Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold311
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: 800152
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 7
Found at i:164536 original size:2 final size:2
Alignment explanation
Indices: 164531--164563 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
164521 ACCTGCGCGC
164531 AT AT 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 AT AT A
164564 AATAATTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:164903 original size:74 final size:75
Alignment explanation
Indices: 164774--164917 Score: 254
Period size: 74 Copynumber: 1.9 Consensus size: 75
164764 CATCAAACTA
*
164774 ATAACATTTGGATTCGACATATATTGGATCACTCGGCCATGAGTAACGAAGGTTTGATCTT-CAA
1 ATAACATTTGGATTCGACATATATTGGACCACTCGGCCATGAGTAACGAAGGTTTGATCTTCCAA
164838 ATATATAAAT
66 ATATATAAAT
* *
164848 ATAACATTTGGATTCGACATATATTGGACCACTCGGCCATGAGTAATGAATGTTTGATCTTCCAA
1 ATAACATTTGGATTCGACATATATTGGACCACTCGGCCATGAGTAACGAAGGTTTGATCTTCCAA
164913 ATATA
66 ATATA
164918 CATACAAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
74 58 0.88
75 8 0.12
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (75 bp):
ATAACATTTGGATTCGACATATATTGGACCACTCGGCCATGAGTAACGAAGGTTTGATCTTCCAA
ATATATAAAT
Found at i:165778 original size:29 final size:29
Alignment explanation
Indices: 165741--165808 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
165731 ATTTGATAAT
*
165741 TTATATTATATTCATATCT-ATATATTTTA
1 TTAT-TTATATTCATATCTAAAATATTTTA
* *
165770 TTATGTTATAATCATATTTAAAATATTTTA
1 TTAT-TTATATTCATATCTAAAATATTTTA
165800 -TATTTATAT
1 TTATTTATAT
165809 AAATTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 5 0.15
29 19 0.58
30 9 0.27
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (29 bp):
TTATTTATATTCATATCTAAAATATTTTA
Found at i:166362 original size:20 final size:20
Alignment explanation
Indices: 166337--166376 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
166327 TTTGTACTAC
166337 TGCAAAATTTAATAGAATTA
1 TGCAAAATTTAATAGAATTA
166357 TGCAAAATTTAATAGAATTA
1 TGCAAAATTTAATAGAATTA
166377 AGGATGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
TGCAAAATTTAATAGAATTA
Found at i:171165 original size:28 final size:28
Alignment explanation
Indices: 171113--171173 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
171103 ACAAGTGGTC
* *
171113 AATTAAAATTTTATATGTAATAAAATTT
1 AATTAAAATTTAATATGTAATAAAATAT
171141 AATTAAGAATTTAATCATGT-A-AAAATAT
1 AATTAA-AATTTAAT-ATGTAATAAAATAT
171169 AATTA
1 AATTA
171174 GGAGACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 17 0.59
29 8 0.28
30 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (28 bp):
AATTAAAATTTAATATGTAATAAAATAT
Found at i:173472 original size:23 final size:24
Alignment explanation
Indices: 173429--173475 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
173419 AAGGGTAAGT
*
173429 GTATTTTGTAGATTTTTTTTATTA
1 GTATTTTGTAGAGTTTTTTTATTA
173453 GTATTTTGTAG-GTTTTTTTATTA
1 GTATTTTGTAGAGTTTTTTTATTA
173476 TAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.66
Consensus pattern (24 bp):
GTATTTTGTAGAGTTTTTTTATTA
Found at i:173943 original size:146 final size:145
Alignment explanation
Indices: 173780--174106 Score: 365
Period size: 146 Copynumber: 2.2 Consensus size: 145
173770 AGGGTATTAT
* * * *
173780 TTATCTTTATTTGTAGAAGTTTAAATTA-TTTTTAGTTATGATTATACGAGTTAAAATTTTTAA-
1 TTATTTTTATTTGTAGAAGTTTAAATTATTTTTTAGGTATGATCATACAAGTTAAAATTTTTAAT
** * * * ** *
173843 GGTATAATTTATTTTTATTTATAGAAGTTTAAATGTGT-TTTTTTGGATATGCTTATACGAGTTT
66 CATATAATTCATTTTTATTTATAGAAATTTAAAT-T-TATTTTTTAGAT-TAATTACACGAGTTT
*
173907 AAAATTTTAATAGTATAAA
128 -AAATTTTAAGAGTATAAA
* * *
173926 TTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTGGGTATGATCATATAAGTTAATATTTTTAA
1 TTATTTTTATTTGTAGAAGTTTAAAT-TATTTTTTAGGTATGATCATACAAGTTAAAATTTTTAA
* ** *
173991 TCATATAATTCATTTTTATTTGTAGAAATTTAAATTTATTTTTTAGATTAATTACGTGAGTTTTA
65 TCATATAATTCATTTTTATTTATAGAAATTTAAATTTATTTTTTAGATTAATTACACGAGTTTAA
* * *
174056 ATTTTTAGGGTATTAA
130 ATTTTAAGAGTATAAA
174072 TTATTTTTATTTGTAGAAGTTTAAATT-TTTATTTA
1 TTATTTTTATTTGTAGAAGTTTAAATTATTT-TTTA
174107 AAGGTTACGT
Statistics
Matches: 152, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
144 3 0.02
145 4 0.03
146 64 0.42
147 13 0.09
148 39 0.26
149 29 0.19
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.53
Consensus pattern (145 bp):
TTATTTTTATTTGTAGAAGTTTAAATTATTTTTTAGGTATGATCATACAAGTTAAAATTTTTAAT
CATATAATTCATTTTTATTTATAGAAATTTAAATTTATTTTTTAGATTAATTACACGAGTTTAAA
TTTTAAGAGTATAAA
Found at i:173959 original size:74 final size:73
Alignment explanation
Indices: 173780--174097 Score: 306
Period size: 74 Copynumber: 4.4 Consensus size: 73
173770 AGGGTATTAT
* *
173780 TTATCTTTATTTGTAGAAGTTTAAAT-TA-TTTTTAGTTATGATTATACGAGTTAAAATTTTTAA
1 TTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGATATGATTATACGAGTTAAAA-TTTTAA
* *
173843 -GGTATAAT
65 TAGTATAAA
* * * *
173851 TTATTTTTATTTATAGAAGTTTAAATGTGTTTTTTTGGATATGCTTATACGAGTTTAAAATTTTA
1 TTATTTTTATTTGTAGAAGTTTAAATGT-ATTTTTTAGATATGATTATACGAG-TTAAAATTTTA
173916 ATAGTATAAA
64 ATAGTATAAA
* * * ** *
173926 TTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTGGGTATGATCATATAAGTTAATATTTTTAA
1 TTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGATATGATTATACGAGTTAA-AATTTTAA
173991 TCA-TAT-AA
65 T-AGTATAAA
* * * *** ** *
173999 TTCATTTTTATTTGTAGAAATTTAAATTTATTTTTTAGAT-TAATTACGTGAGTTTTAATTTTTA
1 TT-ATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGATATGATTATACGAGTTAAAATTTTAA
** *
174063 GGGTATTAA
65 TAGTATAAA
174072 TTATTTTTATTTGTAGAAGTTTAAAT
1 TTATTTTTATTTGTAGAAGTTTAAAT
174098 TTTTATTTAA
Statistics
Matches: 205, Mismatches: 32, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
71 24 0.12
72 33 0.16
73 21 0.10
74 87 0.42
75 40 0.20
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (73 bp):
TTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGATATGATTATACGAGTTAAAATTTTAAT
AGTATAAA
Found at i:177003 original size:2 final size:2
Alignment explanation
Indices: 176996--177035 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
176986 TGAAAGAGCA
*
176996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
177036 GTAAATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:178215 original size:2 final size:2
Alignment explanation
Indices: 178202--178263 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
178192 TCTTAGTATG
* *
178202 AT AT AT AA AT AT AT AT AT TT 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
178244 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
178264 GGTTAAATAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:178537 original size:19 final size:19
Alignment explanation
Indices: 178513--178549 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
178503 AAGTTTATTT
178513 TATTA-TTTATATATTAAAA
1 TATTATTTTAT-TATTAAAA
178532 TATTATTTTATTATTAAA
1 TATTATTTTATTATTAAA
178550 TAATAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATTTTATTATTAAAA
Found at i:178558 original size:19 final size:20
Alignment explanation
Indices: 178518--178558 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
178508 TATTTTATTA
*
178518 TTTATATATTAAAATATTAT
1 TTTATATATTAAAATATAAT
178538 TTTAT-TATT-AAATAATAAT
1 TTTATATATTAAAAT-ATAAT
178557 TT
1 TT
178559 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATATATTAAAATATAAT
Found at i:178559 original size:18 final size:20
Alignment explanation
Indices: 178517--178571 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 20
178507 TTATTTTATT
*
178517 ATTTATATATTAAAATATTA
1 ATTTATATATTAAAATAATA
*
178537 TTTTAT-TATT-AAATAATA
1 ATTTATATATTAAAATAATA
*
178555 ATTTA-A-AATAAAATAAT
1 ATTTATATATTAAAATAAT
178572 TTAAACTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 2 0.07
18 18 0.62
19 4 0.14
20 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATATATTAAAATAATA
Found at i:180745 original size:23 final size:24
Alignment explanation
Indices: 180718--180763 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
180708 TATAATCTTT
*
180718 TTAAAACAACAAT-TTTTTAAAAA
1 TTAAAACAACAATCTTTCTAAAAA
180741 TTAAAACAACAATCTTTCTAAAA
1 TTAAAACAACAATCTTTCTAAAA
180764 TCATTTAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (24 bp):
TTAAAACAACAATCTTTCTAAAAA
Found at i:183273 original size:117 final size:116
Alignment explanation
Indices: 183113--183491 Score: 424
Period size: 117 Copynumber: 3.2 Consensus size: 116
183103 TAATGATCCA
* *
183113 AAAATGCATGAGAATTACTACAAGG-CCTTTAGATTATGGAAAATAATCTAAATGA-CTTCAAAA
1 AAAATGCATGA-AATTACTACATGGTCC-TTAGATTATGAAAAATAA-CTAAATGACCTT-AAAA
* * * *** *
183176 TGC-GGGAAAATTGCAACATAGTTATTAAATTATGAAAAATAATATAAGTGACTTT
62 TGCATGG-AAATTGCTACATGGTCCCTAAATTATGAAAAATAATATAAATGACTTT
* **
183231 AAAATGCATGAAATTGCTACATGGTCCTTAGATTATGAAAAATAACTTCCATGACCTTAAAAT-C
1 AAAATGCATGAAATTACTACATGGTCCTTAGATTATGAAAAATAAC-TAAATGACCTTAAAATGC
* ** * *
183295 ATGGAAATTGCTACATGGTCCGTGGATTATGAAAAATGATATAAATGATTTT
65 ATGGAAATTGCTACATGGTCCCTAAATTATGAAAAATAATATAAATGACTTT
* * * * *
183347 AAAATGCATGAAACTATTAAATGGTCCTTAGATTATAGAAAAAGAACTAAATGACCTTAAGATGC
1 AAAATGCATGAAATTACTACATGGTCCTTAGATTAT-GAAAAATAACTAAATGACCTTAAAATGC
* **
183412 ATGGAAATTGCTACATGGCCCCTAAATTATGAAAAATAACCTAAATGACTTT
65 ATGGAAATTGCTACATGGTCCCTAAATTATGAAAAATAATATAAATGACTTT
*
183464 AAAATGCATGGAAATTGCTACATGGTCC
1 AAAATGCAT-GAAATTACTACATGGTCC
183492 CTAATATGCA
Statistics
Matches: 218, Mismatches: 36, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
116 85 0.39
117 103 0.47
118 30 0.14
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (116 bp):
AAAATGCATGAAATTACTACATGGTCCTTAGATTATGAAAAATAACTAAATGACCTTAAAATGCA
TGGAAATTGCTACATGGTCCCTAAATTATGAAAAATAATATAAATGACTTT
Found at i:183474 original size:59 final size:59
Alignment explanation
Indices: 183113--183491 Score: 378
Period size: 58 Copynumber: 6.5 Consensus size: 59
183103 TAATGATCCA
* * * *
183113 AAAATGCAT-GAGAATTACTACAAGG-CCTTTAGATTATGGAAAATAATCTAAATGACTTC
1 AAAATGCATGGA-AATTGCTACATGGTCC-TTAGATTATGAAAAATAATCTAAATGACTTT
* * * ** * * *
183172 AAAATGC-GGGAAAATTGCAACATAGTTATTAAATTATGAAAAATAATATAAGTGACTTT
1 AAAATGCATGG-AAATTGCTACATGGTCCTTAGATTATGAAAAATAATCTAAATGACTTT
** *
183231 AAAATGCAT-GAAATTGCTACATGGTCCTTAGATTATGAAAAATAA-CTTCCATGACCTT
1 AAAATGCATGGAAATTGCTACATGGTCCTTAGATTATGAAAAATAATC-TAAATGACTTT
* * * * *
183289 AAAAT-CATGGAAATTGCTACATGGTCCGTGGATTATGAAAAATGATATAAATGATTTT
1 AAAATGCATGGAAATTGCTACATGGTCCTTAGATTATGAAAAATAATCTAAATGACTTT
* ** * * *
183347 AAAATGCAT-GAAACTATTAAATGGTCCTTAGATTATAGAAAAAGAA-CTAAATGACCTT
1 AAAATGCATGGAAATTGCTACATGGTCCTTAGATTAT-GAAAAATAATCTAAATGACTTT
* * * * *
183405 AAGATGCATGGAAATTGCTACATGGCCCCTAAATTATGAAAAATAACCTAAATGACTTT
1 AAAATGCATGGAAATTGCTACATGGTCCTTAGATTATGAAAAATAATCTAAATGACTTT
183464 AAAATGCATGGAAATTGCTACATGGTCC
1 AAAATGCATGGAAATTGCTACATGGTCC
183492 CTAATATGCA
Statistics
Matches: 255, Mismatches: 54, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
57 3 0.01
58 133 0.52
59 118 0.46
60 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (59 bp):
AAAATGCATGGAAATTGCTACATGGTCCTTAGATTATGAAAAATAATCTAAATGACTTT
Found at i:184025 original size:20 final size:20
Alignment explanation
Indices: 183993--184070 Score: 86
Period size: 20 Copynumber: 3.8 Consensus size: 20
183983 ACTACCAAGA
*
183993 AAATGTATCGATACATTAAT
1 AAATGTATAGATACATTAAT
* *
184013 AAATGCATAGATACATGCTTCA-
1 AAATGTATAGATACA---TTAAT
*
184035 AAATGTATCGATACATTAAT
1 AAATGTATAGATACATTAAT
184055 AAATGTATAGATACAT
1 AAATGTATAGATACAT
184071 GTTTCAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 3 0.06
20 28 0.60
22 13 0.28
23 3 0.06
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (20 bp):
AAATGTATAGATACATTAAT
Found at i:184047 original size:22 final size:20
Alignment explanation
Indices: 183992--184094 Score: 84
Period size: 20 Copynumber: 5.0 Consensus size: 20
183982 TACTACCAAG
183992 AAAATGTATCGATACA-TTA
1 AAAATGTATCGATACATTTA
* * *
184011 ATAAATGCATAGATACATGCTTC
1 A-AAATGTATCGATACAT--TTA
184034 AAAATGTATCGATACA-TTA
1 AAAATGTATCGATACATTTA
* *
184053 ATAAATGTATAGATACATGTTTC
1 A-AAATGTATCGATACA--TTTA
*
184076 AAATTGTATCGATACATTT
1 AAAATGTATCGATACATTT
184095 CTCATTATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
19 4 0.06
20 30 0.45
22 26 0.39
23 6 0.09
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
AAAATGTATCGATACATTTA
Found at i:184051 original size:42 final size:42
Alignment explanation
Indices: 183992--184093 Score: 177
Period size: 42 Copynumber: 2.4 Consensus size: 42
183982 TACTACCAAG
183992 AAAATGTATCGATACATTAATAAATGCATAGATACATGCTTC
1 AAAATGTATCGATACATTAATAAATGCATAGATACATGCTTC
* *
184034 AAAATGTATCGATACATTAATAAATGTATAGATACATGTTTC
1 AAAATGTATCGATACATTAATAAATGCATAGATACATGCTTC
*
184076 AAATTGTATCGATACATT
1 AAAATGTATCGATACATT
184094 TCTCATTATA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (42 bp):
AAAATGTATCGATACATTAATAAATGCATAGATACATGCTTC
Found at i:187788 original size:10 final size:9
Alignment explanation
Indices: 187783--187819 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
187773 GGTTTTTCAT
187783 TTTTTTTTC
1 TTTTTTTTC
187792 TTTTTTTTCC
1 TTTTTTTT-C
187802 TTTCTTTTTC
1 TTT-TTTTTC
187812 TTTTTTTT
1 TTTTTTTT
187820 TCTTCTGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 13 0.50
10 8 0.31
11 5 0.19
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:187820 original size:10 final size:10
Alignment explanation
Indices: 187775--187823 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
187765 AGTTTAATGG
187775 TTTTTCATTTT
1 TTTTTC-TTTT
187786 TTTTTCTTTT
1 TTTTTCTTTT
* *
187796 TTTTCCTTTC
1 TTTTTCTTTT
187806 TTTTTCTTTT
1 TTTTTCTTTT
187816 TTTTTCTT
1 TTTTTCTT
187824 CTGACCATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 28 0.82
11 6 0.18
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:189041 original size:2 final size:2
Alignment explanation
Indices: 189034--189070 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
189024 TTCAAAGTTA
*
189034 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
189071 ATTGAATTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:192741 original size:19 final size:18
Alignment explanation
Indices: 192701--192748 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
192691 GTAAAAATAA
* *
192701 AAATAATTTAATTGTAATT
1 AAATAATTT-ATTATAAAT
192720 AAATAATTTATTATAAAAT
1 AAATAATTTATTAT-AAAT
*
192739 AAAAAATTTA
1 AAATAATTTA
192749 ACTATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
AAATAATTTATTATAAAT
Found at i:194556 original size:36 final size:33
Alignment explanation
Indices: 194482--194547 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
194472 ATGTTATTTG
*
194482 AAATACAAAAAATTAATATTTTTAAGGAAATTA
1 AAATACAAAAAATTAATATTTTTAAGGAAAATA
*
194515 AAATACAACAAATTAATATTTTT-AGGAAAATA
1 AAATACAAAAAATTAATATTTTTAAGGAAAATA
194547 A
1 A
194548 TTTCAATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.32
Consensus pattern (33 bp):
AAATACAAAAAATTAATATTTTTAAGGAAAATA
Found at i:194645 original size:113 final size:111
Alignment explanation
Indices: 194460--194674 Score: 306
Period size: 113 Copynumber: 1.9 Consensus size: 111
194450 CTTAAAAAAA
*
194460 TCTTATAGCACAATGTTATTTGAAATACAAAAAATTAATATTTTTAAGGAAATTAAAATACAACA
1 TCTTATAGCACAATGTTATTTGAAACACAAAAAATTAATATTTTTAAGGAAATTAAAATACAACA
*
194525 AATTAATATTTTTAGGAAAATAATTTCAATACTGCTTGAAAGAGCG
66 AATTAATATTTTTAAGAAAATAATTTCAATACTGCTTGAAAGAGCG
* * * * * *
194571 TCTTATGGCACTAA-GTTATTTGGAACAGAAGAAATTAATATTTTTTTAAGTAAATTAAAATATA
1 TCTTATAGCAC-AATGTTATTTGAAACACAAAAAATTAATA--TTTTTAAGGAAATTAAAATACA
* *
194635 ATAAATTAATATTTTTAAGAAAATAATTTTAATACTGCTT
63 ACAAATTAATATTTTTAAGAAAATAATTTCAATACTGCTT
194675 AAGAAAACAC
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
111 32 0.35
112 2 0.02
113 57 0.63
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (111 bp):
TCTTATAGCACAATGTTATTTGAAACACAAAAAATTAATATTTTTAAGGAAATTAAAATACAACA
AATTAATATTTTTAAGAAAATAATTTCAATACTGCTTGAAAGAGCG
Found at i:194730 original size:113 final size:110
Alignment explanation
Indices: 194434--194723 Score: 293
Period size: 113 Copynumber: 2.6 Consensus size: 110
194424 AAACTTGTTT
* * *
194434 AATAATATT-AATATTGCTT-AAA-AAAATCTTATAGCACAATGTTATTTGAAATACAAAAAATT
1 AATAAT-TTCAATACTGCTTGAAAGAACATCTTATAGCACAATGTTATTTGGAATACAAAAAATT
*
194496 AATATTTTTAAGGAAATTAAAATACAACAAATTAATATTTTTAGGAA
65 AAT-TTTTTAAGGAAATTAAAATACAACAAATTAATATTTTTAAGAA
* * * * * *
194543 AATAATTTCAATACTGCTTGAAAGAGCGTCTTATGGCACTAA-GTTATTTGGAACAGAAGAAATT
1 AATAATTTCAATACTGCTTGAAAGAACATCTTATAGCAC-AATGTTATTTGGAATACAAAAAATT
* * *
194607 AATATTTTTTTAAGTAAATTAAAATATAATAAATTAATATTTTTAAGAA
65 -A-A-TTTTTTAAGGAAATTAAAATACAACAAATTAATATTTTTAAGAA
* * * *
194656 AATAATTTTAATACTGCTTAAGAAA-ACACATACCTTATAGCACCATGTTATTTGGAATATAACA
1 AATAATTTCAATACTGCTT--GAAAGA-ACAT--CTTATAGCACAATGTTATTTGGAATACAAAA
194720 AATT
61 AATT
194724 CTTTTTTTTT
Statistics
Matches: 147, Mismatches: 21, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
108 2 0.01
109 15 0.10
110 3 0.02
111 29 0.20
112 3 0.02
113 58 0.39
114 2 0.01
115 6 0.04
116 1 0.01
117 28 0.19
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.36
Consensus pattern (110 bp):
AATAATTTCAATACTGCTTGAAAGAACATCTTATAGCACAATGTTATTTGGAATACAAAAAATTA
ATTTTTTAAGGAAATTAAAATACAACAAATTAATATTTTTAAGAA
Found at i:195291 original size:17 final size:18
Alignment explanation
Indices: 195240--195289 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
195230 AACTCCAACA
*
195240 AACTTTAAAGGTATTTTT
1 AACTTTAAAAGTATTTTT
*
195258 AA-TCT-AAA-TATTTTT
1 AACTTTAAAAGTATTTTT
195273 AACTTTAAAAGTATTTT
1 AACTTTAAAAGTATTTT
195290 AAAATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 9 0.35
16 4 0.15
17 5 0.19
18 8 0.31
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
AACTTTAAAAGTATTTTT
Found at i:195363 original size:29 final size:29
Alignment explanation
Indices: 195263--195369 Score: 114
Period size: 29 Copynumber: 3.7 Consensus size: 29
195253 TTTTTAATCT
*
195263 AAATATTTT-TAACTTTAAAAGTATTTTA
1 AAATATTTTCTAACTTTAAAAGTATTTAA
*
195291 AAATATTTTCTAA-TTT--CAGTATTTTAATCTA
1 AAATATTTTCTAACTTTAAAAGTA-TTT-A---A
*
195322 AAATATTTTCTAACTTTAAAAGCATTTAA
1 AAATATTTTCTAACTTTAAAAGTATTTAA
195351 AAATATTTTCTAACTTTAA
1 AAATATTTTCTAACTTTAA
195370 CATAACTCCA
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
26 4 0.06
27 3 0.05
28 12 0.18
29 23 0.35
31 14 0.21
32 4 0.06
33 3 0.05
34 3 0.05
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (29 bp):
AAATATTTTCTAACTTTAAAAGTATTTAA
Found at i:200948 original size:56 final size:56
Alignment explanation
Indices: 200844--200952 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
200834 AATTCAATAT
* * * *
200844 AACTCCAATAAACTTTAAAAGCATTTTTAATTTAAAATATTTTCTAACTTTAACAA
1 AACTCCAACAAACTTTAAAAGCATATTTAATTGAAAACATTTTCTAACTTTAACAA
* *
200900 AACTCCAACAAACTTT-AAAG-GTATTTAAGTTGAAAACATTTTTTTAACTTTAA
1 AACTCCAACAAACTTTAAAAGCATATTTAA-TTGAAAACA-TTTTCTAACTTTAA
200953 AAGCATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 6 0.13
55 11 0.24
56 28 0.62
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (56 bp):
AACTCCAACAAACTTTAAAAGCATATTTAATTGAAAACATTTTCTAACTTTAACAA
Found at i:203976 original size:59 final size:59
Alignment explanation
Indices: 203851--204011 Score: 198
Period size: 59 Copynumber: 2.7 Consensus size: 59
203841 AAATTATCAA
* * * * * * *
203851 AAAATAACATAAATGACCTTAAAATGCATG-AAATTGTTAAATGGTCTTTAGATTATGG
1 AAAATAACCTAAATGACCTTAAAATGCATGAAAATTGCTACATAGCCCTTAAATTATGG
* *
203909 AAAATAACCTAAATGACGTTAAAATGCATGAAAATTCCTACATAGCCCTTAAATTATGG
1 AAAATAACCTAAATGACCTTAAAATGCATGAAAATTGCTACATAGCCCTTAAATTATGG
** **
203968 AGTATAACCTAAATGACCTTAAAACACATGAAAATTGCTACATA
1 AAAATAACCTAAATGACCTTAAAATGCATGAAAATTGCTACATA
204012 ATCCCATATA
Statistics
Matches: 87, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
58 28 0.32
59 59 0.68
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (59 bp):
AAAATAACCTAAATGACCTTAAAATGCATGAAAATTGCTACATAGCCCTTAAATTATGG
Found at i:209295 original size:18 final size:18
Alignment explanation
Indices: 209259--209298 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
209249 CAACAAATTT
209259 AATTTAATATAAAATAAA
1 AATTTAATATAAAATAAA
209277 AATTTGAATATAAAA-AAA
1 AATTT-AATATAAAATAAA
209295 AATT
1 AATT
209299 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AATTTAATATAAAATAAA
Found at i:209483 original size:17 final size:18
Alignment explanation
Indices: 209448--209487 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
209438 TAAAATAAAA
209448 ATTTTAATTATTAATTTT
1 ATTTTAATTATTAATTTT
209466 ATTTTAA-TATCT-ATTTT
1 ATTTTAATTAT-TAATTTT
209483 ATTTT
1 ATTTT
209488 TTAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTAATTATTAATTTT
Found at i:209586 original size:16 final size:17
Alignment explanation
Indices: 209562--209594 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
209552 TAATAATTTC
*
209562 TATTCAAATAAT-AAAT
1 TATTAAAATAATCAAAT
209578 TATTAAAATAATCAAAT
1 TATTAAAATAATCAAAT
209595 ATATATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
TATTAAAATAATCAAAT
Found at i:210266 original size:15 final size:15
Alignment explanation
Indices: 210206--210269 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
210196 TTAAAATATA
*
210206 AAAAAAATTAAATTT
1 AAAATAATTAAATTT
*
210221 AAAA-ATTTTAAATTT
1 AAAATA-ATTAAATTT
* **
210236 AATATAACACAAATTT
1 AAAATAA-TTAAATTT
210252 AAAATAATTAAATTT
1 AAAATAATTAAATTT
210267 AAA
1 AAA
210270 CGTATCCAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 1 0.03
15 24 0.63
16 13 0.34
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATAATTAAATTT
Found at i:210525 original size:19 final size:19
Alignment explanation
Indices: 210501--210538 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
210491 TGCGTCGAGT
210501 GATATAATATAATTATATA
1 GATATAATATAATTATATA
*
210520 GATATAATGTAATTATATA
1 GATATAATATAATTATATA
210539 TAATTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
GATATAATATAATTATATA
Found at i:211287 original size:79 final size:79
Alignment explanation
Indices: 211189--211348 Score: 205
Period size: 79 Copynumber: 2.0 Consensus size: 79
211179 GAAAATACAA
* * * * * * *
211189 TAATTTTTTTAAAAGAAATAATTTTAATATTGCTTAATAAAGCATCTTATAGCATCAAGTTATTT
1 TAATTTTTTTAAAAGAAATAATTTTAATACTACTTAAGAAAGCACCTTACAGCACCAAGTTATGT
211254 GGAATACAAAAAAT
66 GGAATACAAAAAAT
* *
211268 TAATATTTTTTAAGA-AAATAATTTTAATACTACTTAAGAAAGCACCTTACAGCACCATGTTATG
1 TAAT-TTTTTTAAAAGAAATAATTTTAATACTACTTAAGAAAGCACCTTACAGCACCAAGTTATG
* *
211332 TGGAATATAACAAAT
65 TGGAATACAAAAAAT
211347 TA
1 TA
211349 CAATTAGTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
79 60 0.87
80 9 0.13
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (79 bp):
TAATTTTTTTAAAAGAAATAATTTTAATACTACTTAAGAAAGCACCTTACAGCACCAAGTTATGT
GGAATACAAAAAAT
Found at i:211778 original size:35 final size:35
Alignment explanation
Indices: 211739--211821 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
211729 AAATAAATTT
211739 AATTAAATTTAAAAAATTTAATG-TATGATT-TATAA
1 AATTAAATTTAAAAAATTT-ATGATATGATTATAT-A
* * *
211774 AATTAATTGTTAAAATATTTTTGATATGATTATATA
1 AATTAAAT-TTAAAAAATTTATGATATGATTATATA
*
211810 AATTTAATTTAA
1 AATTAAATTTAA
211822 TTTTTTTTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
35 13 0.32
36 24 0.60
37 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (35 bp):
AATTAAATTTAAAAAATTTATGATATGATTATATA
Found at i:216030 original size:52 final size:54
Alignment explanation
Indices: 215930--216051 Score: 128
Period size: 53 Copynumber: 2.3 Consensus size: 54
215920 TTTTTTAAAC
* * *
215930 TTAA-TTAAATATTTTTATTTTATTAAAAATTATAATAAAAACT-TTTTTATTTT
1 TTAATTTAAAT-TTTTTATTTTATTAAAAATCATAATAAAAACTATTTTAATTTG
* *
215983 TTATTTTAAATTTTTTATTTT-TATAAAAA-CATAATAATTAA-TATTTTAATTTG
1 TTAATTTAAATTTTTTATTTTAT-TAAAAATCATAATAA-AAACTATTTTAATTTG
*
216036 TTAATTTAATTTTTTT
1 TTAATTTAAATTTTTT
216052 TAAACTTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
52 9 0.16
53 43 0.74
54 6 0.10
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.59
Consensus pattern (54 bp):
TTAATTTAAATTTTTTATTTTATTAAAAATCATAATAAAAACTATTTTAATTTG
Found at i:216031 original size:126 final size:122
Alignment explanation
Indices: 215856--216237 Score: 370
Period size: 126 Copynumber: 3.2 Consensus size: 122
215846 AATTAATAAA
* * *
215856 ATTTTAATTTAAAATTTTT-TGTTTA-AAAAACATAATAATTAATATTTTAATTTGTTAAAATAA
1 ATTTT-ATTTAAATTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATATAA
215919 ATTTTTTAAACTTAATTAAATATTTTTATTTTATTAAAAATTATAATAAAAACTTTTTT
65 ATTTTTTAAACTTAATTAAATATTTTTATTTTATTAAAAA-TATAATAAAAACTTTTTT
*
215978 ATTTTTTATTTTAAATTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATTT
1 A--TTTTA-TTTAAATTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATAT
* *
216043 AATTTTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAAATATAAACTTT
63 AA-ATTTTTTAAACTTAATT-AA-A-TATTTTT-ATTTTATT-AAAAAT-AT-AATAAAAACTTT
216108 TTT
120 TTT
* *
216111 A----ATTT-AATTTTTTA-TTTT-T---AA-A-AATAATTAATATTTTAA-TTATTAATGTAAA
1 ATTTTATTTAAATTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATATAAA
* * * * *
216163 TTTTTTAAAGTTAATTAAATATTATT-TTTAATTAAAAA-ATAATAATTAATACATTATT
66 TTTTTTAAACTTAATTAAATATTTTTATTTTATTAAAAATATAATAA--AA-ACTTTTTT
216221 -TTTTA-TTAAATTTTTTA
1 ATTTTATTTAAATTTTTTA
216238 AATTAATTAA
Statistics
Matches: 224, Mismatches: 15, Indels: 51
0.77 0.05 0.18
Matches are distributed among these distances:
107 4 0.02
108 2 0.01
109 2 0.01
110 11 0.05
111 6 0.03
112 2 0.01
113 16 0.07
114 1 0.00
115 2 0.01
116 15 0.07
117 10 0.04
118 17 0.08
119 1 0.00
120 2 0.01
122 1 0.00
123 2 0.01
124 19 0.08
125 14 0.06
126 39 0.17
127 17 0.08
128 2 0.01
129 1 0.00
130 7 0.03
131 9 0.04
132 7 0.03
133 15 0.07
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (122 bp):
ATTTTATTTAAATTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATATAAA
TTTTTTAAACTTAATTAAATATTTTTATTTTATTAAAAATATAATAAAAACTTTTTT
Found at i:216060 original size:21 final size:23
Alignment explanation
Indices: 216036--216077 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
216026 TTTTAATTTG
*
216036 TTAATTTAAT-TT-TTTTTAAAC
1 TTAATTAAATATTATTTTTAAAC
216057 TTAATTAAATATTATTTTTAA
1 TTAATTAAATATTATTTTTAA
216078 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTAATTAAATATTATTTTTAAAC
Found at i:216322 original size:16 final size:17
Alignment explanation
Indices: 216293--216344 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
216283 CACGACCCTT
216293 TTTTTTTAAATTTA-AA
1 TTTTTTTAAATTTATAA
**
216309 TTTTTTTATTTTTATAA
1 TTTTTTTAAATTTATAA
216326 TTAATATTTTAAATTTATA
1 TT--T-TTTTAAATTTATA
216345 TATAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 12 0.43
17 4 0.14
19 1 0.04
20 11 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTTAAATTTATAA
Found at i:216329 original size:22 final size:22
Alignment explanation
Indices: 216291--216335 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
216281 CCCACGACCC
216291 TTTTTTTTTAAATTTAA-ATTT
1 TTTTTTTTTAAATTTAATATTT
216312 TTTTATTTTTATAA-TTAATATTT
1 TTTT-TTTTTA-AATTTAATATTT
216335 T
1 T
216336 AAATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 10 0.48
23 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTTTAAATTTAATATTT
Found at i:216397 original size:22 final size:22
Alignment explanation
Indices: 216351--216417 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
216341 TATATATAAT
**
216351 AAAATAAAATAAATTTCA--TA
1 AAAATAAAATAAATTAGATTTA
*
216371 AAAATAAATTAAATTA-ATTTTA
1 AAAATAAAATAAATTAGA-TTTA
216393 AAAATAAAATAAATTAGATTTA
1 AAAATAAAATAAATTAGATTTA
216415 AAA
1 AAA
216418 TTTTTTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.03
20 14 0.35
22 24 0.60
23 1 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (22 bp):
AAAATAAAATAAATTAGATTTA
Found at i:217036 original size:24 final size:24
Alignment explanation
Indices: 217001--217058 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
216991 CAAATGTAAT
*
217001 AAATTA-ATCTTTTAAGAAAACATA
1 AAATTAGA-CTTTGAAGAAAACATA
* *
217025 AAATTAGACTTTGAGGTAAACATA
1 AAATTAGACTTTGAAGAAAACATA
*
217049 AAAGTAGACT
1 AAATTAGACT
217059 CTAGGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (24 bp):
AAATTAGACTTTGAAGAAAACATA
Found at i:217377 original size:22 final size:23
Alignment explanation
Indices: 217345--217394 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
217335 TAAACTTATT
**
217345 TTTAATCTAAAATATTTTCTAAC
1 TTTAATCTAAAATATTCCCTAAC
217368 TTTAAT-TAAAATATTCCCTAAC
1 TTTAATCTAAAATATTCCCTAAC
217390 TTTAA
1 TTTAA
217395 AAGAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAATCTAAAATATTCCCTAAC
Found at i:221043 original size:166 final size:166
Alignment explanation
Indices: 220798--221109 Score: 441
Period size: 166 Copynumber: 1.9 Consensus size: 166
220788 AAAAAAATTC
** *
220798 AAAACTCATGAAAATGAATGAATTTTTTGAAAAATGATTTAATATAAATGAAATAATAATATTTA
1 AAAACTCATGAAAATGAATGAAAGTTTTGAAAAATAATTTAATATAAATGAAATAATAATATTTA
* * *
220863 ATGAATTTTAAAAATTAAAAACTAAAAAAAATCCTCTCAAAAAAATTTACGGAGTAGAAAACT-T
66 ATAAATTTTAAAAATTAAAAACCAAAAAAAATCCTCTC-AAAAAATTTACAGAGTAGAAAACTCT
* *
220927 CGTATTTTGGAAATAAGAGATTTTCATAAAAATAATGA
130 -ATATTTTGGAAACAAGAGATTTTCATAAAAATAATGA
* * *
220965 AAAACTCATGAAAATGAAT-AAAGTTTTGAGAACTAATTTAATGTTAAAT-AAATAATAATATTT
1 AAAACTCATGAAAATGAATGAAAGTTTTGAAAAATAATTTAAT-ATAAATGAAATAATAATATTT
* * * *
221028 GATAAATTTTAAAAATTAAAAACCAAGAAAAATCCTCTCGAAAAATTTACATAGTAGAAAACTCT
65 AATAAATTTTAAAAATTAAAAACCAAAAAAAATCCTCTCAAAAAATTTACAGAGTAGAAAACTCT
221093 ATATTTTGGAAACAAGA
130 ATATTTTGGAAACAAGA
221110 AAATTTCAAA
Statistics
Matches: 128, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
165 36 0.28
166 68 0.53
167 24 0.19
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (166 bp):
AAAACTCATGAAAATGAATGAAAGTTTTGAAAAATAATTTAATATAAATGAAATAATAATATTTA
ATAAATTTTAAAAATTAAAAACCAAAAAAAATCCTCTCAAAAAATTTACAGAGTAGAAAACTCTA
TATTTTGGAAACAAGAGATTTTCATAAAAATAATGA
Found at i:222249 original size:85 final size:83
Alignment explanation
Indices: 222154--223179 Score: 407
Period size: 85 Copynumber: 12.2 Consensus size: 83
222144 ATAAATGAAG
* * * * ** *
222154 GATAAAAAAGTCTCTCGAATCTGAGCCGATGGGCAGACAAAAGATAAAAAAAGTCTTTTAAGTTT
1 GATAAAAAAGTCTC-CGAGTCTAAGCCGATAGGCAGACAAAAGAT-AAAGAAGTCTTTCGAGTCT
* *
222219 GAGCTGACGGGCAAATAAAA
64 GAGCTGACAGGCAGATAAAA
* * *
222239 GATAAAAAAGTCT-CGCAGGTTTAAGCTGATAGGCAGACAAAAGATAAAGAAGTCTCTCGAGTCT
1 GATAAAAAAGTCTCCG-A-GTCTAAGCCGATAGGCAGACAAAAGATAAAGAAGTCTTTCGAGTCT
222303 GAGCTGACAGGCAGATAAAA
64 GAGCTGACAGGCAGATAAAA
* * * *
222323 GATAAAGAAAGTCTCCTGAGTCTTAGTCGGTAGGCAGACAAAAGATAAAGAAGT-TTCCCGAGTC
1 GATAAA-AAAGTCTCC-GAGTCTAAGCCGATAGGCAGACAAAAGATAAAGAAGTCTT-TCGAGTC
222387 TGAGCTGACTA-GCAGATAAAA
63 TGAGCTGAC-AGGCAGATAAAA
* * * * *
222408 GATAAAAAAGTCTCCCGGGTCTAAACTGATGGGCAGAC-AAAGATAAAGAAGTCTATT-GAGTAT
1 GATAAAAAAGTCT-CCGAGTCTAAGCCGATAGGCAGACAAAAGATAAAGAAGTCT-TTCGAGTCT
222471 GA--TG---GGCAGATAAAA
64 GAGCTGACAGGCAGATAAAA
* * * ** * * *
222486 GATAAAAAAATCTTTC-AGTTCTAAGCCAACGGGCAAAC-AAAGAATGAAGAAAG--TTTCCAGG
1 GATAAAAAAGTC-TCCGAG-TCTAAGCCGATAGGCAGACAAAAG-ATAAAG-AAGTCTTTCGA-G
* * * *
222547 TCTGAGCCGACGGGCAGACAAAG
61 TCTGAGCTGACAGGCAGATAAAA
* * ** * *
222570 GATAAAGAAAGTCTTCTGAGTCTAAGTCGACGGGCAAACAAAAGATAAAGAAAGTCTCTCG-GAT
1 GATAAA-AAAGTC-TCCGAGTCTAAGCCGATAGGCAGACAAAAGATAAAG-AAGTCTTTCGAG-T
* * *
222634 CTGAG-TCGACGGGCAGACAAAG
62 CTGAGCT-GACAGGCAGATAAAA
* * * * * *
222656 GATAAAGAAA-TCTCCCGAGTCTGAGCCGATAGGTAGAGAAAAAATAAAGAAGTC-TTCTGGGTT
1 GATAAA-AAAGTCT-CCGAGTCTAAGCCGATAGGCAGACAAAAGATAAAGAAGTCTTTC-GAGTC
* * * *
222719 TGAACCGATAGGCAGACAAAA
63 TGAGCTGACAGGCAGATAAAA
* * * * * * * * * *
222740 GATAAAGAAAGTCTTTCAAGTCTAAGCTGA-CGAGAAGATAAAGGATAAAAAAGTC-TCCTAGGT
1 GATAAA-AAAGTC-TCCGAGTCTAAGCCGATAG-GCAGACAAAAGATAAAGAAGTCTTTCGA-GT
* ** *
222803 TTGAGCCAAC-GAGTAGATAAAA
62 CTGAGCTGACAG-GCAGATAAAA
* ** ** * * *
222825 GATAAAAAAGTCTCTC-AGGTCTGAGCTAACGGGTAGACAAAAGATAAAAAAGTCCTTCGAGTCT
1 GATAAAAAAGTCTC-CGA-GTCTAAGCCGATAGGCAGACAAAAGATAAAGAAGTCTTTCGAGTCT
* * * *
222889 AAGCCGACGGGCAGACAAAA
64 GAGCTGACAGGCAGATAAAA
* * * * * * *** * *
222909 AATAAAGAAAGTCTCTCAAGTTTGAA-TCGATAGACAGACAAAAGATAAGAAAAAGTCACCCAAC
1 GATAAA-AAAGTCTC-CGAGTCT-AAGCCGATAGGCAGACAAAAGAT-A-AAGAAGTCTTTCGAG
* * * *
222973 TTTTAGCTAACAGGCAGACAAAA
61 TCTGAGCTGACAGGCAGATAAAA
* * * * ** * * *
222996 AATAAAGAAGCCTCTCGGGTCCGAGTC-ATTGGGCAGACAAAAGATAAAGAAGTCTCTT-GGGTC
1 GATAAAAAAGTCTC-CGAGTCTAAGCCGA-TAGGCAGACAAAAGATAAAGAAGTCT-TTCGAGTC
* ** *
223059 TAAGCTGACTTGCAGATAAAT
63 TGAGCTGACAGGCAGATAAAA
* * * * * * * *
223080 GATGAAGAAAGTCTCCCGAATCTGAGCTGACAGACA-A-ATAAAGAATAAAGAAAATCTCTCGAG
1 GAT-AAAAAAGTCT-CCGAGTCTAAGCCGATAGGCAGACA-AAAG-ATAAAG-AAGTCTTTCGAG
* *
223143 TCTGAGCCGAC-GAGCAAATAAAA
61 TCTGAGCTGACAG-GCAGATAAAA
*
223166 GATGAAAAAGTCTC
1 GATAAAAAAGTCTC
223180 TCAAGCCTGA
Statistics
Matches: 718, Mismatches: 164, Indels: 119
0.72 0.16 0.12
Matches are distributed among these distances:
77 3 0.00
78 42 0.06
79 11 0.02
80 3 0.00
81 3 0.00
83 28 0.04
84 201 0.28
85 290 0.40
86 99 0.14
87 38 0.05
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.19
Consensus pattern (83 bp):
GATAAAAAAGTCTCCGAGTCTAAGCCGATAGGCAGACAAAAGATAAAGAAGTCTTTCGAGTCTGA
GCTGACAGGCAGATAAAA
Found at i:222266 original size:42 final size:42
Alignment explanation
Indices: 222154--223182 Score: 240
Period size: 42 Copynumber: 24.4 Consensus size: 42
222144 ATAAATGAAG
* * * ** *
222154 GATAAAAAAGTCTCTC-GAATCTGAGCCGATGGGCAGACAAAA
1 GATAAAAAAGTCTCTCAG-GTTTGAGCTGACAGGCAGATAAAA
* * * * *
222196 GATAAAAAAAGTCTTTTAAGTTTGAGCTGACGGGCAAATAAAA
1 GAT-AAAAAAGTCTCTCAGGTTTGAGCTGACAGGCAGATAAAA
* * * *
222239 GATAAAAAAGTCTCGCAGGTTTAAGCTGATAGGCAGACAAAA
1 GATAAAAAAGTCTCTCAGGTTTGAGCTGACAGGCAGATAAAA
* *
222281 GATAAAGAAGTCTCTC-GAGTCTGAGCTGACAGGCAGATAAAA
1 GATAAAAAAGTCTCTCAG-GTTTGAGCTGACAGGCAGATAAAA
* ** *
222323 GATAAAGAAAGTCTC-CTGAGTCTT-AG-TCGGTAGGCAGACAAAA
1 GATAAA-AAAGTCTCTCAG-GT-TTGAGCT-GACAGGCAGATAAAA
* * * *
222366 GATAAAGAAGTTTC-CCGAGTCTGAGCTGACTA-GCAGATAAAA
1 GATAAAAAAGTCTCTCAG-GTTTGAGCTGAC-AGGCAGATAAAA
* * * * * ** *
222408 GATAAAAAAGTCTCCCGGGTCTAAACTGATGGGCAGA-CAAA
1 GATAAAAAAGTCTCTCAGGTTTGAGCTGACAGGCAGATAAAA
* * **
222449 GATAAAGAAG--TCT-A---TTGAGTATGATGGGCAGATAAAA
1 GATAAAAAAGTCTCTCAGGTTTGAG-CTGACAGGCAGATAAAA
* * * ** *
222486 GATAAAAAAATCTTTCA-GTTCTAAGCCAACGGGCA-A-ACAAA
1 GATAAAAAAGTCTCTCAGGTT-TGAGCTGACAGGCAGATA-AAA
* * * * * * *
222527 GAATGAAGAAAGTTTC-CAGGTCTGAGCCGACGGGCAGACAAAG
1 G-AT-AAAAAAGTCTCTCAGGTTTGAGCTGACAGGCAGATAAAA
* * * * * *
222570 GATAAAGAAAGTCT-TCTGAGTCTAAG-TCGACGGGCAAACAAAA
1 GATAAA-AAAGTCTCTCAG-GTTTGAGCT-GACAGGCAGATAAAA
* * * *
222613 GATAAAGAAAGTCTCTC-GGATCTGAG-TCGACGGGCAGACAAAG
1 GATAAA-AAAGTCTCTCAGG-TTTGAGCT-GACAGGCAGATAAAA
* * * * * *
222656 GATAAAGAAA-TCTC-CCGAGTCTGAGCCGATAGGTAGAGAAAA
1 GATAAA-AAAGTCTCTCAG-GTTTGAGCTGACAGGCAGATAAAA
* * * * * * *
222698 AATAAAGAAGTCT-TCTGGGTTTGAACCGATAGGCAGACAAAA
1 GATAAAAAAGTCTCTC-AGGTTTGAGCTGACAGGCAGATAAAA
* * * * * *
222740 GATAAAGAAAGTCTTTCAAGTCTAAGCTGAC-GAGAAGATAAAG
1 GATAAA-AAAGTCTCTCAGGTTTGAGCTGACAG-GCAGATAAAA
** *
222783 GATAAAAAAGTCTC-CTAGGTTTGAGCCAAC-GAGTAGATAAAA
1 GATAAAAAAGTCTCTC-AGGTTTGAGCTGACAG-GCAGATAAAA
* * * * *
222825 GATAAAAAAGTCTCTCAGGTCTGAGCTAACGGGTAGACAAAA
1 GATAAAAAAGTCTCTCAGGTTTGAGCTGACAGGCAGATAAAA
* * * * *
222867 GATAAAAAAGTC-CTTC-GAGTCTAAGCCGACGGGCAGACAAAA
1 GATAAAAAAGTCTC-TCAG-GTTTGAGCTGACAGGCAGATAAAA
* * * * * *
222909 AATAAAGAAAGTCTCTCAAGTTTGA-ATCGATAGACAGACAAAA
1 GATAAA-AAAGTCTCTCAGGTTTGAGCT-GACAGGCAGATAAAA
* * ** * * *
222952 GATAAGAAAAAGTCACCCAACTTTTAGCTAACAGGCAGACAAAA
1 GAT-A-AAAAAGTCTCTCAGGTTTGAGCTGACAGGCAGATAAAA
* * * * ** * ** *
222996 AATAAAGAAGCCTCTCGGGTCCGAG-TCATTGGGCAGACAAAA
1 GATAAAAAAGTCTCTCAGGTTTGAGCTGA-CAGGCAGATAAAA
* ** * * ** *
223038 GATAAAGAAGTCTCTTGGGTCTAAGCTGACTTGCAGATAAAT
1 GATAAAAAAGTCTCTCAGGTTTGAGCTGACAGGCAGATAAAA
* * * * * *
223080 GATGAAGAAAGTCTC-CCGAATCTGAGCTGACAGACAAAT-AAA
1 GAT-AAAAAAGTCTCTCAG-GTTTGAGCTGACAGGCAGATAAAA
* * * *
223122 GAATAAAGAAAATCTCTC-GAGTCTGAGCCGAC-GAGCAAATAAAA
1 G-ATAAA-AAAGTCTCTCAG-GTTTGAGCTGACAG-GCAGATAAAA
*
223166 GATGAAAAAGTCTCTCA
1 GATAAAAAAGTCTCTCA
223183 AGCCTGAACT
Statistics
Matches: 745, Mismatches: 179, Indels: 125
0.71 0.17 0.12
Matches are distributed among these distances:
35 2 0.00
36 11 0.01
37 11 0.01
39 4 0.01
40 2 0.00
41 29 0.04
42 383 0.51
43 259 0.35
44 41 0.06
45 3 0.00
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.19
Consensus pattern (42 bp):
GATAAAAAAGTCTCTCAGGTTTGAGCTGACAGGCAGATAAAA
Found at i:222366 original size:127 final size:124
Alignment explanation
Indices: 222154--222923 Score: 410
Period size: 127 Copynumber: 6.1 Consensus size: 124
222144 ATAAATGAAG
* * * ** * * *
222154 GATAAAAAAGTCTCTCGAATCTGAGCCGATGGGCAGACAAAAGATAAAAAAAGTCTTTTAAGTTT
1 GATAAAGAAGTCTCCCGAGTCTGAGCCGACAGGCAGA-AAAAGAT-AAAGAAGTCTTCTGAGTTT
** * * * * *
222219 GAG-CTGACGGGCAAATAAAAGATAAAAAAGTCTCGCAGGTTTAAGCTGATAGGCAGACAAAA
64 -AGTC-GATAGGCAGACAAAAGATAAAAAAGTCTCTCAGGTCTAAGCTGACAGGCAGACAAAA
* * *
222281 GATAAAGAAGTCTCTCGAGTCTGAGCTGACAGGCAGATAAAAGATAAAGAAAGTCTCCTGAGTCT
1 GATAAAGAAGTCTCCCGAGTCTGAGCCGACAGGCAGA-AAAAGATAAAG-AAGTCTTCTGAGT-T
* * * * * *
222346 TAGTCGGTAGGCAGACAAAAGATAAAGAAGTTTC-CCGAGTCTGAGCTGACTA-GCAGATAAAA
63 TAGTCGATAGGCAGACAAAAGATAAAAAAGTCTCTCAG-GTCTAAGCTGAC-AGGCAGACAAAA
* * * * * ** *
222408 GATAAAAAAGTCTCCCGGGTCTAAACTGATGGGCAGACAAAGATAAAGAAGTCTAT-TGAG--TA
1 GATAAAGAAGTCTCCCGAGTCTGAGCCGACAGGCAGAAAAAGATAAAGAAGTCT-TCTGAGTTTA
* * * * * ** * *
222470 -T-GATGGGCAGATAAAAGATAAAAAAATCTTTCAGTTCTAAGCCAACGGGCAAAC-AAA
65 GTCGATAGGCAGACAAAAGATAAAAAAGTCTCTCAGGTCTAAGCTGACAGGCAGACAAAA
* * * * *
222527 GAATGAAGAAAGTTTCCAG-GTCTGAGCCGACGGGCAGACAAAGGATAAAGAAAGTCTTCTGAGT
1 G-ATAAAG-AAGTCTCCCGAGTCTGAGCCGACAGGCAGA-AAAAGATAAAG-AAGTCTTCTGAGT
* ** * * *
222591 CTAAGTCGACGGGCAAACAAAAGATAAAGAAAGTCTCTC-GGATCTGAG-TCGACGGGCAGACAA
62 -TTAGTCGATAGGCAGACAAAAGATAAA-AAAGTCTCTCAGG-TCTAAGCT-GACAGGCAGACAA
*
222654 AG
123 AA
* * * * *
222656 GATAAAGAAATCTCCCGAGTCTGAGCCGATAGGTAGAGAAAAAATAAAGAAGTCTTCTGGGTTTG
1 GATAAAGAAGTCTCCCGAGTCTGAGCCGACAGGCAGA-AAAAGATAAAGAAGTCTTCTGAGTTT-
** * * * * *
222721 AACCGATAGGCAGACAAAAGATAAAGAAAGTCTTTCAAGTCTAAGCTGAC-GAGAAGATAAAG
64 AGTCGATAGGCAGACAAAAGATAAA-AAAGTCTCTCAGGTCTAAGCTGACAG-GCAGACAAAA
* * * * * * *
222783 GATAAAAAAGTCT-CCTAGGTTTGAGCCAAC-GAGTAGATAAAAGATAAAAAAGTC-TCTCAGGT
1 GATAAAGAAGTCTCCCGA-GTCTGAGCCGACAG-GCAGA-AAAAGATAAAGAAGTCTTCTGA-GT
* * * * *
222845 CTGAG-CTA-ACGGGTAGACAAAAGATAAAAAAGTC-CTTC-GAGTCTAAGCCGACGGGCAGACA
62 -TTAGTCGATA--GGCAGACAAAAGATAAAAAAGTCTC-TCAG-GTCTAAGCTGACAGGCAGACA
222906 AAA
122 AAA
*
222909 AATAAAGAAAGTCTC
1 GATAAAG-AAGTCTC
222924 TCAAGTTTGA
Statistics
Matches: 492, Mismatches: 113, Indels: 75
0.72 0.17 0.11
Matches are distributed among these distances:
119 4 0.01
120 53 0.11
121 21 0.04
122 12 0.02
125 12 0.02
126 58 0.12
127 270 0.55
128 59 0.12
129 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (124 bp):
GATAAAGAAGTCTCCCGAGTCTGAGCCGACAGGCAGAAAAAGATAAAGAAGTCTTCTGAGTTTAG
TCGATAGGCAGACAAAAGATAAAAAAGTCTCTCAGGTCTAAGCTGACAGGCAGACAAAA
Found at i:223108 original size:43 final size:41
Alignment explanation
Indices: 223074--223179 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 41
223064 TGACTTGCAG
223074 ATAAATGATGAAGAAAGTCTCCCGAATCTGAGCTGACAGACAA
1 ATAAA-GATGAAGAAAGTCTCCCGAATCTGAGCTGACAG-CAA
* * * * *
223117 ATAAAGAATAAAGAAAATCTCTCGAGTCTGAGCCGACGAGCAA
1 ATAAAG-ATGAAGAAAGTCTCCCGAATCTGAGCTGAC-AGCAA
223160 ATAAAAGATGAA-AAAGTCTC
1 AT-AAAGATGAAGAAAGTCTC
223180 TCAAGCCTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
42 8 0.15
43 39 0.74
44 6 0.11
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (41 bp):
ATAAAGATGAAGAAAGTCTCCCGAATCTGAGCTGACAGCAA
Found at i:223709 original size:88 final size:88
Alignment explanation
Indices: 223536--223702 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 88
223526 AAGATGGATG
* * * *
223536 CAGATTTGACCAGGGTGGTAACCATAAATTAAATCAGAATGAAAAGAATCTGATAAGGGTGGTAA
1 CAGATTTGACTAAGGTGGCAACCATAAATCAAATCAGAATGAAAAGAATCTGATAAGGGTGGTAA
*
223601 CCATACACTAGACAAAAAAGAAA
66 CCATACACCAGACAAAAAAGAAA
* * * * * *
223624 CAGATTTGACTAAGGTGGCAACCATACATCCAATCGGAATGAAAAGAGTTTGACT-TGGGTGGTA
1 CAGATTTGACTAAGGTGGCAACCATAAATCAAATCAGAATGAAAAGAATCTGA-TAAGGGTGGTA
**
223688 ACCATATGCCAGACA
65 ACCATACACCAGACA
223703 GGAAAGAGAA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
88 64 0.98
89 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (88 bp):
CAGATTTGACTAAGGTGGCAACCATAAATCAAATCAGAATGAAAAGAATCTGATAAGGGTGGTAA
CCATACACCAGACAAAAAAGAAA
Found at i:223775 original size:48 final size:48
Alignment explanation
Indices: 223706--223910 Score: 218
Period size: 48 Copynumber: 4.3 Consensus size: 48
223696 CCAGACAGGA
* * *
223706 AAGAGAAGAGTTTGACTAGGCCTTAATACCAATACAATCAAACAAGAG
1 AAGAAAAGAGTTTGACCAGGCCTTAACACCAATACAATCAAACAAGAG
* * * * *
223754 ATGAAAAGAGTTTGACCAGGCCTTAACACTAATACAGTCAAACGAGGG
1 AAGAAAAGAGTTTGACCAGGCCTTAACACCAATACAATCAAACAAGAG
*** * * *
223802 AAGATTTGAGTTTGACTAGGCCCTAACACCAATACAATCAAACGAATA-
1 AAGAAAAGAGTTTGACCAGGCCTTAACACCAATACAATCAAAC-AAGAG
* *
223850 ATGAAAAGAGTTTGACCAGGTCC-TAACACCAATACAATCAAATAAG-G
1 AAGAAAAGAGTTTGACCAGG-CCTTAACACCAATACAATCAAACAAGAG
223897 AAAGAAAAGAGTTT
1 -AAGAAAAGAGTTT
223911 AACTATGCAC
Statistics
Matches: 126, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
47 2 0.02
48 121 0.96
49 3 0.02
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.20
Consensus pattern (48 bp):
AAGAAAAGAGTTTGACCAGGCCTTAACACCAATACAATCAAACAAGAG
Found at i:223909 original size:96 final size:96
Alignment explanation
Indices: 223702--223960 Score: 285
Period size: 96 Copynumber: 2.7 Consensus size: 96
223692 TATGCCAGAC
* * *
223702 AGGAAAGAGAAGAGTTTGACTAGGCCTTAATACCAATACAATCAAACAAGAGATGAAAAGAGTTT
1 AGGAAAGAAAAGAGTTTGACTAGGCCCTAACACCAATACAATCAAACAAGAGATGAAAAGAGTTT
* * *
223767 GACCAGGCCTTAACACTAATACAGTCAAACG
66 GACCAGGCCTTAACACCAATACAATCAAACA
* *** *
223798 AGGGAAGATTTGAGTTTGACTAGGCCCTAACACCAATACAATCAAACGAATA-ATGAAAAGAGTT
1 AGGAAAGAAAAGAGTTTGACTAGGCCCTAACACCAATACAATCAAAC-AAGAGATGAAAAGAGTT
*
223862 TGACCAGGTCC-TAACACCAATACAATCAAATA
65 TGACCAGG-CCTTAACACCAATACAATCAAACA
* * * * * *
223894 AGGAAAGAAAAGAGTTTAACTATGCACT-ACACTAATACAGTCAAATAA-AGGATGAAAA-ATGT
1 AGGAAAGAAAAGAGTTTGACTAGGCCCTAACACCAATACAATCAAACAAGA-GATGAAAAGA-GT
223956 TTGAC
64 TTGAC
223961 TAGATACAGT
Statistics
Matches: 137, Mismatches: 21, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
93 1 0.01
94 3 0.02
95 29 0.21
96 99 0.72
97 5 0.04
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.20
Consensus pattern (96 bp):
AGGAAAGAAAAGAGTTTGACTAGGCCCTAACACCAATACAATCAAACAAGAGATGAAAAGAGTTT
GACCAGGCCTTAACACCAATACAATCAAACA
Found at i:225450 original size:222 final size:222
Alignment explanation
Indices: 225063--225486 Score: 794
Period size: 222 Copynumber: 1.9 Consensus size: 222
225053 TCTTTCTTTT
* *
225063 TTTTGGGTTAAGACATATAATGTTTAAGTCTCTCAGAAACTAATACTCTTTTATCGAAAATTTTA
1 TTTTGGGTTAAGACATATAATGTTTAAGTCTCTCAAAAACTAATAATCTTTTATCGAAAATTTTA
*
225128 GAATTAAAATTTGGGCTTTTAGCAAAATGGGTTGAAAGGCTAAGAAAACTTTGGTTGGCCCAAGA
66 GAATTAAAATTTGGGCTTTCAGCAAAATGGGTTGAAAGGCTAAGAAAACTTTGGTTGGCCCAAGA
225193 AGATTTCAAAATTGATATGATACATACCCTATTTTCCTAGACACAAATAGATCAGCTCGTATAAA
131 AGATTTCAAAATTGATATGATACATACCCTATTTTCCTAGACACAAATAGATCAGCTCGTATAAA
225258 ACATGAAGATTTCAAAAATCTCTCAGA
196 ACATGAAGATTTCAAAAATCTCTCAGA
225285 TTTTGGGTTAAGACATATAATGTTTAAGTCTCTCAAAAACTAATAATCTTTTATCGAAAATTTTA
1 TTTTGGGTTAAGACATATAATGTTTAAGTCTCTCAAAAACTAATAATCTTTTATCGAAAATTTTA
225350 GAATTAAAATTTGGGCTTTCAGCAAAATGGGTTGAAAGGCTAAGAAAACTTTGGTTGGCCCAAGA
66 GAATTAAAATTTGGGCTTTCAGCAAAATGGGTTGAAAGGCTAAGAAAACTTTGGTTGGCCCAAGA
* * *
225415 AGATTTCAAAATTGATATGATACATACCTTATTTTCCTAGACACGAATAGATCGGCTCGTATAAA
131 AGATTTCAAAATTGATATGATACATACCCTATTTTCCTAGACACAAATAGATCAGCTCGTATAAA
225480 ACATGAA
196 ACATGAA
225487 TTTTTAAAAA
Statistics
Matches: 196, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
222 196 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (222 bp):
TTTTGGGTTAAGACATATAATGTTTAAGTCTCTCAAAAACTAATAATCTTTTATCGAAAATTTTA
GAATTAAAATTTGGGCTTTCAGCAAAATGGGTTGAAAGGCTAAGAAAACTTTGGTTGGCCCAAGA
AGATTTCAAAATTGATATGATACATACCCTATTTTCCTAGACACAAATAGATCAGCTCGTATAAA
ACATGAAGATTTCAAAAATCTCTCAGA
Found at i:225845 original size:16 final size:16
Alignment explanation
Indices: 225818--225863 Score: 83
Period size: 16 Copynumber: 2.8 Consensus size: 16
225808 AACTTCATTC
225818 TTTCTATTTTTTCACTT
1 TTTCT-TTTTTTCACTT
225835 TTTCTTTTTTTCACTT
1 TTTCTTTTTTTCACTT
225851 TTTCTTTTTTTCA
1 TTTCTTTTTTTCA
225864 TCATGCTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 24 0.83
17 5 0.17
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTTTTTCACTT
Found at i:226183 original size:15 final size:16
Alignment explanation
Indices: 226145--226184 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
226135 TCTTTTTCTA
*
226145 CACATTTTCTTCATTG
1 CACATTTTTTTCATTG
*
226161 CACATTTTTTTCATTT
1 CACATTTTTTTCATTG
226177 C-CATTTTT
1 CACATTTTT
226185 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (16 bp):
CACATTTTTTTCATTG
Found at i:230210 original size:155 final size:150
Alignment explanation
Indices: 229750--230219 Score: 403
Period size: 155 Copynumber: 3.0 Consensus size: 150
229740 ACATTCGATG
* * *
229750 TAAAAGTACCCGATA-CTCCTAAAGGATTTAAAAAGGATTA-AATAGGACGAACCTATCCTAAAT
1 TAAAAGTACCCGATACCT-CTAAAGGA-CTAAAAAGGATTACAAAAGGATGAACCTATCCTAAAT
* * * *
229813 ACCACTTTTGCCATAAAAACGAGCCTGGTGACAACCTAAGACTCGATTTTAAAAAATTATCAAAA
64 ACCACTTTCGGCATAAAAGCGA-CCTGGTGACAACCTAAGACTCGATTCTAAAAAATTA-CAAAA
* * ** *
229878 TATCCCTT-GGGGATATCTTCAATA
127 TA-CCCTTATGGGATAACTTTGACA
* * *
229902 TAGAAGTACCCAATATCC-CTAAAGGACTTAAAAAGGATTACAAAATGGGATGAACCTATCCTAG
1 TAAAAGTACCCGATA-CCTCTAAAGGAC-TAAAAAGGATTACAAAA--GGATGAACCTATCCTAA
* * * * * * * * *
229966 ATACCCACTTTCAGCATTAAAGCAGACCCGATGATAACCTAGGACTTGGTTCTTAGAAAATTACA
62 ATA-CCACTTTCGGCATAAAAGC-GACCTGGTGACAACCTAAGACTCGATTC-TAAAAAATTAC-
* * *
230031 AAAATGA-TCTTCA-GAGATACCTTTGACA
123 AAAAT-ACCCTT-ATGGGATAACTTTGACA
* * *
230059 TAAAAGTACCCGGTACCTCTAAAGGACTCAAAAGGATTACAGAAAGGATGAACCTATCATAAATA
1 TAAAAGTACCCGATACCTCTAAAGGACTAAAAAGGATTACA-AAAGGATGAACCTATCCTAAATA
* * * *
230124 CCAACCTTCGGCGTAAAAGCGGACCTGGTGACAACCTATGACTCAATTCTAAAAAATTACGAAAA
65 CC-ACTTTCGGCATAAAAGC-GACCTGGTGACAACCTAAGACTCGATTCTAAAAAATTAC-AAAA
230189 TACCCTTATGGGTATAACTTTGACA
127 TACCCTTATGGG-ATAACTTTGACA
230214 TGAAAA
1 T-AAAA
230220 TATCTTGGTA
Statistics
Matches: 250, Mismatches: 48, Indels: 36
0.75 0.14 0.11
Matches are distributed among these distances:
152 33 0.13
153 5 0.02
154 23 0.09
155 82 0.33
156 56 0.22
157 50 0.20
158 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (150 bp):
TAAAAGTACCCGATACCTCTAAAGGACTAAAAAGGATTACAAAAGGATGAACCTATCCTAAATAC
CACTTTCGGCATAAAAGCGACCTGGTGACAACCTAAGACTCGATTCTAAAAAATTACAAAATACC
CTTATGGGATAACTTTGACA
Found at i:234572 original size:52 final size:52
Alignment explanation
Indices: 234422--234552 Score: 226
Period size: 52 Copynumber: 2.5 Consensus size: 52
234412 CCTGAAATAT
*
234422 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
* *
234474 GAAAATTTGCCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
*
234526 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
234553 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
Found at i:234579 original size:13 final size:13
Alignment explanation
Indices: 234561--234585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234551 CAAAGATCAG
234561 TGTATCGATACAA
1 TGTATCGATACAA
234574 TGTATCGATACA
1 TGTATCGATACA
234586 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:234660 original size:32 final size:33
Alignment explanation
Indices: 234623--234691 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 33
234613 GGCAGTAGCT
234623 TACATTGTATC-ACTACAAAAC-TTATGTATCGA
1 TACATTGTATCGA-TACAAAACTTTATGTATCGA
*
234655 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAACTTTATGTATCGA
234688 TACA
1 TACA
234692 AATCGTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 18 0.53
33 16 0.47
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (33 bp):
TACATTGTATCGATACAAAACTTTATGTATCGA
Found at i:234665 original size:13 final size:13
Alignment explanation
Indices: 234647--234671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234637 ACAAAACTTA
234647 TGTATCGATACAT
1 TGTATCGATACAT
234660 TGTATCGATACA
1 TGTATCGATACA
234672 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:236039 original size:166 final size:165
Alignment explanation
Indices: 235831--236261 Score: 396
Period size: 166 Copynumber: 2.6 Consensus size: 165
235821 GAGAGTTTTG
* * * * *
235831 TAATAATAT-TAGATGAATTTTAAAAGTTTTAAATCGAGAAAAATCCCCCTAAAAAGATTTATGG
1 TAATAATATAT-GATGAATTTTAAAA-ATTAAAACCAAGAAAAATCCCCCTAAAAA-ATTTATAG
* * **
235895 AG-AAAAAAACTCAGT-TTCTCGAAAA-AA-ATAGTCTTCAAAGAAAAA-AATTCAAAACTCATG
63 AGTAAAAAAACTC-GTATT-TCGAAAATAAGAAAAT-TTC-AAGAAAAATAATGAAAAACTCATG
235955 AAAATGAATGAATTTTT-ATAAACTAATTTAATATGAAAGAAA
124 AAAATGAATGAATTTTTGA-AAACTAATTTAATATGAAAGAAA
*
235997 TAATAATA-ATTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCTAAAAAATTTATAG
1 TAATAATATA-TGATGAATTTTAAAAATT-AAAACCAAGAAAAAT-CCCCCTAAAAAATTTATAG
** * **
236061 AGTAAAAAATTTCGTATTTTGAAAATAAGAAAATTTCGTGAAAAATAATGAAAAACTCATGAAAA
63 AGTAAAAAAACTCGTATTTCGAAAATAAGAAAATTTCAAGAAAAATAATGAAAAACTCATGAAAA
* * * * *
236126 TGAATGAATTTTTGAGAATTGATTTAATATTAAATAAA
128 TGAATGAATTTTTGAAAACTAATTTAATATGAAAGAAA
* * * ** * *
236164 TAATAATATATGATTAATTTTAAAAATTAAAACTATGAAAAATCCCTATGAAAAAAATTA-CGAA
1 TAATAATATATGATGAATTTTAAAAATTAAAACCAAGAAAAATCCCCCT-AAAAAATTTATAG-A
* * *
236228 GT-AGAAAACTCCGTATTTCGGAAATAAGAGAATT
64 GTAAAAAAACT-CGTATTTCGAAAATAAGAAAATT
236262 CCACAAGCAA
Statistics
Matches: 217, Mismatches: 34, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
165 12 0.06
166 101 0.47
167 99 0.46
168 5 0.02
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (165 bp):
TAATAATATATGATGAATTTTAAAAATTAAAACCAAGAAAAATCCCCCTAAAAAATTTATAGAGT
AAAAAAACTCGTATTTCGAAAATAAGAAAATTTCAAGAAAAATAATGAAAAACTCATGAAAATGA
ATGAATTTTTGAAAACTAATTTAATATGAAAGAAA
Found at i:236125 original size:20 final size:20
Alignment explanation
Indices: 236080--236133 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
236070 TTTCGTATTT
** *
236080 TGAAAATAA-GAAAATTTCG
1 TGAAAATAATGAAAAACTCA
236099 TGAAAAATAATGAAAAACTCA
1 TG-AAAATAATGAAAAACTCA
236120 TGAAAATGAATGAA
1 TGAAAAT-AATGAA
236134 TTTTTGAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 12 0.41
21 15 0.52
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.22
Consensus pattern (20 bp):
TGAAAATAATGAAAAACTCA
Found at i:237561 original size:20 final size:20
Alignment explanation
Indices: 237533--237607 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
237523 TTTTACCTTG
237533 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
237553 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
237573 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
237593 ATGTATCGATACATT
1 ATGTATCGATACATT
237608 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:237600 original size:40 final size:39
Alignment explanation
Indices: 237533--237610 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
237523 TTTTACCTTG
* *
237533 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
237573 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
237611 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:238544 original size:23 final size:23
Alignment explanation
Indices: 238517--238572 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
238507 AGCCTTTGAC
238517 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
238540 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
238562 CATGCATTTTT
1 CATGCATTTTT
238573 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:238579 original size:20 final size:21
Alignment explanation
Indices: 238525--238579 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
238515 ACCATGCATT
**
238525 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
238546 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
238568 -TTTTTAACATGT
1 TTTTTTAACATGT
238580 CCAGCTTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:240195 original size:12 final size:12
Alignment explanation
Indices: 240178--240202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
240168 AATTTTCTTT
240178 TACTTGTCATTA
1 TACTTGTCATTA
240190 TACTTGTCATTA
1 TACTTGTCATTA
240202 T
1 T
240203 GATGATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTTGTCATTA
Found at i:245018 original size:12 final size:11
Alignment explanation
Indices: 244999--245033 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
244989 CTCACCCAAT
244999 CCAAAAAAAAA
1 CCAAAAAAAAA
245010 CCAAAAAAAAA
1 CCAAAAAAAAA
245021 CCAAAAAAAAA
1 CCAAAAAAAAA
245032 CC
1 CC
245034 TTTTCACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (11 bp):
CCAAAAAAAAA
Found at i:246085 original size:27 final size:27
Alignment explanation
Indices: 246046--246222 Score: 246
Period size: 27 Copynumber: 6.5 Consensus size: 27
246036 AGTGTGAACT
* *
246046 CTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
246073 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
246100 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
246127 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
246155 CTTTTAAGTCTACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
246182 CTTTTAAAGTCCACAACTTCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
246210 CTTTTAAGTCCAC
1 CTTTTAAGTCCAC
246223 TTTTAAGTCC
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 90 0.65
28 49 0.35
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:246227 original size:12 final size:12
Alignment explanation
Indices: 246210--246234 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
246200 TCGTGGCATT
246210 CTTTTAAGTCCA
1 CTTTTAAGTCCA
246222 CTTTTAAGTCCA
1 CTTTTAAGTCCA
246234 C
1 C
246235 AACTTTGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (12 bp):
CTTTTAAGTCCA
Found at i:246237 original size:39 final size:41
Alignment explanation
Indices: 246182--246259 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 41
246172 TCGTGGCATC
*
246182 CTTTTAAAGTCCACAACTTCGTGGCAT-TCTTTTAAGTCCA
1 CTTTTAAAGTCCACAACTTCGTGGCATCCCTTTTAAGTCCA
*
246222 CTTTT-AAGTCCACAACTTTGTGGCATCCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTTCGTGGCATCCCTTTTAAGTC
246260 TACAACTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 20 0.57
40 15 0.43
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (41 bp):
CTTTTAAAGTCCACAACTTCGTGGCATCCCTTTTAAGTCCA
Found at i:246265 original size:67 final size:67
Alignment explanation
Indices: 246155--246283 Score: 206
Period size: 67 Copynumber: 1.9 Consensus size: 67
246145 TGTGGCATCC
* *
246155 CTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGTCCACAACTTCGTGGCATTCTTTTAAGTC
1 CTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAAGTCCACAACTTCGTGGCATCCTTTTAAGTC
246220 CA
66 CA
* *
246222 CTTTTAAGTCCACAACTTTGTGGCATCCCTTTT-AAGTCTACAACTTCGTGGCATCCTTTTAA
1 CTTTTAAGTCCACAACTTCGTGGCAT-CCTTTTAAAGTCCACAACTTCGTGGCATCCTTTTAA
246284 AGTCTACAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
67 51 0.89
68 6 0.11
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (67 bp):
CTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAAGTCCACAACTTCGTGGCATCCTTTTAAGTC
CA
Found at i:246293 original size:95 final size:96
Alignment explanation
Indices: 246127--246720 Score: 364
Period size: 82 Copynumber: 6.9 Consensus size: 96
246117 CTGTGGCACC
246127 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGT
*
246192 CCACAACTTCGTGGCATTCTTTT-AAGTCCA
66 CCACAACTTCGTGGCATCCTTTTAAAGTCCA
*
246222 CTTTTAAGTCCACAACTTTGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGT
*
246287 CTACAACTTCGTGGCATCCTTTTAAAGTCCA
66 CCACAACTTCGTGGCATCCTTTTAAAGTCCA
* * * * * *
246318 C-----A----AC--TTC-GTGGCAT-TCTTTTAAGTCCACAACTCCATGGCACCCTTTT-AAGT
1 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGT
*
246369 CCACAACTCCGTGG----C------A--CC-
66 CCACAACTTCGTGGCATCCTTTTAAAGTCCA
* * * * *
246387 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCCGTGGCACCCTTTT-AAGT
1 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGT
*
246451 CCACAACTCCGTGG----C------A--CC-
66 CCACAACTTCGTGGCATCCTTTTAAAGTCCA
* * * * *
246469 CTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAAC-TCTGTGGCACCCTTTTAAAG
1 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCTACAACTTC-GTGGCATCCTTTTAAAG
*
246533 TCCACAACTCCGT-G--T-C------A--CC-
65 TCCACAACTTCGTGGCATCCTTTTAAAGTCCA
* * * *
246552 CTTTTTAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAAC-TCTGTGGCACCCTTTT-AAG
1 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCTACAACTTC-GTGGCATCCTTTTAAAG
* *
246614 TCTACAACTCCGTGG----C------A--CC-
65 TCCACAACTTCGTGGCATCCTTTTAAAGTCCA
* * *
246633 CTTTTAAGTCCACAACTCTGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
1 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGT
*
246696 CCACAACTCCGTGGCATCCTTTTAA
66 CCACAACTTCGTGGCATCCTTTTAA
246721 GACCACAACT
Statistics
Matches: 442, Mismatches: 28, Indels: 62
0.83 0.05 0.12
Matches are distributed among these distances:
69 1 0.00
70 2 0.00
72 1 0.00
74 1 0.00
78 3 0.01
80 2 0.00
81 98 0.22
82 158 0.36
83 71 0.16
84 7 0.02
85 2 0.00
87 2 0.00
91 1 0.00
95 85 0.19
96 8 0.02
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (96 bp):
CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGT
CCACAACTTCGTGGCATCCTTTTAAAGTCCA
Found at i:246349 original size:27 final size:27
Alignment explanation
Indices: 246222--247434 Score: 889
Period size: 28 Copynumber: 43.0 Consensus size: 27
246212 TTTAAGTCCA
**
246222 CTTTTAAGTCCACAACTTTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
246250 CTTTTAAGTCTACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
246277 CTTTTAAAGTCTACAACTTCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* **
246305 CTTTTAAAGTCCACAACTTCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
246333 CTTTTAAGTCCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
246360 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
246387 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
246415 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
246442 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
246469 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
246497 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
246524 CTTTTAAAGTCCACAACTCCGTGTCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
246552 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
246579 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
246606 CTTTTAAGTCTACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
246633 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
246660 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
246687 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
246714 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
246741 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* **
246769 CTTTTGAGTCCACAACTCTATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
246796 ATTTTAAAATCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
246824 CATTTTAAAATCCACAACTCTGTGGCACC
1 C-TTTT-AAGTCCACAACTCCGTGGCACC
* * * *
246853 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTT-TAAG-TC-CACAACTCCGTGGC-ACC
* * * * *
246885 CATTTCAAAGCCCACACAAGTCGGTGGCAACA
1 C-TTT-TAAG-TC-CACAACTCCGTGGC-ACC
* * *
246917 CTTTTCAAAGCCCACACAAGTCGGTGGCAACAC
1 CTTTT--AAG-TC-CACAACTCCGTGGC-AC-C
* * * *
246950 CTTTCAAAGCCCACACAAGTCGGTGGCACCC
1 CTTT-TAAG-TC-CACAACTCCGTGGCA-CC
** * * *
246981 CTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * ** *
247008 CTTTTAAAGCCCACAAGTTAGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
247036 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
1 CTTTT--AAGTCCACAACTCCGTGGCACC
* * * *
247064 CTTTTCAAAGCCCACAAGTCAGTGGTACC
1 CTTTT--AAGTCCACAACTCCGTGGCACC
* * *
247093 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTT--AAGTCCACAACTCCGTGGCACC
* * * *
247122 CTTTCGAAGCCCACAAGTCAGTGGCACC
1 CTTT-TAAGTCCACAACTCCGTGGCACC
* ** * * * *
247150 ATTACAAAGCCCACAATTCAGTGGCACT
1 CTT-TTAAGTCCACAACTCCGTGGCACC
* * * * *
247178 CTTTCAAAGCCCACACAAGTCAGTGGCACT
1 CTTT-TAAG-TC-CACAACTCCGTGGCACC
* * *
247208 CTTTTAAAGCCCACAAGTCAGTGGCACTC
1 CTTTT-AAGTCCACAACTCCGTGGCAC-C
* * * *
247237 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTT-TAAGTCCACAACTCCGTGGCAC-C
* * * * *
247266 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTT-TAAGTCCACAACTCCGTGGCACC
* * *
247294 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTT--AAGTCCACAACTCCGTGGCACC
* * * *
247323 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTT-TAAGTCCACAACTCCGTGGCACC
* * * **
247351 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTT-TAAGTCCACAACTCCGTGGCACC
* * * *
247379 CTTTCAGAGCCCACAAGTCAGTGGCACC
1 CTTTTA-AGTCCACAACTCCGTGGCACC
* * * *
247407 CTTTCGAAGCCCACAATTCAGTGGCACC
1 CTTT-TAAGTCCACAACTCCGTGGCACC
247435 ATTGCGAAGC
Statistics
Matches: 1069, Mismatches: 84, Indels: 64
0.88 0.07 0.05
Matches are distributed among these distances:
27 339 0.32
28 424 0.40
29 173 0.16
30 28 0.03
31 20 0.02
32 81 0.08
33 4 0.00
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:246391 original size:54 final size:54
Alignment explanation
Indices: 246222--247434 Score: 889
Period size: 54 Copynumber: 21.5 Consensus size: 54
246212 TTTAAGTCCA
** * * *
246222 CTTTTAAGTCCACAACTTTGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* * * * **
246277 CTTTTAAAGTCTACAACTTCGTGGCATCCTTTTAAAGTCCACAACTTCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
*
246333 CTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
246387 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* *
246442 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* *
246497 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGTCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
* *
246552 CTTTTTAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
246606 CTTTTAAGTCTACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
246660 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
246714 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* ** * * *
246769 CTTTTGAGTCCACAACTCTATGGCACCATTTTAAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
* * * * * *
246824 CATTTTAAAATCCACAACTCTGTGGCACCCATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTT-AAGTCCACAACTCCGTGGCACCC-TTT-TAAG-TC-CACAACTCCGTGGC-ACC
* * * * * * * *
246885 CATTTCAAAGCCCACACAAGTCGGTGGCAACACTTTTCAAAGCCCACACAAGTCGGTGGCAACAC
1 C-TTT-TAAG-TC-CACAACTCCGTGGC-ACCCTTTT--AAG-TC-CACAACTCCGTGGC-AC-C
* * * * ** * * *
246950 CTTTCAAAGCCCACACAAGTCGGTGGCACCCCTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTT-TAAG-TC-CACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* * ** * * * *
247008 CTTTTAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-C
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTT--AAGTCCACAACTCCGTGGCACC
* * * * * * *
247064 CTTTTCAAAGCCCACAAGTCAGTGGTACCCTTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTT--AAGTCCACAACTCCGTGGCACCCTTTT--AAGTCCACAACTCCGTGGCACC
* * * * * ** * * * *
247122 CTTTCGAAGCCCACAAGTCAGTGGCACCATTACAAAGCCCACAATTCAGTGGCACT
1 CTTT-TAAGTCCACAACTCCGTGGCACCCTT-TTAAGTCCACAACTCCGTGGCACC
* * * * * * * *
247178 CTTTCAAAGCCCACACAAGTCAGTGGCACTCTTTTAAAGCCCACAAGTCAGTGGCACTC
1 CTTT-TAAG-TC-CACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCAC-C
* * * * * * * * *
247237 CTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTT-TAAGTCCACAACTCCGTGGCAC-CCTTT-TAAGTCCACAACTCCGTGGCACC
* * * * * * *
247294 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTT--AAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAACTCCGTGGCACC
* * * ** * * * *
247351 CTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCACC
1 CTTT-TAAGTCCACAACTCCGTGGCACCCTTTTA-AGTCCACAACTCCGTGGCACC
* * * *
247407 CTTTCGAAGCCCACAATTCAGTGGCACC
1 CTTT-TAAGTCCACAACTCCGTGGCACC
247435 ATTGCGAAGC
Statistics
Matches: 1022, Mismatches: 97, Indels: 77
0.85 0.08 0.06
Matches are distributed among these distances:
54 241 0.24
55 184 0.18
56 200 0.20
57 165 0.16
58 104 0.10
59 12 0.01
60 25 0.02
61 12 0.01
62 4 0.00
63 16 0.02
64 57 0.06
65 2 0.00
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (54 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:247003 original size:28 final size:28
Alignment explanation
Indices: 246353--248476 Score: 1926
Period size: 28 Copynumber: 73.8 Consensus size: 28
246343 CACAACTCCA
* * * *
246353 TGGCACCCTTT-TAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * *
246380 TGGCACCCTTT-TAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * *
246407 TGGCATCCCTTT-TAAGACCACAACTCCG
1 TGGCA-CCCTTTCAAAGCCCACAAGTCAG
* * * *
246435 TGGCACCCTTT-TAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * * *
246462 TGGCACCCTTT-TAAGTCCATAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * * *
246489 TGGCATCTCTTT-TAAGTCCACAACTCTG
1 TGGCA-CCCTTTCAAAGCCCACAAGTCAG
* * * *
246517 TGGCACCCTTTTAAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* ** * * *
246545 TGTCACCCTTT-TTAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * *
246572 TGGCACCCTTT-TAAGTCCACAACTCTG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * * *
246599 TGGCACCCTTT-TAAGTCTACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * *
246626 TGGCACCCTTT-TAAGTCCACAACTCTG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * *
246653 TGGCACCCTTT-TAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * *
246680 TGGCACCCTTT-TAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * * *
246707 TGGCATCCTTT-TAAGACCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * * *
246734 TGGCACCCTTT-TAAGTCCATAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* ** * *
246761 TGGCATCTCTTT-TGAGTCCACAACTCTA-
1 TGGCA-CCCTTTCAAAGCCCACAAGTC-AG
* * ** * *
246789 TGGCACCATTTTAAAATCCACAACTCTG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* ** * *
246817 TGGCACCCATTTTAAAATCCACAACTCTG
1 TGGCACCC-TTTCAAAGCCCACAAGTCAG
*
246846 TGGCACCCATTTCAAAGCCCACACAAGTCGG
1 TGGCACCC-TTTCAAAG-CC-CACAAGTCAG
*
246877 TGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 TGGC-ACCC-TTTCAAAG-CC-CACAAGTCAG
* *
246909 TGGCAACACTTTTCAAAGCCCACACAAGTCGG
1 TGGC-AC-CCTTTCAAAG-CC-CACAAGTCAG
*
246941 TGGCAACACCTTTCAAAGCCCACACAAGTCGG
1 TGGC-AC-CCTTTCAAAG-CC-CACAAGTCAG
*
246973 TGGCACCCCTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* *
247001 TGGCACCCTTTTAAAGCCCACAAGTTAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247029 TGGCACTCTTTTCAAAGCCCACAAGTCAG
1 TGGCAC-CCTTTCAAAGCCCACAAGTCAG
*
247058 TGGCACCTTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247086 TGGTACCCTTTTCAAAGCCCACAAGTCAG
1 TGGCACCC-TTTCAAAGCCCACAAGTCAG
*
247115 TGGCACCCTTTCGAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * *
247143 TGGCACCATTACAAAGCCCACAATTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247171 TGGCACTCTTTCAAAGCCCACACAAGTCAG
1 TGGCACCCTTTCAAAG-CC-CACAAGTCAG
* *
247201 TGGCACTCTTTTAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
247229 TGGCACTCCTTTCAAAGCCCACAAGTCAG
1 TGGCAC-CCTTTCAAAGCCCACAAGTCAG
247258 TGGCACTCCTTTCAAAGCCCACAAGTCAG
1 TGGCAC-CCTTTCAAAGCCCACAAGTCAG
*
247287 TGGCACTCTTTTCAAAGCCCACAAGTCAG
1 TGGCAC-CCTTTCAAAGCCCACAAGTCAG
247316 TGGCACCCTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247344 TGGCACCCTTTCAAAGCCCACAAGTTAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247372 TGGCACCCTTTCAGAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* *
247400 TGGCACCCTTTCGAAGCCCACAATTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * *
247428 TGGCACCATTGCGAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* *
247456 TGGCACTCTTTTAAAGCCCACACAAGTCAG
1 TGGCACCCTTTCAAAG-CC-CACAAGTCAG
* *
247486 TGGCACTCCTTTTAAAGCTCACGCAAGTCAG
1 TGGCAC-CCTTTCAAAGC-C-CACAAGTCAG
* *
247517 TGGCACTCCTTTTAAAGCTCACGCAAGTCAG
1 TGGCAC-CCTTTCAAAGC-C-CACAAGTCAG
* * *
247548 TGGTACTCCTTTTAAAGCTCACGCAAGTCAG
1 TGGCAC-CCTTTCAAAGC-C-CACAAGTCAG
*
247579 TGGCACTCTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247607 TGGCACTCTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247635 TGGCACTCTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247663 TGGCACCCTTTCAAAGCCCACAAGTTAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247691 TGGCACCCCTTTCAAAGCCCACGCAAGTTAG
1 TGGCA-CCCTTTCAAAGCCCA--CAAGTCAG
* *
247722 TGGCACCCTTTTAAAGCCCACAAGTTAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* *
247750 TGGCACCCTTTTAAAGCCCACAAGTTAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* *
247778 TGGCACTCTTTTCAAAGCCCACACAAGTCGG
1 TGGCAC-CCTTTCAAAG-CC-CACAAGTCAG
* *
247809 TGGCAACCCATTCCAAAGCCCACACAAGTCGG
1 TGGC-ACCC-TTTCAAAG-CC-CACAAGTCAG
* *
247841 TGGTAACCTATTCCAAAGCCCACACAAGTCAG
1 TGGCACCCT-TT-CAAAG-CC-CACAAGTCAG
*
247873 TGGCAACCAATTTCAAAGCCCACACAAGTCAG
1 TGGC-ACC-CTTTCAAAG-CC-CACAAGTCAG
*
247905 TGGCACCCTTTCAGAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * * * *
247933 TGGCACCATTGCGAAGCCCACAATTCTG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247961 TGGCACTCTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
247989 TGGCACCCTTTCAAAGCCCACACAAGTCGG
1 TGGCACCCTTTCAAAG-CC-CACAAGTCAG
* *
248019 TGGCAACCCATTCCAAAGCCCACACAAGTCGG
1 TGGC-ACCC-TTTCAAAG-CC-CACAAGTCAG
* *
248051 TGGCAACCTATTTCAAAGCCCACACAAGTCGG
1 TGGC-ACC-CTTTCAAAG-CC-CACAAGTCAG
* *
248083 TGGCAACACTTTTCAAAGCCCACACAAGTCGG
1 TGGC-AC-CCTTTCAAAG-CC-CACAAGTCAG
248115 TGGCACCCTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
248143 TGGCACCCCTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* *
248171 TGGCACCCTTTTAAAGCCCACAAGTTAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
248199 TGGCACTCTTTTCAAAGCCCACAAGTCAG
1 TGGCAC-CCTTTCAAAGCCCACAAGTCAG
* *
248228 TGGCACCTTTTCAAAGCCCACGAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
248256 TGGCACTCTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
*
248284 TGGCACCCTTTC-AAGCCCACGAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * *
248311 TGGTACCTTTTCAAAGCCCACGAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
248339 TGGCA-CCTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* * *
248366 TGGCACTCTTTCAAAGCCCACGAGTTAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAG
* *
248394 TGGTATCCTTTCAAAGCCCACGCAAGTCAG
1 TGGCACCCTTTCAAAGCCCA--CAAGTCAG
*
248424 TGGCACCCTTTTAAAGCCCACGCAAGTCAG
1 TGGCACCCTTTCAAAGCCCA--CAAGTCAG
** *
248454 TAACACTCTTTTCAAAGCCCACA
1 TGGCAC-CCTTTCAAAGCCCACA
248477 TGTGTCAGTG
Statistics
Matches: 1892, Mismatches: 160, Indels: 88
0.88 0.07 0.04
Matches are distributed among these distances:
27 337 0.18
28 775 0.41
29 235 0.12
30 143 0.08
31 151 0.08
32 244 0.13
33 6 0.00
34 1 0.00
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.22
Consensus pattern (28 bp):
TGGCACCCTTTCAAAGCCCACAAGTCAG
Found at i:249115 original size:20 final size:20
Alignment explanation
Indices: 249087--249161 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
249077 TTTTACCTTG
249087 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
249107 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
249127 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
249147 ATGTATCGATACATT
1 ATGTATCGATACATT
249162 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:249154 original size:40 final size:39
Alignment explanation
Indices: 249087--249164 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
249077 TTTTACCTTG
* *
249087 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
249127 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
249165 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:250098 original size:23 final size:23
Alignment explanation
Indices: 250071--250126 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
250061 AGCCTTTGAC
250071 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
250094 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
250116 CATGCATTTTT
1 CATGCATTTTT
250127 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:250133 original size:20 final size:21
Alignment explanation
Indices: 250079--250133 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
250069 ACCATGCATT
**
250079 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
250100 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
250122 -TTTTTAACATGT
1 TTTTTTAACATGT
250134 CCAGCTTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:251748 original size:12 final size:12
Alignment explanation
Indices: 251731--251755 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
251721 AATTTTCTTT
251731 TACTTGTCATTA
1 TACTTGTCATTA
251743 TACTTGTCATTA
1 TACTTGTCATTA
251755 T
1 T
251756 GATGATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTTGTCATTA
Found at i:252992 original size:58 final size:55
Alignment explanation
Indices: 252901--253071 Score: 202
Period size: 58 Copynumber: 3.0 Consensus size: 55
252891 AAAAAACTTA
* * *
252901 AATGACCTCAAAATGCATGAAAATTACTGCATGGTCACTAGATTATGAAAAATAACCT
1 AATGACCTTAAAATGCAT-AAAATT-CTACATGGTC-TTAGATTATGAAAAATAACCT
* *
252959 AAGTGACTTTAAAATGCATAAAATTGCTACATGGTCTTCGAATTATGAAAAATAACCT
1 AA-TGACCTTAAAATGCATAAAATT-CTACATGGTCTTAG-ATTATGAAAAATAACCT
* *
253017 AATGACCTTAAAATACATGAAA-T-TACATGGTCTTTAGATTATGAAAAATAACCT
1 AATGACCTTAAAATGCATAAAATTCTACATGGTC-TTAGATTATGAAAAATAACCT
253071 A
1 A
253072 GATTATGAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
54 27 0.27
55 3 0.03
56 1 0.01
57 19 0.19
58 36 0.36
59 14 0.14
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (55 bp):
AATGACCTTAAAATGCATAAAATTCTACATGGTCTTAGATTATGAAAAATAACCT
Found at i:253084 original size:54 final size:54
Alignment explanation
Indices: 252942--253089 Score: 142
Period size: 54 Copynumber: 2.6 Consensus size: 54
252932 TGGTCACTAG
* * *
252942 ATTATGAAAAATAACCTAAGTGACTTTAAAATG-CATAAAATTGCTACATGGTCTTCGA
1 ATTATGAAAAATAACCTAA-TGAC-TAAAAATGACATGAAA-T--TACATGGTCTTAGA
*
253000 ATTATGAAAAATAACCTAATGACCTTAAAAT-ACATGAAATTACATGGTCTTTAG-
1 ATTATGAAAAATAACCTAATGA-CTAAAAATGACATGAAATTACATGGTC-TTAGA
*
253054 ATTATGAAAAATAACCTAGATTA-TGAAAAATGACAT
1 ATTATGAAAAATAACCTA-ATGACT-AAAAATGACAT
253090 ACATGACCTT
Statistics
Matches: 80, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
53 1 0.01
54 32 0.40
55 10 0.12
56 1 0.01
57 16 0.20
58 20 0.25
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (54 bp):
ATTATGAAAAATAACCTAATGACTAAAAATGACATGAAATTACATGGTCTTAGA
Found at i:259796 original size:13 final size:13
Alignment explanation
Indices: 259778--259803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
259768 TACACCAAGT
259778 ATGTATCGATACA
1 ATGTATCGATACA
259791 ATGTATCGATACA
1 ATGTATCGATACA
259804 CAAAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:265373 original size:13 final size:13
Alignment explanation
Indices: 265355--265380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
265345 TACACCAAGT
265355 ATGTATCGATACA
1 ATGTATCGATACA
265368 ATGTATCGATACA
1 ATGTATCGATACA
265381 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:265378 original size:32 final size:33
Alignment explanation
Indices: 265337--265400 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
265327 TAGCCAAACT
* **
265337 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
265369 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
265401 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:266803 original size:21 final size:22
Alignment explanation
Indices: 266774--266814 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
266764 TAATTTAAAA
266774 TAAATTAAAAATGA-CTAAAATC
1 TAAATTAAAAAT-ATCTAAAATC
266796 TAAA-TAAAAATATCTAAAA
1 TAAATTAAAAATATCTAAAA
266815 CTTAGCTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 13 0.72
22 4 0.22
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAAAAATATCTAAAATC
Found at i:267542 original size:32 final size:33
Alignment explanation
Indices: 267499--267579 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
267489 GTAGATAAAC
267499 AAATAGA-ATATAAATCCATGCACATATAAATG
1 AAATAGATATATAAATCCATGCACATATAAATG
* ** *
267531 AATTA-ATATATAAATTTATGCACATATAAATT
1 AAATAGATATATAAATCCATGCACATATAAATG
*
267563 AAATAGATGTATAAATC
1 AAATAGATATATAAATC
267580 AAGTTTCTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 1 0.03
32 30 0.75
33 9 0.22
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (33 bp):
AAATAGATATATAAATCCATGCACATATAAATG
Found at i:267562 original size:16 final size:16
Alignment explanation
Indices: 267506--267564 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
267496 AACAAATAGA
**
267506 ATATAAATCCATGCAC
1 ATATAAATTAATGCAC
* ** *
267522 ATATAAATGAATTAAT
1 ATATAAATTAATGCAC
*
267538 ATATAAATTTATGCAC
1 ATATAAATTAATGCAC
267554 ATATAAATTAA
1 ATATAAATTAA
267565 ATAGATGTAT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (16 bp):
ATATAAATTAATGCAC
Found at i:268520 original size:33 final size:33
Alignment explanation
Indices: 268478--268545 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
268468 ATAAGAAAAT
268478 TTAAAAACCTTCTTTCCCACTAAACAAACATTA
1 TTAAAAACCTTCTTTCCCACTAAACAAACATTA
* *
268511 TTAAAAACCTTCTTTCCTACTAAACAAGCATTA
1 TTAAAAACCTTCTTTCCCACTAAACAAACATTA
268544 TT
1 TT
268546 GACAATCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (33 bp):
TTAAAAACCTTCTTTCCCACTAAACAAACATTA
Found at i:269451 original size:19 final size:19
Alignment explanation
Indices: 269425--269468 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
269415 TTTAAATTAA
*
269425 AATTATTTTTAATATAATT
1 AATTATTTATAATATAATT
* *
269444 ATTTATTTATAATGTAATT
1 AATTATTTATAATATAATT
269463 AATTAT
1 AATTAT
269469 CAAAATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
AATTATTTATAATATAATT
Found at i:269615 original size:19 final size:21
Alignment explanation
Indices: 269591--269635 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
269581 ATTAATTTAA
269591 TAAAAAA-TAATATAAAAA-T
1 TAAAAAATTAATATAAAAATT
*
269610 TAAAAAATTATTATAAAAATT
1 TAAAAAATTAATATAAAAATT
269631 TAAAA
1 TAAAA
269636 TTATAGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 10 0.43
21 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAAAATTAATATAAAAATT
Found at i:269636 original size:19 final size:20
Alignment explanation
Indices: 269591--269639 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
269581 ATTAATTTAA
*
269591 TAAAAAA-TAATATAAAAAT
1 TAAAAAATTATTATAAAAAT
269610 TAAAAAATTATTATAAAAAT
1 TAAAAAATTATTATAAAAAT
*
269630 T-TAAAATTAT
1 TAAAAAATTAT
269640 AGATATATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAAATTATTATAAAAAT
Found at i:270836 original size:16 final size:16
Alignment explanation
Indices: 270817--270849 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
270807 TTTTAGGTAA
270817 AATATATTAT-TATTTT
1 AATAT-TTATATATTTT
270833 AATATTTATATATTTT
1 AATATTTATATATTTT
270849 A
1 A
270850 TAATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATATTTATATATTTT
Found at i:270856 original size:22 final size:21
Alignment explanation
Indices: 270818--270879 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
270808 TTTAGGTAAA
*
270818 ATATATTATTATTTTAATATTT
1 ATATATT-TTATATTAATATTT
270840 ATATATTTTATAATTAA-ATTT
1 ATATATTTTAT-ATTAATATTT
* *
270861 AAATAATTTTTTTATTAAT
1 ATAT-A-TTTTATATTAAT
270880 TAATAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 11 0.33
22 17 0.52
23 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATATTAATATTT
Found at i:272299 original size:33 final size:33
Alignment explanation
Indices: 272235--272301 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
272225 CATTAATCTA
* **
272235 TAATATTATTAAATTAAAAACAATATTTATTTT
1 TAATATTATTAAATTAAAAACAAAAAATATTTT
* *
272268 TAATATTATTAAATTTAAAATAAAAAATATTTT
1 TAATATTATTAAATTAAAAACAAAAAATATTTT
272301 T
1 T
272302 TTATTATCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (33 bp):
TAATATTATTAAATTAAAAACAAAAAATATTTT
Found at i:272673 original size:2 final size:2
Alignment explanation
Indices: 272666--272698 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
272656 ATTTCGAAAC
272666 AT AT 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 AT AT A
272699 CACTTAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:275589 original size:17 final size:17
Alignment explanation
Indices: 275567--275675 Score: 62
Period size: 18 Copynumber: 6.1 Consensus size: 17
275557 AAAATATAAT
275567 TATATTATAATAATTTA
1 TATATTATAATAATTTA
*
275584 TATATTTATATTATATTTA
1 TATA-TTATAATA-ATTTA
* *
275603 TATATTTTATTATATTATAA
1 TATATTATAATA-ATT-T-A
* *
275623 TCATATTTAAAATATTTTA
1 T-ATA-TTATAATAATTTA
275642 TAT-TTAT-ATAAATTT-
1 TATATTATAAT-AATTTA
*
275657 TAATATAATAATAATTTA
1 T-ATATTATAATAATTTA
275675 T
1 T
275676 TTTTTTAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 21
0.71 0.09 0.21
Matches are distributed among these distances:
15 3 0.04
16 9 0.12
17 12 0.17
18 23 0.32
19 12 0.17
20 3 0.04
21 5 0.07
22 5 0.07
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAATAATTTA
Found at i:275592 original size:23 final size:22
Alignment explanation
Indices: 275560--275616 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
275550 ATACTTAAAA
*
275560 ATATAATTATATTATAATAATTT
1 ATATATTTATATTATAAT-ATTT
275583 ATATATTTATA-T-T-ATATTT
1 ATATATTTATATTATAATATTT
275602 ATATATTT-TATTATA
1 ATATATTTATATTATA
275617 TTATAATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 2 0.07
19 13 0.43
20 3 0.10
21 1 0.03
22 1 0.03
23 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATATTTATATTATAATATTT
Found at i:275597 original size:28 final size:27
Alignment explanation
Indices: 275565--275650 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 27
275555 TAAAAATATA
275565 ATTATATTATAATAATTTATATATTTAT
1 ATTATATT-TAATAATTTATATATTTAT
*
275593 ATTATATTTATATATTTTAT-TATATTAT
1 ATTATATTTA-ATAATTTATATAT-TTAT
* *
275621 AATCATATTTAA-AATATTTTATATTTAT
1 -ATTATATTTAATAAT-TTATATATTTAT
275649 AT
1 AT
275651 AAATTTTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 9 0.18
28 28 0.57
29 12 0.24
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTATATTTAATAATTTATATATTTAT
Found at i:275628 original size:23 final size:22
Alignment explanation
Indices: 275560--275628 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
275550 ATACTTAAAA
275560 ATATA-ATTATATTATAATAAT
1 ATATATATTATATTATAATAAT
* * *
275581 TTATATATTTATATTATATTTAT
1 ATATATA-TTATATTATAATAAT
* *
275604 ATATTTTATTATATTATAATCAT
1 ATA-TATATTATATTATAATAAT
275627 AT
1 AT
275629 TTAAAATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 4 0.11
22 1 0.03
23 30 0.79
24 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATATATTATATTATAATAAT
Found at i:278719 original size:44 final size:43
Alignment explanation
Indices: 278669--278758 Score: 162
Period size: 44 Copynumber: 2.1 Consensus size: 43
278659 GAAAAATTCT
278669 ATCTTTCTGTTCTACATTCCTTATTCTCTTTATTATTTTTTTTC
1 ATCTTTCTGTTCTACATTCCTTATTCTCTTTATTA-TTTTTTTC
*
278713 ATCTTTCTGTTTTACATTCCTTATTCTCTTTATTATTTTTTTC
1 ATCTTTCTGTTCTACATTCCTTATTCTCTTTATTATTTTTTTC
278756 ATC
1 ATC
278759 ATATTTTCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 11 0.24
44 34 0.76
ACGTcount: A:0.14, C:0.20, G:0.02, T:0.63
Consensus pattern (43 bp):
ATCTTTCTGTTCTACATTCCTTATTCTCTTTATTATTTTTTTC
Found at i:291988 original size:13 final size:13
Alignment explanation
Indices: 291970--291994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291960 ATTACTCAAA
291970 TGTATCGATACAT
1 TGTATCGATACAT
291983 TGTATCGATACA
1 TGTATCGATACA
291995 CTGATCTTTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:292045 original size:52 final size:53
Alignment explanation
Indices: 291983--292127 Score: 188
Period size: 52 Copynumber: 2.8 Consensus size: 53
291973 ATCGATACAT
***
291983 TGTATCGATACACTGAT-CTTTATATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATATATCGATACATGCAGGCAAATTTGCCCAGA
* * *
292035 TGTATCGATACA-TTATAAAATGTATCGGTACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATATATCGATACATGCAGGCAAATTTGCCCAGA
* * *
292087 TGTATCGATACACT-ATTAAATGTATCGATACATGCAAGCAA
1 TGTATCGATACACTGATAAAATATATCGATACATGCAGGCAA
292128 CTTTTCATAT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
51 3 0.04
52 78 0.95
53 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (53 bp):
TGTATCGATACACTGATAAAATATATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:299318 original size:29 final size:31
Alignment explanation
Indices: 299278--299349 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 31
299268 GTTCTTTTCC
299278 AAAAAAAGAAAC-A-AAACAAAAAATAAGAA-
1 AAAAAAAGAAACAACAAACAAAAAA-AAGAAG
299307 AAAAAAAGAAACAAACAAACAAAAAAAAGAAG
1 AAAAAAAGAAAC-AACAAACAAAAAAAAGAAG
299339 AAGAAAAAGAA
1 AA-AAAAAGAA
299350 GGGAAAACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
29 12 0.32
31 6 0.16
32 12 0.32
33 8 0.21
ACGTcount: A:0.82, C:0.07, G:0.10, T:0.01
Consensus pattern (31 bp):
AAAAAAAGAAACAACAAACAAAAAAAAGAAG
Found at i:299332 original size:24 final size:23
Alignment explanation
Indices: 299278--299337 Score: 50
Period size: 25 Copynumber: 2.4 Consensus size: 23
299268 GTTCTTTTCC
299278 AAAAAAAGAAACAAAACAA-AAAA
1 AAAAAAAGAAACAAAA-AACAAAA
* *
299301 TAAGAAAAAAAAAGAAACAAACAAACA
1 -AA-AAAAAGAAACAAA-AAACAAA-A
299328 AAAAAAAGAA
1 AAAAAAAGAA
299338 GAAGAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
24 2 0.07
25 20 0.69
26 6 0.21
27 1 0.03
ACGTcount: A:0.83, C:0.08, G:0.07, T:0.02
Consensus pattern (23 bp):
AAAAAAAGAAACAAAAAACAAAA
Found at i:299339 original size:24 final size:24
Alignment explanation
Indices: 299291--299340 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
299281 AAAAGAAACA
*
299291 AAACAAAAAATAAGAAAAAAAAAG
1 AAACAAAAAACAAGAAAAAAAAAG
*
299315 AAACAAACAAACAA-AAAAAAGAAG
1 AAACAAA-AAACAAGAAAAAAAAAG
299339 AA
1 AA
299341 GAAAAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.02
Consensus pattern (24 bp):
AAACAAAAAACAAGAAAAAAAAAG
Found at i:300390 original size:30 final size:31
Alignment explanation
Indices: 300339--300424 Score: 104
Period size: 30 Copynumber: 2.8 Consensus size: 31
300329 CACAACTCCG
* * *
300339 TGGCACCTTCTTCTTTAAAGTCCACGACTTAG
1 TGGCATCTT-TTCTTCAAAGTCCACGACTTAA
300371 TGGCAT-TTTGTC-TCAAAGTCCACGACTTAA
1 TGGCATCTTT-TCTTCAAAGTCCACGACTTAA
*
300401 TGGCATCTTTTCTTCAAAGCCCAC
1 TGGCATCTTTTCTTCAAAGTCCAC
300425 AACTCCGTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
30 25 0.53
31 17 0.36
32 5 0.11
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (31 bp):
TGGCATCTTTTCTTCAAAGTCCACGACTTAA
Found at i:300456 original size:34 final size:34
Alignment explanation
Indices: 300401--301037 Score: 294
Period size: 34 Copynumber: 19.8 Consensus size: 34
300391 CACGACTTAA
*
300401 TGGCA-TC-TTTT-CTTCAAAGCCCACAACTCCG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
300432 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* * * *
300466 TGGCACTC-TTATCCGTT-TAAGTCCGCGACTCCG
1 TGGCACTCTTTTTCC-TTCTAAGCCCACAACTCCG
* * * * * *
300499 TGGCACTTTTTTTCTTTTTAAAGTCCACGACTCAG
1 TGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCG
*
300534 TGGCA-T-TTTCTT--TTCAAAGCCCACAACTCCG
1 TGGCACTCTTT-TTCCTTCTAAGCCCACAACTCCG
* *
300565 TGGCAC-C-----CGTT-TAAGCCCACAACTCTG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* * * * *
300592 TGGCACTCTTTTTCCCTTTTAAGTCTACAATTTCG
1 TGGCACTCTTTTT-CCTTCTAAGCCCACAACTCCG
* *
300627 TGGCA--C-----CCTTTTAAGTCCACAACTCCG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* *
300654 TGGCA--C-----CCTTTTAAGCCCACAACTCTG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* * * *
300681 TGGCATTCTTTTTCCTTTTAAGTCCACGACTCCG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* * * **
300715 TGGCAC-CTTCTT--TTCAAAGCCCACAGCAT-AT
1 TGGCACTCTTTTTCCTTCTAAGCCCACAAC-TCCG
* * *
300746 TGGCACTCTTTTTCCTTCTAAGTCCATAACTCTG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* * *
300780 TGGCAC-C---AT--TT-TAAGCCTACAACTCTG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* * *
300807 TGGCACTCTGTTTCCTTCTAAGTCCACAACTCTG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* * *
300841 TGGCAC-C--CTT--TT-AAAGCCCATAACTCCG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* *
300869 TGGCACTCTTTTTCCCTTTTTAAAGTCCACAACTCCG
1 TGGCACTCTTTTT-CC-TTCT-AAGCCCACAACTCCG
* *
300906 TGGCAC-CTTTTTCCCTTTTCAAAGCCCACAACTCTG
1 TGGCACTCTTTTT-CC--TTCTAAGCCCACAACTCCG
* * *
300942 TGGCATTCTTTTTCCTTTTAAGTCCACAACTCCG
1 TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
* * ** *
300976 TGGCAC-CTTTTTCTTTTTTAAGTTCACAACTCTG
1 TGGCACTCTTTTTC-CTTCTAAGCCCACAACTCCG
*
301010 TGGCAC-CTTTTTCTTTCTAAAGCCCACA
1 TGGCACTCTTTTTCCTTCT-AAGCCCACA
301038 CAAGTCGATG
Statistics
Matches: 475, Mismatches: 79, Indels: 101
0.73 0.12 0.15
Matches are distributed among these distances:
27 87 0.18
28 24 0.05
29 4 0.01
30 1 0.00
31 43 0.09
32 10 0.02
33 56 0.12
34 157 0.33
35 36 0.08
36 29 0.06
37 28 0.06
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.35
Consensus pattern (34 bp):
TGGCACTCTTTTTCCTTCTAAGCCCACAACTCCG
Found at i:300588 original size:27 final size:27
Alignment explanation
Indices: 300550--300685 Score: 128
Period size: 27 Copynumber: 4.7 Consensus size: 27
300540 TTTCTTTTCA
*
300550 AAGCCCACAACTCCGTGGCACCCGTTT
1 AAGCCCACAACTCCGTGGCACCCTTTT
*
300577 AAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
1 AAGCCCACAACTCCGTGGCA--------CCCTTTT
* * * *
300612 AAGTCTACAATTTCGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACCCTTTT
*
300639 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACCCTTTT
*
300666 AAGCCCACAACTCTGTGGCA
1 AAGCCCACAACTCCGTGGCA
300686 TTCTTTTTCC
Statistics
Matches: 89, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
27 68 0.76
35 21 0.24
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (27 bp):
AAGCCCACAACTCCGTGGCACCCTTTT
Found at i:300713 original size:61 final size:62
Alignment explanation
Indices: 300633--300987 Score: 410
Period size: 61 Copynumber: 5.5 Consensus size: 62
300623 TTCGTGGCAC
*
300633 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGCCCACAACTCTGTGGCATTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
* * *
300694 CCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAGCATAT-TGGCACTCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACC--CTTTT-AAAGCCCACAAC-TCTGTGGCACTCTTTT
300758 T
62 T
* * * * * *
300759 CCTTCTAAGTCCATAACTCTGTGGCACCATTTT-AAGCCTACAACTCTGTGGCACTCTGTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
* * * *
300820 CCTTCTAAGTCCACAACTCTGTGGCACCCTTTTAAAGCCCATAACTCCGTGGCACTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
300882 CCCTTTTTAAAGTCCACAACTCCGTGGCACCTTTTTCCCTTTTCAAAGCCCACAACTCTGTGGCA
1 -CC-TTTT-AAGTCCACAACTCCGTGGCA-------CCCTTTT-AAAGCCCACAACTCTGTGGCA
*
300947 TTCTTTTT
55 CTCTTTTT
*
300955 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
300988 CTTTTTTAAG
Statistics
Matches: 251, Mismatches: 25, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
60 2 0.01
61 79 0.31
62 24 0.10
63 17 0.07
64 3 0.01
65 65 0.26
66 2 0.01
70 20 0.08
71 4 0.02
72 9 0.04
73 26 0.10
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (62 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
Found at i:300777 original size:126 final size:126
Alignment explanation
Indices: 300632--300984 Score: 435
Period size: 126 Copynumber: 2.7 Consensus size: 126
300622 TTTCGTGGCA
300632 CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCTGTGGCATTCTTTTTCCT
1 CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCTGTGGCATTCTTTTTCCT
* * *
300697 TTTAAGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAGCAT-ATTGGCACTCTTTTT
66 TTTAAGTCCACAACTCCGTGGCACCTTCTTTT-AAAGCCCACAAC-TCAGTGGCACTCTTTTT
* * * * * * *
300759 -CCTTCTAAGTCCATAACTCTGTGGCACCATTTTAAGCCTACAACTCTGTGGCACTCTGTTTCCT
1 CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCTGTGGCATTCTTTTTCCT
* * * *
300823 TCTAAGTCCACAACTCTGTGGCACC--CTTTTAAAGCCCATAACTCCGTGGCACTCTTTTT
66 TTTAAGTCCACAACTCCGTGGCACCTTCTTTTAAAGCCCACAACTCAGTGGCACTCTTTTT
300882 CCCTTTTTAAAGTCCACAACTCCGTGGCACCTTTTTCCCTTTTCAAAGCCCACAACTCTGTGGCA
1 CCC-TTTT-AAGTCCACAACTCCGTGGCA-------CCCTTTT--AAGCCCACAACTCTGTGGCA
300947 TTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTT
55 TTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTT
300985 TTTCTTTTTT
Statistics
Matches: 188, Mismatches: 23, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
122 1 0.01
123 23 0.12
124 7 0.04
125 3 0.02
126 97 0.52
133 6 0.03
135 51 0.27
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (126 bp):
CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCTGTGGCATTCTTTTTCCT
TTTAAGTCCACAACTCCGTGGCACCTTCTTTTAAAGCCCACAACTCAGTGGCACTCTTTTT
Found at i:300988 original size:70 final size:70
Alignment explanation
Indices: 300846--301037 Score: 239
Period size: 70 Copynumber: 2.7 Consensus size: 70
300836 CTCTGTGGCA
* *
300846 CCCTTTTAAAGCCCATAACTCCGTGGCACTCTTTTTCCCTTTTTAAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAAGCCCACAACTCTGTGGCA-TCTTTTT-CCTTTTTAAAGTCCACAACTCCGTGGCA
300911 CCTTTTT
64 CCTTTTT
300918 CCCTTTTCAAAGCCCACAACTCTGTGGCATTCTTTTTCC-TTTT-AAGTCCACAACTCCGTGGCA
1 CCCTTTT-AAAGCCCACAACTCTGTGGCA-TCTTTTTCCTTTTTAAAGTCCACAACTCCGTGGCA
300981 CCTTTTT
64 CCTTTTT
* * ** * * *
300988 -CTTTTTTAAGTTCACAACTCTGTGGCACCTTTTT-CTTTCTAAAGCCCACA
1 CCCTTTTAAAGCCCACAACTCTGTGGCATCTTTTTCCTTTTTAAAGTCCACA
301038 CAAGTCGATG
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
66 1 0.01
67 9 0.08
68 26 0.24
69 5 0.05
70 27 0.25
71 4 0.04
72 9 0.08
73 26 0.24
ACGTcount: A:0.20, C:0.32, G:0.11, T:0.38
Consensus pattern (70 bp):
CCCTTTTAAAGCCCACAACTCTGTGGCATCTTTTTCCTTTTTAAAGTCCACAACTCCGTGGCACC
TTTTT
Found at i:301103 original size:33 final size:33
Alignment explanation
Indices: 301024--301250 Score: 356
Period size: 33 Copynumber: 7.0 Consensus size: 33
301014 ACCTTTTTCT
*
301024 TTCTAAAGCCCACACAAGTCGATGGCAACC--C
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
*
301055 TTCTCAAAGCTCACACAAGTCGGTGGCAACCTTC
1 TTCT-AAAGCCCACACAAGTCGGTGGCAACCTTC
301089 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTT-
1 TTCTAAAGCCCACACAAGTCGGTGGCAA-CCTTC
301122 TTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
* * *
301155 TTCTAAAGCCTACACAAATCGGTGGCAACCCTC
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
301188 -TCTAAAGCCCACACAAGTCGGTGGCAACCTTC
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
301220 TTCTAAAGCCCACACAAGTCGGTGGC-ACCTT
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCTT
301251 TAAGTCCAAT
Statistics
Matches: 181, Mismatches: 9, Indels: 11
0.90 0.04 0.05
Matches are distributed among these distances:
31 4 0.02
32 62 0.34
33 106 0.59
34 9 0.05
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (33 bp):
TTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
Found at i:301104 original size:65 final size:66
Alignment explanation
Indices: 301024--301246 Score: 387
Period size: 65 Copynumber: 3.4 Consensus size: 66
301014 ACCTTTTTCT
* *
301024 TTCTAAAGCCCACACAAGTCGATGGCAACCCTTCTC-AAAGCTCACACAAGTCGGTGGCAACCTT
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTT
301088 C
66 C
*
301089 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCTT
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTT
301154 C
66 C
* *
301155 TTCTAAAGCCTACACAAATCGGTGGCAACCC-TCTCTAAAGCCCACACAAGTCGGTGGCAACCTT
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTT
301219 C
66 C
301220 TTCTAAAGCCCACACAAGTCGGTGGCA
1 TTCTAAAGCCCACACAAGTCGGTGGCA
301247 CCTTTAAGTC
Statistics
Matches: 149, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
65 92 0.62
66 57 0.38
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (66 bp):
TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTT
C
Found at i:301139 original size:98 final size:97
Alignment explanation
Indices: 301023--301250 Score: 356
Period size: 98 Copynumber: 2.3 Consensus size: 97
301013 CACCTTTTTC
* *
301023 TTTCTAAAGCCCACACAAGTCGATGGCAACC--CTTCTCAAAG-CTCACACAAGTCGGTGGCAAC
1 TTTCTAAAGCCCACACAAGTCGGTGGCAACCTTCTTCT-AAAGCCT-ACACAAATCGGTGGCAAC
*
301085 CTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCT
64 CCTC-TCTAAAGCCCACACAAGTCGGTGGCAA-CCT
301121 TTTCTAAAGCCCACACAAGTCGGTGGCAACCTTCTTCTAAAGCCTACACAAATCGGTGGCAACCC
1 TTTCTAAAGCCCACACAAGTCGGTGGCAACCTTCTTCTAAAGCCTACACAAATCGGTGGCAACCC
301186 TCTCTAAAGCCCACACAAGTCGGTGGCAACCT
66 TCTCTAAAGCCCACACAAGTCGGTGGCAACCT
301218 TCTTCTAAAGCCCACACAAGTCGGTGGC-ACCTT
1 T-TTCTAAAGCCCACACAAGTCGGTGGCAACCTT
301251 TAAGTCCAAT
Statistics
Matches: 123, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
97 9 0.07
98 83 0.67
99 24 0.20
100 7 0.06
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (97 bp):
TTTCTAAAGCCCACACAAGTCGGTGGCAACCTTCTTCTAAAGCCTACACAAATCGGTGGCAACCC
TCTCTAAAGCCCACACAAGTCGGTGGCAACCT
Found at i:301324 original size:52 final size:51
Alignment explanation
Indices: 301248--301918 Score: 546
Period size: 52 Copynumber: 13.9 Consensus size: 51
301238 TCGGTGGCAC
* *
301248 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTTTCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
*
301299 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTTTCTA
1 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTC-A
* * *
301351 TCTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC----T--
1 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
* *
301397 C--TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-------C-
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
301438 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTTCTT--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT-TTCA
* *
301487 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC----T--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
* *
301532 C--TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTT--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
* * *
301579 CTTT-AGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCACC----T--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
* * *
301623 C--TAAGCCCAAATATAGCTGGCCTTGAATCAGTATATTGGCACCTTCTT--
1 CTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
* * *
301671 CTTT-AGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACC----T--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
* *
301715 C--TAAG-CCTAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCA
1 CTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
*
301764 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCA
1 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
* * * * *
301816 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTCA
1 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-CTTTT-TCA
* * * * * *
301871 TCTTTAAGCCCAATATCA-TTGGCCGTGAATCAACATAGTGGCATCTTT
1 -CTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCACCTTT
301919 ATCAATTTTC
Statistics
Matches: 526, Mismatches: 51, Indels: 83
0.80 0.08 0.13
Matches are distributed among these distances:
41 1 0.00
42 4 0.01
43 150 0.29
44 34 0.06
45 3 0.01
47 2 0.00
48 67 0.13
49 46 0.09
50 3 0.01
51 5 0.01
52 166 0.32
53 6 0.01
54 4 0.01
55 34 0.06
56 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (51 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
Found at i:301413 original size:43 final size:43
Alignment explanation
Indices: 301352--301855 Score: 497
Period size: 43 Copynumber: 10.9 Consensus size: 43
301342 CCTTTTCTAT
301352 CTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
301395 CTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
301438 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
301481 TTTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 ---C-TC--TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
301530 CTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 CTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C
* *
301574 TTCTTCTTTAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCAC
1 --C-TC-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
301621 CTCTAAGCCCAAATATAGCTGGCCTTGAATCAGTATATTGGCACC
1 CTCTAAGTCC-AATGTAGCTGGCCTTGAATCAGCACATTGGCA-C
* *
301666 TTCTTCTTTAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
1 --C-TC-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
301713 CTCTAAG-CCTAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCAC
1 CTCTAAGTCC-AATGTAGCTGGCCTTGAATCAGCACATTGG---------CAC
* * *
301765 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC
1 CTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA------C
*
301814 CATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 C-TC--TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
301856 ACATCTTTTT
Statistics
Matches: 389, Mismatches: 35, Indels: 65
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.01
43 156 0.40
44 33 0.08
45 5 0.01
46 3 0.01
47 6 0.02
48 64 0.16
49 45 0.12
50 1 0.00
52 72 0.19
53 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
CTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:301527 original size:92 final size:92
Alignment explanation
Indices: 301352--301809 Score: 691
Period size: 92 Copynumber: 5.0 Consensus size: 92
301342 CCTTTTCTAT
* * *
301352 CTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--C-TC--TAAGTCCAATGTA
1 CTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
301411 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
301438 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTCTTCTTTAAGTCCAATGTA
1 CTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
301503 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
301530 CTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTT-AGTCCAATGTA
1 CTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
*
301594 GTTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
301621 CTCTAAGCCCAAATATAGCTGGCCTTGAATCAGTATATTGGCACCTTCTTCTTT-AGTCCAATGT
1 CTCTAAGCCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
*
301685 AGCTGGCCTTGAATCAGCACATTGACAC
65 AGCTGGCCTTGAATCAGCACATTGGCAC
* *
301713 CTCTAAGCCTAATATAGCTGGCCTTGAATCAGCATATTGGCACATT-TTCCACCTTTAAGTCCAA
1 CTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTT----CTTTAAGTCCAA
* *
301777 TATAGCTGGCCTTGAATCAGCATATTGGCAC
62 TGTAGCTGGCCTTGAATCAGCACATTGGCAC
301808 CT
1 CT
301810 TTTCCATCTT
Statistics
Matches: 343, Mismatches: 17, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
86 39 0.11
89 1 0.00
90 4 0.01
91 81 0.24
92 177 0.52
94 4 0.01
95 37 0.11
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (92 bp):
CTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Done.