Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015265.1 Kokia drynarioides strain JFW-HI SEQ_130310, 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: 306283
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 149 characters in sequence are not A, C, G, or T
Found at i:5052 original size:18 final size:18
Alignment explanation
Indices: 5029--5063 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5019 AAGGAGAAGC
5029 TTGAAG-AGAAGAAGGAAA
1 TTGAAGAAG-AGAAGGAAA
5047 TTGAAGAAGAGAAGGAA
1 TTGAAGAAGAGAAGGAA
5064 TAAGAGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.00, G:0.34, T:0.11
Consensus pattern (18 bp):
TTGAAGAAGAGAAGGAAA
Found at i:10360 original size:23 final size:23
Alignment explanation
Indices: 10334--11068 Score: 909
Period size: 23 Copynumber: 32.3 Consensus size: 23
10324 CTTATATCTA
10334 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
10357 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
10380 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
10403 TGCATAAGTATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
10426 TGCTTAAATATTAATGTTATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
10449 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
** * *
10472 TAATTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
10495 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
10518 TGCTTAAGTATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
10541 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
10564 TGCTCAAATATTAATTTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
10587 TGTTTAAATATTAATATGA--TG
1 TGCTTAAATATTAATGTGATTTG
*
10608 TGCTTAAATATTGATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
10631 TGTTTAAAATATTAATCTGATTTG
1 TGCTT-AAATATTAATGTGATTTG
*
10655 TG-TTCAAATATTAATGTGATTTA
1 TGCTT-AAATATTAATGTGATTTG
10678 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
10701 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
10724 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
10747 TGCTAAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
10770 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
10793 TGTTTAAATATTAATCTAATTTG
1 TGCTTAAATATTAATGTGATTTG
*
10816 TG-TTCAAATATTAATGTGATTTA
1 TGCTT-AAATATTAATGTGATTTG
** *
10839 TGCTTAAATATTAATCCGACTTG
1 TGCTTAAATATTAATGTGATTTG
* *
10862 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
10885 TACTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
10908 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
10931 TGCTCAAATATT--T-TG---TG
1 TGCTTAAATATTAATGTGATTTG
* *
10948 -C-TTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
10969 TGATAAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
10992 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
11015 TTCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
11038 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
11061 TGCTTAAA
1 TGCTTAAA
11069 GAATTAAGAT
Statistics
Matches: 612, Mismatches: 86, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.01
17 3 0.00
18 2 0.00
20 2 0.00
21 21 0.03
22 2 0.00
23 552 0.90
24 22 0.04
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:10947 original size:15 final size:15
Alignment explanation
Indices: 10927--10957 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10917 ATTAATATGA
10927 TTTGTGCTCAAATAT
1 TTTGTGCTCAAATAT
*
10942 TTTGTGCTTAAATAT
1 TTTGTGCTCAAATAT
10957 T
1 T
10958 AATATGATTT
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:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (15 bp):
TTTGTGCTCAAATAT
Found at i:10955 original size:38 final size:38
Alignment explanation
Indices: 10904--10980 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
10894 ATTAATGTGA
* *
10904 TTTGTGCTTAAATATTAATATGATTTGTGCTCAAATAT
1 TTTGTGCTTAAATATTAATATGATTTGTGATAAAATAT
10942 TTTGTGCTTAAATATTAATATGATTTGTGATAAAATAT
1 TTTGTGCTTAAATATTAATATGATTTGTGATAAAATAT
10980 T
1 T
10981 AATGTGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (38 bp):
TTTGTGCTTAAATATTAATATGATTTGTGATAAAATAT
Found at i:11000 original size:84 final size:84
Alignment explanation
Indices: 10859--11026 Score: 248
Period size: 84 Copynumber: 2.0 Consensus size: 84
10849 TTAATCCGAC
* * *
10859 TTGTGCTCAAATATTAATGTGATTTATACTTAAATATTAATGTGATTTGTGCTTAAATATTAATA
1 TTGTGCTCAAATATTAATATGATTTATACTAAAATATTAATGTGATTTATGCTTAAATATTAATA
10924 TGATTTGTGCTCAAATATT
66 TGATTTGTGCTCAAATATT
* *
10943 TTGTGCTTAAATATTAATATGATTTGTGA-TAAAATATTAATGTGATTTATGCTTAAATATTAAT
1 TTGTGCTCAAATATTAATATGATTTAT-ACTAAAATATTAATGTGATTTATGCTTAAATATTAAT
* * *
11007 GTGATTTGTTCTTAAATATT
65 ATGATTTGTGCTCAAATATT
11027 AATATGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
84 74 0.99
85 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (84 bp):
TTGTGCTCAAATATTAATATGATTTATACTAAAATATTAATGTGATTTATGCTTAAATATTAATA
TGATTTGTGCTCAAATATT
Found at i:11185 original size:36 final size:36
Alignment explanation
Indices: 11145--11261 Score: 189
Period size: 36 Copynumber: 3.2 Consensus size: 36
11135 TGTGAAAGTG
* * *
11145 AATATATGAGTATGTTCTTCATGCTATGTGATAGAA
1 AATATGTGGGTATGTTCTTCATGCCATGTGATAGAA
11181 AATATGTGGGTATGTTCTTCATGCCATGTGATAGAA
1 AATATGTGGGTATGTTCTTCATGCCATGTGATAGAA
*
11217 AATATGTGGGTATGTTCTTCATGCCATGTGACAGAA
1 AATATGTGGGTATGTTCTTCATGCCATGTGATAGAA
11253 AATAGTGTG
1 AATA-TGTG
11262 ATAATTAAGT
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 72 0.95
37 4 0.05
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (36 bp):
AATATGTGGGTATGTTCTTCATGCCATGTGATAGAA
Found at i:16028 original size:11 final size:11
Alignment explanation
Indices: 15964--16032 Score: 57
Period size: 11 Copynumber: 5.6 Consensus size: 11
15954 TCACGTCAAC
*
15964 AAATAATTTTA
1 AAATTATTTTA
*
15975 AAATTAATTTA
1 AAATTATTTTA
15986 AAATTAATTTTTA
1 AAATT-A-TTTTA
15999 AAATATAAATTTATTA
1 AAAT-T--A-TT-TTA
16015 AAATTATTTTA
1 AAATTATTTTA
16026 AAATTAT
1 AAATTAT
16033 AATCATTATC
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 24 0.48
12 3 0.06
13 9 0.18
14 1 0.02
15 6 0.12
16 7 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:17065 original size:34 final size:34
Alignment explanation
Indices: 17003--17174 Score: 191
Period size: 34 Copynumber: 5.0 Consensus size: 34
16993 GTGATTTTGA
* *
17003 TGAGAAGAAGAAGTGGTGTGTTAGATGGAAGAATGG
1 TGAGAAGGAGAAGT-G-GTGTTAAATGGAAGAATGG
17039 TGAGAAGGAGAAGTGGTGTTAAATGGAAGAATGG
1 TGAGAAGGAGAAGTGGTGTTAAATGGAAGAATGG
* *
17073 TGAGAAGGAAAAGTGGTGTTAAATGGAAGAGTGG
1 TGAGAAGGAGAAGTGGTGTTAAATGGAAGAATGG
* * * * * *
17107 TAAGAAGAAGAAATGATGTAAAAGGGAAGAATGG
1 TGAGAAGGAGAAGTGGTGTTAAATGGAAGAATGG
* * * * *
17141 TAAGAAGGAGAAATGGTATTAGATGGAAAAATGG
1 TGAGAAGGAGAAGTGGTGTTAAATGGAAGAATGG
17175 GGAAGAAGAT
Statistics
Matches: 117, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
34 103 0.88
35 1 0.01
36 13 0.11
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (34 bp):
TGAGAAGGAGAAGTGGTGTTAAATGGAAGAATGG
Found at i:17105 original size:18 final size:18
Alignment explanation
Indices: 17050--17107 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
17040 GAGAAGGAGA
17050 AGTGGTGTTAAATGGAAG
1 AGTGGTGTTAAATGGAAG
* *
17068 AATGGTG--AGAA-GGAAA
1 AGTGGTGTTA-AATGGAAG
17084 AGTGGTGTTAAATGGAAG
1 AGTGGTGTTAAATGGAAG
17102 AGTGGT
1 AGTGGT
17108 AAGAAGAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 11 0.34
17 4 0.12
18 17 0.53
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (18 bp):
AGTGGTGTTAAATGGAAG
Found at i:17155 original size:16 final size:16
Alignment explanation
Indices: 17104--17158 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
17094 AATGGAAGAG
*
17104 TGGTAAGAAGAAGAAA
1 TGGTAAGAAGGAGAAA
17120 TGATGTAA-AAGG-GAAGAA
1 TG--GTAAGAAGGAG-A-AA
17138 TGGTAAGAAGGAGAAA
1 TGGTAAGAAGGAGAAA
17154 TGGTA
1 TGGTA
17159 TTAGATGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
16 14 0.44
17 9 0.28
18 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.35, T:0.16
Consensus pattern (16 bp):
TGGTAAGAAGGAGAAA
Found at i:17246 original size:17 final size:17
Alignment explanation
Indices: 17205--17246 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
17195 ATTAAAATTA
17205 TTTAATAATTTTATATTT
1 TTTAA-AATTTTATATTT
**
17223 TAAAAAATTTTATATTT
1 TTTAAAATTTTATATTT
17240 TTTAAAA
1 TTTAAAA
17247 AATAATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAAATTTTATATTT
Found at i:17631 original size:12 final size:13
Alignment explanation
Indices: 17609--17637 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
17599 GGAACCTAAA
17609 TAAATTTTAAATT
1 TAAATTTTAAATT
17622 TAAA-TTTAAATT
1 TAAATTTTAAATT
17634 TAAA
1 TAAA
17638 ATGTCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTTTAAATT
Found at i:18741 original size:29 final size:29
Alignment explanation
Indices: 18650--18914 Score: 286
Period size: 30 Copynumber: 9.0 Consensus size: 29
18640 ATTGACTCTC
* *
18650 AAACTTTTCCAAAATTATATTTTGACCCCTT
1 AAACTTTTCCAAAATTACATTTT-AACCC-T
* * *
18681 AAACTTCTT--AAAATTATATTTTGACACAT
1 AAACTT-TTCCAAAATTACATTTTAAC-CCT
18710 AAACTTTTCCAAAATTACATTTTAACCCT
1 AAACTTTTCCAAAATTACATTTTAACCCT
18739 AAACTTTTCCAAAATTACATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCC-T
*
18769 GAACTTTTCCAAAATTACATTTTAACCCT
1 AAACTTTTCCAAAATTACATTTTAACCCT
*
18798 CAAACCTTTT-CAAAATCACATTTTAACCCT
1 -AAA-CTTTTCCAAAATTACATTTTAACCCT
* * * ** *
18828 AAACATCTCCAAAATCATGTTTTGACCCT
1 AAACTTTTCCAAAATTACATTTTAACCCT
* *
18857 AAACTTTCCCAAAATTACATTTTTACCTCCT
1 AAACTTTTCCAAAATTACA-TTTTAAC-CCT
18888 -AACTTTTCCAAAATTACATTTTAACCC
1 AAACTTTTCCAAAATTACATTTTAACCC
18915 GAATTCTCTG
Statistics
Matches: 200, Mismatches: 24, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
28 7 0.04
29 78 0.39
30 99 0.50
31 14 0.07
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
AAACTTTTCCAAAATTACATTTTAACCCT
Found at i:18779 original size:59 final size:57
Alignment explanation
Indices: 18623--18914 Score: 286
Period size: 59 Copynumber: 5.0 Consensus size: 57
18613 TTGACCCCCG
* * * *
18623 AACTTCTTCAAAATTACA--TTGACTCTCAAACTTTTCCAAAATTATATTTTGACCCCTTA
1 AACTT-TTCAAAATTACATTTTAACCCT-AAACTTTTCCAAAATTACATTTT-AACCC-TA
* * *
18682 AACTTCTT-AAAATTATATTTTGACACATAAACTTTTCCAAAATTACATTTTAACCCTA
1 AACTT-TTCAAAATTACATTTTAAC-CCTAAACTTTTCCAAAATTACATTTTAACCCTA
*
18740 AACTTTTCCAAAATTACATTTTAACCCTTGAACTTTTCCAAAATTACATTTTAACCCTCA
1 AACTTTT-CAAAATTACATTTTAACCC-TAAACTTTTCCAAAATTACATTTTAACCCT-A
* * * * ** *
18800 AACCTTTTCAAAATCACATTTTAACCCTAAACATCTCCAAAATCATGTTTTGACCCTA
1 AA-CTTTTCAAAATTACATTTTAACCCTAAACTTTTCCAAAATTACATTTTAACCCTA
* *
18858 AACTTTCCCAAAATTACATTTTTACCTCCT-AACTTTTCCAAAATTACATTTTAACCC
1 AACTTT-TCAAAATTACA-TTTTAAC-CCTAAACTTTTCCAAAATTACATTTTAACCC
18915 GAATTCTCTG
Statistics
Matches: 196, Mismatches: 26, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
57 6 0.03
58 28 0.14
59 105 0.54
60 51 0.26
61 6 0.03
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (57 bp):
AACTTTTCAAAATTACATTTTAACCCTAAACTTTTCCAAAATTACATTTTAACCCTA
Found at i:26744 original size:18 final size:18
Alignment explanation
Indices: 26721--26759 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
26711 GACTCGATAT
26721 GTTAAATACTCAGAATGG
1 GTTAAATACTCAGAATGG
*
26739 GTTAAATACTTAGAATGG
1 GTTAAATACTCAGAATGG
26757 GTT
1 GTT
26760 GCCAATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (18 bp):
GTTAAATACTCAGAATGG
Found at i:30831 original size:22 final size:22
Alignment explanation
Indices: 30803--30845 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
30793 GGGTCAAAGC
30803 AATATAGTGGTCGTCTTCCTGT
1 AATATAGTGGTCGTCTTCCTGT
30825 AATATAGTGGTCGTCTTCCTG
1 AATATAGTGGTCGTCTTCCTG
30846 ATAAGATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (22 bp):
AATATAGTGGTCGTCTTCCTGT
Found at i:31244 original size:209 final size:209
Alignment explanation
Indices: 30849--31245 Score: 505
Period size: 209 Copynumber: 1.9 Consensus size: 209
30839 CTTCCTGATA
** *
30849 AGATACAGAGAAATGGACCAAATCCGTCTCCCTGATGAGATACAGAGAAGCAGATTAAAACAAAT
1 AGATACAGAGAAATAAACCAAATCCGTCTCCCTGATGAGATACAGAGAAACAGATTAAAACAAAT
* * * *
30914 GAGGCGGTCATCTTCCTGATACGATATAAAGAAGTAGACCGAATCAATGAAGCAAAGCTCAATGT
66 GAAGCGATCATCTTCCTAATACGATACAAAGAAGTAGACCGAATCAATGAAGCAAAGCTCAATGT
* ***
30979 GAGTGAAAATTCAAGCCCCATCTTCCTAATGAGATATTGAGAAGTAGGATGAAGCAATAGAGTGT
131 GAGTGAAAATTCAAACCCCATCTTCCTAATGAGATACAAAGAAGTAGGATGAAGCAATAGAGTGT
31044 TCATCTTCTTGACG
196 TCATCTTCTTGACG
* * * * **
31058 AGATACAGAGAAGTAAATCAAATCTGTCTTCCTGATGAGATACAGAGAAATGGATTAAAAC-AAT
1 AGATACAGAGAAATAAACCAAATCCGTCTCCCTGATGAGATACAGAGAAACAGATTAAAACAAAT
* *
31122 GAAGCGATCATCTTCCTAATGA-GATACGAAGAAGTAGA-CTAATTCAATGAAGCAAAGCTCAAT
66 GAAGCGATCATCTTCCTAAT-ACGATACAAAGAAGTAGACCGAA-TCAATGAAGCAAAGCTCAAT
* * * * * *
31185 GTGAGTGAAATTTCCAAACCTCATCTTCTTGATGAGATACAAATAAGT-GGGTCGAAGCAAT
129 GTGAGTGAAAATT-CAAACCCCATCTTCCTAATGAGATACAAAGAAGTAGGAT-GAAGCAAT
31246 GAAGCAGTCA
Statistics
Matches: 159, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
207 3 0.02
208 69 0.43
209 87 0.55
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (209 bp):
AGATACAGAGAAATAAACCAAATCCGTCTCCCTGATGAGATACAGAGAAACAGATTAAAACAAAT
GAAGCGATCATCTTCCTAATACGATACAAAGAAGTAGACCGAATCAATGAAGCAAAGCTCAATGT
GAGTGAAAATTCAAACCCCATCTTCCTAATGAGATACAAAGAAGTAGGATGAAGCAATAGAGTGT
TCATCTTCTTGACG
Found at i:31259 original size:209 final size:209
Alignment explanation
Indices: 30838--31281 Score: 504
Period size: 209 Copynumber: 2.1 Consensus size: 209
30828 ATAGTGGTCG
** * ** *
30838 TCTTCCTGATAAGATACAGAGAAATGGACCAAATCCGTCTCCCTGATGAGATACAGAGAAGCAGA
1 TCTTCCTGACGAGATACAGAGAAGTAAACCAAATCCGTCTCCCTGATGAGATACAGAGAAACAGA
* * * *
30903 TTAAAACAAATGAGGCGGTCATCTTCCTGATACGATATAAAGAAGTAGACCGAATCAATGAAGCA
66 TTAAAACAAATGAAGCGATCATCTTCCTAATACGATACAAAGAAGTAGACCGAATCAATGAAGCA
* ***
30968 AAGCTCAATGTGAGTGAAAATTCAAGCCCCATCTTCCTAATGAGATATTGAGAAGTAGGATGAAG
131 AAGCTCAATGTGAGTGAAAATTCAAACCCCATCTTCCTAATGAGATACAAAGAAGTAGGATGAAG
*
31033 CAATAGAGTGTTCA
196 CAATAGAGAGTTCA
* * * * **
31047 TCTTCTTGACGAGATACAGAGAAGTAAATCAAATCTGTCTTCCTGATGAGATACAGAGAAATGGA
1 TCTTCCTGACGAGATACAGAGAAGTAAACCAAATCCGTCTCCCTGATGAGATACAGAGAAACAGA
* *
31112 TTAAAAC-AATGAAGCGATCATCTTCCTAATGA-GATACGAAGAAGTAGA-CTAATTCAATGAAG
66 TTAAAACAAATGAAGCGATCATCTTCCTAAT-ACGATACAAAGAAGTAGACCGAA-TCAATGAAG
* * * * * *
31174 CAAAGCTCAATGTGAGTGAAATTTCCAAACCTCATCTTCTTGATGAGATACAAATAAGT-GGGTC
129 CAAAGCTCAATGTGAGTGAAAATT-CAAACCCCATCTTCCTAATGAGATACAAAGAAGTAGGAT-
31238 GAAGCAAT-GAAGCAG-TCA
192 GAAGCAATAG-AG-AGTTCA
* * *
31256 TCTTCCTGATGAAATATAGAGAAGTA
1 TCTTCCTGACGAGATACAGAGAAGTA
31282 GATCGAGAGA
Statistics
Matches: 196, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
207 3 0.02
208 70 0.36
209 122 0.62
210 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (209 bp):
TCTTCCTGACGAGATACAGAGAAGTAAACCAAATCCGTCTCCCTGATGAGATACAGAGAAACAGA
TTAAAACAAATGAAGCGATCATCTTCCTAATACGATACAAAGAAGTAGACCGAATCAATGAAGCA
AAGCTCAATGTGAGTGAAAATTCAAACCCCATCTTCCTAATGAGATACAAAGAAGTAGGATGAAG
CAATAGAGAGTTCA
Found at i:33404 original size:60 final size:58
Alignment explanation
Indices: 33338--33648 Score: 259
Period size: 60 Copynumber: 5.2 Consensus size: 58
33328 TAAGATCATG
* * * *
33338 AACTTTTCAAAAATCATATTTTGATCCTCGAACTTCTCCAAAATTATATTTTGACCCTCA
1 AACTTTTCCAAAATCATATTTTGA-CCCCAAACTT-TCCAAAATTACATTTTGACCCTCA
** * * * *
33398 AACTTTTGTAAAATCACATTTTGACCCCTAAGCTTTTCCAAAATTACATTTCGACCCTTA
1 AACTTTTCCAAAATCATATTTTGACCCC-AAAC-TTTCCAAAATTACATTTTGACCCTCA
* * * * *
33458 AGCTTTTCCAAAATTATGTTTTGACCACCAAACTTTCAAAAATTACATTTTAACCC-CTA
1 AACTTTTCCAAAATCATATTTTGACC-CCAAACTTTCCAAAATTACATTTTGACCCTC-A
* * * * *
33517 AACTTTTCCAAAATCATATTTTAATCACTAAACCTTTCCAAAATCACATTTTAACCC-CA
1 AACTTTTCCAAAATCATATTTTGA-CCCCAAA-CTTTCCAAAATTACATTTTGACCCTCA
** * * * ** *
33576 AAAATCTCCAAAATCACATTTTAACCTTAAACTTTCCCAAAATTACATTTTTA-CCTCA
1 AACTTTTCCAAAATCATATTTTGACCCCAAACTTT-CCAAAATTACATTTTGACCCTCA
33634 TAACTTTTCCAAAAT
1 -AACTTTTCCAAAAT
33649 TACGTTTTAA
Statistics
Matches: 203, Mismatches: 39, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
57 6 0.03
58 22 0.11
59 80 0.39
60 91 0.45
61 4 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (58 bp):
AACTTTTCCAAAATCATATTTTGACCCCAAACTTTCCAAAATTACATTTTGACCCTCA
Found at i:33524 original size:59 final size:58
Alignment explanation
Indices: 33368--33660 Score: 255
Period size: 59 Copynumber: 4.9 Consensus size: 58
33358 TTGATCCTCG
* * ** * *
33368 AACTTCTCCAAAATTATATTTTGACCCTCAAACTTTTGTAAAATCACATTTTGACCCCTA
1 AACTT-TCCAAAATTACATTTTAACCC-CAAACTTTTCCAAAATCACATTTTAACCACTA
* ** * * * ** * *
33428 AGCTTTTCCAAAATTACATTTCGACCCTTAAGCTTTTCCAAAATTATGTTTTGACCACCA
1 AAC-TTTCCAAAATTACATTTTAACCC-CAAACTTTTCCAAAATCACATTTTAACCACTA
* * *
33488 AACTTTCAAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTAATCACTA
1 AACTTTCCAAAATTACATTTTAACCCC-AAACTTTTCCAAAATCACATTTTAACCACTA
* ** * *
33547 AACCTTTCCAAAATCACATTTTAACCCCAAAAATCTCCAAAATCACATTTTAACC-TTA
1 AA-CTTTCCAAAATTACATTTTAACCCCAAACTTTTCCAAAATCACATTTTAACCACTA
* * * *
33605 AACTTTCCCAAAATTACATTTTTACCTCATAACTTTTCCAAAATTACGTTTTAACC
1 AACTTT-CCAAAATTACATTTTAACCCCA-AACTTTTCCAAAATCACATTTTAACC
33661 CGAATTCTCT
Statistics
Matches: 189, Mismatches: 39, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
57 4 0.02
58 23 0.12
59 90 0.48
60 70 0.37
61 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (58 bp):
AACTTTCCAAAATTACATTTTAACCCCAAACTTTTCCAAAATCACATTTTAACCACTA
Found at i:33539 original size:30 final size:30
Alignment explanation
Indices: 33338--33648 Score: 222
Period size: 30 Copynumber: 10.5 Consensus size: 30
33328 TAAGATCATG
* * * *
33338 AACTTTTCAAAAATCATATTTTGA-TCCTCG
1 AACTTTTCCAAAATCACATTTTGACCCCT-A
* * *
33368 AACTTCTCCAAAATTATATTTTGA-CCCTCA
1 AACTTTTCCAAAATCACATTTTGACCCCT-A
**
33398 AACTTTTGTAAAATCACATTTTGACCCCTA
1 AACTTTTCCAAAATCACATTTTGACCCCTA
* * * *
33428 AGCTTTTCCAAAATTACATTTCGACCCTTA
1 AACTTTTCCAAAATCACATTTTGACCCCTA
* * **
33458 AGCTTTTCCAAAATTATGTTTTGACCACC-A
1 AACTTTTCCAAAATCACATTTTGACC-CCTA
* * *
33488 AAC-TTTCAAAAATTACATTTTAACCCCTA
1 AACTTTTCCAAAATCACATTTTGACCCCTA
* * * *
33517 AACTTTTCCAAAATCATATTTTAATCACTA
1 AACTTTTCCAAAATCACATTTTGACCCCTA
* *
33547 AACCTTTCCAAAATCACATTTTAACCCC-A
1 AACTTTTCCAAAATCACATTTTGACCCCTA
** * * *
33576 AAAATCTCCAAAATCACATTTT-AACCTTA
1 AACTTTTCCAAAATCACATTTTGACCCCTA
* * * *
33605 AACTTTCCCAAAATTACATTTTTACCTC-A
1 AACTTTTCCAAAATCACATTTTGACCCCTA
33634 TAACTTTTCCAAAAT
1 -AACTTTTCCAAAAT
33649 TACGTTTTAA
Statistics
Matches: 226, Mismatches: 48, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
28 5 0.02
29 61 0.27
30 155 0.69
31 5 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
AACTTTTCCAAAATCACATTTTGACCCCTA
Found at i:34134 original size:36 final size:36
Alignment explanation
Indices: 34053--34136 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
34043 AAGTAAAAAT
* * *
34053 TTTGAAAAGAAAGTAAAAGAAAAAATATTTTGAAGG
1 TTTGAAAAGTAAGTAAAAGAAAAAAGATTTTAAAGG
34089 TTTGAAAAGTAAGTAAAAGAAAAAAGATTTTAAAGG
1 TTTGAAAAGTAAGTAAAAGAAAAAAGATTTTAAAGG
34125 TTTGAAAAGTAA
1 TTTGAAAAGTAA
34137 AAGTTTCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (36 bp):
TTTGAAAAGTAAGTAAAAGAAAAAAGATTTTAAAGG
Found at i:34261 original size:26 final size:26
Alignment explanation
Indices: 34232--34327 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
34222 ATTTTACTTA
34232 TTTTAAACTCTCAAAACTTTTTTTTC
1 TTTTAAACTCTCAAAACTTTTTTTTC
* *
34258 TTTTAAACTTTTACTTTCTATAAA-TATTTTACTTA
1 TTTTAAAC---T-C--TC-A-AAACT-TTTT-TTTC
34293 TTTTAAACTCTCAAAACTTTTTTTTC
1 TTTTAAACTCTCAAAACTTTTTTTTC
34319 TTTTAAACT
1 TTTTAAACT
34328 TTTTTTTTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 22
0.68 0.05 0.27
Matches are distributed among these distances:
26 19 0.35
27 7 0.13
28 2 0.04
29 3 0.05
30 1 0.02
31 1 0.02
32 3 0.05
33 2 0.04
34 7 0.13
35 10 0.18
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTAAACTCTCAAAACTTTTTTTTC
Found at i:34337 original size:61 final size:61
Alignment explanation
Indices: 34195--34330 Score: 263
Period size: 61 Copynumber: 2.2 Consensus size: 61
34185 GAAAAAGTTC
*
34195 TCTTTAAAACTTTTACTTTCTATAAATATTTTACTTATTTTAAACTCTCAAAACTTTTTTT
1 TCTTTTAAACTTTTACTTTCTATAAATATTTTACTTATTTTAAACTCTCAAAACTTTTTTT
34256 TCTTTTAAACTTTTACTTTCTATAAATATTTTACTTATTTTAAACTCTCAAAACTTTTTTT
1 TCTTTTAAACTTTTACTTTCTATAAATATTTTACTTATTTTAAACTCTCAAAACTTTTTTT
34317 TCTTTTAAACTTTT
1 TCTTTTAAACTTTT
34331 TTTTTCTTTT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 74 1.00
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (61 bp):
TCTTTTAAACTTTTACTTTCTATAAATATTTTACTTATTTTAAACTCTCAAAACTTTTTTT
Found at i:34350 original size:17 final size:18
Alignment explanation
Indices: 34306--34350 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
34296 TAAACTCTCA
34306 AAACTT-TTTTTTCTTTT
1 AAACTTCTTTTTTCTTTT
*
34323 AAACTTTTTTTTTCTTTT
1 AAACTTCTTTTTTCTTTT
*
34341 -ACCTTCTTTT
1 AAACTTCTTTT
34351 CTAAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (18 bp):
AAACTTCTTTTTTCTTTT
Found at i:34350 original size:18 final size:18
Alignment explanation
Indices: 34306--34341 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
34296 TAAACTCTCA
34306 AAAC-TTTTTTTTCTTTT
1 AAACTTTTTTTTTCTTTT
34323 AAACTTTTTTTTTCTTTT
1 AAACTTTTTTTTTCTTTT
34341 A
1 A
34342 CCTTCTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.69
Consensus pattern (18 bp):
AAACTTTTTTTTTCTTTT
Found at i:34544 original size:26 final size:24
Alignment explanation
Indices: 34469--34548 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 24
34459 AAATTAAATT
34469 TTAAAATTTAAATTATT-T-ATTTA
1 TTAAAATTT-AATTATTATAATTTA
* * *
34492 ATAATATTAAATTATTATCAATTTTA
1 TTAAAATTTAATTATTAT-AA-TTTA
34518 TTAAAATTTAATTATTGATAATATTA
1 TTAAAATTTAATTATT-ATAAT-TTA
34544 -TAAAA
1 TTAAAA
34549 CATTCGTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
22 7 0.16
23 7 0.16
25 7 0.16
26 22 0.49
27 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (24 bp):
TTAAAATTTAATTATTATAATTTA
Found at i:36393 original size:12 final size:12
Alignment explanation
Indices: 36369--36411 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
36359 GTTTTGCTAC
*
36369 TATTTTTGCTGT
1 TATTTTTGTTGT
36381 TATTTTTGTTGT
1 TATTTTTGTTGT
* * *
36393 TGTTTTAGTTTT
1 TATTTTTGTTGT
36405 TATTTTT
1 TATTTTT
36412 ACGACTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.09, C:0.02, G:0.14, T:0.74
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:36430 original size:21 final size:21
Alignment explanation
Indices: 36404--36444 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
36394 GTTTTAGTTT
36404 TTATTTTTACGACTATTTTTG
1 TTATTTTTACGACTATTTTTG
* *
36425 TTATTTTTACTATTATTTTT
1 TTATTTTTACGACTATTTTT
36445 TATGTATGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (21 bp):
TTATTTTTACGACTATTTTTG
Found at i:38179 original size:16 final size:15
Alignment explanation
Indices: 38157--38197 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
38147 TCCCTTTTAA
38157 AAATATATATAAAAT
1 AAATATATATAAAAT
38172 ATAATATA-ATAAAAT
1 A-AATATATATAAAAT
*
38187 AAAAATATATA
1 AAATATATATA
38198 CTAATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 12 0.52
16 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATATATAAAAT
Found at i:39006 original size:23 final size:22
Alignment explanation
Indices: 38963--39011 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
38953 GAATTCTTGT
**
38963 TAAAATAAAATTCAGTACTAAAA
1 TAAAATAAAATAAAGTACT-AAA
38986 TAAAATAAAAGTAAAGT-CTAAA
1 TAAAATAAAA-TAAAGTACTAAA
39008 TAAA
1 TAAA
39012 CTAGACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 12 0.52
24 4 0.17
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.24
Consensus pattern (22 bp):
TAAAATAAAATAAAGTACTAAA
Found at i:49375 original size:23 final size:23
Alignment explanation
Indices: 49349--49403 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
49339 TGACGTGGCA
*
49349 TCCAGTCAGCAGCTTCTAGAAGG
1 TCCAGTCAGCAGCTTCTAGAAGC
49372 TCCAGTCAGCAGCTTCTAGAAGC
1 TCCAGTCAGCAGCTTCTAGAAGC
*
49395 TCTAGTCAG
1 TCCAGTCAG
49404 TAATGATGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
TCCAGTCAGCAGCTTCTAGAAGC
Found at i:56813 original size:15 final size:15
Alignment explanation
Indices: 56793--56823 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56783 AAAGAGTTCG
56793 AATAAAGAAGAAAAA
1 AATAAAGAAGAAAAA
56808 AATAAAGAAGAAAAA
1 AATAAAGAAGAAAAA
56823 A
1 A
56824 GAGAATAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (15 bp):
AATAAAGAAGAAAAA
Found at i:63713 original size:23 final size:24
Alignment explanation
Indices: 63675--63722 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
63665 TTTTAGAGAA
63675 TTTTGTGTTTACG-TTTTGAGGGTT
1 TTTTGTGTTTACGTTTTTG-GGGTT
*
63699 TTTTGTTTTTA-GTTTTTGGGGTT
1 TTTTGTGTTTACGTTTTTGGGGTT
63722 T
1 T
63723 AGTTTCATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.06, C:0.02, G:0.27, T:0.65
Consensus pattern (24 bp):
TTTTGTGTTTACGTTTTTGGGGTT
Found at i:65846 original size:3 final size:3
Alignment explanation
Indices: 65840--65891 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
65830 ATTTTTTATT
65840 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
65888 ATA A
1 ATA A
65892 AAGCAAAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:67188 original size:10 final size:9
Alignment explanation
Indices: 67174--67262 Score: 65
Period size: 9 Copynumber: 9.7 Consensus size: 9
67164 ATAAAAAGCA
67174 ATAAAAATT
1 ATAAAAATT
**
67183 ATTAAATTTT
1 A-TAAAAATT
67193 AATAAAAA-T
1 -ATAAAAATT
*
67202 ATAAAAAAT
1 ATAAAAATT
**
67211 AGGAAAATT
1 ATAAAAATT
67220 ATAAAAAATT
1 AT-AAAAATT
67230 ATAAAAATGT
1 ATAAAAAT-T
**
67240 A-AAATTTT
1 ATAAAAATT
67248 ATAAAAATT
1 ATAAAAATT
67257 ATAAAA
1 ATAAAA
67263 GGTGAAGATT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
8 9 0.15
9 31 0.51
10 20 0.33
11 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:67226 original size:27 final size:27
Alignment explanation
Indices: 67196--67262 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
67186 AAATTTTAAT
67196 AAAAATATAAAAAATAGGAAAA-TTATA
1 AAAAATATAAAAAAT-GGAAAATTTATA
*
67223 AAAAAT-TATAAAAATGTAAAATTTTATA
1 AAAAATATA-AAAAATGGAAAA-TTTATA
*
67251 AAAATTATAAAA
1 AAAAATATAAAA
67263 GGTGAAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 7 0.21
27 12 0.35
28 13 0.38
29 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAAATATAAAAAATGGAAAATTTATA
Found at i:67234 original size:36 final size:35
Alignment explanation
Indices: 67152--67262 Score: 91
Period size: 37 Copynumber: 3.0 Consensus size: 35
67142 TGTGGCAAAT
*
67152 AAATTATAAGAAATA-AAAAGCAATAAAAATTATTAA
1 AAATTATAA-AAATATAAAA-CAATAAAAATTATAAA
**
67188 ATTTTAATAAAAATATAAAA-AATAGGAAAATTATAAA
1 AAATT-ATAAAAATATAAAACAATA--AAAATTATAAA
* **
67225 AAATTATAAAAATGTAAAATTTTATAAAAATTATAAA
1 AAATTATAAAAATATAAAA--CAATAAAAATTATAAA
67262 A
1 A
67263 GGTGAAGATT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
35 4 0.07
36 21 0.34
37 33 0.54
39 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.30
Consensus pattern (35 bp):
AAATTATAAAAATATAAAACAATAAAAATTATAAA
Found at i:67275 original size:26 final size:28
Alignment explanation
Indices: 67186--67262 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
67176 AAAAATTATT
*
67186 AAATTTTA-ATAAAAA-TATAAAAAATAGGA
1 AAATTTTATA-AAAAATTAT-AAAAAT-GTA
67215 AAA--TTATAAAAAATTATAAAAATGTA
1 AAATTTTATAAAAAATTATAAAAATGTA
67241 AAATTTTAT-AAAAATTATAAAA
1 AAATTTTATAAAAAATTATAAAA
67263 GGTGAAGATT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
26 5 0.12
27 27 0.63
28 8 0.19
29 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (28 bp):
AAATTTTATAAAAAATTATAAAAATGTA
Found at i:67651 original size:18 final size:18
Alignment explanation
Indices: 67628--67666 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
67618 ATTGTTTTTC
* *
67628 AAAAATATTTTTAAGATA
1 AAAAATACTTTTAAAATA
67646 AAAAATACTTTTAAAATA
1 AAAAATACTTTTAAAATA
67664 AAA
1 AAA
67667 GAACTGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAATACTTTTAAAATA
Found at i:67745 original size:16 final size:16
Alignment explanation
Indices: 67715--67748 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
67705 GCTTTTGAAA
**
67715 TAAAAAATATTTTTTT
1 TAAAAAATACATTTTT
67731 TAAAAAATACATTTTT
1 TAAAAAATACATTTTT
67747 TA
1 TA
67749 GTAAAAAAGA
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAAAATACATTTTT
Found at i:68087 original size:23 final size:25
Alignment explanation
Indices: 68043--68093 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
68033 TTACTAGGAC
*
68043 GATTTTAAGCTAATTTTACTATCTG
1 GATTTTAAGCTAATTCTACTATCTG
* *
68068 GATTTT-AGC-AATTCTGCTATGTG
1 GATTTTAAGCTAATTCTACTATCTG
68091 GAT
1 GAT
68094 AATGACCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 14 0.61
24 3 0.13
25 6 0.26
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (25 bp):
GATTTTAAGCTAATTCTACTATCTG
Found at i:89738 original size:20 final size:20
Alignment explanation
Indices: 89715--89815 Score: 75
Period size: 19 Copynumber: 5.0 Consensus size: 20
89705 GCTGGTTTGG
89715 TTGTTGTTTTTTTGTTGTTT
1 TTGTTGTTTTTTTGTTGTTT
**
89735 TTG-TGTTTTTTAATTG-TT
1 TTGTTGTTTTTTTGTTGTTT
*
89753 TTGGTGTTTTTTT-TACTGTTT
1 TTGTTGTTTTTTTGT--TGTTT
* *
89774 TGGTTATTATTTTCGTGTTG-TT
1 TTGTTGTT-TTTT--TGTTGTTT
89796 TTGTTGTTGTTTTTGTTGTT
1 TTGTTGTT-TTTTTGTTGTT
89816 ATTTTTAATG
Statistics
Matches: 63, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
18 6 0.10
19 19 0.30
20 10 0.16
21 8 0.13
22 16 0.25
23 2 0.03
24 1 0.02
25 1 0.02
ACGTcount: A:0.05, C:0.02, G:0.21, T:0.72
Consensus pattern (20 bp):
TTGTTGTTTTTTTGTTGTTT
Found at i:89808 original size:34 final size:34
Alignment explanation
Indices: 89769--89842 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
89759 TTTTTTTTAC
**
89769 TGTTTTGGTTATTA-TTTTCGTGTTGTTTTGTTGT
1 TGTTTTGGTTATTATTTTTAATGTTG-TTTGTTGT
* *
89803 TGTTTTTGTTGTTATTTTTAATGTTGTTTGTTGT
1 TGTTTTGGTTATTATTTTTAATGTTGTTTGTTGT
*
89837 TATTTT
1 TGTTTT
89843 TGCTAGTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 25 0.74
35 9 0.26
ACGTcount: A:0.08, C:0.01, G:0.20, T:0.70
Consensus pattern (34 bp):
TGTTTTGGTTATTATTTTTAATGTTGTTTGTTGT
Found at i:89811 original size:12 final size:12
Alignment explanation
Indices: 89692--89871 Score: 70
Period size: 12 Copynumber: 15.2 Consensus size: 12
89682 AAAATTTATA
89692 TTGTTG-TTTTG
1 TTGTTGTTTTTG
* * * *
89703 GTGCTGGTTTGG
1 TTGTTGTTTTTG
89715 TTGTTGTTTTT-
1 TTGTTGTTTTTG
89726 TTGTTGTTTTTG
1 TTGTTGTTTTTG
*
89738 -TGTTTTTTAATTG
1 TTGTTGTTT--TTG
* *
89751 TTTTGGTGTTTTTT
1 --TTGTTGTTTTTG
** *
89765 TTACTGTTTTGG
1 TTGTTGTTTTTG
* * *
89777 TTATTATTTTCG
1 TTGTTGTTTTTG
89789 -TGTTG-TTTTG
1 TTGTTGTTTTTG
89799 TTGTTGTTTTTG
1 TTGTTGTTTTTG
* *
89811 TTGTTATTTTTA
1 TTGTTGTTTTTG
*
89823 ATGTTG--TTTG
1 TTGTTGTTTTTG
*
89833 TTGTTATTTTTG
1 TTGTTGTTTTTG
* * *
89845 CTAG-TATTTTGG
1 -TTGTTGTTTTTG
*
89857 TTGTTATTTTTG
1 TTGTTGTTTTTG
89869 TTG
1 TTG
89872 CTTGAATGTT
Statistics
Matches: 124, Mismatches: 32, Indels: 25
0.69 0.18 0.14
Matches are distributed among these distances:
10 11 0.09
11 32 0.26
12 68 0.55
13 5 0.04
14 2 0.02
16 6 0.05
ACGTcount: A:0.07, C:0.02, G:0.23, T:0.68
Consensus pattern (12 bp):
TTGTTGTTTTTG
Found at i:89835 original size:22 final size:21
Alignment explanation
Indices: 89803--89867 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 21
89793 GTTTTGTTGT
89803 TGTTTTTGTTGTTATTTTTAA
1 TGTTTTTGTTGTTATTTTTAA
**
89824 TGTTGTTTGTTGTTATTTTTGC
1 TGTT-TTTGTTGTTATTTTTAA
89846 TAGTATTTTGGTTGTTATTTTT
1 T-GT-TTTT-GTTGTTATTTTT
89868 GTTGCTTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 4 0.11
22 16 0.42
23 5 0.13
24 13 0.34
ACGTcount: A:0.11, C:0.02, G:0.18, T:0.69
Consensus pattern (21 bp):
TGTTTTTGTTGTTATTTTTAA
Found at i:89853 original size:34 final size:35
Alignment explanation
Indices: 89789--89854 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
89779 ATTATTTTCG
* *
89789 TGTTGTTTTGTTGTTGTTTTTGTTGTTATTTTTAA
1 TGTTGTTTTGTTGTTATTTTTGTAGTTATTTTTAA
89824 TGTTG-TTTGTTGTTATTTTTGCTAG-TATTTT
1 TGTTGTTTTGTTGTTATTTTTG-TAGTTATTTT
89855 GGTTGTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 21 0.75
35 7 0.25
ACGTcount: A:0.09, C:0.02, G:0.20, T:0.70
Consensus pattern (35 bp):
TGTTGTTTTGTTGTTATTTTTGTAGTTATTTTTAA
Found at i:90634 original size:32 final size:31
Alignment explanation
Indices: 90559--90636 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 31
90549 TAGGTCCAAT
* * *
90559 TTGGTACTTAAATTTAACACTTTTTCTTCAT
1 TTGGTACTTAAACTTAACACTTTTTCTTAAG
* * *
90590 TTGATAAC-TAAACTTGACACTTTTTTTTTAAG
1 TTGGT-ACTTAAACTTAACAC-TTTTTCTTAAG
90622 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
90637 TTTGGAGTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
31 16 0.43
32 21 0.57
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (31 bp):
TTGGTACTTAAACTTAACACTTTTTCTTAAG
Found at i:92021 original size:12 final size:12
Alignment explanation
Indices: 92004--92036 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
91994 AATTGAAAAA
92004 AAAAAAAGAATG
1 AAAAAAAGAATG
92016 -AAAAAA-AATG
1 AAAAAAAGAATG
92026 AAAAAAAGAAT
1 AAAAAAAGAAT
92037 TAATGGACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.21
11 12 0.63
12 3 0.16
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (12 bp):
AAAAAAAGAATG
Found at i:96680 original size:27 final size:27
Alignment explanation
Indices: 96625--96678 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
96615 AATTACAAAG
96625 TTAAAAATTTAAAATAATATATAAAAA
1 TTAAAAATTTAAAATAATATATAAAAA
*
96652 TTAAAAATTGTTAAAATAATATTTAAA
1 TTAAAAA-T-TTAAAATAATATATAAA
96679 TTTCAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.29
28 1 0.04
29 16 0.67
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
TTAAAAATTTAAAATAATATATAAAAA
Found at i:97192 original size:20 final size:21
Alignment explanation
Indices: 97153--97192 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
97143 ATTAATTAAG
* *
97153 CCTAAAAAGAAATACACTATC
1 CCTAAAAACAAAAACACTATC
97174 CCTAAAAACAAAAAC-CTAT
1 CCTAAAAACAAAAACACTAT
97193 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.25, G:0.03, T:0.17
Consensus pattern (21 bp):
CCTAAAAACAAAAACACTATC
Found at i:106610 original size:7 final size:7
Alignment explanation
Indices: 106584--106628 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
106574 AGAAAACCCT
106584 CTTTCCC
1 CTTTCCC
106591 C-TTCCC
1 CTTTCCC
**
106597 CCATCCC
1 CTTTCCC
106604 CTTTCCC
1 CTTTCCC
106611 CTTTCCC
1 CTTTCCC
*
106618 CTTTCTC
1 CTTTCCC
106625 CTTT
1 CTTT
106629 GTTGCAACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.02, C:0.56, G:0.00, T:0.42
Consensus pattern (7 bp):
CTTTCCC
Found at i:114446 original size:20 final size:20
Alignment explanation
Indices: 114423--114465 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
114413 CCAAACACCA
114423 AAAAAT-ATTAATTTTTCCAG
1 AAAAATAATTAATTTTT-CAG
* *
114443 AAAAGTAATTCATTTTTCAG
1 AAAAATAATTAATTTTTCAG
114463 AAA
1 AAA
114466 TCATTTTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (20 bp):
AAAAATAATTAATTTTTCAG
Found at i:114471 original size:14 final size:14
Alignment explanation
Indices: 114452--114487 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
114442 GAAAAGTAAT
* *
114452 TCATTTTTCAGAAA
1 TCATTTTCCAAAAA
114466 TCATTTTCCAAAAA
1 TCATTTTCCAAAAA
114480 TCATTTTC
1 TCATTTTC
114488 AATCAAACAA
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:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (14 bp):
TCATTTTCCAAAAA
Found at i:117449 original size:249 final size:252
Alignment explanation
Indices: 116999--117502 Score: 933
Period size: 249 Copynumber: 2.0 Consensus size: 252
116989 TTATTACATG
116999 TTTTTTTATTATTTTTCTTTATAATATTATATATATTAAATATATAATTAATCTTAAATAAATTA
1 TTTTTTTA-TATTTTTCTTTATAATATTATATATATTAAATATATAATTAATCTTAAATAAATTA
*
117064 TCCTTTTATTTTTATTTTGGTGGATATTATCTTTTGATTTTAAGAATTTACTTAATTGAATAATG
65 TCCTTTTATTTTTATTTTGGTGGATATTATCTTTTGATTTTAAAAATTTACTTAATTGAATAATG
*
117129 TTATAATATTAAAATTAATAAATATAAAAATTTTAAGCTTAAAATATGCTTTAAAAAAACACATA
130 TTATAATATTAAAATTAATAAATATAAAAATTTTAAGCTTAAAACATGCTTTAAAAAAACACATA
117194 TTAATAACATTTATCAAATTAAATTTATATATTTTAAATATAATAAAATTTAATTACA
195 TTAATAACATTTATCAAATTAAATTTATATATTTTAAATATAATAAAATTTAATTACA
117252 TTTTTTTA-ATTTTTCTTTATAATATTATATATATTAAATATATAATTAATCTTAAATAAATTAT
1 TTTTTTTATATTTTTCTTTATAATATTATATATATTAAATATATAATTAATCTTAAATAAATTAT
* *
117316 CTTTTTA-TTTT-TTTTGGTGGATATTATCTTTTGATTTTAAAAATTTACTTAATTGAGTAATGT
66 CCTTTTATTTTTATTTTGGTGGATATTATCTTTTGATTTTAAAAATTTACTTAATTGAATAATGT
*
117379 TATAATATTAAAATTAATAAATATAAAAATTTTAAGCTTAAAACATGCTTTGAAAAAACACATAT
131 TATAATATTAAAATTAATAAATATAAAAATTTTAAGCTTAAAACATGCTTTAAAAAAACACATAT
117444 TAATAACATTTATCAAATTAAATTTATATATTTTAAATATAATAAAATTTAATTACA
196 TAATAACATTTATCAAATTAAATTTATATATTTTAAATATAATAAAATTTAATTACA
117501 TT
1 TT
117503 ATTTGGTCAA
Statistics
Matches: 246, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
249 172 0.70
250 4 0.02
251 62 0.25
253 8 0.03
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (252 bp):
TTTTTTTATATTTTTCTTTATAATATTATATATATTAAATATATAATTAATCTTAAATAAATTAT
CCTTTTATTTTTATTTTGGTGGATATTATCTTTTGATTTTAAAAATTTACTTAATTGAATAATGT
TATAATATTAAAATTAATAAATATAAAAATTTTAAGCTTAAAACATGCTTTAAAAAAACACATAT
TAATAACATTTATCAAATTAAATTTATATATTTTAAATATAATAAAATTTAATTACA
Found at i:119587 original size:29 final size:29
Alignment explanation
Indices: 119509--119592 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
119499 CGAGTTGGAG
*
119509 CACGAGGGTGTGTCA-AGGTGTATGTGGCA
1 CACGAGGGTGTGTCAGA-GTGTGTGTGGCA
*
119538 CACG-GAGGTGTGTCAGGGTGTGTGTGGCA
1 CACGAG-GGTGTGTCAGAGTGTGTGTGGCA
*
119567 CACGAGGGTGTGTTAGAGTGTGTGTG
1 CACGAGGGTGTGTCAGAGTGTGTGTG
119593 TTTATTATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.02
29 46 0.96
30 1 0.02
ACGTcount: A:0.17, C:0.12, G:0.45, T:0.26
Consensus pattern (29 bp):
CACGAGGGTGTGTCAGAGTGTGTGTGGCA
Found at i:120177 original size:40 final size:40
Alignment explanation
Indices: 120133--120245 Score: 174
Period size: 40 Copynumber: 2.8 Consensus size: 40
120123 AGAATATTTA
120133 ACTGAACCGGCAGTGACATTGTAAACACTGCAAGGTTACC
1 ACTGAACCGGCAGTGACATTGTAAACACTGCAAGGTTACC
* *
120173 ACTGAACTGGCAGTGACATTGTAAACACTGTAAGGTTACC
1 ACTGAACCGGCAGTGACATTGTAAACACTGCAAGGTTACC
* *
120213 ACTAAACTC-GCAGTGACACTGTAAACACTGCAA
1 ACTGAAC-CGGCAGTGACATTGTAAACACTGCAA
120246 CATGTCATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (40 bp):
ACTGAACCGGCAGTGACATTGTAAACACTGCAAGGTTACC
Found at i:120357 original size:29 final size:29
Alignment explanation
Indices: 120308--120392 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
120298 ACGGATGGGG
* *
120308 GTATCATGTTTGAATCTGTAACTGTATCT
1 GTATCATGTCTGCATCTGTAACTGTATCT
* *
120337 GTATCATGTCTGCATCCGTAACTATATCT
1 GTATCATGTCTGCATCTGTAACTGTATCT
*
120366 GTGA-CATGACTGCATCTGTAACTGTAT
1 GT-ATCATGTCTGCATCTGTAACTGTAT
120393 ATCTAATTCG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 47 0.98
30 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (29 bp):
GTATCATGTCTGCATCTGTAACTGTATCT
Found at i:120434 original size:29 final size:29
Alignment explanation
Indices: 120355--120440 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
120345 TCTGCATCCG
* * * *
120355 TAACTATATCTGTGACATGACTGCATCTG
1 TAACTGTATCTCTGACATGACTGTATCTA
*
120384 TAACTGTATATCT-A-ATTCGACTGTATCTA
1 TAACTGTATCTCTGACA-T-GACTGTATCTA
120413 TAACTGTATCTCTGACATGACTGTATCT
1 TAACTGTATCTCTGACATGACTGTATCT
120441 GTATTATTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
27 1 0.02
28 2 0.04
29 41 0.87
30 2 0.04
31 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (29 bp):
TAACTGTATCTCTGACATGACTGTATCTA
Found at i:122133 original size:37 final size:38
Alignment explanation
Indices: 122085--122165 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
122075 GTAGTGATAT
* *
122085 TCTTGGGTGCAA-TTGAAGAATACTTATGCAGCGATAG
1 TCTTGGATGCAATTTGAAGAATACTTATGCAGCGACAG
* * *
122122 TTTTGGATGCAATTTGAAGAATATTTATTCAGCGACAG
1 TCTTGGATGCAATTTGAAGAATACTTATGCAGCGACAG
122160 TCTTGG
1 TCTTGG
122166 GTACTTTCCG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 10 0.27
38 27 0.73
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (38 bp):
TCTTGGATGCAATTTGAAGAATACTTATGCAGCGACAG
Found at i:126316 original size:17 final size:18
Alignment explanation
Indices: 126284--126317 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
126274 CAATAATTAA
*
126284 ATAAATAATTAAAAATTC
1 ATAAATAATAAAAAATTC
126302 ATAAA-AATAAAAAATT
1 ATAAATAATAAAAAATT
126318 ATTAAACCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATAATAAAAAATTC
Found at i:127338 original size:20 final size:20
Alignment explanation
Indices: 127313--127377 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
127303 AATGTTTTGT
127313 TTATGTTTGTTTATTTAAAA
1 TTATGTTTGTTTATTTAAAA
*
127333 TTATGTTTGTTCA--T---A
1 TTATGTTTGTTTATTTAAAA
*
127348 TT-CGTTTGTTTATTTAAAA
1 TTATGTTTGTTTATTTAAAA
127367 TTATGTTTGTT
1 TTATGTTTGTT
127378 CATATTCGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
14 8 0.23
15 3 0.09
16 1 0.03
18 1 0.03
19 3 0.09
20 19 0.54
ACGTcount: A:0.23, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
TTATGTTTGTTTATTTAAAA
Found at i:127356 original size:34 final size:34
Alignment explanation
Indices: 127317--127393 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
127307 TTTTGTTTAT
127317 GTTTGTTTATTTAAAATTATGTTTGTTCATATTC
1 GTTTGTTTATTTAAAATTATGTTTGTTCATATTC
127351 GTTTGTTTATTTAAAATTATGTTTGTTCATATTC
1 GTTTGTTTATTTAAAATTATGTTTGTTCATATTC
127385 GTTTGTTTA
1 GTTTGTTTA
127394 ATGTTCACGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.22, C:0.05, G:0.13, T:0.60
Consensus pattern (34 bp):
GTTTGTTTATTTAAAATTATGTTTGTTCATATTC
Found at i:127431 original size:23 final size:23
Alignment explanation
Indices: 127400--127511 Score: 136
Period size: 23 Copynumber: 4.8 Consensus size: 23
127390 TTTAATGTTC
*
127400 ACGAACATGTTCATTCAAC-TTAA
1 ACGAACATGTTCA-TGAACATTAA
*
127423 TCGAACATGTTCATGAACATTAA
1 ACGAACATGTTCATGAACATTAA
*
127446 ACGAATATGTTCATGAACATTAA
1 ACGAACATGTTCATGAACATTAA
*
127469 ACGAATATGTTCATGAACATATAA
1 ACGAACATGTTCATGAACAT-TAA
** *
127493 TTGAACATGTTCACGAACA
1 ACGAACATGTTCATGAACA
127512 ATGTTAATGA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
22 4 0.05
23 57 0.72
24 18 0.23
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (23 bp):
ACGAACATGTTCATGAACATTAA
Found at i:127442 original size:12 final size:12
Alignment explanation
Indices: 127419--127522 Score: 52
Period size: 12 Copynumber: 8.7 Consensus size: 12
127409 TTCATTCAAC
127419 TTAATCGAACATG
1 TTAAT-GAACATG
*
127432 TTCATGAACAT-
1 TTAATGAACATG
* * *
127443 TAAACGAATATG
1 TTAATGAACATG
*
127455 TTCATGAACAT-
1 TTAATGAACATG
* * *
127466 TAAACGAATATG
1 TTAATGAACATG
*
127478 TTCATGAACAT-
1 TTAATGAACATG
*
127489 ATAATTGAACATG
1 TTAA-TGAACATG
* *
127502 TTCACGAACAATG
1 TTAATGAAC-ATG
127515 TTAATGAA
1 TTAATGAA
127523 TAATAAACAA
Statistics
Matches: 62, Mismatches: 24, Indels: 10
0.65 0.25 0.10
Matches are distributed among these distances:
11 16 0.26
12 31 0.50
13 15 0.24
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (12 bp):
TTAATGAACATG
Found at i:127842 original size:22 final size:22
Alignment explanation
Indices: 127817--127862 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
127807 AAATATTCGT
*
127817 ATTTTTTATAATAT-TTAATTTA
1 ATTTTTCATAATATATT-ATTTA
*
127839 ATTTTTCATTATATATTATTTA
1 ATTTTTCATAATATATTATTTA
127861 AT
1 AT
127863 AACAGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTTCATAATATATTATTTA
Found at i:128061 original size:6 final size:6
Alignment explanation
Indices: 128043--128100 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
128033 TTAAGTTGGG
**
128043 TTTAAA TTT--A TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
128087 TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TT
128101 GATTTAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 4 0.10
5 7 0.17
6 31 0.74
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:128075 original size:17 final size:17
Alignment explanation
Indices: 128043--128115 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
128033 TTAAGTTGGG
128043 TTTAAATTT-ATTTAAA
1 TTTAAATTTGATTTAAA
*
128059 TTTAAATTTGCTTTAAA
1 TTTAAATTTGATTTAAA
* *
128076 TTTAAATTTAATTAAAA
1 TTTAAATTTGATTTAAA
128093 TTTAAA-TTGATTTAAAA
1 TTTAAATTTGATTT-AAA
128110 TTTAAA
1 TTTAAA
128116 ACTTAACATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
16 14 0.29
17 35 0.71
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTAAATTTGATTTAAA
Found at i:128088 original size:11 final size:11
Alignment explanation
Indices: 128043--128097 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
128033 TTAAGTTGGG
128043 TTTAAATTT-A
1 TTTAAATTTAA
128053 TTTAAATTTAAA
1 TTTAAATTT-AA
**
128065 TTT-GCTTTAAA
1 TTTAAATTT-AA
128076 TTTAAATTTAA
1 TTTAAATTTAA
*
128087 TTAAAATTTAA
1 TTTAAATTTAA
128098 ATTGATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
10 9 0.24
11 21 0.57
12 7 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:128835 original size:18 final size:18
Alignment explanation
Indices: 128809--128843 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
128799 ATTGATGATA
128809 ATTAATATTAATAATAAT
1 ATTAATATTAATAATAAT
*
128827 ATTATTATTAATAATAA
1 ATTAATATTAATAATAA
128844 CAGTAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAATATTAATAATAAT
Found at i:130022 original size:30 final size:30
Alignment explanation
Indices: 129883--130030 Score: 158
Period size: 30 Copynumber: 4.9 Consensus size: 30
129873 CCTTGGAAGT
* *
129883 CCCTAAAC-TATCCAAAAAT-CATATTTTGAC
1 CCCTAAACTTTTCCAAAATTACAT-TTTT-AC
* *
129913 CCCTAAACTTTTCCAAAATTATATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTTAC
* * *
129943 CCCTAAACTTTTCCGAAATTAAATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTTAC
* *
129973 CCTTAAACTTCTCCAAAATTACATTTTTAC
1 CCCTAAACTTTTCCAAAATTACATTTTTAC
*
130003 CCCTTAAAC-TTTCTAAAATTACATTTTT
1 CCC-TAAACTTTTCCAAAATTACATTTTT
130031 GGCCTCGATT
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
30 82 0.81
31 17 0.17
32 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.39
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTACATTTTTAC
Found at i:130067 original size:30 final size:30
Alignment explanation
Indices: 130033--130415 Score: 189
Period size: 30 Copynumber: 13.1 Consensus size: 30
130023 ACATTTTTGG
*
130033 CCTCGATTTTTCTAAAAATTACCATTTTAC
1 CCTCGATTTTTCCAAAAATTACCATTTTAC
** * *
130063 CCTCGA-ACTCCCAAAAATT-CTATCTTTGA-
1 CCTCGATTTTTCCAAAAATTACCAT-TTT-AC
* * *
130092 CCTCGATTTTACAAAAAATTACTATTTTAC
1 CCTCGATTTTTCCAAAAATTACCATTTTAC
** *
130122 CCTCGAACTTT-GAAAAATT-CCATTTTTAAC
1 CCTCGATTTTTCCAAAAATTACCA-TTTT-AC
*
130152 CCT-GATTTTTCCAAAATTTACCATTTTAC
1 CCTCGATTTTTCCAAAAATTACCATTTTAC
*
130181 CCTCGA-ATTTCCAAAAATT-CCATTTTTGAC
1 CCTCGATTTTTCCAAAAATTACCA-TTTT-AC
* * **
130211 CC-CTATTTTTCTAGGAATTACCA-TTTAC
1 CCTCGATTTTTCCAAAAATTACCATTTTAC
* *
130239 CC-CTGA-ATTTCCAAAAAAT-CCATTTTTGAC
1 CCTC-GATTTTTCCAAAAATTACCA-TTTT-AC
* *
130269 ACT-AATTTTTCC-AAAATTACCATTTTA-
1 CCTCGATTTTTCCAAAAATTACCATTTTAC
* *** *
130296 CCT-TAAACTTCCCAAAATT-CCATTTTTGA-
1 CCTCGATTTTTCCAAAAATTACCA-TTTT-AC
* *
130325 TC-CGATTCTTTCCAAAAATTATCATTTTAC
1 CCTCGATT-TTTCCAAAAATTACCATTTTAC
* ** *
130355 CCCCGA-ACTTCCAAAAATT-CCATTTTTAA
1 CCTCGATTTTTCCAAAAATTACCA-TTTTAC
* *
130384 CCTCGATTCTTCCAAAAAGTACCATTTTAC
1 CCTCGATTTTTCCAAAAATTACCATTTTAC
130414 CC
1 CC
130416 CCAGATGTCT
Statistics
Matches: 265, Mismatches: 56, Indels: 64
0.69 0.15 0.17
Matches are distributed among these distances:
27 13 0.05
28 34 0.13
29 99 0.37
30 101 0.38
31 18 0.07
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (30 bp):
CCTCGATTTTTCCAAAAATTACCATTTTAC
Found at i:130148 original size:29 final size:30
Alignment explanation
Indices: 130041--130411 Score: 124
Period size: 29 Copynumber: 12.6 Consensus size: 30
130031 GGCCTCGATT
*
130041 TTTCTAAAAATTACCA-TTTT-ACCCTCGAA
1 TTTCCAAAAATT-CCATTTTTAACCCTCGAA
* * * * * *
130070 CTCCCAAAAATTCTATCTTTGA-CCTCGAT
1 TTTCCAAAAATTCCATTTTTAACCCTCGAA
* *
130099 TTTACAAAAAATTAC-TATTTT-ACCCTCGAA
1 TTT-CCAAAAATTCCAT-TTTTAACCCTCGAA
* *
130129 CTTT-GAAAAATTCCATTTTTAACCCT-GATT
1 -TTTCCAAAAATTCCATTTTTAACCCTCGA-A
*
130159 TTTCCAAAATTTACCA-TTTT-ACCCTCGAA
1 TTTCCAAAAATT-CCATTTTTAACCCTCGAA
* * *
130188 TTTCCAAAAATTCCATTTTTGACCC-CTATT
1 TTTCCAAAAATTCCATTTTTAACCCTCGA-A
* ** *
130218 TTTCTAGGAATTACCA--TTTACCCCT-GAA
1 TTTCCAAAAATT-CCATTTTTAACCCTCGAA
* * *
130246 TTTCCAAAAAATCCATTTTTGACACT--AA
1 TTTCCAAAAATTCCATTTTTAACCCTCGAA
**
130274 TTTTTCC-AAAATTACCA-TTTT-A-CCTTAAA
1 --TTTCCAAAAATT-CCATTTTTAACCCTCGAA
* * * * *
130303 CTTCCCAAAATTCCATTTTTGA-TC-CGATTC
1 TTTCCAAAAATTCCATTTTTAACCCTCGA--A
* *
130333 TTTCCAAAAATTATCA-TTTT-ACCCCCGAA
1 TTTCCAAAAATT-CCATTTTTAACCCTCGAA
* *
130362 CTTCCAAAAATTCCATTTTTAA-CCTCGAT
1 TTTCCAAAAATTCCATTTTTAACCCTCGAA
*
130391 TCTTCCAAAAAGTACCATTTT
1 T-TTCCAAAAA-TTCCATTTT
130412 ACCCCCAGAT
Statistics
Matches: 252, Mismatches: 54, Indels: 70
0.67 0.14 0.19
Matches are distributed among these distances:
27 12 0.05
28 29 0.12
29 107 0.42
30 82 0.33
31 22 0.09
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.39
Consensus pattern (30 bp):
TTTCCAAAAATTCCATTTTTAACCCTCGAA
Found at i:130266 original size:58 final size:57
Alignment explanation
Indices: 129984--130473 Score: 343
Period size: 59 Copynumber: 8.4 Consensus size: 57
129974 CTTAAACTTC
* * * * * *
129984 TCCAAAATTA-CATTTTTACCCCTTAAACTTTCTAAAATTACATTTTTG-GCCTCGATTTT
1 TCCAAAATTACCA-TTTTA-CCC-TGAACTTCCAAAAATTCCATTTTTGACCCT-AATTTT
* * * * *
130043 TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATTCTATCTTTGA-CCTCGATTTT
1 TC-CAAAATTACCATTTTACCCT-GAACTTCCAAAAATTCCATTTTTGACCCT-AATTTT
* * * ** * *
130102 ACAAAAAATTACTATTTTACCCTCGAACTTTGAAAAATTCCATTTTTAACCCTGATTTT
1 TC-CAAAATTACCATTTTACCCT-GAACTTCCAAAAATTCCATTTTTGACCCTAATTTT
*
130161 TCCAAAATTTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCCCT-ATTTT
1 TCCAAAA-TTACCATTTTACCCT-GAACTTCCAAAAATTCCATTTTTGA-CCCTAATTTT
* * * * *
130220 TCTAGGAATTACCA-TTTACCCCTGAATTTCCAAAAAATCCATTTTTGACACTAATTTT
1 TCCA-AAATTACCATTTTA-CCCTGAACTTCCAAAAATTCCATTTTTGACCCTAATTTT
* * * * *
130278 TCCAAAATTACCATTTTACCTTAAACTTCCCAAAATTCCATTTTTGATCC-GATTCTT
1 TCCAAAATTACCATTTTACCCTGAACTTCCAAAAATTCCATTTTTGACCCTAATT-TT
* * * * *
130335 TCCAAAAATTATCATTTTACCCCCGAACTTCCAAAAATTCCATTTTT-AACCTCGATTCT
1 TCC-AAAATTACCATTTTA-CCCTGAACTTCCAAAAATTCCATTTTTGACCCT-AATTTT
* ** * * *
130394 TCCAAAAAGTACCATTTTACCCCCAGA-TGT-CTAAAATTCTATTTTTGACCCTTAA-CTT
1 TCC-AAAATTACCATTTTACCCTGA-ACT-TCCAAAAATTCCATTTTTGACCC-TAATTTT
130452 TCCTAAAATTACCATTTTACCC
1 TCC-AAAATTACCATTTTACCC
130474 CTCCGAGTAT
Statistics
Matches: 355, Mismatches: 56, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
56 3 0.01
57 41 0.12
58 103 0.29
59 180 0.51
60 26 0.07
61 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (57 bp):
TCCAAAATTACCATTTTACCCTGAACTTCCAAAAATTCCATTTTTGACCCTAATTTT
Found at i:130409 original size:174 final size:175
Alignment explanation
Indices: 130135--130472 Score: 416
Period size: 174 Copynumber: 1.9 Consensus size: 175
130125 CGAACTTTGA
* * *
130135 AAAATTCCATTTTTAACCCTGATTTTTCCAAAATTTACCATTTTACCCTCGAATTTCCAAAAATT
1 AAAATTCCATTTTTAACCCTGATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATT
* * * * ** * * *
130200 CCATTTTTGACCCCTATTTTTCTAGGAATTACCA-TTTA-CCCCTGAATTTCCAAAAAATCCATT
66 CCATTTTTAACCCCGATTCTTCCAAAAAGTACCATTTTACCCCCAG-ATGT-CAAAAAATCCATT
*
130263 TTTGACAC-TAATTTTTCC-AAAATTACCATTTTACCTTAAACTTCCC
129 TTTGACACTTAA-CTTTCCTAAAATTACCATTTTACCTTAAACTTCCC
* * *
130309 AAAATTCCATTTTTGATCC-GATTCTTTCCAAAAATTATCATTTTACCCCCGAACTTCCAAAAAT
1 AAAATTCCATTTTTAACCCTGATT-TTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT
* * * *
130373 TCCATTTTTAACCTCGATTCTTCCAAAAAGTACCATTTTACCCCCAGATGTCTAAAATTCTATTT
65 TCCATTTTTAACCCCGATTCTTCCAAAAAGTACCATTTTACCCCCAGATGTCAAAAAATCCATTT
*
130438 TTGACCCTTAACTTTCCTAAAATTACCATTTTACC
130 TTGACACTTAACTTTCCTAAAATTACCATTTTACC
130473 CCTCCGAGTA
Statistics
Matches: 138, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
173 4 0.03
174 102 0.74
175 27 0.20
176 5 0.04
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (175 bp):
AAAATTCCATTTTTAACCCTGATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATT
CCATTTTTAACCCCGATTCTTCCAAAAAGTACCATTTTACCCCCAGATGTCAAAAAATCCATTTT
TGACACTTAACTTTCCTAAAATTACCATTTTACCTTAAACTTCCC
Found at i:130417 original size:59 final size:59
Alignment explanation
Indices: 130017--130415 Score: 434
Period size: 59 Copynumber: 6.8 Consensus size: 59
130007 TAAACTTTCT
* * * *
130017 AAAATTACATTTTTGGCCTCGATTTTTCTAAAAATTACCATTTTACCCTCGAACTCCCA
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
* * * * * **
130076 AAAATTCTATCTTTGACCTCGATTTTACAAAAAATTACTATTTTACCCTCGAACTTTGA
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
* * *
130135 AAAATTCCATTTTTAACC-CTGATTTTTCCAAAATTTACCATTTTACCCTCGAATTTCCA
1 AAAATTCCATTTTTGACCTC-GATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
* * * ** *
130194 AAAATTCCATTTTTGACCCCTATTTTTCTAGGAATTACCA-TTTACCC-CTGAATTTCCA
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCTC-GAACTTCCA
* * ** *
130252 AAAAATCCATTTTTGACACT-AATTTTTCC-AAAATTACCATTTTA-CCTTAAACTTCCC
1 AAAATTCCATTTTTGAC-CTCGATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
* * *
130309 AAAATTCCATTTTTGATC-CGATTCTTTCCAAAAATTATCATTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTGACCTCGATT-TTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
* * *
130368 AAAATTCCATTTTTAACCTCGATTCTTCCAAAAAGTACCATTTTACCC
1 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCC
130416 CCAGATGTCT
Statistics
Matches: 280, Mismatches: 49, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
56 4 0.01
57 37 0.13
58 58 0.21
59 175 0.62
60 6 0.02
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (59 bp):
AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
Found at i:138463 original size:21 final size:21
Alignment explanation
Indices: 138433--138479 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
138423 TAACATGGAA
*
138433 GAAGAGTCTGAGAATTCTGAG
1 GAAGAATCTGAGAATTCTGAG
138454 GAAGAATCTGAGAATTCTGAG
1 GAAGAATCTGAGAATTCTGAG
138475 GAAGA
1 GAAGA
138480 TCAAAGCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (21 bp):
GAAGAATCTGAGAATTCTGAG
Found at i:147830 original size:21 final size:21
Alignment explanation
Indices: 147806--147849 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
147796 TAACGCTTCA
147806 CAAAACGCTTC-TCTTTCAACT
1 CAAAACG-TTCTTCTTTCAACT
**
147827 CAAATTGTTCTTCTTTCAACT
1 CAAAACGTTCTTCTTTCAACT
147848 CA
1 CA
147850 TACTCGCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.39
Consensus pattern (21 bp):
CAAAACGTTCTTCTTTCAACT
Found at i:148004 original size:231 final size:231
Alignment explanation
Indices: 147717--148201 Score: 596
Period size: 231 Copynumber: 2.1 Consensus size: 231
147707 TCTCATATTT
* * * ** *
147717 CTGCTCATACTGTTTTACATTAACTTCAAGATCTCTACAACATTCTTTGAAAGCCTTCTCTTCCC
1 CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTACAACATTCTTCCAAAGCCTTCTCTTCCA
* * * *
147782 TCTCAAACTCCAAATAACGCTTCACAAAACGCTTCTCTTTCAACTCAAATTGTTCTTCTTTCAAC
66 ACTCAAACTCCAAACAACGCTTCACAAAACGCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
* * * * * * * *
147847 TCATACTCGCTCAAGCACTTCTCCAAAT-ATTTCTCTTTCACCCCAACTTCCTCGAACTTATCTT
131 ACATAATCCCTCAAGCAATTCTCCAAATCA-TTCTCTTTCAACCCAACTTCCCCCAACTTATCAT
* *
147911 TTACTGA-TTTCTCCGTCAACTTAAACTCTTCACACTG
195 TTAC-CACTTTCTCCATCAACTTAAACTCTTCACACTG
* * * *
147948 CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTGCGACGTTCTTCCAAAGCCTTTTCTTCCA
1 CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTACAACATTCTTCCAAAGCCTTCTCTTCCA
* * * * * * *
148013 ACTGAAATTCCATACACCGCTTCTCAAAACTCTTCTCTTTCAACCCAAATTGTTGTTCTCTCAAC
66 ACTCAAACTCCAAACAACGCTTCACAAAACGCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
* * *
148078 ACATAATCCCTCAAGCAATTCTCCAAATCATTCTCTTTTAACCGAATTTCCCCCAACTTATCATT
131 ACATAATCCCTCAAGCAATTCTCCAAATCATTCTCTTTCAACCCAACTTCCCCCAACTTATCATT
* * *
148143 TACCACTTTCTCCATCAACTTAACCTCTTTACATTG
196 TACCACTTTCTCCATCAACTTAAACTCTTCACACTG
*
148179 CTGCTCACATTGTTCTACACTAA
1 CTGCTCACATTGTTTTACACTAA
148202 ATTGGAGATC
Statistics
Matches: 214, Mismatches: 38, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
230 1 0.00
231 212 0.99
232 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.36
Consensus pattern (231 bp):
CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTACAACATTCTTCCAAAGCCTTCTCTTCCA
ACTCAAACTCCAAACAACGCTTCACAAAACGCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
ACATAATCCCTCAAGCAATTCTCCAAATCATTCTCTTTCAACCCAACTTCCCCCAACTTATCATT
TACCACTTTCTCCATCAACTTAAACTCTTCACACTG
Found at i:148246 original size:231 final size:230
Alignment explanation
Indices: 147717--148280 Score: 580
Period size: 231 Copynumber: 2.4 Consensus size: 230
147707 TCTCATATTT
* * * * * * * * ** * *
147717 CTGCTCATACTGTTTTACATTAACTTCAAGATCTCTACAACATTCTTTGAAAGCCTTCTCTTCCC
1 CTGCTCACATTGTTCTACACTAAATTCAAGATCTCTACGACGTGCTTCCAAAGCCTTTTCTTCCA
* * * * * * *
147782 TCTCAAACTCCAAATAACGCTTCACAAAACGCTTCTCTTTCAACTCAAATTGTTCTTCTTTCAAC
66 ACTCAAAATCCATACAACGCTTCTCAAAAC-CTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
* * * * * * * *
147847 TCATACTCGCTCAAGCACTTCTCCAAATATTTCTCTTTCACCCCAACTTCCTCGAACTTATCTTT
130 ACATAATCCCTCAAGCAATTCTCCAAATATTTCTCTTTCAACCCAACTTCCCCCAACTTATCATT
* *
147912 TACTGATTTCTCCGTCAACTTAAACTCTTCACACTG
195 TACTCATTTCTCCATCAACTTAAACTCTTCACACTG
* * * *
147948 CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTGCGACGTTCTTCCAAAGCCTTTTCTTCCA
1 CTGCTCACATTGTTCTACACTAAATTCAAGATCTCTACGACGTGCTTCCAAAGCCTTTTCTTCCA
* * * *
148013 ACTGAAATTCCATACACCGCTTCTCAAAACTCTTCTCTTTCAACCCAAATTGTTGTTCTCTCAAC
66 ACTCAAAATCCATACAACGCTTCTCAAAAC-CTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
* * *
148078 ACATAATCCCTCAAGCAATTCTCCAAATCA-TTCTCTTTTAACCGAATTTCCCCCAACTTATCAT
130 ACATAATCCCTCAAGCAATTCTCCAAAT-ATTTCTCTTTCAACCCAACTTCCCCCAACTTATCAT
* * *
148142 TTAC-CACTTTCTCCATCAACTTAACCTCTTTACATTG
194 TTACTCA-TTTCTCCATCAACTTAAACTCTTCACACTG
** * *
148179 CTGCTCACATTGTTCTACACTAAATTGGAGATCTTTACGAC-TGCGTT-CAAGATCCTTCTTC-T
1 CTGCTCACATTGTTCTACACTAAATTCAAGATCTCTACGACGTGC-TTCCAA-AGCCTT-TTCTT
* *
148241 CCAACTCAAAATCCCTACAACACTTCTCAAAAGCCTTCTC
63 CCAACTCAAAATCCATACAACGCTTCTCAAAA-CCTTCTC
148281 CTTTAACACA
Statistics
Matches: 277, Mismatches: 50, Indels: 12
0.82 0.15 0.04
Matches are distributed among these distances:
230 6 0.02
231 266 0.96
232 5 0.02
ACGTcount: A:0.26, C:0.32, G:0.07, T:0.35
Consensus pattern (230 bp):
CTGCTCACATTGTTCTACACTAAATTCAAGATCTCTACGACGTGCTTCCAAAGCCTTTTCTTCCA
ACTCAAAATCCATACAACGCTTCTCAAAACCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAACA
CATAATCCCTCAAGCAATTCTCCAAATATTTCTCTTTCAACCCAACTTCCCCCAACTTATCATTT
ACTCATTTCTCCATCAACTTAAACTCTTCACACTG
Found at i:156812 original size:37 final size:37
Alignment explanation
Indices: 156737--156913 Score: 185
Period size: 37 Copynumber: 4.8 Consensus size: 37
156727 GGATTATCGA
* * * *
156737 CACAAAACCTGCTAGGCACATGGCC-CAAATACACCGG
1 CACAAAGCCTACTAGGCACATAGCCTGAAA-ACACCGG
** * *
156774 CATGAAGCCTATTAGGCACATAGCCTGAAAACATCGG
1 CACAAAGCCTACTAGGCACATAGCCTGAAAACACCGG
** * *
156811 CATGAAGCTTACTAGGCACATAGCCTGAATACACCGG
1 CACAAAGCCTACTAGGCACATAGCCTGAAAACACCGG
* * * *
156848 CACAAAGCTTATTAGGCACATAGCCTGAAGACACCAG
1 CACAAAGCCTACTAGGCACATAGCCTGAAAACACCGG
*
156885 CACAAAGCCTACTAGGCACGTAGCCTGAA
1 CACAAAGCCTACTAGGCACATAGCCTGAA
156914 TATTTAGATG
Statistics
Matches: 119, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
37 116 0.97
38 3 0.03
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (37 bp):
CACAAAGCCTACTAGGCACATAGCCTGAAAACACCGG
Found at i:156869 original size:74 final size:74
Alignment explanation
Indices: 156737--156915 Score: 223
Period size: 74 Copynumber: 2.4 Consensus size: 74
156727 GGATTATCGA
* * * ** **
156737 CACAAAACCTGCTAGGCACATGGCCCAAATACACCGGCATGAAGCCTATTAGGCACATAGCCTGA
1 CACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCACAAAGCCTATTAGGCACATAGCCTGA
* *
156802 AAACATCGG
66 AAACACCAG
** * *
156811 CATGAAGCTTACTAGGCACATAGCCTGAATACACCGGCACAAAGCTTATTAGGCACATAGCCTGA
1 CACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCACAAAGCCTATTAGGCACATAGCCTGA
*
156876 AGACACCAG
66 AAACACCAG
*
156885 CACAAAGCCTACTAGGCACGTAGCCTGAATA
1 CACAAAGCCTACTAGGCACATAGCCTGAATA
156916 TTTAGATGCA
Statistics
Matches: 87, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
74 87 1.00
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.16
Consensus pattern (74 bp):
CACAAAGCCTACTAGGCACATAGCCTGAATACACCGGCACAAAGCCTATTAGGCACATAGCCTGA
AAACACCAG
Found at i:158640 original size:21 final size:19
Alignment explanation
Indices: 158589--158643 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
158579 TACAAAATCT
158589 AAATTTAATGAT-TATATA
1 AAATTTAATGATGTATATA
158607 AAATATATAATGATGTATTATA
1 AAAT-T-TAATGATGTA-TATA
*
158629 TTAATTTAATGATGT
1 -AAATTTAATGATGT
158644 TAAAATTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.13
19 1 0.03
20 7 0.23
21 11 0.35
22 5 0.16
23 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (19 bp):
AAATTTAATGATGTATATA
Found at i:158657 original size:20 final size:21
Alignment explanation
Indices: 158614--158657 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
158604 ATAAAATATA
* * *
158614 TAATGATGTATTATATTAATT
1 TAATGATGTATAAAATTAAGT
158635 TAATGATGT-TAAAATTAAGT
1 TAATGATGTATAAAATTAAGT
158655 TAA
1 TAA
158658 GCTTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (21 bp):
TAATGATGTATAAAATTAAGT
Found at i:162441 original size:33 final size:31
Alignment explanation
Indices: 162382--162442 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
162372 GATATCTTAA
*
162382 AATAATATTTTAGTCTTAAACAAATTAAAAC
1 AATAATATTTTAATCTTAAACAAATTAAAAC
* *
162413 AATAATGATTTTAATTTATAAATAAATTAA
1 AATAAT-ATTTTAATCT-TAAACAAATTAA
162443 TATTTATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 6 0.24
32 8 0.32
33 11 0.44
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.39
Consensus pattern (31 bp):
AATAATATTTTAATCTTAAACAAATTAAAAC
Found at i:169690 original size:23 final size:23
Alignment explanation
Indices: 169646--169722 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
169636 TCGGGCTCGA
* * *
169646 TTCGTTTAGCGTTCACGTACATG
1 TTCGTTTAACGTTCGCGAACATG
*
169669 TTCGTTTAACGTTCGCAAACATG
1 TTCGTTTAACGTTCGCGAACATG
* * *
169692 TTTGTTTATATGTTCGTGAACATG
1 TTCGTTTA-ACGTTCGCGAACATG
169716 TTCGTTT
1 TTCGTTT
169723 TTGTTCACGA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 26 0.59
24 18 0.41
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (23 bp):
TTCGTTTAACGTTCGCGAACATG
Found at i:173705 original size:20 final size:20
Alignment explanation
Indices: 173678--173735 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
173668 GTAATTTCTC
173678 TAATCTAATATTTAAATTTT
1 TAATCTAATATTTAAATTTT
* *
173698 TTATCTAAT-TTTATATTTT
1 TAATCTAATATTTAAATTTT
* *
173717 TAATTTTATATTTAAATTT
1 TAATCTAATATTTAAATTT
173736 AATTTGATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATCTAATATTTAAATTTT
Found at i:173716 original size:18 final size:20
Alignment explanation
Indices: 173680--173735 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
173670 AATTTCTCTA
173680 ATCTAATATTTAAATTTTTT
1 ATCTAATATTTAAATTTTTT
* *
173700 ATCTAAT-TTTATATTTTTA
1 ATCTAATATTTAAATTTTTT
* *
173719 ATTTTATATTTAAATTT
1 ATCTAATATTTAAATTT
173736 AATTTGATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
ATCTAATATTTAAATTTTTT
Found at i:173722 original size:14 final size:14
Alignment explanation
Indices: 173703--173729 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
173693 ATTTTTTATC
173703 TAATTTTATATTTT
1 TAATTTTATATTTT
173717 TAATTTTATATTT
1 TAATTTTATATTT
173730 AAATTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TAATTTTATATTTT
Found at i:173736 original size:26 final size:25
Alignment explanation
Indices: 173683--173740 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
173673 TTCTCTAATC
* * *
173683 TAATATTTAAATTTTTTATCTAATTT
1 TAAT-TTTTAATTTTATATCTAAATT
*
173709 TATATTTTTAATTTTATATTTAAATT
1 TA-ATTTTTAATTTTATATCTAAATT
173735 TAATTT
1 TAATTT
173741 GATAATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.15
26 21 0.78
27 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TAATTTTTAATTTTATATCTAAATT
Found at i:174384 original size:135 final size:135
Alignment explanation
Indices: 174239--174509 Score: 542
Period size: 135 Copynumber: 2.0 Consensus size: 135
174229 TTTTATGGGT
174239 TAAATTAGGTTATTAGTTCATTTAATTTACAATTATGATTTTTTTTATACTTTAATTTGAGAATT
1 TAAATTAGGTTATTAGTTCATTTAATTTACAATTATGATTTTTTTTATACTTTAATTTGAGAATT
174304 TTTTGTTTTGTATTTATAAATTTTAAAATTATAGTTTTTTTTTCGAGAATTGTTAAGTTCATCAA
66 TTTTGTTTTGTATTTATAAATTTTAAAATTATAGTTTTTTTTTCGAGAATTGTTAAGTTCATCAA
174369 TTAAG
131 TTAAG
174374 TAAATTAGGTTATTAGTTCATTTAATTTACAATTATGATTTTTTTTATACTTTAATTTGAGAATT
1 TAAATTAGGTTATTAGTTCATTTAATTTACAATTATGATTTTTTTTATACTTTAATTTGAGAATT
174439 TTTTGTTTTGTATTTATAAATTTTAAAATTATAGTTTTTTTTTCGAGAATTGTTAAGTTCATCAA
66 TTTTGTTTTGTATTTATAAATTTTAAAATTATAGTTTTTTTTTCGAGAATTGTTAAGTTCATCAA
174504 TTAAG
131 TTAAG
174509 T
1 T
174510 TTTGATATTT
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54
Consensus pattern (135 bp):
TAAATTAGGTTATTAGTTCATTTAATTTACAATTATGATTTTTTTTATACTTTAATTTGAGAATT
TTTTGTTTTGTATTTATAAATTTTAAAATTATAGTTTTTTTTTCGAGAATTGTTAAGTTCATCAA
TTAAG
Found at i:176165 original size:16 final size:16
Alignment explanation
Indices: 176144--176175 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
176134 ACTAAAATTC
*
176144 AAAATTAGAGTTTTTT
1 AAAATTAGAATTTTTT
176160 AAAATTAGAATTTTTT
1 AAAATTAGAATTTTTT
176176 GCAGATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
AAAATTAGAATTTTTT
Found at i:187580 original size:3 final size:3
Alignment explanation
Indices: 187572--187633 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
187562 GCTTGTAGAC
187572 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
187620 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
187634 ATAAAATGTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:203282 original size:87 final size:87
Alignment explanation
Indices: 203185--203357 Score: 337
Period size: 87 Copynumber: 2.0 Consensus size: 87
203175 TCGTAATTAA
*
203185 AATTAATTAATTACTAGCTTTGTTGATCATCGTTATTCAAATAAAATAAAATGATATTATATGTG
1 AATTAATTAATTACTAGCTTTGTTGATCATCGTTATTCAAACAAAATAAAATGATATTATATGTG
203250 CCGTTTGGATACGTGGAAAAAG
66 CCGTTTGGATACGTGGAAAAAG
203272 AATTAATTAATTACTAGCTTTGTTGATCATCGTTATTCAAACAAAATAAAATGATATTATATGTG
1 AATTAATTAATTACTAGCTTTGTTGATCATCGTTATTCAAACAAAATAAAATGATATTATATGTG
203337 CCGTTTGGATACGTGGAAAAA
66 CCGTTTGGATACGTGGAAAAA
203358 TAATGCTACG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (87 bp):
AATTAATTAATTACTAGCTTTGTTGATCATCGTTATTCAAACAAAATAAAATGATATTATATGTG
CCGTTTGGATACGTGGAAAAAG
Found at i:205430 original size:18 final size:18
Alignment explanation
Indices: 205407--205444 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
205397 ACTCAACCTA
*
205407 AATTTTTTCAAAAAAAAT
1 AATTTTATCAAAAAAAAT
*
205425 AATTTTATCAAAGAAAAT
1 AATTTTATCAAAAAAAAT
205443 AA
1 AA
205445 CTTAACTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (18 bp):
AATTTTATCAAAAAAAAT
Found at i:206232 original size:9 final size:9
Alignment explanation
Indices: 206218--206325 Score: 78
Period size: 9 Copynumber: 11.9 Consensus size: 9
206208 ATATAATTTT
206218 TTTTTATAA
1 TTTTTATAA
206227 TTTTTATAAA
1 TTTTTAT-AA
*
206237 TTATTATAAA
1 TTTTTAT-AA
**
206247 TTTTCGTAA
1 TTTTTATAA
*
206256 TTTCTATATA
1 TTTTTATA-A
206266 TTTTTAT-A
1 TTTTTATAA
*
206274 -TTTTATAT
1 TTTTTATAA
*
206282 TTTTTATGA
1 TTTTTATAA
206291 TTTTTATAA
1 TTTTTATAA
* *
206300 TATTTATCA
1 TTTTTATAA
*
206309 TTTTCA-ATA
1 TTTTTATA-A
206318 TTTTTATA
1 TTTTTATA
206326 TTGTAGAAAT
Statistics
Matches: 75, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
7 6 0.08
8 1 0.01
9 45 0.60
10 23 0.31
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:206238 original size:10 final size:10
Alignment explanation
Indices: 206218--206273 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
206208 ATATAATTTT
206218 TTTTTAT-AA
1 TTTTTATAAA
206227 TTTTTATAAA
1 TTTTTATAAA
*
206237 TTATTATAAA
1 TTTTTATAAA
**
206247 TTTTCGT-AA
1 TTTTTATAAA
* *
206256 TTTCTATATA
1 TTTTTATAAA
206266 TTTTTATA
1 TTTTTATA
206274 TTTTATATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
9 13 0.36
10 23 0.64
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:221068 original size:100 final size:100
Alignment explanation
Indices: 220887--221082 Score: 272
Period size: 100 Copynumber: 2.0 Consensus size: 100
220877 TCTTCTGGAG
* * *
220887 TCATCTTATTCCTCGGGTGCCAAGCTTTATCTGCTAAAAACCCTTTGCTTTATGTTTGTTTGATA
1 TCATCTTATTCCTCGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGATA
* * * *
220952 ATATATTTCTTAAAATTATTCGATGCCATGTTCCA
66 ATACATTTATTAAAATTATTCAATACCATGTTCCA
*
220987 TCATCTTATTCCTTGAGG-GCCAAGCTTTATCTGCTAAAAAACCATTTGCTTAATGTCTGTTTG-
1 TCATCTTATTCCTCG-GGTGCCAAGCTTTATCTGCT-AAAAACCATTTGCTTAATGTCTGTTTGA
221050 TGAATACATTTATT-AAATTATTCAATACCATGT
64 T-AATACATTTATTAAAATTATTCAATACCATGT
221083 GTCATTACTG
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
100 49 0.58
101 36 0.42
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.42
Consensus pattern (100 bp):
TCATCTTATTCCTCGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGATA
ATACATTTATTAAAATTATTCAATACCATGTTCCA
Found at i:224779 original size:20 final size:20
Alignment explanation
Indices: 224756--224804 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
224746 AATTTTTTTA
*
224756 AAAAATTATAA-AAATTATTT
1 AAAAATTATAACAAA-TATAT
*
224776 AAAAATCATAACAAATATAT
1 AAAAATTATAACAAATATAT
*
224796 AAAATTTAT
1 AAAAATTAT
224805 TTAATAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTATAACAAATATAT
Found at i:227899 original size:106 final size:107
Alignment explanation
Indices: 227759--227973 Score: 414
Period size: 106 Copynumber: 2.0 Consensus size: 107
227749 AAATCACCAG
227759 CAGCATTCATGGTGATGAATTTTGAATCAGACAAATGTAGAAAATATGTGATCCAAGAACGCATA
1 CAGCATTCATGGTGATGAATTTTGAATCAGACAAATGTAGAAAATATGTGATCCAAGAACGCATA
227824 CCCATGTCAATCCTATTTGAGCAGATTCTTTAATAACATCAC
66 CCCATGTCAATCCTATTTGAGCAGATTCTTTAATAACATCAC
227866 CAGCATTCATGGTGAT-AATTTTGAATCAGACAAATGTAGAAAATATGTGATCCAAGAACGCATA
1 CAGCATTCATGGTGATGAATTTTGAATCAGACAAATGTAGAAAATATGTGATCCAAGAACGCATA
*
227930 CCCATGTCAATGCTATTTGAGCAGATTCTTTAATAACATCAC
66 CCCATGTCAATCCTATTTGAGCAGATTCTTTAATAACATCAC
227972 CA
1 CA
227974 AGTTGCCCAG
Statistics
Matches: 107, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
106 91 0.85
107 16 0.15
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (107 bp):
CAGCATTCATGGTGATGAATTTTGAATCAGACAAATGTAGAAAATATGTGATCCAAGAACGCATA
CCCATGTCAATCCTATTTGAGCAGATTCTTTAATAACATCAC
Found at i:235121 original size:75 final size:75
Alignment explanation
Indices: 234998--235148 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
234988 AGAATAAATA
*
234998 AAGAATATGTATTGCATTCTATATCTTCATCCCATTTACAAGTAGCATACTCCTTTATATATATA
1 AAGAATATGTATTGCATTCTATATCTTCATCCCATTTACAAGTAGCATACTCCTCTATATATATA
235063 GGGAGATTCG
66 GGGAGATTCG
235073 AAGAATATGTATTGCATTCTATATCTTCATCCCATTTACAAGTAGCATACTCCTCTATATATATA
1 AAGAATATGTATTGCATTCTATATCTTCATCCCATTTACAAGTAGCATACTCCTCTATATATATA
235138 GGGAGATTCG
66 GGGAGATTCG
235148 A
1 A
235149 CACTTCATAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.36
Consensus pattern (75 bp):
AAGAATATGTATTGCATTCTATATCTTCATCCCATTTACAAGTAGCATACTCCTCTATATATATA
GGGAGATTCG
Found at i:243036 original size:21 final size:23
Alignment explanation
Indices: 242994--243036 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
242984 ACTTTTTTTA
242994 ATTATTTTGTGGTTTTAATTAAAT
1 ATTATTTTGTGGTTTT-ATTAAAT
243018 ATTATTTTGT-GTTTT-TTAA
1 ATTATTTTGTGGTTTTATTAA
243037 TGGATGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
23 5 0.26
24 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (23 bp):
ATTATTTTGTGGTTTTATTAAAT
Found at i:244410 original size:21 final size:22
Alignment explanation
Indices: 244367--244410 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
244357 GAAGGAGGAG
* * *
244367 AGTAAAGAGGTTGAGTGTGAAA
1 AGTAAAGAGGCTGAGGGTAAAA
244389 AGTAAA-AGGCTGAGGGTAAAA
1 AGTAAAGAGGCTGAGGGTAAAA
244410 A
1 A
244411 TGTGGCTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.34, T:0.18
Consensus pattern (22 bp):
AGTAAAGAGGCTGAGGGTAAAA
Found at i:245094 original size:28 final size:27
Alignment explanation
Indices: 245059--245118 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 27
245049 AATTTTTTAA
245059 ATTTT-AAAAATAAAAAGTATAAAAAAT
1 ATTTTAAAAAATAAAAA-TATAAAAAAT
245086 CATTTTAAAAAATAAAAATATAAAAAAT
1 -ATTTTAAAAAATAAAAATATAAAAAAT
245114 ATTTT
1 ATTTT
245119 CTTAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 5 0.16
28 15 0.48
29 11 0.35
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (27 bp):
ATTTTAAAAAATAAAAATATAAAAAAT
Found at i:247630 original size:29 final size:30
Alignment explanation
Indices: 247597--247665 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 30
247587 TAAAATATAT
* *
247597 ATTTTAGAAAAATCTAAAAAGTAAATAA-A
1 ATTTTAGAAAAATATAAAAAATAAATAAGA
* * *
247626 ATTTT-CAAAAATATAAAAAATAATTAAGT
1 ATTTTAGAAAAATATAAAAAATAAATAAGA
247655 ATTTTAGAAAA
1 ATTTTAGAAAA
247666 TTCAAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 18 0.56
29 10 0.31
30 4 0.12
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (30 bp):
ATTTTAGAAAAATATAAAAAATAAATAAGA
Found at i:247666 original size:29 final size:28
Alignment explanation
Indices: 247589--247666 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
247579 AATATTAATA
* *
247589 AAATATATATTTTAGAAAAATCTAAAAAGT
1 AAATA-ATATTTTAG-AAAATATAAAAAAT
*
247619 AAATAAAATTTTCA-AAAATATAAAAAAT
1 AAATAATATTTT-AGAAAATATAAAAAAT
*
247647 AATTAAGTATTTTAGAAAAT
1 AAATAA-TATTTTAGAAAAT
247667 TCAAAATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
28 18 0.45
29 16 0.40
30 6 0.15
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATAATATTTTAGAAAATATAAAAAAT
Found at i:247690 original size:25 final size:25
Alignment explanation
Indices: 247642--247704 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 25
247632 AAAAATATAA
*
247642 AAAATAATTAAGTATTTTAGAAAATTC
1 AAAATAA-TAAAT-TTTTAGAAAATTC
247669 AAAATATATAAATTTTTA-AAAATTC
1 AAAATA-ATAAATTTTTAGAAAATTC
247694 AAAATAATAAA
1 AAAATAATAAA
247705 AAATCAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
24 5 0.15
25 13 0.38
26 5 0.15
27 10 0.29
28 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (25 bp):
AAAATAATAAATTTTTAGAAAATTC
Found at i:275360 original size:10 final size:10
Alignment explanation
Indices: 275345--275374 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
275335 GCTCACAGAC
275345 CTTATTTAAT
1 CTTATTTAAT
275355 CTTATTTAAT
1 CTTATTTAAT
275365 CTTATTTAAT
1 CTTATTTAAT
275375 AGTTACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (10 bp):
CTTATTTAAT
Found at i:283080 original size:25 final size:27
Alignment explanation
Indices: 283052--283103 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
283042 GCCAAGTGGC
*
283052 AAAACATTC-CTTAGTGCCGCCACTTA
1 AAAACATTCTATTAGTGCCGCCACTTA
* *
283078 AAAACCTTCTATTTGTGCCGCCACTT
1 AAAACATTCTATTAGTGCCGCCACTT
283104 TGTGTTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (27 bp):
AAAACATTCTATTAGTGCCGCCACTTA
Done.