Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008183.1 Hibiscus syriacus cultivar Beakdansim tig00110783_pilon, whole genome shotgun sequence
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: 2364390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:908340 original size:13 final size:13
Alignment explanation
Indices: 908322--908349 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
908312 ATTATTATAA
908322 AAAATAATAATTT
1 AAAATAATAATTT
908335 AAAATAATAATTT
1 AAAATAATAATTT
908348 AA
1 AA
908350 CTTTGAGTTA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATAATAATTT
Found at i:909824 original size:46 final size:45
Alignment explanation
Indices: 909773--909876 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
909763 ACATACCATG
* *
909773 CATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATC
1 CATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTGATC
* * *
909819 CATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATG
1 CATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATC
909864 CATCGATGCACTC
1 CATCGATGCACTC
909877 TTAGTGCACC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 32 0.62
46 17 0.33
47 3 0.06
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (45 bp):
CATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATC
Found at i:909874 original size:17 final size:19
Alignment explanation
Indices: 909846--909894 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
909836 TATTTTGAAA
909846 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
909864 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
909883 CACCGATGCACT
1 CATCGATGCACT
909895 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:910709 original size:17 final size:17
Alignment explanation
Indices: 910687--910724 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
910677 ACTTCAAATG
910687 TCGACTCCGGTCTCGAT
1 TCGACTCCGGTCTCGAT
910704 TCGACTCCGGTCTCGAT
1 TCGACTCCGGTCTCGAT
910721 TCGA
1 TCGA
910725 TGCCCGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.13, C:0.34, G:0.24, T:0.29
Consensus pattern (17 bp):
TCGACTCCGGTCTCGAT
Found at i:917303 original size:21 final size:21
Alignment explanation
Indices: 917261--917304 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
917251 ACTCCGGGAG
* *
917261 CTAGCTCTTCACGAGTTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
917282 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
917303 CT
1 CT
917305 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:918382 original size:45 final size:46
Alignment explanation
Indices: 918326--918433 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 46
918316 TGCACCAATC
918326 CATGCATCGATGCACCATGA-ATTAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCACCATGAGATTAAA-TGAAACATCGAATGCATTT
**
918371 CATGCATCGATGCA-C-TGAGGATTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACCATGA-GATTAAATG-AAACATCGAATGCATTT
*
918417 GATGCATCGATGCACCA
1 CATGCATCGATGCACCA
918434 GCCATGCATC
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
43 3 0.06
44 3 0.06
45 18 0.33
46 29 0.54
47 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (46 bp):
CATGCATCGATGCACCATGAGATTAAATGAAACATCGAATGCATTT
Found at i:918483 original size:64 final size:65
Alignment explanation
Indices: 918371--918495 Score: 191
Period size: 64 Copynumber: 1.9 Consensus size: 65
918361 GAATGCATTT
* *
918371 CATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
1 CATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTGATGCATCGATGCACCAGC
* *
918436 CATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCACTTGATGCATCGATGCAC
1 CATGCATCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCACTTGATGCATCGATGCAC
918496 TCTTAGTGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 31 0.56
65 21 0.38
66 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (65 bp):
CATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTGATGCATCGATGCACCAGC
Found at i:918495 original size:17 final size:19
Alignment explanation
Indices: 918467--918515 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
918457 TATTTTGAAA
918467 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
918485 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
918504 CACCGATGCACT
1 CATCGATGCACT
918516 AAGGATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:919563 original size:2 final size:2
Alignment explanation
Indices: 919556--919591 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
919546 TCATTTTCCA
919556 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
919592 TAAATTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:921986 original size:16 final size:17
Alignment explanation
Indices: 921965--921998 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
921955 AAGATAAATA
*
921965 TTTTTGATATTAT-TTT
1 TTTTTGAAATTATCTTT
921981 TTTTTGAAATTATCTTT
1 TTTTTGAAATTATCTTT
921998 T
1 T
921999 CAATTTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTTTGAAATTATCTTT
Found at i:924430 original size:2 final size:2
Alignment explanation
Indices: 924423--924457 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
924413 TATGTAAGTG
924423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
924458 GAATTACTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:927093 original size:2 final size:2
Alignment explanation
Indices: 927086--927175 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
927076 ATCTTATCTC
927086 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
927128 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
927170 AT AT AT
1 AT AT AT
927176 GACCATTGGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:928110 original size:45 final size:45
Alignment explanation
Indices: 928059--928320 Score: 330
Period size: 45 Copynumber: 5.8 Consensus size: 45
928049 GTTATAACAT
* *
928059 CTTTTCTATTGATAATGTACCCATATGCATTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
*
928104 CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* * *
928149 -TTATTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATG
1 CTT-TTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* * * * *
928194 CTCTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* ** * * * * *
928239 C-TTTCTGTTGATAATGCATTCATATGCATTTCAACCAAATTATG
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
928283 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTA
928321 GGGCATCCTT
Statistics
Matches: 188, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
44 37 0.20
45 150 0.80
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
Found at i:928294 original size:134 final size:135
Alignment explanation
Indices: 928062--928319 Score: 394
Period size: 134 Copynumber: 1.9 Consensus size: 135
928052 ATAACATCTT
* * *
928062 TTCTATTGATAATGTACCCATATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGTACCCA
1 TTCTATTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
*
928127 TATACATTTCAACCATAGTATATTATTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCA
66 TATACATTTCAACCAAAGTATATTATTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCA
928192 TGCTC
131 TGCTC
* * **
928197 TTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATAC-TTTCTGTTGATAATGCATTCA
1 TTCTATTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
* * *
928261 TATGCATTTCAACCAAATTATGCTT-TTCTGTTGATAATGTACCCATATACATTTCAACT
66 TATACATTTCAACCAAAGTAT-ATTATTCTGTTGATAATGTACCCATATACATTTCAACT
928320 AGGGCATCCT
Statistics
Matches: 111, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
134 70 0.63
135 41 0.37
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.40
Consensus pattern (135 bp):
TTCTATTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
TATACATTTCAACCAAAGTATATTATTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCA
TGCTC
Found at i:928345 original size:134 final size:135
Alignment explanation
Indices: 928072--928358 Score: 373
Period size: 134 Copynumber: 2.1 Consensus size: 135
928062 TTCTATTGAT
* * *
928072 AATGTACCCATATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* ** *
928137 AACCATAGTATATTATTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATGCTCTTCTG
66 AACCAAAGTATATTATTCTGTTGATAATGTACCCATATACATTTCAACTAGAGCATCCTCTTCTG
*** *
928202 TTGAT
131 CCAAC
* ** *
928207 AATGCACCCATATGCATTTCAACTCTAGCATAC-TTTCTGTTGATAATGCATTCATATGCATTTC
1 AATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* * *
928271 AACCAAATTATGCTT-TTCTGTTGATAATGTACCCATATACATTTCAACTAGGGCATCCT-TTCA
66 AACCAAAGTAT-ATTATTCTGTTGATAATGTACCCATATACATTTCAACTAGAGCATCCTCTTC-
928334 TGCCAAC
129 TGCCAAC
928341 AATGCACCCATATGCATT
1 AATGCACCCATATGCATT
928359 ATTATTTTCA
Statistics
Matches: 132, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
133 3 0.02
134 97 0.73
135 32 0.24
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (135 bp):
AATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
AACCAAAGTATATTATTCTGTTGATAATGTACCCATATACATTTCAACTAGAGCATCCTCTTCTG
CCAAC
Found at i:928924 original size:100 final size:100
Alignment explanation
Indices: 928800--928981 Score: 258
Period size: 100 Copynumber: 1.8 Consensus size: 100
928790 ACCCTATTAG
* * *
928800 GGTATCAATACCCCCTTCATGTATCAATACCAAAATTAGCTTCGATATAGCCTGGTATCGATACC
1 GGTATCAATACCCCCTTCAGGTATCAATACCAAAATTAGATTCGATATAGACTGGTATCGATACC
928865 CTCACCATAGTATCGATACCCCTATGCTATGCTAT
66 CTCACCATAGTATCGATACCCCTATGCTATGCTAT
* * * **
928900 GGTATCAATACTCCC-TCTAGGTATCGATACCAAAATTAGATTCGATGTTTACTGGTATCGATAC
1 GGTATCAATACCCCCTTC-AGGTATCAATACCAAAATTAGATTCGATATAGACTGGTATCGATAC
* *
928964 CCTTACCATGGTATCGAT
65 CCTCACCATAGTATCGAT
928982 GCCCATTGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 2 0.03
100 69 0.97
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (100 bp):
GGTATCAATACCCCCTTCAGGTATCAATACCAAAATTAGATTCGATATAGACTGGTATCGATACC
CTCACCATAGTATCGATACCCCTATGCTATGCTAT
Found at i:932105 original size:35 final size:35
Alignment explanation
Indices: 932066--932134 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
932056 ATATTTAAGT
*
932066 TTTATATTT-AGATTATGCAATTTGAATTTTTAAAC
1 TTTATATTTCA-ATTATGCAATTCGAATTTTTAAAC
* *
932101 TTTATGTTTCAATTATGTAATTCGAATTTTTAAA
1 TTTATATTTCAATTATGCAATTCGAATTTTTAAA
932135 TGTTTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (35 bp):
TTTATATTTCAATTATGCAATTCGAATTTTTAAAC
Found at i:932696 original size:24 final size:24
Alignment explanation
Indices: 932669--932714 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
932659 GTTACATTGC
932669 TTGTTGTGCATGAGTCTGTTAGAG
1 TTGTTGTGCATGAGTCTGTTAGAG
*
932693 TTGTTGTGCATGAGTTTGTTAG
1 TTGTTGTGCATGAGTCTGTTAG
932715 GCAGCTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.07, G:0.33, T:0.46
Consensus pattern (24 bp):
TTGTTGTGCATGAGTCTGTTAGAG
Found at i:948330 original size:13 final size:13
Alignment explanation
Indices: 948312--948341 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
948302 TCAATATTAT
*
948312 TTTTGAAAAGTGA
1 TTTTGAAAAATGA
948325 TTTTGAAAAATGA
1 TTTTGAAAAATGA
948338 TTTT
1 TTTT
948342 TTTAAAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.47
Consensus pattern (13 bp):
TTTTGAAAAATGA
Found at i:948982 original size:17 final size:17
Alignment explanation
Indices: 948960--948994 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
948950 TACAATCAGA
948960 TTTGTTCATA-TTTATCT
1 TTTGTTCA-AGTTTATCT
948977 TTTGTTCAAGTTTATCT
1 TTTGTTCAAGTTTATCT
948994 T
1 T
948995 GTTATGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (17 bp):
TTTGTTCAAGTTTATCT
Found at i:950196 original size:172 final size:171
Alignment explanation
Indices: 949904--950382 Score: 735
Period size: 171 Copynumber: 2.8 Consensus size: 171
949894 TAACTTTCAT
* * * *
949904 GAGCAGCAGTTGATCAGCCACTCACGAACCA-TTAAAGGAAACTGTCAATATTTTCTCACTCAGT
1 GAGCACCAGTTGATCAGCCACTCACGTACCACTT-AAGGAAACTGCCAATATTTTTTCACTCAGT
* * *
949968 TCGTAATGACCATGAATACTTAAAGTTTGAATCGAAGTAATCAATCACCTTCAAATTATCTATTC
65 TTGTAATGACCATGAATACTTAAAGTCTGAATCGAAGTAGTCAATCACCTTCAAATTATCTATTC
950033 ATTTATAAATAAGCATATAGTCCTTTGTCCCTTTTAGGTATAC
130 ATTTATAAATAAGCATATAG-CCTTTGTCCCTTTTAGGTATAC
* *
950076 GAGCACCAGTTGATCAACCACTCATGTACCACTTAAGGAAACTGCCAATATTTTTTCACTCAGTT
1 GAGCACCAGTTGATCAGCCACTCACGTACCACTTAAGGAAACTGCCAATATTTTTTCACTCAGTT
950141 TGTAATGACCATGAATACTTAAAGTCTGAATCGAAGTAGTCAATCACCTTCAAATTATCTATTCA
66 TGTAATGACCATGAATACTTAAAGTCTGAATCGAAGTAGTCAATCACCTTCAAATTATCTATTCA
* * * *
950206 TTTATACATAAGCATGTAGCTTTTGTCCCTTTTAGGTGTAC
131 TTTATAAATAAGCATATAGCCTTTGTCCCTTTTAGGTATAC
* * * * * * * *
950247 GAGCACCAATTGTTTAGCCACTCACGTACCACTAAAGAAAACTGCCAAAAATTTTTCATTCAGTT
1 GAGCACCAGTTGATCAGCCACTCACGTACCACTTAAGGAAACTGCCAATATTTTTTCACTCAGTT
*
950312 TGTAATGACCATGAATACTTAAAGTCTGAATCAAAGTAGTCAATCACCTTCAAATTATCTATTCA
66 TGTAATGACCATGAATACTTAAAGTCTGAATCGAAGTAGTCAATCACCTTCAAATTATCTATTCA
950377 TTTATA
131 TTTATA
950383 CATATGTAAC
Statistics
Matches: 282, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
171 145 0.51
172 135 0.48
173 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (171 bp):
GAGCACCAGTTGATCAGCCACTCACGTACCACTTAAGGAAACTGCCAATATTTTTTCACTCAGTT
TGTAATGACCATGAATACTTAAAGTCTGAATCGAAGTAGTCAATCACCTTCAAATTATCTATTCA
TTTATAAATAAGCATATAGCCTTTGTCCCTTTTAGGTATAC
Found at i:952125 original size:31 final size:31
Alignment explanation
Indices: 951970--952110 Score: 246
Period size: 31 Copynumber: 4.5 Consensus size: 31
951960 AGGGTCGAGG
951970 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
952001 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
952032 GTTTGCCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
952063 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
952094 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
952111 AGAATCTATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:953274 original size:16 final size:17
Alignment explanation
Indices: 953244--953276 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
953234 AATAATATTC
953244 AAATAAATATATTTGTA
1 AAATAAATATATTTGTA
*
953261 AAAT-AATATTTTTGTA
1 AAATAAATATATTTGTA
953277 GTTATAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
AAATAAATATATTTGTA
Found at i:953682 original size:25 final size:22
Alignment explanation
Indices: 953654--953698 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
953644 AATATGAGGG
953654 TAAAATTAATTATTTTATATTAAAT
1 TAAAATT-ATT-TTTTA-ATTAAAT
953679 TAAAATTATTTTTTAATTAA
1 TAAAATTATTTTTTAATTAA
953699 CATTTTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 5 0.25
24 3 0.15
25 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAAATTATTTTTTAATTAAAT
Found at i:961211 original size:40 final size:40
Alignment explanation
Indices: 961156--961235 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
961146 TTGAACTGTT
961156 AAAATATTGTAAGTTGAATGCTTTAAACTCACATGATGTG
1 AAAATATTGTAAGTTGAATGCTTTAAACTCACATGATGTG
* *
961196 AAAATATTGTAAGTTGAATGCTTTAAATTCGCATGATGTG
1 AAAATATTGTAAGTTGAATGCTTTAAACTCACATGATGTG
961236 TGTATTATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (40 bp):
AAAATATTGTAAGTTGAATGCTTTAAACTCACATGATGTG
Found at i:973837 original size:21 final size:23
Alignment explanation
Indices: 973803--973845 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
973793 CCCCTGTGGG
*
973803 GGGGGGGAGAATCGGTTCCCTCA
1 GGGGGGGAGAATCGATTCCCTCA
973826 GGGGGGG-G-ATCGATTCCCTC
1 GGGGGGGAGAATCGATTCCCTC
973846 TGCACCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.14, C:0.23, G:0.44, T:0.19
Consensus pattern (23 bp):
GGGGGGGAGAATCGATTCCCTCA
Found at i:979721 original size:31 final size:31
Alignment explanation
Indices: 979686--979782 Score: 72
Period size: 31 Copynumber: 3.2 Consensus size: 31
979676 AGTTAGAACT
979686 TTATTTAAGTATATTAAAAAATATTAGGCCC
1 TTATTTAAGTATATTAAAAAATATTAGGCCC
* * * *** * * *
979717 TTATTAAACTCT-TTTTGAAAGATTAAGTCC
1 TTATTTAAGTATATTAAAAAATATTAGGCCC
* *
979747 TCATTTGAGTATA-TACAAAAATATTAGGCCC
1 TTATTTAAGTATATTA-AAAAATATTAGGCCC
979778 TTATT
1 TTATT
979783 CAACTCTTTT
Statistics
Matches: 43, Mismatches: 21, Indels: 4
0.63 0.31 0.06
Matches are distributed among these distances:
30 20 0.47
31 23 0.53
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (31 bp):
TTATTTAAGTATATTAAAAAATATTAGGCCC
Found at i:979821 original size:60 final size:61
Alignment explanation
Indices: 979688--979834 Score: 235
Period size: 60 Copynumber: 2.4 Consensus size: 61
979678 TTAGAACTTT
*
979688 ATTTAAGTATATTA-AAAAATATTAGGCCCTTATTAAACTCTTTTTGAAAGATTAAGTCCTC
1 ATTTGAGTATA-TACAAAAATATTAGGCCCTTATTAAACTCTTTTTGAAAGATTAAGTCCTC
* *
979749 ATTTGAGTATATACAAAAATATTAGGCCCTTATTCAACTC-TTTTGAAAGATTAAGTCTTC
1 ATTTGAGTATATACAAAAATATTAGGCCCTTATTAAACTCTTTTTGAAAGATTAAGTCCTC
*
979809 ATTTGAGTATATACGAAAATATTAGG
1 ATTTGAGTATATACAAAAATATTAGG
979835 TTCCTATTAA
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
60 46 0.57
61 35 0.43
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (61 bp):
ATTTGAGTATATACAAAAATATTAGGCCCTTATTAAACTCTTTTTGAAAGATTAAGTCCTC
Found at i:983999 original size:4 final size:4
Alignment explanation
Indices: 983992--984263 Score: 535
Period size: 4 Copynumber: 68.0 Consensus size: 4
983982 CACATGCATG
983992 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
984040 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
984088 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
984136 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
984184 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA TATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
984232 CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
984264 ACCATAAGAG
Statistics
Matches: 266, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 266 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:986023 original size:47 final size:48
Alignment explanation
Indices: 985931--986023 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 48
985921 TATAGTTTGA
* *
985931 GATGAAATTAAAATGTTGAAAAAGTTTAGGGACCAATTTAGAATGAAG
1 GATGAAACTAAAATGTTGAAAAAGTTTAGGGACCAATTTAAAATGAAG
*
985979 GATGAAACTAAAATGTTG-AAAAGTTT-GAGGACTAATTTAAAATGA
1 GATGAAACTAAAATGTTGAAAAAGTTTAG-GGACCAATTTAAAATGA
986024 TAATCATAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
46 1 0.02
47 23 0.56
48 17 0.41
ACGTcount: A:0.46, C:0.04, G:0.22, T:0.28
Consensus pattern (48 bp):
GATGAAACTAAAATGTTGAAAAAGTTTAGGGACCAATTTAAAATGAAG
Found at i:989518 original size:13 final size:13
Alignment explanation
Indices: 989500--989525 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
989490 TTTATGAATT
989500 TATACTTTTATTA
1 TATACTTTTATTA
989513 TATACTTTTATTA
1 TATACTTTTATTA
989526 AATATTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
TATACTTTTATTA
Found at i:989850 original size:19 final size:19
Alignment explanation
Indices: 989819--989857 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
989809 TATCTGATTT
989819 AAATTATCTAAAAATTTAA
1 AAATTATCTAAAAATTTAA
*
989838 AAATATATC-AAAATTTTAA
1 AAAT-TATCTAAAAATTTAA
989857 A
1 A
989858 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTATCTAAAAATTTAA
Found at i:993062 original size:6 final size:7
Alignment explanation
Indices: 993045--993070 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
993035 TTTCCCTAAA
993045 TTTTTTG
1 TTTTTTG
993052 TTTTTTG
1 TTTTTTG
993059 TTTTTTG
1 TTTTTTG
993066 TTTTT
1 TTTTT
993071 ACATTACTTC
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTTG
Found at i:993599 original size:4 final size:4
Alignment explanation
Indices: 993590--993625 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
993580 GTATGCATTT
*
993590 TTTG TTTG TTTG TTTG CTTG TTTG TTATG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TT-TG TTTG TTT
993626 TGCATGTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.03, C:0.03, G:0.22, T:0.72
Consensus pattern (4 bp):
TTTG
Found at i:994980 original size:20 final size:20
Alignment explanation
Indices: 994957--994995 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
994947 ATCGGTACAA
994957 GAAGAACAATATCGATACTG
1 GAAGAACAATATCGATACTG
* *
994977 GAAGAACAGTATTGATACT
1 GAAGAACAATATCGATACT
994996 ATAAGGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.23
Consensus pattern (20 bp):
GAAGAACAATATCGATACTG
Found at i:1008281 original size:3 final size:3
Alignment explanation
Indices: 1008273--1008297 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1008263 TTGTTTACAG
1008273 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1008298 ATGCCCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1013572 original size:29 final size:29
Alignment explanation
Indices: 1013539--1013618 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
1013529 ATTAAAGGCG
*
1013539 AATTTAAATTTATAAAATTTTAAAAAATA
1 AATTTGAATTTATAAAATTTTAAAAAATA
* * * *
1013568 AATTTGTACTTATAAAATTTTAAGAGATA
1 AATTTGAATTTATAAAATTTTAAAAAATA
*
1013597 AACTTGAATTTATAAAATTTTA
1 AATTTGAATTTATAAAATTTTA
1013619 GGAGACATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (29 bp):
AATTTGAATTTATAAAATTTTAAAAAATA
Found at i:1013636 original size:29 final size:28
Alignment explanation
Indices: 1013545--1013633 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 28
1013535 GGCGAATTTA
* * **
1013545 AATTTATAAAATTTTAAAAAATAAATTT
1 AATTTATAAAATTTTAAGACATAAACAT
* * * *
1013573 GTACTTATAAAATTTTAAGAGATAAACTT
1 -AATTTATAAAATTTTAAGACATAAACAT
1013602 GAATTTATAAAATTTTAGGAGACATAAACAT
1 -AATTTATAAAATTTTA--AGACATAAACAT
1013633 A
1 A
1013634 TTTTCAATAG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 38 0.78
30 1 0.02
31 10 0.20
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (28 bp):
AATTTATAAAATTTTAAGACATAAACAT
Found at i:1014233 original size:20 final size:21
Alignment explanation
Indices: 1014202--1014240 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1014192 ATGGTGAAGA
1014202 AAAATGTATTAGTTGTCATGC
1 AAAATGTATTAGTTGTCATGC
1014223 AAAAT-TATTAGTTGTCAT
1 AAAATGTATTAGTTGTCAT
1014241 ACAACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (21 bp):
AAAATGTATTAGTTGTCATGC
Found at i:1018938 original size:21 final size:20
Alignment explanation
Indices: 1018914--1018955 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1018904 GTCATACAAC
*
1018914 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
1018935 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
1018955 T
1 T
1018956 TGTAAGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:1019922 original size:23 final size:24
Alignment explanation
Indices: 1019889--1019934 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1019879 AGACATACTA
*
1019889 AAAATTGTAGAG-TATAAAATTAT
1 AAAATTGTAGAGATACAAAATTAT
*
1019912 AAAATTTTAGAGATACAAAATTA
1 AAAATTGTAGAGATACAAAATTA
1019935 AATTGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (24 bp):
AAAATTGTAGAGATACAAAATTAT
Found at i:1020504 original size:2 final size:2
Alignment explanation
Indices: 1020497--1020524 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1020487 ACATAGTAAT
1020497 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
1020525 ACTGATATAC
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:1023934 original size:5 final size:5
Alignment explanation
Indices: 1023926--1023950 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1023916 CCCTTCCCTC
1023926 CTAAT CTAAT CTAAT CTAAT CTAAT
1 CTAAT CTAAT CTAAT CTAAT CTAAT
1023951 ATTTATAACT
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:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
CTAAT
Found at i:1026285 original size:34 final size:34
Alignment explanation
Indices: 1026244--1026353 Score: 102
Period size: 34 Copynumber: 3.2 Consensus size: 34
1026234 GTGGTAAGAA
* * *
1026244 ATTTATTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTTATTTTATATTAATATATTTATGTAAATA-TT
1026277 ATTATATTTTATATTAATATATTTATGTAAATATT
1 ATT-TATTTTATATTAATATATTTATGTAAATATT
* * *
1026312 ATTT-TTTTAT-TAAAATAATATTTATATAATTATT
1 ATTTATTTTATAT-TAAT-ATATTTATGTAAATATT
1026346 ATTTATTT
1 ATTTATTT
1026354 AGAATTATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
32 1 0.02
33 12 0.18
34 34 0.52
35 11 0.17
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (34 bp):
ATTTATTTTATATTAATATATTTATGTAAATATT
Found at i:1028108 original size:21 final size:21
Alignment explanation
Indices: 1028078--1028125 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1028068 GCATGGGTAC
* *
1028078 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1028099 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1028120 ATGCCA
1 ATGCCA
1028126 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1028155 original size:21 final size:21
Alignment explanation
Indices: 1028129--1028222 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
1028119 TATGCCATCT
1028129 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
1028150 CCGCAGGGATACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
1028171 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
1028192 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
1028213 CCGCAGGGTT
1 CCGCAGGGTT
1028223 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.34, G:0.28, T:0.19
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:1028848 original size:34 final size:33
Alignment explanation
Indices: 1028742--1028848 Score: 126
Period size: 34 Copynumber: 3.2 Consensus size: 33
1028732 ATAAATGTTT
1028742 TTAAAATACAAAA-TATATTATTCGAAATTTAAAA
1 TTAAAATA-AAAATTATATTATTCGAAATTT-AAA
* *
1028776 TAAAAATAAAAATAATATTATTCGAAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* * *
1028809 TTTAAAATATAAATTATAGTATTCGAAGTTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
1028844 TTAAA
1 TTAAA
1028849 TTTCAACTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
33 7 0.11
34 55 0.87
35 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:1029698 original size:128 final size:127
Alignment explanation
Indices: 1029470--1029841 Score: 656
Period size: 128 Copynumber: 2.9 Consensus size: 127
1029460 GGAAATCATT
1029470 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1029535 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
1029598 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATATCATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1029663 TGACAAAATAATGGAAGGCGCGCCCTCGGGAACGCGCCTTTATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCC-CGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1029726 TACTGATATATCTAGTGTCCCCAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1029790 TGACAAAATAATGGAAGGCGCGTCCCCAGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGT
1029842 ACTCCGATTA
Statistics
Matches: 233, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
127 49 0.21
128 184 0.79
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (127 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1029925 original size:8 final size:8
Alignment explanation
Indices: 1029912--1029952 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1029902 TCACAAGCTT
1029912 TCAAATTC
1 TCAAATTC
1029920 TCAAATTC
1 TCAAATTC
* *
1029928 CCAAACTC
1 TCAAATTC
1029936 T-AAATTC
1 TCAAATTC
1029943 TCAAATTC
1 TCAAATTC
1029951 TC
1 TC
1029953 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1037948 original size:16 final size:15
Alignment explanation
Indices: 1037924--1037959 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1037914 GGAATAGTAC
*
1037924 TTTACTCTTATATATT
1 TTTAATCTTATAT-TT
1037940 TTTAATCTTATATTT
1 TTTAATCTTATATTT
1037955 TTTAA
1 TTTAA
1037960 CTTTTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATCTTATATTT
Found at i:1045916 original size:392 final size:392
Alignment explanation
Indices: 1045192--1045978 Score: 1556
Period size: 392 Copynumber: 2.0 Consensus size: 392
1045182 ACTTAATTTA
1045192 TTGAAACTTGATAAATGAATTTTGAAACTTACTAAATATAGTTTCATAAATGTTCGACTTTATGG
1 TTGAAACTTGATAAATGAATTTTGAAACTTACTAAATATAGTTTCATAAATGTTCGACTTTATGG
1045257 AGGCCTTGCAGGGTTATCTTGAGTGCTTTCTAAGTGGTAAATTTACCCTTTTCTGTAGTAAAGTT
66 AGGCCTTGCAGGGTTATCTTGAGTGCTTTCTAAGTGGTAAATTTACCCTTTTCTGTAGTAAAGTT
1045322 TTAGTAGAAGGTTATGTAGTAATGCTAGAGAGATTAAAGTATTTCATGCTTTTACACCATTCTAT
131 TTAGTAGAAGGTTATGTAGTAATGCTAGAGAGATTAAAGTATTTCATGCTTTTACACCATTCTAT
1045387 TAATGCATCCTTGTCATATTTGAGTTACGAATCAAATTTTTTTCGTGTTTCCATGTATATGGCAA
196 TAATGCATCCTTGTCATATTTGAGTTACGAATCAAATTTTTTTCGTGTTTCCATGTATATGGCAA
1045452 AAAGCAAGGTCCAGTCATGATAATCCGGACATGGTATCCATAATAAATGTTGGCTCTTTTTTTGT
261 AAAGCAAGGTCCAGTCATGATAATCCGGACATGGTATCCATAATAAATGTTGGCTCTTTTTTTGT
1045517 GTTGTGGTTCTTACTTGCTATGATAAGTAATGCCTGCTAATGATATTTCCTGGTTGATTGGTGAA
326 GTTGTGGTTCTTACTTGCTATGATAAGTAATGCCTGCTAATGATATTTCCTGGTTGATTGGTGAA
1045582 TT
391 TT
1045584 TTGAAACTTGATAAATGAATTTTGAAACTTACTAAATATAGTTTCATAAATGTTCGACTTTATGG
1 TTGAAACTTGATAAATGAATTTTGAAACTTACTAAATATAGTTTCATAAATGTTCGACTTTATGG
1045649 AGGCCTTGCAGGGTTATCTTGAGTGCTTTCTAAGTGGTAAATTTACCCTTTTCTGTAGTAAAGTT
66 AGGCCTTGCAGGGTTATCTTGAGTGCTTTCTAAGTGGTAAATTTACCCTTTTCTGTAGTAAAGTT
1045714 TTAGTAGAAGGTTATGTAGTAATGCTAGAGAGATTAAAGTATTTCATGCTTTTACACCATTCTAT
131 TTAGTAGAAGGTTATGTAGTAATGCTAGAGAGATTAAAGTATTTCATGCTTTTACACCATTCTAT
1045779 TAATGCATCCTTGTCATATTTGAGTTACGAATCAAATTTTTTTCGTGTTTCCATGTATATGGCAA
196 TAATGCATCCTTGTCATATTTGAGTTACGAATCAAATTTTTTTCGTGTTTCCATGTATATGGCAA
1045844 AAAGCAAGGTCCAGTCATGATAATCCGGACATGGTATCCATAATAAATGTTGGCTCTTTTTTTGT
261 AAAGCAAGGTCCAGTCATGATAATCCGGACATGGTATCCATAATAAATGTTGGCTCTTTTTTTGT
* *
1045909 GTTGTGGTTCTTACTTGCTATGATGAGTAATGCCTGTTAATGATATTTCCTGGTTGATTGGTGAA
326 GTTGTGGTTCTTACTTGCTATGATAAGTAATGCCTGCTAATGATATTTCCTGGTTGATTGGTGAA
1045974 TT
391 TT
1045976 TTG
1 TTG
1045979 CAGGTTCTTA
Statistics
Matches: 393, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
392 393 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (392 bp):
TTGAAACTTGATAAATGAATTTTGAAACTTACTAAATATAGTTTCATAAATGTTCGACTTTATGG
AGGCCTTGCAGGGTTATCTTGAGTGCTTTCTAAGTGGTAAATTTACCCTTTTCTGTAGTAAAGTT
TTAGTAGAAGGTTATGTAGTAATGCTAGAGAGATTAAAGTATTTCATGCTTTTACACCATTCTAT
TAATGCATCCTTGTCATATTTGAGTTACGAATCAAATTTTTTTCGTGTTTCCATGTATATGGCAA
AAAGCAAGGTCCAGTCATGATAATCCGGACATGGTATCCATAATAAATGTTGGCTCTTTTTTTGT
GTTGTGGTTCTTACTTGCTATGATAAGTAATGCCTGCTAATGATATTTCCTGGTTGATTGGTGAA
TT
Found at i:1049190 original size:21 final size:21
Alignment explanation
Indices: 1049161--1049213 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1049151 ATTCTGACTA
1049161 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
1049182 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
* *
1049203 TCACAATGCGA
1 TCGCATTGCGA
1049214 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1049264 original size:20 final size:20
Alignment explanation
Indices: 1049206--1049354 Score: 212
Period size: 20 Copynumber: 7.5 Consensus size: 20
1049196 TCCTAATTCA
1049206 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* ** *
1049226 CAA--AGAATTTGGAAAATCG
1 CAATGCGAA-TACGTAAATCG
1049245 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
1049265 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
1049285 CAATGTGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
1049305 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
1049325 CAATGCGAATATGTAAATCG
1 CAATGCGAATACGTAAATCG
*
1049345 CAACGCGAAT
1 CAATGCGAAT
1049355 CTGACTATCG
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
18 3 0.03
19 11 0.10
20 97 0.85
21 3 0.03
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:1049576 original size:22 final size:22
Alignment explanation
Indices: 1049551--1049615 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
1049541 GCGACATCCG
1049551 TCCCCATCTCCGACGAAATCAA
1 TCCCCATCTCCGACGAAATCAA
* *
1049573 TCCCCATCTCCGACGATATCAG
1 TCCCCATCTCCGACGAAATCAA
* *
1049595 TCTCCATCTCCGGCGAAATCA
1 TCCCCATCTCCGACGAAATCA
1049616 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.22
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAA
Found at i:1050048 original size:20 final size:20
Alignment explanation
Indices: 1049952--1050041 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
1049942 CGATTTTGTC
1049952 GTTGCGATTTTCA-TTTCGCT
1 GTTGCGATTTTCATTTTCG-T
** **
1049972 -TTGCGATAGTCAAATTCGT
1 GTTGCGATTTTCATTTTCGT
** *
1049991 GTTGCGATAGTCATTTTTGT
1 GTTGCGATTTTCATTTTCGT
1050011 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1050031 GTTGCGATTTT
1 GTTGCGATTTT
1050042 AAGTTTCAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.19
20 48 0.81
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:1051934 original size:20 final size:20
Alignment explanation
Indices: 1051909--1052080 Score: 131
Period size: 20 Copynumber: 9.3 Consensus size: 20
1051899 AGAATAGTTT
1051909 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1051929 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1051949 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1051965 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
1051982 AAAACCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
* *
1051998 A--ATCGCAACGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
1052016 ACTATCGCAATG-AAAAATG
1 ACTATCGCAATGCGAAAATG
1052035 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
1052055 ACTATCGCAATGTGAATTTG
1 ACTATCGCAATGCGAAAATG
1052075 ACTATC
1 ACTATC
1052081 ATAATGAAAG
Statistics
Matches: 127, Mismatches: 10, Indels: 30
0.76 0.06 0.18
Matches are distributed among these distances:
14 13 0.10
16 10 0.08
17 8 0.06
18 5 0.04
19 25 0.20
20 66 0.52
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1052156 original size:20 final size:20
Alignment explanation
Indices: 1052131--1052197 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1052121 GATTCTCTCG
**
1052131 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1052151 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
1052171 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
1052191 TTGCGAT
1 TTGCGAT
1052198 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1052772 original size:21 final size:21
Alignment explanation
Indices: 1052681--1052785 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
1052671 GAATCACCTG
*
1052681 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1052703 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1052723 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1052744 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1052765 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1052786 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1052778 original size:42 final size:42
Alignment explanation
Indices: 1052678--1052788 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1052668 CCCGAATCAC
* * * *
1052678 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1052720 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1052762 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1052789 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1054188 original size:14 final size:14
Alignment explanation
Indices: 1054169--1054204 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1054159 ATTGTTTAAT
1054169 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1054183 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1054197 TGATTTGT
1 TGATTTGT
1054205 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1054360 original size:33 final size:33
Alignment explanation
Indices: 1054310--1054405 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
1054300 AAAACAGACT
* **
1054310 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1054344 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1054377 ATAGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1054406 CGAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1054464 original size:34 final size:34
Alignment explanation
Indices: 1054421--1054515 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 34
1054411 CTAAATTCAT
*
1054421 GTTGTGATTTTCATTTTCGCATTGCGATTCACTC
1 GTTGCGATTTTCATTTTCGCATTGCGATTCACTC
*
1054455 GTTGCGATTTTCA-TTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTTCGCATTGCGATTCACTC
** * *
1054488 GTTGCGATAGTCATTTACGCGTTGCGAT
1 GTTGCGATTTTCATTTTCGCATTGCGAT
1054516 AGTCATATTC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (34 bp):
GTTGCGATTTTCATTTTCGCATTGCGATTCACTC
Found at i:1054512 original size:20 final size:20
Alignment explanation
Indices: 1054487--1054535 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1054477 GCGATTCTCT
1054487 CGTTGCGATAGTCAT-TTACG
1 CGTTGCGATAGTCATATT-CG
1054507 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATATTCG
1054527 CGTTGCGAT
1 CGTTGCGAT
1054536 TTCCGCATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATATTCG
Found at i:1056982 original size:24 final size:24
Alignment explanation
Indices: 1056948--1057001 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1056938 CTGAAACATC
1056948 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1056972 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1056996 ATCAAA
1 ATCAAA
1057002 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1057868 original size:20 final size:20
Alignment explanation
Indices: 1057843--1057889 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1057833 AAATTCAGTA
1057843 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
1057863 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
1057883 TTGCGAT
1 TTGCGAT
1057890 TTACAGATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:1057896 original size:20 final size:20
Alignment explanation
Indices: 1057853--1057933 Score: 85
Period size: 20 Copynumber: 4.0 Consensus size: 20
1057843 TTGCGATAGT
* *
1057853 CAGAATCTCGTTGCGATAGT-
1 CAGAATCGCGTTGCGAT-TTA
*
1057873 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
*
1057893 CAGATTCGCGTTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
*
1057913 C-GTATTCGCGTTGCGATTTA
1 CAG-AATCGCGTTGCGATTTA
1057933 C
1 C
1057934 GTATTCACAT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 2 0.04
20 54 0.96
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (20 bp):
CAGAATCGCGTTGCGATTTA
Found at i:1057948 original size:20 final size:20
Alignment explanation
Indices: 1057881--1057939 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
1057871 GTCAGAATCT
1057881 CGTTGCGATTTACAG-ATTCG
1 CGTTGCGATTTAC-GTATTCG
1057901 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
1057921 CGTTGCGATTTACGTATTC
1 CGTTGCGATTTACGTATTC
1057940 ACATTGCGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:1062879 original size:2 final size:2
Alignment explanation
Indices: 1062872--1062896 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1062862 ATAGTTCTGC
1062872 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1062897 GAGTTAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1069462 original size:15 final size:15
Alignment explanation
Indices: 1069442--1069497 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
1069432 GTACAAACTT
*
1069442 TTAAAAATATATATA
1 TTAAAAATATAAATA
* *
1069457 TT-AAAATTTAAAAAA
1 TTAAAAATAT-AAATA
1069472 TTAAAAAT-TAAATTA
1 TTAAAAATATAAA-TA
1069487 TTAAAAATATA
1 TTAAAAATATA
1069498 TTTAAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 9 0.27
15 17 0.52
16 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAAAATATAAATA
Found at i:1069469 original size:22 final size:22
Alignment explanation
Indices: 1069441--1069498 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1069431 AGTACAAACT
*
1069441 TTTAAAAATATATATATTAAAA
1 TTTAAAAATATATAAATTAAAA
* *
1069463 TTTAAAAA-ATTAAAAATTAAAT
1 TTTAAAAATA-TATAAATTAAAA
1069485 TATTAAAAATATAT
1 T-TTAAAAATATAT
1069499 TTAAATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 18 0.62
23 9 0.31
24 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAAATATATAAATTAAAA
Found at i:1073515 original size:24 final size:20
Alignment explanation
Indices: 1073462--1073519 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1073452 TTCCCATTAA
*
1073462 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
1073482 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
1073505 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1073520 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:1078571 original size:21 final size:21
Alignment explanation
Indices: 1078520--1078572 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1078510 ATTATTACTA
*
1078520 TCGCAATGCGATTTTTCAATT
1 TCGCAATGCGATTTTCCAATT
***
1078541 TCGTGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1078562 TCGCAATGCGA
1 TCGCAATGCGA
1078573 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1078627 original size:20 final size:19
Alignment explanation
Indices: 1078602--1078716 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 19
1078592 AATTTGGAAA
*
1078602 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
1078622 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
1078643 ATCGCAACGCGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
1078663 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATAC-TACT
* * *
1078683 TTCGCAACGAGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
1078703 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
1078717 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.06
20 47 0.59
21 24 0.30
22 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:1078644 original size:41 final size:41
Alignment explanation
Indices: 1078599--1078676 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
1078589 GCGAATTTGG
*
1078599 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
1078640 AAAATCGCAACGCGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
1078677 CTTACTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1078931 original size:20 final size:21
Alignment explanation
Indices: 1078886--1078933 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1078876 TCTCTCACCC
*
1078886 ATCTCCGACGAAATCCGTCCCT
1 ATCTCCGACAAAATCCGT-CCT
*
1078908 ATCTCCGGCAAAATCCGT-CT
1 ATCTCCGACAAAATCCGTCCT
1078928 ATCTCC
1 ATCTCC
1078934 ATCTCTCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
22 16 0.67
ACGTcount: A:0.23, C:0.40, G:0.12, T:0.25
Consensus pattern (21 bp):
ATCTCCGACAAAATCCGTCCT
Found at i:1079229 original size:20 final size:20
Alignment explanation
Indices: 1079180--1079238 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1079170 TTTATTCTCT
* **
1079180 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1079200 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
1079220 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
1079239 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1080583 original size:18 final size:18
Alignment explanation
Indices: 1080557--1080604 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1080547 TCCACTTCGG
1080557 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1080575 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1080593 GAGCCATCACCT
1 GAGCCATCACCT
1080605 GATCGACCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1081192 original size:19 final size:20
Alignment explanation
Indices: 1081138--1081204 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1081128 TAGTTTACTT
* *
1081138 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1081158 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1081178 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1081197 TCGCAACG
1 TCGCAACG
1081205 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1081231 original size:19 final size:19
Alignment explanation
Indices: 1081138--1081235 Score: 71
Period size: 20 Copynumber: 5.3 Consensus size: 19
1081128 TAGTTTACTT
* **
1081138 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1081158 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1081178 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1081197 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1081211 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1081230 TCGCAA
1 TCGCAA
1081236 TGTGATTTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 23 0.36
20 24 0.38
21 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1081339 original size:20 final size:20
Alignment explanation
Indices: 1081310--1081370 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
1081300 TTTGCATTGT
1081310 GATA-CCATTTCCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
1081329 GATAGCCATTTCCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
* *
1081349 GATAGTCATTTTCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
1081369 GA
1 GA
1081371 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 4 0.10
20 35 0.90
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.33
Consensus pattern (20 bp):
GATAGCCATTTCCGCGTTGC
Found at i:1081770 original size:21 final size:20
Alignment explanation
Indices: 1081718--1081778 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
1081708 GGCTCACCTG
1081718 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
1081738 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
1081759 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
1081779 CCCACCTTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:1081777 original size:42 final size:41
Alignment explanation
Indices: 1081718--1081796 Score: 122
Period size: 42 Copynumber: 1.9 Consensus size: 41
1081708 GGCTCACCTG
*
1081718 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCAACCGTTCAAGAGGCCCCTA
* *
1081760 TCATCCCTCAAGAGTCCCCCCCACCTTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCCCCCAACCGTTCAAGAGGCC
1081797 ATTTTCATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 15 0.44
42 19 0.56
ACGTcount: A:0.23, C:0.43, G:0.14, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCAACCGTTCAAGAGGCCCCTA
Found at i:1083247 original size:14 final size:14
Alignment explanation
Indices: 1083213--1083251 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1083203 TTGATTGTTT
1083213 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1083227 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1083241 TGTTGATTTGT
1 AATTGATTTGT
1083252 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1083415 original size:19 final size:19
Alignment explanation
Indices: 1083391--1083436 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1083381 GCAACGAGAG
1083391 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1083410 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1083429 AATCGCAA
1 AATCGCAA
1083437 CAAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1083443 original size:19 final size:19
Alignment explanation
Indices: 1083402--1083443 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1083392 ATCGCAATGC
***
1083402 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACAA
1083421 GAAATGAAAATCGCAACAA
1 GAAATGAAAATCGCAACAA
1083440 GAAA
1 GAAA
1083444 ATCGCAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.14, G:0.19, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACAA
Found at i:1083499 original size:20 final size:20
Alignment explanation
Indices: 1083474--1083516 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1083464 TCGCATTGCG
*
1083474 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1083494 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
1083514 ATT
1 ATT
1083517 GATTTCCCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1084090 original size:20 final size:20
Alignment explanation
Indices: 1084069--1084156 Score: 133
Period size: 20 Copynumber: 4.4 Consensus size: 20
1084059 TGTATTATCT
*
1084069 CGTTGC-AATAGTCAGAATCT
1 CGTTGCGAA-AGTCAGAATCG
1084089 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
1084109 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
1084129 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
1084149 CATTGCGA
1 CGTTGCGA
1084157 TTTTCCAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:1084239 original size:21 final size:22
Alignment explanation
Indices: 1084187--1084239 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1084177 ATTTATTTAT
1084187 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1084208 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1084229 TCGCATTGCGA
1 TCGCATTGCGA
1084240 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1084297 original size:20 final size:20
Alignment explanation
Indices: 1084274--1084319 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1084264 GGAAACTGAT
*
1084274 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
1084294 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
1084313 TTGCGAT
1 TTGCGAT
1084320 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:1087957 original size:41 final size:39
Alignment explanation
Indices: 1087869--1087949 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 39
1087859 GGTGATTATT
1087869 TTAATT-TTTTAAATTTTAATAATAAAAATATTATTTTA
1 TTAATTATTTTAAATTTTAATAATAAAAATATTATTTTA
* * *
1087907 TTATTTATTTTAAATTTTTTATATTAAATAATATT-TTTT-
1 TTAATTATTTTAAA-TTTTAATAATAAA-AATATTATTTTA
1087946 TTAA
1 TTAA
1087950 AATTATTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
38 5 0.14
39 10 0.28
40 15 0.42
41 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (39 bp):
TTAATTATTTTAAATTTTAATAATAAAAATATTATTTTA
Found at i:1088179 original size:5 final size:5
Alignment explanation
Indices: 1088169--1088195 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1088159 ATAAGTTGCC
1088169 AGCAG AGCAG AGCAG AGCAG AGCAG AG
1 AGCAG AGCAG AGCAG AGCAG AGCAG AG
1088196 TCCATTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.41, T:0.00
Consensus pattern (5 bp):
AGCAG
Found at i:1089019 original size:60 final size:60
Alignment explanation
Indices: 1088950--1089062 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
1088940 AATGGTCCAT
* * *
1088950 CGACTATAAGAAGTTAG-TTTGTTGAGTCTCTCTACTATTAAAAGTTATAAAATAGTTCTC
1 CGACTATAAGAAGTT-GTTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATAGTTCTC
* *
1089010 CGACTATAAGATGTTGTTTTGTTGAGTCTCCCGATTATTAAAAGTTACAAAAT
1 CGACTATAAGAAGTTGTTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAAT
1089063 TTTCACTTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (60 bp):
CGACTATAAGAAGTTGTTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATAGTTCTC
Found at i:1092214 original size:87 final size:86
Alignment explanation
Indices: 1092019--1092224 Score: 241
Period size: 87 Copynumber: 2.4 Consensus size: 86
1092009 GTACACTTGA
* * * * *** *
1092019 GAGGTTGAGTTTATACTCTTAATGAATCCATAGCCCGTGATTTGGGTGGTCCTAGTGAGATGGAC
1 GAGGTTGAGTTTACACTCTTAATGAATCCATAACCCATGACTTAAATGGTCCTAGTGAGACGGAC
*
1092084 TTGATGAATACATCAATTTAT
66 TTGATGAATACATAAATTTAT
* * *
1092105 GAGGTTAAGTTTTACACCCTTAATGAATCCATAACCCATGACTTAAATGGTCTTAGTGAGACGGA
1 GAGGTTGAG-TTTACACTCTTAATGAATCCATAACCCATGACTTAAATGGTCCTAGTGAGACGGA
* *
1092170 CTTGGTGAATACATAAATTTGT
65 CTTGATGAATACATAAATTTAT
* * *
1092192 GAGGTTGAGTTTCCAACTCTTAACGAATTCATA
1 GAGGTTGAGTTTAC-ACTCTTAATGAATCCATA
1092225 GCTTGAGTCT
Statistics
Matches: 99, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
86 12 0.12
87 87 0.88
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (86 bp):
GAGGTTGAGTTTACACTCTTAATGAATCCATAACCCATGACTTAAATGGTCCTAGTGAGACGGAC
TTGATGAATACATAAATTTAT
Found at i:1093425 original size:14 final size:14
Alignment explanation
Indices: 1093382--1093429 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
1093372 GCAGAGAGCT
1093382 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
* * *
1093396 CGTTCGGT-A-ATA
1 TGTTCGTTCATTTA
1093408 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
1093422 TGTTCGTT
1 TGTTCGTT
1093430 TATGTACGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 8 0.31
13 2 0.08
14 16 0.62
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.52
Consensus pattern (14 bp):
TGTTCGTTCATTTA
Found at i:1093439 original size:24 final size:26
Alignment explanation
Indices: 1093386--1093449 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
1093376 AGAGCTTGTT
* *
1093386 CGTTCATTTACGTTCGGTAATATGTT
1 CGTTCATTTATGTTCGGTAATATGTA
*
1093412 CGTTCATTTATGTTC-GT-TTATGTA
1 CGTTCATTTATGTTCGGTAATATGTA
*
1093436 CGTTTATTTATGTT
1 CGTTCATTTATGTT
1093450 TAGCCCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 18 0.53
25 2 0.06
26 14 0.41
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.53
Consensus pattern (26 bp):
CGTTCATTTATGTTCGGTAATATGTA
Found at i:1093642 original size:14 final size:14
Alignment explanation
Indices: 1093623--1093666 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
1093613 TTTCATTTGT
1093623 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1093637 GTTCGTTTAT-TGT-
1 GTTCGTTTATGT-TC
1093650 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1093664 GTT
1 GTT
1093667 TACATCCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.07, C:0.11, G:0.23, T:0.59
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:1093655 original size:13 final size:13
Alignment explanation
Indices: 1093619--1093659 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
1093609 CTATTTTCAT
1093619 TTGTGTTCGTTTA
1 TTGTGTTCGTTTA
1093632 -TGTTCGTTCGTTTA
1 TTG-T-GTTCGTTTA
1093646 TTGTGTTCGTTTA
1 TTGTGTTCGTTTA
1093659 T
1 T
1093660 GTTCGTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.08
13 11 0.44
14 10 0.40
15 2 0.08
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.61
Consensus pattern (13 bp):
TTGTGTTCGTTTA
Found at i:1106527 original size:18 final size:17
Alignment explanation
Indices: 1106503--1106544 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1106493 CTATATTTTA
* *
1106503 TAAATATATTTAATAAT
1 TAAATATAATAAATAAT
1106520 TCAAATATAATAAATAAT
1 T-AAATATAATAAATAAT
1106538 TAAATAT
1 TAAATAT
1106545 CTTAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATAATAAATAAT
Found at i:1122730 original size:2 final size:2
Alignment explanation
Indices: 1122723--1122750 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1122713 AAAGGGTTTG
1122723 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
1122751 GTAATATCTA
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):
AT
Found at i:1126833 original size:12 final size:12
Alignment explanation
Indices: 1126816--1126840 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1126806 TCGTTGGTGC
1126816 CGCCTTTGTCAT
1 CGCCTTTGTCAT
1126828 CGCCTTTGTCAT
1 CGCCTTTGTCAT
1126840 C
1 C
1126841 TTCGTAGTCT
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:0.08, C:0.36, G:0.16, T:0.40
Consensus pattern (12 bp):
CGCCTTTGTCAT
Found at i:1127772 original size:15 final size:15
Alignment explanation
Indices: 1127752--1127780 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1127742 TCTAATTTTT
1127752 TTTTGAGTTCAAGTC
1 TTTTGAGTTCAAGTC
1127767 TTTTGAGTTCAAGT
1 TTTTGAGTTCAAGT
1127781 TTCAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (15 bp):
TTTTGAGTTCAAGTC
Found at i:1129553 original size:29 final size:29
Alignment explanation
Indices: 1129518--1129599 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
1129508 AAACTAAATT
*
1129518 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1129547 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1129576 GATATCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1129600 GTTAGGTGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1134311 original size:29 final size:29
Alignment explanation
Indices: 1134276--1134357 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1134266 AAACTAAATT
*
1134276 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1134305 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1134334 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1134358 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1136314 original size:2 final size:2
Alignment explanation
Indices: 1136307--1136336 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1136297 TACCATATTA
1136307 AT AT AT AT AT AT A- 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
1136337 ACTACGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1138088 original size:25 final size:25
Alignment explanation
Indices: 1138041--1138090 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1138031 AGGTCCCTTC
1138041 CTCAATGGAGATAAGTTCTCCCCAT
1 CTCAATGGAGATAAGTTCTCCCCAT
1138066 CTCAATGGAGATAAGTTCTCCCCAT
1 CTCAATGGAGATAAGTTCTCCCCAT
1138091 TTACCTGCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (25 bp):
CTCAATGGAGATAAGTTCTCCCCAT
Found at i:1145576 original size:80 final size:80
Alignment explanation
Indices: 1145443--1145738 Score: 477
Period size: 80 Copynumber: 3.7 Consensus size: 80
1145433 TGTAAGTCAT
*
1145443 TACGGACCTAAGGATATCTTGGATAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1145508 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
* *
1145523 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCTTTTGTTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1145588 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
* * *
1145603 TACGGATCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
*
1145668 TGCTTAAGGTAACCC
66 TGCATAAGGTAACCC
* * * *
1145683 TACGGATCTAAGGATGTCCTTGGGTAGAT-CCAAGGTATATCCTTAGGTTGGCTCCC
1 TACGGACCTAAGGATAT-CTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCC
1145739 CTTTTTGCTG
Statistics
Matches: 202, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
80 193 0.96
81 9 0.04
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (80 bp):
TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
TGCATAAGGTAACCC
Found at i:1147417 original size:17 final size:17
Alignment explanation
Indices: 1147395--1147428 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1147385 TTGGCTTTGA
1147395 CCAAAAAGTCAAATTTT
1 CCAAAAAGTCAAATTTT
*
1147412 CCAAAAAGTCATATTTT
1 CCAAAAAGTCAAATTTT
1147429 ATGTTTTTCG
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:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (17 bp):
CCAAAAAGTCAAATTTT
Found at i:1150663 original size:2 final size:2
Alignment explanation
Indices: 1150656--1150686 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1150646 ATACCTTGTA
*
1150656 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1150687 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1154429 original size:2 final size:2
Alignment explanation
Indices: 1154420--1154482 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
1154410 AAAATATAAA
* * *
1154420 AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1154457 -T 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 A
1154483 ATCGGGGCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
1 6 0.12
2 46 0.88
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1154430 original size:35 final size:33
Alignment explanation
Indices: 1154382--1154466 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
1154372 CCCGAACCCG
*
1154382 AAAATATTTTATATATAATTAATATAAAAAAATAT
1 AAAATATTATATATATAATTAATAT--AAAAATAT
1154417 AAAATATTATATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
1154450 AAAATATTATATATATA
1 AAAATATTATATATATA
1154467 TATATATATA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 25 0.51
35 24 0.49
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAATAT
Found at i:1154467 original size:35 final size:35
Alignment explanation
Indices: 1154382--1154468 Score: 135
Period size: 35 Copynumber: 2.5 Consensus size: 35
1154372 CCCGAACCCG
1154382 AAAATATTT-TATATATAATTAATATAAAAAAATAT
1 AAAATATTTATATATATAATTAATAT-AAAAAATAT
1154417 AAAATA-TTATATATATAATTAATAT-AAAAATAT
1 AAAATATTTATATATATAATTAATATAAAAAATAT
1154450 AAAATATTATATATATATA
1 AAAATATT-TATATATATA
1154469 TATATATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
33 14 0.29
34 3 0.06
35 32 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (35 bp):
AAAATATTTATATATATAATTAATATAAAAAATAT
Found at i:1156039 original size:108 final size:108
Alignment explanation
Indices: 1155905--1156171 Score: 311
Period size: 108 Copynumber: 2.5 Consensus size: 108
1155895 AAACGGTAAG
* * *
1155905 AAAATAAGTTAATTA-TTATTTTGTTATTAATATTTTTAACATATTAGGTTACACCTAATATATT
1 AAAATAAGTTAATTACTTATTTTGTTATAAATATTATTAACATATTAGGTTACACCTAAAATATT
** * * * ** * * * *
1155969 ATGAGAGTTTAAGATGATGGGGCCTTAGAAGTCTCATGATAAC
66 ACCAAAGTTTAAGATAATAGAACATTAGAAATCTCACGACAAC
* * * *
1156012 AAAATAAGTTAATTACTTATTTTGTTATGAATATTATCAACATATTAGGTTGCACTTAAAATATT
1 AAAATAAGTTAATTACTTATTTTGTTATAAATATTATTAACATATTAGGTTACACCTAAAATATT
* *
1156077 ACCAAAGTTTAAGCTAATAGAACATTATAAATCTCACGACAAC
66 ACCAAAGTTTAAGATAATAGAACATTAGAAATCTCACGACAAC
* * *
1156120 AAAATAAGTTAAATACTTATTTTGTTATAAATAAATATTAACGTATTAGGTT
1 AAAATAAGTTAATTACTTATTTTGTTATAAAT-ATTATTAACATATTAGGTT
1156172 GCAACAAATA
Statistics
Matches: 134, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
107 15 0.11
108 103 0.77
109 16 0.12
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (108 bp):
AAAATAAGTTAATTACTTATTTTGTTATAAATATTATTAACATATTAGGTTACACCTAAAATATT
ACCAAAGTTTAAGATAATAGAACATTAGAAATCTCACGACAAC
Found at i:1157073 original size:100 final size:98
Alignment explanation
Indices: 1156899--1157199 Score: 347
Period size: 100 Copynumber: 3.0 Consensus size: 98
1156889 AAGTTGTAAA
* * * * * *
1156899 ACCGTTTATAGTATTAATATAACC-TTAAACAAACCGATAGTTAGTTTAACGTAATATGTTGCAC
1 ACCGTTTACATTATT-ATAT-ACCTTTAAACAAAACGGTAGCTAGTTTAACGTAATATGTTGCGC
*
1156963 CTATTATATTTTAACTGGTTAAGTTGTAAATATTTT
64 CTATTTTATTTTAACT-GTTAAGTTGTAAATATTTT
**
1156999 ACCGTTTACATTATTATTATACCTTTAAACAAAACGGTAGCTAGTTTAACGTAATATGTTGCGTG
1 ACCGTTTACATTATTA-TATACCTTTAAACAAAACGGTAGCTAGTTTAACGTAATATGTTGCGCC
*
1157064 TATTTTATTTTAACTGATAAGTTG-AAATATTTT
65 TATTTTATTTTAACTGTTAAGTTGTAAATATTTT
* * * * *
1157097 ACTGTTTACATTTTTATATACCTTTAAAC-AAACTAGTAACTAGTTTAAACGTAATAGGTTGCGC
1 ACCGTTTACATTATTATATACCTTTAAACAAAAC-GGTAGCTAGTTT-AACGTAATATGTTGCGC
* * *
1157161 CTATTTCATTTTAACTAGTTAAGTCGTAATTATTATT
64 CTATTTTATTTTAACT-GTTAAGTTGTAAATATT-TT
1157198 AC
1 AC
1157200 ATTATCGATA
Statistics
Matches: 173, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
96 4 0.02
97 23 0.13
98 52 0.30
99 19 0.11
100 71 0.41
101 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.42
Consensus pattern (98 bp):
ACCGTTTACATTATTATATACCTTTAAACAAAACGGTAGCTAGTTTAACGTAATATGTTGCGCCT
ATTTTATTTTAACTGTTAAGTTGTAAATATTTT
Found at i:1157158 original size:98 final size:100
Alignment explanation
Indices: 1156940--1157199 Score: 330
Period size: 98 Copynumber: 2.6 Consensus size: 100
1156930 AACCGATAGT
* * *
1156940 TAGTTTAACGTAATATGTTGCACCTATTATATTTTAACTGGTTAAGTTGTAAATATTTTACCGTT
1 TAGTTTAACGTAATATGTTGCGCCTATTTTATTTTAACTGGATAAGTTGTAAATATTTTACCGTT
* *
1157005 TACATTATTATTATACCTTTAAACAAAACGGTAGC
66 TACATTATTATTATACCTTTAAACAAAACAGTAAC
** *
1157040 TAGTTTAACGTAATATGTTGCGTGTATTTTATTTTAACT-GATAAGTTG-AAATATTTTACTGTT
1 TAGTTTAACGTAATATGTTGCGCCTATTTTATTTTAACTGGATAAGTTGTAAATATTTTACCGTT
*
1157103 TACATTTTTA-TATACCTTTAAAC-AAACTAGTAAC
66 TACATTATTATTATACCTTTAAACAAAAC-AGTAAC
* * * * * *
1157137 TAGTTTAAACGTAATAGGTTGCGCCTATTTCATTTTAACTAGTTAAGTCGTAATTATTATTAC
1 TAGTTT-AACGTAATATGTTGCGCCTATTTTATTTTAACTGGATAAGTTGTAAATATT-TTAC
1157200 ATTATCGATA
Statistics
Matches: 139, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
96 4 0.03
97 23 0.17
98 52 0.37
99 15 0.11
100 41 0.29
101 4 0.03
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (100 bp):
TAGTTTAACGTAATATGTTGCGCCTATTTTATTTTAACTGGATAAGTTGTAAATATTTTACCGTT
TACATTATTATTATACCTTTAAACAAAACAGTAAC
Found at i:1157579 original size:19 final size:20
Alignment explanation
Indices: 1157555--1157601 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1157545 GACCAACAAA
*
1157555 TTCGCAACGCGATCT-CAAT
1 TTCGCAACGCGAACTCCAAT
*
1157574 TTCGCAACGGGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
1157594 TTCGCAAC
1 TTCGCAAC
1157602 CCAGTTTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:1157638 original size:20 final size:20
Alignment explanation
Indices: 1157615--1157702 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
1157605 GTTTCCAATT
* *
1157615 TCGCAACACGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
** * **
1157635 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATTTGTAAA
*
1157655 TTCGCAACGCGAATCTGTAAA
1 -TCGCAACGCGAATTTGTAAA
1157676 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
1157696 TCGCAAC
1 TCGCAAC
1157703 ACAAAAGTCA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 39 0.74
21 14 0.26
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:1157719 original size:20 final size:20
Alignment explanation
Indices: 1157696--1157870 Score: 170
Period size: 20 Copynumber: 8.3 Consensus size: 20
1157686 AATTTGTAAA
1157696 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
1157716 TCGCAACACAAAAGTTAAAT
1 TCGCAACACAAAAGTCAAAT
* *
1157736 CCGCAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * * *
1157756 TCGCAACGCGATAGCCAAAT
1 TCGCAACACAAAAGTCAAAT
*
1157776 TCGAAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
1157796 TCGCAACACAAAAATAAAATTAGCAAAT
1 TCGCAACAC------AAAAGT--CAAAT
*
1157824 TCGAAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
1157844 TCGCAACACAAAAATAAAAT
1 TCGCAACACAAAAGTCAAAT
1157864 TCGCAAC
1 TCGCAAC
1157871 GCGATAGGAA
Statistics
Matches: 125, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
20 102 0.82
22 5 0.04
26 5 0.04
28 13 0.10
ACGTcount: A:0.50, C:0.23, G:0.10, T:0.16
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:1157720 original size:40 final size:39
Alignment explanation
Indices: 1157676--1157802 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 39
1157666 AATCTGTAAA
1157676 TCGCAACGCGAATTTGTAAATCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAA-TTGTAAATCGCAACACAAAAGTCAAAT
* ** *
1157716 TCGCAACAC-AAAAGTTAAATCCGCAACACATAAGTCAAAT
1 TCGCAACGCGAATTG-TAAAT-CGCAACACAAAAGTCAAAT
* * *
1157756 TCGCAACGCG-ATAGCCAAATTCGAAACACAAAAGTCAAAT
1 TCGCAACGCGAATTG-TAAA-TCGCAACACAAAAGTCAAAT
1157796 TCGCAAC
1 TCGCAAC
1157803 ACAAAAATAA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 7 0.10
40 64 0.88
41 1 0.01
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.17
Consensus pattern (39 bp):
TCGCAACGCGAATTGTAAATCGCAACACAAAAGTCAAAT
Found at i:1157842 original size:48 final size:48
Alignment explanation
Indices: 1157771--1157869 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
1157761 ACGCGATAGC
1157771 CAAATTCGAAACACAAAAGTCAAATTCGCAACACAAAAATAAAATTAG
1 CAAATTCGAAACACAAAAGTCAAATTCGCAACACAAAAATAAAATTAG
*
1157819 CAAATTCGAAACACAAAAGTCAAATTCGCAACACAAAAATAAAATTCG
1 CAAATTCGAAACACAAAAGTCAAATTCGCAACACAAAAATAAAATTAG
1157867 CAA
1 CAA
1157870 CGCGATAGGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (48 bp):
CAAATTCGAAACACAAAAGTCAAATTCGCAACACAAAAATAAAATTAG
Found at i:1158427 original size:14 final size:14
Alignment explanation
Indices: 1158395--1158428 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1158385 ATACGAAAAT
1158395 GAAAATCGCAACAC
1 GAAAATCGCAACAC
* *
1158409 CAAAATCGCAACGC
1 GAAAATCGCAACAC
1158423 GAAAAT
1 GAAAAT
1158429 GAAAATCGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACAC
Done.