Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 153 of 198
Found at i:48472460 original size:24 final size:24
Alignment explanation
Indices: 48472405--48472461 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
48472395 AAGATTTAGT
* * *
48472405 ATTTATGAGTATAACATATTTAGC
1 ATTTATTAGCATAACATATTTAAC
*
48472429 ATTTATTAGCATAATATATTTAAC
1 ATTTATTAGCATAACATATTTAAC
48472453 -TTTGATTAG
1 ATTT-ATTAG
48472462 AATTAGATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (24 bp):
ATTTATTAGCATAACATATTTAAC
Found at i:48476650 original size:24 final size:24
Alignment explanation
Indices: 48476616--48476667 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
48476606 TTTTTAGAAG
* *
48476616 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
* *
48476640 ATTTAGCATTTGTTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
48476664 ATTT
1 ATTT
48476668 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:48485908 original size:27 final size:27
Alignment explanation
Indices: 48485875--48486129 Score: 254
Period size: 27 Copynumber: 9.5 Consensus size: 27
48485865 CCCTAAAATA
** *
48485875 GGTAAAATGACCAAAATACCCCTAAAG
1 GGTAAAATGACTGAAATACCCCTATAG
* ** *
48485902 GGTAAAATAACT-ATTTTACCCTTAATA-
1 GGTAAAATGACTGA-AATACCCCT-ATAG
*
48485929 GATGAAAATGACTGAAATA-CCCTCATAG
1 GGT-AAAATGACTGAAATACCCCT-ATAG
*
48485957 GGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCTATAG
**
48485984 GGTAAAATGACCAAAATACCCCTATAG
1 GGTAAAATGACTGAAATACCCCTATAG
*
48486011 AGTAAAATGA-TCGAAATACCCC-ATAG
1 GGTAAAATGACT-GAAATACCCCTATAG
* *
48486037 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCTATAG
* *
48486064 GATAAAATAACTGAAATACCCCTATAG
1 GGTAAAATGACTGAAATACCCCTATAG
*
48486091 GG-AAAATGACTGAAATACCTCC-ATAC
1 GGTAAAATGACTGAAATACC-CCTATAG
48486117 GGTAAAATGACTG
1 GGTAAAATGACTG
48486130 TTATAGCCTT
Statistics
Matches: 188, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
26 45 0.24
27 125 0.66
28 17 0.09
29 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCCTATAG
Found at i:48486056 original size:53 final size:52
Alignment explanation
Indices: 48485933--48486129 Score: 240
Period size: 53 Copynumber: 3.7 Consensus size: 52
48485923 TTAATAGATG
*
48485933 AAAATGACTGAAATA-CCCTCATAGGGTAAAATGACTGAAATACCCCCATAGGGT
1 AAAATGACCGAAATACCCCT-ATA-GGTAAAATGACTGAAATA-CCCCATAGGGT
*
48485987 AAAATGACCAAAATACCCCTATAGAGTAAAATGA-TCGAAATACCCCATAGGGT
1 AAAATGACCGAAATACCCCTATAG-GTAAAATGACT-GAAATACCCCATAGGGT
* *
48486040 AAAATGACCGAAATACCCCCATAGGATAAAATAACTGAAATACCCCTATAGGG-
1 AAAATGACCGAAATACCCCTATAGG-TAAAATGACTGAAATACCCC-ATAGGGT
*
48486093 AAAATGACTGAAATACCTCC-ATACGGTAAAATGACTG
1 AAAATGACCGAAATACC-CCTATA-GGTAAAATGACTG
48486130 TTATAGCCTT
Statistics
Matches: 128, Mismatches: 7, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
52 1 0.01
53 81 0.63
54 42 0.33
55 4 0.03
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (52 bp):
AAAATGACCGAAATACCCCTATAGGTAAAATGACTGAAATACCCCATAGGGT
Found at i:48486056 original size:80 final size:80
Alignment explanation
Indices: 48485875--48486127 Score: 314
Period size: 80 Copynumber: 3.1 Consensus size: 80
48485865 CCCTAAAATA
* * * *** *
48485875 GGTAAAATGACCAAAATACCCCTAAAGGGTAAAATAACTATTTTACCCTTAATAGA-TGAAAATG
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATAACTAAAATACCCCT-ATAGAGT-AAAATG
48485939 ACTGAAATACCCTCATAG
64 ACTGAAATACCC-CATAG
* * *
48485957 GGTAAAATGACTGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTATAGAGTAAAATGA-
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATAACTAAAATACCCCTATAGAGTAAAATGAC
48486021 TCGAAATACCCCATAG
66 T-GAAATACCCCATAG
* * *
48486037 GGTAAAATGACCGAAATACCCCCATAGGATAAAATAACTGAAATACCCCTATAG-GGAAAATGAC
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAATAACTAAAATACCCCTATAGAGTAAAATGAC
*
48486101 TGAAATACCTCCATAC
66 TGAAATACC-CCATAG
48486117 GGTAAAATGAC
1 GGTAAAATGAC
48486128 TGTTATAGCC
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
79 16 0.11
80 72 0.48
81 21 0.14
82 41 0.27
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (80 bp):
GGTAAAATGACCGAAATACCCCCATAGGGTAAAATAACTAAAATACCCCTATAGAGTAAAATGAC
TGAAATACCCCATAG
Found at i:48486370 original size:26 final size:26
Alignment explanation
Indices: 48486334--48486414 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
48486324 TTTGCCACAT
* * *
48486334 ATACTGTTACTGGCAACTTTACTACG
1 ATACTGATACTGGCAGCTTTACTGCG
*
48486360 ATACTGATACTGGCAGCTCTACTGCG
1 ATACTGATACTGGCAGCTTTACTGCG
* *
48486386 AT-GTTATTACTGGCAGCTTTACTGCG
1 ATACTGA-TACTGGCAGCTTTACTGCG
48486412 ATA
1 ATA
48486415 TTGGTGTGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
25 2 0.04
26 44 0.96
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTACTGCG
Found at i:48486557 original size:28 final size:28
Alignment explanation
Indices: 48486517--48486604 Score: 158
Period size: 28 Copynumber: 3.1 Consensus size: 28
48486507 TTGCACTGCG
48486517 CTGTTACTGTATTGAGCTAAGGCCCACA
1 CTGTTACTGTATTGAGCTAAGGCCCACA
* *
48486545 CTGTTATTGTATTGGGCTAAGGCCCACA
1 CTGTTACTGTATTGAGCTAAGGCCCACA
48486573 CTGTTACTGTATTGAGCTAAGGCCCACA
1 CTGTTACTGTATTGAGCTAAGGCCCACA
48486601 CTGT
1 CTGT
48486605 ACTATCACTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (28 bp):
CTGTTACTGTATTGAGCTAAGGCCCACA
Found at i:48488336 original size:18 final size:19
Alignment explanation
Indices: 48488313--48488353 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
48488303 AAAAATTTTA
48488313 AAAC-TTAAAAATTTGGAG
1 AAACTTTAAAAATTTGGAG
* *
48488331 AAACTTTGAAACTTTGGAG
1 AAACTTTAAAAATTTGGAG
48488350 AAAC
1 AAAC
48488354 AAGTTTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (19 bp):
AAACTTTAAAAATTTGGAG
Found at i:48491873 original size:18 final size:19
Alignment explanation
Indices: 48491844--48491879 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
48491834 GTGAAAATTT
*
48491844 TGAAATTTAGGGATTTAAG
1 TGAAATTTAGGGAGTTAAG
48491863 TGAAA-TTAGGGAGTTAA
1 TGAAATTTAGGGAGTTAA
48491880 ATTTAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGGGAGTTAAG
Found at i:48494341 original size:9 final size:10
Alignment explanation
Indices: 48494315--48494340 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
48494305 TGTAAATCTG
48494315 TCAAAAATAA
1 TCAAAAATAA
48494325 TCAAAAATAA
1 TCAAAAATAA
48494335 TCAAAA
1 TCAAAA
48494341 TTTATTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (10 bp):
TCAAAAATAA
Found at i:48495074 original size:6 final size:6
Alignment explanation
Indices: 48495063--48495096 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
48495053 ATGCTCTCCT
*
48495063 TTTTTC TTTTTC TTTTTC TTTTT- TTCTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
48495097 TTTCACGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:48495087 original size:20 final size:20
Alignment explanation
Indices: 48495062--48495100 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
48495052 TATGCTCTCC
48495062 TTTTTTCTT-TTTCTTTTTCT
1 TTTTTTCTTCTTT-TTTTTCT
48495082 TTTTTTCTTCTTTTTTTTC
1 TTTTTTCTTCTTTTTTTTC
48495101 ACGAGCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTCTTCTTTTTTTTCT
Found at i:48495100 original size:12 final size:11
Alignment explanation
Indices: 48495062--48495099 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
48495052 TATGCTCTCC
48495062 TTTTTTCTTTT
1 TTTTTTCTTTT
48495073 TCTTTTTCTTTT
1 T-TTTTTCTTTT
*
48495085 TTTCTTCTTTT
1 TTTTTTCTTTT
48495096 TTTT
1 TTTT
48495100 CACGAGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:48497537 original size:16 final size:16
Alignment explanation
Indices: 48497516--48497547 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48497506 GGTTTGATGA
48497516 GTGATGAATGATGGAG
1 GTGATGAATGATGGAG
48497532 GTGATGAATGATGGAG
1 GTGATGAATGATGGAG
48497548 AAGGTTGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (16 bp):
GTGATGAATGATGGAG
Found at i:48497921 original size:29 final size:30
Alignment explanation
Indices: 48497864--48497921 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
48497854 TCTTTTGAAG
*
48497864 ATATTTACAAAAAGAGACATCTAATTTTTA
1 ATATTTACAAAAAGAGACATCTAAATTTTA
*
48497894 ATATTTATAAAAAGAGTA-A-CTAAATTTT
1 ATATTTACAAAAAGAG-ACATCTAAATTTT
48497922 GAAAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 16 0.64
31 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (30 bp):
ATATTTACAAAAAGAGACATCTAAATTTTA
Found at i:48506393 original size:7 final size:7
Alignment explanation
Indices: 48506381--48506410 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
48506371 GTATATGTAT
48506381 TATATAA
1 TATATAA
48506388 TATATAA
1 TATATAA
48506395 TATATAA
1 TATATAA
48506402 TATATAA
1 TATATAA
48506409 TA
1 TA
48506411 AATGAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TATATAA
Found at i:48506503 original size:12 final size:12
Alignment explanation
Indices: 48506473--48506511 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
48506463 ATTAAATAGA
48506473 AAGAAAAGAAAG
1 AAGAAAAGAAAG
48506485 -A-AAAAGAAAG
1 AAGAAAAGAAAG
*
48506495 AAGAAAAGAAGG
1 AAGAAAAGAAAG
48506507 AAGAA
1 AAGAA
48506512 CGCACAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.38
11 2 0.08
12 13 0.54
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAAAGAAAG
Found at i:48508630 original size:30 final size:30
Alignment explanation
Indices: 48508594--48508655 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
48508584 ACATGGGGTA
*
48508594 TGTCACACACGAGCAACACACATGGGCATG
1 TGTCACACACGAGCAACACACATGGACATG
*
48508624 TGTCACACACGGGCAACACACATGGACATG
1 TGTCACACACGAGCAACACACATGGACATG
48508654 TG
1 TG
48508656 ACCCATATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (30 bp):
TGTCACACACGAGCAACACACATGGACATG
Found at i:48512041 original size:41 final size:42
Alignment explanation
Indices: 48511942--48512077 Score: 150
Period size: 42 Copynumber: 3.3 Consensus size: 42
48511932 GTTTGTCCGC
* * * * * *
48511942 TGATGCACTTACGTGGCAATATAATTGCTTTGGA-ATATCCGA
1 TGATGCACTTACGTGCCAGTATATTTGC-TTCGATACATCTGA
* *
48511984 TGATGCACTTATGTGCCAGTATATTTGCTTCGATATAT-TGA
1 TGATGCACTTACGTGCCAGTATATTTGCTTCGATACATCTGA
** *
48512025 TGATGTGCTTACGTGCCAGTATATTTTCTTCGATACATCTGA
1 TGATGCACTTACGTGCCAGTATATTTGCTTCGATACATCTGA
48512067 TGATGCACTTA
1 TGATGCACTTA
48512078 GGTACCAACA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 39 0.49
42 40 0.51
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (42 bp):
TGATGCACTTACGTGCCAGTATATTTGCTTCGATACATCTGA
Found at i:48513357 original size:24 final size:22
Alignment explanation
Indices: 48513299--48513357 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 22
48513289 ATATGTATAC
*
48513299 TAAAATAAAT-ATATACATATAGA
1 TAAAA-AAATAAT-TACATATAAA
48513322 TAAAAAAATAATTACATATAAA
1 TAAAAAAATAATTACATATAAA
48513344 TAAATAAAAATAAT
1 T-AA-AAAAATAAT
48513358 AATTATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 14 0.44
23 9 0.28
24 9 0.28
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAAAAAATAATTACATATAAA
Found at i:48513414 original size:21 final size:21
Alignment explanation
Indices: 48513375--48513415 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48513365 TTATACTACA
* *
48513375 AAAAATAAATATGCGTATATG
1 AAAAATAAATATACATATATG
*
48513396 AAAAATATATATACATATAT
1 AAAAATAAATATACATATAT
48513416 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAATAAATATACATATATG
Found at i:48514001 original size:22 final size:21
Alignment explanation
Indices: 48513966--48514099 Score: 84
Period size: 19 Copynumber: 6.5 Consensus size: 21
48513956 AAAGGGTATC
* *
48513966 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
48513987 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
*
48514010 TACATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
48514029 TGCATAT-ATTATATCTAAGAT
1 TACAAATCA-TATCTCTAAGAT
*
48514050 TGCATATATCATA--TCTAAGAT
1 TACA-A-ATCATATCTCTAAGAT
* *
48514071 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
48514090 TACATATCAT
1 TACAAATCAT
48514100 CGAAGATTAT
Statistics
Matches: 98, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
18 1 0.01
19 39 0.40
21 27 0.28
22 15 0.15
23 15 0.15
24 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:48514009 original size:23 final size:22
Alignment explanation
Indices: 48513966--48514023 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
48513956 AAAGGGTATC
* *
48513966 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
48513987 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
48514010 TACATATCATATCT
1 TACAAATCATATCT
48514024 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:48514026 original size:19 final size:19
Alignment explanation
Indices: 48513979--48514099 Score: 125
Period size: 21 Copynumber: 5.9 Consensus size: 19
48513969 AAATTAAATC
*
48513979 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
48513999 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
* *
48514021 TCTAAGATTGCATATATTATA
1 TCTAAGATT--ACATATCATA
*
48514042 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
48514063 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
48514082 TCTAAGATTACATATCAT
1 TCTAAGATTACATATCAT
48514100 CGAAGATTAT
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
19 34 0.38
21 37 0.42
22 7 0.08
23 11 0.12
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:48514042 original size:21 final size:21
Alignment explanation
Indices: 48514013--48514096 Score: 136
Period size: 21 Copynumber: 4.1 Consensus size: 21
48514003 CTAAGATTAC
48514013 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
48514034 ATATTATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
48514055 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
*
48514074 ATATCATATCTAAGATTACAT
1 ATATCATATCTAAGATTGCAT
48514095 AT
1 AT
48514097 CATCGAAGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 18 0.31
21 40 0.69
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:48514059 original size:42 final size:40
Alignment explanation
Indices: 48513995--48514096 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
48513985 ATTACAAAAT
48513995 CATATC-T-TCTAAGATTAC--ATATCATATCTAAGATTG
1 CATATCATATCTAAGATTACATATATCATATCTAAGATTG
* *
48514031 CATATATTATATCTAAGATTGCATATATCATATCTAAGATTG
1 C--ATATCATATCTAAGATTACATATATCATATCTAAGATTG
48514073 CATATCATATCTAAGATTACATAT
1 CATATCATATCTAAGATTACATAT
48514097 CATCGAAGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
36 1 0.02
38 4 0.07
39 1 0.02
40 31 0.55
42 19 0.34
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (40 bp):
CATATCATATCTAAGATTACATATATCATATCTAAGATTG
Found at i:48514526 original size:44 final size:43
Alignment explanation
Indices: 48514476--48515118 Score: 621
Period size: 44 Copynumber: 14.6 Consensus size: 43
48514466 CCACTTTACT
* *
48514476 ACCAATATAAGAAGACAGGATCTGCTATCTTCGATCTACTTCAC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-C
* * * *
48514520 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTTGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTAC-TT-CC
* * * *
48514565 ACCAGTATATGAAGACAAGATCTGCTTTCTTCGATCTATTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTT--CC
* * *
48514610 ACCAATATGGGAAGATAAGATCTGC-ATCTTTGATCTACTTCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCC
* *
48514652 TACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCTC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-C
* * * *
48514697 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTT--CC
* * *
48514742 ACCAATATGGGAAGCCAAGATCTGC-ATCTTCGATCCACTTCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCC
* *
48514784 TACCATTATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-C
* * * * *
48514829 GCCAATACATGAGGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTT--CC
* * * * *
48514874 ACCAATATGGGATGATAAGATCTAC-ATCTTCGATCCACTTCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCC
* * *
48514916 TACCAATATAGGAAGACAGGACCTGCTATCTTTGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-C
* * * * * * *
48514961 GCCAATACATGAAGAGAAGATCTACTTTTTTCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTT--CC
* *
48515006 ACTAATAT-GAGAAGACAAGATCTGC-ATCTTCGATCCACTTCC
1 ACCAATATAG-GAAGACAAGATCTGCTATCTTCGATCTACTTCC
*
48515048 TACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-C
* * *
48515093 GCCAATACATGAAGACAAGATCTGCT
1 ACCAATATAGGAAGACAAGATCTGCT
48515119 TTTTCATTGA
Statistics
Matches: 489, Mismatches: 87, Indels: 46
0.79 0.14 0.07
Matches are distributed among these distances:
42 8 0.02
43 84 0.17
44 268 0.55
45 125 0.26
46 4 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (43 bp):
ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCC
Found at i:48515122 original size:132 final size:132
Alignment explanation
Indices: 48514476--48515120 Score: 961
Period size: 132 Copynumber: 4.9 Consensus size: 132
48514466 CCACTTTACT
** * * * * * *
48514476 ACCAATATAAGAAGACAGGATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGA
1 ACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGA
* * * * *
48514540 TCTGCTTTCTTCGATCTACTTTGC-CACCAGTATATGAAGACAAGATCTGCTTTCTTCGATCTAT
64 TCTGCTATCTTCGATCTAC-TT-CACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
48514604 TTCGCC
127 TTCGCC
* * * *
48514610 ACCAATATGGGAAGATAAGATCTGCATCTTTGATCTACTTCCTACCAATATAGGAAGATAGGATC
1 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATC
*
48514675 TGCTATCTTCGATCTACTTCTCGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCG
66 TGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCG
48514740 CC
131 CC
* *
48514742 ACCAATATGGGAAGCCAAGATCTGCATCTTCGATCCACTTCCTACCATTATAGGAAGACAGGATC
1 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATC
*
48514807 TGCTATCTTCGATCTACTTCACGCCAATACATGAGGACAAGATCTGCTTTCTTCGATCTACTTCG
66 TGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCG
48514872 CC
131 CC
* * * *
48514874 ACCAATATGGGATGATAAGATCTACATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACC
1 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATC
* * * *
48514939 TGCTATCTTTGATCTACTTCACGCCAATACATGAAGAGAAGATCTACTTTTTTCGATCTACTTCG
66 TGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCG
48515004 CC
131 CC
* *
48515006 ACTAATATGAGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATC
1 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATC
48515071 TGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
66 TGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
48515121 TTCATTGATC
Statistics
Matches: 466, Mismatches: 43, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
131 1 0.00
132 396 0.85
133 48 0.10
134 21 0.05
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (132 bp):
ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATC
TGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCG
CC
Found at i:48516441 original size:9 final size:9
Alignment explanation
Indices: 48516424--48516469 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
48516414 TGAGTTTTCG
48516424 AATTCGAAT
1 AATTCGAAT
*
48516433 AACTCGAAT
1 AATTCGAAT
48516442 AATTCGAAT
1 AATTCGAAT
48516451 AATTCGAAT
1 AATTCGAAT
48516460 AATTCGAAT
1 AATTCGAAT
48516469 A
1 A
48516470 TCAAACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:48516716 original size:30 final size:30
Alignment explanation
Indices: 48516682--48516738 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
48516672 AAACCTTTTA
*
48516682 TTTTCCCCCAAAATTTTTACTCCCTTCAAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCAAC
* * *
48516712 TTTTCCCCTAATACTTTTATTCCCTTC
1 TTTTCCCCCAAAACTTTTACTCCCTTC
48516739 CCATCTCACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (30 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCAAC
Found at i:48517514 original size:15 final size:15
Alignment explanation
Indices: 48517496--48517526 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
48517486 CTCGAAAATT
48517496 TTCGATTCGATTCAA
1 TTCGATTCGATTCAA
48517511 TTCGATTCGATTCAA
1 TTCGATTCGATTCAA
48517526 T
1 T
48517527 CAAATGCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (15 bp):
TTCGATTCGATTCAA
Found at i:48517667 original size:27 final size:26
Alignment explanation
Indices: 48517605--48517669 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
48517595 CTCCATTTTT
* * * *
48517605 CTTTTCTTTTTATTTTCTTTTTATCA
1 CTTTTTTTTTTATTTTATTTTGACCA
*
48517631 CTTTTATTTTTTATTTTGATTTTGACCC
1 CTTTT-TTTTTTATTTT-ATTTTGACCA
48517659 CTTTTTTTTTT
1 CTTTTTTTTTT
48517670 GAATCTGAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 5 0.16
27 16 0.50
28 11 0.34
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.72
Consensus pattern (26 bp):
CTTTTTTTTTTATTTTATTTTGACCA
Found at i:48520725 original size:23 final size:23
Alignment explanation
Indices: 48520693--48520750 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
48520683 ATATGTATAC
* *
48520693 TAAAATAAATA-TATACATATAGA
1 TAAAAAAAATAGT-TACATATAAA
48520716 TAAAAAAAATAGTTACATATAAA
1 TAAAAAAAATAGTTACATATAAA
48520739 TAAATAAAAATA
1 TAAA-AAAAATA
48520751 ATAATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 23 0.74
24 8 0.26
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (23 bp):
TAAAAAAAATAGTTACATATAAA
Found at i:48520809 original size:21 final size:21
Alignment explanation
Indices: 48520770--48520810 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48520760 TTATACTACA
* *
48520770 AAAAATAAATATGCGTATATG
1 AAAAATAAATATACATATATG
*
48520791 AAAAATATATATACATATAT
1 AAAAATAAATATACATATAT
48520811 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAATAAATATACATATATG
Found at i:48521405 original size:23 final size:22
Alignment explanation
Indices: 48521360--48521417 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
48521350 AAAGGGTATC
* *
48521360 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
48521381 TACAAAATCATATCTTCTAATAT
1 TAC-AAATCATATCTTCTAAGAT
*
48521404 TACATATCATATCT
1 TACAAATCATATCT
48521418 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:48521428 original size:19 final size:19
Alignment explanation
Indices: 48521373--48521472 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 19
48521363 AAATTAAATC
*
48521373 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
48521393 TCTTCTAATATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
48521415 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
48521436 TCTAAGATTGTATATATCATA
1 TCTAAGA-T-TACATATCATA
*
48521457 TCTAATATTACATATC
1 TCTAAGATTACATATC
48521473 CTCGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
19 15 0.22
20 1 0.01
21 32 0.48
22 8 0.12
23 11 0.16
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:48521433 original size:21 final size:21
Alignment explanation
Indices: 48521407--48521471 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
48521397 CTAATATTAC
48521407 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
48521428 ATATCATATCTAAGATTGTAT
1 ATATCATATCTAAGATTGCAT
* *
48521449 ATATCATATCTAATATTACAT
1 ATATCATATCTAAGATTGCAT
48521470 AT
1 AT
48521472 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:48524052 original size:27 final size:27
Alignment explanation
Indices: 48524022--48524075 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
48524012 AAGGCAATTC
*
48524022 GTGAAGTTCTTTTACGTCATTGCCTTA
1 GTGAAGTTCTTTTACGCCATTGCCTTA
*
48524049 GTGAAGTTCTTTTATGCCATTGCCTTA
1 GTGAAGTTCTTTTACGCCATTGCCTTA
48524076 ATGTGGATAT
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:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (27 bp):
GTGAAGTTCTTTTACGCCATTGCCTTA
Found at i:48527470 original size:50 final size:50
Alignment explanation
Indices: 48527356--48527832 Score: 516
Period size: 50 Copynumber: 9.7 Consensus size: 50
48527346 TCACATATCA
* * *
48527356 GTGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCACTCATC--T-C
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCTCTGTCC
** *
48527403 AAGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTCTGTCC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCTCTGTCC
* *
48527453 GTGCCGATGCCATGTCCCAGACATGGTCTTACACT-AGCACTCCTCGGTCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CACTCCTCTGTCC
* * *
48527503 GTGCCAATGCCATGTCCAAGACATGGTCTTACACTGACACTCATCT-T--
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCTCTGTCC
* * * *
48527550 GAGCCGATGCCATGTCACAGACATGGTCTAAGACTGA-ATCTCCTCTGTCC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACA-CTCCTCTGTCC
* * *
48527600 GTGCCGATGCCATGTCCCAAACATAGTCTTACACT-AGCACTCCT-TGGTCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CACTCCTCT-GTCC
* * *
48527650 GTGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATC--T-C
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCTCTGTCC
* * * *
48527697 GAGCCGATGTCATGTCCCAGACATGGTCTTACACTGACTCTCATCTGTCC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCTCTGTCC
* * *
48527747 GTGCCGATGTCATGTCCCAGACATGGTCTTACACT-AGCATTCCT-TGGTCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CACTCCTCT-GTCC
* * *
48527797 GTACCGATGCCATGTCCCAAACATGGTCGTACACTG
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTG
48527833 GCACACTCAC
Statistics
Matches: 361, Mismatches: 49, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
46 1 0.00
47 116 0.32
48 2 0.01
49 8 0.02
50 232 0.64
51 2 0.01
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (50 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCTCTGTCC
Found at i:48527478 original size:97 final size:98
Alignment explanation
Indices: 48527314--48527841 Score: 531
Period size: 97 Copynumber: 5.4 Consensus size: 98
48527304 TAGGGTGCCA
* * ** * * *
48527314 ATGCCATATCCCAGATATGGTCTTACA-TGGGA-TCA-CATATCAGTGCCGATGCCATGTCCCAA
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACTCATC-TGTCCGTGCCGATGCCATGTCCCAG
*
48527376 ACATGGTCTTACACTGGCACTCATC-TCAAGCCG
65 ACATGGTCTTACACTGGCACTCATCGTCGAGCCG
* *
48527409 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTCTGTCCGTGCCGATGCCATGTCCCAGA
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACTCATCTGTCCGTGCCGATGCCATGTCCCAGA
* * * *
48527474 CATGGTCTTACACTAGCACTCCTCGGTCTGTGCCA
66 CATGGTCTTACACTGGCACTCATC-GTC-GAGCCG
* * *
48527509 ATGCCATGTCCAAGACATGGTCTTACACTGACACTCATCT-T--GAGCCGATGCCATGTCACAGA
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACTCATCTGTCCGTGCCGATGCCATGTCCCAGA
* * * * *
48527571 CATGGTCTAAGACT-GAATCTCCTCTGTCCGTGCCG
66 CATGGTCTTACACTGGCA-CTCATC-GT-CGAGCCG
* * * * *
48527606 ATGCCATGTCCCAAACATAGTCTTACACT-AGCACTCCT-TGGTCTGTGCTGATGCCATGTCCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CACTCATCT-GTCCGTGCCGATGCCATGTCCCA
48527669 GACATGGTCTTACACTGGCACTCATC-TCGAGCCG
64 GACATGGTCTTACACTGGCACTCATCGTCGAGCCG
* * *
48527703 ATGTCATGTCCCAGACATGGTCTTACACTGACTCTCATCTGTCCGTGCCGATGTCATGTCCCAGA
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACTCATCTGTCCGTGCCGATGCCATGTCCCAGA
* * * *
48527768 CATGGTCTTACACTAGCATTCCTTGGTCTGTA-CCG
66 CATGGTCTTACACTGGCACT-CATCGTC-G-AGCCG
* *
48527803 ATGCCATGTCCCAAACATGGTCGTACACTGGCACACTCA
1 ATGCCATGTCCCAGACATGGTCTTACACT-G-ACACTCA
48527842 CTACCATGGT
Statistics
Matches: 359, Mismatches: 52, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
95 25 0.07
96 6 0.02
97 200 0.56
98 8 0.02
99 5 0.01
100 105 0.29
101 4 0.01
102 6 0.02
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (98 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACACTCATCTGTCCGTGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGGCACTCATCGTCGAGCCG
Found at i:48527573 original size:147 final size:147
Alignment explanation
Indices: 48527356--48527841 Score: 758
Period size: 147 Copynumber: 3.3 Consensus size: 147
48527346 TCACATATCA
* *
48527356 GTGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCACTCATCTCAAGCCGATGCCATGTCCC
1 GTGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACTCATCTCGAGCCGATGCCATGTCCC
48527421 AGACATGGTCTTACACTGACTCTCCTCTGTCCGTGCCGATGCCATGTCCCAGACATGGTCTTACA
66 AGACATGGTCTTACACTGACTCTCCTCTGTCCGTGCCGATGCCATGTCCCAGACATGGTCTTACA
*
48527486 CTAGCACTCCTCGGTCT
131 CTAGCACTCCTTGGTCT
* * *
48527503 GTGCCAATGCCATGT-CCAAGACATGGTCTTACACTGACACTCATCTTGAGCCGATGCCATGTCA
1 GTGCCGATGCCATGTCCCAA-ACATGGTCTTACACTGACACTCATCTCGAGCCGATGCCATGTCC
* * * * *
48527567 CAGACATGGTCTAAGACTGAATCTCCTCTGTCCGTGCCGATGCCATGTCCCAAACATAGTCTTAC
65 CAGACATGGTCTTACACTGACTCTCCTCTGTCCGTGCCGATGCCATGTCCCAGACATGGTCTTAC
48527632 ACTAGCACTCCTTGGTCT
130 ACTAGCACTCCTTGGTCT
* * * *
48527650 GTGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATCTCGAGCCGATGTCATGTCCC
1 GTGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACTCATCTCGAGCCGATGCCATGTCCC
* *
48527715 AGACATGGTCTTACACTGACTCTCATCTGTCCGTGCCGATGTCATGTCCCAGACATGGTCTTACA
66 AGACATGGTCTTACACTGACTCTCCTCTGTCCGTGCCGATGCCATGTCCCAGACATGGTCTTACA
*
48527780 CTAGCATTCCTTGGTCT
131 CTAGCACTCCTTGGTCT
* *
48527797 GTACCGATGCCATGTCCCAAACATGGTCGTACACTGGCACACTCA
1 GTGCCGATGCCATGTCCCAAACATGGTCTTACACT-G-ACACTCA
48527842 CTACCATGGT
Statistics
Matches: 304, Mismatches: 31, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
146 4 0.01
147 290 0.95
148 4 0.01
149 6 0.02
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (147 bp):
GTGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACTCATCTCGAGCCGATGCCATGTCCC
AGACATGGTCTTACACTGACTCTCCTCTGTCCGTGCCGATGCCATGTCCCAGACATGGTCTTACA
CTAGCACTCCTTGGTCT
Found at i:48527661 original size:197 final size:195
Alignment explanation
Indices: 48527405--48527832 Score: 551
Period size: 197 Copynumber: 2.2 Consensus size: 195
48527395 CTCATCTCAA
* *
48527405 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTCTGTCCGTGCCGATGCCATGTCC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTG-CACTCCTCTGTCCGTGCCGATGCCATGTCC
* *
48527470 CAGACATGGTCTTACACTAGCACTCCTCGGTCTGTGCCAATGCCATGTCCAAGACATGGTCTTAC
65 CAGACATGGTCTTACACTAGCACTCATC--TC-GAGCCAATGCCATGTCCAAGACATGGTCTTAC
*
48527535 ACTGACACTCATCT-T-GAGCCGATGCCATGTCACAGACATGGTCTAAGACT-GAATCTCCTCT-
127 ACTGACACTCATCTGTCGAGCCGATGCCATGTCACAGACATGGTCTAACACTAGAAT-TCCT-TG
48527596 GTCCGT
190 GTCCGT
* * *
48527602 GCCGATGCCATGTCCCAAACATAGTCTTACACTAGCACTCCT-TGGTCTGTGCTGATGCCATGTC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACT-GCACTCCTCT-GTCCGTGCCGATGCCATGTC
* * * *
48527666 CCAGACATGGTCTTACACTGGCACTCATCTCGAGCCGATGTCATGTCCCAGACATGGTCTTACAC
64 CCAGACATGGTCTTACACTAGCACTCATCTCGAGCCAATGCCATGTCCAAGACATGGTCTTACAC
* * * * * *
48527731 TGACTCTCATCTGTCCGTGCCGATGTCATGTCCCAGACATGGTCTTACACTAGCATTCCTTGGTC
129 TGACACTCATCTGT-CGAGCCGATGCCATGTCACAGACATGGTCTAACACTAGAATTCCTTGGTC
*
48527796 TGT
193 CGT
* *
48527799 ACCGATGCCATGTCCCAAACATGGTCGTACACTG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTG
48527833 GCACACTCAC
Statistics
Matches: 202, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
194 41 0.20
195 3 0.01
196 3 0.01
197 151 0.75
198 4 0.02
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (195 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTGCACTCCTCTGTCCGTGCCGATGCCATGTCCC
AGACATGGTCTTACACTAGCACTCATCTCGAGCCAATGCCATGTCCAAGACATGGTCTTACACTG
ACACTCATCTGTCGAGCCGATGCCATGTCACAGACATGGTCTAACACTAGAATTCCTTGGTCCGT
Found at i:48540233 original size:56 final size:56
Alignment explanation
Indices: 48540080--48540236 Score: 260
Period size: 56 Copynumber: 2.8 Consensus size: 56
48540070 AGTATTTATG
* * * * *
48540080 TAGGAATCAAAATGCGAAGAGATAATATCTCATAATAATATCCTATAATATCCCAT
1 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATTCTATAACATCCCAT
48540136 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATTCTATAACATCCCAT
1 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATTCTATAACATCCCAT
*
48540192 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATTCTA
1 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATTCTA
48540237 ACACCCCCTC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 95 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (56 bp):
TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATTCTATAACATCCCAT
Found at i:48555564 original size:26 final size:27
Alignment explanation
Indices: 48555535--48555601 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 27
48555525 CCTGTTATAT
48555535 GGCTCTTCGTGAGCTTTCC-AATTAAA
1 GGCTCTTCGTGAGCTTTCCTAATTAAA
* * *
48555561 GGCTCTTTGTGAGC-TTCCTGATTAAT
1 GGCTCTTCGTGAGCTTTCCTAATTAAA
48555587 GGCTCTTCG-GAGCTT
1 GGCTCTTCGTGAGCTT
48555602 CCCGATATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 8 0.23
26 27 0.77
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.37
Consensus pattern (27 bp):
GGCTCTTCGTGAGCTTTCCTAATTAAA
Found at i:48555599 original size:25 final size:25
Alignment explanation
Indices: 48555519--48555677 Score: 109
Period size: 25 Copynumber: 6.4 Consensus size: 25
48555509 CAGCTCTTAT
*
48555519 GAGCGTCCTG-TTATATGGCTCTTCG
1 GAGCTTCCTGATTA-ATGGCTCTTCG
* * *
48555544 TGAGCTTTCC-AATTAAAGGCTCTTTG
1 -GAGC-TTCCTGATTAATGGCTCTTCG
48555570 TGAGCTTCCTGATTAATGGCTCTTCG
1 -GAGCTTCCTGATTAATGGCTCTTCG
*
48555596 GAGCTTCCCGA-T-ATGGCTCGCTT--
1 GAGCTTCCTGATTAATGGCT--CTTCG
* * *
48555619 GAACTTCCTGA-TATATGGCTATCCG
1 GAGCTTCCTGATTA-ATGGCTCTTCG
*
48555644 GAGCTTCC-CATTAATGGCTCTTCG
1 GAGCTTCCTGATTAATGGCTCTTCG
*
48555668 GAGCTACCTG
1 GAGCTTCCTG
48555678 TTATTGACTC
Statistics
Matches: 104, Mismatches: 18, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
23 17 0.16
24 18 0.17
25 32 0.31
26 31 0.30
27 6 0.06
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (25 bp):
GAGCTTCCTGATTAATGGCTCTTCG
Found at i:48555637 original size:48 final size:51
Alignment explanation
Indices: 48555524--48555663 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 51
48555514 CTTATGAGCG
* * ** *
48555524 TCCTGTTATATGGCTCTTCGTGAGCTTTCCAATTAAAGGCTCTTTGTGAGCT
1 TCCTGATATATGGCTCTTCG-GAGCTTCCCAATTAAAGGCTCGCTGTGAACT
* *
48555576 TCCTGAT-TAATGGCTCTTCGGAGCTTCCCGA-T-ATGGCTCGCT-TGAACT
1 TCCTGATAT-ATGGCTCTTCGGAGCTTCCCAATTAAAGGCTCGCTGTGAACT
* * *
48555624 TCCTGATATATGGCTATCCGGAGCTTCCC-ATTAATGGCTC
1 TCCTGATATATGGCTCTTCGGAGCTTCCCAATTAAAGGCTC
48555664 TTCGGAGCTA
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
47 1 0.01
48 31 0.41
49 15 0.20
50 1 0.01
51 10 0.13
52 17 0.23
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (51 bp):
TCCTGATATATGGCTCTTCGGAGCTTCCCAATTAAAGGCTCGCTGTGAACT
Found at i:48555708 original size:72 final size:73
Alignment explanation
Indices: 48555571--48555710 Score: 178
Period size: 72 Copynumber: 1.9 Consensus size: 73
48555561 GGCTCTTTGT
* * * *
48555571 GAGCTTCCTGATTAATGGCTCTTCGGAGCTTCCCGATATGGCTCGCTTGAACTTCCTGATATATG
1 GAGCTTCCTCATTAATGGCTCTTCGGAGCTACCCGATATGACTCGCATGAACTTCCTGATATATG
48555636 GCTATCCG
66 GCTATCCG
* * *
48555644 GAGCTTCC-CATTAATGGCTCTTCGGAGCTACCTGTTATTGACTCGCATGAGCTTTCC-GAT-TA
1 GAGCTTCCTCATTAATGGCTCTTCGGAGCTACCCGATA-TGACTCGCATGAAC-TTCCTGATATA
48555706 TGGCT
64 TGGCT
48555711 CTTATGAGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
72 32 0.55
73 22 0.38
74 4 0.07
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.34
Consensus pattern (73 bp):
GAGCTTCCTCATTAATGGCTCTTCGGAGCTACCCGATATGACTCGCATGAACTTCCTGATATATG
GCTATCCG
Found at i:48555720 original size:72 final size:71
Alignment explanation
Indices: 48555544--48555724 Score: 175
Period size: 72 Copynumber: 2.5 Consensus size: 71
48555534 TGGCTCTTCG
* * * * *
48555544 TGAGCTTTCCAATTAAAGGCTCTTTGTGAGCTTCCTGATTAATGGCTCTTCGGAGCTTCCCGATA
1 TGAGCTTTCCGATT-ATGGCTC-TTATGAGCTTCC-CATTAATGGCTCTTCGGAGCTACCCGATA
* *
48555609 TGGCTCGCT
63 TGACTCGCA
* * *** * *
48555618 TGAAC-TTCCTGATATATGGCTATCCGGAGCTTCCCATTAATGGCTCTTCGGAGCTACCTGTTAT
1 TGAGCTTTCC-GAT-TATGGCTCTTATGAGCTTCCCATTAATGGCTCTTCGGAGCTACCCGATA-
48555682 TGACTCGCA
63 TGACTCGCA
48555691 TGAGCTTTCCGATTATGGCTCTTATGAGCTTCCC
1 TGAGCTTTCCGATTATGGCTCTTATGAGCTTCCC
48555725 GTTATACAAC
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
72 42 0.49
73 27 0.32
74 15 0.18
75 1 0.01
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (71 bp):
TGAGCTTTCCGATTATGGCTCTTATGAGCTTCCCATTAATGGCTCTTCGGAGCTACCCGATATGA
CTCGCA
Found at i:48562066 original size:32 final size:32
Alignment explanation
Indices: 48562021--48562092 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
48562011 CTTGTTTTAA
48562021 AGTTCTTTTACTTCACGTGCCAAAACTCTAATC
1 AGTTC-TTTACTTCACGTGCCAAAACTCTAATC
48562054 AGTTCTTTACTTCACGTGCCAAAACTCTAATC
1 AGTTCTTTACTTCACGTGCCAAAACTCTAATC
48562086 AGTTCTT
1 AGTTCTT
48562093 CAGAATACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 34 0.87
33 5 0.13
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (32 bp):
AGTTCTTTACTTCACGTGCCAAAACTCTAATC
Found at i:48564000 original size:54 final size:54
Alignment explanation
Indices: 48563920--48564022 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
48563910 TACATGCTCA
48563920 TGTGTCCAACCGTGTGCTCACCCGTGTAACTCACTGACTTAGTTCACACGTCTG
1 TGTGTCCAACCGTGTGCTCACCCGTGTAACTCACTGACTTAGTTCACACGTCTG
* *
48563974 TGTGT-CAACTCGTGTGCT-AGCCCGTGTAACTTACTGACTTGGTTCACAC
1 TGTGTCCAAC-CGTGTGCTCA-CCCGTGTAACTCACTGACTTAGTTCACAC
48564023 ACCCAAGTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
53 5 0.11
54 40 0.89
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.31
Consensus pattern (54 bp):
TGTGTCCAACCGTGTGCTCACCCGTGTAACTCACTGACTTAGTTCACACGTCTG
Found at i:48565939 original size:32 final size:32
Alignment explanation
Indices: 48565868--48565942 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
48565858 GAAAGATGCA
*
48565868 ATTATTCTAAATACAACCTATTCCAAACAATG
1 ATTATTCTAAATACAACCTATTCCAAACAATC
* *
48565900 ATCATTCTAAATATAA-CTATTCCTGAAACAA-C
1 ATTATTCTAAATACAACCTATTCC--AAACAATC
48565932 ATTATTCTAAA
1 ATTATTCTAAA
48565943 CAAAAGTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 7 0.19
32 24 0.65
33 6 0.16
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (32 bp):
ATTATTCTAAATACAACCTATTCCAAACAATC
Found at i:48566100 original size:16 final size:16
Alignment explanation
Indices: 48566042--48566100 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
48566032 TGTTTTGAGC
48566042 ATAACTATTCT-AGA-A
1 ATAACTATTCTGA-ACA
* *
48566057 ATAGCTATCCTTGAACA
1 ATAACTATTC-TGAACA
* *
48566074 ATAATTGTTCTGAACA
1 ATAACTATTCTGAACA
48566090 ATAACTATTCT
1 ATAACTATTCT
48566101 AAATAAGATT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 8 0.24
16 17 0.52
17 8 0.24
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (16 bp):
ATAACTATTCTGAACA
Found at i:48566721 original size:28 final size:28
Alignment explanation
Indices: 48566687--48566742 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
48566677 TTATTTATGT
*
48566687 TATAAAATTAAAAGAAATATAGAATGGA
1 TATAAAACTAAAAGAAATATAGAATGGA
*
48566715 TATAAAACTAAAAGAAGTATAGAATGGA
1 TATAAAACTAAAAGAAATATAGAATGGA
48566743 CAAAAGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.16, T:0.23
Consensus pattern (28 bp):
TATAAAACTAAAAGAAATATAGAATGGA
Found at i:48573645 original size:3 final size:3
Alignment explanation
Indices: 48573637--48573664 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
48573627 TAGCTAGCGA
48573637 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
48573665 CCCTTTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:48574982 original size:69 final size:69
Alignment explanation
Indices: 48574866--48575007 Score: 250
Period size: 69 Copynumber: 2.1 Consensus size: 69
48574856 CATCCGATGC
*
48574866 ATTAGTTTTACAAAAAGATATCATATTATAATTGAAGGGTTAGGAGTG-TTGAAATTTAGATTCA
1 ATTAGTTTTACAAAAAGATATCATATTATAATTGAAGGGTTAAGAGTGCTT-AAATTTAGATTCA
48574930 ACTTG
65 ACTTG
*
48574935 ATTAGTTTTACAAAAAGATATTATATTATAATTGAAGGGTTAAGAGTGCTTAAATTTAGATTCAA
1 ATTAGTTTTACAAAAAGATATCATATTATAATTGAAGGGTTAAGAGTGCTTAAATTTAGATTCAA
48575000 CTTG
66 CTTG
48575004 ATTA
1 ATTA
48575008 ATAATCAGGT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
69 68 0.97
70 2 0.03
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (69 bp):
ATTAGTTTTACAAAAAGATATCATATTATAATTGAAGGGTTAAGAGTGCTTAAATTTAGATTCAA
CTTG
Found at i:48575742 original size:24 final size:24
Alignment explanation
Indices: 48575715--48575764 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
48575705 TTTGCCGCCT
*
48575715 CCATGCTTTCCGTGCTTAAATTTC
1 CCATGCTTCCCGTGCTTAAATTTC
*
48575739 CCATGCTTCCCGTGCTTGAATTTC
1 CCATGCTTCCCGTGCTTAAATTTC
48575763 CC
1 CC
48575765 CCCATGATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.34, G:0.14, T:0.38
Consensus pattern (24 bp):
CCATGCTTCCCGTGCTTAAATTTC
Found at i:48575784 original size:21 final size:22
Alignment explanation
Indices: 48575751--48575809 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
48575741 ATGCTTCCCG
*
48575751 TGCTTGAATTTCCCC-CCATGA
1 TGCTTGAACTTCCCCACCATGA
*
48575772 TGCTTAAACTTCCCACCACCATGA
1 TGCTTGAACTT-CC-CCACCATGA
*
48575796 TGTTTGAACTTCCC
1 TGCTTGAACTTCCC
48575810 ATGATGACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 9 0.29
22 3 0.10
23 4 0.13
24 15 0.48
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (22 bp):
TGCTTGAACTTCCCCACCATGA
Found at i:48575841 original size:9 final size:9
Alignment explanation
Indices: 48575829--48575871 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
48575819 ATGACCAAAC
*
48575829 CCATGAGCG
1 CCATGAGCA
*
48575838 CCATAAGCA
1 CCATGAGCA
48575847 CCATGAGCA
1 CCATGAGCA
48575856 CCATGAGCA
1 CCATGAGCA
48575865 CCATGAG
1 CCATGAG
48575872 ACACGTGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.12
Consensus pattern (9 bp):
CCATGAGCA
Found at i:48576148 original size:30 final size:32
Alignment explanation
Indices: 48576114--48576175 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
48576104 GGGGTATCCT
*
48576114 CCTTGAGGAGGGTA-G-CCAGCTGGTGGATAG
1 CCTTGAGGAGGGTACGCCCAGCCGGTGGATAG
*
48576144 CCTTGAGGGGGGTACGCTCCAGCCGGTGGATA
1 CCTTGAGGAGGGTACGC-CCAGCCGGTGGATA
48576176 TCCGCCAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 13 0.48
31 1 0.04
33 13 0.48
ACGTcount: A:0.18, C:0.21, G:0.42, T:0.19
Consensus pattern (32 bp):
CCTTGAGGAGGGTACGCCCAGCCGGTGGATAG
Found at i:48578766 original size:56 final size:56
Alignment explanation
Indices: 48578677--48578792 Score: 171
Period size: 56 Copynumber: 2.1 Consensus size: 56
48578667 TTACTAAAAA
*
48578677 AAATAAGAAGAGATTTTGATGATCAAAACGAAAGTGACCTAAAACTTGGGATGACCG
1 AAATAAGAAGAGATTTTAATGATCAAAACGAAAGTGACCTAAAACTT-GGATGACCG
* * * *
48578734 AAAT-AGAAGAGATTTTAATGATTAAAATGAAAGTGACCTAACACTTGGATGACTG
1 AAATAAGAAGAGATTTTAATGATCAAAACGAAAGTGACCTAAAACTTGGATGACCG
48578789 AAAT
1 AAAT
48578793 GAAAGTGTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 12 0.22
56 38 0.70
57 4 0.07
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (56 bp):
AAATAAGAAGAGATTTTAATGATCAAAACGAAAGTGACCTAAAACTTGGATGACCG
Found at i:48579118 original size:22 final size:22
Alignment explanation
Indices: 48579093--48579138 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
48579083 CCTCCGCAGA
48579093 TTTATGTCTTCATATTATTCTC
1 TTTATGTCTTCATATTATTCTC
48579115 TTTATGTCTTCATATTATTCTC
1 TTTATGTCTTCATATTATTCTC
48579137 TT
1 TT
48579139 ACATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTATGTCTTCATATTATTCTC
Found at i:48585653 original size:42 final size:41
Alignment explanation
Indices: 48585607--48585695 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
48585597 GTGCTAAATA
* * *
48585607 GAAACCGATAAGGGTTGAATG-AAAGCTCATAAGAGCTTAACG
1 GAAACCCATAAGGGTT-AA-GCAAAGCTCAAAAGAGCTGAACG
* *
48585649 GAAACCCATAATGGTTAAGCTAAAGTTCAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAGC-AAAGCTCAAAAGAGCTGAACG
48585691 GAAAC
1 GAAAC
48585696 TGAATAGGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 1 0.03
41 2 0.05
42 37 0.93
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.18
Consensus pattern (41 bp):
GAAACCCATAAGGGTTAAGCAAAGCTCAAAAGAGCTGAACG
Found at i:48587552 original size:5 final size:5
Alignment explanation
Indices: 48587540--48587577 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
48587530 AAAAGTTAAG
48587540 TATA- TATAT TATA- TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
48587578 AATAAAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.25
5 24 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:48588577 original size:22 final size:23
Alignment explanation
Indices: 48588551--48588612 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
48588541 TTCTGATTAC
*
48588551 TAGCACGTTAGTGCTCTCCAT-T-
1 TAGCACATTAGTGCTCTCC-TGTA
*
48588573 TAGCACATTTGTGCTC-CCTGTA
1 TAGCACATTAGTGCTCTCCTGTA
*
48588595 TAGCACTTTAGTGCTCTC
1 TAGCACATTAGTGCTCTC
48588613 TATTCATTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 3 0.09
22 28 0.85
23 1 0.03
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (23 bp):
TAGCACATTAGTGCTCTCCTGTA
Found at i:48589647 original size:30 final size:30
Alignment explanation
Indices: 48589613--48589672 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
48589603 TGAAGATTAT
48589613 TTGGGATACGTAATGTCGTTATTAAGGAAG
1 TTGGGATACGTAATGTCGTTATTAAGGAAG
48589643 TTGGGATACGTAATGTCGTTATTAAGGAAG
1 TTGGGATACGTAATGTCGTTATTAAGGAAG
48589673 AAGTTATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (30 bp):
TTGGGATACGTAATGTCGTTATTAAGGAAG
Found at i:48593043 original size:22 final size:23
Alignment explanation
Indices: 48592990--48593045 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
48592980 CTAGCAAGTC
* *
48592990 AGTGCTCTCCGTTTAGCACATTT
1 AGTGCTCTCTGTATAGCACATTT
48593013 -GTGCTCTCTGTATAGCAC-TTT
1 AGTGCTCTCTGTATAGCACATTT
48593034 AGTGCTCTCTGT
1 AGTGCTCTCTGT
48593046 TATTAGTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (23 bp):
AGTGCTCTCTGTATAGCACATTT
Found at i:48599474 original size:51 final size:49
Alignment explanation
Indices: 48599398--48599535 Score: 159
Period size: 50 Copynumber: 2.8 Consensus size: 49
48599388 TATAAACACG
* * * *
48599398 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAG-T-ATGATCACA
* * * * *
48599449 TGTGTAGTACTATGTGTAGGCTACTACGTGAACCGGAAAGTTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GAAAGTATGATCACA
*
48599499 TGTGTAGTACTATGTGAAGGCTAGTACGTGTATCGAA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAA
48599536 TGACAATAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
49 3 0.04
50 36 0.49
51 31 0.42
52 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAGTATGATCACA
Found at i:48602302 original size:21 final size:21
Alignment explanation
Indices: 48602278--48602358 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
48602268 AACAGAAACC
*
48602278 CATAAGGGTTGAACGAAAGCT
1 CATAAGAGTTGAACGAAAGCT
* *
48602299 CATAAGAGCTGAGCGGAAA-CT
1 CATAAGAGTTGAAC-GAAAGCT
* * *
48602320 CATAAGGGTT-AAGGTGAAGCT
1 CATAAGAGTTGAACG-AAAGCT
*
48602341 CAAAAGAGTTGAACGAAA
1 CATAAGAGTTGAACGAAA
48602359 CCCTAATAGG
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 33 0.75
22 7 0.16
ACGTcount: A:0.41, C:0.14, G:0.28, T:0.17
Consensus pattern (21 bp):
CATAAGAGTTGAACGAAAGCT
Found at i:48609181 original size:36 final size:36
Alignment explanation
Indices: 48609134--48609215 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 36
48609124 TAAATAGCTA
* * * *
48609134 GCTGATATAATATCGTAGTTGATATCGTTAAGGTTT
1 GCTGATTTAATATCATAGTTGATATCATTAAAGTTT
48609170 GCTGATTTAATATCATAGTTGATATCATTAAAGTTT
1 GCTGATTTAATATCATAGTTGATATCATTAAAGTTT
*
48609206 GTTGATTTAA
1 GCTGATTTAA
48609216 GATTACAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.44
Consensus pattern (36 bp):
GCTGATTTAATATCATAGTTGATATCATTAAAGTTT
Found at i:48609381 original size:95 final size:95
Alignment explanation
Indices: 48609271--48609473 Score: 307
Period size: 95 Copynumber: 2.1 Consensus size: 95
48609261 TCTGAGTTAG
*
48609271 TTGATTTAATATCGCTACTCTAAACAACTCGCTGATTTAATATCGCAGCTAATATCGTTAAGATT
1 TTGATTTAATATCGCTACTCTAAACAACTCGCTGATTTAAGATCGCAGCTAATATCGTTAAGATT
*
48609336 CGCTGATTTAAGATCACAACGTAAGTTCAT
66 CGCTGATTTAAGATCACAACCTAAGTTCAT
* * * * * *
48609366 TTGATTTAATATCGCTATTCTAAACAACTTGTTGATTTAAGATCGCAGCTGATATTGTTAAGGTT
1 TTGATTTAATATCGCTACTCTAAACAACTCGCTGATTTAAGATCGCAGCTAATATCGTTAAGATT
**
48609431 CGCTGATTTAAGATTGCAACCTAAGTTCAT
66 CGCTGATTTAAGATCACAACCTAAGTTCAT
*
48609461 TCGATTTAATATC
1 TTGATTTAATATC
48609474 ATGAACAATC
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (95 bp):
TTGATTTAATATCGCTACTCTAAACAACTCGCTGATTTAAGATCGCAGCTAATATCGTTAAGATT
CGCTGATTTAAGATCACAACCTAAGTTCAT
Found at i:48609505 original size:64 final size:63
Alignment explanation
Indices: 48609436--48609897 Score: 197
Period size: 64 Copynumber: 7.1 Consensus size: 63
48609426 AGGTTCGCTG
*
48609436 ATTTAAGATTGCAACCTAAGTTCATTCGATTTAATATCATGAACAATCTTATCTAAGTTAGCTA
1 ATTTAAGATCGCAACCTAAGTTCATT-GATTTAATATCATGAACAATCTTATCTAAGTTAGCTA
* * * * *** * * * *
48609500 ATTTAATATCGCTACTCTAAACATTTCGTTGATTTAATATCATTG-TTGATATTGT-TAGGGTTT
1 ATTTAAGATCGCAAC-CT--A-AGTTCATTGATTTAATATCA-TGAACAATCTTATCTA-AGTTA
* *
48609563 GTTG
60 GCTA
*
48609567 ATTTAAGATCGCAACATAAGTTCATTTGATTTAATATCATGAACAATCTTATCTAAGTTAGCTA
1 ATTTAAGATCGCAACCTAAGTTCA-TTGATTTAATATCATGAACAATCTTATCTAAGTTAGCTA
* * * * * * *** * * * *
48609631 ATTTTATATCACTACTCTAAACATTTCGTTGATTTAATATCATTG-TTGATATTGT-TAGGGTTT
1 ATTTAAGATCGCAAC-CT--A-AGTTCATTGATTTAATATCA-TGAACAATCTTATCTA-AGTTA
* *
48609694 GTTG
60 GCTA
* * * * *
48609698 ATTTAAGATCGCAACATAAGTTCATTTGATTTAATATTATGAACAATTTTATCTGAGTTAGCTG
1 ATTTAAGATCGCAACCTAAGTTCA-TTGATTTAATATCATGAACAATCTTATCTAAGTTAGCTA
* * * * * *
48609762 ATTTAATATCGCTACTCTAAACGACTCACTAATTTAAGATC--G--CAA-CTGATATCGTTAAGG
1 ATTTAAGATCGCAAC-CT-AA-G-TTCATTGATTTAATATCATGAACAATCT--TATC--TAA-G
*
48609822 TTCA-CTG
57 TT-AGCTA
* * * * *
48609829 ATTTAAGATTGCAACCTAAGTTCATTCAATTTAATATCATGAACAATCTTATTTGAGTTAGCTT
1 ATTTAAGATCGCAACCTAAGTTCATT-GATTTAATATCATGAACAATCTTATCTAAGTTAGCTA
48609893 ATTTA
1 ATTTA
48609898 GTATCACTAT
Statistics
Matches: 283, Mismatches: 80, Indels: 70
0.65 0.18 0.16
Matches are distributed among these distances:
62 1 0.00
63 20 0.07
64 111 0.39
65 12 0.04
66 13 0.05
67 103 0.36
68 21 0.07
69 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (63 bp):
ATTTAAGATCGCAACCTAAGTTCATTGATTTAATATCATGAACAATCTTATCTAAGTTAGCTA
Found at i:48609507 original size:131 final size:130
Alignment explanation
Indices: 48609369--48610008 Score: 742
Period size: 131 Copynumber: 4.9 Consensus size: 130
48609359 AGTTCATTTG
* * *
48609369 ATTTAATATCGCTATTCTAAACAACTTGTTGATTTAAGATCGCAGCTGATATTGTTAAGGTTCGC
1 ATTTAATATCGCTACTCTAAAC-ACTTGTTGATTTAATATCGCAGTTGATATTGTTAAGGTTCGC
48609434 TGATTTAAGATTGCAACCTAAGTTCATTCGATTTAATATCATGAACAATCTTATCTAAGTTAGCT
65 TGATTTAAGATTGCAACCTAAGTTCATTCGATTTAATATCATGAACAATCTTATCTAAGTTAGCT
48609499 A
130 A
* *** * * *
48609500 ATTTAATATCGCTACTCTAAACATTTCGTTGATTTAATATCATTGTTGATATTGTTAGGGTTTGT
1 ATTTAATATCGCTACTCTAAACACTT-GTTGATTTAATATCGCAGTTGATATTGTTAAGGTTCGC
* * *
48609565 TGATTTAAGATCGCAACATAAGTTCATTTGATTTAATATCATGAACAATCTTATCTAAGTTAGCT
65 TGATTTAAGATTGCAACCTAAGTTCATTCGATTTAATATCATGAACAATCTTATCTAAGTTAGCT
48609630 A
130 A
* * * *** * * *
48609631 ATTTTATATCACTACTCTAAACATTTCGTTGATTTAATATCATTGTTGATATTGTTAGGGTTTGT
1 ATTTAATATCGCTACTCTAAACACTT-GTTGATTTAATATCGCAGTTGATATTGTTAAGGTTCGC
* * * * * *
48609696 TGATTTAAGATCGCAACATAAGTTCATTTGATTTAATATTATGAACAATTTTATCTGAGTTAGCT
65 TGATTTAAGATTGCAACCTAAGTTCATTCGATTTAATATCATGAACAATCTTATCTAAGTTAGCT
*
48609761 G
130 A
*** * * ** * *
48609762 ATTTAATATCGCTACTCTAAACGACTCACTAATTTAAGATCGCAACTGATATCGTTAAGGTTCAC
1 ATTTAATATCGCTACTCTAAAC-ACTTGTTGATTTAATATCGCAGTTGATATTGTTAAGGTTCGC
* * *
48609827 TGATTTAAGATTGCAACCTAAGTTCATTCAATTTAATATCATGAACAATCTTATTTGAGTTAGCT
65 TGATTTAAGATTGCAACCTAAGTTCATTCGATTTAATATCATGAACAATCTTATCTAAGTTAGCT
*
48609892 T
130 A
* * * * * * * *
48609893 ATTTAGTATCACTATTCTAACCAACTTGCTAATTTAATATTGCAGTTGATATCGTTAAGGTTCGC
1 ATTTAATATCGCTACTCTAAAC-ACTTGTTGATTTAATATCGCAGTTGATATTGTTAAGGTTCGC
* * *
48609958 T-ATTTTAAGATTACAACCTAATTTCATTCCATTTAATATCATGAACAATCT
65 TGA-TTTAAGATTGCAACCTAAGTTCATTCGATTTAATATCATGAACAATCT
48610009 CATTTGTGTT
Statistics
Matches: 446, Mismatches: 60, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
130 4 0.01
131 440 0.99
132 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (130 bp):
ATTTAATATCGCTACTCTAAACACTTGTTGATTTAATATCGCAGTTGATATTGTTAAGGTTCGCT
GATTTAAGATTGCAACCTAAGTTCATTCGATTTAATATCATGAACAATCTTATCTAAGTTAGCTA
Found at i:48609578 original size:67 final size:67
Alignment explanation
Indices: 48609500--48609709 Score: 198
Period size: 67 Copynumber: 3.2 Consensus size: 67
48609490 AAGTTAGCTA
*
48609500 ATTTAATATCGCTACTCTAAACATTTCGTTGATTTAATATCATTGTTGATATTGTTAGGGTTTGT
1 ATTTAAGATCGCTACTCTAAACATTTCGTTGATTTAATATCATTGTTGATATTGTTAGGGTTTGT
48609565 TG
66 TG
* * * * *** * * *
48609567 ATTTAAGATCGC-A-AC-ATA-AGTTCATTTGATTTAATATCA-TGAACAATCTTATCTA-AGTT
1 ATTTAAGATCGCTACTCTAAACATTTC-GTTGATTTAATATCATTG-TTGATATTGT-TAGGGTT
* * *
48609626 AGCTA
63 TGTTG
* * *
48609631 ATTTTATATCACTACTCTAAACATTTCGTTGATTTAATATCATTGTTGATATTGTTAGGGTTTGT
1 ATTTAAGATCGCTACTCTAAACATTTCGTTGATTTAATATCATTGTTGATATTGTTAGGGTTTGT
48609696 TG
66 TG
48609698 ATTTAAGATCGC
1 ATTTAAGATCGC
48609710 AACATAAGTT
Statistics
Matches: 101, Mismatches: 33, Indels: 18
0.66 0.22 0.12
Matches are distributed among these distances:
63 6 0.06
64 35 0.35
65 4 0.04
66 4 0.04
67 46 0.46
68 6 0.06
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (67 bp):
ATTTAAGATCGCTACTCTAAACATTTCGTTGATTTAATATCATTGTTGATATTGTTAGGGTTTGT
TG
Found at i:48609667 original size:226 final size:223
Alignment explanation
Indices: 48609199--48609604 Score: 515
Period size: 226 Copynumber: 1.8 Consensus size: 223
48609189 TGATATCATT
*
48609199 AAAGTTTGTTGATTTAAGATTACAACCTAAGTTCATTCAATCTAATATCATGAACAATCTTATCT
1 AAAGTTCGTTGATTTAAGATTACAACCTAAGTTCATTCAATCTAATATCATGAACAATCTTATCT
* * * *
48609264 GAGTTAGTTGATTTAATATCGCTACTCTAAACAACTCGCTGATTTAATATCGCAGCTAATATCGT
66 AAGTTAGCTAATTTAATATCGCTACTCTAAACAACTCGCTGATTTAATATCACAGCTAATATCGT
* *
48609329 TAAGATTCGCTGATTTAAGATCACAACGTAAGTTCATTTGATTTAATATCGCTATTCTAAACAAC
131 TAAGATTCGCTGATTTAAGATCACAACATAAGTTCATTTGATTTAATATCGCTAATCTAAACAAC
* * * * *
48609394 TTGTTGATTTAAGATCGCAGCTGATATTGTT
196 TTGCTAATTTAAGATC-CAGC--ATACTCTA
* * * * *
48609425 AAGGTTCGCTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAATATCATGAACAATCTTATCT
1 AAAGTTCGTTGATTTAAGATTACAACCTAAGTTCATTCAATCTAATATCATGAACAATCTTATCT
** * ** * * *
48609490 AAGTTAGCTAATTTAATATCGCTACTCTAAACATTTCGTTGATTTAATATCATTGTTGATATTGT
66 AAGTTAGCTAATTTAATATCGCTACTCTAAACAACTCGCTGATTTAATATCACAGCTAATATCGT
* * * * *
48609555 TAGGGTTTGTTGATTTAAGATCGCAACATAAGTTCATTTGATTTAATATC
131 TAAGATTCGCTGATTTAAGATCACAACATAAGTTCATTTGATTTAATATC
48609605 ATGAACAATC
Statistics
Matches: 156, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
226 156 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (223 bp):
AAAGTTCGTTGATTTAAGATTACAACCTAAGTTCATTCAATCTAATATCATGAACAATCTTATCT
AAGTTAGCTAATTTAATATCGCTACTCTAAACAACTCGCTGATTTAATATCACAGCTAATATCGT
TAAGATTCGCTGATTTAAGATCACAACATAAGTTCATTTGATTTAATATCGCTAATCTAAACAAC
TTGCTAATTTAAGATCCAGCATACTCTA
Found at i:48624049 original size:26 final size:26
Alignment explanation
Indices: 48623995--48624049 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
48623985 ATAATTATTA
* *
48623995 TAAATTAATTAAAAATTATAAAATTT
1 TAAATTAATTAAAAACTATAAAATAT
*
48624021 TAAATTTATTAAAAACTATAACAA-AT
1 TAAATTAATTAAAAACTATAA-AATAT
48624047 TAA
1 TAA
48624050 TAATGTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
TAAATTAATTAAAAACTATAAAATAT
Found at i:48624636 original size:18 final size:17
Alignment explanation
Indices: 48624610--48624649 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
48624600 TTTAAAATAA
*
48624610 TTTTAAAATATTCTTTAT
1 TTTTTAAAT-TTCTTTAT
*
48624628 TTTTTAAATTTTTTTAT
1 TTTTTAAATTTCTTTAT
48624645 TTTTT
1 TTTTT
48624650 CTAATGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTAAATTTCTTTAT
Found at i:48626287 original size:8 final size:7
Alignment explanation
Indices: 48626265--48626299 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
48626255 CCTTTTGTAT
48626265 GGTTTAG
1 GGTTTAG
48626272 GGTTTAG
1 GGTTTAG
48626279 GGTTTTAG
1 GG-TTTAG
48626287 GGTTTAG
1 GGTTTAG
48626294 GGTTTA
1 GGTTTA
48626300 TGTCTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.14, C:0.00, G:0.40, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:48626287 original size:15 final size:15
Alignment explanation
Indices: 48626267--48626298 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
48626257 TTTTGTATGG
48626267 TTTAGGGTTTAGGGT
1 TTTAGGGTTTAGGGT
48626282 TTTAGGGTTTAGGGT
1 TTTAGGGTTTAGGGT
48626297 TT
1 TT
48626299 ATGTCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (15 bp):
TTTAGGGTTTAGGGT
Found at i:48626835 original size:202 final size:202
Alignment explanation
Indices: 48626489--48626902 Score: 702
Period size: 202 Copynumber: 2.0 Consensus size: 202
48626479 GCATTTGATT
* *
48626489 TAAATACTAATAAGAATTATAATGTCATCTACAAATCCAATTGGGGAGATGACTAGTCTTGGCTA
1 TAAATACTGATAAGAATTATAATGTCATCTACAAACCCAATTGGGGAGATGACTAGTCTTGGCTA
* * *
48626554 TCGGAGCAGTTGTTTCCACGAGTAGAGACATAGATGTATTCATTTGTAGAATGATACATTGGACT
66 CCAGAGCAGTTGTTTCCACGAGTAGAGACATAGATGTATTCATTGGTAGAATGATACATTGGACT
*
48626619 GGACTCACGATGAATTAATTCTGAATCCGTTTGTGAATTAATTCACTTGTGATGTTCATGGTATG
131 GGACTCACGATGAATTAATTCTGAATCCATTTGTGAATTAATTCACTTGTGATGTTCATGGTATG
48626684 ATTTATC
196 ATTTATC
* * * *
48626691 TAAATACTGATAAGAATTATTATGTCGTTTACAAACCCAATTGGGGAGATGGCTAGTCTTGGCTA
1 TAAATACTGATAAGAATTATAATGTCATCTACAAACCCAATTGGGGAGATGACTAGTCTTGGCTA
* *
48626756 CCAGAGCAGTTGTTTCCTCGAGTAGAGACATAGATGTATTCATTGGTAGAATGATACATTGGATT
66 CCAGAGCAGTTGTTTCCACGAGTAGAGACATAGATGTATTCATTGGTAGAATGATACATTGGACT
*
48626821 GGACTCACGATGAATTAATTCTGAATCCATTTGTGAATTAATTCACTTGTGATGTTCATGGTGTG
131 GGACTCACGATGAATTAATTCTGAATCCATTTGTGAATTAATTCACTTGTGATGTTCATGGTATG
48626886 ATTTATC
196 ATTTATC
*
48626893 TAAATCCTGA
1 TAAATACTGA
48626903 GTTCATCACT
Statistics
Matches: 198, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
202 198 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (202 bp):
TAAATACTGATAAGAATTATAATGTCATCTACAAACCCAATTGGGGAGATGACTAGTCTTGGCTA
CCAGAGCAGTTGTTTCCACGAGTAGAGACATAGATGTATTCATTGGTAGAATGATACATTGGACT
GGACTCACGATGAATTAATTCTGAATCCATTTGTGAATTAATTCACTTGTGATGTTCATGGTATG
ATTTATC
Found at i:48628180 original size:37 final size:35
Alignment explanation
Indices: 48628129--48628199 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
48628119 ATTCCAAAAA
*
48628129 TAATATTATTTTAATAGT-TTAATATTAAATTTAATT
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATT
*
48628165 TAATACTTATCTTAATAGTATTTTATTAATTTAAT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAAT
48628200 ATTGAGGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.42
37 16 0.52
38 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (35 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATT
Found at i:48629658 original size:13 final size:13
Alignment explanation
Indices: 48629596--48629658 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
48629586 TCTTCATTGT
*
48629596 TTTTGAGAAGTGC
1 TTTTGAAAAGTGC
* *
48629609 TGTGGAAAAGTGC
1 TTTTGAAAAGTGC
48629622 TTTTGAGAAA-TGC
1 TTTTGA-AAAGTGC
* *
48629635 TTTTGAGAAGTGT
1 TTTTGAAAAGTGC
48629648 TTTTGAAAAGT
1 TTTTGAAAAGT
48629659 TTGATTTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 2 0.05
13 35 0.88
14 3 0.08
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:48634673 original size:6 final size:6
Alignment explanation
Indices: 48634664--48634695 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
48634654 TTGGTGGATA
48634664 GTGCTG GTGCTG GTGCTG GTGCTG GTG-TG GTG
1 GTGCTG GTGCTG GTGCTG GTGCTG GTGCTG GTG
48634696 GGGAATGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.12, G:0.53, T:0.34
Consensus pattern (6 bp):
GTGCTG
Found at i:48634813 original size:16 final size:16
Alignment explanation
Indices: 48634784--48634818 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
48634774 TTGTAGGAGG
*
48634784 GAGGGAGAGCGAGAGA
1 GAGGGAGAGAGAGAGA
*
48634800 GAGGGGGAGAGAGAGA
1 GAGGGAGAGAGAGAGA
48634816 GAG
1 GAG
48634819 AAACAAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.60, T:0.00
Consensus pattern (16 bp):
GAGGGAGAGAGAGAGA
Found at i:48640167 original size:17 final size:17
Alignment explanation
Indices: 48640129--48640170 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
48640119 TTTTAATATT
*
48640129 TTTTTAGTTCAAAACATA
1 TTTTTA-TTCAAAACAAA
*
48640147 -TTTTATTGAAAACAAA
1 TTTTTATTCAAAACAAA
48640163 TTTTTATT
1 TTTTTATT
48640171 ACTTTCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTTTATTCAAAACAAA
Found at i:48653306 original size:51 final size:51
Alignment explanation
Indices: 48653192--48653451 Score: 340
Period size: 51 Copynumber: 5.3 Consensus size: 51
48653182 CTTACGTATG
* * * *
48653192 ATCACTTATCACTTGTCCCTAATCAGATAAATGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
**
48653242 ATCACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
48653293 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCAC-T
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
48653343 -T-AC----CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * * *
48653388 ATCACTTGCCACTAT-TCACTGATCAGATAAGTGTATCTGAAGCTACTACTT
1 ATCACTTGTCACT-TGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
48653439 ATCACTTGTCACT
1 ATCACTTGTCACT
48653452 GATCAGAAGT
Statistics
Matches: 187, Mismatches: 14, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
44 38 0.20
45 1 0.01
46 1 0.01
47 2 0.01
48 2 0.01
49 1 0.01
50 35 0.19
51 106 0.57
52 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:48653370 original size:95 final size:95
Alignment explanation
Indices: 48653244--48653458 Score: 369
Period size: 95 Copynumber: 2.3 Consensus size: 95
48653234 TACCACTTAT
*
48653244 CACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACT-TG
1 CACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTAT-
48653308 TCACTGATCAGATAAGTGTAGCTGAAGCTAC
65 TCACTGATCAGATAAGTGTAGCTGAAGCTAC
*
48653339 CACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTGCCACTATT
1 CACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTATT
*
48653404 CACTGATCAGATAAGTGTATCTGAAGCTAC
66 CACTGATCAGATAAGTGTAGCTGAAGCTAC
* *
48653434 TACTTATCACTTGTCACTGATCAGA
1 CACTTACCACTTGTCACTGATCAGA
48653459 AGTACTCAAA
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 113 0.99
96 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (95 bp):
CACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTATT
CACTGATCAGATAAGTGTAGCTGAAGCTAC
Found at i:48653387 original size:37 final size:39
Alignment explanation
Indices: 48653301--48653393 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 39
48653291 TTATCACTTG
*
48653301 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCAC
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCT--CAC
48653342 TTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCT-A-
1 -T--CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTCAC
*
48653382 TCACTTATCACT
1 TCACTTGTCACT
48653394 TGCCACTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
37 10 0.21
39 1 0.02
41 1 0.02
42 1 0.02
44 34 0.72
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (39 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTCAC
Found at i:48654439 original size:44 final size:44
Alignment explanation
Indices: 48654389--48654478 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
48654379 AGTGAAAAAT
48654389 GTTAATTTCCATTTTGCCCCAAATTTCACAGCTTATACAATTCA
1 GTTAATTTCCATTTTGCCCCAAATTTCACAGCTTATACAATTCA
*
48654433 GTTAATTTCCATTTTGCCCCAAATTTCACAGTTTATACAATTCA
1 GTTAATTTCCATTTTGCCCCAAATTTCACAGCTTATACAATTCA
48654477 GT
1 GT
48654479 CATTTCTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (44 bp):
GTTAATTTCCATTTTGCCCCAAATTTCACAGCTTATACAATTCA
Found at i:48656875 original size:19 final size:19
Alignment explanation
Indices: 48656851--48656890 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
48656841 AAGGAATGGT
48656851 GCCTGAACTAAAGAAAGTA
1 GCCTGAACTAAAGAAAGTA
*
48656870 GCCTGAACTAATGAAAGTA
1 GCCTGAACTAAAGAAAGTA
48656889 GC
1 GC
48656891 AAACGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (19 bp):
GCCTGAACTAAAGAAAGTA
Found at i:48667421 original size:2 final size:2
Alignment explanation
Indices: 48667414--48667440 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48667404 ACAATGACAT
48667414 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
48667441 TTATTTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48670324 original size:11 final size:12
Alignment explanation
Indices: 48670307--48670339 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
48670297 ATCATTAATA
48670307 AATAAACGAGTC
1 AATAAACGAGTC
*
48670319 -ATAAACAAGTC
1 AATAAACGAGTC
48670330 AATAAACGAG
1 AATAAACGAG
48670340 CTTGTTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:48675242 original size:41 final size:41
Alignment explanation
Indices: 48675148--48675277 Score: 163
Period size: 41 Copynumber: 3.2 Consensus size: 41
48675138 GCTAACCGAA
* * * * *
48675148 AAACACCGCAAAAGGTAAAGCATTAACGGCGTTTTT-GCAT
1 AAACGCCGTAAAAGGTAAAGCAATAGCGGCGTTTTTCCCAT
* * *
48675188 AAACACCGTAAAAGGTAAAGCAATAGCGGTGTTTTTCTCAT
1 AAACGCCGTAAAAGGTAAAGCAATAGCGGCGTTTTTCCCAT
* *
48675229 AAACGTCGTAAAAGGTAAAACAATAGCGGCGTTTTTCCCAT
1 AAACGCCGTAAAAGGTAAAGCAATAGCGGCGTTTTTCCCAT
48675270 AAACGCCG
1 AAACGCCG
48675278 CAAATATTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 32 0.41
41 46 0.59
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (41 bp):
AAACGCCGTAAAAGGTAAAGCAATAGCGGCGTTTTTCCCAT
Found at i:48675509 original size:23 final size:24
Alignment explanation
Indices: 48675479--48675530 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
48675469 ATCTTTCAAA
*
48675479 TCTTCGCTCAAATTTAT-TTGTTC
1 TCTTCGCTCAAATTTATCTCGTTC
*
48675502 TCTTCGCTCAAATTTCTCTCGTTC
1 TCTTCGCTCAAATTTATCTCGTTC
48675526 TCTTC
1 TCTTC
48675531 ATTCAAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.13, C:0.29, G:0.08, T:0.50
Consensus pattern (24 bp):
TCTTCGCTCAAATTTATCTCGTTC
Found at i:48676970 original size:16 final size:16
Alignment explanation
Indices: 48676949--48676980 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48676939 AGACTGCTTG
48676949 TCATGTGATTTTAATA
1 TCATGTGATTTTAATA
48676965 TCATGTGATTTTAATA
1 TCATGTGATTTTAATA
48676981 CCTTGTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TCATGTGATTTTAATA
Found at i:48678646 original size:32 final size:32
Alignment explanation
Indices: 48678604--48678683 Score: 108
Period size: 35 Copynumber: 2.4 Consensus size: 32
48678594 ATTAAAGGGT
*
48678604 TAAA-ATTTAAAGATGATAATTATAACTTACA
1 TAAACATTTAAAGATGATAATCATAACTTACA
*
48678635 TAAACATTTAAAGTTTATGATTATCATAACTTACA
1 TAAACATTTAAAG---ATGATAATCATAACTTACA
48678670 TAAACATTTAAAGA
1 TAAACATTTAAAGA
48678684 ATAAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 4 0.09
32 9 0.21
35 30 0.70
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (32 bp):
TAAACATTTAAAGATGATAATCATAACTTACA
Found at i:48678664 original size:35 final size:35
Alignment explanation
Indices: 48678616--48678682 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
48678606 AAATTTAAAG
*
48678616 ATGATAATTATAACTTACATAAACATTTAAAGTTT
1 ATGATAATCATAACTTACATAAACATTTAAAGTTT
*
48678651 ATGATTATCATAACTTACATAAACATTTAAAG
1 ATGATAATCATAACTTACATAAACATTTAAAG
48678683 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.37
Consensus pattern (35 bp):
ATGATAATCATAACTTACATAAACATTTAAAGTTT
Found at i:48678797 original size:43 final size:44
Alignment explanation
Indices: 48678703--48678813 Score: 113
Period size: 43 Copynumber: 2.5 Consensus size: 44
48678693 AAAACTTTGG
* *
48678703 ATCATAACTTACATAATACATAAATATATATCATATCACAACTT
1 ATCATAACTTACATAATACATAAATATATATAATATCACAACAT
* * *
48678747 A-CGTAACTTACATAACTTACAT-AATATATA-AATAT-ATATCAT
1 ATCATAACTTACATAA--TACATAAATATATATAATATCACAACAT
*
48678789 ATCATAACTTACATAAATATATAAA
1 ATCATAACTTACAT-AATACATAAA
48678814 AATCACAGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
42 9 0.16
43 30 0.55
44 11 0.20
45 5 0.09
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (44 bp):
ATCATAACTTACATAATACATAAATATATATAATATCACAACAT
Found at i:48703726 original size:31 final size:31
Alignment explanation
Indices: 48703688--48703749 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
48703678 ATACATTTAG
48703688 GTTTAACTGTTAGCAT-TAATTGTTTTGTTAA
1 GTTTAACTGTTAGCATGT-ATTGTTTTGTTAA
*
48703719 GTTTAACTGTTAGTATGTATTGTTTTGTTAA
1 GTTTAACTGTTAGCATGTATTGTTTTGTTAA
48703750 ATTTGTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.24, C:0.05, G:0.18, T:0.53
Consensus pattern (31 bp):
GTTTAACTGTTAGCATGTATTGTTTTGTTAA
Found at i:48708892 original size:26 final size:26
Alignment explanation
Indices: 48708833--48708893 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
48708823 ATGTATATAA
*
48708833 AAAATATTTAAAAATATTAAATGAATT
1 AAAATATTAAAAAATATTAAAT-AATT
*
48708860 -AAA-ATTAAATAAATTTTAAAT-ATT
1 AAAATATTAAA-AAATATTAAATAATT
48708884 AAAATATTAA
1 AAAATATTAA
48708894 TTAATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
24 3 0.10
25 8 0.28
26 18 0.62
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAATATTAAAAAATATTAAATAATT
Found at i:48710435 original size:11 final size:11
Alignment explanation
Indices: 48710419--48710452 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
48710409 TTGACCATTC
48710419 AAACATG-CACA
1 AAACATGTC-CA
48710430 AAACATGTCCA
1 AAACATGTCCA
48710441 AAACATGTCCA
1 AAACATGTCCA
48710452 A
1 A
48710453 CTATTCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 21 0.95
12 1 0.05
ACGTcount: A:0.50, C:0.26, G:0.09, T:0.15
Consensus pattern (11 bp):
AAACATGTCCA
Found at i:48716664 original size:41 final size:41
Alignment explanation
Indices: 48716607--48716688 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
48716597 AAATATTTTG
*
48716607 CTAGCATGGGTTTGTATTAGAAATGGTTAATTTGCATGATT
1 CTAGCATGGGTTTGTATTAAAAATGGTTAATTTGCATGATT
48716648 CTAGCATGGGTTTGTATTAAAAATGGTTAATTTGCATGATT
1 CTAGCATGGGTTTGTATTAAAAATGGTTAATTTGCATGATT
48716689 TGGACTCAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.41
Consensus pattern (41 bp):
CTAGCATGGGTTTGTATTAAAAATGGTTAATTTGCATGATT
Found at i:48719063 original size:33 final size:33
Alignment explanation
Indices: 48719026--48719127 Score: 134
Period size: 33 Copynumber: 3.1 Consensus size: 33
48719016 ATCCCTCCAA
* *
48719026 CACACCAATGTTCATAAGAGCTAATCCAACCAT
1 CACACCAATGCTCATAAGAGCTAAACCAACCAT
*
48719059 CACACCAATGCTCAT-AGAGCTAAACAAACCAT
1 CACACCAATGCTCATAAGAGCTAAACCAACCAT
* * * *
48719091 CACACTAATGCTCATAAAAGTTAAAACAACCAT
1 CACACCAATGCTCATAAGAGCTAAACCAACCAT
48719124 CACA
1 CACA
48719128 ACAAACAGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 29 0.48
33 31 0.52
ACGTcount: A:0.44, C:0.29, G:0.08, T:0.19
Consensus pattern (33 bp):
CACACCAATGCTCATAAGAGCTAAACCAACCAT
Found at i:48719089 original size:32 final size:32
Alignment explanation
Indices: 48719026--48719106 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
48719016 ATCCCTCCAA
* * *
48719026 CACACCAATGTTCATAAGAGCTAATCCAACCAT
1 CACACCAATGCTCAT-AGAGCTAAACAAACCAT
48719059 CACACCAATGCTCATAGAGCTAAACAAACCAT
1 CACACCAATGCTCATAGAGCTAAACAAACCAT
*
48719091 CACACTAATGCTCATA
1 CACACCAATGCTCATA
48719107 AAAGTTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 30 0.68
33 14 0.32
ACGTcount: A:0.41, C:0.31, G:0.09, T:0.20
Consensus pattern (32 bp):
CACACCAATGCTCATAGAGCTAAACAAACCAT
Found at i:48724974 original size:5 final size:5
Alignment explanation
Indices: 48724966--48725031 Score: 57
Period size: 5 Copynumber: 13.2 Consensus size: 5
48724956 TATTTAATTT
* *
48724966 ATATA ATATA ATACA ATATA ATATA TTATATT ATATA ATA-A A-ATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA
*
48725015 ATATA TATATA ACATA A
1 ATATA -ATATA ATATA A
48725032 AAATCTAAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.16
5 32 0.64
6 5 0.10
7 4 0.08
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:48728952 original size:15 final size:15
Alignment explanation
Indices: 48728932--48728962 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
48728922 AATTATTTTC
*
48728932 ATTATTATTGTTATT
1 ATTATTAATGTTATT
48728947 ATTATTAATGTTATT
1 ATTATTAATGTTATT
48728962 A
1 A
48728963 GAACTATTAG
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:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTATTAATGTTATT
Found at i:48729333 original size:11 final size:11
Alignment explanation
Indices: 48729319--48729376 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 11
48729309 TCTTTAACCG
48729319 TATTTTAAATT
1 TATTTTAAATT
*
48729330 TATTTCAAATTT
1 TATTTTAAA-TT
48729342 TCATTTATATATTATT
1 T-ATTT-TA-A--ATT
48729358 TATTTTAAATT
1 TATTTTAAATT
48729369 TATTTTAA
1 TATTTTAA
48729377 TATATAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
11 19 0.49
12 3 0.08
13 5 0.13
14 3 0.08
15 5 0.13
16 3 0.08
17 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTAAATT
Found at i:48729379 original size:28 final size:27
Alignment explanation
Indices: 48729326--48729391 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
48729316 CCGTATTTTA
*
48729326 AATTTATTTCAAATTTTCATTTATATAT
1 AATTTATTTTAAATTTT-ATTTATATAT
*
48729354 TATTTATTTTAAA-TTTATTTTAATATAT
1 AATTTATTTTAAATTTTA-TTT-ATATAT
*
48729382 AATTTCTTTT
1 AATTTATTTT
48729392 CTTTCGTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 6 0.19
28 25 0.78
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (27 bp):
AATTTATTTTAAATTTTATTTATATAT
Found at i:48737721 original size:11 final size:11
Alignment explanation
Indices: 48737698--48737742 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
48737688 AACAAATCCT
48737698 CTCTCATATTTC
1 CTCTCA-ATTTC
48737710 CTCTCAATTTC
1 CTCTCAATTTC
*
48737721 CTCTCAATTTT
1 CTCTCAATTTC
48737732 CTCTCAATTTC
1 CTCTCAATTTC
48737743 TTTCCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:48737781 original size:51 final size:51
Alignment explanation
Indices: 48737724--48737844 Score: 181
Period size: 51 Copynumber: 2.4 Consensus size: 51
48737714 CAATTTCCTC
* * * *
48737724 TCAATTTTCTCTCAATTTCTTTCCAAAATTCTCAT-AAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCATTCCAAAAATCTC-TCAAACCCATATTTAATT
48737775 TCAATTTCCTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATT
*
48737826 TCAATTTGCTCTCAATTTC
1 TCAATTTCCTCTCAATTTC
48737845 CTTTTTTAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 1 0.02
51 63 0.98
ACGTcount: A:0.31, C:0.25, G:0.01, T:0.44
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATT
Found at i:48738975 original size:7 final size:7
Alignment explanation
Indices: 48738959--48738990 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
48738949 TGCAAATAGA
*
48738959 TATTTTG
1 TATTTAG
48738966 TATTTAG
1 TATTTAG
48738973 TATTTAG
1 TATTTAG
48738980 TATTTAG
1 TATTTAG
48738987 TATT
1 TATT
48738991 ATGTATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TATTTAG
Found at i:48738996 original size:14 final size:13
Alignment explanation
Indices: 48738962--48738996 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
48738952 AAATAGATAT
48738962 TTTGTATTTAGTA
1 TTTGTATTTAGTA
48738975 TTTAGTATTTAGTA
1 TTT-GTATTTAGTA
48738989 TTATGTAT
1 TT-TGTAT
48738997 ATAACTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (13 bp):
TTTGTATTTAGTA
Found at i:48747113 original size:31 final size:32
Alignment explanation
Indices: 48747054--48747118 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
48747044 GACAAATTAC
48747054 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
48747086 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
48747117 AA
1 AA
48747119 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:48748267 original size:5 final size:5
Alignment explanation
Indices: 48748259--48748288 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
48748249 ATACCACAAA
*
48748259 AAAAT AAAAT AAAGT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
48748289 GAGATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:48750554 original size:10 final size:9
Alignment explanation
Indices: 48750527--48750576 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 9
48750517 TTTTTGAAAA
*
48750527 TTTAACTTT
1 TTTAAATTT
*
48750536 TTT-ATTTT
1 TTTAAATTT
48750544 TTTAGAATTT
1 TTTA-AATTT
48750554 TTTAAA-TT
1 TTTAAATTT
*
48750562 TTTAATTTT
1 TTTAAATTT
48750571 TTTAAA
1 TTTAAA
48750577 AATATATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 14 0.41
9 12 0.35
10 8 0.24
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTAAATTT
Found at i:48750586 original size:27 final size:25
Alignment explanation
Indices: 48750512--48750609 Score: 70
Period size: 27 Copynumber: 3.7 Consensus size: 25
48750502 ATTATTTTAG
* *
48750512 AATTATTTTTGAAAATTTAACTTTTT
1 AATT-TTTTTAAAAATTTAAATTTTT
* **
48750538 TATTTTTTTAGAATTTTTTAAATTTTT
1 AATTTTTTTA-AA-AATTTAAATTTTT
*
48750565 AATTTTTTTAAAAATATATAAATTTTAG
1 AATTTTTTTAAAAAT-T-TAAATTTT-T
* *
48750593 AATTTTTATAAATATTT
1 AATTTTTTTAAAAATTT
48750610 TGAAATTTAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
25 6 0.11
26 9 0.16
27 28 0.50
28 13 0.23
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (25 bp):
AATTTTTTTAAAAATTTAAATTTTT
Found at i:48756598 original size:24 final size:24
Alignment explanation
Indices: 48756571--48756617 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
48756561 TCATTTTCGC
* *
48756571 TTTTAATATTTATTTTTTAATTAA
1 TTTTAACATATATTTTTTAATTAA
**
48756595 TTTTGCCATATATTTTTTAATTA
1 TTTTAACATATATTTTTTAATTA
48756618 CTTCCAAACC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTAACATATATTTTTTAATTAA
Found at i:48764078 original size:3 final size:3
Alignment explanation
Indices: 48764070--48764099 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
48764060 AATGACAATT
48764070 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
48764100 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CTA
Found at i:48765863 original size:3 final size:3
Alignment explanation
Indices: 48765848--48765879 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
48765838 TTCATTCTCC
*
48765848 TCT TCT TCC TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
48765880 ATTGTCATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:48768551 original size:18 final size:17
Alignment explanation
Indices: 48768528--48768589 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 17
48768518 TAAATACTCT
48768528 TTATAAATTTAAAAATAA
1 TTAT-AATTTAAAAATAA
*
48768546 TTATAATTT---AATAG
1 TTATAATTTAAAAATAA
*
48768560 TTATATATTTCAAAATAA
1 TTATA-ATTTAAAAATAA
48768578 TTATAATTTAAA
1 TTATAATTTAAA
48768590 CTACAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
17 11 0.30
18 13 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTATAATTTAAAAATAA
Found at i:48768563 original size:14 final size:14
Alignment explanation
Indices: 48768541--48768588 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
48768531 TAAATTTAAA
48768541 AATAATTATAATTT
1 AATAATTATAATTT
*
48768555 AATAGTTATATATTT
1 AATAATTATA-ATTT
48768570 CAAAATAATTATAATTT
1 ---AATAATTATAATTT
48768587 AA
1 AA
48768589 ACTACAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 11 0.39
15 4 0.14
17 4 0.14
18 9 0.32
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (14 bp):
AATAATTATAATTT
Done.