Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2057
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: 447875
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 3
Found at i:273496 original size:20 final size:19
Alignment explanation
Indices: 273471--273544 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
273461 TTTACCCAGA
*
273471 TGTATCGATACATTTTGCAT
1 TGTATCAATACATTTT-CAT
* *
273491 TGTATCGATACATTGCTCAT
1 TGTATCAATACATT-TTCAT
*
273511 TGTATCAATATATTTTACAAT
1 TGTATCAATACATTTT-C-AT
273532 T-TATCAATACATT
1 TGTATCAATACATT
273545 CAGGCATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 1 0.02
20 41 0.89
21 4 0.09
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (19 bp):
TGTATCAATACATTTTCAT
Found at i:282874 original size:13 final size:13
Alignment explanation
Indices: 282856--282881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
282846 CAATTTTTTG
282856 TGTATCGATACAT
1 TGTATCGATACAT
282869 TGTATCGATACAT
1 TGTATCGATACAT
282882 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:287559 original size:17 final size:17
Alignment explanation
Indices: 287516--287562 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
287506 TCTAAAAAAG
*
287516 TTTAAATTATTTTTGAA
1 TTTAAATTATTTTTAAA
**
287533 -TTATTGTTATTTTTAAA
1 TTTA-AATTATTTTTAAA
287550 TTTAAATTATTTT
1 TTTAAATTATTTT
287563 ATATTAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TTTAAATTATTTTTAAA
Found at i:288110 original size:16 final size:16
Alignment explanation
Indices: 288089--288121 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
288079 ATAATTTTAA
288089 ATTTTAAAATTAAATT
1 ATTTTAAAATTAAATT
*
288105 ATTTTAAATTTAAATT
1 ATTTTAAAATTAAATT
288121 A
1 A
288122 AATAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTAAAATTAAATT
Found at i:288130 original size:22 final size:23
Alignment explanation
Indices: 288079--288133 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
288069 GTCAAGTTTT
288079 ATAATTTTAAATTTTAAAATTAA
1 ATAATTTTAAATTTTAAAATTAA
*
288102 ATTATTTTAAA-TTT-AAATTAA
1 ATAATTTTAAATTTTAAAATTAA
288123 ATAAATTTTAA
1 AT-AATTTTAA
288134 GTTATTCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.31
22 10 0.34
23 10 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATTTTAAATTTTAAAATTAA
Found at i:292010 original size:2 final size:2
Alignment explanation
Indices: 292003--292039 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
291993 CTTTTGCTGC
292003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
292040 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:292044 original size:2 final size:2
Alignment explanation
Indices: 292039--292066 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
292029 ATATATATAT
292039 AG 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 AG
292067 GATGGATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:292375 original size:2 final size:2
Alignment explanation
Indices: 292368--292413 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
292358 AAACGAAGAA
*
292368 AT AT AT AT CT AT AT AT AT AT -T AT A- AT AT -T 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
292407 AT AT AT A
1 AT AT AT A
292414 AGCCTTTGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:294021 original size:20 final size:20
Alignment explanation
Indices: 293996--294057 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
293986 TAAAGCAATA
293996 TATCGATACAGTTCATCATG
1 TATCGATACAGTTCATCATG
294016 TATCGAT--A---CAT--TG
1 TATCGATACAGTTCATCATG
294029 TAT-GATACAGTTCATCATG
1 TATCGATACAGTTCATCATG
294048 TATCGATACA
1 TATCGATACA
294058 TTGTATCGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 1 0.03
15 3 0.09
17 3 0.09
18 1 0.03
19 5 0.15
20 13 0.38
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (20 bp):
TATCGATACAGTTCATCATG
Found at i:294041 original size:32 final size:33
Alignment explanation
Indices: 293996--294070 Score: 143
Period size: 32 Copynumber: 2.3 Consensus size: 33
293986 TAAAGCAATA
293996 TATCGATACAGTTCATCATGTATCGATACATTG
1 TATCGATACAGTTCATCATGTATCGATACATTG
294029 TAT-GATACAGTTCATCATGTATCGATACATTG
1 TATCGATACAGTTCATCATGTATCGATACATTG
294061 TATCGATACA
1 TATCGATACA
294071 ATGTGCCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 32 0.78
33 9 0.22
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (33 bp):
TATCGATACAGTTCATCATGTATCGATACATTG
Found at i:294064 original size:13 final size:12
Alignment explanation
Indices: 293996--294070 Score: 69
Period size: 13 Copynumber: 6.8 Consensus size: 12
293986 TAAAGCAATA
293996 TATCGATACA-G
1 TATCGATACATG
294007 T-TC-AT-CATG
1 TATCGATACATG
294016 TATCGATACATTG
1 TATCGATACA-TG
294029 TAT-GATACA-G
1 TATCGATACATG
294039 T-TC-AT-CATG
1 TATCGATACATG
294048 TATCGATACATTG
1 TATCGATACA-TG
294061 TATCGATACA
1 TATCGATACA
294071 ATGTGCCATG
Statistics
Matches: 53, Mismatches: 0, Indels: 20
0.73 0.00 0.27
Matches are distributed among these distances:
8 4 0.08
9 9 0.17
10 8 0.15
11 5 0.09
12 10 0.19
13 17 0.32
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (12 bp):
TATCGATACATG
Found at i:294081 original size:33 final size:31
Alignment explanation
Indices: 294000--294090 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 31
293990 GCAATATATC
*
294000 GATACAGTTCATCATGTATCGATACATTGTAT
1 GATACAGTGCA-CATGTATCGATACATTGTAT
*
294032 GATACAGTTCATCATGTATCGATACATTGTAT
1 GATACAGTGCA-CATGTATCGATACATTGTAT
294064 CGATACAATGTGC-CATGTATCGATACA
1 -GATAC-A-GTGCACATGTATCGATACA
294091 AACAGTGGTA
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
32 32 0.58
33 19 0.35
34 1 0.02
35 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (31 bp):
GATACAGTGCACATGTATCGATACATTGTAT
Found at i:294164 original size:19 final size:20
Alignment explanation
Indices: 294120--294172 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
294110 TTGTCAGTTT
* **
294120 CATGTATTGATACAATTGTG
1 CATGTATCGATACAATTGAA
294140 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
294159 CATGTATCAATACA
1 CATGTATCGATACA
294173 TCTGGATGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:294327 original size:21 final size:21
Alignment explanation
Indices: 294277--294332 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
294267 GAATATTTTC
*
294277 ACTCAAAAACATTTGATTTAA
1 ACTCAAAAACATTTGATTCAA
*
294298 ATTCAAAAACATTTG-TTCATA
1 ACTCAAAAACATTTGATTCA-A
*
294319 ACTCTAAAACATTT
1 ACTCAAAAACATTT
294333 ATTAATGTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (21 bp):
ACTCAAAAACATTTGATTCAA
Found at i:295805 original size:18 final size:18
Alignment explanation
Indices: 295775--295817 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
295765 TTAATATACT
* *
295775 AAAA-TAAATTTTATTAA
1 AAAATTAAAATTTAATAA
295792 AAAATTAAAATTTAATAA
1 AAAATTAAAATTTAATAA
*
295810 AATATTAA
1 AAAATTAA
295818 TTAACACCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTAAAATTTAATAA
Found at i:296266 original size:30 final size:30
Alignment explanation
Indices: 296230--296291 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
296220 TATGTGTGTT
296230 TATATATATATATATGTATATTTTTCTTTG
1 TATATATATATATATGTATATTTTTCTTTG
296260 TATATATATATATATGTATATTTTTCTTTG
1 TATATATATATATATGTATATTTTTCTTTG
296290 TA
1 TA
296292 GGTCTTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (30 bp):
TATATATATATATATGTATATTTTTCTTTG
Found at i:297123 original size:21 final size:20
Alignment explanation
Indices: 297084--297123 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
297074 AATCTTGTTC
*
297084 AAAATATT-TTAATTCTGAT
1 AAAATATTATTAAATCTGAT
297103 AAAATATTATCTAAATCTGAT
1 AAAATATTAT-TAAATCTGAT
297124 TCAATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
AAAATATTATTAAATCTGAT
Found at i:298125 original size:26 final size:27
Alignment explanation
Indices: 298095--298150 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
298085 ATATTTAGTT
*
298095 AAAATATTATTGAA-ATATA-AAAAATA
1 AAAATATT-TTAAATATATAGAAAAATA
298121 AAAATATTTTAAATATATAGAAAAATA
1 AAAATATTTTAAATATATAGAAAAATA
298148 AAA
1 AAA
298151 GTAACTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 13 0.48
27 10 0.37
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (27 bp):
AAAATATTTTAAATATATAGAAAAATA
Found at i:299390 original size:19 final size:20
Alignment explanation
Indices: 299345--299396 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
299335 TACCAGTTTC
*
299345 ATGTATCGATACAATTTAAT
1 ATGTATCGATACAATTGAAT
* *
299365 TTGTATCGATACTA-TGAAT
1 ATGTATCGATACAATTGAAT
299384 ATGTATCGATACA
1 ATGTATCGATACA
299397 TCTGGGTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAT
Found at i:300121 original size:24 final size:25
Alignment explanation
Indices: 300084--300142 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 25
300074 TAACAAATTG
300084 TCCCCTTTTAAAAAATTCATACTTC
1 TCCCCTTTTAAAAAATTCATACTTC
*
300109 TCCCC-TTTAAAAAATTCGTACTTC
1 TCCCCTTTTAAAAAATTCATACTTC
300133 TCCCCCTTTT
1 T-CCCCTTTT
300143 TGTAATCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 19 0.61
25 9 0.29
26 3 0.10
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (25 bp):
TCCCCTTTTAAAAAATTCATACTTC
Found at i:306496 original size:3 final size:3
Alignment explanation
Indices: 306488--306524 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
306478 CAAGTCAACT
* *
306488 TCA TCA TCA TCA TCA TCA TTA TCA TCT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
306525 TGATGGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:308432 original size:20 final size:19
Alignment explanation
Indices: 308386--308442 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
308376 TTATATTGGT
* *
308386 ACATTATATCGATACATGT
1 ACATTGTATCGATACATGC
*
308405 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
308424 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
308443 AAACTGGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:308520 original size:20 final size:20
Alignment explanation
Indices: 308495--308560 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
308485 GGCACATTAA
308495 TGTATCGATACATGATGAAT
1 TGTATCGATACATGATGAAT
308515 TGTATCGATAC------AA-
1 TGTATCGATACATGATGAAT
*
308528 TGTATCAATACATGATGAAT
1 TGTATCGATACATGATGAAT
308548 TGTATCGATACAT
1 TGTATCGATACAT
308561 TACTTTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.27
14 2 0.05
19 2 0.05
20 23 0.62
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATGATGAAT
Found at i:308539 original size:33 final size:33
Alignment explanation
Indices: 308493--308559 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
308483 ATGGCACATT
*
308493 AATGTATCGATACATGATGAATTGTATCGATAC
1 AATGTATCAATACATGATGAATTGTATCGATAC
308526 AATGTATCAATACATGATGAATTGTATCGATAC
1 AATGTATCAATACATGATGAATTGTATCGATAC
308559 A
1 A
308560 TTACTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (33 bp):
AATGTATCAATACATGATGAATTGTATCGATAC
Found at i:319869 original size:20 final size:20
Alignment explanation
Indices: 319844--319911 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
319834 ATTTGCTTGC
319844 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
319864 ATGTATCGATAC-------A
1 ATGTATCGATACATTGAATA
* *
319877 ATGTATTGATATATTGAATA
1 ATGTATCGATACATTGAATA
319897 ATGTATCGATACATT
1 ATGTATCGATACATT
319912 TCCTTGGCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
13 11 0.30
20 26 0.70
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:319881 original size:33 final size:33
Alignment explanation
Indices: 319844--319909 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
319834 ATTTGCTTGC
319844 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACATTGAATAATGTATCGATACA
* *
319877 ATGTATTGATATATTGAATAATGTATCGATACA
1 ATGTATCGATACATTGAATAATGTATCGATACA
319910 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGAATAATGTATCGATACA
Found at i:320926 original size:49 final size:49
Alignment explanation
Indices: 320808--321769 Score: 643
Period size: 49 Copynumber: 20.8 Consensus size: 49
320798 AAAAAAGAAC
* ** * * * *
320808 GCCAATGTGCTGAGACAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGAT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GATGAAGGT
* * * *
320860 GCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* * *
320909 GCCAATGTACTGATTCAAGGCCA-CTGACATTGCTCTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGC-GACATTGGTCTTAAAGATGAAGGT
* * *
320958 GCCACTATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--AA-GT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* * *
321001 GCCAATGTGCTGATTCAAGGCTAGC-AGCATTGGAT-TTAAAGATGGTTAAGAT
1 GCCAATATGCTGATTCAAGGCCAGCGA-CATTGG-TCTTAAAGAT-G--AAGGT
* ** * *
321053 GCCAATGTATTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* * *
321102 GCCAATATGCTGATTCAAGGCCAACGATATTGGTCTT--AGAGGCAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG-AAGGT
*
321150 GCCAATATGCTGATTCAAGGCCAGCGATATTAGG-C-T-----T--A--T
1 GCCAATATGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGATGAAGGT
* * **
321189 GCTAATGTGCTGATTCAAGGCCAATGACATTGGTCTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* * * * *
321238 GCCAATATACTGATTTAAGGCCAACGATATTGGGC-T-----T----GT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* *
321277 GCCAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* * * * *
321326 GCCAATATGCTGATTTAAGGCTAACGATATTGGGC-T-----T----GT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* *
321365 GCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* * *
321414 GCCACTATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T----GT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* *
321453 GCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAG--GCAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG-AAGGT
*
321501 GCCAATATGCTGATTCAAGGCCAGCGATATTAGG-C-T-----T--A--T
1 GCCAATATGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGATGAAGGT
* *
321540 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* * *
321588 GCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT-AAGATGGTAAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-G--AAGGT
* *
321639 GCCAATATGCTGATTC-AGG-GAGCGACATTGGACTT----A--AAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* * * *
321680 GCCAATGTGCTAATTCAAGGCTAGCGACATTGGTCTTAAAGATAAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
* * * *
321729 GCCAATATGTTGATTCAAGGCCAGTGATATTGGACTTAAAG
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG
321770 GTGCCACAGA
Statistics
Matches: 718, Mismatches: 109, Indels: 169
0.72 0.11 0.17
Matches are distributed among these distances:
38 4 0.01
39 151 0.21
40 5 0.01
41 21 0.03
42 4 0.01
43 48 0.07
44 2 0.00
45 4 0.01
46 4 0.01
47 13 0.02
48 105 0.15
49 259 0.36
50 6 0.01
51 25 0.03
52 66 0.09
53 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGT
Found at i:321093 original size:144 final size:142
Alignment explanation
Indices: 320854--321722 Score: 576
Period size: 136 Copynumber: 6.3 Consensus size: 142
320844 TAGGAATGTT
* * * * * *
320854 AAAGATGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGAT-G--AAGGTGCCAATG
1 AAAG-TGCCAATGTGCTGATTCAAGGCCAGCG-CATT-GATTTAAAGATGGTTAAGATGCCAATG
* *
320916 TACTGATTCAAGGCC-ACTGACATTGCTCTTAAAGATGAAGGTGCCACTATGCTGATTCAAGGCC
63 TACTGATTCAAGGCCAAC-GACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
*
320980 AGCGATATTGGACTTA
127 AACGATATTGGACTTA
*
320996 AAAGTGCCAATGTGCTGATTCAAGGCTAGCAGCATTGGATTTAAAGATGGTTAAGATGCCAATGT
1 AAAGTGCCAATGTGCTGATTCAAGGCCAGC-GCATT-GATTTAAAGATGGTTAAGATGCCAATGT
* *
321061 ATTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAA
64 ACTGATTCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAA
*
321126 CGATATTGGTCTTA
129 CGATATTGGACTTA
* * *
321140 GAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCG-A-T-A-TT--AG--GCTT---ATGCTAA
1 -A---AA-GTGCCAATGTGCTGATTCAAGGCCAGCGCATTGATTTAAAGATGGTTAAGATGCCAA
* * * *
321194 TGTGCTGATTCAAGGCCAATGACATTGGTCTTAAAGATGAAGGTGCCAATATACTGATTTAAGGC
61 TGTACTGATTCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGC
*
321259 CAACGATATTGGGCTT-
126 CAACGATATTGGACTTA
* *
321275 ---GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGAT-G--AAGGTGCCAATAT
1 AAAGTGCCAATGTGCTGATTCAAGGCCAGCG-CATTGAT-TTAAAGATGGTTAAGATGCCAATGT
* * * * * * * *
321334 GCTGATTTAAGGCTAACGATATTGGGC-T-----T----GTGCCAATGTGTTGATTCAAGGCCAG
64 ACTGATTCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAA
* *
321389 CGACATTGGTCTTAAA
129 CGATATTGGACTT--A
* *
321405 GATGAAGGTGCCACTATGCTGATTCAAGGCCAGCG-A-T-A-TT---G--GGCTT--G-TGCCAA
1 -A--AA-GTGCCAATGTGCTGATTCAAGGCCAGCGCATTGATTTAAAGATGG-TTAAGATGCCAA
* * *
321458 TGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAG--GCAAGGTGCCAATATGCTGATTCAAGG
61 TGTACTGATTCAAGGCCAACGACATTGGTCTTAAAGATG-AAGGTGCCAATATGCTGATTCAAGG
*
321521 CCAGCGATATTAGG-CTT-
125 CCAACGATATT-GGACTTA
* * * *
321538 --A-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA----CAAGGTGCCAATAT
1 AAAGTGCCAATGTGCTGATTCAAGGCCAGCG-CATTGAT-TTAAAGATGGTTAAGATGCCAATGT
* * * * *
321596 GCTGATTCAAGGCCAGCGATATTAGACTT-AAGATGGTAAAGGTGCCAATATGCTGATTC-AGG-
64 ACTGATTCAAGGCCAACGACATTGGTCTTAAAGAT-G--AAGGTGCCAATATGCTGATTCAAGGC
* * *
321658 GAGCGACATTGGACTTA
126 CAACGATATTGGACTTA
* * * *
321675 AAGGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGTCTTAAAGAT
1 AAAGTGCCAATGTGCTGATTCAAGGCCAGCG-CATTGAT-TTAAAGAT
321723 AAAGGTGCCA
Statistics
Matches: 588, Mismatches: 68, Indels: 143
0.74 0.09 0.18
Matches are distributed among these distances:
126 25 0.04
127 89 0.15
128 5 0.01
129 2 0.00
130 1 0.00
131 4 0.01
132 2 0.00
133 3 0.01
134 5 0.01
135 39 0.07
136 125 0.21
137 61 0.10
138 21 0.04
139 3 0.01
140 41 0.07
141 38 0.06
142 6 0.01
143 2 0.00
144 83 0.14
145 3 0.01
146 1 0.00
147 1 0.00
148 3 0.01
149 25 0.04
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (142 bp):
AAAGTGCCAATGTGCTGATTCAAGGCCAGCGCATTGATTTAAAGATGGTTAAGATGCCAATGTAC
TGATTCAAGGCCAACGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAACG
ATATTGGACTTA
Found at i:321266 original size:88 final size:88
Alignment explanation
Indices: 321101--321625 Score: 772
Period size: 88 Copynumber: 6.0 Consensus size: 88
321091 AAGATGAAGG
* * * *
321101 TGCCAATATGCTGATTCAAGGCCAACGATATTGGTCTT--AGAGGCAAGGTGCCAATATGCTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG-AAGGTGCCAATATGCTGAT
321164 TCAAGGCCAGCGATATTAGGCTTA
65 TCAAGGCCAGCGATATTAGGCTTA
* ** *
321188 TGCTAATGTGCTGATTCAAGGCCAATGACATTGGTCTTAAAGATGAAGGTGCCAATATACTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATT
* * * *
321253 TAAGGCCAACGATATTGGGCTTG
66 CAAGGCCAGCGATATTAGGCTTA
*
321276 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGATGAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATT
* * * * *
321341 TAAGGCTAACGATATTGGGCTTG
66 CAAGGCCAGCGATATTAGGCTTA
* *
321364 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCACTATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATT
* *
321429 CAAGGCCAGCGATATTGGGCTTG
66 CAAGGCCAGCGATATTAGGCTTA
*
321452 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAG--GCAAGGTGCCAATATGCTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG-AAGGTGCCAATATGCTGAT
321515 TCAAGGCCAGCGATATTAGGCTTA
65 TCAAGGCCAGCGATATTAGGCTTA
*
321539 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATT
*
321603 CAAGGCCAGCGATATTAGACTTA
66 CAAGGCCAGCGATATTAGGCTTA
321626 AGATGGTAAA
Statistics
Matches: 404, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
86 1 0.00
87 157 0.39
88 242 0.60
89 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (88 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTAGGCTTA
Found at i:321290 original size:39 final size:39
Alignment explanation
Indices: 321236--321572 Score: 206
Period size: 39 Copynumber: 7.9 Consensus size: 39
321226 AAAGATGAAG
* * * *
321236 GTGCCAATATACTGATTTAAGGCCAACGATATTGGGCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT
* **
321275 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGC-T-----T
* * * *
321320 GAAGGTGCCAATATGCTGATTTAAGGCTAACGATATTGGGCTT
1 ----GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT
* * *
321363 GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGC-T-----T
* *
321408 GAAGGTGCCACTATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 ----GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT
* * *
321451 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT
* *
321490 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTT
1 ---------GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT
* *
321538 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGG
321573 TCTTAAAGAC
Statistics
Matches: 229, Mismatches: 40, Indels: 58
0.70 0.12 0.18
Matches are distributed among these distances:
39 125 0.55
40 2 0.01
43 2 0.01
45 2 0.01
48 36 0.16
49 62 0.27
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (39 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT
Found at i:321761 original size:92 final size:92
Alignment explanation
Indices: 321539--321775 Score: 262
Period size: 92 Copynumber: 2.5 Consensus size: 92
321529 ATTAGGCTTA
* * *
321539 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATATGCTGATTC-AGG-CAGCGACATTGGACTT----A-AAGGTGCCAATATGCTAATTC
* *
321604 AAGGCCAGCGATATTAGACTTAAGATGGTAAAGG
59 AAGGCCAGCGACATTAGACTTAAGATGATAAAGG
* * *
321638 TGCCAATATGCTGATTCAGGGAGCGACATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCTA
1 TGCCAATATGCTGATTCAGGCAGCGACATTGGACTTAAAGGTGCCAATATGCTAATTCAAGGCCA
* *
321703 GCGACATTGGTCTTAA-A-GATAAAGG
66 GCGACATTAGACTTAAGATGATAAAGG
* * *
321728 TGCCAATATGTTGATTCAAGGCCAGTGATATTGGACTTAAAGGTGCCA
1 TGCCAATATGCTGATTC-AGG-CAGCGACATTGGACTTAAAGGTGCCA
321776 CAGAGTTGTG
Statistics
Matches: 122, Mismatches: 14, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
90 23 0.19
91 4 0.03
92 61 0.50
93 1 0.01
97 14 0.11
98 3 0.02
99 16 0.13
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (92 bp):
TGCCAATATGCTGATTCAGGCAGCGACATTGGACTTAAAGGTGCCAATATGCTAATTCAAGGCCA
GCGACATTAGACTTAAGATGATAAAGG
Found at i:321905 original size:33 final size:33
Alignment explanation
Indices: 321766--322306 Score: 532
Period size: 34 Copynumber: 16.8 Consensus size: 33
321756 TATTGGACTT
*
321766 AAAGGTGCCACAGAGTTGTGGACTT-AAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* **
321798 AAGGGTATCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAA-GGAA
* * *
321832 AAGGGTGCCACGGAGTCGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
321865 AAA-GTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
321897 CAAGGTGCCACGGAGTTGTGAACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
321930 AAAGATGTCACGGAGTTATGGACTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
321960 ---GGTGCCACGGAGTTGTAGACTTAAAAGGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGG-AA
* *
321991 AAAGGATGCCACAGAGGTGT-GACTTAAAA-G--
1 AAAGG-TGCCACGGAGTTGTGGACTTAAAAGGAA
* *
322021 ---GGTGCCACAGAGTTGTGGACTTAAAAGTAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAG-GAA
* * * * *
322052 AAAAGTGCCACAGAGGTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
*
322086 AAAGGTGGCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
322119 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
322152 AATGAGTGCCATGGAGTTGTGGGCTTAAAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
322186 AAAGAGTGCTACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGAC-TTAAAAGGAA
322221 AAAGGTGCCACGGAGTTGTGGACTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
322251 ---GGTGCCACAGAGTTGTGGACTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* *
322282 AAAGGTGCCACAGAGTCGTGGACTT
1 AAAGGTGCCACGGAGTTGTGGACTT
322307 TGGGAAGAAA
Statistics
Matches: 429, Mismatches: 51, Indels: 57
0.80 0.09 0.11
Matches are distributed among these distances:
26 13 0.03
27 52 0.12
28 3 0.01
29 5 0.01
32 52 0.12
33 111 0.26
34 162 0.38
35 31 0.07
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.20
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:322026 original size:26 final size:27
Alignment explanation
Indices: 321990--322047 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
321980 TTAAAAGGAA
321990 AAAAGGATGCCACAGAGGTGT-GACTT
1 AAAAGGATGCCACAGAGGTGTGGACTT
* *
322016 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGATGCCACAGAGGTGTGGACTT
322043 AAAAG
1 AAAAG
322048 TAAAAAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (27 bp):
AAAAGGATGCCACAGAGGTGTGGACTT
Found at i:322257 original size:27 final size:27
Alignment explanation
Indices: 322219--322272 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
322209 CTTTAAAAAG
*
322219 AAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAAGGTGCCACAGAGTTGTGGACTT
*
322246 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAAGGTGCCACAGAGTTGTGGACTT
322273 TGAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (27 bp):
AAAAAGGTGCCACAGAGTTGTGGACTT
Found at i:322280 original size:61 final size:61
Alignment explanation
Indices: 322185--322306 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 61
322175 CTTAAAAGGA
* * * * *
322185 AAAAGAGTGCTACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACAGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACAGAGTCGTGGACTT
* *
322246 AAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTT
1 AAAAGAGTGCCACAGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACAGAGTCGTGGACTT
322307 TGGGAAGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (61 bp):
AAAAGAGTGCCACAGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACAGAGTCGTGGACTT
Found at i:322355 original size:31 final size:30
Alignment explanation
Indices: 322287--322598 Score: 354
Period size: 32 Copynumber: 10.0 Consensus size: 30
322277 AAGAAAAAGG
* * *
322287 TGCCACAGAGTCGTGGACTTTGGGAAGAAA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
322317 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
*
322347 TTGCCACTGAGTCGTGGACTTTGAAGAAAAGA
1 -TGCCACTGAGTCGTGGACTTTG-AGAAGAGA
*
322379 TGCCACTGAGTCGTGGACTTTGCAGAAAAGA
1 TGCCACTGAGTCGTGGACTTTG-AGAAGAGA
** * *
322410 TGCCACTGAGTTATAGACTTTGGGAAAAGAGA
1 TGCCACTGAGTCGTGGACTTT--GAGAAGAGA
* *
322442 TGCCACTAAGTCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTG-AG--AAGAGA
* * *
322475 TGCCACTAAGTTGTGGACTTTGAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAG--AAGAGA
**
322507 TGCCACTGAGTTATGGACTTTGAGAAGAAAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAG--AGA
*
322539 TGCCACTGAGTTGTGGACTTTGAGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
*
322569 TGCCATTGAGTCGTGGACTTTGAGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
322599 GATTTGAAGA
Statistics
Matches: 250, Mismatches: 23, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
30 61 0.24
31 71 0.28
32 91 0.36
33 27 0.11
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGA
Found at i:322398 original size:62 final size:61
Alignment explanation
Indices: 322287--322598 Score: 353
Period size: 62 Copynumber: 5.0 Consensus size: 61
322277 AAGAAAAAGG
* * *
322287 TGCCACAGAGTCGTGGACTTTG-GGAAGAA-ATGCCACTGAGTCGTGGACTTTGAGAAGAGA
1 TGCCACTGAGTTGTGGACTTTGAAGAA-AAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA
* *
322347 TTGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGCAGAAAAGA
1 -TGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTG-AGAAGAGA
* * * * *
322410 TGCCACTGAGTTATAGACTTTGGGAA-AAGAGATGCCACTAAGTCGTGGACTTTGAAGAAAAAAG
1 TGCCACTGAGTTGTGGACTTT--GAAGAAAAGATGCCACTGAGTCGTGGACTTTG-AG--AAGAG
322474 A
61 A
* * **
322475 TGCCACTAAGTTGTGGACTTTGAGAAAAAAGATGCCACTGAGTTATGGACTTTGAGAAGAAAGA
1 TGCCACTGAGTTGTGGACTTTGA-AGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAG--AGA
* *
322539 TGCCACTGAGTTGTGGACTTTG-AGAAGAGATGCCATTGAGTCGTGGACTTTGAGAAGAGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA
322599 GATTTGAAGA
Statistics
Matches: 217, Mismatches: 23, Indels: 23
0.83 0.09 0.09
Matches are distributed among these distances:
60 3 0.01
61 23 0.11
62 76 0.35
63 37 0.17
64 30 0.14
65 48 0.22
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (61 bp):
TGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA
Found at i:324537 original size:33 final size:33
Alignment explanation
Indices: 324500--324566 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
324490 TTCAACGATT
324500 TGTATCGATACATAAAATATTGTATCGATACAA
1 TGTATCGATACATAAAATATTGTATCGATACAA
*** *
324533 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATATTGTATCGATACAA
324566 T
1 T
324567 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATATTGTATCGATACAA
Found at i:324538 original size:13 final size:13
Alignment explanation
Indices: 324520--324544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
324510 CATAAAATAT
324520 TGTATCGATACAA
1 TGTATCGATACAA
324533 TGTATCGATACA
1 TGTATCGATACA
324545 TATTTTTTTG
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:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:324628 original size:13 final size:13
Alignment explanation
Indices: 324610--324634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
324600 ATTACTCACA
324610 TGTATCGATACAT
1 TGTATCGATACAT
324623 TGTATCGATACA
1 TGTATCGATACA
324635 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:324771 original size:52 final size:52
Alignment explanation
Indices: 324643--324763 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
324633 CACTGATCTT
*
324643 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
324695 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
324747 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
324764 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:331652 original size:1 final size:1
Alignment explanation
Indices: 331646--331714 Score: 84
Period size: 1 Copynumber: 69.0 Consensus size: 1
331636 GAGTTCCCTT
* * * * * *
331646 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAACACAAAAAAAAAAACAACACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
331711 AAAA
1 AAAA
331715 TGCAAAGGCA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:331975 original size:17 final size:17
Alignment explanation
Indices: 331954--331985 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
331944 TCTTTTCCAA
331954 AAAAAAG-AAACAAAAC
1 AAAAAAGAAAACAAAAC
331970 AAAAAAGAAAACAAAA
1 AAAAAAGAAAACAAAA
331986 GAGGAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAACAAAAC
Found at i:333053 original size:61 final size:61
Alignment explanation
Indices: 332988--333667 Score: 398
Period size: 71 Copynumber: 10.0 Consensus size: 61
332978 GCATTTTTTC
* *
332988 TTTAAAGCCCATAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCT
* * * * *
333049 TTTAAAGCCCACAATTCTGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-TTTAAGTCCACAACTCCGTGGCACCCT
* * *
333111 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCAC-----C
333175 CT
60 CT
333177 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAGTCCACAACTCCGTGGCA------
333242 TCCCT
58 -CCCT
* * * * *
333247 TCCTAAAGCCCACACAAGTCGGTGGCAACCTTCTT-CTTTTAAAGCCCACAACTCCGTGGCACTC
1 T-TTAAAG-CC-CACAACTCCGTGGC-ACCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCA---
333311 TTTTTCCCT
58 -----CCCT
* * * * *
333320 TTT-AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAACTCCGTGGCAACC
1 TTTAAAGCCCACAACTCCGTGGCACCTTT-TTCCTT--TTAAG-TC-CACAACTCCGTGGC-A-C
333384 TTCTTCT
59 --C--CT
* * * **
333391 TTTCAAAGACCACAACTCCGTGGCACCTTCTT-CTTTTAAAGCCCACAACTTTGTGGCACTCTTT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCA--C---
333455 TTTCCT
59 ---CCT
* *
333461 TTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCC-TTTTAAGTCCACAACTCCGTGGCA------
333526 TTCCCT
58 --CCCT
* *
333532 TTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTCT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCC-TTTTAAGTCCACAACTCCGTGGCA------
333597 TTCCCT
58 --CCCT
* *
333603 TTTCAAAGCCCACAACTCCGTGGCA-CTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCACCCT
333665 TTT
1 TTT
333668 TCCCTTTTAA
Statistics
Matches: 519, Mismatches: 49, Indels: 101
0.78 0.07 0.15
Matches are distributed among these distances:
60 3 0.01
61 74 0.14
62 35 0.07
66 4 0.01
67 23 0.04
68 42 0.08
69 25 0.05
70 70 0.13
71 141 0.27
72 32 0.06
73 64 0.12
74 3 0.01
75 1 0.00
77 2 0.00
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.32
Consensus pattern (61 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCT
Found at i:333095 original size:34 final size:33
Alignment explanation
Indices: 332965--333707 Score: 496
Period size: 34 Copynumber: 21.8 Consensus size: 33
332955 GTCTCAAAGT
* * *
332965 CCACGACTCAGTGGCA-TTTTTTCT-TTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
* * * *
332996 CCATAACTCCGTGGCACCTTGTTC-CTTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCTC-TTTAAGC
*
333029 CCACAACTCCGTGGCAC-----CCT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* * *
333057 CCACAATTCTGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-TCTTTAAGC
333091 CCACAACTCCGTGGCAC------C-CGTTTAAGC
1 CCACAACTCCGTGGCACTTTTTTCTC-TTTAAGC
* *
333118 CCACAACTCCGTGGCACCTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
333152 CCACAACTCCGTGGCACTTTTTTCT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* *
333185 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTTAAGC
* *
333220 CCACAACTCCGTGGCA-TCTTTCTCCCTTCCTAAAGCC
1 CCACAACTCCGTGGCACT-TTTTTCTCTT--T-AAG-C
* * * *
333257 CACACAAGTCGGTGGCAACCTTCTTCT-TTTAAAGC
1 C-CACAACTCCGTGGC-ACTTTTTTCTCTTT-AAGC
* *
333292 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTTAAGC
* *
333327 CCACAACTCCGTGGCA-TCTTTCTCCCTTCCTAAAGCC
1 CCACAACTCCGTGGCACT-TTTTTCTCTT--T-AAG-C
* * *
333364 CACACAACTCCGTGGCAACCTTCTTCT-TTTCAAAGA
1 C-CACAACTCCGTGGC-ACTTTTTTCTCTTT--AAGC
* *
333400 CCACAACTCCGTGGCACCTTCTTCT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
**
333433 CCACAACTTTGTGGCACTCTTTTT-TCCTTTTCAAAGC
1 CCACAACTCCGTGGCACT-TTTTTCT-C-TTT--AAGC
*
333470 CCACAACTCCGTGGCACCTTTTTC-CGTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTC-TTT-AAGC
*
333504 CCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGC
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTT--AAGC
*
333541 CCACAACTCCGTGGCACCTTTTTC-CGTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTC-TTT-AAGC
* *
333575 CCACAACTCCGTGGCACTCTCTTTCCCTTTTCAAAGC
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTT--AAGC
*
333612 CCACAACTCCGTGGCACTTTTTCCT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTCTTT-AAGC
* *
333645 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTTTTCTC-TTTAAGC
333680 CCACAACTCCGTGGCATCTTTTTT-TCTT
1 CCACAACTCCGTGGCA-CTTTTTTCTCTT
333708 CCCAAAGCCC
Statistics
Matches: 589, Mismatches: 65, Indels: 114
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.00
27 26 0.04
28 20 0.03
31 13 0.02
32 5 0.01
33 103 0.17
34 158 0.27
35 102 0.17
36 50 0.08
37 71 0.12
38 30 0.05
39 10 0.02
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (33 bp):
CCACAACTCCGTGGCACTTTTTTCTCTTTAAGC
Found at i:333272 original size:38 final size:35
Alignment explanation
Indices: 333114--333700 Score: 502
Period size: 34 Copynumber: 16.7 Consensus size: 35
333104 GCACCCGTTT
* * * *
333114 AAGCCCACAACTCCGTGGCACCTTT-TTCTTTTTA
1 AAGCCCACAACTCCGTGGCATCTTTCTCCCTTCTA
** *
333148 AAGCCCACAACTCCGTGGCA-CTTT-TTTCTTTTA
1 AAGCCCACAACTCCGTGGCATCTTTCTCCCTTCTA
* *
333181 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTT-TT
1 AAGCCCACAACTCCGTGGCA-TCTTTCTCCCTTCTA
*
333216 AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTA
1 AAGCCCACAACTCCGTGGCATCTTTCTCCCTT-CTA
* * * * * *
333252 AAGCCCACACAAGTCGGTGGCAACCTTCT-TCTTTTA
1 AAG-CC-CACAACTCCGTGGCATCTTTCTCCCTTCTA
* *
333288 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTT-TT
1 AAGCCCACAACTCCGTGGCA-TCTTTCTCCCTTCTA
*
333323 AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTA
1 AAGCCCACAACTCCGTGGCATCTTTCTCCCTT-CTA
* * * *
333359 AAGCCCACACAACTCCGTGGCAACCTTCT-TCTTTTCA
1 AAG-CC-CACAACTCCGTGGCATCTTTCTCCCTTCT-A
* * * *
333396 AAGACCACAACTCCGTGGCA-CCTTCT-TCTTTTA
1 AAGCCCACAACTCCGTGGCATCTTTCTCCCTTCTA
** * * *
333429 AAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTCA
1 AAGCCCACAACTCCGTGGCA-TCTTTCTCCCTTCT-A
* * *
333466 AAGCCCACAACTCCGTGGCACCTTTTTCCGTT-TA
1 AAGCCCACAACTCCGTGGCATCTTTCTCCCTTCTA
* *
333500 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCA-TCTTTCTCCCTTCT-A
* * *
333537 AAGCCCACAACTCCGTGGCACCTTTTTCCGTT-TA
1 AAGCCCACAACTCCGTGGCATCTTTCTCCCTTCTA
*
333571 AAGCCCACAACTCCGTGGCACTCTCTT-TCCCTTTTCA
1 AAGCCCACAACTCCGTGGCA-TCT-TTCTCCCTTCT-A
* *
333608 AAGCCCACAACTCCGTGGCA-CTTT-TTCCTTTTA
1 AAGCCCACAACTCCGTGGCATCTTTCTCCCTTCTA
* *
333641 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTT-TT
1 AAGCCCACAACTCCGTGGCA-TCTTTCTCCCTTCTA
*
333676 AAGTCCACAACTCCGTGGCATCTTT
1 AAGCCCACAACTCCGTGGCATCTTT
333701 TTTTCTTCCC
Statistics
Matches: 473, Mismatches: 52, Indels: 56
0.81 0.09 0.10
Matches are distributed among these distances:
33 70 0.15
34 123 0.26
35 114 0.24
36 55 0.12
37 73 0.15
38 38 0.08
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (35 bp):
AAGCCCACAACTCCGTGGCATCTTTCTCCCTTCTA
Found at i:333286 original size:71 final size:70
Alignment explanation
Indices: 333114--333702 Score: 754
Period size: 71 Copynumber: 8.4 Consensus size: 70
333104 GCACCCGTTT
*
333114 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT-TTTTT--C
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
333176 TTTTA
66 TTTTA
* *
333181 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCCGTGGCA-TCTTTCTC
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
*
333244 CCTTCCTA
64 CCTT-TTA
* * *
333252 AAGCCCACACAAGTCGGTGGCAACCTTCTT-CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 AAG-CC-CACAACTCCGTGGC-ACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
333316 CCCTTTT-
63 CCCTTTTA
* * * * *
333323 AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAACTCCGTGGCAAC-CTTC
1 AAGCCCACAACTCCGTGGCACCTTT-TTCCTT-TTAAAG-CC-CACAACTCCGTGGC-ACTCTTT
333387 TT--CTTTTCA
61 TTCCCTTTT-A
* * ** *
333396 AAGACCACAACTCCGTGGCACCTTCTT-CTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCC
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
333460 TTTTCA
66 TTTT-A
*
333466 AAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
333531 TTTTCA
66 TTTT-A
* *
333537 AAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTCTTTCCC
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
333602 TTTTCA
66 TTTT-A
333608 AAGCCCACAACTCCGTGGCA-CTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
333672 TTTT-
66 TTTTA
* *
333676 AAGTCCACAACTCCGTGGCATCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTT
333703 TTCTTCCCAA
Statistics
Matches: 462, Mismatches: 36, Indels: 46
0.85 0.07 0.08
Matches are distributed among these distances:
67 24 0.05
68 69 0.15
69 26 0.06
70 90 0.19
71 155 0.34
72 25 0.05
73 69 0.15
74 4 0.01
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (70 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
TTTTA
Found at i:333301 original size:107 final size:104
Alignment explanation
Indices: 333114--333695 Score: 702
Period size: 107 Copynumber: 5.5 Consensus size: 104
333104 GCACCCGTTT
* * * * *
333114 AAGCCCACAACTCCGTGGCACCTTTTT-CTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTT
1 AAGCCCACAACTCCGTGGCATCTTTTTCCCTTCTAAAGCCCACAACTCCGTGGCACCTTCTTCTT
333178 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-
66 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTA
* * * *
333216 AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAACCTTCT
1 AAGCCCACAACTCCGTGGCATCTTTTTCCCTT-CTAAAG-CC-CACAACTCCGTGGC-ACCTTCT
333281 TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-
62 TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTA
* *
333323 AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAACTCCGTGGCAACCTTCT
1 AAGCCCACAACTCCGTGGCATCTTTTTCCCTT-CTAAAG-CC-CACAACTCCGTGGC-ACCTTCT
* *
333388 TCTTTTCAAAGACCACAACTCCGTGGCAC-CTTCTT--CTTTTA
62 TCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTA
** * * *
333429 AAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 AAGCCCACAACTCCGTGGCA-TCTTTTTCCCTTCT-AAAGCCCACAACTCCGTGGCACCTTCTT-
*
333494 CGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCA
63 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-A
* *
333537 AAGCCCACAACTCCGTGGCACCTTTTTCCGTT-TAAAGCCCACAACTCCGTGGCA-CTCTCTTTC
1 AAGCCCACAACTCCGTGGCATCTTTTTCCCTTCTAAAGCCCACAACTCCGTGGCACCT-TC-TT-
333600 CCTTTTCAAAGCCCACAACTCCGTGGCA--CTTTTT-CCTTTTA
63 -CTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTA
* *
333641 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTT-TTAAGTCCACAACTCCGTGGCA
1 AAGCCCACAACTCCGTGGCA-TCTTTTTCCCTTCTAAAGCCCACAACTCCGTGGCA
333696 TCTTTTTTTC
Statistics
Matches: 427, Mismatches: 34, Indels: 35
0.86 0.07 0.07
Matches are distributed among these distances:
102 24 0.06
103 3 0.01
104 56 0.13
105 88 0.21
106 41 0.10
107 154 0.36
108 61 0.14
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (104 bp):
AAGCCCACAACTCCGTGGCATCTTTTTCCCTTCTAAAGCCCACAACTCCGTGGCACCTTCTTCTT
TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTA
Found at i:333705 original size:141 final size:138
Alignment explanation
Indices: 332987--333702 Score: 759
Period size: 141 Copynumber: 5.2 Consensus size: 138
332977 GGCATTTTTT
* * * *
332987 CTTTAAAGCCCATAACTCCGTGGCACCTTGTTCCTTTT-AAGTCCACAACTCCGTGGCA------
1 CTTTTAAGCCCACAACTCCGTGGCACCTT-TTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
* * * * *
333045 --CCCTTTTAAAGCCCACAATTCTGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCA
65 TTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-TTTAAAGCCCACAACTCCGTGGCA
333107 --------CC
129 CTCTTTTTCC
*
333109 CGTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT-TTT
1 CTTTTAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACTCTTT
*
333173 TT--CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCCGTGGC
65 TTCCCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAAGCCCACAACTCCGTGGC
*
333235 A-TCTTTCTCC
128 ACTCTTTTTCC
* * * *
333245 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACT
1 CTT--TTAAG-CC-CACAACTCCGTGGC-ACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACT
* * * *
333310 CTTTTTCCCTTTT-AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAACTC
61 CTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTT-TTCCTT-TTAAAG-CC-CACAACTC
*
333374 CGTGGCAAC-CTTCTT--
122 CGTGGC-ACTCTTTTTCC
* * **
333389 CTTTTCAAAGACCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTT
1 CTTTT--AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
* *
333454 TTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGC
64 TTTCCCTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGC
333519 ACTCTTTTTCC
128 ACTCTTTTTCC
*
333530 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCT
1 CTTTT--AAGCCCACAACTCCGTGGCACCTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTCT
*
333595 CTTTCCCTTTTCAAAGCCCACAACTCCGTGGCA-CTTTTTCCTTTTAAAGCCCACAACTCCGTGG
63 TTTTCCCTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGG
333659 CACTCTTTTTCC
127 CACTCTTTTTCC
* *
333671 CTTTTAAGTCCACAACTCCGTGGCATCTTTTT
1 CTTTTAAGCCCACAACTCCGTGGCACCTTTTT
333703 TTCTTCCCAA
Statistics
Matches: 509, Mismatches: 44, Indels: 65
0.82 0.07 0.11
Matches are distributed among these distances:
121 3 0.01
122 30 0.06
123 19 0.04
128 25 0.05
129 28 0.06
130 2 0.00
136 4 0.01
138 6 0.01
139 46 0.09
140 41 0.08
141 151 0.30
142 96 0.19
143 32 0.06
144 7 0.01
145 14 0.03
146 5 0.01
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.32
Consensus pattern (138 bp):
CTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
TCCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACT
CTTTTTCC
Found at i:333748 original size:33 final size:34
Alignment explanation
Indices: 333703--333769 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
333693 GCATCTTTTT
333703 TTCTTCCCAAAGCCCACACAAGTCGGTGGCAACC
1 TTCTTCCCAAAGCCCACACAAGTCGGTGGCAACC
333737 TTCTT-CCAAAGCCCACACAAGTCGGTGGCAACC
1 TTCTTCCCAAAGCCCACACAAGTCGGTGGCAACC
333770 CCTCTAAGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 28 0.85
34 5 0.15
ACGTcount: A:0.27, C:0.37, G:0.18, T:0.18
Consensus pattern (34 bp):
TTCTTCCCAAAGCCCACACAAGTCGGTGGCAACC
Found at i:333862 original size:52 final size:51
Alignment explanation
Indices: 333774--334412 Score: 671
Period size: 52 Copynumber: 13.0 Consensus size: 51
333764 GCAACCCCTC
* *
333774 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTT-CATCTT
*
333826 TAAGTCCAATATAGCTGGCCTTGACTCAGCACATTGGCACC--TTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
* * *
333875 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--TCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
* *
333924 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC-TTT-ATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
* * * *
333973 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC---CCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
*
334021 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA------C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
* *
334064 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTT-CATCTT
*
334116 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA------C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
* *
334159 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTT-CATCTT
*
334211 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA------C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
* *
334254 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTT-CATCTT
* * * *
334306 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CC--TTT-TCATCTT
* * * * * * *
334361 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA-CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTT-TCATCTT
334412 T
1 T
334413 TCTCATCATC
Statistics
Matches: 503, Mismatches: 48, Indels: 73
0.81 0.08 0.12
Matches are distributed among these distances:
43 117 0.23
45 3 0.01
48 42 0.08
49 130 0.26
50 7 0.01
51 4 0.01
52 159 0.32
53 1 0.00
54 1 0.00
55 38 0.08
56 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (51 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
Found at i:334081 original size:43 final size:43
Alignment explanation
Indices: 333970--334293 Score: 360
Period size: 43 Copynumber: 7.0 Consensus size: 43
333960 GCACCTTTAT
333970 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----CAC
*
334018 CATTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
334061 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-------C
334111 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
334156 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-------C
334206 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
334251 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
334294 ATTTTCCATC
Statistics
Matches: 242, Mismatches: 16, Indels: 41
0.81 0.05 0.14
Matches are distributed among these distances:
43 121 0.50
45 2 0.01
48 39 0.16
50 2 0.01
52 78 0.32
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:334153 original size:95 final size:95
Alignment explanation
Indices: 333970--334337 Score: 636
Period size: 95 Copynumber: 3.9 Consensus size: 95
333960 GCACCTTTAT
* * * * *
333970 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC----CCACCATTAAGTCCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAAT
334031 GTAGCTGGCCTTGAATCAGCACATTGGCAC
66 GTAGCTGGCCTTGAATCAGCACATTGGCAC
334061 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAAT
334126 GTAGCTGGCCTTGAATCAGCACATTGGCAC
66 GTAGCTGGCCTTGAATCAGCACATTGGCAC
334156 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAAT
334221 GTAGCTGGCCTTGAATCAGCACATTGGCAC
66 GTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
334251 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAAT
334316 GTAGCTGGCCTTGAATCAGCAC
66 GTAGCTGGCCTTGAATCAGCAC
334338 GTTGACATCC
Statistics
Matches: 265, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
91 41 0.15
95 224 0.85
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (95 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:334380 original size:55 final size:55
Alignment explanation
Indices: 334251--334634 Score: 264
Period size: 67 Copynumber: 6.7 Consensus size: 55
334241 ACATTGGCAC
* *
334251 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
334303 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
334358 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
* * *
334422 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATGGGCAT-C----T-TCAT
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
334474 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * * *
334529 CTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-C-TTT-T--TC-TC
334594 AT
54 AT
*
334596 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
334635 GCACCTTCAT
Statistics
Matches: 255, Mismatches: 44, Indels: 52
0.73 0.13 0.15
Matches are distributed among these distances:
49 35 0.14
50 1 0.00
52 42 0.16
54 8 0.03
55 64 0.25
56 2 0.01
57 2 0.01
58 2 0.01
59 1 0.00
61 8 0.03
62 6 0.02
63 5 0.02
64 7 0.03
66 4 0.02
67 68 0.27
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:334541 original size:171 final size:171
Alignment explanation
Indices: 334251--334645 Score: 682
Period size: 171 Copynumber: 2.3 Consensus size: 171
334241 ACATTGGCAC
* *
334251 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA-TGG-GCATCTT-CATCTTTAAGTTCAAT
334316 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
334381 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
128 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* *
334425 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATGGGCATCTTCATCTTTAAGTTCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATGGGCATCTTCATCTTTAAGTTCAATGTA
*
334490 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
*
334555 AATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
131 AATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* * *
334596 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATGGGCATCTTCATC
334646 ATCTCTAAAA
Statistics
Matches: 211, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
171 169 0.80
172 5 0.02
173 3 0.01
174 34 0.16
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (171 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATGGGCATCTTCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
AATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
Found at i:335481 original size:33 final size:33
Alignment explanation
Indices: 335444--335510 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
335434 TTCAACGATT
335444 TGTATCGATACATAAAATATTGTATCGATACAA
1 TGTATCGATACATAAAATATTGTATCGATACAA
*** *
335477 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATATTGTATCGATACAA
335510 T
1 T
335511 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATATTGTATCGATACAA
Found at i:335482 original size:13 final size:13
Alignment explanation
Indices: 335464--335488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
335454 CATAAAATAT
335464 TGTATCGATACAA
1 TGTATCGATACAA
335477 TGTATCGATACA
1 TGTATCGATACA
335489 TATTTTTTTG
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:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:335571 original size:13 final size:13
Alignment explanation
Indices: 335553--335577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
335543 ATTACTCACA
335553 TGTATCGATACAT
1 TGTATCGATACAT
335566 TGTATCGATACA
1 TGTATCGATACA
335578 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:335714 original size:52 final size:52
Alignment explanation
Indices: 335586--335706 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
335576 CACTGATCTT
*
335586 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
335638 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
335690 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
335707 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:343236 original size:13 final size:13
Alignment explanation
Indices: 343218--343242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343208 TACTATGAAC
343218 ATGTATCGATACA
1 ATGTATCGATACA
343231 ATGTATCGATAC
1 ATGTATCGATAC
343243 TAAGCAATAT
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:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:343241 original size:32 final size:33
Alignment explanation
Indices: 343200--343263 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
343190 CAATTTAATT
*
343200 TGTATCGATACTATG-AACATGTATCGATACAA
1 TGTATCGATACTAAGCAACATGTATCGATACAA
*
343232 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
343264 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:345020 original size:3 final size:3
Alignment explanation
Indices: 345012--345037 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
345002 TAATTTCATT
345012 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
345038 TAAAATACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:359878 original size:12 final size:11
Alignment explanation
Indices: 359855--359924 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 11
359845 GTCCTCCGCA
359855 AAAAAAAGAAAG
1 AAAAAAA-AAAG
359867 AAGAAAAAAAAG
1 AA-AAAAAAAAG
*
359879 AAAAAAAACAAAC
1 -AAAAAAA-AAAG
*
359892 AAACAAAAAAAT
1 AAA-AAAAAAAG
* *
359904 AACAAAATAAAC
1 AA-AAAAAAAAG
359916 AAAAAAAAA
1 AAAAAAAAA
359925 CCAAACAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 6 0.12
12 27 0.56
13 15 0.31
ACGTcount: A:0.84, C:0.07, G:0.06, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:359881 original size:9 final size:9
Alignment explanation
Indices: 359870--359953 Score: 71
Period size: 10 Copynumber: 8.8 Consensus size: 9
359860 AAGAAAGAAG
*
359870 AAAAAAAAG
1 AAAAAAAAC
359879 AAAAAAAAC
1 AAAAAAAAC
359888 AAACAAACAA-
1 AAA-AAA-AAC
*
359898 AAAAATAAC
1 AAAAAAAAC
*
359907 AAAATAAAC
1 AAAAAAAAC
359916 AAAAAAAAACC
1 -AAAAAAAA-C
*
359927 AAACAAAAC
1 AAAAAAAAC
359936 AAAAAAAAAC
1 -AAAAAAAAC
359946 AACAAAAA
1 AA-AAAAA
359954 GGGTCCGAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
8 2 0.03
9 23 0.38
10 33 0.54
11 3 0.05
ACGTcount: A:0.83, C:0.13, G:0.01, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:359899 original size:24 final size:24
Alignment explanation
Indices: 359873--359953 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
359863 AAAGAAGAAA
* *
359873 AAAAAGAAAA-AAAACAAACAAAC
1 AAAAAAAAAACAAAACAAACAAAA
* *
359896 AAAAAAATAACAAAATAAACAAAA
1 AAAAAAAAAACAAAACAAACAAAA
**
359920 AAAAACCAAACAAAACAAA-AAAA
1 AAAAAAAAAACAAAACAAACAAAA
*
359943 AACAACAAAAA
1 AA-AAAAAAAA
359954 GGGTCCGAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
23 14 0.31
24 31 0.69
ACGTcount: A:0.83, C:0.14, G:0.01, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAACAAAACAAACAAAA
Found at i:359930 original size:5 final size:5
Alignment explanation
Indices: 359870--359947 Score: 58
Period size: 5 Copynumber: 16.4 Consensus size: 5
359860 AAGAAAGAAG
* * *
359870 AAAA- AAAAG AAAA- AAAAC -AAAC -AAAC AAAAA AATAAC AAAA- TAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AA-AAC AAAAC AAAAC
* * *
359916 AAAAA AAAAC CAAAC AAAAC AAAAA AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AA
359948 CAAAAAGGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
4 19 0.32
5 36 0.61
6 4 0.07
ACGTcount: A:0.83, C:0.13, G:0.01, T:0.03
Consensus pattern (5 bp):
AAAAC
Found at i:359953 original size:19 final size:18
Alignment explanation
Indices: 359870--359953 Score: 98
Period size: 20 Copynumber: 4.4 Consensus size: 18
359860 AAGAAAGAAG
359870 AAAAAAA-AGAAAAAAAAC
1 AAAAAAACA-AAAAAAAAC
*
359888 AAACAAACAAAAAAATAAC
1 AAAAAAACAAAAAAA-AAC
359907 AAAATAAACAAAAAAAAACC
1 AAAA-AAACAAAAAAAAA-C
359927 AAACAAAACAAAAAAAAAC
1 AAA-AAAACAAAAAAAAAC
359946 AACAAAAA
1 AA-AAAAA
359954 GGGTCCGAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
18 12 0.21
19 16 0.28
20 29 0.50
21 1 0.02
ACGTcount: A:0.83, C:0.13, G:0.01, T:0.02
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAAC
Found at i:361415 original size:29 final size:29
Alignment explanation
Indices: 361373--361828 Score: 566
Period size: 29 Copynumber: 15.9 Consensus size: 29
361363 CAATCCTCAC
361373 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* *
361402 CTTTTCCAAAGCCCAAAAGTCAGTGGCAA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* *
361431 C-CTTCAAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* *
361459 CTTTTCCAAAGCCAACAAGTCAGTGGCAA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* * *
361488 C-CTTCAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-T
361517 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* *
361546 CTTTTCCAAAG-CCACAAGTTAGTGGCAA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* * *
361574 CCTTT-AAAAGCTCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* * *
361602 CTTTTCCAAAGCCCATAAGTCAGTAGCAA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* * *
361631 C-CTTCAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-T
361660 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
*
361689 CTTTTCCAAAGCCCACAAGTCAGTGGCAA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* * *
361718 C-CTTCAAAAGCCCACAAGTTAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* *
361746 CTTTTCCAAAGCCCACAAATCAGTGGCAA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
** * * *
361775 C-CCTCAAAATCCCACAAGTTAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
361803 CTTTTCCAAAGCCCACAAGTCAGTGG
1 CTTTTCCAAAGCCCACAAGTCAGTGG
361829 TAACCTTCAA
Statistics
Matches: 358, Mismatches: 60, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.01
28 151 0.42
29 155 0.43
30 48 0.13
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.21
Consensus pattern (29 bp):
CTTTTCCAAAGCCCACAAGTCAGTGGCAT
Found at i:361449 original size:28 final size:28
Alignment explanation
Indices: 361376--361850 Score: 511
Period size: 28 Copynumber: 16.6 Consensus size: 28
361366 TCCTCACCTT
* *
361376 TTCCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCCAAAGCCCACAAGTCAGTGGCAAC-C
*
361405 TTCCAAAGCCCAAAAGTCAGTGGCAACC
1 TTCCAAAGCCCACAAGTCAGTGGCAACC
* * *
361433 TTCAAAAGCCCACAAGTCAGTGGCATCTT
1 TTCCAAAGCCCACAAGTCAGTGGCAAC-C
*
361462 TTCCAAAGCCAACAAGTCAGTGGCAACC
1 TTCCAAAGCCCACAAGTCAGTGGCAACC
* *
361490 TTCAAAAGCCCACAAGTCAGTGGCACCC
1 TTCCAAAGCCCACAAGTCAGTGGCAACC
* *
361518 TTTTCCAAAGCCCACAAGTCAGTGGCATCTT
1 --TTCCAAAGCCCACAAGTCAGTGGCAAC-C
*
361549 TTCCAAAG-CCACAAGTTAGTGGCAACC
1 TTCCAAAGCCCACAAGTCAGTGGCAACC
** * * *
361576 TTTAAAAGCTCACAAGTCAGTGGCATCTT
1 TTCCAAAGCCCACAAGTCAGTGGCAAC-C
* *
361605 TTCCAAAGCCCATAAGTCAGTAGCAACC
1 TTCCAAAGCCCACAAGTCAGTGGCAACC
* *
361633 TTCAAAAGCCCACAAGTCAGTGGCACCC
1 TTCCAAAGCCCACAAGTCAGTGGCAACC
* *
361661 TTTTCCAAAGCCCACAAGTCAGTGGCATCTT
1 --TTCCAAAGCCCACAAGTCAGTGGCAAC-C
361692 TTCCAAAGCCCACAAGTCAGTGGCAACC
1 TTCCAAAGCCCACAAGTCAGTGGCAACC
* * * *
361720 TTCAAAAGCCCACAAGTTAGTGGCATCTT
1 TTCCAAAGCCCACAAGTCAGTGGCAAC-C
*
361749 TTCCAAAGCCCACAAATCAGTGGCAACC
1 TTCCAAAGCCCACAAGTCAGTGGCAACC
* * * * * *
361777 CTCAAAATCCCACAAGTTAGTGGCATCTT
1 TTCCAAAGCCCACAAGTCAGTGGCAAC-C
*
361806 TTCCAAAGCCCACAAGTCAGTGGTAACC
1 TTCCAAAGCCCACAAGTCAGTGGCAACC
* *
361834 TTCAAAAGCACACAAGT
1 TTCCAAAGCCCACAAGT
361851 TGGTGCAACC
Statistics
Matches: 368, Mismatches: 67, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
27 6 0.02
28 164 0.45
29 148 0.40
30 50 0.14
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (28 bp):
TTCCAAAGCCCACAAGTCAGTGGCAACC
Found at i:361631 original size:143 final size:144
Alignment explanation
Indices: 361372--361828 Score: 783
Period size: 143 Copynumber: 3.2 Consensus size: 144
361362 ACAATCCTCA
*
361372 CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCAAAAGTCAGTGGCAACCTTCA
1 CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
*
361437 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCAACAAGTCAGTGGCAACCTTCAAAAGCCCA
66 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCA
361502 CAAGTCAGTGGCAC
131 CAAGTCAGTGGCAC
* *
361516 CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAG-CCACAAGTTAGTGGCAACCTTTA
1 CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
361580 AAAGCTCACAAGTCAGTGGCATCTTTTCCAAAGCCCATAAGTCAGTAGCAACCTTCAAAAGCCCA
66 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCA
361645 CAAGTCAGTGGCAC
131 CAAGTCAGTGGCAC
361659 CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
361724 AAAGCCCACAAGTTAGTGGCATCTTTTCCAAAGCCCACAAATCAGTGGCAACCCTCAAAATCCCA
66 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCA
*
361789 CAAGTTAGTGGCA-
131 CAAGTCAGTGGCAC
*
361802 TCTTTTCCAAAGCCCACAAGTCAGTGG
1 CCTTTTCCAAAGCCCACAAGTCAGTGG
361829 TAACCTTCAA
Statistics
Matches: 294, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
143 162 0.55
144 132 0.45
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (144 bp):
CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCA
CAAGTCAGTGGCAC
Found at i:361851 original size:57 final size:57
Alignment explanation
Indices: 361380--361850 Score: 624
Period size: 57 Copynumber: 8.2 Consensus size: 57
361370 CACCTTTTCC
*
361380 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCAAAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
*
361437 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCAACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
361494 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCAAC-CTTCA
* * * * * * * *
361553 AAAG-CCACAAGTTAGTGGCAACCTTT-AAAAGCTCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAAC-CTTCA
* * * * * * *
361609 AAAGCCCATAAGTCAGTAGCAAC-CTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACC--TTCA
361667 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
361724 AAAGCCCACAAGTTAGTGGCATCTTTTCCAAAGCCCACAAATCAGTGGCAACCCTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
361781 AAATCCCACAAGTTAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGTAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
*
361838 AAAGCACACAAGT
1 AAAGCCCACAAGT
361851 TGGTGCAACC
Statistics
Matches: 372, Mismatches: 35, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
56 34 0.09
57 238 0.64
58 67 0.18
59 33 0.09
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:362023 original size:52 final size:49
Alignment explanation
Indices: 361893--362129 Score: 206
Period size: 52 Copynumber: 4.9 Consensus size: 49
361883 GGTGGCATCT
* *
361893 TCTTCTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACTTTCA
1 TCTT-TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTCA
* *
361943 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTATCA
1 TCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC-TT-TCA
* * * * * *
361995 TTTTTAAGACCAATGTTGCTGGCCTTGAATTAGCACATT---A---GCA
1 TCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTCA
*
362038 -C---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
1 TCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCA-C--TTTCA
* * * *
362086 TTTTTAAGACCAATGTTGCTGGCCTTGAATCAGCAAATTGGCAC
1 TCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
362130 AAGTCCAATA
Statistics
Matches: 149, Mismatches: 22, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
39 29 0.19
42 1 0.01
43 2 0.01
48 2 0.01
49 37 0.25
50 5 0.03
51 3 0.02
52 70 0.47
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (49 bp):
TCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTCA
Found at i:362217 original size:91 final size:91
Alignment explanation
Indices: 361948--362217 Score: 423
Period size: 91 Copynumber: 3.0 Consensus size: 91
361938 TTTCATCTTT
361948 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTATCATTTTTAAGACCAATGTTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTATCATTTTTAAGACCAATGTTG
* *
362013 CTGGCCTTGAATTAGCACATTAGCAC
66 CTGGCCTTGAATCAGCACATTGGCAC
* *
362039 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATTTTTAAGACCAATGTTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTATCATTTTTAAGACCAATGTTG
*
362104 CTGGCCTTGAATCAGCAAATTGGCAC
66 CTGGCCTTGAATCAGCACATTGGCAC
* * ** * *
362130 AAGTCCAATATCGCTAGCCTTGAATCGGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTATCATTTTTAAGACCAATGTTG
* *
362195 CCGGCCTTGAATCGGCACATTGG
66 CTGGCCTTGAATCAGCACATTGG
362218 TATCTTCATC
Statistics
Matches: 164, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 164 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (91 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTATCATTTTTAAGACCAATGTTG
CTGGCCTTGAATCAGCACATTGGCAC
Found at i:363102 original size:19 final size:19
Alignment explanation
Indices: 363078--363127 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
363068 AAACAGTAAC
363078 TGTATCGATACATAAATGT
1 TGTATCGATACATAAATGT
*
363097 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAATGT
363116 TGTATCGATACA
1 TGTATCGATACA
363128 ATGTATTGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATAAATGT
Found at i:367755 original size:165 final size:166
Alignment explanation
Indices: 367221--367999 Score: 858
Period size: 164 Copynumber: 4.7 Consensus size: 166
367211 TGAAATAATT
* * * * *
367221 TGAATTTTTCAAAAATGATTTAATGTAAATTTAATAACAATA-TTAGATGAATTTTAAAAATTAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTA-ATGAATTTTAAAAATTAA
*** * * * * *
367285 AAACCAAGAAAAATCCCCCCAAAAATATTTACGGAGCAGAAAACTCCGTATTTTAGAAATAGGAG
65 AAACCAAGAAAAATCCCCTTGAAAATATTTACGAAGTAGAAAACTCCGTATTTCAGAAACAAGAG
* * ** *
367350 AATTTCAAGGAAAAACTGAAACATTTATAAAAATGAA
130 AATTTCAAGGAAAAAATGAAAAATGAATGAAAATGAA
* * * * * * **
367387 TAAATTTCTGAAAACTAATTAAATATGAATTAAATAATAATATTTGACAAATTTTAAAAATTAAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
* ** * *
367452 AACCAAGAAAAATCCCCTTGAAAATGTTTAC-AATGTAGAAAACTTTGTATTTCAAAAAC-TGA-
66 AACCAAGAAAAATCCCCTTGAAAATATTTACGAA-GTAGAAAACTCCGTATTTCAGAAACAAGAG
* *
367514 TATTTCAAGGAAAAAAAGAAAAATGAATGAAAATGAA
130 AATTTCAAGGAAAAAATGAAAAATGAATGAAAATGAA
*
367551 TGAATTTTTGAAAAATGATTTAATACGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
* * * * * *
367616 GACCAAGAAAACTCCCCTTGAAAACATTTACGGAGTAAAAAACTCTGTATTTCAGAAACAAGAGA
66 AACCAAGAAAAATCCCCTTGAAAATATTTACGAAGTAGAAAACTCCGTATTTCAGAAACAAGAGA
367681 ATTTCAA-GAAAAAATGAAAAATGAATGAAAATGAA
131 ATTTCAAGGAAAAAATGAAAAATGAATGAAAATGAA
367716 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATT-AA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
* * ** * * *
367780 AACTATGAAAAATCTCCC-TGAAAATATTTAAAAAGTAGAAAACTCCGCATTTTAGAAA-TAGAA
66 AACCAAGAAAAATC-CCCTTGAAAATATTTACGAAGTAGAAAACTCCGTATTTCAGAAACAAG-A
* * * *
367843 AAATTTCTAGGAAAAAATGAGAAACT-CATGAAAATGAA
129 GAATTTCAAGGAAAAAATGA-AAAATGAATGAAAATGAA
* * * * * **
367881 TGAATTTTTGAAGAATGAATTACTATAAATTAAATAATAATATTTGACAAATTTTAAAAATTAAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
* *** * *
367946 AACCCAA-AAAAACCCCCCCAAAAATATTTACAAAGTAGAAAACTTCGTATTTCA
66 AA-CCAAGAAAAATCCCCTTGAAAATATTTACGAAGTAGAAAACTCCGTATTTCA
368000 AATGTAAAGG
Statistics
Matches: 515, Mismatches: 86, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
163 2 0.00
164 187 0.36
165 176 0.34
166 146 0.28
167 4 0.01
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (166 bp):
TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
AACCAAGAAAAATCCCCTTGAAAATATTTACGAAGTAGAAAACTCCGTATTTCAGAAACAAGAGA
ATTTCAAGGAAAAAATGAAAAATGAATGAAAATGAA
Found at i:367857 original size:330 final size:330
Alignment explanation
Indices: 367221--367999 Score: 915
Period size: 330 Copynumber: 2.4 Consensus size: 330
367211 TGAAATAATT
* * * *
367221 TGAATTTTTCAAAAATGATTTAATGTAAATTTAATAACAATA-TTAGATGAATTTTAAAAATTAA
1 TGAATTTTTGAAAAATGATTTAATATAAATTAAATAATAATATTTA-ATGAATTTTAAAAATTAA
* * * * * *
367285 AAACCAAGAAAAATCCCCCCAAAAATATTTACGGAGCAGAAAACTCCGTATTTTAGAAATAGGAG
65 AAACCAAGAAAACTCCCCCCAAAAACATTTACGGAGCAAAAAACTCCGTATTTCAGAAACAAGAG
* * ** *
367350 AATTTCAAGGAAAAACTGAAACATTTATAAAAATGAATAAATTTCTGAAAACTAATTAAATATGA
130 AATTTCAAGGAAAAAATGAAAAATGAATAAAAATGAATAAATTTCTGAAAAATAATTAAATATGA
* *
367415 ATTAAATAATAATATTTGACAAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTTGAAAATGTT
195 ATTAAATAATAATATTTAACAAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTTGAAAATATT
* * ** * *
367480 TACAATGTAGAAAACTTTGTATTTCAAAAACTGATATTTCAAGGAAAAAAAGA-AAAATGAATGA
260 TAAAAAGTAGAAAACTCCGCATTTCAAAAACTGAAATTTCAAGGAAAAAAAGAGAAAAT-AATGA
367544 AAATGAA
324 AAATGAA
**
367551 TGAATTTTTGAAAAATGATTTAATACGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
1 TGAATTTTTGAAAAATGATTTAATATAAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
* *** * *
367616 GACCAAGAAAACTCCCCTTGAAAACATTTACGGAGTAAAAAACTCTGTATTTCAGAAACAAGAGA
66 AACCAAGAAAACTCCCCCCAAAAACATTTACGGAGCAAAAAACTCCGTATTTCAGAAACAAGAGA
* * * * *
367681 ATTTCAA-GAAAAAATGAAAAATGAATGAAAATGAATGAATTTTTGAAAAATGATTTAATATGAA
131 ATTTCAAGGAAAAAATGAAAAATGAATAAAAATGAATAAATTTCTGAAAAATAATTAAATATGAA
** * *
367745 TTAAATAATAATATTTAATGAATTTTAAAAATT-AAAACTATGAAAAATCTCCC-TGAAAATATT
196 TTAAATAATAATATTTAACAAATTTTAAAAATTAAAAACCAAGAAAAATC-CCCTTGAAAATATT
* * * * * *
367808 TAAAAAGTAGAAAACTCCGCATTTTAGAAA-TAGAAAAATTTCTAGGAAAAAATGAGAAACTCAT
260 TAAAAAGTAGAAAACTCCGCATTTCAAAAACT-G--AAATTTCAAGGAAAAAAAGAGAAAATAAT
367872 GAAAATGAA
322 GAAAATGAA
* * * * **
367881 TGAATTTTTGAAGAATGAATTACTATAAATTAAATAATAATATTTGACAAATTTTAAAAATTAAA
1 TGAATTTTTGAAAAATGATTTAATATAAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
* * ** * * *
367946 AACCCAAAAAAAC-CCCCCCAAAAATATTTACAAAGTAGAAAACTTCGTATTTCA
66 AA-CCAAGAAAACTCCCCCCAAAAACATTTACGGAGCAAAAAACTCCGTATTTCA
368000 AATGTAAAGG
Statistics
Matches: 377, Mismatches: 65, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
327 1 0.00
328 47 0.12
329 80 0.21
330 233 0.62
331 16 0.04
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (330 bp):
TGAATTTTTGAAAAATGATTTAATATAAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
AACCAAGAAAACTCCCCCCAAAAACATTTACGGAGCAAAAAACTCCGTATTTCAGAAACAAGAGA
ATTTCAAGGAAAAAATGAAAAATGAATAAAAATGAATAAATTTCTGAAAAATAATTAAATATGAA
TTAAATAATAATATTTAACAAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTTGAAAATATTT
AAAAAGTAGAAAACTCCGCATTTCAAAAACTGAAATTTCAAGGAAAAAAAGAGAAAATAATGAAA
ATGAA
Found at i:368580 original size:21 final size:21
Alignment explanation
Indices: 368535--368580 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
368525 TTTTTGCCAA
* **
368535 AATGTATCGATACATGCTCTT
1 AATGTATCGATACAAGCTCCC
*
368556 AATGTATCGATACAAGGTCCC
1 AATGTATCGATACAAGCTCCC
368577 AATG
1 AATG
368581 GTCAAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (21 bp):
AATGTATCGATACAAGCTCCC
Found at i:368738 original size:50 final size:51
Alignment explanation
Indices: 368607--368741 Score: 204
Period size: 50 Copynumber: 2.7 Consensus size: 51
368597 TTCCATAATT
*
368607 TGTATCGATACA-TTCTTCATTGTATCGATACATTCTGGGTTTTACCCAGA
1 TGTATCGATACATTTCTTCATTGTATCGATACATTCTAGGTTTTACCCAGA
* * *
368657 TGTATCGATACATTT-TTCATTATATCAATACATTCTAGGTTTTACCCGGA
1 TGTATCGATACATTTCTTCATTGTATCGATACATTCTAGGTTTTACCCAGA
*
368707 TGTATCGATACATTTCTT-AATGTATCGATACATTC
1 TGTATCGATACATTTCTTCATTGTATCGATACATTC
368742 AGGCATTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 72 0.95
51 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (51 bp):
TGTATCGATACATTTCTTCATTGTATCGATACATTCTAGGTTTTACCCAGA
Found at i:371379 original size:157 final size:158
Alignment explanation
Indices: 371083--371384 Score: 371
Period size: 157 Copynumber: 1.9 Consensus size: 158
371073 TTCATGTTTC
* * * **
371083 TATTTCCAAAACATCGATTTTTCACAATCGGGGATACTCAAATTCTGTTATTTCTGAGGGAATAC
1 TATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCAAACCCTGTTATTTCTGAGGGAATAC
* * * * *
371148 TCTAACCCCGGTCTTATTTCCAAAACACTATTTTTTCACAATCAGAGATACTCCATCCCGTTATT
66 TCTAACCCCAGTCTTATTTCCAAAACACGATTTTTTCACAATCAAAGATACTCCACCCCATTATT
*
371213 TTTGAAGGG-ATACTACAACTCTGGTAT
131 TTCGAAGGGAATACTACAACTCTGGTAT
* * *
371240 TATTTCCAAAATACCAATTTTTCACAATCGAGGATACTCCAACCCTGTTATTT-TCGAGGGGATA
1 TATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCAAACCCTGTTATTTCT-GAGGGAATA
* * * *
371304 CT-TCAACCTCAGTTTTATTTCCAAAACATCGA-TTTTTCACAATTAAAGGTACTCCAACCCCAT
65 CTCT-AACCCCAGTCTTATTTCCAAAACA-CGATTTTTTCACAATCAAAGATACTCC-ACCCCAT
371367 TATTTTCG-AGGGAATACT
127 TATTTTCGAAGGGAATACT
371385 CTAAACTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
156 2 0.02
157 101 0.83
158 19 0.16
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (158 bp):
TATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCAAACCCTGTTATTTCTGAGGGAATAC
TCTAACCCCAGTCTTATTTCCAAAACACGATTTTTTCACAATCAAAGATACTCCACCCCATTATT
TTCGAAGGGAATACTACAACTCTGGTAT
Found at i:371399 original size:79 final size:79
Alignment explanation
Indices: 371078--371408 Score: 284
Period size: 79 Copynumber: 4.2 Consensus size: 79
371068 TTTCATTCAT
* * * ** *
371078 GTTTCTATTTCCAAAACATCGATTTTTCACAATCGGGGATACTCAAATTCTGTTA-TTTCTGAGG
1 GTTT-TATTTCCAAAACATCGATTTTTCACAATAGAGGATACTCCAACCCCGTTATTTTC-GAGG
* * *
371142 GAATACTCTAACCCCG
64 GAATACTCTAAACTCA
* * * *
371158 GTCTTATTTCCAAAACA-CTATTTTTTCACAATCAGA-GATACTCC-ATCCCGTTATTTTTGAAG
1 GTTTTATTTCCAAAACATCGA-TTTTTCACAAT-AGAGGATACTCCAACCCCGTTATTTTCG-AG
*
371220 GG-ATA--CTACAACTCTG
63 GGAATACTCTA-AACTC-A
* * * * * * *
371236 GTATTATTTCCAAAATACCAATTTTTCACAATCGAGGATACTCCAACCCTGTTATTTTCGAGGGG
1 GTTTTATTTCCAAAACATCGATTTTTCACAATAGAGGATACTCCAACCCCGTTATTTTCGAGGGA
*
371301 ATACT-TCAACCTCA
66 ATACTCT-AAACTCA
* *
371315 GTTTTATTTCCAAAACATCGATTTTTCACAATTAAAGG-TACTCCAACCCCATTATTTTCGAGGG
1 GTTTTATTTCCAAAACATCGATTTTTCACAA-TAGAGGATACTCCAACCCCGTTATTTTCGAGGG
371379 AATACTCTAAACTCA
65 AATACTCTAAACTCA
* *
371394 ATTTTATCTCCAAAA
1 GTTTTATTTCCAAAA
371409 TATTAAACTT
Statistics
Matches: 205, Mismatches: 31, Indels: 31
0.77 0.12 0.12
Matches are distributed among these distances:
76 3 0.01
77 5 0.02
78 52 0.25
79 130 0.63
80 14 0.07
81 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (79 bp):
GTTTTATTTCCAAAACATCGATTTTTCACAATAGAGGATACTCCAACCCCGTTATTTTCGAGGGA
ATACTCTAAACTCA
Found at i:376011 original size:79 final size:79
Alignment explanation
Indices: 375868--376019 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 79
375858 ATTTTCTAAT
* * * * *
375868 ATTTTTCACAATCGGGGATACTCCAACCACATTATTTCTGAGGGGATACTCCAACCTTGGTTTTA
1 ATTTTTCACAATCGGAGATACTCCAACCACATTATTTCTGAAGGGATACTCAAACCCTGATTTTA
*
375933 TTTCCAAAACACCG
66 TCTCCAAAACACCG
* * * *
375947 ATTTTTCACAATCGGAGATACTTCAACCCCGTTATTTTTGAAGGGATACTCAAACCCTGATTTTA
1 ATTTTTCACAATCGGAGATACTCCAACCACATTATTTCTGAAGGGATACTCAAACCCTGATTTTA
376012 TCTCCAAA
66 TCTCCAAA
376020 CTATTAAACT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (79 bp):
ATTTTTCACAATCGGAGATACTCCAACCACATTATTTCTGAAGGGATACTCAAACCCTGATTTTA
TCTCCAAAACACCG
Found at i:379129 original size:13 final size:13
Alignment explanation
Indices: 379111--379135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
379101 CAATTCAACA
379111 TGTATCAATACAT
1 TGTATCAATACAT
379124 TGTATCAATACA
1 TGTATCAATACA
379136 ATGTGCCAAT
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:379814 original size:21 final size:21
Alignment explanation
Indices: 379788--379829 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
379778 GGCTCTCGTT
* *
379788 AAAAAATTTTCCCTTTGATAA
1 AAAAAATTCTCCCCTTGATAA
379809 AAAAAATTCTCCCCTTGATAA
1 AAAAAATTCTCCCCTTGATAA
379830 TCGGTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAAAATTCTCCCCTTGATAA
Found at i:381748 original size:17 final size:17
Alignment explanation
Indices: 381726--381758 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
381716 AAATAGTAAC
381726 CCTTGTATCCATACATT
1 CCTTGTATCCATACATT
*
381743 CCTTGTATCGATACAT
1 CCTTGTATCCATACAT
381759 CTGGGTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.39
Consensus pattern (17 bp):
CCTTGTATCCATACATT
Found at i:386278 original size:3 final size:3
Alignment explanation
Indices: 386270--386300 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
386260 TCCGAGTCAC
*
386270 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
386301 TTTGATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:388029 original size:19 final size:19
Alignment explanation
Indices: 387986--388057 Score: 90
Period size: 20 Copynumber: 3.7 Consensus size: 19
387976 TGCCAGTTTC
**
387986 ATGTATCGATACAATTGTCT
1 ATGTATCGATACAA-TGAAT
388006 ATGTATCGATACAATGAAT
1 ATGTATCGATACAATGAAT
* *
388025 ATGTATCGATACAAAGCAT
1 ATGTATCGATACAATGAAT
388044 AATGTATCGATACA
1 -ATGTATCGATACA
388058 TCTGGGTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
19 20 0.43
20 27 0.57
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACAATGAAT
Found at i:394257 original size:3 final size:3
Alignment explanation
Indices: 394249--394279 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
394239 TCCGAGTCAC
*
394249 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
394280 TTTGATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:396008 original size:19 final size:19
Alignment explanation
Indices: 395965--396036 Score: 90
Period size: 20 Copynumber: 3.7 Consensus size: 19
395955 TGCCAGTTTC
**
395965 ATGTATCGATACAATTGTCT
1 ATGTATCGATACAA-TGAAT
395985 ATGTATCGATACAATGAAT
1 ATGTATCGATACAATGAAT
* *
396004 ATGTATCGATACAAAGCAT
1 ATGTATCGATACAATGAAT
396023 AATGTATCGATACA
1 -ATGTATCGATACA
396037 TCTGGGTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
19 20 0.43
20 27 0.57
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACAATGAAT
Found at i:402956 original size:52 final size:52
Alignment explanation
Indices: 402808--402936 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
402798 CAAAATATGA
*
402808 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
402860 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
402912 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
402937 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:402963 original size:13 final size:13
Alignment explanation
Indices: 402945--402969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
402935 CAAAGATCAG
402945 TGTATCGATACAA
1 TGTATCGATACAA
402958 TGTATCGATACA
1 TGTATCGATACA
402970 TTTGAGTAAT
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:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:403046 original size:19 final size:18
Alignment explanation
Indices: 403022--403084 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
403012 AGCGATACAT
403022 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
*
403041 TGTATCAATAC--A--T-
1 TGTATCGATACAAACTTA
403054 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
403073 TATATCGATACA
1 TGTATCGATACA
403085 TTGTATCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 10 0.29
14 1 0.03
16 2 0.06
18 1 0.03
19 21 0.60
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:403057 original size:32 final size:32
Alignment explanation
Indices: 403016--403099 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
403006 CTTCATAGCG
*
403016 ATACATTGTATCGATACAAAACTTATGTATCA
1 ATACATTGTATCGATACAAAACTTATATATCA
* *
403048 ATACATTGTATCGATACAACACTTATATATCG
1 ATACATTGTATCGATACAAAACTTATATATCA
403080 ATACATTGTATCGATACAAA
1 ATACATTGTATCGATACAAA
403100 TCATTGAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (32 bp):
ATACATTGTATCGATACAAAACTTATATATCA
Found at i:406631 original size:21 final size:21
Alignment explanation
Indices: 406605--406664 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
406595 TTTTTATTAG
406605 CTAACTCA-TCATTTTCATTTT
1 CTAACTCATTCATTTTC-TTTT
406626 GC-AACTCATTTC-TTTTCTTTT
1 -CTAACTCA-TTCATTTTCTTTT
406647 CTAACTCATTCATTTTCT
1 CTAACTCATTCATTTTCT
406665 CCTCTAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.12
21 22 0.65
22 6 0.18
23 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.02, T:0.53
Consensus pattern (21 bp):
CTAACTCATTCATTTTCTTTT
Found at i:406670 original size:21 final size:21
Alignment explanation
Indices: 406628--406671 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
406618 TTCATTTTGC
**
406628 AACTCATTTCTTTTCTTTTCT
1 AACTCATTTCTTTTCTCCTCT
406649 AACTCA-TTCATTTTCTCCTCT
1 AACTCATTTC-TTTTCTCCTCT
406670 AA
1 AA
406672 TTCACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.52
Consensus pattern (21 bp):
AACTCATTTCTTTTCTCCTCT
Found at i:408333 original size:13 final size:13
Alignment explanation
Indices: 408315--408340 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
408305 TACACCAAGT
408315 ATGTATCGATACA
1 ATGTATCGATACA
408328 ATGTATCGATACA
1 ATGTATCGATACA
408341 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:408338 original size:32 final size:33
Alignment explanation
Indices: 408297--408360 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
408287 TAGCCAAACT
* **
408297 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
408329 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
408361 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:412426 original size:15 final size:15
Alignment explanation
Indices: 412406--412436 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
412396 TAAAAATGTC
*
412406 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
412421 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
412436 C
1 C
412437 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:414534 original size:13 final size:13
Alignment explanation
Indices: 414516--414554 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
414506 ACATTTTTCT
414516 TTGTATCGATACA
1 TTGTATCGATACA
414529 TTGTATCGATACA
1 TTGTATCGATACA
* *
414542 CTGTATTGATACA
1 TTGTATCGATACA
414555 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:414709 original size:20 final size:20
Alignment explanation
Indices: 414666--414711 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
414656 AAATCTTTTG
414666 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
414687 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
414707 CAAAA
1 CAAAA
414712 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:417131 original size:13 final size:13
Alignment explanation
Indices: 417113--417138 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
417103 TACACCAAGT
417113 ATGTATCGATACA
1 ATGTATCGATACA
417126 ATGTATCGATACA
1 ATGTATCGATACA
417139 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:417136 original size:32 final size:33
Alignment explanation
Indices: 417095--417158 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
417085 TAGCCAAACT
* **
417095 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
417127 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
417159 TTAGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:418833 original size:19 final size:19
Alignment explanation
Indices: 418794--418833 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
418784 TGAACAGTGA
* * *
418794 TGTATCGATACATGAATAG
1 TGTATCAATACATAAACAG
418813 TGTATCAATACATAAACAG
1 TGTATCAATACATAAACAG
418832 TG
1 TG
418834 ATGAACAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (19 bp):
TGTATCAATACATAAACAG
Found at i:418891 original size:13 final size:13
Alignment explanation
Indices: 418873--418897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
418863 TGCCAGTTTT
418873 ATGTATCGATACA
1 ATGTATCGATACA
418886 ATGTATCGATAC
1 ATGTATCGATAC
418898 TAAGCAAAAT
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:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:426367 original size:13 final size:13
Alignment explanation
Indices: 426349--426374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
426339 CAATTTTTTA
426349 TGTATCGATACAT
1 TGTATCGATACAT
426362 TGTATCGATACAT
1 TGTATCGATACAT
426375 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:426390 original size:32 final size:33
Alignment explanation
Indices: 426329--426392 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
426319 TACAAGCCAA
**
426329 TGTATCGATACAATTTTTTATGTATCGATACAT
1 TGTATCGATACAATACTTTATGTATCGATACAT
*
426362 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTATGTATCGATACA
426393 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTATGTATCGATACAT
Found at i:426497 original size:20 final size:20
Alignment explanation
Indices: 426445--426499 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
426435 CATCTTTTTC
*
426445 ATGTATCGATACATTGCAAT
1 ATGTATCGATACTTTGCAAT
426465 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-T
*
426485 GTGTATCGATACTTT
1 ATGTATCGATACTTT
426500 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAT
Found at i:431783 original size:11 final size:11
Alignment explanation
Indices: 431767--431807 Score: 57
Period size: 10 Copynumber: 3.6 Consensus size: 11
431757 CCTTCTTTTA
431767 AAAAAAACAAC
1 AAAAAAACAAC
431778 AAAAAAACAAAAC
1 AAAAAAAC--AAC
431791 AAAAAAA-AAC
1 AAAAAAACAAC
431801 AAAAAAA
1 AAAAAAA
431808 ACAAAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.36
11 8 0.29
13 10 0.36
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:431794 original size:24 final size:24
Alignment explanation
Indices: 431766--431824 Score: 91
Period size: 24 Copynumber: 2.3 Consensus size: 24
431756 ACCTTCTTTT
431766 AAAAAAAACAACAAAAAAACAAAACA
1 AAAAAAAAC-A-AAAAAAACAAAACA
431792 AAAAAAAACAAAAAAAACAAAACA
1 AAAAAAAACAAAAAAAACAAAACA
431816 AAGAAAAAA
1 AA-AAAAAA
431825 GGAGAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 16 0.50
25 7 0.22
26 9 0.28
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (24 bp):
AAAAAAAACAAAAAAAACAAAACA
Found at i:431823 original size:10 final size:9
Alignment explanation
Indices: 431766--431824 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
431756 ACCTTCTTTT
431766 AAAAAAAAC
1 AAAAAAAAC
*
431775 -AACAAAA-
1 AAAAAAAAC
*
431782 AAACAAAAC
1 AAAAAAAAC
431791 AAAAAAAAAC
1 -AAAAAAAAC
431801 AAAAAAAAC
1 AAAAAAAAC
* *
431810 AAAACAAAG
1 AAAAAAAAC
431819 AAAAAA
1 AAAAAA
431825 GGAGAGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 13 0.31
9 21 0.50
10 8 0.19
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:433036 original size:55 final size:55
Alignment explanation
Indices: 432841--433899 Score: 308
Period size: 61 Copynumber: 18.1 Consensus size: 55
432831 GATGCCTTCT
* * *
432841 CCTTTTAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTACTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTT--AGTACTCAAAGAGCAGGACG
* * * * *
432896 CCTTTCAAAGCCCACACAAGCGGGTGGCACC-TTCAGTCCTCAAAGAGCGGGATG
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTACTCAAAGAGCAGGACG
* *
432950 CCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTTCTCAAAGAGCAGGACG
1 CC-TTT-C----AAAGCCCACACAAGCTGGTGGCACCTTTTAGTACTCAAAGAGCAGGACG
* * * * * * *
433011 CCTTTCAAAGCCTACAAAAGCTGGTGGCACC-TTCAATCCTCAAAGAGCGGGGAAGCATTTT
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTACTCAAAGAGC-AGG-A-C----G
* * * *
433072 CCCTTCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTT--AGTACTCAAAGAGCAGGACG
* * * ** * *
433127 CTTTTCAAAGCCCACATAAGTTGGTGG-TGCTTTTCAGTCCTCAAGGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTT-AGTACTCAAAGAGCAGGACG
* * * * * *
433182 CCTTTTCCTTCAAAAGCCCACACAAGTTGGTGGCA-TTTTCTAATCCTCAAAGAGTAGGACA
1 CC---T--TTC-AAAGCCCACACAAGCTGGTGGCACCTTT-TAGTACTCAAAGAGCAGGACG
** * ***
433243 CCTTTCAAAGCCCACACAAGCTAGG-GGCACC-TTCCGTCCTC--A-A--A-GTTT
1 CCTTTCAAAGCCCACACAAGCT-GGTGGCACCTTTTAGTACTCAAAGAGCAGGACG
* * * * * *
433291 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCTAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTACTCAAAGAGCAGGACG
* * * *
433346 CCATTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTTAAAGAGCAGGATG
1 CC-TTT-C----AAAGCCCACACAAGCTGGTGGCACCTTTT-AGTACTCAAAGAGCAGGACG
* * * * * * * * *
433407 CCTTTTCCTTTTAAAGCCAACACAAGTTGCTGACA-CTTTTCAGTCCTTAAGGAGTAGGATG
1 CC-TTT-C----AAAGCCCACACAAGCTGGTGGCACCTTTT-AGTACTCAAAGAGCAGGACG
* * * * * *
433468 CCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTGTCGTCCTCAAAGAGTAGGATG
1 CC-TTT-C----AAAGCCCACACAAGCTGGTGGCACCTTT-TAGTACTCAAAGAGCAGGACG
* * * * *
433530 CCTTTTCCTTTTAAAGTCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACG
1 CC-TTT-C----AAAGCCCACACAAGCTGGTGGCACCTTTTAGTACTCAAAGAGCAGGACG
* * * * **
433591 CCTTTTTCTTTTAAAGCCTACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAATAGGACG
1 CC--TTTC----AAAGCCCACACAAGCTGGTGGCACCTTTTAGTACTCAAAGAGCAGGACG
* ** * *
433652 TATTTTTCTTTCAAAGCCCATGCAAG-TGGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATG
1 ------CCTTTCAAAGCCCACACAAGCT-GGTGGCACCTTTTAGTACTCAAAGAGCAGGACG
* * * *
433713 CCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCA-CTTTTCAAT-CTTCAAGGAGCAGGACG
1 CC-TTT-C----AAAGCCCACACAAGCTGGTGGCACCTTTT-AGTAC-TCAAAGAGCAGGACG
* * * * * *
433774 CCTTTTTTTTTAAAGCCAACACAAGTTAGTGGCA-CTTTTCAGTCCTCAAAGAGTAGGACG
1 CC-----TTTCAAAGCCCACACAAGCTGGTGGCACCTTTT-AGTACTCAAAGAGCAGGACG
* * * * * * *
433834 CCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACCTTCTAGTCCTCGAAGAGCAAGACA
1 CC-TTT-C----AAAGCCCACACAAGCTGGTGGCACCTTTTAGTACTCAAAGAGCAGGACG
433895 CCTTT
1 CCTTT
433900 TCCTTTTAAA
Statistics
Matches: 810, Mismatches: 118, Indels: 147
0.75 0.11 0.14
Matches are distributed among these distances:
47 2 0.00
48 27 0.03
49 8 0.01
51 2 0.00
52 2 0.00
54 38 0.05
55 123 0.15
56 23 0.03
57 2 0.00
58 2 0.00
59 1 0.00
60 89 0.11
61 401 0.50
62 80 0.10
63 1 0.00
65 8 0.01
67 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTACTCAAAGAGCAGGACG
Found at i:433209 original size:61 final size:61
Alignment explanation
Indices: 433127--433930 Score: 782
Period size: 61 Copynumber: 13.5 Consensus size: 61
433117 GAGCAGGATG
* ** *
433127 CTTTTCAAAGCCCACATAAGTTGGTGGTGCTTTTCAGTCCTCAAGGAGCAGGACGCCTTTTC
1 CTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
** * * *
433189 CTTCAAAAGCCCACACAAGTTGGTGGCA-TTTTCTAATCCTCAAAGAGTAGGACACC-TTT-
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* * *
433248 C----AAAGCCCACACAAGCTAGG-GGCAC-CTTCCGTCCTC----A--A--A-G---TTTC
1 CTTTTAAAGCCCACACAAG-TTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
** * *
433292 CTTTTAAAGCCCACACAAGTTGGTGGCAC-CCTCTAGTCCTCAAAGAGCAGGATGCCATTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* *
433353 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTTAAAGAGCAGGATGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * * * * *
433414 CTTTTAAAGCCAACACAAGTTGCTGACACTTTTCAGTCCTTAAGGAGTAGGATGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* *
433475 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTGTC-GTCCTCAAAGAGTAGGATGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCAC-TTT-TCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
433537 CTTTTAAAGTCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAAGACGCCTTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* * ** ** *
433598 CTTTTAAAGCCTACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAATAGGACGTATTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* ** * *
433659 CTTTCAAAGCCCATGCAAGTGGGTGGCACCTTTT-AGTCCTCAAAGAGCAGGATGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
433720 CTTTTAAAGCCTACACAAGTTGGTGGCACTTTTCAATCTTCAAGGAGCAGGACGCCTTTT-
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
433780 TTTTTAAAGCCAACACAAGTTAGTGGCACTTTTCAGTCCTCAAAGAGTAGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * * *
433841 CTTTTAAAGCCTACACAAGTTGGTGGCAC-CTTCTAGTCCTCGAAGAGCAAGACACCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
*** *
433902 CTTTTAAAGTGAACACAAGTTAGTGGCAC
1 CTTTTAAAGCCCACACAAGTTGGTGGCAC
433931 CTTCTAATCC
Statistics
Matches: 626, Mismatches: 84, Indels: 65
0.81 0.11 0.08
Matches are distributed among these distances:
43 3 0.00
44 1 0.00
46 1 0.00
47 3 0.00
48 23 0.04
49 6 0.01
50 1 0.00
53 1 0.00
54 5 0.01
55 22 0.04
56 3 0.00
57 1 0.00
58 1 0.00
59 3 0.00
60 70 0.11
61 417 0.67
62 61 0.10
63 4 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (61 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
Found at i:433320 original size:48 final size:49
Alignment explanation
Indices: 433243--433336 Score: 129
Period size: 48 Copynumber: 1.9 Consensus size: 49
433233 GAGTAGGACA
* *
433243 CCTTTCAAAGCCCACACAAGCTAGGGGCACCTTC-CGTCCTCAAAGTTT
1 CCTTTCAAAGCCCACACAAGCTAGGGGCACCCTCTAGTCCTCAAAGTTT
* *
433291 CCTTTTAAAGCCCACACAAG-TTGGTGGCACCCTCTAGTCCTCAAAG
1 CCTTTCAAAGCCCACACAAGCTAGG-GGCACCCTCTAGTCCTCAAAG
433337 AGCAGGATGC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 3 0.08
48 27 0.68
49 10 0.25
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (49 bp):
CCTTTCAAAGCCCACACAAGCTAGGGGCACCCTCTAGTCCTCAAAGTTT
Found at i:433718 original size:245 final size:243
Alignment explanation
Indices: 433288--433921 Score: 783
Period size: 245 Copynumber: 2.6 Consensus size: 243
433278 GTCCTCAAAG
* * *
433288 TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCTAGTCCTCAAAGAGCAGGATGCCATTTC
1 TTTCCTTTTAAAG-CCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * * * *
433353 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTTAAAGAGCAGGATGCCTTTTCCTT
65 CTTTTAAAGCCTACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAACAGGACGCATTTTCCTT
* * * * *
433417 TTAAAGCCAACACAAGTTGCTGACACTTTTCAGTCCTTAAGGAGTAGGATGCCTTTTCCTTTTAA
129 TCAAAGCCAACACAAGTGGCTGACACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAA
* * *
433482 AGCCCACACAAGTTGGTGGCACTTTTGTC-GTCCTCAAAGAGTAGGATGCCT
194 AGCCCACACAAGTTGGTGGCAC-TTT-TCAATCCTCAAAGAGCAGGACGCCT
* *
433533 TTTCCTTTTAAAGTCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCCTTTTT
1 TTTCCTTTTAAAG-CCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
* * *
433598 CTTTTAAAGCCTACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAATAGGACGTATTTTTCTTT
65 CTTTTAAAGCCTACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAACAGGACGCATTTTCCTTT
* ** * *
433663 CAAAGCCCATGCAAGTGGGTGGCACCTTTT-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAA
130 CAAAGCCAACACAAGTGGCTGACA-CTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAA
* * *
433727 AGCCTACACAAGTTGGTGGCACTTTTCAATCTTCAAGGAGCAGGACGCCT
194 AGCCCACACAAGTTGGTGGCACTTTTCAATCCTCAAAGAGCAGGACGCCT
* * * *
433777 TTT-TTTTTAAAGCCAACACAAGTTAGTGGCA-CTTTTCAGTCCTCAAAGAGTAGGACGCCTTTT
1 TTTCCTTTTAAAGCC-ACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
433840 CCTTTTAAAGCCTACACAAGTTGGTGGCACCTTCTAGTCCTCGAAGAGCAAGACACCTTTTCCTT
64 CCTTTTAAAGCCTACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAACAGGACGCATTTTCCTT
* **
433905 TTAAAGTGAACACAAGT
129 TCAAAGCCAACACAAGT
433922 TAGTGGCACC
Statistics
Matches: 333, Mismatches: 51, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
242 6 0.02
243 116 0.35
244 23 0.07
245 179 0.54
246 9 0.03
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (243 bp):
TTTCCTTTTAAAGCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCC
TTTTAAAGCCTACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAACAGGACGCATTTTCCTTTC
AAAGCCAACACAAGTGGCTGACACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAG
CCCACACAAGTTGGTGGCACTTTTCAATCCTCAAAGAGCAGGACGCCT
Found at i:434683 original size:49 final size:50
Alignment explanation
Indices: 434571--434704 Score: 207
Period size: 49 Copynumber: 2.7 Consensus size: 50
434561 TTTCACAATT
* *
434571 TGTATCGATACATTGTTCATTGTATCGATACATTCTAGGTTTTACCCAGA
1 TGTATCGATACATTGTTCATTGTATCGATACATTCTAGGGTTTACCCAAA
* *
434621 TATATCCATACATTGTTCATTGTATCGATACATTCT-GGGTTTACCCAAA
1 TGTATCGATACATTGTTCATTGTATCGATACATTCTAGGGTTTACCCAAA
* *
434670 TGTATCGATACATTTTTCAATGTATCGATACATTC
1 TGTATCGATACATTGTTCATTGTATCGATACATTC
434705 AAGCATTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 42 0.55
50 34 0.45
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (50 bp):
TGTATCGATACATTGTTCATTGTATCGATACATTCTAGGGTTTACCCAAA
Found at i:437122 original size:51 final size:51
Alignment explanation
Indices: 437062--437181 Score: 204
Period size: 51 Copynumber: 2.4 Consensus size: 51
437052 TTATTTCTGA
* *
437062 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCGAAAACACCAAATTTTCACAATC
**
437113 GGGGATACTCCAACTTCGATTTTATTTCGAAAACACCAAATTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCGAAAACACCAAATTTTCACAATC
437164 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
437182 TTATTTCCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCGAAAACACCAAATTTTCACAATC
Found at i:437241 original size:130 final size:128
Alignment explanation
Indices: 436986--437387 Score: 383
Period size: 130 Copynumber: 3.1 Consensus size: 128
436976 TTCATCTCGA
* * *
436986 GGATACTCCAACGC-CGGTTTATTTCCAAAACATTAATTTTTCATAATCGGGGATACTCCAATCC
1 GGATACTCCAAC-CTCGCTTTATTTCCAAAACA-TAAATTTTCACAATCGGGGATACTCCAATCC
* *
437050 CGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGG
64 CGTTATTTCCGAGGGGATACTCCAACACCGATTTTATTTCTAAAACACCAATTTTTCACAATCGG
* * * * *
437115 GGATACTCCAACTTCGATTTTATTTCGAAAACACCAAATTTTCACAATCGGGGATACTCCAACCC
1 GGATACTCCAACCTCG-CTTTATTTCCAAAACA-TAAATTTTCACAATCGGGGATACTCCAATCC
* * * * *** *
437180 CGTTATTTCCGAGGGGATACTCTAACACCGGTTTTATTTTTAAAATATTGATTTTTTACAATCGG
64 CGTTATTTCCGAGGGGATACTCCAACACCGATTTTATTTCTAAAACACCAATTTTTCACAATCGG
* * * * ** *
437245 GAATACTCTAACCTCGGCTTTATTTCTAAAATATTGATTTCTCACAATCAGGGATACTCCAATCC
1 GGATACTCCAACCTC-GCTTTATTTCCAAAACATAAATTT-TCACAATCGGGGATACTCCAATCC
* ** * * * *** * * * *
437310 TGTTATTTTTGCGGTGATACTCCAACCCCGGCCTTATTTCTAAAGCATCAATTTTCCACAATTGG
64 CGTTATTTCCGAGGGGATACTCCAACACCGATTTTATTTCTAAAACACCAATTTTTCACAATCGG
* *
437375 AGATACTCTAACC
1 GGATACTCCAACC
437388 CTATTATTTT
Statistics
Matches: 221, Mismatches: 48, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
129 18 0.08
130 202 0.91
131 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (128 bp):
GGATACTCCAACCTCGCTTTATTTCCAAAACATAAATTTTCACAATCGGGGATACTCCAATCCCG
TTATTTCCGAGGGGATACTCCAACACCGATTTTATTTCTAAAACACCAATTTTTCACAATCGG
Found at i:437275 original size:51 final size:51
Alignment explanation
Indices: 437193--437303 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
437183 TATTTCCGAG
* * * *
437193 GGGATACTCTAACACCGGTTTTATTTTTAAAATATTGATTTTTTACAATC-
1 GGGATACTCTAACACCGGCTTTATTTCTAAAATATTGATTTCTCACAATCA
437243 GGGAATACTCTAAC-CTCGGCTTTATTTCTAAAATATTGATTTCTCACAATCA
1 GGG-ATACTCTAACAC-CGGCTTTATTTCTAAAATATTGATTTCTCACAATCA
437295 GGGATACTC
1 GGGATACTC
437304 CAATCCTGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
50 4 0.07
51 47 0.87
52 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (51 bp):
GGGATACTCTAACACCGGCTTTATTTCTAAAATATTGATTTCTCACAATCA
Found at i:437426 original size:79 final size:79
Alignment explanation
Indices: 437282--437540 Score: 252
Period size: 79 Copynumber: 3.3 Consensus size: 79
437272 AAAATATTGA
* * * ** * ***
437282 TTTCTCACAATCAGGGATACTCCAATCCTGTTATTTTTGCGGTGATACTCCAACCCCGGCCTTA-
1 TTTC-CACAATCAAGGATACTCTAACCCTGTTATTTTTAAGGGGATACTCCAACCCCGATTTTAT
* *
437346 TTTCTAAAGCATCAAT
65 TTTC-AAAACACCAAT
** *
437362 TTTCCACAAT-TGGAGATACTCTAACCCTATTATTTTTAAGGGGATACTCCAACCCCGATTTTAT
1 TTTCCACAATCAAG-GATACTCTAACCCTGTTATTTTTAAGGGGATACTCCAACCCCGATTTTAT
*
437426 TTTCAAAACACCGAT
65 TTTCAAAACACCAAT
* * * * *
437441 TTTCTATAATCAAGGATACTTTAACCCTGTTATTTTCAAGGGGATACTCCAACCTCGATTTTATT
1 TTTCCACAATCAAGGATACTCTAACCCTGTTATTTTTAAGGGGATACTCCAACCCCGATTTTATT
* *
437506 TTCAGAACACCGAT
66 TTCAAAACACCAAT
* **
437520 TTTCCATAATCGGGGATACTC
1 TTTCCACAATCAAGGATACTC
437541 CAGCCCCGTT
Statistics
Matches: 150, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
78 2 0.01
79 139 0.93
80 9 0.06
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (79 bp):
TTTCCACAATCAAGGATACTCTAACCCTGTTATTTTTAAGGGGATACTCCAACCCCGATTTTATT
TTCAAAACACCAAT
Found at i:440699 original size:4 final size:4
Alignment explanation
Indices: 440690--440728 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
440680 TTTTAAGGTG
*
440690 TTTA TTTA TTTA TTTA TTCA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
440729 TGTTTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:445834 original size:15 final size:16
Alignment explanation
Indices: 445799--445834 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
445789 GATAAAAATG
445799 TCCAAAATGAGGAAGC
1 TCCAAAATGAGGAAGC
445815 T-CAAAATGA-GAAGC
1 TCCAAAATGAGGAAGC
445829 TCCAAA
1 TCCAAA
445835 CGAAATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.32
15 12 0.63
16 1 0.05
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (16 bp):
TCCAAAATGAGGAAGC
Done.