Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 193 of 208
Found at i:58820155 original size:26 final size:26
Alignment explanation
Indices: 58820105--58820175 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
58820095 AGCCATATCG
* *
58820105 AGAAGCTC-CGGAGAGCCATTGATCA
1 AGAAGCTCACGAAGAGCCATTAATCA
* *
58820130 GGAAGCTCACGAAGAGCCTTTAATCA
1 AGAAGCTCACGAAGAGCCATTAATCA
*
58820156 AGAAGCTCATGAAGAGCCAT
1 AGAAGCTCACGAAGAGCCAT
58820176 ATAACGAGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 7 0.18
26 31 0.82
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (26 bp):
AGAAGCTCACGAAGAGCCATTAATCA
Found at i:58829500 original size:27 final size:25
Alignment explanation
Indices: 58829465--58829514 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
58829455 ATGTTACTAT
58829465 TTTAATAATATATATATTTCATCATTA
1 TTTAATAATA-A-ATATTTCATCATTA
*
58829492 TTTAATAATAAATGTTTCATCAT
1 TTTAATAATAAATATTTCATCAT
58829515 AGAAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 1 0.05
27 10 0.45
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTAATAATAAATATTTCATCATTA
Found at i:58830161 original size:41 final size:40
Alignment explanation
Indices: 58830072--58830163 Score: 94
Period size: 41 Copynumber: 2.3 Consensus size: 40
58830062 TATCTCAGCC
* *
58830072 ATATGATTATTGTGATATTAATATTAAAATAATACTTTAA
1 ATATTATTATTGTGATATTAAAATTAAAATAATACTTTAA
* * * * * **
58830112 ATAATATTATTGTGTTTTTTAAAATTAATATAATATTTTGG
1 ATATTATTATTGTG-ATATTAAAATTAAAATAATACTTTAA
58830153 ATATTATTATT
1 ATATTATTATT
58830164 AACTAAAACT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
40 12 0.29
41 29 0.71
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (40 bp):
ATATTATTATTGTGATATTAAAATTAAAATAATACTTTAA
Found at i:58832702 original size:17 final size:17
Alignment explanation
Indices: 58832680--58832720 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
58832670 TATTTTCTTT
58832680 CAAAGTTAACTAATAGA
1 CAAAGTTAACTAATAGA
**
58832697 CAAAGTTGGCTAATAGA
1 CAAAGTTAACTAATAGA
*
58832714 TAAAGTT
1 CAAAGTT
58832721 GGAGAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (17 bp):
CAAAGTTAACTAATAGA
Found at i:58832721 original size:17 final size:17
Alignment explanation
Indices: 58832689--58832722 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58832679 TCAAAGTTAA
58832689 CTAATAGACAAAGTTGG
1 CTAATAGACAAAGTTGG
*
58832706 CTAATAGATAAAGTTGG
1 CTAATAGACAAAGTTGG
58832723 AGAAGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (17 bp):
CTAATAGACAAAGTTGG
Found at i:58832977 original size:14 final size:14
Alignment explanation
Indices: 58832936--58832978 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
58832926 CAAACCCGAG
*
58832936 GCCCAACTACCTCAA
1 GCCCAA-TACCTAAA
* *
58832951 GCCCAAAATCTAAA
1 GCCCAATACCTAAA
58832965 GCCCAATACCTAAA
1 GCCCAATACCTAAA
58832979 ATACCCTAGC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.42, C:0.37, G:0.07, T:0.14
Consensus pattern (14 bp):
GCCCAATACCTAAA
Found at i:58836896 original size:2 final size:2
Alignment explanation
Indices: 58836889--58836914 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58836879 CATACCTCAA
58836889 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
58836915 CAAAACATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58839064 original size:20 final size:20
Alignment explanation
Indices: 58839021--58839066 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
58839011 ATTAACTTGG
*
58839021 TTTAATTAAGTTAATCATGT
1 TTTAATTAAGTTAATCATGC
*
58839041 TTTAATTAATTTAATTCAT-C
1 TTTAATTAAGTTAA-TCATGC
58839061 TTTAAT
1 TTTAAT
58839067 CAAGAATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTAATTAAGTTAATCATGC
Found at i:58841060 original size:20 final size:21
Alignment explanation
Indices: 58841035--58841073 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58841025 TATATAATCG
58841035 TATTAAAA-TGATTAAAAAAT
1 TATTAAAACTGATTAAAAAAT
*
58841055 TATTAAAACTTATTAAAAA
1 TATTAAAACTGATTAAAAA
58841074 GTTACAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (21 bp):
TATTAAAACTGATTAAAAAAT
Found at i:58841409 original size:19 final size:20
Alignment explanation
Indices: 58841385--58841422 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
58841375 TTAGAAATTA
*
58841385 TTAAAATATTATA-AAAATG
1 TTAAAAAATTATAGAAAATG
58841404 TTAAAAAATTATAGAAAAT
1 TTAAAAAATTATAGAAAAT
58841423 TATATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
TTAAAAAATTATAGAAAATG
Found at i:58841414 original size:30 final size:30
Alignment explanation
Indices: 58841379--58841449 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
58841369 AAGCTTTTAG
*
58841379 AAATTATTA-AAATATTATA-AAAATGTTAAA
1 AAATTA-TAGAAA-ATTATATAAAATATTAAA
*
58841409 AAATTATAGAAAATTATATAAATTATTAAA
1 AAATTATAGAAAATTATATAAAATATTAAA
*
58841439 AAAAT-TAGAAA
1 AAATTATAGAAA
58841450 TTACTACGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (30 bp):
AAATTATAGAAAATTATATAAAATATTAAA
Found at i:58842355 original size:22 final size:21
Alignment explanation
Indices: 58842330--58842373 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
58842320 ATTTCAACTA
* *
58842330 AAACCTTATTTATTTTTAACAT
1 AAACCTTATATATATTT-ACAT
*
58842352 AAACTTTATATATATTTACAT
1 AAACCTTATATATATTTACAT
58842373 A
1 A
58842374 TTTGTTTCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (21 bp):
AAACCTTATATATATTTACAT
Found at i:58843043 original size:2 final size:2
Alignment explanation
Indices: 58843038--58843067 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
58843028 TGAAAAAAAC
58843038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58843068 AAGGAATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58850601 original size:41 final size:41
Alignment explanation
Indices: 58850544--58850626 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
58850534 CCATGAAACA
58850544 AAGGAGAGGAAAAAACAATGTGAAAAATCTAAAAAAAGCAT
1 AAGGAGAGGAAAAAACAATGTGAAAAATCTAAAAAAAGCAT
58850585 AAGGAGAGGAAAAAACAATGTGAAAAATCTAAAAAAAGCAT
1 AAGGAGAGGAAAAAACAATGTGAAAAATCTAAAAAAAGCAT
58850626 A
1 A
58850627 CTCTCAAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.61, C:0.07, G:0.19, T:0.12
Consensus pattern (41 bp):
AAGGAGAGGAAAAAACAATGTGAAAAATCTAAAAAAAGCAT
Found at i:58857603 original size:21 final size:21
Alignment explanation
Indices: 58857578--58857625 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
58857568 GGGTAAAAAA
58857578 ACTCTTAAGAGATAATGTGTT
1 ACTCTTAAGAGATAATGTGTT
58857599 ACTCTTAAGAGATAATGTGTT
1 ACTCTTAAGAGATAATGTGTT
58857620 A-TCTTA
1 ACTCTTA
58857626 TCAAATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
ACTCTTAAGAGATAATGTGTT
Found at i:58859482 original size:16 final size:16
Alignment explanation
Indices: 58859463--58859500 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
58859453 TTTTATATAT
*
58859463 TTTTAATAATAATTAA
1 TTTTAATAACAATTAA
*
58859479 TTTTAATAACAATTAG
1 TTTTAATAACAATTAA
58859495 TTTTAA
1 TTTTAA
58859501 GTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTTAATAACAATTAA
Found at i:58870475 original size:2 final size:2
Alignment explanation
Indices: 58870468--58870504 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
58870458 CCCTTTTTAA
58870468 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
58870505 CTATTACTAA
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:58872240 original size:22 final size:24
Alignment explanation
Indices: 58872212--58872256 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
58872202 CTTTGACTTA
*
58872212 TTTTTTAA-A-TTCTATAATATAT
1 TTTTTTAATATTTATATAATATAT
58872234 TTTTTTAATATTTATATAATATA
1 TTTTTTAATATTTATATAATATA
58872257 AAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 1 0.05
24 11 0.55
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTTTAATATTTATATAATATAT
Found at i:58873557 original size:22 final size:21
Alignment explanation
Indices: 58873524--58873565 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
58873514 AATATGATTA
*
58873524 AAATATATTAATTTATAAATTC
1 AAATATATTAATATA-AAATTC
58873546 AAATAT-TATAATATAAAATT
1 AAATATAT-TAATATAAAATT
58873566 TTAAAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATATATTAATATAAAATTC
Found at i:58878521 original size:2 final size:2
Alignment explanation
Indices: 58878514--58878551 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
58878504 CATGTATCTC
58878514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58878552 TCATGTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58878764 original size:50 final size:49
Alignment explanation
Indices: 58878702--58878801 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 49
58878692 TCATATGAGT
** *
58878702 TGTAAACGGAAAGCTC-CTCAGAGTTGAATATCGAGAAGCTCATGCAAGC
1 TGTAAACGGAAAGCTCAAGC-GAGCTGAATATCGAGAAGCTCATGCAAGC
*
58878751 TGTATAACGGAAAGCTCAAGCGAGCTGAATATCGGGAAGCTCATGCAAGC
1 TGTA-AACGGAAAGCTCAAGCGAGCTGAATATCGAGAAGCTCATGCAAGC
58878801 T
1 T
58878802 ATGGTGTGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
49 4 0.09
50 40 0.89
51 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (49 bp):
TGTAAACGGAAAGCTCAAGCGAGCTGAATATCGAGAAGCTCATGCAAGC
Found at i:58878765 original size:25 final size:25
Alignment explanation
Indices: 58878706--58878801 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
58878696 ATGAGTTGTA
* *
58878706 AACGGAAAGCTCCT-CAGAGTTGAAT
1 AACGGAAAGCTCATGCA-AGCTGAAT
* *
58878731 ATC-GAGAAGCTCATGCAAGCTGTAT
1 AACGGA-AAGCTCATGCAAGCTGAAT
* *
58878756 AACGGAAAGCTCAAGCGAGCTGAAT
1 AACGGAAAGCTCATGCAAGCTGAAT
* *
58878781 ATCGGGAAGCTCATGCAAGCT
1 AACGGAAAGCTCATGCAAGCT
58878802 ATGGTGTGTC
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
24 2 0.04
25 50 0.89
26 4 0.07
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (25 bp):
AACGGAAAGCTCATGCAAGCTGAAT
Found at i:58881042 original size:17 final size:19
Alignment explanation
Indices: 58881006--58881044 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
58880996 TAGCATTTAA
*
58881006 TTTTAGAATATATATCTAT
1 TTTTAAAATATATATCTAT
58881025 TTTTAAAATATA-AT-TAT
1 TTTTAAAATATATATCTAT
58881042 TTT
1 TTT
58881045 GTTGATTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAATATATATCTAT
Found at i:58886121 original size:34 final size:34
Alignment explanation
Indices: 58886083--58886222 Score: 156
Period size: 34 Copynumber: 4.1 Consensus size: 34
58886073 ACTACTTTAA
* *
58886083 TGATTTGTTAGAAGCATATGAATTGCTACCATAT
1 TGATCTGTTAGAAGCATATTAATTGCTACCATAT
* * *
58886117 TGATTTGTT-GTAAGCATATAAATTGCTATCATAT
1 TGATCTGTTAG-AAGCATATTAATTGCTACCATAT
* * ** *
58886151 TGATCTGTTATAAGCATATTAATTACTACTGTAC
1 TGATCTGTTAGAAGCATATTAATTGCTACCATAT
* *
58886185 TGATCTGTTACAAGCATATTAATTGCTACCGTAT
1 TGATCTGTTAGAAGCATATTAATTGCTACCATAT
58886219 TGAT
1 TGAT
58886223 ATGTGCATGT
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
33 1 0.01
34 89 0.99
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (34 bp):
TGATCTGTTAGAAGCATATTAATTGCTACCATAT
Found at i:58886464 original size:43 final size:43
Alignment explanation
Indices: 58886383--58886464 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
58886373 CCTTTAACTA
* * * ** *
58886383 CAAATATGTTGTGCATGCACAACCCAATGTTAGTTTTTACATG
1 CAAACATGTTGTCCATCCACAACCCAATGGCAGATTTTACATG
*
58886426 CAAACATGTTGTCCATCCACAGCCCAATGGCAGATTTTA
1 CAAACATGTTGTCCATCCACAACCCAATGGCAGATTTTA
58886465 TCTACGAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (43 bp):
CAAACATGTTGTCCATCCACAACCCAATGGCAGATTTTACATG
Found at i:58889941 original size:60 final size:60
Alignment explanation
Indices: 58889874--58889992 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
58889864 ATATTATATC
* *
58889874 AATAATTAGATAAAATCAAAATTCATGTAAAAAATTGCATATTAAACCATAGTTGATGTT
1 AATAATTAGATAAAATCAAAATTCATGTAAAAAATTACATATAAAACCATAGTTGATGTT
* *
58889934 AATAATTAGATCAAATCAAAATTCATGTAAACAATTACATATAAAACCATAGTTGATGT
1 AATAATTAGATAAAATCAAAATTCATGTAAAAAATTACATATAAAACCATAGTTGATGT
58889993 ATAACTTTGA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (60 bp):
AATAATTAGATAAAATCAAAATTCATGTAAAAAATTACATATAAAACCATAGTTGATGTT
Found at i:58889993 original size:31 final size:30
Alignment explanation
Indices: 58889898--58889993 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 30
58889888 ATCAAAATTC
*
58889898 ATGTAAAAAATTGCATATTAAACCATAGTTG
1 ATGTAAAAAATT-CATATAAAACCATAGTTG
* * * * * * * *
58889929 ATGTTAATAATT-AGATCAAATCAAAATTC
1 ATGTAAAAAATTCATATAAAACCATAGTTG
*
58889958 ATGTAAACAATTACATATAAAACCATAGTTG
1 ATGTAAAAAATT-CATATAAAACCATAGTTG
58889989 ATGTA
1 ATGTA
58889994 TAACTTTGAG
Statistics
Matches: 47, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
29 21 0.45
31 26 0.55
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (30 bp):
ATGTAAAAAATTCATATAAAACCATAGTTG
Found at i:58899957 original size:45 final size:45
Alignment explanation
Indices: 58899893--58899982 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
58899883 GAACATAAAA
58899893 AAAGGAAGAGAGCTGAGAGGTCATTATTTAAGTAATAAATTAAGT
1 AAAGGAAGAGAGCTGAGAGGTCATTATTTAAGTAATAAATTAAGT
58899938 AAAGGAAGAGAGCTGAGAGGTCATTATTTAAGTAATAAATTAAGT
1 AAAGGAAGAGAGCTGAGAGGTCATTATTTAAGTAATAAATTAAGT
58899983 GATGGGGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.27
Consensus pattern (45 bp):
AAAGGAAGAGAGCTGAGAGGTCATTATTTAAGTAATAAATTAAGT
Found at i:58902650 original size:53 final size:53
Alignment explanation
Indices: 58902589--58902699 Score: 222
Period size: 53 Copynumber: 2.1 Consensus size: 53
58902579 GTCCTTGTAC
58902589 ATTTTGTAAAATTGAAATTTAGTTCATTTTTAATTGTTAACACTATTAAAATT
1 ATTTTGTAAAATTGAAATTTAGTTCATTTTTAATTGTTAACACTATTAAAATT
58902642 ATTTTGTAAAATTGAAATTTAGTTCATTTTTAATTGTTAACACTATTAAAATT
1 ATTTTGTAAAATTGAAATTTAGTTCATTTTTAATTGTTAACACTATTAAAATT
58902695 ATTTT
1 ATTTT
58902700 TCTTAAATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.50
Consensus pattern (53 bp):
ATTTTGTAAAATTGAAATTTAGTTCATTTTTAATTGTTAACACTATTAAAATT
Found at i:58906376 original size:9 final size:9
Alignment explanation
Indices: 58906362--58906411 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
58906352 TTCTTTTTAA
58906362 TTTTTATAT
1 TTTTTATAT
58906371 TTTTTATAT
1 TTTTTATAT
*
58906380 TATTTA-AT
1 TTTTTATAT
58906388 TTTTTGA-AT
1 TTTTT-ATAT
* *
58906397 GTTTTATAA
1 TTTTTATAT
58906406 TTTTTA
1 TTTTTA
58906412 AATGGGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
8 7 0.21
9 27 0.79
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (9 bp):
TTTTTATAT
Found at i:58906389 original size:17 final size:16
Alignment explanation
Indices: 58906355--58906412 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
58906345 TTTATGCTTC
58906355 TTTTTAATTTTTATAT
1 TTTTTAATTTTTATAT
58906371 TTTTTATATTATTTA-AT
1 TTTTTA-ATT-TTTATAT
*
58906388 TTTTTGAATGTTTTATAA
1 TTTTT-AAT-TTTTATAT
58906406 TTTTTAA
1 TTTTTAA
58906413 ATGGGTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 6 0.17
17 18 0.50
18 12 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTTTAATTTTTATAT
Found at i:58907840 original size:2 final size:2
Alignment explanation
Indices: 58907828--58907879 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
58907818 ACTTTACCCC
58907828 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58907869 AT AT AT AT AT A
1 AT AT AT AT AT A
58907880 CTCTTNNNNN
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58908302 original size:2 final size:2
Alignment explanation
Indices: 58908295--58908363 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
58908285 TTTAATACAA
58908295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58908337 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 A
58908364 CTCCTTGTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58911640 original size:29 final size:30
Alignment explanation
Indices: 58911607--58911674 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
58911597 TCAAAACTTT
58911607 ATGTATAAAATTGCACA-AAATCAAAGTTC
1 ATGTATAAAATTGCACATAAATCAAAGTTC
*** *
58911636 ATGTATGGCATTGCACATTAGATCAAAGTTC
1 ATGTATAAAATTGCACA-TAAATCAAAGTTC
58911667 ATGTATAA
1 ATGTATAA
58911675 TTTTGATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 14 0.45
31 17 0.55
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (30 bp):
ATGTATAAAATTGCACATAAATCAAAGTTC
Found at i:58911786 original size:32 final size:29
Alignment explanation
Indices: 58911749--58911809 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 29
58911739 TAAAAATCTC
58911749 ATTTTTTATAAATAATTATTGGG-TTAGGCTG
1 ATTTTTTAT-AA-AATTA-TGGGATTAGGCTG
*
58911780 ATTTTTTGTAAAATTATGGGATTAGGCTG
1 ATTTTTTATAAAATTATGGGATTAGGCTG
58911809 A
1 A
58911810 AATAACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 14 0.50
30 2 0.07
31 8 0.29
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (29 bp):
ATTTTTTATAAAATTATGGGATTAGGCTG
Found at i:58914882 original size:6 final size:6
Alignment explanation
Indices: 58914871--58914895 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58914861 AGATTGGATA
58914871 TGGGCT TGGGCT TGGGCT TGGGCT T
1 TGGGCT TGGGCT TGGGCT TGGGCT T
58914896 AGTTGAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TGGGCT
Found at i:58916187 original size:11 final size:11
Alignment explanation
Indices: 58916173--58916227 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
58916163 TTAAATATGG
58916173 ATTTGAGAGAA
1 ATTTGAGAGAA
* *
58916184 ATTTGAAAGGA
1 ATTTGAGAGAA
58916195 ATTTGAGAGCAA
1 ATTTGAGAG-AA
58916207 A-TTGAGAGGAA
1 ATTTGAGA-GAA
58916218 ATTTGAGAGA
1 ATTTGAGAGA
58916228 GGATTAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.44, C:0.02, G:0.29, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:58916202 original size:40 final size:40
Alignment explanation
Indices: 58916085--58916187 Score: 188
Period size: 40 Copynumber: 2.6 Consensus size: 40
58916075 AATTATTTAA
* *
58916085 AAATAGGGATTTAAGAGAAATTTAAGAGCAAATTGAGATT
1 AAATATGGATTTGAGAGAAATTTAAGAGCAAATTGAGATT
58916125 AAATATGGATTTGAGAGAAATTTAAGAGCAAATTGAGATT
1 AAATATGGATTTGAGAGAAATTTAAGAGCAAATTGAGATT
58916165 AAATATGGATTTGAGAGAAATTT
1 AAATATGGATTTGAGAGAAATTT
58916188 GAAAGGAATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.46, C:0.02, G:0.22, T:0.30
Consensus pattern (40 bp):
AAATATGGATTTGAGAGAAATTTAAGAGCAAATTGAGATT
Found at i:58916220 original size:23 final size:22
Alignment explanation
Indices: 58916173--58916227 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
58916163 TTAAATATGG
58916173 ATTTGAGAGAAATTTGAAAGGA
1 ATTTGAGAGAAATTTGAAAGGA
*
58916195 ATTTGAGAGCAAA-TTGAGAGGAA
1 ATTTGAGAG-AAATTTGAAAGG-A
58916218 ATTTGAGAGA
1 ATTTGAGAGA
58916228 GGATTAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.44, C:0.02, G:0.29, T:0.25
Consensus pattern (22 bp):
ATTTGAGAGAAATTTGAAAGGA
Found at i:58918127 original size:23 final size:24
Alignment explanation
Indices: 58918097--58918145 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
58918087 CGTTATTGGG
58918097 AAAGGATGAATTGACG-AAAATGT
1 AAAGGATGAATTGACGAAAAATGT
58918120 AAAGGATGAATTGACGAAAAATGT
1 AAAGGATGAATTGACGAAAAATGT
58918144 AA
1 AA
58918146 GAAGAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.20
Consensus pattern (24 bp):
AAAGGATGAATTGACGAAAAATGT
Found at i:58918183 original size:23 final size:23
Alignment explanation
Indices: 58918153--58918200 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
58918143 TAAGAAGAAA
58918153 AATGTAAAGGATGAATTGACAGT
1 AATGTAAAGGATGAATTGACAGT
* *
58918176 AATGTAAATGATGAATTGACGGT
1 AATGTAAAGGATGAATTGACAGT
58918199 AA
1 AA
58918201 GTTATCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.25, T:0.27
Consensus pattern (23 bp):
AATGTAAAGGATGAATTGACAGT
Found at i:58919936 original size:83 final size:82
Alignment explanation
Indices: 58919769--58919936 Score: 212
Period size: 83 Copynumber: 2.0 Consensus size: 82
58919759 AAAAAATGAT
* *
58919769 TATTGAATCAATTTATAAGTTGTTTAAATTTTTTACTTTTTACTTGTTTATTTAATCATTGTTCG
1 TATTGAATCAATTTATAAGTTGTTTAAATTTTTTACTTTTTACTTGTTTAATTAATCATTATTCG
* ** *
58919834 AATGGCGATTGAATGAA
66 AATGACGACCGAATCAA
* *
58919851 TATTGAA-CTAATTTATAAGTTGTTTAATTTTTGTTATTTTTTACTTGTTTAATTAATCATTATT
1 TATTGAATC-AATTTATAAGTTGTTTAAATTTT-TTACTTTTTACTTGTTTAATTAATCATTATT
* * *
58919915 GGAATGACGGCCGGATCAA
64 CGAATGACGACCGAATCAA
58919934 TAT
1 TAT
58919937 GGTTTTCAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 1 0.01
82 29 0.40
83 43 0.59
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (82 bp):
TATTGAATCAATTTATAAGTTGTTTAAATTTTTTACTTTTTACTTGTTTAATTAATCATTATTCG
AATGACGACCGAATCAA
Found at i:58923864 original size:72 final size:72
Alignment explanation
Indices: 58923751--58923935 Score: 273
Period size: 72 Copynumber: 2.6 Consensus size: 72
58923741 AACAAATTTT
* * * *
58923751 ATATCC-AAAATCAAACATAAACTACTATTGATAAAATTAGATTATACATAAATAAGTAGAACAT
1 ATATCCAAAAATCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTACAACAT
58923815 AAATTCA
66 AAATTCA
* * * *
58923822 ATATCCAAAAACCAAACATAAGCAACTATTGATACAACTAGATTACACATAAATAAGTACAATAT
1 ATATCCAAAAATCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTACAACAT
58923887 AAATTCA
66 AAATTCA
*
58923894 ATATCCAAAAATCAAACATAAACAACAATTGATAAAAACTAG
1 ATATCCAAAAATCAAACATAAACAACTATTGAT-AAAACTAG
58923936 TTTTGCATTG
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
71 6 0.06
72 87 0.87
73 7 0.07
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.24
Consensus pattern (72 bp):
ATATCCAAAAATCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTACAACAT
AAATTCA
Found at i:58925098 original size:14 final size:15
Alignment explanation
Indices: 58925067--58925099 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
58925057 ATTTACCTCT
*
58925067 AAAGGAGAAAGTAAA
1 AAAGGAAAAAGTAAA
58925082 AAAGGAAAAAG-AAA
1 AAAGGAAAAAGTAAA
58925096 AAAG
1 AAAG
58925100 AAGCATACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (15 bp):
AAAGGAAAAAGTAAA
Found at i:58930984 original size:21 final size:20
Alignment explanation
Indices: 58930949--58930994 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
58930939 CTATATGGGT
* *
58930949 AAATTTAACTCAATTTAATG
1 AAATTTAACTCAATTCAATC
*
58930969 AAATTTATATTCAATTCAATC
1 AAATTTA-ACTCAATTCAATC
58930990 AAATT
1 AAATT
58930995 CACATTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATTTAACTCAATTCAATC
Found at i:58932855 original size:29 final size:30
Alignment explanation
Indices: 58932796--58932853 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
58932786 TTCGAGCCTT
*
58932796 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
58932826 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
58932854 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:58933083 original size:13 final size:13
Alignment explanation
Indices: 58933065--58933096 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
58933055 TTTCCAGCAA
58933065 TTATGAATTTATT
1 TTATGAATTTATT
58933078 TTATGAATTTATT
1 TTATGAATTTATT
*
58933091 TGATGA
1 TTATGA
58933097 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:58933304 original size:50 final size:50
Alignment explanation
Indices: 58933191--58933432 Score: 277
Period size: 50 Copynumber: 4.7 Consensus size: 50
58933181 ATTTGGGTAA
* * *
58933191 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--CAAGA-C--G
* *
58933247 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * * *
58933297 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
58933347 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
58933397 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
58933433 TTTGGCATGT
Statistics
Matches: 164, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
50 91 0.55
51 29 0.18
52 1 0.01
53 3 0.02
55 1 0.01
56 39 0.24
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:58933379 original size:100 final size:103
Alignment explanation
Indices: 58933191--58933440 Score: 344
Period size: 100 Copynumber: 2.4 Consensus size: 103
58933181 ATTTGGGTAA
58933191 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC--T-AGATCATGAGAGGTCCC
* * *
58933256 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * * * *
58933297 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCA-C-CGA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTAGATCATGAGAGGTCCCCTA
*
58933359 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
58933397 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
58933441 GTTATTATCA
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
100 51 0.40
101 38 0.29
105 1 0.01
106 39 0.30
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:58936970 original size:19 final size:19
Alignment explanation
Indices: 58936941--58936978 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
58936931 TAATAAAGTG
58936941 TACATAATAAAATTAAAATA
1 TACATAAT-AAATTAAAATA
58936961 TACA-AATAAATTAAAATA
1 TACATAATAAATTAAAATA
58936979 AAACTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 3 0.17
20 4 0.22
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
TACATAATAAATTAAAATA
Found at i:58939242 original size:15 final size:14
Alignment explanation
Indices: 58939222--58939282 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 14
58939212 AGACAACGCC
58939222 CAGCAGCAACAGCAG
1 CAGCAGCAACAG-AG
*
58939237 CAGCAGCCACAAGAG
1 CAGCAGCAAC-AGAG
58939252 CAGCAGCAACA-AG
1 CAGCAGCAACAGAG
*
58939265 -AGCAACAACAGCAG
1 CAGCAGCAACAG-AG
58939279 CAGC
1 CAGC
58939283 CACAACCGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 9 0.23
13 2 0.05
14 3 0.08
15 23 0.59
16 2 0.05
ACGTcount: A:0.43, C:0.33, G:0.25, T:0.00
Consensus pattern (14 bp):
CAGCAGCAACAGAG
Found at i:58939287 original size:15 final size:15
Alignment explanation
Indices: 58939222--58939294 Score: 59
Period size: 15 Copynumber: 5.3 Consensus size: 15
58939212 AGACAACGCC
*
58939222 CAGCAGCAACAGCAG
1 CAGCAGCAACAACAG
*
58939237 CAGCAGCCAC-A-AG
1 CAGCAGCAACAACAG
*
58939250 -AGCAGCAGCAACA-
1 CAGCAGCAACAACAG
58939263 -AG-AGCAACAACAG
1 CAGCAGCAACAACAG
* *
58939276 CAGCAGCCACAACCG
1 CAGCAGCAACAACAG
58939291 CAGC
1 CAGC
58939295 TGCCGCGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 16 0.35
13 5 0.11
14 3 0.07
15 22 0.48
ACGTcount: A:0.41, C:0.36, G:0.23, T:0.00
Consensus pattern (15 bp):
CAGCAGCAACAACAG
Found at i:58939357 original size:18 final size:18
Alignment explanation
Indices: 58939323--58939361 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58939313 AACTGGTCAA
*
58939323 GGTTAAGAAAGTAGTGGT
1 GGTTAAGAAAGAAGTGGT
58939341 GGTTAAG-AAGAAGGTGGT
1 GGTTAAGAAAGAA-GTGGT
58939359 GGT
1 GGT
58939362 GGGAGCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.26
Consensus pattern (18 bp):
GGTTAAGAAAGAAGTGGT
Found at i:58939371 original size:3 final size:3
Alignment explanation
Indices: 58939365--58939401 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
58939355 TGGTGGTGGG
* *
58939365 AGC AGC AGC AGC AGC AGC AGC AGC CGC AGC CGC AGC A
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC A
58939402 ACATCACAGA
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:0.38, G:0.32, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:58960248 original size:24 final size:24
Alignment explanation
Indices: 58960184--58960237 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
58960174 TTTTTCTAGA
* * **
58960184 ATATTTAATATTTATGAGTATAAT
1 ATATTTAGTATTTATTAAAATAAT
58960208 ATATTTAGTATTTATTAAAATAAT
1 ATATTTAGTATTTATTAAAATAAT
58960232 ATATTT
1 ATATTT
58960238 GACTTTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
ATATTTAGTATTTATTAAAATAAT
Found at i:58975287 original size:10 final size:10
Alignment explanation
Indices: 58975272--58975301 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
58975262 AATAAACTCA
58975272 AATTAATTTT
1 AATTAATTTT
*
58975282 AATTAATTAT
1 AATTAATTTT
58975292 AATTAATTTT
1 AATTAATTTT
58975302 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
AATTAATTTT
Found at i:58977671 original size:46 final size:46
Alignment explanation
Indices: 58977618--58977756 Score: 190
Period size: 46 Copynumber: 3.0 Consensus size: 46
58977608 ACAATGCTAT
* * * *
58977618 AACTCAGTATGATTTT-TGTTATTGAAATACTATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCT-TTACTGAAATACCATACCTACGTTCCAC
* *
58977664 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACATTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
* *
58977710 AACTCAGTATGGTTTTCTTTACTGAATTACCATACCTACGTCCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
58977756 A
1 A
58977757 CTTTGCCATG
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 81 0.99
47 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
Found at i:58980734 original size:22 final size:22
Alignment explanation
Indices: 58980709--58980775 Score: 84
Period size: 20 Copynumber: 3.1 Consensus size: 22
58980699 TATAATAATC
* *
58980709 AATAGAAATAATAAAACAAAAA
1 AATAAAAATAAAAAAACAAAAA
58980731 AATAAAAATAAAAAAAC--AAA
1 AATAAAAATAAAAAAACAAAAA
*
58980751 AATAAAAATAAAATACACAAAAA
1 AATAAAAATAAAA-AAACAAAAA
58980774 AA
1 AA
58980776 GAATAATCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
20 16 0.41
21 3 0.08
22 15 0.38
23 5 0.13
ACGTcount: A:0.81, C:0.06, G:0.01, T:0.12
Consensus pattern (22 bp):
AATAAAAATAAAAAAACAAAAA
Found at i:58980743 original size:14 final size:14
Alignment explanation
Indices: 58980721--58980758 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
58980711 TAGAAATAAT
* *
58980721 AAAACAAAAAAATA
1 AAAATAAAAAAACA
58980735 AAAATAAAAAAACA
1 AAAATAAAAAAACA
58980749 AAAATAAAAA
1 AAAATAAAAA
58980759 TAAAATACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.87, C:0.05, G:0.00, T:0.08
Consensus pattern (14 bp):
AAAATAAAAAAACA
Found at i:58980772 original size:26 final size:26
Alignment explanation
Indices: 58980728--58980781 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
58980718 AATAAAACAA
58980728 AAAAATAAAAATAAAAAAACAAA-AAT
1 AAAAATAAAAATAAAAAAA-AAAGAAT
*
58980754 AAAAAT-AAAATACACAAAAAAAGAAT
1 AAAAATAAAAATA-AAAAAAAAAGAAT
58980780 AA
1 AA
58980782 TCTATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (26 bp):
AAAAATAAAAATAAAAAAAAAAGAAT
Found at i:58982782 original size:2 final size:2
Alignment explanation
Indices: 58982775--58982819 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
58982765 TGGTGTTACA
58982775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58982817 AT A
1 AT A
58982820 GCAATAGCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58984039 original size:2 final size:2
Alignment explanation
Indices: 58984032--58984066 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58984022 TGCACATGTT
58984032 TA TA TA TA 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 TA TA TA TA T
58984067 CCAAACTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58988978 original size:24 final size:24
Alignment explanation
Indices: 58988946--58988994 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
58988936 GATAAAGAAG
58988946 ATTAAAACTTATGTTAATTTTTCT
1 ATTAAAACTTATGTTAATTTTTCT
*
58988970 ATTAAAACTTCTGTTAATTTTTCT
1 ATTAAAACTTATGTTAATTTTTCT
58988994 A
1 A
58988995 GTGTCTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTAAAACTTATGTTAATTTTTCT
Found at i:58989299 original size:12 final size:12
Alignment explanation
Indices: 58989282--58989332 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
58989272 TGCTTCCTTC
58989282 GTACGTACGTAT
1 GTACGTACGTAT
58989294 GTACGTACGTAT
1 GTACGTACGTAT
* *
58989306 GTATGTATGTAT
1 GTACGTACGTAT
* *
58989318 GTATGTATGTAT
1 GTACGTACGTAT
58989330 GTA
1 GTA
58989333 TGTATGTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.41
Consensus pattern (12 bp):
GTACGTACGTAT
Found at i:58989309 original size:4 final size:4
Alignment explanation
Indices: 58989290--58989340 Score: 84
Period size: 4 Copynumber: 12.8 Consensus size: 4
58989280 TCGTACGTAC
* *
58989290 GTAT GTAC GTAC GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
58989338 GTA
1 GTA
58989341 CATGTGTGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.45
Consensus pattern (4 bp):
GTAT
Found at i:59002927 original size:14 final size:15
Alignment explanation
Indices: 59002908--59002936 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59002898 TTAGCTTGAC
59002908 AAACAAAAA-TAAAT
1 AAACAAAAACTAAAT
59002922 AAACAAAAACTAAAT
1 AAACAAAAACTAAAT
59002937 TTTTCATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (15 bp):
AAACAAAAACTAAAT
Found at i:59005241 original size:16 final size:15
Alignment explanation
Indices: 59005220--59005262 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
59005210 AACAACAATG
59005220 AATATAATAAAAATAA
1 AATAT-ATAAAAATAA
* *
59005236 AATATATATATATAA
1 AATATATAAAAATAA
59005251 AACTATATAAAA
1 AA-TATATAAAA
59005263 GAAAAATGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AATATATAAAAATAA
Found at i:59006427 original size:31 final size:32
Alignment explanation
Indices: 59006389--59006451 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
59006379 AGGCAAATTA
59006389 CAAGAGTAATTG-AATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAAATCCTAATAAAACTCTTT
59006420 CAAGAGTAATTGAAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAAATCCTAATAAAACTCTTT
59006452 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAAATCCTAATAAAACTCTTT
Found at i:59007367 original size:18 final size:18
Alignment explanation
Indices: 59007346--59007394 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
59007336 AGACTTGCAA
59007346 AAGA-AAAAAGAATAAAAT
1 AAGATAAAAAGAAT-AAAT
59007364 AAGATAAAACA-AATAAAT
1 AAGATAAAA-AGAATAAAT
*
59007382 AAAATAAAAAGAA
1 AAGATAAAAAGAA
59007395 AACGAAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.04
18 18 0.67
19 7 0.26
20 1 0.04
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (18 bp):
AAGATAAAAAGAATAAAT
Found at i:59008280 original size:50 final size:50
Alignment explanation
Indices: 59008198--59008541 Score: 158
Period size: 50 Copynumber: 6.9 Consensus size: 50
59008188 TGTAATGTCG
* * * * * * * *
59008198 GGGAAGCAAGATTCGTCGTCGTAACTTTAATCTGCTCCACTGCATTGCTA
1 GGGAAGCAAGATTCGCCGTTGCAGCTTCAATCTGTTCAACTGCAATGCTA
* * * *
59008248 GGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAATTGCAATG-TCA
1 GGGAAGCAAGATTCGCCGTTGCAGCTTCAATCTGTTCAACTGCAATGCT-A
* * * * * * * * *
59008298 GAGAAGCAAGATTCGCCATCGTAGTTTCAATCTGCTCTACTGCATTGCCA
1 GGGAAGCAAGATTCGCCGTTGCAGCTTCAATCTGTTCAACTGCAATGCTA
*** * * * * *
59008348 TAAAAGTAAGATTCGCCGTTGCGGCTTCAATCAT-TTTAATTGCAATG-TCG
1 GGGAAGCAAGATTCGCCGTTGCAGCTTCAATC-TGTTCAACTGCAATGCT-A
* *** * * * * *
59008398 GGGAAACAAGATTCATTGTTGTAGCTCCAATCTGTTCCACTGCACTGCCA
1 GGGAAGCAAGATTCGCCGTTGCAGCTTCAATCTGTTCAACTGCAATGCTA
* * * * * *
59008448 GGGAAGTAAGATTCGCCGTTGC-GACTTCAATATTTTTAATTGCAATG-TCG
1 GGGAAGCAAGATTCGCCGTTGCAG-CTTCAATCTGTTCAACTGCAATGCT-A
* * * * * *
59008498 GGGAAGCAGGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCA
1 GGGAAGCAAGATTCGCCGTTGCAGCTTCAATCTGTTCAACTGCA
59008542 CCGCTTGGAA
Statistics
Matches: 202, Mismatches: 83, Indels: 18
0.67 0.27 0.06
Matches are distributed among these distances:
49 3 0.01
50 197 0.98
51 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (50 bp):
GGGAAGCAAGATTCGCCGTTGCAGCTTCAATCTGTTCAACTGCAATGCTA
Found at i:59008542 original size:100 final size:100
Alignment explanation
Indices: 59008191--59008542 Score: 431
Period size: 100 Copynumber: 3.5 Consensus size: 100
59008181 AATCCGATGT
** * * *
59008191 AATGTCGGGGAAGCAAGATTCGTCGTCGTAACTTTAATCTGCTCCACTGCATTGCTAGGGAAGTA
1 AATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAAGTA
*
59008256 AGATTCGCCGTTGC-AGCTTCAATCTTTTTAATTGC
66 AGATTCGCCGTTGCGA-CTTCAATATTTTTAATTGC
* * * * * * ***
59008291 AATGTCAGAGAAGCAAGATTCGCCATCGTAG-TTTCAATCTGCTCTACTGCATTGCCATAAAAGT
1 AATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTT-AATCTGCTCCACTGCACTGCCAGGGAAGT
*
59008355 AAGATTCGCCGTTGCGGCTTCAATCA-TTTTAATTGC
65 AAGATTCGCCGTTGCGACTTCAAT-ATTTTTAATTGC
* ** * ** *
59008391 AATGTCGGGGAAACAAGATTCATTGTTGTAGCTCCAATCTGTTCCACTGCACTGCCAGGGAAGTA
1 AATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAAGTA
59008456 AGATTCGCCGTTGCGACTTCAATATTTTTAATTGC
66 AGATTCGCCGTTGCGACTTCAATATTTTTAATTGC
* *
59008491 AATGTCGGGGAAGCAGGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCAC
1 AATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCAC
59008543 CGCTTGGAAA
Statistics
Matches: 211, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
99 4 0.02
100 206 0.98
101 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (100 bp):
AATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAAGTA
AGATTCGCCGTTGCGACTTCAATATTTTTAATTGC
Found at i:59008718 original size:45 final size:45
Alignment explanation
Indices: 59008657--59009050 Score: 456
Period size: 45 Copynumber: 8.8 Consensus size: 45
59008647 CTGGTGCTTC
* * * * *
59008657 CGATCTGCTTCACTGCCAGTACAGGAAGATAAGATCTGCTATATT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* * * *
59008702 C-AGTCTGCTTTGCTGCCAATACAGGAAGACAAGA-CTTGTTAACTT
1 CGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTT
* *
59008747 CGATCTACTTCGCTGCCAATACAGGAAGACAAGACCTGTTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* * * *
59008792 CGATTTACTTCACTGCCAATACAGGAAAACAAAATCTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* * *
59008837 CGATCCACTTCACTGCCAATACAAGAAGACAAGATCTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* *
59008882 CGATCCACTTCGCTGCCAATACAGGAAGACAAGATCTTCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* * *
59008927 CGATCCACTTTGCTGCCAATACAGGAAGATAAGATCTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* * * *
59008972 C-AGTCTAATTCACTGCCAATACAGGAAGACAAGA-CTTGTTATATT
1 CGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTT
*
59009017 -TAGTCTACTTCGCTGCCAATACAGGAAGACAAGA
1 CGA-TCTACTTCGCTGCCAATACAGGAAGACAAGA
59009051 CTTGCTTTCT
Statistics
Matches: 306, Mismatches: 36, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
44 4 0.01
45 300 0.98
46 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (45 bp):
CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
Found at i:59009062 original size:135 final size:136
Alignment explanation
Indices: 59008664--59009062 Score: 524
Period size: 135 Copynumber: 3.0 Consensus size: 136
59008654 TTCCGATCTG
* * * **
59008664 CTTCACTGCCAGTACAGGAAGATAAGATCTGCTATATTCAGTCTGCTTTGCTGCCAATACAGGAA
1 CTTCACTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAA
*
59008729 GACAAGACTTGTTA-ACTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGACCTG-TTATCTT
66 GACAAGACTTGTTATACTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGACTTGCTT-TCTT
**
59008792 CGATTTA
130 CGATCCA
* * * * *
59008799 CTTCACTGCCAATACAGGAAAACAAAATCTGCTATCTTC-GATCCACTTCACTGCCAATACAAGA
1 CTTCACTGCCAATACAGGAAGATAAGATCTGCTATCTTCAG-TCTACTTCACTGCCAATACAGGA
* * *
59008863 AGACAAGA-TCTGCTAT-CTTCGATCCACTTCGCTGCCAATACAGGAAGACAAGATCTT-CTATC
65 AGACAAGACT-TGTTATACTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGA-CTTGCTTTC
59008925 TTCGATCCA
128 TTCGATCCA
** *
59008934 CTTTGCTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTAATTCACTGCCAATACAGGAA
1 CTTCACTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAA
* *
59008999 GACAAGACTTGTTATATTTAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACTTGCTTTCTTC
66 GACAAGACTTGTTATACTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGACTTGCTTTCTTC
59009063 AACTTTCTCC
Statistics
Matches: 226, Mismatches: 29, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
134 5 0.02
135 213 0.94
136 8 0.04
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (136 bp):
CTTCACTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAA
GACAAGACTTGTTATACTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGACTTGCTTTCTTC
GATCCA
Found at i:59010133 original size:17 final size:17
Alignment explanation
Indices: 59010113--59010151 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
59010103 TCTTTTTCTT
59010113 TTTTCATTCTTCTTTTC
1 TTTTCATTCTTCTTTTC
* *
59010130 TTTTCTTTTTTCTTTTC
1 TTTTCATTCTTCTTTTC
*
59010147 ATTTC
1 TTTTC
59010152 TTTTTTTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCATTCTTCTTTTC
Found at i:59010136 original size:30 final size:30
Alignment explanation
Indices: 59010102--59010159 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
59010092 CATTGGCCTC
*
59010102 TTCTTTTTCTTTTTTCA-TTCTTCTTTTCTT
1 TTCTTTTT-TCTTTTCATTTCTTCTTTTCTT
*
59010132 TTCTTTTTTCTTTTCATTTCTTTTTTTC
1 TTCTTTTTTCTTTTCATTTCTTCTTTTC
59010160 AAGTGAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (30 bp):
TTCTTTTTTCTTTTCATTTCTTCTTTTCTT
Found at i:59010138 original size:24 final size:22
Alignment explanation
Indices: 59010106--59010155 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
59010096 GGCCTCTTCT
*
59010106 TTTTCTTTTTTCATTCTTCTTTTC
1 TTTTCTTTTTTC-TT-TTCATTTC
59010130 TTTTCTTTTTTCTTTTCATTTC
1 TTTTCTTTTTTCTTTTCATTTC
59010152 TTTT
1 TTTT
59010156 TTTCAAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.44
23 2 0.08
24 12 0.48
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTTTCTTTTCATTTC
Found at i:59010152 original size:17 final size:17
Alignment explanation
Indices: 59010122--59010157 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
59010112 TTTTTCATTC
*
59010122 TTCTTTTCTTTTCTTTT
1 TTCTTTTCATTTCTTTT
59010139 TTCTTTTCATTTCTTTT
1 TTCTTTTCATTTCTTTT
59010156 TT
1 TT
59010158 TCAAGTGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTCTTTTCATTTCTTTT
Found at i:59010616 original size:21 final size:19
Alignment explanation
Indices: 59010599--59010651 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
59010589 TTTTTTTATC
59010599 TTTTTGTTTTTTCATTTTT
1 TTTTTGTTTTTTCATTTTT
**
59010618 AATTTTTAATTTTTCATTTTT
1 --TTTTTGTTTTTTCATTTTT
59010639 TGTTTTGTTTTTT
1 T-TTTTGTTTTTT
59010652 TTGTTTGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 9 0.33
21 17 0.63
ACGTcount: A:0.11, C:0.04, G:0.06, T:0.79
Consensus pattern (19 bp):
TTTTTGTTTTTTCATTTTT
Found at i:59010662 original size:14 final size:14
Alignment explanation
Indices: 59010634--59010668 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
59010624 TAATTTTTCA
*
59010634 TTTTTTGTTTTGTT
1 TTTTTTGTTTGGTT
59010648 TTTTTTGTTTGGTT
1 TTTTTTGTTTGGTT
59010662 TTTTTTG
1 TTTTTTG
59010669 CCTCCACTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (14 bp):
TTTTTTGTTTGGTT
Found at i:59017996 original size:45 final size:45
Alignment explanation
Indices: 59017922--59018180 Score: 259
Period size: 45 Copynumber: 5.8 Consensus size: 45
59017912 ACAATTAGGT
* * * *
59017922 TATACATATAACAGGTATTATGTATCGGTGTTGGCTATCATGTCA
1 TATACATACAACAGGTACTATGTAACGGTGTTGGCTATCATGCCA
** * *
59017967 TATACATACAGTAGGTACTACGTAACGGTGTCGGCTATCATGCCA
1 TATACATACAACAGGTACTATGTAACGGTGTTGGCTATCATGCCA
* * * * * *
59018012 TATACATACAACAAGTACTATGTATCGGTATCGACTTTCATGCCA
1 TATACATACAACAGGTACTATGTAACGGTGTTGGCTATCATGCCA
* * * * * *
59018057 TATAAATACAACAGGTACCATATATCGGTGTTAGCTATCATACCA
1 TATACATACAACAGGTACTATGTAACGGTGTTGGCTATCATGCCA
* * * *
59018102 TATACATACAACATGTATTATGTACCGGTGTTGGCTTTCATGCCA
1 TATACATACAACAGGTACTATGTAACGGTGTTGGCTATCATGCCA
* * *
59018147 TATAAATATAGCAGGTACTATGT-ACTGGTGTTGG
1 TATACATACAACAGGTACTATGTAAC-GGTGTTGG
59018181 TTATTTTGTC
Statistics
Matches: 172, Mismatches: 41, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
44 1 0.01
45 171 0.99
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (45 bp):
TATACATACAACAGGTACTATGTAACGGTGTTGGCTATCATGCCA
Found at i:59018177 original size:90 final size:90
Alignment explanation
Indices: 59017922--59018178 Score: 302
Period size: 90 Copynumber: 2.9 Consensus size: 90
59017912 ACAATTAGGT
* * * * * *
59017922 TATACATATAACAGGTATTATGTATCGGTGTTGGCTATCATGTCATATACATACAGTAGGTACTA
1 TATACATACAACAAGTATTATGTATCGGTGTTGGCTTTCATGCCATATAAATACAGCAGGTACTA
* ** *
59017987 CGTAAC-GGTGTCGGCTATCATGCCA
66 TGT-ACTGGTGTTAGCTATCATACCA
* * * * * *
59018012 TATACATACAACAAGTACTATGTATCGGTATCGACTTTCATGCCATATAAATACAACAGGTACCA
1 TATACATACAACAAGTATTATGTATCGGTGTTGGCTTTCATGCCATATAAATACAGCAGGTACTA
*
59018077 TATA-TCGGTGTTAGCTATCATACCA
66 TGTACT-GGTGTTAGCTATCATACCA
* * *
59018102 TATACATACAACATGTATTATGTACCGGTGTTGGCTTTCATGCCATATAAATATAGCAGGTACTA
1 TATACATACAACAAGTATTATGTATCGGTGTTGGCTTTCATGCCATATAAATACAGCAGGTACTA
59018167 TGTACTGGTGTT
66 TGTACTGGTGTT
59018179 GGTTATTTTG
Statistics
Matches: 137, Mismatches: 27, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
89 1 0.01
90 135 0.99
91 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (90 bp):
TATACATACAACAAGTATTATGTATCGGTGTTGGCTTTCATGCCATATAAATACAGCAGGTACTA
TGTACTGGTGTTAGCTATCATACCA
Found at i:59019787 original size:21 final size:24
Alignment explanation
Indices: 59019747--59019797 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
59019737 CCAATAAAAT
*
59019747 GAAAAACACTTGGGGTTTTAT-AG
1 GAAAAACACTTGGAGTTTTATAAG
59019770 GAAAAA-ACTT-GAGTTTTATAAG
1 GAAAAACACTTGGAGTTTTATAAG
59019792 GAAAAA
1 GAAAAA
59019798 GCATTTCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.31
22 12 0.46
23 6 0.23
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.27
Consensus pattern (24 bp):
GAAAAACACTTGGAGTTTTATAAG
Found at i:59020119 original size:19 final size:20
Alignment explanation
Indices: 59020095--59020135 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
59020085 AAAACAACTA
59020095 AAAGAAGAAAT-TTAAAAAC
1 AAAGAAGAAATATTAAAAAC
* *
59020114 AAAGAATAAATATTTAAAAC
1 AAAGAAGAAATATTAAAAAC
59020134 AA
1 AA
59020136 TAAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAGAAGAAATATTAAAAAC
Found at i:59020150 original size:20 final size:20
Alignment explanation
Indices: 59020109--59020150 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
59020099 AAGAAATTTA
*
59020109 AAAACAAAGAATAAATATTT
1 AAAACAAAGAATAAATAATT
*
59020129 AAAACAATA-AATAATTAATT
1 AAAACAA-AGAATAAATAATT
59020149 AA
1 AA
59020151 TTAAAAGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAACAAAGAATAAATAATT
Found at i:59020984 original size:22 final size:22
Alignment explanation
Indices: 59020937--59021024 Score: 61
Period size: 22 Copynumber: 3.9 Consensus size: 22
59020927 CTATTAAATA
* * *
59020937 GAGAGCACTAAA-GTGTTATACA
1 GAGAGCAC-AAATGTGCTAAACG
59020959 GAGAGCACAAATGTGCTAAACG
1 GAGAGCACAAATGTGCTAAACG
* * *
59020981 GAGAACACTATTGTGCTAATAATCG
1 GAGAGCACAAATGTGCT-A-AA-CG
* *
59021006 GAGAGCACTAACGTGCTAA
1 GAGAGCACAAATGTGCTAA
59021025 TAATCAGAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.06
22 29 0.55
23 2 0.04
24 3 0.06
25 16 0.30
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (22 bp):
GAGAGCACAAATGTGCTAAACG
Found at i:59021014 original size:25 final size:25
Alignment explanation
Indices: 59020959--59021036 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
59020949 GTGTTATACA
*
59020959 GAGAGCACAAATGTGCT-A-AA-CG
1 GAGAGCACTAATGTGCTAATAATCG
* *
59020981 GAGAACACTATTGTGCTAATAATCG
1 GAGAGCACTAATGTGCTAATAATCG
* *
59021006 GAGAGCACTAACGTGCTAATAATCA
1 GAGAGCACTAATGTGCTAATAATCG
59021031 GAGAGC
1 GAGAGC
59021037 GCGCTAGGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
22 14 0.30
23 1 0.02
24 2 0.04
25 29 0.63
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.19
Consensus pattern (25 bp):
GAGAGCACTAATGTGCTAATAATCG
Found at i:59023425 original size:19 final size:19
Alignment explanation
Indices: 59023401--59023442 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
59023391 TAAATTTCGA
59023401 AATAAATAAATAATAAA-AT
1 AATAAA-AAATAATAAATAT
*
59023420 AATAAAAACTAATAAATAT
1 AATAAAAAATAATAAATAT
59023439 AATA
1 AATA
59023443 TTGGGCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAAATAATAAATAT
Found at i:59026908 original size:2 final size:2
Alignment explanation
Indices: 59026901--59026925 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59026891 CCCCGAGTTC
59026901 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
59026926 GTCTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:59036030 original size:43 final size:43
Alignment explanation
Indices: 59035983--59036065 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
59035973 ATGCACCTCG
**
59035983 TGTGCTAGTATAATTGCTTCAGTTTGCCCAATGATGCACTATA
1 TGTGCTAGTATAATTGCTTCAGTTCACCCAATGATGCACTATA
* ** *
59036026 TGTGCTAGTATATTTTTTTCAGTTCATCCAATGATGCACT
1 TGTGCTAGTATAATTGCTTCAGTTCACCCAATGATGCACT
59036066 GTGGTGCCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (43 bp):
TGTGCTAGTATAATTGCTTCAGTTCACCCAATGATGCACTATA
Found at i:59043611 original size:26 final size:26
Alignment explanation
Indices: 59043576--59043635 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
59043566 TTGAAAAGTG
59043576 TTTCAAAAGTG-TTGTGGAAAAGTACT
1 TTTCAAAAGTGCTT-TGGAAAAGTACT
* * *
59043602 TTTCAGAAGTGCTTTTGAGAAGTACT
1 TTTCAAAAGTGCTTTGGAAAAGTACT
*
59043628 TTTGAAAA
1 TTTCAAAA
59043636 TTTTGAGTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (26 bp):
TTTCAAAAGTGCTTTGGAAAAGTACT
Found at i:59043631 original size:13 final size:13
Alignment explanation
Indices: 59043595--59043632 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
59043585 TGTTGTGGAA
*
59043595 AAGTACTTTTCAG
1 AAGTACTTTTGAG
*
59043608 AAGTGCTTTTGAG
1 AAGTACTTTTGAG
59043621 AAGTACTTTTGA
1 AAGTACTTTTGA
59043633 AAATTTTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (13 bp):
AAGTACTTTTGAG
Found at i:59044652 original size:13 final size:13
Alignment explanation
Indices: 59044634--59044663 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
59044624 AGCCCAAACT
59044634 CAATTACCCAACC
1 CAATTACCCAACC
59044647 CAATTACCCAACC
1 CAATTACCCAACC
59044660 CAAT
1 CAAT
59044664 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:59044816 original size:9 final size:9
Alignment explanation
Indices: 59044804--59044853 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
59044794 AAATAAAAAA
59044804 AATTCGGGT
1 AATTCGGGT
59044813 AATTCGGGT
1 AATTCGGGT
*
59044822 ATTTTTC-GGT
1 A--ATTCGGGT
*
59044832 AATTCGGTT
1 AATTCGGGT
59044841 AATTCGGGT
1 AATTCGGGT
59044850 AATT
1 AATT
59044854 TTTAATCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 3 0.09
9 24 0.71
10 4 0.12
11 3 0.09
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:59047262 original size:16 final size:15
Alignment explanation
Indices: 59047237--59047270 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
59047227 AAAGTTGATA
*
59047237 ATAATTAATATATATT
1 ATAATAAATATA-ATT
59047253 ATAATAAATATAATT
1 ATAATAAATATAATT
59047268 ATA
1 ATA
59047271 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:59047392 original size:30 final size:30
Alignment explanation
Indices: 59047335--59047393 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
59047325 GCCTTTTGAA
* * *
59047335 AATATTTAGAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
59047365 AATATTTACAAAAAGA-GCAACCAAATTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTT
59047394 GAAAATAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:59050821 original size:107 final size:107
Alignment explanation
Indices: 59050634--59050853 Score: 377
Period size: 107 Copynumber: 2.1 Consensus size: 107
59050624 TAACTCCAAA
**
59050634 GATTCAAAGCAGGATTGCGGATTAAATCCTTTTCATCACTTGGAGGGTCTGATGTCAAAATTTGT
1 GATTCAAAGCAGGATTGCAAATTAAATCCTTTTCATCACTTGGAGGGTCTGATGTCAAAATTTGT
*
59050699 TCCAATAGGTTCTCAACATAGTTGAGTTCCTTTTCCATGATT
66 TCCAATAGGTCCTCAACATAGTTGAGTTCCTTTTCCATGATT
* *
59050741 GATTCAAAGTAGGATTGCAAATTAAATCCTTTTCATCACTTGGAGGGTCTGATGTTAAAATTTGT
1 GATTCAAAGCAGGATTGCAAATTAAATCCTTTTCATCACTTGGAGGGTCTGATGTCAAAATTTGT
*
59050806 TCCAATAGGTCCTCAATATAGTTGAGTTCCTTTTCCATGATT
66 TCCAATAGGTCCTCAACATAGTTGAGTTCCTTTTCCATGATT
*
59050848 AATTCA
1 GATTCA
59050854 TATAAATCGA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 106 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (107 bp):
GATTCAAAGCAGGATTGCAAATTAAATCCTTTTCATCACTTGGAGGGTCTGATGTCAAAATTTGT
TCCAATAGGTCCTCAACATAGTTGAGTTCCTTTTCCATGATT
Found at i:59059486 original size:13 final size:13
Alignment explanation
Indices: 59059468--59059544 Score: 75
Period size: 13 Copynumber: 5.9 Consensus size: 13
59059458 AGTTCTTCAT
59059468 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
59059481 TGCTTTTCAAAAG
1 TGCTTTTGAAAAG
*
59059494 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
* * *
59059507 TACTTTTCAGAAG
1 TGCTTTTGAAAAG
*
59059520 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
59059533 TACTTTTGAAAA
1 TGCTTTTGAAAA
59059545 TTTTGAGTGT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
12 2 0.04
13 47 0.92
14 2 0.04
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:59059533 original size:26 final size:26
Alignment explanation
Indices: 59059468--59059544 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
59059458 AGTTCTTCAT
*
59059468 TGCTTTTGAAAAGTGCTTTTCAAAAG
1 TGCTTTTGAAAAGTACTTTTCAAAAG
* *
59059494 TG-TTGTGGAAAAGTACTTTTCAGAAG
1 TGCTT-TTGAAAAGTACTTTTCAAAAG
* *
59059520 TGCTTTTGAGAAGTACTTTTGAAAA
1 TGCTTTTGAAAAGTACTTTTCAAAA
59059545 TTTTGAGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.05
26 38 0.90
27 2 0.05
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (26 bp):
TGCTTTTGAAAAGTACTTTTCAAAAG
Found at i:59061687 original size:72 final size:71
Alignment explanation
Indices: 59061594--59061768 Score: 235
Period size: 72 Copynumber: 2.4 Consensus size: 71
59061584 AAAATCACAT
* * * *
59061594 ATAAACAACTATTGATAAAACTAATTTAGTAAAAGATAAGTAGAATATAAATTCAATATCTAAAG
1 ATAAACAACTATTGATAAAACTAATTTAGCAAAA-ATAAGTAGAACATAAATTCAATATCCAAAA
59061659 ACCAAAC
65 ACCAAAC
* * *
59061666 ATAAACAACTTTTAATAAAACTAGATTTCA-CATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTA-ATTT-AGCAAAAATAAGTAGAACATAAATTCAATATCCAAA
59061730 AACCAAAC
64 AACCAAAC
* *
59061738 ATAAATAACTATTGATAAAACTAGTTTAGCA
1 ATAAACAACTATTGATAAAACTAATTTAGCA
59061769 TTGTTGTTTA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
70 1 0.01
71 5 0.06
72 75 0.84
73 7 0.08
74 1 0.01
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (71 bp):
ATAAACAACTATTGATAAAACTAATTTAGCAAAAATAAGTAGAACATAAATTCAATATCCAAAAA
CCAAAC
Found at i:59062213 original size:18 final size:18
Alignment explanation
Indices: 59062190--59062237 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
59062180 TCCATCAATT
*
59062190 TGAACATCATTTGAAATG
1 TGAACATCATTTAAAATG
59062208 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
59062226 TGAACATCATTT
1 TGAACATCATTT
59062238 CTCATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTAAAATG
Found at i:59064367 original size:19 final size:19
Alignment explanation
Indices: 59064329--59064367 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
59064319 GTGGTGGAGA
**
59064329 AGAGGAACAAAGCACCAGC
1 AGAGGAACAAAAAACCAGC
*
59064348 AGAGGAACAAAAAACTAGC
1 AGAGGAACAAAAAACCAGC
59064367 A
1 A
59064368 CTAGCACCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.21, G:0.23, T:0.03
Consensus pattern (19 bp):
AGAGGAACAAAAAACCAGC
Found at i:59064377 original size:31 final size:31
Alignment explanation
Indices: 59064339--59064404 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
59064329 AGAGGAACAA
* * *
59064339 AGCACCAGCAGAGGAACAAAAAACTAGCACT
1 AGCACCAGCAGAAGAACAAAAAACCAGCACC
* *
59064370 AGCACCAGTAGAAGAACAAAGAACCAGCACC
1 AGCACCAGCAGAAGAACAAAAAACCAGCACC
59064401 AGCA
1 AGCA
59064405 GAGGATCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.27, G:0.20, T:0.05
Consensus pattern (31 bp):
AGCACCAGCAGAAGAACAAAAAACCAGCACC
Found at i:59064414 original size:25 final size:25
Alignment explanation
Indices: 59064370--59064423 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
59064360 AACTAGCACT
*
59064370 AGCACCAGTAGAAGAACAAAGAACC
1 AGCACCAGCAGAAGAACAAAGAACC
* * *
59064395 AGCACCAGCAGAGGATCAAAGAAGC
1 AGCACCAGCAGAAGAACAAAGAACC
59064420 AGCA
1 AGCA
59064424 GAGGAACAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.24, T:0.04
Consensus pattern (25 bp):
AGCACCAGCAGAAGAACAAAGAACC
Found at i:59064424 original size:19 final size:19
Alignment explanation
Indices: 59064398--59064446 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
59064388 AAGAACCAGC
*
59064398 ACCAGCAGAGGATCAAAGA
1 ACCAGCAGAGGAACAAAGA
*
59064417 AGCAGCAGAGGAACAAAGA
1 ACCAGCAGAGGAACAAAGA
59064436 ACCAGCGAGAG
1 ACCAGC-AGAG
59064447 AAGAGATGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.47, C:0.20, G:0.31, T:0.02
Consensus pattern (19 bp):
ACCAGCAGAGGAACAAAGA
Found at i:59065676 original size:120 final size:119
Alignment explanation
Indices: 59065439--59065810 Score: 552
Period size: 120 Copynumber: 3.1 Consensus size: 119
59065429 GAAGCTGCAA
** *
59065439 CAGTTTGAGATTGAGGAGCCGCCGTCGTCATTGGTGGTTTAGGCTCAGTTACAGCC-TT--TGGA
1 CAGTTTGAGCCTGAGGAGCCGCCGTCGCCATTGGTGGTTTAGGCTCAGTTACAGCCTTTGGTGGA
* *
59065501 GATGACGGTACTTTCTCGTCTCTTTGTTTTTCAATACTGGAGGCTGAAGCTACAG
66 GGTGACGGTACTTTCTGGTCTCTTTGTTTTTCAATACTGGAGGCTGAAGC-ACAG
* * *
59065556 CAGTTTGAGCCTGAGGAACCGCCGTCGCCATTTGTGGTTTAGGCTCAGTTACATCCTTTGGTGGA
1 CAGTTTGAGCCTGAGGAGCCGCCGTCGCCATTGGTGGTTTAGGCTCAGTTACAGCCTTTGGTGGA
* * *
59065621 GGTGACGGTACTTTCTGGTCTCTCTGTTTTTCAACACTGGAGGTTGAAGCGACAG
66 GGTGACGGTACTTTCTGGTCTCTTTGTTTTTCAATACTGGAGGCTGAAGC-ACAG
* *
59065676 CAGTTTGAGCCTGAGGAGCCGTCGTCGCCATTGGTGGTTTAGGCTCAGATACAGCCTTTGGTGGA
1 CAGTTTGAGCCTGAGGAGCCGCCGTCGCCATTGGTGGTTTAGGCTCAGTTACAGCCTTTGGTGGA
* * *
59065741 GGTGACGGTACTTTTTGGCCTCTTTGTTTTTCAATACCGGAGGCTGAAGCAGCAG
66 GGTGACGGTACTTTCTGGTCTCTTTGTTTTTCAATACTGGAGGCTGAAGCA-CAG
59065796 CAGTTTGAGCCTGAG
1 CAGTTTGAGCCTGAG
59065811 CCGTTGGCAA
Statistics
Matches: 228, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
117 50 0.22
118 2 0.01
119 1 0.00
120 175 0.77
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (119 bp):
CAGTTTGAGCCTGAGGAGCCGCCGTCGCCATTGGTGGTTTAGGCTCAGTTACAGCCTTTGGTGGA
GGTGACGGTACTTTCTGGTCTCTTTGTTTTTCAATACTGGAGGCTGAAGCACAG
Found at i:59079852 original size:12 final size:12
Alignment explanation
Indices: 59079835--59079859 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59079825 AGTTACCCAC
59079835 TGGCTAAAGTTT
1 TGGCTAAAGTTT
59079847 TGGCTAAAGTTT
1 TGGCTAAAGTTT
59079859 T
1 T
59079860 CGATTCATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (12 bp):
TGGCTAAAGTTT
Found at i:59090306 original size:76 final size:76
Alignment explanation
Indices: 59090221--59090376 Score: 260
Period size: 76 Copynumber: 2.1 Consensus size: 76
59090211 AACCACTTAA
* * *
59090221 TTAAGAATTTTCAAGTTAAATCAATTTAAGGAAAAATA-AGTTTTTTTAGTTGCATTTATCTCAC
1 TTAAGAATTTTCAAGTTAAATCAATTTAAGGAAAAATATA-TTTTTGTAGTTACATTTATCTCAA
59090285 ATATTTTCCTTT
65 ATATTTTCCTTT
*
59090297 TTAAGAATTTTCAAGTTAAATCAATTTAAGGAAAGATATATTTTTGTAGTTACATTTATCTCAAA
1 TTAAGAATTTTCAAGTTAAATCAATTTAAGGAAAAATATATTTTTGTAGTTACATTTATCTCAAA
59090362 TATTTTCCTTT
66 TATTTTCCTTT
59090373 TTAA
1 TTAA
59090377 ATTTTACCAA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
76 74 0.99
77 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (76 bp):
TTAAGAATTTTCAAGTTAAATCAATTTAAGGAAAAATATATTTTTGTAGTTACATTTATCTCAAA
TATTTTCCTTT
Found at i:59096549 original size:38 final size:39
Alignment explanation
Indices: 59096507--59096616 Score: 107
Period size: 38 Copynumber: 2.8 Consensus size: 39
59096497 TCGGATAGTT
* *
59096507 CGAAGCAAAGTTGACACCCAGTGTCTCATC-AGCCTAGC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
* * * * *
59096545 CGAAGTAAAG-TGATACCTAGTATCTCATCGAATCTATC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
* *
59096583 TGAAGTAAAATAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAAAGT--TGACACCCAGTGTCTCATCGA
59096617 CTCGAGGTCG
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
37 16 0.29
38 22 0.39
41 18 0.32
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (39 bp):
CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:59096612 original size:41 final size:38
Alignment explanation
Indices: 59096507--59096616 Score: 105
Period size: 41 Copynumber: 2.8 Consensus size: 38
59096497 TCGGATAGTT
* *
59096507 CGAAGCAAAGTTGACACCCAGTGTCTCATC-AGCCTAGC
1 CGAAGTAAAG-TGACACCCAGTGTCTCATCGAACCTAGC
* * * * *
59096545 CGAAGTAAAGTGATACCTAGTATCTCATCGAATCTATC
1 CGAAGTAAAGTGACACCCAGTGTCTCATCGAACCTAGC
*
59096583 TGAAGTAAAATAGTGACACCCAGTGTCTCATCGA
1 CGAAGT--AA-AGTGACACCCAGTGTCTCATCGA
59096617 CTCGAGGTCG
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
37 16 0.28
38 19 0.33
40 2 0.04
41 20 0.35
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (38 bp):
CGAAGTAAAGTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:59098566 original size:31 final size:31
Alignment explanation
Indices: 59098531--59098594 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
59098521 CTCATATACT
*
59098531 AAATATAATATAAAATAATA-ATATCTCATTA
1 AAATATAA-ATAAAATAATATATATCTAATTA
* *
59098562 AAATATTAATAAAATAATATTTATCTAATTA
1 AAATATAAATAAAATAATATATATCTAATTA
59098593 AA
1 AA
59098595 TAATCATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATATAAATAAAATAATATATATCTAATTA
Found at i:59098575 original size:30 final size:30
Alignment explanation
Indices: 59098530--59098607 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
59098520 GCTCATATAC
* *
59098530 TAAATATAATATAAAATAATA-ATATCTCAT
1 TAAATATTA-ATAAAATAATATATATCTAAT
*
59098560 TAAAATATTAATAAAATAATATTTATCTAAT
1 T-AAATATTAATAAAATAATATATATCTAAT
* *
59098591 TAAATAATCATAAAATA
1 TAAATATTAATAAAATA
59098608 TTAAAATATC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 26 0.63
31 15 0.37
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (30 bp):
TAAATATTAATAAAATAATATATATCTAAT
Found at i:59101671 original size:25 final size:25
Alignment explanation
Indices: 59101640--59101757 Score: 114
Period size: 25 Copynumber: 4.8 Consensus size: 25
59101630 ATGAGTTATA
* *
59101640 AACGGGAAGCTCCTCCGAGCTGAAT
1 AACGGGAAGCTCATACGAGCTGAAT
* * *
59101665 AATGGGAAGCTCATGCGAGCTAAAT
1 AACGGGAAGCTCATACGAGCTGAAT
*
59101690 AACGGGAAGCTCATACGAGCTGCAT
1 AACGGGAAGCTCATACGAGCTGAAT
* * * *
59101715 TACAGAAAGCTCATGCGAGCT-ATAT
1 AACGGGAAGCTCATACGAGCTGA-AT
*
59101740 AAC-AGAAGCTCATACGAG
1 AACGGGAAGCTCATACGAG
59101758 TTGTGGTGTG
Statistics
Matches: 75, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
24 12 0.16
25 63 0.84
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (25 bp):
AACGGGAAGCTCATACGAGCTGAAT
Found at i:59101698 original size:50 final size:50
Alignment explanation
Indices: 59101640--59101757 Score: 148
Period size: 50 Copynumber: 2.4 Consensus size: 50
59101630 ATGAGTTATA
* * ** *
59101640 AACGGGAAGCTCCTCCGAGCTGAATAATGGGAAGCTCATGCGAGCTAAAT
1 AACGGGAAGCTCATACGAGCTGAATAACAGAAAGCTCATGCGAGCTAAAT
* * *
59101690 AACGGGAAGCTCATACGAGCTGCATTACAGAAAGCTCATGCGAGCTATAT
1 AACGGGAAGCTCATACGAGCTGAATAACAGAAAGCTCATGCGAGCTAAAT
*
59101740 AAC-AGAAGCTCATACGAG
1 AACGGGAAGCTCATACGAG
59101758 TTGTGGTGTG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 14 0.24
50 45 0.76
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (50 bp):
AACGGGAAGCTCATACGAGCTGAATAACAGAAAGCTCATGCGAGCTAAAT
Found at i:59104045 original size:11 final size:12
Alignment explanation
Indices: 59104010--59104055 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
59104000 ACATATATAC
59104010 ATATAT-ATAAA
1 ATATATAATAAA
*
59104021 ACTATGAAAATAAA
1 A-TAT-ATAATAAA
59104035 ATA-ATAATAAA
1 ATATATAATAAA
59104046 ATATATAATA
1 ATATATAATA
59104056 TATGTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 11 0.38
12 9 0.31
13 3 0.10
14 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (12 bp):
ATATATAATAAA
Found at i:59104045 original size:61 final size:60
Alignment explanation
Indices: 59103933--59104058 Score: 132
Period size: 61 Copynumber: 2.1 Consensus size: 60
59103923 AACAAAGGAT
* * * * *
59103933 ATATAAACATATATATATATATATAGATTATAAAATATGGAAAATGTAT-AAATATTATAAA
1 ATATAAACATATATACATATATATAAACTATAAAATA-GAAAAATGAATAAAATA-TATAAA
*
59103994 ATATAAACATATATACATATATATAAAACTATGAAAATA-AAATAAT-AATAAAATATATAAT
1 ATATAAACATATATACATATATAT-AAACTAT-AAAATAGAAA-AATGAATAAAATATATAAA
59104055 ATAT
1 ATAT
59104059 GTATATATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
61 36 0.65
62 13 0.24
63 6 0.11
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (60 bp):
ATATAAACATATATACATATATATAAACTATAAAATAGAAAAATGAATAAAATATATAAA
Found at i:59119573 original size:18 final size:17
Alignment explanation
Indices: 59119552--59119586 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
59119542 AGGAAAGAGG
59119552 TTCCTTTTTTTCTTTTTT
1 TTCCTTTTTTT-TTTTTT
59119570 TTCCTTTTTTTTTTTTT
1 TTCCTTTTTTTTTTTTT
59119587 CTGGTTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTCCTTTTTTTTTTTTT
Found at i:59119582 original size:15 final size:16
Alignment explanation
Indices: 59119558--59119587 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59119548 GAGGTTCCTT
59119558 TTTTTCTTTTTTTTCC
1 TTTTTCTTTTTTTTCC
59119574 TTTTT-TTTTTTTTC
1 TTTTTCTTTTTTTTC
59119588 TGGTTGGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTCTTTTTTTTCC
Found at i:59131433 original size:25 final size:25
Alignment explanation
Indices: 59131399--59131446 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
59131389 CCTGCGAAGC
59131399 CAAAAGAAAAAATAAAGAA-AGAATT
1 CAAAAGAAAAAA-AAAGAACAGAATT
*
59131424 CAAAAGAAAATAAAAGAACAGAA
1 CAAAAGAAAAAAAAAGAACAGAA
59131447 ATGAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.73, C:0.06, G:0.12, T:0.08
Consensus pattern (25 bp):
CAAAAGAAAAAAAAAGAACAGAATT
Found at i:59131453 original size:25 final size:26
Alignment explanation
Indices: 59131400--59131458 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
59131390 CTGCGAAGCC
*
59131400 AAAAGAAAAAATAAAGAAAGAATTC-
1 AAAAGAAAAAATAAAGAAAGAAATCA
* *
59131425 AAAAGAAAATA-AAAGAACAGAAATGA
1 AAAAGAAAAAATAAAGAA-AGAAATCA
59131451 AAAAGAAA
1 AAAAGAAA
59131459 CGAAAAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 15 0.52
26 8 0.28
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.08
Consensus pattern (26 bp):
AAAAGAAAAAATAAAGAAAGAAATCA
Found at i:59131542 original size:17 final size:17
Alignment explanation
Indices: 59131520--59131557 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
59131510 CAAACACTGT
59131520 ATTGGCGTGAAAT-CAAA
1 ATTGGC-TGAAATGCAAA
*
59131537 ATTGGCTTAAATGCAAA
1 ATTGGCTGAAATGCAAA
59131554 ATTG
1 ATTG
59131558 ACCTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (17 bp):
ATTGGCTGAAATGCAAA
Done.