Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 71 of 325
Found at i:19605881 original size:3 final size:3
Alignment explanation
Indices: 19605868--19605898 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
19605858 ATTCTATGTT
19605868 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19605899 TGTGAATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:19607586 original size:26 final size:26
Alignment explanation
Indices: 19607549--19607632 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
19607539 TGATACAAAT
*
19607549 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
19607575 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
19607601 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
19607627 TGATAA
1 TGATAA
19607633 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:19610551 original size:24 final size:24
Alignment explanation
Indices: 19610480--19610551 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
19610470 GACTCACCAC
* * *
19610480 AGCTCGTATGAGCTTACCGATATATC
1 AGCTCGTAAGAGCTTACCG-T-TTTT
**
19610506 AGCTCGTAAGAGCTTATTGTTTTT
1 AGCTCGTAAGAGCTTACCGTTTTT
19610530 AGCTCGTCAA-AGCTTACCGTTT
1 AGCTCGT-AAGAGCTTACCGTTT
19610552 CAGCTCAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 19 0.50
25 3 0.08
26 16 0.42
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (24 bp):
AGCTCGTAAGAGCTTACCGTTTTT
Found at i:19610774 original size:20 final size:19
Alignment explanation
Indices: 19610745--19610807 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
19610735 AGTTATGTGT
*
19610745 TTATACGGATGAATTACTG
1 TTATATGGATGAATTACTG
* *
19610764 CTTATATGGATGAAGTATTG
1 -TTATATGGATGAATTACTG
* *
19610784 TTTATATAGATGAGTTACTG
1 -TTATATGGATGAATTACTG
19610804 TTAT
1 TTAT
19610808 CAAATGAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (19 bp):
TTATATGGATGAATTACTG
Found at i:19613837 original size:20 final size:20
Alignment explanation
Indices: 19613798--19613852 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
19613788 AGTCATAATA
*
19613798 AAATGATAAAAAATGT-AAAG
1 AAAT-ATAAAAATTGTAAAAG
*
19613818 AAATATAAAATTTGTAAAAG
1 AAATATAAAAATTGTAAAAG
*
19613838 AATTATAAAAATTGT
1 AAATATAAAAATTGT
19613853 CATACCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (20 bp):
AAATATAAAAATTGTAAAAG
Found at i:19614040 original size:20 final size:20
Alignment explanation
Indices: 19614011--19614049 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19614001 TTAAAGGGCC
19614011 TTTTTGATGAGTTTTATAAT
1 TTTTTGATGAGTTTTATAAT
* *
19614031 TTTTTTATGATTTTTATAA
1 TTTTTGATGAGTTTTATAA
19614050 AAATTTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (20 bp):
TTTTTGATGAGTTTTATAAT
Found at i:19614094 original size:28 final size:27
Alignment explanation
Indices: 19614063--19614135 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 27
19614053 TTTACAATTA
19614063 TTTATATTTTTACTACTTTTTAGTAAA-T
1 TTTATATTTTTA-TA-TTTTTAGTAAAGT
*
19614091 TTTAAATATTTTTTATATTTTTATTAAAGT
1 TTT--ATA-TTTTTATATTTTTAGTAAAGT
*
19614121 TTAATAATTTTTATA
1 TTTAT-ATTTTTATA
19614136 ACTTGTATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
28 13 0.34
29 11 0.29
30 8 0.21
31 6 0.16
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTATATTTTTATATTTTTAGTAAAGT
Found at i:19614112 original size:29 final size:29
Alignment explanation
Indices: 19614068--19614135 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
19614058 AATTATTTAT
*
19614068 ATTTTTACTACTTTTTAGTAAATTTTAAATA
1 ATTTTTA-TACTTTTTAGTAAAGTTT-AATA
* *
19614099 TTTTTTATA-TTTTTATTAAAGTTTAATA
1 ATTTTTATACTTTTTAGTAAAGTTTAATA
19614127 ATTTTTATA
1 ATTTTTATA
19614136 ACTTGTATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 12 0.36
29 13 0.39
30 2 0.06
31 6 0.18
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (29 bp):
ATTTTTATACTTTTTAGTAAAGTTTAATA
Found at i:19614144 original size:29 final size:29
Alignment explanation
Indices: 19614068--19614144 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 29
19614058 AATTATTTAT
* * *
19614068 ATTTTTACTACTTTTTAGTAAATTTTAAATA
1 ATTTTTA-TAC-TTGTATTAAAGTTTAAATA
* * *
19614099 TTTTTTATATTTTTATTAAAGTTT-AATA
1 ATTTTTATACTTGTATTAAAGTTTAAATA
19614127 ATTTTTATAACTTGTATT
1 ATTTTTAT-ACTTGTATT
19614145 GATTTTTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 11 0.29
29 19 0.50
30 2 0.05
31 6 0.16
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (29 bp):
ATTTTTATACTTGTATTAAAGTTTAAATA
Found at i:19616341 original size:2 final size:2
Alignment explanation
Indices: 19616334--19616364 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19616324 ACATTAATTA
19616334 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 A
19616365 GAAATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19616926 original size:7 final size:7
Alignment explanation
Indices: 19616910--19617016 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
19616900 AATAAATGAA
*
19616910 ATAATTT
1 ATAATAT
19616917 ATAATAT
1 ATAATAT
19616924 ATAATAT
1 ATAATAT
*
19616931 A-AAAAT
1 ATAATAT
* *
19616937 GTAAGTTT
1 ATAA-TAT
*
19616945 TTAA-A-
1 ATAATAT
*
19616950 ATAATGT
1 ATAATAT
19616957 ATAATAT
1 ATAATAT
*
19616964 A-AATAA
1 ATAATAT
19616970 ATAAATAT
1 AT-AATAT
19616978 ATAAGATAT
1 AT-A-ATAT
19616987 ATAAGT-T
1 ATAA-TAT
19616994 A-AA-AT
1 ATAATAT
19616999 ATAATAT
1 ATAATAT
19617006 ATAATA-
1 ATAATAT
19617012 ATAAT
1 ATAAT
19617017 TTACAAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
5 5 0.06
6 18 0.23
7 34 0.44
8 14 0.18
9 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:19616980 original size:21 final size:21
Alignment explanation
Indices: 19616948--19617012 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
19616938 TAAGTTTTTA
*
19616948 AAAT-AATGTATAATATAAAT
1 AAATAAATATATAATATAAAT
* *
19616968 AAATAAATATATAAGATATAT
1 AAATAAATATATAATATAAAT
*
19616989 AAGTTAAA-ATATAATATATAAT
1 AA-ATAAATATATAATATA-AAT
19617011 AA
1 AA
19617013 TAATTTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 24 0.67
22 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATAAATATATAATATAAAT
Found at i:19616981 original size:28 final size:29
Alignment explanation
Indices: 19616950--19617010 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
19616940 AGTTTTTAAA
19616950 ATAATGTATAATATAA-AT-AAATA-AATAT
1 ATAATG-AT-ATATAAGATAAAATATAATAT
*
19616978 ATAA-GATATATAAGTTAAAATATAATAT
1 ATAATGATATATAAGATAAAATATAATAT
19617006 ATAAT
1 ATAAT
19617011 AATAATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 6 0.21
28 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
ATAATGATATATAAGATAAAATATAATAT
Found at i:19617051 original size:12 final size:13
Alignment explanation
Indices: 19617032--19617062 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
19617022 AATTTTGAAA
19617032 ATATAAATAATAT
1 ATATAAATAATAT
19617045 A-ATAAATAATAT
1 ATATAAATAATAT
19617057 ATATAA
1 ATATAA
19617063 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:19617060 original size:16 final size:15
Alignment explanation
Indices: 19617037--19617067 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
19617027 TGAAAATATA
19617037 AATAATATAATAAAT
1 AATAATATAATAAAT
19617052 AATATATATAATAAAT
1 AATA-ATATAATAAAT
19617068 TAAAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATAATAAAT
Found at i:19617414 original size:35 final size:34
Alignment explanation
Indices: 19617370--19617500 Score: 210
Period size: 35 Copynumber: 3.8 Consensus size: 34
19617360 AATCATATCT
19617370 TCTAAGATTGTATATCATATCTAAGATTGCAAT-TA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATATA
19617405 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAAT-ATA
19617440 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAAT-ATA
*
19617475 TTTAAGATTGTATCATATCTAAGATT
1 TCTAAGATTGTATCATATCTAAGATT
19617501 ACATATCATT
Statistics
Matches: 93, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
33 21 0.23
35 72 0.77
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (34 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATATA
Found at i:19617425 original size:17 final size:17
Alignment explanation
Indices: 19617370--19617500 Score: 167
Period size: 17 Copynumber: 7.5 Consensus size: 17
19617360 AATCATATCT
19617370 TCTAAGATTGTATATCATA
1 TCTAAGATTG--TATCATA
*
19617389 TCTAAGATTGCA--ATTA
1 TCTAAGATTGTATCA-TA
19617405 TCTAAGATTGTATCATA
1 TCTAAGATTGTATCATA
*
19617422 TCTAAGATTGCAATCATA
1 TCTAAGATTG-TATCATA
19617440 TCTAAGATTGTATCATA
1 TCTAAGATTGTATCATA
*
19617457 TCTAAGATTGCAATCATA
1 TCTAAGATTG-TATCATA
*
19617475 TTTAAGATTGTATCATA
1 TCTAAGATTGTATCATA
19617492 TCTAAGATT
1 TCTAAGATT
19617501 ACATATCATT
Statistics
Matches: 99, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.01
16 13 0.13
17 43 0.43
18 32 0.32
19 10 0.10
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (17 bp):
TCTAAGATTGTATCATA
Found at i:19617484 original size:70 final size:70
Alignment explanation
Indices: 19617363--19617509 Score: 221
Period size: 70 Copynumber: 2.1 Consensus size: 70
19617353 ATTACAAAAT
19617363 CATATC-T-TCTAAGATTGTATATCATATCTAAGATTGCAATTATCTAAGATTGTATCATATCTA
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTGCAATTATCTAAGATTGTATCATATCTA
*
19617426 AGATTG
65 AGATTA
*
19617432 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTGCAATCATATTTAAGATTGTATCATATCT
1 CATATCATATCTAAGATTGATATCATATCTAAGATTGCAAT--TATCTAAGATTGTATCATATCT
19617495 AAGATTA
64 AAGATTA
19617502 CATATCAT
1 CATATCAT
19617510 TGAAGTTATA
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
68 24 0.34
69 3 0.04
70 39 0.55
71 5 0.07
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (70 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTGCAATTATCTAAGATTGTATCATATCTAA
GATTA
Found at i:19618110 original size:83 final size:83
Alignment explanation
Indices: 19617891--19618242 Score: 625
Period size: 83 Copynumber: 4.2 Consensus size: 83
19617881 TTCGATTTGT
* * *
19617891 AAGGATGTCAAATCATC-TGAGTCTGTTTGAGAACATTTGAGAATCATATCTGCAAGGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCGA
*
19617955 CTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
*
19617973 AAGGATGCCTAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATGTCTGCAAGGTCCTCG
1 AAGGATGCC-AAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCG
19618038 ATTTGTTCCTTGTAAGCAC
65 ATTTGTTCCTTGTAAGCAC
*
19618057 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCGA
19618122 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
*
19618140 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCGA
19618205 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
19618223 AAGGATGCCAAACCATCTTG
1 AAGGATGCCAAACCATCTTG
19618243 GATCTGCTTC
Statistics
Matches: 261, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
82 8 0.03
83 182 0.70
84 71 0.27
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (83 bp):
AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCGA
TTTGTTCCTTGTAAGCAC
Found at i:19618515 original size:119 final size:119
Alignment explanation
Indices: 19618166--19618645 Score: 845
Period size: 119 Copynumber: 4.0 Consensus size: 119
19618156 CTTGAGTCTG
* * * * * * *
19618166 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
*
19618231 CAAACCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
19618285 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTT-CTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
*
19618349 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGTTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
19618403 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCAATTTGTTCCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
19618468 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
19618522 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
*
19618587 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATC
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
19618641 TTTGA
1 TTTGA
19618646 TCTGTTCCCT
Statistics
Matches: 346, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
118 112 0.32
119 234 0.68
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (119 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:19618713 original size:43 final size:44
Alignment explanation
Indices: 19618631--19618809 Score: 170
Period size: 44 Copynumber: 4.1 Consensus size: 44
19618621 TGAAGGTTAG
**
19618631 ATCTGCTATCTTTGATCTGTTCCCTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
19618675 ATCTGCTATCTTCAA-CTTGTT-CCTATAAACACAGGGATGCC--
1 ATCTGCTATCTTCAATC-TGTTCCCTATAAACACAGGGATGCCAA
** * * * * * *
19618716 ATGCTGAAATCTTCAATCTGCTTCGC-AGAGAGCACAGGAATGTCAG
1 AT-CTGCTATCTTCAATCTG-TTCCCTATA-AACACAGGGATGCCAA
* * *
19618762 ATCTACTATCTTCTATCTGTTCCCTATAAACATAGGGATGCCAA
1 ATCTGCTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
19618806 ATCT
1 ATCT
19618810 TGTTTCTTTG
Statistics
Matches: 106, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
41 2 0.02
42 13 0.12
43 26 0.25
44 48 0.45
45 15 0.14
46 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (44 bp):
ATCTGCTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
Found at i:19619709 original size:13 final size:12
Alignment explanation
Indices: 19619688--19619734 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
19619678 CTCTCCATTT
19619688 TTTTTTTTTCTC
1 TTTTTTTTTCTC
19619700 TTTATTTTTTTCTC
1 -TT-TTTTTTTCTC
19619714 TTTTTCTTTTCT-
1 TTTTT-TTTTCTC
19619726 TTTTTTTTT
1 TTTTTTTTT
19619735 TTTTTTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.12
12 8 0.25
13 10 0.31
14 10 0.31
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:19619709 original size:14 final size:13
Alignment explanation
Indices: 19619687--19619735 Score: 73
Period size: 14 Copynumber: 3.8 Consensus size: 13
19619677 CCTCTCCATT
19619687 TTTTTTTTTTCTC
1 TTTTTTTTTTCTC
19619700 TTTATTTTTTTCTC
1 TTT-TTTTTTTCTC
*
19619714 TTTTTCTTTTCT-
1 TTTTTTTTTTCTC
19619726 TTTTTTTTTT
1 TTTTTTTTTT
19619736 TTTTTGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 9 0.27
13 11 0.33
14 13 0.39
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTTCTC
Found at i:19625034 original size:2 final size:2
Alignment explanation
Indices: 19625027--19625056 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19625017 ATACATTAAT
19625027 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
19625057 AGAAATATAA
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:19625615 original size:7 final size:7
Alignment explanation
Indices: 19625599--19625705 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
19625589 AATAAATGAA
*
19625599 ATAATTT
1 ATAATAT
19625606 ATAATAT
1 ATAATAT
19625613 ATAATAT
1 ATAATAT
*
19625620 A-AAAAT
1 ATAATAT
* *
19625626 GTAAGTTT
1 ATAA-TAT
*
19625634 TTAA-A-
1 ATAATAT
*
19625639 ATAATGT
1 ATAATAT
19625646 ATAATAT
1 ATAATAT
*
19625653 A-AATAA
1 ATAATAT
19625659 ATAAATAT
1 AT-AATAT
19625667 ATAAGATAT
1 AT-A-ATAT
19625676 ATAAGT-T
1 ATAA-TAT
19625683 A-AA-AT
1 ATAATAT
19625688 ATAATAT
1 ATAATAT
19625695 ATAATA-
1 ATAATAT
19625701 ATAAT
1 ATAAT
19625706 TTACAAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
5 5 0.06
6 18 0.23
7 34 0.44
8 14 0.18
9 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:19625669 original size:21 final size:21
Alignment explanation
Indices: 19625637--19625701 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
19625627 TAAGTTTTTA
*
19625637 AAAT-AATGTATAATATAAAT
1 AAATAAATATATAATATAAAT
* *
19625657 AAATAAATATATAAGATATAT
1 AAATAAATATATAATATAAAT
*
19625678 AAGTTAAA-ATATAATATATAAT
1 AA-ATAAATATATAATATA-AAT
19625700 AA
1 AA
19625702 TAATTTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 24 0.67
22 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATAAATATATAATATAAAT
Found at i:19625670 original size:28 final size:29
Alignment explanation
Indices: 19625639--19625699 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
19625629 AGTTTTTAAA
19625639 ATAATGTATAATATAA-AT-AAATA-AATAT
1 ATAATG-AT-ATATAAGATAAAATATAATAT
*
19625667 ATAA-GATATATAAGTTAAAATATAATAT
1 ATAATGATATATAAGATAAAATATAATAT
19625695 ATAAT
1 ATAAT
19625700 AATAATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 6 0.21
28 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
ATAATGATATATAAGATAAAATATAATAT
Found at i:19625740 original size:12 final size:13
Alignment explanation
Indices: 19625721--19625751 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
19625711 AATTTTGAAA
19625721 ATATAAATAATAT
1 ATATAAATAATAT
19625734 A-ATAAATAATAT
1 ATATAAATAATAT
19625746 ATATAA
1 ATATAA
19625752 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:19625749 original size:16 final size:15
Alignment explanation
Indices: 19625726--19625756 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
19625716 TGAAAATATA
19625726 AATAATATAATAAAT
1 AATAATATAATAAAT
19625741 AATATATATAATAAAT
1 AATA-ATATAATAAAT
19625757 TAAAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATAATAAAT
Found at i:19626093 original size:18 final size:18
Alignment explanation
Indices: 19626057--19626172 Score: 173
Period size: 18 Copynumber: 6.5 Consensus size: 18
19626047 AATCATATCT
*
19626057 TCTAAGATTGTATATCATA
1 TCTAAGATTGCA-ATCATA
19626076 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
19626094 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
19626112 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
19626129 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
* *
19626147 TTTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
19626164 TCTAAGATT
1 TCTAAGATT
19626173 ACATATCATT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
17 30 0.33
18 49 0.54
19 11 0.12
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:19626134 original size:35 final size:36
Alignment explanation
Indices: 19626057--19626181 Score: 191
Period size: 35 Copynumber: 3.5 Consensus size: 36
19626047 AATCATATCT
* *
19626057 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGCATATCATATCTAAGATTG-TATCATA
19626094 TCTAAGATTGCA-ATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGTATCATA
*
19626129 TCTAAGATTGCA-ATCATATTTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGTATCATA
*
19626164 TCTAAGATTACATATCAT
1 TCTAAGATTGCATATCAT
19626182 TGAAGATTAT
Statistics
Matches: 83, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
35 51 0.61
36 21 0.25
37 11 0.13
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (36 bp):
TCTAAGATTGCATATCATATCTAAGATTGTATCATA
Found at i:19626136 original size:53 final size:53
Alignment explanation
Indices: 19626057--19626181 Score: 189
Period size: 53 Copynumber: 2.3 Consensus size: 53
19626047 AATCATATCT
19626057 TCTAAGATTGTATATCATATCTAAGATTGCAATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCAATCATATCTAAGATTG-AATCATA
* *
19626112 TCTAAGATTG-TATCATATCTAAGATTGCAATCATATTTAAGATTGTATCATA
1 TCTAAGATTGATATCATATCTAAGATTGCAATCATATCTAAGATTGAATCATA
*
19626164 TCTAAGATTACATATCAT
1 TCTAAGATT-GATATCAT
19626182 TGAAGATTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
52 15 0.23
53 34 0.52
54 6 0.09
55 10 0.15
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (53 bp):
TCTAAGATTGATATCATATCTAAGATTGCAATCATATCTAAGATTGAATCATA
Found at i:19627327 original size:2 final size:2
Alignment explanation
Indices: 19627320--19627387 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
19627310 GATTGTGAGT
19627320 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19627362 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
19627388 ATGAGTTTGC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19629509 original size:41 final size:41
Alignment explanation
Indices: 19629455--19629536 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
19629445 AAGAAAAGAA
*
19629455 AGAAAAAGTAAAAGAGAAAGAAGAAAGAAAGACGCACGGCT
1 AGAAAAAGAAAAAGAGAAAGAAGAAAGAAAGACGCACGGCT
19629496 AGAAAAAGAAAAAGAGAAAGAAGAAAGAAAGACGCACGGCT
1 AGAAAAAGAAAAAGAGAAAGAAGAAAGAAAGACGCACGGCT
19629537 TAGGGACTTC
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:0.60, C:0.10, G:0.27, T:0.04
Consensus pattern (41 bp):
AGAAAAAGAAAAAGAGAAAGAAGAAAGAAAGACGCACGGCT
Found at i:19633272 original size:19 final size:20
Alignment explanation
Indices: 19633248--19633285 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19633238 TAAATTTTCC
19633248 TTTTCTT-TTTCTTTCCCTT
1 TTTTCTTCTTTCTTTCCCTT
19633267 TTTTCTTCTTTCTTTCCCT
1 TTTTCTTCTTTCTTTCCCT
19633286 GCTATTCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCTTCTTTCTTTCCCTT
Found at i:19633275 original size:16 final size:17
Alignment explanation
Indices: 19633246--19633278 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19633236 CCTAAATTTT
*
19633246 CCTTTTCTTTTTCTTTC
1 CCTTTTCTTCTTCTTTC
19633263 CCTTTT-TTCTTCTTTC
1 CCTTTTCTTCTTCTTTC
19633279 TTTCCCTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
CCTTTTCTTCTTCTTTC
Found at i:19633359 original size:24 final size:23
Alignment explanation
Indices: 19633332--19633382 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
19633322 TTTTATTCTT
19633332 TTATTTATTATAACTATTAT-ATTA
1 TTATTTATTATAA--ATTATAATTA
*
19633356 TTA--TATTTTAAATTATAATTA
1 TTATTTATTATAAATTATAATTA
19633377 TTATTT
1 TTATTT
19633383 CTTAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
22 7 0.30
23 1 0.04
24 3 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATTTATTATAAATTATAATTA
Found at i:19633379 original size:21 final size:21
Alignment explanation
Indices: 19633347--19633394 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
19633337 TATTATAACT
19633347 ATTAT-ATTATTATATT-TTAA
1 ATTATAATTATTAT-TTCTTAA
19633367 ATTATAATTATTATTTCTTAA
1 ATTATAATTATTATTTCTTAA
*
19633388 ATAATAA
1 ATTATAA
19633395 GTAAATACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATAATTATTATTTCTTAA
Found at i:19639115 original size:11 final size:11
Alignment explanation
Indices: 19639089--19639117 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
19639079 AGATAACAAA
19639089 GAAAGAAAAAG
1 GAAAGAAAAAG
19639100 G-AAGAAAAAG
1 GAAAGAAAAAG
19639110 GAAAGAAA
1 GAAAGAAA
19639118 CAAATGTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
GAAAGAAAAAG
Found at i:19646303 original size:10 final size:10
Alignment explanation
Indices: 19646288--19646326 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
19646278 CTAGGATGAT
19646288 TGTTTTGACA
1 TGTTTTGACA
19646298 TGTTTTGA-A
1 TGTTTTGACA
19646307 TGTATTTGATCA
1 TGT-TTTGA-CA
19646319 TGTTTTGA
1 TGTTTTGA
19646327 ACTGGTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.15
10 13 0.50
11 5 0.19
12 4 0.15
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.54
Consensus pattern (10 bp):
TGTTTTGACA
Found at i:19647648 original size:2 final size:2
Alignment explanation
Indices: 19647641--19647675 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19647631 GCATAAAAAC
19647641 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 A
19647676 AGTCATTCAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19651999 original size:21 final size:19
Alignment explanation
Indices: 19651973--19652011 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
19651963 TAGTCCTTTA
19651973 CTAATTATTCTATCAATTGAG
1 CTAATT-TT-TATCAATTGAG
*
19651994 CTAATTTTTCTCAATTGA
1 CTAATTTTTATCAATTGA
19652012 AAATTTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (19 bp):
CTAATTTTTATCAATTGAG
Found at i:19653227 original size:13 final size:13
Alignment explanation
Indices: 19653188--19653240 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
19653178 AGTTTGGCAA
19653188 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
19653201 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
19653214 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
19653227 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
19653240 T
1 T
19653241 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.09
13 28 0.82
14 3 0.09
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:19660657 original size:27 final size:24
Alignment explanation
Indices: 19660627--19660675 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 24
19660617 CGAGGTAAGT
19660627 TTGTATGTAAAATAAGCTTTAATATAA
1 TTGTAT-TAAAAT--GCTTTAATATAA
*
19660654 TTGTATTTAAATGCTTTAATAT
1 TTGTATTAAAATGCTTTAATAT
19660676 TTCATGAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
26 5 0.24
27 6 0.29
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (24 bp):
TTGTATTAAAATGCTTTAATATAA
Found at i:19660947 original size:28 final size:28
Alignment explanation
Indices: 19660907--19660962 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
19660897 ACAGCTTGTG
19660907 TGAGCAGCACCGAGTAGCTATGTAACAC
1 TGAGCAGCACCGAGTAGCTATGTAACAC
19660935 TGAGCAGCACCGAGTAGCTATGTAACAC
1 TGAGCAGCACCGAGTAGCTATGTAACAC
19660963 CCCTATACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (28 bp):
TGAGCAGCACCGAGTAGCTATGTAACAC
Found at i:19664343 original size:26 final size:26
Alignment explanation
Indices: 19664312--19664419 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
19664302 TGAAATGCCC
*
19664312 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
19664338 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
19664364 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
19664390 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
19664416 ATCA
1 ATCA
19664420 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:19665518 original size:8 final size:8
Alignment explanation
Indices: 19665505--19665535 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
19665495 AATTTTTAAT
19665505 ATAATATA
1 ATAATATA
19665513 ATAATATA
1 ATAATATA
*
19665521 ATAATAAA
1 ATAATATA
19665529 ATAATAT
1 ATAATAT
19665536 TTACTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAATATA
Found at i:19666892 original size:21 final size:21
Alignment explanation
Indices: 19666866--19666915 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
19666856 ATGAATTCTT
19666866 AAATTAGAGGTCCTTAAATGG
1 AAATTAGAGGTCCTTAAATGG
19666887 AAATTAGAGGTCCTTAAATGG
1 AAATTAGAGGTCCTTAAATGG
*
19666908 TAATTAGA
1 AAATTAGA
19666916 CCATTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (21 bp):
AAATTAGAGGTCCTTAAATGG
Found at i:19681821 original size:7 final size:7
Alignment explanation
Indices: 19681809--19681833 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19681799 GTTGTCTTCT
19681809 TGTTTGA
1 TGTTTGA
19681816 TGTTTGA
1 TGTTTGA
19681823 TGTTTGA
1 TGTTTGA
19681830 TGTT
1 TGTT
19681834 GTGGTGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TGTTTGA
Found at i:19682763 original size:27 final size:28
Alignment explanation
Indices: 19682707--19682775 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
19682697 AAATTTGTAC
*
19682707 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCAAGTTTGATTATAT
* *
19682735 AGCACTAGGTGTGCAAG-TTGATTTTAT
1 AGCACTAAGTGTGCAAGTTTGATTATAT
19682762 AGCACTAAGTGTGC
1 AGCACTAAGTGTGC
19682776 GGACTCACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCAAGTTTGATTATAT
Found at i:19686010 original size:12 final size:12
Alignment explanation
Indices: 19685989--19686019 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19685979 AAAGTTGTGC
19685989 TAATTATAATTG
1 TAATTATAATTG
*
19686001 TAATTGTAATTG
1 TAATTATAATTG
19686013 TAATTAT
1 TAATTAT
19686020 TACTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (12 bp):
TAATTATAATTG
Found at i:19686224 original size:25 final size:25
Alignment explanation
Indices: 19686196--19686247 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
19686186 CATAAAATAA
19686196 AACTACATTTTATGTTGAATATGTT
1 AACTACATTTTATGTTGAATATGTT
19686221 AACTACATTTTATGTTGAATATGTT
1 AACTACATTTTATGTTGAATATGTT
19686246 AA
1 AA
19686248 AAATACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.46
Consensus pattern (25 bp):
AACTACATTTTATGTTGAATATGTT
Found at i:19686257 original size:25 final size:25
Alignment explanation
Indices: 19686204--19686257 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
19686194 AAAACTACAT
** *
19686204 TTTATGTTGAATATGTTAACTACAT
1 TTTATGTTGAATATGTTAAAAACAC
*
19686229 TTTATGTTGAATATGTTAAAAATAC
1 TTTATGTTGAATATGTTAAAAACAC
19686254 TTTA
1 TTTA
19686258 ATTAACTATT
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:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (25 bp):
TTTATGTTGAATATGTTAAAAACAC
Found at i:19690852 original size:16 final size:15
Alignment explanation
Indices: 19690833--19690866 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
19690823 TATTTTTCAT
19690833 TTTATATATTTTAAAA
1 TTTATA-ATTTTAAAA
*
19690849 TTTATAATTTTTAAA
1 TTTATAATTTTAAAA
19690864 TTT
1 TTT
19690867 TGTTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATAATTTTAAAA
Found at i:19690867 original size:32 final size:32
Alignment explanation
Indices: 19690761--19690867 Score: 78
Period size: 31 Copynumber: 3.4 Consensus size: 32
19690751 ATTTTGGAAT
* * * *
19690761 TTTTTATATTTTAAAATATTTTAAAA--AATCA
1 TTTTTAAATTTT-ATATATTTTAAAATTTATAA
* * * *
19690792 TTTTTTAATTTTTTAAATTTTAAAGAATTT-TTA
1 TTTTTAAATTTTATATATTTT-AA-AATTTATAA
*
19690825 TTTTT-CATTTTATATATTTTAAAATTTATAA
1 TTTTTAAATTTTATATATTTTAAAATTTATAA
19690856 TTTTTAAATTTT
1 TTTTTAAATTTT
19690868 GTTTAAATAG
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
30 11 0.19
31 21 0.36
32 19 0.33
33 7 0.12
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (32 bp):
TTTTTAAATTTTATATATTTTAAAATTTATAA
Found at i:19712856 original size:15 final size:15
Alignment explanation
Indices: 19712836--19712864 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19712826 TTTAATAATG
19712836 TATTAAATTATTTTT
1 TATTAAATTATTTTT
19712851 TATTAAATTATTTT
1 TATTAAATTATTTT
19712865 AATAATAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTAAATTATTTTT
Found at i:19714535 original size:20 final size:19
Alignment explanation
Indices: 19714490--19714585 Score: 67
Period size: 20 Copynumber: 5.1 Consensus size: 19
19714480 ATTAAATACA
19714490 AATTAATAAAATAATATAT
1 AATTAATAAAATAATATAT
19714509 AATTTAATAAAAT-ATA-AT
1 AA-TTAATAAAATAATATAT
* * *
19714527 TATTATTAAAATACTA-ATT
1 AATTAATAAAATAATATA-T
*
19714546 AA-TAA-AATTATAATATAT
1 AATTAATAA-AATAATATAT
* *
19714564 AATATTATAAAATAACATAT
1 AAT-TAATAAAATAATATAT
19714584 AA
1 AA
19714586 CCTACTTTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
17 11 0.19
18 16 0.27
19 8 0.14
20 22 0.37
21 2 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTAATAAAATAATATAT
Found at i:19714559 original size:15 final size:15
Alignment explanation
Indices: 19714500--19714565 Score: 57
Period size: 15 Copynumber: 4.3 Consensus size: 15
19714490 AATTAATAAA
*
19714500 ATAATATATAATT-T
1 ATAAAATATAATTAT
19714514 AATAAAATATAATTATT
1 -ATAAAATATAATTA-T
19714531 ATTAAAATACTAATTA-
1 A-TAAAATA-TAATTAT
19714547 ATAAAATTATAA-TAT
1 ATAAAA-TATAATTAT
19714562 ATAA
1 ATAA
19714566 TATTATAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
14 2 0.05
15 24 0.55
16 4 0.09
17 8 0.18
18 6 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAATATAATTAT
Found at i:19714575 original size:55 final size:51
Alignment explanation
Indices: 19714471--19714577 Score: 144
Period size: 55 Copynumber: 2.0 Consensus size: 51
19714461 ATATTTTAAC
*
19714471 ATAATTTTTATTAAATACAAATTAATAAAATAATATATAATTTAATAAAAT
1 ATAATTATTATTAAATACAAATTAATAAAATAATATATAATTTAATAAAAT
*
19714522 ATAATTATTATTAAAATACTAATTAATAAAATTATAATATATAATATT-ATAAAAT
1 ATAATTATTATT-AAATACAAATTAAT-AAA--ATAATATATAAT-TTAATAAAAT
19714577 A
1 A
19714578 ACATATAACC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
51 11 0.22
52 13 0.27
53 3 0.06
55 20 0.41
56 2 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (51 bp):
ATAATTATTATTAAATACAAATTAATAAAATAATATATAATTTAATAAAAT
Found at i:19715204 original size:14 final size:14
Alignment explanation
Indices: 19715182--19715215 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19715172 ATCATCCATC
*
19715182 TCTTTTTTTCTTTTT
1 TCTTTTTTT-TTTGT
19715197 TCTTTTTTTTTTGT
1 TCTTTTTTTTTTGT
19715211 TCTTT
1 TCTTT
19715216 GAAGATGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (14 bp):
TCTTTTTTTTTTGT
Found at i:19719177 original size:11 final size:10
Alignment explanation
Indices: 19719157--19719189 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
19719147 GGAAAGATAT
19719157 AAAAATGAAA
1 AAAAATGAAA
19719167 AAAAATGGAAA
1 AAAAAT-GAAA
19719178 AAAAATGAAA
1 AAAAATGAAA
19719188 AA
1 AA
19719190 GATCAAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:19727638 original size:13 final size:13
Alignment explanation
Indices: 19727620--19727644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19727610 AATAGGGGAC
19727620 ACATGACCGTGTA
1 ACATGACCGTGTA
19727633 ACATGACCGTGT
1 ACATGACCGTGT
19727645 GACGCACATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (13 bp):
ACATGACCGTGTA
Found at i:19731174 original size:40 final size:40
Alignment explanation
Indices: 19731129--19731224 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
19731119 TCGGTATCGT
*
19731129 ACACATAGTGCCATTTATTCAGCTATCGTTGTATATTCTC
1 ACACATAGTGCCATTTATTCAGCTATAGTTGTATATTCTC
19731169 ACACATAGTGCCATTTATTCAGCTATAGTTGTATATTCTC
1 ACACATAGTGCCATTTATTCAGCTATAGTTGTATATTCTC
*
19731209 GCACACTCAGTGCCAT
1 ACACA-T-AGTGCCAT
19731225 ATTTAATAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 43 0.83
41 1 0.02
42 8 0.15
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (40 bp):
ACACATAGTGCCATTTATTCAGCTATAGTTGTATATTCTC
Found at i:19732286 original size:13 final size:13
Alignment explanation
Indices: 19732268--19732292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19732258 CATAAACGAT
19732268 AAAATTTTCACAC
1 AAAATTTTCACAC
19732281 AAAATTTTCACA
1 AAAATTTTCACA
19732293 GATATCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:19732834 original size:15 final size:15
Alignment explanation
Indices: 19732814--19732843 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19732804 TCGAATGGCT
19732814 CATTCCATTCAACCA
1 CATTCCATTCAACCA
*
19732829 CATTCCGTTCAACCA
1 CATTCCATTCAACCA
19732844 AACAGGCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.40, G:0.03, T:0.27
Consensus pattern (15 bp):
CATTCCATTCAACCA
Found at i:19742339 original size:14 final size:14
Alignment explanation
Indices: 19742311--19742352 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
19742301 TTCAATTTAG
*
19742311 AATTATTAATATTA
1 AATTATTATTATTA
19742325 ATATTATT-TTATTA
1 A-ATTATTATTATTA
*
19742339 AATTCTTATTATTA
1 AATTATTATTATTA
19742353 TAATGTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.21
14 13 0.54
15 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTATTATTATTA
Found at i:19745364 original size:16 final size:16
Alignment explanation
Indices: 19745343--19745373 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19745333 ATTGAAAAAT
19745343 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
19745359 TTTCAAATTTATATG
1 TTTCAAATATATATG
19745374 CTTTAACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:19745927 original size:2 final size:2
Alignment explanation
Indices: 19745922--19745947 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19745912 ATTTTTTGTC
19745922 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
19745948 AATTAACCAC
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):
TA
Found at i:19754600 original size:18 final size:18
Alignment explanation
Indices: 19754573--19754706 Score: 160
Period size: 18 Copynumber: 7.4 Consensus size: 18
19754563 TATCAATATC
*
19754573 ATTCAGTAACAGTCGGTT
1 ATTCAGTAACAGTCAGTT
* **
19754591 ATTCAATAACAGTTGGTT
1 ATTCAGTAACAGTCAGTT
*
19754609 ATTCAGTAACAGTCAATT
1 ATTCAGTAACAGTCAGTT
* *
19754627 ATTCAGTAATAATCAGTT
1 ATTCAGTAACAGTCAGTT
*
19754645 ATTCAGTAACAGTCATTT
1 ATTCAGTAACAGTCAGTT
* *
19754663 ATTCAGTAACAGTTAATT
1 ATTCAGTAACAGTCAGTT
* *
19754681 ATTCAGTAGCAATCAGTT
1 ATTCAGTAACAGTCAGTT
19754699 ATTCAGTA
1 ATTCAGTA
19754707 CCTTTATTTA
Statistics
Matches: 98, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 98 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (18 bp):
ATTCAGTAACAGTCAGTT
Found at i:19754704 original size:54 final size:54
Alignment explanation
Indices: 19754573--19754706 Score: 187
Period size: 54 Copynumber: 2.5 Consensus size: 54
19754563 TATCAATATC
* * * **
19754573 ATTCAGTAACAGTCGGTTATTCAATAACAGTTGGTTATTCAGTAACAGTCAATT
1 ATTCAGTAACAATCAGTTATTCAGTAACAGTCAGTTATTCAGTAACAGTCAATT
* * *
19754627 ATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTAACAGTTAATT
1 ATTCAGTAACAATCAGTTATTCAGTAACAGTCAGTTATTCAGTAACAGTCAATT
*
19754681 ATTCAGTAGCAATCAGTTATTCAGTA
1 ATTCAGTAACAATCAGTTATTCAGTA
19754707 CCTTTATTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (54 bp):
ATTCAGTAACAATCAGTTATTCAGTAACAGTCAGTTATTCAGTAACAGTCAATT
Found at i:19755638 original size:17 final size:16
Alignment explanation
Indices: 19755607--19755642 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
19755597 TGAAATTTCC
*
19755607 CTTTCTTCTTTCTTTT
1 CTTTCTTCCTTCTTTT
19755623 CTTTCTTTCCTTCTTTT
1 CTTTC-TTCCTTCTTTT
19755640 CTT
1 CTT
19755643 CTCTGTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
CTTTCTTCCTTCTTTT
Found at i:19755888 original size:17 final size:18
Alignment explanation
Indices: 19755868--19755902 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
19755858 ATATATATTT
19755868 TTTATAAATAA-TAAATA
1 TTTATAAATAATTAAATA
19755885 TTTATAAATAATTAAATA
1 TTTATAAATAATTAAATA
19755903 CATGTATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTATAAATAATTAAATA
Found at i:19756150 original size:15 final size:16
Alignment explanation
Indices: 19756116--19756161 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
19756106 ATTTATTTCA
19756116 TAATAAAATATCAAAT
1 TAATAAAATATCAAAT
19756132 TAATAAAA-AT-AACAT
1 TAATAAAATATCAA-AT
19756147 TAAT-AAATATCAAAT
1 TAATAAAATATCAAAT
19756162 ATAAAACCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.19
15 12 0.44
16 10 0.37
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATAAAATATCAAAT
Found at i:19756178 original size:3 final size:3
Alignment explanation
Indices: 19756170--19756204 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19756160 ATATAAAACC
19756170 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
19756205 TATTATTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:19756181 original size:30 final size:30
Alignment explanation
Indices: 19756115--19756182 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
19756105 AATTTATTTC
19756115 ATAATAAAATATCAAATTAATAAAAATAACA
1 ATAAT-AAATATCAAATTAATAAAAATAACA
* *
19756146 TTAATAAATATCAAA-T-ATAAAACCATAATA
1 ATAATAAATATCAAATTAATAAAA--ATAACA
19756176 ATAATAA
1 ATAATAA
19756183 TAATAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 6 0.19
29 1 0.03
30 21 0.66
31 4 0.12
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (30 bp):
ATAATAAATATCAAATTAATAAAAATAACA
Found at i:19766086 original size:15 final size:16
Alignment explanation
Indices: 19766066--19766096 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19766056 TTATTTAAAA
19766066 TTTAAAA-TTATTATT
1 TTTAAAATTTATTATT
19766081 TTTAAAATTTATTATT
1 TTTAAAATTTATTATT
19766097 AAAATAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTTATTATT
Found at i:19766124 original size:17 final size:17
Alignment explanation
Indices: 19766084--19766125 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
19766074 TATTATTTTT
*
19766084 AAAATT-TATTATTAAA
1 AAAATTATAATATTAAA
19766100 ATAGAATTATAATATTAAA
1 A-A-AATTATAATATTAAA
19766119 AAAATTA
1 AAAATTA
19766126 CTAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 1 0.05
17 6 0.27
18 5 0.23
19 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATTATAATATTAAA
Found at i:19779845 original size:32 final size:32
Alignment explanation
Indices: 19779778--19779845 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
19779768 TAACTTATTA
* *
19779778 TATATTATATGTTATATTATATAATAGAAATG
1 TATATTATACGTTATATTATATAAAAGAAATG
*
19779810 TATA-TATACGTTATAATTATAATAAAATAAA-G
1 TATATTATACGTTAT-ATTAT-ATAAAAGAAATG
19779842 TATA
1 TATA
19779846 ATAAAACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 9 0.29
32 14 0.45
33 8 0.26
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (32 bp):
TATATTATACGTTATATTATATAAAAGAAATG
Found at i:19783879 original size:21 final size:20
Alignment explanation
Indices: 19783816--19783882 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
19783806 GAGCTTAACA
19783816 GAAACCCATAAGGGTTAAACT
1 GAAACCCA-AAGGGTTAAACT
* ** * * *
19783837 GAAGCTTAAAAGATTGAACT
1 GAAACCCAAAGGGTTAAACT
19783857 GAAACCCAGAAGGGTTAAACT
1 GAAACCCA-AAGGGTTAAACT
19783878 GAAAC
1 GAAAC
19783883 TCATATGAGT
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (20 bp):
GAAACCCAAAGGGTTAAACT
Found at i:19783899 original size:41 final size:41
Alignment explanation
Indices: 19783787--19783900 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
19783777 ACCCGTGTGA
* * * * *
19783787 GTTAAACGGAAGCTCATAGGAGCTTAACAGAAACCCATAAGG
1 GTTAAACTGAAGCTCATAAGAG-TTGACTGAAACCCAGAAGG
* *
19783829 GTTAAACTGAAGCTTAAAAGA-TTGAACTGAAACCCAGAAGG
1 GTTAAACTGAAGCTCATAAGAGTTG-ACTGAAACCCAGAAGG
* *
19783870 GTTAAACTGAAACTCATATGAGTTGACTGAA
1 GTTAAACTGAAGCTCATAAGAGTTGACTGAA
19783901 GCTCATGAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
40 2 0.03
41 37 0.63
42 20 0.34
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (41 bp):
GTTAAACTGAAGCTCATAAGAGTTGACTGAAACCCAGAAGG
Found at i:19785868 original size:27 final size:27
Alignment explanation
Indices: 19785634--19785867 Score: 310
Period size: 27 Copynumber: 8.7 Consensus size: 27
19785624 CCAAAGTACT
*
19785634 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
19785661 CTC-AGTTTATAGAATTACCGTTTTACC
1 CTCGA-TTTATAGAATTACCGTTTTACC
*
19785688 CTC-AGTTTATAGAATTACTGTTTTACC
1 CTCGA-TTTATAGAATTACCGTTTTACC
* *
19785715 CTCGATTTGTAAAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
19785742 CTCGATTTATAGAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* * * *
19785769 CTCGATTTACAGTATTTCCATTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
*
19785796 CTCGATTTATAGAATTACTGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* * *
19785823 CTTGATTTACAGAATTACTGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* *
19785850 CTCGATTTACAAAATTAC
1 CTCGATTTATAGAATTAC
19785868 TAAAATACCC
Statistics
Matches: 185, Mismatches: 20, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 183 0.99
28 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (27 bp):
CTCGATTTATAGAATTACCGTTTTACC
Found at i:19785877 original size:81 final size:81
Alignment explanation
Indices: 19785617--19785878 Score: 285
Period size: 81 Copynumber: 3.2 Consensus size: 81
19785607 CTCGACTTGT
* * * *
19785617 AAAATTACCAAAGTACTCTCGATTTACAGAATTACCGTTTTACCC-TCAGTTTATAGAATTACCG
1 AAAATTACCAAATTACCCTCGATTTATAGAATTACCGTTTTACCCTTGA-TTTATAGAATTACCG
*
19785681 TTTTACCCTC-AGTTTAT
65 TTTTACCCTCGA-TTTAC
* **** * * *
19785698 AGAATTACTGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGT
1 AAAATTACCAAATTACCCTCGATTTATAGAATTACCGTTTTACCCTTGATTTATAGAATTACCGT
19785763 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
** * ** * * *
19785779 AGTATTTCCATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGT
1 AAAATTACCAAATTACCCTCGATTTATAGAATTACCGTTTTACCCTTGATTTATAGAATTACCGT
19785844 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
* *
19785860 AAAATTACTAAAATACCCT
1 AAAATTACCAAATTACCCT
19785879 TGGTTTGTGA
Statistics
Matches: 149, Mismatches: 30, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
81 147 0.99
82 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.40
Consensus pattern (81 bp):
AAAATTACCAAATTACCCTCGATTTATAGAATTACCGTTTTACCCTTGATTTATAGAATTACCGT
TTTACCCTCGATTTAC
Found at i:19785893 original size:81 final size:80
Alignment explanation
Indices: 19785646--19785896 Score: 290
Period size: 81 Copynumber: 3.1 Consensus size: 80
19785636 CGATTTACAG
* * *
19785646 AATTACCGTTTTACCC-TCAGTTTATAGAATTACCGTTTTACCCTC-AGTTTATAGAATTACTGT
1 AATTACCGTTTTACCCTTGA-TTTATAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACTAT
19785709 TTTACCCTCGATTTGTAA
64 TTTACCCTCGATTTGT-A
* * * *
19785727 AATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGTATTTCCATTT
1 AATTACCGTTTTACCCTTGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTT
*
19785792 TACCCTCGATTTATA
66 TACCCTCGATTTGTA
* * * * **
19785807 GAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAA
1 -AATTACCGTTTTACCCTTGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATT
* * *
19785872 ATACCCTTGGTTTGTGA
65 TTACCCTCGATTTGT-A
19785889 AATTACCG
1 AATTACCG
19785897 CAATACCCTC
Statistics
Matches: 143, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
80 1 0.01
81 139 0.97
82 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (80 bp):
AATTACCGTTTTACCCTTGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTT
TACCCTCGATTTGTA
Found at i:19787133 original size:25 final size:25
Alignment explanation
Indices: 19787105--19787152 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
19787095 TTATACCATG
* * *
19787105 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
19787130 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
19787153 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:19787255 original size:20 final size:20
Alignment explanation
Indices: 19787195--19787255 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
19787185 ATAAATATGG
*
19787195 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
19787215 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
19787235 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
19787255 T
1 T
19787256 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:19787383 original size:23 final size:23
Alignment explanation
Indices: 19787305--19787471 Score: 246
Period size: 24 Copynumber: 7.0 Consensus size: 23
19787295 GAGGAAGTGA
19787305 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
19787328 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
19787352 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
19787376 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
19787399 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
* *
19787423 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
19787447 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
19787471 A
1 A
19787472 TGATAAAGCA
Statistics
Matches: 135, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
23 45 0.33
24 80 0.59
25 10 0.07
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:19787398 original size:47 final size:46
Alignment explanation
Indices: 19787305--19787471 Score: 246
Period size: 47 Copynumber: 3.5 Consensus size: 46
19787295 GAGGAAGTGA
19787305 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTAT
19787352 CAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
* *
19787399 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAGGGCTTATGCCCCAGTTA-T
*
19787447 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
19787472 TGATAAAGCA
Statistics
Matches: 111, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
46 22 0.20
47 44 0.40
48 35 0.32
49 10 0.09
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
Found at i:19787697 original size:31 final size:31
Alignment explanation
Indices: 19787662--19787725 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
19787652 CGTTTACAGT
*
19787662 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
19787693 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
19787724 AA
1 AA
19787726 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:19790796 original size:27 final size:27
Alignment explanation
Indices: 19790562--19790795 Score: 310
Period size: 27 Copynumber: 8.7 Consensus size: 27
19790552 CCAAAGTACT
*
19790562 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
19790589 CTC-AGTTTATAGAATTACCGTTTTACC
1 CTCGA-TTTATAGAATTACCGTTTTACC
*
19790616 CTC-AGTTTATAGAATTACTGTTTTACC
1 CTCGA-TTTATAGAATTACCGTTTTACC
* *
19790643 CTCGATTTGTAAAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
19790670 CTCGATTTATAGAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* * * *
19790697 CTCGATTTACAGTATTTCCATTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
*
19790724 CTCGATTTATAGAATTACTGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* * *
19790751 CTTGATTTACAGAATTACTGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* *
19790778 CTCGATTTACAAAATTAC
1 CTCGATTTATAGAATTAC
19790796 TAAAATACCC
Statistics
Matches: 185, Mismatches: 20, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 183 0.99
28 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (27 bp):
CTCGATTTATAGAATTACCGTTTTACC
Found at i:19790805 original size:81 final size:81
Alignment explanation
Indices: 19790545--19790806 Score: 285
Period size: 81 Copynumber: 3.2 Consensus size: 81
19790535 CTCGACTTGT
* * * *
19790545 AAAATTACCAAAGTACTCTCGATTTACAGAATTACCGTTTTACCC-TCAGTTTATAGAATTACCG
1 AAAATTACCAAATTACCCTCGATTTATAGAATTACCGTTTTACCCTTGA-TTTATAGAATTACCG
*
19790609 TTTTACCCTC-AGTTTAT
65 TTTTACCCTCGA-TTTAC
* **** * * *
19790626 AGAATTACTGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGT
1 AAAATTACCAAATTACCCTCGATTTATAGAATTACCGTTTTACCCTTGATTTATAGAATTACCGT
19790691 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
** * ** * * *
19790707 AGTATTTCCATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGT
1 AAAATTACCAAATTACCCTCGATTTATAGAATTACCGTTTTACCCTTGATTTATAGAATTACCGT
19790772 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
* *
19790788 AAAATTACTAAAATACCCT
1 AAAATTACCAAATTACCCT
19790807 TGGTTTGTGA
Statistics
Matches: 149, Mismatches: 30, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
81 147 0.99
82 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.40
Consensus pattern (81 bp):
AAAATTACCAAATTACCCTCGATTTATAGAATTACCGTTTTACCCTTGATTTATAGAATTACCGT
TTTACCCTCGATTTAC
Found at i:19790821 original size:81 final size:80
Alignment explanation
Indices: 19790574--19790824 Score: 290
Period size: 81 Copynumber: 3.1 Consensus size: 80
19790564 CGATTTACAG
* * *
19790574 AATTACCGTTTTACCC-TCAGTTTATAGAATTACCGTTTTACCCTC-AGTTTATAGAATTACTGT
1 AATTACCGTTTTACCCTTGA-TTTATAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACTAT
19790637 TTTACCCTCGATTTGTAA
64 TTTACCCTCGATTTGT-A
* * * *
19790655 AATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGTATTTCCATTT
1 AATTACCGTTTTACCCTTGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTT
*
19790720 TACCCTCGATTTATA
66 TACCCTCGATTTGTA
* * * * **
19790735 GAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAA
1 -AATTACCGTTTTACCCTTGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATT
* * *
19790800 ATACCCTTGGTTTGTGA
65 TTACCCTCGATTTGT-A
19790817 AATTACCG
1 AATTACCG
19790825 CAATACCCTC
Statistics
Matches: 143, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
80 1 0.01
81 139 0.97
82 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (80 bp):
AATTACCGTTTTACCCTTGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTT
TACCCTCGATTTGTA
Found at i:19792062 original size:25 final size:25
Alignment explanation
Indices: 19792034--19792081 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
19792024 TTATACCATG
* * *
19792034 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
19792059 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
19792082 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:19792184 original size:20 final size:20
Alignment explanation
Indices: 19792124--19792184 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
19792114 ATAAATATGG
*
19792124 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
19792144 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
19792164 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
19792184 T
1 T
19792185 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:19792312 original size:23 final size:23
Alignment explanation
Indices: 19792234--19792400 Score: 246
Period size: 24 Copynumber: 7.0 Consensus size: 23
19792224 GAGGAAGTGA
19792234 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
19792257 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
19792281 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
19792305 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
19792328 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
* *
19792352 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
19792376 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
19792400 A
1 A
19792401 TGATAAAGCA
Statistics
Matches: 135, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
23 45 0.33
24 80 0.59
25 10 0.07
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:19792327 original size:47 final size:46
Alignment explanation
Indices: 19792234--19792400 Score: 246
Period size: 47 Copynumber: 3.5 Consensus size: 46
19792224 GAGGAAGTGA
19792234 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTAT
19792281 CAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
* *
19792328 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAGGGCTTATGCCCCAGTTA-T
*
19792376 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
19792401 TGATAAAGCA
Statistics
Matches: 111, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
46 22 0.20
47 44 0.40
48 35 0.32
49 10 0.09
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
Found at i:19792628 original size:31 final size:31
Alignment explanation
Indices: 19792590--19792653 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
19792580 CATTTACAGT
*
19792590 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
19792621 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
19792652 AA
1 AA
19792654 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:19794341 original size:11 final size:11
Alignment explanation
Indices: 19794325--19794381 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
19794315 TTATATACTA
19794325 AATAAAATAAT
1 AATAAAATAAT
19794336 AATAAAAT-AT
1 AATAAAATAAT
*
19794346 AATTAAA-AAT
1 AATAAAATAAT
*
19794356 CAAATCAAAATATT
1 --AAT-AAAATAAT
19794370 AATAAAATAAT
1 AATAAAATAAT
19794381 A
1 A
19794382 TTTATTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
10 10 0.27
11 16 0.43
12 6 0.16
13 3 0.08
14 2 0.05
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:19794355 original size:23 final size:23
Alignment explanation
Indices: 19794325--19794381 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
19794315 TTATATACTA
19794325 AATAAAATAATAAT-AAAATA-T
1 AATAAAATAATAATCAAAATATT
*
19794346 AATTAAA-AATCAAATCAAAATATT
1 AATAAAATAAT--AATCAAAATATT
19794370 AATAAAATAATA
1 AATAAAATAATA
19794382 TTTATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 3 0.10
21 6 0.21
22 3 0.10
23 7 0.24
24 7 0.24
25 3 0.10
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AATAAAATAATAATCAAAATATT
Found at i:19800021 original size:21 final size:21
Alignment explanation
Indices: 19799991--19800031 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19799981 AAGGGAAGGA
19799991 GGTGGCGGCGTCACCGGCGGC
1 GGTGGCGGCGTCACCGGCGGC
* **
19800012 GGTGGTGGCGTTGCCGGCGG
1 GGTGGCGGCGTCACCGGCGG
19800032 TGGAGGTGAG
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:0.02, C:0.27, G:0.56, T:0.15
Consensus pattern (21 bp):
GGTGGCGGCGTCACCGGCGGC
Found at i:19801472 original size:2 final size:2
Alignment explanation
Indices: 19801465--19801493 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19801455 GGTACAGATA
19801465 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 A
19801494 AAGAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19802525 original size:14 final size:14
Alignment explanation
Indices: 19802506--19802539 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
19802496 GCCTTGATTT
19802506 TTTCTTC-TCGTTTC
1 TTTCTTCTTC-TTTC
19802520 TTTCTTCTTCTTTC
1 TTTCTTCTTCTTTC
19802534 TTTCTT
1 TTTCTT
19802540 TTTTTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTCTTCTTCTTTC
Found at i:19804662 original size:24 final size:24
Alignment explanation
Indices: 19804630--19804686 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
19804620 TTTGCTGGCA
*
19804630 CAGGTTCATATACCTATGAGTTTT
1 CAGGCTCATATACCTATGAGTTTT
19804654 CAGGCTCATATACCTATGAGTTTT
1 CAGGCTCATATACCTATGAGTTTT
**
19804678 TGGGCTCAT
1 CAGGCTCAT
19804687 GCTTTCATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (24 bp):
CAGGCTCATATACCTATGAGTTTT
Found at i:19810481 original size:19 final size:19
Alignment explanation
Indices: 19810459--19810497 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19810449 TTATAATTGT
*
19810459 AATAAATATT-AATTATTAA
1 AATAAA-ATTGAAATATTAA
19810478 AATAAAATTGAAATATTAA
1 AATAAAATTGAAATATTAA
19810497 A
1 A
19810498 TAATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AATAAAATTGAAATATTAA
Found at i:19810752 original size:18 final size:19
Alignment explanation
Indices: 19810731--19810770 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
19810721 CTTACGCTTT
19810731 AAAAGTTG-TTTATAGAAA
1 AAAAGTTGATTTATAGAAA
19810749 AAAAGTTGATTTTATAGAAA
1 AAAAGTTGA-TTTATAGAAA
19810769 AA
1 AA
19810771 TAACTAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (19 bp):
AAAAGTTGATTTATAGAAA
Found at i:19811704 original size:6 final size:6
Alignment explanation
Indices: 19811680--19811723 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
19811670 TAATAAGAAT
*
19811680 AATAAG AATAAA TAA-AAA AAT-AA AATAAA AATAAA AATAAA AAT
1 AATAAA AATAAA -AATAAA AATAAA AATAAA AATAAA AATAAA AAT
19811724 TAGGTTGCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
5 7 0.21
6 25 0.74
7 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:19811708 original size:17 final size:17
Alignment explanation
Indices: 19811680--19811721 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
19811670 TAATAAGAAT
19811680 AATAAGAATAAATAA-AAA
1 AATAA-AATAAA-AATAAA
19811698 AATAAAATAAAAATAAA
1 AATAAAATAAAAATAAA
19811715 AATAAAA
1 AATAAAA
19811722 ATTAGGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 16 0.70
18 5 0.22
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (17 bp):
AATAAAATAAAAATAAA
Found at i:19811712 original size:23 final size:23
Alignment explanation
Indices: 19811680--19811723 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
19811670 TAATAAGAAT
*
19811680 AATAAGAATAAATAA-AAAAATAA
1 AATAAAAATAAA-AATAAAAATAA
19811703 AATAAAAATAAAAATAAAAAT
1 AATAAAAATAAAAATAAAAAT
19811724 TAGGTTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (23 bp):
AATAAAAATAAAAATAAAAATAA
Found at i:19815383 original size:10 final size:10
Alignment explanation
Indices: 19815356--19815405 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
19815346 TTAAATTCTA
19815356 AAAGATAAAT
1 AAAGATAAAT
19815366 ACAA-ATAAAT
1 A-AAGATAAAT
*
19815376 AAAGATAATT
1 AAAGATAAAT
*
19815386 AAAGACAAAT
1 AAAGATAAAT
19815396 GAAA-ATAAAT
1 -AAAGATAAAT
19815406 CCTAAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 2 0.06
10 26 0.79
11 5 0.15
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:19815438 original size:13 final size:12
Alignment explanation
Indices: 19815422--19815451 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
19815412 ATTAAATCTA
19815422 AATAATTATCCTT
1 AATAATTATCC-T
19815435 AATAATTATCCT
1 AATAATTATCCT
19815447 AATAA
1 AATAA
19815452 AATTGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAATTATCCT
Found at i:19816505 original size:17 final size:17
Alignment explanation
Indices: 19816485--19816517 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19816475 TAAAATTGAG
19816485 TTGAGAACA-TAATTTAA
1 TTGAGAA-ATTAATTTAA
19816502 TTGAGAAATTAATTTA
1 TTGAGAAATTAATTTA
19816518 GTTAAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (17 bp):
TTGAGAAATTAATTTAA
Found at i:19817480 original size:50 final size:51
Alignment explanation
Indices: 19817399--19817494 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 51
19817389 AACAACATCA
* * * *
19817399 TCTTCTTTTAAAGACTCGACATCATCTTCATCCC-AATGCCTTCACATGTC
1 TCTTCATTTAAAGACTCAACATCACCCTCATCCCTAATGCCTTCACATGTC
* * *
19817449 TCTTCATTTGAAGACTCAACGTCACCCTCATCCCTAATGGCTTCAC
1 TCTTCATTTAAAGACTCAACATCACCCTCATCCCTAATGCCTTCAC
19817495 CTGTTGTGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 28 0.74
51 10 0.26
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (51 bp):
TCTTCATTTAAAGACTCAACATCACCCTCATCCCTAATGCCTTCACATGTC
Found at i:19819165 original size:24 final size:24
Alignment explanation
Indices: 19819138--19819183 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
19819128 TTAAAAAAAA
19819138 AATTTATGA-ACTTTTTATAATTTT
1 AATTTATGATACTTTTTA-AATTTT
*
19819162 AATTTTTGATACTTTTTAAATT
1 AATTTATGATACTTTTTAAATT
19819184 CTTTGTTGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (24 bp):
AATTTATGATACTTTTTAAATTTT
Found at i:19820152 original size:2 final size:2
Alignment explanation
Indices: 19820145--19820170 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19820135 TTGCCGGATA
19820145 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
19820171 GAGTAGGTTT
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:19823688 original size:24 final size:24
Alignment explanation
Indices: 19823656--19823705 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
19823646 TGCTCTAACT
*
19823656 TAATTTAATAGTAATATAGAGTAG
1 TAATTTAATAGTAATAAAGAGTAG
*
19823680 TAATTTAATAGTAATAAATAGTAG
1 TAATTTAATAGTAATAAAGAGTAG
19823704 TA
1 TA
19823706 GGATCGATCC
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:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (24 bp):
TAATTTAATAGTAATAAAGAGTAG
Found at i:19823693 original size:11 final size:11
Alignment explanation
Indices: 19823656--19823694 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
19823646 TGCTCTAACT
19823656 TAATTTAATAG
1 TAATTTAATAG
*
19823667 TAATATAGAGTAG
1 TAATTTA-A-TAG
19823680 TAATTTAATAG
1 TAATTTAATAG
19823691 TAAT
1 TAAT
19823695 AAATAGTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 13 0.54
12 2 0.08
13 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (11 bp):
TAATTTAATAG
Found at i:19824979 original size:30 final size:31
Alignment explanation
Indices: 19824943--19825006 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
19824933 AATTATTTTA
*
19824943 TTGTTAA-TTTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTTATTATTATTTTAGAA-GCAT
19824973 TTGTTAATTTTTATTATTATTTTAGAAGCAT
1 TTGTTAATTTTTATTATTATTTTAGAAGCAT
19825004 TTG
1 TTG
19825007 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 7 0.23
31 22 0.71
32 2 0.06
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.58
Consensus pattern (31 bp):
TTGTTAATTTTTATTATTATTTTAGAAGCAT
Found at i:19830938 original size:23 final size:21
Alignment explanation
Indices: 19830905--19830978 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 21
19830895 AACATATATA
19830905 ATTTTTTTAAAAAGTTTAAAAT
1 ATTTTTTTAAAAA-TTTAAAAT
*
19830927 ATTTTTTATAAAATTTTAAAAT
1 ATTTTTT-TAAAAATTTAAAAT
* *
19830949 ATAATTTTTTATAAATTTAAATT
1 AT--TTTTTTAAAAATTTAAAAT
*
19830972 AATTTTT
1 ATTTTTT
19830979 ATATATTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.11
22 17 0.39
23 17 0.39
24 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (21 bp):
ATTTTTTTAAAAATTTAAAAT
Found at i:19830983 original size:22 final size:23
Alignment explanation
Indices: 19830903--19830983 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
19830893 ATAACATATA
* * *
19830903 TAATTTTTTTAAAAAGTTTAAAA
1 TAATTTTTATATAAAGTTTAAAT
* *
19830926 TATTTTTTATA-AAATTTTAAAAT
1 TAATTTTTATATAAAGTTT-AAAT
19830949 ATAATTTTT-TATAAA-TTTAAAT
1 -TAATTTTTATATAAAGTTTAAAT
19830971 TAATTTTTATATA
1 TAATTTTTATATA
19830984 TTATTTTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
21 8 0.16
22 14 0.29
23 17 0.35
24 10 0.20
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
TAATTTTTATATAAAGTTTAAAT
Found at i:19831007 original size:30 final size:32
Alignment explanation
Indices: 19830930--19831035 Score: 96
Period size: 32 Copynumber: 3.3 Consensus size: 32
19830920 TTAAAATATT
* * *
19830930 TTTTATAAAATTTTAAAATATAATTTTTTATAAA
1 TTTTATAAAATTTTTAATTAT-ATATTTTA-AAA
*
19830964 -TTTA-AATTAATTTTT-A-TATATTATTTTGAAA
1 TTTTATAA--AATTTTTAATTATA-TATTTTAAAA
19830995 TTTT-TAAAATTTTTAATTATATATTTTAAAA
1 TTTTATAAAATTTTTAATTATATATTTTAAAA
19831026 TTTTATAAAA
1 TTTTATAAAA
19831036 AAATTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
30 7 0.12
31 18 0.30
32 24 0.40
33 5 0.08
34 6 0.10
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TTTTATAAAATTTTTAATTATATATTTTAAAA
Found at i:19831221 original size:15 final size:16
Alignment explanation
Indices: 19831201--19831230 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19831191 AATAGTCTTT
19831201 TTTAATATT-TAAATA
1 TTTAATATTATAAATA
19831216 TTTAATATTATAAAT
1 TTTAATATTATAAAT
19831231 TTATATTTTA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATATTATAAATA
Done.