Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1497
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: 67107
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:5152 original size:12 final size:12
Alignment explanation
Indices: 5137--5171 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
5127 GTCAACCATC
5137 AATGATGATGAA
1 AATGATGATGAA
*
5149 AATGATGATGAT
1 AATGATGATGAA
5161 AATGATGATGA
1 AATGATGATGA
5172 GGTTGACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (12 bp):
AATGATGATGAA
Found at i:11788 original size:13 final size:12
Alignment explanation
Indices: 11772--11815 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
11762 TTCTTTTTTC
11772 TTTTTTCTTTCAT
1 TTTTTTCTTT-AT
11785 TTTTTTCTTTAT
1 TTTTTTCTTTAT
11797 TTTTCCTT-TTTAT
1 TTTT--TTCTTTAT
11810 TTTTTT
1 TTTTTT
11816 TTATTTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.07
12 6 0.21
13 19 0.66
14 2 0.07
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTCTTTAT
Found at i:11790 original size:31 final size:31
Alignment explanation
Indices: 11746--11872 Score: 93
Period size: 31 Copynumber: 4.0 Consensus size: 31
11736 ACAAGAAAAA
11746 ATTTATATTT-TTTTCTTTCTTTTTTCTTTTT
1 ATTT-TATTTATTTTCTTTCTTTTTTCTTTTT
* *
11777 -TCTTTCATTT-TTTTCTTTATTTTTCCTTTTT
1 AT-TTT-ATTTATTTTCTTTCTTTTTTCTTTTT
* *
11808 ATTTTTTTTTATTTTCCTTATC-TTTCTCTGTTTT
1 A-TTTTATTTATTTT-CTT-TCTTTTTTCT-TTTT
**
11842 -TTTTATTTCCTTTCTTTCTTTTTATCTTTTT
1 ATTTTATTTATTTTCTTTCTTTTT-TCTTTTT
11873 GTCTTTATGA
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
30 4 0.05
31 38 0.50
32 20 0.26
33 9 0.12
34 5 0.07
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (31 bp):
ATTTTATTTATTTTCTTTCTTTTTTCTTTTT
Found at i:11832 original size:27 final size:26
Alignment explanation
Indices: 11775--11860 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 26
11765 TTTTTTCTTT
*
11775 TTTCTTTC-ATTTTTTTCTTTATTT--
1 TTTCTTTCTATGTTTTT-TTTATTTCC
* *
11799 TTCCTTTTTAT-TTTTTTTTATTTTCC
1 TTTCTTTCTATGTTTTTTTTA-TTTCC
*
11825 TTATCTTTCTCTGTTTTTTTTATTTCC
1 TT-TCTTTCTATGTTTTTTTTATTTCC
11852 TTTCTTTCT
1 TTTCTTTCT
11861 TTTTATCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
23 4 0.08
24 14 0.27
25 2 0.04
26 9 0.18
27 13 0.25
28 9 0.18
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.76
Consensus pattern (26 bp):
TTTCTTTCTATGTTTTTTTTATTTCC
Found at i:15766 original size:60 final size:59
Alignment explanation
Indices: 15642--15754 Score: 131
Period size: 60 Copynumber: 1.9 Consensus size: 59
15632 CCGTAGTTCA
* **
15642 ATTTTTTTTGCCCTAACTTTTGTCTAAATTGTCCTAAAAAAGGATTTTCATGTTAACAGC
1 ATTTTTTTTGCCCTAACTTTTGACTAAATTGTCCT-AAAAAGGATTTTCAACTTAACAGC
** * *
15702 -TTTTTTCTTGCTTTAACTTTTGACTAAGTTGTCCT-TAAAGGATTTTCAACTTA
1 ATTTTTT-TTGCCCTAACTTTTGACTAAATTGTCCTAAAAAGGATTTTCAACTTA
15755 GTAGGCATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
58 15 0.33
59 6 0.13
60 24 0.53
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (59 bp):
ATTTTTTTTGCCCTAACTTTTGACTAAATTGTCCTAAAAAGGATTTTCAACTTAACAGC
Found at i:16121 original size:13 final size:13
Alignment explanation
Indices: 16103--16128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16093 CATTTTTCTG
16103 TGTATCGATACAT
1 TGTATCGATACAT
16116 TGTATCGATACAT
1 TGTATCGATACAT
16129 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16140 original size:33 final size:33
Alignment explanation
Indices: 16083--16149 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
16073 GCCAAGGAAA
***
16083 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
* *
16116 TGTATCGATACATGGATCTTTGTATTGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
16149 T
1 T
16150 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:18663 original size:28 final size:27
Alignment explanation
Indices: 18593--18668 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
18583 TTTCTTCACA
*
18593 ATCGGGGACACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
18620 ATCGGGGATACTCCAACCCCGTTACT-
1 ATCGGGGATACTCCAACCCCGTTAATC
*
18646 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
18669 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.05
27 24 0.55
28 18 0.41
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.20
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:18778 original size:53 final size:52
Alignment explanation
Indices: 18487--18824 Score: 208
Period size: 51 Copynumber: 6.4 Consensus size: 52
18477 AATTCTCCAC
* * * *
18487 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAACTTTTCTAT
* * *
18538 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTC-AC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAACACCAACTT-TTCTAT
* * * ** * * * *
18592 AATCGGGGACACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTACT-T
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAA---CTTTTCTAT
* * ***
18647 --TCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGACTTTTC-AT
1 AATC--GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAACTTTTCTAT
* * * *
18698 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAACTTTT-CTAT
* * * * *
18751 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACTAATTTTTC-AC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAACTTTTCTAT
* *
18803 AATCGAGGACACTCCAACCCCG
1 AATCGGGGATACTCCAACCCCG
18825 TTACTTCCGA
Statistics
Matches: 218, Mismatches: 48, Indels: 41
0.71 0.16 0.13
Matches are distributed among these distances:
51 72 0.33
52 24 0.11
53 54 0.25
54 39 0.18
55 22 0.10
56 3 0.01
57 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAACTTTTCTAT
Found at i:18842 original size:105 final size:105
Alignment explanation
Indices: 18537--18842 Score: 277
Period size: 105 Copynumber: 2.9 Consensus size: 105
18527 TAATTTTCTA
* *
18537 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGAC
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACTAATTT-TTCACAATCGGGGAC
* *
18602 ACTCCAACCCCGTTAATCATCG-GGGATACTCCAACCCCGTTACTT
64 ACTCCAACCCCGTTATTC--CGAGGGA-ACACCAA-CCCGTTACTT
* * * * * * * *
18647 TCGA--GGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGACTTTTCATAATCGGGGATA
1 T-AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACTAATTTTTCACAATCGGGGACA
* * *** *
18709 CTCCAACCCCGGTTTTATTTTC-A--AAACACCAA-TTTTTCCTT
65 CTCCAACCCC-G--TTA-TTCCGAGGGAACACCAACCCGTTACTT
*
18750 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACTAATTTTTCACAATCGAGGACAC
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACTAATTTTTCACAATCGGGGACAC
18815 TCCAACCCCGTTACTTCCGAGGGAACAC
66 TCCAACCCCGTTA-TTCCGAGGGAACAC
18843 TCCAACCCTG
Statistics
Matches: 154, Mismatches: 30, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
102 7 0.05
103 7 0.05
104 28 0.18
105 44 0.29
106 25 0.16
107 9 0.06
108 1 0.01
109 30 0.19
110 2 0.01
111 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.29
Consensus pattern (105 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACTAATTTTTCACAATCGGGGACAC
TCCAACCCCGTTATTCCGAGGGAACACCAACCCGTTACTT
Found at i:23127 original size:13 final size:13
Alignment explanation
Indices: 23109--23134 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23099 CAATTTTTTG
23109 TGTATCGATACAT
1 TGTATCGATACAT
23122 TGTATCGATACAT
1 TGTATCGATACAT
23135 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25531 original size:21 final size:21
Alignment explanation
Indices: 25507--25553 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
25497 TTTGATGCTG
25507 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
25527 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
25548 ATTTTG
1 ATTTTG
25554 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:25697 original size:13 final size:13
Alignment explanation
Indices: 25679--25717 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
25669 ATAATCACCC
*
25679 TGTATCGATACAG
1 TGTATCGATACAA
25692 TGTATCGATACAA
1 TGTATCGATACAA
25705 TGTATCGATACAA
1 TGTATCGATACAA
25718 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:25728 original size:20 final size:20
Alignment explanation
Indices: 25703--25781 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
25693 GTATCGATAC
25703 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
* *
25723 AATGTATTGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
25748 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
25768 CATGTATCGATACA
1 AATGTATCGATACA
25782 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
25 17 0.35
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:27724 original size:20 final size:20
Alignment explanation
Indices: 27701--27773 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
27691 ACAATTCAAA
27701 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
27721 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
27742 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
27762 GTATCGATACAT
1 GTATCGATACAT
27774 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:27745 original size:21 final size:21
Alignment explanation
Indices: 27719--27794 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
27709 ACATGTTGCA
27719 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
27740 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
27760 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
27781 TTGTATCGATACAT
1 ATGTATCGATACAT
27795 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:27752 original size:41 final size:41
Alignment explanation
Indices: 27701--27794 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
27691 ACAATTCAAA
*
27701 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
27742 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
27783 GTATCGATACAT
1 GTATCGATACAT
27795 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:27851 original size:13 final size:13
Alignment explanation
Indices: 27833--27858 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27823 TACAGCAAGT
27833 ATGTATCGATACA
1 ATGTATCGATACA
27846 ATGTATCGATACA
1 ATGTATCGATACA
27859 CAAAAAATTG
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:31929 original size:15 final size:15
Alignment explanation
Indices: 31909--31939 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31899 TAAAAATGTC
*
31909 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
31924 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
31939 C
1 C
31940 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:33982 original size:20 final size:20
Alignment explanation
Indices: 33956--34033 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
33946 AATGTCCAAA
33956 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
33976 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T-G--TTTCT
*
34001 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
34021 TTGTATCGATACA
1 ATGTATCGATACA
34034 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:34040 original size:13 final size:13
Alignment explanation
Indices: 34022--34059 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
34012 CATTTTTCTT
34022 TGTATCGATACAA
1 TGTATCGATACAA
*
34035 TGTATCGATACAC
1 TGTATCGATACAA
34048 TGTATCGATACA
1 TGTATCGATACA
34060 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:35880 original size:23 final size:23
Alignment explanation
Indices: 35850--35896 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
35840 GTGCAAATAA
35850 ATTTTGATATGAATTACTTGATT
1 ATTTTGATATGAATTACTTGATT
35873 ATTTTGATATGAATTACTTGATT
1 ATTTTGATATGAATTACTTGATT
35896 A
1 A
35897 AGGGGGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
ATTTTGATATGAATTACTTGATT
Found at i:36556 original size:20 final size:20
Alignment explanation
Indices: 36533--36605 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
36523 ACAATTCAAA
36533 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
36553 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
36574 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
36594 GTATCGATACAT
1 GTATCGATACAT
36606 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:36577 original size:21 final size:21
Alignment explanation
Indices: 36551--36626 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
36541 ACATGTTGCA
36551 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
36572 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
36592 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
36613 TTGTATCGATACAT
1 ATGTATCGATACAT
36627 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:36584 original size:41 final size:41
Alignment explanation
Indices: 36533--36626 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
36523 ACAATTCAAA
*
36533 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
36574 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
36615 GTATCGATACAT
1 GTATCGATACAT
36627 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:36683 original size:13 final size:13
Alignment explanation
Indices: 36665--36690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36655 TACAGCAAGT
36665 ATGTATCGATACA
1 ATGTATCGATACA
36678 ATGTATCGATACA
1 ATGTATCGATACA
36691 CAAAAAATTG
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:37853 original size:15 final size:15
Alignment explanation
Indices: 37833--37863 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37823 ATTTCGTTTG
*
37833 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
37848 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
37863 G
1 G
37864 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:39696 original size:21 final size:21
Alignment explanation
Indices: 39667--39711 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
39657 AAGTTTTCAT
*
39667 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
39687 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
39709 TTT
1 TTT
39712 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:41904 original size:13 final size:13
Alignment explanation
Indices: 41886--41911 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41876 CAATTTTTTG
41886 TGTATCGATACAT
1 TGTATCGATACAT
41899 TGTATCGATACAT
1 TGTATCGATACAT
41912 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:51171 original size:16 final size:15
Alignment explanation
Indices: 51150--51190 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
51140 CCTTCTCTTC
51150 AAAAAAAAAGCAAAA
1 AAAAAAAAAGCAAAA
*
51165 GAAAAAAAAAGGAAAA
1 -AAAAAAAAAGCAAAA
51181 AAAAACAAAA
1 AAAAA-AAAA
51191 AAACAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGCAAAA
Found at i:51180 original size:27 final size:28
Alignment explanation
Indices: 51150--51226 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 28
51140 CCTTCTCTTC
51150 AAAAAAAAAGCAAAAGAAAAAAA-A-AGG
1 AAAAAAAAAGCAAAAGAAAAAAACACA-G
51177 AAAAAAAAA-CAAAA-AAACAAAACACAG
1 AAAAAAAAAGCAAAAGAAA-AAAACACAG
* *
51204 AAAAAGAGAG-AAAAGAAAAAAAC
1 AAAAAAAAAGCAAAAGAAAAAAAC
51227 CTACTTAAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
25 3 0.07
26 9 0.21
27 27 0.63
28 4 0.09
ACGTcount: A:0.81, C:0.08, G:0.12, T:0.00
Consensus pattern (28 bp):
AAAAAAAAAGCAAAAGAAAAAAACACAG
Found at i:52277 original size:55 final size:55
Alignment explanation
Indices: 52192--52768 Score: 707
Period size: 55 Copynumber: 10.3 Consensus size: 55
52182 TCCGCTTTTT
52192 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
52247 GGTCCTCAAAGATCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCCTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
52302 AGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACATAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
52357 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* ** *
52412 AGTCC-CTAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCATTTTTT
1 AGTCCTC-AAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
52467 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
52522 AGTCCCCAAAGACCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC-TTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * ** *
52576 AGTTCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACC-TTC
1 AGTCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTC
* ** *
52635 AGTCCTCAAAGAGTAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
** * * *
52696 AGTCCTCAAAGAGCAGGATGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
52751 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
52769 TACACTTTAT
Statistics
Matches: 454, Mismatches: 50, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
54 23 0.05
55 329 0.72
56 8 0.02
57 2 0.00
59 46 0.10
60 24 0.05
61 21 0.05
64 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:52573 original size:29 final size:29
Alignment explanation
Indices: 52485--52573 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
52475 AAGAGCAGGA
52485 CACCTCTTAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
* *** *
52514 CACCT-TT-CAGTCCC-CA-AAGACCAG-GA
1 CACCTCTTAAAG-CCCACACAAG-TTGGTGG
52540 CACCTCTTAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
52569 CACCT
1 CACCT
52574 TCAGTTCTCA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 9 0.21
27 10 0.23
28 10 0.23
29 14 0.33
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.19
Consensus pattern (29 bp):
CACCTCTTAAAGCCCACACAAGTTGGTGG
Found at i:53566 original size:19 final size:19
Alignment explanation
Indices: 53542--53606 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
53532 AATTCAACAA
53542 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
53561 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
53576 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
53593 ATTGTATCGATACA
1 TTTGTATCGATACA
53607 ATGTATCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 25 0.62
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:53581 original size:13 final size:13
Alignment explanation
Indices: 53563--53619 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
53553 ACATAAGTTT
53563 TGTATCGATACAA
1 TGTATCGATACAA
53576 TGTATCGATACATAAGTA
1 TGTATCGATAC---A--A
53594 TTGTATCGATACAA
1 -TGTATCGATACAA
53608 TGTATCGATACA
1 TGTATCGATACA
53620 TAATTAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:53585 original size:32 final size:32
Alignment explanation
Indices: 53544--53622 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
53534 TTCAACAATT
*
53544 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
53576 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
53608 TGTATCGATACATAA
1 TGTATCGATACATAA
53623 TTAGCTACTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:56209 original size:28 final size:27
Alignment explanation
Indices: 56139--56214 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
56129 TTTCTTCACA
*
56139 ATCGGGGACACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
56166 ATCGGGGATACTCCAACCCCGTTACT-
1 ATCGGGGATACTCCAACCCCGTTAATC
*
56192 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
56215 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.05
27 24 0.55
28 18 0.41
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.20
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:56324 original size:53 final size:54
Alignment explanation
Indices: 56033--56370 Score: 204
Period size: 51 Copynumber: 6.4 Consensus size: 54
56023 AATTCTCCAC
* * * *
56033 AATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTT-CTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCCTAT
* *
56084 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT-C-AC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAAACACCAATTT-TTCCTAT
* * * *** * * *** *
56138 AATCGGGGACACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTACT-T
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC-CAAAAACACCAA--TTTTTCCTAT
* * *** *
56193 --TCGAGGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGACTTTT-C-AT
1 AATC--GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCCTAT
* * *
56244 AATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCCTAT
* * *
56297 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-C-AC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCCTAT
* *
56349 AATCGAGGACACTCCAACCCCG
1 AATCGGGGATACTCCAACCCCG
56371 TTACTTCCGA
Statistics
Matches: 219, Mismatches: 48, Indels: 39
0.72 0.16 0.13
Matches are distributed among these distances:
51 69 0.32
52 27 0.12
53 54 0.25
54 42 0.19
55 21 0.10
56 2 0.01
57 4 0.02
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (54 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCCTAT
Found at i:56388 original size:105 final size:105
Alignment explanation
Indices: 56083--56388 Score: 277
Period size: 105 Copynumber: 2.9 Consensus size: 105
56073 TAATTTTCTA
*
56083 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGAC
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGGGGAC
* *
56148 ACTCCAACCCCGTTAATCATCG-GGGATACTCCAACCCCGTTACTT
64 ACTCCAACCCCGTTATTC--CGAGGGA-ACACCAA-CCCGTTACTT
* * * *** * * *
56193 TCGA--GGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGACTTTTCATAATCGGGGATA
1 T-AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGGGGACA
* * *** *
56255 CTCCAACCCCGGTTTTATTTTC-A--AAACACCAA-TTTTTCCTT
65 CTCCAACCCC-G--TTA-TTCCGAGGGAACACCAACCCGTTACTT
*
56296 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGACAC
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGGGGACAC
56361 TCCAACCCCGTTACTTCCGAGGGAACAC
66 TCCAACCCCGTTA-TTCCGAGGGAACAC
56389 TCCAACCCCA
Statistics
Matches: 153, Mismatches: 31, Indels: 29
0.72 0.15 0.14
Matches are distributed among these distances:
102 7 0.05
103 7 0.05
104 28 0.18
105 43 0.28
106 25 0.16
107 9 0.06
108 1 0.01
109 30 0.20
110 2 0.01
111 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (105 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGGGGACAC
TCCAACCCCGTTATTCCGAGGGAACACCAACCCGTTACTT
Found at i:58669 original size:28 final size:28
Alignment explanation
Indices: 58629--58700 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
58619 AAAAAAAAAT
* ** *
58629 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCAAGGAAATAA
*
58657 CGGGGTTGGAGTATCCCCAATGAAATAA
1 CGGGGTTGGAGTATCCCCAAGGAAATAA
*
58685 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
58701 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCAAGGAAATAA
Found at i:58751 original size:52 final size:50
Alignment explanation
Indices: 58689--58858 Score: 155
Period size: 52 Copynumber: 3.3 Consensus size: 50
58679 AAATAACGAG
* *
58689 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGT-TTTTTAGAAATAAAA-CGGA
** * **
58741 GTTGGAGTATCCCCGATTAACGGAAAATTAGCGTTTT-GAAAATAAAACCGG-
1 GTTGGAGTATCCCCGATT-GTGAAAAATTAGTTTTTTAG-AAATAAAA-CGGA
* ** *
58792 GATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCGATAAAACCGA
1 G-TTGGAGTATCCCCGATTGT-GAAAAATTAGTTTTTTAGAAATAAAACGGA
58844 GGTTGGAGTATCCCC
1 -GTTGGAGTATCCCC
58859 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
51 4 0.04
52 82 0.85
53 10 0.10
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGTTTTTTAGAAATAAAACGGA
Found at i:58810 original size:104 final size:102
Alignment explanation
Indices: 58690--59025 Score: 272
Period size: 104 Copynumber: 3.2 Consensus size: 102
58680 AATAACGAGG
* *
58690 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTAGAAATAAAATCGGAGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTGTGAAAAATTGGT-TTTTTAGAAATAAAATCAGAGTTGGAGTATCCCC
*
58755 GATTAACGGAAAATTAGCGTTTTGAAAATAAAACCGGGA
65 GATTAACGGAAAATTAGAGTTTTGAAAATAAAA-CGGGA
* * ** *
58794 TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCGATAAAA-CCGAGGTTGGAGTATCCC
1 TTGGAGTATCCCCGATTGT-GAAAAATTGGTTTTTTAGAAATAAAATCAGA-GTTGGAGTAT-CC
* ** * ** ** * *
58858 CTCAGAAATAACGG--GGTTGGAGTATCCCCGATGAT-TAACGGGG
63 C-C-G-ATTAACGGAAAATTAGAGT-T--TTGAAAATAAAACGGGA
* *
58901 TTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGTTAGAGTATCC
1 TTGGAGTATCCCCGATTGTGAA-AAATT-G-GTTTTTTAGAAATAAAATCAGAGTTGGAGTATCC
*
58966 CCGATTATA--GAAAATTAGTGTTTTGAAAATAAAATC-GGA
63 CCGATTA-ACGGAAAATTAGAGTTTTGAAAATAAAA-CGGGA
*
59005 GTTGGAATATCCCCGATTGTG
1 -TTGGAGTATCCCCGATTGTG
59026 GAGAATTGAG
Statistics
Matches: 177, Mismatches: 36, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
103 7 0.04
104 45 0.25
105 37 0.21
106 16 0.09
107 31 0.18
108 12 0.07
109 26 0.15
110 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (102 bp):
TTGGAGTATCCCCGATTGTGAAAAATTGGTTTTTTAGAAATAAAATCAGAGTTGGAGTATCCCCG
ATTAACGGAAAATTAGAGTTTTGAAAATAAAACGGGA
Found at i:58904 original size:27 final size:28
Alignment explanation
Indices: 58844--58916 Score: 105
Period size: 27 Copynumber: 2.6 Consensus size: 28
58834 ATAAAACCGA
*
58844 GGTTGGAGTATCCCCTCA-GAAATAACGG
1 GGTTGGAGTATCCCC-GATGAAATAACGG
*
58872 GGTTGGAGTATCCCCGATG-ATTAACGG
1 GGTTGGAGTATCCCCGATGAAATAACGG
58899 GGTTGGAGTATCCCCGAT
1 GGTTGGAGTATCCCCGAT
58917 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
27 26 0.62
28 16 0.38
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGATGAAATAACGG
Found at i:58930 original size:212 final size:212
Alignment explanation
Indices: 58634--59027 Score: 607
Period size: 212 Copynumber: 1.9 Consensus size: 212
58624 AAAATCGGGA
* *
58634 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTAT
1 TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTAT
* * *
58699 CCTCGATTGTGAAAAATTGGT-ATTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTA-AC
66 CCCCGATTGTGAAAAATTGGTGATTTTTAGAAATAAAATCAGAGTTAGAGTATCCCCGATTATA-
*
58762 GGAAAATTAGCGTTTTGAAAATAAAACCGG-GATTGGAGTATCCCCGATTGTGGAAAAATTAGTG
130 -GAAAATTAGCGTTTTGAAAATAAAACCGGAG-TTGGAATATCCCCGATTGTGGAAAAATTAGTG
58826 TTTTAGCGATAAAACCGAGG
193 TTTTAGCGATAAAACCGAGG
* * *
58846 TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTAT
1 TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTAT
* *
58910 CCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGTTAGAGTATCCCCGATTATA
66 CCCCGATTGTGAA-AAATTGGTGATTTTTAGAAATAAAATCAGAGTTAGAGTATCCCCGATTATA
* *
58975 GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
130 GAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
59028 GAATTGAGAA
Statistics
Matches: 165, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
211 29 0.18
212 98 0.59
213 37 0.22
214 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (212 bp):
TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTAT
CCCCGATTGTGAAAAATTGGTGATTTTTAGAAATAAAATCAGAGTTAGAGTATCCCCGATTATAG
AAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTT
TAGCGATAAAACCGAGG
Found at i:59000 original size:51 final size:53
Alignment explanation
Indices: 58904--59022 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
58894 AACGGGGTTG
* * *
58904 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCAGAGTTA
* *
58958 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCAGAGTTA
*
59009 GAATATCCCCGATT
1 GAGTATCCCCGATT
59023 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCAGAGTTA
Found at i:61170 original size:19 final size:18
Alignment explanation
Indices: 61146--61213 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
61136 CAGTAGCTAA
61146 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
61165 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
61180 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
61197 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
61214 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:61186 original size:13 final size:13
Alignment explanation
Indices: 61168--61192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61158 ACAATACTTA
61168 TGTATCGATACAT
1 TGTATCGATACAT
61181 TGTATCGATACA
1 TGTATCGATACA
61193 AAACTTATGT
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:61190 original size:32 final size:32
Alignment explanation
Indices: 61149--61211 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
61139 TAGCTAATTA
*
61149 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
61181 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
61212 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:61275 original size:21 final size:20
Alignment explanation
Indices: 61249--61327 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 20
61239 GTTGGGACCC
61249 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTA-AA
***
61270 TGTATCGATACATTCCACAAA
1 TGTATCGATACATT-TGTAAA
61291 TGTATCGATACATTCT-TCAAA
1 TGTATCGATACATT-TGT-AAA
61312 TGTATCGATACATTTG
1 TGTATCGATACATTTG
61328 GATAAATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.02
21 48 0.96
22 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTTGTAAA
Found at i:62144 original size:55 final size:55
Alignment explanation
Indices: 62060--62594 Score: 567
Period size: 55 Copynumber: 9.4 Consensus size: 55
62050 AAAGTGTATT
* * * * *
62060 CTGCTCTTTGAGGACTAAAAAGTACCACCAACTCGTGTGGGGTTTGAAAGGCGTC
1 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
* *
62115 CTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGCGTC
1 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
62170 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCGTC
1 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCGTC
* *
62230 CCGCTCTTTGAGGACTG-GAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAGAAGGCGTC
1 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-A-AAGGCGTC
* * *
62290 CTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGGGTC
1 CTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
* * *
62345 CTGCTCTTTGGGGAC-GAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGGGTC
1 CTGCTCTTTGAGGACTG-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
* * * *
62400 CTGCTCTTTGGGGACGGAAAGGTGCCACCAACTTATGTGGGCTTTGAAGAAAAGACGTC
1 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---G-AAAGGCGTC
* * * *
62459 CCGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGTTTTAAAAGGAGAAGGCATC
1 CTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCGTC
* * **
62520 CTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGTATC
1 CTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
62575 CTGCTCTTTGAGGACTGAAA
1 CTGCTCTTTGAGGACTGAAA
62595 AGTGGAAGGA
Statistics
Matches: 422, Mismatches: 39, Indels: 39
0.84 0.08 0.08
Matches are distributed among these distances:
53 1 0.00
54 5 0.01
55 211 0.50
56 3 0.01
59 74 0.18
60 53 0.13
61 74 0.18
62 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (55 bp):
CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTC
Found at i:62191 original size:26 final size:26
Alignment explanation
Indices: 62104--62191 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
62094 GTGTGGGGTT
*
62104 TGAAAGGCGTCCTGCTTTTTGAGGAC
1 TGAAAGGCGTCCTGCTCTTTGAGGAC
* ** * * *
62130 TGAAAGGTG-CCACCAACTTATGTGGGC
1 TGAAAGGCGTCCTGC-TCTT-TGAGGAC
62157 TTTGAAAGGCGTCCTGCTCTTTGAGGAC
1 --TGAAAGGCGTCCTGCTCTTTGAGGAC
62185 TGAAAGG
1 TGAAAGG
62192 TGCCACCAAC
Statistics
Matches: 44, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
25 3 0.07
26 17 0.39
27 5 0.11
28 5 0.11
29 11 0.25
30 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (26 bp):
TGAAAGGCGTCCTGCTCTTTGAGGAC
Found at i:62487 original size:230 final size:231
Alignment explanation
Indices: 62060--62596 Score: 828
Period size: 230 Copynumber: 2.3 Consensus size: 231
62050 AAAGTGTATT
*** * * * * *
62060 CTGCTCTTTGAGGACTAAAAAGTACCACCAACTCGTGTGGGGTTTGAAAGGCGTCCTGCTTTTTG
1 CTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTG
* *
62125 AGGACTG-AAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAA
66 AGGACTGAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACGGAA
* * **
62189 AGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGGAGGTGC
131 AGGTGCCACCAACTTATGTGGGCTTTGAAAGAAAAGACGTCCCGCTCTTTGAGGACTGGAAATGC
*
62254 CACCAACTTGTGTGGGCTTTAAAAGAAGAAGGCGTC
196 CACCAACTTGTGTGGGCTTTAAAAGAAGAAGGCATC
*
62290 CTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGGTCCTGCTCTTTG
1 CTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTG
* * * *
62355 GGGAC-GAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGGGTCCTGCTCTTTGGGGACGGAA
66 AGGACTGAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACGGAA
62419 AGGTGCCACCAACTTATGTGGGCTTTG-AAGAAAAGACGTCCCGCTCTTTGAGGACTGGAAAATG
131 AGGTGCCACCAACTTATGTGGGCTTTGAAAGAAAAGACGTCCCGCTCTTTGAGGACTGG-AAATG
* *
62483 CCACCAACTTGTGTGGGTTTTAAAAGGAGAAGGCATC
195 CCACCAACTTGTGTGGGCTTTAAAAGAAGAAGGCATC
**
62520 CTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGTATCCTGCTCTTTG
1 CTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTG
62585 AGGACTGAAAAG
66 AGGACTGAAAAG
62597 TGGAAGGAGA
Statistics
Matches: 279, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
229 31 0.11
230 242 0.87
231 6 0.02
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (231 bp):
CTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTG
AGGACTGAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACGGAA
AGGTGCCACCAACTTATGTGGGCTTTGAAAGAAAAGACGTCCCGCTCTTTGAGGACTGGAAATGC
CACCAACTTGTGTGGGCTTTAAAAGAAGAAGGCATC
Found at i:62579 original size:175 final size:175
Alignment explanation
Indices: 62106--62594 Score: 605
Period size: 175 Copynumber: 2.8 Consensus size: 175
62096 GTGGGGTTTG
* *
62106 AAAGGCGTCCTGCTTTTTGAGGACT-GAAAGGTGCCACCAACTTATGTGGGCTTT----GA-AAG
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAG
62165 GCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCGT
65 GC-TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGCGT
* *
62229 CCCGCTCTTTGAGGACTGG--AGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
124 CCTGCTCTTTGAGGAC-GGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGA
*
62280 AGAAGGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAG-G--G
1 A-AAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAG
* * *
62342 G-TCCTGCTCTTTGGGGAC-GAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGGGTCCTGCT
65 GCTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCT
* *
62405 CTTTGGGGACGGAAAGGTGCCACCAACTTATGTGGGCTTT-GAAGA
130 CTTTGAGGACGGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGA
* * * *
62450 AAAGACGTCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGTTTTAAAAGGAGAAG
1 AAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAGAAG
* **
62515 GCATCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGTATCCTGC
65 GC-TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGC
*
62579 TCTTTGAGGACTGAAA
129 TCTTTGAGGACGGAAA
62595 AGTGGAAGGA
Statistics
Matches: 276, Mismatches: 22, Indels: 33
0.83 0.07 0.10
Matches are distributed among these distances:
169 54 0.20
170 28 0.10
171 26 0.09
173 2 0.01
174 1 0.00
175 156 0.57
176 6 0.02
177 2 0.01
179 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (175 bp):
AAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGG
CTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTC
TTTGAGGACGGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGA
Found at i:63567 original size:1 final size:1
Alignment explanation
Indices: 63557--63621 Score: 67
Period size: 1 Copynumber: 65.0 Consensus size: 1
63547 CTTAAGCAGA
* * * * * * *
63557 TTTTTCTTTTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTGTTTTTGTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
63622 AAAGAGAAGG
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:63584 original size:15 final size:14
Alignment explanation
Indices: 63563--63613 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
63553 CAGATTTTTC
63563 TTTTTTTTTTGTTT
1 TTTTTTTTTTGTTT
63577 TGTTTTTTTTTGTTT
1 T-TTTTTTTTTGTTT
*
63592 TTTTGTTTTTGTTT
1 TTTTTTTTTTGTTT
63606 TTTTTTTT
1 TTTTTTTT
63614 CTTTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 20 0.59
15 14 0.41
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:63586 original size:18 final size:17
Alignment explanation
Indices: 63563--63621 Score: 82
Period size: 18 Copynumber: 3.4 Consensus size: 17
63553 CAGATTTTTC
*
63563 TTTTTTTTTTGTTTTGT
1 TTTTTTTTTTTTTTTGT
63580 TTTTTTTTGTTTTTTTGT
1 TTTTTTTT-TTTTTTTGT
*
63598 TTTTGTTTTTTTTTTTCT
1 TTTT-TTTTTTTTTTTGT
63616 TTTTTT
1 TTTTTT
63622 AAAGAGAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.26
18 24 0.63
19 4 0.11
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTGT
Found at i:63600 original size:29 final size:26
Alignment explanation
Indices: 63563--63621 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 26
63553 CAGATTTTTC
*
63563 TTTTTTTTTTGTTTTGTTTTTTTTTGTT
1 TTTTTTTTTTGTTTT-TTTTTTTCT-TT
63591 TTTTTGTTTTTGTTTTTTTTTTTCTTT
1 TTTTT-TTTTTGTTTTTTTTTTTCTTT
63618 TTTT
1 TTTT
63622 AAAGAGAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.21
28 13 0.45
29 10 0.34
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (26 bp):
TTTTTTTTTTGTTTTTTTTTTTCTTT
Done.