Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 82 of 193
Found at i:27151898 original size:7 final size:7
Alignment explanation
Indices: 27151887--27152039 Score: 144
Period size: 7 Copynumber: 21.9 Consensus size: 7
27151877 ATCGTTGATA
27151887 GTTGACC
1 GTTGACC
* *
27151894 ATTGATC
1 GTTGACC
27151901 GTTGACC
1 GTTGACC
*
27151908 GTTGACT
1 GTTGACC
*
27151915 GTTGATC
1 GTTGACC
*
27151922 GTTGACT
1 GTTGACC
*
27151929 GTTGATC
1 GTTGACC
*
27151936 GTTGACT
1 GTTGACC
*
27151943 GTTGACT
1 GTTGACC
*
27151950 GTTGATC
1 GTTGACC
*
27151957 GTTGATC
1 GTTGACC
27151964 GTTGACC
1 GTTGACC
*
27151971 GTTGACT
1 GTTGACC
*
27151978 GTTGATC
1 GTTGACC
*
27151985 GTTGACT
1 GTTGACC
*
27151992 GTTGATC
1 GTTGACC
*
27151999 GTTGACT
1 GTTGACC
*
27152006 GTTGACT
1 GTTGACC
*
27152013 GTTGATC
1 GTTGACC
*
27152020 GTTGATC
1 GTTGACC
27152027 GTTGACC
1 GTTGACC
27152034 GTTGAC
1 GTTGAC
27152040 TTTTTTTGAA
Statistics
Matches: 118, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 118 1.00
ACGTcount: A:0.15, C:0.17, G:0.28, T:0.40
Consensus pattern (7 bp):
GTTGACC
Found at i:27151903 original size:21 final size:21
Alignment explanation
Indices: 27151895--27152038 Score: 188
Period size: 21 Copynumber: 6.9 Consensus size: 21
27151885 TAGTTGACCA
27151895 TTGATCGTTGACCGTTGACT-G
1 TTGATCGTTGACCGTTGA-TCG
*
27151916 TTGATCGTTGACTGTTGATCG
1 TTGATCGTTGACCGTTGATCG
*
27151937 TTGACT-GTTGACTGTTGATCG
1 TTGA-TCGTTGACCGTTGATCG
27151958 TTGATCGTTGACCGTTGA-CTG
1 TTGATCGTTGACCGTTGATC-G
*
27151979 TTGATCGTTGACTGTTGATCG
1 TTGATCGTTGACCGTTGATCG
*
27152000 TTGA-CTGTTGACTGTTGATCG
1 TTGATC-GTTGACCGTTGATCG
27152021 TTGATCGTTGACCGTTGA
1 TTGATCGTTGACCGTTGA
27152039 CTTTTTTTGA
Statistics
Matches: 112, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
20 4 0.04
21 105 0.94
22 3 0.03
ACGTcount: A:0.15, C:0.16, G:0.28, T:0.41
Consensus pattern (21 bp):
TTGATCGTTGACCGTTGATCG
Found at i:27153151 original size:3 final size:3
Alignment explanation
Indices: 27153101--27153140 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
27153091 ACATTATTTA
27153101 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
27153141 TTGGATTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:27160278 original size:3 final size:3
Alignment explanation
Indices: 27160219--27160267 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
27160209 ACAAATTTAC
27160219 ATT ATT -TT A-T 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 ATT ATT ATT
27160265 ATT
1 ATT
27160268 TTGGATTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:27170513 original size:51 final size:49
Alignment explanation
Indices: 27170458--27170673 Score: 154
Period size: 51 Copynumber: 4.3 Consensus size: 49
27170448 ACTTTACTTC
*
27170458 AAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGTTTA
1 AAAATCTAAACTTTTATTT-GAAATA-TTAAAAAAATCAAAACTTTGTTTA
* * *** *
27170509 AAAATTTAAACTTTT-TCTTTAAA-ATTACTAAAAAA-CATATTTTATTTTTTA
1 AAAATCTAAACTTTTAT-TTGAAATATTA--AAAAAATCA-AAACT-TTGTTTA
* ** * ** **
27170560 AAAATCTGAAC-TTTATTT-ATTTATTAATGAAAATCACTACTTTACTTA
1 AAAATCTAAACTTTTATTTGAAATATTAA-AAAAATCAAAACTTTGTTTA
*
27170608 AAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGTTTA
1 AAAATCTAAACTTTTATTT-GAAATA-TTAAAAAAATCAAAACTTTGTTTA
*
27170659 AAAATTTAAACTTTT
1 AAAATCTAAACTTTT
27170674 TCTTTAAAAT
Statistics
Matches: 124, Mismatches: 28, Indels: 26
0.70 0.16 0.15
Matches are distributed among these distances:
48 18 0.15
49 17 0.14
50 23 0.19
51 62 0.50
52 4 0.03
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (49 bp):
AAAATCTAAACTTTTATTTGAAATATTAAAAAAATCAAAACTTTGTTTA
Found at i:27170601 original size:150 final size:150
Alignment explanation
Indices: 27170439--27170785 Score: 554
Period size: 150 Copynumber: 2.3 Consensus size: 150
27170429 TGATTAAAAT
*
27170439 AAAATCATTACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCATTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
27170504 GTTTAAAAATTTAAACTTTTTCTTTAAAATTACTAAAAAACATA-TTTTATTTTTT-AAAAATCT
66 GTTTAAAAATTTAAACTTTTTCTTTAAAATCACT--AAAACATATTTTTATTTTTTAAAAAATCT
*
27170567 GAACTTTATTTATTTATTAATG
129 AAACTTTATTTATTTATTAATG
* *
27170589 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCATTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
27170654 GTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAACATATTTTTATTTTTTAAAAAATCTAA
66 GTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAACATATTTTTATTTTTTAAAAAATCTAA
* * *
27170719 ACTTTCTTTCTTTTTTAATG
131 ACTTTATTTATTTATTAATG
* * * *
27170739 AAAATCATTATTTTACTTAAAAATCTAAACTTTTGTTTTGAAATAGT
1 AAAATCATTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGT
27170786 ACTTTATTTA
Statistics
Matches: 182, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
148 8 0.04
149 11 0.06
150 163 0.90
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (150 bp):
AAAATCATTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAACATATTTTTATTTTTTAAAAAATCTAA
ACTTTATTTATTTATTAATG
Found at i:27170817 original size:150 final size:145
Alignment explanation
Indices: 27170439--27170942 Score: 496
Period size: 150 Copynumber: 3.5 Consensus size: 145
27170429 TGATTAAAAT
* * *
27170439 AAAATCATTACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
27170504 GTTTAAAAATTTAAACTTTTTCTTTAAAATTACTAAAAAACATATTTTATTTTTTAAAAATCTGA
66 GTTT----ATTTAAACTTTTTCTTTAAAATCACT-AAAAACATATTTTATTTTTTAAAAATCTAA
27170569 ACTTTATTTATTTATTAATG
126 ACTTTATTTATTTATTAATG
27170589 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
27170654 GTTTAAAAATTTAAACTTTTTCTTTAAAATCACT-AAAACATATTTTTATTTTTTAAAAAATCTA
66 GTTT----ATTTAAACTTTTTCTTTAAAATCACTAAAAACATA-TTTTATTTTTT-AAAAATCTA
* * *
27170718 AACTTTCTTTCTTTTTTAATG
125 AACTTTATTTATTTATTAATG
* * * * * **** * *
27170739 AAAATCATTATTTTACTTAAAAATCTAAACTTTTGTTTTGAAATAG-TACTTTATTTAAAA----
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * * *** * *
27170799 ----ATTTAAACTTTTTTTTTAAAATAACTAAAAAACAGATTTT-TTTAAAAAAAATATAAACTC
66 GTTTATTTAAACTTTTTCTTTAAAATCACT-AAAAACATATTTTATTTTTTAAAAATCTAAACTT
* * **
27170859 T-CTT-TTTA-AAAAA
130 TATTTATTTATTAATG
* *
27170872 AAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
27170937 TGTTTA
65 TGTTTA
27170943 AAAATTTAAA
Statistics
Matches: 299, Mismatches: 41, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
133 45 0.15
134 4 0.01
135 9 0.03
136 13 0.04
137 27 0.09
138 4 0.01
139 7 0.02
143 1 0.00
148 8 0.03
149 19 0.06
150 162 0.54
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (145 bp):
AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTTATTTAAACTTTTTCTTTAAAATCACTAAAAACATATTTTATTTTTTAAAAATCTAAACTTT
ATTTATTTATTAATG
Found at i:27170905 original size:133 final size:135
Alignment explanation
Indices: 27170649--27170918 Score: 348
Period size: 133 Copynumber: 2.0 Consensus size: 135
27170639 AAAAATCAAA
* * * * ** **
27170649 ACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAACATATTTTTATTTTTTAAAAAA
1 ACTTTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTATTTTAAAAAAAA
* * ** * * *
27170714 TCTAAACTTTCTTTCTTTTTTAATGAAAATCATTATTTTACTTAAAAATCTAAACTTTTGTTTTG
66 TATAAAC-TTC-TTCTTTTTAAAAAAAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCG
27170779 AAATAGT
129 AAATAGT
*
27170786 ACTTTATTTAAAAATTTAAACTTTTTTTTTAAAATAACTAAAAAACAGATTT-TTTTAAAAAAAA
1 ACTTTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTATTTTAAAAAAAA
27170850 TATAAAC-TC-TCTTTTTAAAAAAAAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGA
66 TATAAACTTCTTCTTTTT-AAAAAAAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGA
27170913 AATAGT
130 AATAGT
27170919 TAAAAAAAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
132 7 0.06
133 46 0.40
134 2 0.02
136 16 0.14
137 45 0.39
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (135 bp):
ACTTTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTATTTTAAAAAAAA
TATAAACTTCTTCTTTTTAAAAAAAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAA
ATAGT
Found at i:27170930 original size:52 final size:52
Alignment explanation
Indices: 27170868--27171024 Score: 166
Period size: 45 Copynumber: 3.1 Consensus size: 52
27170858 CTCTTTTTAA
* *
27170868 AAAAAAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTT
1 AAAAAAAATCAATATTTTACTTAAAAATCTAAACTTTTATTTCGAAATATTT
* * ** * *
27170920 AAAAAAAATCAAAACTTTGTTTAAAAATTTAAA--TTT-TTTC----TTTTT
1 AAAAAAAATCAATATTTTACTTAAAAATCTAAACTTTTATTTCGAAATATTT
* *
27170965 AAAGAAAATCAATATTTTACTTAAAAATCAAAACTTTTATTTCGAAATTATTT
1 AAAAAAAATCAATATTTTACTTAAAAATCTAAACTTTTATTTCGAAA-TATTT
27171018 AAAAAAA
1 AAAAAAA
27171025 CCAAAACTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 15
0.71 0.15 0.13
Matches are distributed among these distances:
45 29 0.36
47 3 0.04
48 4 0.05
49 4 0.05
50 3 0.04
52 27 0.34
53 10 0.12
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (52 bp):
AAAAAAAATCAATATTTTACTTAAAAATCTAAACTTTTATTTCGAAATATTT
Found at i:27174579 original size:11 final size:11
Alignment explanation
Indices: 27174558--27174587 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
27174548 TTACATTATT
27174558 TATTATTTTTAA
1 TATT-TTTTTAA
27174570 TATTTTTTTAA
1 TATTTTTTTAA
27174581 TATTTTT
1 TATTTTT
27174588 ATTCAATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTTTTTAA
Found at i:27175504 original size:3 final size:3
Alignment explanation
Indices: 27175498--27175540 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
27175488 CAACAACAAC
27175498 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27175541 AAGACTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:27181093 original size:14 final size:14
Alignment explanation
Indices: 27181055--27181097 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
27181045 CAAAATGTAC
27181055 AATATAATTAAA-T
1 AATATAATTAAATT
27181068 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
27181083 AA-ATAATTTAATT
1 AATATAATTAAATT
27181096 AA
1 AA
27181098 CTATTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:27184106 original size:30 final size:30
Alignment explanation
Indices: 27184047--27184201 Score: 127
Period size: 30 Copynumber: 5.2 Consensus size: 30
27184037 TTAAATTTGA
* * *
27184047 CCCTAAAATTT-TTAAACTTTCATTTTTAAC
1 CCCTTAAATTTCTAAAAATTTCA-TTTTAAC
*
27184077 CCCTTAACTTTCTAAAAATTTCATTTTAA-
1 CCCTTAAATTTCTAAAAATTTCATTTTAAC
* * *
27184106 CCCTTGAATTTTTTGAAAAATTTCATTTTGAC
1 CCCTT-AAATTTCT-AAAAATTTCATTTTAAC
* * * * *
27184138 CCCTAAAATTTTTGAAAATTACATTTTGAC
1 CCCTTAAATTTCTAAAAATTTCATTTTAAC
** *
27184168 CCCAAAAATTTCTAAAAATTACA-TTTAAC
1 CCCTTAAATTTCTAAAAATTTCATTTTAAC
27184197 CCCTT
1 CCCTT
27184202 TTTTACTCTT
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
29 13 0.12
30 56 0.54
31 31 0.30
32 4 0.04
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (30 bp):
CCCTTAAATTTCTAAAAATTTCATTTTAAC
Found at i:27184201 original size:91 final size:90
Alignment explanation
Indices: 27184031--27184198 Score: 223
Period size: 91 Copynumber: 1.9 Consensus size: 90
27184021 AAACTTTTCC
* * ** *
27184031 AAAAATTTAAATTTGACCCTAAAATTTTTAAACTTTCATTTTTAACCCCTTAACTTTCTAAAAAT
1 AAAAATTTAAATTTGACCCTAAAATTTTTAAAATTACATTTTTAACCCCAAAAATTTCTAAAAAT
*
27184096 TTCATTTTAACCCTTGAATTTTTTG
66 TACATTTTAACCCTTGAATTTTTTG
* * *
27184121 AAAAATTTCATTTTGACCCCTAAAATTTTTGAAAATTACA-TTTTGACCCCAAAAATTTCTAAAA
1 AAAAATTTAAATTTGA-CCCTAAAATTTTT-AAAATTACATTTTTAACCCCAAAAATTTCTAAAA
27184185 ATTACA-TTTAACCC
64 ATTACATTTTAACCC
27184199 CTTTTTTACT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
90 22 0.33
91 38 0.57
92 7 0.10
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.41
Consensus pattern (90 bp):
AAAAATTTAAATTTGACCCTAAAATTTTTAAAATTACATTTTTAACCCCAAAAATTTCTAAAAAT
TACATTTTAACCCTTGAATTTTTTG
Found at i:27203685 original size:158 final size:158
Alignment explanation
Indices: 27203391--27203872 Score: 660
Period size: 158 Copynumber: 3.1 Consensus size: 158
27203381 ATCATCATAT
* *
27203391 CATGTAATGCTCACACGAGCTGTGAAATGGGCCTGCTCACATGAGTTGTGGGTCGAGATGTTAAG
1 CATGTAATGCTCACACGAGCTGTGAAATGGGCTTGCTCACATGAGTTGTGGGTCGAGATGTTGAG
* * * * * * * *
27203456 CTACACAATGATGCTCACACGAGCTATAGAGAATCCACAATAATTATCGGATCTCAGTCATCGAT
66 CTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAATAATTGTCGGATCTCAGCCATCAAT
* *
27203521 AAGACATTTAATACCAGCACCCATATAA
131 AAGACATCTAAGACCAGCACCCATATAA
* * * * *
27203549 CATGTAATGCTCACACGAGCTGTGAAATGGGCTTGTTCACACGAGCTATGGGTTGAGATGTTGAG
1 CATGTAATGCTCACACGAGCTGTGAAATGGGCTTGCTCACATGAGTTGTGGGTCGAGATGTTGAG
* * *
27203614 CTACACGATGCTACTCACACGAGCTGTGGAGAATCCGCAATAATTGTCGAATCTCAACCATCAAT
66 CTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAATAATTGTCGGATCTCAGCCATCAAT
*
27203679 AGGACATCTAAGACCAGCACCCATATAA
131 AAGACATCTAAGACCAGCACCCATATAA
* * * * *
27203707 CCTATAATGCTCACACGAGCTGTTACATGGG-TCTGGTCACATGAGTTGTGGGTCGAGATGTTGA
1 CATGTAATGCTCACACGAGCTGTGAAATGGGCT-TGCTCACATGAGTTGTGGGTCGAGATGTTGA
* *
27203771 GCTACACGATACTGCTCACACGAGCTGTGGAGAATCCGCAATAATTGTCGGATCTCAGCCATCAG
65 GCTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAATAATTGTCGGATCTCAGCCATCAA
* * *
27203836 TAAGACATCTAAGACCAACACGCGTATAA
130 TAAGACATCTAAGACCAGCACCCATATAA
*
27203865 CCTGTAAT
1 CATGTAAT
27203873 CCCGATGACG
Statistics
Matches: 283, Mismatches: 40, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
157 1 0.00
158 282 1.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (158 bp):
CATGTAATGCTCACACGAGCTGTGAAATGGGCTTGCTCACATGAGTTGTGGGTCGAGATGTTGAG
CTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAATAATTGTCGGATCTCAGCCATCAAT
AAGACATCTAAGACCAGCACCCATATAA
Found at i:27206080 original size:3 final size:3
Alignment explanation
Indices: 27206072--27206129 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
27206062 TTAGGTTTAG
* * * *
27206072 TTA TTA TTA TTA TTA TTA TTT TTCT TTA TTA TTA TTA TTA TTC CTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
27206118 TTA -TA TTA TTA T
1 TTA TTA TTA TTA T
27206130 CCTATGCTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27206089 original size:25 final size:25
Alignment explanation
Indices: 27206060--27206113 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
27206050 CTGCATTTAA
27206060 TATTAGGTTTAGTTATTATTATTAT
1 TATTAGGTTTAGTTATTATTATTAT
** **
27206085 TATTATTTTTCTTTATTATTATTAT
1 TATTAGGTTTAGTTATTATTATTAT
27206110 TATT
1 TATT
27206114 CCTATTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.67
Consensus pattern (25 bp):
TATTAGGTTTAGTTATTATTATTAT
Found at i:27216096 original size:19 final size:21
Alignment explanation
Indices: 27216072--27216111 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
27216062 GAAAATCGAA
27216072 TGTAATA-AATAC-GAAATTT
1 TGTAATAGAATACGGAAATTT
*
27216091 TGTAATAGCATACGGAAATTT
1 TGTAATAGAATACGGAAATTT
27216112 CGAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (21 bp):
TGTAATAGAATACGGAAATTT
Found at i:27216118 original size:21 final size:20
Alignment explanation
Indices: 27216080--27216118 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
27216070 AATGTAATAA
* *
27216080 ATACGAAATTTTGTAATAGC
1 ATACGAAATTTCGAAATAGC
27216100 ATACGGAAATTTCGAAATA
1 ATAC-GAAATTTCGAAATA
27216119 AAAATTCAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (20 bp):
ATACGAAATTTCGAAATAGC
Found at i:27216983 original size:12 final size:11
Alignment explanation
Indices: 27216968--27217078 Score: 59
Period size: 12 Copynumber: 9.7 Consensus size: 11
27216958 TTATTTTAGC
27216968 ATTTAATTTTTT
1 ATTT-ATTTTTT
27216980 ATTTAATTTTTT
1 ATTT-ATTTTTT
*
27216992 A-TTATTTATT
1 ATTTATTTTTT
27217002 ATTTATTTATTT
1 ATTTATTT-TTT
* *
27217014 ATGTGATATTTT
1 AT-TTATTTTTT
27217026 ATGTTATTTAATTT
1 AT-TTATTT--TTT
**
27217040 -TTT-GCTTTT
1 ATTTATTTTTT
*
27217049 ATTTA-ATTTT
1 ATTTATTTTTT
*
27217059 ATTGATATTTTT
1 ATTTAT-TTTTT
27217071 ATTTATTT
1 ATTTATTT
27217079 GCATACTATA
Statistics
Matches: 78, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
9 3 0.04
10 18 0.23
11 11 0.14
12 38 0.49
13 5 0.06
14 3 0.04
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.70
Consensus pattern (11 bp):
ATTTATTTTTT
Found at i:27217000 original size:4 final size:4
Alignment explanation
Indices: 27216968--27217015 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
27216958 TTATTTTAGC
27216968 ATTT AATTT -TTT ATTT AATTT -TTT A-TT ATTT A-TT ATTT ATTT ATTT
1 ATTT -ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
27217014 AT
1 AT
27217016 GTGATATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
3 12 0.32
4 18 0.47
5 8 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:27217015 original size:15 final size:15
Alignment explanation
Indices: 27216973--27217015 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
27216963 TTAGCATTTA
27216973 ATTT-TTTATTTAATT
1 ATTTATTTATTT-ATT
*
27216988 TTTTA-TTATTTATT
1 ATTTATTTATTTATT
27217002 ATTTATTTATTTAT
1 ATTTATTTATTTAT
27217016 GTGATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTATTTATTTATT
Found at i:27217023 original size:22 final size:21
Alignment explanation
Indices: 27216998--27217078 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 21
27216988 TTTTATTATT
27216998 TATTATTTATTTATTTATGTGA
1 TATTATTTATTTATTTAT-TGA
* *
27217020 TATTTTATGTTATTTAATTTTTTGC
1 TA--TTAT-TTATTT-ATTTATTGA
* *
27217045 TTTTATTTA-AT-TTTATTGA
1 TATTATTTATTTATTTATTGA
27217064 TATT-TTTATTTATTT
1 TATTATTTATTTATTT
27217079 GCATACTATA
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
18 4 0.09
19 10 0.22
20 3 0.07
21 1 0.02
22 5 0.11
23 4 0.09
24 4 0.09
25 9 0.20
26 5 0.11
ACGTcount: A:0.23, C:0.01, G:0.06, T:0.69
Consensus pattern (21 bp):
TATTATTTATTTATTTATTGA
Found at i:27217071 original size:18 final size:18
Alignment explanation
Indices: 27217029--27217071 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
27217019 ATATTTTATG
* *
27217029 TTATTTAATTTTTTGCTT
1 TTATTTAATTTTTTGATA
27217047 TTATTTAATTTTATTGATA
1 TTATTTAATTTT-TTGATA
27217066 TT-TTTA
1 TTATTTA
27217072 TTTATTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (18 bp):
TTATTTAATTTTTTGATA
Found at i:27220780 original size:21 final size:20
Alignment explanation
Indices: 27220720--27220794 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
27220710 GGAGTTTTTA
* *
27220720 GTATCGATAGAAGCATGACTT
1 GTATCGGTAGAA-CATCACTT
* * *
27220741 GTTTCGGTAAAAGATTCACTT
1 GTATCGGTAGAACA-TCACTT
**
27220762 GTATCGGTAGAACAGTCACAG
1 GTATCGGTAGAACA-TCACTT
27220783 GTATCGGTAGAA
1 GTATCGGTAGAA
27220795 GTCTGCACTA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (20 bp):
GTATCGGTAGAACATCACTT
Found at i:27231560 original size:21 final size:20
Alignment explanation
Indices: 27231511--27231561 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
27231501 GGAGCAAGAA
*
27231511 TATCGATACCTTAGAGAAAG
1 TATCGATACCTTACAGAAAG
**
27231531 TATTAATACCTTTACA-AAAGG
1 TATCGATACC-TTACAGAAA-G
27231552 TATCGATACC
1 TATCGATACC
27231562 AAATCGATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (20 bp):
TATCGATACCTTACAGAAAG
Found at i:27235926 original size:24 final size:24
Alignment explanation
Indices: 27235893--27235951 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
27235883 GACTTGAGTT
* *
27235893 GTATCAGTAGTTCTTCCCATAGGA
1 GTATCGGTAGTTCTGCCCATAGGA
27235917 GTATCGGTAGTTCTGCCCATAGGA
1 GTATCGGTAGTTCTGCCCATAGGA
27235941 GTATCGGTAGT
1 GTATCGGTAGT
27235952 ATATGTACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (24 bp):
GTATCGGTAGTTCTGCCCATAGGA
Found at i:27238372 original size:28 final size:27
Alignment explanation
Indices: 27238322--27238374 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
27238312 AAAATTATTA
*
27238322 TTTTTAAAATTTTAACTTTTTTAAATT
1 TTTTTAAAATTTTAACTCTTTTAAATT
27238349 TTTTTAAAAATTTATAA-TCTTTTAAA
1 TTTTT-AAAATTT-TAACTCTTTTAAA
27238375 ACATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 15 0.65
29 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTTAAAATTTTAACTCTTTTAAATT
Found at i:27238408 original size:27 final size:28
Alignment explanation
Indices: 27238378--27238433 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
27238368 TTTTAAAACA
*
27238378 TAAATTTTGAAAATT-TTATAAA-TATTT
1 TAAA-TTTAAAAATTATTATAAATTATTT
*
27238405 TAAATTTAAAAATTATTTTAAATTATTT
1 TAAATTTAAAAATTATTATAAATTATTT
27238433 T
1 T
27238434 GTAATTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.36
27 10 0.40
28 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TAAATTTAAAAATTATTATAAATTATTT
Found at i:27238409 original size:18 final size:19
Alignment explanation
Indices: 27238388--27238428 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
27238378 TAAATTTTGA
*
27238388 AAATTTTATAAA-TATTTT
1 AAATTTTAAAAATTATTTT
27238406 AAA-TTTAAAAATTATTTT
1 AAATTTTAAAAATTATTTT
27238424 AAATT
1 AAATT
27238429 ATTTTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 12 0.60
19 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTTTAAAAATTATTTT
Found at i:27252807 original size:51 final size:51
Alignment explanation
Indices: 27252733--27252913 Score: 301
Period size: 51 Copynumber: 3.5 Consensus size: 51
27252723 AAACGAAAGG
*
27252733 GGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATTAAA
* * *
27252784 GGTCCGATGACTAAGTGTTATCGTGAGTAAATGAATCCTTTACGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATTAAA
27252835 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATG-ATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCC-TGTATGGATTAAA
*
27252886 GGTCCGATGACTTAGTGTCATCGTGAGT
1 GGTCCGATGACTAAGTGTCATCGTGAGT
27252914 GTATGAATTC
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 120 0.99
52 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATTAAA
Found at i:27253713 original size:21 final size:22
Alignment explanation
Indices: 27253688--27253739 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
27253678 TGAAATGTAC
**
27253688 CGGTAGAAATTA-TACTTGTAT
1 CGGTAGAAATTAGTACAGGTAT
* *
27253709 TGGTA-AAACTAGTACAGGTAT
1 CGGTAGAAATTAGTACAGGTAT
27253730 CGGTAGAAAT
1 CGGTAGAAAT
27253740 CTGCACTGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
20 5 0.22
21 15 0.65
22 3 0.13
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (22 bp):
CGGTAGAAATTAGTACAGGTAT
Found at i:27255692 original size:67 final size:67
Alignment explanation
Indices: 27255579--27255711 Score: 185
Period size: 67 Copynumber: 2.0 Consensus size: 67
27255569 TTTTCGACAG
* * * * *
27255579 AATAACAATCTATCTTAGTTGTGTAATTAGCTCTATCGGTGTCATCTATTTATAAGAAGAAAAGG
1 AATAACAATCTATCTTAGTTATGTAAATAGCTCTACCGGTGCCATCTATATATAAGAAGAAAAGG
27255644 TC
66 TC
* * * *
27255646 AATAACAATCTCTTTTAGTTATGTAAATAGCTCTACCGGTGCCATCTATATATAGGAAGAGAAGG
1 AATAACAATCTATCTTAGTTATGTAAATAGCTCTACCGGTGCCATCTATATATAAGAAGAAAAGG
27255711 T
66 T
27255712 AGAACTCTTG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (67 bp):
AATAACAATCTATCTTAGTTATGTAAATAGCTCTACCGGTGCCATCTATATATAAGAAGAAAAGG
TC
Found at i:27257219 original size:30 final size:34
Alignment explanation
Indices: 27257170--27257257 Score: 131
Period size: 34 Copynumber: 2.6 Consensus size: 34
27257160 TTACAGTGTT
* *
27257170 ATCTAGTGTGTTGGTTGGTTTGGCTCATACGAGC
1 ATCTGGTGTGTTGGTTGGTTTGGCTCATACAAGC
* *
27257204 ATTTGGTGTGTTGGTTGGTTTGGCTTATACAAGC
1 ATCTGGTGTGTTGGTTGGTTTGGCTCATACAAGC
*
27257238 ATCTGGTGTGTTGGATGGTT
1 ATCTGGTGTGTTGGTTGGTT
27257258 AACTGTGTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.14, C:0.10, G:0.34, T:0.42
Consensus pattern (34 bp):
ATCTGGTGTGTTGGTTGGTTTGGCTCATACAAGC
Found at i:27270086 original size:31 final size:30
Alignment explanation
Indices: 27270050--27270150 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
27270040 AAAAGCTTAG
27270050 GTACCAAATTAGGAAAAAATGGCAAGTTTAA
1 GTACCAAATTAGGAAAAAAT-GCAAGTTTAA
* *
27270081 GTACCAAATT-GGTTAAAAA---AAGTTTAG
1 GTACCAAATTAGG-AAAAAATGCAAGTTTAA
* * * *
27270108 GTATCAAATTAAGAAAAAGTGTCAAGTTCAA
1 GTACCAAATTAGGAAAAAATG-CAAGTTTAA
27270139 GTACCAAATTAG
1 GTACCAAATTAG
27270151 ATAATAAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
27 20 0.37
28 1 0.02
30 2 0.04
31 31 0.57
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.26
Consensus pattern (30 bp):
GTACCAAATTAGGAAAAAATGCAAGTTTAA
Found at i:27270117 original size:58 final size:57
Alignment explanation
Indices: 27270035--27270196 Score: 200
Period size: 58 Copynumber: 2.8 Consensus size: 57
27270025 AAATTGAATC
* * *
27270035 TTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGGCAAGTTTAAGTACCAAATTGG
1 TTAAAAAAAGATTAGGTACCAAATTA-GAAAAAATGTCAAGTTTAAGTACCAAATTAG
* * * *
27270093 TTAAAAAAAGTTTAGGTATCAAATTAAGAAAAAGTGTCAAGTTCAAGTACCAAATTAG
1 TTAAAAAAAGATTAGGTACCAAATT-AGAAAAAATGTCAAGTTTAAGTACCAAATTAG
* *
27270151 ATAATAAAAA-ATTAGGTACCAAATCAGAAAAAAGTGTCAAGTTTAA
1 TTAA-AAAAAGATTAGGTACCAAATTAGAAAAAA-TGTCAAGTTTAA
27270197 ATATTAAAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
57 7 0.08
58 76 0.85
59 6 0.07
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (57 bp):
TTAAAAAAAGATTAGGTACCAAATTAGAAAAAATGTCAAGTTTAAGTACCAAATTAG
Found at i:27270125 original size:27 final size:27
Alignment explanation
Indices: 27270037--27270125 Score: 81
Period size: 27 Copynumber: 3.1 Consensus size: 27
27270027 ATTGAATCTT
*
27270037 AAAAAAAGCTTAGGTACCAAATTAGGA
1 AAAAAAAGTTTAGGTACCAAATTAGGA
* *
27270064 AAAAATGGCAAGTTTAAGTACCAAATT-GGTT
1 AAAAA----AAGTTTAGGTACCAAATTAGG-A
* *
27270095 AAAAAAAGTTTAGGTATCAAATTAAGA
1 AAAAAAAGTTTAGGTACCAAATTAGGA
27270122 AAAA
1 AAAA
27270126 GTGTCAAGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
27 25 0.51
28 1 0.02
30 2 0.04
31 21 0.43
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.24
Consensus pattern (27 bp):
AAAAAAAGTTTAGGTACCAAATTAGGA
Found at i:27270252 original size:30 final size:29
Alignment explanation
Indices: 27270192--27270255 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
27270182 AAGTGTCAAG
*
27270192 TTTAAATATTAAAATTAAAAATTGTATAT
1 TTTAAATACTAAAATTAAAAATTGTATAT
* *
27270221 TTTACAATACTAAAATT-ACAATTTTATTAT
1 TTTA-AATACTAAAATTAAAAATTGTA-TAT
27270251 TTTAA
1 TTTAA
27270256 TAGTCTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTAAATACTAAAATTAAAAATTGTATAT
Found at i:27276437 original size:16 final size:17
Alignment explanation
Indices: 27276416--27276448 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
27276406 CCAATTATAA
27276416 TAAAAATAAA-AACAAT
1 TAAAAATAAATAACAAT
27276432 TAAAAATAAATAACAAT
1 TAAAAATAAATAACAAT
27276449 ACTCCATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAATAAATAACAAT
Found at i:27281617 original size:13 final size:12
Alignment explanation
Indices: 27281582--27281617 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
27281572 TACAAAAAGA
*
27281582 TAAACATAAATT
1 TAAATATAAATT
27281594 TAAATATAAATT
1 TAAATATAAATT
27281606 TAAATAATAAAT
1 TAAAT-ATAAAT
27281618 AATATCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAATATAAATT
Found at i:27281618 original size:19 final size:19
Alignment explanation
Indices: 27281594--27281636 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
27281584 AACATAAATT
27281594 TAAATATAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
27281613 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
27281632 TAAAT
1 TAAAT
27281637 CTTAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:27282479 original size:102 final size:101
Alignment explanation
Indices: 27282307--27282496 Score: 240
Period size: 102 Copynumber: 1.9 Consensus size: 101
27282297 ATACATTGGA
* * * **
27282307 CCTTTTGATGCGAAATGAAATGACAACCAAACACTCCATCTCGATTACTCAGCCCAACATGCTCT
1 CCTTTTGACGCGAAATGAAATGACAACCAAACACTCCACCCCGATTACTCAGCCCAACACACTCT
* * *
27282372 CAATTTTTTTTCTTTTTTTTTTTTAAAATGTGTTAGC
66 CAA-TTTATTTATTTATTTTTTTTAAAATGTGTTAGC
* * *
27282409 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCC-AGTTACTCAGTCTAACACACTC
1 CCTTTTGACGCGAAATGAAATGACAACCAAACACTCCACCCCGA-TTACTCAGCCCAACACACTC
27282473 -CGAATTTATTTATTTATTTTTTTT
65 TC-AATTTATTTATTTATTTTTTTT
27282497 CTTCCGGTTA
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
101 19 0.25
102 56 0.75
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (101 bp):
CCTTTTGACGCGAAATGAAATGACAACCAAACACTCCACCCCGATTACTCAGCCCAACACACTCT
CAATTTATTTATTTATTTTTTTTAAAATGTGTTAGC
Found at i:27290318 original size:14 final size:14
Alignment explanation
Indices: 27290299--27290333 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
27290289 AAAAAAGAGA
27290299 AGAAAGCTAGAAAT
1 AGAAAGCTAGAAAT
27290313 AGAAAGCTAGAAAT
1 AGAAAGCTAGAAAT
27290327 AGAAAGC
1 AGAAAGC
27290334 ATTAAGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.57, C:0.09, G:0.23, T:0.11
Consensus pattern (14 bp):
AGAAAGCTAGAAAT
Found at i:27296046 original size:16 final size:14
Alignment explanation
Indices: 27296026--27296060 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
27296016 AGAAAATGAG
27296026 AAGAAAATAAAAGAA
1 AAGAAAA-AAAAGAA
27296041 AGAGAAAAAAAAGAA
1 A-AGAAAAAAAAGAA
27296056 AAGAA
1 AAGAA
27296061 TGAATAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 9 0.47
16 6 0.32
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:27305998 original size:177 final size:178
Alignment explanation
Indices: 27305663--27306005 Score: 395
Period size: 177 Copynumber: 1.9 Consensus size: 178
27305653 ATGAGTAAAG
* * ** * *
27305663 AATCCAAGAATGGATTACAAGCCCTACGATGGCTAAGATTTATGCGTAAGTGCATATTCTCGATA
1 AATCCAAGAATGGATTACAAGCCCTACGATGGCTAAGACTTATGCATAAGTGCATACACCCGAAA
* * * * * *
27305728 GCTTGTGTGCGCAGCATCGTTAGGGAACAATTATATGCACATATACCGTATCGATGGTTGAGGTA
66 GCTCGTGTGAG-AGCATCGTTAGAGAACAATTATATGCACAGACACCGTACCGATGGTTGAGGTA
* * * * *
27305793 CCGCATATGTTGCAAGTTCTCGACAGCTCGTGTGAGTAGCATGCTGAGT
130 CCACAGATGTTGCAAGTCCTCAACAGCTCGTATGAGTAGCATGCTGAGT
* * * * *
27305842 AATCCTAGAATGGATTACAGGCTCTGCGATGGCTGAGACTTATGCATAAGTGCATACACCCGAAA
1 AATCCAAGAATGGATTACAAGCCCTACGATGGCTAAGACTTATGCATAAGTGCATACACCCGAAA
* *
27305907 GCTCGTGTGAG-GCATCGTTA-AGAGACAGTTATATAG-ACAGACATCGTACCGATGGTTGAGGT
66 GCTCGTGTGAGAGCATCGTTAGAGA-ACAATTATAT-GCACAGACACCGTACCGATGGTTGAGGT
* **
27305969 ACCATAGATGTTGTGAGTCCTCAACAGCTCGTATGAG
129 ACCACAGATGTTGCAAGTCCTCAACAGCTCGTATGAG
27306006 CAATATCGGG
Statistics
Matches: 135, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
176 2 0.01
177 69 0.51
178 1 0.01
179 63 0.47
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (178 bp):
AATCCAAGAATGGATTACAAGCCCTACGATGGCTAAGACTTATGCATAAGTGCATACACCCGAAA
GCTCGTGTGAGAGCATCGTTAGAGAACAATTATATGCACAGACACCGTACCGATGGTTGAGGTAC
CACAGATGTTGCAAGTCCTCAACAGCTCGTATGAGTAGCATGCTGAGT
Found at i:27306974 original size:21 final size:20
Alignment explanation
Indices: 27306921--27306975 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
27306911 TGTAGCTTAG
*
27306921 ATGATATTGTGATAT-TATGT
1 ATGATA-TGTGATATGGATGT
27306941 -TGATATG-GAATATGGATGT
1 ATGATATGTG-ATATGGATGT
27306960 CATGATATGTGATATG
1 -ATGATATGTGATATG
27306976 AATATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
17 1 0.03
18 6 0.21
19 9 0.31
21 12 0.41
22 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.25, T:0.42
Consensus pattern (20 bp):
ATGATATGTGATATGGATGT
Found at i:27308156 original size:25 final size:25
Alignment explanation
Indices: 27308103--27308148 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
27308093 GTTGGATCCA
27308103 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
27308128 AATTAAA-TCT-AAAAGATAATT
1 AATTAAATTCTAAAAAGATAATT
27308149 CCCTAATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 11 0.52
24 3 0.14
25 7 0.33
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:27309183 original size:20 final size:20
Alignment explanation
Indices: 27309160--27309199 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
27309150 TTTCTTCTAT
27309160 TTTTTTCTCAATTTTTTTGA
1 TTTTTTCTCAATTTTTTTGA
* **
27309180 TTTTTTTTCGTTTTTTTTGA
1 TTTTTTCTCAATTTTTTTGA
27309200 CTCTTTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.75
Consensus pattern (20 bp):
TTTTTTCTCAATTTTTTTGA
Found at i:27312211 original size:22 final size:20
Alignment explanation
Indices: 27312173--27312219 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
27312163 AAAATAGAAT
*
27312173 AAAAAAATTAAATTAAAAAC
1 AAAAAAATTAAAATAAAAAC
*
27312193 AAAAAAATATGAAAATAAAAAT
1 AAAAAAAT-T-AAAATAAAAAC
27312215 AAAAA
1 AAAAA
27312220 TGGCTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 1 0.04
22 14 0.61
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAAAAATTAAAATAAAAAC
Found at i:27313153 original size:19 final size:18
Alignment explanation
Indices: 27313108--27313153 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
27313098 GATAACAACT
*
27313108 AAAATAAATAGTCATATG
1 AAAATAAATAGTCATATC
27313126 AATAA-AAATAGTGCATATC
1 AA-AATAAATAGT-CATATC
27313145 AAAATAAAT
1 AAAATAAAT
27313154 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.26
Consensus pattern (18 bp):
AAAATAAATAGTCATATC
Found at i:27313176 original size:17 final size:16
Alignment explanation
Indices: 27313145--27313179 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
27313135 AGTGCATATC
*
27313145 AAAATAAATTAAAAAT
1 AAAATAAAATAAAAAT
27313161 AAAATGAAAATAAAAAT
1 AAAAT-AAAATAAAAAT
27313178 AA
1 AA
27313180 TTGTACTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:27313235 original size:12 final size:11
Alignment explanation
Indices: 27313207--27313234 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
27313197 AATTTGTCTA
27313207 TTTTTTCAACT
1 TTTTTTCAACT
27313218 TTTTTTCAACT
1 TTTTTTCAACT
27313229 TTTTTT
1 TTTTTT
27313235 TAAAATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTTCAACT
Found at i:27315219 original size:19 final size:19
Alignment explanation
Indices: 27315192--27315246 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
27315182 AAAGAACCTA
27315192 TAAAATAAAATAAAAAATT
1 TAAAATAAAATAAAAAATT
* *
27315211 TAAATTAAAACAAAAAATT
1 TAAAATAAAATAAAAAATT
27315230 TGAAAATAAAATAAAAA
1 T-AAAATAAAATAAAAA
27315247 TGGCTAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
TAAAATAAAATAAAAAATT
Found at i:27316375 original size:13 final size:13
Alignment explanation
Indices: 27316359--27316392 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27316349 ACAATAAAAT
27316359 AATAATAATCCTA
1 AATAATAATCCTA
*
27316372 AATATTAATCCTA
1 AATAATAATCCTA
*
27316385 AAAAATAA
1 AATAATAA
27316393 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:27318068 original size:18 final size:18
Alignment explanation
Indices: 27318045--27318092 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
27318035 ACAATTGATA
27318045 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * *
27318063 TCACTTTCACTTTCACTT
1 TCACTTTCAATTCCAATT
*
27318081 TCACTCTCAATT
1 TCACTTTCAATT
27318093 TTAATCACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:27318070 original size:6 final size:6
Alignment explanation
Indices: 27318045--27318085 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
27318035 ACAATTGATA
* * *
27318045 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACT
27318086 CTCAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:27320723 original size:17 final size:17
Alignment explanation
Indices: 27320701--27320736 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
27320691 TTCTTGTAAT
27320701 ATTGCCTAGATTAACTA
1 ATTGCCTAGATTAACTA
27320718 ATTGCCTAGATTAACTA
1 ATTGCCTAGATTAACTA
27320735 AT
1 AT
27320737 GTATCTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (17 bp):
ATTGCCTAGATTAACTA
Found at i:27323399 original size:195 final size:195
Alignment explanation
Indices: 27323055--27323502 Score: 541
Period size: 195 Copynumber: 2.3 Consensus size: 195
27323045 TGAAACAACA
* * * *
27323055 CGATGGTTGAGGTACCGCATATGTTGCGA-TTCCTCGACAGCTTGTGTGAGCAACATTGTGAGTT
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTT-CTCGACAGCTCGTGTGAGCAACATCGTGAGTC
* * * * *
27323119 GGGAAATGAGTAAAGAATCCTAGAATGGATTACAGGCCCTACGATGGCTGAGATTTATGCATAAG
65 AGAAAAAGAGTAAAGAATCCTAAAATGGATTACAGGCCCTACGATGGCTGAGACTTATGCATAAG
* ** * * * *
27323184 TGTATATTCTTGATAGCTCGTGTAAGCAGCATCGTTAGG-GAACAGTTGTAT-GCACAGATA-CA
130 TGCATAAACTCGACAGCTCGTGTAAGCAGCATCGTTAGGAG-ACAGTTATATAG-ACAGACATC-
27323246 GTAT
192 GTAT
*
27323250 CGATGGCTGAGGTACCGCATATGTTGCGAGTTCTCGACAGCTCATGTGAGCAACATCGTGAGTCA
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTTCTCGACAGCTCGTGTGAGCAACATCGTGAGTCA
* * *
27323315 GAAAAAGAG-ATATGAATCCTAAAATGGATTACAGGCCCTACGATGGTTGGGACTTATGCATAAG
66 GAAAAAGAGTA-AAGAATCCTAAAATGGATTACAGGCCCTACGATGGCTGAGACTTATGCATAAG
* * *
27323379 TGCATACAAC-CGACAGCTCGTGTGAGTAGCATCGTTAGGAGACAGTTATATAGACGGACATCGT
130 TGCATA-AACTCGACAGCTCGTGTAAGCAGCATCGTTAGGAGACAGTTATATAGACAGACATCGT
27323443 AT
194 AT
* * * *
27323445 CGATGGCT-AGGGTACCGTATATGTTGCGAGTCCTTGATAGCTCGTGTGAGCAACATCG
1 CGATGGCTGA-GGTACCGCATATGTTGCGAGTTCTCGACAGCTCGTGTGAGCAACATCG
27323503 GGTACAGGTA
Statistics
Matches: 218, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
194 2 0.01
195 210 0.96
196 6 0.03
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (195 bp):
CGATGGCTGAGGTACCGCATATGTTGCGAGTTCTCGACAGCTCGTGTGAGCAACATCGTGAGTCA
GAAAAAGAGTAAAGAATCCTAAAATGGATTACAGGCCCTACGATGGCTGAGACTTATGCATAAGT
GCATAAACTCGACAGCTCGTGTAAGCAGCATCGTTAGGAGACAGTTATATAGACAGACATCGTAT
Found at i:27327895 original size:18 final size:17
Alignment explanation
Indices: 27327848--27327896 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
27327838 ATTTACAGGT
27327848 ATAAATAATAAGAAAACA
1 ATAAATAATAA-AAAACA
* *
27327866 ATATATACATAAAACACA
1 ATAAATA-ATAAAAAACA
27327884 ATAAGATAATAAA
1 ATAA-ATAATAAA
27327897 TTGAGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.20
Consensus pattern (17 bp):
ATAAATAATAAAAAACA
Found at i:27327960 original size:3 final size:3
Alignment explanation
Indices: 27327952--27327986 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
27327942 AAAGGAATTA
27327952 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27327987 AACATGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27328107 original size:30 final size:30
Alignment explanation
Indices: 27328062--27328217 Score: 142
Period size: 30 Copynumber: 5.3 Consensus size: 30
27328052 CATTAAAACC
* * *
27328062 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
1 GGGTTAAATTGGAATTTTTAGAAAGTTTAA
*
27328092 GGGTTAAATTGGAATTTTTAGAAA-ATTAA
1 GGGTTAAATTGGAATTTTTAGAAAGTTTAA
* *
27328121 GGG-TCAATTGGAATTTTTAGAAGGTTT--
1 GGGTTAAATTGGAATTTTTAGAAAGTTTAA
** *
27328148 GGGTGTCAAATTCAAATTTTTGGAAA-TTTCAA
1 GGGT-T-AAATTGGAATTTTTAGAAAGTTT-AA
* * *
27328180 GGGTTAAATTTGAATTTTTAGAAAGGTTAG
1 GGGTTAAATTGGAATTTTTAGAAAGTTTAA
27328210 GGGTTAAA
1 GGGTTAAA
27328218 GCATAATTTC
Statistics
Matches: 101, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
27 3 0.03
28 18 0.18
29 13 0.13
30 60 0.59
31 3 0.03
32 4 0.04
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGTTAAATTGGAATTTTTAGAAAGTTTAA
Found at i:27328159 original size:58 final size:58
Alignment explanation
Indices: 27328062--27328217 Score: 156
Period size: 58 Copynumber: 2.6 Consensus size: 58
27328052 CATTAAAACC
* * **
27328062 GGGTCAAATTTGAATTTTTGGAAAGTTTAAGGGTTAAATTGGAATTTTTAGAAAATT-AA
1 GGGTC-AATTTGAATTTTTAGAAGGTTT-AGGGTTAAATTCAAATTTTTAGAAAATTCAA
* * *
27328121 GGGTCAATTGGAATTTTTAGAAGGTTT-GGGTGTCAAATTCAAATTTTTGGAAATTTCAA
1 GGGTCAATTTGAATTTTTAGAAGGTTTAGGGT-T-AAATTCAAATTTTTAGAAAATTCAA
*
27328180 GGGTTAAATTTGAATTTTTAGAAAGG-TTAGGGGTTAAA
1 GGG-TCAATTTGAATTTTTAG-AAGGTTTA-GGGTTAAA
27328218 GCATAATTTC
Statistics
Matches: 81, Mismatches: 9, Indels: 13
0.79 0.09 0.13
Matches are distributed among these distances:
56 4 0.05
57 1 0.01
58 37 0.46
59 10 0.12
60 20 0.25
61 5 0.06
62 4 0.05
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (58 bp):
GGGTCAATTTGAATTTTTAGAAGGTTTAGGGTTAAATTCAAATTTTTAGAAAATTCAA
Found at i:27330166 original size:50 final size:50
Alignment explanation
Indices: 27330091--27330216 Score: 180
Period size: 50 Copynumber: 2.5 Consensus size: 50
27330081 CAGGAGTATA
* * *
27330091 AGATTCACCCTTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
1 AGATTCGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
* *
27330141 AGATTCGCCATTGCGGCTTCAATCTGCCCTTCTACAGCTTTAGGTGTATG
1 AGATTCGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
* * *
27330191 ATATTTGCCATTACGGCTTCAATCTG
1 AGATTCGCCATTGCGGCTTCAATCTG
27330217 TTCCTCCTCT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (50 bp):
AGATTCGCCATTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
Found at i:27341765 original size:37 final size:36
Alignment explanation
Indices: 27341695--27341767 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
27341685 CATGTTATGC
*
27341695 AAAAAATATATACATAATTACACAGGTAAATAATAAT
1 AAAAAATATATACATAAATACACA-GTAAATAATAAT
27341732 AAAAAATATTATACATGAAATACA-A-TAAGATAATAA
1 AAAAAATA-TATACAT-AAATACACAGTAA-ATAATAA
27341768 ATGAGTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 3 0.09
37 15 0.47
38 8 0.25
39 6 0.19
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (36 bp):
AAAAAATATATACATAAATACACAGTAAATAATAAT
Found at i:27350622 original size:21 final size:21
Alignment explanation
Indices: 27350598--27350639 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27350588 ATATTTTTTT
*
27350598 AAATATT-ATTTAAAATTATTA
1 AAATATTAATATAAAA-TATTA
27350619 AAATATTAATATAAAATATTA
1 AAATATTAATATAAAATATTA
27350640 TATTTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATATTAATATAAAATATTA
Found at i:27350724 original size:30 final size:31
Alignment explanation
Indices: 27350690--27350755 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
27350680 TTTAATCATA
27350690 AATAAATTA-TTAATA-TAAAATTATTATTTT
1 AATAAATTATTTAATATTAAAATT-TTATTTT
**
27350720 AATAAATTATTTAATATTTCAATTTTATTTT
1 AATAAATTATTTAATATTAAAATTTTATTTT
27350751 AATAA
1 AATAA
27350756 TAAATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 9 0.28
31 18 0.56
32 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
AATAAATTATTTAATATTAAAATTTTATTTT
Found at i:27350776 original size:14 final size:15
Alignment explanation
Indices: 27350751--27350785 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
27350741 ATTTTATTTT
27350751 AATAATAAATTTTAA
1 AATAATAAATTTTAA
27350766 AATAA-AAATTTT-A
1 AATAATAAATTTTAA
27350779 AATAATA
1 AATAATA
27350786 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.32
14 8 0.42
15 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAATAAATTTTAA
Found at i:27359673 original size:31 final size:33
Alignment explanation
Indices: 27359603--27359681 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
27359593 CCAAAACGGA
* *
27359603 CATTTATTTGAAGAAGGAAATTAGGCAACAAAG
1 CATTAATTTCAAGAAGGAAATTAGGCAACAAAG
*
27359636 CATTAATTTCAAGAAGGAAATTAGGC-A-AAGG
1 CATTAATTTCAAGAAGGAAATTAGGCAACAAAG
*
27359667 CATTAATATCAAGAA
1 CATTAATTTCAAGAA
27359682 AGATATTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 17 0.40
32 1 0.02
33 24 0.57
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (33 bp):
CATTAATTTCAAGAAGGAAATTAGGCAACAAAG
Found at i:27363283 original size:15 final size:16
Alignment explanation
Indices: 27363248--27363290 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
27363238 CAAATCTATG
27363248 ATTTTCTACTA-ATGGT
1 ATTTTCTA-TAGATGGT
27363264 A-TTTCTATAGA-GGT
1 ATTTTCTATAGATGGT
27363278 ATTTTCTATAGAT
1 ATTTTCTATAGAT
27363291 AGCATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.25
15 17 0.71
16 1 0.04
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (16 bp):
ATTTTCTATAGATGGT
Found at i:27369269 original size:17 final size:17
Alignment explanation
Indices: 27369247--27369279 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27369237 ACACACACGC
*
27369247 ACAAAGAGAGAAAAAAT
1 ACAAAGAAAGAAAAAAT
27369264 ACAAAGAAAGAAAAAA
1 ACAAAGAAAGAAAAAA
27369280 GAGAAGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (17 bp):
ACAAAGAAAGAAAAAAT
Found at i:27369979 original size:12 final size:11
Alignment explanation
Indices: 27369920--27370047 Score: 62
Period size: 11 Copynumber: 11.6 Consensus size: 11
27369910 AAATGTCTCG
27369920 AATAATA-TAA
1 AATAATATTAA
*
27369930 AATAATA-TATT
1 AATAATATTA-A
27369941 AAT-ATATT-A
1 AATAATATTAA
*
27369950 AA-AAT-TAAA
1 AATAATATTAA
27369959 ATATAATATTAA
1 A-ATAATATTAA
27369971 AAGTAATA-TAA
1 AA-TAATATTAA
27369982 AATATTATATT--
1 AATA--ATATTAA
27369993 AATAATATTAA
1 AATAATATTAA
27370004 AAGTAATAATATAA
1 AA-TAAT-AT-TAA
27370018 AATATTATATT--
1 AATA--ATATTAA
27370029 AATAATATTAA
1 AATAATATTAA
27370040 AAGTAATA
1 AA-TAATA
27370048 AATAAGTATT
Statistics
Matches: 93, Mismatches: 4, Indels: 40
0.68 0.03 0.29
Matches are distributed among these distances:
8 1 0.01
9 16 0.17
10 15 0.16
11 25 0.27
12 21 0.23
13 6 0.06
14 7 0.08
15 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
AATAATATTAA
Found at i:27369984 original size:24 final size:23
Alignment explanation
Indices: 27369921--27370047 Score: 85
Period size: 24 Copynumber: 5.7 Consensus size: 23
27369911 AATGTCTCGA
**
27369921 ATAATA-TAAAATAATATATTA-
1 ATAATATTAAAATAATATAAAAT
27369942 AT-ATATT-AAA-AAT-TAAAAT
1 ATAATATTAAAATAATATAAAAT
27369961 ATAATATTAAAAGTAATATAAAAT
1 ATAATATTAAAA-TAATATAAAAT
*
27369985 ATTATATT--AATAATATTAAAAGT
1 ATAATATTAAAATAATA-TAAAA-T
* **
27370008 AATAATA-TAAAATATTATATTA-
1 -ATAATATTAAAATAATATAAAAT
27370030 ATAATATTAAAAGTAATA
1 ATAATATTAAAA-TAATA
27370048 AATAAGTATT
Statistics
Matches: 84, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
18 3 0.04
19 5 0.06
20 11 0.13
21 17 0.20
22 12 0.14
23 9 0.11
24 21 0.25
25 6 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
ATAATATTAAAATAATATAAAAT
Found at i:27369985 original size:19 final size:18
Alignment explanation
Indices: 27369923--27370024 Score: 59
Period size: 19 Copynumber: 5.4 Consensus size: 18
27369913 TGTCTCGAAT
27369923 AATA-TAAAATAATATATTA
1 AATATTAAAATAATATA--A
* *
27369942 ATATATTAAAAATTAAAATAT
1 A-ATATT-AAAA-TAATATAA
27369963 AATATTAAAAGTAATATAA
1 AATATTAAAA-TAATATAA
*
27369982 AATATTATATTAATAATATTA
1 AATATTA-A--AATAATATAA
*
27370003 AA-AGT--AATAATATAA
1 AATATTAAAATAATATAA
27370018 AATATTA
1 AATATTA
27370025 TATTAATAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
15 11 0.17
16 2 0.03
19 18 0.28
20 11 0.17
21 11 0.17
22 6 0.09
23 6 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATATTAAAATAATATAA
Found at i:27370021 original size:36 final size:36
Alignment explanation
Indices: 27369961--27370052 Score: 156
Period size: 36 Copynumber: 2.7 Consensus size: 36
27369951 AAATTAAAAT
27369961 ATAATATTAAAAG---TAATATAAAATATTATATTA
1 ATAATATTAAAAGTAATAATATAAAATATTATATTA
27369994 ATAATATTAAAAGTAATAATATAAAATATTATATTA
1 ATAATATTAAAAGTAATAATATAAAATATTATATTA
27370030 ATAATATTAAAAGTAATAA-ATAA
1 ATAATATTAAAAGTAATAATATAA
27370053 GTATTTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
33 13 0.23
35 4 0.07
36 39 0.70
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (36 bp):
ATAATATTAAAAGTAATAATATAAAATATTATATTA
Found at i:27371530 original size:18 final size:18
Alignment explanation
Indices: 27371474--27371539 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
27371464 TCAGCTGGCT
* * *
27371474 GAGCCTGAGCCCAAGCTT
1 GAGCCTGAGCCCGATCTA
* * * *
27371492 GAGCCAGAGCACGGTCCA
1 GAGCCTGAGCCCGATCTA
27371510 GAGCCTGAGCCCGATCTA
1 GAGCCTGAGCCCGATCTA
*
27371528 GAGCCCGAGCCC
1 GAGCCTGAGCCC
27371540 AAGCCTAACC
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.23, C:0.36, G:0.30, T:0.11
Consensus pattern (18 bp):
GAGCCTGAGCCCGATCTA
Found at i:27371973 original size:6 final size:6
Alignment explanation
Indices: 27371964--27371993 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
27371954 TGGAATTAAA
*
27371964 TATGTT TATGTT TATGCT TATGTT TATGTT
1 TATGTT TATGTT TATGTT TATGTT TATGTT
27371994 CGTATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (6 bp):
TATGTT
Found at i:27372201 original size:71 final size:72
Alignment explanation
Indices: 27372066--27372202 Score: 206
Period size: 71 Copynumber: 1.9 Consensus size: 72
27372056 ATTTTGTATT
* *
27372066 TAAAACCATAAACTTAAAGCCTTAAACCTTAAAATCAAAACCCTAACCCTAAACCCTAAAAATCT
1 TAAAACCATAAACTTAAAGCCTTAAACCCTAAAATCAAAACCCTAACCCTAAACACTAAAAATCT
27372131 TAAGCAC
66 TAAGCAC
* * *
27372138 TAAAATCAT-AACTTTAAA-CCTTAAACCCTAAAATCAAAACCCTAACCCTAAATACTAATAATC
1 TAAAACCATAAAC-TTAAAGCCTTAAACCCTAAAATCAAAACCCTAACCCTAAACACTAAAAATC
27372201 TT
65 TT
27372203 TAATACCAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
71 46 0.78
72 13 0.22
ACGTcount: A:0.48, C:0.26, G:0.01, T:0.24
Consensus pattern (72 bp):
TAAAACCATAAACTTAAAGCCTTAAACCCTAAAATCAAAACCCTAACCCTAAACACTAAAAATCT
TAAGCAC
Found at i:27372294 original size:4 final size:4
Alignment explanation
Indices: 27372285--27372311 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
27372275 ATTATTGATA
27372285 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
27372312 ATGATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:27375604 original size:10 final size:9
Alignment explanation
Indices: 27375574--27375604 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
27375564 TTATAAAAAA
27375574 AATATTTTT
1 AATATTTTT
27375583 AATATTTTT
1 AATATTTTT
27375592 AATATTTTAT
1 AATATTTT-T
27375602 AAT
1 AAT
27375605 TGGAAAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
AATATTTTT
Found at i:27375751 original size:27 final size:27
Alignment explanation
Indices: 27375712--27375814 Score: 143
Period size: 27 Copynumber: 3.8 Consensus size: 27
27375702 GAGTTTGATA
*
27375712 CCGCCTGTCAGGTAGGCACCATTGGTG
1 CCGCCTATCAGGTAGGCACCATTGGTG
* * *
27375739 CCGCCTATTAGGTAAGCACCATTAGTG
1 CCGCCTATCAGGTAGGCACCATTGGTG
* * *
27375766 CCGTCTGTCAGGTAGGCACCTTTGGTG
1 CCGCCTATCAGGTAGGCACCATTGGTG
27375793 CCGCCTATCAGGTAGGCACCAT
1 CCGCCTATCAGGTAGGCACCAT
27375815 CCTGTTATAT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.24
Consensus pattern (27 bp):
CCGCCTATCAGGTAGGCACCATTGGTG
Found at i:27378381 original size:23 final size:23
Alignment explanation
Indices: 27378355--27378401 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
27378345 TAACTGTATT
*
27378355 TGTAAT-ATATTTGTATTTGTAAC
1 TGTAATCATA-TTCTATTTGTAAC
*
27378378 TGTATTCATATTCTATTTGTAAC
1 TGTAATCATATTCTATTTGTAAC
27378401 T
1 T
27378402 ATATTTAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.53
Consensus pattern (23 bp):
TGTAATCATATTCTATTTGTAAC
Found at i:27378394 original size:29 final size:29
Alignment explanation
Indices: 27378340--27378398 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
27378330 AGGAAACTGC
**
27378340 ATTTGTAACTGTATTTGTAATATATTTGT
1 ATTTGTAACTGTATTCATAATATATTTGT
* *
27378369 ATTTGTAACTGTATTCATATTCTATTTGT
1 ATTTGTAACTGTATTCATAATATATTTGT
27378398 A
1 A
27378399 ACTATATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (29 bp):
ATTTGTAACTGTATTCATAATATATTTGT
Found at i:27380595 original size:18 final size:17
Alignment explanation
Indices: 27380515--27380602 Score: 54
Period size: 17 Copynumber: 4.9 Consensus size: 17
27380505 TAATCTTTTT
*
27380515 ATAATTTTTAATATTT-T
1 ATAATTTTTAAT-TTTAA
* *
27380532 GTAATATTTAGATTTTAA
1 ATAATTTTTA-ATTTTAA
27380550 ATAATATTTTACAATTTT-A
1 ATAAT-TTTT--AATTTTAA
*
27380569 GTAAGTTTTGTAATTTTAA
1 ATAA-TTTT-TAATTTTAA
*
27380588 ATAATTTTTTATTTT
1 ATAATTTTTAATTTT
27380603 TTAAATATGT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
17 17 0.31
18 16 0.29
19 14 0.25
20 7 0.13
21 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (17 bp):
ATAATTTTTAATTTTAA
Found at i:27381163 original size:15 final size:16
Alignment explanation
Indices: 27381128--27381164 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
27381118 TCTAAATTAC
27381128 ATTAT-ATATAAAAAT
1 ATTATAATATAAAAAT
*
27381143 AATATAATAT-AAAAT
1 ATTATAATATAAAAAT
27381158 ATTATAA
1 ATTATAA
27381165 ACTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTATAATATAAAAAT
Found at i:27383901 original size:19 final size:20
Alignment explanation
Indices: 27383879--27383925 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
27383869 ACTTTAATTT
*
27383879 TAATTAAATTATTTA-AAAA
1 TAATTAAAATATTTATAAAA
27383898 TAATTAAAATATTTATAAAA
1 TAATTAAAATATTTATAAAA
*
27383918 TAAATAAA
1 TAATTAAA
27383926 CATGTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATTAAAATATTTATAAAA
Found at i:27384237 original size:16 final size:17
Alignment explanation
Indices: 27384210--27384243 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27384200 ATTAATATTT
*
27384210 AAAATAATAATTTGATA
1 AAAATAATAATTTAATA
27384227 AAAATAA-AATTTAATA
1 AAAATAATAATTTAATA
27384243 A
1 A
27384244 TTATAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AAAATAATAATTTAATA
Found at i:27412818 original size:17 final size:17
Alignment explanation
Indices: 27412792--27412824 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27412782 GATTTTAAAT
27412792 ATTTAATTTTAGTTTCA
1 ATTTAATTTTAGTTTCA
*
27412809 ATTTAGTTTTAGTTTC
1 ATTTAATTTTAGTTTC
27412825 TTTACATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (17 bp):
ATTTAATTTTAGTTTCA
Found at i:27413890 original size:42 final size:42
Alignment explanation
Indices: 27413824--27413907 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
27413814 AAGCTTTTCA
* * * * *
27413824 AAGTTGGAATCCTCGTTTTGATGATGTAATCGAAGAGTTTGG
1 AAGTTGGAATCCTCATTCTAATGATGCAATCAAAGAGTTTGG
* *
27413866 AAGTTGGAATCTTCATTCTAATGATGCAATCAAATAGTTTGG
1 AAGTTGGAATCCTCATTCTAATGATGCAATCAAAGAGTTTGG
27413908 TTATATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.36
Consensus pattern (42 bp):
AAGTTGGAATCCTCATTCTAATGATGCAATCAAAGAGTTTGG
Found at i:27415225 original size:45 final size:44
Alignment explanation
Indices: 27415145--27415230 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 44
27415135 ATACATATTT
*
27415145 AATTATTTATATTTAATAATATAATACATTATTAATATAATTTAA
1 AATTATTTATATTTAATAATATAAGACATTATTAATA-AATTTAA
*
27415190 AATTATTTAATATTTTATAATATAAGA-A-TATTTAATAAATT
1 AATTATTT-ATATTTAATAATATAAGACATTA-TTAATAAATT
27415231 ATTTAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
44 6 0.16
45 15 0.41
46 16 0.43
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (44 bp):
AATTATTTATATTTAATAATATAAGACATTATTAATAAATTTAA
Found at i:27415232 original size:25 final size:25
Alignment explanation
Indices: 27415180--27415232 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
27415170 ACATTATTAA
* **
27415180 TATAATTTAAAATTATTTAATATTT
1 TATAATATAAAATTATTTAATAAAT
27415205 TATAATATAAGAA-TATTTAATAAAT
1 TATAATATAA-AATTATTTAATAAAT
27415230 TAT
1 TAT
27415233 TTAAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TATAATATAAAATTATTTAATAAAT
Found at i:27415297 original size:13 final size:14
Alignment explanation
Indices: 27415281--27415322 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
27415271 TTTCAATTTT
27415281 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
27415294 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
27415309 ATTTTAAATAATAT
1 ATTTT-AATAATAT
27415323 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:27415307 original size:16 final size:16
Alignment explanation
Indices: 27415285--27415321 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
27415275 AATTTTATTT
27415285 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
27415302 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
27415317 TAATA
1 TAATA
27415322 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:27416184 original size:18 final size:19
Alignment explanation
Indices: 27416140--27416184 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
27416130 TAATCGAAAT
*
27416140 TTATTTTATACTAAGATAA
1 TTATTTTATAATAAGATAA
27416159 -TATTTTATAATAA-ATAA
1 TTATTTTATAATAAGATAA
*
27416176 TTATGTTAT
1 TTATTTTAT
27416185 TTAATGCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (19 bp):
TTATTTTATAATAAGATAA
Found at i:27416337 original size:3 final size:3
Alignment explanation
Indices: 27416329--27416358 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
27416319 TCGCTTCATT
27416329 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
27416359 TTCCACAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:27421367 original size:18 final size:18
Alignment explanation
Indices: 27421346--27421380 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27421336 TTGAAACAAC
*
27421346 AATTTTTTATTTAGTTGT
1 AATTTTTGATTTAGTTGT
*
27421364 AATTTTTGCTTTAGTTG
1 AATTTTTGATTTAGTTG
27421381 GAACAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (18 bp):
AATTTTTGATTTAGTTGT
Found at i:27425378 original size:27 final size:27
Alignment explanation
Indices: 27425343--27425412 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
27425333 AATTTTGATT
* *
27425343 TTTAATTAAGTTTGAA-TTGATTTTAAA
1 TTTAATTAAATTTAAATTTG-TTTTAAA
*
27425370 TTTATTTAAATTTAAATTTGTTTTAAA
1 TTTAATTAAATTTAAATTTGTTTTAAA
* *
27425397 TTTAAATACATTTAAA
1 TTTAATTAAATTTAAA
27425413 ATAGTTGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 33 0.92
28 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (27 bp):
TTTAATTAAATTTAAATTTGTTTTAAA
Found at i:27425385 original size:16 final size:17
Alignment explanation
Indices: 27425364--27425403 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
27425354 TTGAATTGAT
27425364 TTTAAATTT-ATTTAAA
1 TTTAAATTTGATTTAAA
*
27425380 TTTAAATTTGTTTTAAA
1 TTTAAATTTGATTTAAA
27425397 TTTAAAT
1 TTTAAAT
27425404 ACATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTGATTTAAA
Found at i:27425680 original size:26 final size:26
Alignment explanation
Indices: 27425651--27425701 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
27425641 GATCGCCACG
27425651 TCAGCAGCAACTTGCCACCACCATCT
1 TCAGCAGCAACTTGCCACCACCATCT
* * *
27425677 TCAGCATCAACTTGCCTCTACCATC
1 TCAGCAGCAACTTGCCACCACCATC
27425702 AGCTACCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.41, G:0.10, T:0.24
Consensus pattern (26 bp):
TCAGCAGCAACTTGCCACCACCATCT
Found at i:27426238 original size:19 final size:20
Alignment explanation
Indices: 27426210--27426259 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
27426200 GTATTAAAGA
27426210 TATT-ATTAATAATAATATT
1 TATTAATTAATAATAATATT
*
27426229 T-TTAATTAATAATAGTATT
1 TATTAATTAATAATAATATT
27426248 TATTAA-TAATAA
1 TATTAATTAATAA
27426260 AAAAAGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 22 0.79
20 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TATTAATTAATAATAATATT
Found at i:27426240 original size:16 final size:16
Alignment explanation
Indices: 27426209--27426258 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
27426199 AGTATTAAAG
*
27426209 ATATTATTAA-TAATA
1 ATATTTTTAATTAATA
27426224 ATATTTTTAATTAATA
1 ATATTTTTAATTAATA
*
27426240 ATAGTATTT-ATTAATA
1 ATA-TTTTTAATTAATA
27426256 ATA
1 ATA
27426259 AAAAAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
15 9 0.29
16 18 0.58
17 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATTTTTAATTAATA
Found at i:27427435 original size:28 final size:29
Alignment explanation
Indices: 27427403--27427553 Score: 114
Period size: 29 Copynumber: 5.2 Consensus size: 29
27427393 TCGAAACTTT
*
27427403 CAAAAATTACCATTTTACCCCCGAATGTC
1 CAAAAACTACCATTTTACCCCCGAATGTC
* **
27427432 AAAAAACT-CCATTTTTGA-CCCAAAACT-TC
1 CAAAAACTACCA-TTTT-ACCCCCGAA-TGTC
* *
27427461 CAAAAACTACCATTTTACCCCTGGATGTC
1 CAAAAACTACCATTTTACCCCCGAATGTC
***
27427490 CAAAAACT-CCATTTTTGACCCGAAACT-TC
1 CAAAAACTACCATTTTACCCCCG-AA-TGTC
* * *
27427519 CAAAAATTATCATTTTACCCCCGGATGTC
1 CAAAAACTACCATTTTACCCCCGAATGTC
27427548 CAAAAA
1 CAAAAA
27427554 TTCCGTTTTT
Statistics
Matches: 93, Mismatches: 19, Indels: 20
0.70 0.14 0.15
Matches are distributed among these distances:
28 16 0.17
29 61 0.66
30 16 0.17
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.27
Consensus pattern (29 bp):
CAAAAACTACCATTTTACCCCCGAATGTC
Found at i:27427472 original size:58 final size:58
Alignment explanation
Indices: 27427396--27427565 Score: 259
Period size: 58 Copynumber: 2.9 Consensus size: 58
27427386 TCTAACCTCG
* * *
27427396 AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCAAAAAACTCCATTTTTGACCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGGATGTCCAAAAACTCCATTTTTGACCCA
* * *
27427454 AAACTTCCAAAAACTACCATTTTACCCCTGGATGTCCAAAAACTCCATTTTTGACCCG
1 AAACTTCCAAAAATTACCATTTTACCCCCGGATGTCCAAAAACTCCATTTTTGACCCA
* * *
27427512 AAACTTCCAAAAATTATCATTTTACCCCCGGATGTCCAAAAATTCCGTTTTTGA
1 AAACTTCCAAAAATTACCATTTTACCCCCGGATGTCCAAAAACTCCATTTTTGA
27427566 TCTCGGTCTT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 101 1.00
ACGTcount: A:0.35, C:0.28, G:0.08, T:0.30
Consensus pattern (58 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGGATGTCCAAAAACTCCATTTTTGACCCA
Found at i:27427606 original size:59 final size:57
Alignment explanation
Indices: 27427336--27427611 Score: 241
Period size: 58 Copynumber: 4.7 Consensus size: 57
27427326 GAGGTCCCTA
* * * * * *
27427336 AACTGTCCAAAAATTA-TATTCTGACCCCCGAACT-TCTCCAAAATTCCATTTCTAACCTCG
1 AACT-TCCAAAAATTACCATT-TTACCCCCGAA-TGTC-CAAAAACTCCATTTTTGACC-CG
* * *
27427396 AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCAAAAAACTCCATTTTTGACCCAA
1 -AACTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCC-G
* * *
27427455 AACTTCCAAAAACTACCATTTTACCCCTGGATGTCCAAAAACTCCATTTTTGACCCG
1 AACTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCCG
* * * * *
27427512 AAACTTCCAAAAATTATCATTTTACCCCCGGATGTCCAAAAATTCCGTTTTTGATCTCG
1 -AACTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGA-CCCG
** * * * *
27427571 GTCTTTCTAAAAATTACCGTTTTACCCTCGAATGTCTAAAA
1 AAC-TTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAA
27427612 TGTCATTTTT
Statistics
Matches: 180, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
58 101 0.56
59 50 0.28
60 22 0.12
61 7 0.04
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (57 bp):
AACTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCCG
Found at i:27434193 original size:51 final size:49
Alignment explanation
Indices: 27434037--27434410 Score: 236
Period size: 49 Copynumber: 7.5 Consensus size: 49
27434027 GAAACACAAC
** * * *
27434037 GGGAAAGATCTAAGACCATAACGGCAGATCCAGTACCGCAA-AGATACA-AAA
1 GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTA-C-CAAGA-AGACATGAA
* * * * * * * *
27434088 GGGAAAGGTCTAAGTCACAACGGCAGA-CCGTGTACCTTAGAAGACACGAC
1 GGGAAAGATCTAAGCCGCAACGGCGGATCC-AGTACC-AAGAAGACATGAA
* *
27434138 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAAAAAGATA-GAA
1 GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACC--AAGAAGACATGAA
* * * **
27434189 GGGAAAGATCTAAGACAGCAATGGCAGATCCAGTACCGCGAAGACAT-AA
1 GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCAAGAAGACATGAA
* ** * * * *
27434238 GGGAAAGATCTAAGCCGTAATAGAGGATCTAGCACCACGAAGACATGAA
1 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAAGAAGACATGAA
* * *
27434287 GGGAAAGATCTAAGCCGCGACGGCGGATCTAGTACCACGAAGACATGAA
1 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAAGAAGACATGAA
* * * * * * **
27434336 GAGAAAGATCTAAGCCGCGACGGCGAATCTAGTATCACCGAAGATTTGAA
1 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCA-AGAAGACATGAA
* * * *
27434386 GGGAAAGGTTTAAGTCGCAATGGCG
1 GGGAAAGATCTAAGCCGCAACGGCG
27434411 AACTTGGTAC
Statistics
Matches: 264, Mismatches: 49, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
48 25 0.09
49 108 0.41
50 58 0.22
51 64 0.24
52 9 0.03
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (49 bp):
GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAAGAAGACATGAA
Found at i:27434232 original size:101 final size:98
Alignment explanation
Indices: 27434037--27434369 Score: 271
Period size: 101 Copynumber: 3.3 Consensus size: 98
27434027 GAAACACAAC
** * * * * *
27434037 GGGAAAGATCTAAGACCATAACGGCAGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAG
1 GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCG-AAAAAGACAGAAGGGAAAGATCTAAG
* *
27434102 TCA-CAACGGCAGA-CCGTGTACCTTA-GAAGACACGAC
64 -CAGCAACGGCAGATCC-AGTACC--ACGAAGACACGAA
*
27434138 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAAAAAGATAGAAGGGAAAGATCTAAG
1 GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCG-AAAAAGACAGAAGGGAAAGATCTAAG
* * *
27434203 ACAGCAATGGCAGATCCAGTACCGCGAAGACA-TAA
64 -CAGCAACGGCAGATCCAGTACCACGAAGACACGAA
* ** * * * **
27434238 GGGAAAGATCTAAGCCGTAATAGAGGATCTAGCACC-ACGAAGACATGAAGGGAAAGATCTAAGC
1 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGAAAAAGACA-GAAGGGAAAGATCTAAGC
* * * * *
27434302 CGCGACGGCGGATCTAGTACCACGAAGACATGAA
65 AGCAACGGCAGATCCAGTACCACGAAGACACGAA
* * * *
27434336 GAGAAAGATCTAAGCCGCGACGGCGAATCTAGTA
1 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTA
27434370 TCACCGAAGA
Statistics
Matches: 188, Mismatches: 39, Indels: 13
0.78 0.16 0.05
Matches are distributed among these distances:
97 31 0.16
98 45 0.24
99 16 0.09
100 15 0.08
101 65 0.35
102 14 0.07
103 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.27, T:0.13
Consensus pattern (98 bp):
GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGAAAAAGACAGAAGGGAAAGATCTAAGCA
GCAACGGCAGATCCAGTACCACGAAGACACGAA
Found at i:27434289 original size:49 final size:49
Alignment explanation
Indices: 27434127--27434408 Score: 237
Period size: 49 Copynumber: 5.7 Consensus size: 49
27434117 GTGTACCTTA
* * * * * *
27434127 GAAGACACGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAA
1 GAAGACATGAAGGGAAAGATCTAAG-CCGCAATGGAGGATCTAGTACC--AC
* * * * *
27434179 AAAGATA-GAAGGGAAAGATCTAAGACAGCAATGGCA-GATCCAGTACCGC
1 GAAGACATGAAGGGAAAGATCTAAG-CCGCAATGG-AGGATCTAGTACCAC
* * *
27434228 GAAGACAT-AAGGGAAAGATCTAAGCCGTAATAGAGGATCTAGCACCAC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAATGGAGGATCTAGTACCAC
* * *
27434276 GAAGACATGAAGGGAAAGATCTAAGCCGCGACGGCGGATCTAGTACCAC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAATGGAGGATCTAGTACCAC
* * * * * *
27434325 GAAGACATGAAGAGAAAGATCTAAGCCGCGACGGCGAATCTAGTATCACC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAATGGAGGATCTAGTACCA-C
** * * *
27434375 GAAGATTTGAAGGGAAAGGTTTAAGTCGCAATGG
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAATGG
27434409 CGAACTTGGT
Statistics
Matches: 192, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
47 1 0.01
48 24 0.12
49 100 0.52
50 27 0.14
51 35 0.18
52 5 0.03
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (49 bp):
GAAGACATGAAGGGAAAGATCTAAGCCGCAATGGAGGATCTAGTACCAC
Found at i:27435297 original size:206 final size:206
Alignment explanation
Indices: 27434939--27435649 Score: 1075
Period size: 206 Copynumber: 3.4 Consensus size: 206
27434929 GCAATAAAAT
* * *
27434939 AATTCGTCTTCCTGATGAGATACAGAGAA-ACAGATTGAAACAAACAACGCGGTCATCTTCCTTA
1 AATTCGTCTTCCTGATGAGATACAGAGAAGA-GGATTGAAACAAACGACGCGGTCATCTTCCTGA
*
27435003 TGAGATACAGAGAAAAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAGC
65 TGAGATACAGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAGC
* * *
27435068 TTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACCTTCCTAATGAGATACTG
130 TTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTG
*
27435133 AGAAGTGAACCA
195 AGAAGTGGACCA
27435145 AATTCGTCTTCCTGATGAGATACAGAGAAGAGGATTGAAACAAACGACGCGGTCATCTTCCTGAT
1 AATTCGTCTTCCTGATGAGATACAGAGAAGAGGATTGAAACAAACGACGCGGTCATCTTCCTGAT
* * ** *
27435210 GAGATACAGAGAAGAAGACCAAATCAAACTGACGCTGGATGCGAGCAAATCTTTGAACCCCAGCT
66 GAGATACAGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAGCT
* * *
27435275 TCCTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAAATGGTTAGCTTCTTGATGAGATACTGA
131 TCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGA
27435340 GAAGTGGACCA
196 GAAGTGGACCA
* * *
27435351 AATTCGTCTTCTTGATGAGATACAGAGAAGCA-GATTGAAACAAACGACGTGATCATCTTCCTGA
1 AATTCGTCTTCCTGATGAGATACAGAGAAG-AGGATTGAAACAAACGACGCGGTCATCTTCCTGA
*
27435415 TGAGATACAGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCCAGC
65 TGAGATACAGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAGC
** * * * *
27435480 TTCCTGATGAGATACTGAGAAATAGGTTGAAGCAATAAAACGGTTAGTTTCCTGATGAGATATTG
130 TTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTG
27435545 AGAAGTGGACCA
195 AGAAGTGGACCA
* * **
27435557 AATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAAACAAACGATACGGTCATCTTCCTGA
1 AATTCGTCTTCCTGATGAGATACAGAGAAGAGGATTG-AAACAAACGACGCGGTCATCTTCCTGA
* * * *
27435622 TGGGATACTGAGAAGAAGGCCAAGTCAA
65 TGAGATACAGAGAAGAAGACCAAATCAA
27435650 TGAAACCAGA
Statistics
Matches: 458, Mismatches: 43, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
206 409 0.89
207 49 0.11
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (206 bp):
AATTCGTCTTCCTGATGAGATACAGAGAAGAGGATTGAAACAAACGACGCGGTCATCTTCCTGAT
GAGATACAGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAGCT
TCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGA
GAAGTGGACCA
Found at i:27436028 original size:23 final size:23
Alignment explanation
Indices: 27435990--27436033 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
27435980 GATCAAAATT
*
27435990 TTGATTTTTAAATTAAGTTTGAA
1 TTGATTTTTAAATTAAATTTGAA
27436013 TTGA-TTTTAAATTTAAATTTG
1 TTGATTTTTAAA-TTAAATTTG
27436034 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (23 bp):
TTGATTTTTAAATTAAATTTGAA
Found at i:27436031 original size:17 final size:16
Alignment explanation
Indices: 27436011--27436047 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
27436001 ATTAAGTTTG
27436011 AATTGATTTTAAATTTA
1 AATTG-TTTTAAATTTA
27436028 AATTTGTTTTAAATTTA
1 AA-TTGTTTTAAATTTA
27436045 AAT
1 AAT
27436048 ACATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.05
17 15 0.79
18 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
AATTGTTTTAAATTTA
Found at i:27436862 original size:19 final size:20
Alignment explanation
Indices: 27436838--27436883 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
27436828 TATTAAAGAT
27436838 ATTAATAATAATATTT-TTA
1 ATTAATAATAATATTTATTA
*
27436857 ATTAATAATAGTATTTATTA
1 ATTAATAATAATATTTATTA
27436877 A-TAATAA
1 ATTAATAA
27436884 AAAAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTAATAATAATATTTATTA
Found at i:27436864 original size:16 final size:17
Alignment explanation
Indices: 27436839--27436882 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
27436829 ATTAAAGATA
*
27436839 TTAA-TAATAATA-TTT
1 TTAATTAATAATAGTAT
27436854 TTAATTAATAATAGTAT
1 TTAATTAATAATAGTAT
27436871 TT-ATTAATAATA
1 TTAATTAATAATA
27436883 AAAAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 18 0.69
17 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAATTAATAATAGTAT
Found at i:27438028 original size:30 final size:29
Alignment explanation
Indices: 27437988--27438102 Score: 105
Period size: 28 Copynumber: 3.9 Consensus size: 29
27437978 CTGACCCTCG
*
27437988 AACTTCTCCAAAATT-CCATTTTTAACCCTAA
1 AACTTC-CAAAAATTACCATTTTT-ACCC-AA
**
27438019 AACTTTCCAAAAATTACCA-TTTTACCCCCG
1 AAC-TTCCAAAAATTACCATTTTTA-CCCAA
*
27438049 AACTTCC-AAAATT-CCATTTTTGACCCGA
1 AACTTCCAAAAATTACCATTTTT-ACCCAA
27438077 AACTTCCAAAAATTACCA-TTTTACCC
1 AACTTCCAAAAATTACCATTTTTACCC
27438103 CGGATATCCA
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
27 3 0.04
28 24 0.33
29 15 0.21
30 7 0.10
31 17 0.24
32 6 0.08
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTACCATTTTTACCCAA
Found at i:27438069 original size:28 final size:28
Alignment explanation
Indices: 27437994--27438125 Score: 103
Period size: 28 Copynumber: 4.6 Consensus size: 28
27437984 CTCGAACTTC
**
27437994 TCCAAAATTCCATTTTTAACCCTAAAACTT
1 TCCAAAATTCCATTTTTAACCC-CGAAC-T
*
27438024 TCCAAAAATTACCA-TTTTACCCCCGAACT
1 TCC-AAAATT-CCATTTTTAACCCCGAACT
*
27438053 TCCAAAATTCCATTTTTGA-CCCGAAACT
1 TCCAAAATTCCATTTTTAACCCCG-AACT
*
27438081 TCCAAAAATTACCA-TTTT-ACCCCGGA-T
1 TCC-AAAATT-CCATTTTTAACCCCGAACT
*
27438108 ATCCAAAACTCCATTTTT
1 -TCCAAAATTCCATTTTT
27438126 GATCCCGATC
Statistics
Matches: 86, Mismatches: 7, Indels: 21
0.75 0.06 0.18
Matches are distributed among these distances:
26 3 0.03
27 17 0.20
28 22 0.26
29 18 0.21
30 9 0.10
31 14 0.16
32 3 0.03
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (28 bp):
TCCAAAATTCCATTTTTAACCCCGAACT
Found at i:27438096 original size:57 final size:58
Alignment explanation
Indices: 27437994--27438158 Score: 212
Period size: 57 Copynumber: 2.9 Consensus size: 58
27437984 CTCGAACTTC
* *
27437994 TCCAAAATTCCATTTTTAACCCTAAAACTTTCCAAAAATTACCATTTTACCCCCGAACT-
1 TCCAAAATTCCATTTTTGACCC-GAAACTTTCCAAAAATTACCATTTTACCCCCGAA-TA
*
27438053 TCCAAAATTCCATTTTTGACCCGAAAC-TTCCAAAAATTACCATTTTA-CCCCGGATA
1 TCCAAAATTCCATTTTTGACCCGAAACTTTCCAAAAATTACCATTTTACCCCCGAATA
* * * *
27438109 TCCAAAACTCCATTTTTGATCCCG-ATCTTTCTAAAAATTACTATTTTACC
1 TCCAAAATTCCATTTTTGA-CCCGAAACTTTCCAAAAATTACCATTTTACC
27438159 TGAATATCTA
Statistics
Matches: 95, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
55 1 0.01
56 26 0.27
57 42 0.44
58 5 0.05
59 21 0.22
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
TCCAAAATTCCATTTTTGACCCGAAACTTTCCAAAAATTACCATTTTACCCCCGAATA
Found at i:27440572 original size:6 final size:6
Alignment explanation
Indices: 27440561--27440593 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
27440551 TGATCAAAAT
*
27440561 TGAAAG TGAAAG TGAAAG TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
27440594 TATGAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:27445498 original size:17 final size:16
Alignment explanation
Indices: 27445476--27445513 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
27445466 AAAAAATATT
27445476 TTTTTCT-TTTTTCCGTA
1 TTTTTCTATTTTT--GTA
27445493 TTTTTCTATTTTTGTA
1 TTTTTCTATTTTTGTA
27445509 TTTTT
1 TTTTT
27445514 TCAATCACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTTTCTATTTTTGTA
Found at i:27445514 original size:17 final size:17
Alignment explanation
Indices: 27445475--27445515 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
27445465 CAAAAAATAT
27445475 TTTTTTCTTTTTTCCGTA
1 TTTTTTCTTTTTT-CGTA
27445493 -TTTTTCTATTTTT-GTA
1 TTTTTTCT-TTTTTCGTA
27445509 TTTTTTC
1 TTTTTTC
27445516 AATCACCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 13 0.62
18 5 0.24
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTTTTTCGTA
Found at i:27446479 original size:35 final size:34
Alignment explanation
Indices: 27446426--27446508 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 34
27446416 AAAAGAGAGG
*
27446426 TCTATCTCGAGATCTAGTCTCGAGACATGAGGGAC
1 TCTACCTCGAGA-CTAGTCTCGAGACATGAGGGAC
* *
27446461 TCTACCTCGAGACGTAGTCTCGGGACATTAGGGAC
1 TCTACCTCGAGAC-TAGTCTCGAGACATGAGGGAC
* *
27446496 CCTACCTTGAGAC
1 TCTACCTCGAGAC
27446509 ACAATTTCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 1 0.02
35 41 0.98
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (34 bp):
TCTACCTCGAGACTAGTCTCGAGACATGAGGGAC
Found at i:27449733 original size:28 final size:29
Alignment explanation
Indices: 27449673--27449741 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
27449663 TAAATCTTAA
*
27449673 AATTATAA-ATGAAGTTTAATTTAATGTGT
1 AATTATAACATGAAGTTTAATTT-AGGTGT
27449702 AATTATATACATGAA-TTTAATTT-GGTGT
1 AATTATA-ACATGAAGTTTAATTTAGGTGT
27449730 AATTATACACAT
1 AATTATA-ACAT
27449742 AAAATTCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 15 0.42
29 7 0.19
30 9 0.25
31 5 0.14
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (29 bp):
AATTATAACATGAAGTTTAATTTAGGTGT
Found at i:27454138 original size:15 final size:15
Alignment explanation
Indices: 27454118--27454163 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
27454108 ACAAAATATT
27454118 AACATAAGTGACTAA
1 AACATAAGTGACTAA
* *
27454133 AACATAA-T-ATTTCA
1 AACATAAGTGA-CTAA
27454147 AACATAAGTGACTAA
1 AACATAAGTGACTAA
27454162 AA
1 AA
27454164 TGTAACCTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 12 0.50
16 1 0.04
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (15 bp):
AACATAAGTGACTAA
Done.