Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 168 of 322
Found at i:54897629 original size:20 final size:19
Alignment explanation
Indices: 54897600--54897648 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
54897590 CATCTATTAA
54897600 TTAA-TTTTTTAATTCATTT
1 TTAATTTTTTTAA-TCATTT
*
54897619 TTAATTTTTTTAATGATTT
1 TTAATTTTTTTAATCATTT
54897638 TTATATTTTTT
1 TTA-ATTTTTT
54897649 ATTAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTAATTTTTTTAATCATTT
Found at i:54900208 original size:24 final size:24
Alignment explanation
Indices: 54900119--54900211 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 24
54900109 TCGATATATC
*
54900119 AGCTCGTAAGAGCTTACTGTTTTC
1 AGCTCGTAAGAGCTTACTGTTTTT
* * ** * *
54900143 AACTTGTTGGAGCTTACTATTTCT
1 AGCTCGTAAGAGCTTACTGTTTTT
** *
54900167 -GCTTATAAAAGCTTACTGTTTTT
1 AGCTCGTAAGAGCTTACTGTTTTT
*
54900190 AGCTCGTTAGAGCTTACTGTTT
1 AGCTCGTAAGAGCTTACTGTTT
54900212 CAGCTCAATA
Statistics
Matches: 50, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
23 16 0.32
24 34 0.68
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (24 bp):
AGCTCGTAAGAGCTTACTGTTTTT
Found at i:54900223 original size:23 final size:23
Alignment explanation
Indices: 54900176--54900232 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
54900166 TGCTTATAAA
* **
54900176 AGCTTACTGTTTTTAGCTCGTTAG
1 AGCTTACTG-TTTCAGCTCAATAG
54900200 AGCTTACTGTTTCAGCTCAATAG
1 AGCTTACTGTTTCAGCTCAATAG
*
54900223 AGTTTACTGT
1 AGCTTACTGT
54900233 CCATCAGCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (23 bp):
AGCTTACTGTTTCAGCTCAATAG
Found at i:54900413 original size:20 final size:20
Alignment explanation
Indices: 54900367--54900407 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
54900357 CAACGAGCAT
*
54900367 AAATACTGTTTATTTGGATG
1 AAATACTGTTTATATGGATG
54900387 AAATACTGTTTATATGGATG
1 AAATACTGTTTATATGGATG
54900407 A
1 A
54900408 GCTACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (20 bp):
AAATACTGTTTATATGGATG
Found at i:54904989 original size:5 final size:5
Alignment explanation
Indices: 54904979--54905007 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
54904969 TTCTTTATTT
54904979 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
54905008 TCATAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:54918324 original size:9 final size:9
Alignment explanation
Indices: 54918311--54918378 Score: 82
Period size: 9 Copynumber: 7.6 Consensus size: 9
54918301 ATAATTATAA
*
54918311 AATTAACCA
1 AATTAACCG
**
54918320 AATTAATTG
1 AATTAACCG
54918329 AATTAACCG
1 AATTAACCG
*
54918338 AATTACCCG
1 AATTAACCG
* *
54918347 AATTATCCA
1 AATTAACCG
54918356 AATTAACCG
1 AATTAACCG
54918365 AATTAACCG
1 AATTAACCG
54918374 AATTA
1 AATTA
54918379 TTTGTATAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:54918414 original size:5 final size:6
Alignment explanation
Indices: 54918399--54918439 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
54918389 ATTATATGTT
*
54918399 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
54918440 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:54918486 original size:18 final size:18
Alignment explanation
Indices: 54918463--54918499 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
54918453 TAATTTTTAT
54918463 GATTGGGTTGGGTAATTG
1 GATTGGGTTGGGTAATTG
*
54918481 GATTGGGTTGGGTACTTG
1 GATTGGGTTGGGTAATTG
54918499 G
1 G
54918500 GTTAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.03, G:0.46, T:0.38
Consensus pattern (18 bp):
GATTGGGTTGGGTAATTG
Found at i:54937845 original size:13 final size:13
Alignment explanation
Indices: 54937827--54937851 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54937817 CTTATAATGT
54937827 TGATTGTACAAGC
1 TGATTGTACAAGC
54937840 TGATTGTACAAG
1 TGATTGTACAAG
54937852 TTTACTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (13 bp):
TGATTGTACAAGC
Found at i:54959722 original size:13 final size:13
Alignment explanation
Indices: 54959704--54959728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54959694 ACTTCTATTT
54959704 TACTTATTACTAA
1 TACTTATTACTAA
54959717 TACTTATTACTA
1 TACTTATTACTA
54959729 GCATAATCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TACTTATTACTAA
Found at i:54975888 original size:13 final size:15
Alignment explanation
Indices: 54975859--54975890 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
54975849 GAAAAAGGCG
54975859 GATTCAGAGGCAAGA
1 GATTCAGAGGCAAGA
54975874 GATTC-GAGG-AAGA
1 GATTCAGAGGCAAGA
54975887 GATT
1 GATT
54975891 GATGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.19
Consensus pattern (15 bp):
GATTCAGAGGCAAGA
Found at i:54975947 original size:44 final size:44
Alignment explanation
Indices: 54975884--54976050 Score: 325
Period size: 44 Copynumber: 3.8 Consensus size: 44
54975874 GATTCGAGGA
*
54975884 AGAGATTGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
1 AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
54975928 AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
1 AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
54975972 AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
1 AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
54976016 AGAGATCGATGAATAAATCTTATCATTCCTCATCA
1 AGAGATCGATGAATAAATCTTATCATTCCTCATCA
54976051 GCAGGATATC
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 122 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (44 bp):
AGAGATCGATGAATAAATCTTATCATTCCTCATCAAAGAAACCT
Found at i:54986116 original size:55 final size:55
Alignment explanation
Indices: 54986026--54986155 Score: 145
Period size: 55 Copynumber: 2.4 Consensus size: 55
54986016 GTGTATGTAG
* * *
54986026 TGTTAATCTGACAGGTTCGCCCATGGTTGCTAGGCACGGACGTGTCGCAAGCCCA
1 TGTTAATTTGACAGGTTCGCCCACGGTTGCTAGGCACGGACATGTCGCAAGCCCA
* * * * *
54986081 TGTTAATTTGACAGGTTCGGCCACGGTT-TTCAGGCACGGGCATGTCGCACGCCCG
1 TGTTAATTTGACAGGTTCGCCCACGGTTGCT-AGGCACGGACATGTCGCAAGCCCA
** *
54986136 TGTTGTTTTGGCAGGTTCGC
1 TGTTAATTTGACAGGTTCGC
54986156 ACGGCCATGG
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
54 1 0.02
55 61 0.98
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (55 bp):
TGTTAATTTGACAGGTTCGCCCACGGTTGCTAGGCACGGACATGTCGCAAGCCCA
Found at i:54986467 original size:52 final size:53
Alignment explanation
Indices: 54986384--54986483 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 53
54986374 GACTTACCTC
*
54986384 TCCATTGAATGGTCATGGTGGTTCGAGGAGTTTATACTCCTTATTCCTACTTT
1 TCCATTGAATGGTCATGGTGGTTCGAGGAGTTTATACTCCTCATTCCTACTTT
* *
54986437 TCCATTGAATGGT-ATGGTTGTTTGAGGAGTTTATACTCCTCATTCCT
1 TCCATTGAATGGTCATGGTGGTTCGAGGAGTTTATACTCCTCATTCCT
54986484 GCTGTGAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 31 0.70
53 13 0.30
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (53 bp):
TCCATTGAATGGTCATGGTGGTTCGAGGAGTTTATACTCCTCATTCCTACTTT
Found at i:54992306 original size:22 final size:22
Alignment explanation
Indices: 54992278--54992342 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
54992268 AGATTACCGA
54992278 TTCAGCTCGTATA-AGCTTACTG
1 TTCAGCTCG-ATAGAGCTTACTG
54992300 TTCAGCTCGATAGAGCTTAC-G
1 TTCAGCTCGATAGAGCTTACTG
* *
54992321 TTTTAGCTCAATAGAGCTTACT
1 -TTCAGCTCGATAGAGCTTACT
54992343 ATTTATCAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 4 0.11
22 34 0.89
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (22 bp):
TTCAGCTCGATAGAGCTTACTG
Found at i:54992347 original size:22 final size:22
Alignment explanation
Indices: 54992234--54992347 Score: 72
Period size: 22 Copynumber: 5.0 Consensus size: 22
54992224 TCGATATATC
54992234 AGCTC-ATAAGAGCTTACTATTT
1 AGCTCAAT-AGAGCTTACTATTT
* * * * *
54992256 ACAGCTCATTGGAGATTACCGATTC
1 --AGCTCAATAGAGCTTA-CTATTT
* * *
54992281 AGCTCGTATA-AGCTTACTGTTC
1 AGCTC-AATAGAGCTTACTATTT
*
54992303 AGCTCGATAGAGCTTACGT-TTT
1 AGCTCAATAGAGCTTAC-TATTT
54992325 AGCTCAATAGAGCTTACTATTT
1 AGCTCAATAGAGCTTACTATTT
54992347 A
1 A
54992348 TCAGCTCAGG
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
21 4 0.06
22 38 0.54
23 11 0.16
24 12 0.17
25 5 0.07
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (22 bp):
AGCTCAATAGAGCTTACTATTT
Found at i:54992536 original size:20 final size:20
Alignment explanation
Indices: 54992511--54992576 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
54992501 GAATAAGCTA
54992511 TGTTGAAATGAATGAATTAC
1 TGTTGAAATGAATGAATTAC
54992531 TGTTGAAATGAATGAATTAC
1 TGTTGAAATGAATGAATTAC
* * * * *
54992551 TATTGATACGGATGAATTAT
1 TGTTGAAATGAATGAATTAC
54992571 TGTTGA
1 TGTTGA
54992577 TATAAATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (20 bp):
TGTTGAAATGAATGAATTAC
Found at i:54992567 original size:40 final size:40
Alignment explanation
Indices: 54992522--54992612 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 40
54992512 GTTGAAATGA
* *
54992522 ATGAATTACTGTTGAAATGAATGAATTACTATTGA-TACGG
1 ATGAATTACTGTTGAAATAAATAAATTACTATT-ATTACGG
* * * *
54992562 ATGAATTATTGTTGATATAAATAAATTATTGTTATTACGG
1 ATGAATTACTGTTGAAATAAATAAATTACTATTATTACGG
54992602 ATGAATTACTG
1 ATGAATTACTG
54992613 GTTATATAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 1 0.02
40 42 0.98
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (40 bp):
ATGAATTACTGTTGAAATAAATAAATTACTATTATTACGG
Found at i:54992577 original size:20 final size:20
Alignment explanation
Indices: 54992520--54992663 Score: 89
Period size: 20 Copynumber: 7.2 Consensus size: 20
54992510 ATGTTGAAAT
* *
54992520 GAATGAATTACTGTTGAAAT
1 GAATGAATTACTGTTGATAC
*
54992540 GAATGAATTACTATTGATAC
1 GAATGAATTACTGTTGATAC
* * *
54992560 GGATGAATTATTGTTGATAT
1 GAATGAATTACTGTTGATAC
* * *
54992580 AAATAAATTATTGTT-ATTAC
1 GAATGAATTACTGTTGA-TAC
*
54992600 GGATGAATTACTGGTT-ATA-
1 GAATGAATTACT-GTTGATAC
* * *
54992619 TAGATGAACTACTAGTT-ATAT
1 GA-ATGAATTACT-GTTGATAC
* *
54992640 GAATGAATTACAGTTTATAC
1 GAATGAATTACTGTTGATAC
54992660 GAAT
1 GAAT
54992664 AAAAATGAAT
Statistics
Matches: 96, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
19 4 0.04
20 87 0.91
21 5 0.05
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (20 bp):
GAATGAATTACTGTTGATAC
Found at i:55000684 original size:16 final size:16
Alignment explanation
Indices: 55000652--55000692 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
55000642 TTTAATCAAG
*
55000652 TCGAGTGGAATGAAAT
1 TCGAGTAGAATGAAAT
55000668 TCGAGTAGAATCG-AAT
1 TCGAGTAGAAT-GAAAT
55000684 T-GAGTAGAA
1 TCGAGTAGAA
55000693 CCCTAACTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 14 0.61
17 1 0.04
ACGTcount: A:0.39, C:0.07, G:0.29, T:0.24
Consensus pattern (16 bp):
TCGAGTAGAATGAAAT
Found at i:55014174 original size:72 final size:72
Alignment explanation
Indices: 55013837--55014148 Score: 421
Period size: 72 Copynumber: 4.3 Consensus size: 72
55013827 AAAATCATAT
* * *** * *
55013837 ATAAACAACAATTGTTAAAACTA-ATTTTGCATAAATAAGTAAAACATAAATTTAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
*
55013901 ATCAAAC
66 ACCAAAC
* ** *
55013908 ATAAACAATTATTGATAAAACTAGCCCTA-AGCATAAATAAGTAGACCATAAATTCAATATCCAA
1 ATAAACAACTATTGATAAAACTAG-ATTACA-CATAAATAAGTAGAACATAAATTCAATATCCAA
*
55013972 AGACCAAAC
64 AAACCAAAC
* * *
55013981 ATAAACAACTATTAATAGAACAAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
55014046 ACCAAAC
66 ACCAAAC
* *
55014053 ATAAACAACCATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTTAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
55014118 ACCAAAC
66 ACCAAAC
*
55014125 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTGATAAAACTAG
55014149 TTTAGCATTG
Statistics
Matches: 210, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
71 20 0.10
72 131 0.62
73 59 0.28
ACGTcount: A:0.54, C:0.16, G:0.06, T:0.24
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:55014174 original size:144 final size:145
Alignment explanation
Indices: 55013866--55014145 Score: 420
Period size: 145 Copynumber: 1.9 Consensus size: 145
55013856 ACTAATTTTG
* * * **
55013866 CATAAATAAGTAAAACATAAATTTAATATCCAAAAATCAAACATAAACAATTATTGATAAAACTA
1 CATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACCATTGATAAAACTA
* * *
55013931 GCCCTAAGCATAAATAAGTAGACCATAAATTCAATATCCAAAGACCAAACATAAACAACTATTAA
66 GCACTAAGCATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAA
*
55013996 TAGAACAAGATTACA
131 TAAAACAAGATTACA
55014011 CATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACCATTGATAAAACTA
1 CATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACCATTGATAAAACTA
* * * *
55014076 G-ATTACA-CATAAATAAGTAGAACATAAATTTAATATCCAAAAACCAAACATAAATAACTATTG
66 GCACTA-AGCATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTA
55014139 ATAAAAC
130 ATAAAAC
55014146 TAGTTTAGCA
Statistics
Matches: 121, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
144 59 0.49
145 62 0.51
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.23
Consensus pattern (145 bp):
CATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACCATTGATAAAACTA
GCACTAAGCATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAA
TAAAACAAGATTACA
Found at i:55014599 original size:18 final size:18
Alignment explanation
Indices: 55014576--55014623 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
55014566 TTCCATCAAT
*
55014576 TGAACATCATTTGAAATG
1 TGAACATCATTTAAAATG
55014594 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
55014612 TGAACATCATTT
1 TGAACATCATTT
55014624 CTCACATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTAAAATG
Found at i:55021078 original size:39 final size:39
Alignment explanation
Indices: 55021034--55021115 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
55021024 AATTATATTA
55021034 CCAGCACAAAGCCTGC-GGAACTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCAGG-ACTTTAGCCCGGATACATTT
*
55021073 CCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCAGGACTTTAGCCCGGATACATTT
55021112 CCAG
1 CCAG
55021116 TGTCTTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 39 0.95
40 2 0.05
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.20
Consensus pattern (39 bp):
CCAGCACAAAGCCTGCAGGACTTTAGCCCGGATACATTT
Found at i:55028180 original size:3 final size:3
Alignment explanation
Indices: 55028172--55028417 Score: 492
Period size: 3 Copynumber: 82.0 Consensus size: 3
55028162 TATTTGTGCC
55028172 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
55028220 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
55028268 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
55028316 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
55028364 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
55028412 ATT ATT
1 ATT ATT
55028418 TATTCATTAA
Statistics
Matches: 243, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 243 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:55032156 original size:19 final size:19
Alignment explanation
Indices: 55032132--55032169 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55032122 ACAAGAACAG
55032132 CTTCACTGATCTCAAGATC
1 CTTCACTGATCTCAAGATC
55032151 CTTCACTGATCTCAAGATC
1 CTTCACTGATCTCAAGATC
55032170 GGGTCAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (19 bp):
CTTCACTGATCTCAAGATC
Found at i:55038672 original size:36 final size:36
Alignment explanation
Indices: 55038625--55038699 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
55038615 AAAAGGAGAA
55038625 AGGATCAGGTGCTACTAAGGTGTGTAAACGCTGTCG
1 AGGATCAGGTGCTACTAAGGTGTGTAAACGCTGTCG
55038661 AGGATCAGGTGCTACTAAGGTGTGTAAACGCTGTCG
1 AGGATCAGGTGCTACTAAGGTGTGTAAACGCTGTCG
55038697 AGG
1 AGG
55038700 CTAAGAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (36 bp):
AGGATCAGGTGCTACTAAGGTGTGTAAACGCTGTCG
Found at i:55040927 original size:44 final size:45
Alignment explanation
Indices: 55040877--55040989 Score: 147
Period size: 44 Copynumber: 2.5 Consensus size: 45
55040867 ATGGCAAATT
* * **
55040877 TTATCTCCCTGAAGTTGCAGTGGATCAGATGGAAGCCA-TTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATGGAAGACAGAGAATC
* * *
55040921 TTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATAGAGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATGGAAGACAGAGAATC
*
55040966 TTATTTCCCTGAAGTTGCAGTGGA
1 TTATCTCCCTGAAGTTGCAGTGGA
55040990 ATAGATTAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
44 33 0.56
45 26 0.44
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATGGAAGACAGAGAATC
Found at i:55040972 original size:190 final size:190
Alignment explanation
Indices: 55040674--55041095 Score: 553
Period size: 190 Copynumber: 2.2 Consensus size: 190
55040664 GATTATAGTC
* *
55040674 ATCATGGCAAATCTTATCTCCTTAAAATTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCTCC
1 ATCATGGCAAATCTTATCTCCCTAAAATTGCAGTGGAGCAGATGGAAGCCACTAATCTTATCTCC
* * *
55040739 CTAAAGTTACGATGGAGCAGATTGAAGATAGTGAATTTTATTTCCCTGAAGTTGTAGTGAAATAG
66 CTAAAGTTACGATGGAGCAGATTGAAGATAGAGAATCTTATTTCCCTGAAGTTGCAGTGAAATAG
* * *
55040804 ATTAAAGCTACAAGTTACAAGTCCTAGACCTCTGAAGTTACAGTAGGTCAGATCAAATCT
131 ATTAAAGCTACAAGTCACAAATCCTAGACCTCTAAAGTTACAGTAGGTCAGATCAAATCT
* * * * *
55040864 ATCATGGCAAATTTTATCTCCCTGAAGTTGCAGTGGATCAGATGGAAGCCATTAATCTTATCTCC
1 ATCATGGCAAATCTTATCTCCCTAAAATTGCAGTGGAGCAGATGGAAGCCACTAATCTTATCTCC
* *
55040929 CTGAAGTTAC-AGTGGAGCAGATTGAAGATAGAGAATCTTATTTCCCTGAAGTTGCAGTGGAATA
66 CTAAAGTTACGA-TGGAGCAGATTGAAGATAGAGAATCTTATTTCCCTGAAGTTGCAGTGAAATA
* * * * ** *
55040993 GATTAAAGCTACAAGTCACAAATCTTATACCTCTAAAGTTGCAGAAAATCGGATCAAATCT
130 GATTAAAGCTACAAGTCACAAATCCTAGACCTCTAAAGTTACAGTAGGTCAGATCAAATCT
* * * * * *
55041054 ACCATAGG--AATCTTATTTCTCTAAAGTTGTAGTGGAACAGAT
1 ATCAT-GGCAAATCTTATCTCCCTAAAATTGCAGTGGAGCAGAT
55041096 TAAAGCTGCA
Statistics
Matches: 201, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
189 29 0.14
190 170 0.85
191 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (190 bp):
ATCATGGCAAATCTTATCTCCCTAAAATTGCAGTGGAGCAGATGGAAGCCACTAATCTTATCTCC
CTAAAGTTACGATGGAGCAGATTGAAGATAGAGAATCTTATTTCCCTGAAGTTGCAGTGAAATAG
ATTAAAGCTACAAGTCACAAATCCTAGACCTCTAAAGTTACAGTAGGTCAGATCAAATCT
Found at i:55043002 original size:3 final size:3
Alignment explanation
Indices: 55042994--55043018 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55042984 TTTGTGCCTA
55042994 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
55043019 TATTCATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:55043290 original size:3 final size:3
Alignment explanation
Indices: 55043282--55043324 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
55043272 CTCACACACT
55043282 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55043325 CTCATCTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55045423 original size:18 final size:18
Alignment explanation
Indices: 55045375--55045450 Score: 71
Period size: 18 Copynumber: 3.9 Consensus size: 18
55045365 AGACTTTTTC
*
55045375 AATATACAAATTGAAAAAA
1 AATATAAAAATT-AAAAAA
*
55045394 ATATATTAAAAATTACAAAA
1 A-ATA-TAAAAATTAAAAAA
*
55045414 AATATAAAAATTATAAAA
1 AATATAAAAATTAAAAAA
*
55045432 ATTATAAAATTATTAAAAA
1 AATATAAAA--ATTAAAAA
55045451 TTATGTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
18 21 0.44
19 4 0.08
20 16 0.33
21 7 0.15
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (18 bp):
AATATAAAAATTAAAAAA
Found at i:55045440 original size:27 final size:27
Alignment explanation
Indices: 55045390--55045454 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 27
55045380 ACAAATTGAA
55045390 AAAAATATATTAAAAATTACAAAAA-ATAT
1 AAAAAT-TA-TAAAAATTACAAAAATAT-T
* *
55045419 AAAAATTATAAAAATTATAAAATTATT
1 AAAAATTATAAAAATTACAAAAATATT
55045446 AAAAATTAT
1 AAAAATTAT
55045455 GTAAAAGAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.70
28 4 0.12
29 6 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAAATTATAAAAATTACAAAAATATT
Found at i:55045448 original size:9 final size:9
Alignment explanation
Indices: 55045391--55045460 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
55045381 CAAATTGAAA
55045391 AAAATATATT
1 AAAAT-TATT
**
55045401 AAAAATTACA
1 -AAAATTATT
* *
55045411 AAAAATATA
1 AAAATTATT
*
55045420 AAAATTATA
1 AAAATTATT
55045429 AAAATTA-T
1 AAAATTATT
55045437 AAAATTATT
1 AAAATTATT
55045446 AAAAATTATGT
1 -AAAATTAT-T
55045457 AAAA
1 AAAA
55045461 GAGTTTGCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
8 7 0.14
9 23 0.46
10 14 0.28
11 6 0.12
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAATTATT
Found at i:55045680 original size:10 final size:10
Alignment explanation
Indices: 55045619--55045680 Score: 56
Period size: 11 Copynumber: 6.0 Consensus size: 10
55045609 CCATAAAAAA
55045619 TATAATTTTT
1 TATAATTTTT
*
55045629 TAT-ATTTTCA
1 TATAATTTT-T
55045639 TATAATTTTT
1 TATAATTTTT
55045649 TAATAATTTTT
1 T-ATAATTTTT
*
55045660 T-TGCAAATTTT
1 TAT--AATTTTT
55045671 TATAATTTTT
1 TATAATTTTT
55045681 GAAAAATCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 6 0.14
10 13 0.31
11 22 0.52
12 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (10 bp):
TATAATTTTT
Found at i:55045702 original size:25 final size:26
Alignment explanation
Indices: 55045665--55045727 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
55045655 TTTTTTTGCA
* **
55045665 AATTT-TTATAATTTTTGAAAAATCT
1 AATTTATTTTAATTTTCCAAAAATCT
* *
55045690 -CTTTATTTTAATTTTCCAAAATTCT
1 AATTTATTTTAATTTTCCAAAAATCT
55045715 AATTTATTTTAAT
1 AATTTATTTTAAT
55045728 AATTATTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 3 0.10
25 16 0.53
26 11 0.37
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.56
Consensus pattern (26 bp):
AATTTATTTTAATTTTCCAAAAATCT
Found at i:55046050 original size:21 final size:21
Alignment explanation
Indices: 55046000--55046057 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
55045990 TTTTTAATTA
55046000 TTATAA-TTATTAT-AA-TTTT
1 TTATAACTT-TTATAAATTTTT
** *
55046019 TTATATTTTTTGTAAATTTTT
1 TTATAACTTTTATAAATTTTT
55046040 TTATAACTTTTATAAATT
1 TTATAACTTTTATAAATT
55046058 CTATTTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 8 0.26
20 4 0.13
21 19 0.61
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTATAACTTTTATAAATTTTT
Found at i:55053419 original size:23 final size:25
Alignment explanation
Indices: 55053374--55053420 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
55053364 AATAAATATA
*
55053374 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
55053399 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
55053421 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:55054340 original size:31 final size:32
Alignment explanation
Indices: 55054304--55054369 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
55054294 TTTTTTAGCT
55054304 AAATTTGACTC-TCAAC-TTTTTAAAAAGAATC
1 AAATTTGAC-CATCAACATTTTTAAAAAGAATC
*
55054335 AAATTTGACCATCAACATTTTTAAAAAGAGTC
1 AAATTTGACCATCAACATTTTTAAAAAGAATC
55054367 AAA
1 AAA
55054370 ATGATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 1 0.03
31 14 0.44
32 17 0.53
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (32 bp):
AAATTTGACCATCAACATTTTTAAAAAGAATC
Found at i:55064916 original size:60 final size:58
Alignment explanation
Indices: 55064850--55064974 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 58
55064840 TTTTAATAGG
*
55064850 ATTATTATTAAAAATAATTTAATAAAATAAAAATAAATACTTTAAT-CATATTTCAATATA
1 ATTATTATTAAAAATAATTTAAT-AAA-AAAAATAAATAATTTAATACAT-TTTCAATATA
* * * *
55064910 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAAAAAATAAATAATTTAAT-ACATTTTCAATATA
55064969 ATTATT
1 ATTATT
55064975 TTTATATTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
58 15 0.26
59 18 0.31
60 25 0.43
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAAAAAATAAATAATTTAATACATTTTCAATATA
Found at i:55065035 original size:25 final size:25
Alignment explanation
Indices: 55065007--55065059 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
55064997 TATTTTTTAG
55065007 TTTTATATCAAATTATATTAAAATA
1 TTTTATATCAAATTATATTAAAATA
* * *
55065032 TTTTATATTAAGTTTTATTAAAATA
1 TTTTATATCAAATTATATTAAAATA
55065057 TTT
1 TTT
55065060 CAAATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTATATCAAATTATATTAAAATA
Found at i:55065058 original size:33 final size:32
Alignment explanation
Indices: 55064979--55065073 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 32
55064969 ATTATTTTTA
55064979 TATTAAATTATATTAAAATA-TTT-TTTAGTTT
1 TATTAAA-TATATTAAAATATTTTATTTAGTTT
55065010 TATATCAAATTATATTAAAATATTTTATATTAAGTTT
1 TAT-T-AAA-TATATTAAAATATTTTAT-TT-AGTTT
*
55065047 TATTAAA-ATATTTCAAATATTTTATTT
1 TATTAAATATA-TTAAAATATTTTATTT
55065074 TATATTTTCT
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
31 3 0.05
32 1 0.02
33 21 0.38
34 16 0.29
35 4 0.07
36 3 0.05
37 8 0.14
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (32 bp):
TATTAAATATATTAAAATATTTTATTTAGTTT
Found at i:55066653 original size:75 final size:74
Alignment explanation
Indices: 55066574--55066748 Score: 187
Period size: 75 Copynumber: 2.4 Consensus size: 74
55066564 AAAATTTCAT
*
55066574 TTTTTTCGTAGATTGTAAATAAGTATA-TTATT-AAA-AAGACATACGATAGAATACAATACAAG
1 TTTTTTCGTAGATTGTAAATAAGTATAGTTATTGAAATAA-A-ATA-AATAGAATACAATACAA-
* ** *
55066636 CCTTTTTTTTAAC
62 ACAATTTTTAAAC
* * *
55066649 TTTTTT-TTAGATTGTAAATAAGTATATGTTATTGAAATAAAATAAATATAATACAATATAAACA
1 TTTTTTCGTAGATTGTAAATAAGTATA-GTTATTGAAATAAAATAAATAGAATACAATACAAACA
*
55066713 ATTTTTAAAT
65 ATTTTTAAAC
*
55066723 TTTTTTCGTTGATTGTAAATAAGTAT
1 TTTTTTCGTAGATTGTAAATAAGTAT
55066749 TATTGATGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
74 33 0.39
75 37 0.44
76 8 0.10
77 4 0.05
78 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (74 bp):
TTTTTTCGTAGATTGTAAATAAGTATAGTTATTGAAATAAAATAAATAGAATACAATACAAACAA
TTTTTAAAC
Found at i:55067241 original size:18 final size:19
Alignment explanation
Indices: 55067218--55067259 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
55067208 TACTATTATT
*
55067218 TTTGAA-TAATTGTTTCTA
1 TTTGAAGTAAATGTTTCTA
55067236 TTTGAAGTTAAATGTTTCTA
1 TTTGAAG-TAAATGTTTCTA
55067256 TTTG
1 TTTG
55067260 TATTGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (19 bp):
TTTGAAGTAAATGTTTCTA
Found at i:55069100 original size:41 final size:41
Alignment explanation
Indices: 55069022--55069100 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
55069012 ATGTTTGTAA
*
55069022 TGTTCGAGCTTTGAGCCTAGCAAGCCTTGTGCTGGTGACTT
1 TGTTCGAGCTTTGAGCCTAGCAAGCCTTGTGCCGGTGACTT
* * *
55069063 TGTTCGGGCTTTGTGCCTAGC-AGGCTTAGTGCCGGTGA
1 TGTTCGAGCTTTGAGCCTAGCAAGCCTT-GTGCCGGTGA
55069101 ATGAATTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.33
Consensus pattern (41 bp):
TGTTCGAGCTTTGAGCCTAGCAAGCCTTGTGCCGGTGACTT
Found at i:55069333 original size:35 final size:35
Alignment explanation
Indices: 55069294--55069369 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
55069284 ACAAGTAAGC
*
55069294 TTATATCAAACTTGAGTATTCGGTTACATGTGAAT
1 TTATATCAAACATGAGTATTCGGTTACATGTGAAT
** * * * *
55069329 TTATATTGAACATGTGTATTTGGTTACCTGTGAGT
1 TTATATCAAACATGAGTATTCGGTTACATGTGAAT
55069364 TTATAT
1 TTATAT
55069370 TGAGCTTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (35 bp):
TTATATCAAACATGAGTATTCGGTTACATGTGAAT
Found at i:55077182 original size:35 final size:35
Alignment explanation
Indices: 55077143--55077218 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
55077133 ACAAGTAAGC
*
55077143 TTATATCAAACTTGAGTATTCGGTTACATGTGAAT
1 TTATATCAAACATGAGTATTCGGTTACATGTGAAT
** * * *
55077178 TTATATTGAACATGTGTATTTGGTTACATGTGAGT
1 TTATATCAAACATGAGTATTCGGTTACATGTGAAT
55077213 TTATAT
1 TTATAT
55077219 TGAGCTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (35 bp):
TTATATCAAACATGAGTATTCGGTTACATGTGAAT
Found at i:55079095 original size:12 final size:12
Alignment explanation
Indices: 55079077--55079110 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
55079067 TAAGGTTCTA
55079077 AAAATGGAAATG
1 AAAATGGAAATG
*
55079089 GAAATGGAAATG
1 AAAATGGAAATG
*
55079101 AAAATAGAAA
1 AAAATGGAAA
55079111 CTTATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:55094964 original size:20 final size:20
Alignment explanation
Indices: 55094909--55094952 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
55094899 ACTAAATTTT
*
55094909 AAAAATAAAACTAAAATAAA
1 AAAAATATAACTAAAATAAA
*
55094929 AAAAATATAACCAAAATAAA
1 AAAAATATAACTAAAATAAA
55094949 AAAA
1 AAAA
55094953 TTAACTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.14
Consensus pattern (20 bp):
AAAAATATAACTAAAATAAA
Found at i:55095606 original size:11 final size:11
Alignment explanation
Indices: 55095592--55095637 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
55095582 ATCCTCTCAC
55095592 AATTCTCTCTA
1 AATTCTCTCTA
*
55095603 AATTCTTTCTA
1 AATTCTCTCTA
55095614 AATTCTCTC-A
1 AATTCTCTCTA
*
55095624 AATT-TCTCTT
1 AATTCTCTCTA
55095634 AATT
1 AATT
55095638 TTTGTCAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 4 0.13
10 9 0.29
11 18 0.58
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTCTCTCTA
Found at i:55097302 original size:13 final size:14
Alignment explanation
Indices: 55097286--55097321 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
55097276 CAATCTCATA
55097286 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
55097299 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
55097312 TCTC-ATTTCA
1 TCTCAATTTCA
55097322 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:55097311 original size:18 final size:19
Alignment explanation
Indices: 55097273--55097313 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
55097263 TGGTTCATGT
55097273 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
55097292 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
55097310 TTTC
1 TTTC
55097314 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:55097503 original size:39 final size:38
Alignment explanation
Indices: 55097436--55097570 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
55097426 ACCAATATGG
* * *
55097436 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
55097475 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
55097513 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
55097554 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
55097571 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:55097836 original size:18 final size:19
Alignment explanation
Indices: 55097810--55097848 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
55097800 TTTCAATTCA
55097810 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
55097829 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
55097847 AT
1 AT
55097849 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:55099174 original size:5 final size:5
Alignment explanation
Indices: 55099164--55099216 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
55099154 TTACTTATTT
* *
55099164 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
55099212 ATATA
1 ATATA
55099217 TATTTTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:55099180 original size:12 final size:12
Alignment explanation
Indices: 55099163--55099218 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
55099153 TTTACTTATT
55099163 TATATAATATAA
1 TATATAATATAA
55099175 TATATAATATAATA
1 TATATAATAT-A-A
55099189 TACTATAATATAA
1 TA-TATAATATAA
*
55099202 TA-ATAATTTAA
1 TATATAATATAA
55099213 TATATA
1 TATATA
55099219 TTTTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:55099819 original size:7 final size:7
Alignment explanation
Indices: 55099807--55099832 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55099797 TAGTCGTTTC
55099807 GTATTTA
1 GTATTTA
55099814 GTATTTA
1 GTATTTA
55099821 GTATTTA
1 GTATTTA
55099828 GTATT
1 GTATT
55099833 ACCTGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:55100492 original size:18 final size:18
Alignment explanation
Indices: 55100450--55100486 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55100440 TGCCAGGTGC
*
55100450 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
*
55100468 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
55100486 G
1 G
55100487 CTTCCTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.41
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:55101163 original size:130 final size:129
Alignment explanation
Indices: 55100899--55101275 Score: 639
Period size: 129 Copynumber: 2.9 Consensus size: 129
55100889 TGTAGAAACT
*
55100899 TTTTTTATATAG-TTTCATATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
1 TTTTTTATATAGTTTTAAT-TAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
55100963 TTTTTGAATTTTATTAAAATAAATGTTCTTTTAAATTAGTCAATATTTTTATTATTTTTATATTT
65 TTTTT-AATTTTATTAAAATAAATGTTCTTTTAAATTAGTCAATATTTTTATTATTTTTATATTT
55101028 A
129 A
*
55101029 TTTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTGCTTT
1 TTTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
55101094 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGTCAATATTTTTATTATTTTTATATTTA
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGTCAATATTTTTATTATTTTTATATTTA
* * **
55101158 TTTTTTATTTAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACCAT
1 TTTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
* * *
55101223 TTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGCCAATAATTTTTATTA
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGTCAAT-ATTTTTATTA
55101276 AAATAAATGT
Statistics
Matches: 235, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
129 159 0.68
130 71 0.30
131 5 0.02
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (129 bp):
TTTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGTCAATATTTTTATTATTTTTATATTTA
Found at i:55101304 original size:39 final size:38
Alignment explanation
Indices: 55101229--55101316 Score: 104
Period size: 39 Copynumber: 2.3 Consensus size: 38
55101219 CCATTTTTAA
* * * *
55101229 TTTTAATACAATAAATGTTCTTTTAAATTAGCCAATAAT
1 TTTTAATAAAATAAATGTTATTTTAAATGAGACAAT-AT
* * *
55101268 TTTTATTAAAATAAATGTTATTTTGAATGCGACAATAT
1 TTTTAATAAAATAAATGTTATTTTAAATGAGACAATAT
55101306 TTTTAATAAAA
1 TTTTAATAAAA
55101317 CATAAATAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 12 0.29
39 29 0.71
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (38 bp):
TTTTAATAAAATAAATGTTATTTTAAATGAGACAATAT
Found at i:55102086 original size:217 final size:217
Alignment explanation
Indices: 55101711--55102142 Score: 749
Period size: 217 Copynumber: 2.0 Consensus size: 217
55101701 CACCCCATAG
* *
55101711 TCGCATGTCCTATTTCTCAAGTGTACACGATATTGCCCACAGATAATACCTTGGTTCGGTCTGTC
1 TCGCATGTCCTATTTCTCAAGCGTACACGATATTGCCCACAGATAATACCTTGGTTCGGTCTATC
* *
55101776 AAACTCTGTAACACAAAACCATAGGTTATCGCGATCGTGACACACTATGTGCATGGTGTTGGCTC
66 AAACTCCGTAACACAAAACCATAGGTTATCGCGATCATGACACACTATGTGCATGGTGTTGGCTC
* * *
55101841 GTACCTTCGCCTTGTTAATCTCTCGCAATACCTTCGCGTACCATACATGGCCTCCTTGCATTTGG
131 ATACCTTCGCCTTGTTAATCTCTCGCAATACCTTCGCGCACCATACATGGCCTCCCTGCATTTGG
55101906 CCTTTATAACTCGCTGCTCATT
196 CCTTTATAACTCGCTGCTCATT
*
55101928 TCGCATGTTCTATTTCTCAAGCGTACACGATATTGCCCACCA-ATAATACCTTGGTTCGGTCTAT
1 TCGCATGTCCTATTTCTCAAGCGTACACGATATTGCCCA-CAGATAATACCTTGGTTCGGTCTAT
* *
55101992 CAAACTCCGTAACACGAAACCATAGGTTGTCGCGATCATGACACACTATGTGCATGGTGTTGGCT
65 CAAACTCCGTAACACAAAACCATAGGTTATCGCGATCATGACACACTATGTGCATGGTGTTGGCT
*
55102057 CATACCTTCGCCTTGTTAATCTCTCGCAATACCTTCGCGCACCATATATGGCCTCCCTGCATTTG
130 CATACCTTCGCCTTGTTAATCTCTCGCAATACCTTCGCGCACCATACATGGCCTCCCTGCATTTG
55102122 GCCTTTATAACTCGCTGCTCA
195 GCCTTTATAACTCGCTGCTCA
55102143 CTTTGGAAAT
Statistics
Matches: 203, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
217 201 0.99
218 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.31
Consensus pattern (217 bp):
TCGCATGTCCTATTTCTCAAGCGTACACGATATTGCCCACAGATAATACCTTGGTTCGGTCTATC
AAACTCCGTAACACAAAACCATAGGTTATCGCGATCATGACACACTATGTGCATGGTGTTGGCTC
ATACCTTCGCCTTGTTAATCTCTCGCAATACCTTCGCGCACCATACATGGCCTCCCTGCATTTGG
CCTTTATAACTCGCTGCTCATT
Found at i:55104790 original size:126 final size:126
Alignment explanation
Indices: 55104565--55104873 Score: 521
Period size: 126 Copynumber: 2.5 Consensus size: 126
55104555 AGTATAAGGC
* * *
55104565 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCTACGTGGGAG-TTTGTTTCCATAATTTTGCTGA
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTT-TTTCCGTAATTTTGCTAA
* *
55104629 CAGTGCATCCTTCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAATTTAT
65 CACTGCATCCTTCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTAT
*
55104691 TTTTTCAGATACTACTGTAGCAAAAGAACGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTAAC
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTAAC
55104756 ACTGCATCCTTCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTAT
66 ACTGCATCCTTCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTAT
* * *
55104817 TTTTTCAGATACTACTATAGCAAAAGAGCGTCCACATGGGAGCTTTTTTTCGTAATT
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATT
55104874 AATAGTTAAT
Statistics
Matches: 172, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
126 169 0.98
127 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (126 bp):
TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTAAC
ACTGCATCCTTCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTAT
Found at i:55105020 original size:24 final size:24
Alignment explanation
Indices: 55104993--55105041 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
55104983 TTATTTTTTT
55104993 CTTAAAAATACTAAAACC-TTAAAC
1 CTTAAAAA-ACTAAAACCATTAAAC
* *
55105017 CTTAAAAACCTTAAACCATTAAAC
1 CTTAAAAAACTAAAACCATTAAAC
55105041 C
1 C
55105042 CTAACCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (24 bp):
CTTAAAAAACTAAAACCATTAAAC
Found at i:55105026 original size:16 final size:17
Alignment explanation
Indices: 55105005--55105039 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
55104995 TAAAAATACT
55105005 AAAACCTTAAACC-TTA
1 AAAACCTTAAACCATTA
55105021 AAAACCTTAAACCATTA
1 AAAACCTTAAACCATTA
55105038 AA
1 AA
55105040 CCCTAACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAACCTTAAACCATTA
Found at i:55105954 original size:46 final size:46
Alignment explanation
Indices: 55105773--55105954 Score: 258
Period size: 46 Copynumber: 4.0 Consensus size: 46
55105763 TTTGACATGA
* * * * * *
55105773 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
55105819 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
55105865 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
55105911 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
55105955 AGAGCACACT
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.03
46 120 0.97
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:55125202 original size:20 final size:19
Alignment explanation
Indices: 55125174--55125232 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
55125164 TAAAAATTTC
*
55125174 AAATATTAAAAAGTAGAAAA
1 AAATTTTAAAAA-TAGAAAA
* * *
55125194 AAATTTTAAAAATATATAG
1 AAATTTTAAAAATAGAAAA
*
55125213 AAATTTTAAAAATATAAAA
1 AAATTTTAAAAATAGAAAA
55125232 A
1 A
55125233 TTGCAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 22 0.67
20 11 0.33
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATTTTAAAAATAGAAAA
Found at i:55125264 original size:47 final size:46
Alignment explanation
Indices: 55125165--55125324 Score: 119
Period size: 47 Copynumber: 3.4 Consensus size: 46
55125155 AAATTTTAAT
* * * * * *
55125165 AAAAATTTCAAATATTAAAAAGTAGAAAAAAATTT-TAAAAATA-TAT
1 AAAAATTTTAAAAATTAAAAA-T-TACAAAATTTTATAAAAATAGTAA
* * **
55125211 AGAAATTTTAAAAATATAAAAATTGCAATTTTTTATAAAAATAGTAA
1 AAAAATTTTAAAAAT-TAAAAATTACAAAATTTTATAAAAATAGTAA
* * *
55125258 AAAAATTTAAAAAATTATAAAATTATAAAATTTTAT-AAAATTGTAA
1 AAAAATTTTAAAAATTA-AAAATTACAAAATTTTATAAAAATAGTAA
*
55125304 GAAAATTTTACAAAATGTAAA
1 AAAAATTTTA-AAAAT-TAAA
55125325 GAAATATAAA
Statistics
Matches: 89, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
45 5 0.06
46 40 0.45
47 42 0.47
48 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (46 bp):
AAAAATTTTAAAAATTAAAAATTACAAAATTTTATAAAAATAGTAA
Found at i:55125329 original size:20 final size:21
Alignment explanation
Indices: 55125284--55125328 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
55125274 ATAAAATTAT
*
55125284 AAAATTTTATAAAATTGTAAG
1 AAAATTTTACAAAATTGTAAG
55125305 AAAATTTTACAAAA-TGTAAAG
1 AAAATTTTACAAAATTGT-AAG
55125326 AAA
1 AAA
55125329 TATAAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (21 bp):
AAAATTTTACAAAATTGTAAG
Found at i:55125337 original size:47 final size:47
Alignment explanation
Indices: 55125241--55125334 Score: 111
Period size: 47 Copynumber: 2.0 Consensus size: 47
55125231 AATTGCAATT
*
55125241 TTTTATAAAAATAGTAAAAAAATTTAAAAAATTATAAAATTATAAAA
1 TTTTATAAAAATAGTAAAAAAATTTAAAAAATTATAAAAATATAAAA
* * *
55125288 TTTTAT-AAAATTGTAAGAAAATTTTACAAAATGTA-AAGAAATATAAA
1 TTTTATAAAAATAGTAA-AAAAATTTAAAAAAT-TATAA-AAATATAAA
55125335 TTTCGTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
46 9 0.22
47 21 0.52
48 10 0.25
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (47 bp):
TTTTATAAAAATAGTAAAAAAATTTAAAAAATTATAAAAATATAAAA
Found at i:55125603 original size:20 final size:20
Alignment explanation
Indices: 55125565--55125602 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55125555 TAATAAAAAT
*
55125565 TTAAAATTTTTATATTTTTA
1 TTAAAATTTATATATTTTTA
55125585 TTAAAATTTATAT-TTTTT
1 TTAAAATTTATATATTTTT
55125603 TCTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTAAAATTTATATATTTTTA
Found at i:55129155 original size:2 final size:2
Alignment explanation
Indices: 55129150--55129174 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55129140 ATCATCGATT
55129150 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
55129175 TTTTAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:55130511 original size:17 final size:17
Alignment explanation
Indices: 55130489--55130524 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
55130479 CGTTGCCTAC
55130489 AATCAGTCTAGATTTAG
1 AATCAGTCTAGATTTAG
55130506 AATCAGTCTAGATTTAG
1 AATCAGTCTAGATTTAG
55130523 AA
1 AA
55130525 AAATGATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (17 bp):
AATCAGTCTAGATTTAG
Found at i:55130620 original size:20 final size:20
Alignment explanation
Indices: 55130595--55130641 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
55130585 ACACCAGTAT
*
55130595 TTTTATTTTGAATTTTAGGA
1 TTTTATCTTGAATTTTAGGA
55130615 TTTTATCTTGAATTTTAGGA
1 TTTTATCTTGAATTTTAGGA
55130635 TTTTATC
1 TTTTATC
55130642 CGGAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.04, G:0.13, T:0.60
Consensus pattern (20 bp):
TTTTATCTTGAATTTTAGGA
Found at i:55131054 original size:55 final size:54
Alignment explanation
Indices: 55130984--55131088 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 54
55130974 ACATATTTAG
* * * * *
55130984 CCTCAATATTTACAAAGTTTTTCATTTTAGTT-TGAATTCTAAAAATAAATTTAAC
1 CCTCAAAATTTACAAAATTTGTCACTTTAATTCT-AATTCTAAAAA-AAATTTAAC
55131039 CCTCAAAATTTACAAAATTTGTCACTTTAATTCTAATTCTAAAAAAAATT
1 CCTCAAAATTTACAAAATTTGTCACTTTAATTCTAATTCTAAAAAAAATT
55131089 CAACAAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
54 5 0.11
55 38 0.86
56 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (54 bp):
CCTCAAAATTTACAAAATTTGTCACTTTAATTCTAATTCTAAAAAAAATTTAAC
Found at i:55133838 original size:5 final size:5
Alignment explanation
Indices: 55133789--55133898 Score: 71
Period size: 5 Copynumber: 22.0 Consensus size: 5
55133779 ACAAACCCAT
* * * * *
55133789 CAGAA CA-AGA CAGAG CAGAA CAAAA CA-AA GCAAAA CTGAA TAGAA CAGAA
1 CAGAA CAGA-A CAGAA CAGAA CAGAA CAGAA -CAGAA CAGAA CAGAA CAGAA
* * * * * * * *
55133839 TAGAG CAGAG CAGAG CAGAG CAGAA CAGAA TAGAA CAGAA TAGAG CAGAA
1 CAGAA CAGAA CAGAA CAGAA CAGAA CAGAA CAGAA CAGAA CAGAA CAGAA
55133889 CAGAA CAGAA
1 CAGAA CAGAA
55133899 TAGAGCAGAG
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
4 3 0.04
5 77 0.93
6 3 0.04
ACGTcount: A:0.55, C:0.16, G:0.24, T:0.05
Consensus pattern (5 bp):
CAGAA
Found at i:55133844 original size:40 final size:40
Alignment explanation
Indices: 55133800--55133895 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
55133790 AGAACAAGAC
* *
55133800 AGAGCAGAACAAAACAAAGCAAAACTGAATAGAACAGAAT
1 AGAGCAGAACAGAACAAAGCAAAACAGAATAGAACAGAAT
* * * *
55133840 AGAGCAGAGCAGAGCAGAGCAGAACAGAATAGAACAGAAT
1 AGAGCAGAACAGAACAAAGCAAAACAGAATAGAACAGAAT
55133880 AGAGCAGAACAGAACA
1 AGAGCAGAACAGAACA
55133896 GAATAGAGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.55, C:0.16, G:0.24, T:0.05
Consensus pattern (40 bp):
AGAGCAGAACAGAACAAAGCAAAACAGAATAGAACAGAAT
Found at i:55133864 original size:30 final size:30
Alignment explanation
Indices: 55133830--55133918 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
55133820 AAAACTGAAT
* *
55133830 AGAACAGAATAGAGCAGAGCAGAGCAGAGC
1 AGAACAGAATAGAGCAGAGAAGAGCAGAAC
*
55133860 AGAACAGAATAGAACAGA-ATAGAGCAGAAC
1 AGAACAGAATAGAGCAGAGA-AGAGCAGAAC
55133890 AGAACAGAATAGAGCAGAGAAGAGCAGAA
1 AGAACAGAATAGAGCAGAGAAGAGCAGAA
55133919 TGGAATAAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
30 52 0.98
31 1 0.02
ACGTcount: A:0.53, C:0.13, G:0.29, T:0.04
Consensus pattern (30 bp):
AGAACAGAATAGAGCAGAGAAGAGCAGAAC
Found at i:55133908 original size:5 final size:5
Alignment explanation
Indices: 55133840--55133917 Score: 57
Period size: 5 Copynumber: 15.6 Consensus size: 5
55133830 AGAACAGAAT
* ** * ** *
55133840 AGAGC AGAGC AGAGC AGAGC AGAAC AGAAT AGAAC AGAAT AGAGC AGAAC
1 AGAGC AGAGC AGAGC AGAGC AGAGC AGAGC AGAGC AGAGC AGAGC AGAGC
* ** *
55133890 AGAAC AGAAT AGAGC AGAGA AGAGC AGA
1 AGAGC AGAGC AGAGC AGAGC AGAGC AGA
55133918 ATGGAATAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 61 1.00
ACGTcount: A:0.51, C:0.14, G:0.31, T:0.04
Consensus pattern (5 bp):
AGAGC
Found at i:55133913 original size:10 final size:10
Alignment explanation
Indices: 55133826--55133919 Score: 91
Period size: 10 Copynumber: 9.4 Consensus size: 10
55133816 AAGCAAAACT
*
55133826 GAATAGAACA
1 GAATAGAGCA
55133836 GAATAGAGCA
1 GAATAGAGCA
**
55133846 GAGCAGAGCA
1 GAATAGAGCA
** *
55133856 GAGCAGAACA
1 GAATAGAGCA
*
55133866 GAATAGAACA
1 GAATAGAGCA
55133876 GAATAGAGCA
1 GAATAGAGCA
* *
55133886 GAACAGAACA
1 GAATAGAGCA
55133896 GAATAGAGCA
1 GAATAGAGCA
55133906 GAGA-AGAGCA
1 GA-ATAGAGCA
55133916 GAAT
1 GAAT
55133920 GGAATAAAGC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
9 1 0.01
10 69 0.97
11 1 0.01
ACGTcount: A:0.52, C:0.13, G:0.29, T:0.06
Consensus pattern (10 bp):
GAATAGAGCA
Found at i:55137376 original size:2 final size:2
Alignment explanation
Indices: 55137369--55137399 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55137359 TTGTTGCCAT
55137369 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
55137400 TCATGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:55140255 original size:17 final size:16
Alignment explanation
Indices: 55140205--55140263 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 16
55140195 TAATTACTTT
55140205 AATATTAAATT-AATA
1 AATATTAAATTAAATA
*
55140220 TAATATT-TATTAAGATA
1 -AATATTAAATTAA-ATA
55140237 AATATTAAATTAAATTA
1 AATATTAAATTAAA-TA
55140254 AATATTAAAT
1 AATATTAAAT
55140264 CTTATTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
15 3 0.08
16 14 0.38
17 20 0.54
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
AATATTAAATTAAATA
Found at i:55140310 original size:62 final size:59
Alignment explanation
Indices: 55140207--55140323 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
55140197 ATTACTTTAA
* * *
55140207 TATTAAATTAATATAATATTTATTAAGATAAATATTAAATTAAATTAAATATTAAATCT
1 TATTAAAATAATAGAATATTTATTAAGATAAATAGTAAATTAAATTAAATATTAAATCT
* *
55140266 TATTAAAATAATAGAATTTTTATCTACAAGATAAATAGTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTAT-T--AAGATAAATAGTAAATTAAATTAAATATTAA
55140324 TATAAACATT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
60 1 0.02
62 29 0.58
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATTAAGATAAATAGTAAATTAAATTAAATATTAAATCT
Found at i:55140396 original size:37 final size:36
Alignment explanation
Indices: 55140304--55140409 Score: 109
Period size: 37 Copynumber: 3.1 Consensus size: 36
55140294 AGATAAATAG
*
55140304 TAAATTAAATTTAATATT-AA-TA-T-AAA-CATTT
1 TAAATTAAATTTAATATTAAACTATTAAAATAATTT
* *
55140335 TAATGTTAAA-TTAATA-AAATACTATTAAAATAATTAT
1 TAA-ATTAAATTTAATATTAA-ACTATTAAAATAATT-T
55140372 TAAATTAAATTTAATATTAAACTATTAAAATAATTT
1 TAAATTAAATTTAATATTAAACTATTAAAATAATTT
55140408 TA
1 TA
55140410 TTTTTGGAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
31 10 0.17
32 6 0.10
33 2 0.03
34 1 0.02
35 3 0.05
36 11 0.18
37 25 0.42
38 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (36 bp):
TAAATTAAATTTAATATTAAACTATTAAAATAATTT
Found at i:55140509 original size:37 final size:36
Alignment explanation
Indices: 55140458--55140533 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
55140448 ATTCTAAAAA
*
55140458 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATAT
*
55140494 TAATACTTATCTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAATAT
55140531 TAA
1 TAA
55140534 AGTAATTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATAT
Found at i:55140619 original size:62 final size:59
Alignment explanation
Indices: 55140546--55140659 Score: 156
Period size: 62 Copynumber: 1.9 Consensus size: 59
55140536 TAATTATCTT
* * * *
55140546 ATATTAAATTTAATTTAATGTTTATCTACAAGATAAATATTCTATTATTTTAATAAGATTTA
1 ATATTAAATTTAATCTAATATTTATCT---AGATAAATATTATATTAATTTAATAAGATTTA
*
55140608 ATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 ATATTAAATTTAATCTAATATTTATCTAGATAAATATTATATTAATTTAATA
55140660 TTAAAGTGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
59 22 0.47
62 25 0.53
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (59 bp):
ATATTAAATTTAATCTAATATTTATCTAGATAAATATTATATTAATTTAATAAGATTTA
Found at i:55148898 original size:34 final size:34
Alignment explanation
Indices: 55148855--55148924 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
55148845 TTCTCTTGAA
55148855 TTAAAGTGTGTGTAAATAATGACCCAAGACTGTC
1 TTAAAGTGTGTGTAAATAATGACCCAAGACTGTC
*
55148889 TTAAAGTGTGTGTAAATAATGACCCAATACTGTC
1 TTAAAGTGTGTGTAAATAATGACCCAAGACTGTC
55148923 TT
1 TT
55148925 TATATAGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (34 bp):
TTAAAGTGTGTGTAAATAATGACCCAAGACTGTC
Found at i:55149473 original size:19 final size:17
Alignment explanation
Indices: 55149441--55149489 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 17
55149431 GACTGAAAAA
55149441 AAATAAA-G-AAATTGG
1 AAATAAAGGAAAATTGG
*
55149456 GAATAAGAGGTAAAATTGG
1 AAATAA-AGG-AAAATTGG
55149475 AAATAAAGGAAAATT
1 AAATAAAGGAAAATT
55149490 TAATAAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 5 0.18
16 1 0.04
17 7 0.25
18 3 0.11
19 12 0.43
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.20
Consensus pattern (17 bp):
AAATAAAGGAAAATTGG
Found at i:55150609 original size:75 final size:75
Alignment explanation
Indices: 55150456--55150609 Score: 195
Period size: 75 Copynumber: 2.1 Consensus size: 75
55150446 GTTATATATG
* * * **
55150456 TGTGCAAGTGTAAGACCATAGTTAAGCTATGATAATGTGATTAGTGTGTGATCATGGCAAGGCCA
1 TGTGCAAGTGCAAGACCATAATTAAGCTATGACAATGTGAAAAGTGTGTGATCATGGCAAGGCCA
*
55150521 TGGTAAAATA
66 TGATAAAATA
* * *
55150531 TGTGCAAGTGCAAGACCATAATTAAGTTGTGGCAATGTGACAAAGTGTGTGATCATGGCTAA-GC
1 TGTGCAAGTGCAAGACCATAATTAAGCTATGACAATGTGA-AAAGTGTGTGATCATGGC-AAGGC
55150595 CATGATAAAA-A
64 CATGATAAAATA
55150606 TGTG
1 TGTG
55150610 TACAAAACCA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 39 0.57
76 27 0.40
77 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.28
Consensus pattern (75 bp):
TGTGCAAGTGCAAGACCATAATTAAGCTATGACAATGTGAAAAGTGTGTGATCATGGCAAGGCCA
TGATAAAATA
Found at i:55156559 original size:48 final size:48
Alignment explanation
Indices: 55156469--55156563 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
55156459 GCTCAATATT
* * *
55156469 AGTCAATATTTTTCAATATCAATTAATTTATCAATATCATTCAGTAAC
1 AGTCAATATTTTTCAATAGCAATCAATTGATCAATATCATTCAGTAAC
* ** *
55156517 AGTCAATATTTTTCAATAGCGATCAATTGATCTTTATTATTCAGTAA
1 AGTCAATATTTTTCAATAGCAATCAATTGATCAATATCATTCAGTAA
55156564 TAGTTAACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (48 bp):
AGTCAATATTTTTCAATAGCAATCAATTGATCAATATCATTCAGTAAC
Found at i:55161861 original size:24 final size:24
Alignment explanation
Indices: 55161829--55161879 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
55161819 TCGTGAATCT
*
55161829 TAATTCTCAAGACTCTATACAAAC
1 TAATTCTCAAGACTCCATACAAAC
55161853 TAATTCTCAAGACTCCATACAAAC
1 TAATTCTCAAGACTCCATACAAAC
55161877 TAA
1 TAA
55161880 CGATCGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.25, G:0.04, T:0.27
Consensus pattern (24 bp):
TAATTCTCAAGACTCCATACAAAC
Found at i:55164299 original size:12 final size:13
Alignment explanation
Indices: 55164284--55164317 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
55164274 TTTTCAAATT
*
55164284 AATTTTTTAAT-A
1 AATTCTTTAATCA
55164296 AATTCTTTAATCA
1 AATTCTTTAATCA
55164309 AATTCTTTA
1 AATTCTTTA
55164318 GTTAAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTCTTTAATCA
Found at i:55168602 original size:30 final size:31
Alignment explanation
Indices: 55168566--55168649 Score: 127
Period size: 30 Copynumber: 2.8 Consensus size: 31
55168556 TTTTTATTTA
55168566 AAAATAATAGGAAATTATTAAAAAGT-GTTT
1 AAAATAATAGGAAATTATTAAAAAGTAGTTT
* * *
55168596 AAAATAATAGGAATTTCTTAAAAAGTATTTT
1 AAAATAATAGGAAATTATTAAAAAGTAGTTT
55168627 AAAA-AATAGGAAATTATTAAAAA
1 AAAATAATAGGAAATTATTAAAAA
55168650 TTAAAAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 41 0.85
31 7 0.15
ACGTcount: A:0.56, C:0.01, G:0.11, T:0.32
Consensus pattern (31 bp):
AAAATAATAGGAAATTATTAAAAAGTAGTTT
Found at i:55169594 original size:16 final size:16
Alignment explanation
Indices: 55169573--55169634 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
55169563 TTTGGTTCAG
*
55169573 TGTAATGGAATAGGGT
1 TGTAATGGAATAGAGT
**
55169589 TGTAATGGAATAGAAC
1 TGTAATGGAATAGAGT
55169605 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGT
*
55169621 TGTAATAGAATAGA
1 TGTAATGGAATAGA
55169635 ACTGTAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.40, C:0.02, G:0.29, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:55169609 original size:32 final size:32
Alignment explanation
Indices: 55169573--55169642 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
55169563 TTTGGTTCAG
* *
55169573 TGTAATGGAATAGGGTTGTAATGGAATAGAAC
1 TGTAATGGAATAGAGTTGTAATAGAATAGAAC
55169605 TGTAATGGAATAGAGTTGTAATAGAATAGAAC
1 TGTAATGGAATAGAGTTGTAATAGAATAGAAC
55169637 TGTAAT
1 TGTAAT
55169643 AACAATTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.27, T:0.30
Consensus pattern (32 bp):
TGTAATGGAATAGAGTTGTAATAGAATAGAAC
Found at i:55169640 original size:16 final size:16
Alignment explanation
Indices: 55169589--55169643 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
55169579 GGAATAGGGT
*
55169589 TGTAATGGAATAGAAC
1 TGTAATAGAATAGAAC
* **
55169605 TGTAATGGAATAGAGT
1 TGTAATAGAATAGAAC
55169621 TGTAATAGAATAGAAC
1 TGTAATAGAATAGAAC
55169637 TGTAATA
1 TGTAATA
55169644 ACAATTCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.29
Consensus pattern (16 bp):
TGTAATAGAATAGAAC
Found at i:55169714 original size:44 final size:45
Alignment explanation
Indices: 55169628--55169715 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
55169618 AGTTGTAATA
55169628 GAATAGAACTGTAATAACAATTCAATTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATAACAATTCAATTGTTTGGTTGAATGGAATG
* *
55169673 GAATAGAACTGTAATAA-TATTC-TTGTGTTTGGTTGAATGGAAT
1 GAATAGAACTGTAATAACAATTCAAT-TGTTTGGTTGAATGGAAT
55169716 AAAGTTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 1 0.03
44 22 0.55
45 17 0.43
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (45 bp):
GAATAGAACTGTAATAACAATTCAATTGTTTGGTTGAATGGAATG
Found at i:55169879 original size:61 final size:60
Alignment explanation
Indices: 55169814--55169966 Score: 150
Period size: 58 Copynumber: 2.5 Consensus size: 60
55169804 TTTAATAGGA
** *
55169814 TTATTATTAGATATAATTTAATAAAAATAATAATACATAATTTAACCCTATT-TTAATAAAT
1 TTATTATTA-ATATAA-TTAATAAAAATAATAATACATAATTTAACAATATTCTTAATAAAG
* * * *
55169875 TTATTATTAATTATAATT--TAACAATAATAATATATAATTTAATAATATTCTTAATATAG
1 TTATTATTAA-TATAATTAATAAAAATAATAATACATAATTTAACAATATTCTTAATAAAG
**
55169934 CAATTATTAAAATATAAATTAATAAAAATAATA
1 TTATTATT--AATAT-AATTAATAAAAATAATA
55169967 TATAATATTA
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
58 26 0.35
59 13 0.17
60 6 0.08
61 20 0.27
63 10 0.13
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (60 bp):
TTATTATTAATATAATTAATAAAAATAATAATACATAATTTAACAATATTCTTAATAAAG
Found at i:55169910 original size:21 final size:20
Alignment explanation
Indices: 55169882--55169921 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
55169872 AATTTATTAT
55169882 TAATTATAATTTAACAATAA
1 TAATTATAATTTAACAATAA
*
55169902 TAATATATAATTTAATAATA
1 TAAT-TATAATTTAACAATA
55169922 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATTATAATTTAACAATAA
Found at i:55169982 original size:22 final size:21
Alignment explanation
Indices: 55169945--55169990 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
55169935 AATTATTAAA
55169945 ATATAAATTAATAAAAATAAT
1 ATATAAATTAATAAAAATAAT
55169966 ATATAATATTACA-AAAAATAAT
1 ATATAA-ATTA-ATAAAAATAAT
55169988 ATA
1 ATA
55169991 CAACCTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 16 0.70
23 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATAAATTAATAAAAATAAT
Found at i:55170123 original size:12 final size:12
Alignment explanation
Indices: 55170093--55170127 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
55170083 TCTATGTTAC
55170093 TTAAAGAATAAT
1 TTAAAGAATAAT
55170105 TTAAAAGAATAAT
1 TT-AAAGAATAAT
55170118 TTAAAGAATA
1 TTAAAGAATA
55170128 TATTGTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (12 bp):
TTAAAGAATAAT
Found at i:55170899 original size:5 final size:5
Alignment explanation
Indices: 55170891--55170916 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55170881 GATACAAATC
55170891 AAAGA AAAGA AAAGA AAAGA AAAGA A
1 AAAGA AAAGA AAAGA AAAGA AAAGA A
55170917 CATATATAAT
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):
AAAGA
Found at i:55174886 original size:18 final size:17
Alignment explanation
Indices: 55174847--55174888 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
55174837 TCTCTCTCCT
*
55174847 TTTTTTTTGTTTTTTAA
1 TTTTATTTGTTTTTTAA
*
55174864 -ATTATTTGTTTTTTATA
1 TTTTATTTGTTTTTTA-A
55174881 TTTTATTT
1 TTTTATTT
55174889 TGCTTAGCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 13 0.65
17 1 0.05
18 6 0.30
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTATTTGTTTTTTAA
Found at i:55176541 original size:16 final size:17
Alignment explanation
Indices: 55176511--55176545 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
55176501 ATTCTGTCTT
*
55176511 ATTTTTATCATTTTAAA
1 ATTTTTATCACTTTAAA
55176528 ATTTTT-TCACTTTAAA
1 ATTTTTATCACTTTAAA
55176544 AT
1 AT
55176546 AAAATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTTATCACTTTAAA
Found at i:55183845 original size:4 final size:4
Alignment explanation
Indices: 55183836--55183860 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55183826 GAGCGGCTGA
55183836 GCCT GCCT GCCT GCCT GCCT GCCT G
1 GCCT GCCT GCCT GCCT GCCT GCCT G
55183861 AGATGTCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.28, T:0.24
Consensus pattern (4 bp):
GCCT
Found at i:55186355 original size:6 final size:6
Alignment explanation
Indices: 55186346--55186379 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
55186336 AAGTGAACTG
*
55186346 CAAAAC CAAAAC CAAAAC CAAAAC CAAAAT CAAA
1 CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAA
55186380 TTCCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.68, C:0.29, G:0.00, T:0.03
Consensus pattern (6 bp):
CAAAAC
Found at i:55189187 original size:4 final size:4
Alignment explanation
Indices: 55189178--55189202 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55189168 GAGCGGCTGA
55189178 GCCT GCCT GCCT GCCT GCCT GCCT G
1 GCCT GCCT GCCT GCCT GCCT GCCT G
55189203 AGATGTCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.28, T:0.24
Consensus pattern (4 bp):
GCCT
Found at i:55193116 original size:5 final size:5
Alignment explanation
Indices: 55193106--55193130 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55193096 ACTGATAGCC
55193106 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
55193131 TATAGGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:55196726 original size:33 final size:33
Alignment explanation
Indices: 55196688--55196794 Score: 110
Period size: 33 Copynumber: 3.3 Consensus size: 33
55196678 ATGATACAAT
** *
55196688 TTGAAAAGGTTAGGTATACTTTGTGTATACCA-
1 TTGAAAAGGAAAGGTATACTTTCTGTATACCAC
* *
55196720 TATGAAAAGGAAATGTATGCTTTCTGTATACCAC
1 T-TGAAAAGGAAAGGTATACTTTCTGTATACCAC
* * * *
55196754 TTGAAAAGGAAAGGTACACTATATGTGTA-CAC
1 TTGAAAAGGAAAGGTATACTTTCTGTATACCAC
55196786 TTGAAAAGG
1 TTGAAAAGG
55196795 CTATGTGCAC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 13 0.21
33 48 0.77
34 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (33 bp):
TTGAAAAGGAAAGGTATACTTTCTGTATACCAC
Found at i:55196826 original size:33 final size:33
Alignment explanation
Indices: 55196777--55196893 Score: 137
Period size: 33 Copynumber: 3.6 Consensus size: 33
55196767 GTACACTATA
* *
55196777 TGTGTAC-ACTTGAAAAGGCTATGTGCACTTTG
1 TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
* *
55196809 TGTGTACAAATTGAAAAGGGTATGTACACTTCG
1 TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
* * * *
55196842 TGTGTACCACTTGAAAGGGGAATGTGCACCTCG
1 TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
* *
55196875 GGTGTACAACTAGAAAAGG
1 TGTGTACAACTTGAAAAGG
55196894 AAAGGTCTAT
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
32 7 0.10
33 63 0.90
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (33 bp):
TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
Found at i:55202885 original size:13 final size:13
Alignment explanation
Indices: 55202867--55202893 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55202857 GGAATATTGC
55202867 TTGAAAATTTTTA
1 TTGAAAATTTTTA
55202880 TTGAAAATTTTTA
1 TTGAAAATTTTTA
55202893 T
1 T
55202894 CAATTATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TTGAAAATTTTTA
Found at i:55203911 original size:32 final size:27
Alignment explanation
Indices: 55203841--55203895 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
55203831 TTGTAATTGG
55203841 TATGTACATGTAATAAATCAACCTTGA
1 TATGTACATGTAATAAATCAACCTTGA
*
55203868 TATGTACATGTAATAAATCAATCTTGA
1 TATGTACATGTAATAAATCAACCTTGA
55203895 T
1 T
55203896 TTGTGATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (27 bp):
TATGTACATGTAATAAATCAACCTTGA
Found at i:55204144 original size:33 final size:33
Alignment explanation
Indices: 55204106--55204180 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
55204096 ATGGTACAAT
**
55204106 TTGAAAAGGTTAGGTATACTTTGTGTATACCA-
1 TTGAAAAGGAAAGGTATACTTTGTGTATACCAC
*
55204138 TATGAAAAAGAAAGGTATACTTTGTGTATACCAC
1 T-TGAAAAGGAAAGGTATACTTTGTGTATACCAC
55204172 TTGAAAAGG
1 TTGAAAAGG
55204181 CTATGTGCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 1 0.03
33 35 0.95
34 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.32
Consensus pattern (33 bp):
TTGAAAAGGAAAGGTATACTTTGTGTATACCAC
Found at i:55204193 original size:33 final size:33
Alignment explanation
Indices: 55204156--55204279 Score: 122
Period size: 33 Copynumber: 3.8 Consensus size: 33
55204146 AGAAAGGTAT
* *
55204156 ACTTTGTGTATACCACTTGAAAAGGCTATGTGC
1 ACTTTGTGTGTACCACTTGAAAAGGGTATGTGC
* * * **
55204189 ACTTTGTGTGTTCAAATTGAAAAGGGTATGTAA
1 ACTTTGTGTGTACCACTTGAAAAGGGTATGTGC
* *
55204222 AATTTGTGTGTACCACTTGAAAAGGGAATGTGC
1 ACTTTGTGTGTACCACTTGAAAAGGGTATGTGC
* * * * *
55204255 ACCTCGGGTGTACAACTAGAAAAGG
1 ACTTTGTGTGTACCACTTGAAAAGG
55204280 AAAGGTCTAT
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (33 bp):
ACTTTGTGTGTACCACTTGAAAAGGGTATGTGC
Found at i:55212838 original size:32 final size:31
Alignment explanation
Indices: 55212755--55212845 Score: 82
Period size: 32 Copynumber: 2.8 Consensus size: 31
55212745 TAAACGCGTG
55212755 ATTTTGTGAAATAATAACAAATATTAGCT-TTCTT
1 ATTTTGTGAAAT-ATAAC-AA-ATTA-CTATTCTT
*
55212789 -TTTTTTGAAATATTAACAAATTACTATT-TT
1 ATTTTGTGAAATA-TAACAAATTACTATTCTT
55212819 AATTTTGTGAAATGATAACAAA-TACTA
1 -ATTTTGTGAAAT-ATAACAAATTACTA
55212846 ACTTGGTATG
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
30 4 0.08
31 11 0.22
32 20 0.40
33 15 0.30
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (31 bp):
ATTTTGTGAAATATAACAAATTACTATTCTT
Found at i:55212911 original size:18 final size:18
Alignment explanation
Indices: 55212885--55212922 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
55212875 AAAACATAAT
55212885 AATAAAAAT-TATCGATAC
1 AATAAAAATGT-TCGATAC
*
55212903 AATATAAATGTTCGATAC
1 AATAAAAATGTTCGATAC
55212921 AA
1 AA
55212923 CGATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.29
Consensus pattern (18 bp):
AATAAAAATGTTCGATAC
Found at i:55218398 original size:19 final size:20
Alignment explanation
Indices: 55218376--55218416 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
55218366 TTCTATTCTG
*
55218376 TTTCTTTTCTTTCTTTT-TT
1 TTTCTATTCTTTCTTTTGTT
55218395 TTTCTATTCTTTCTTTTGTT
1 TTTCTATTCTTTCTTTTGTT
55218415 TT
1 TT
55218417 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTCTATTCTTTCTTTTGTT
Found at i:55218404 original size:15 final size:15
Alignment explanation
Indices: 55218366--55218411 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
55218356 GTTTCGTCTC
*
55218366 TTCTATTCTGTTTCTT
1 TTCTATTCT-TTTTTT
55218382 TTCT-TTCTTTTTTT
1 TTCTATTCTTTTTTT
55218396 TTCTATTCTTTCTTTT
1 TTCTATTCTTT-TTTT
55218412 GTTTTATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 9 0.33
15 10 0.37
16 8 0.30
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.76
Consensus pattern (15 bp):
TTCTATTCTTTTTTT
Found at i:55218433 original size:5 final size:5
Alignment explanation
Indices: 55218420--55218464 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
55218410 TTGTTTTATG
55218420 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA
55218465 AAACATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 23 0.64
6 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:55218445 original size:19 final size:19
Alignment explanation
Indices: 55218421--55218463 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
55218411 TGTTTTATGT
55218421 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
55218440 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
55218459 ATATA
1 ATATA
55218464 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:55218473 original size:24 final size:24
Alignment explanation
Indices: 55218427--55218492 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
55218417 ATGTATATAT
* *
55218427 ATAATATAATATAATATATTAATA
1 ATAATATAATATAATAAAATAATA
55218451 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAAT-A
* **
55218476 TTCCTATAATATAATAA
1 ATAATATAATATAATAA
55218493 TATTTCTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 12 0.35
26 2 0.06
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATA
Done.