Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold23
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: 3125668
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 362582 characters in sequence are not A, C, G, or T
File 18 of 18
Found at i:3007851 original size:1 final size:1
Alignment explanation
Indices: 3007847--3007898 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
3007837 TTTTTCATGG
* * ** * *
3007847 TTTTTTTTGTTTTTTTCTTTTTTTTGGTTTTTTTTTATTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3007899 GGGTATAAAG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.04, C:0.02, G:0.06, T:0.88
Consensus pattern (1 bp):
T
Found at i:3007869 original size:17 final size:16
Alignment explanation
Indices: 3007847--3007898 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
3007837 TTTTTCATGG
3007847 TTTTTTTTGTTTTTTT
1 TTTTTTTTGTTTTTTT
3007863 CTTTTTTTTGGTTTTTTT
1 -TTTTTTTT-GTTTTTTT
*
3007881 TTATTTTTTATTTTTTT
1 TT-TTTTTTGTTTTTTT
3007898 T
1 T
3007899 GGGTATAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.04, C:0.02, G:0.06, T:0.88
Consensus pattern (16 bp):
TTTTTTTTGTTTTTTT
Found at i:3007875 original size:27 final size:27
Alignment explanation
Indices: 3007834--3007900 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
3007824 ATTTTTTCGC
*
3007834 TATTTTTTCATGGTTTTTTTTGT-TTTTT
1 TATTTTTT-TTGGTTTTTTTT-TATTTTT
*
3007862 TCTTTTTTTTGGTTTTTTTTTATTTTT
1 TATTTTTTTTGGTTTTTTTTTATTTTT
3007889 TATTTTTTTTGG
1 TATTTTTTTTGG
3007901 GTATAAAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 27 0.77
28 7 0.20
ACGTcount: A:0.06, C:0.03, G:0.10, T:0.81
Consensus pattern (27 bp):
TATTTTTTTTGGTTTTTTTTTATTTTT
Found at i:3012995 original size:19 final size:20
Alignment explanation
Indices: 3012950--3013001 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3012940 TTACAAGCCA
**
3012950 ATGTATCGATACATTTTATG
1 ATGTATCGATACATACTATG
*
3012970 ATGTATCGATACATACTGTG
1 ATGTATCGATACATACTATG
3012990 -TGTATCGATACA
1 ATGTATCGATACA
3013002 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATACTATG
Found at i:3013061 original size:21 final size:21
Alignment explanation
Indices: 3013035--3013088 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
3013025 CCAATGACCT
*
3013035 GTATCGATACAACTTT-TTCAA
1 GTATCGATACAA-TTTGGTCAA
*
3013056 GTATCGATAC-ATTTGGTCAT
1 GTATCGATACAATTTGGTCAA
3013076 GTATCGATACAAT
1 GTATCGATACAAT
3013089 GTATCGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 14 0.48
21 12 0.41
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (21 bp):
GTATCGATACAATTTGGTCAA
Found at i:3013092 original size:13 final size:13
Alignment explanation
Indices: 3013074--3013102 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3013064 ACATTTGGTC
3013074 ATGTATCGATACA
1 ATGTATCGATACA
3013087 ATGTATCGATACA
1 ATGTATCGATACA
3013100 ATG
1 ATG
3013103 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3013113 original size:20 final size:20
Alignment explanation
Indices: 3013088--3013138 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3013078 ATCGATACAA
*
3013088 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
3013108 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
3013128 TGTATCGATAC
1 TGTATCGATAC
3013139 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:3023773 original size:28 final size:28
Alignment explanation
Indices: 3023644--3024301 Score: 592
Period size: 28 Copynumber: 22.9 Consensus size: 28
3023634 AAAAAAAGAA
* *
3023644 GTGCCACTAACTTGTGTGGGCTTTGAAAAAAG
1 GTGCCACTGAC-T-TGTGGGCTTTG--AAAGG
* *
3023676 TTGCCATTGACTCGTGTGGGCTTTGAAAAGAG
1 GTGCCACTGACT--TGTGGGCTTTG-AAAG-G
* * * * *
3023708 TTACCACTAACTTATGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
3023737 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
3023765 GTGCTACTGACTTGTGGGCTTTAAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
3023793 GTACCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * * *
3023821 ATGCCACTAATTTGTGGGCTTTGAGAAGA
1 GTGCCACTGACTTGTGGGCTTTGA-AAGG
*
3023850 GTGCCACTAACTTG-GAGGCTTTGAAAGG
1 GTGCCACTGACTTGTG-GGCTTTGAAAGG
* * * *
3023878 GTGCCACTGGCTTGTAGGCATTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
*
3023907 GTGCCACTGACTTGTGGG-TGTG---GG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* ** ** * **** * *
3023931 CTTTGAAAGAG-CTTTTTTTTTTTAAAAAAAAG
1 --GTGCCACTGACTTGTGGGCTTT---GAAAGG
* * *
3023963 ATGCCACTAACTTGCGTGAGCTTTGAAA-G
1 GTGCCACTGACTT--GTGGGCTTTGAAAGG
*
3023992 GTGCCACTGACTTGTGGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
3024020 ATGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
3024048 GTGCCACTGACTTTTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
* *
3024077 GTGCCACTGACTTGTGGACTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
3024105 GTGCCACTGACTTGCGTGGGCTTTGAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAGG
*
3024135 GTGCCACTAACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * * *
3024163 ATGCCACTAACTTATGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
*
3024192 GTGCTACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
3024220 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
3024248 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
*
3024277 GTGCCACTAACTTGTGGGCTTTGAA
1 GTGCCACTGACTTGTGGGCTTTGAA
3024302 GAGATTAACG
Statistics
Matches: 515, Mismatches: 87, Indels: 52
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.00
25 4 0.01
26 6 0.01
27 12 0.02
28 255 0.50
29 148 0.29
30 46 0.09
31 8 0.02
32 31 0.06
33 4 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGG
Found at i:3023813 original size:85 final size:85
Alignment explanation
Indices: 3023637--3024301 Score: 621
Period size: 85 Copynumber: 7.7 Consensus size: 85
3023627 TTTTTATAAA
* * * *
3023637 AAAAGAAGTGCCACTAACTTGTGTGGGCTTTGAAAAAAGTTGCCATTGACTCGTGTGGGCTTTGA
1 AAAAG-AGTGCCACTGAC-T-TGTGGGCTTTG--AAAGGGTGCCACTGACT--TGTGGGCTTTG-
* * * *
3023702 AAAGAGTTACCACTAACTTATGGGCTTTG
58 AAAG-GGTGCCACTGACTTGTGGGCTTTG
* * *
3023731 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCTACTGACTTGTGGGCTTTAAAAGGGTA
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
3023796 CCACTGACTTGTGGGCTTTG
66 CCACTGACTTGTGGGCTTTG
* * * * *
3023816 AAAGGA-TGCCACTAATTTGTGGGCTTTGAGAAGAGTGCCACTAACTTG-GAGGCTTTGAAAGGG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGA-AAGGGTGCCACTGACTTGTG-GGCTTTGAAAGGG
* * *
3023879 TGCCACTGGCTTGTAGGCATTG
64 TGCCACTGACTTGTGGGCTTTG
* * *** ** * **** * *
3023901 AAAAGAGTGCCACTGACTTGTGGG-TGTG---GGCTTTGAAAGAGCTTTTTTTTTTTAAAAAAAA
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA-CTTGTGGGCTTT---GAAAG
* * *
3023962 GATGCCACTAACTTGCGTGAGCTTTG
62 GGTGCCACTGACTT--GTGGGCTTTG
* *
3023988 -AAAG-GTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
*
3024051 CCACTGACTTTTGGGCTTTG
66 CCACTGACTTGTGGGCTTTG
* *
3024071 AAAAGAGTGCCACTGACTTGTGGACTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTGAAAGGG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGG
*
3024136 TGCCACTAACTTGTGGGCTTTG
64 TGCCACTGACTTGTGGGCTTTG
* * * * *
3024158 AAAGGA-TGCCACTAACTTATGGGCTTTGAAAAGAGTGCTACTGACTTGTGGGCTTTGAAAGGGT
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGT
3024222 GCCACTGACTTGTGGGCTTTG
65 GCCACTGACTTGTGGGCTTTG
* * *
3024243 -AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAA
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAA
3024302 GAGATTAACG
Statistics
Matches: 469, Mismatches: 82, Indels: 49
0.78 0.14 0.08
Matches are distributed among these distances:
81 4 0.01
82 6 0.01
83 8 0.02
84 29 0.06
85 251 0.54
86 45 0.10
87 73 0.16
88 7 0.01
89 18 0.04
91 11 0.02
92 1 0.00
93 11 0.02
94 5 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (85 bp):
AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
CCACTGACTTGTGGGCTTTG
Found at i:3023876 original size:57 final size:57
Alignment explanation
Indices: 3023645--3024301 Score: 645
Period size: 57 Copynumber: 11.4 Consensus size: 57
3023635 AAAAAAGAAG
* * *
3023645 TGCCACTAACTTGTGTGGGCTTTGAAAAAAGTTGCCATTGACTCGTGTGGGCTTTGAAAAGAGT
1 TGCCACTAAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTG-AAAG-GA
* * *
3023709 TACCACTAACTTATGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
3023766 TGCTACTGACTTGTGGGCTTT-AAAAGGGTACCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
3023822 TGCCACTAATTTGTGGGCTTTGAGAAGAGTGCCACTAACTTG-GAGGCTTTGAAAGGG
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG-GGCTTTGAAAGGA
** * * * *
3023879 TGCCACTGGCTTGTAGGCATTGAAAAGAGTGCCACTGACTTGTGGG-TGTG---GGCTT
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG--A
* ** * * **** * * * *
3023934 TG-AAAGAGCTTTTTTTTTTTAAAAAAAAGATGCCACTAACTTGCGTGAGCTTTGAAAGG-
1 TGCCACTAACTTGTGGGCTTT-GAAAAGAG-TGCCACTGACTT--GTGGGCTTTGAAAGGA
* *
3023993 TGCCACTGACTTGTGGGCTTTGAAAAGA-TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
3024049 TGCCACTGACTTTTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGACTTTGAAAAGG-
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGA
* * *
3024106 TGCCACTGACTTGCGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGA
1 TGCCACTAACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
3024164 TGCCACTAACTTATGGGCTTTGAAAAGAGTGCTACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
3024221 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
3024277 GTGCCACTAACTTGTGGGCTTTGAA
1 -TGCCACTAACTTGTGGGCTTTGAA
3024302 GAGATTAACG
Statistics
Matches: 493, Mismatches: 77, Indels: 52
0.79 0.12 0.08
Matches are distributed among these distances:
53 2 0.00
54 8 0.02
55 22 0.04
56 131 0.27
57 203 0.41
58 51 0.10
59 30 0.06
60 8 0.02
61 10 0.02
62 18 0.04
63 1 0.00
64 9 0.02
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (57 bp):
TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:3024518 original size:16 final size:15
Alignment explanation
Indices: 3024490--3024519 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
3024480 TACAAAAATG
3024490 ATGAATGATGATATT
1 ATGAATGATGATATT
3024505 ATGAATGCATGATAT
1 ATGAATG-ATGATAT
3024520 GGAATTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (15 bp):
ATGAATGATGATATT
Found at i:3026555 original size:20 final size:19
Alignment explanation
Indices: 3026510--3026566 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
3026500 TGTATCGATA
*
3026510 CATTGTACCGATACATGAT
1 CATTGTATCGATACATGAT
3026529 CATTGTATCGATACATGCA-
1 CATTGTATCGATACATG-AT
3026548 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
3026567 AACTAGCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:3028236 original size:15 final size:15
Alignment explanation
Indices: 3028213--3028252 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3028203 AAGTCAACCA
*
3028213 TTAAAGATGATGAAG
1 TTAATGATGATGAAG
*
3028228 TTAATGATGATGATG
1 TTAATGATGATGAAG
*
3028243 ATAATGATGA
1 TTAATGATGA
3028253 AGTTGACTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (15 bp):
TTAATGATGATGAAG
Found at i:3029487 original size:33 final size:32
Alignment explanation
Indices: 3029441--3029508 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
3029431 CGTTACAAGC
* **
3029441 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATAGATACATACTATG-TGTATCGATA
*
3029474 CAATGTATAGATACATACTGTGTGTATCGATA
1 CAATGTATAGATACATACTATGTGTATCGATA
3029506 CAA
1 CAA
3029509 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATAGATACATACTATGTGTATCGATA
Found at i:3029588 original size:20 final size:21
Alignment explanation
Indices: 3029541--3029593 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3029531 GCCAATGACC
**
3029541 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
3029562 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
3029582 TGTATCGATACA
1 TGTATCGATACA
3029594 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:3029599 original size:13 final size:13
Alignment explanation
Indices: 3029581--3029609 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3029571 ACATTTGGTC
3029581 ATGTATCGATACA
1 ATGTATCGATACA
3029594 ATGTATCGATACA
1 ATGTATCGATACA
3029607 ATG
1 ATG
3029610 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3029620 original size:20 final size:20
Alignment explanation
Indices: 3029595--3029645 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3029585 ATCGATACAA
*
3029595 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
3029615 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
3029635 TGTATCGATAC
1 TGTATCGATAC
3029646 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:3031587 original size:20 final size:21
Alignment explanation
Indices: 3031558--3031599 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
3031548 TAGGGGCTGC
*
3031558 CCGGTTGCGACCTGG-AGGTG
1 CCGGTCGCGACCTGGTAGGTG
3031578 CCGGTCGCGACCTGGTAGGTG
1 CCGGTCGCGACCTGGTAGGTG
3031599 C
1 C
3031600 TGCCTAGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.10, C:0.29, G:0.43, T:0.19
Consensus pattern (21 bp):
CCGGTCGCGACCTGGTAGGTG
Found at i:3032053 original size:13 final size:13
Alignment explanation
Indices: 3032035--3032065 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3032025 AACCCCTTGC
*
3032035 ATCGATACACTGT
1 ATCGATACAATGT
3032048 ATCGATACAATGT
1 ATCGATACAATGT
3032061 ATCGA
1 ATCGA
3032066 CACAGAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (13 bp):
ATCGATACAATGT
Found at i:3038244 original size:13 final size:13
Alignment explanation
Indices: 3038226--3038251 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3038216 ACATTTTATG
3038226 ATGTATCGATACA
1 ATGTATCGATACA
3038239 ATGTATCGATACA
1 ATGTATCGATACA
3038252 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3038246 original size:33 final size:32
Alignment explanation
Indices: 3038204--3038271 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
3038194 CGTTACAAGC
**
3038204 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATACTATG-TGTATCGATA
*
3038237 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
3038269 CAA
1 CAA
3038272 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:3038350 original size:20 final size:21
Alignment explanation
Indices: 3038303--3038355 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3038293 GCCAATGACC
**
3038303 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
3038324 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
3038344 TGTATCGATACA
1 TGTATCGATACA
3038356 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:3038361 original size:13 final size:13
Alignment explanation
Indices: 3038343--3038371 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3038333 ACATTTGGTC
3038343 ATGTATCGATACA
1 ATGTATCGATACA
3038356 ATGTATCGATACA
1 ATGTATCGATACA
3038369 ATG
1 ATG
3038372 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3038382 original size:20 final size:20
Alignment explanation
Indices: 3038357--3038407 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3038347 ATCGATACAA
*
3038357 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
3038377 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
3038397 TGTATCGATAC
1 TGTATCGATAC
3038408 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:3039067 original size:13 final size:13
Alignment explanation
Indices: 3039049--3039073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3039039 ATAATGCACA
3039049 GTATCGATACATT
1 GTATCGATACATT
3039062 GTATCGATACAT
1 GTATCGATACAT
3039074 GACCATTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:3046347 original size:21 final size:22
Alignment explanation
Indices: 3046323--3046371 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3046313 ATCTAAAAAA
*
3046323 TGAAAAATTAAAA-AATAAATT
1 TGAAAAATGAAAATAATAAATT
*
3046344 TG-AAAATGAAAATAATGAATT
1 TGAAAAATGAAAATAATAAATT
3046365 T-AAAAAT
1 TGAAAAAT
3046372 ATAATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (22 bp):
TGAAAAATGAAAATAATAAATT
Found at i:3052641 original size:19 final size:19
Alignment explanation
Indices: 3052617--3052682 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
3052607 TGTCAACGAT
3052617 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
3052636 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
3052650 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
3052668 TTGTATCGATACATA
1 TTGTATCGATACATA
3052683 TTAAGCTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.27
15 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:3052654 original size:32 final size:32
Alignment explanation
Indices: 3052618--3052680 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
3052608 GTCAACGATT
3052618 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3052650 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
3052681 TATTAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:3052655 original size:13 final size:13
Alignment explanation
Indices: 3052637--3052661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3052627 ACATAAGTGT
3052637 TGTATCGATACAA
1 TGTATCGATACAA
3052650 TGTATCGATACA
1 TGTATCGATACA
3052662 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3052742 original size:13 final size:13
Alignment explanation
Indices: 3052724--3052748 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3052714 ATTACTCAAA
3052724 TGTATCGATACAT
1 TGTATCGATACAT
3052737 TGTATCGATACA
1 TGTATCGATACA
3052749 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3052813 original size:52 final size:52
Alignment explanation
Indices: 3052757--3052887 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
3052747 CACTGATCTT
* **
3052757 TGTATCGATACATGCAGGCAAATTTTCTCAGATGTATCGATACATTATGAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACCATGAAA
*
3052809 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACCATGAAA
*
3052861 TGTATCGATACATGCAGGCAAAATTTC
1 TGTATCGATACATGCAGGCAAATTTTC
3052888 ATATTTCGGG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACCATGAAA
Found at i:3057628 original size:4 final size:4
Alignment explanation
Indices: 3057619--3057649 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3057609 TGGTTCTTCT
*
3057619 TTTA TTTA TTTA TTTA TTTA TTTA CTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3057650 TTTCCAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:3058440 original size:14 final size:14
Alignment explanation
Indices: 3058421--3058524 Score: 70
Period size: 15 Copynumber: 7.3 Consensus size: 14
3058411 AATCATAATT
3058421 AAATTTAAAATCTA
1 AAATTTAAAATCTA
*
3058435 AAATTTTGAAATC-A
1 AAA-TTTAAAATCTA
**
3058449 AAATTTAAACA-AAA
1 AAATTTAAA-ATCTA
* *
3058463 AAATTTTAAATTTA
1 AAATTTAAAATCTA
* * *
3058477 TGAATTTAAAAACCA
1 -AAATTTAAAATCTA
3058492 TAAATTTAAAATCTA
1 -AAATTTAAAATCTA
3058507 AAATCTTAAAAT-TA
1 AAAT-TTAAAATCTA
3058521 AAAT
1 AAAT
3058525 ACAAATTTAA
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
13 6 0.09
14 28 0.40
15 36 0.51
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (14 bp):
AAATTTAAAATCTA
Found at i:3059910 original size:14 final size:14
Alignment explanation
Indices: 3059891--3059921 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3059881 TAGTTTTCAC
3059891 TTTCAATTCTCAAT
1 TTTCAATTCTCAAT
3059905 TTTCAATTCTCAAT
1 TTTCAATTCTCAAT
3059919 TTT
1 TTT
3059922 GAATATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTCAATTCTCAAT
Found at i:3061413 original size:3 final size:3
Alignment explanation
Indices: 3061399--3061442 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3061389 GAATTAACTT
*
3061399 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3061443 TTGCTAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3065274 original size:28 final size:32
Alignment explanation
Indices: 3065207--3065274 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 32
3065197 TAATTTTTAG
* *
3065207 TTAAATAATTATTTTACTATAGTTAATTTTAT
1 TTAAATAATTATTTTACTATAATTAATTCTAT
**
3065239 TTTGATAATTA-TTT-C-ATAATT-ATTCTAT
1 TTAAATAATTATTTTACTATAATTAATTCTAT
3065267 TTAAATAA
1 TTAAATAA
3065275 GATTGCTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
28 12 0.40
29 5 0.17
30 1 0.03
31 3 0.10
32 9 0.30
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (32 bp):
TTAAATAATTATTTTACTATAATTAATTCTAT
Found at i:3071459 original size:21 final size:19
Alignment explanation
Indices: 3071412--3071466 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
3071402 GCAAGGCAAC
3071412 TTTGTATCGATACAACACT
1 TTTGTATCGATACAACACT
* **
3071431 TATGTATCGATACATTTACT
1 TTTGTATCGATACA-ACACT
3071451 GTTTGTATCGATACAA
1 -TTTGTATCGATACAA
3071467 ATTGTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACAACACT
Found at i:3074717 original size:51 final size:51
Alignment explanation
Indices: 3074631--3074768 Score: 145
Period size: 51 Copynumber: 2.7 Consensus size: 51
3074621 AATAGCCTCT
* * * *
3074631 ATGTATCGATACATTGAAGAACGTAAT-AATACATTTGG-ATCAAAACCCAAA
1 ATGTATCAATACAATGAA-AATGT-ATCAATACATTTGGCATAAAAACCCAAA
** * *
3074682 ATGTATTGATATAATGAAAAATGTATCAATACATTTGGCTTAAAAACCCAAA
1 ATGTATCAATACAATG-AAAATGTATCAATACATTTGGCATAAAAACCCAAA
**
3074734 ATGTATCAATACAATGAAAATGTATCGGTACATTT
1 ATGTATCAATACAATGAAAATGTATCAATACATTT
3074769 TCTTTTCAGT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 2 0.03
51 45 0.62
52 26 0.36
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (51 bp):
ATGTATCAATACAATGAAAATGTATCAATACATTTGGCATAAAAACCCAAA
Found at i:3079056 original size:23 final size:22
Alignment explanation
Indices: 3079009--3079073 Score: 105
Period size: 23 Copynumber: 3.0 Consensus size: 22
3078999 CAATTTATAA
3079009 CTCCCCCTTAATAAAAT-TTTT
1 CTCCCCCTTAATAAAATATTTT
3079030 CTCCCCCTTAATAAAATTATTTT
1 CTCCCCCTTAATAAAA-TATTTT
*
3079053 CTCCCCTTTAATAAAATATTT
1 CTCCCCCTTAATAAAATATTT
3079074 AATGCTTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 16 0.39
22 6 0.15
23 19 0.46
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (22 bp):
CTCCCCCTTAATAAAATATTTT
Found at i:3083578 original size:21 final size:21
Alignment explanation
Indices: 3083553--3083593 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3083543 AACTTCCTGC
*
3083553 AATTCATTTA-TTCTCTTTTCT
1 AATTCATCTACTT-TCTTTTCT
3083574 AATTCATCTACTTTCTTTTC
1 AATTCATCTACTTTCTTTTC
3083594 AAACACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTCATCTACTTTCTTTTCT
Found at i:3084629 original size:51 final size:50
Alignment explanation
Indices: 3084559--3084690 Score: 156
Period size: 51 Copynumber: 2.6 Consensus size: 50
3084549 TTTTACTCAT
* * **
3084559 TGTATCGATACAATATTCATTGTATCGATACATTCTAGGCTTTTACTTAGA
1 TGTATCGATAC-ATCTTCATTGTATCGATACATTATAGGCTTTTACCCAGA
* * *
3084610 TGTATCGATACATTCTTCATTGTATTGATACATTATGGGTTTTTACCCAGA
1 TGTATCGATACA-TCTTCATTGTATCGATACATTATAGGCTTTTACCCAGA
* *
3084661 TGTATCGATACATCATTCAATGCATCGATA
1 TGTATCGATACATC-TTCATTGTATCGATA
3084691 TATGCAGGCA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 3 0.04
51 66 0.96
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (50 bp):
TGTATCGATACATCTTCATTGTATCGATACATTATAGGCTTTTACCCAGA
Found at i:3086556 original size:11 final size:10
Alignment explanation
Indices: 3086532--3086556 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3086522 GTTTGAAATG
3086532 TTTTTCTAGA
1 TTTTTCTAGA
3086542 TTTTTCTAGA
1 TTTTTCTAGA
3086552 TTTTT
1 TTTTT
3086557 GAAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTTTCTAGA
Found at i:3093832 original size:15 final size:15
Alignment explanation
Indices: 3093812--3093850 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3093802 CGATCCTTAC
* *
3093812 TACCCAAGTGCACTT
1 TACCCAAGCGCACCT
3093827 TACCCAAGCGCACCT
1 TACCCAAGCGCACCT
3093842 TACCCAAGC
1 TACCCAAGC
3093851 CCTATCATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.28, C:0.41, G:0.13, T:0.18
Consensus pattern (15 bp):
TACCCAAGCGCACCT
Found at i:3096320 original size:20 final size:20
Alignment explanation
Indices: 3096295--3096348 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3096285 GTTACAAGCA
* *
3096295 ATGTATCGACACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
3096315 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
3096335 ATGTATCGATACAA
1 ATGTATCGATACAA
3096349 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:3096421 original size:19 final size:18
Alignment explanation
Indices: 3096376--3096433 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
3096366 ACTACTAGTT
3096376 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
3096395 TCCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
3096414 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
3096433 T
1 T
3096434 ATCGATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.54
20 16 0.43
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:3096435 original size:13 final size:13
Alignment explanation
Indices: 3096417--3096443 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3096407 TACAATGATC
3096417 ATGTATCGATACA
1 ATGTATCGATACA
3096430 ATGTATCGATACA
1 ATGTATCGATACA
3096443 A
1 A
3096444 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3097797 original size:13 final size:13
Alignment explanation
Indices: 3097779--3097803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3097769 ATAATGCACA
3097779 GTATCGATACATT
1 GTATCGATACATT
3097792 GTATCGATACAT
1 GTATCGATACAT
3097804 GACCACTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:3097936 original size:33 final size:33
Alignment explanation
Indices: 3097872--3097972 Score: 152
Period size: 33 Copynumber: 3.1 Consensus size: 33
3097862 CCTTAACTAT
* *
3097872 TTGTATCGATACAT-A-CAAGACGTATCGATACA
1 TTGTATCAATACATGACCAA-ATGTATCGATACA
*
3097904 TTGTATCAATACATGACCAAATTTATCGATACA
1 TTGTATCAATACATGACCAAATGTATCGATACA
3097937 TTGTATCAATACATGACCAAATGTATCGATACA
1 TTGTATCAATACATGACCAAATGTATCGATACA
3097970 TTG
1 TTG
3097973 GCTTGTAACG
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 13 0.21
33 47 0.75
34 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (33 bp):
TTGTATCAATACATGACCAAATGTATCGATACA
Found at i:3105134 original size:19 final size:21
Alignment explanation
Indices: 3105110--3105165 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
3105100 CAGTATCAAT
3105110 ACATTGTATCGATACAT-G-A
1 ACATTGTATCGATACATAGAA
*
3105129 ACATTGTATTGATAC-TAGCAA
1 ACATTGTATCGATACATAG-AA
*
3105150 AGATTGTATCGATACA
1 ACATTGTATCGATACA
3105166 GGTGATTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
21 14 0.47
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (21 bp):
ACATTGTATCGATACATAGAA
Found at i:3105233 original size:13 final size:13
Alignment explanation
Indices: 3105215--3105273 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
3105205 ATATACAAGA
3105215 TGTATCGATACAT
1 TGTATCGATACAT
3105228 TGTATCGATACA-
1 TGTATCGATACAT
*
3105240 TG-A-CCA-A-A-
1 TGTATCGATACAT
3105248 TGTATCGATACAT
1 TGTATCGATACAT
3105261 TGTATCGATACAT
1 TGTATCGATACAT
3105274 GACCAAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 3 0.08
9 2 0.05
10 4 0.10
11 2 0.05
12 3 0.08
13 25 0.64
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3105253 original size:20 final size:20
Alignment explanation
Indices: 3105228--3105293 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
3105218 ATCGATACAT
3105228 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
3105248 TGTATCGATACAT-------
1 TGTATCGATACATGACCAAA
3105261 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
3105281 TGTATCGATACAT
1 TGTATCGATACAT
3105294 TGGCTTGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:3105256 original size:33 final size:33
Alignment explanation
Indices: 3105195--3105295 Score: 170
Period size: 33 Copynumber: 3.1 Consensus size: 33
3105185 CCTTAACTGT
*
3105195 TTGTATCGATATAT-A-CAAGATGTATCGATACA
1 TTGTATCGATACATGACCAA-ATGTATCGATACA
3105227 TTGTATCGATACATGACCAAATGTATCGATACA
1 TTGTATCGATACATGACCAAATGTATCGATACA
3105260 TTGTATCGATACATGACCAAATGTATCGATACA
1 TTGTATCGATACATGACCAAATGTATCGATACA
3105293 TTG
1 TTG
3105296 GCTTGTAACG
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
32 13 0.20
33 50 0.76
34 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACA
Found at i:3106166 original size:33 final size:31
Alignment explanation
Indices: 3106099--3106568 Score: 262
Period size: 27 Copynumber: 15.7 Consensus size: 31
3106089 TCTTCTTTGG
**
3106099 GTCCACAACTCCCTGGCACCTTTCCTTTTAA
1 GTCCACAACTCTGTGGCACCTTTCCTTTTAA
3106130 GTCCACAACTCTGTGGCACCTCTTCCTTTTTAA
1 GTCCACAACTCTGTGGCACCT-TTCC-TTTTAA
* *
3106163 GTCCACAGCTCTGTGGCACCTTTTCCTTTCAA
1 GTCCACAACTCTGTGGCACC-TTTCCTTTTAA
* * *
3106195 GTCTACAACTTTGTGGCACC--T--TTTTAT
1 GTCCACAACTCTGTGGCACCTTTCCTTTTAA
*
3106222 GTCCACAACTCTGTGGCACCTTTTTCCTTTCAA
1 GTCCACAACTCTGTGGCACC--TTTCCTTTTAA
*
3106255 GTCCATAACTCTGTGGCA-C---CCTTTTAA
1 GTCCACAACTCTGTGGCACCTTTCCTTTTAA
*** *
3106282 GTTTGCAACTTTGTGGCA-C---CCTTTTAA
1 GTCCACAACTCTGTGGCACCTTTCCTTTTAA
* * ** **
3106309 GCCCACAAATCCATGGCACCATTTTGTTTTCAA
1 GTCCACAACTCTGTGGCACC-TTTCCTTTT-AA
* *
3106342 ATCCATAACT-TCGTGGCA-C---CCTTTTAA
1 GTCCACAACTCT-GTGGCACCTTTCCTTTTAA
* *
3106369 GTCCACAACTCTGTGGCACATTTTCCTTTCAA
1 GTCCACAACTCTGTGGCAC-CTTTCCTTTTAA
*
3106401 GTCCCCAACTC-GATGGCACC--T--TTTTAA
1 GTCCACAACTCTG-TGGCACCTTTCCTTTTAA
** * *
3106428 GTCCACAACTCCATGGCACATTTTCTTTTCAA
1 GTCCACAACTCTGTGGCACCTTTCCTTTT-AA
* ** *
3106460 GTCCATAACTCCATGGCA-C--T-ATTTTAA
1 GTCCACAACTCTGTGGCACCTTTCCTTTTAA
** *
3106487 GTCCACAACTCCATGGCACCTTTTCTTTTCAA
1 GTCCACAACTCTGTGGCACCTTTCCTTTT-AA
* ** *
3106519 GTCCATAACTCCATGGCA-C---CATTTTAA
1 GTCCACAACTCTGTGGCACCTTTCCTTTTAA
*
3106546 GTCCACAAATCTGTGGCACCTTT
1 GTCCACAACTCTGTGGCACCTTT
3106569 ATCCTTCTTA
Statistics
Matches: 341, Mismatches: 60, Indels: 76
0.71 0.13 0.16
Matches are distributed among these distances:
27 133 0.39
28 16 0.05
29 4 0.01
30 1 0.00
31 30 0.09
32 93 0.27
33 63 0.18
34 1 0.00
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (31 bp):
GTCCACAACTCTGTGGCACCTTTCCTTTTAA
Found at i:3106291 original size:60 final size:59
Alignment explanation
Indices: 3106099--3106306 Score: 220
Period size: 60 Copynumber: 3.4 Consensus size: 59
3106089 TCTTCTTTGG
** *
3106099 GTCCACAACTCCCTGGCACC-TTTCCTTTTAAGTCCACAACTCTGTGGCACCTCTTCCTTTTTAA
1 GTCCACAACTCTGTGGCACCTTTTCCTTTCAAGTCCACAACTCTGTGGCA---C--CC-TTTTAA
* * * * *
3106163 GTCCACAGCTCTGTGGCACCTTTTCCTTTCAAGTCTACAACTTTGTGGCACCTTTTTAT
1 GTCCACAACTCTGTGGCACCTTTTCCTTTCAAGTCCACAACTCTGTGGCACCCTTTTAA
*
3106222 GTCCACAACTCTGTGGCACCTTTTTCCTTTCAAGTCCATAACTCTGTGGCACCCTTTTAA
1 GTCCACAACTCTGTGGCACC-TTTTCCTTTCAAGTCCACAACTCTGTGGCACCCTTTTAA
*** *
3106282 GTTTGCAACTTTGTGGCACCCTTTT
1 GTCCACAACTCTGTGGCA-CCTTTT
3106307 AAGCCCACAA
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
59 24 0.20
60 53 0.43
61 2 0.02
62 1 0.01
64 17 0.14
65 26 0.21
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.37
Consensus pattern (59 bp):
GTCCACAACTCTGTGGCACCTTTTCCTTTCAAGTCCACAACTCTGTGGCACCCTTTTAA
Found at i:3106378 original size:87 final size:87
Alignment explanation
Indices: 3106187--3106387 Score: 251
Period size: 87 Copynumber: 2.3 Consensus size: 87
3106177 GGCACCTTTT
* * * * * ** *
3106187 CCTTTCAAGTCTACAACTTTGTGGCACCTTTTTATGTCCACAACTCTGTGGCACCTTTTTCCTTT
1 CCTTTTAAGTCTACAACTTTGTGGCACCCTTTTAAGCCCACAAATCCATGGCACCATTTTCCTTT
*
3106252 CAAGTCCATAACTCTGTGGCAC
66 CAAATCCATAACTCTGTGGCAC
* * **
3106274 CCTTTTAAGTTTGCAACTTTGTGGCACCCTTTTAAGCCCACAAATCCATGGCACCATTTTGTTTT
1 CCTTTTAAGTCTACAACTTTGTGGCACCCTTTTAAGCCCACAAATCCATGGCACCATTTTCCTTT
3106339 CAAATCCATAACT-TCGTGGCAC
66 CAAATCCATAACTCT-GTGGCAC
* *
3106361 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCTACAACTTTGTGGCAC
3106388 ATTTTCCTTT
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
86 1 0.01
87 95 0.99
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.35
Consensus pattern (87 bp):
CCTTTTAAGTCTACAACTTTGTGGCACCCTTTTAAGCCCACAAATCCATGGCACCATTTTCCTTT
CAAATCCATAACTCTGTGGCAC
Found at i:3106403 original size:32 final size:31
Alignment explanation
Indices: 3106362--3106543 Score: 182
Period size: 32 Copynumber: 6.0 Consensus size: 31
3106352 TCGTGGCACC
* **
3106362 CTTTTAAGTCCACAACTCTGTGGCACATTTT
1 CTTTCAAGTCCACAACTCCATGGCACATTTT
* * *
3106393 CCTTTCAAGTCCCCAACTCGATGGCAC--CTT
1 -CTTTCAAGTCCACAACTCCATGGCACATTTT
3106423 -TTT-AAGTCCACAACTCCATGGCACATTTT
1 CTTTCAAGTCCACAACTCCATGGCACATTTT
* *
3106452 CTTTTCAAGTCCATAACTCCATGGCAC--TAT
1 C-TTTCAAGTCCACAACTCCATGGCACATTTT
*
3106482 -TTT-AAGTCCACAACTCCATGGCACCTTTT
1 CTTTCAAGTCCACAACTCCATGGCACATTTT
*
3106511 CTTTTCAAGTCCATAACTCCATGGCACCATTTT
1 C-TTTCAAGTCCACAACTCCATGGCA-CATTTT
3106544 AAGTCCACAA
Statistics
Matches: 125, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
27 39 0.31
28 6 0.05
29 4 0.03
30 4 0.03
31 6 0.05
32 61 0.49
33 5 0.04
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.34
Consensus pattern (31 bp):
CTTTCAAGTCCACAACTCCATGGCACATTTT
Found at i:3106420 original size:59 final size:59
Alignment explanation
Indices: 3106295--3106553 Score: 356
Period size: 59 Copynumber: 4.4 Consensus size: 59
3106285 TGCAACTTTG
* * * * * * *
3106295 TGGCACCCTTTTAAGCCCACAAATCCATGGCACCATTTTGTTTTCAAATCCATAACTTCG
1 TGGCACCATTTTAAGTCCACAACTCCATGGCA-CATTTTCTTTTCAAGTCCATAACTCCA
* ** * ** *
3106355 TGGCACCCTTTTAAGTCCACAACTCTGTGGCACATTTTCCTTTCAAGTCCCCAACTCGA
1 TGGCACCATTTTAAGTCCACAACTCCATGGCACATTTTCTTTTCAAGTCCATAACTCCA
*
3106414 TGGCACCTTTTTAAGTCCACAACTCCATGGCACATTTTCTTTTCAAGTCCATAACTCCA
1 TGGCACCATTTTAAGTCCACAACTCCATGGCACATTTTCTTTTCAAGTCCATAACTCCA
* *
3106473 TGGCACTATTTTAAGTCCACAACTCCATGGCACCTTTTCTTTTCAAGTCCATAACTCCA
1 TGGCACCATTTTAAGTCCACAACTCCATGGCACATTTTCTTTTCAAGTCCATAACTCCA
3106532 TGGCACCATTTTAAGTCCACAA
1 TGGCACCATTTTAAGTCCACAA
3106554 ATCTGTGGCA
Statistics
Matches: 176, Mismatches: 23, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
59 148 0.84
60 28 0.16
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (59 bp):
TGGCACCATTTTAAGTCCACAACTCCATGGCACATTTTCTTTTCAAGTCCATAACTCCA
Found at i:3106623 original size:32 final size:32
Alignment explanation
Indices: 3106577--3106996 Score: 411
Period size: 32 Copynumber: 13.1 Consensus size: 32
3106567 TTATCCTTCT
*
3106577 TAAAGCCCATACAAGTTGGTGGCAACCCTTTC
1 TAAAGCCCACACAAGTTGGTGGCAACCCTTTC
* * *
3106609 TAAAGCCCACACAAGTCGATGGCAACCTTCTTC
1 TAAAGCCCACACAAGTTGGTGGCAACCCT-TTC
*
3106642 -AAAGCCCACACAAGTTGGTGGCGACCCTTTC
1 TAAAGCCCACACAAGTTGGTGGCAACCCTTTC
* *
3106673 TAAAGCCCACACAAGTCGGTGGCAACCTTCTTC
1 TAAAGCCCACACAAGTTGGTGGCAACCCT-TTC
* * *
3106706 -AAATCCCACATAAGTTGGTGGCGACCCTTTC
1 TAAAGCCCACACAAGTTGGTGGCAACCCTTTC
* * * * *
3106737 CAATGCCCAAACAAGTTGGTGGTAACCATTTC
1 TAAAGCCCACACAAGTTGGTGGCAACCCTTTC
*
3106769 TAAAGCCCACACAAGTTGGTGGTGAA-CCTTTC
1 TAAAGCCCACACAAGTTGGTGG-CAACCCTTTC
*
3106801 TAAAGCCCACACAAGTTGGTGGCGACCCTTTC
1 TAAAGCCCACACAAGTTGGTGGCAACCCTTTC
* ** ** * *
3106833 TAAAGCCCACATAAGTCAGTGGTGACCTTTTT
1 TAAAGCCCACACAAGTTGGTGGCAACCCTTTC
* * *
3106865 TAAAGGCCCACACAAGTCGATGGCAA-CCTTTT
1 TAAA-GCCCACACAAGTTGGTGGCAACCCTTTC
*
3106897 TCAAAACCCACACAAGTTGGTGGCAACCC-TTC
1 T-AAAGCCCACACAAGTTGGTGGCAACCCTTTC
** * * *
3106929 TTAAAGCTTACCCATGTCGGTGGCAACCCTTT-
1 -TAAAGCCCACACAAGTTGGTGGCAACCCTTTC
* * *
3106961 TAAAAGCCCACATAAGTTGGTGGCATCTCTTTC
1 T-AAAGCCCACACAAGTTGGTGGCAACCCTTTC
3106994 TAA
1 TAA
3106997 GCCTAATGTC
Statistics
Matches: 315, Mismatches: 60, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
31 8 0.03
32 274 0.87
33 33 0.10
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (32 bp):
TAAAGCCCACACAAGTTGGTGGCAACCCTTTC
Found at i:3107990 original size:51 final size:51
Alignment explanation
Indices: 3107934--3108066 Score: 194
Period size: 51 Copynumber: 2.6 Consensus size: 51
3107924 TGATTGATTA
* * * *
3107934 TATCGATACAATATTCATTGTATCGATACATACTGGGTTTTTACCTAGATG
1 TATCGATACATTATTCATTGTATCGATACATACTAGATTTTTACCCAGATG
* *
3107985 TATCGATACATTTTTCATTGTATCGATACATTCTAGATTTTTACCCAGATG
1 TATCGATACATTATTCATTGTATCGATACATACTAGATTTTTACCCAGATG
* *
3108036 TATCGATACATTATTCAATATATCGATACAT
1 TATCGATACATTATTCATTGTATCGATACAT
3108067 GTAGGCAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 73 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (51 bp):
TATCGATACATTATTCATTGTATCGATACATACTAGATTTTTACCCAGATG
Found at i:3110662 original size:18 final size:18
Alignment explanation
Indices: 3110639--3110674 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3110629 AAGTAAGGTA
3110639 ATGTTCCGTATCGGTATC
1 ATGTTCCGTATCGGTATC
3110657 ATGTTCCGTATCGGTATC
1 ATGTTCCGTATCGGTATC
3110675 TCTCTAGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (18 bp):
ATGTTCCGTATCGGTATC
Found at i:3112729 original size:33 final size:32
Alignment explanation
Indices: 3112668--3112729 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
3112658 ATTTACTATA
**
3112668 TATCGATACCAAGAACATGTATTGATACAATG
1 TATCGATACCAAGAACATGTATCAATACAATG
* *
3112700 TATCGATACTAAGCAATATGTATCAATACA
1 TATCGATACCAAG-AACATGTATCAATACA
3112730 TCTGTGCGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 12 0.48
33 13 0.52
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (32 bp):
TATCGATACCAAGAACATGTATCAATACAATG
Found at i:3113124 original size:18 final size:18
Alignment explanation
Indices: 3113088--3113124 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3113078 TTTTTGTGCC
*
3113088 TTATAGGATTCACAGGCT
1 TTATAGGATTCACAAGCT
*
3113106 TTATAGGATTCATAAGCT
1 TTATAGGATTCACAAGCT
3113124 T
1 T
3113125 AGTGAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (18 bp):
TTATAGGATTCACAAGCT
Done.