Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 156 of 160
Found at i:31799417 original size:17 final size:17
Alignment explanation
Indices: 31799377--31799421 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
31799367 ATCATGCATC
*
31799377 AATATAAAAAAATACTT
1 AATATAAAAAAATACAT
*
31799394 AAAATAACAAAAATA-AT
1 AATATAA-AAAAATACAT
31799411 AATATAAAAAA
1 AATATAAAAAA
31799422 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 4 0.17
17 13 0.54
18 7 0.29
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (17 bp):
AATATAAAAAAATACAT
Found at i:31800813 original size:74 final size:74
Alignment explanation
Indices: 31800673--31800813 Score: 158
Period size: 74 Copynumber: 1.9 Consensus size: 74
31800663 TCAAGTAATA
* * * *
31800673 AAAAAAATGATCAGGACGACACCGCAAGTCGAGAAGTAAGAAAACAATCGGGACAACACTGCAAG
1 AAAAAAATGATCAAGACAACACCGCAAGTCGAGAAGTAAGAAAACAATCGAGACAACACCGCAAG
31800738 TCGAAAAGT
66 TCGAAAAGT
* * * * * * * *
31800747 AAAAAAATGATCAAGATAACATCGCGAGTTGAGAAGTAA-ATAATCGATCGAGATAACACCGTAA
1 AAAAAAATGATCAAGACAACACCGCAAGTCGAGAAGTAAGA-AAACAATCGAGACAACACCGCAA
31800811 GTC
65 GTC
31800814 AAGAAATTAT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
73 1 0.02
74 53 0.98
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (74 bp):
AAAAAAATGATCAAGACAACACCGCAAGTCGAGAAGTAAGAAAACAATCGAGACAACACCGCAAG
TCGAAAAGT
Found at i:31801108 original size:87 final size:86
Alignment explanation
Indices: 31800838--31801086 Score: 302
Period size: 87 Copynumber: 2.9 Consensus size: 86
31800828 GAAGGTCTTA
* * * * * * *
31800838 GAAATCATGCCCGAAGGTCTTATAAAATCGACTGAGACAACACTGCAAGCCAAAATTAATGAATC
1 GAAATCATGCCCGAAGGTCTTACAGAATCGACTGGGATAACACTGCAAGTCAAAATTAAAGAATT
31800903 GATCGGGATAACACGTGAATC
66 GATCGGGATAACACGTGAATC
* * * * *
31800924 GAAATTATGCCCGAAAGTCTTACAGAATCGA-TCAGGATAACACCGTAAGTCAAAATTAAAGAAT
1 GAAATCATGCCCGAAGGTCTTACAGAATCGACT-GGGATAACACTGCAAGTCAAAATTAAAGAAT
* *
31800988 TGATCGGGATAACACCATGAATT
65 TGATCGGGATAACA-CGTGAATC
* * * *
31801011 GAAATCATGCCCGGAGGTCTCACAGAATCGACTGGGATAACACTGCAAGTCGAGATTAAAGAATT
1 GAAATCATGCCCGAAGGTCTTACAGAATCGACTGGGATAACACTGCAAGTCAAAATTAAAGAATT
*
31801076 GATTGGGATAA
66 GATCGGGATAA
31801087 TATCGCGAAT
Statistics
Matches: 136, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
85 1 0.01
86 64 0.47
87 70 0.51
88 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (86 bp):
GAAATCATGCCCGAAGGTCTTACAGAATCGACTGGGATAACACTGCAAGTCAAAATTAAAGAATT
GATCGGGATAACACGTGAATC
Found at i:31801255 original size:132 final size:131
Alignment explanation
Indices: 31801015--31801260 Score: 298
Period size: 132 Copynumber: 1.9 Consensus size: 131
31801005 TGAATTGAAA
* * ** * * * *
31801015 TCATGCCCGGAGGTCTCACAGAATCGACTGGGATAACACTGCAAGTCGAGATTAAAGAATTGATT
1 TCATGCCCGGAAGTCTCACAGAATCGACCGGGATAACACCACAAGTCAAAATTAAAGAATCGATC
* *
31801080 GGGATAATATCGCGAATCAAAATTATGCCTGAATGTCTGAGAAATCATGCTCGAAGGTTTTAGAA
66 GGGATAATATCGCAAATCAAAATTATGCCTGAAGGTCTGAGAAATCATGCTCGAAGGTTTTAGAA
31801145 G
131 G
* * *
31801146 TCATGCCTGGAAGTCTTACAGAATCGACCGGGATAACACCACAAAGTCAAAATTAGAGAATCGAT
1 TCATGCCCGGAAGTCTCACAGAATCGACCGGGATAACACCAC-AAGTCAAAATTAAAGAATCGAT
* * * *
31801211 CGGGATAAT-CCTGCAAATCAAAATTATG-ATCGGAGGTCTTAGAAATCATG
65 CGGGATAATATC-GCAAATCAAAATTATGCCT-GAAGGTCTGAGAAATCATG
31801261 ATTTTTAAAT
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
131 38 0.40
132 57 0.60
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (131 bp):
TCATGCCCGGAAGTCTCACAGAATCGACCGGGATAACACCACAAGTCAAAATTAAAGAATCGATC
GGGATAATATCGCAAATCAAAATTATGCCTGAAGGTCTGAGAAATCATGCTCGAAGGTTTTAGAA
G
Found at i:31801845 original size:33 final size:33
Alignment explanation
Indices: 31801808--31802147 Score: 113
Period size: 33 Copynumber: 10.4 Consensus size: 33
31801798 CCTTGAAAGT
* *
31801808 TTAAAACTTCTTTTGGGGCCAAATAAACTGAGC
1 TTAAAACTTCTTTTGAGGCCAGATAAACTGAGC
* * *
31801841 TT-AAA-TT-TTATTGAAGGCTAGCTAAACTGGGC
1 TTAAAACTTCTT-TTG-AGGCCAGATAAACTGAGC
* * * *
31801873 TTAAAACCTCATTTGAGGCCAGGTAAACTAAGC
1 TTAAAACTTCTTTTGAGGCCAGATAAACTGAGC
* * *
31801906 TTAAAACTTC-ATTGATGGTCAGATAAACTG-GG
1 TTAAAACTTCTTTTGA-GGCCAGATAAACTGAGC
* * *
31801938 TTTAAA-TGTC-ATTGATGGTCAGATAAACT-AGGC
1 TTAAAACT-TCTTTTGA-GGCCAGATAAACTGA-GC
* * * * *
31801971 TT-AAA-TGTC-ATTAATGGCTAGATAAATTGGGC
1 TTAAAACT-TCTTTTGA-GGCCAGATAAACTGAGC
* * * *
31802003 TTAAAGCTTC-ATTAACGGTCAGATAAACTGAGC
1 TTAAAACTTCTTTTGA-GGCCAGATAAACTGAGC
* * *
31802036 TT-AAA-TATC-ATTGATGGCCAAATAAACTGGGC
1 TTAAAACT-TCTTTTGA-GGCCAGATAAACTGAGC
* * * *
31802068 TTAAAA-TT-TTATTAATGACCAAATAAACTGGGC
1 TTAAAACTTCTT-TTGA-GGCCAGATAAACTGAGC
* * *
31802101 TTAAAACTTC-ATTAATGGTCAGATAAACTGAGC
1 TTAAAACTTCTTTTGA-GGCCAGATAAACTGAGC
*
31802134 TTAAAACTTTTTTT
1 TTAAAACTTCTTTT
31802148 TTGGCGATCC
Statistics
Matches: 242, Mismatches: 46, Indels: 37
0.74 0.14 0.11
Matches are distributed among these distances:
30 2 0.01
31 7 0.03
32 100 0.41
33 123 0.51
34 9 0.04
35 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (33 bp):
TTAAAACTTCTTTTGAGGCCAGATAAACTGAGC
Found at i:31801950 original size:65 final size:65
Alignment explanation
Indices: 31801824--31802139 Score: 216
Period size: 65 Copynumber: 4.8 Consensus size: 65
31801814 CTTCTTTTGG
* * * * * **
31801824 GGCCAAATAAACTGAGCTTAAATTTTATTGAA-GG-CTAGCTAAACTGGGCTTAAAACCTCATTT
1 GGCCAGATAAACTAAGCTTAAATATCATT-AATGGTC-AGATAAACTGGGCTTAAAATGTCA-TT
31801887 GA-
63 GAC
* * *
31801889 GGCCAGGTAAACTAAGCTTAAA-ACTTCATTGATGGTCAGATAAACTGGG-TTTAAATGTCATTG
1 GGCCAGATAAACTAAGCTTAAATA--TCATTAATGGTCAGATAAACTGGGCTTAAAATGTCATTG
*
31801952 AT
64 AC
* * * * * *
31801954 GGTCAGATAAACTAGGCTTAAATGTCATTAATGG-CTAGATAAATTGGGCTTAAAGCT-TCATTA
1 GGCCAGATAAACTAAGCTTAAATATCATTAATGGTC-AGATAAACTGGGCTTAAA-ATGTCATTG
31802017 AC
64 AC
* * * * * * * * *
31802019 GGTCAGATAAACTGAGCTTAAATATCATTGATGGCCAAATAAACTGGGCTTAAAATTTTATTAAT
1 GGCCAGATAAACTAAGCTTAAATATCATTAATGGTCAGATAAACTGGGCTTAAAATGTCATTGAC
* * ** *
31802084 GACCAAATAAACTGGGCTTAAA-ACTTCATTAATGGTCAGATAAACTGAGCTTAAAA
1 GGCCAGATAAACTAAGCTTAAATA--TCATTAATGGTCAGATAAACTGGGCTTAAAA
31802140 CTTTTTTTTT
Statistics
Matches: 201, Mismatches: 37, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
63 1 0.00
64 26 0.13
65 127 0.63
66 46 0.23
67 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (65 bp):
GGCCAGATAAACTAAGCTTAAATATCATTAATGGTCAGATAAACTGGGCTTAAAATGTCATTGAC
Found at i:31801955 original size:32 final size:32
Alignment explanation
Indices: 31801914--31802138 Score: 222
Period size: 32 Copynumber: 6.9 Consensus size: 32
31801904 GCTTAAAACT
* *
31801914 TCATTGATGGTCAGATAAACTGGGTTTAAATG
1 TCATTAATGGTCAGATAAACTGGGCTTAAATG
* *
31801946 TCATTGATGGTCAGATAAACTAGGCTTAAATG
1 TCATTAATGGTCAGATAAACTGGGCTTAAATG
*
31801978 TCATTAATGG-CTAGATAAATTGGGCTTAAA-G
1 TCATTAATGGTC-AGATAAACTGGGCTTAAATG
* * *
31802009 CTTCATTAACGGTCAGATAAACTGAGCTTAAATA
1 --TCATTAATGGTCAGATAAACTGGGCTTAAATG
* * * *
31802043 TCATTGATGGCCAAATAAACTGGGCTTAAAATT
1 TCATTAATGGTCAGATAAACTGGGCTT-AAATG
* ** *
31802076 TTATTAATGACCAAATAAACTGGGCTTAAAACT-
1 TCATTAATGGTCAGATAAACTGGGCTT-AAA-TG
*
31802109 TCATTAATGGTCAGATAAACTGAGCTTAAA
1 TCATTAATGGTCAGATAAACTGGGCTTAAA
31802139 ACTTTTTTTT
Statistics
Matches: 163, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.01
32 80 0.49
33 79 0.48
34 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (32 bp):
TCATTAATGGTCAGATAAACTGGGCTTAAATG
Found at i:31809474 original size:19 final size:19
Alignment explanation
Indices: 31809450--31809493 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
31809440 TCCTTAAAAT
31809450 AAAATAATAATCTTTATAG
1 AAAATAATAATCTTTATAG
*
31809469 AAAAT-A-AGTCTTTATAG
1 AAAATAATAATCTTTATAG
*
31809486 AAGATAAT
1 AAAATAAT
31809494 TGTTAGTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 14 0.67
18 2 0.10
19 5 0.24
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (19 bp):
AAAATAATAATCTTTATAG
Found at i:31809482 original size:17 final size:16
Alignment explanation
Indices: 31809455--31809493 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
31809445 AAAATAAAAT
31809455 AATAATCTTTATAGAA
1 AATAATCTTTATAGAA
31809471 AATAAGTCTTTATAGAA
1 AATAA-TCTTTATAGAA
*
31809488 GATAAT
1 AATAAT
31809494 TGTTAGTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (16 bp):
AATAATCTTTATAGAA
Found at i:31819483 original size:21 final size:18
Alignment explanation
Indices: 31819459--31819506 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 18
31819449 ATATTTACTA
31819459 TTAATTAATTATGAATCAAAT
1 TTAATTAATTAT--AT-AAAT
31819480 TTAATT-ATT-TATAAAT
1 TTAATTAATTATATAAAT
31819496 TTAATTAATTA
1 TTAATTAATTA
31819507 AAAATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 10 0.40
17 5 0.20
19 1 0.04
20 3 0.12
21 6 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAATTAATTATATAAAT
Found at i:31819511 original size:16 final size:16
Alignment explanation
Indices: 31819476--31819511 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31819466 ATTATGAATC
* *
31819476 AAATTTAATTATTTAT
1 AAATTTAATTAATTAA
31819492 AAATTTAATTAATTAA
1 AAATTTAATTAATTAA
31819508 AAAT
1 AAAT
31819512 AAATATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTAATTAATTAA
Found at i:31822960 original size:70 final size:71
Alignment explanation
Indices: 31822886--31823019 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 71
31822876 AAAATGAGGC
*
31822886 AGAAAAGAAAAAAAGA-ACATATATATACACACAAC-AAAAAAATATACAACATGAAAAATCTTA
1 AGAAAA-AAAAAAAGATACATATATATACACACAACAAAAAAAATATACAAAATGAAAAATCTTA
31822949 GAAAAAA
65 GAAAAAA
* * * * *
31822956 AGAAAAAAATATATATATATATATATATACACAACAAAAAAAATATACAAAATGAAAAATCTTA
1 AGAAAAAAAAAAAGATACATATATATACACACAACAAAAAAAATATACAAAATGAAAAATCTTA
31823020 AGGAATGAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
69 6 0.11
70 23 0.41
71 27 0.48
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.19
Consensus pattern (71 bp):
AGAAAAAAAAAAAGATACATATATATACACACAACAAAAAAAATATACAAAATGAAAAATCTTAG
AAAAAA
Found at i:31825260 original size:76 final size:77
Alignment explanation
Indices: 31825107--31825248 Score: 241
Period size: 76 Copynumber: 1.9 Consensus size: 77
31825097 CATTTATAAT
* * * *
31825107 TTAATACATTGTTTTTTTTTCAATTAAACAACAATCCATTAATTATGCTTTTTAATTTAAATATC
1 TTAATACATTGTTTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATC
31825172 ACCATTAACATA
66 ACCATTAACATA
31825184 TTAATACATTG-TTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATC
1 TTAATACATTGTTTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATC
31825248 A
66 A
31825249 TTGTTGACAT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
76 50 0.82
77 11 0.18
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (77 bp):
TTAATACATTGTTTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATC
ACCATTAACATA
Found at i:31833484 original size:21 final size:18
Alignment explanation
Indices: 31833460--31833507 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 18
31833450 ATATTTACTA
31833460 TTAATTAATTATGAATCAAAT
1 TTAATTAATTAT--AT-AAAT
31833481 TTAATT-ATT-TATAAAT
1 TTAATTAATTATATAAAT
31833497 TTAATTAATTA
1 TTAATTAATTA
31833508 AAAATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 10 0.40
17 5 0.20
19 1 0.04
20 3 0.12
21 6 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAATTAATTATATAAAT
Found at i:31833512 original size:16 final size:16
Alignment explanation
Indices: 31833477--31833512 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31833467 ATTATGAATC
* *
31833477 AAATTTAATTATTTAT
1 AAATTTAATTAATTAA
31833493 AAATTTAATTAATTAA
1 AAATTTAATTAATTAA
31833509 AAAT
1 AAAT
31833513 AAATATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTAATTAATTAA
Found at i:31839254 original size:76 final size:75
Alignment explanation
Indices: 31839103--31839241 Score: 226
Period size: 75 Copynumber: 1.9 Consensus size: 75
31839093 TTTTATTAAT
* * * *
31839103 TTAATACATTGTTTTTTTTCAATTAAACAACATCCATTAATTATGCTTTTTAATTTAAATATCAC
1 TTAATACATTGTTCTTTTTCAATTAAAAAACATACATTAATTATACTTTTTAATTTAAATATCAC
31839168 CATTAACATA
66 CATTAACATA
31839178 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTT-ATTTAAATATCA
1 TTAATACATTGTTCTTTTTCAATTAAAAAAC-ATACATTAATTATACTTTTTAATTTAAATATCA
31839242 TTGTTTGACA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 41 0.69
76 18 0.31
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (75 bp):
TTAATACATTGTTCTTTTTCAATTAAAAAACATACATTAATTATACTTTTTAATTTAAATATCAC
CATTAACATA
Found at i:31847429 original size:21 final size:18
Alignment explanation
Indices: 31847405--31847452 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 18
31847395 ATATTTACTA
31847405 TTAATTAATTATGAATCAAAT
1 TTAATTAATTAT--AT-AAAT
31847426 TTAATT-ATT-TATAAAT
1 TTAATTAATTATATAAAT
31847442 TTAATTAATTA
1 TTAATTAATTA
31847453 AAAATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 10 0.40
17 5 0.20
19 1 0.04
20 3 0.12
21 6 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAATTAATTATATAAAT
Found at i:31847457 original size:16 final size:16
Alignment explanation
Indices: 31847422--31847457 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31847412 ATTATGAATC
* *
31847422 AAATTTAATTATTTAT
1 AAATTTAATTAATTAA
31847438 AAATTTAATTAATTAA
1 AAATTTAATTAATTAA
31847454 AAAT
1 AAAT
31847458 AAATATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTAATTAATTAA
Found at i:31847912 original size:37 final size:37
Alignment explanation
Indices: 31847795--31847912 Score: 102
Period size: 37 Copynumber: 3.1 Consensus size: 37
31847785 CATTTATAAT
*
31847795 TTAATACATTGTTCTCTTTCAATTAAAAAACAATACA
1 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACA
* * *
31847832 TTAAT-TA-TG--CTTTTT-AATTTAAATATCACCATTAACATA
1 TTAATACATTGTTCTTTTTCAA-TTAAA-A--AACAAT-AC--A
31847871 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACA
1 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACA
31847908 TTAAT
1 TTAAT
31847913 TATACTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 24
0.67 0.08 0.26
Matches are distributed among these distances:
32 2 0.03
33 10 0.16
34 1 0.02
35 2 0.03
36 5 0.08
37 13 0.21
39 8 0.13
40 5 0.08
41 2 0.03
42 1 0.02
43 11 0.18
44 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.42
Consensus pattern (37 bp):
TTAATACATTGTTCTTTTTCAATTAAAAAACAATACA
Found at i:31847947 original size:76 final size:76
Alignment explanation
Indices: 31847795--31847935 Score: 264
Period size: 76 Copynumber: 1.9 Consensus size: 76
31847785 CATTTATAAT
*
31847795 TTAATACATTGTTCTCTTTCAATTAAAAAACAATACATTAATTATGCTTTTTAATTTAAATATCA
1 TTAATACATTGTTCTCTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATCA
31847860 CCATTAACATA
66 CCATTAACATA
*
31847871 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATCA
1 TTAATACATTGTTCTCTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATCA
31847936 TTGTTGACAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 63 1.00
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.44
Consensus pattern (76 bp):
TTAATACATTGTTCTCTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATCA
CCATTAACATA
Found at i:31849820 original size:15 final size:15
Alignment explanation
Indices: 31849802--31849832 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31849792 TTCTGCTTCT
31849802 TCTTCTTCATCATCA
1 TCTTCTTCATCATCA
*
31849817 TCTTCTTCATCTTCA
1 TCTTCTTCATCATCA
31849832 T
1 T
31849833 TTTCGACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (15 bp):
TCTTCTTCATCATCA
Found at i:31850120 original size:2 final size:2
Alignment explanation
Indices: 31850107--31850145 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
31850097 ATATAGAATG
*
31850107 AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
31850146 TATATATCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:31858211 original size:18 final size:18
Alignment explanation
Indices: 31858188--31858222 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31858178 GAATTTGGGT
*
31858188 GAAGATGCTGATGATGAA
1 GAAGATGATGATGATGAA
31858206 GAAGATGATGATGATGA
1 GAAGATGATGATGATGA
31858223 TGAGGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.34, T:0.23
Consensus pattern (18 bp):
GAAGATGATGATGATGAA
Found at i:31875359 original size:3 final size:3
Alignment explanation
Indices: 31875353--31875387 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31875343 TAACAACAAC
31875353 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
31875388 AAAGATTAAA
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:31876020 original size:54 final size:53
Alignment explanation
Indices: 31875946--31876081 Score: 182
Period size: 54 Copynumber: 2.5 Consensus size: 53
31875936 TCCTAAAAAA
* * * *
31875946 ATTGAAATAACTCGTTGAAATTGTAAAATAACCCATGTAAATTACGTAAAGTTT
1 ATTGAAACAATTCGTTGAAATTATAAAATAACCCATGTAAATTAC-TAAACTTT
* * *
31876000 ATTGGAGCAATTCGTTGAAATTATAAAATGACCCATGTAAATTACTAAACTTT
1 ATTGAAACAATTCGTTGAAATTATAAAATAACCCATGTAAATTACTAAACTTT
* *
31876053 ATTGAAACAATTCGTTAAAATTACAAAAT
1 ATTGAAACAATTCGTTGAAATTATAAAAT
31876082 GATCCCTATA
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
53 32 0.45
54 39 0.55
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (53 bp):
ATTGAAACAATTCGTTGAAATTATAAAATAACCCATGTAAATTACTAAACTTT
Found at i:31876075 original size:53 final size:54
Alignment explanation
Indices: 31875946--31876096 Score: 189
Period size: 53 Copynumber: 2.8 Consensus size: 54
31875936 TCCTAAAAAA
* * * * *
31875946 ATTGAAATAACTCGTTGAAATTGTAAAATAACCCATGTAAATTACGTAAAGTTT
1 ATTGAAACAATTCGTTGAAATTATAAAATGACCCATGTAAATTACGTAAACTTT
* *
31876000 ATTGGAGCAATTCGTTGAAATTATAAAATGACCCATGTAAATTAC-TAAACTTT
1 ATTGAAACAATTCGTTGAAATTATAAAATGACCCATGTAAATTACGTAAACTTT
* * *
31876053 ATTGAAACAATTCGTTAAAATTACAAAATGATCCC-TATAAATTA
1 ATTGAAACAATTCGTTGAAATTATAAAATGA-CCCATGTAAATTA
31876097 TATGAACTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
53 42 0.50
54 42 0.50
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (54 bp):
ATTGAAACAATTCGTTGAAATTATAAAATGACCCATGTAAATTACGTAAACTTT
Found at i:31880301 original size:14 final size:15
Alignment explanation
Indices: 31880282--31880311 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31880272 AATGCAACTG
31880282 AATTTTT-TTAATTA
1 AATTTTTGTTAATTA
31880296 AATTTTTGTTAATTA
1 AATTTTTGTTAATTA
31880311 A
1 A
31880312 TTAATCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
AATTTTTGTTAATTA
Found at i:31896431 original size:39 final size:39
Alignment explanation
Indices: 31896354--31896432 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
31896344 GGATGGTTCC
* * * * *
31896354 TAATTATACAGAAGCAACCTTATTAGGTCATTTTTTAGT
1 TAATGATACACAAACAACCTTATTAGGTCAGTTATTAGT
* *
31896393 TAATGATACACAAACAACCTTATTATGTTAGTTATTAGT
1 TAATGATACACAAACAACCTTATTAGGTCAGTTATTAGT
31896432 T
1 T
31896433 TTGTATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (39 bp):
TAATGATACACAAACAACCTTATTAGGTCAGTTATTAGT
Found at i:31912432 original size:21 final size:21
Alignment explanation
Indices: 31912393--31912432 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31912383 TTAGTCGCTC
*
31912393 CTCTTTTTTCCTTTCAATTTT
1 CTCTTTTTTCCTTTAAATTTT
**
31912414 CTCTTTTTTTTTTTAAATT
1 CTCTTTTTTCCTTTAAATT
31912433 AAAAAGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.70
Consensus pattern (21 bp):
CTCTTTTTTCCTTTAAATTTT
Found at i:31926440 original size:22 final size:22
Alignment explanation
Indices: 31926406--31926452 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
31926396 GAGTCCATTT
* *
31926406 ATAATTACCAAGAATTA-CAAA
1 ATAATAACCAAGAAGTAGCAAA
31926427 ATAATAACACAAGAAGTAGCAAA
1 ATAATAAC-CAAGAAGTAGCAAA
31926450 ATA
1 ATA
31926453 CCATACGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAATAACCAAGAAGTAGCAAA
Found at i:31943580 original size:24 final size:23
Alignment explanation
Indices: 31943544--31943588 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
31943534 AATTTATCAC
*
31943544 ATATATTATAAA-TATTATTTTGA
1 ATATATTAAAAATTA-TATTTTGA
31943567 ATATAATTAAAAATTATATTTT
1 ATAT-ATTAAAAATTATATTTT
31943589 TATACTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 13 0.68
25 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATATTAAAAATTATATTTTGA
Found at i:31952049 original size:27 final size:28
Alignment explanation
Indices: 31951999--31952055 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
31951989 AAGTTATTCT
*
31951999 AAAAATCAAGTTTAGATAGGGAAAGAAG
1 AAAAATCAAGTTTAGATAGCGAAAGAAG
31952027 AAAAATCAAGTTTAGATA-CGAAAGAAG
1 AAAAATCAAGTTTAGATAGCGAAAGAAG
31952054 AA
1 AA
31952056 GAGTGAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (28 bp):
AAAAATCAAGTTTAGATAGCGAAAGAAG
Found at i:31953570 original size:4 final size:4
Alignment explanation
Indices: 31953552--31953586 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
31953542 AAGAAAATAT
* *
31953552 ATAC ATGC ATGC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
31953587 GATATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:31954909 original size:2 final size:2
Alignment explanation
Indices: 31954896--31954925 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31954886 ATCACTTTAA
*
31954896 AT AT AT AA 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
31954926 GAATTGCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31965636 original size:34 final size:31
Alignment explanation
Indices: 31965554--31965636 Score: 78
Period size: 34 Copynumber: 2.5 Consensus size: 31
31965544 ATATAATACG
*
31965554 ATAAAATAATAAAAATTTTCATATAAAAAAAT
1 ATAATATAATAAAAA-TTTCATATAAAAAAAT
* *
31965586 ATAATATAATTTAAAATTTCAATATAAATTAAAT
1 ATAATATAA-TAAAAATTTC-ATATAAA-AAAAT
31965620 ATAAGT-TCAATAAAAAT
1 ATAA-TAT-AATAAAAAT
31965637 ATATGTTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
32 12 0.29
33 12 0.29
34 15 0.36
35 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (31 bp):
ATAATATAATAAAAATTTCATATAAAAAAAT
Found at i:31966453 original size:12 final size:12
Alignment explanation
Indices: 31966436--31966461 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31966426 TTTTAAAATA
31966436 TAAATATTTTAT
1 TAAATATTTTAT
31966448 TAAATATTTTAT
1 TAAATATTTTAT
31966460 TA
1 TA
31966462 TAATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAATATTTTAT
Found at i:31968980 original size:18 final size:18
Alignment explanation
Indices: 31968957--31968996 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
31968947 AAAAAAAAGA
31968957 AAACCACTCTTATCTAGT
1 AAACCACTCTTATCTAGT
* *
31968975 AAACCACTGTTCTCTAGT
1 AAACCACTCTTATCTAGT
31968993 AAAC
1 AAAC
31968997 TTTAATGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (18 bp):
AAACCACTCTTATCTAGT
Found at i:31972118 original size:18 final size:18
Alignment explanation
Indices: 31972095--31972166 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 18
31972085 TTGAAATTAA
31972095 AATAATATAATAATTTTT
1 AATAATATAATAATTTTT
* * *
31972113 AATAATTTATTAA-TATT
1 AATAATATAATAATTTTT
* *
31972130 AAGTAATCTAA-AACTTTT
1 AA-TAATATAATAATTTTT
*
31972148 -ATGATAT-ATAATTTTT
1 AATAATATAATAATTTTT
31972164 AAT
1 AAT
31972167 CTAATACTTC
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
15 1 0.02
16 10 0.24
17 10 0.24
18 20 0.49
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
AATAATATAATAATTTTT
Found at i:31990711 original size:17 final size:17
Alignment explanation
Indices: 31990689--31990721 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31990679 TTTTGTACAG
31990689 TCCCTTCCAAATACAAT
1 TCCCTTCCAAATACAAT
31990706 TCCCTTCCAAATACAA
1 TCCCTTCCAAATACAA
31990722 ATATAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.27
Consensus pattern (17 bp):
TCCCTTCCAAATACAAT
Found at i:31993867 original size:15 final size:16
Alignment explanation
Indices: 31993843--31993875 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31993833 TGCGTAAATA
31993843 TACTTAATTT-CTTCT
1 TACTTAATTTACTTCT
*
31993858 TACTTCATTTACTTCT
1 TACTTAATTTACTTCT
31993874 TA
1 TA
31993876 GAGCTTGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (16 bp):
TACTTAATTTACTTCT
Found at i:31996689 original size:97 final size:97
Alignment explanation
Indices: 31996523--31996721 Score: 380
Period size: 97 Copynumber: 2.1 Consensus size: 97
31996513 GCCAATATCA
31996523 ATGGATTATACAGTGCCAAGCTTTGAAGAAAAATAAAATGTCATTAAGCCAATTCTACCACGACA
1 ATGGATTATACAGTGCCAAGCTTTGAAGAAAAATAAAATGTCATTAAGCCAATTCTACCACGACA
31996588 CTATGATACAAGCAACCACTACATATAATTGT
66 CTATGATACAAGCAACCACTACATATAATTGT
* *
31996620 ATGGATTATACAGTGCCAAGCTTTGAAGAAGAATAAAATGTCATTAAGCCAATTCTACCACGATA
1 ATGGATTATACAGTGCCAAGCTTTGAAGAAAAATAAAATGTCATTAAGCCAATTCTACCACGACA
31996685 CTATGATACAAGCAACCACTACATATAATTGT
66 CTATGATACAAGCAACCACTACATATAATTGT
31996717 ATGGA
1 ATGGA
31996722 GAAAACTGTT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 100 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (97 bp):
ATGGATTATACAGTGCCAAGCTTTGAAGAAAAATAAAATGTCATTAAGCCAATTCTACCACGACA
CTATGATACAAGCAACCACTACATATAATTGT
Found at i:32015730 original size:27 final size:27
Alignment explanation
Indices: 32015678--32015730 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
32015668 CTTATGAAAT
* * *
32015678 AAAAATAATAAATAAATAAAAGAAAGG
1 AAAAATAAAAAAAAAATAAAACAAAGG
*
32015705 AAAAATAAAAAAAAAATAAGACAAAG
1 AAAAATAAAAAAAAAATAAAACAAAG
32015731 AAGCAATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.11
Consensus pattern (27 bp):
AAAAATAAAAAAAAAATAAAACAAAGG
Found at i:32019280 original size:15 final size:15
Alignment explanation
Indices: 32019256--32019293 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
32019246 ACCTAGCCTC
32019256 AAAAAA-AAAAAAAA
1 AAAAAACAAAAAAAA
*
32019270 AAAAAACAAAATAAA
1 AAAAAACAAAAAAAA
*
32019285 ACAAAACAA
1 AAAAAACAA
32019294 GGGAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAAAACAAAAAAAA
Found at i:32019818 original size:12 final size:12
Alignment explanation
Indices: 32019783--32019827 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
32019773 ATCATATGGC
*
32019783 CCATGATCATCA
1 CCATCATCATCA
32019795 CCATCA-CGATCA
1 CCATCATC-ATCA
32019807 CCATCATCATCA
1 CCATCATCATCA
*
32019819 TCATCATCA
1 CCATCATCA
32019828 GCAGCAGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 1 0.03
12 27 0.93
13 1 0.03
ACGTcount: A:0.33, C:0.38, G:0.04, T:0.24
Consensus pattern (12 bp):
CCATCATCATCA
Found at i:32022058 original size:26 final size:27
Alignment explanation
Indices: 32022017--32022082 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 27
32022007 TCCATGTTGG
32022017 AAAGAAAGAGAAAGAACAAAAGCAAAAAT
1 AAAGAAA-AGAAAGAACAAAAG-AAAAAT
**
32022046 -AAG-AAAGAAAGAAGGAAAGAAAAAT
1 AAAGAAAAGAAAGAACAAAAGAAAAAT
32022071 AAAGAAAAGAAA
1 AAAGAAAAGAAA
32022083 AGAAACCAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 6 0.18
26 15 0.45
27 9 0.27
28 3 0.09
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.03
Consensus pattern (27 bp):
AAAGAAAAGAAAGAACAAAAGAAAAAT
Found at i:32036048 original size:17 final size:17
Alignment explanation
Indices: 32036026--32036062 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
32036016 TTGTTTTGTC
32036026 TTTTTTTCCTTTGTTTT
1 TTTTTTTCCTTTGTTTT
**
32036043 TTTTTTTTTTTTGTTTT
1 TTTTTTTCCTTTGTTTT
32036060 TTT
1 TTT
32036063 GATGGACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.89
Consensus pattern (17 bp):
TTTTTTTCCTTTGTTTT
Found at i:32037183 original size:21 final size:21
Alignment explanation
Indices: 32037158--32037200 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
32037148 ATCGATCTAA
*
32037158 TGCATGTATCTAAAGTCAAGT
1 TGCATGTACCTAAAGTCAAGT
32037179 TGCATGTACCTAAAGTCAAGT
1 TGCATGTACCTAAAGTCAAGT
32037200 T
1 T
32037201 CGAATCCGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (21 bp):
TGCATGTACCTAAAGTCAAGT
Found at i:32038214 original size:2 final size:2
Alignment explanation
Indices: 32038207--32038241 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
32038197 ATTATTGTTA
* *
32038207 AT AT AT AT AT AT AT AT AT CT AT AG AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32038242 CCAGCTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:32045867 original size:2 final size:2
Alignment explanation
Indices: 32045860--32045884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32045850 AATTAATAAT
32045860 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
32045885 AAAGTAGCAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:32059969 original size:20 final size:20
Alignment explanation
Indices: 32059944--32060006 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 20
32059934 TACAGGTTGG
32059944 ATGCAAAATAACAAGTGCAA
1 ATGCAAAATAACAAGTGCAA
* * *
32059964 ATGC-AACTAA-AGGTTG--G
1 ATGCAAAATAACAAG-TGCAA
*
32059981 ATGCACAATAACAAGTGCAA
1 ATGCAAAATAACAAGTGCAA
32060001 ATGCAA
1 ATGCAA
32060007 CTAAAAGTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 4 0.13
18 8 0.27
19 9 0.30
20 9 0.30
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (20 bp):
ATGCAAAATAACAAGTGCAA
Found at i:32059991 original size:37 final size:37
Alignment explanation
Indices: 32059937--32060011 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
32059927 ATGTCAATAC
32059937 AGGTTGGATGCAAAATAACAAGTGCAAATGCAACTAA
1 AGGTTGGATGCAAAATAACAAGTGCAAATGCAACTAA
*
32059974 AGGTTGGATGCACAATAACAAGTGCAAATGCAACTAA
1 AGGTTGGATGCAAAATAACAAGTGCAAATGCAACTAA
32060011 A
1 A
32060012 AGTTTCAGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (37 bp):
AGGTTGGATGCAAAATAACAAGTGCAAATGCAACTAA
Found at i:32067249 original size:22 final size:23
Alignment explanation
Indices: 32067224--32067275 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
32067214 GTAAATTTAA
32067224 TTTTATAAATT-AAAAATAAAAT
1 TTTTATAAATTAAAAAATAAAAT
** *
32067246 TTTT-TATTTTAAAAAATAAATT
1 TTTTATAAATTAAAAAATAAAAT
32067268 TATTTATA
1 T-TTTATA
32067276 CAAATAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 4 0.17
22 15 0.62
23 3 0.12
24 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTATAAATTAAAAAATAAAAT
Found at i:32086016 original size:2 final size:2
Alignment explanation
Indices: 32086009--32086039 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32085999 TTATTAGGCG
32086009 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 T
32086040 TGGCAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32105044 original size:3 final size:3
Alignment explanation
Indices: 32105030--32105059 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
32105020 TGAGGATGAT
32105030 AAG AACG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AA-G AAG AAG AAG AAG AAG AAG AAG AA
32105060 TCAATCTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.03, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:32110106 original size:3 final size:3
Alignment explanation
Indices: 32110098--32110137 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
32110088 CTCTCTATAT
32110098 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
32110138 CTAAGACTTT
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:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:32111176 original size:51 final size:52
Alignment explanation
Indices: 32111060--32111214 Score: 138
Period size: 51 Copynumber: 3.0 Consensus size: 52
32111050 TATAACCATA
* * * * * * *
32111060 CAAACTTGCCCATTAAAAATC-TCTCTCCTCTTAAAATT-TTTTTTCTGTAAGT
1 CAAACTTACCTATTAAAAATCACCT-TTCTCTTAAAATTCTTCTCT-TGCAAGT
* * *
32111112 CAAACTTACCTATTAAGAATC-CCTTTACTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAAAATCACCTTT-CTCTTAAAATTCTTCTCTTGCAAGT
* * *
32111164 C-AACTTACCTATTAAAAATCATCTTTCTCTTAAAATTCTTCTTTTGTAAGT
1 CAAACTTACCTATTAAAAATCACCTTTCTCTTAAAATTCTTCTCTTGCAAGT
32111215 TTTCTTGTCA
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
51 40 0.48
52 40 0.48
53 4 0.05
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.43
Consensus pattern (52 bp):
CAAACTTACCTATTAAAAATCACCTTTCTCTTAAAATTCTTCTCTTGCAAGT
Found at i:32111265 original size:22 final size:22
Alignment explanation
Indices: 32111240--32111282 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
32111230 GCAATATCTG
*
32111240 ACAAATCTTAAATAAATCTCTA
1 ACAAATCTCAAATAAATCTCTA
32111262 ACAAATCTCAAATAAATCTCT
1 ACAAATCTCAAATAAATCTCT
32111283 TATAGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (22 bp):
ACAAATCTCAAATAAATCTCTA
Found at i:32111281 original size:11 final size:11
Alignment explanation
Indices: 32111242--32111281 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
32111232 AATATCTGAC
*
32111242 AAATCTTAAAT
1 AAATCTCAAAT
* *
32111253 AAATCTCTAAC
1 AAATCTCAAAT
32111264 AAATCTCAAAT
1 AAATCTCAAAT
32111275 AAATCTC
1 AAATCTC
32111282 TTATAGATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATCTCAAAT
Found at i:32113822 original size:2 final size:2
Alignment explanation
Indices: 32113815--32113856 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
32113805 TACGTATGTG
* *
32113815 TA TA TA TA TA TA TA TA TA TA TA TA TGC TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA T
32113857 GCATTTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 34 0.97
3 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32117494 original size:8 final size:8
Alignment explanation
Indices: 32117481--32117512 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
32117471 ATCTATCATC
32117481 TTATATAT
1 TTATATAT
32117489 TTATATAT
1 TTATATAT
*
32117497 ATATATAT
1 TTATATAT
32117505 TTATATAT
1 TTATATAT
32117513 GTTCATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATATAT
Found at i:32124725 original size:17 final size:18
Alignment explanation
Indices: 32124703--32124738 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
32124693 CTATTTTCAA
32124703 ATTTTTATATT-ATATTT
1 ATTTTTATATTCATATTT
*
32124720 ATTTTTGTATTCATATTT
1 ATTTTTATATTCATATTT
32124738 A
1 A
32124739 ATAGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTTTTATATTCATATTT
Found at i:32124917 original size:27 final size:25
Alignment explanation
Indices: 32124860--32124923 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 25
32124850 TTTTTTTTTT
*
32124860 ATATATTTAAGTAATATTTTTAGAAAT
1 ATATA-TTAA-TAATATTTTTAGAAAA
*
32124887 ATATATTAATATATATTTTTAATAAAA
1 ATATATTAATA-ATATTTTT-AGAAAA
32124914 ATATATTAAT
1 ATATATTAAT
32124924 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 2 0.06
26 12 0.36
27 19 0.58
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
ATATATTAATAATATTTTTAGAAAA
Found at i:32124988 original size:22 final size:21
Alignment explanation
Indices: 32124934--32124983 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
32124924 TTTAATTAAT
32124934 TTAAA-ATAATAATTTATATTA
1 TTAAATATAA-AATTTATATTA
32124955 TTAAATATAAAATTTAT-TTA
1 TTAAATATAAAATTTATATTA
32124975 TTAAATATA
1 TTAAATATA
32124984 TAAAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.43
21 12 0.43
22 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATATAAAATTTATATTA
Found at i:32125263 original size:32 final size:32
Alignment explanation
Indices: 32125222--32125287 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
32125212 AAAACATTTT
32125222 AATTAAAATGTTACGAATGCTACAAAAATAGA
1 AATTAAAATGTTACGAATGCTACAAAAATAGA
32125254 AATTAAAATGTTACGAATGCTACAAAAATAGA
1 AATTAAAATGTTACGAATGCTACAAAAATAGA
32125286 AA
1 AA
32125288 GGTGTTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (32 bp):
AATTAAAATGTTACGAATGCTACAAAAATAGA
Found at i:32128273 original size:10 final size:10
Alignment explanation
Indices: 32128249--32128285 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
32128239 TATTTTGCTC
*
32128249 GCTCTCTC-G
1 GCTCTCTCTA
32128258 GCTCTCTCTA
1 GCTCTCTCTA
32128268 GCTCTCTCTA
1 GCTCTCTCTA
32128278 GCTCTCTC
1 GCTCTCTC
32128286 GCTTCACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.05, C:0.43, G:0.14, T:0.38
Consensus pattern (10 bp):
GCTCTCTCTA
Found at i:32130020 original size:12 final size:12
Alignment explanation
Indices: 32129977--32130021 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
32129967 TAATTCAGTG
32129977 TACATATCATATA
1 TACATAT-ATATA
* *
32129990 TACATACATACA
1 TACATATATATA
32130002 TACATATATATA
1 TACATATATATA
*
32130014 TATATATA
1 TACATATA
32130022 GTCCTCTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 21 0.78
13 6 0.22
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (12 bp):
TACATATATATA
Found at i:32137384 original size:20 final size:20
Alignment explanation
Indices: 32137359--32137421 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
32137349 TAGTAGATTG
32137359 ATCAGAATCATTCTAGTGGC
1 ATCAGAATCATTCTAGTGGC
*
32137379 ATCAGAATCATTCTAGTAGC
1 ATCAGAATCATTCTAGTGGC
* *
32137399 ATCGGAATCATTTTAGTGGC
1 ATCAGAATCATTCTAGTGGC
32137419 ATC
1 ATC
32137422 CTTGTCAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (20 bp):
ATCAGAATCATTCTAGTGGC
Found at i:32137598 original size:2 final size:2
Alignment explanation
Indices: 32137591--32137620 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32137581 CGTATGTCTC
32137591 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
32137621 AGACATCACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:32140650 original size:16 final size:16
Alignment explanation
Indices: 32140629--32140660 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
32140619 TTATGAAACT
32140629 ATAGTAAAGCAAAGAC
1 ATAGTAAAGCAAAGAC
32140645 ATAGTAAAGCAAAGAC
1 ATAGTAAAGCAAAGAC
32140661 CTTTCCGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.12
Consensus pattern (16 bp):
ATAGTAAAGCAAAGAC
Found at i:32145298 original size:15 final size:15
Alignment explanation
Indices: 32145278--32145321 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
32145268 AAAATAAAAC
32145278 AAAATTATAAATATT
1 AAAATTATAAATATT
32145293 AAAATT-TAAA-ATTT
1 AAAATTATAAATA-TT
32145307 AAAATTATTAAATAT
1 AAAATTA-TAAATAT
32145322 CACATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.04
14 12 0.48
15 6 0.24
16 5 0.20
17 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:32146357 original size:16 final size:15
Alignment explanation
Indices: 32146336--32146366 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
32146326 TTTTATAAAA
32146336 AAATTAAATTTCTATT
1 AAATTAAATTT-TATT
32146352 AAATTAAATTTTATT
1 AAATTAAATTTTATT
32146367 TATTTTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATTAAATTTTATT
Found at i:32147086 original size:3 final size:3
Alignment explanation
Indices: 32147078--32147108 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
32147068 TCTTTTATTG
*
32147078 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
32147109 CGGATTTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:32151652 original size:26 final size:26
Alignment explanation
Indices: 32151616--32151668 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
32151606 GTTAACCTAT
32151616 TCCATAGCCCAAAGTTCAAACAAGAA
1 TCCATAGCCCAAAGTTCAAACAAGAA
32151642 TCCATAGCCCAAAGTTCAAACAAGAA
1 TCCATAGCCCAAAGTTCAAACAAGAA
32151668 T
1 T
32151669 AGAGCCCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.17
Consensus pattern (26 bp):
TCCATAGCCCAAAGTTCAAACAAGAA
Found at i:32156467 original size:13 final size:13
Alignment explanation
Indices: 32156454--32156502 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
32156444 GGTAAAATTT
32156454 ATAAAATATTTTTA
1 ATAAAATA-TTTTA
*
32156468 A-AAAATAATTTA
1 ATAAAATATTTTA
32156480 ATAAAAT-TTTTA
1 ATAAAATATTTTA
*
32156492 ATAAAAAATTT
1 ATAAAATATTT
32156503 AAATTTATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 15 0.50
13 14 0.47
14 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAAAATATTTTA
Found at i:32160880 original size:16 final size:16
Alignment explanation
Indices: 32160861--32160894 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
32160851 ACCCTAATTG
32160861 CCCCAAAAAAAAAAAA
1 CCCCAAAAAAAAAAAA
* *
32160877 CCCCAAAAGAAAGAAA
1 CCCCAAAAAAAAAAAA
32160893 CC
1 CC
32160895 AAAGCACACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.29, G:0.06, T:0.00
Consensus pattern (16 bp):
CCCCAAAAAAAAAAAA
Found at i:32166340 original size:2 final size:2
Alignment explanation
Indices: 32166327--32166357 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
32166317 GCCTCAATTG
*
32166327 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32166358 ATAAAAATAA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:32167519 original size:23 final size:21
Alignment explanation
Indices: 32167493--32167534 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
32167483 ATGTTATAAA
*
32167493 TGGAAGGAAGATCTCTTATCTCC
1 TGGAAAGAAGAT-TC-TATCTCC
32167516 TGGAAAGAAGATTCTATCT
1 TGGAAAGAAGATTCTATCT
32167535 TTTCTCGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (21 bp):
TGGAAAGAAGATTCTATCTCC
Found at i:32175250 original size:77 final size:77
Alignment explanation
Indices: 32175163--32175312 Score: 282
Period size: 77 Copynumber: 1.9 Consensus size: 77
32175153 TTCTTTCCCG
32175163 TCTTTTTTGTCTTTTAGGCCTTTTGTTTCCATTATTTTGCTTACTTTTCGGCATAGATTACAATT
1 TCTTTTTTGTCTTTTAGGCCTTTTGTTTCCATTATTTTGCTTACTTTTCGGCATAGATTACAATT
32175228 TAACTTTCCTTT
66 TAACTTTCCTTT
* *
32175240 TCTTTTTTGTCTTTTAGGCCTTTTGTTTCCATTATTTTGTTTACTTTTCGGCATAGATTATAATT
1 TCTTTTTTGTCTTTTAGGCCTTTTGTTTCCATTATTTTGCTTACTTTTCGGCATAGATTACAATT
32175305 TAACTTTC
66 TAACTTTC
32175313 TATTATAATT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.16, C:0.17, G:0.11, T:0.57
Consensus pattern (77 bp):
TCTTTTTTGTCTTTTAGGCCTTTTGTTTCCATTATTTTGCTTACTTTTCGGCATAGATTACAATT
TAACTTTCCTTT
Found at i:32186504 original size:38 final size:38
Alignment explanation
Indices: 32186462--32186541 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
32186452 AGATTTGAGC
* *
32186462 ATTTGATATTTTAGATTAATTTATTTATTATGATTTTT
1 ATTTGATATTTTAAATTAATTTATTTATTATGATTTAT
32186500 ATTTGATATTTTAAATTAATTTATTTATTATGATTTAT
1 ATTTGATATTTTAAATTAATTTATTTATTATGATTTAT
32186538 ATTT
1 ATTT
32186542 TTATGAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (38 bp):
ATTTGATATTTTAAATTAATTTATTTATTATGATTTAT
Found at i:32189237 original size:8 final size:8
Alignment explanation
Indices: 32189224--32189248 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
32189214 GCCAAGCAGT
32189224 TGCTTAAA
1 TGCTTAAA
32189232 TGCTTAAA
1 TGCTTAAA
32189240 TGCTTAAA
1 TGCTTAAA
32189248 T
1 T
32189249 TATCGAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (8 bp):
TGCTTAAA
Found at i:32191606 original size:26 final size:23
Alignment explanation
Indices: 32191559--32191609 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
32191549 TTATTTATTA
*
32191559 TTAATTAATTTTAAATCGAATAT
1 TTAATTAATTTTAAATCAAATAT
32191582 TTAATATAATATTTAAATCTAAATAT
1 TTAAT-TAAT-TTTAAATC-AAATAT
32191608 TT
1 TT
32191610 CTTTCCTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 8 0.33
26 7 0.29
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAATTAATTTTAAATCAAATAT
Found at i:32193471 original size:7 final size:7
Alignment explanation
Indices: 32193456--32193484 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
32193446 TTTTTTCCAC
32193456 AAAAA-A
1 AAAAAGA
32193462 AAAAAGA
1 AAAAAGA
32193469 AAAAAGA
1 AAAAAGA
32193476 AAAAAGA
1 AAAAAGA
32193483 AA
1 AA
32193485 TGTACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:32194473 original size:14 final size:14
Alignment explanation
Indices: 32194451--32194485 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
32194441 GTAAACGAGA
32194451 TTAAAATGAATTTT
1 TTAAAATGAATTTT
*
32194465 TTTAAATGAATTTT
1 TTAAAATGAATTTT
32194479 TTAAAAT
1 TTAAAAT
32194486 ATATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (14 bp):
TTAAAATGAATTTT
Found at i:32195032 original size:14 final size:15
Alignment explanation
Indices: 32195013--32195046 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
32195003 TGTCTCAAAT
32195013 TTTTAAAAAATA-AA
1 TTTTAAAAAATATAA
*
32195027 TTTTAAATAATATAA
1 TTTTAAAAAATATAA
32195042 TTTTA
1 TTTTA
32195047 GGTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTTAAAAAATATAA
Found at i:32208564 original size:12 final size:12
Alignment explanation
Indices: 32208547--32208571 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32208537 ATTTCGGGTC
32208547 ACACACACACAT
1 ACACACACACAT
32208559 ACACACACACAT
1 ACACACACACAT
32208571 A
1 A
32208572 TATATATATA
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:0.52, C:0.40, G:0.00, T:0.08
Consensus pattern (12 bp):
ACACACACACAT
Found at i:32216284 original size:27 final size:27
Alignment explanation
Indices: 32216231--32216305 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
32216221 ACATTGGGTA
* *
32216231 GGTTGAGAATCTGGTTTTGAAATGGCT
1 GGTTGAGAATCTAGTTTTGAAACGGCT
*
32216258 GGTTGAGATTCTAGTTTT-AAAGCGGCT
1 GGTTGAGAATCTAGTTTTGAAA-CGGCT
* * * *
32216285 AGTTGGGAATATGGTTTTGAA
1 GGTTGAGAATCTAGTTTTGAA
32216306 GGGGTTGGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 3 0.08
27 33 0.87
28 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.32, T:0.37
Consensus pattern (27 bp):
GGTTGAGAATCTAGTTTTGAAACGGCT
Found at i:32220671 original size:14 final size:14
Alignment explanation
Indices: 32220652--32220682 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
32220642 AATTAAATTA
32220652 AAAAGAAGAAGAAG
1 AAAAGAAGAAGAAG
32220666 AAAAGAAGAAGAAG
1 AAAAGAAGAAGAAG
32220680 AAA
1 AAA
32220683 GCTTTGGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAGAAG
Found at i:32226128 original size:4 final size:4
Alignment explanation
Indices: 32226121--32226155 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
32226111 TTCATGCATG
32226121 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CAT
32226156 TGCAATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:32228761 original size:15 final size:16
Alignment explanation
Indices: 32228736--32228776 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
32228726 CAAATGAGAG
32228736 ATTTATCCTTTTC-CTT
1 ATTT-TCCTTTTCACTT
32228752 ATTTTCC-TTTCACTT
1 ATTTTCCTTTTCACTT
*
32228767 ATTTCCCTTT
1 ATTTTCCTTT
32228777 ATTTTCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.18
15 12 0.55
16 6 0.27
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTCCTTTTCACTT
Found at i:32236309 original size:21 final size:19
Alignment explanation
Indices: 32236267--32236301 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
32236257 GAAAAAAATA
32236267 ATTT-ATTATAATAATTTT
1 ATTTAATTATAATAATTTT
32236285 -TTTAATTATAATAATTT
1 ATTTAATTATAATAATTT
32236302 ATTATTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTAATTATAATAATTTT
Found at i:32236576 original size:18 final size:18
Alignment explanation
Indices: 32236553--32236595 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
32236543 CAAATTAAGA
32236553 TATTAAAAAAATAAAAAT
1 TATTAAAAAAATAAAAAT
* * *
32236571 TATTAATAAATTAAATAT
1 TATTAAAAAAATAAAAAT
32236589 TATTAAA
1 TATTAAA
32236596 TATTTATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATTAAAAAAATAAAAAT
Found at i:32253818 original size:17 final size:17
Alignment explanation
Indices: 32253796--32253832 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
32253786 ATAGCTTTTG
32253796 TATATATAAAAAAATAT
1 TATATATAAAAAAATAT
32253813 TATATATAAAAAAATAT
1 TATATATAAAAAAATAT
32253830 TAT
1 TAT
32253833 TAGCACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATATATAAAAAAATAT
Found at i:32262149 original size:22 final size:22
Alignment explanation
Indices: 32262123--32262164 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
32262113 GTAAAATAAA
32262123 AGTATAAAATTTATCAAAAATG
1 AGTATAAAATTTATCAAAAATG
* *
32262145 AGTATTAAATTTATTAAAAA
1 AGTATAAAATTTATCAAAAA
32262165 GTAACACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (22 bp):
AGTATAAAATTTATCAAAAATG
Found at i:32288747 original size:22 final size:22
Alignment explanation
Indices: 32288722--32288763 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
32288712 TTATTTTTAA
* *
32288722 TTTCATCGAAATTAATATCATT
1 TTTCATCAAAATCAATATCATT
*
32288744 TTTCATTAAAATCAATATCA
1 TTTCATCAAAATCAATATCA
32288764 ACGTCTATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.43
Consensus pattern (22 bp):
TTTCATCAAAATCAATATCATT
Found at i:32294133 original size:20 final size:21
Alignment explanation
Indices: 32294108--32294157 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
32294098 TATTTTAAGA
*
32294108 TTTATTTATATTCATTTA-GG
1 TTTATTTATATTCATTTATAG
*
32294128 TTTATTTATATTTATTTATAG
1 TTTATTTATATTCATTTATAG
32294149 TTTATTTAT
1 TTTATTTAT
32294158 TTAAATTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (21 bp):
TTTATTTATATTCATTTATAG
Found at i:32298947 original size:15 final size:15
Alignment explanation
Indices: 32298915--32298958 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
32298905 GTTCTCAGAA
*
32298915 TTTTGAATTTTAAAG
1 TTTTGGATTTTAAAG
**
32298930 TTTTGGATTTTACGG
1 TTTTGGATTTTAAAG
*
32298945 TTTAGGATTTTAAA
1 TTTTGGATTTTAAA
32298959 TTTAAGGGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.27, C:0.02, G:0.18, T:0.52
Consensus pattern (15 bp):
TTTTGGATTTTAAAG
Found at i:32298997 original size:30 final size:30
Alignment explanation
Indices: 32298963--32299108 Score: 102
Period size: 29 Copynumber: 5.0 Consensus size: 30
32298953 TTTAAATTTA
*
32298963 AGGGTTCGAGGTTTTAGTTTTAGGGTTTTG
1 AGGGTTTGAGGTTTTAGTTTTAGGGTTTTG
* * * ** *
32298993 AGGGTTTGGGGTTTCAATTTCGGGGTTTAG
1 AGGGTTTGAGGTTTTAGTTTTAGGGTTTTG
*
32299023 A-GGTTTTAGAG-TTTAGTTTTAGGGTTTTG
1 AGGGTTTGAG-GTTTTAGTTTTAGGGTTTTG
* * * * * *
32299052 AGGGTTTAAGGTTTCA-ATTTCGGGGTTTA
1 AGGGTTTGAGGTTTTAGTTTTAGGGTTTTG
* **
32299081 AGGGTTTG-GATTTTAGGGTTAGGGTTTT
1 AGGGTTTGAGGTTTTAGTTTTAGGGTTTT
32299109 AAGGTTTAGA
Statistics
Matches: 85, Mismatches: 27, Indels: 9
0.70 0.22 0.07
Matches are distributed among these distances:
28 5 0.06
29 45 0.53
30 35 0.41
ACGTcount: A:0.16, C:0.03, G:0.36, T:0.45
Consensus pattern (30 bp):
AGGGTTTGAGGTTTTAGTTTTAGGGTTTTG
Found at i:32299039 original size:59 final size:58
Alignment explanation
Indices: 32298975--32299116 Score: 196
Period size: 59 Copynumber: 2.4 Consensus size: 58
32298965 GGTTCGAGGT
** *
32298975 TTTAGTTTTAGGGTTTTGAGGGTTTGGGGTTTCAATTTCGGGGTTTAGAGGTTTTAGAG
1 TTTAGTTTTAGGGTTTTGAGGGTTTAAGGTTTCAATTTCGGGGTTTA-AGGGTTTAGAG
* *
32299034 TTTAGTTTTAGGGTTTTGAGGGTTTAAGGTTTCAATTTCGGGGTTTAAGGGTTTGGAT
1 TTTAGTTTTAGGGTTTTGAGGGTTTAAGGTTTCAATTTCGGGGTTTAAGGGTTTAGAG
** *
32299092 TTTAGGGTTAGGGTTTT-AAGGTTTA
1 TTTAGTTTTAGGGTTTTGAGGGTTTA
32299117 GATTTTTTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
57 7 0.09
58 23 0.31
59 45 0.60
ACGTcount: A:0.17, C:0.03, G:0.34, T:0.46
Consensus pattern (58 bp):
TTTAGTTTTAGGGTTTTGAGGGTTTAAGGTTTCAATTTCGGGGTTTAAGGGTTTAGAG
Found at i:32299043 original size:22 final size:22
Alignment explanation
Indices: 32299018--32299059 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
32299008 AATTTCGGGG
32299018 TTTAGAGGTTTT-AGAGTTTAGT
1 TTTAG-GGTTTTGAGAGTTTAGT
*
32299040 TTTAGGGTTTTGAGGGTTTA
1 TTTAGGGTTTTGAGAGTTTA
32299060 AGGTTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (22 bp):
TTTAGGGTTTTGAGAGTTTAGT
Found at i:32299047 original size:29 final size:29
Alignment explanation
Indices: 32298975--32299059 Score: 98
Period size: 30 Copynumber: 2.9 Consensus size: 29
32298965 GGTTCGAGGT
* *
32298975 TTTAGTTTTAGGGTTTTGAGGGTTTGGGG
1 TTTAGTTTTAGGGTTTTGAGGGTTTAGAG
* ** * *
32299004 TTTCAATTTCGGGGTTTAGAGGTTTTAGAG
1 TTT-AGTTTTAGGGTTTTGAGGGTTTAGAG
32299034 TTTAGTTTTAGGGTTTTGAGGGTTTA
1 TTTAGTTTTAGGGTTTTGAGGGTTTA
32299060 AGGTTTCAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
29 21 0.49
30 22 0.51
ACGTcount: A:0.15, C:0.02, G:0.34, T:0.48
Consensus pattern (29 bp):
TTTAGTTTTAGGGTTTTGAGGGTTTAGAG
Found at i:32299099 original size:22 final size:22
Alignment explanation
Indices: 32299047--32299107 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
32299037 AGTTTTAGGG
32299047 TTTTGAGGGTTTAA-GGTTTCAA
1 TTTT-AGGGTTTAAGGGTTTCAA
** **
32299069 TTTCGGGGTTTAAGGGTTTGGA
1 TTTTAGGGTTTAAGGGTTTCAA
32299091 TTTTAGGG-TT-AGGGTTT
1 TTTTAGGGTTTAAGGGTTT
32299108 TAAGGTTTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 7 0.22
21 10 0.31
22 15 0.47
ACGTcount: A:0.16, C:0.03, G:0.34, T:0.46
Consensus pattern (22 bp):
TTTTAGGGTTTAAGGGTTTCAA
Found at i:32299260 original size:35 final size:32
Alignment explanation
Indices: 32299202--32299284 Score: 85
Period size: 35 Copynumber: 2.5 Consensus size: 32
32299192 ATTTTTACGA
32299202 TTTTTGAAAATTAATTAAAAATTTTCATATATTT
1 TTTTTGAAAATTAATTAAAAA-TTT-ATATATTT
* ** *
32299236 TTTTATGAAAATTTATTATTAATTTATTTATTT
1 TTTT-TGAAAATTAATTAAAAATTTATATATTT
* *
32299269 TTTTTAAAAAATAATT
1 TTTTTGAAAATTAATT
32299285 TTTCAACATC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 9 0.22
33 11 0.27
34 7 0.17
35 14 0.34
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (32 bp):
TTTTTGAAAATTAATTAAAAATTTATATATTT
Found at i:32299375 original size:3 final size:3
Alignment explanation
Indices: 32299369--32299410 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
32299359 AAAAAAAAAT
*
32299369 TTA TTA TTA TTA TTA TTA TT- TTA -GA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
32299411 TTTTAAGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 32 0.91
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:32299399 original size:22 final size:22
Alignment explanation
Indices: 32299371--32299412 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
32299361 AAAAAAATTT
32299371 ATTATTATTATTATTATTTTAG
1 ATTATTATTATTATTATTTTAG
32299393 ATTATTATTATTATTATTTT
1 ATTATTATTATTATTATTTT
32299413 TTAAGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTATTATTATTTTAG
Found at i:32299403 original size:25 final size:24
Alignment explanation
Indices: 32299369--32299447 Score: 92
Period size: 25 Copynumber: 3.3 Consensus size: 24
32299359 AAAAAAAAAT
32299369 TTATTATTATTATTATTATTTTAGA
1 TTATTATTATTATTATT-TTTTAGA
32299394 TTATTATTATTATTATTTTTTAAGCA
1 TTATTATTATTATTATTTTTT-AG-A
* *
32299420 TTTTTACTA-TA-TATTTTTTAG-
1 TTATTATTATTATTATTTTTTAGA
32299441 TTATTAT
1 TTATTAT
32299448 CCTATTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
21 5 0.10
23 2 0.04
24 12 0.25
25 21 0.44
26 8 0.17
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.65
Consensus pattern (24 bp):
TTATTATTATTATTATTTTTTAGA
Found at i:32300588 original size:3 final size:3
Alignment explanation
Indices: 32300580--32300623 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
32300570 ATTAAACCAA
32300580 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
32300624 AACAAGTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:32301160 original size:20 final size:19
Alignment explanation
Indices: 32301123--32301162 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
32301113 AATTTTTCAA
*
32301123 TGAATTTTTCGACCAATTT
1 TGAATTTTTCGACAAATTT
*
32301142 TGAATTTTTTGATCAAATTT
1 TGAATTTTTCGA-CAAATTT
32301162 T
1 T
32301163 CCAGTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (19 bp):
TGAATTTTTCGACAAATTT
Found at i:32301573 original size:17 final size:18
Alignment explanation
Indices: 32301551--32301588 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
32301541 TTTTTTTTAA
*
32301551 ATTTATTTGTTTATT-TT
1 ATTTATTTATTTATTATT
32301568 ATTTATTTATTTATTATT
1 ATTTATTTATTTATTATT
32301586 ATT
1 ATT
32301589 ATTAGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTATTTATTTATTATT
Found at i:32301856 original size:57 final size:56
Alignment explanation
Indices: 32301661--32302141 Score: 201
Period size: 58 Copynumber: 8.2 Consensus size: 56
32301651 TGATTTTCCT
* * * * * *
32301661 AAAATAAAATTTCAAAAAAAAATTTGAGA-AAAAGT-TAAAAGTATCAATTTTTCTTG
1 AAAATAAAATTT-AAAAAATATTTTTAAAGAAAAGTGGAAAA-TATCAATTTTTCTTA
* ** * *
32301717 AAAATAAAATTTTTAAATAAAATATTTTTGAAAG-AAAGTTGAATGTATCAA-TTTCCTTTC
1 AAAATAAAA--TTT-AA-AAAATATTTTT-AAAGAAAAGTGGAAAATATCAATTTTTC-TTA
* * * *** *
32301777 AACACAAAA-TAAAAAAATATATTTTTGGGAGCAAGTGGAAAATATCAATTTTTCTTGA
1 AAAATAAAATTTAAAAAATAT-TTTTAAAGA-AAAGTGGAAAATATCAATTTTTCTT-A
* *
32301835 AAAA-AAAGATTTAAAAAATATTTTTAAAGAAAAGTTGAAAGTATCAATTTTTCTTA
1 AAAATAAA-ATTTAAAAAATATTTTTAAAGAAAAGTGGAAAATATCAATTTTTCTTA
* ** * *
32301891 AAAATAAAATTTAAAAAATATATTTTTTTTAAA-AAAAGTTGAATGTATCAA-TTTCCTTG
1 AAAATAAAATTT-AAAAA-ATA---TTTTTAAAGAAAAGTGGAAAATATCAATTTTTCTTA
* * * * *
32301950 ACAACAAAATTTCTTTTTAAAAAAAAGATATTTTT-GAGAAAAAGTTGAAAGTATCAATTTTTCT
1 AAAATAAAA------TTT---AAAAA-ATATTTTTAAAG-AAAAGTGGAAAATATCAATTTTTCT
*
32302014 TG
55 TA
* * * * * *
32302016 AAATTAAAATTTCAAAAAAAATATTTT-GAGAAAAAGTTGAAAGTACCAATTTTTCTTA
1 AAAATAAAATTT-AAAAAATAT-TTTTAAAG-AAAAGTGGAAAATATCAATTTTTCTTA
* * * *
32302074 AAAGTAAAATTATCAGGAAAAATATTTTTAAAGAAAAGTTGAAAGTATGAATTTTTCTT-
1 AAAATAAAATT-T-A--AAAAATATTTTTAAAGAAAAGTGGAAAATATCAATTTTTCTTA
32302133 AAAATAAAA
1 AAAATAAAA
32302142 ACCTTCAAAT
Statistics
Matches: 337, Mismatches: 52, Indels: 69
0.74 0.11 0.15
Matches are distributed among these distances:
55 8 0.02
56 24 0.07
57 52 0.15
58 70 0.21
59 46 0.14
60 70 0.21
61 19 0.06
63 1 0.00
64 5 0.01
65 20 0.06
66 13 0.04
67 9 0.03
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.36
Consensus pattern (56 bp):
AAAATAAAATTTAAAAAATATTTTTAAAGAAAAGTGGAAAATATCAATTTTTCTTA
Found at i:32302048 original size:58 final size:58
Alignment explanation
Indices: 32301661--32302141 Score: 387
Period size: 60 Copynumber: 8.2 Consensus size: 58
32301651 TGATTTTCCT
*
32301661 AAAATAAAATTTCAAAAAAAA-A-TTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTG
1 AAAATAAAATTTCAAAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
* * * * *
32301717 AAAATAAAATTTTTAAATAAAATATTTTTGA-AAGAAAGTTGAATGTATCAA-TTTCCTTTC
1 AAAATAAAA-TTTCAAAAAAAATA-TTTTGAGAA-AAAGTTGAAAGTATCAATTTTTC-TTG
* * * ** * *
32301777 AACACAAAA--T-AAAAAAATATATTTTTGGGAGCAAGTGGAAAATATCAATTTTTCTTG
1 AAAATAAAATTTCAAAAAAA-ATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
* * * *
32301834 AAAAAAAAGATTT---AAAAAATATTTTTAAAGAAAAGTTGAAAGTATCAATTTTTCTTA
1 AAAATAAA-ATTTCAAAAAAAATATTTTGAGA-AAAAGTTGAAAGTATCAATTTTTCTTG
* * * * *
32301891 AAAATAAAATTT-AAAAAATATATTTTTTTTAAAAAAAGTTGAATGTATCAA-TTTCCTTG
1 AAAATAAAATTTCAAAAAA-A-A-TATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
* *
32301950 ACAACAAAATTTCTTTTTAAAAAAAAGATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAATAAAATTTC------AAAAAAA-ATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
32302015 G
58 G
* *
32302016 AAATTAAAATTTCAAAAAAAATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTT-
1 AAAATAAAATTTCAAAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
** * * *
32302073 AAAAGTAAAATTATCAGGAAAAATATTTTTAAAGAAAAGTTGAAAGTATGAATTTTTCTT-
1 AAAA-TAAAATT-TCAAAAAAAATATTTTGAGA-AAAAGTTGAAAGTATCAATTTTTCTTG
32302133 AAAATAAAA
1 AAAATAAAA
32302142 ACCTTCAAAT
Statistics
Matches: 344, Mismatches: 51, Indels: 57
0.76 0.11 0.13
Matches are distributed among these distances:
56 24 0.07
57 76 0.22
58 56 0.16
59 47 0.14
60 83 0.24
61 9 0.03
64 1 0.00
65 25 0.07
66 23 0.07
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.36
Consensus pattern (58 bp):
AAAATAAAATTTCAAAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:32305159 original size:23 final size:23
Alignment explanation
Indices: 32305129--32305185 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
32305119 GTTATTTTAG
32305129 GATTTCTTTTAAAGTAATGTTAA
1 GATTTCTTTTAAAGTAATGTTAA
32305152 GATTTCTTTTAAAGTAATGTTAA
1 GATTTCTTTTAAAGTAATGTTAA
32305175 GATTTCTTTTA
1 GATTTCTTTTA
32305186 TGCAATAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (23 bp):
GATTTCTTTTAAAGTAATGTTAA
Found at i:32305715 original size:19 final size:18
Alignment explanation
Indices: 32305684--32305728 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
32305674 TCAAAGATAG
*
32305684 AAAGAAAAGAAAGAAAAA
1 AAAGAAAACAAAGAAAAA
32305702 AAAGCAAAACAAAGAAAAA
1 AAAG-AAAACAAAGAAAAA
*
32305721 AGAGAAAA
1 AAAGAAAA
32305729 AAAAAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAGAAAACAAAGAAAAA
Found at i:32305729 original size:9 final size:8
Alignment explanation
Indices: 32305684--32305731 Score: 51
Period size: 9 Copynumber: 5.4 Consensus size: 8
32305674 TCAAAGATAG
32305684 AAAGAAAA
1 AAAGAAAA
32305692 GAAAGAAAAA
1 -AAAG-AAAA
32305702 AAAGCAAAA
1 AAAG-AAAA
32305711 CAAAGAAAA
1 -AAAGAAAA
32305720 AAGAGAAAA
1 AA-AGAAAA
32305729 AAA
1 AAA
32305732 AAATGAATGC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
8 3 0.09
9 24 0.69
10 8 0.23
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:32306132 original size:7 final size:7
Alignment explanation
Indices: 32306130--32306188 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 7
32306120 GAAAAAAATA
32306130 AAAAAATG
1 AAAAAA-G
32306138 AAAAAAG
1 AAAAAAG
32306145 AGAAAAAG
1 A-AAAAAG
32306153 AAAAAAG
1 AAAAAAG
32306160 AAAAAAATG
1 -AAAAAA-G
*
32306169 AAAAAGG
1 AAAAAAG
**
32306176 ATGAAAG
1 AAAAAAG
32306183 AAAAAA
1 AAAAAA
32306189 AAAGATTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
7 17 0.40
8 24 0.57
9 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:32306135 original size:21 final size:21
Alignment explanation
Indices: 32306094--32306137 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
32306084 GATGAAAAAA
32306094 GATGAAAAAAAAAAGGGAAAATG
1 GATGAAAAAAAAAA--GAAAATG
32306117 GATGAAAAAAATAAA-AAAATG
1 GATGAAAAAAA-AAAGAAAATG
32306138 AAAAAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
23 11 0.55
24 3 0.15
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.11
Consensus pattern (21 bp):
GATGAAAAAAAAAAGAAAATG
Found at i:32306157 original size:31 final size:33
Alignment explanation
Indices: 32306121--32306193 Score: 105
Period size: 31 Copynumber: 2.3 Consensus size: 33
32306111 AAAATGGATG
*
32306121 AAAAAAATAAAAAAATGAAAAAAGA-GAAA-AA
1 AAAAAAAGAAAAAAATGAAAAAAGATGAAAGAA
* *
32306152 GAAAAAAGAAAAAAATGAAAAAGGATGAAAGAA
1 AAAAAAAGAAAAAAATGAAAAAAGATGAAAGAA
32306185 AAAAAAAGA
1 AAAAAAAGA
32306194 TTCAAATTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 22 0.61
32 4 0.11
33 10 0.28
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (33 bp):
AAAAAAAGAAAAAAATGAAAAAAGATGAAAGAA
Found at i:32306174 original size:15 final size:16
Alignment explanation
Indices: 32306122--32306173 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
32306112 AAATGGATGA
*
32306122 AAAAAATAAAAAAATG
1 AAAAAAGAAAAAAATG
*
32306138 AAAAAAGAGAAAAA-G
1 AAAAAAGAAAAAAATG
32306153 AAAAAAGAAAAAAATG
1 AAAAAAGAAAAAAATG
32306169 AAAAA
1 AAAAA
32306174 GGATGAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 14 0.44
16 18 0.56
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAAAGAAAAAAATG
Found at i:32307308 original size:21 final size:21
Alignment explanation
Indices: 32307279--32307322 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
32307269 TTCTTAAATG
** *
32307279 AAATGTCAAGTGAGAATTTTT
1 AAATGTCAAAAGAGAATCTTT
*
32307300 AAATTTCAAAAGAGAATCTTT
1 AAATGTCAAAAGAGAATCTTT
32307321 AA
1 AA
32307323 GGTGTGAAAC
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:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (21 bp):
AAATGTCAAAAGAGAATCTTT
Found at i:32307411 original size:21 final size:21
Alignment explanation
Indices: 32307350--32307423 Score: 105
Period size: 22 Copynumber: 3.5 Consensus size: 21
32307340 TTATCGAATA
*
32307350 AGAATCTTCGAA-TTCAAATG
1 AGAATCTTTGAATTTCAAATG
*
32307370 AGAATCTTTGAATCCTCAAATG
1 AGAATCTTTGAAT-TTCAAATG
*
32307392 AGAATCTTTGAATTTCAAATA
1 AGAATCTTTGAATTTCAAATG
32307413 AGAATCTTTGA
1 AGAATCTTTGA
32307424 GGTGTGAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
20 11 0.23
21 17 0.35
22 20 0.42
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (21 bp):
AGAATCTTTGAATTTCAAATG
Found at i:32307427 original size:101 final size:100
Alignment explanation
Indices: 32307284--32307502 Score: 307
Period size: 101 Copynumber: 2.2 Consensus size: 100
32307274 AAATGAAATG
* * *
32307284 TCAAGTGAGAATTTTTAAATTTCAAAAGAGAATCTTTAAGGTGTGAAA-CTCAAAATTTATCGAA
1 TCAAATGAGAATATTTGAATTTCAAAAGAGAATCTTTAAGGTGTGAAACCT-AAAATTTATCGAA
*
32307348 TAAGAATCTTCGAATTCAAATGAGAATCTTTGAATCC
65 TAAGAATCTTCAAATTCAAATGAGAATCTTTGAAT-C
* *
32307385 TCAAATGAGAATCTTTGAATTTCAAATA-AGAATCTTTGAGGTGTGAAACCTAAAATTTATCGAA
1 TCAAATGAGAATATTTGAATTTCAAA-AGAGAATCTTTAAGGTGTGAAACCTAAAATTTATCGAA
* * * *
32307449 TATGAATCTTTAAATTCAAATGAGAATCTTTGAGTT
65 TAAGAATCTTCAAATTCAAATGAGAATCTTTGAATC
32307485 TCAAATGAGAATATTTGA
1 TCAAATGAGAATATTTGA
32307503 GATGTAAAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
100 17 0.16
101 86 0.81
102 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (100 bp):
TCAAATGAGAATATTTGAATTTCAAAAGAGAATCTTTAAGGTGTGAAACCTAAAATTTATCGAAT
AAGAATCTTCAAATTCAAATGAGAATCTTTGAATC
Done.