Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 72 of 345
Found at i:19624909 original size:19 final size:19
Alignment explanation
Indices: 19624885--19624922 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19624875 ACACACATAC
*
19624885 AACATATGCAGGTTGAATT
1 AACATATACAGGTTGAATT
19624904 AACATATACAGGTTGAATT
1 AACATATACAGGTTGAATT
19624923 TTCCGATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (19 bp):
AACATATACAGGTTGAATT
Found at i:19628252 original size:3 final size:3
Alignment explanation
Indices: 19628241--19628296 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
19628231 AATTTAATAA
19628241 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19628287 TAT TAT TAT T
1 TAT TAT TAT T
19628297 GTTGTTACAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19628666 original size:23 final size:22
Alignment explanation
Indices: 19628635--19628682 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 22
19628625 TTTTTTTTCC
*
19628635 TTTCTCTTCTACTTCTCCCTCTAT
1 TTTCTCTTC-A-TTCTCCATCTAT
*
19628659 TTTC-CTTCATTCTCCATCTCT
1 TTTCTCTTCATTCTCCATCTAT
19628680 TTT
1 TTT
19628683 AACTTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 13 0.59
22 1 0.05
23 4 0.18
24 4 0.18
ACGTcount: A:0.08, C:0.35, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTCTCTTCATTCTCCATCTAT
Found at i:19637504 original size:75 final size:73
Alignment explanation
Indices: 19637416--19637587 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
19637406 GGTTTTCCTC
*** * * **
19637416 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
19637480 TCAGTATGG
65 TCAGTATGG
*
19637489 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
19637554 CTCAGTATGG
64 CTCAGTATGG
19637564 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
19637588 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:19637585 original size:35 final size:35
Alignment explanation
Indices: 19637421--19637587 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
19637411 TCCTCATTGA
*** *
19637421 AATACCATACCTACATTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
19637456 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
19637496 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
19637531 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
19637566 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
19637588 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 88 0.75
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:19644985 original size:35 final size:35
Alignment explanation
Indices: 19644918--19645085 Score: 185
Period size: 35 Copynumber: 4.6 Consensus size: 35
19644908 TCCTCATTGA
*** *
19644918 AATACCATACCTACATTTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACA-TTTCACAACTCAGTAT-GGAT
* **
19644954 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
19644994 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
19645029 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
19645064 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
19645086 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
35 74 0.63
36 14 0.12
39 3 0.03
40 27 0.23
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:19645044 original size:75 final size:73
Alignment explanation
Indices: 19644913--19645085 Score: 210
Period size: 75 Copynumber: 2.4 Consensus size: 73
19644903 GGTTTTCCTC
*** * * **
19644913 ATTGAAATACCATACCTACATTTTTTTAACTCGGTATGGGAAATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACA-TTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAAC
19644978 TCAGTATGG
65 TCAGTATGG
*
19644987 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-GGATAATACCATACCTACATTTCACA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGGA-AATACCATACCTACATTTCACA
19645051 ACTCAGTATGG
63 ACTCAGTATGG
19645062 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
19645086 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 2 0.02
74 4 0.05
75 46 0.52
76 15 0.17
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:19656735 original size:43 final size:42
Alignment explanation
Indices: 19656688--19656772 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
19656678 ATTATGCTTG
19656688 AAAAAAAAGGAAATCAAGATGAAAACCCGAAAAAGGGCATCTTA
1 AAAAAAAAGG-AATCAAGATGAAAACCCG-AAAAGGGCATCTTA
* * *
19656732 AAAAAAAAGGGATCAAGGTGAAAACCCGAAAAGGGCGTCTT
1 AAAAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCATCTT
19656773 GATTAACACA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 12 0.32
43 16 0.42
44 10 0.26
ACGTcount: A:0.52, C:0.14, G:0.22, T:0.12
Consensus pattern (42 bp):
AAAAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCATCTTA
Found at i:19657648 original size:14 final size:14
Alignment explanation
Indices: 19657629--19657663 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19657619 CGCTGAGGTA
* *
19657629 TTTTCAATTTCTGT
1 TTTTCAATTTATAT
19657643 TTTTCAATTTATAT
1 TTTTCAATTTATAT
19657657 TTTTCAA
1 TTTTCAA
19657664 AAATCAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTATAT
Found at i:19657777 original size:88 final size:87
Alignment explanation
Indices: 19657580--19658352 Score: 386
Period size: 87 Copynumber: 8.8 Consensus size: 87
19657570 GTATTTTGAT
* ** ** * **
19657580 TCAACTTATATTGCGAGAAATGAGTTGAGCCTTAGGATACGCTGAGGTATTTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTATTTTCAAAATCTGTTT
*
19657645 TTCAATTTATATTTTTCAAAAA
66 TTCAATTTATATTTGTCAAAAA
* *
19657667 TCAACTCATATTGCGAGAGGTGAGTTAAGCCCCAGGGCACGCTGAGGTATTTTCAAAATCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTATTTTCAAAATCTGTTT
*
19657732 TTCAAATTTATGTTTGTCAAAAA
66 TTC-AATTTATATTTGTCAAAAA
* ** *
19657755 TTAACTCATATTGCGAGAGGTGAGTTGAG-CCTTGGCTCACATGCTGAGGTATTTTC--AA----
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGG---ACACGCTGAGGTATTTTCAAAATCTG
* *
19657813 TTTTT--A--TA-CTTT-TAAAAAA
63 TTTTTCAATTTATATTTGTCAAAAA
* * * * * * *
19657832 TCAACTCATATGGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGATATTTTCAAATTCTGT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGG--ACACGCTGAGGTATTTTCAAAATCTGT
* * * *
19657897 TGTTCAAATTTTGTTTTTAATTTCTACTTTTCCAAAA
64 TTTTC-AA-------TTT-A----TATTTGTCAAAAA
* ** ** *
19657934 TCAACTCATATCGCGAGAGGTGAGTTGAG-CCTTGGCTCACACGCTGAGGTATTTTCAATTTTTG
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGG---ACACGCTGAGGTATTTTCAAAATCTG
* *
19657998 TTTTTCAATTTCTGCTTT-TCAAAAAA
63 TTTTTCAATTTAT-ATTTGTC-AAAAA
* * * *** *
19658024 GTCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAGTTTTTGTT
1 -TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTATTTTCAAAATCTGTT
*
19658089 TTTCAATTTATATTTTTCAAAAAAAAA
65 TTTCAATTTATATTTGTC----AAAAA
* * * *
19658116 TCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGGTCACATG-TCGAGGTATTTTCAAAATCTG
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGG--ACACGCT-GAGGTATTTTCAAAATCTG
*
19658180 CTTTT--A---A-A-TT-TCAAAAAGA
63 TTTTTCAATTTATATTTGTC-AAAA-A
* * ** * * **
19658199 CCAACTCATATGGCGAGAGGTGAGTTGAG-CCTTGGCTCACGTACTGAGCTATTTTCAATTTCTG
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGG-ACACG--CTGAGGTATTTTCAAAATCTG
* *
19658263 -TTTT-AATGTT-TGTTT-T--TAAA
63 TTTTTCAAT-TTATATTTGTCAAAAA
** * *
19658283 TCAACTCATATTGCGAGAGGTGAGTTGAGCATCAGGACACGATGAGGTATTTT-AAATTTCTGTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTATTTTCAAA-ATCTGTT
*
19658347 TGTCAA
65 TTTCAA
19658353 AAATTAACTC
Statistics
Matches: 539, Mismatches: 90, Indels: 117
0.72 0.12 0.16
Matches are distributed among these distances:
77 51 0.09
78 6 0.01
79 3 0.01
81 7 0.01
82 27 0.05
83 51 0.09
84 40 0.07
85 6 0.01
86 3 0.01
87 63 0.12
88 53 0.10
89 41 0.08
90 22 0.04
91 61 0.11
92 10 0.02
93 22 0.04
94 3 0.01
95 1 0.00
96 1 0.00
101 7 0.01
102 61 0.11
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (87 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGACACGCTGAGGTATTTTCAAAATCTGTTT
TTCAATTTATATTTGTCAAAAA
Found at i:19658004 original size:14 final size:14
Alignment explanation
Indices: 19657985--19658019 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19657975 CGCTGAGGTA
* *
19657985 TTTTCAATTTTTGT
1 TTTTCAATTTCTGC
19657999 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
19658013 TTTTCAA
1 TTTTCAA
19658020 AAAAGTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:19658005 original size:102 final size:102
Alignment explanation
Indices: 19657819--19658005 Score: 275
Period size: 102 Copynumber: 1.8 Consensus size: 102
19657809 TCAATTTTTA
* * *
19657819 TACTTTTAAAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGATAT
1 TACTTTTAAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCCGAGATAT
19657884 TTTCAAATTCTGTTGTTCAAATTTTGTTTTTAATTTC
66 TTTCAAATTCTGTTGTTCAAATTTTGTTTTTAATTTC
** * * *
19657921 TACTTTTCCAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTAT
1 TACTTTTAAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCCGAGATAT
* * *
19657986 TTTCAATTTTTGTTTTTCAA
66 TTTCAAATTCTGTTGTTCAA
19658006 TTTCTGCTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 74 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (102 bp):
TACTTTTAAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCCGAGATAT
TTTCAAATTCTGTTGTTCAAATTTTGTTTTTAATTTC
Found at i:19658120 original size:91 final size:90
Alignment explanation
Indices: 19657899--19658352 Score: 362
Period size: 91 Copynumber: 5.2 Consensus size: 90
19657889 AATTCTGTTG
* * * *
19657899 TTCAAATTTTGTTTTT-AATTTCTACTTTTC--CAAAATCAACTCATATCGCGAGAGGTGAGTTG
1 TTCAATTTTTGTTTTTCAATTTATACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
*
19657961 AGCCT-TGGCTCACACGCTGAGGTATT
66 AGCCTCAGG--CACACGCTGAGGTATT
* * * *
19657987 TTCAATTTTTGTTTTTCAATTTCTGCTTTTCAAAAAAGTCAACTCATATTGCGAAAGGTGAGTTG
1 TTCAATTTTTGTTTTTCAATTTATACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
*
19658052 AGCCTCAGG-GCACGCTGAGGTATT
66 AGCCTCAGGCACACGCTGAGGTATT
* * *
19658076 TTCAGTTTTTGTTTTTCAATTTATATTTTTCAAAAAAAAATCAACTCATATTGCGAGAGATGAGT
1 TTCAATTTTTGTTTTTCAATTTATACTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGT
* *
19658141 TGAGCCTCGGGTCACATG-TCGAGGTATT
64 TGAGCCTCAGG-CACACGCT-GAGGTATT
** * * * * *
19658169 TTCAAAATCTGCTTTT--A---A-A--TTTCAAAAAGACCAACTCATATGGCGAGAGGTGAGTTG
1 TTCAATTTTTGTTTTTCAATTTATACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* * *
19658226 AGCCT-TGGCTCACGTACTGAGCTATT
66 AGCCTCAGGCACACG--CTGAGGTATT
* * *
19658252 TTCAATTTCTG-TTTT-AATGTT-T-GTTTT----TAAATCAACTCATATTGCGAGAGGTGAGTT
1 TTCAATTTTTGTTTTTCAAT-TTATACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* *
19658309 GAGCATCAGG-ACACGATGAGGTATT
65 GAGCCTCAGGCACACGCTGAGGTATT
* * *
19658334 TTAAATTTCTGTTTGTCAA
1 TTCAATTTTTGTTTTTCAA
19658353 AAATTAACTC
Statistics
Matches: 299, Mismatches: 44, Indels: 50
0.76 0.11 0.13
Matches are distributed among these distances:
81 4 0.01
82 24 0.08
83 55 0.18
84 38 0.13
85 6 0.02
87 1 0.00
88 19 0.06
89 54 0.18
91 73 0.24
92 3 0.01
93 22 0.07
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (90 bp):
TTCAATTTTTGTTTTTCAATTTATACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
AGCCTCAGGCACACGCTGAGGTATT
Found at i:19660202 original size:18 final size:18
Alignment explanation
Indices: 19660179--19660213 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19660169 ATATCATTGT
19660179 TATTTAATATTATTATTA
1 TATTTAATATTATTATTA
* *
19660197 TATTTACTCTTATTATT
1 TATTTAATATTATTATT
19660214 TAAAAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTAATATTATTATTA
Found at i:19660692 original size:15 final size:16
Alignment explanation
Indices: 19660672--19660704 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19660662 ATATATATTT
19660672 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
19660687 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
19660704 T
1 T
19660705 ATAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:19660776 original size:21 final size:21
Alignment explanation
Indices: 19660752--19660810 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
19660742 GTTTGAAGAA
19660752 TTGTTTTAATATTATTTTTAT
1 TTGTTTTAATATTATTTTTAT
*
19660773 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATA-TTATTTTTAT
*
19660795 GT-TTTTAA-ATATATTT
1 TTGTTTTAATAT-TATTT
19660811 GATTTATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 17 0.52
22 10 0.30
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (21 bp):
TTGTTTTAATATTATTTTTAT
Found at i:19660785 original size:12 final size:12
Alignment explanation
Indices: 19660752--19660791 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
19660742 GTTTGAAGAA
19660752 TTGTTTTAATA-
1 TTGTTTTAATAT
*
19660763 TTATTTT--TAT
1 TTGTTTTAATAT
19660773 TTGTTTTAATAT
1 TTGTTTTAATAT
19660785 TTGTTTT
1 TTGTTTT
19660792 TATGTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 2 0.08
10 6 0.25
11 6 0.25
12 10 0.42
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:19660825 original size:26 final size:24
Alignment explanation
Indices: 19660781--19660830 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
19660771 ATTTGTTTTA
*
19660781 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
19660805 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
19660831 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:19661173 original size:2 final size:2
Alignment explanation
Indices: 19661166--19661195 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19661156 CATTATTATT
19661166 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
19661196 CTTTATGCAA
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:19662934 original size:14 final size:16
Alignment explanation
Indices: 19662898--19662927 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19662888 TTATTTATTA
19662898 AAAT-AAAAAATTTAT
1 AAATAAAAAAATTTAT
19662913 AAATAAAAAAATTTA
1 AAATAAAAAAATTTA
19662928 AGAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAAAATTTAT
Found at i:19665736 original size:12 final size:12
Alignment explanation
Indices: 19665719--19665754 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
19665709 TGAGGATGGA
*
19665719 GTGAGGGTGAGG
1 GTGAGGGTCAGG
19665731 GTGAGGGTCAGG
1 GTGAGGGTCAGG
*
19665743 GTCAGGGTCAGG
1 GTGAGGGTCAGG
19665755 CACATGAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.08, G:0.58, T:0.17
Consensus pattern (12 bp):
GTGAGGGTCAGG
Found at i:19666285 original size:2 final size:2
Alignment explanation
Indices: 19666278--19666302 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19666268 CTTTTACTGT
19666278 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 T
19666303 TTTTTTTGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19675231 original size:2 final size:2
Alignment explanation
Indices: 19675224--19675248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19675214 AATGAAATTA
19675224 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 A
19675249 AAATGAGATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19676700 original size:30 final size:30
Alignment explanation
Indices: 19676644--19676702 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
19676634 TCCCAAGTAG
***
19676644 TTATATACTTTCACTTAATTGCATATAAAA
1 TTATATACTTTCACTTAATCAAATATAAAA
19676674 TTATATACTTTCACTCT-ATCAAATATAAA
1 TTATATACTTTCACT-TAATCAAATATAAA
19676703 TTACTTGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.42
Consensus pattern (30 bp):
TTATATACTTTCACTTAATCAAATATAAAA
Found at i:19679368 original size:39 final size:39
Alignment explanation
Indices: 19679314--19679393 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
19679304 TGTCAATCCC
19679314 TCCACCTTTCAAAATAAATATAGAAAAATCATATAATTA
1 TCCACCTTTCAAAATAAATATAGAAAAATCATATAATTA
*
19679353 TCCACCTTTCAAAATAAATATAGAACAATCATATAATTA
1 TCCACCTTTCAAAATAAATATAGAAAAATCATATAATTA
19679392 TC
1 TC
19679394 ATATGCTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (39 bp):
TCCACCTTTCAAAATAAATATAGAAAAATCATATAATTA
Found at i:19684528 original size:16 final size:17
Alignment explanation
Indices: 19684501--19684545 Score: 67
Period size: 15 Copynumber: 2.7 Consensus size: 17
19684491 AGCCTAATCC
19684501 TAAATTAATAAAATAAAA
1 TAAA-TAATAAAATAAAA
19684519 TAAA-AAT-AAATAAAA
1 TAAATAATAAAATAAAA
19684534 TAAATAATAAAA
1 TAAATAATAAAA
19684546 CCAAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.48
16 6 0.24
17 3 0.12
18 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATAATAAAATAAAA
Found at i:19684533 original size:9 final size:9
Alignment explanation
Indices: 19684502--19684540 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
19684492 GCCTAATCCT
*
19684502 AAATTAATA
1 AAATAAATA
19684511 AAATAAAATAA
1 AAAT-AAAT-A
19684522 AAATAAATA
1 AAATAAATA
19684531 AAATAAATA
1 AAATAAATA
19684540 A
1 A
19684541 TAAAACCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 15 0.56
10 7 0.26
11 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAAATA
Found at i:19708833 original size:23 final size:23
Alignment explanation
Indices: 19708807--19708850 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
19708797 GGGTAGGGTT
19708807 GGGATTGTTGTGAAGAGAAGGGA
1 GGGATTGTTGTGAAGAGAAGGGA
19708830 GGGATTGTTGTGAAGAGAAGG
1 GGGATTGTTGTGAAGAGAAGG
19708851 AAGTCTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.23
Consensus pattern (23 bp):
GGGATTGTTGTGAAGAGAAGGGA
Found at i:19710180 original size:3 final size:3
Alignment explanation
Indices: 19710172--19710236 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
19710162 AGATGATTTA
19710172 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19710220 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
19710237 AGGCACAAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19710352 original size:2 final size:2
Alignment explanation
Indices: 19710345--19710404 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
19710335 CAAATGAATA
*
19710345 AT AT AT AT AT AT AA 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
19710387 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
19710405 GTACAAGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19712022 original size:20 final size:20
Alignment explanation
Indices: 19711992--19712042 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
19711982 ACAGGGCTTA
* *
19711992 TATAATGTATTGGACTAATC
1 TATAATATATTCGACTAATC
* *
19712012 TCTAATATATTCGATTAATC
1 TATAATATATTCGACTAATC
*
19712032 TATAACATATT
1 TATAATATATT
19712043 ATTAATAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (20 bp):
TATAATATATTCGACTAATC
Found at i:19716533 original size:26 final size:25
Alignment explanation
Indices: 19716495--19716557 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
19716485 AACCTTTTGA
*
19716495 TTCATGTTTTCAATCTC-ATATCTCAAT
1 TTCA-GTTCTCAAT-TCAATATCTC-AT
*
19716522 TTCAGTTCTCAATTCAATTTCTCAT
1 TTCAGTTCTCAATTCAATATCTCAT
19716547 TTCA-TTC-CAAT
1 TTCAGTTCTCAAT
19716558 AGCTCAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 4 0.12
24 3 0.09
25 8 0.24
26 14 0.42
27 4 0.12
ACGTcount: A:0.25, C:0.24, G:0.03, T:0.48
Consensus pattern (25 bp):
TTCAGTTCTCAATTCAATATCTCAT
Found at i:19716677 original size:23 final size:23
Alignment explanation
Indices: 19716647--19716704 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
19716637 GTGGATTCCT
19716647 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
19716670 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
19716693 CCCAAACACACC
1 CCCAAACACACC
19716705 CGGAATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.47, C:0.43, G:0.03, T:0.07
Consensus pattern (23 bp):
CCCAAACACACCAGAATATCCAA
Found at i:19717226 original size:15 final size:15
Alignment explanation
Indices: 19717206--19717252 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
19717196 TAATATATAT
19717206 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
19717221 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
19717236 TTCAATCAATATAAA
1 TTCAATCAATATAAA
19717251 TT
1 TT
19717253 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:19718543 original size:13 final size:13
Alignment explanation
Indices: 19718525--19718556 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
19718515 TTTTATTTCA
19718525 TTTATTTCTTTAT
1 TTTATTTCTTTAT
19718538 TTTATTTCTTTAT
1 TTTATTTCTTTAT
19718551 TTTATT
1 TTTATT
19718557 ATTAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTCTTTAT
Found at i:19723450 original size:23 final size:21
Alignment explanation
Indices: 19723325--19723463 Score: 98
Period size: 22 Copynumber: 6.1 Consensus size: 21
19723315 TACCAATATA
*
19723325 TTAGCTCATAAGAGCTTACTATT
1 TTAGCTCAT-AGAGCTTACT-GT
*
19723348 TTCAGCTCATTAGAGCTTACCGAT
1 TT-AGCTCA-TAGAGCTTACTG-T
* *
19723372 TCAGCTCGTATGAGCTTACTGT
1 TTAGCTCATA-GAGCTTACTGT
* * *
19723394 TTAGTTCGATAAAGTTTACTGT
1 TTAGCTC-ATAGAGCTTACTGT
* *
19723416 TTAGCTGGATAGAGCTTACCGTT
1 TTAGCT-CATAGAGCTTACTG-T
*
19723439 TTAGCTCAATAGAGCTTACTAT
1 TTAGCTC-ATAGAGCTTACTGT
19723461 TTA
1 TTA
19723464 TTAGCTCAGA
Statistics
Matches: 90, Mismatches: 18, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
22 36 0.40
23 36 0.40
24 17 0.19
25 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (21 bp):
TTAGCTCATAGAGCTTACTGT
Found at i:19723654 original size:20 final size:20
Alignment explanation
Indices: 19723629--19723666 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19723619 ATAAGCTATG
19723629 TTGAAATAAATGAATTACTA
1 TTGAAATAAATGAATTACTA
*
19723649 TTGAAATGAATGAATTAC
1 TTGAAATAAATGAATTAC
19723667 AGTTTATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (20 bp):
TTGAAATAAATGAATTACTA
Found at i:19725488 original size:3 final size:3
Alignment explanation
Indices: 19725475--19725513 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
19725465 TAAATAGATA
*
19725475 AAT AGAT AAT AAT AA- AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19725514 GGCACAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19725492 original size:23 final size:23
Alignment explanation
Indices: 19725441--19725509 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
19725431 TTAAGTATGT
* * *
19725441 ATAAAA-AAATAAAGAGGTAATA
1 ATAAAATAGATAAATAGATAATA
19725463 A-ATAAATAGATAAATAGATAATA
1 ATA-AAATAGATAAATAGATAATA
19725486 ATAAAATAG-T-AATA-ATAATA
1 ATAAAATAGATAAATAGATAATA
19725506 ATAA
1 ATAA
19725510 TAATGGCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.24
21 5 0.12
22 5 0.12
23 20 0.49
24 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.25
Consensus pattern (23 bp):
ATAAAATAGATAAATAGATAATA
Found at i:19726938 original size:19 final size:20
Alignment explanation
Indices: 19726906--19726943 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
19726896 TTATATGGAC
* *
19726906 TTTTGATTTTTTTTTTTTGG
1 TTTTGATTTATTTTATTTGG
19726926 TTTT-ATTTATTTTATTTG
1 TTTTGATTTATTTTATTTG
19726944 ATTTCTGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (20 bp):
TTTTGATTTATTTTATTTGG
Found at i:19728685 original size:44 final size:44
Alignment explanation
Indices: 19728637--19729603 Score: 559
Period size: 44 Copynumber: 21.2 Consensus size: 44
19728627 TCTGAGTGAA
* * *
19728637 ATAAGATTTGTAGTTTCAATCTGCTCCACTACAACTTTAGGGGG
1 ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * *
19728681 ATAAGATTTATAACTTGTAGCTTT-AATCTGTTCCACTGCAACTTCAGGAAA
1 ATAAG----AT---TTGTAG-TTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * *
19728732 ATAAGATTTGTAGCTTCAATCTGCTCCACTGTAA-TTCTAGAGAG
1 ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTC-AGGGAG
* * * * * * * *
19728776 ATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCTCTGAAACTTTATGAAA
1 ATAAGATTTGT-A---GT---TTCAATCTGCTCCACTGCAACTTCAGGGAG
* *
19728827 ATAAGATTTGTAGCTTT-AATTTGCTCCACTGCAACTCCAGGGAG
1 ATAAGATTTGTAG-TTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * *
19728871 ATAAGATTTGTCGTTTCAATCTGTTCCATTGCAACTTCAGTGAG
1 ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* **
19728915 ATAAGATTTGTTATTTTTCAATCCACTCCACTGCAACTTCAGGGAG
1 ATAAGATTTG-TA-GTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* *
19728961 ATAAGATTTGTAGCTTCAATCTGCTCTTCCACTGCAACTTCAGAGAG
1 ATAAGATTTGTAGTTTCAATCTG--C-TCCACTGCAACTTCAGGGAG
* * * *
19729008 ATAAAATTTGTAGCTTCAATCTGCTCCATTGCAACTTTAGGGAG
1 ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * * *
19729052 ATAAGATTTGTAACTTATAGCTTTAATCTGTTCCACTGCAATTTTA-GGAA
1 ATAAGATTTGT-AGTT-T--C---AATCTGCTCCACTGCAACTTCAGGGAG
* * * * * * *
19729102 ACAAAATTTATAGCTTCAATCTGCTGCACTGCAACTCCAAGGAG
1 ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* ** * * *
19729146 ATAAAATTTGTCA-TTTCAATCTATTCCACTACAACTCCAAGGAG
1 ATAAGATTTGT-AGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* ** * * *
19729190 ATAAGATTTGTTGTTTCAATCTATTCCACTACAACTACAGAGAG
1 ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * * *
19729234 ATAAGGTTTGTAGCTTCAATCTACTCCACTGTAAC-TCTAGGAAG
1 ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTC-AGGGAG
* * * *
19729278 ATAAGATTTGTAACTTGTAGCTTTC-ATCTGTTCCACTGTAATTTCAGGGAA
1 ATAAGA----T---TTGTAG-TTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * * *
19729329 ATAATATTTGTAGCTTCAATCTGCTTCACTGCAACTCCAGTGAG
1 ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* ** * * *
19729373 ATAAGATTTGTCGTTTCAATCTATTCCAATACAACTTTAGGGAG
1 ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
*** * * * *
19729417 ATAAGACTCACTATTTTTCAATCTGCTCCATTGTAACTTCAAGGAG
1 ATAAGA-TTTGTA-GTTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * * *
19729463 ATAAGATTTGTGGCTTT-AATCTGCTCTATTGCAACCTCAAGGAG
1 ATAAGATTTGTAG-TTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * ** * * * *
19729507 ATACGATTTGTGGCTTT-AATCTATTACACTACAAATTTAGGGAG
1 ATAAGATTTGTAG-TTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * * *
19729551 ATAAGATTTGTGGCTTT-AATATGCTCCATTACAAATTCAGGGAG
1 ATAAGATTTGTAG-TTTCAATCTGCTCCACTGCAACTTCAGGGAG
19729595 ATAAGATTT
1 ATAAGATTT
19729604 TCCACGATGG
Statistics
Matches: 717, Mismatches: 157, Indels: 98
0.74 0.16 0.10
Matches are distributed among these distances:
43 29 0.04
44 417 0.58
45 17 0.02
46 69 0.10
47 45 0.06
48 7 0.01
49 2 0.00
50 12 0.02
51 109 0.15
52 10 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (44 bp):
ATAAGATTTGTAGTTTCAATCTGCTCCACTGCAACTTCAGGGAG
Found at i:19728717 original size:95 final size:95
Alignment explanation
Indices: 19728554--19729245 Score: 606
Period size: 95 Copynumber: 7.5 Consensus size: 95
19728544 CGAATATCAC
* * * * *
19728554 GTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGTTTTGTAACTTGTAACTTTAATTTATCC
1 GTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTC
*
19728619 CACTGCAA-TCTGAGTGAAATAAGATTTGTA
66 CACTGCAACT-TCAGTGAAATAAGATTTGTA
* * * *
19728649 GTTTCAATCTGCTCCACTACAACTTTAGGGGGATAAGATTTATAACTTGTAGCTTTAATCTGTTC
1 GTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTC
19728714 CACTGCAACTTCAG-GAAAATAAGATTTGTA
66 CACTGCAACTTCAGTG-AAATAAGATTTGTA
* * *
19728744 GCTTCAATCTGCTCCACTGTAA-TTCTAGAGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTT
1 GTTTCAATCTGCTCCACTGCAACTTC-AGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTT
* * *
19728808 CCTCTGAAACTTTA-TGAAAATAAGATTTGTA
65 CCACTGCAACTTCAGTG-AAATAAGATTTGTA
* * *
19728839 GCTTT-AATTTGCTCCACTGCAACTCCAGGGAGATAAGATTTGT--C--GT---TTCAATCTGTT
1 G-TTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTT
* *
19728896 CCATTGCAACTTCAGTGAGATAAGATTTGTTA
65 CCACTGCAACTTCAGTGAAATAAGATTTG-TA
* ** * * * * * *
19728928 TTTTTCAATCCACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTT-CA-ATCT--GCTCTT
1 -GTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTT
* * *
19728989 CCACTGCAACTTCAGAGAGATAAAATTTGTA
65 CCACTGCAACTTCAGTGAAATAAGATTTGTA
* * * *
19729020 GCTTCAATCTGCTCCATTGCAACTTTAGGGAGATAAGATTTGTAACTTATAGCTTTAATCTGTTC
1 GTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTC
* * * * *
19729085 CACTGCAATTTTAG-GAAACAAAATTTATA
66 CACTGCAACTTCAGTGAAATAAGATTTGTA
* * * * * * *
19729114 GCTTCAATCTGCTGCACTGCAACTCCAAGGAGATAAAATTTGTCA-TT-T--C---AATCTATTC
1 GTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTC
* * * *
19729172 CACTACAACTCCAAG-GAGATAAGATTTGTT
66 CACTGCAACTTC-AGTGAAATAAGATTTGTA
** * * * *
19729202 GTTTCAATCTATTCCACTACAACTACAGAGAGATAAGGTTTGTA
1 GTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTA
19729246 GCTTCAATCT
Statistics
Matches: 487, Mismatches: 89, Indels: 49
0.78 0.14 0.08
Matches are distributed among these distances:
87 16 0.03
88 76 0.16
89 7 0.01
90 35 0.07
91 43 0.09
92 5 0.01
93 35 0.07
94 53 0.11
95 212 0.44
96 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (95 bp):
GTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTC
CACTGCAACTTCAGTGAAATAAGATTTGTA
Found at i:19729252 original size:226 final size:229
Alignment explanation
Indices: 19728837--19729422 Score: 712
Period size: 226 Copynumber: 2.6 Consensus size: 229
19728827 ATAAGATTTG
* * * * * * * * * * * *
19728837 TAGCTTTAATTTGCTCCACTGCAACTCCAGGGAGATAAGATTTGTCGTTTCAATCTGTTCCATTG
1 TAGCTTTAATCTGTTCCACTGCAATTTCAGGGAAACAAAATTTATAGCTTCAATCTGCTCCACTG
* * * * *
19728902 CAACTTCAGTGAGATAAGATTTGTTATTTTTCAATCCACTCCACTGCAACTTCAGGGAGATAAGA
66 CAACTCCAGTGAGATAAGATTTGTCA--TTTCAATCTATTCCACTACAACTTCAGGGAGATAAGA
* * * *
19728967 TTTGTAGCTTCAATCTGCTCTTCCACTGCAACTTCAGAGAGATAAAATTTGTAGCTTCAATCTGC
129 TTTGTAGCTTCAA-CTGCTATTCCACTACAACTACAGAGAGATAAAATTTGTAGCTTCAATCTAC
* * *
19729032 TCCATTGCAACTTTAGGGAGATAAGATTTGTAACTTA
193 TCCACTGCAACTCTAGGAAGATAAGATTTGTAACTTA
* *
19729069 TAGCTTTAATCTGTTCCACTGCAATTTTA-GGAAACAAAATTTATAGCTTCAATCTGCTGCACTG
1 TAGCTTTAATCTGTTCCACTGCAATTTCAGGGAAACAAAATTTATAGCTTCAATCTGCTCCACTG
* * *
19729133 CAACTCCAAG-GAGATAAAATTTGTCATTTCAATCTATTCCACTACAACTCCAAGGAGATAAGAT
66 CAACTCC-AGTGAGATAAGATTTGTCATTTCAATCTATTCCACTACAACTTCAGGGAGATAAGAT
* * **
19729197 TTGTTGTTTCAA-T-CTATTCCACTACAACTACAGAGAGATAAGGTTTGTAGCTTCAATCTACTC
130 TTGTAGCTTCAACTGCTATTCCACTACAACTACAGAGAGATAAAATTTGTAGCTTCAATCTACTC
* *
19729260 CACTGTAACTCTAGGAAGATAAGATTTGTAACTTG
195 CACTGCAACTCTAGGAAGATAAGATTTGTAACTTA
* * * * * *
19729295 TAGCTTTCATCTGTTCCACTGTAATTTCAGGGAAATAATATTTGTAGCTTCAATCTGCTTCACTG
1 TAGCTTTAATCTGTTCCACTGCAATTTCAGGGAAACAAAATTTATAGCTTCAATCTGCTCCACTG
* * *
19729360 CAACTCCAGTGAGATAAGATTTGTCGTTTCAATCTATTCCAATACAACTTTAGGGAGATAAGA
66 CAACTCCAGTGAGATAAGATTTGTCATTTCAATCTATTCCACTACAACTTCAGGGAGATAAGA
19729423 CTCACTATTT
Statistics
Matches: 303, Mismatches: 48, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
226 102 0.34
227 86 0.28
229 43 0.14
231 46 0.15
232 26 0.09
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (229 bp):
TAGCTTTAATCTGTTCCACTGCAATTTCAGGGAAACAAAATTTATAGCTTCAATCTGCTCCACTG
CAACTCCAGTGAGATAAGATTTGTCATTTCAATCTATTCCACTACAACTTCAGGGAGATAAGATT
TGTAGCTTCAACTGCTATTCCACTACAACTACAGAGAGATAAAATTTGTAGCTTCAATCTACTCC
ACTGCAACTCTAGGAAGATAAGATTTGTAACTTA
Found at i:19729506 original size:317 final size:314
Alignment explanation
Indices: 19728827--19729561 Score: 716
Period size: 317 Copynumber: 2.3 Consensus size: 314
19728817 CTTTATGAAA
* *
19728827 ATAAGATTTGTAGCTTTAATTTGCTCCACTGCAACTCCAGGGAGATAAGATTTGTCGTTTCAATC
1 ATAAGATTTGT-GCTTTAATCTGCTCCACTGCAACTCCAAGGAGATAAGATTTGTCGTTTCAATC
* * * * * **
19728892 TGTTCCATTGCAACTTCAGTGAGATAAGATTTGTTATTTTTCAATCCACTCCACTGCAACTTCAG
65 TATTCCACTACAACTACAGAGAGATAAGATTTGTTATGCTTCAATCCACTCCACTGCAACTTCAG
* * * *
19728957 GGAGATAAGATTTGTAGCTTCAATCTGCTCTTCCACTGCAACTTCAGAGAGATAAAATTTGTAGC
130 GAAGATAAGATTTGTAACTTCAAGCTGCTCTTCCACTGCAACTTCAGAGAAATAAAATTTGTAGC
* ** *
19729022 TTCAATCTGCTCCATTGCAACTTTAGGGAGATAAGATTTGTAACTTATAGCTTTAATCTGTTCCA
195 TTCAATCTGCTCCACTGCAACTCCAGGGAGATAAGATTTGT-ACTTATA-C--TAATCTATTCCA
* * * * * *
19729087 CTGCAATTTTAGGAAACAAAATTTATAGCTTCAATCTGCTGCACTGCAACTCCAAGGAG
256 ATACAACTTTAGGAAACAAAACTCATAGCTTCAATCTGCTCCACTGCAACTCCAAGGAG
* ** * *
19729146 ATAAAATTTGT-CATTTCAATCTATTCCACTACAACTCCAAGGAGATAAGATTTGTTGTTTCAAT
1 ATAAGATTTGTGC-TTT-AATCTGCTCCACTGCAACTCCAAGGAGATAAGATTTGTCGTTTCAAT
* * *
19729210 CTATTCCACTACAACTACAGAGAGATAAGGTTTG-TA-GCTTCAATCTACTCCACTGTAAC-TCT
64 CTATTCCACTACAACTACAGAGAGATAAGATTTGTTATGCTTCAATCCACTCCACTGCAACTTC-
** * * * * *
19729272 AGGAAGATAAGATTTGTAACTTGTAGCTTTCATCTGTTCCACTGTAATTTCAGGGAAATAATATT
128 AGGAAGATAAGATTTGTAACTTCAAGC-TGC-TC--TTCCACTGCAACTTCAGAGAAATAAAATT
* *
19729337 TGTAGCTTCAATCTGCTTCACTGCAACTCCAGTGAGATAAGATTTGT-CGTT-T-C-AATCTATT
189 TGTAGCTTCAATCTGCTCCACTGCAACTCCAGGGAGATAAGATTTGTAC-TTATACTAATCTATT
* * * ** * * *
19729398 CCAATACAACTTTAGGGAGATAAGACTCACTATTTTTCAATCTGCTCCATTGTAACTTCAAGGAG
253 CCAATACAACTTTA-GGAAACAAAACTCA-TA-GCTTCAATCTGCTCCACTGCAACTCCAAGGAG
* * * *
19729463 ATAAGATTTGTGGCTTTAATCTGCTCTATTGCAAC-CTCAAGGAGATACGATTTGTGGCTTT-AA
1 ATAAGATTTGT-GCTTTAATCTGCTCCACTGCAACTC-CAAGGAGATAAGATTTGTCG-TTTCAA
* * ** *
19729526 TCTATTACACTACAAATTTAGGGAGATAAGATTTGT
63 TCTATTCCACTACAACTACAGAGAGATAAGATTTGT
19729562 GGCTTTAATA
Statistics
Matches: 338, Mismatches: 62, Indels: 33
0.78 0.14 0.08
Matches are distributed among these distances:
314 18 0.05
315 9 0.03
316 5 0.01
317 141 0.42
318 13 0.04
319 84 0.25
320 2 0.01
321 66 0.20
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (314 bp):
ATAAGATTTGTGCTTTAATCTGCTCCACTGCAACTCCAAGGAGATAAGATTTGTCGTTTCAATCT
ATTCCACTACAACTACAGAGAGATAAGATTTGTTATGCTTCAATCCACTCCACTGCAACTTCAGG
AAGATAAGATTTGTAACTTCAAGCTGCTCTTCCACTGCAACTTCAGAGAAATAAAATTTGTAGCT
TCAATCTGCTCCACTGCAACTCCAGGGAGATAAGATTTGTACTTATACTAATCTATTCCAATACA
ACTTTAGGAAACAAAACTCATAGCTTCAATCTGCTCCACTGCAACTCCAAGGAG
Found at i:19729508 original size:134 final size:133
Alignment explanation
Indices: 19729299--19729556 Score: 324
Period size: 134 Copynumber: 1.9 Consensus size: 133
19729289 AACTTGTAGC
* * * *
19729299 TTTCATCTGTTCCACTGTAATTTCAGGGAAATAATATTTGTAGCTTCAATCTGCTTCACTGCAAC
1 TTTCATCTGCTCCACTGTAACTTCAAGGAAATAAGATTTGTAGCTTCAATCTGCTTCACTGCAAC
* * *
19729364 TCCAGTGAGATAAGATTTGTCG-TTTCAATCTATTCCAATACAACTTTAGGGAGATAAGACTCAC
66 TCAAGTGAGATAAGATTTGTCGCTTT-AATCTATTACAATACAAATTTAGGGAGATAAGACTCAC
19729428 TATT
130 TATT
* * * * *
19729432 TTTCAATCTGCTCCATTGTAACTTCAAGGAGATAAGATTTGTGGCTTTAATCTGC-TCTATTGCA
1 TTTC-ATCTGCTCCACTGTAACTTCAAGGAAATAAGATTTGTAGCTTCAATCTGCTTC-ACTGCA
* * *
19729496 ACCTCAAG-GAGATACGATTTGTGGCTTTAATCTATTACACTACAAATTTAGGGAGATAAGA
64 A-CTCAAGTGAGATAAGATTTGTCGCTTTAATCTATTACAATACAAATTTAGGGAGATAAGA
19729557 TTTGTGGCTT
Statistics
Matches: 106, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
133 6 0.06
134 92 0.87
135 8 0.08
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (133 bp):
TTTCATCTGCTCCACTGTAACTTCAAGGAAATAAGATTTGTAGCTTCAATCTGCTTCACTGCAAC
TCAAGTGAGATAAGATTTGTCGCTTTAATCTATTACAATACAAATTTAGGGAGATAAGACTCACT
ATT
Found at i:19730560 original size:19 final size:19
Alignment explanation
Indices: 19730532--19730582 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
19730522 CCACAAAAGG
19730532 TCCTCCAGAAAATTAACGC
1 TCCTCCAGAAAATTAACGC
*
19730551 TCCTCTAGAAAATTAACGC
1 TCCTCCAGAAAATTAACGC
* *
19730570 TTCTCCAAAAAAT
1 TCCTCCAGAAAAT
19730583 GTCTTCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (19 bp):
TCCTCCAGAAAATTAACGC
Found at i:19756670 original size:27 final size:27
Alignment explanation
Indices: 19756639--19756690 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
19756629 CCTAATATTG
*
19756639 GTAAAATTATCGAAATACCCTTGTAGT
1 GTAAAATTATCGAAATACCCCTGTAGT
*
19756666 GTAAAATTATCGTAATACCCCTGTA
1 GTAAAATTATCGAAATACCCCTGTA
19756691 TGGTAGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (27 bp):
GTAAAATTATCGAAATACCCCTGTAGT
Found at i:19756970 original size:22 final size:22
Alignment explanation
Indices: 19756942--19756998 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
19756932 TTTACTGTGA
19756942 TGAGCCGTCCTGTCTACGGCGT
1 TGAGCCGTCCTGTCTACGGCGT
* * *
19756964 TGAGCCGTCTTGTCTAGGGTGT
1 TGAGCCGTCCTGTCTACGGCGT
*
19756986 TGAGCCGTTCTGT
1 TGAGCCGTCCTGT
19756999 TGACTTAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.09, C:0.25, G:0.33, T:0.33
Consensus pattern (22 bp):
TGAGCCGTCCTGTCTACGGCGT
Found at i:19759297 original size:12 final size:12
Alignment explanation
Indices: 19759282--19759313 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
19759272 AACATAATTA
19759282 TAATATTAATAT
1 TAATATTAATAT
19759294 TAATATTAATAT
1 TAATATTAATAT
19759306 TAATATTA
1 TAATATTA
19759314 TAGTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATATTAATAT
Found at i:19759339 original size:19 final size:19
Alignment explanation
Indices: 19759315--19759353 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19759305 TTAATATTAT
19759315 AGTAATAATAA-ATAAATGA
1 AGTAAT-ATAAGATAAATGA
*
19759334 AGTAATTTAAGATAAATGA
1 AGTAATATAAGATAAATGA
19759353 A
1 A
19759354 AAATGGAAGA
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:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (19 bp):
AGTAATATAAGATAAATGA
Found at i:19759431 original size:20 final size:19
Alignment explanation
Indices: 19759406--19759468 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 19
19759396 GAAAGTGCCA
*
19759406 AAAATAATAAGAGAAATAAT
1 AAAATAAAAAGA-AAATAAT
*
19759426 AAAATAACAAGAACAAACTAA-
1 AAAATAAAAAG-A-AAA-TAAT
*
19759447 AAAATAAAAATAAAATAAT
1 AAAATAAAAAGAAAATAAT
19759466 AAA
1 AAA
19759469 TGACAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 3 0.08
19 6 0.17
20 11 0.31
21 13 0.36
22 3 0.08
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAATAAAAAGAAAATAAT
Found at i:19759683 original size:4 final size:4
Alignment explanation
Indices: 19759674--19759774 Score: 55
Period size: 4 Copynumber: 25.5 Consensus size: 4
19759664 ATGAAGGAAT
* * * * * *
19759674 AATA AATA AATG AATAA AATG ATTA AA-A AATA AGTG AAT- AATA GATA
1 AATA AATA AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA
* * * * * *
19759721 AATA GATA AGTA TATG AGTA AATA AATA AATA AA-A AAGTA AATA AATG
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA-TA AATA AATA
19759769 AATA AA
1 AATA AA
19759775 AGAATTAAAA
Statistics
Matches: 69, Mismatches: 23, Indels: 10
0.68 0.23 0.10
Matches are distributed among these distances:
3 9 0.13
4 54 0.78
5 6 0.09
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:19759760 original size:20 final size:20
Alignment explanation
Indices: 19759737--19759775 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19759727 TAAGTATATG
19759737 AGTAAATAAATAAATAAAAA
1 AGTAAATAAATAAATAAAAA
*
19759757 AGTAAATAAATGAATAAAA
1 AGTAAATAAATAAATAAAA
19759776 GAATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (20 bp):
AGTAAATAAATAAATAAAAA
Found at i:19759762 original size:16 final size:16
Alignment explanation
Indices: 19759743--19759790 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
19759733 TATGAGTAAA
19759743 TAAATAAATAAAAAAG
1 TAAATAAATAAAAAAG
19759759 TAAATAAATGAATAAAAG
1 TAAATAAAT-AA-AAAAG
*
19759777 -AATTAAAATAAAAA
1 TAAAT-AAATAAAAA
19759791 GGACTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 12 0.43
17 7 0.25
18 9 0.32
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (16 bp):
TAAATAAATAAAAAAG
Found at i:19763768 original size:18 final size:18
Alignment explanation
Indices: 19763744--19763793 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
19763734 TAAGTAATAT
*
19763744 TCATTTATTCAGTACCAG
1 TCATTTATTCAGTAACAG
* *
19763762 TCGTTTATTCTGTAACAG
1 TCATTTATTCAGTAACAG
*
19763780 TCAATTATTCAGTA
1 TCATTTATTCAGTA
19763794 GCAGACAGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (18 bp):
TCATTTATTCAGTAACAG
Found at i:19764328 original size:37 final size:37
Alignment explanation
Indices: 19764279--19764350 Score: 87
Period size: 37 Copynumber: 1.9 Consensus size: 37
19764269 TTCAATTTTC
19764279 CACTCAATATTCAT--ATATTCTATTCAATATCAATAAT
1 CACTCAATATTCATGAAT-TTCTATTCAAT-TCAATAAT
*
19764316 CACT-AATAATTCATGAATTTTTATTCAATTCAATA
1 CACTCAAT-ATTCATGAATTTCTATTCAATTCAATA
19764351 CCATAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
36 3 0.10
37 16 0.52
38 10 0.32
39 2 0.06
ACGTcount: A:0.40, C:0.17, G:0.01, T:0.42
Consensus pattern (37 bp):
CACTCAATATTCATGAATTTCTATTCAATTCAATAAT
Found at i:19764361 original size:3 final size:3
Alignment explanation
Indices: 19764353--19764394 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
19764343 ATTCAATACC
19764353 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19764395 CTTGCAATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19769468 original size:18 final size:18
Alignment explanation
Indices: 19769447--19769506 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
19769437 AATTGGTTAA
*
19769447 TCAGTAATATTCATTTAT
1 TCAGTAATAGTCATTTAT
** *
19769465 TCAGTACCAGTCGTTTAT
1 TCAGTAATAGTCATTTAT
*
19769483 TCTA-TAATAGTCAATTAT
1 TC-AGTAATAGTCATTTAT
19769501 TCAGTA
1 TCAGTA
19769507 GCAGACAATC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 1 0.03
18 30 0.94
19 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (18 bp):
TCAGTAATAGTCATTTAT
Found at i:19770074 original size:3 final size:3
Alignment explanation
Indices: 19770066--19770091 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19770056 ATTCAATACC
19770066 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
19770092 CCTTACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:19792308 original size:13 final size:13
Alignment explanation
Indices: 19792290--19792354 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
19792280 AATTTTCAAA
19792290 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
19792303 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
19792316 TGC-TGTGGAAAT
1 TGCTTTTGAAAAG
*
19792328 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
19792341 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
19792354 T
1 T
19792355 TTGGATTAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
12 9 0.21
13 33 0.79
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:19792563 original size:31 final size:33
Alignment explanation
Indices: 19792527--19792638 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 33
19792517 TAATTTGCTT
*
19792527 TAATATTTTAATATATGAAATATAAATT-TTTA
1 TAATATTTTAATATATGAAATATAAATTACTTA
*
19792559 -AATATTTTTAAGTA-AT-AAATATTAATTACTTA
1 TAATA-TTTTAA-TATATGAAATATAAATTACTTA
*
19792591 TAATA-TTTAA-ATA-GAATATATAAATTACATTT
1 TAATATTTTAATATATGAA-ATATAAATTAC-TTA
*
19792623 TAAATATTTAAATATA
1 T-AATATTTTAATATA
19792639 ACCATTAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 19
0.73 0.06 0.22
Matches are distributed among these distances:
29 1 0.02
30 3 0.05
31 29 0.45
32 14 0.22
33 10 0.16
34 4 0.06
35 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (33 bp):
TAATATTTTAATATATGAAATATAAATTACTTA
Found at i:19792982 original size:13 final size:13
Alignment explanation
Indices: 19792966--19793031 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
19792956 TTTAAATCAA
19792966 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
19792979 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
19792992 ATTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
19793005 ACTTTTCAAAATC
1 ACTTTTCAAAAGC
*
19793018 ACTTTCCAAAAGC
1 ACTTTTCAAAAGC
19793031 A
1 A
19793032 TTGCCAAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 4 0.09
13 35 0.81
14 4 0.09
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:19795871 original size:40 final size:40
Alignment explanation
Indices: 19795815--19795908 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 40
19795805 CGTTTTAATA
*
19795815 AAAAAACACCGCTAAATATCGAGAATTAGCGACACTTTCT
1 AAAAAACGCCGCTAAATATCGAGAATTAGCGACACTTTCT
** * * *
19795855 TTAAAATGCCGCTAAATATCGAGCATTAGCGGCACTTTCT
1 AAAAAACGCCGCTAAATATCGAGAATTAGCGACACTTTCT
19795895 AAAAAACGCCGCTA
1 AAAAAACGCCGCTA
19795909 TAGGATCACC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (40 bp):
AAAAAACGCCGCTAAATATCGAGAATTAGCGACACTTTCT
Found at i:19796166 original size:174 final size:176
Alignment explanation
Indices: 19795857--19796174 Score: 487
Period size: 174 Copynumber: 1.8 Consensus size: 176
19795847 CACTTTCTTT
* * *
19795857 AAAATGCCGCTAAATATCGAGCATTAGCGGCACTTTCTAAAAAACGCCGCTATAGGATCACCTTT
1 AAAAAGCCGCTAAATATCGAGCAATAGCGGCACTTTCTAAAAAACGCCGCTATAGGAACACCTTT
* *
19795922 AGCGGCGTTTTTTAGAAAGCACCACAAAAAATTATGCGCAACGTTGTCATTTTGTACTAAGCATT
66 AGCGGCGTTTCTTAGAAAGCACCACAAAAAATTATGCGCAACGTCGTCATTTTGTACTAAGCATT
19795987 AGCGGCGATTTTTTGCTATAGATCGACTTTTAGCGGCGCTTATTTA
131 AGCGGCGATTTTTTGCTATAGATCGACTTTTAGCGGCGCTTATTTA
* * * * *
19796033 AAAAAGCC-CTAAATATCGATCAATAGCGGCGCTTTTTAAAAAATGTCGCTATAGGAACACCTTT
1 AAAAAGCCGCTAAATATCGAGCAATAGCGGCACTTTCTAAAAAACGCCGCTATAGGAACACCTTT
* ** *
19796097 AGC-GTGTTTCTTAGAAAGTGCCACAAAAAATTATGCGCAACGTCGTCGTTTTGTACTAAGCATT
66 AGCGGCGTTTCTTAGAAAGCACCACAAAAAATTATGCGCAACGTCGTCATTTTGTACTAAGCATT
*
19796161 AGCGGCGCTTTTTT
131 AGCGGCGATTTTTT
19796175 AAAAACACCG
Statistics
Matches: 127, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
174 68 0.54
175 52 0.41
176 7 0.06
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (176 bp):
AAAAAGCCGCTAAATATCGAGCAATAGCGGCACTTTCTAAAAAACGCCGCTATAGGAACACCTTT
AGCGGCGTTTCTTAGAAAGCACCACAAAAAATTATGCGCAACGTCGTCATTTTGTACTAAGCATT
AGCGGCGATTTTTTGCTATAGATCGACTTTTAGCGGCGCTTATTTA
Found at i:19796262 original size:40 final size:40
Alignment explanation
Indices: 19796157--19796270 Score: 106
Period size: 40 Copynumber: 2.8 Consensus size: 40
19796147 TTGTACTAAG
* *
19796157 CATTAGCGGCGCTTTTTTAAAAACACCGCTAT-AGATCGAA
1 CATTAGCGGCGC-TTTTTAAAAACGCCGCTATAAGATCCAA
** * * *
19796197 TTTTAGCAGCGCTTATTTAAGAACGCCGCTATAAG-TCCAC
1 CATTAGCGGCGCTT-TTTAAAAACGCCGCTATAAGATCCAA
* *
19796237 CATTAGCGGCGCTTTCCTAAAAACGCCGCAATAA
1 CATTAGCGGCGCTTT-TTAAAAACGCCGCTATAA
19796271 ATTATGCACA
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
39 3 0.05
40 53 0.91
41 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (40 bp):
CATTAGCGGCGCTTTTTAAAAACGCCGCTATAAGATCCAA
Found at i:19796513 original size:15 final size:15
Alignment explanation
Indices: 19796493--19796523 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19796483 ATGAAAAAAA
19796493 TTAAAATAATTTTAT
1 TTAAAATAATTTTAT
19796508 TTAAAATAATTTTAT
1 TTAAAATAATTTTAT
19796523 T
1 T
19796524 GTTTTTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAAATAATTTTAT
Found at i:19796644 original size:7 final size:7
Alignment explanation
Indices: 19796628--19796674 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
19796618 TATCATTATA
19796628 GTTTAAG
1 GTTTAAG
*
19796635 GTTTATG
1 GTTTAAG
19796642 GTTT-AG
1 GTTTAAG
* *
19796648 GATATATG
1 G-TTTAAG
19796656 GTTTAAG
1 GTTTAAG
19796663 GTTTAAG
1 GTTTAAG
19796670 GTTTA
1 GTTTA
19796675 GGAGTTAGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
6 2 0.06
7 28 0.88
8 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:19796645 original size:14 final size:14
Alignment explanation
Indices: 19796623--19796674 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
19796613 TTAATTATCA
*
19796623 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
19796637 TTATGGTTT-AGGAT
1 TTATGGTTTAAGG-T
*
19796651 ATATGGTTTAAGGT
1 TTATGGTTTAAGGT
*
19796665 TTAAGGTTTA
1 TTATGGTTTA
19796675 GGAGTTAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 3 0.09
14 26 0.81
15 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:19796767 original size:21 final size:21
Alignment explanation
Indices: 19796706--19796779 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
19796696 ATGAATTATG
* * *
19796706 GGTTTAGGGATTA-TGGTTTA
1 GGTTTAGGGGTTAGAGGTTAA
* *
19796726 GGATTTA-GGGTTGGAGTTTAA
1 GG-TTTAGGGGTTAGAGGTTAA
19796747 GGTTTAGGGGTTAGAGGTTAA
1 GGTTTAGGGGTTAGAGGTTAA
* *
19796768 GGGTTAGAGGTT
1 GGTTTAGGGGTT
19796780 TTATGGTTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 10 0.24
21 32 0.76
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.38
Consensus pattern (21 bp):
GGTTTAGGGGTTAGAGGTTAA
Found at i:19796817 original size:14 final size:15
Alignment explanation
Indices: 19796800--19796828 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19796790 AAGCCTAAAG
19796800 GTTAAGGG-TTAGGA
1 GTTAAGGGTTTAGGA
19796814 GTTAAGGGTTTAGGA
1 GTTAAGGGTTTAGGA
19796829 TTTATGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.41, T:0.31
Consensus pattern (15 bp):
GTTAAGGGTTTAGGA
Found at i:19798305 original size:46 final size:44
Alignment explanation
Indices: 19798246--19798360 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
19798236 ACAGGACAGA
* *
19798246 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
19798292 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
19798336 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
19798361 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:19798341 original size:44 final size:45
Alignment explanation
Indices: 19798246--19798379 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
19798236 ACAGGACAGA
* *
19798246 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
19798292 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
19798336 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
19798380 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:19803065 original size:26 final size:26
Alignment explanation
Indices: 19803029--19803163 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
19803019 TGATACAAAT
* *
19803029 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
19803055 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
19803081 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
19803107 TGATAATGGGTTA-GTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
19803132 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
19803158 TGATAA
1 TGATAA
19803164 GAATTTCATG
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
25 25 0.24
26 81 0.76
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:19803145 original size:51 final size:52
Alignment explanation
Indices: 19803029--19803163 Score: 227
Period size: 51 Copynumber: 2.6 Consensus size: 52
19803019 TGATACAAAT
* *
19803029 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCA
* *
19803081 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGGTTA-GTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCA
19803132 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATGGGTTAGGTAAATGTTTCATGATAA
19803164 GAATTTCATG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 43 0.54
52 36 0.46
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.37
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCA
Found at i:19808781 original size:26 final size:26
Alignment explanation
Indices: 19808745--19808830 Score: 163
Period size: 26 Copynumber: 3.3 Consensus size: 26
19808735 ATCCATTATC
19808745 CATGATAATGGGTTAGGTAAATGTTT
1 CATGATAATGGGTTAGGTAAATGTTT
*
19808771 CATGATAATGGGTTAGGTAAATGTTC
1 CATGATAATGGGTTAGGTAAATGTTT
19808797 CATGATAATGGGTTAGGTAAATGTTT
1 CATGATAATGGGTTAGGTAAATGTTT
19808823 CATGATAA
1 CATGATAA
19808831 GAATTTCATG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 58 1.00
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.36
Consensus pattern (26 bp):
CATGATAATGGGTTAGGTAAATGTTT
Found at i:19811589 original size:2 final size:2
Alignment explanation
Indices: 19811584--19811611 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19811574 ACACACATAC
19811584 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
19811612 TCATTCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19812220 original size:99 final size:99
Alignment explanation
Indices: 19812053--19812413 Score: 422
Period size: 99 Copynumber: 3.5 Consensus size: 99
19812043 GTTTTCTTTA
* *
19812053 ATTTTATTTTCAATTTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATTTTATT
1 ATTTTATTTTCAAATTACATAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATTTTATT
19812118 TTATTTGAATCACGAAAATTAATTTCAATATTTT
66 TTATTTGAATCACGAAAATTAATTTCAATATTTT
* * * *
19812152 ATTTTATTTT-AACATTACATAATTAAACTAAGTTGTATTTAAAGTTTTATTTTAAATATTTTAA
1 ATTTTATTTTCAA-ATTACATAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATTTT-A
* * *** *
19812216 TTTATTTCACTTTAATTTAATCACGAAAAAT-ATTTTGTTTTCTTT
64 --T-TTT-A---T--TTGAATCACGAAAATTAATTTCAATAT-TTT
* *
19812261 AATTTTATTTTCAATTTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATTTTAT
1 -ATTTTATTTTCAAATTACATAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATTTTAT
19812326 TTTATTTGAATCACGAAAATTAATTTCAATATTTT
65 TTTATTTGAATCACGAAAATTAATTTCAATATTTT
* * *
19812361 ATTTTATTTT-AACATTACATAATTAAATTAAGTTGTATTTAAAGTTTTATTTT
1 ATTTTATTTTCAA-ATTACATAATTAAATTAAATTATATTTAAAGTTTCATTTT
19812414 CAATTTACCT
Statistics
Matches: 217, Mismatches: 29, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
98 4 0.02
99 98 0.45
100 18 0.08
101 6 0.03
102 2 0.01
103 3 0.01
104 1 0.00
105 1 0.00
106 3 0.01
107 2 0.01
108 6 0.03
109 18 0.08
110 53 0.24
111 2 0.01
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.53
Consensus pattern (99 bp):
ATTTTATTTTCAAATTACATAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATTTTATT
TTATTTGAATCACGAAAATTAATTTCAATATTTT
Found at i:19812409 original size:43 final size:43
Alignment explanation
Indices: 19812362--19812443 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
19812352 CAATATTTTA
19812362 TTTTATTTT-AACATTACATAATTAAATTAAGTTGTATTTAAAG
1 TTTTATTTTCAA-ATTACATAATTAAATTAAGTTGTATTTAAAG
* * *
19812405 TTTTATTTTCAATTTACCTAATTAAATTAAGTTTTATTT
1 TTTTATTTTCAAATTACATAATTAAATTAAGTTGTATTT
19812444 TCAAGTTCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
43 33 0.94
44 2 0.06
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (43 bp):
TTTTATTTTCAAATTACATAATTAAATTAAGTTGTATTTAAAG
Found at i:19812548 original size:64 final size:64
Alignment explanation
Indices: 19812463--19812813 Score: 621
Period size: 64 Copynumber: 5.5 Consensus size: 64
19812453 CCAGCAAGTC
* *
19812463 ACATAATTTACATAATTTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATAACTT
1 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTT
* * * * * *
19812527 ACATAATTTAAAAAACGTACATAATACATAACTAATATAATTTAAAGTTCAAATTTCATAACTT
1 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTT
19812591 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTT
1 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTT
*
19812655 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTTATAACTT
1 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTT
19812719 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTT
1 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTT
19812783 ACATAATTTACATAACTTACATAATACATAA
1 ACATAATTTACATAACTTACATAATACATAA
19812814 ATATATATCA
Statistics
Matches: 273, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 273 1.00
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.36
Consensus pattern (64 bp):
ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTT
Found at i:19817890 original size:13 final size:14
Alignment explanation
Indices: 19817874--19817902 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19817864 TTATAAATAT
19817874 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
19817887 TTATAATGGTTTAA
1 TTATAATGGTTTAA
19817901 TT
1 TT
19817903 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:19818343 original size:21 final size:21
Alignment explanation
Indices: 19818314--19818361 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
19818304 ACGGATGCAG
*
19818314 CAGCAAGGGAGACAGCGGCAA
1 CAGCGAGGGAGACAGCGGCAA
** *
19818335 CAGCGAGGGAGGTAGCGGCAG
1 CAGCGAGGGAGACAGCGGCAA
19818356 CAGCGA
1 CAGCGA
19818362 TGGCAGTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.23, G:0.44, T:0.02
Consensus pattern (21 bp):
CAGCGAGGGAGACAGCGGCAA
Found at i:19818370 original size:21 final size:21
Alignment explanation
Indices: 19818327--19818367 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19818317 CAAGGGAGAC
*
19818327 AGCGGCAACAGCGAGGGAGGT
1 AGCGGCAACAGCGAGGCAGGT
*
19818348 AGCGGCAGCAGCGATGGCAG
1 AGCGGCAACAGCGA-GGCAG
19818368 TAGAGTAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.27, C:0.22, G:0.46, T:0.05
Consensus pattern (21 bp):
AGCGGCAACAGCGAGGCAGGT
Found at i:19818679 original size:31 final size:31
Alignment explanation
Indices: 19818614--19818672 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
19818604 TGTATTTTTT
*
19818614 ATGCTACATTTGTTGTTTTTGGTTGGATCCA
1 ATGCTACATTTGTTGTATTTGGTTGGATCCA
*
19818645 ATGCTATATTTGTTGTATTTGGTTGGAT
1 ATGCTACATTTGTTGTATTTGGTTGGAT
19818673 TTAATGCAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.17, C:0.08, G:0.24, T:0.51
Consensus pattern (31 bp):
ATGCTACATTTGTTGTATTTGGTTGGATCCA
Found at i:19818805 original size:43 final size:42
Alignment explanation
Indices: 19818758--19818947 Score: 170
Period size: 43 Copynumber: 4.4 Consensus size: 42
19818748 AAGCGCCGCC
*
19818758 AAAAGCCATGACTTTTAGCAGTGCTTTTCCCACAAAAGCTGCT
1 AAAAGCCATGACTTTTAGC-GCGCTTTTCCCACAAAAGCTGCT
* *
19818801 AAAAGTCATGA-TCTTTAGCGGCGC-TTTCCTCACAAACGCTGCT
1 AAAAGCCATGACT-TTTAGC-GCGCTTTTCC-CACAAAAGCTGCT
* * * *
19818844 AAAAGCCATGACTTTTAGCGACACTTTCCCCACAAATGCCGCT
1 AAAAGCCATGACTTTTAGCG-CGCTTTTCCCACAAAAGCTGCT
* ** * *
19818887 AAAAGCCATGA-TCTTTAGCGACACTTTTCTTACAAACGCCGCT
1 AAAAGCCATGACT-TTTAGCG-CGCTTTTCCCACAAAAGCTGCT
*
19818930 AAAAGTCATGATCTTTTA
1 AAAAGCCATGA-CTTTTA
19818948 TGGCGTTTTT
Statistics
Matches: 125, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
42 8 0.06
43 107 0.86
44 9 0.07
45 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (42 bp):
AAAAGCCATGACTTTTAGCGCGCTTTTCCCACAAAAGCTGCT
Found at i:19818876 original size:86 final size:86
Alignment explanation
Indices: 19818751--19818947 Score: 252
Period size: 86 Copynumber: 2.3 Consensus size: 86
19818741 GTAAAAAAAG
* ** * * *
19818751 CGCCGCCAAAAGCCATGACTTTTAGCAGTGCTTTTCCCACAAAAGCTGCTAAAAGTCATGATCTT
1 CGCCGCTAAAAGCCATGACTTTTAGCAGCACTTTCCCCACAAAAGCCGCTAAAAGCCATGATCTT
* *
19818816 TAGCGGCGCTTTCCTCACAAA
66 TAGCGACACTTTCCTCACAAA
* *
19818837 CGCTGCTAAAAGCCATGACTTTTAGC-GACACTTTCCCCACAAATGCCGCTAAAAGCCATGATCT
1 CGCCGCTAAAAGCCATGACTTTTAGCAG-CACTTTCCCCACAAAAGCCGCTAAAAGCCATGATCT
* *
19818901 TTAGCGACACTTTTCTTACAAA
65 TTAGCGACACTTTCCTCACAAA
*
19818923 CGCCGCTAAAAGTCATGATCTTTTA
1 CGCCGCTAAAAGCCATGA-CTTTTA
19818948 TGGCGTTTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
85 1 0.01
86 88 0.93
87 6 0.06
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (86 bp):
CGCCGCTAAAAGCCATGACTTTTAGCAGCACTTTCCCCACAAAAGCCGCTAAAAGCCATGATCTT
TAGCGACACTTTCCTCACAAA
Found at i:19820678 original size:15 final size:15
Alignment explanation
Indices: 19820655--19820689 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
19820645 AGATAATGAC
* *
19820655 ACAAAAATAATAATA
1 ACAATAATAAGAATA
19820670 ACAATAATAAGAATA
1 ACAATAATAAGAATA
19820685 ACAAT
1 ACAAT
19820690 GATGAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.20
Consensus pattern (15 bp):
ACAATAATAAGAATA
Found at i:19821406 original size:35 final size:34
Alignment explanation
Indices: 19821327--19821406 Score: 79
Period size: 35 Copynumber: 2.3 Consensus size: 34
19821317 GAAATAATAG
**
19821327 TAATAATAAAATAAAGAATAACAATAATACATTAA
1 TAAT-ATAAAATAAAGAATAACAATAATACAACAA
* * * *
19821362 TAACAATAAAATCAGGAATAATAATAATAACAACAA
1 TAA-TATAAAATAAAGAATAACAATAAT-ACAACAA
19821398 TAATATAAA
1 TAATATAAA
19821407 TAATAATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
35 28 0.78
36 8 0.22
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (34 bp):
TAATATAAAATAAAGAATAACAATAATACAACAA
Found at i:19821472 original size:3 final size:3
Alignment explanation
Indices: 19821180--19821457 Score: 136
Period size: 3 Copynumber: 93.7 Consensus size: 3
19821170 AGATATCAAA
* * *
19821180 AAT AGT AAT AAT AAT AAA AAT AAC AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
** *
19821226 GCT AA- AAT AATT AAT AAT AA- AAT AAT AAGT AGAT AA- ACTT AA- AA-
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AA-T A-AT AAT A-AT AAT AAT
* * * ** *
19821270 AAG AA- AAT -AT AAT CAT AAT AAA AAT AAT AGC CAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
19821316 AGA- AAT AAT AGT AAT AAT AA- AAT AAAG AAT AAC AAT AAT ACATT AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A-A-T AAT
* ** * *
19821363 AAC AAT AA- AAT CAGG AAT AAT AAT AAT AAC AAC AAT AAT -AT AAAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * *
19821408 AAT AAT -AT AA- AA- AAT AAT AAT AGT AAT AACT -AT AAT AGT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
19821450 AAT AAT AA
1 AAT AAT AA
19821458 GAACAGAAAA
Statistics
Matches: 208, Mismatches: 42, Indels: 50
0.69 0.14 0.17
Matches are distributed among these distances:
2 27 0.13
3 158 0.76
4 20 0.10
5 3 0.01
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:19824792 original size:30 final size:30
Alignment explanation
Indices: 19824758--19824820 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
19824748 ATCCAAATTA
*
19824758 TATTTTTATTATATAACATTTATTATATTT
1 TATTTTTATTATATAACACTTATTATATTT
* ** *
19824788 TATTTTTATTCTATATTACTTATTATTTTT
1 TATTTTTATTATATAACACTTATTATATTT
19824818 TAT
1 TAT
19824821 ATATGTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (30 bp):
TATTTTTATTATATAACACTTATTATATTT
Found at i:19824842 original size:39 final size:39
Alignment explanation
Indices: 19824780--19824876 Score: 96
Period size: 39 Copynumber: 2.5 Consensus size: 39
19824770 ATAACATTTA
* *
19824780 TTATAT-TTTATTTTTATTCTATATTA-CTTATTAT-TT-T
1 TTATATATTTA-TTATATTATATATTATC-TATTATATTAT
19824817 TTATATATGTTATGTATATTATATATTATCTATTATATTAT
1 TTATATAT-TTAT-TATATTATATATTATCTATTATATTAT
*
19824858 TTAT-TATTCATTATATTAT
1 TTATATATTTATTATATTAT
19824877 TTAAAATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
37 6 0.12
38 10 0.20
39 24 0.47
40 6 0.12
41 5 0.10
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (39 bp):
TTATATATTTATTATATTATATATTATCTATTATATTAT
Found at i:19824877 original size:19 final size:19
Alignment explanation
Indices: 19824831--19824879 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
19824821 ATATGTTATG
*
19824831 TATATTATATATTATCTAT
1 TATATTATTTATTATCTAT
19824850 TATATTATTTATTAT-TCAT
1 TATATTATTTATTATCT-AT
19824869 TATATTATTTA
1 TATATTATTTA
19824880 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTATTTATTATCTAT
Found at i:19825077 original size:24 final size:24
Alignment explanation
Indices: 19825050--19825097 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
19825040 AAAAAAACCC
19825050 AATATATT-TTATCATTCTTTTATA
1 AATATATTGTTATCA-TCTTTTATA
* *
19825074 AATATTTTGTTATCATGTTTTATA
1 AATATATTGTTATCATCTTTTATA
19825098 TATTGTATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (24 bp):
AATATATTGTTATCATCTTTTATA
Found at i:19831082 original size:26 final size:26
Alignment explanation
Indices: 19831046--19831154 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
19831036 CATGAAATTC
19831046 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAAACCA
*
19831072 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAAACCA
* * *
19831098 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAAACCA
*
19831124 TTATCATGGAACATTTACCT-AACCA
1 TTATCATGAAACATTTACCTAAACCA
19831149 TTATCA
1 TTATCA
19831155 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 10 0.13
26 67 0.87
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAAACCA
Found at i:19834658 original size:7 final size:7
Alignment explanation
Indices: 19834646--19834774 Score: 82
Period size: 7 Copynumber: 18.1 Consensus size: 7
19834636 ACTAATTAAT
19834646 CTAAACC
1 CTAAACC
19834653 CTAAACC
1 CTAAACC
*
19834660 TCTTAACCC
1 -C-TAAACC
*
19834669 CT-ATCC
1 CTAAACC
*
19834675 CATAAACA
1 C-TAAACC
*
19834683 CTAAACT
1 CTAAACC
19834690 CTAAACC
1 CTAAACC
*
19834697 CTTAACC
1 CTAAACC
*
19834704 CTTAACC
1 CTAAACC
*
19834711 CCAAACC
1 CTAAACC
*
19834718 CTTACACC
1 C-TAAACC
* *
19834726 TTAAACT
1 CTAAACC
19834733 CT-AACC
1 CTAAACC
*
19834739 CTAACCC
1 CTAAACC
19834746 CTAAACC
1 CTAAACC
*
19834753 CTAAATC
1 CTAAACC
* *
19834760 ATAATCC
1 CTAAACC
19834767 CTAAACC
1 CTAAACC
19834774 C
1 C
19834775 ATAATTCATC
Statistics
Matches: 92, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
6 9 0.10
7 69 0.75
8 9 0.10
9 5 0.05
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:19834914 original size:7 final size:7
Alignment explanation
Indices: 19834899--19834952 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
19834889 TTAATTATCA
*
19834899 TTATAGT
1 TTATGGT
19834906 TTATGGT
1 TTATGGT
19834913 TTATGGT
1 TTATGGT
* *
19834920 TTAAGAT
1 TTATGGT
*
19834927 ATATGGT
1 TTATGGT
*
19834934 TTAGGGT
1 TTATGGT
*
19834941 TTAAGGT
1 TTATGGT
19834948 TTATG
1 TTATG
19834953 AGTTAACTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (7 bp):
TTATGGT
Found at i:19834931 original size:21 final size:21
Alignment explanation
Indices: 19834907--19834991 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
19834897 CATTATAGTT
*
19834907 TATGGTTTATGGTTTAAGATA
1 TATGGTTTAGGGTTTAAGATA
* *
19834928 TATGGTTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
**
19834949 TATGAGTTAACTATAGTTTAAGATA
1 TATG-GTT---TAGGGTTTAAGATA
19834974 TATGGTTTAGGGTTTAAG
1 TATGGTTTAGGGTTTAAG
19834992 GTTTAGGAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
21 31 0.61
22 3 0.06
24 3 0.06
25 14 0.27
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (21 bp):
TATGGTTTAGGGTTTAAGATA
Found at i:19834970 original size:46 final size:46
Alignment explanation
Indices: 19834918--19835007 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
19834908 ATGGTTTATG
*
19834918 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAACTATA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTATA
19834964 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTA
19835008 GTATTTGAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (46 bp):
GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTATA
Found at i:19835063 original size:7 final size:7
Alignment explanation
Indices: 19835034--19835169 Score: 87
Period size: 7 Copynumber: 19.1 Consensus size: 7
19835024 GATGAATTAT
19835034 GGGTTTA
1 GGGTTTA
*
19835041 GGGATTA
1 GGGTTTA
* *
19835048 TGATTTA
1 GGGTTTA
19835055 GGGTTTA
1 GGGTTTA
*
19835062 GGGGTTA
1 GGGTTTA
19835069 GGG-TTA
1 GGGTTTA
*
19835075 GAGTTTA
1 GGGTTTA
* *
19835082 AGGTGTAA
1 GGGT-TTA
*
19835090 GGGTTTG
1 GGGTTTA
*
19835097 GGGTTAA
1 GGGTTTA
*
19835104 GGGTTAA
1 GGGTTTA
*
19835111 GGGTTAA
1 GGGTTTA
19835118 GGGTTTA
1 GGGTTTA
*
19835125 GAGTTTA
1 GGGTTTA
*
19835132 GTGTTTA
1 GGGTTTA
*
19835139 TGGG-ATA
1 -GGGTTTA
*
19835146 GGGGTTAA
1 -GGGTTTA
19835154 GAGGTTTA
1 G-GGTTTA
19835162 GGGTTTA
1 GGGTTTA
19835169 G
1 G
19835170 ATTAATTAGT
Statistics
Matches: 99, Mismatches: 25, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
6 5 0.05
7 80 0.81
8 14 0.14
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (7 bp):
GGGTTTA
Found at i:19835897 original size:12 final size:12
Alignment explanation
Indices: 19835880--19835907 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19835870 AATATACATT
19835880 TAAAAACGCCGC
1 TAAAAACGCCGC
19835892 TAAAAACGCCGC
1 TAAAAACGCCGC
19835904 TAAA
1 TAAA
19835908 GCCCTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.29, G:0.14, T:0.11
Consensus pattern (12 bp):
TAAAAACGCCGC
Found at i:19835989 original size:30 final size:31
Alignment explanation
Indices: 19835927--19835989 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
19835917 TCTTGTAGTG
19835927 ATCATACATTATTTAATTATTACTTTTTTGTAT
1 ATCATACATTATTTAATTATTAC--TTTTGTAT
*
19835960 ATCATGCATTATTTAATTATTAC-TTTGTAT
1 ATCATACATTATTTAATTATTACTTTTGTAT
19835990 GTTTGTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
33 22 0.76
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.56
Consensus pattern (31 bp):
ATCATACATTATTTAATTATTACTTTTGTAT
Found at i:19837894 original size:2 final size:2
Alignment explanation
Indices: 19837889--19837919 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19837879 AAAAATTATC
19837889 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
19837920 CACTTTAAAA
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:19839932 original size:22 final size:21
Alignment explanation
Indices: 19839893--19839937 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
19839883 TTTTGAGCAA
19839893 TTTAAATTTTTTCTTTTATGTT
1 TTTAAATTTTTTCTTTTAT-TT
19839915 TTTAACATTTTTTC-TTTATTT
1 TTTAA-ATTTTTTCTTTTATTT
19839936 TT
1 TT
19839938 CAGTCTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.18
22 10 0.45
23 8 0.36
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTAAATTTTTTCTTTTATTT
Found at i:19841423 original size:34 final size:29
Alignment explanation
Indices: 19841384--19841470 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 29
19841374 GTAATTTATA
19841384 AAATTTTAAATTAATAATAATAAAATTATATTTT
1 AAATTTTAAA--AATAATAA-AAAA-T-TATTTT
19841418 AAATTTTTCAAAAATAATAAAAAATTATTTT
1 AAA-TTTT-AAAAATAATAAAAAATTATTTT
*
19841449 AATATTTTAAAAATTATAAAAA
1 AA-ATTTTAAAAATAATAAAAA
19841471 TATAAATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
30 13 0.27
31 12 0.24
32 2 0.04
33 4 0.08
34 11 0.22
35 4 0.08
36 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATTTTAAAAATAATAAAAAATTATTTT
Found at i:19841437 original size:31 final size:29
Alignment explanation
Indices: 19841394--19841474 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 29
19841384 AAATTTTAAA
*
19841394 TTAATAATAATAAAATTATATTTTAA-ATTT
1 TTAAAAATAATAAAA-TATATTTTAATA-TT
*
19841424 TTCAAAAATAATAAAAAATTATTTTAATATT
1 TT-AAAAATAATAAAATA-TATTTTAATATT
*
19841455 TTAAAAATTATAAAAATATA
1 TTAAAAATAAT-AAAATATA
19841475 AATAATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
30 13 0.30
31 29 0.67
32 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAAAAATAATAAAATATATTTTAATATT
Found at i:19842038 original size:16 final size:16
Alignment explanation
Indices: 19842016--19842072 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
19842006 CGTTTGGTTG
*
19842016 GCTGTAATGGAATAG-
1 GCTGTAATAGAATAGA
*
19842031 GACTGTAATTGAATAGA
1 G-CTGTAATAGAATAGA
19842048 GCTGTAATAGAATAGA
1 GCTGTAATAGAATAGA
19842064 GCTGTAATA
1 GCTGTAATA
19842073 AGTAATTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 1 0.03
16 36 0.95
17 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:19842142 original size:44 final size:46
Alignment explanation
Indices: 19842057--19842146 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
19842047 AGCTGTAATA
*
19842057 GAATAGAGCTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
***
19842103 GAATAGAACTGTAAT-AGT-ATTCTTGTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
19842147 ATGTTGTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 23 0.57
45 3 0.08
46 14 0.35
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.36
Consensus pattern (46 bp):
GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
Found at i:19846049 original size:5 final size:5
Alignment explanation
Indices: 19846039--19846064 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19846029 ATTTACCTCC
19846039 TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA T
19846065 ATTTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:19851576 original size:22 final size:23
Alignment explanation
Indices: 19851546--19851612 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
19851536 TATAGCATGA
*
19851546 CCTAAGGTTCGTATGTCATAA-T
1 CCTAGGGTTCGTATGTCATAAGT
***
19851568 CCTAGGGTTCACGTGTCA-AAGT
1 CCTAGGGTTCGTATGTCATAAGT
*
19851590 CCTAGGGTTCGTATGTAATAAGT
1 CCTAGGGTTCGTATGTCATAAGT
19851613 TTGCTTGTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 2 0.06
22 29 0.83
23 4 0.11
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (23 bp):
CCTAGGGTTCGTATGTCATAAGT
Found at i:19851631 original size:37 final size:37
Alignment explanation
Indices: 19851581--19851651 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
19851571 AGGGTTCACG
*
19851581 TGTCAAAGTCCTAGGGTTCGTATGTAATAAGTTTGCT
1 TGTCAAAGTCCTAGGGTTCGCATGTAATAAGTTTGCT
*
19851618 TGTCATAA-TCCTAGGGTTTGCATGTAATAAGTTT
1 TGTCA-AAGTCCTAGGGTTCGCATGTAATAAGTTT
19851652 ACGTGATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 29 0.94
38 2 0.06
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (37 bp):
TGTCAAAGTCCTAGGGTTCGCATGTAATAAGTTTGCT
Found at i:19854353 original size:22 final size:22
Alignment explanation
Indices: 19854310--19854354 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19854300 ATTATAAATT
*
19854310 AATTAAATATTAATTTAGTTAAA
1 AATTAAATATT-ATTTAATTAAA
19854333 AATTAAAATATT-TTTAATTAAA
1 AATT-AAATATTATTTAATTAAA
19854355 TATAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTAAATATTATTTAATTAAA
Found at i:19855019 original size:73 final size:73
Alignment explanation
Indices: 19854900--19855046 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
19854890 TATAAGAACC
19854900 AAGTGGTGTTTAGAAACAAACTAGATGAGAGTGATAACAGTTAGAAATAAGGCTAAATTAATTTC
1 AAGTGGTGTTTAGAAACAAACTAGATGAGAGTGATAACAGTTAGAAATAAGGCTAAATTAATTTC
19854965 TTAAAGCT
66 TTAAAGCT
19854973 AAGTGGTGTTTAGAAACAAACTAGATGAGAGTGATAACAGTTAGAAATAAGGCTAAATTAATTTC
1 AAGTGGTGTTTAGAAACAAACTAGATGAGAGTGATAACAGTTAGAAATAAGGCTAAATTAATTTC
19855038 TTAAAGCT
66 TTAAAGCT
19855046 A
1 A
19855047 TAGTCAAGAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (73 bp):
AAGTGGTGTTTAGAAACAAACTAGATGAGAGTGATAACAGTTAGAAATAAGGCTAAATTAATTTC
TTAAAGCT
Found at i:19861754 original size:15 final size:13
Alignment explanation
Indices: 19861720--19861752 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
19861710 TGCATTTAGG
*
19861720 GACACACGGCCTA
1 GACACACGGCCAA
19861733 GACACACGGCCAA
1 GACACACGGCCAA
19861746 GACACAC
1 GACACAC
19861753 ACCCATATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.39, G:0.21, T:0.03
Consensus pattern (13 bp):
GACACACGGCCAA
Found at i:19866178 original size:33 final size:33
Alignment explanation
Indices: 19866132--19866200 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
19866122 GTAGAATTTG
*
19866132 ACTGCTTCATTTAATTGTTCTACAAAAATTTAA
1 ACTGCTTCATTTAATTGTCCTACAAAAATTTAA
* * *
19866165 ACTGTTTCCTTTAATTGTCCTACTAAAATTTAA
1 ACTGCTTCATTTAATTGTCCTACAAAAATTTAA
19866198 ACT
1 ACT
19866201 ATTTTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.43
Consensus pattern (33 bp):
ACTGCTTCATTTAATTGTCCTACAAAAATTTAA
Found at i:19867657 original size:18 final size:17
Alignment explanation
Indices: 19867624--19867657 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19867614 TTTATATTTT
*
19867624 TTTAAAAATAATAATAA
1 TTTAAAAATAAAAATAA
19867641 TTTAAAAATTAAAAATA
1 TTTAAAAA-TAAAAATA
19867658 TACAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTAAAAATAAAAATAA
Found at i:19867769 original size:18 final size:17
Alignment explanation
Indices: 19867727--19867771 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
19867717 TTTTGATGTG
19867727 AAAAATTTTATACTTTTT
1 AAAAATTTTATA-TTTTT
**
19867745 ATGAATTTATATATTTTT
1 AAAAATTT-TATATTTTT
19867763 AAAAATTTT
1 AAAAATTTT
19867772 TAATTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 1 0.05
18 17 0.77
19 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
AAAAATTTTATATTTTT
Found at i:19868949 original size:13 final size:13
Alignment explanation
Indices: 19868931--19868956 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19868921 CATTTCCAGG
19868931 TCATTTTCATTTT
1 TCATTTTCATTTT
19868944 TCATTTTCATTTT
1 TCATTTTCATTTT
19868957 GGAGAAAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:19869946 original size:12 final size:12
Alignment explanation
Indices: 19869924--19869959 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
19869914 AACAAAAAAT
19869924 TGAAGTAAATAAG
1 TGAA-TAAATAAG
19869937 TGAATAAATAAG
1 TGAATAAATAAG
*
19869949 TGAGTAAATAA
1 TGAATAAATAA
19869960 CTAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (12 bp):
TGAATAAATAAG
Found at i:19876578 original size:11 final size:11
Alignment explanation
Indices: 19876562--19876593 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19876552 AAATGGTAAT
19876562 ATGCAATTAAC
1 ATGCAATTAAC
19876573 ATGCAATTAAC
1 ATGCAATTAAC
*
19876584 ATGCCATTAA
1 ATGCAATTAA
19876594 TGCAATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (11 bp):
ATGCAATTAAC
Found at i:19877074 original size:25 final size:28
Alignment explanation
Indices: 19877024--19877075 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
19877014 CAATATTTTT
*
19877024 GCATGAAAATTGATATGATAGGAAAATC
1 GCATGAAAATTGATATGATAGAAAAATC
19877052 GCATGAAAA-T-AT-TGATAGAAAAAT
1 GCATGAAAATTGATATGATAGAAAAAT
19877076 TTTACCGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 2 0.09
27 1 0.04
28 9 0.39
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (28 bp):
GCATGAAAATTGATATGATAGAAAAATC
Found at i:19880916 original size:174 final size:175
Alignment explanation
Indices: 19880625--19880966 Score: 533
Period size: 174 Copynumber: 2.0 Consensus size: 175
19880615 TTTATTCGAC
* * *
19880625 CGAGTAGTCTTCTTCGCTATCCTTAAGATCACGTTTGTCGAGTGTGGGCTAGCTTCTAATCAGAA
1 CGAGTAGTCTTCTTCGCTATCCTCAAGATCACGTTTGTCGAGTGTGGGCTAGCTTCAAATCAAAA
*** * * *
19880690 AATTTTTCACAAAAATTACCAGTGGGGTAATTTTACAATTTCTCTAAACTTTTGGGTCAAGTTGT
66 AAAAATTCACAAAAATTACCAGTAGGGTAATATTACAATTTCTCTAAACTTTTGGGTAAAGTTGT
* *
19880755 AAATCAGAAAAATATCTCTAGAAATTTTTTAGAATAATATTTAAT
131 AAATCAAAAAAATATCTCTAGAAAATTTTTAGAATAATATTTAAT
* * * *
19880800 CGAGTAGTCTTCTTCGCTATCCTCAAGCTCAC-TTTTTTGAGTGTGGGCTCGCTTCAAATCAAAA
1 CGAGTAGTCTTCTTCGCTATCCTCAAGATCACGTTTGTCGAGTGTGGGCTAGCTTCAAATCAAAA
*
19880864 AAAAATTCACAAAAATTACTAGTAGGGTAATATTACAATTTCTCTAAACTTTTGGGTAAAGTTGT
66 AAAAATTCACAAAAATTACCAGTAGGGTAATATTACAATTTCTCTAAACTTTTGGGTAAAGTTGT
19880929 AAATCAAAAAAATATCTCTAGAAAATTTTTAGAATAAT
131 AAATCAAAAAAATATCTCTAGAAAATTTTTAGAATAAT
19880967 CTCTTCAAAA
Statistics
Matches: 151, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
174 121 0.80
175 30 0.20
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (175 bp):
CGAGTAGTCTTCTTCGCTATCCTCAAGATCACGTTTGTCGAGTGTGGGCTAGCTTCAAATCAAAA
AAAAATTCACAAAAATTACCAGTAGGGTAATATTACAATTTCTCTAAACTTTTGGGTAAAGTTGT
AAATCAAAAAAATATCTCTAGAAAATTTTTAGAATAATATTTAAT
Done.