGGC
* *
21284763 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATATTCCAAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
* *
21284828 CATGGTTTTACACTAGCCCACATGTTGAGGCCCATGCCATGTTCCAAACATGGTCTTACACTAGC
66 CATGGTCTTACACTAGCCCACATGTTGAGGCCGATGCCATGTTCCAAACATGGTCTTACACTAGC
21284893 CCACATGTCGAGGC
131 CCACATGTCGAGGC
*
21284907 TGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
* *
21284972 CATGGTCTTACACTGGCTCACAT
66 CATGGTCTTACACTAGCCCACAT
21284995 AACCCTACTA
Statistics
Matches: 330, Mismatches: 45, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
144 175 0.53
145 1 0.00
146 150 0.45
148 4 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (144 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
CATGGTCTTACACTAGCCCACATGTTGAGGCCGATGCCATGTTCCAAACATGGTCTTACACTAGC
CCACATGTCGAGGC
Found at i:21284994 original size:96 final size:96
Alignment explanation
Indices: 21284471--21284995 Score: 538
Period size: 96 Copynumber: 5.4 Consensus size: 96
21284461 GGTAAGATGT
* * *
21284471 CGATGCCATG-TCCTAGACATGGTCTTACACTGGCTCTCATATATCG-GTGCCGATACCATGTTC
1 CGATGCCATGTTCC-AGACATGGTCTTACACTAGCTCACATATA--GAG-GCCGATGCCATGTTC
21284534 CAAACATGGTCTTACACTAGCCCACA-AGTCGAGGC
62 CAAACATGGTCTTACACTAGCCCACATA-TCGAGGC
* * * *
21284569 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTC-TATATAAATGCCGATGCCATGTTCCAA
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGC-TCACATATAGAGGCCGATGCCATGTTCCAA
* * ** *
21284633 ACATGGTCATACACTGGCTCTCGTATATCG-GTGT
65 ACATGGTCTTACACTAGC-C-CACATATCGAG-GC
* * * * * * *
21284667 TGATGCCATGTTCCGGACATGGTCTTACACTACCCCACATGTTGAGGTCGATGCCATGTTCCAAA
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGCTCACATATAGAGGCCGATGCCATGTTCCAAA
*
21284732 CATGGTCTTACACTAGCCCACATGTCGAGGC
66 CATGGTCTTACACTAGCCCACATATCGAGGC
* * * * * *
21284763 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATATTCCAAT
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGCTCACATATAGAGGCCGATGCCATGTTCCAAA
* * *
21284828 CATGGTTTTACACTAGCCCACATGTTGAGGC
66 CATGGTCTTACACTAGCCCACATATCGAGGC
* * * * * * * *
21284859 CCATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATGTCGAGGCTGATGCCATGTCCCAGA
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGCTCACATATAGAGGCCGATGCCATGTTCCAAA
* * ** *
21284924 CATGGTCTTACACTAGCTCTCATATAAATGC
66 CATGGTCTTACACTAGCCCACATATCGAGGC
* *
21284955 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATA
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGCTCACATA
21284996 ACCCTACTAT
Statistics
Matches: 350, Mismatches: 68, Indels: 20
0.80 0.16 0.05
Matches are distributed among these distances:
96 233 0.67
97 5 0.01
98 107 0.31
99 5 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (96 bp):
CGATGCCATGTTCCAGACATGGTCTTACACTAGCTCACATATAGAGGCCGATGCCATGTTCCAAA
CATGGTCTTACACTAGCCCACATATCGAGGC
Found at i:21288192 original size:28 final size:27
Alignment explanation
Indices: 21288125--21288213 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 27
21288115 ATATGACATC
* *
21288125 GTGCTAAGGGAAATAAGACCATGGCA-
1 GTGCTAAGTGAAATAAGTCCATGGCAT
21288151 -T-CTAAGTGAAATAAGTCCATGGCAAT
1 GTGCTAAGTGAAATAAGTCCATGGC-AT
*
21288177 GTGCTAAGTGAAATAAGTCCATGGCTTT
1 GTGCTAAGTGAAATAAGTCCATGGC-AT
21288205 GTGCTAAGT
1 GTGCTAAGT
21288214 TAGAAATTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
24 20 0.36
25 2 0.04
27 1 0.02
28 32 0.58
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (27 bp):
GTGCTAAGTGAAATAAGTCCATGGCAT
Found at i:21288517 original size:51 final size:51
Alignment explanation
Indices: 21288239--21288509 Score: 434
Period size: 51 Copynumber: 5.3 Consensus size: 51
21288229 TGAACCTTAG
*
21288239 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * ** *
21288290 GAATATAATAGCTTTGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
*
21288341 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * ** *
21288392 GAATATAATAGCTTTGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
21288443 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
21288494 GAATAAAATAGCTTTG
1 GAATAAAATAGCTTTG
21288510 CCTACAAGGG
Statistics
Matches: 197, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 197 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:21288533 original size:102 final size:102
Alignment explanation
Indices: 21288239--21288509 Score: 524
Period size: 102 Copynumber: 2.7 Consensus size: 102
21288229 TGAACCTTAG
21288239 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATATAATAGCTT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATATAATAGCTT
21288304 TGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
66 TGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
21288341 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATATAATAGCTT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATATAATAGCTT
21288406 TGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
66 TGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
* *
21288443 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAAAATAGCTT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATATAATAGCTT
21288508 TG
66 TG
21288510 CCTACAAGGG
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 167 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (102 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGACCACTTTGTGAATATAATAGCTT
TGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
Found at i:21291166 original size:42 final size:43
Alignment explanation
Indices: 21291008--21291166 Score: 153
Period size: 42 Copynumber: 3.6 Consensus size: 43
21290998 CTTAGGAAAA
* * * * * *
21291008 TCGCACACTTAGTGCCAAATAAATAGCTGAAGCTGTATCAATC
1 TCGCACACTAAGTGCCAAATAAATAGCAGAAGCTATCTCGATT
21291051 TCGCACACTAAGTGCCAATATGTATATATAGCAGAAGCTATCTCGATCT
1 TCGCACACTAAGTGCCAA-A--TA-A-ATAGCAGAAGCTATCTCGAT-T
* * *
21291100 T-GCACACTAAGCG-CAAATATATAGCCGAAGCTATCTCGATT
1 TCGCACACTAAGTGCCAAATAAATAGCAGAAGCTATCTCGATT
*
21291141 TCGCACACTAAGTGCC-CATAAATAGC
1 TCGCACACTAAGTGCCAAATAAATAGC
21291167 TGAATCATCG
Statistics
Matches: 96, Mismatches: 12, Indels: 17
0.77 0.10 0.14
Matches are distributed among these distances:
41 2 0.02
42 38 0.40
43 18 0.19
44 3 0.03
46 3 0.03
47 4 0.04
48 27 0.28
49 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (43 bp):
TCGCACACTAAGTGCCAAATAAATAGCAGAAGCTATCTCGATT
Found at i:21293127 original size:17 final size:17
Alignment explanation
Indices: 21293105--21293138 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21293095 CGTGTGGTTG
21293105 GCTGTGTGCGAGACACA
1 GCTGTGTGCGAGACACA
21293122 GCTGTGTGCGAGACACA
1 GCTGTGTGCGAGACACA
21293139 TGCATGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (17 bp):
GCTGTGTGCGAGACACA
Found at i:21296226 original size:18 final size:18
Alignment explanation
Indices: 21296174--21296226 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
21296164 CAAATCCTAT
*
21296174 TCTTTCAATTCTTTCTAA
1 TCTTTCAATTCTTTCAAA
* *
21296192 TCTCTT-AACTCTCTCAAA
1 TCT-TTCAATTCTTTCAAA
*
21296210 TCTTTCAATTTTTTCAA
1 TCTTTCAATTCTTTCAA
21296227 GTTTTTGTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (18 bp):
TCTTTCAATTCTTTCAAA
Found at i:21303861 original size:29 final size:27
Alignment explanation
Indices: 21303770--21303884 Score: 95
Period size: 29 Copynumber: 4.1 Consensus size: 27
21303760 TTCACATACC
* * * *
21303770 TTATCTGGCCCATTAAGCCCATTCATA
1 TTATATGGCCCATTAGGCCCAATCACA
* * *
21303797 TTCATATGGCCTATTAGGCTCAAATCACC
1 TT-ATATGGCCCATTAGGC-CCAATCACA
21303826 TGTATATGGCCCATTAGGCCCAAATCACA
1 T-TATATGGCCCATTAGGCCC-AATCACA
* * *
21303855 TTAATATAGCCCGTTAGGCCCAGTCACA
1 TT-ATATGGCCCATTAGGCCCAATCACA
21303883 TT
1 TT
21303885 CATAATCATG
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
27 2 0.03
28 23 0.33
29 44 0.63
30 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (27 bp):
TTATATGGCCCATTAGGCCCAATCACA
Found at i:21317486 original size:33 final size:32
Alignment explanation
Indices: 21317431--21317511 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 32
21317421 TTTTTTACAT
*
21317431 ATATATATTATATA-AAACATGA-CCTTGAAATGC
1 ATATATATTATATATAAACATGACCCAT-AAA--C
**
21317464 ATATATATTATATATTTA-ATGACCCATAAAC
1 ATATATATTATATATAAACATGACCCATAAAC
21317495 ATATATATTATATATAA
1 ATATATATTATATATAA
21317512 CAAATATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
31 16 0.39
33 21 0.51
34 4 0.10
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (32 bp):
ATATATATTATATATAAACATGACCCATAAAC
Found at i:21317518 original size:18 final size:18
Alignment explanation
Indices: 21317492--21317532 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
21317482 ATGACCCATA
*
21317492 AACATATATATTATATAT
1 AACAAATATATTATATAT
*
21317510 AACAAATATTTTATATAT
1 AACAAATATATTATATAT
21317528 AACAA
1 AACAA
21317533 GATGCATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (18 bp):
AACAAATATATTATATAT
Found at i:21317787 original size:31 final size:30
Alignment explanation
Indices: 21317688--21317787 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 30
21317678 CAACACGCAT
* *
21317688 ATATATATTGTATATATAACATAACCATGACGC
1 ATATATATTATATATATAACA-AA-C-TCACGC
* * *
21317721 ATATATTTTATATATATAACAAAATC-CAC
1 ATATATATTATATATATAACAAACTCACGC
*
21317750 ACATATATTATATATATAACGAAACTCACGC
1 ATATATATTATATATATAAC-AAACTCACGC
21317781 ATATATA
1 ATATATA
21317788 GGTATTATGT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
29 20 0.36
30 6 0.11
31 8 0.15
32 2 0.04
33 19 0.35
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (30 bp):
ATATATATTATATATATAACAAACTCACGC
Found at i:21321162 original size:40 final size:39
Alignment explanation
Indices: 21321118--21321222 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
21321108 AGTGACCATA
*
21321118 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
21321158 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
21321196 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
21321223 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:21321179 original size:39 final size:40
Alignment explanation
Indices: 21321078--21321241 Score: 169
Period size: 40 Copynumber: 4.1 Consensus size: 40
21321068 TTGAATGATG
* *
21321078 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATA
*
21321118 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA
*
21321157 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
* * **
21321197 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATA-CTATA
21321237 TCCGG
1 TCCGG
21321242 TTAAATTCCG
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 36 0.34
40 59 0.56
41 10 0.09
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
Found at i:21321241 original size:79 final size:80
Alignment explanation
Indices: 21321078--21321228 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
21321068 TTGAATGATG
*
21321078 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
21321143 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * *
21321158 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
21321220 TTGAACGAG
64 TTGAACGAG
21321229 TAGCTATATC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.69
80 18 0.30
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:21324962 original size:45 final size:45
Alignment explanation
Indices: 21324876--21324963 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
21324866 TAATCGAATA
* * * * *
21324876 CGATGCCGATGTCCCAGACATTGTCTTACACGTAACCACATATAT
1 CGATGCCAACGTCCCAGACATGGTCTTACACGAAAACACATATAT
* *
21324921 CGATGCCAACGTCCCAGACGTGGTCTTACACGAAAATACATAT
1 CGATGCCAACGTCCCAGACATGGTCTTACACGAAAACACATAT
21324964 CGAACATCCT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (45 bp):
CGATGCCAACGTCCCAGACATGGTCTTACACGAAAACACATATAT
Found at i:21325792 original size:16 final size:18
Alignment explanation
Indices: 21325773--21325805 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
21325763 CATACAAATT
21325773 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
21325789 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
21325806 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:21326435 original size:43 final size:43
Alignment explanation
Indices: 21326367--21326488 Score: 219
Period size: 43 Copynumber: 2.8 Consensus size: 43
21326357 CTGAACTCAT
21326367 TCACCGGCATTAT-GCCTGCTAGGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
21326409 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
*
21326452 TCACCGACATTATAGCCTGCTAGGCTCGAAGTCCCGA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAG-CCCGA
21326489 ATAGTACTGT
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
42 13 0.17
43 59 0.77
44 5 0.06
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
Found at i:21328896 original size:14 final size:14
Alignment explanation
Indices: 21328879--21328906 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21328869 TCACGAAAAT
21328879 TTCACACATATAAA
1 TTCACACATATAAA
21328893 TTCACACATATAAA
1 TTCACACATATAAA
21328907 CATAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
TTCACACATATAAA
Found at i:21337106 original size:27 final size:26
Alignment explanation
Indices: 21337075--21337252 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
21337065 TAAATTGTAC
21337075 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
21337102 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
21337128 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
21337156 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
21337184 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
21337211 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
21337238 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21337253 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 25 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:21337191 original size:82 final size:81
Alignment explanation
Indices: 21337076--21337231 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
21337066 AAATTGTACA
* *
21337076 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
21337140 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
21337157 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
21337222 TGCGAGTTGA
65 TGCGAATTGA
21337232 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:21337243 original size:82 final size:81
Alignment explanation
Indices: 21337072--21337252 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
21337062 GATTAAATTG
* *
21337072 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
21337137 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
21337153 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
21337217 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
21337235 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
21337253 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:21337263 original size:27 final size:27
Alignment explanation
Indices: 21337157--21337263 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
21337147 TGACCATGCG
* * * *
21337157 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
21337185 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
21337212 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
21337239 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
21337264 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:21345171 original size:27 final size:27
Alignment explanation
Indices: 21345140--21345317 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21345130 TAAATTGTAC
21345140 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
21345167 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21345193 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
21345221 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
21345249 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21345276 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
21345303 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21345318 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:21345254 original size:82 final size:81
Alignment explanation
Indices: 21345141--21345296 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
21345131 AAATTGTACA
* *
21345141 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
21345205 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
21345222 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
21345287 TGCGAGTTGA
65 TGCGAATTGA
21345297 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:21345308 original size:82 final size:81
Alignment explanation
Indices: 21345137--21345317 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
21345127 GATTAAATTG
* *
21345137 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
21345202 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
21345218 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
21345282 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
21345300 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
21345318 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:21348315 original size:14 final size:15
Alignment explanation
Indices: 21348296--21348324 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21348286 TTACGAAAGT
21348296 TTCACACAT-ATAAA
1 TTCACACATAATAAA
21348310 TTCACACATAATAAA
1 TTCACACATAATAAA
21348325 AAAAGAAAAT
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:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:21348961 original size:13 final size:13
Alignment explanation
Indices: 21348943--21348971 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21348933 TATTAAAAAC
21348943 CCTAATATTTAAA
1 CCTAATATTTAAA
21348956 CCTAATATTTAAA
1 CCTAATATTTAAA
21348969 CCT
1 CCT
21348972 TAAAAGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (13 bp):
CCTAATATTTAAA
Found at i:21353483 original size:15 final size:16
Alignment explanation
Indices: 21353463--21353492 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21353453 CACAATTTAA
21353463 TTATAC-GATATGGAT
1 TTATACGGATATGGAT
21353478 TTATACGGATATGGA
1 TTATACGGATATGGA
21353493 GGCGATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (16 bp):
TTATACGGATATGGAT
Found at i:21373485 original size:22 final size:22
Alignment explanation
Indices: 21373459--21373506 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
21373449 CAAAGTTAAC
* *
21373459 AAATCAACCGAATAGAAATTTT
1 AAATCAACCAAACAGAAATTTT
21373481 AAATCAACCAAACAGAAATTTT
1 AAATCAACCAAACAGAAATTTT
21373503 AAAT
1 AAAT
21373507 AGCTTGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (22 bp):
AAATCAACCAAACAGAAATTTT
Found at i:21375772 original size:17 final size:17
Alignment explanation
Indices: 21375750--21375785 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
21375740 GCATCATCAC
21375750 GTGCCCATATGAAATTT
1 GTGCCCATATGAAATTT
21375767 GTGCCCATATGAAATTT
1 GTGCCCATATGAAATTT
21375784 GT
1 GT
21375786 TCATACTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (17 bp):
GTGCCCATATGAAATTT
Found at i:21382159 original size:3 final size:3
Alignment explanation
Indices: 21382146--21382178 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
21382136 TTAGGTAAAG
21382146 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
21382179 GGTAAGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:21383870 original size:45 final size:45
Alignment explanation
Indices: 21383810--21383897 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
21383800 AAATTATGTA
*
21383810 ATCTGAACTCATTGAGTTGTGGTCTGAGTTTATGATATATGTGAC
1 ATCTGAACTCATTGAGTTGTAGTCTGAGTTTATGATATATGTGAC
* *
21383855 ATCTGAACTCGTTGAGTTGTAGTCTGAGTTTGTGATATATGTG
1 ATCTGAACTCATTGAGTTGTAGTCTGAGTTTATGATATATGTG
21383898 GCACATGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (45 bp):
ATCTGAACTCATTGAGTTGTAGTCTGAGTTTATGATATATGTGAC
Found at i:21385867 original size:35 final size:34
Alignment explanation
Indices: 21385803--21385876 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 34
21385793 AACTTGTCTG
*
21385803 ACTAGTGCTGGGCACACAACCGTTAGTTTATCCA
1 ACTAGCGCTGGGCACACAACCGTTAGTTTATCCA
*
21385837 ACTAGCGCTGGGCACA-ATCACCGTTGGTTTATCCA
1 ACTAGCGCTGGGCACACA--ACCGTTAGTTTATCCA
21385872 ACTAG
1 ACTAG
21385877 AGTTGCGCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 1 0.03
34 15 0.42
35 20 0.56
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (34 bp):
ACTAGCGCTGGGCACACAACCGTTAGTTTATCCA
Found at i:21385999 original size:76 final size:76
Alignment explanation
Indices: 21385859--21386004 Score: 197
Period size: 76 Copynumber: 1.9 Consensus size: 76
21385849 CACAATCACC
* *
21385859 GTTGGTTTATCCAACTAGAGTTGCGCTCACAATTATTACCATCAGTATATCCAACTAGAACTGGG
1 GTTGGGTTATCCAACCAGAGTTGCGCTCACAATTATTACCATCAGTATATCCAACTAGAACTGGG
*
21385924 TGCAAAATATT
66 CGCAAAATATT
* * **
21385935 GTTGGGTTATCCAACCAGAGTTGGGCTCAC-ATTCATTACCATCAGT-TCATCCGACTAGTGCTG
1 GTTGGGTTATCCAACCAGAGTTGCGCTCACAATT-ATTACCATCAGTAT-ATCCAACTAGAACTG
21385998 GGCGCAA
64 GGCGCAA
21386005 CACCTTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
75 4 0.07
76 57 0.93
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (76 bp):
GTTGGGTTATCCAACCAGAGTTGCGCTCACAATTATTACCATCAGTATATCCAACTAGAACTGGG
CGCAAAATATT
Found at i:21403596 original size:29 final size:29
Alignment explanation
Indices: 21403547--21403608 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
21403537 TGCCTAGTCG
*
21403547 TGTGGTTGGCCATGCGCGAGACACGGCCA
1 TGTGGTTGGCCATGCACGAGACACGGCCA
* * *
21403576 TGTGGTTGGCCGTGCATGAGACACGGTCA
1 TGTGGTTGGCCATGCACGAGACACGGCCA
21403605 TGTG
1 TGTG
21403609 TTCGACGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.39, T:0.23
Consensus pattern (29 bp):
TGTGGTTGGCCATGCACGAGACACGGCCA
Found at i:21409305 original size:40 final size:40
Alignment explanation
Indices: 21409026--21409293 Score: 378
Period size: 40 Copynumber: 6.7 Consensus size: 40
21409016 AGGTCTCGAC
* *
21409026 GATG-ATCCGGGCTAACTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
21409065 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
21409105 GATGTACCCGGGGTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
21409145 GATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
21409185 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * * *
21409225 AATATATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCTAGT
* * *
21409265 GTTATATCCGGGCTAGGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCA
21409294 ATCATGCTGG
Statistics
Matches: 204, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 5 0.02
40 197 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:21415746 original size:21 final size:22
Alignment explanation
Indices: 21415720--21415760 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
21415710 CATTAACGAG
21415720 TCAATGTTGTGACA-TCAACAT
1 TCAATGTTGTGACACTCAACAT
21415741 TCAATGTTGTGACACTCAAC
1 TCAATGTTGTGACACTCAAC
21415761 TTTGAGGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (22 bp):
TCAATGTTGTGACACTCAACAT
Found at i:21416359 original size:22 final size:22
Alignment explanation
Indices: 21416334--21416379 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
21416324 TTTAGGTAGA
21416334 TGTGGTCAAAAGAATAGTCTAC
1 TGTGGTCAAAAGAATAGTCTAC
21416356 TGTGGTCAAAAGAATAGTCTAC
1 TGTGGTCAAAAGAATAGTCTAC
21416378 TG
1 TG
21416380 AGCATCTTTT
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:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (22 bp):
TGTGGTCAAAAGAATAGTCTAC
Found at i:21420096 original size:25 final size:25
Alignment explanation
Indices: 21420030--21420124 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
21420020 AGCTTCTCTT
* * * **
21420030 GAGCCATATAACAAGAAGCTCATGT
1 GAGCTATATAACAGGAAGCTTATCC
*
21420055 GAGCTATATGAA-GGGAAGCTTATCC
1 GAGCTATAT-AACAGGAAGCTTATCC
21420080 GAGCTATATAACAGGAAGCTTATCC
1 GAGCTATATAACAGGAAGCTTATCC
* *
21420105 GGGCTATATAACAGAAAGCT
1 GAGCTATATAACAGGAAGCT
21420125 CATAAGAGCC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
24 2 0.03
25 55 0.93
26 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (25 bp):
GAGCTATATAACAGGAAGCTTATCC
Found at i:21420111 original size:50 final size:51
Alignment explanation
Indices: 21420016--21420113 Score: 117
Period size: 50 Copynumber: 1.9 Consensus size: 51
21420006 GCACATAATC
* * **
21420016 GGGAAGCTTCTCTTGAGCCATATAACAAGAAGCTCATGTGAGCTATATGAA
1 GGGAAGCTTATCTCGAGCCATATAACAAGAAGCTCATCCGAGCTATATGAA
* * * *
21420067 GGGAAGCTTATC-CGAGCTATATAACAGGAAGCTTATCCGGGCTATAT
1 GGGAAGCTTATCTCGAGCCATATAACAAGAAGCTCATCCGAGCTATAT
21420114 AACAGAAAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
50 28 0.72
51 11 0.28
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (51 bp):
GGGAAGCTTATCTCGAGCCATATAACAAGAAGCTCATCCGAGCTATATGAA
Found at i:21420138 original size:25 final size:25
Alignment explanation
Indices: 21420110--21420164 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
21420100 TATCCGGGCT
21420110 ATATAACAGAAAGCTCATAAGAGCC
1 ATATAACAGAAAGCTCATAAGAGCC
** **
21420135 ATAT-TTAGAAAGCTCATGCGAGCC
1 ATATAACAGAAAGCTCATAAGAGCC
21420159 A-ATAAC
1 ATATAAC
21420165 TGGTAGCTCC
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
23 2 0.09
24 17 0.74
25 4 0.17
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (25 bp):
ATATAACAGAAAGCTCATAAGAGCC
Found at i:21420291 original size:26 final size:26
Alignment explanation
Indices: 21420249--21420298 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
21420239 GGAAGCTTCG
*
21420249 AAGAGTCATTAATTAGGAAGCTCACA
1 AAGAGCCATTAATTAGGAAGCTCACA
*
21420275 AAGAGCCATATAA-TAGGACGCTCA
1 AAGAGCCAT-TAATTAGGAAGCTCA
21420299 TAAGATCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (26 bp):
AAGAGCCATTAATTAGGAAGCTCACA
Found at i:21420767 original size:21 final size:21
Alignment explanation
Indices: 21420743--21420784 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21420733 TAAATTTATC
*
21420743 TCAATTTAATACAATTCATAT
1 TCAATTCAATACAATTCATAT
*
21420764 TCAATTCAATTCAATTCATAT
1 TCAATTCAATACAATTCATAT
21420785 CCTAGGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (21 bp):
TCAATTCAATACAATTCATAT
Found at i:21420772 original size:5 final size:5
Alignment explanation
Indices: 21420743--21420781 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
21420733 TAAATTTATC
* *
21420743 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
21420782 TATCCTAGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:21423327 original size:14 final size:14
Alignment explanation
Indices: 21423310--21423338 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21423300 TATTATAATC
21423310 ATTAAGTTTAATTA
1 ATTAAGTTTAATTA
21423324 ATTAAGTTTAATTA
1 ATTAAGTTTAATTA
21423338 A
1 A
21423339 ACCTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATTAAGTTTAATTA
Found at i:21425881 original size:682 final size:682
Alignment explanation
Indices: 21424569--21425933 Score: 2329
Period size: 682 Copynumber: 2.0 Consensus size: 682
21424559 GTGGTCAGGT
*
21424569 CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACTAA
1 CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
* *
21424634 TTAAGATCACACGGCCAAGTCACACACCCGTGTGCTAGGCCATGCGGAAAATTAATTTTCATAAA
66 TTAAGATCACACAGCCAAGTCACACACCCGTGTGCTAGGCCATGCGAAAAATTAATTTTCATAAA
* **
21424699 ATAGGTGCAGACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTCGTGCCGTCTACATGGCT
131 ATAGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTCGTGCCGTCTACACAGCT
* * *
21424764 GAGGCACACTCCCATGTCTCTTCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAAGG
196 GAGACACACGCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAAGG
* *
21424829 TGCAGGGGACACATGGCCAACACACATTCCCATGGGACAGGCCATGTGTCACACACAGTCTAGAC
261 TGCAGGGGACACATGGCCAACACACATCCCCATGGGACAGGCCATGTATCACACACAGTCTAGAC
* *
21424894 ACATGCACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCTTA
326 ACATACACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCCTA
* * **
21424959 ATTCACACATACACTTACACCAATTAAAAGGCACAAAACATAATATACTTAGGCAATGAAACATC
391 ATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACATC
* * * *
21425024 CATAATTATGACCTACACATGCCAATACAATATCAGCATCGATCATACTCACAATATTTATTATG
456 CACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTATA
* * *
21425089 CTCTAACTCAATCATGCAAATTTCCAGTCATCAAGCCTCAATTAACTACTTTCAAGTTACCTAAT
521 CCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTAAT
*
21425154 TGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGCTATAAA
586 TGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGATATAAA
21425219 TCACTTTCCATCATACACCAAGCATACCATGA
651 TCACTTTCCATCATACACCAAGCATACCATGA
* * *
21425251 CGTGTGGTCACACATGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAGCAAA
1 CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
* *
21425316 TTAAGATCACACAGCCAAGTCACACACCTGTGTGCTAGGCTATGCGAAAAATTAATTTTCAT-AA
66 TTAAGATCACACAGCCAAGTCACACACCCGTGTGCTAGGCCATGCGAAAAATTAATTTTCATAAA
21425380 ATAAGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGG-CTGTGCCGTCTACACAG
131 AT-AGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTC-GTGCCGTCTACACAG
* * *
21425444 CTGAGACACACGCCCGTGTCTCTGCCCGTGTGCTCAATTCTGAGTATTTTGTTTCTCAAAATTAG
194 CTGAGACACACGCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAA
* *
21425509 GGTGCAGGGGGCACATGGCCAACACACATCCCCATGGGACAGGCCGTGTATCACACACAGTCTAG
259 GGTGCAGGGGACACATGGCCAACACACATCCCCATGGGACAGGCCATGTATCACACACAGTCTAG
* *
21425574 ACACATACACGTGTGTCTACCCTTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCC
324 ACACATACACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCC
21425639 TAATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACA
389 TAATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACA
21425704 TCCACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTA
454 TCCACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTA
21425769 TACCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTA
519 TACCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTA
* ***
21425834 ATTGTACATAAATTTATCATCTCATCAATCTTTCACATTTCCAAACATTTCACTTTCATGATATA
584 ATTGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGATATA
21425899 AATCACTTTCCATCATACACCAAGCATACCATGA
649 AATCACTTTCCATCATACACCAAGCATACCATGA
21425933 C
1 C
21425934 TATAACACCA
Statistics
Matches: 640, Mismatches: 41, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
681 5 0.01
682 635 0.99
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (682 bp):
CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
TTAAGATCACACAGCCAAGTCACACACCCGTGTGCTAGGCCATGCGAAAAATTAATTTTCATAAA
ATAGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTCGTGCCGTCTACACAGCT
GAGACACACGCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAAGG
TGCAGGGGACACATGGCCAACACACATCCCCATGGGACAGGCCATGTATCACACACAGTCTAGAC
ACATACACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCCTA
ATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACATC
CACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTATA
CCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTAAT
TGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGATATAAA
TCACTTTCCATCATACACCAAGCATACCATGA
Found at i:21434500 original size:50 final size:50
Alignment explanation
Indices: 21434409--21434747 Score: 439
Period size: 50 Copynumber: 7.0 Consensus size: 50
21434399 TTTGACCACA
**
21434409 TAGGTAAGTACATATGTGATG-TATATTGAACCTTGTGTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* *
21434458 TAGGTAAGTATTTATGTGATGATATATTGAAGCTTGTTTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* *
21434508 TAGGTAAGTATTTATGTGATGATAAATTGAACCTTCTGTATTCGGCC---
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* *
21434555 -----AAGTATTTATGTGATGATATATTGAACCTTCTGTATTCAGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
21434600 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* * * *
21434650 TAGGTAAGTATTCATGTGATGATATATTGAACCTTGTATATTTGGCCATA
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* * **
21434700 T-GAGTATGTATTTATGTGATGATATACTTG-ATCTTGCATATTCGGCCA
1 TAG-GTAAGTATTTATGTGATGATATA-TTGAACCTTGTGTATTCGGCCA
21434748 AATGAATGGT
Statistics
Matches: 258, Mismatches: 21, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
42 40 0.16
49 20 0.08
50 195 0.76
51 3 0.01
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (50 bp):
TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
Found at i:21434572 original size:92 final size:92
Alignment explanation
Indices: 21434463--21434723 Score: 344
Period size: 92 Copynumber: 2.8 Consensus size: 92
21434453 CCATGTAGGT
* *
21434463 AAGTATTTATGTGATGATATATTGAAGCTTGTTTATTCGGCCATGTAGGTAAGTATTTATGTGAT
1 AAGTATTTATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAGGTAAGTATTTATGTGAT
21434528 GATAAATTGAACCTTCTGTATTCGGCC
66 GATAAATTGAACCTTCTGTATTCGGCC
* * *
21434555 AAGTATTTATGTGATGATATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGAT
1 AAGTATTTATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAGGTAAGTATTTATGTGAT
* *
21434620 GATATATTGAACCTTGTGTATTCGGCC
66 GATAAATTGAACCTTCTGTATTCGGCC
* * *
21434647 ATGTAGGTAAGTATTCATGTGATGATATATTGAACCTTGTATATTTGGCCATAT-GAGTATGTAT
1 A---A-GT-A-T-TT-ATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAG-GTAAGTAT
21434711 TTATGTGATGATA
57 TTATGTGATGATA
21434724 TACTTGATCT
Statistics
Matches: 148, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
92 87 0.59
95 1 0.01
96 2 0.01
97 1 0.01
98 1 0.01
99 3 0.02
100 53 0.36
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (92 bp):
AAGTATTTATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAGGTAAGTATTTATGTGAT
GATAAATTGAACCTTCTGTATTCGGCC
Found at i:21434598 original size:142 final size:141
Alignment explanation
Indices: 21434421--21434684 Score: 465
Period size: 142 Copynumber: 1.9 Consensus size: 141
21434411 GGTAAGTACA
* *
21434421 TATGTGATGTATATTGAACCTTGTGTATTCGGCCATGTAGGTAAGTATTTATGTGATGATATATT
1 TATGTGATGTATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGATGATATATT
* * *
21434486 GAAGCTTGTTTATTCGGCCATGTAGGTAAGTATTTATGTGATGATAAATTGAACCTTCTGTATTC
66 GAACCTTGTGTATTCGGCCATGTAGGTAAGTATTCATGTGATGATAAATTGAACCTTCTGTATTC
21434551 GGCCAAGTATT
131 GGCCAAGTATT
21434562 TATGTGATGATATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGATGATATAT
1 TATGTGATG-TATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGATGATATAT
*
21434627 TGAACCTTGTGTATTCGGCCATGTAGGTAAGTATTCATGTGATGATATATTGAACCTT
65 TGAACCTTGTGTATTCGGCCATGTAGGTAAGTATTCATGTGATGATAAATTGAACCTT
21434685 GTATATTTGG
Statistics
Matches: 116, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
141 9 0.08
142 107 0.92
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (141 bp):
TATGTGATGTATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGATGATATATT
GAACCTTGTGTATTCGGCCATGTAGGTAAGTATTCATGTGATGATAAATTGAACCTTCTGTATTC
GGCCAAGTATT
Found at i:21441400 original size:9 final size:9
Alignment explanation
Indices: 21441386--21441424 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
21441376 ACATATACTC
21441386 CTTTTTTTT
1 CTTTTTTTT
*
21441395 CTTTTTCTT
1 CTTTTTTTT
*
21441404 -TTTTTTCT
1 CTTTTTTTT
21441412 CTTTTTTTT
1 CTTTTTTTT
21441421 CTTT
1 CTTT
21441425 CAAGATCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:21441406 original size:15 final size:16
Alignment explanation
Indices: 21441386--21441425 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
21441376 ACATATACTC
21441386 CTTTTTTTTCT-TTTT
1 CTTTTTTTTCTCTTTT
21441401 CTTTTTTTTCTCTTTT
1 CTTTTTTTTCTCTTTT
*
21441417 -TTTTCTTTC
1 CTTTTTTTTC
21441426 AAGATCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (16 bp):
CTTTTTTTTCTCTTTT
Found at i:21444141 original size:77 final size:77
Alignment explanation
Indices: 21444048--21444206 Score: 221
Period size: 77 Copynumber: 2.1 Consensus size: 77
21444038 ACTGGGAGCA
* * * * * *
21444048 AGCTGTTGGCTGTTGGCGCACG-CGAGCTGGAGCTAGAAGTAGGCCTGGTGTGTGCGACAGTAGC
1 AGCTGTTGGCTATTGGCGCACGAGGA-CTGGAGCTAGAAGCAAGCCTGGCGTGTGCGACAGTAAC
21444112 AGCGTACATATGG
65 AGCGTACATATGG
*
21444125 AGCTGTTGGCTATTGGCGCACGAGGACTGGAGCTAGAAGCAAGCCTGGCGTGTGCGGCAGTAACA
1 AGCTGTTGGCTATTGGCGCACGAGGACTGGAGCTAGAAGCAAGCCTGGCGTGTGCGACAGTAACA
* *
21444190 GCGTGCATGTGG
66 GCGTACATATGG
21444202 AGCTG
1 AGCTG
21444207 CTAGCCGAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 70 0.97
78 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.39, T:0.21
Consensus pattern (77 bp):
AGCTGTTGGCTATTGGCGCACGAGGACTGGAGCTAGAAGCAAGCCTGGCGTGTGCGACAGTAACA
GCGTACATATGG
Found at i:21455161 original size:19 final size:19
Alignment explanation
Indices: 21455139--21455193 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
21455129 TAATAGTATT
21455139 TTATTAATTTAATTTTAAA
1 TTATTAATTTAATTTTAAA
*
21455158 TTATT-ATCTTAATATTAAA
1 TTATTAAT-TTAATTTTAAA
21455177 -T-TTAATTTAATGTTTAA
1 TTATTAATTTAAT-TTTAA
21455194 TAAACATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 7 0.23
18 9 0.29
19 15 0.48
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTAATTTAATTTTAAA
Found at i:21457565 original size:43 final size:43
Alignment explanation
Indices: 21457496--21457622 Score: 211
Period size: 42 Copynumber: 3.0 Consensus size: 43
21457486 ATATGCAACG
*
21457496 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTTTAAAAAACA
1 CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAACA
* * *
21457539 CCGCTAAAGACCAGGACCTTTCGCGGCGCTTTTAT-AAAAACG
1 CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAACA
21457581 CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAAC
1 CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAAC
21457623 GCCATGAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 39 0.51
43 38 0.49
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (43 bp):
CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAACA
Found at i:21457591 original size:42 final size:43
Alignment explanation
Indices: 21457492--21457625 Score: 225
Period size: 43 Copynumber: 3.1 Consensus size: 43
21457482 CATTATATGC
*
21457492 AACGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTTTAAAA
1 AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
* * *
21457535 AACACCGCTAAAGACCAGGACCTTTCGCGGCGCTTTTAT-AAA
1 AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
21457577 AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
1 AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
21457620 AACGCC
1 AACGCC
21457626 ATGAATTTGC
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.47
43 44 0.53
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (43 bp):
AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
Found at i:21462248 original size:41 final size:41
Alignment explanation
Indices: 21462204--21462402 Score: 206
Period size: 41 Copynumber: 4.9 Consensus size: 41
21462194 GTTATACGAC
* * * *
21462204 TTTTAGCGGCATTTTACCAAAAGCGCCGCTAATGCTCCGGC
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCCGGT
* * ** *
21462245 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTTTGTT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCCGGT
* * * **
21462286 TTTTAGTGGCGTTTTACCAAAAACGCAGCTATTTCT-CTAT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCCGGT
* * *
21462326 TTTTAGAGGCGTTTTAACAAAAAACGCCGGTATTGCTCC-GT
1 TTTTAGCGGCGTTTT-ACCAAAAACGCCGCTATTGCTCCGGT
*
21462367 TTTTAGCGGCGTTTTA-CTAAAACGCCGCTATTGCTC
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTC
21462403 TGTGTTTTAC
Statistics
Matches: 133, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 17 0.13
40 16 0.12
41 99 0.74
42 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCCGGT
Found at i:21462784 original size:43 final size:42
Alignment explanation
Indices: 21462737--21462856 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 42
21462727 AATGCCAACA
* * *
21462737 TCCCAGACGTGGTATTACATGTAATCAGATATCGATGCC-ACTG
1 TCCCAGACGTGGTCTTACACG-AATCACATATCGATGCCGA-TG
21462780 TCCCAGACAG-GGTCTTACACGAATCACATATACGATGCCGATG
1 TCCCAGAC-GTGGTCTTACACGAATCACATAT-CGATGCCGATG
*
21462823 TCCCAGACATGGTCTTACACGCAATCACATATCG
1 TCCCAGACGTGGTCTTACACG-AATCACATATCG
21462857 TAAATCCTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
42 9 0.13
43 47 0.69
44 12 0.18
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (42 bp):
TCCCAGACGTGGTCTTACACGAATCACATATCGATGCCGATG
Found at i:21466884 original size:67 final size:67
Alignment explanation
Indices: 21466810--21466936 Score: 227
Period size: 67 Copynumber: 1.9 Consensus size: 67
21466800 GTCTATCTAG
* * *
21466810 ATCTATACGAGTGAATTTAACATTAATTTATCATTTTTTACATTCATATGGACTAAATTTAACAT
1 ATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTTAACAT
21466875 TA
66 TA
21466877 ATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTT
1 ATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTT
21466937 TCATCCTAGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (67 bp):
ATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTTAACAT
TA
Found at i:21470616 original size:19 final size:19
Alignment explanation
Indices: 21470594--21470636 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
21470584 ATTTTTACCC
21470594 TTAAATTAAAAATAAATTA
1 TTAAATTAAAAATAAATTA
* **
21470613 TTAAA-TGAAAATTTATTA
1 TTAAATTAAAAATAAATTA
21470631 TTAAAT
1 TTAAAT
21470637 AATATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TTAAATTAAAAATAAATTA
Found at i:21470645 original size:18 final size:18
Alignment explanation
Indices: 21470609--21470660 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
21470599 TTAAAAATAA
*
21470609 ATTATTAAATGAA-AATTT
1 ATTATTAAAT-AATATTTT
21470627 ATTATTAAATAATATTTT
1 ATTATTAAATAATATTTT
*
21470645 AATATTATAATAATAT
1 ATTATTA-AATAATAT
21470661 GTAATAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 20 0.67
19 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTATTAAATAATATTTT
Found at i:21470712 original size:19 final size:21
Alignment explanation
Indices: 21470688--21470743 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
21470678 AATAGTTTTA
*
21470688 AATAACCTAT-TTAA-ATCTT
1 AATAACATATATTAATATCTT
21470707 AATAACATATATTAATATCTT
1 AATAACATATATTAATATCTT
*
21470728 AAAAATCATATATTAA
1 AATAA-CATATATTAA
21470744 AATAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 9 0.28
20 4 0.12
21 9 0.28
22 10 0.31
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAACATATATTAATATCTT
Found at i:21470726 original size:21 final size:20
Alignment explanation
Indices: 21470688--21470744 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
21470678 AATAGTTTTA
*
21470688 AATAACCTAT-TTAAATCTT
1 AATAACATATATTAAATCTT
21470707 AATAACATATATTAATATCTT
1 AATAACATATATTAA-ATCTT
*
21470728 AAAAATCATATATTAAA
1 AATAA-CATATATTAAA
21470745 ATAATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.27
20 4 0.12
21 10 0.30
22 10 0.30
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAACATATATTAAATCTT
Found at i:21473975 original size:3 final size:3
Alignment explanation
Indices: 21473967--21474012 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
21473957 TATAAATTGA
21473967 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
21474013 GATATAAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:21479812 original size:21 final size:22
Alignment explanation
Indices: 21479758--21479812 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
21479748 TAGGTAAGAC
**
21479758 ATTTTACGGGAATAAGAAAATA
1 ATTTTACGTTAATAAGAAAATA
** *
21479780 ATTTTATATTAATTAGAAAAT-
1 ATTTTACGTTAATAAGAAAATA
21479801 ATTTTACGTTAA
1 ATTTTACGTTAA
21479813 CCATCCTATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (22 bp):
ATTTTACGTTAATAAGAAAATA
Found at i:21481262 original size:15 final size:15
Alignment explanation
Indices: 21481229--21481275 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
21481219 CTGAAAACTC
* *
21481229 TAAAATTTATA-AAA
1 TAAAATTAATATATA
21481243 TAAAATTAATATATA
1 TAAAATTAATATATA
*
21481258 TAAAATAAATATATA
1 TAAAATTAATATATA
21481273 TAA
1 TAA
21481276 TTGTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATTAATATATA
Found at i:21481295 original size:28 final size:27
Alignment explanation
Indices: 21481264--21481328 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
21481254 TATATAAAAT
*
21481264 AAATATATATAA-TTGTTTAAAAAATTTA
1 AAATATATAGAACTT-TTTAAAAAA-TTA
*
21481292 AAATATGTCAGAACTTTTTAAAAAATTA
1 AAATATAT-AGAACTTTTTAAAAAATTA
*
21481320 AAAAATATA
1 AAATATATA
21481329 AAATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
27 1 0.03
28 16 0.52
29 12 0.39
30 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (27 bp):
AAATATATAGAACTTTTTAAAAAATTA
Found at i:21484783 original size:22 final size:23
Alignment explanation
Indices: 21484758--21484803 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
21484748 CAACCAAATC
21484758 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
21484780 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
21484803 A
1 A
21484804 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:21484809 original size:23 final size:23
Alignment explanation
Indices: 21484765--21484809 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21484755 ATCAATTCAA
*
21484765 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
21484788 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
21484810 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:21491840 original size:25 final size:24
Alignment explanation
Indices: 21491806--21491855 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
21491796 TATAACACTA
21491806 ATTATCATATTATTAAATTAATTT
1 ATTATCATATTATTAAATTAATTT
*
21491830 ATTATACATATTATTAATTTAATTT
1 ATTAT-CATATTATTAAATTAATTT
21491855 A
1 A
21491856 AATTTTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTATCATATTATTAAATTAATTT
Found at i:21491863 original size:20 final size:20
Alignment explanation
Indices: 21491822--21491863 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
21491812 ATATTATTAA
*
21491822 ATTAATTTATTATACATATT
1 ATTAATTTATTATAAATATT
*
21491842 ATTAATTTAATT-TAAATTTT
1 ATTAATTT-ATTATAAATATT
21491862 AT
1 AT
21491864 AGATTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTAATTTATTATAAATATT
Found at i:21497963 original size:30 final size:31
Alignment explanation
Indices: 21497929--21497987 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
21497919 TTAGATATTG
21497929 ATTATG-TTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTAAGCTTGTTAGATATTGAATTT
*
21497959 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATG-TTTAAGCTTGTTAGATATTGAA
21497988 ATGATTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 6 0.23
32 20 0.77
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.49
Consensus pattern (31 bp):
ATTATGTTTAAGCTTGTTAGATATTGAATTT
Found at i:21499265 original size:22 final size:20
Alignment explanation
Indices: 21499225--21499273 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
21499215 TAATTTAAAA
21499225 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
21499245 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
21499265 TGTAAAAAT
1 TATAAAAAT
21499274 AACTTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:21499386 original size:20 final size:20
Alignment explanation
Indices: 21499361--21499400 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
21499351 AAATATTTTC
21499361 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
*
21499381 AGTAAATCGTTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
21499401 TCATTTTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:21512273 original size:22 final size:23
Alignment explanation
Indices: 21512233--21512296 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
21512223 AATGGCAGCG
* *
21512233 AAACAACATAATAAACAACTA-CA
1 AAACAACACAAAAAACAAC-ACCA
*
21512256 AAACAACA-ATAAAACAACACCA
1 AAACAACACAAAAAACAACACCA
*
21512278 AATCAACACAAAAAACAAC
1 AAACAACACAAAAAACAAC
21512297 CTGCAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 17 0.49
23 17 0.49
ACGTcount: A:0.67, C:0.25, G:0.00, T:0.08
Consensus pattern (23 bp):
AAACAACACAAAAAACAACACCA
Found at i:21527926 original size:22 final size:22
Alignment explanation
Indices: 21527887--21527945 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
21527877 TAGCTCGTAT
21527887 GAGCTTACCGTTTTAGCTCTACA
1 GAGCTTACCG-TTTAGCTCTACA
*
21527910 GAGCTTACCGTTTAGCTCTTCA
1 GAGCTTACCGTTTAGCTCTACA
* *
21527932 TAGTTTACCGTTTA
1 GAGCTTACCGTTTA
21527946 TCAGCTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 23 0.70
23 10 0.30
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (22 bp):
GAGCTTACCGTTTAGCTCTACA
Found at i:21532181 original size:39 final size:41
Alignment explanation
Indices: 21532099--21532181 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 41
21532089 TATGCATATA
** *
21532099 GTATCTGAGATGGGCTAAGGCCCTAATTTATATCTGAGGCT
1 GTATCTGAGATGGGCTAAGGCCCTAAACTATATCTGAAGCT
* *
21532140 GTATCTGA-ATGGGCTAAGG-CCTAAACTGTATCTGAATCT
1 GTATCTGAGATGGGCTAAGGCCCTAAACTATATCTGAAGCT
21532179 GTA
1 GTA
21532182 ATGGGCTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 18 0.49
40 11 0.30
41 8 0.22
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (41 bp):
GTATCTGAGATGGGCTAAGGCCCTAAACTATATCTGAAGCT
Found at i:21538573 original size:7 final size:7
Alignment explanation
Indices: 21538557--21538598 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
21538547 ATTTAAAAAA
21538557 AATTGAG
1 AATTGAG
*
21538564 AATTGGG
1 AATTGAG
21538571 AATTGAG
1 AATTGAG
*
21538578 GATTGAG
1 AATTGAG
21538585 AATTGAG
1 AATTGAG
*
21538592 GATTGAG
1 AATTGAG
21538599 TTAAAAAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (7 bp):
AATTGAG
Found at i:21538576 original size:14 final size:14
Alignment explanation
Indices: 21538557--21538598 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
21538547 ATTTAAAAAA
* *
21538557 AATTGAGAATTGGG
1 AATTGAGGATTGAG
21538571 AATTGAGGATTGAG
1 AATTGAGGATTGAG
21538585 AATTGAGGATTGAG
1 AATTGAGGATTGAG
21538599 TTAAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (14 bp):
AATTGAGGATTGAG
Found at i:21538582 original size:21 final size:21
Alignment explanation
Indices: 21538558--21538598 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21538548 TTTAAAAAAA
21538558 ATTGAGAATTG-GGAATTGAGG
1 ATTGAGAATTGAGG-ATTGAGG
21538579 ATTGAGAATTGAGGATTGAG
1 ATTGAGAATTGAGGATTGAG
21538599 TTAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (21 bp):
ATTGAGAATTGAGGATTGAGG
Found at i:21553324 original size:30 final size:30
Alignment explanation
Indices: 21553266--21553338 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
21553256 TTTGTTAATG
* * **
21553266 AATAAGTAATTTAATATATTTATTTTTAAA
1 AATAAATAATTTAAAATATTTAAATTTAAA
* *
21553296 TAAT-ATTAATTTAAAATTTTTAAATTTAAA
1 -AATAAATAATTTAAAATATTTAAATTTAAA
21553326 AATAAATAATTTA
1 AATAAATAATTTA
21553339 TTTCAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 3 0.09
30 29 0.83
31 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
AATAAATAATTTAAAATATTTAAATTTAAA
Found at i:21553651 original size:33 final size:33
Alignment explanation
Indices: 21553614--21553688 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
21553604 GATGTTCATT
* *
21553614 GATAAATAATGTGCCTCGTTAAAACCTTACTAA
1 GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
21553647 GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
1 GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
21553680 GATAAAAAA
1 GATAAAAAA
21553689 ATCTTAGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (33 bp):
GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
Found at i:21556533 original size:25 final size:26
Alignment explanation
Indices: 21556505--21556554 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
21556495 CAACAAAACT
* *
21556505 AAAATCTAACCTA-AAAAGAAAAGAG
1 AAAACCTAAACTAGAAAAGAAAAGAG
*
21556530 AAAACCTAAACTAGAAATGAAAAGA
1 AAAACCTAAACTAGAAAAGAAAAGA
21556555 ACAAAAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12
Consensus pattern (26 bp):
AAAACCTAAACTAGAAAAGAAAAGAG
Found at i:21563556 original size:27 final size:25
Alignment explanation
Indices: 21563513--21563570 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
21563503 AAATTATAAA
*
21563513 AAAATTTAATATTTATTTTAAAATAT-
1 AAAA-TTAATATTTATTATAAAA-ATC
21563539 AAAATTAATATTAATATTATAAAAATC
1 AAAATTAATATT--TATTATAAAAATC
21563566 AAAAT
1 AAAAT
21563571 ATAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.29
26 6 0.21
27 14 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATTAATATTTATTATAAAAATC
Found at i:21567011 original size:129 final size:129
Alignment explanation
Indices: 21566774--21567025 Score: 355
Period size: 129 Copynumber: 2.0 Consensus size: 129
21566764 ATTTATTTAA
** ** *
21566774 AAATTCTTTAAAACGAAGGCGGTGTTCGATATTTGGCAATTCGCGGAATCGTGCTCTAACATGCT
1 AAATTCTCCAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACATGCT
*
21566839 GGGTTGCAATTCCTCGTTTGCTCAAAATAATTGAATGTCCCTTTAGAATTTCATTCATGCGTTT
66 GGGTTGCAATTCCTCGTTTGCTCAAAATAATTGAATGTCCCTTTAGAATTTCACTCATGCGTTT
* * *
21566903 AAATTCTCCAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCATGCT
1 AAATTCTCCAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACATGCT
* * * *
21566968 GGGTTGTAATTTCCT-GTTTGTTCAAAATGATTGAA-GATTCCTTTAGAATTTCACTCAT
66 GGGTTGCAA-TTCCTCGTTTGCTCAAAATAATTGAATG-TCCCTTTAGAATTTCACTCAT
21567026 ATTCTCTAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
128 1 0.01
129 102 0.94
130 5 0.05
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (129 bp):
AAATTCTCCAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACATGCT
GGGTTGCAATTCCTCGTTTGCTCAAAATAATTGAATGTCCCTTTAGAATTTCACTCATGCGTTT
Found at i:21593980 original size:28 final size:28
Alignment explanation
Indices: 21593947--21594008 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
21593937 CCACAAATAC
* *
21593947 AGGTTCATAATTAGGGCTCGCACATGTA
1 AGGTTCACAACTAGGGCTCGCACATGTA
* * * *
21593975 GGGTTCGCACCTAGGGTTCGCACATGTA
1 AGGTTCACAACTAGGGCTCGCACATGTA
21594003 AGGTTC
1 AGGTTC
21594009 GCGTATGCGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (28 bp):
AGGTTCACAACTAGGGCTCGCACATGTA
Found at i:21593982 original size:15 final size:15
Alignment explanation
Indices: 21593958--21594010 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
21593948 GGTTCATAAT
*
21593958 TAGGGCTCGCACATG
1 TAGGGTTCGCACATG
*
21593973 TAGGGTTCGCAC--C
1 TAGGGTTCGCACATG
21593986 TAGGGTTCGCACATG
1 TAGGGTTCGCACATG
*
21594001 TAAGGTTCGC
1 TAGGGTTCGC
21594011 GTATGCGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.38
15 20 0.62
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.25
Consensus pattern (15 bp):
TAGGGTTCGCACATG
Found at i:21593991 original size:13 final size:13
Alignment explanation
Indices: 21593973--21593997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21593963 CTCGCACATG
21593973 TAGGGTTCGCACC
1 TAGGGTTCGCACC
21593986 TAGGGTTCGCAC
1 TAGGGTTCGCAC
21593998 ATGTAAGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.24
Consensus pattern (13 bp):
TAGGGTTCGCACC
Found at i:21594073 original size:21 final size:20
Alignment explanation
Indices: 21594047--21594100 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
21594037 GACATATATA
21594047 AGGTTCGCATAAAAAGCACAT
1 AGGTTCGCATAAAAA-CACAT
* * *
21594068 AGGTTCACATAAATACATAT
1 AGGTTCGCATAAAAACACAT
21594088 AGGGTTCGCATAA
1 A-GGTTCGCATAA
21594101 CATGGCTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (20 bp):
AGGTTCGCATAAAAACACAT
Found at i:21594337 original size:25 final size:25
Alignment explanation
Indices: 21594309--21594361 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
21594299 TTATGACTCG
*
21594309 CATGTGACAAACAACAGGTGACACA
1 CATGTAACAAACAACAGGTGACACA
* ** *
21594334 CATGTAATATTCAACAGGTGACTCA
1 CATGTAACAAACAACAGGTGACACA
21594359 CAT
1 CAT
21594362 ATACAACAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (25 bp):
CATGTAACAAACAACAGGTGACACA
Found at i:21595653 original size:48 final size:48
Alignment explanation
Indices: 21595582--21595678 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
21595572 TATATAGGGA
21595582 TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
1 TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
21595630 TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
1 TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
21595678 T
1 T
21595679 TAGTCTCTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.16, C:0.27, G:0.12, T:0.44
Consensus pattern (48 bp):
TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
Found at i:21599150 original size:27 final size:26
Alignment explanation
Indices: 21599115--21599226 Score: 118
Period size: 27 Copynumber: 4.2 Consensus size: 26
21599105 AGCATGGCTG
* *
21599115 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
21599141 CCAGATACAGATAACCGTGGCAGAGCCA
1 CCAGA-ACAGATAA-TGTGGCAGAGCCA
*
21599169 CCAGAACAGATATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
21599196 CCA-AATCAGATAATTGTGGCATAGCAA
1 CCAGAA-CAGATAA-TGTGGCAGAGCCA
21599223 CCAG
1 CCAG
21599227 GACGCTTCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.11
27 48 0.67
28 16 0.22
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:21599179 original size:54 final size:54
Alignment explanation
Indices: 21599115--21599226 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
21599105 AGCATGGCTG
* * *
21599115 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAACCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAAAT-CAGATAACCGTGGCAGAGCAA
** ** *
21599169 CCAGAACAGATATATGTGGTAGAGCCACCAAATCAGATAATTGTGGCATAGCAA
1 CCAGAACAGATATATGTGACAGAGCCACCAAATCAGATAACCGTGGCAGAGCAA
21599223 CCAG
1 CCAG
21599227 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 33 0.67
55 16 0.33
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAAATCAGATAACCGTGGCAGAGCAA
Found at i:21606030 original size:16 final size:16
Alignment explanation
Indices: 21606005--21606036 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21605995 CAATCTTTAT
*
21606005 AAAATTTTTATTTTCG
1 AAAATCTTTATTTTCG
21606021 AAAATCTTTATTTTCG
1 AAAATCTTTATTTTCG
21606037 TAAACCCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (16 bp):
AAAATCTTTATTTTCG
Found at i:21607070 original size:27 final size:26
Alignment explanation
Indices: 21607008--21607119 Score: 89
Period size: 27 Copynumber: 4.2 Consensus size: 26
21606998 AACATGGCTG
* ** *
21607008 CCAGAATAGAAAATGTGATAGAGTCA
1 CCAGAACAGAAAATGTGGCAGAGCCA
**
21607034 TTAGATACAGAAAATCGTGGCAGAGCCA
1 CCAGA-ACAGAAAAT-GTGGCAGAGCCA
* *
21607062 CCAGAACAGATATATGTGGTAGAGCCA
1 CCAGAACAGA-AAATGTGGCAGAGCCA
* * *
21607089 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGA-AAATGTGGCAGAGCCA
21607116 CCAG
1 CCAG
21607120 GACGCTTCCT
Statistics
Matches: 68, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
26 3 0.04
27 50 0.74
28 15 0.22
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (26 bp):
CCAGAACAGAAAATGTGGCAGAGCCA
Found at i:21609398 original size:29 final size:29
Alignment explanation
Indices: 21609364--21609434 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
21609354 TGAGAACTTA
21609364 TGATATGTGAGCCTTTATGGCTGAATCTC
1 TGATATGTGAGCCTTTATGGCTGAATCTC
*
21609393 TGATATATGAGCCTTTATGGCTGAATCTC
1 TGATATGTGAGCCTTTATGGCTGAATCTC
21609422 TGATATGTGAGCC
1 TGATATGTGAGCC
21609435 CGTCTAGCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (29 bp):
TGATATGTGAGCCTTTATGGCTGAATCTC
Found at i:21609564 original size:65 final size:65
Alignment explanation
Indices: 21609441--21609572 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 65
21609431 AGCCCGTCTA
* * * * *
21609441 GCGAAGATTGTTTGAATGCAAGTTGGTGTCTTAATAGTTGTTCCTGTTACATGTGTGCCCTTGTG
1 GCGAAGATTGTTTGAATGCAAGTGGGTGTCTTAATAGCTATTCATGATACATGTGTGCCCTTGTG
* * * *
21609506 GCGAAGATTGTTTGAATGCAGGTGGGTGTCTTAATGGCTATCTGATGATGCATG-GTGCCCTTGT
1 GCGAAGATTGTTTGAATGCAAGTGGGTGTCTTAATAGCTAT-TCATGATACATGTGTGCCCTTGT
21609570 G
65 G
21609571 GC
1 GC
21609573 TATATGTTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 49 0.86
66 8 0.14
ACGTcount: A:0.18, C:0.14, G:0.31, T:0.36
Consensus pattern (65 bp):
GCGAAGATTGTTTGAATGCAAGTGGGTGTCTTAATAGCTATTCATGATACATGTGTGCCCTTGTG
Found at i:21624242 original size:30 final size:31
Alignment explanation
Indices: 21624202--21624260 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
21624192 ATCTATTTAC
* *
21624202 TTTCCTCCAAAATTTTTACTCC-CTCCCACT
1 TTTCCACCAAAACTTTTACTCCTCTCCCACT
*
21624232 TTTCCACCAAAACTTTTATTCCTCTCCCA
1 TTTCCACCAAAACTTTTACTCCTCTCCCA
21624261 TCCCACCCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (31 bp):
TTTCCACCAAAACTTTTACTCCTCTCCCACT
Found at i:21624384 original size:125 final size:128
Alignment explanation
Indices: 21624238--21624474 Score: 349
Period size: 125 Copynumber: 1.9 Consensus size: 128
21624228 CACTTTTCCA
* * * * *
21624238 CCAAAACTTTTATTCCTCTCCCATCCCACCCCCCTTCTA-CCCAAACTCATCCCCTCC-CCCC-C
1 CCAAAACGTTTACTCCCCTCCCATCCCACCCCCCTTCTACCCCAAACCCA-CCCC-CCACCCCAA
* *
21624300 CTTTTTTTTAATATT-TCC-CCCCAAAATTTTACTCCTTCAACCCCCAAAACTTTTTATTTTCTC
64 ATTTTTTTTAATATTCTCCTCCCCAAAATTTTACTCCCTCAACCCCCAAAACTTTTTATTTTCTC
*
21624363 CCAAAACGTTTACTCCCCTCCCATTCCACCCCCCTTCTACCCCAAACCCACCCCCCACCCCAAAT
1 CCAAAACGTTTACTCCCCTCCCATCCCACCCCCCTTCTACCCCAAACCCACCCCCCACCCCAAAT
21624428 TTTTTTTAATATTCTCCTCCCCAAAATTTTACTCCCTCAACCCCCAA
66 TTTTTTTAATATTCTCCTCCCCAAAATTTTACTCCCTCAACCCCCAA
21624475 TTTTTTTTTA
Statistics
Matches: 99, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
124 2 0.02
125 43 0.43
126 23 0.23
127 3 0.03
128 28 0.28
ACGTcount: A:0.23, C:0.46, G:0.00, T:0.31
Consensus pattern (128 bp):
CCAAAACGTTTACTCCCCTCCCATCCCACCCCCCTTCTACCCCAAACCCACCCCCCACCCCAAAT
TTTTTTTAATATTCTCCTCCCCAAAATTTTACTCCCTCAACCCCCAAAACTTTTTATTTTCTC
Found at i:21625047 original size:30 final size:30
Alignment explanation
Indices: 21625011--21625079 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
21625001 TATATTTGAT
*
21625011 TCGATTCGATTGAATTACATCTCATTCGAC
1 TCGATTCGATTGAATTACATCTCACTCGAC
* *
21625041 TCGATTCGATTGAATTCCATCTCACTCGGC
1 TCGATTCGATTGAATTACATCTCACTCGAC
21625071 TCGATTCGA
1 TCGATTCGA
21625080 GAAAATTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (30 bp):
TCGATTCGATTGAATTACATCTCACTCGAC
Found at i:21625244 original size:17 final size:18
Alignment explanation
Indices: 21625211--21625244 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21625201 TAGAAGTATT
21625211 AATAATTATACATTTAAA
1 AATAATTATACATTTAAA
*
21625229 AATATTTATA-ATTTAA
1 AATAATTATACATTTAA
21625245 TATAAGTTGT
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:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAATTATACATTTAAA
Found at i:21629513 original size:13 final size:12
Alignment explanation
Indices: 21629489--21629516 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
21629479 AATAGTCATC
21629489 TATCAGTTTTTT
1 TATCAGTTTTTT
21629501 TATCAGTTTTTT
1 TATCAGTTTTTT
21629513 TATC
1 TATC
21629517 TTTATTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.64
Consensus pattern (12 bp):
TATCAGTTTTTT
Found at i:21629652 original size:15 final size:15
Alignment explanation
Indices: 21629632--21629663 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21629622 GGTAACGTTG
21629632 TAACTAAGGGTTGAA
1 TAACTAAGGGTTGAA
21629647 TAACTAAGGGTTGAA
1 TAACTAAGGGTTGAA
21629662 TA
1 TA
21629664 CAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (15 bp):
TAACTAAGGGTTGAA
Found at i:21632259 original size:41 final size:40
Alignment explanation
Indices: 21632194--21632288 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 40
21632184 ATAATAAATC
*
21632194 AAATATATTTAAAACAAATATTAAAATAAGAAACAAATAAA
1 AAATATA-ATAAAACAAATATTAAAATAAGAAACAAATAAA
* * * * * *
21632235 AAATGATACTAAAACAATTCTTAAAATAATACACAAATTAA
1 AAAT-ATAATAAAACAAATATTAAAATAAGAAACAAATAAA
21632276 AAATATAATAAAA
1 AAATATAATAAAA
21632289 AGTGATTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 8 0.17
41 35 0.76
42 3 0.07
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.25
Consensus pattern (40 bp):
AAATATAATAAAACAAATATTAAAATAAGAAACAAATAAA
Found at i:21632339 original size:28 final size:27
Alignment explanation
Indices: 21632271--21632339 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
21632261 TAATACACAA
* * *
21632271 ATTAAAAATATAATAAAAAGTGATTAT
1 ATTAAAAATAAAATAAAAAGTAAATAT
* *
21632298 ATTAAAATTGAAAATAAAATGTAAATAT
1 ATTAAAAAT-AAAATAAAAAGTAAATAT
21632326 GATTAAAAATAAAA
1 -ATTAAAAATAAAA
21632340 AATATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 8 0.24
28 18 0.53
29 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (27 bp):
ATTAAAAATAAAATAAAAAGTAAATAT
Found at i:21640654 original size:3 final size:3
Alignment explanation
Indices: 21640646--21640671 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21640636 GTGATAGAAA
21640646 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
21640672 CCTTCATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21643553 original size:19 final size:18
Alignment explanation
Indices: 21643505--21643545 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
21643495 TTTTAAAAGG
* *
21643505 AAAACAAATGAATTTTAA
1 AAAACAAATGAATCTAAA
21643523 AAAACAAATGAATCTAAA
1 AAAACAAATGAATCTAAA
21643541 AAAAC
1 AAAAC
21643546 TTAATGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAACAAATGAATCTAAA
Found at i:21645518 original size:17 final size:18
Alignment explanation
Indices: 21645486--21645520 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
21645476 ATAATTTTTA
21645486 AATGTGTCTAAATTAATT
1 AATGTGTCTAAATTAATT
*
21645504 AATGTG-CTGAATTAATT
1 AATGTGTCTAAATTAATT
21645521 TGTGTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (18 bp):
AATGTGTCTAAATTAATT
Found at i:21650065 original size:27 final size:27
Alignment explanation
Indices: 21650035--21650088 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21650025 GCTTCTTGTG
21650035 TTAGCTTCTTTTCAGATTTCGCTAAAT
1 TTAGCTTCTTTTCAGATTTCGCTAAAT
21650062 TTAGCTTCTTTTCAGATTTCGCTAAAT
1 TTAGCTTCTTTTCAGATTTCGCTAAAT
21650089 CTTTTCCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (27 bp):
TTAGCTTCTTTTCAGATTTCGCTAAAT
Found at i:21654004 original size:74 final size:74
Alignment explanation
Indices: 21653905--21654047 Score: 205
Period size: 74 Copynumber: 1.9 Consensus size: 74
21653895 TAGTGCTAGG
* * * * *
21653905 CGCAAATATTGTTAGTAAATCCAACTAGAGCTGGGCTCACTATTTATTCGTCGGTTTATCCGACC
1 CGCAAATACTATTAGTAAATCCAACTAGAGCTGGGCTCACAAATTATTCGTCGGTTTACCCGACC
21653970 AGCGCCGGA
66 AGCGCCGGA
* * * *
21653979 CGCAAATACTATTGGTATATCCAACTAGAGCTGGGCTCACAAATTATTTGTCGGTTTACCCGACT
1 CGCAAATACTATTAGTAAATCCAACTAGAGCTGGGCTCACAAATTATTCGTCGGTTTACCCGACC
21654044 AGCG
66 AGCG
21654048 TTGAGCACAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (74 bp):
CGCAAATACTATTAGTAAATCCAACTAGAGCTGGGCTCACAAATTATTCGTCGGTTTACCCGACC
AGCGCCGGA
Found at i:21660154 original size:426 final size:427
Alignment explanation
Indices: 21659361--21660218 Score: 1691
Period size: 426 Copynumber: 2.0 Consensus size: 427
21659351 ATCAAAAGAC
*
21659361 ATGAAATATAAATATATATGAATTGCTTAACTACAGAGAAGAGATGTAAAATGAATGTAAGGGGT
1 ATGAAATATAAATATATATGAATTGCTTAACTACAGAGAAGAGATGTAAAATGAACGTAAGGGGT
21659426 GAAGCTATTAAGATTATGAAAGTAAAAAGTTTAAGTTACAATGTATATTCATAGCTTATTATTGT
66 GAAGCTATTAAGATTATGAAAGTAAAAAGTTTAAGTTACAATGTATATTCATAGCTTATTATTGT
21659491 TTTAAGTATTAGTTTATAGAAATACCACTGAGTGTATACTCAGCGTACGGTATGTTTCAGTACAC
131 TTTAAGTATTAGTTTATAGAAATACCACTGAGTGTATACTCAGCGTACGGTATGTTTCAGTACAC
21659556 AGGACTAGGTACGAAAGAAAGCTAAGGGCTCAGCATCCAAGCCAATCCGGGATTTAAAGTGGTGA
196 AGGACTAGGTACGAAAGAAAGCTAAGGGCTCAGCATCCAAGCCAATCCGGGATTTAAAGTGGTGA
21659621 ATACTTTTCTTTTGGTAAAATGGCATGTACCTAGGTTGTTAAGGTGTTATTTTGTACATGATAGT
261 ATACTTTTCTTTTGGTAAAATGGCATGTACCTAGGTTGTTAAGGTGTTATTTTGTACATGATAGT
21659686 GAATAAGCATGAAAGTTGTTGAAGTATGGTATGAAATATGCATATTTTGGAAGTTAAACTTATAT
326 GAATAAGCATGAAAGTTGTTGAAGTATGGTATGAAATATGCATATTTTGGAAGTTAAACTTATAT
21659751 GAGTTTGACTAGTATGATAATGTAATATAATTTTG-T
391 GAGTTTGACTAGTATGATAATGTAATATAATTTTGTT
*
21659787 ATGAAATATAAATATATATGAATTGCTTAACTACAGAGAAGAGATGTAAAATGAACGTAATGGGT
1 ATGAAATATAAATATATATGAATTGCTTAACTACAGAGAAGAGATGTAAAATGAACGTAAGGGGT
21659852 GAAGCTATTAAGATTATGAAAGTAAAAAGTTTAAGTTACAATGTATATTCATAGCTTATTATTGT
66 GAAGCTATTAAGATTATGAAAGTAAAAAGTTTAAGTTACAATGTATATTCATAGCTTATTATTGT
21659917 TTTAAGTATTAGTTTATAGAAATACCACTGAGTGTATACTCAGCGTACGGTATGTTTCAGTACAC
131 TTTAAGTATTAGTTTATAGAAATACCACTGAGTGTATACTCAGCGTACGGTATGTTTCAGTACAC
21659982 AGGACTAGGTACGAAAGAAAGCTAAGGGCTCAGCATCCAAGCCAATCCGGGATTTAAAGTGGTGA
196 AGGACTAGGTACGAAAGAAAGCTAAGGGCTCAGCATCCAAGCCAATCCGGGATTTAAAGTGGTGA
21660047 ATACTTTTCTTTTGGTAAAATGGCATGTACCTAGGTTGTTAAGGTGTTATTTTGTACATGATAGT
261 ATACTTTTCTTTTGGTAAAATGGCATGTACCTAGGTTGTTAAGGTGTTATTTTGTACATGATAGT
21660112 GAATAAGCATGAAAGTTGTTGAAGTATGGTATGAAATATGCATATTTTGGAAGTTAAACTTATAT
326 GAATAAGCATGAAAGTTGTTGAAGTATGGTATGAAATATGCATATTTTGGAAGTTAAACTTATAT
21660177 GAGTTTGACTAGTATGATAATGTAATATAATTTTGTT
391 GAGTTTGACTAGTATGATAATGTAATATAATTTTGTT
21660214 ATGAA
1 ATGAA
21660219 TTGTGGTACA
Statistics
Matches: 429, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
426 423 0.99
427 6 0.01
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (427 bp):
ATGAAATATAAATATATATGAATTGCTTAACTACAGAGAAGAGATGTAAAATGAACGTAAGGGGT
GAAGCTATTAAGATTATGAAAGTAAAAAGTTTAAGTTACAATGTATATTCATAGCTTATTATTGT
TTTAAGTATTAGTTTATAGAAATACCACTGAGTGTATACTCAGCGTACGGTATGTTTCAGTACAC
AGGACTAGGTACGAAAGAAAGCTAAGGGCTCAGCATCCAAGCCAATCCGGGATTTAAAGTGGTGA
ATACTTTTCTTTTGGTAAAATGGCATGTACCTAGGTTGTTAAGGTGTTATTTTGTACATGATAGT
GAATAAGCATGAAAGTTGTTGAAGTATGGTATGAAATATGCATATTTTGGAAGTTAAACTTATAT
GAGTTTGACTAGTATGATAATGTAATATAATTTTGTT
Found at i:21662885 original size:31 final size:30
Alignment explanation
Indices: 21662850--21662921 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
21662840 ATTATTAAAG
* *
21662850 TAAAATTATACTTTGACCTTTTTTA-AAATTA
1 TAAAATTATAATTT-A-ATTTTTTATAAATTA
21662881 TAAAAATT-TAATTTAATTTTTTATAAATTA
1 T-AAAATTATAATTTAATTTTTTATAAATTA
*
21662911 TAAAAATATAA
1 TAAAATTATAA
21662922 ACTATAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
29 12 0.34
30 11 0.31
31 6 0.17
32 6 0.17
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (30 bp):
TAAAATTATAATTTAATTTTTTATAAATTA
Found at i:21662922 original size:15 final size:15
Alignment explanation
Indices: 21662902--21662931 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21662892 TTTAATTTTT
*
21662902 TATAAATTATAAAAA
1 TATAAACTATAAAAA
21662917 TATAAACTATAAAAA
1 TATAAACTATAAAAA
21662932 ATTCAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:21673827 original size:52 final size:48
Alignment explanation
Indices: 21673765--21673957 Score: 187
Period size: 47 Copynumber: 4.0 Consensus size: 48
21673755 GAAATGTGAT
* * *
21673765 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATTTGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
21673817 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * *
21673864 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * * *
21673910 ATCCGTGTAAGACCATGGCTGGGCTATGGCCTCG-GTATGTGATATGTG
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAG--TGTGATATGTG
21673958 ACTATGTGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
46 26 0.21
47 53 0.44
48 11 0.09
50 1 0.01
51 1 0.01
52 29 0.24
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:21677781 original size:27 final size:27
Alignment explanation
Indices: 21677751--21677928 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21677741 ATATTGAGTC
* * * *
21677751 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
21677778 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
21677805 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
21677833 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
21677860 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
21677887 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
21677914 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
21677929 GTACAATAAA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:21677890 original size:82 final size:81
Alignment explanation
Indices: 21677772--21677927 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
21677762 TGCTATATAA
* *
21677772 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
21677837 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
21677854 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
21677918 CACTTAGTGC
65 CACTTAGTGC
21677928 TGTACAATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:21678433 original size:12 final size:12
Alignment explanation
Indices: 21678416--21678441 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21678406 ATGGCATACT
21678416 TATGTATATATA
1 TATGTATATATA
21678428 TATGTATATATA
1 TATGTATATATA
21678440 TA
1 TA
21678442 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:21679986 original size:29 final size:28
Alignment explanation
Indices: 21679954--21680048 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 28
21679944 TTGAGATACT
21679954 AAATTGAACCTAAAAAAAGTTTAGGTACC
1 AAATTGAA-CTAAAAAAAGTTTAGGTACC
* *
21679983 AAATTAAGAA-AAAAATACCAAGTTAAGGTACC
1 AAATT--GAACTAAAA-A--AAGTTTAGGTACC
**
21680015 AAATTGGGCTTAAAAAAAGTTTAGGTACC
1 AAATTGAAC-TAAAAAAAGTTTAGGTACC
21680044 AAATT
1 AAATT
21680049 AAGAAAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
29 26 0.49
30 2 0.04
31 4 0.08
32 21 0.40
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (28 bp):
AAATTGAACTAAAAAAAGTTTAGGTACC
Found at i:21680036 original size:61 final size:60
Alignment explanation
Indices: 21679964--21680118 Score: 215
Period size: 59 Copynumber: 2.6 Consensus size: 60
21679954 AAATTGAACC
* *
21679964 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGGTACCAAATTGGGCT
1 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGATACCAAATTAGG-T
** *
21680025 TAAAAAAAGTTTAGGTACCAAATTAAG-AAAAAATGTCAAGTTCAGATACCAAATTAGGT
1 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGATACCAAATTAGGT
* * *
21680084 AAAAAAAAGTTTAGGTACTAAATT-AGAACAAAATA
1 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATA
21680119 GTAAGTTGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.02
59 29 0.35
60 26 0.31
61 27 0.32
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.24
Consensus pattern (60 bp):
TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGATACCAAATTAGGT
Done.