Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 36 of 190
Found at i:10204617 original size:20 final size:19
Alignment explanation
Indices: 10204592--10204636 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
10204582 AATAAACACC
10204592 AAAAAAA-ATTTTAGAAAACT
1 AAAAAAAGATTTTA-AAAA-T
10204612 AAAAAAAGTATTTTAAAAAT
1 AAAAAAAG-ATTTTAAAAAT
10204632 AAAAA
1 AAAAA
10204637 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 13 0.57
21 4 0.17
22 6 0.26
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAAAAAGATTTTAAAAAT
Found at i:10204617 original size:22 final size:20
Alignment explanation
Indices: 10204592--10204636 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
10204582 AATAAACACC
10204592 AAAAAAAATTTTAGAAAACTAA
1 AAAAAAAATTTTA-AAAA-TAA
**
10204614 AAAAAGTATTTTAAAAATAA
1 AAAAAAAATTTTAAAAATAA
10204634 AAA
1 AAA
10204637 GTATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 4 0.19
22 11 0.52
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAAAAAATTTTAAAAATAA
Found at i:10211347 original size:2 final size:2
Alignment explanation
Indices: 10211340--10211379 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
10211330 GATGTTTTGA
10211340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10211380 TGAAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10222324 original size:25 final size:25
Alignment explanation
Indices: 10222290--10222338 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
10222280 TTTAATTAAT
*
10222290 ACAAGACTTTGGACTGTTCTAAGAC
1 ACAAGACTTTGGACTGTTCCAAGAC
*
10222315 ACAAGACTTTGGATTGTTCCAAGA
1 ACAAGACTTTGGACTGTTCCAAGA
10222339 TGGTCTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (25 bp):
ACAAGACTTTGGACTGTTCCAAGAC
Found at i:10236896 original size:12 final size:12
Alignment explanation
Indices: 10236879--10236906 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10236869 GCACACAGTC
10236879 GTGTCCTGACCT
1 GTGTCCTGACCT
10236891 GTGTCCTGACCT
1 GTGTCCTGACCT
10236903 GTGT
1 GTGT
10236907 AACTCTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.29, G:0.29, T:0.36
Consensus pattern (12 bp):
GTGTCCTGACCT
Found at i:10237926 original size:42 final size:41
Alignment explanation
Indices: 10237880--10237990 Score: 114
Period size: 42 Copynumber: 2.7 Consensus size: 41
10237870 GCACATAAGT
* * * *
10237880 GCTAAACGGAAACCCATGAGGGTTGAACAGAAGCTTATAGGA
1 GCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTCAGA-GA
* * *
10237922 GCTAAACAGAAACCCAAAAGGGTTAAACTGAAGCTCAGAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTCAGAGA
* * * *
10237963 GCTGAACGGAAACTCATTAGGGATAAAC
1 GCTAAACGGAAACCCATAAGGGTTAAAC
10237991 TAAAACTCAT
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 24 0.43
42 32 0.57
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.15
Consensus pattern (41 bp):
GCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTCAGAGA
Found at i:10241226 original size:16 final size:16
Alignment explanation
Indices: 10241205--10241269 Score: 87
Period size: 16 Copynumber: 4.1 Consensus size: 16
10241195 CGCTGTATTG
10241205 GAATAGAGGCGTAATA
1 GAATAGAGGCGTAATA
*
10241221 GAATAGAGGCGTAATG
1 GAATAGAGGCGTAATA
*
10241237 GAATAGAGGTGTAAT-
1 GAATAGAGGCGTAATA
*
10241252 GAAATAGAGGTGTAATA
1 G-AATAGAGGCGTAATA
10241269 G
1 G
10241270 CAAATCAACT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
15 1 0.02
16 43 0.96
17 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.34, T:0.22
Consensus pattern (16 bp):
GAATAGAGGCGTAATA
Found at i:10241244 original size:32 final size:32
Alignment explanation
Indices: 10241203--10241267 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
10241193 TTCGCTGTAT
10241203 TGGAATAGAGGCGTAAT-AGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAATGA-AATAGAGGCGTAA
* *
10241235 TGGAATAGAGGTGTAATGAAATAGAGGTGTAA
1 TGGAATAGAGGCGTAATGAAATAGAGGCGTAA
10241267 T
1 T
10241268 AGCAAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.34, T:0.23
Consensus pattern (32 bp):
TGGAATAGAGGCGTAATGAAATAGAGGCGTAA
Found at i:10241521 original size:18 final size:17
Alignment explanation
Indices: 10241500--10241534 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10241490 TTATTATTAA
*
10241500 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
10241518 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
10241535 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:10241641 original size:18 final size:17
Alignment explanation
Indices: 10241618--10241654 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
10241608 AATTATTATT
10241618 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
10241634 AAATATATGATTTAATA
1 AAATATATGATTTAATA
10241651 AAAT
1 AAAT
10241655 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:10241693 original size:120 final size:120
Alignment explanation
Indices: 10241480--10241843 Score: 676
Period size: 120 Copynumber: 3.0 Consensus size: 120
10241470 TTAATCATAT
*
10241480 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
*
10241545 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
10241600 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
10241665 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
*
10241720 TTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTAAATAA
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAA
10241784 TCAATATTCTTATATGAATTTACTTAAAATCATAATATATGATACTATAAAATATAA
65 TCAATATTCTTATATGAATTTAC-TAAAATCATAATATATGATACTATAAAATATAA
10241841 TTT
1 TTT
10241844 GAAATNNNNN
Statistics
Matches: 239, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
120 201 0.84
121 38 0.16
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:10241761 original size:18 final size:17
Alignment explanation
Indices: 10241738--10241774 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
10241728 AATTATTATT
10241738 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
10241754 AAATATATGATTTAATA
1 AAATATATGATTTAATA
10241771 AAAT
1 AAAT
10241775 TCTAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:10242222 original size:47 final size:47
Alignment explanation
Indices: 10242100--10242236 Score: 151
Period size: 47 Copynumber: 3.0 Consensus size: 47
10242090 NNNNNNNNNN
* * *
10242100 TATATAATTTCATAAAACTCTTGATAATAAATATTCTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATATTCTTATATGAATA
** *
10242147 TATATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATGA
1 TATATAATTTCATAAAATTCTTAATAATAAATAT--TCTTATATGAAT-A
10242191 TATATAATTTCATAAAATTCTTAATAATAAATATTCTTATATGAAT
1 TATATAATTTCATAAAATTCTTAATAATAAATATTCTTATATGAAT
10242237 TTACTAAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
43 3 0.04
44 26 0.36
45 6 0.08
46 6 0.08
47 28 0.39
48 3 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (47 bp):
TATATAATTTCATAAAATTCTTAATAATAAATATTCTTATATGAATA
Found at i:10245274 original size:45 final size:41
Alignment explanation
Indices: 10245215--10245324 Score: 107
Period size: 45 Copynumber: 2.6 Consensus size: 41
10245205 TTTGGTTCGC
* *
10245215 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
10245257 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
10245300 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
10245325 TAATGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 21 0.38
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:10245491 original size:18 final size:17
Alignment explanation
Indices: 10245470--10245504 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10245460 TTATTATTAA
*
10245470 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
10245488 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
10245505 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:10245619 original size:14 final size:15
Alignment explanation
Indices: 10245541--10245621 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 15
10245531 AATTTACTCA
*
10245541 AATTATAATATATGAT
1 AATTA-AATATATTAT
*
10245557 ACTGTAAA-ATA-TA-
1 AAT-TAAATATATTAT
10245570 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
10245585 TATTAAATATATTAT
1 AATTAAATATATTAT
10245600 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
10245613 AATTTAATA
1 AATTAAATA
10245622 AAATTCTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
12 3 0.06
13 13 0.25
14 11 0.21
15 19 0.37
16 4 0.08
17 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:10245739 original size:14 final size:15
Alignment explanation
Indices: 10245690--10245741 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
10245680 GTAAAATATA
10245690 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
10245705 TATTAAATATATTAT
1 AATTAAATATATTAT
10245720 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
10245733 AATTTAATA
1 AATTAAATA
10245742 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:10245804 original size:61 final size:61
Alignment explanation
Indices: 10245498--10245804 Score: 228
Period size: 61 Copynumber: 5.1 Consensus size: 61
10245488 ATATAATTTA
*
10245498 ATAAAATTCTTAATAATTAATATTCTTATATATAATTTACTCAAATTATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTATTATATA-AATTTACTCAAATTATAATATATGATACT
* * * * * * *
10245560 GTAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTATTATATAAATTTACTCA-AATTATAATATATGATACT
* * *
10245618 AATAAAATTCTTAATAATTAATATTTTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTATTATATAAATTTACTCAAATTATAATATATGATACT
* * * * * * *
10245680 GTAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTATTATATAAATTTACTCA-AATTATAATATATGATACT
* * *
10245738 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTATTATATAAATTTACTCAAATTATAATATATGATACT
10245800 ATAAA
1 ATAAA
10245805 TGAAAATTTG
Statistics
Matches: 183, Mismatches: 38, Indels: 49
0.68 0.14 0.18
Matches are distributed among these distances:
57 4 0.02
58 12 0.07
59 53 0.29
60 29 0.16
61 62 0.34
62 15 0.08
63 8 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTATTATATAAATTTACTCAAATTATAATATATGATACT
Found at i:10245877 original size:120 final size:120
Alignment explanation
Indices: 10245453--10245866 Score: 699
Period size: 120 Copynumber: 3.4 Consensus size: 120
10245443 ATCATATTTA
*
10245453 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
10245518 TATTCTTATATATAATTTACTCAAATTATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATAT-GAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
10245574 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
10245639 TATTTTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
10245694 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
10245759 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAAA-TT
* * *
10245814 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
10245867 TAAAATAATT
Statistics
Matches: 281, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
119 7 0.02
120 198 0.70
121 76 0.27
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:10249201 original size:33 final size:33
Alignment explanation
Indices: 10249162--10249237 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
10249152 ATTATAAAGC
*
10249162 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
10249195 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
10249228 ATGTATAATT
1 ATGTATAATT
10249238 CAAGCTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:10249335 original size:37 final size:37
Alignment explanation
Indices: 10249280--10249361 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
10249270 GTATAAATAT
* *
10249280 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
*
10249317 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
10249354 ATTGATTA
1 ATTGATTA
10249362 ATAAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
Found at i:10252575 original size:5 final size:5
Alignment explanation
Indices: 10252535--10252560 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
10252525 GCAAATCGGC
10252535 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
10252561 TCGGATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:10254517 original size:30 final size:30
Alignment explanation
Indices: 10254481--10254537 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
10254471 TTTTACATAT
10254481 ATATTTTGAATTTTTATAAAAT-TTTTATTC
1 ATATTTTGAATTTTTA-AAAATATTTTATTC
*
10254511 ATATTTTTAATTTTTAAAAATATTTTA
1 ATATTTTGAATTTTTAAAAATATTTTA
10254538 ACGTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (30 bp):
ATATTTTGAATTTTTAAAAATATTTTATTC
Found at i:10254593 original size:22 final size:20
Alignment explanation
Indices: 10254551--10254597 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
10254541 TGAATTTCAA
*
10254551 TATTTTTAATAATTTATATT
1 TATTTTTAATAATTTAAATT
10254571 TATTTTTAATATATTTTAAATT
1 TATTTTTAATA-A-TTTAAATT
10254593 T-TTTT
1 TATTTT
10254598 AAAAATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 5 0.21
22 8 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTTTAATAATTTAAATT
Found at i:10265260 original size:21 final size:21
Alignment explanation
Indices: 10265236--10265292 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
10265226 ATTGGGTGGA
* *
10265236 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTAT
10265257 TCAGCTCTTACGAGCTTCTAT
1 TCAGCTCTTACGAGCTTCTAT
*
10265278 TCAACT-TT-CGAGCTT
1 TCAGCTCTTACGAGCTT
10265293 TTGTTGGCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 7 0.21
20 2 0.06
21 24 0.73
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.40
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTAT
Found at i:10276501 original size:31 final size:31
Alignment explanation
Indices: 10276462--10276530 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
10276452 TATGTCGCAG
10276462 TTAA-TCTATTTCTAAATTGTGCCAATCAAT
1 TTAATTCTATTTCTAAATTGTGCCAATCAAT
10276492 TTAATTCTATTTCTAAATTGTGCCAATCAAT
1 TTAATTCTATTTCTAAATTGTGCCAATCAAT
10276523 TTAATTCT
1 TTAATTCT
10276531 TCATAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (31 bp):
TTAATTCTATTTCTAAATTGTGCCAATCAAT
Found at i:10277487 original size:23 final size:23
Alignment explanation
Indices: 10277455--10277498 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
10277445 AATACCATTT
10277455 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
10277478 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
10277499 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:10277491 original size:13 final size:11
Alignment explanation
Indices: 10277459--10277501 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
10277449 CCATTTTCTA
*
10277459 AATAAAATAAT
1 AATAAAATATT
10277470 AAT-AAATATCT
1 AATAAAATAT-T
10277481 AAGTAAAATATT
1 AA-TAAAATATT
10277493 AATAAAATA
1 AATAAAATA
10277502 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:10281259 original size:30 final size:30
Alignment explanation
Indices: 10281152--10281261 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 30
10281142 GTTTTGTTAT
* * ** *
10281152 TTATATATATAATATATATGGGTTTTGCTG
1 TTATATGTATAATATATTTGGGTCATGGTG
* **
10281182 TTATA--TATAATATATGTACGTGCATGGGTG
1 TTATATGTATAATATATTTGGGT-CAT-GGTG
*
10281212 TTATATGAATAATATATTTGGGTCATGGTG
1 TTATATGTATAATATATTTGGGTCATGGTG
10281242 TTATATGTATAATATATTTG
1 TTATATGTATAATATATTTG
10281262 CGTGGGTCAG
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
28 13 0.20
29 1 0.02
30 36 0.55
31 3 0.05
32 12 0.18
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (30 bp):
TTATATGTATAATATATTTGGGTCATGGTG
Found at i:10289478 original size:2 final size:2
Alignment explanation
Indices: 10289471--10289570 Score: 139
Period size: 2 Copynumber: 47.5 Consensus size: 2
10289461 TCTCAATTAC
10289471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10289513 AT AT AT ACT ACT ACT ACT ACT ACT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT A-T A-T A-T A-T A-T A-T AT AT AT AT AT AT AT AT AT AT
10289556 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
10289571 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.01
2 78 0.81
3 17 0.18
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10290093 original size:2 final size:2
Alignment explanation
Indices: 10290086--10290137 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
10290076 CTACTACTAC
10290086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10290128 TA TA TA TA TA
1 TA TA TA TA TA
10290138 CACTACATCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10310472 original size:29 final size:31
Alignment explanation
Indices: 10310419--10310478 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
10310409 AACCTCTTCG
10310419 CTTTCCTCTCAAAACTTTTACT-CCCTCCCA
1 CTTTCCTCTCAAAACTTTTACTCCCCTCCCA
* **
10310449 CTTTCC-CTCATAACTTTTGTTCCCCTCCCA
1 CTTTCCTCTCAAAACTTTTACTCCCCTCCCA
10310479 TCCTACCCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.17, C:0.43, G:0.02, T:0.38
Consensus pattern (31 bp):
CTTTCCTCTCAAAACTTTTACTCCCCTCCCA
Found at i:10317489 original size:69 final size:68
Alignment explanation
Indices: 10317379--10317513 Score: 234
Period size: 69 Copynumber: 2.0 Consensus size: 68
10317369 CGTTGAGCGC
* *
10317379 ACATAAAAAAATCTAACACTCGTCATCATTATCAAATTATTGTGAAATGCAAATGTGAGTTATGG
1 ACATAAAAAAATCTAACACTCATCATCATTATCAAATTATTGTGAAATGCAAATGTCAGTTATGG
10317444 CGG
66 CGG
*
10317447 ACATAAAAAAAATCTAACACTCATCATCATTATCAAATTATTGTGAAATGTAAATGTCAGTTATG
1 ACAT-AAAAAAATCTAACACTCATCATCATTATCAAATTATTGTGAAATGCAAATGTCAGTTATG
10317512 GC
65 GC
10317514 AGTTGTATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 4 0.06
69 59 0.94
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (68 bp):
ACATAAAAAAATCTAACACTCATCATCATTATCAAATTATTGTGAAATGCAAATGTCAGTTATGG
CGG
Found at i:10318031 original size:9 final size:8
Alignment explanation
Indices: 10318005--10318084 Score: 115
Period size: 8 Copynumber: 9.5 Consensus size: 8
10317995 TTTGGTTAAA
10318005 AATTACCG
1 AATTACCG
10318013 AATTACCG
1 AATTACCG
10318021 AATTAACCG
1 AATT-ACCG
10318030 AATTACCG
1 AATTACCG
10318038 AATTAACCG
1 AATT-ACCG
10318047 AATTAACCG
1 AATT-ACCG
10318056 AATTACCG
1 AATTACCG
*
10318064 AAAATACCG
1 -AATTACCG
10318073 AATTACCG
1 AATTACCG
10318081 AATT
1 AATT
10318085 TTTTTTATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
8 35 0.52
9 32 0.48
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (8 bp):
AATTACCG
Found at i:10318031 original size:17 final size:16
Alignment explanation
Indices: 10318005--10318084 Score: 115
Period size: 17 Copynumber: 4.8 Consensus size: 16
10317995 TTTGGTTAAA
10318005 AATTACCGAATTACCG
1 AATTACCGAATTACCG
10318021 AATTAACCGAATTACCG
1 AATT-ACCGAATTACCG
10318038 AATTAACCGAATTAACCG
1 AATT-ACCGAATT-ACCG
*
10318056 AATTACCGAAAATACCG
1 AATTACCG-AATTACCG
10318073 AATTACCGAATT
1 AATTACCGAATT
10318085 TTTTTTATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.12
17 41 0.69
18 11 0.19
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (16 bp):
AATTACCGAATTACCG
Found at i:10321824 original size:32 final size:32
Alignment explanation
Indices: 10321763--10321825 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
10321753 TGCATGAGCT
*
10321763 ACACGGGTTGAACCATTACATACGACCAGACC
1 ACACGGGTTGAACCATTACACACGACCAGACC
* * * *
10321795 ACACTGGTTGAACCATTTCACATGGCCAGAC
1 ACACGGGTTGAACCATTACACACGACCAGAC
10321826 AACATAGCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (32 bp):
ACACGGGTTGAACCATTACACACGACCAGACC
Found at i:10324243 original size:30 final size:29
Alignment explanation
Indices: 10324189--10324248 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
10324179 CGAGCCTTGG
10324189 GGCAAAAATGTAATTATGTAAAAGTTTAGA
1 GGCAAAAATGTAATTATGTAAAAG-TTAGA
* *
10324219 GGCAAAATTGTAATTTTG-ACAAAGTTAGA
1 GGCAAAAATGTAATTATGTA-AAAGTTAGA
10324248 G
1 G
10324249 TCGAGGGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (29 bp):
GGCAAAAATGTAATTATGTAAAAGTTAGA
Found at i:10324445 original size:50 final size:50
Alignment explanation
Indices: 10324370--10324689 Score: 399
Period size: 50 Copynumber: 6.4 Consensus size: 50
10324360 GTTGGTGAAT
10324370 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
* * *
10324420 TGGGATATGGCGTTGGTACCGAGATGAGAGGTCCCATGTAAGACCATATC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
* **
10324470 TGAGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
* * * * **
10324520 TGGGACATGGCATGGGCACCGATATAAGAACATCCCATGTAAGACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTC
* *
10324571 TGGGACATGGTGTTGGCACCGAGATGAGAGGTCCC-TCGTAAAACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCAT-GTAAGACCATGTC
* * * * **
10324621 TGGGGCATGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTC
* * *
10324672 TGAGACATAGCTTTGGCA
1 TGGGACATGGCGTTGGCA
10324690 TGTTATGATC
Statistics
Matches: 227, Mismatches: 39, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
49 1 0.00
50 154 0.68
51 71 0.31
52 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
Found at i:10324604 original size:101 final size:101
Alignment explanation
Indices: 10324373--10324689 Score: 465
Period size: 101 Copynumber: 3.1 Consensus size: 101
10324363 GGTGAATTGG
* * * * *
10324373 GACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTGGTA
1 GACATGGCGTTGGCACCGAGATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA
* ** *
10324438 CCGAGATGAG-AGGTCCCATGTAAGACCATATCTGA
66 CCGATATGAGAACATCCCATGTAAGACCATGTCTGA
*
10324473 GACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCA
1 GACATGGCGTTGGCACCGAGATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA
* *
10324538 CCGATATAAGAACATCCCATGTAAGACCATGTCTGG
66 CCGATATGAGAACATCCCATGTAAGACCATGTCTGA
* * * *
10324574 GACATGGTGTTGGCACCGAGATGAGAGGTCCCTCGTAAAACCATGTCTGGGGCATGGCATGGGCA
1 GACATGGCGTTGGCACCGAGATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA
10324639 CCGATATGAGAACATCCCATGTAAGACCATGTCTGA
66 CCGATATGAGAACATCCCATGTAAGACCATGTCTGA
* *
10324675 GACATAGCTTTGGCA
1 GACATGGCGTTGGCA
10324690 TGTTATGATC
Statistics
Matches: 195, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
100 67 0.34
101 128 0.66
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (101 bp):
GACATGGCGTTGGCACCGAGATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA
CCGATATGAGAACATCCCATGTAAGACCATGTCTGA
Found at i:10328195 original size:9 final size:9
Alignment explanation
Indices: 10328183--10328211 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
10328173 TGACGGAAAT
10328183 GGTGGTGGA
1 GGTGGTGGA
10328192 GGTGGTGGA
1 GGTGGTGGA
10328201 GGTGGTGGA
1 GGTGGTGGA
10328210 GG
1 GG
10328212 CAGTGGGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.69, T:0.21
Consensus pattern (9 bp):
GGTGGTGGA
Found at i:10328217 original size:18 final size:18
Alignment explanation
Indices: 10328183--10328217 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10328173 TGACGGAAAT
**
10328183 GGTGGTGGAGGTGGTGGA
1 GGTGGTGGAGGCAGTGGA
10328201 GGTGGTGGAGGCAGTGG
1 GGTGGTGGAGGCAGTGG
10328218 GGGAGGAGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.03, G:0.66, T:0.20
Consensus pattern (18 bp):
GGTGGTGGAGGCAGTGGA
Found at i:10329662 original size:24 final size:24
Alignment explanation
Indices: 10329595--10329662 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
10329585 TGGAGGAACA
10329595 ATAATACTTCCATTGAAAATATCC
1 ATAATACTTCCATTGAAAATATCC
*
10329619 ---ATA-TT--ATTGAGAAACA-CC
1 ATAATACTTCCATTGA-AAATATCC
10329637 ATAATACTTCCATTGAAAATATCC
1 ATAATACTTCCATTGAAAATATCC
10329661 AT
1 AT
10329663 GTTATTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 2 0.06
21 6 0.18
22 2 0.06
23 4 0.12
24 9 0.26
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (24 bp):
ATAATACTTCCATTGAAAATATCC
Found at i:10336097 original size:51 final size:51
Alignment explanation
Indices: 10336038--10336138 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
10336028 CAAGACTTAG
10336038 TCAATTATCTCGAAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAAA
1 TCAATTATCTCGAAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAAA
*
10336089 TCAATTATCTCGCAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAA
1 TCAATTATCTCGAAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAA
10336139 CTCTTATTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (51 bp):
TCAATTATCTCGAAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAAA
Found at i:10340148 original size:23 final size:23
Alignment explanation
Indices: 10340119--10340166 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
10340109 TTCCTAATTA
*
10340119 ATGGCTCTCCT-AAGCTTCCCGAT
1 ATGGCTCGCCTGAA-CTTCCCGAT
*
10340142 ATGGCTCGCTTGAACTTCCCGAT
1 ATGGCTCGCCTGAACTTCCCGAT
10340165 AT
1 AT
10340167 ATGGCTATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (23 bp):
ATGGCTCGCCTGAACTTCCCGAT
Found at i:10340184 original size:25 final size:25
Alignment explanation
Indices: 10340156--10340221 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
10340146 CTCGCTTGAA
*
10340156 CTTCCCGATATATGGCTATCCGGAG
1 CTTCCCGATATATGGCTATACGGAG
* * *
10340181 CTTCCTGATAAATGGCTCTACGGAG
1 CTTCCCGATATATGGCTATACGGAG
* *
10340206 CTACCCGTTAT-TGGCT
1 CTTCCCGATATATGGCT
10340222 TGCATGAGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 5 0.15
25 28 0.85
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (25 bp):
CTTCCCGATATATGGCTATACGGAG
Found at i:10340296 original size:25 final size:25
Alignment explanation
Indices: 10340238--10340320 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
10340228 AGCTTCTTGA
* *
10340238 ATATGGCTCTGATGAGCTTCCCCTT
1 ATATGGCTCGGATAAGCTTCCCCTT
**
10340263 ATACAGCTCGGATAAGCTTCCCCTT
1 ATATGGCTCGGATAAGCTTCCCCTT
* *
10340288 ATATGGCTCGAGAGAGAGCTTCCCGTTT
1 ATATGGCTCG-GATA-AGCTTCCC-CTT
10340316 ATATG
1 ATATG
10340321 CTCATATGAG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 29 0.62
26 3 0.06
27 8 0.17
28 7 0.15
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (25 bp):
ATATGGCTCGGATAAGCTTCCCCTT
Found at i:10342377 original size:25 final size:25
Alignment explanation
Indices: 10342299--10342459 Score: 107
Period size: 25 Copynumber: 6.4 Consensus size: 25
10342289 AATTCATATT
*
10342299 CGGGAATGCTCATATGAGCACATA-AA
1 CGGGAA-GCTCATCTGAGC-CATATAA
* *
10342325 CAGGAAGCTCTCTCTCGAGCCATATAA
1 CGGGAAGCTC-ATCT-GAGCCATATAA
* *
10342352 CGGGAAGCTCATGTGAGCCATGTAA
1 CGGGAAGCTCATCTGAGCCATATAA
* * *
10342377 CGGGAAGCTTATCTGAGCAATATGA
1 CGGGAAGCTCATCTGAGCCATATAA
** ** * *
10342402 CAAGAAGCTCATAAGAGCTATATTTA
1 CGGGAAGCTCATCTGAGCCATA-TAA
10342428 --GGAAGCTCATGC-GAGCCA-ATAA
1 CGGGAAGCTCAT-CTGAGCCATATAA
10342450 CGGGAAGCTC
1 CGGGAAGCTC
10342460 TGAAGAGCCA
Statistics
Matches: 105, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
22 2 0.02
23 1 0.01
24 22 0.21
25 50 0.48
26 15 0.14
27 15 0.14
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (25 bp):
CGGGAAGCTCATCTGAGCCATATAA
Found at i:10342525 original size:23 final size:23
Alignment explanation
Indices: 10342499--10342544 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
10342489 TAGTCATATA
* *
10342499 TCGGGAAGTTCAAGCGAGCCATT
1 TCGGGAAGCTCAAGAGAGCCATT
*
10342522 TCGGGAAGCTCCAGAGAGCCATT
1 TCGGGAAGCTCAAGAGAGCCATT
10342545 AATTAGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (23 bp):
TCGGGAAGCTCAAGAGAGCCATT
Found at i:10342572 original size:26 final size:26
Alignment explanation
Indices: 10342525--10342595 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
10342515 AGCCATTTCG
* *
10342525 GGAAGCTC-CAGAGAGCCATTAATTA
1 GGAAGCTCACAAAGAGCCATTAATGA
* *
10342550 GGAAGCTCACAAAGAGCCTTTAATGC
1 GGAAGCTCACAAAGAGCCATTAATGA
*
10342576 GGAAGCTCACGAAGAGCCAT
1 GGAAGCTCACAAAGAGCCAT
10342596 ATATCGGGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 8 0.21
26 31 0.79
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCATTAATGA
Found at i:10356739 original size:25 final size:26
Alignment explanation
Indices: 10356702--10356750 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
10356692 AAAACTAAAG
*
10356702 AAAAATATAAAAAATTTAAATTTATT
1 AAAAATATAAAAAAATTAAATTTATT
*
10356728 AAAAATAT-AAAAAATTAGATTTA
1 AAAAATATAAAAAAATTAAATTTA
10356751 AAGTTGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AAAAATATAAAAAAATTAAATTTATT
Found at i:10356877 original size:25 final size:26
Alignment explanation
Indices: 10356848--10356905 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
10356838 AAAATATAGG
10356848 GAAAATAGAAAAAATTA-TAAAAATAT
1 GAAAATAGAAAAAATTATTAAAAAT-T
** *
10356874 -AAAATATCAAAATTTATTAAAAATT
1 GAAAATAGAAAAAATTATTAAAAATT
10356899 GAAAATA
1 GAAAATA
10356906 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (26 bp):
GAAAATAGAAAAAATTATTAAAAATT
Found at i:10358827 original size:25 final size:26
Alignment explanation
Indices: 10358784--10358832 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
10358774 TATAAAAAAG
10358784 TTTAATAATATTTATTTTTATATATT
1 TTTAATAATATTTATTTTTATATATT
*
10358810 TTTAATAAT-TTTATTTTTTTATA
1 TTTAATAATATTTATTTTTATATA
10358833 AATTTTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTAATAATATTTATTTTTATATATT
Found at i:10358830 original size:17 final size:18
Alignment explanation
Indices: 10358807--10358868 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
10358797 ATTTTTATAT
10358807 ATTTTTAATAATTTTAT-
1 ATTTTTAATAATTTTATC
*
10358824 -TTTTTTATAAATTTTATC
1 ATTTTTAAT-AATTTTATC
* *
10358842 ATTTTTACTAATTATAATC
1 ATTTTTAATAATT-TTATC
10358861 ATATTTTA
1 AT-TTTTA
10358869 TCTTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 7 0.19
17 8 0.22
18 4 0.11
19 12 0.33
20 5 0.14
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTAATAATTTTATC
Found at i:10358838 original size:26 final size:26
Alignment explanation
Indices: 10358784--10358839 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
10358774 TATAAAAAAG
*
10358784 TTTAATAATATTTATTTTTATATATT
1 TTTAATAATATTTATTTTTATATAAT
*
10358810 TTTAATAAT-TTTATTTTTTTATAAAT
1 TTTAATAATATTTATTTTTATAT-AAT
10358836 TTTA
1 TTTA
10358840 TCATTTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTAATAATATTTATTTTTATATAAT
Found at i:10359026 original size:25 final size:27
Alignment explanation
Indices: 10358976--10359028 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
10358966 ATGAATTATC
10358976 TATATTTTTATATATTATAATAATTTT
1 TATATTTTTATATATTATAATAATTTT
* *
10359003 TATA-TTTTAT-TATTTTAATTATTTT
1 TATATTTTTATATATTATAATAATTTT
10359028 T
1 T
10359029 TCTAACTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
26 6 0.25
27 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
TATATTTTTATATATTATAATAATTTT
Found at i:10366487 original size:3 final size:3
Alignment explanation
Indices: 10366479--10366510 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
10366469 TTTTTTGTCA
10366479 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10366511 ATTAATGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10373856 original size:62 final size:61
Alignment explanation
Indices: 10373699--10373911 Score: 209
Period size: 61 Copynumber: 3.4 Consensus size: 61
10373689 ATCCAATGCT
* * * * *
10373699 CAAATCAATTCAACAATATATATATTCATATACGAACCAAATTTGACAATGTATATCTATATA
1 CAAATAAATTCAACAATGTATA-A-CCATATACGAATCAAATTTGACAATGTATATCTATAGA
* * * *
10373762 CAAATCAATTCGACAATGTATAACCATATACGAATCAAGTTTGGCAATGTATAATC-ATAGA
1 CAAATAAATTCAACAATGTATAACCATATACGAATCAAATTTGACAATGTAT-ATCTATAGA
* * *
10373823 CAAATTAAATTCAACAGTGTATAACCATATACGAATC--ATTTCGACAACT-TATATCCATATA
1 CAAA-TAAATTCAACAATGTATAACCATATACGAATCAAATTT-GACAA-TGTATATCTATAGA
* *
10373884 CAATTCAATTTCAACAATGTATAACCAT
1 CAAAT-AAATTCAACAATGTATAACCAT
10373912 GTACAAATTA
Statistics
Matches: 128, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
60 7 0.05
61 67 0.52
62 34 0.27
63 20 0.16
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (61 bp):
CAAATAAATTCAACAATGTATAACCATATACGAATCAAATTTGACAATGTATATCTATAGA
Found at i:10374133 original size:31 final size:31
Alignment explanation
Indices: 10373699--10374134 Score: 213
Period size: 31 Copynumber: 14.2 Consensus size: 31
10373689 ATCCAATGCT
*
10373699 CAAATCAA-TTCAACAATATATATATTCATATA
1 CAAATTAATTTCAACAATATATA-A-TCATATA
*** * *
10373731 CGAACCAAATTT-GACAATGTAT-ATCTATATA
1 C-AAATTAATTTCAACAATATATAATC-ATATA
* * * *
10373762 CAAATCAA-TTCGACAATGTATAACCATATA
1 CAAATTAATTTCAACAATATATAATCATATA
* * ** * *
10373792 CGAATCAAGTTT-GGCAATGTATAATCATAGA
1 CAAATTAA-TTTCAACAATATATAATCATATA
* * * *
10373823 CAAATTAAATTCAACAGTGTATAACCATATA
1 CAAATTAATTTCAACAATATATAATCATATA
* * *
10373854 CGAA-TCATTTCGACAACT-TAT-ATCCATATA
1 CAAATTAATTTCAACAA-TATATAAT-CATATA
* * *
10373884 C-AATTCAATTTCAACAATGTATAACCATGTA
1 CAAATT-AATTTCAACAATATATAATCATATA
** * *
10373915 CAAATTAACATCAGCAATATGTAATCATATA
1 CAAATTAATTTCAACAATATATAATCATATA
*
10373946 CAAATCAATTT-AACAACT-TAT-ATCCATATA
1 CAAATTAATTTCAACAA-TATATAAT-CATATA
* * *
10373976 C-AATTCAATTTCAACAATGTATAACCATGTA
1 CAAATT-AATTTCAACAATATATAATCATATA
* *
10374007 CAAATTAATTTCAGCAATAGATAATCATATA
1 CAAATTAATTTCAACAATATATAATCATATA
* **
10374038 CAAATCAA-TTCGGCAACT-TAT-ATCCATATA
1 CAAATTAATTTCAACAA-TATATAAT-CATATA
** * **
10374068 C-AATTCAATTTCAACAACGTATAACCATGCA
1 CAAATT-AATTTCAACAATATATAATCATATA
* *
10374099 CAAATTAATTTCAGCAATATACAATCATATA
1 CAAATTAATTTCAACAATATATAATCATATA
10374130 CAAAT
1 CAAAT
10374135 CAAGTCGGCC
Statistics
Matches: 307, Mismatches: 68, Indels: 59
0.71 0.16 0.14
Matches are distributed among these distances:
29 15 0.05
30 87 0.28
31 173 0.56
32 18 0.06
33 12 0.04
34 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.31
Consensus pattern (31 bp):
CAAATTAATTTCAACAATATATAATCATATA
Found at i:10374211 original size:92 final size:92
Alignment explanation
Indices: 10373757--10374184 Score: 531
Period size: 92 Copynumber: 4.7 Consensus size: 92
10373747 ATGTATATCT
* * ** *
10373757 ATATACAAATCAATTCGACAA-TGTATAACCATATACGAA-TCAAGTTT-GGCAATGTATAATCA
1 ATATACAAATCAATTCGGCAACT-TATATCCATATAC-AATTCAA-TTTCAACAATGTATAACCA
* * * * *
10373819 TAG-ACAAATTAAATTCAACAGTGTATAACC
63 T-GTACAAATTAATTTCAGCAATATATAATC
* * *
10373849 ATATACGAATCATTTCGACAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
1 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
** *
10373914 ACAAATTAACATCAGCAATATGTAATC
66 ACAAATTAATTTCAGCAATATATAATC
***
10373941 ATATACAAATCAATTTAACAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
1 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
*
10374006 ACAAATTAATTTCAGCAATAGATAATC
66 ACAAATTAATTTCAGCAATATATAATC
* *
10374033 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAACGTATAACCATGC
1 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
*
10374098 ACAAATTAATTTCAGCAATATACAATC
66 ACAAATTAATTTCAGCAATATATAATC
* * * * **
10374125 ATATACAAATCAAGTCGGCCACTTATATCCATATGCAAATCAATTTTGACAATGTATAAC
1 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAAC
10374185 TATAAAAAAT
Statistics
Matches: 297, Mismatches: 35, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
91 6 0.02
92 290 0.98
93 1 0.00
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.30
Consensus pattern (92 bp):
ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
ACAAATTAATTTCAGCAATATATAATC
Found at i:10374213 original size:25 final size:25
Alignment explanation
Indices: 10374185--10374238 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
10374175 AATGTATAAC
*
10374185 TATAAAA-AATTCGAATTCGGCAATA
1 TATAAAACAA-TCAAATTCGGCAATA
*
10374210 TATAAAACAATCAAATTCGGCAATG
1 TATAAAACAATCAAATTCGGCAATA
10374235 TATA
1 TATA
10374239 TCTATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (25 bp):
TATAAAACAATCAAATTCGGCAATA
Found at i:10379616 original size:34 final size:34
Alignment explanation
Indices: 10379522--10379617 Score: 111
Period size: 34 Copynumber: 2.8 Consensus size: 34
10379512 ACATTACCAA
* * *
10379522 AAACATATATCCGATCAAAATGCCATATTTCTAG
1 AAACACATATCAGATCAAAATGTCATATTTCTAG
* * *
10379556 AAACATATATCAGATCAAAATATCATATTTTTAG
1 AAACACATATCAGATCAAAATGTCATATTTCTAG
** *
10379590 AAGTACATATCATATCAAAATGTCATAT
1 AAACACATATCAGATCAAAATGTCATAT
10379618 CATATTAGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (34 bp):
AAACACATATCAGATCAAAATGTCATATTTCTAG
Found at i:10382458 original size:21 final size:20
Alignment explanation
Indices: 10382434--10382522 Score: 55
Period size: 21 Copynumber: 4.5 Consensus size: 20
10382424 TTAAAAATTC
10382434 TTTAATAT-ATGATTTGAAAAT
1 TTTAATATAAT-ATTT-AAAAT
* *
10382455 TTTATTATAATATTTAAATT
1 TTTAATATAATATTTAAAAT
*
10382475 TTTAA-ATAA-ATTAATATATAT
1 TTTAATATAATATT--TA-AAAT
*
10382496 TTTAAT-T-ATATTTAAAAA
1 TTTAATATAATATTTAAAAT
10382514 TTTAA-ATAA
1 TTTAATATAA
10382523 GAAATATTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
18 11 0.21
19 7 0.13
20 11 0.21
21 22 0.42
22 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAATATAATATTTAAAAT
Found at i:10387000 original size:18 final size:18
Alignment explanation
Indices: 10386977--10387020 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
10386967 TAGCGACATT
10386977 TTTTAGCGCCGCAAATAC
1 TTTTAGCGCCGCAAATAC
10386995 TTTTAGCGCCGCAAATAC
1 TTTTAGCGCCGCAAATAC
10387013 TTTTAGCG
1 TTTTAGCG
10387021 GCGCTTTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (18 bp):
TTTTAGCGCCGCAAATAC
Found at i:10387608 original size:43 final size:43
Alignment explanation
Indices: 10387143--10387608 Score: 781
Period size: 43 Copynumber: 10.9 Consensus size: 43
10387133 GCAACGCCGT
* * *
10387143 TATAGACCATGGTCTTTAGCGGCGCTTAGCCTAAAAATGTCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
10387186 TATAGACCATGGTCTTTAGCGGCGCTTAGCCGAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
* * *
10387229 TATAGATCATTGTCTTTAGCGGCGCTTAGCCACAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
10387272 TATAGACCATGGTCTTTAGCGGCGTTTAGCCAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
10387315 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAATGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
* * *
10387358 TAGAGATCATGGTCTTTAGCGGCGCTTAGCCACAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
10387401 TATAGACCATGGTCTTTAGCGGCGCTTAGCCACAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
10387444 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAA-GCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
10387486 TATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
10387529 TATAGACCATGGTCTTTAGCGGCGCTTAGCCGAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
10387572 TATAGACCATGGTCTTTAGCGGCGCTTATCCAAAAAA
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAA
10387609 TGCCGCTAAT
Statistics
Matches: 397, Mismatches: 25, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
42 41 0.10
43 356 0.90
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (43 bp):
TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
Found at i:10387694 original size:14 final size:14
Alignment explanation
Indices: 10387677--10387706 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
10387667 AATCAGAAGA
10387677 AACCAAATCTAACC
1 AACCAAATCTAACC
10387691 AACCAAATCTAACC
1 AACCAAATCTAACC
10387705 AA
1 AA
10387707 ATCTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (14 bp):
AACCAAATCTAACC
Found at i:10387963 original size:21 final size:21
Alignment explanation
Indices: 10387915--10387968 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
10387905 TTATGCTGAT
*
10387915 CTGCTTCCCTCGCTGCAGCCT
1 CTGCTTCCCTCGCTGCAGCCG
*
10387936 CTACTTCCCTCGCTGCAGCCG
1 CTGCTTCCCTCGCTGCAGCCG
*
10387957 CTGCTTCTCTCG
1 CTGCTTCCCTCG
10387969 TTGCCGCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.06, C:0.46, G:0.19, T:0.30
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCG
Found at i:10388049 original size:21 final size:21
Alignment explanation
Indices: 10388020--10388070 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
10388010 TTTCGTTGAA
* *
10388020 CCTCAGCTTCTCTCGCTGCTG
1 CCTCTGCTTCTCTCGCTGCCG
10388041 CCTCTGCTTCTCTCGCTGCCG
1 CCTCTGCTTCTCTCGCTGCCG
*
10388062 CATCTGCTT
1 CCTCTGCTT
10388071 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCCG
Found at i:10388095 original size:87 final size:87
Alignment explanation
Indices: 10387939--10388136 Score: 231
Period size: 87 Copynumber: 2.3 Consensus size: 87
10387929 GCAGCCTCTA
* * * * *
10387939 CTTCCCTCGCTGCAGCCGCTGCTTCTCTCGTTGCCGCATCTTCTTTAAGCTGCTACTGCAGTTGC
1 CTTCTCTCGCTGCTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGCTACTGCAGTTGC
10388004 TCATA-CTTTCGTTGAACCTCAG
66 TCATATCTTT-GTTGAACCTCAG
* *
10388026 CTTCTCTCGCTGCTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTTG-TAGCTGGAGTT-
1 CTTCTCTCGCTGCTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGCTA-CTGCAGTTG
* **
10388089 CTTCATATCTTTTTTGAACCTTGG
65 C-TCATATCTTTGTTGAACCTCAG
* * *
10388113 CTTCTCTCGATGTTGCCTCCGCTT
1 CTTCTCTCGCTGCTGCCTCTGCTT
10388137 TAAGTTGTGT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
86 3 0.03
87 88 0.93
88 4 0.04
ACGTcount: A:0.11, C:0.32, G:0.19, T:0.38
Consensus pattern (87 bp):
CTTCTCTCGCTGCTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGCTACTGCAGTTGC
TCATATCTTTGTTGAACCTCAG
Found at i:10394523 original size:28 final size:28
Alignment explanation
Indices: 10394492--10394550 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
10394482 AAAATAATGT
*
10394492 AATTTTTAAAAATTGTTAATACAATTAA
1 AATTTTTAAAAATTGTTAATACAAATAA
10394520 AA-TTTTAAAAATTGTTAATACAAATAA
1 AATTTTTAAAAATTGTTAATACAAATAA
10394547 AATT
1 AATT
10394551 ATCTATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (28 bp):
AATTTTTAAAAATTGTTAATACAAATAA
Found at i:10395712 original size:16 final size:16
Alignment explanation
Indices: 10395691--10395721 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10395681 CGTTTATGAG
10395691 TTAGGGATTTCAGAAC
1 TTAGGGATTTCAGAAC
*
10395707 TTAGGGATTTTAGAA
1 TTAGGGATTTCAGAA
10395722 TAGGGAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
TTAGGGATTTCAGAAC
Found at i:10396513 original size:23 final size:23
Alignment explanation
Indices: 10396470--10396514 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
10396460 TGCTTTTGTA
*
10396470 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
10396493 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
10396515 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:10397469 original size:41 final size:41
Alignment explanation
Indices: 10397378--10397510 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
10397368 AATATTTCTA
* * * * ** *
10397378 ATTAGCGGCGTTTTTACACAAACGCCGCTATAG-ACCCAAG
1 ATTAGCGGCGATTCTCCAGAAACGCCGCTATAGAACGGAAC
* * *
10397418 AGTTACCGGCGCTTCTCCAGGAACGCCGCTATAGAACGGAAC
1 A-TTAGCGGCGATTCTCCAGAAACGCCGCTATAGAACGGAAC
* * * *
10397460 ATTAGCGGCGATTCTCCATAAACGCCGCTTTAGAGCGGAGC
1 ATTAGCGGCGATTCTCCAGAAACGCCGCTATAGAACGGAAC
*
10397501 ATCAGCGGCG
1 ATTAGCGGCG
10397511 GTTTATGAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
40 1 0.01
41 68 0.92
42 5 0.07
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGATTCTCCAGAAACGCCGCTATAGAACGGAAC
Found at i:10397802 original size:114 final size:113
Alignment explanation
Indices: 10397603--10397949 Score: 577
Period size: 113 Copynumber: 3.1 Consensus size: 113
10397593 GCTTAACGCC
* * *
10397603 AAACGCCGCTGAAGAACGGATTATTAGCGGCGTTTGGGCAAAAACCGCCACTAGTGTTCCCAAAT
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGC-AAAACCGCCACTAATGTTCCCAAAT
*
10397668 ATATGAAAACGGCGTCGTTCTGTGTTACTCTATTTGCGACGCTTTTTGTA
65 ATATGAAAACGGCGTCGTTCTGTGTTACTCTA-TTGCGGCGCTTTTTGTA
*
10397718 AAACGCCGCTGAAGAATGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* *
10397783 TATGAAAACGGCGTCGTTCTGTGTTACTCCATTGCGGCGCTTTTTATA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
* *
10397831 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* *
10397896 TATGAAAACGGCGTTGTTCTGTGTGACTCTATTGCGGCGCTTTTTGTA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
10397944 AAACGC
1 AAACGC
10397950 TGCTAATGCT
Statistics
Matches: 218, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 127 0.58
114 55 0.25
115 36 0.17
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (113 bp):
AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
Found at i:10400603 original size:23 final size:23
Alignment explanation
Indices: 10400573--10400639 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
10400563 ACATACATTC
10400573 ACGGGTCTTAAATCGAGCCTACG
1 ACGGGTCTTAAATCGAGCCTACG
10400596 ACGGGTCTTAAATCGAGCCTACG
1 ACGGGTCTTAAATCGAGCCTACG
*
10400619 ATGGGTCTTAAATCGAGCCTA
1 ACGGGTCTTAAATCGAGCCTA
10400640 TGAGGCCTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (23 bp):
ACGGGTCTTAAATCGAGCCTACG
Found at i:10403413 original size:16 final size:17
Alignment explanation
Indices: 10403392--10403435 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
10403382 AATGAGTTTT
10403392 ATTTTTATAATTTT-CA
1 ATTTTTATAATTTTACA
*
10403408 ATTTTTATAATTTTATA
1 ATTTTTATAATTTTACA
10403425 ATTTTT-TAATT
1 ATTTTTATAATT
10403436 ATATAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTATAATTTTACA
Found at i:10403440 original size:16 final size:17
Alignment explanation
Indices: 10403392--10403441 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
10403382 AATGAGTTTT
10403392 ATTTTTATAATT-T-TCA
1 ATTTTTATAATTATAT-A
*
10403408 ATTTTTATAATTTTATA
1 ATTTTTATAATTATATA
10403425 ATTTTT-TAATTATATA
1 ATTTTTATAATTATATA
10403441 A
1 A
10403442 AAATTAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 22 0.71
17 8 0.26
18 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTATAATTATATA
Found at i:10407103 original size:28 final size:28
Alignment explanation
Indices: 10407082--10407145 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
10407072 TTTTCAGAGT
10407082 TTCCCGATTTAAAGGCTCTTTTATGAGC
1 TTCCCGATTTAAAGGCTCTTTTATGAGC
*
10407110 TTCCCGATTTAAATGCTCTTTTATGAGC
1 TTCCCGATTTAAAGGCTCTTTTATGAGC
*
10407138 TTCTCGAT
1 TTCCCGAT
10407146 ATTGGCTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (28 bp):
TTCCCGATTTAAAGGCTCTTTTATGAGC
Found at i:10407159 original size:24 final size:24
Alignment explanation
Indices: 10407132--10407312 Score: 143
Period size: 24 Copynumber: 7.5 Consensus size: 24
10407122 ATGCTCTTTT
*
10407132 ATGAGCTTCTCGATATTGGCTCGC
1 ATGAGCTTCCCGATATTGGCTCGC
*
10407156 ATGAGCTTCCCGATATTAGCTCGC
1 ATGAGCTTCCCGATATTGGCTCGC
*
10407180 ATGAGCTTCCCGATATTGGCTTGC
1 ATGAGCTTCCCGATATTGGCTCGC
* * * * * *
10407204 TTGAACTTCTCGACATTGACTCGT
1 ATGAGCTTCCCGATATTGGCTCGC
* * *
10407228 ATGAGCTTCCCGTTAATGGCTCTC
1 ATGAGCTTCCCGATATTGGCTCGC
** * *
10407252 CGGAG-TTCCC-ATTACATGGCTCAC
1 ATGAGCTTCCCGA-TA-TTGGCTCGC
*
10407276 ATGAGCTTCCC-ATTATATGGCTCGA
1 ATGAGCTTCCCGA-TAT-TGGCTCGC
*
10407301 AAGAGCTTCCCG
1 ATGAGCTTCCCG
10407313 TTTATATGCT
Statistics
Matches: 122, Mismatches: 30, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
23 7 0.06
24 90 0.74
25 25 0.20
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.31
Consensus pattern (24 bp):
ATGAGCTTCCCGATATTGGCTCGC
Found at i:10407295 original size:25 final size:25
Alignment explanation
Indices: 10407228--10407320 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 25
10407218 ATTGACTCGT
* *
10407228 ATGAGCTTCCCGTTA-ATGGCTCTC
1 ATGAGCTTCCCATTATATGGCTCAC
** *
10407252 CGGAG-TTCCCATTACATGGCTCAC
1 ATGAGCTTCCCATTATATGGCTCAC
10407276 ATGAGCTTCCCATTATATGGCTCGA-
1 ATGAGCTTCCCATTATATGGCTC-AC
* *
10407301 AAGAGCTTCCCGTTTATATG
1 ATGAGCTTCCC-ATTATATG
10407321 CTTGTATGAG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
23 8 0.14
24 14 0.25
25 26 0.46
26 8 0.14
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCATTATATGGCTCAC
Found at i:10407331 original size:25 final size:25
Alignment explanation
Indices: 10407223--10407337 Score: 76
Period size: 25 Copynumber: 4.6 Consensus size: 25
10407213 TCGACATTGA
* *
10407223 CTCGTATGAGCTTCCCGTTA-ATGG
1 CTCGAATGAGCTTCCCATTATATGG
**** *
10407247 CTCTCCGGAG-TTCCCATTACATGG
1 CTCGAATGAGCTTCCCATTATATGG
10407271 CTC-ACATGAGCTTCCCATTATATGG
1 CTCGA-ATGAGCTTCCCATTATATGG
* *
10407296 CTCGAAAGAGCTTCCCGTTTATAT-G
1 CTCGAATGAGCTTCCC-ATTATATGG
* *
10407321 CTTGTATGAGCATTCCC
1 CTCGAATGAGC-TTCCC
10407338 CAATATGAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 10
0.75 0.15 0.11
Matches are distributed among these distances:
23 8 0.11
24 16 0.23
25 35 0.49
26 12 0.17
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (25 bp):
CTCGAATGAGCTTCCCATTATATGG
Found at i:10409401 original size:9 final size:9
Alignment explanation
Indices: 10409387--10409414 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
10409377 ACATTCGGCT
10409387 TCAAAGAAA
1 TCAAAGAAA
10409396 TCAAAGAAA
1 TCAAAGAAA
10409405 TCAAAGAAA
1 TCAAAGAAA
10409414 T
1 T
10409415 ATCATGATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (9 bp):
TCAAAGAAA
Found at i:10410358 original size:22 final size:22
Alignment explanation
Indices: 10410333--10410377 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
10410323 ATGTCAATTG
10410333 TTTGTGAATATCCTGATGTATT
1 TTTGTGAATATCCTGATGTATT
10410355 TTTGTGAATATCCTGATGTATT
1 TTTGTGAATATCCTGATGTATT
10410377 T
1 T
10410378 CCCGAAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (22 bp):
TTTGTGAATATCCTGATGTATT
Found at i:10414656 original size:25 final size:25
Alignment explanation
Indices: 10414602--10414673 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
10414592 ATTGGCTTGT
* *
10414602 ATGAGCTTCCCGTTAATGGCTCTTC
1 ATGAACTTCCCGTTAATGGCTCTAC
*
10414627 -GGAACTTCCCGTTACATGGCTC-AC
1 ATGAACTTCCCGTTA-ATGGCTCTAC
*
10414651 ATGAACTTCTCGTTATATGGCTC
1 ATGAACTTCCCGTTA-ATGGCTC
10414674 GAAAAAGCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 13 0.33
25 26 0.67
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.33
Consensus pattern (25 bp):
ATGAACTTCCCGTTAATGGCTCTAC
Found at i:10417612 original size:15 final size:15
Alignment explanation
Indices: 10417557--10417613 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
10417547 TTTATATTAC
*
10417557 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
10417572 AACATATTTATAATTGT
1 AAAATATTTATTA-T-T
10417589 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
10417606 AAAATATT
1 AAAATATT
10417614 AATGTTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:10417677 original size:16 final size:16
Alignment explanation
Indices: 10417646--10417682 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
10417636 ATGTGAAGAA
10417646 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
10417662 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
10417678 TATTA
1 TATTA
10417683 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:10417831 original size:9 final size:9
Alignment explanation
Indices: 10417817--10417845 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
10417807 ATTTTATATT
10417817 AATATTTTA
1 AATATTTTA
10417826 AATATTTTA
1 AATATTTTA
10417835 AATATTTTA
1 AATATTTTA
10417844 AA
1 AA
10417846 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AATATTTTA
Found at i:10420800 original size:61 final size:61
Alignment explanation
Indices: 10420732--10420857 Score: 162
Period size: 61 Copynumber: 2.1 Consensus size: 61
10420722 TATTTTTAAC
* * * * ** *
10420732 TTTTAGAATTAGAACTAAATTGAAAAATTTTGTAAATGTTGGGGGCTAAATTTATTGAATT
1 TTTTAGAACTAAAACTAAAATGAAAAATTTTATAAACATTGAGGGCTAAATTTATTGAATT
* * *
10420793 TTTTAGAACTAAAACTAAAATGACAACTTTTATAAACATTGAGGGCTAAATTTGTTGAATT
1 TTTTAGAACTAAAACTAAAATGAAAAATTTTATAAACATTGAGGGCTAAATTTATTGAATT
10420854 TTTT
1 TTTT
10420858 GGATTTAGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (61 bp):
TTTTAGAACTAAAACTAAAATGAAAAATTTTATAAACATTGAGGGCTAAATTTATTGAATT
Found at i:10421274 original size:11 final size:12
Alignment explanation
Indices: 10421244--10421277 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
10421234 CGGCTAACCC
10421244 ATATTAATTTTT
1 ATATTAATTTTT
10421256 ATATTAATTTTT
1 ATATTAATTTTT
10421268 ATA-TAATTTT
1 ATATTAATTTT
10421278 AATTATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:10421442 original size:30 final size:30
Alignment explanation
Indices: 10421398--10421460 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
10421388 ACTTAACATG
*
10421398 CAAATGCCTCTAAAATAATAACAAAACTAA
1 CAAATGCCTCTAAAATAAAAACAAAACTAA
* * *
10421428 CAAATGTCTTTAAAATAAAAACAAAATTAA
1 CAAATGCCTCTAAAATAAAAACAAAACTAA
10421458 CAA
1 CAA
10421461 TATAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.59, C:0.16, G:0.03, T:0.22
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAAAAACAAAACTAA
Found at i:10438820 original size:44 final size:44
Alignment explanation
Indices: 10438772--10438856 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
10438762 TAGGAACTAA
*
10438772 AGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAGGATTATT
1 AGCTTCAATCTACTCCACTACAACTTCAGAGAGATAGGATTATT
* * * *
10438816 AGCTTTAATCTGCTCCACTACAATTTCAGGGAGATAGGATT
1 AGCTTCAATCTACTCCACTACAACTTCAGAGAGATAGGATT
10438857 CGCCATCTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
AGCTTCAATCTACTCCACTACAACTTCAGAGAGATAGGATTATT
Found at i:10439202 original size:50 final size:50
Alignment explanation
Indices: 10439148--10439328 Score: 168
Period size: 50 Copynumber: 3.6 Consensus size: 50
10439138 ACTAGGGAGA
*
10439148 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCACTACAACGCCAGGGAAG
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCATTACAACGCCAGGGAAG
* * * * * ** ** * ** *
10439198 TAAGACTCGCAGTCGCGGCTTCAGTCTTTTAAATTACAATGTTGAGGAAACG
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCATTACAACG-CCAGGGAA-G
* * * *
10439250 --AGATTCACCGTCGTAGCTTCAATCTGTTCCATTATACCGCCAGGGAAG
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCATTACAACGCCAGGGAAG
10439298 TAAGATTCACCGTCGTGGCTTCAATCTGCTC
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTC
10439329 TACTGTAATG
Statistics
Matches: 96, Mismatches: 31, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
48 1 0.01
49 5 0.05
50 84 0.88
51 5 0.05
52 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (50 bp):
TAAGATTCACCGTCGTGGCTTCAATCTGCTCCATTACAACGCCAGGGAAG
Found at i:10439364 original size:267 final size:267
Alignment explanation
Indices: 10438882--10439469 Score: 933
Period size: 267 Copynumber: 2.2 Consensus size: 267
10438872 TTGAAATTCC
* * * * * *
10438882 AAGATTCGCCGTCATAGCTTCAATTTGTTTCGCTACAACGCCAGGGAAGTAAGACTCGCCGTCGC
1 AAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAGTAAGACTCGCAGTCGC
* * *
10438947 GGCTTCAGTCTTTTAAATTGCAATGTTGAGGAAACGAGATTCGCCGTTGTAGCTTCAATCTATTC
66 GGCTTCAGTCTTTTAAATTACAATGTTGAGGAAACGAGATTCACCGTCGTAGCTTCAATCTATTC
* *
10439012 CACTACACCGCCAGGGAAGTAAGATTCACCGTCGTGGTTTTAATCTGCTCCACTGTAATGCTAAA
131 CACTACACCGCCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTGCTCCACTGTAATGCTAAA
* *
10439077 GAGATAGGATTCGCTGCCCACAGCTTTAATCCACTCCACTTCAGCTAATCCAAACCTTAACACTA
196 GAGATAGGATTCACTGCCCACAACTTTAATCCACTCCACTTCAGCTAATCCAAACCTTAACACTA
10439142 GGGAGAT
261 GGGAGAT
* *
10439149 AAGATTCACCGTCGTGGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAGACTCGCAGTCGC
1 AAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAGTAAGACTCGCAGTCGC
*
10439214 GGCTTCAGTCTTTTAAATTACAATGTTGAGGAAACGAGATTCACCGTCGTAGCTTCAATCTGTTC
66 GGCTTCAGTCTTTTAAATTACAATGTTGAGGAAACGAGATTCACCGTCGTAGCTTCAATCTATTC
* * *
10439279 CATTATACCGCCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTGCTCTACTGTAATGCTAAA
131 CACTACACCGCCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTGCTCCACTGTAATGCTAAA
* * * *
10439344 GAGATAGGATTCATTGCCCACAACTTTAATCCGCTCCACTTCAGCTACTCCAAGCCTTAACACTA
196 GAGATAGGATTCACTGCCCACAACTTTAATCCACTCCACTTCAGCTAATCCAAACCTTAACACTA
10439409 GGGAGAT
261 GGGAGAT
** * *
10439416 AAGATTCGTTGTCGTGGCTTCAATCTGCTCCGCTACAATGCCAGGGAAATAAGA
1 AAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAGTAAGA
10439470 TTCCCCGTTG
Statistics
Matches: 292, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
267 292 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (267 bp):
AAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAGTAAGACTCGCAGTCGC
GGCTTCAGTCTTTTAAATTACAATGTTGAGGAAACGAGATTCACCGTCGTAGCTTCAATCTATTC
CACTACACCGCCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTGCTCCACTGTAATGCTAAA
GAGATAGGATTCACTGCCCACAACTTTAATCCACTCCACTTCAGCTAATCCAAACCTTAACACTA
GGGAGAT
Found at i:10445808 original size:19 final size:19
Alignment explanation
Indices: 10445784--10445826 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
10445774 CGTAATTCCA
10445784 TGGTACTTTTTTACTATCT
1 TGGTACTTTTTTACTATCT
10445803 TGGTACTTTTTTACTATCT
1 TGGTACTTTTTTACTATCT
10445822 TGGTA
1 TGGTA
10445827 AGAAAAGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.56
Consensus pattern (19 bp):
TGGTACTTTTTTACTATCT
Found at i:10451396 original size:15 final size:15
Alignment explanation
Indices: 10451376--10451405 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10451366 ATAGATGTCG
10451376 CAATAACAAATACAA
1 CAATAACAAATACAA
*
10451391 CAATAATAAATACAA
1 CAATAACAAATACAA
10451406 TAACGGCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (15 bp):
CAATAACAAATACAA
Found at i:10451877 original size:21 final size:21
Alignment explanation
Indices: 10451829--10451880 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
10451819 ATATATAGAT
10451829 ATTAAAAAATAATTACATAAA
1 ATTAAAAAATAATTACATAAA
* * *
10451850 ATAAAAAAATAATTACATTAC
1 ATTAAAAAATAATTACATAAA
10451871 ATTAAAAAAT
1 ATTAAAAAAT
10451881 TTAAATATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (21 bp):
ATTAAAAAATAATTACATAAA
Found at i:10452414 original size:12 final size:12
Alignment explanation
Indices: 10452397--10452422 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10452387 TATTCTTCCT
10452397 TCCAAAAAAAAC
1 TCCAAAAAAAAC
10452409 TCCAAAAAAAAC
1 TCCAAAAAAAAC
10452421 TC
1 TC
10452423 TCGCCCCCAT
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:0.62, C:0.27, G:0.00, T:0.12
Consensus pattern (12 bp):
TCCAAAAAAAAC
Found at i:10459957 original size:30 final size:30
Alignment explanation
Indices: 10459919--10460044 Score: 137
Period size: 30 Copynumber: 4.2 Consensus size: 30
10459909 TTAGCCCGAA
* *
10459919 TGAG-AAATCTATTATAATGTCAGCTTGTA
1 TGAGCAAATCTATTATAATGACAGCTTGTG
** *
10459948 TGAGCAAATCTATTATAACAACAACTTGTG
1 TGAGCAAATCTATTATAATGACAGCTTGTG
*
10459978 TGAGCAAATCCATTATAATGACAGCTTGTG
1 TGAGCAAATCTATTATAATGACAGCTTGTG
* * * * **
10460008 TGAGCAATTTTATCATACTGTTAGCTTGTG
1 TGAGCAAATCTATTATAATGACAGCTTGTG
10460038 TGAGCAA
1 TGAGCAA
10460045 TATATTAACC
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
29 4 0.05
30 76 0.95
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (30 bp):
TGAGCAAATCTATTATAATGACAGCTTGTG
Found at i:10469949 original size:17 final size:17
Alignment explanation
Indices: 10469929--10469973 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
10469919 TAAAAAAACA
10469929 AAAAGAAAATA-AAATTT
1 AAAA-AAAATATAAATTT
*
10469946 AAAAAAAAGTATCAATTT
1 AAAAAAAA-TATAAATTT
10469964 AAAAAAAATA
1 AAAAAAAATA
10469974 CAGAAAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
17 8 0.32
18 13 0.52
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (17 bp):
AAAAAAAATATAAATTT
Found at i:10474824 original size:50 final size:50
Alignment explanation
Indices: 10474709--10474901 Score: 273
Period size: 50 Copynumber: 3.8 Consensus size: 50
10474699 GATATTAACA
* ** *
10474709 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *
10474760 TGTCC-ATGTCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TG-CCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTCGG
*
10474810 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACGTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
10474860 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGTACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
10474902 TTACCCAAAT
Statistics
Matches: 128, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
49 3 0.02
50 92 0.72
51 30 0.23
52 3 0.02
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:10474901 original size:100 final size:101
Alignment explanation
Indices: 10474709--10474890 Score: 296
Period size: 101 Copynumber: 1.8 Consensus size: 101
10474699 GATATTAACA
* * *
10474709 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGTCCATGTCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACGTTCTCATATCGGTGTCCACGCCATGT
10474774 CCCAGACATGGTCTTACGAGGGACCTCTCATCTCGG
66 CCCAGACATGGTCTTACGAGGGACCTCTCATCTCGG
* *
10474810 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACG-TCTCATCTCGGTG-CCAACGCCATG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACGTTCTCATATCGGTGTCC-ACGCCATG
10474873 TCCCAGACATGGTCTTAC
65 TCCCAGACATGGTCTTAC
10474891 ATGGTACCTC
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
99 2 0.03
100 36 0.48
101 37 0.49
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACGTTCTCATATCGGTGTCCACGCCATGT
CCCAGACATGGTCTTACGAGGGACCTCTCATCTCGG
Found at i:10487425 original size:2 final size:2
Alignment explanation
Indices: 10487418--10487443 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10487408 ACAATAAGAA
10487418 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
10487444 TTCATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10492327 original size:21 final size:20
Alignment explanation
Indices: 10492291--10492330 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
10492281 GAAAATGGTT
*
10492291 TAAAATTAATTATTAATTTA
1 TAAAATTAAATATTAATTTA
10492311 TAAAATTGAAATATTAATTT
1 TAAAATT-AAATATTAATTT
10492331 TTTGAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TAAAATTAAATATTAATTTA
Found at i:10495051 original size:24 final size:26
Alignment explanation
Indices: 10495018--10495065 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
10495008 GCTAGAGGAC
*
10495018 ATTTTCTACTGTG-A-GACTTATGTT
1 ATTTTCTACTATGCATGACTTATGTT
*
10495042 ATTTTGTACTATGCATGACTTATG
1 ATTTTCTACTATGCATGACTTATG
10495066 GGGGGTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 1 0.05
26 8 0.40
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (26 bp):
ATTTTCTACTATGCATGACTTATGTT
Found at i:10498053 original size:21 final size:21
Alignment explanation
Indices: 10498027--10498087 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
10498017 ACGCACCAAT
*
10498027 AGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCAAAAGAGCTGAAC
*
10498048 AGAAGCTCAAAAGAGCTGAAT
1 AGAAGCTCAAAAGAGCTGAAC
*
10498069 AGAAGCTTAAAAGAGCTGA
1 AGAAGCTCAAAAGAGCTGA
10498088 TCCACTAGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.15
Consensus pattern (21 bp):
AGAAGCTCAAAAGAGCTGAAC
Found at i:10499899 original size:26 final size:26
Alignment explanation
Indices: 10499869--10499927 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
10499859 GAAGCTCCGG
*
10499869 GAGCCATTAATCAGGAAGTTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* * * *
10499895 GAGCCTTTAATCGGGTAGCTCACGAA
1 GAGCCATTAATCAGGAAGCTCACAAA
10499921 GAGCCAT
1 GAGCCAT
10499928 ATATCGGGAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACAAA
Found at i:10500037 original size:25 final size:25
Alignment explanation
Indices: 10500009--10500072 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
10499999 GAAAAGCTAT
*
10500009 TAACGGGAAGCTTGCAAGAACCATA
1 TAACGGGAAGCTCGCAAGAACCATA
10500034 TAACGGGAAGCTCGCAAGAACCATA
1 TAACGGGAAGCTCGCAAGAACCATA
* **
10500059 GAATAGGAAGCTCG
1 TAACGGGAAGCTCG
10500073 AGAGAGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (25 bp):
TAACGGGAAGCTCGCAAGAACCATA
Found at i:10505035 original size:23 final size:23
Alignment explanation
Indices: 10505009--10505070 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
10504999 TAATATCCCA
*
10505009 AAAATTACTACTGTAATACTTCG
1 AAAATTACTACTGTAATACCTCG
10505032 AAAATTACTACTGTAATACCTCG
1 AAAATTACTACTGTAATACCTCG
* *
10505055 AAAATTAATACAGTAA
1 AAAATTACTACTGTAA
10505071 GAAAGTAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (23 bp):
AAAATTACTACTGTAATACCTCG
Found at i:10508197 original size:50 final size:50
Alignment explanation
Indices: 10508143--10508629 Score: 613
Period size: 50 Copynumber: 9.8 Consensus size: 50
10508133 CATTGAAATT
*
10508143 ATGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCACTGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAG
* *
10508193 ATGAGAGGTCCCATGTAAAACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAG
* * *
10508243 ATGAGAGGTCCTATGTAAGACCATGTCTAGGACATGG-AGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCACTGAG
* * *
10508293 ATGAGAGGTCCTATGTAAGACTATGTCTGGGACATGGCGTTGGCACTGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAG
*
10508343 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACTGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAG
* *
10508393 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAG
* *
10508443 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCAC-GAGG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGA-G
* ** * * *
10508493 ATGAAAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCA-TCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACT-GAG
** * * * * * * *
10508543 ATGAGAACTCCCATGTAATAACATATCTGGGATATGACATTGGCAGT-AC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAG
* * ** *
10508592 AAGAAACATCTCATGTAAGACCATGTCTGGGACATGGC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
10508630 TTTGACATGT
Statistics
Matches: 382, Mismatches: 49, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
49 32 0.08
50 347 0.91
51 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAG
Found at i:10510159 original size:23 final size:23
Alignment explanation
Indices: 10510121--10510171 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
10510111 GGGAGAGAAA
*
10510121 TGTAATATCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
10510144 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
10510167 AGTAA
1 TGTAA
10510172 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:10516350 original size:18 final size:18
Alignment explanation
Indices: 10516310--10516350 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
10516300 TTAATCTTTG
10516310 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTTT
*
10516327 AGTTATTTATTTTAATTTT
1 ATTTATTTATTTT-ATTTT
10516346 -TTTAT
1 ATTTAT
10516351 CTGACTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:10517106 original size:30 final size:30
Alignment explanation
Indices: 10517070--10517142 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
10517060 TATTTTTTAT
10517070 TTTTTTAATTTTAAAATACTTTTTTTAAAAT--
1 TTTTTTAATTTT-AAA-A-TTTTTTTAAAATAC
* *
10517101 TTTTTAAAATTTAAAATTTTTTTAAAATAC
1 TTTTTTAATTTTAAAATTTTTTTAAAATAC
10517131 TTTTTTAATTTT
1 TTTTTTAATTTT
10517143 TTTTAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 12 0.33
29 1 0.03
30 13 0.36
31 10 0.28
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTTAATTTTAAAATTTTTTTAAAATAC
Found at i:10517114 original size:31 final size:30
Alignment explanation
Indices: 10517067--10517138 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
10517057 TATTATTTTT
* * *
10517067 TATTTTTTTAATTTTAAAATACTTTTTTTAAA
1 TATTTTTTAAAATTTAAAAT--TTTTTTAAAA
10517099 -ATTTTTTAAAATTTAAAATTTTTTTAAAA
1 TATTTTTTAAAATTTAAAATTTTTTTAAAA
10517128 TACTTTTTTAA
1 TA-TTTTTTAA
10517139 TTTTTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 1 0.03
31 25 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TATTTTTTAAAATTTAAAATTTTTTTAAAA
Found at i:10517115 original size:17 final size:18
Alignment explanation
Indices: 10517093--10517208 Score: 90
Period size: 18 Copynumber: 6.1 Consensus size: 18
10517083 AAATACTTTT
10517093 TTTAAAA-TTTTTTAAAA
1 TTTAAAATTTTTTTAAAA
10517110 TTTAAAATTTTTTTAAAATA
1 TTTAAAATTTTTTT-AAA-A
** *
10517130 CTTTTTTAATTTTTTTTAAA
1 --TTTAAAATTTTTTTAAAA
10517150 TTTAAAATTTTTTTAAAATA
1 TTTAAAATTTTTTT-AAA-A
** *
10517170 CTTTTTTAATTTTTTTTAAA
1 --TTTAAAATTTTTTTAAAA
*
10517190 TTTAAAATATTTTTAAAA
1 TTTAAAATTTTTTTAAAA
10517208 T
1 T
10517209 ACTTTTTTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
17 7 0.09
18 33 0.43
19 5 0.06
20 4 0.05
21 4 0.05
22 24 0.31
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAAAATTTTTTTAAAA
Found at i:10517151 original size:40 final size:41
Alignment explanation
Indices: 10517078--10517235 Score: 239
Period size: 40 Copynumber: 3.8 Consensus size: 41
10517068 ATTTTTTTAA
* *
10517078 TTTTAAAATACTTTTTTTAAAATTTTTTAAAATTTAAAATTT
1 TTTTAAAATACTTTTTTT-AATTTTTTTTAAATTTAAAATTT
10517120 TTTTAAAATAC-TTTTTTAATTTTTTTTAAATTTAAAATTT
1 TTTTAAAATACTTTTTTTAATTTTTTTTAAATTTAAAATTT
*
10517160 TTTTAAAATAC-TTTTTTAATTTTTTTTAAATTTAAAATAT
1 TTTTAAAATACTTTTTTTAATTTTTTTTAAATTTAAAATTT
*
10517200 TTTTAAAATACTTTTTTTTAATTTTTGTTTTAATTT
1 TTTTAAAATAC-TTTTTTTAATTTTT-TTTAAATTT
10517236 TTAAAATAAA
Statistics
Matches: 109, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
40 71 0.65
41 6 0.06
42 24 0.22
43 8 0.07
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (41 bp):
TTTTAAAATACTTTTTTTAATTTTTTTTAAATTTAAAATTT
Found at i:10517176 original size:13 final size:11
Alignment explanation
Indices: 10517089--10517189 Score: 64
Period size: 11 Copynumber: 9.9 Consensus size: 11
10517079 TTTAAAATAC
10517089 TTTTTTTAAAA
1 TTTTTTTAAAA
10517100 -TTTTTTAAAA
1 TTTTTTTAAAA
10517110 ----TTTAAAA
1 TTTTTTTAAAA
10517117 TTTTTTTAAAA
1 TTTTTTTAAAA
10517128 TACTTTTTT--AA
1 T--TTTTTTAAAA
*
10517139 TTTTTTTTAAA
1 TTTTTTTAAAA
10517150 ----TTTAAAA
1 TTTTTTTAAAA
10517157 TTTTTTTAAAA
1 TTTTTTTAAAA
*
10517168 TACTTTTTT-AAT
1 T--TTTTTTAAAA
10517180 TTTTTTTAAA
1 TTTTTTTAAA
10517190 TTTAAAATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 30
0.70 0.02 0.29
Matches are distributed among these distances:
7 13 0.18
9 6 0.08
10 16 0.22
11 23 0.32
12 3 0.04
13 12 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTTTTAAAA
Found at i:10532984 original size:57 final size:57
Alignment explanation
Indices: 10532881--10533006 Score: 173
Period size: 57 Copynumber: 2.2 Consensus size: 57
10532871 GAATAAAAAT
* * *
10532881 AATGAAAATGGAGAAATGATAAATATTTGGAAATAATTATAGTTTTCTTCAAAATGAA
1 AATGAAAATGAAGAAATGA-AAATATTTAGAAATAATTATAGTTTTCTCCAAAATGAA
* * *
10532939 AATGAAAATGAATAAATG-AAATCATTTAGAAATGATTATGGTTTTCTCCAAAATGAA
1 AATGAAAATGAAGAAATGAAAAT-ATTTAGAAATAATTATAGTTTTCTCCAAAATGAA
10532996 AATGAAAATGA
1 AATGAAAATGA
10533007 CCTGGAAATG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
56 4 0.07
57 41 0.67
58 16 0.26
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (57 bp):
AATGAAAATGAAGAAATGAAAATATTTAGAAATAATTATAGTTTTCTCCAAAATGAA
Found at i:10539732 original size:10 final size:11
Alignment explanation
Indices: 10539706--10539731 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10539696 TAAAAAAATA
10539706 AAAAATATTTT
1 AAAAATATTTT
10539717 AAAAATATTTT
1 AAAAATATTTT
10539728 AAAA
1 AAAA
10539732 TTAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:10539745 original size:7 final size:8
Alignment explanation
Indices: 10539728--10539756 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
10539718 AAAATATTTT
10539728 AAAATTAA
1 AAAATTAA
10539736 AAAATTAA
1 AAAATTAA
10539744 AAAATTAA
1 AAAATTAA
10539752 AAAAT
1 AAAAT
10539757 ATTTATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:10555011 original size:16 final size:16
Alignment explanation
Indices: 10554990--10555088 Score: 119
Period size: 16 Copynumber: 6.2 Consensus size: 16
10554980 TGAATTATTG
*
10554990 ATTACAGCTCTATTAC
1 ATTACAGCTCTATTCC
*
10555006 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
* *
10555022 ATTACAACTTTATTCC
1 ATTACAGCTCTATTCC
*
10555038 ATTATAGC-CTTATTCC
1 ATTACAGCTC-TATTCC
10555054 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* *
10555070 ATTATAGCCCTATTCC
1 ATTACAGCTCTATTCC
10555086 ATT
1 ATT
10555089 CCAGTGAACC
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
16 71 0.99
17 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:10555026 original size:32 final size:32
Alignment explanation
Indices: 10554990--10555088 Score: 144
Period size: 32 Copynumber: 3.1 Consensus size: 32
10554980 TGAATTATTG
* * *
10554990 ATTACAGCTCTATTACATTACAGCTTTATTCC
1 ATTACAGCTCTATTCCATTATAGCCTTATTCC
* *
10555022 ATTACAACTTTATTCCATTATAGCCTTATTCC
1 ATTACAGCTCTATTCCATTATAGCCTTATTCC
*
10555054 ATTACAGCTCTATTCCATTATAGCCCTATTCC
1 ATTACAGCTCTATTCCATTATAGCCTTATTCC
10555086 ATT
1 ATT
10555089 CCAGTGAACC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.27, C:0.26, G:0.05, T:0.41
Consensus pattern (32 bp):
ATTACAGCTCTATTCCATTATAGCCTTATTCC
Done.