Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 126 of 135
Found at i:38245337 original size:30 final size:30
Alignment explanation
Indices: 38245301--38245363 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
38245291 TCAAAGAATG
38245301 TACATATATATCTTTTGTATGGTGTGTTCC
1 TACATATATATCTTTTGTATGGTGTGTTCC
38245331 TACATATATATCTTTTGTATGGTGTGTTCC
1 TACATATATATCTTTTGTATGGTGTGTTCC
38245361 TAC
1 TAC
38245364 TATGCTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (30 bp):
TACATATATATCTTTTGTATGGTGTGTTCC
Found at i:38251052 original size:20 final size:20
Alignment explanation
Indices: 38251027--38251065 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
38251017 TTTTCTTCGT
38251027 ATGGTTCAAGAAAAAAAATG
1 ATGGTTCAAGAAAAAAAATG
38251047 ATGGTTCAAGAAAAAAAAT
1 ATGGTTCAAGAAAAAAAAT
38251066 TATTAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (20 bp):
ATGGTTCAAGAAAAAAAATG
Found at i:38251075 original size:21 final size:20
Alignment explanation
Indices: 38251031--38251076 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
38251021 CTTCGTATGG
**
38251031 TTCAAGAAAAAAAATGATGG
1 TTCAAGAAAAAAAATGATAA
*
38251051 TTCAAGAAAAAAAATTATTAA
1 TTCAAGAAAAAAAATGA-TAA
38251072 TTCAA
1 TTCAA
38251077 AGTTATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.57, C:0.07, G:0.11, T:0.26
Consensus pattern (20 bp):
TTCAAGAAAAAAAATGATAA
Found at i:38253126 original size:60 final size:60
Alignment explanation
Indices: 38253062--38253190 Score: 195
Period size: 60 Copynumber: 2.1 Consensus size: 60
38253052 ATCGAATCAA
** * * *
38253062 AATTATTAATTATCCAATTTCGAACCGATTTCGAAATATAATTAACTGATTTCAGTTATT
1 AATTATTAATTATCCAATTTCGAACAAATTTCAAAATATAATTAACCGATTTCAATTATT
* *
38253122 AATTATTAATTATTCGATTTCGAACAAATTTCAAAATATAATTAACCGATTTCAATTATT
1 AATTATTAATTATCCAATTTCGAACAAATTTCAAAATATAATTAACCGATTTCAATTATT
38253182 AATTATTAA
1 AATTATTAA
38253191 GTTCAATTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (60 bp):
AATTATTAATTATCCAATTTCGAACAAATTTCAAAATATAATTAACCGATTTCAATTATT
Found at i:38259468 original size:20 final size:19
Alignment explanation
Indices: 38259424--38259573 Score: 60
Period size: 20 Copynumber: 7.6 Consensus size: 19
38259414 AAGATGTACA
38259424 AAAAAACTATGAGGGAATA-C
1 AAAAAA-TATGA-GGAATATC
38259444 TAAAAAATATGAGGAAGTATC
1 -AAAAAATATGAGGAA-TATC
* * *
38259465 -AAAATTACGAGAGAATACC
1 AAAAAATATGAG-GAATATC
* *
38259484 ATAAAACT-TGAAGAAATAT-
1 A-AAAAATATG-AGGAATATC
* *
38259503 AAAAAA-ATGAGGATGTACC
1 AAAAAATATGAGGA-ATATC
* *
38259522 AAAACATATAAGGAAGTA-C
1 AAAAAATATGAGGAA-TATC
*
38259541 AAAAAATTATGAGAGAATATAA
1 AAAAAA-TATGAG-GAATAT-C
38259563 AAAAAATATGA
1 AAAAAATATGA
38259574 TGATATAAAA
Statistics
Matches: 97, Mismatches: 17, Indels: 30
0.67 0.12 0.21
Matches are distributed among these distances:
17 3 0.03
18 8 0.08
19 28 0.29
20 30 0.31
21 22 0.23
22 6 0.06
ACGTcount: A:0.57, C:0.07, G:0.16, T:0.19
Consensus pattern (19 bp):
AAAAAATATGAGGAATATC
Found at i:38259565 original size:21 final size:19
Alignment explanation
Indices: 38259541--38259590 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
38259531 AAGGAAGTAC
38259541 AAAAAATTATGAGAGAATATA
1 AAAAAATTATGA-AG-ATATA
* *
38259562 AAAAAAATATGATGATATA
1 AAAAAATTATGAAGATATA
*
38259581 AAAATATTAT
1 AAAAAATTAT
38259591 TTACCAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 13 0.52
20 1 0.04
21 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (19 bp):
AAAAAATTATGAAGATATA
Found at i:38259671 original size:20 final size:20
Alignment explanation
Indices: 38259625--38259672 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
38259615 AAAAATTACA
38259625 AGAGAATACCAAAAAATAAG
1 AGAGAATACCAAAAAATAAG
* * ** *
38259645 AGGGAATATCAAAATTTATG
1 AGAGAATACCAAAAAATAAG
38259665 AGAGAATA
1 AGAGAATA
38259673 ACATAAAACC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (20 bp):
AGAGAATACCAAAAAATAAG
Found at i:38259968 original size:20 final size:19
Alignment explanation
Indices: 38259945--38260006 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
38259935 CAAAAAAAAA
38259945 ATGAGAATATATAAAAATTT
1 ATGAGAATATATAAAAA-TT
* * *
38259965 ATGAGAAAATAAAAAAATA
1 ATGAGAATATATAAAAATT
*
38259984 AAGA-AATAT-TAAAAATT
1 ATGAGAATATATAAAAATT
38260001 ATGAGA
1 ATGAGA
38260007 GAATATCAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 9 0.27
18 5 0.15
19 4 0.12
20 15 0.45
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (19 bp):
ATGAGAATATATAAAAATT
Found at i:38260003 original size:36 final size:40
Alignment explanation
Indices: 38259920--38260016 Score: 121
Period size: 36 Copynumber: 2.5 Consensus size: 40
38259910 AAATACCAAG
*
38259920 AATTATGAGGGAATACAAAAAAAAAATGAGAATATATAAA
1 AATTATGAGAGAATACAAAAAAAAAATGAGAATATATAAA
* *
38259960 AATTTATGAGAAAATA-AAAAAATAAA-GA-AATAT-TAAA
1 AA-TTATGAGAGAATACAAAAAAAAAATGAGAATATATAAA
38259997 AATTATGAGAGAATATCAAA
1 AATTATGAGAGAATA-CAAA
38260017 TAACATGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
36 12 0.24
37 6 0.12
38 8 0.16
39 2 0.04
40 11 0.22
41 11 0.22
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (40 bp):
AATTATGAGAGAATACAAAAAAAAAATGAGAATATATAAA
Found at i:38260011 original size:20 final size:20
Alignment explanation
Indices: 38259947--38260045 Score: 64
Period size: 20 Copynumber: 5.0 Consensus size: 20
38259937 AAAAAAAAAT
38259947 GAGAATATATAAAAATTTATGA
1 GAGAATAT-TAAAAA-TTATGA
* * *
38259969 GA-AA-ATAAAAAAATA-AA
1 GAGAATATTAAAAATTATGA
38259986 GA-AATATTAAAAATTATGA
1 GAGAATATTAAAAATTATGA
* *
38260005 GAGAATATCAAATAA-CATGA
1 GAGAATATTAAA-AATTATGA
* * *
38260025 GAGGATACTAAAAATTGTGA
1 GAGAATATTAAAAATTATGA
38260045 G
1 G
38260046 GGATATCAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
17 5 0.08
18 11 0.19
19 10 0.17
20 27 0.46
21 4 0.07
22 2 0.03
ACGTcount: A:0.58, C:0.03, G:0.15, T:0.24
Consensus pattern (20 bp):
GAGAATATTAAAAATTATGA
Found at i:38263074 original size:60 final size:59
Alignment explanation
Indices: 38262957--38263233 Score: 262
Period size: 59 Copynumber: 4.6 Consensus size: 59
38262947 AATTGCATGA
* * **
38262957 CCGACACCCTCTTTTAATTTGAT-AAAAAATCAAA-TTTTTGGGTGTTGGTCATGCAATGG
1 CCGACACCC-CTTTT-ATCTGATAAAAAAATTAAATTTTTTTTGTGTTGGTCATGCAATGG
*
38263016 CCGACACCCCTATTTATCTGATAAAAAAATTAAATTTTTTTTGTGTTGGTCATACAATGG
1 CCGACACCCCT-TTTATCTGATAAAAAAATTAAATTTTTTTTGTGTTGGTCATGCAATGG
* ** *
38263076 CCGATACCGTTATTTAT-TGATAAAAAAATTCAAA-TTTTTTAGTGTTGGTCATGCAATGG
1 CCGACACCCCT-TTTATCTGATAAAAAAATT-AAATTTTTTTTGTGTTGGTCATGCAATGG
* * * * * *
38263135 TCGACACCCCCTTTT-TCAGATAAAAAATTTCAAATTTTTTTTGTGTAGGCCATTG-TATGG
1 CCGACA-CCCCTTTTATCTGATAAAAAAATT-AAATTTTTTTTGTGTTGGTCA-TGCAATGG
**
38263195 CCGACACTCTTTTTTATCTGA-ATAAAAAATTAAATTTTT
1 CCGACAC-CCCTTTTATCTGATA-AAAAAATTAAATTTTT
38263234 GGGTTTGTCA
Statistics
Matches: 182, Mismatches: 25, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
58 9 0.05
59 81 0.45
60 79 0.43
61 13 0.07
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (59 bp):
CCGACACCCCTTTTATCTGATAAAAAAATTAAATTTTTTTTGTGTTGGTCATGCAATGG
Found at i:38263195 original size:119 final size:119
Alignment explanation
Indices: 38262975--38263234 Score: 318
Period size: 119 Copynumber: 2.2 Consensus size: 119
38262965 CTCTTTTAAT
* *
38262975 TTGAT-AAAAAA-TCAAATTTTTGGGTGTTGGTCATGCAATGGCCGACACCCCTATTTATCTGAT
1 TTGATAAAAAAATTCAAATTTTTGAGTGTTGGTCATGCAATGGCCGACACCCCTATTTATCAGAT
* * *
38263038 AAAAAAATTAAATTTTTTTTGTGTTGGTCATACAATGGCCGATAC-CGTTATTTA
66 AAAAAAATTAAATTTTTTTTGTGTAGGCCATACAATGGCCGACACTC-TTATTTA
* *
38263092 TTGATAAAAAAATTCAAATTTTTTAGTGTTGGTCATGCAATGGTCGACACCCCCT-TTT-TCAGA
1 TTGATAAAAAAATTCAAATTTTTGAGTGTTGGTCATGCAATGGCCGACA-CCCCTATTTATCAGA
* *** *
38263155 TAAAAAATTTCAAATTTTTTTTGTGTAGGCCATTGTATGGCCGACACTCTTTTTTA
65 TAAAAAAATT-AAATTTTTTTTGTGTAGGCCATACAATGGCCGACACTCTTATTTA
38263211 TCTGA-ATAAAAAATT-AAATTTTTG
1 T-TGATA-AAAAAATTCAAATTTTTG
38263235 GGTTTGTCAG
Statistics
Matches: 123, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
117 5 0.04
118 19 0.15
119 82 0.67
120 17 0.14
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (119 bp):
TTGATAAAAAAATTCAAATTTTTGAGTGTTGGTCATGCAATGGCCGACACCCCTATTTATCAGAT
AAAAAAATTAAATTTTTTTTGTGTAGGCCATACAATGGCCGACACTCTTATTTA
Found at i:38263288 original size:89 final size:91
Alignment explanation
Indices: 38263150--38263322 Score: 232
Period size: 89 Copynumber: 1.9 Consensus size: 91
38263140 ACCCCCTTTT
*
38263150 TCAGATAAAAAATTTCAAATTTTTTTTGTGTAGGCCATTGTATGGCCGACA-CTCTTTTTTATCT
1 TCAGATAAAAAATTTCAAATTTTTTTTGTGTAGGCCATTGTATGACCGACACCTC-TTTTTATCT
38263214 GA-ATAAAAAATTAAATTTTTGGGTTTG
65 GATA-AAAAAATTAAATTTTTGGGTTTG
*
38263241 TCAGATAAAAAA-TTCGAA-TTTTTTTGTGTTA-GCCA-TGTCATGACCGACACCTCTTTTTATC
1 TCAGATAAAAAATTTCAAATTTTTTTTGTG-TAGGCCATTGT-ATGACCGACACCTCTTTTTATC
* *
38263302 TGGTAAAAAAATTAATTTTTT
64 TGATAAAAAAATTAAATTTTT
38263323 TTGTTATTGG
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
88 3 0.04
89 48 0.65
90 11 0.15
91 12 0.16
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (91 bp):
TCAGATAAAAAATTTCAAATTTTTTTTGTGTAGGCCATTGTATGACCGACACCTCTTTTTATCTG
ATAAAAAAATTAAATTTTTGGGTTTG
Found at i:38263289 original size:149 final size:148
Alignment explanation
Indices: 38263098--38263382 Score: 319
Period size: 149 Copynumber: 1.9 Consensus size: 148
38263088 TTTATTGATA
* * **
38263098 AAAAAATTCAAATTTTTTAGTGTTGGTCATGCAATGGTCGACACCCCCTTTT-TCAGATAAAAAA
1 AAAAAATTCAAATTTTTTAGTGTTAGCCATGCAATGACCGACACCCCCTTTTATCAGATAAAAAA
* * * *
38263162 TTTCAAATTTTTTTTGTGTA-GGCCATTG-TATGGCCGACACTCT-TTTTTATCTGAATAAAAAA
66 ATT--AATTTTTTTTGT-TATGGCCA-TGCAATGGCCGACACCCTCTTTTTATC-AAATAAAAAA
38263224 TTAAATTTTTGGGTTTGTCAGAT
126 TTAAATTTTTGGGTTTGTCAGAT
* * * * * *
38263247 AAAAAATTCGAATTTTTTTGTGTTAGCCATGTC-ATGACCGACACCTCTTTTTATCTGGTAAAAA
1 AAAAAATTCAAATTTTTTAGTGTTAGCCATG-CAATGACCGACACCCCCTTTTATCAGATAAAAA
* * *
38263311 AATTAATTTTTTTTGTTATTGGCTATGCAATGGCCGACACCCTCTTTTTGTCAAATAAAAAATTT
65 AATTAATTTTTTTTGTTA-TGGCCATGCAATGGCCGACACCCTCTTTTTATCAAATAAAAAATTA
38263376 AATTTTT
129 AATTTTT
38263383 TTTGTGTTGG
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
147 2 0.02
148 14 0.12
149 77 0.68
150 20 0.18
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (148 bp):
AAAAAATTCAAATTTTTTAGTGTTAGCCATGCAATGACCGACACCCCCTTTTATCAGATAAAAAA
ATTAATTTTTTTTGTTATGGCCATGCAATGGCCGACACCCTCTTTTTATCAAATAAAAAATTAAA
TTTTTGGGTTTGTCAGAT
Found at i:38263313 original size:60 final size:57
Alignment explanation
Indices: 38263246--38263472 Score: 181
Period size: 60 Copynumber: 3.8 Consensus size: 57
38263236 GTTTGTCAGA
38263246 TAAAAAATTCGAATTTTTTTGTGTTAGCCATGTC-ATGACCGACACCTCTTTTTATCTGG
1 TAAAAAATT--AATTTTTTTGTGTTAGCCATG-CAATGACCGACACCTCTTTTTATCTGG
* * * ***
38263305 TAAAAAAATTAATTTTTTT-TGTTATTGGCTATGCAATGGCCGACACCCTCTTTTTGTCAAA
1 T-AAAAAATTAATTTTTTTGTGTTA---GCCATGCAATGACCGACA-CCTCTTTTTATCTGG
* ** **
38263366 TAAAAAATTTAATTTTTTTTGTGTTGGCCATGCCGTGGTCGACA-CTCTTTTTTAATCTGG
1 TAAAAAA-TTAA-TTTTTTTGTGTTAGCCATGCAATGACCGACACCTC-TTTTT-ATCTGG
* *
38263426 TAAAAAATTAAAATTTTTTTGGTGTTGGTCATGCAATGACCGACACC
1 TAAAAAATT--AATTTTTTT-GTGTTAGCCATGCAATGACCGACACC
38263473 AACTTTCTCT
Statistics
Matches: 133, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
57 5 0.04
58 12 0.09
59 9 0.07
60 58 0.44
61 37 0.28
62 8 0.06
63 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (57 bp):
TAAAAAATTAATTTTTTTGTGTTAGCCATGCAATGACCGACACCTCTTTTTATCTGG
Found at i:38263369 original size:120 final size:121
Alignment explanation
Indices: 38263237--38263472 Score: 302
Period size: 120 Copynumber: 2.0 Consensus size: 121
38263227 AATTTTTGGG
* *
38263237 TTTGTCAGATAAAAAATTCGAA-TTTTTTTGTGTTAGCCATGTCATGACCGACAC-CTCTTTTT-
1 TTTGTCAAATAAAAAATT-GAATTTTTTTTGTGTTAGCCATGCCATGACCGACACTCT-TTTTTA
* * *
38263299 ATCTGGTAAAAAAATT-AATTTTTTTTGTTATTGG-CTATGCAATGGCCGACACCCTCTT
64 ATCTGGT-AAAAAATTAAAATTTTTTTGGTATTGGTC-ATGCAATGACCGACACCCTCTT
* * * **
38263357 TTTGTCAAATAAAAAATTTAATTTTTTTTGTGTTGGCCATGCCGTGGTCGACACTCTTTTTTAAT
1 TTTGTCAAATAAAAAATTGAATTTTTTTTGTGTTAGCCATGCCATGACCGACACTCTTTTTTAAT
*
38263422 CTGGTAAAAAATTAAAATTTTTTTGGTGTTGGTCATGCAATGACCGACACC
66 CTGGTAAAAAATTAAAATTTTTTTGGTATTGGTCATGCAATGACCGACACC
38263473 AACTTTCTCT
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
119 2 0.02
120 57 0.57
121 40 0.40
122 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (121 bp):
TTTGTCAAATAAAAAATTGAATTTTTTTTGTGTTAGCCATGCCATGACCGACACTCTTTTTTAAT
CTGGTAAAAAATTAAAATTTTTTTGGTATTGGTCATGCAATGACCGACACCCTCTT
Found at i:38263432 original size:61 final size:59
Alignment explanation
Indices: 38263246--38263472 Score: 215
Period size: 61 Copynumber: 3.8 Consensus size: 59
38263236 GTTTGTCAGA
* * * *
38263246 TAAAAAATTCGAA-TTTTTTTGTGTTAGCCATGTCATGACCGACACCTCTTTTTATCTGG
1 TAAAAAATT-TAATTTTTTTTGTGTTGGCCATGCCATGGCCGACACCTCTTTTTATCTGG
* * * * * ***
38263305 TAAAAAAATTAATTTTTTTTGTTATTGGCTATGCAATGGCCGACACCCTCTTTTTGTCAAA
1 TAAAAAATTTAATTTTTTTTG-TGTTGGCCATGCCATGGCCGACA-CCTCTTTTTATCTGG
* *
38263366 TAAAAAATTTAATTTTTTTTGTGTTGGCCATGCCGTGGTCGACA-CTCTTTTTTAATCTGG
1 TAAAAAATTTAATTTTTTTTGTGTTGGCCATGCCATGGCCGACACCTC-TTTTT-ATCTGG
* * * * *
38263426 TAAAAAATTAAAATTTTTTTGGTGTTGGTCATGCAATGACCGACACC
1 TAAAAAATT-TAATTTTTTTTGTGTTGGCCATGCCATGGCCGACACC
38263473 AACTTTCTCT
Statistics
Matches: 132, Mismatches: 29, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
58 5 0.04
59 21 0.16
60 46 0.35
61 59 0.45
62 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (59 bp):
TAAAAAATTTAATTTTTTTTGTGTTGGCCATGCCATGGCCGACACCTCTTTTTATCTGG
Found at i:38264263 original size:30 final size:28
Alignment explanation
Indices: 38264227--38264338 Score: 104
Period size: 30 Copynumber: 3.8 Consensus size: 28
38264217 AAAAAAGAAT
38264227 AATTAGAAATTAAATTTAAAAGATGAATAA
1 AATTAGAAATTAAATTTAAAA-AT-AATAA
38264257 AATTAGAAATTTAAA--TAAAAATATATAGGA
1 AATTAGAAA-TTAAATTTAAAAATA-ATA--A
38264287 AATTAGAAATTAAATTT-AAAATAAAGTCAA
1 AATTAGAAATTAAATTTAAAAAT-AA-T-AA
* *
38264317 AATTACAAATTGAATTTAAAAA
1 AATTAGAAATTAAATTTAAAAA
38264339 GTAAACGGAA
Statistics
Matches: 70, Mismatches: 2, Indels: 19
0.77 0.02 0.21
Matches are distributed among these distances:
27 1 0.01
28 5 0.07
29 10 0.14
30 41 0.59
31 12 0.17
32 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (28 bp):
AATTAGAAATTAAATTTAAAAATAATAA
Found at i:38265483 original size:13 final size:13
Alignment explanation
Indices: 38265465--38265489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38265455 ATTTCCAAAA
38265465 TGTAAAAAATATT
1 TGTAAAAAATATT
38265478 TGTAAAAAATAT
1 TGTAAAAAATAT
38265490 CAGATTTTTG
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTAAAAAATATT
Found at i:38265539 original size:20 final size:20
Alignment explanation
Indices: 38265514--38265551 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38265504 TTAAAAATTC
*
38265514 GAAAATATAAAAAATATTTT
1 GAAAATAGAAAAAATATTTT
38265534 GAAAATAGAAAAAATATT
1 GAAAATAGAAAAAATATT
38265552 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
GAAAATAGAAAAAATATTTT
Found at i:38265558 original size:20 final size:20
Alignment explanation
Indices: 38265515--38265558 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
38265505 TAAAAATTCG
* * *
38265515 AAAATATAAAAAATATTTTG
1 AAAATAGAAAAAATATTATA
38265535 AAAATAGAAAAAATATTATA
1 AAAATAGAAAAAATATTATA
38265555 AAAA
1 AAAA
38265559 ATTCAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAATAGAAAAAATATTATA
Found at i:38266611 original size:22 final size:22
Alignment explanation
Indices: 38266562--38266613 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
38266552 TTGGGGTGTT
* * *
38266562 GGTGAGTTGGAATTTCGGTTTT
1 GGTGAGCTGAAATTTCGGTTTA
* *
38266584 GATGAGCTGAAATTTTGGTTTA
1 GGTGAGCTGAAATTTCGGTTTA
38266606 GGTGAGCT
1 GGTGAGCT
38266614 AGAATTTGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.06, G:0.35, T:0.40
Consensus pattern (22 bp):
GGTGAGCTGAAATTTCGGTTTA
Found at i:38266619 original size:22 final size:21
Alignment explanation
Indices: 38266562--38266620 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
38266552 TTGGGGTGTT
* *
38266562 GGTGAGTTGGAATTTCGGTTTT
1 GGTGAGCT-GAATTTCGGTTTA
* *
38266584 GATGAGCTGAAATTTTGGTTTA
1 GGTGAGCTG-AATTTCGGTTTA
38266606 GGTGAGCTAGAATTT
1 GGTGAGCT-GAATTT
38266621 GGGTGGTCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.22, C:0.05, G:0.32, T:0.41
Consensus pattern (21 bp):
GGTGAGCTGAATTTCGGTTTA
Found at i:38267022 original size:83 final size:84
Alignment explanation
Indices: 38266712--38267484 Score: 1135
Period size: 84 Copynumber: 9.2 Consensus size: 84
38266702 TAAATTTAAA
* * * *
38266712 ATTTGATAAAAATTATAATATAATAATAATTTTTTATTCAAATATTTAAAATTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAGTAAATAATGT
*
38266777 ATTGTCAAATCCACACATT
66 ATTGTCAAATCAACACATT
*
38266796 ATTTGATAAAAATTATAATATAATAATAATTTTTTATTTAAATATTCAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAGTAAATAATGT
38266861 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* *
38266880 ATTTGATAAAAATTGTAATATAATAATAATTTTTGT-TTTAAATGTTCAAATTTAATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTT-TATTTAAATATTCAAATTTAGTAAATAATG
* * * *
38266944 TAATGTTAAATCAATATATT
65 TATTGTCAAATCAACACATT
* * *
38266964 ATTTGAT-AAAATTATTATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAGTAAATAATGT
* *
38267028 ATTGTCAAATAAACATATT
66 ATTGTCAAATCAACACATT
*
38267047 ATTTGATAAAAATTGTAATATAATAAT-ATTTTTTATTTAAATATTCAAATTTAATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAGTAAATAATGT
38267111 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* * * *
38267130 ATTTCATAAAAATTGTAATATAATAATAA-TTTTTATTTAAATGTTTAAATTTAGTAAATAATTT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAGTAAATAATGT
38267194 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* *
38267213 ATTTGATAAAAATTATAATATAATAATAATTTTTTATTTAAATATTAAAATTT-GATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAG-TAAATAATG
*
38267277 TATTATCAAATCAACACATT
65 TATTGTCAAATCAACACATT
* * *
38267297 ATTTGATAAAAGTTGTAATATAATAATGATTTTTGATTTAAATATTCAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAGTAAATAATGT
*
38267362 ATTATCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* * ** *
38267381 ATTTGATAAAAATTGTAATATAATAATAATTTGTAATTTAAATATGAAAATTT-GATTAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAG-TAAATAATG
* *
38267445 TATTGTCAAATTAACACAAT
65 TATTGTCAAATCAACACATT
* *
38267465 ATTTGATATAAATTGAAATA
1 ATTTGATAAAAATTGTAATA
38267485 ATCTTTTTTA
Statistics
Matches: 627, Mismatches: 54, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
82 1 0.00
83 229 0.37
84 395 0.63
85 2 0.00
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (84 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAGTAAATAATGT
ATTGTCAAATCAACACATT
Found at i:38267647 original size:16 final size:17
Alignment explanation
Indices: 38267626--38267660 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38267616 CTTAATTTTC
*
38267626 AAATTAATT-TCAACTT
1 AAATTAATTATCAAATT
38267642 AAATTAATTATCAAATT
1 AAATTAATTATCAAATT
38267659 AA
1 AA
38267661 TTTTTTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTAATTATCAAATT
Found at i:38271619 original size:121 final size:116
Alignment explanation
Indices: 38271408--38271711 Score: 297
Period size: 121 Copynumber: 2.5 Consensus size: 116
38271398 CATGACTAAC
* * *
38271408 AAAAAAATTAATTTTTTTACCAGATAAAAAAGAGGTGTCGGCCATGGCATGGCCAACA-CAAAAA
1 AAAAAAATTGATTTTTTTATCAGAT-AAAAAG-GGTGTCGGCCAT-GCATGACCAACACCAAAAA
** * * * * * *
38271472 AATTCGAATTTTTTATCTGACAAAAAGGGGGTGTTGGCTATGGCATGACCGACACC
63 AATTAAAATTTTTTATCTG--AAAAAGGAGGTGTCGGCCATGACATGACCAACACA
* *
38271528 CAAAAATTTGATTTTTTTTATTCAGATAAAAAGGGATGTCGGCCATGCAATGACCAACACCAAAA
1 AAAAAAATTGA-TTTTTTTA-TCAGATAAAAAGGG-TGTCGGCCATGC-ATGACCAACACCAAAA
* * *
38271593 AATTTTAAAATTTTTTTATCTG-AAAAGGAGGTGTCGGCCATTACATGATCAACACA
62 AA-ATTAAAA-TTTTTTATCTGAAAAAGGAGGTGTCGGCCATGACATGACCAACACA
* * * *
38271649 AAAAAAATTGATTTTTTTATCAAATAAATAGGGGTGTCGGCCATTGCATGACTAACACTAAAA
1 AAAAAAATTGATTTTTTTATCAGATAAA-AAGGGTGTCGGCCA-TGCATGACCAACACCAAAA
38271712 TTTTTTTCTG
Statistics
Matches: 153, Mismatches: 22, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
119 31 0.20
120 27 0.18
121 68 0.44
122 12 0.08
123 4 0.03
124 11 0.07
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (116 bp):
AAAAAAATTGATTTTTTTATCAGATAAAAAGGGTGTCGGCCATGCATGACCAACACCAAAAAAAT
TAAAATTTTTTATCTGAAAAAGGAGGTGTCGGCCATGACATGACCAACACA
Found at i:38271706 original size:59 final size:58
Alignment explanation
Indices: 38271384--38271711 Score: 263
Period size: 60 Copynumber: 5.5 Consensus size: 58
38271374 AGGAAAAGTT
* * * * *
38271384 GGTGTCGACCATTGCATGA-CTA-ACAAAAAAATTAATTTTTTTACCAGATAAAAAAGA
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAATTGATTTTTTTATCAGAT-AAAAAGG
* * * * *
38271441 GGTGTCGGCCATGGCATGGCCAACACAAAAAAATTCGAATTTTTTATCTGACAAAAAGGG
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAATT-GATTTTTTTATCAGATAAAAA-GG
* * * * * *
38271501 GGTGTTGGCTATGGCATGACCGACACCCAAAAATTTGATTTTTTTTATTCAGATAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACA-CAAAAAAATTGA-TTTTTTTA-TCAGATAAAAAGG
* * * *
38271562 GATGTCGGCCA-TGCAATGACCAACACCAAAAAATTTTAAAATTTTTTTATC---TGAAAAGG
1 GGTGTCGGCCATTGC-ATGACCAACA-CAAAAAA-ATT--GATTTTTTTATCAGATAAAAAGG
* * * *
38271621 AGGTGTCGGCCATTACATGATCAACACAAAAAAAATTGATTTTTTTATCAAATAAATAGG
1 -GGTGTCGGCCATTGCATGACCAACAC-AAAAAAATTGATTTTTTTATCAGATAAAAAGG
* *
38271681 GGTGTCGGCCATTGCATGACTAACACTAAAA
1 GGTGTCGGCCATTGCATGACCAACACAAAAA
38271712 TTTTTTTCTG
Statistics
Matches: 216, Mismatches: 38, Indels: 33
0.75 0.13 0.11
Matches are distributed among these distances:
57 27 0.12
58 6 0.03
59 49 0.23
60 68 0.31
61 43 0.20
62 14 0.06
63 8 0.04
64 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (58 bp):
GGTGTCGGCCATTGCATGACCAACACAAAAAAATTGATTTTTTTATCAGATAAAAAGG
Found at i:38279803 original size:30 final size:30
Alignment explanation
Indices: 38279767--38279856 Score: 180
Period size: 30 Copynumber: 3.0 Consensus size: 30
38279757 ATGAATTAAA
38279767 TTCCTAAATACCAATAAATACTTTGATTTT
1 TTCCTAAATACCAATAAATACTTTGATTTT
38279797 TTCCTAAATACCAATAAATACTTTGATTTT
1 TTCCTAAATACCAATAAATACTTTGATTTT
38279827 TTCCTAAATACCAATAAATACTTTGATTTT
1 TTCCTAAATACCAATAAATACTTTGATTTT
38279857 GTTCTCAATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (30 bp):
TTCCTAAATACCAATAAATACTTTGATTTT
Found at i:38285144 original size:10 final size:10
Alignment explanation
Indices: 38285129--38285160 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
38285119 GAAACAAAGC
38285129 AAAAAAAGAA
1 AAAAAAAGAA
38285139 AAAAAAAGAA
1 AAAAAAAGAA
38285149 AAAAAAAGAA
1 AAAAAAAGAA
38285159 AA
1 AA
38285161 GGAGGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:38302106 original size:29 final size:30
Alignment explanation
Indices: 38302043--38302122 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
38302033 ATCTCAAAAC
* *
38302043 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTTTGATTT-ATGTGCAATTG
*
38302074 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTTTGATTTATGTGCAATTG
*
38302103 TATACATGAAATCTTGATTT
1 TATACATGAACT-TTGATTT
38302123 GATCCAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 20 0.45
30 7 0.16
31 17 0.39
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTG
Found at i:38302131 original size:30 final size:29
Alignment explanation
Indices: 38302068--38302133 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
38302058 GTTTAATGTG
* * *
38302068 CAATTGTATACATGAACTTTGATTTTGTG
1 CAATTTTATACATGAAATTTGATTTTGTC
38302097 CAATTTTATACATGAAATCTTGA-TTTGATC
1 CAATTTTATACATGAAAT-TTGATTTTG-TC
38302127 CAATTTT
1 CAATTTT
38302134 TGTAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (29 bp):
CAATTTTATACATGAAATTTGATTTTGTC
Found at i:38302637 original size:19 final size:21
Alignment explanation
Indices: 38302600--38302640 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
38302590 GTTGAAACTA
*
38302600 TTTAATATCAAATATAAAATT
1 TTTAATATCAAATACAAAATT
38302621 TTTAA-ATCAAAT-CAAAATT
1 TTTAATATCAAATACAAAATT
38302640 T
1 T
38302641 AGGTCCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAATATCAAATACAAAATT
Found at i:38303679 original size:14 final size:13
Alignment explanation
Indices: 38303657--38303690 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
38303647 TTTAATCTAT
38303657 TTTTCAGAAATCA
1 TTTTCAGAAATCA
*
38303670 TTTTCTAGAAATTA
1 TTTTC-AGAAATCA
38303684 TTTTCAG
1 TTTTCAG
38303691 CGAATTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (13 bp):
TTTTCAGAAATCA
Found at i:38303928 original size:14 final size:14
Alignment explanation
Indices: 38303909--38303939 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38303899 GATCTGTCCG
*
38303909 TATTAATTTTTTTA
1 TATTAATATTTTTA
38303923 TATTAATATTTTTA
1 TATTAATATTTTTA
38303937 TAT
1 TAT
38303940 AAAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTAATATTTTTA
Found at i:38305606 original size:53 final size:52
Alignment explanation
Indices: 38305507--38305606 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 52
38305497 ACTGTGTACG
* *
38305507 CTGATAGTATCTGTGTAATACTCACATCGTGATGATTTGTAGGTAATATAAA
1 CTGATAGTATCTGTGTAATACTCACATCGTGAGGAGTTGTAGGTAATATAAA
*
38305559 CTGATAGTATCTGTGTATATACTCACATCGTGAGGCAGTT-TATGTAAT
1 CTGATAGTATCTGTGTA-ATACTCACATCGTGAGG-AGTTGTAGGTAAT
38305607 CCTTGCACCT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 17 0.40
53 23 0.53
54 3 0.07
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (52 bp):
CTGATAGTATCTGTGTAATACTCACATCGTGAGGAGTTGTAGGTAATATAAA
Found at i:38332785 original size:23 final size:23
Alignment explanation
Indices: 38332759--38332806 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
38332749 CATAAGGCAG
*
38332759 AAGCATGCCACAAGGCAAAGGAA
1 AAGCATACCACAAGGCAAAGGAA
* *
38332782 AAGCGTACCACAAGGCAGAGGAA
1 AAGCATACCACAAGGCAAAGGAA
38332805 AA
1 AA
38332807 ATGTGCCACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.21, G:0.27, T:0.04
Consensus pattern (23 bp):
AAGCATACCACAAGGCAAAGGAA
Found at i:38332815 original size:23 final size:23
Alignment explanation
Indices: 38332764--38332847 Score: 105
Period size: 23 Copynumber: 3.6 Consensus size: 23
38332754 GGCAGAAGCA
* *
38332764 TGCCACAAGGCAAAGGAAAAGCG
1 TGCCACAAGGCAGAGGAAAAACG
* *
38332787 TACCACAAGGCAGAGGAAAAATG
1 TGCCACAAGGCAGAGGAAAAACG
* *
38332810 TGCCACAAGGTAGAGAAAAAACG
1 TGCCACAAGGCAGAGGAAAAACG
38332833 TGCCACAAAGGCAGA
1 TGCCAC-AAGGCAGA
38332848 AAAAATTTAG
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
23 44 0.86
24 7 0.14
ACGTcount: A:0.45, C:0.20, G:0.27, T:0.07
Consensus pattern (23 bp):
TGCCACAAGGCAGAGGAAAAACG
Found at i:38335052 original size:3 final size:3
Alignment explanation
Indices: 38335044--38335082 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
38335034 TCAATCAAAT
38335044 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
38335083 AACCCTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:38341823 original size:20 final size:22
Alignment explanation
Indices: 38341800--38341840 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
38341790 GAAAGGTAAT
38341800 ATTT-AATTTTAT-AATTATTA
1 ATTTAAATTTTATAAATTATTA
38341820 ATTTAAAATTTTATAAATTAT
1 ATTT-AAATTTTATAAATTAT
38341841 AAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTAAATTTTATAAATTATTA
Found at i:38341833 original size:16 final size:16
Alignment explanation
Indices: 38341814--38341863 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
38341804 AATTTTATAA
38341814 TTATTAATTTAAAATT
1 TTATTAATTTAAAATT
*
38341830 TTATAAATTATAAAA-T
1 TTATTAATT-TAAAATT
*
38341846 AT-TTAATTTAAAATT
1 TTATTAATTTAAAATT
38341861 TTA
1 TTA
38341864 CCATATTGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
16 10 0.37
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTAATTTAAAATT
Found at i:38349607 original size:1 final size:1
Alignment explanation
Indices: 38349601--38349630 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
38349591 TAAGTCCACA
*
38349601 TTTTTTTTTGTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38349631 ATATACAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:38359163 original size:23 final size:23
Alignment explanation
Indices: 38359137--38359185 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
38359127 ATATTTTAAA
*
38359137 AAACAAAAAATAATTATTAAGTT
1 AAACAAAAAATAAATATTAAGTT
** *
38359160 AAACAAATTATAAATATTAATTT
1 AAACAAAAAATAAATATTAAGTT
38359183 AAA
1 AAA
38359186 ATTTAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
AAACAAAAAATAAATATTAAGTT
Found at i:38361512 original size:2 final size:2
Alignment explanation
Indices: 38361505--38361535 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38361495 AAAATACTCA
38361505 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 A
38361536 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38361540 original size:2 final size:2
Alignment explanation
Indices: 38361535--38361608 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
38361525 ATATATATAT
38361535 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38361577 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38361609 TAGTCAAGAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38371502 original size:5 final size:5
Alignment explanation
Indices: 38371492--38371522 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
38371482 AACAATAGTG
*
38371492 ATAAA ATAAA ATACA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
38371523 AGTAAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:38373413 original size:6 final size:7
Alignment explanation
Indices: 38373387--38373412 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38373377 TTCTTTTTAA
38373387 AAAAAAT
1 AAAAAAT
38373394 AAAAAAT
1 AAAAAAT
38373401 AAAAAAT
1 AAAAAAT
38373408 AAAAA
1 AAAAA
38373413 TCTTCAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:38395931 original size:2 final size:2
Alignment explanation
Indices: 38395926--38395953 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38395916 AACATTCTAT
38395926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38395954 ATTTATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38401521 original size:51 final size:51
Alignment explanation
Indices: 38401445--38401553 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 51
38401435 TGATTTAAGG
* * * *
38401445 TTGGATCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATATCTGGGAGAAGT
1 TTGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTAGCAGAAGT
* *
38401496 TTGGAGCAGGCTGCTGATTCAAGAAACGAAGTTGGAATAACTAGCAGAAGT
1 TTGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTAGCAGAAGT
*
38401547 TTAGAGC
1 TTGGAGC
38401554 CAAGTCAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (51 bp):
TTGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTAGCAGAAGT
Found at i:38401655 original size:60 final size:61
Alignment explanation
Indices: 38401504--38401661 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 61
38401494 GTTTGGAGCA
* * * * * * * *
38401504 GGCTGCTGATTCAAGAAACGAAGTTGGAATAACT-AGCAGAAGTTTAGAGCCAAGTCAAGT
1 GGCTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAAGAAGTTTAGAGCCAAGCCAACT
** *
38401564 GGCTGCTGAATCTAGAAAAGAAGCCGAAATAGCTGGGAAG-AGTTTAGAGCCAAGCCAACT
1 GGCTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAAGAAGTTTAGAGCCAAGCCAACT
* *
38401624 GGCTGCTGAGTCTAGAAAAGAAGTTGGAATAGTTGGGA
1 GGCTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGA
38401662 GAACTTTGGA
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 78 0.96
61 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (61 bp):
GGCTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAAGAAGTTTAGAGCCAAGCCAACT
Found at i:38406761 original size:13 final size:13
Alignment explanation
Indices: 38406728--38406764 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
38406718 CTCTCAGAAC
38406728 TAAATAAAATATT
1 TAAATAAAATATT
*
38406741 T-TATAAAATATT
1 TAAATAAAATATT
38406753 TAAATAAAATAT
1 TAAATAAAATAT
38406765 ATTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAATAAAATATT
Found at i:38407570 original size:110 final size:110
Alignment explanation
Indices: 38407243--38407570 Score: 425
Period size: 109 Copynumber: 3.0 Consensus size: 110
38407233 TGAACTATAG
* * * *
38407243 AATAGAAAGGGAGTGAGAGCTTTTGATTGGTGC-AGACAATGCAAAC-AATAAGGCCACACAACA
1 AATAGAAAGGGAGTGAGAACATTTGATTGGTGCAAG-CAATGCAAACAAAGAAGGCCATACAACA
* * *
38407306 ACAGT-TTTAACAGTCCAATGACTTAAATGAGAACTTATGAATAATT
65 ACA-TATTTAACAGTCTAATGACTTAAATGAAAACTTATGAATAGTT
* * *
38407352 AACAGAAAGAGAGTGAGAACATTTGATTGGTGCAGGCAATGCAAACAAAGAA-GCCATACAACAA
1 AATAGAAAGGGAGTGAGAACATTTGATTGGTGCAAGCAATGCAAACAAAGAAGGCCATACAACAA
*
38407416 CA-ATTTTAACAAT-TCAATGACTTAAATGAAAACTTATGAATAGTT
66 CATA-TTTAACAGTCT-AATGACTTAAATGAAAACTTATGAATAGTT
* * * *
38407461 AATAGAAAGGGAGTGCGAACATTTGAGTGGTGCAAGCAATGCAAGCAAAGAAGGTCATACAACAA
1 AATAGAAAGGGAGTGAGAACATTTGATTGGTGCAAGCAATGCAAACAAAGAAGGCCATACAACAA
* *
38407526 CATATTTAATAGTCTAGTGACTTAAATGAAAACTTATGAATAGTT
66 CATATTTAACAGTCTAATGACTTAAATGAAAACTTATGAATAGTT
38407571 CTATAACGAT
Statistics
Matches: 190, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
109 134 0.71
110 54 0.28
111 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (110 bp):
AATAGAAAGGGAGTGAGAACATTTGATTGGTGCAAGCAATGCAAACAAAGAAGGCCATACAACAA
CATATTTAACAGTCTAATGACTTAAATGAAAACTTATGAATAGTT
Found at i:38417799 original size:15 final size:15
Alignment explanation
Indices: 38417779--38417808 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38417769 TTTAAAATTA
38417779 AAAAAAATATAAAAC
1 AAAAAAATATAAAAC
*
38417794 AAAAAAATATTAAAC
1 AAAAAAATATAAAAC
38417809 TAAAGTACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAAATATAAAAC
Found at i:38431326 original size:19 final size:19
Alignment explanation
Indices: 38431294--38431332 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
38431284 CTTATTTTTC
38431294 AAATTTAATATTTTTTAAA
1 AAATTTAATATTTTTTAAA
38431313 AAATTATAAT-TTTTTTAAA
1 AAATT-TAATATTTTTTAAA
38431332 A
1 A
38431333 TTTTTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTTAATATTTTTTAAA
Found at i:38431332 original size:17 final size:17
Alignment explanation
Indices: 38431288--38431335 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
38431278 TTTTTTCTTA
*
38431288 TTTTTCAAATTTAATAT
1 TTTTTAAAATTTAATAT
38431305 TTTTTAAAAAATTATAAT-T
1 TTTTT--AAAATT-TAATAT
38431324 TTTTTAAAATTT
1 TTTTTAAAATTT
38431336 TTTAAAGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.04
17 11 0.41
19 11 0.41
20 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTAAAATTTAATAT
Found at i:38437896 original size:17 final size:17
Alignment explanation
Indices: 38437874--38437906 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38437864 ATTAAATGCA
38437874 TATTTAATAAA-ATTTAT
1 TATTTAA-AAATATTTAT
38437891 TATTTAAAAATATTTA
1 TATTTAAAAATATTTA
38437907 AAATTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTAAAAATATTTAT
Found at i:38437916 original size:13 final size:13
Alignment explanation
Indices: 38437881--38437920 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 13
38437871 GCATATTTAA
38437881 TAAAATTTATTATT
1 TAAAATTTA-TATT
38437895 TAAAA---ATATT
1 TAAAATTTATATT
38437905 TAAAATTTATATT
1 TAAAATTTATATT
38437918 TAA
1 TAA
38437921 TATATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
13 8 0.35
14 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAAATTTATATT
Found at i:38438796 original size:41 final size:41
Alignment explanation
Indices: 38438750--38438829 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
38438740 TACACTAAAA
* *
38438750 ATATTAAAATAAATATTAAAACAACAAACAAATTAAAAACG
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
* * *
38438791 ATATTAAAACAATTCGTAAAACAACAAACAAATTGAAAA
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAA
38438830 TACAAAAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (41 bp):
ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
Found at i:38439502 original size:24 final size:24
Alignment explanation
Indices: 38439475--38439527 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
38439465 ATTCAATCAT
* *
38439475 TATTACAAGCAAAAAAAAAATTAG
1 TATTAAAAACAAAAAAAAAATTAG
* * *
38439499 TATTAAAAATAAAAATAAAATTAT
1 TATTAAAAACAAAAAAAAAATTAG
38439523 TATTA
1 TATTA
38439528 TAAATTCGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (24 bp):
TATTAAAAACAAAAAAAAAATTAG
Found at i:38439532 original size:24 final size:24
Alignment explanation
Indices: 38439485--38439532 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
38439475 TATTACAAGC
38439485 AAAAAAAAAATTAGTATTAAAAAT
1 AAAAAAAAAATTAGTATTAAAAAT
* * *
38439509 AAAAATAAAATTATTATTATAAAT
1 AAAAAAAAAATTAGTATTAAAAAT
38439533 TCGGGCCAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAAAAAAAATTAGTATTAAAAAT
Found at i:38450234 original size:27 final size:28
Alignment explanation
Indices: 38450144--38450234 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 28
38450134 CCGAATCTTG
* * * *
38450144 AACCCTAAA-TCATAAACTTTAAGCTTA
1 AACCATAAACTCATAAACCTCAAACTTA
* *
38450171 AACCGTAAA-TCATAAACCTCGAACTTA
1 AACCATAAACTCATAAACCTCAAACTTA
*
38450198 AACCATAAACTCA-AAATCTCAAACTTA
1 AACCATAAACTCATAAACCTCAAACTTA
*
38450225 AACCCTAAAC
1 AACCATAAAC
38450235 CTTAAGTTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 51 0.94
28 3 0.06
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.23
Consensus pattern (28 bp):
AACCATAAACTCATAAACCTCAAACTTA
Found at i:38453513 original size:15 final size:15
Alignment explanation
Indices: 38453492--38453534 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
38453482 TTATGTTTTC
38453492 AAATAATATATTAAT
1 AAATAATATATTAAT
*
38453507 TAATAATA-ATATAAT
1 AAATAATATAT-TAAT
38453522 AAATAATAATATT
1 AAATAAT-ATATT
38453535 TTATTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 2 0.09
15 17 0.74
16 2 0.09
17 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAATATATTAAT
Found at i:38453516 original size:18 final size:18
Alignment explanation
Indices: 38453493--38453547 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
38453483 TATGTTTTCA
38453493 AATAATATATTAATTAAT
1 AATAATATATTAATTAAT
* *
38453511 AATAATATAATAAATAAT
1 AATAATATATTAATTAAT
* * *
38453529 AATATTTTATTATTTAAT
1 AATAATATATTAATTAAT
38453547 A
1 A
38453548 TTATAAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAATATATTAATTAAT
Found at i:38455590 original size:29 final size:29
Alignment explanation
Indices: 38455558--38455667 Score: 71
Period size: 29 Copynumber: 3.8 Consensus size: 29
38455548 GAAGTCGAAC
38455558 TTTTAGAAAATTGAGGGTAAAATAGTAAT
1 TTTTAGAAAATTGAGGGTAAAATAGTAAT
* *** * * *
38455587 TTTTGGATTCTCGAGGGTAAAATGGTGAT
1 TTTTAGAAAATTGAGGGTAAAATAGTAAT
* * * *
38455616 TTTT-GGAAGTTCGGGGGCAAAATA-TAATTT
1 TTTTAGAAAATT-GAGGGTAAAATAGTAA--T
*
38455646 TTTTAGAAATTTGAGGGTAAAA
1 TTTTAGAAAATTGAGGGTAAAA
38455668 ATGTGATTTT
Statistics
Matches: 57, Mismatches: 20, Indels: 7
0.68 0.24 0.08
Matches are distributed among these distances:
28 4 0.07
29 35 0.61
30 13 0.23
31 5 0.09
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
TTTTAGAAAATTGAGGGTAAAATAGTAAT
Found at i:38455678 original size:30 final size:30
Alignment explanation
Indices: 38455634--38455737 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 30
38455624 GTTCGGGGGC
* *
38455634 AAAATATAATTTTTTTAGAAATTTGAGGGTA
1 AAAATGTAA-TTTTTTAGAAGTTTGAGGGTA
* * * *
38455665 AAAATGTGA-TTTTTGGAAGTTTAAGGGCA
1 AAAATGTAATTTTTTAGAAGTTTGAGGGTA
* * * *
38455694 AAAATGTAATTTTTGAGAAGTTCGAGGATC
1 AAAATGTAATTTTTTAGAAGTTTGAGGGTA
38455724 AAAATGTAATTTTT
1 AAAATGTAATTTTT
38455738 GGATAGTTTA
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
29 24 0.41
30 27 0.47
31 7 0.12
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTTAGAAGTTTGAGGGTA
Found at i:38455693 original size:59 final size:58
Alignment explanation
Indices: 38455576--38455750 Score: 176
Period size: 59 Copynumber: 2.9 Consensus size: 58
38455566 AATTGAGGGT
* ***
38455576 AAAATAGTAATTTTTG-G-ATTCTCGAGGGTAAAATGGTGATTTTTGGAAGTTCGGGGGC-
1 AAAATA-TAATTTTTGAGAAAT-TCGAGGGTAAAAT-GTGATTTTTGGAAGTTTAAGGGCA
* *
38455634 AAAATATAATTTTTTTAGAAATTTGAGGGTAAAAATGTGATTTTTGGAAGTTTAAGGGCA
1 AAAATATAA-TTTTTGAGAAATTCGAGGGT-AAAATGTGATTTTTGGAAGTTTAAGGGCA
* * * *
38455694 AAAATGTAATTTTTGAGAAGTTCGAGGATCAAAATGTAATTTTTGGATAGTTTAAGG
1 AAAATATAATTTTTGAGAAATTCGAGGGT-AAAATGTGATTTTTGGA-AGTTTAAGG
38455751 ACCTTTCGGG
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
57 3 0.03
58 11 0.11
59 60 0.61
60 24 0.24
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (58 bp):
AAAATATAATTTTTGAGAAATTCGAGGGTAAAATGTGATTTTTGGAAGTTTAAGGGCA
Found at i:38455738 original size:30 final size:29
Alignment explanation
Indices: 38455570--38455745 Score: 137
Period size: 29 Copynumber: 6.0 Consensus size: 29
38455560 TTAGAAAATT
*
38455570 GAGGGT-AAAATAGTAATTTTTGG-ATTCTC
1 GAGGGTCAAAAT-GTAATTTTTGGAAGT-TC
*
38455599 GAGGGT-AAAATGGTGATTTTTGGAAGTTC
1 GAGGGTCAAAAT-GTAATTTTTGGAAGTTC
* * * * *
38455628 G-GGGGCAAAATATAATTTTTTTAGAAATTT
1 GAGGGTCAAAATGTAA--TTTTTGGAAGTTC
* * *
38455658 GAGGGTAAAAATGTGATTTTTGGAAGTTT
1 GAGGGTCAAAATGTAATTTTTGGAAGTTC
*
38455687 AAGGG-CAAAAATGTAATTTTTGAGAAGTTC
1 GAGGGTC-AAAATGTAATTTTTG-GAAGTTC
*
38455717 GAGGATCAAAATGTAATTTTTGGATAGTT
1 GAGGGTCAAAATGTAATTTTTGGA-AGTT
38455746 TAAGGACCTT
Statistics
Matches: 117, Mismatches: 21, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
28 5 0.04
29 60 0.51
30 41 0.35
31 11 0.09
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
GAGGGTCAAAATGTAATTTTTGGAAGTTC
Found at i:38457100 original size:6 final size:6
Alignment explanation
Indices: 38457089--38457160 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
38457079 TTTTGGACAT
* * * *
38457089 TTTAAA TTTAAA TTTTAG TTTAAA -ATAAA TTTAAA TTTAAA -AT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
38457134 TTTAAAA TTTAAAA TTTAAAA TTTAAA
1 TTT-AAA TTT-AAA TTT-AAA TTTAAA
38457161 ATTGAGCTCC
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
4 2 0.04
5 6 0.11
6 27 0.50
7 19 0.35
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:38457119 original size:17 final size:17
Alignment explanation
Indices: 38457097--38457148 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
38457087 ATTTTAAATT
* *
38457097 TAAATTTTAGTTTAAAA
1 TAAATTTAAATTTAAAA
38457114 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
38457131 T-AATTTAAAATTTAAAA
1 TAAATTT-AAATTTAAAA
38457148 T
1 T
38457149 TTAAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.16
17 27 0.84
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:38457161 original size:7 final size:7
Alignment explanation
Indices: 38457132--38457163 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
38457122 AATTTAAAAT
38457132 AATTTAA
1 AATTTAA
38457139 AATTTAA
1 AATTTAA
38457146 AATTTAA
1 AATTTAA
38457153 AATTTAA
1 AATTTAA
38457160 AATT
1 AATT
38457164 GAGCTCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:38458620 original size:21 final size:22
Alignment explanation
Indices: 38458594--38458635 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38458584 ATATCAAAAA
38458594 AAAATA-AATTTAAAAAGACTG
1 AAAATATAATTTAAAAAGACTG
**
38458615 AAAATATTTTTTAAAAAGACT
1 AAAATATAATTTAAAAAGACT
38458636 TAAATTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (22 bp):
AAAATATAATTTAAAAAGACTG
Found at i:38458714 original size:31 final size:30
Alignment explanation
Indices: 38458667--38458772 Score: 76
Period size: 31 Copynumber: 3.6 Consensus size: 30
38458657 TTAATATAAC
* *
38458667 ATTTGGTACTTGAACTTGACATTTTTTCCTA
1 ATTTGGTACCTAAACTTGA-ATTTTTTCCTA
** *
38458698 ATTTGGTACCTAAACTT---TTTTGACCCA
1 ATTTGGTACCTAAACTTGAATTTTTTCCTA
* * *
38458725 ATTTGGAACTTGAAA-TTGATATTTTTTTCTA
1 ATTTGGTACCT-AAACTTGA-ATTTTTTCCTA
*
38458756 ATTTGATACCTAAACTT
1 ATTTGGTACCTAAACTT
38458773 TTTTTAGATC
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
27 18 0.33
28 3 0.05
30 3 0.05
31 31 0.56
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.46
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGAATTTTTTCCTA
Found at i:38458738 original size:58 final size:58
Alignment explanation
Indices: 38458667--38458776 Score: 175
Period size: 58 Copynumber: 1.9 Consensus size: 58
38458657 TTAATATAAC
* * *
38458667 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTGACCCA
1 ATTTGGAACTTGAAATTGACATTTTTTCCTAATTTGATACCTAAACTTTTTTGACCCA
* *
38458725 ATTTGGAACTTGAAATTGATATTTTTTTCTAATTTGATACCTAAACTTTTTT
1 ATTTGGAACTTGAAATTGACATTTTTTCCTAATTTGATACCTAAACTTTTTT
38458777 TAGATCCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (58 bp):
ATTTGGAACTTGAAATTGACATTTTTTCCTAATTTGATACCTAAACTTTTTTGACCCA
Found at i:38459031 original size:30 final size:28
Alignment explanation
Indices: 38458996--38459075 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 28
38458986 GGAGCCCAAA
38458996 AAGTTTAAGTACAAATTAGG-AAAAAGTATC
1 AAGTTT-AGTACAAATTAGGAAAAAAG--TC
*
38459026 AAGTTTAGATATCAAATTAAGAAAAAAGTC
1 AAGTTTAG-TA-CAAATTAGGAAAAAAGTC
38459056 AAGTTTGAGTACTAAATTAG
1 AAGTTT-AGTAC-AAATTAG
38459076 ACCAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
29 3 0.07
30 24 0.56
31 10 0.23
32 6 0.14
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (28 bp):
AAGTTTAGTACAAATTAGGAAAAAAGTC
Found at i:38463529 original size:7 final size:8
Alignment explanation
Indices: 38463507--38463533 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
38463497 TATTTTAAAA
38463507 ATATTTTT
1 ATATTTTT
38463515 ATATTTTT
1 ATATTTTT
38463523 ATATTTTT
1 ATATTTTT
38463531 ATA
1 ATA
38463534 CCAAACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
ATATTTTT
Found at i:38465754 original size:2 final size:2
Alignment explanation
Indices: 38465747--38465784 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
38465737 TTAATAGTTT
38465747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38465785 GGAAATGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38500495 original size:31 final size:31
Alignment explanation
Indices: 38500460--38500531 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
38500450 TAACAACCCT
38500460 ATGACTTAAAT-AAAAGCTTTT-GAATAGTTCA
1 ATGACTTAAATGAAAA--TTTTCGAATAGTTCA
38500491 ATGACTTAAATGAAAATTTTCGAATAGTTCA
1 ATGACTTAAATGAAAATTTTCGAATAGTTCA
38500522 ATGAC-TAAAT
1 ATGACTTAAAT
38500532 TATAACTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
30 9 0.23
31 26 0.67
32 4 0.10
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (31 bp):
ATGACTTAAATGAAAATTTTCGAATAGTTCA
Found at i:38507399 original size:18 final size:20
Alignment explanation
Indices: 38507362--38507400 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
38507352 GATTGAGCTT
*
38507362 ATATTAAATAATTATGCATG
1 ATATTAAATAATTATACATG
38507382 ATATT-AAT-ATTATACATG
1 ATATTAAATAATTATACATG
38507400 A
1 A
38507401 ATAAATCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (20 bp):
ATATTAAATAATTATACATG
Found at i:38507733 original size:18 final size:18
Alignment explanation
Indices: 38507710--38507744 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38507700 ATAAAATTAT
38507710 ATTAATA-TTAATAATAAC
1 ATTAATAGTT-ATAATAAC
38507728 ATTAATAGTTATAATAA
1 ATTAATAGTTATAATAA
38507745 GTGAAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAATAGTTATAATAAC
Found at i:38515112 original size:29 final size:27
Alignment explanation
Indices: 38515047--38515178 Score: 97
Period size: 29 Copynumber: 4.6 Consensus size: 27
38515037 AGTTTTAATT
* * * *
38515047 TTTTAAATATTTTTACACTTTTCTATA-
1 TTTTATATATTTTTA-AATTTTTTTTAC
38515074 TTTTATTATATTTTTAACATTTTTTTTCAC
1 TTTTA-TATATTTTTAA-ATTTTTTTT-AC
*
38515104 TTTTATATATTTTTATAATTTTTTTTAG
1 TTTTATATATTTTTA-AATTTTTTTTAC
* *
38515132 TTTGTATATATTATTTTGAATTTTTTTATAA
1 TTT-TATATA-T-TTTTAAATTTTTTT-TAC
38515163 TTTT-TATAATTTTTAA
1 TTTTATAT-ATTTTTAA
38515179 TGATTTTAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
27 6 0.07
28 24 0.28
29 30 0.34
30 18 0.21
31 9 0.10
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTTATATATTTTTAAATTTTTTTTAC
Found at i:38515117 original size:10 final size:10
Alignment explanation
Indices: 38515065--38515177 Score: 53
Period size: 9 Copynumber: 11.5 Consensus size: 10
38515055 ATTTTTACAC
*
38515065 TTTTCTATA-
1 TTTTATATAT
38515074 TTTTATTATAT
1 TTTTA-TATAT
*
38515085 TTTTA-ACAT
1 TTTTATATAT
* *
38515094 TTTT-TTTCAC
1 TTTTATAT-AT
38515104 TTTTATATAT
1 TTTTATATAT
38515114 TTTTATA-AT
1 TTTTATATAT
*
38515123 TTTT-TTTAGT
1 TTTTATATA-T
*
38515133 TTGTATATAT
1 TTTTATATAT
38515143 TATTT-TGA-AT
1 T-TTTAT-ATAT
*
38515153 TTTTTTATAAT
1 TTTTATAT-AT
38515164 TTTTATA-AT
1 TTTTATATAT
38515173 TTTTA
1 TTTTA
38515178 ATGATTTTAA
Statistics
Matches: 79, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
8 1 0.01
9 29 0.37
10 28 0.35
11 21 0.27
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.68
Consensus pattern (10 bp):
TTTTATATAT
Found at i:38515127 original size:39 final size:37
Alignment explanation
Indices: 38515042--38515127 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 37
38515032 TTTACAGTTT
*
38515042 TAATTTTTTAAATATTTTTACACTTTTCTATATTTTA
1 TAATTTTTTAAATATTTTTACACTTTTATATATTTTA
* * *
38515079 TTATATTTTTAACATTTTTTTTCACTTTTATATATTTTTA
1 TAAT-TTTTTAA-ATATTTTTACACTTTTATATA-TTTTA
38515119 TAATTTTTT
1 TAATTTTTT
38515128 TTAGTTTGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 3 0.07
38 7 0.17
39 23 0.56
40 8 0.20
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (37 bp):
TAATTTTTTAAATATTTTTACACTTTTATATATTTTA
Found at i:38515997 original size:18 final size:19
Alignment explanation
Indices: 38515962--38516001 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
38515952 CCACATTTTT
*
38515962 AATTAAATAAATTATTAAA
1 AATTAAATAAAATATTAAA
38515981 AATTAAA-AAAATATTAAA
1 AATTAAATAAAATATTAAA
38515999 AAT
1 AAT
38516002 ATATATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTAAATAAAATATTAAA
Found at i:38518065 original size:27 final size:27
Alignment explanation
Indices: 38517998--38518067 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
38517988 TTACAAGGGG
* *
38517998 TGGTGCCTACCTGACAGGCGGCACTAG
1 TGGTGCCTACCTGTCAGGCGGCACTAA
38518025 TGGTGCCTACCTGTCAGGCGGCACTAA
1 TGGTGCCTACCTGTCAGGCGGCACTAA
*
38518052 TGGTGCCTTCCTGTCA
1 TGGTGCCTACCTGTCA
38518068 CGCGACACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (27 bp):
TGGTGCCTACCTGTCAGGCGGCACTAA
Found at i:38522382 original size:28 final size:28
Alignment explanation
Indices: 38522329--38522386 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
38522319 CATTTTTCTG
*
38522329 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATAATTGAAT
**
38522357 TTGGAATTAATTCTGTTTA-AATTTGAAT
1 TTGGAATTAATTAAGTTTATAA-TTGAAT
38522385 TT
1 TT
38522387 ATTTAATGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAGTTTATAATTGAAT
Found at i:38524610 original size:30 final size:30
Alignment explanation
Indices: 38524562--38524618 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
38524552 ATCATCCTTA
*
38524562 ATTATTTTT-AAAATTTTAAATTGAAATTT
1 ATTATTTTTAAAAATTTAAAATTGAAATTT
38524591 ATTATTTATTAAAAATTTAAAATTGAAA
1 ATTATTT-TTAAAAATTTAAAATTGAAA
38524619 GATTCAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.28
30 2 0.08
31 16 0.64
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (30 bp):
ATTATTTTTAAAAATTTAAAATTGAAATTT
Found at i:38525292 original size:17 final size:17
Alignment explanation
Indices: 38525270--38525303 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38525260 CTTACAATAA
*
38525270 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
38525287 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
38525304 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:38537229 original size:13 final size:13
Alignment explanation
Indices: 38537211--38537238 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38537201 CTTGTATTTC
38537211 TGTTGTTAGAAAT
1 TGTTGTTAGAAAT
38537224 TGTTGTTAGAAAT
1 TGTTGTTAGAAAT
38537237 TG
1 TG
38537239 ATCTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (13 bp):
TGTTGTTAGAAAT
Found at i:38537349 original size:34 final size:35
Alignment explanation
Indices: 38537270--38537351 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 35
38537260 TGAAATCTTA
* * * *
38537270 ATAAAA-AAAATTAATTTAATTTTTAATCTAATGT
1 ATAAAATATAATTTATTTAATTTTTAATCAAAAGT
38537304 ATAAAAT-TAATTTATTTAATTTTTTAAT-AAAAG-
1 ATAAAATATAATTTATTTAA-TTTTTAATCAAAAGT
38537337 ATAAAATATAATTTA
1 ATAAAATATAATTTA
38537352 ACTTAAGGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 7 0.17
34 26 0.63
35 8 0.20
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (35 bp):
ATAAAATATAATTTATTTAATTTTTAATCAAAAGT
Found at i:38542642 original size:23 final size:22
Alignment explanation
Indices: 38542612--38542737 Score: 126
Period size: 23 Copynumber: 5.4 Consensus size: 22
38542602 CACTAGCACA
*
38542612 CTCTCTGTTTAGCACGTCTCGTG
1 CTCTCTGTTTAGCACGTGT-GTG
38542635 CTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTG-T-TTAGCAC-GTGTGTG
* *
38542660 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGTTTAGCAC-GTGTGTG
* * * *
38542683 CTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCAC-GTGTGTG
38542706 CTCTCTGTTTAGCACTGTGTGTG
1 CTCTCTGTTTAGCAC-GTGTGTG
38542729 CTCTCTGTT
1 CTCTCTGTT
38542738 GCCCAGCACT
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
23 70 0.77
24 1 0.01
25 17 0.19
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (22 bp):
CTCTCTGTTTAGCACGTGTGTG
Found at i:38542711 original size:46 final size:47
Alignment explanation
Indices: 38542611--38542736 Score: 157
Period size: 46 Copynumber: 2.7 Consensus size: 47
38542601 ACACTAGCAC
* *
38542611 ACTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGT
1 ACTCTCTGATTAGCACTGTGT-GTGCTCTCTG-TATTAGCACTGTGTGT
* * * *
38542659 GCTCTCTGATTAGCACTTTGTGTGCTCTCTG-ATTAGTACTTTGTGT
1 ACTCTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGT
*
38542705 ACTCTCTGTTTAGCACTGTGTGTGCTCTCTGT
1 ACTCTCTGATTAGCACTGTGTGTGCTCTCTGT
38542737 TGCCCAGCAC
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 41 0.61
48 24 0.36
49 2 0.03
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (47 bp):
ACTCTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGT
Found at i:38542735 original size:69 final size:66
Alignment explanation
Indices: 38542635--38542784 Score: 194
Period size: 69 Copynumber: 2.2 Consensus size: 66
38542625 ACGTCTCGTG
*
38542635 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACT
1 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACT
38542699 TTGTGTA
61 TTG-GTA
*
38542706 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTTTGTTAGTACTTT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTT
38542771 GGTA
63 GGTA
38542775 CTCTCTGTTT
1 CTCTCTGTTT
38542785 GTTCTGTATA
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
68 2 0.03
69 35 0.48
70 12 0.16
71 19 0.26
72 5 0.07
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (66 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGT
A
Found at i:38543985 original size:28 final size:28
Alignment explanation
Indices: 38543930--38543985 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
38543920 GTAGACTCAT
* ** *
38543930 CTCGTGTTTATTATCCCGACGGATTTAC
1 CTCGTGTTTACTATCCCGACAAAATTAC
*
38543958 CTCGTGTTTACTATCCTGACAAAATTAC
1 CTCGTGTTTACTATCCCGACAAAATTAC
38543986 TTTGTTCCGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (28 bp):
CTCGTGTTTACTATCCCGACAAAATTAC
Found at i:38545964 original size:41 final size:41
Alignment explanation
Indices: 38545907--38545988 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
38545897 TTTAAGGTTA
38545907 TGATAGCATTCTTATCATAATACAGTATATATTCAATGTTT
1 TGATAGCATTCTTATCATAATACAGTATATATTCAATGTTT
38545948 TGATAGCATTCTTATCATAATACAGTATATATTCAATGTTT
1 TGATAGCATTCTTATCATAATACAGTATATATTCAATGTTT
38545989 GTTGCTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (41 bp):
TGATAGCATTCTTATCATAATACAGTATATATTCAATGTTT
Found at i:38549374 original size:29 final size:30
Alignment explanation
Indices: 38549304--38549379 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
38549294 AATTCTAAAA
*
38549304 TTATACATGAATTATGATTTAATGTGCAATT
1 TTATACATGAATTTTGATTTAATGT-CAATT
** * *
38549335 GCATAAATGAATTTTGATTTTATGT-AATT
1 TTATACATGAATTTTGATTTAATGTCAATT
38549364 TTATACATGAAATTTT
1 TTATACATG-AATTTT
38549380 TTATTTGATC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 10 0.28
30 6 0.17
31 20 0.56
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (30 bp):
TTATACATGAATTTTGATTTAATGTCAATT
Found at i:38553624 original size:29 final size:29
Alignment explanation
Indices: 38553563--38553634 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
38553553 GTTTAGTTTG
38553563 GGTACCAAATTGGACATTAAAACCAAAATTA
1 GGTACCAAATTGGACA-TAAAA-CAAAATTA
38553594 GGTACCAAATTGTGACA-AAAA-AAAACTTA
1 GGTACCAAATTG-GACATAAAACAAAA-TTA
*
38553623 GGTATCAAATTG
1 GGTACCAAATTG
38553635 AATATTGAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 4 0.11
29 14 0.37
30 4 0.11
31 12 0.32
32 4 0.11
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (29 bp):
GGTACCAAATTGGACATAAAACAAAATTA
Found at i:38555403 original size:20 final size:20
Alignment explanation
Indices: 38555375--38555413 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38555365 AGATATGACC
*
38555375 CATTAAAAACCTTCTAAATA
1 CATTAAAAACCTTCGAAATA
* *
38555395 CATTGAAAAGCTTCGAAAT
1 CATTAAAAACCTTCGAAAT
38555414 TTCGAATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (20 bp):
CATTAAAAACCTTCGAAATA
Found at i:38558508 original size:41 final size:41
Alignment explanation
Indices: 38558451--38558530 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
38558441 TTTAGGAAAA
38558451 CAAGAGTGGGTAAATAGTAAATAAAAAAAATGAAGAGCATC
1 CAAGAGTGGGTAAATAGTAAATAAAAAAAATGAAGAGCATC
38558492 CAAGAGTGGGTAAATAGTAAATAAAAAAAATGAAGAGCA
1 CAAGAGTGGGTAAATAGTAAATAAAAAAAATGAAGAGCA
38558531 ACCCCTCCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.16
Consensus pattern (41 bp):
CAAGAGTGGGTAAATAGTAAATAAAAAAAATGAAGAGCATC
Found at i:38559884 original size:39 final size:40
Alignment explanation
Indices: 38559826--38559903 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 40
38559816 TGATTCAAGT
* * *
38559826 TCTAAAAAATATCTAAAAATTATATACAATTTATAAAAAA
1 TCTAAAAAATATCAAAAAATAATATAAAATTTATAAAAAA
* * *
38559866 TCTAAAGAA-ATCAAAAAATAATGTAAAATTTATGAAAA
1 TCTAAAAAATATCAAAAAATAATATAAAATTTATAAAAA
38559904 TTCGTATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
39 24 0.75
40 8 0.25
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.29
Consensus pattern (40 bp):
TCTAAAAAATATCAAAAAATAATATAAAATTTATAAAAAA
Found at i:38560886 original size:2 final size:2
Alignment explanation
Indices: 38560879--38560917 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
38560869 TTTGTTTACA
38560879 AT AT AT 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 AT AT AT A
38560918 ATGCAAATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38571248 original size:13 final size:13
Alignment explanation
Indices: 38571217--38571251 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
38571207 TAGATAAAAA
*
38571217 AAAATTAAGTATC
1 AAAATTAAATATC
38571230 -AAATTAAATATC
1 AAAATTAAATATC
38571242 AAAATTAAAT
1 AAAATTAAAT
38571252 TTAAATACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (13 bp):
AAAATTAAATATC
Found at i:38572214 original size:22 final size:22
Alignment explanation
Indices: 38572174--38572216 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38572164 TGAGTTTAAA
*
38572174 AAAATATATAATCCAAGAAAAT
1 AAAATATATAATACAAGAAAAT
38572196 AAAATATATATATAC-AGAAAA
1 AAAATATATA-ATACAAGAAAA
38572217 AACTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (22 bp):
AAAATATATAATACAAGAAAAT
Found at i:38580181 original size:15 final size:15
Alignment explanation
Indices: 38580161--38580191 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38580151 AAGTTTTGGT
38580161 CTTTTGTCTCAGCAA
1 CTTTTGTCTCAGCAA
*
38580176 CTTTTGTCTCATCAA
1 CTTTTGTCTCAGCAA
38580191 C
1 C
38580192 CAAGCGTAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.42
Consensus pattern (15 bp):
CTTTTGTCTCAGCAA
Found at i:38581735 original size:2 final size:2
Alignment explanation
Indices: 38581728--38581773 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
38581718 TCTATTTGAA
38581728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38581770 AT AT
1 AT AT
38581774 TGATGCCAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38589048 original size:12 final size:12
Alignment explanation
Indices: 38589031--38589055 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38589021 TAATTTTGCA
38589031 AATTTTTTATAT
1 AATTTTTTATAT
38589043 AATTTTTTATAT
1 AATTTTTTATAT
38589055 A
1 A
38589056 TTACTATTTC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTTTTTATAT
Found at i:38589891 original size:5 final size:5
Alignment explanation
Indices: 38589881--38589905 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38589871 GGGTAAATGA
38589881 CCGGG CCGGG CCGGG CCGGG CCGGG
1 CCGGG CCGGG CCGGG CCGGG CCGGG
38589906 TTGAGCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.60, T:0.00
Consensus pattern (5 bp):
CCGGG
Found at i:38593559 original size:20 final size:20
Alignment explanation
Indices: 38593528--38593568 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
38593518 AAGCAATAAG
38593528 AAGAAAAAGAAGCAGA-AAC
1 AAGAAAAAGAAGCAGAGAAC
38593547 AAGAAACAAGAAGCAGAGAAC
1 AAGAAA-AAGAAGCAGAGAAC
38593568 A
1 A
38593569 CACCTTGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 10 0.50
21 4 0.20
ACGTcount: A:0.66, C:0.12, G:0.22, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAGCAGAGAAC
Found at i:38598237 original size:14 final size:15
Alignment explanation
Indices: 38598213--38598241 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38598203 TATGTGTCTT
38598213 TTTTTTAAATATTTA
1 TTTTTTAAATATTTA
38598228 TTTTTT-AATATTTA
1 TTTTTTAAATATTTA
38598242 ATATTTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTAAATATTTA
Found at i:38599460 original size:57 final size:57
Alignment explanation
Indices: 38599394--38599505 Score: 215
Period size: 57 Copynumber: 2.0 Consensus size: 57
38599384 TAATAAAATC
38599394 ATTAAAAAATGTAAATAATGTATTTATTATTTGGATTTAAAATTTTTAAAATAATGT
1 ATTAAAAAATGTAAATAATGTATTTATTATTTGGATTTAAAATTTTTAAAATAATGT
*
38599451 ATTAAAAAATGTAAATAATGTATTTATTATTTGGGTTTAAAATTTTTAAAATAAT
1 ATTAAAAAATGTAAATAATGTATTTATTATTTGGATTTAAAATTTTTAAAATAAT
38599506 ATATGTACTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (57 bp):
ATTAAAAAATGTAAATAATGTATTTATTATTTGGATTTAAAATTTTTAAAATAATGT
Found at i:38607809 original size:24 final size:24
Alignment explanation
Indices: 38607772--38607821 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
38607762 AACTTAACCT
*
38607772 AAAAATTAAATAAA-TAAGAAAATA
1 AAAAATCAAATAAATTAA-AAAATA
*
38607796 AAAAATCAATTAAATTAAAAAATA
1 AAAAATCAAATAAATTAAAAAATA
38607820 AA
1 AA
38607822 GATGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAAATCAAATAAATTAAAAAATA
Found at i:38609051 original size:18 final size:20
Alignment explanation
Indices: 38609011--38609063 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
38609001 GTCGTTCAAG
* *
38609011 TAATTATTTATTTTAATTAA
1 TAATTATATATTTAAATTAA
38609031 TAATTATATA-TTAAATT-A
1 TAATTATATATTTAAATTAA
38609049 TAATTAT-T-TTTAAAT
1 TAATTATATATTTAAAT
38609064 ATTTTTTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 7 0.23
18 8 0.27
19 6 0.20
20 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATTATATATTTAAATTAA
Found at i:38612756 original size:3 final size:3
Alignment explanation
Indices: 38612748--38612786 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
38612738 TTTTTATAGC
38612748 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
38612787 TTCTTCAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:38613868 original size:3 final size:3
Alignment explanation
Indices: 38613860--38613898 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
38613850 GACCTCCCTT
38613860 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38613899 AGATATTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38620771 original size:22 final size:23
Alignment explanation
Indices: 38620709--38620784 Score: 77
Period size: 22 Copynumber: 3.4 Consensus size: 23
38620699 ATTATATTAT
* * *
38620709 TGTTTTGGTGCTGTTTTTTTTAC
1 TGTTTTGATGTTGCTTTTTTTAC
*
38620732 TATTTTG--GTTGCTATTTTTTAC
1 TGTTTTGATGTTGCT-TTTTTTAC
*
38620754 TGTTTTGATGTTG-TTTTTTTAT
1 TGTTTTGATGTTGCTTTTTTTAC
38620776 TGTTTTGAT
1 TGTTTTGAT
38620785 TACTATTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.09
22 30 0.67
23 7 0.16
24 4 0.09
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.67
Consensus pattern (23 bp):
TGTTTTGATGTTGCTTTTTTTAC
Found at i:38620791 original size:44 final size:45
Alignment explanation
Indices: 38620709--38620793 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 45
38620699 ATTATATTAT
* * *
38620709 TGTTTTGGTGCTGTTTTTTTTACTATTTTGGTTGCTATTTTTTAC
1 TGTTTTGATGCTGTTTTTTTTACTATTTTGATTACTATTTTTTAC
* * *
38620754 TGTTTTGATGTTG-TTTTTTTATTGTTTTGATTACTATTTT
1 TGTTTTGATGCTGTTTTTTTTACTATTTTGATTACTATTTT
38620794 GATGCTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 23 0.68
45 11 0.32
ACGTcount: A:0.11, C:0.06, G:0.16, T:0.67
Consensus pattern (45 bp):
TGTTTTGATGCTGTTTTTTTTACTATTTTGATTACTATTTTTTAC
Found at i:38620793 original size:22 final size:22
Alignment explanation
Indices: 38620724--38620793 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
38620714 TGGTGCTGTT
* * *
38620724 TTTTTTACTATTTTGGTTGCTA
1 TTTTTTACTGTTTTGATTACTA
**
38620746 TTTTTTACTGTTTTGATGTTGT-
1 TTTTTTACTGTTTTGAT-TACTA
*
38620768 TTTTTTATTGTTTTGATTACTA
1 TTTTTTACTGTTTTGATTACTA
38620790 TTTT
1 TTTT
38620794 GATGCTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.05
22 35 0.90
23 2 0.05
ACGTcount: A:0.13, C:0.06, G:0.13, T:0.69
Consensus pattern (22 bp):
TTTTTTACTGTTTTGATTACTA
Found at i:38620802 original size:21 final size:21
Alignment explanation
Indices: 38620778--38620818 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38620768 TTTTTTATTG
38620778 TTTTGATTACTATTTTGATGC
1 TTTTGATTACTATTTTGATGC
** *
38620799 TTTTTTTTACTGTTTTGATG
1 TTTTGATTACTATTTTGATG
38620819 TTATTTTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (21 bp):
TTTTGATTACTATTTTGATGC
Found at i:38620813 original size:33 final size:34
Alignment explanation
Indices: 38620750--38620838 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 34
38620740 TTGCTATTTT
* * *
38620750 TTACTGTTTTGATGTTGTTTTTTTATTGTTTTGA
1 TTACTATTTTGATGCTGTTTTTTTACTGTTTTGA
38620784 TTACTATTTTGATGCT-TTTTTTTACTGTTTTGA
1 TTACTATTTTGATGCTGTTTTTTTACTGTTTTGA
*
38620817 TGT--TATTTTTGTTGCTGTTTTT
1 T-TACTA-TTTTGATGCTGTTTTT
38620839 GTTTTTATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 2 0.04
33 26 0.54
34 20 0.42
ACGTcount: A:0.11, C:0.06, G:0.16, T:0.67
Consensus pattern (34 bp):
TTACTATTTTGATGCTGTTTTTTTACTGTTTTGA
Found at i:38620825 original size:21 final size:21
Alignment explanation
Indices: 38620784--38620826 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
38620774 ATTGTTTTGA
38620784 TTACTATTTTGATGCTTTTTT
1 TTACTATTTTGATGCTTTTTT
* *
38620805 TTACTGTTTTGATG-TTATTT
1 TTACTATTTTGATGCTTTTTT
38620825 TT
1 TT
38620827 GTTGCTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.67
Consensus pattern (21 bp):
TTACTATTTTGATGCTTTTTT
Found at i:38620826 original size:12 final size:12
Alignment explanation
Indices: 38620811--38620853 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
38620801 TTTTTTACTG
*
38620811 TTTTGATGTTAT
1 TTTTGTTGTTAT
* *
38620823 TTTTGTTGCTGT
1 TTTTGTTGTTAT
*
38620835 TTTTGTTTTTAT
1 TTTTGTTGTTAT
38620847 TTTTGTT
1 TTTTGTT
38620854 ATTTTACTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.07, C:0.02, G:0.16, T:0.74
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:38620838 original size:24 final size:23
Alignment explanation
Indices: 38620778--38620854 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 23
38620768 TTTTTTATTG
* *
38620778 TTTTGATTACTATTTTGATGCT-T
1 TTTTG-TTACTGTTTTGATGTTAT
38620801 TTTT-TTACTGTTTTGATGTTAT
1 TTTTGTTACTGTTTTGATGTTAT
* * *
38620823 TTTTGTTGCTGTTTTTGTTTTTAT
1 TTTTGTTACTG-TTTTGATGTTAT
38620847 TTTTGTTA
1 TTTTGTTA
38620855 TTTTACTGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.31
22 5 0.11
23 9 0.20
24 17 0.38
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.69
Consensus pattern (23 bp):
TTTTGTTACTGTTTTGATGTTAT
Done.