Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 133 of 168
Found at i:38860442 original size:49 final size:49
Alignment explanation
Indices: 38860385--38860484 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
38860375 TGTATCGAAC
38860385 AAAGTCTAAAAACTTTACTACTTACACTATCTTGACAAATTTAGGACAT
1 AAAGTCTAAAAACTTTACTACTTACACTATCTTGACAAATTTAGGACAT
38860434 AAAGTCTAAAAACTTTACTACTTACACTATCTTGACAAATTTAGGACAT
1 AAAGTCTAAAAACTTTACTACTTACACTATCTTGACAAATTTAGGACAT
38860483 AA
1 AA
38860485 CAAAAAAGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (49 bp):
AAAGTCTAAAAACTTTACTACTTACACTATCTTGACAAATTTAGGACAT
Found at i:38863810 original size:25 final size:25
Alignment explanation
Indices: 38863743--38863803 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
38863733 ATTATATATT
*
38863743 AAATATATTTTTTTTATTTTTAATC
1 AAATATATATTTTTTATTTTTAATC
38863768 AAATATATATTTTTTATTTTTAATC
1 AAATATATATTTTTTATTTTTAATC
38863793 AAATATATATT
1 AAATATATATT
38863804 ATATATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
AAATATATATTTTTTATTTTTAATC
Found at i:38865062 original size:9 final size:9
Alignment explanation
Indices: 38865048--38865094 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
38865038 CATTTCTTCA
38865048 CTTCTTGTT
1 CTTCTTGTT
38865057 CTTCTTGTT
1 CTTCTTGTT
*
38865066 C-TCGTTTTT
1 CTTC-TTGTT
*
38865075 GTTCTTGTT
1 CTTCTTGTT
*
38865084 CTTCTTTTT
1 CTTCTTGTT
38865093 CT
1 CT
38865095 CTTCTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
8 2 0.06
9 27 0.87
10 2 0.06
ACGTcount: A:0.00, C:0.21, G:0.11, T:0.68
Consensus pattern (9 bp):
CTTCTTGTT
Found at i:38865091 original size:18 final size:18
Alignment explanation
Indices: 38865048--38865094 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
38865038 CATTTCTTCA
*
38865048 CTTCTTGTTCTTCTTGTT
1 CTTCTTTTTCTTCTTGTT
*
38865066 C-TCGTTTTTGTTCTTGTT
1 CTTC-TTTTTCTTCTTGTT
38865084 CTTCTTTTTCT
1 CTTCTTTTTCT
38865095 CTTCTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.00, C:0.21, G:0.11, T:0.68
Consensus pattern (18 bp):
CTTCTTTTTCTTCTTGTT
Found at i:38868017 original size:33 final size:34
Alignment explanation
Indices: 38867980--38868127 Score: 98
Period size: 33 Copynumber: 4.4 Consensus size: 34
38867970 GTGGAATTAG
38867980 CACTTAGCAACCACCAAT-GAATAGGGGAATCAA
1 CACTTAGCAACCACCAATAGAATAGGGGAATCAA
* *
38868013 CACTTAGCAACC-CC--TCG----GGGGAATCAG
1 CACTTAGCAACCACCAATAGAATAGGGGAATCAA
* * *
38868040 CACTTAGCAACCCCCTCTCACATTTAAAATACGGTGGAATCAG
1 CACTTAGCAA---CCAC-CA-A--TAGAATA-GG-GGAATCAA
*
38868083 CACTTAGCAACCACCAATA-ATTAGGGGAATCAA
1 CACTTAGCAACCACCAATAGAATAGGGGAATCAA
38868116 CACTTAGCAACC
1 CACTTAGCAACC
38868128 CCTCGGGGGA
Statistics
Matches: 92, Mismatches: 6, Indels: 34
0.70 0.05 0.26
Matches are distributed among these distances:
27 19 0.21
30 3 0.03
31 2 0.02
32 3 0.03
33 31 0.34
34 2 0.02
35 3 0.03
36 2 0.02
37 1 0.01
38 1 0.01
39 2 0.02
40 3 0.03
42 2 0.02
43 18 0.20
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.18
Consensus pattern (34 bp):
CACTTAGCAACCACCAATAGAATAGGGGAATCAA
Found at i:38868044 original size:103 final size:103
Alignment explanation
Indices: 38867865--38868233 Score: 614
Period size: 103 Copynumber: 3.6 Consensus size: 103
38867855 TAACCGTTAT
* *
38867865 CGGTGGATTCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACACAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAACACACAGCAACCCCTCGGGG
38867930 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
* **
38867968 CGGTGGAATTAGCACTTAGCAACCACCAATGAATAGGGGAATCAACACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAACACACAGCAACCCCTCGGGG
38868033 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
**
38868071 CGGTGGAATCAGCACTTAGCAACCACCAAT-AATTAGGGGAATCAACACTTAGCAACCCCTCGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAA-TAGGGGAATCAACACACAGCAACCCCTCGGG
*
38868135 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
65 GGAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
* * * *
38868174 CGGTGGGATCAGCACTTAGCAATCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAACACACAGCAACCCCT
38868234 TTATATGCAA
Statistics
Matches: 251, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
102 2 0.01
103 247 0.98
104 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.18
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAACACACAGCAACCCCTCGGGG
GAATCAGCACTTAGCAACCCCCTCTCACATTTAAAATA
Found at i:38870251 original size:12 final size:12
Alignment explanation
Indices: 38870234--38870258 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38870224 ACCATCCATT
38870234 TCAATATATTAC
1 TCAATATATTAC
38870246 TCAATATATTAC
1 TCAATATATTAC
38870258 T
1 T
38870259 AAATTCCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAATATATTAC
Found at i:38871652 original size:39 final size:39
Alignment explanation
Indices: 38871594--38871669 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
38871584 AAAACATTTG
38871594 AAATATTTTAATATAATTTAATAATATTTTTA-TAAATAA
1 AAATATTTTAATATAATTT-ATAATATTTTTATTAAATAA
* **
38871633 AAATATTATTAA-ATTATTTATTTTATTTTTATTAAAT
1 AAATATT-TTAATATAATTTATAATATTTTTATTAAAT
38871670 TATATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 10 0.31
39 18 0.56
40 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (39 bp):
AAATATTTTAATATAATTTATAATATTTTTATTAAATAA
Found at i:38871686 original size:16 final size:16
Alignment explanation
Indices: 38871667--38871737 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
38871657 ATTTTTATTA
38871667 AATTATATTTAATAAT
1 AATTATATTTAATAAT
*
38871683 AATTATA-TTAAAACAT
1 AATTATATTTAATA-AT
* *
38871699 AATTAAATTATTTATTATT
1 AATT--A-TATTTAATAAT
*
38871718 AAATTATTTTTAATAAT
1 -AATTATATTTAATAAT
38871735 AAT
1 AAT
38871738 CCTATTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
15 5 0.12
16 16 0.38
17 8 0.19
18 2 0.05
19 3 0.07
20 8 0.19
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTATATTTAATAAT
Found at i:38871691 original size:26 final size:26
Alignment explanation
Indices: 38871662--38871746 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
38871652 ATTTTATTTT
38871662 TATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATTTAATAATAATTA
** * * *
38871688 TATTAAAACATAATTAA-ATTATTTA
1 TATTAAATTATATTTAATAATAATTA
* **
38871713 TTATTAAATTATTTTTAATAATAATCC
1 -TATTAAATTATATTTAATAATAATTA
38871740 TATTAAA
1 TATTAAA
38871747 ATTTAATAAC
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
25 6 0.14
26 34 0.77
27 4 0.09
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTAAATTATATTTAATAATAATTA
Found at i:38875565 original size:42 final size:42
Alignment explanation
Indices: 38875473--38875567 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
38875463 TATACGAATG
* * * *
38875473 GCACTAAGCGTGTGAAACTAAAATGACAATGGCGAATAACGG
1 GCACTAAGTGTGCGAAACTAAAACGACAATGGCGAATAACGA
* **
38875515 GTACTAAGTGTGCGAAACTAAAACGACAATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAAACGACAATGGCGAATAACGA
38875557 GCACTAAGTGT
1 GCACTAAGTGT
38875568 ATGATACCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (42 bp):
GCACTAAGTGTGCGAAACTAAAACGACAATGGCGAATAACGA
Found at i:38883778 original size:21 final size:21
Alignment explanation
Indices: 38883752--38883791 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
38883742 AAAAAAAATT
38883752 AAACTTTACCAA-TTTTCTCCA
1 AAACTTT-CCAACTTTTCTCCA
38883773 AAACTTTCCAACTTTTCTC
1 AAACTTTCCAACTTTTCTC
38883792 ATATTTTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (21 bp):
AAACTTTCCAACTTTTCTCCA
Found at i:38885004 original size:36 final size:36
Alignment explanation
Indices: 38884933--38885005 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
38884923 TCGGAAAAAC
*
38884933 TGTTTTTACATATATTAATAGATTTATATTTTAAAT
1 TGTTTTTACATATATTAATAGATTTATATTATAAAT
*
38884969 TGTTTTTACATATATTGCAGT-GATTTAT-TTATAAAT
1 TGTTTTTACATATATT--AATAGATTTATATTATAAAT
38885005 T
1 T
38885006 AAATTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 24 0.73
37 7 0.21
38 2 0.06
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (36 bp):
TGTTTTTACATATATTAATAGATTTATATTATAAAT
Found at i:38886049 original size:2 final size:2
Alignment explanation
Indices: 38886044--38886080 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
38886034 TGTGTGTGTG
*
38886044 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38886081 TTCAATCCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:38887551 original size:5 final size:5
Alignment explanation
Indices: 38887543--38887571 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
38887533 GTTAAGTTTA
38887543 TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATA
38887572 AAAGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:38888364 original size:30 final size:30
Alignment explanation
Indices: 38888324--38888387 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
38888314 ATGGATTGTC
38888324 TTGATATGTGATGAAATTATATTAGTTGAA
1 TTGATATGTGATGAAATTATATTAGTTGAA
* *
38888354 TTGATTTGTGATGAAATTATATTGGTTGAA
1 TTGATATGTGATGAAATTATATTAGTTGAA
38888384 TTGA
1 TTGA
38888388 ATTGGAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (30 bp):
TTGATATGTGATGAAATTATATTAGTTGAA
Found at i:38888412 original size:15 final size:16
Alignment explanation
Indices: 38888392--38888423 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
38888382 AATTGAATTG
38888392 GAATATATATAT-TAT
1 GAATATATATATATAT
38888407 GAATATATATATATAT
1 GAATATATATATATAT
38888423 G
1 G
38888424 TGTGTGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
GAATATATATATATAT
Found at i:38888617 original size:22 final size:22
Alignment explanation
Indices: 38888592--38888641 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
38888582 GTTAGTGCTT
*
38888592 TCTGTTTAGCACATCTGCGCTC
1 TCTGTTTAGCACATCAGCGCTC
* * *
38888614 TCTGTCTAGCACTTCAGTGCTC
1 TCTGTTTAGCACATCAGCGCTC
38888636 TCTGTT
1 TCTGTT
38888642 CATTAGTGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.40
Consensus pattern (22 bp):
TCTGTTTAGCACATCAGCGCTC
Found at i:38890266 original size:25 final size:25
Alignment explanation
Indices: 38890238--38890309 Score: 135
Period size: 25 Copynumber: 2.9 Consensus size: 25
38890228 GCGAGCACTT
38890238 TGATTATTAGCACGTTGGTGCTCTC
1 TGATTATTAGCACGTTGGTGCTCTC
*
38890263 TGATTATTAGCATGTTGGTGCTCTC
1 TGATTATTAGCACGTTGGTGCTCTC
38890288 TGATTATTAGCACGTTGGTGCT
1 TGATTATTAGCACGTTGGTGCT
38890310 ATTTAGCACT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.42
Consensus pattern (25 bp):
TGATTATTAGCACGTTGGTGCTCTC
Found at i:38890336 original size:22 final size:22
Alignment explanation
Indices: 38890308--38890375 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
38890298 CACGTTGGTG
*
38890308 CTATTTAGCACTTCAGTGCTTT
1 CTATTTAGCACTTCAGTGCTCT
38890330 CTATTTAGCACTTCAGTGCTCT
1 CTATTTAGCACTTCAGTGCTCT
* *
38890352 CTGTATAGCACTTCAGTGCTCT
1 CTATTTAGCACTTCAGTGCTCT
38890374 CT
1 CT
38890376 GTTCATTAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (22 bp):
CTATTTAGCACTTCAGTGCTCT
Found at i:38894240 original size:5 final size:5
Alignment explanation
Indices: 38894223--38894261 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
38894213 GTTAAGTTTA
38894223 TATAT TATA- TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
38894262 AATAAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:38895258 original size:25 final size:25
Alignment explanation
Indices: 38895228--38895306 Score: 113
Period size: 25 Copynumber: 3.2 Consensus size: 25
38895218 TAGCGCGCTA
38895228 TCTGATTATTAGCACGTTGGTGCTC
1 TCTGATTATTAGCACGTTGGTGCTC
* *
38895253 TTTGATTATTATCACGTTGGTGCTC
1 TCTGATTATTAGCACGTTGGTGCTC
* **
38895278 TCTGATTATTAGCGCGTCAGTGCTC
1 TCTGATTATTAGCACGTTGGTGCTC
38895303 TCTG
1 TCTG
38895307 TTTAGCACAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (25 bp):
TCTGATTATTAGCACGTTGGTGCTC
Found at i:38895322 original size:22 final size:22
Alignment explanation
Indices: 38895294--38895352 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
38895284 TATTAGCGCG
38895294 TCAGTGCTCTCTGTTTAGCACA
1 TCAGTGCTCTCTGTTTAGCACA
* * *
38895316 TCTGTGCTCTCTGTATAGCACT
1 TCAGTGCTCTCTGTTTAGCACA
38895338 TCAGTGCTCTCTGTT
1 TCAGTGCTCTCTGTT
38895353 CATTAGTGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.41
Consensus pattern (22 bp):
TCAGTGCTCTCTGTTTAGCACA
Found at i:38901874 original size:46 final size:45
Alignment explanation
Indices: 38901783--38901874 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 45
38901773 GTTAAGTAAT
** *
38901783 AGAAGCAATTTCAATTCACATACAGAACATATCAGCTACATATGC
1 AGAAGCAATTTCAATTCACATACAGAACATATCAAATACAAATGC
* * * *
38901828 AGAAGCAATTTTAGTTTCATATACAGAACATATCAAATTCAAATGC
1 AGAAGCAATTTCA-ATTCACATACAGAACATATCAAATACAAATGC
38901874 A
1 A
38901875 ATTATTCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 12 0.31
46 27 0.69
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (45 bp):
AGAAGCAATTTCAATTCACATACAGAACATATCAAATACAAATGC
Found at i:38902431 original size:42 final size:42
Alignment explanation
Indices: 38902384--38902488 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 42
38902374 GGACCCACGT
* *
38902384 CCATGTCCTTGCCTGTGTGGCTCACACGGCTTGG-GCACATAC
1 CCATGTCCTTGCCTGTGTGGCTCAAACGGCTTGGAG-ACACAC
* * ** *
38902426 CCATGTTCTTACCCT-TGTGTTTCAAACGGCTTGGAGACACGC
1 CCATGTCCTT-GCCTGTGTGGCTCAAACGGCTTGGAGACACAC
38902468 CCATGTCCTCTGCCTGTGTGG
1 CCATGTCCT-TGCCTGTGTGG
38902489 TTCTAAAACG
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
42 40 0.82
43 9 0.18
ACGTcount: A:0.14, C:0.31, G:0.25, T:0.30
Consensus pattern (42 bp):
CCATGTCCTTGCCTGTGTGGCTCAAACGGCTTGGAGACACAC
Found at i:38903245 original size:20 final size:21
Alignment explanation
Indices: 38903200--38903252 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
38903190 AGAATGAAGC
38903200 AAAAATAAAAGAATTGGAAAA
1 AAAAATAAAAGAATTGGAAAA
38903221 GAAAAA-AAAAGAA-T-GATAAA
1 -AAAAATAAAAGAATTGGA-AAA
38903241 AAAAATAAAAGA
1 AAAAATAAAAGA
38903253 GGAAGAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.24
20 10 0.34
21 7 0.24
22 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.11
Consensus pattern (21 bp):
AAAAATAAAAGAATTGGAAAA
Found at i:38903907 original size:15 final size:15
Alignment explanation
Indices: 38903887--38903935 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
38903877 TCGTCTGGGC
38903887 ACAAACAAAAAAAAA
1 ACAAACAAAAAAAAA
*
38903902 ACAAAC-AAAACAAA
1 ACAAACAAAAAAAAA
* *
38903916 ATAAATAAAACAAAAA
1 ACAAACAAAA-AAAAA
38903932 ACAA
1 ACAA
38903936 TTAAAGTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 11 0.41
15 9 0.33
16 7 0.26
ACGTcount: A:0.82, C:0.14, G:0.00, T:0.04
Consensus pattern (15 bp):
ACAAACAAAAAAAAA
Found at i:38905367 original size:63 final size:63
Alignment explanation
Indices: 38905221--38905370 Score: 178
Period size: 63 Copynumber: 2.4 Consensus size: 63
38905211 ATATTACTTT
* * * * * *
38905221 ATTTATTTATTCATTCTTTTACTTTTTAAATACTTAAATTTAATATTATTTGTTTTTCCTATTT
1 ATTTATTTATT-ATTCTTTTATTTTTTAAATACTTAAATTTAATATTACTTATCTTCCCTATTC
* *
38905285 ATTTATTTATTATTCTTTTATTTTTTAAATATTTAAATTTGATATTACTTATACTTCCCT-TTC
1 ATTTATTTATTATTCTTTTATTTTTTAAATACTTAAATTTAATATTACTTAT-CTTCCCTATTC
*
38905348 ATTTCATTTTTTATT-TTTTATTT
1 ATTT-ATTTATTATTCTTTTATTT
38905371 GAAAGTTACT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 50 0.67
64 25 0.33
ACGTcount: A:0.25, C:0.09, G:0.01, T:0.64
Consensus pattern (63 bp):
ATTTATTTATTATTCTTTTATTTTTTAAATACTTAAATTTAATATTACTTATCTTCCCTATTC
Found at i:38915189 original size:18 final size:18
Alignment explanation
Indices: 38915154--38915187 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38915144 GTCATTCACT
*
38915154 CTTTCTTTTTCAGTTTTA
1 CTTTATTTTTCAGTTTTA
38915172 CTTTATTTTT-AGTTTT
1 CTTTATTTTTCAGTTTT
38915188 TAATTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.71
Consensus pattern (18 bp):
CTTTATTTTTCAGTTTTA
Found at i:38929129 original size:18 final size:18
Alignment explanation
Indices: 38929106--38929141 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38929096 AAATTATAAT
*
38929106 AATAAAATTAAACCCAAA
1 AATAAAACTAAACCCAAA
*
38929124 AATAAAACTAAATCCAAA
1 AATAAAACTAAACCCAAA
38929142 TTAATTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
AATAAAACTAAACCCAAA
Found at i:38930769 original size:43 final size:43
Alignment explanation
Indices: 38930716--38931609 Score: 937
Period size: 43 Copynumber: 20.8 Consensus size: 43
38930706 ACATGTTATT
* * * *
38930716 ACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGAAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* *
38930759 ATATAACGATGTCAATGTCCCAGACATGGTCTTATACGTAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * *
38930802 ACAGT-ACAATGCCAATGTCTCAGACATGGTCTTACTTA--TTATC
1 ACA-TAACGATGCCAATGTCCCAGACATGGTCTTA--TACGTAATC
* * * *
38930845 ACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGAAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * *
38930888 ATATAACGGTGCCAATTTCCCAAACATGGTCTTATACGTAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * * *
38930931 ACAGT-ACAATGTCAATGTCCCAGACATGGTCTTACATGTTATC
1 ACA-TAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * * *
38930974 ACATATCGATGCCACTATCCCAGACAGGGTCTTATACGAAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * *
38931017 ATATAACGATGTCAATGTCCTAGACATGGTCTTATACGTAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* *
38931060 ACAGT-ACAATGCCAATGTCCCAGACATGGTCTTACTTA--TTATC
1 ACA-TAACGATGCCAATGTCCCAGACATGGTCTTA--TACGTAATC
* * * **
38931103 ACATATCGATGCCACTGTCCCAGACAGGGTCTTATACAAAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* *
38931146 ATATAACGATGCCAATTTCCCAGACATGGTCTTATACGTAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * * *
38931189 ACAGT-ACAATGCCAATGTCCCAGACATGATCTTACATGTTATC
1 ACA-TAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * *
38931232 ACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGAAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
*
38931275 ATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * *
38931318 ACAGT-ACAATGCCAATGTCCCAGACATGGTCTTACATGTTATC
1 ACA-TAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * *
38931361 ACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGAAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * * *
38931404 ATATAACAATGCCAATGCCCCATACATGGTCTTATATGTAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * *
38931447 ACAGT-ACAATGCCAATGTCCCAGACATGGTCTTACATGTTATC
1 ACA-TAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* * * * * *
38931490 ACATATCGATGTCACTATCCCAGACAAGGTCTTATACGAAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
*
38931533 ATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
1 ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
* *
38931576 ACAGT-ACAATGCCAATGTCCCAAACATGGTCTTA
1 ACA-TAACGATGCCAATGTCCCAGACATGGTCTTA
38931610 CATGTTATCA
Statistics
Matches: 691, Mismatches: 139, Indels: 42
0.79 0.16 0.05
Matches are distributed among these distances:
41 4 0.01
42 6 0.01
43 670 0.97
44 7 0.01
45 4 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (43 bp):
ACATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATC
Found at i:38930932 original size:129 final size:129
Alignment explanation
Indices: 38930690--38931619 Score: 1617
Period size: 129 Copynumber: 7.2 Consensus size: 129
38930680 TAATGTCATA
* * *
38930690 TCCCAGATATGTTCTTACATGTTATTACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
1 TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
*
38930755 AATCATATAACGATGTCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
66 AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
* * *
38930819 TCTCAGACATGGTCTTACTTATTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
1 TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
* * * *
38930884 AATCATATAACGGTGCCAATTTCCCAAACATGGTCTTATACGTAATCACAGTACAATGTCAATG
66 AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
*
38930948 TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTATCCCAGACAGGGTCTTATACGA
1 TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
* *
38931013 AATCATATAACGATGTCAATGTCCTAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
66 AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
* * *
38931077 TCCCAGACATGGTCTTACTTATTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACAA
1 TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
*
38931142 AATCATATAACGATGCCAATTTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
66 AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
*
38931206 TCCCAGACATGATCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
1 TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
38931271 AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
66 AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
38931335 TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
1 TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
* * * *
38931400 AATCATATAACAATGCCAATGCCCCATACATGGTCTTATATGTAATCACAGTACAATGCCAATG
66 AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
* * *
38931464 TCCCAGACATGGTCTTACATGTTATCACATATCGATGTCACTATCCCAGACAAGGTCTTATACGA
1 TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
38931529 AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
66 AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
*
38931593 TCCCAAACATGGTCTTACATGTTATCA
1 TCCCAGACATGGTCTTACATGTTATCA
38931620 AATCTTGGTA
Statistics
Matches: 755, Mismatches: 46, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 755 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (129 bp):
TCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGA
AATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAGTACAATGCCAATG
Found at i:38935670 original size:25 final size:24
Alignment explanation
Indices: 38935642--38935713 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
38935632 GTTCTGTGGA
38935642 AAAGGATGAATTGACGGTAAAATGC
1 AAAGGATGAATTGACGGT-AAATGC
**
38935667 AAAGGATGAATTGACGGTATGTGC
1 AAAGGATGAATTGACGGTAAATGC
*
38935691 AAAGGATGAATTGACGGCAAATG
1 AAAGGATGAATTGACGGTAAATG
38935714 TACCCAAGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 24 0.57
25 18 0.43
ACGTcount: A:0.40, C:0.08, G:0.31, T:0.21
Consensus pattern (24 bp):
AAAGGATGAATTGACGGTAAATGC
Found at i:38935892 original size:21 final size:21
Alignment explanation
Indices: 38935834--38935895 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
38935824 GCTTCAATTT
38935834 AACCCTTATGGGTTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
* * *** *
38935855 AGCTCTTACAAGCTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
38935876 AACCCTTATGGGTTTCCGTT
1 AACCCTTATGGGTTTCCGTT
38935896 TAGCTCTCAT
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCGTTC
Found at i:38935918 original size:42 final size:42
Alignment explanation
Indices: 38935763--38935918 Score: 134
Period size: 42 Copynumber: 3.7 Consensus size: 42
38935753 TCGTGTTTAC
* * * * * *
38935763 TTTCCGTTTAGCTCACACGAGCTTCTGCT-AACTCATATGAG
1 TTTCCGTTCAGCTCTCACGAGCTTCTGTTCAACCCTTATGGG
* *** ** *
38935804 TTTCCATTCAGCTCTTTTGAGCTTCAATTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTCACGAGCTTCTGTTCAACCCTTATGGG
* * *
38935846 TTTCCGTTCAGCTCTTACAAGCTTCCGTTCAACCCTTATGGG
1 TTTCCGTTCAGCTCTCACGAGCTTCTGTTCAACCCTTATGGG
* * *
38935888 TTTCCGTTTAGCTCTCATGAGTTTCTGTTCA
1 TTTCCGTTCAGCTCTCACGAGCTTCTGTTCA
38935919 GCCTTCGGGC
Statistics
Matches: 89, Mismatches: 25, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
41 20 0.22
42 69 0.78
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.40
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTCACGAGCTTCTGTTCAACCCTTATGGG
Found at i:38944256 original size:4 final size:4
Alignment explanation
Indices: 38944247--38944271 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
38944237 ATAATTTAAC
38944247 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
38944272 TGGTATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:38945593 original size:18 final size:19
Alignment explanation
Indices: 38945570--38945606 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
38945560 AACAAATTAT
*
38945570 GAATTTTATTAT-TTTTTA
1 GAATTTTATCATATTTTTA
38945588 GAATTTTATCATATTTTTA
1 GAATTTTATCATATTTTTA
38945607 TATTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
GAATTTTATCATATTTTTA
Found at i:38958379 original size:19 final size:17
Alignment explanation
Indices: 38958355--38958398 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
38958345 TAACAACCTA
38958355 AATAATAAAATGAAATGAC
1 AATAATAAAATG-AAT-AC
**
38958374 AATAATATGATGAATAC
1 AATAATAAAATGAATAC
38958391 AATAATAA
1 AATAATAA
38958399 GAAATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 9 0.41
18 3 0.14
19 10 0.45
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (17 bp):
AATAATAAAATGAATAC
Found at i:38962171 original size:21 final size:21
Alignment explanation
Indices: 38962147--38962289 Score: 103
Period size: 21 Copynumber: 6.9 Consensus size: 21
38962137 TGTGTTTGCT
*
38962147 TTCAGTTTAGCTCTTATGAGC
1 TTCAGTTTAACTCTTATGAGC
* *
38962168 TTCAG-TTAACTCATATGAGT
1 TTCAGTTTAACTCTTATGAGC
* * *
38962188 TTCAGTTTAAC-CATTTTGGGT
1 TTCAGTTTAACTC-TTATGAGC
* * *
38962209 TTCAGTTTAGCTTTTTTGAGC
1 TTCAGTTTAACTCTTATGAGC
* * *
38962230 TTCAGTTTAACCCTTATGGGTT
1 TTCAGTTTAACTCTTATGAG-C
* *
38962252 TTC-GTTCAACTCTTATGAGT
1 TTCAGTTTAACTCTTATGAGC
* *
38962272 TTCTGTTTAAATCTTATG
1 TTCAGTTTAACTCTTATG
38962290 GGTTTTTGTT
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
20 22 0.23
21 71 0.74
22 3 0.03
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCAGTTTAACTCTTATGAGC
Found at i:38962186 original size:20 final size:20
Alignment explanation
Indices: 38962147--38962194 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38962137 TGTGTTTGCT
* *
38962147 TTCAGTTTAGCTCTTATGAGC
1 TTCAG-TTAACTCATATGAGC
*
38962168 TTCAGTTAACTCATATGAGT
1 TTCAGTTAACTCATATGAGC
38962188 TTCAGTT
1 TTCAGTT
38962195 TAACCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (20 bp):
TTCAGTTAACTCATATGAGC
Found at i:38962280 original size:42 final size:43
Alignment explanation
Indices: 38962146--38962295 Score: 137
Period size: 42 Copynumber: 3.6 Consensus size: 43
38962136 TTGTGTTTGC
* * * * *
38962146 TTTCAGTTTAGCTCTTATGAG-CTTCAGTT-AACTCATATGAG
1 TTTCAGTTTAACCCTTATGGGTTTTCAGTTCAACTCTTATGAG
* * * * * *
38962187 TTTCAGTTTAACCATTTTGGG-TTTCAGTTTAGCTTTTTTGAG
1 TTTCAGTTTAACCCTTATGGGTTTTCAGTTCAACTCTTATGAG
*
38962229 CTTCAGTTTAACCCTTATGGGTTTTC-GTTCAACTCTTATGAG
1 TTTCAGTTTAACCCTTATGGGTTTTCAGTTCAACTCTTATGAG
* **
38962271 TTTCTGTTTAAATCTTATGGGTTTT
1 TTTCAGTTTAACCCTTATGGGTTTT
38962296 TGTTTAGCAC
Statistics
Matches: 86, Mismatches: 21, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
41 23 0.27
42 59 0.69
43 4 0.05
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.48
Consensus pattern (43 bp):
TTTCAGTTTAACCCTTATGGGTTTTCAGTTCAACTCTTATGAG
Found at i:38962294 original size:21 final size:20
Alignment explanation
Indices: 38962242--38962301 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
38962232 CAGTTTAACC
* *
38962242 CTTATGGGTTTTCGTTCAACT
1 CTTATGGGTTTT-GTTTAAAT
*
38962263 CTTATGAGTTTCTGTTTAAAT
1 CTTATGGGTTT-TGTTTAAAT
38962284 CTTATGGGTTTTTGTTTA
1 CTTATGGG-TTTTGTTTA
38962302 GCACTTATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.53
Consensus pattern (20 bp):
CTTATGGGTTTTGTTTAAAT
Found at i:38962308 original size:21 final size:20
Alignment explanation
Indices: 38962242--38962310 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
38962232 CAGTTTAACC
* * *
38962242 CTTATGGGTTTTCGTTCAACT
1 CTTATGGGTTTTTGTT-TACA
* * *
38962263 CTTATGAGTTTCTGTTTAAA
1 CTTATGGGTTTTTGTTTACA
38962283 TCTTATGGGTTTTTGTTTAGCA
1 -CTTATGGGTTTTTGTTTA-CA
38962305 CTTATG
1 CTTATG
38962311 TACTTTTGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.17, C:0.13, G:0.19, T:0.51
Consensus pattern (20 bp):
CTTATGGGTTTTTGTTTACA
Found at i:38967371 original size:27 final size:27
Alignment explanation
Indices: 38967341--38967394 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
38967331 CTTTGTCAAA
*
38967341 AATCAAATGATATAACTCTTGATTAAT
1 AATCAAAAGATATAACTCTTGATTAAT
*
38967368 AATCAAAAGATATAACTTTTGATTAAT
1 AATCAAAAGATATAACTCTTGATTAAT
38967395 TACACTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.37
Consensus pattern (27 bp):
AATCAAAAGATATAACTCTTGATTAAT
Found at i:38968319 original size:9 final size:9
Alignment explanation
Indices: 38968307--38968383 Score: 93
Period size: 9 Copynumber: 8.4 Consensus size: 9
38968297 AAAATAAAAA
38968307 AATTCGGGT
1 AATTCGGGT
38968316 AATTCGGGT
1 AATTCGGGT
*
38968325 ATTTTTC-GGT
1 A--ATTCGGGT
*
38968335 AATTCGGTT
1 AATTCGGGT
*
38968344 AATTCGGTT
1 AATTCGGGT
38968353 AATTCGGGT
1 AATTCGGGT
*
38968362 AATTCGGTT
1 AATTCGGGT
38968371 AATTCGGGT
1 AATTCGGGT
38968380 AATT
1 AATT
38968384 TTTAACCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
8 3 0.05
9 49 0.83
10 4 0.07
11 3 0.05
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:38968561 original size:12 final size:12
Alignment explanation
Indices: 38968544--38968568 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38968534 AGTAATTTCG
38968544 GGTCGGTTAACC
1 GGTCGGTTAACC
38968556 GGTCGGTTAACC
1 GGTCGGTTAACC
38968568 G
1 G
38968569 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:38976171 original size:18 final size:18
Alignment explanation
Indices: 38976130--38976164 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38976120 CACAATTAGG
38976130 ATTAGATTAGTGAGCATA
1 ATTAGATTAGTGAGCATA
38976148 ACTTAGATTA-TGAGCAT
1 A-TTAGATTAGTGAGCAT
38976165 TTATTAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (18 bp):
ATTAGATTAGTGAGCATA
Found at i:38979195 original size:18 final size:17
Alignment explanation
Indices: 38979162--38979194 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
38979152 AGATACTAAA
38979162 TTAAACAAAAAAAAAAC
1 TTAAACAAAAAAAAAAC
38979179 TTAAACAAAAAAAAAA
1 TTAAACAAAAAAAAAA
38979195 ATATAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (17 bp):
TTAAACAAAAAAAAAAC
Found at i:38985266 original size:11 final size:11
Alignment explanation
Indices: 38985250--38985283 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
38985240 TCAAATATTT
38985250 TCTCAATTTCC
1 TCTCAATTTCC
*
38985261 TCTCAATTTGC
1 TCTCAATTTCC
38985272 TCTCAATTTCC
1 TCTCAATTTCC
38985283 T
1 T
38985284 TCCGAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.03, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:38985278 original size:22 final size:22
Alignment explanation
Indices: 38985246--38985299 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
38985236 TCTCTCAAAT
38985246 ATTT-TCTCAATTTCC-TCTC-A
1 ATTTCTCTCAATTTCCTTC-CGA
38985266 ATTTGCTCTCAATTTCCTTCCGA
1 ATTT-CTCTCAATTTCCTTCCGA
38985289 ATTTCTCTCAA
1 ATTTCTCTCAA
38985300 ATCCATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.20, C:0.30, G:0.04, T:0.46
Consensus pattern (22 bp):
ATTTCTCTCAATTTCCTTCCGA
Found at i:38985332 original size:49 final size:50
Alignment explanation
Indices: 38985263--38985358 Score: 133
Period size: 49 Copynumber: 1.9 Consensus size: 50
38985253 CAATTTCCTC
*
38985263 TCAATTTGCTCTCAATTTCCT-TCCGAATTTCTCTCAAATCCATATTTAATT
1 TCAATTTGC-CTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAATT
* *
38985314 TCAATTTG-CTCAATTTCCTCTTAAATTTCTCTTAAATCCATATTT
1 TCAATTTGCCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
38985359 TTAATTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
49 32 0.78
50 1 0.02
51 8 0.20
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (50 bp):
TCAATTTGCCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAATT
Found at i:38985423 original size:13 final size:14
Alignment explanation
Indices: 38985387--38985423 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
38985377 ATTAATTTAA
*
38985387 AAACCCTAAACCCT
1 AAACCCTTAACCCT
38985401 AAACCC-TAACCCT
1 AAACCCTTAACCCT
38985414 -AACCCTTAAC
1 AAACCCTTAAC
38985424 TTAAAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 5 0.24
13 10 0.48
14 6 0.29
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (14 bp):
AAACCCTTAACCCT
Found at i:38985439 original size:7 final size:7
Alignment explanation
Indices: 38985387--38985419 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
38985377 ATTAATTTAA
38985387 AAACCCT
1 AAACCCT
38985394 AAACCCT
1 AAACCCT
38985401 AAACCCT
1 AAACCCT
38985408 -AACCCT
1 AAACCCT
38985414 -AACCCT
1 AAACCCT
38985420 TAACTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCCT
Found at i:38985515 original size:22 final size:22
Alignment explanation
Indices: 38985408--38985506 Score: 150
Period size: 22 Copynumber: 4.6 Consensus size: 22
38985398 CCTAAACCCT
*
38985408 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCATTAACTTAAA
38985429 AACCCTAAACCATTAACTTAAA
1 AACCCTAAACCATTAACTTAAA
*
38985451 AACCCTAACCCATTAACTTAAA
1 AACCCTAAACCATTAACTTAAA
38985473 AACCCTAAACTC-TTAACTTAAA
1 AACCCTAAAC-CATTAACTTAAA
38985495 AACCCT-AACCAT
1 AACCCTAAACCAT
38985507 AACCCTTAAC
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.01
21 10 0.14
22 60 0.83
23 1 0.01
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.23
Consensus pattern (22 bp):
AACCCTAAACCATTAACTTAAA
Found at i:38985515 original size:44 final size:44
Alignment explanation
Indices: 38985408--38985504 Score: 171
Period size: 44 Copynumber: 2.2 Consensus size: 44
38985398 CCTAAACCCT
38985408 AACCCTAACCC-TTAACTTAAAAACCCTAAACCATTAACTTAAA
1 AACCCTAACCCATTAACTTAAAAACCCTAAACCATTAACTTAAA
38985451 AACCCTAACCCATTAACTTAAAAACCCTAAACTC-TTAACTTAAA
1 AACCCTAACCCATTAACTTAAAAACCCTAAAC-CATTAACTTAAA
38985495 AACCCTAACC
1 AACCCTAACC
38985505 ATAACCCTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
43 11 0.21
44 40 0.77
45 1 0.02
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (44 bp):
AACCCTAACCCATTAACTTAAAAACCCTAAACCATTAACTTAAA
Found at i:38985532 original size:22 final size:22
Alignment explanation
Indices: 38985414--38985524 Score: 116
Period size: 22 Copynumber: 4.8 Consensus size: 22
38985404 CCCTAACCCT
*
38985414 AACCCTTAACTTAAAAACCCTA
1 AACCCTTAACTTAAAAACCCAA
* *
38985436 AACCATTAACTTAAAAACCC-T
1 AACCCTTAACTTAAAAACCCAA
*
38985457 AACCCATTAACTTAAAAACCCTA
1 AACCC-TTAACTTAAAAACCCAA
*
38985480 AACTCTTAACTTAAAAACCCTAACCA
1 AACCCTTAACTTAAAAACCC--A--A
38985506 TAACCCTTAACTTAAAAAC
1 -AACCCTTAACTTAAAAAC
38985525 TAAAAACCTT
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
21 4 0.05
22 49 0.65
23 4 0.05
26 1 0.01
27 17 0.23
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (22 bp):
AACCCTTAACTTAAAAACCCAA
Found at i:38985563 original size:21 final size:22
Alignment explanation
Indices: 38985524--38985565 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
38985514 AACTTAAAAA
* *
38985524 CTAAAAACCTTAAACCCTAACC
1 CTAAAAACCTCAAAACCTAACC
38985546 CTAAAAACC-CAAAACCTAAC
1 CTAAAAACCTCAAAACCTAAC
38985566 GTGGGAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (22 bp):
CTAAAAACCTCAAAACCTAACC
Found at i:38985649 original size:40 final size:40
Alignment explanation
Indices: 38985604--38985681 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
38985594 AGGGGCGCGC
* * *
38985604 TACGTGGCAGCAAAACACGTCCACGTCAGCGCGCTTTGCA
1 TACGTGGCAACAAAACACGTCCACGTAAGCACGCTTTGCA
* *
38985644 TACGTGGCAACAAAGCGCGTCCACGTAAGCACGCTTTG
1 TACGTGGCAACAAAACACGTCCACGTAAGCACGCTTTG
38985682 TTGCCACGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.18
Consensus pattern (40 bp):
TACGTGGCAACAAAACACGTCCACGTAAGCACGCTTTGCA
Found at i:38988255 original size:40 final size:40
Alignment explanation
Indices: 38988201--38988335 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
38988191 CGTTTGGACA
* * * *
38988201 AAAAACGCCACTAAAAATGAAGCAGTAGGGGCGCTTTTGG
1 AAAAACGCCGCTAAAAATGAAGCATTAGCGGCGATTTTGG
** * **
38988241 AAAAACGCCGCTAAAGGTCG-ATCATTAGCGGCGATTTTTA
1 AAAAACGCCGCTAAAAAT-GAAGCATTAGCGGCGATTTTGG
*
38988281 AAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGTTTTTTGG
1 AAAAACGCCGCTAAAAATGAAGCATTAGCGGCG-ATTTTGG
*
38988321 -AAAGCGCCGC-AAAAA
1 AAAAACGCCGCTAAAAA
38988336 GCCTAAGCCA
Statistics
Matches: 76, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
38 5 0.07
39 21 0.28
40 49 0.64
41 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATGAAGCATTAGCGGCGATTTTGG
Found at i:38988426 original size:41 final size:41
Alignment explanation
Indices: 38988369--38988606 Score: 338
Period size: 41 Copynumber: 5.8 Consensus size: 41
38988359 AGTTTTTTGG
*
38988369 GGTCTTTAGCGGCATTTTCTGAA-AAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTT-TGAATAAGCGCCGCTAATGCTCA
* *
38988410 GGTCTTTAGCGGCATTTTTGAATAAGCGTCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCA
38988451 GGTCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCA
* *
38988492 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGATCA
1 GGTCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCA
* *
38988533 TGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTC-
1 GGTCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCA
**
38988573 -GTACCTTTAGCGGCGTTTTTTGAGGAAGCGCCGC
1 GGT--CTTTAGCGGCG-TTTTTGAATAAGCGCCGC
38988607 AAAAACATTT
Statistics
Matches: 183, Mismatches: 10, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
39 2 0.01
40 4 0.02
41 162 0.89
42 15 0.08
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.33
Consensus pattern (41 bp):
GGTCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCA
Found at i:38988751 original size:26 final size:26
Alignment explanation
Indices: 38988703--38988753 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
38988693 AAAATGGATA
** * *
38988703 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
38988729 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
38988754 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:38990206 original size:38 final size:38
Alignment explanation
Indices: 38990159--38990286 Score: 229
Period size: 38 Copynumber: 3.4 Consensus size: 38
38990149 ACTTAGATAA
38990159 TCCTGTCATTTATCCGGTTTGTTTGAATAATTTCAACT
1 TCCTGTCATTTATCCGGTTTGTTTGAATAATTTCAACT
* * *
38990197 TCCAGTCATTTATCCGATTTGTTTGAATAAATTCAACT
1 TCCTGTCATTTATCCGGTTTGTTTGAATAATTTCAACT
38990235 TCCTGTCATTTATCCGGTTTGTTTGAATAATTTCAACT
1 TCCTGTCATTTATCCGGTTTGTTTGAATAATTTCAACT
38990273 TCCTGTCATTTATC
1 TCCTGTCATTTATC
38990287 ATTACAAATT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 84 1.00
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.46
Consensus pattern (38 bp):
TCCTGTCATTTATCCGGTTTGTTTGAATAATTTCAACT
Found at i:38991657 original size:9 final size:9
Alignment explanation
Indices: 38991645--38991711 Score: 58
Period size: 9 Copynumber: 7.9 Consensus size: 9
38991635 TTAAAATAGT
38991645 TAACTTACA
1 TAACTTACA
38991654 TAACTTA-A
1 TAACTTACA
38991662 TTAA-TTA-A
1 -TAACTTACA
38991670 T-A-TTATCTA
1 TAACTTA-C-A
38991679 TAACTTACA
1 TAACTTACA
38991688 TAACTTAC-
1 TAACTTACA
38991696 -AACTTACA
1 TAACTTACA
38991704 TAACTTAC
1 TAACTTAC
38991712 GAATTATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
6 4 0.08
7 8 0.16
8 5 0.10
9 28 0.56
10 2 0.04
11 3 0.06
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (9 bp):
TAACTTACA
Found at i:38991701 original size:16 final size:16
Alignment explanation
Indices: 38991680--38991711 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38991670 TATTATCTAT
38991680 AACTTACATAACTTAC
1 AACTTACATAACTTAC
38991696 AACTTACATAACTTAC
1 AACTTACATAACTTAC
38991712 GAATTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:38993575 original size:66 final size:66
Alignment explanation
Indices: 38993469--38993636 Score: 232
Period size: 66 Copynumber: 2.5 Consensus size: 66
38993459 CAAATTACTT
* * * *
38993469 AACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCT
1 AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-
38993533 A-C
64 AGC
*
38993535 AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAG
1 AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAG
38993600 C
66 C
* * *
38993601 AGCTTAAAGCAGATGCAGCAGCAAGAGAAGCAGAGG
1 AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
38993637 CGGCAGCGAG
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
65 1 0.01
66 87 0.95
67 4 0.04
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.13
Consensus pattern (66 bp):
AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAG
C
Found at i:38993633 original size:21 final size:21
Alignment explanation
Indices: 38993607--38993723 Score: 69
Period size: 21 Copynumber: 5.6 Consensus size: 21
38993597 CAGCAGCTTA
*
38993607 AAGCAGATGCAGCAGCAAGAG
1 AAGCAGAGGCAGCAGCAAGAG
* *
38993628 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAGCAAGAG
* * * * *
38993649 AAGTACAGGCTA-TAGCGAGGG
1 AAGCAGAGGC-AGCAGCAAGAG
* * *
38993670 AAGCAGAGGCTA-AAGCGAGGG
1 AAGCAGAGGC-AGCAGCAAGAG
* * *
38993691 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCAGCAGCAAGAG
38993712 AAGCAGA-GCAGC
1 AAGCAGAGGCAGC
38993724 GTCAAAAGTT
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
20 4 0.05
21 76 0.95
ACGTcount: A:0.36, C:0.18, G:0.41, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCAAGAG
Found at i:38993673 original size:42 final size:42
Alignment explanation
Indices: 38993627--38993719 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
38993617 AGCAGCAAGA
** * *
38993627 GAAGCAGAGGCGGCAGCGAGAGAAGTACAGGCTATAGCGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCTACAGCGAGG
* * * *
38993669 GAAGCAGAGGCTAAAGCGAGGGAAGCAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCTACAGCGAGG
38993711 GAAGCAGAG
1 GAAGCAGAG
38993720 CAGCGTCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.16, G:0.44, T:0.05
Consensus pattern (42 bp):
GAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCTACAGCGAGG
Found at i:38994225 original size:43 final size:42
Alignment explanation
Indices: 38994071--38994227 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 42
38994061 AGGTGTTGGC
*
38994071 CTTTAGTGGCGTTTCTGGTAAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAA-GGT
* * * * * *
38994114 CTTTCGCGGCGTTT-TCGGAAAAAGCACCCCTAAAGATCATGGT
1 CTTTAGTGGCGTTTGT-GGTAAAAGCGCCGCTAAAGAT-AAGGT
** *
38994157 CTTTAGTGGCGTTTGTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGG-T
* **
38994200 CTCTAGTGGCGTTTGTGGTCGAAGCGCC
1 CTTTAGTGGCGTTTGTGGTAAAAGCGCC
38994228 ACTATAGACC
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
42 3 0.03
43 87 0.95
44 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.28
Consensus pattern (42 bp):
CTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGGT
Found at i:38995008 original size:30 final size:30
Alignment explanation
Indices: 38994972--38995046 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
38994962 TAATGTGTCA
*
38994972 GTGATCAACTTGTAACTTTCGAATAGTTCG
1 GTGATCAACTTGTAACTTTCAAATAGTTCG
* *
38995002 GTGATCAACTTATAACTTTCAAATAGTTTG
1 GTGATCAACTTGTAACTTTCAAATAGTTCG
* *
38995032 GTGAACAAATTGTAA
1 GTGATCAACTTGTAA
38995047 TTTTTTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (30 bp):
GTGATCAACTTGTAACTTTCAAATAGTTCG
Found at i:38999972 original size:24 final size:24
Alignment explanation
Indices: 38999938--38999989 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
38999928 TTTCTAAAAG
* *
38999938 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
38999962 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
38999986 ATTT
1 ATTT
38999990 TACTCTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:39004414 original size:24 final size:24
Alignment explanation
Indices: 39004351--39004402 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
39004341 TTTCTAAAAG
* *
39004351 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
39004375 ATTTAGCATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
39004399 ATTT
1 ATTT
39004403 GACTTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:39004772 original size:67 final size:67
Alignment explanation
Indices: 39004664--39004797 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
39004654 GTGCACTTGT
39004664 CTTAGTCAGATTTTTAGTTAATTTATGACTGCATCATTGACAAATTTATTCTAATTCAATAAGTG
1 CTTAGTCAGATTTTTAGTTAATTTATGACTGCATCATTGACAAATTTATTCTAATTCAATAAGTG
39004729 TG
66 TG
39004731 CTTAGTCAGATTTTTAGTTAATTTATGACTGCATCATTGACAAATTTATTCTAATTCAATAAGTG
1 CTTAGTCAGATTTTTAGTTAATTTATGACTGCATCATTGACAAATTTATTCTAATTCAATAAGTG
39004796 TG
66 TG
39004798 TTTTTGTTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (67 bp):
CTTAGTCAGATTTTTAGTTAATTTATGACTGCATCATTGACAAATTTATTCTAATTCAATAAGTG
TG
Found at i:39004786 original size:33 final size:33
Alignment explanation
Indices: 39004682--39004786 Score: 83
Period size: 33 Copynumber: 3.2 Consensus size: 33
39004672 GATTTTTAGT
39004682 TAATTTATGACTGCATCATTGACAAATTTATTC
1 TAATTTATGACTGCATCATTGACAAATTTATTC
* * * * * *
39004715 TAATTCAATAAGTG--TGC-TTAGTCAGATTT-TTAGT
1 TAATT-TATGACTGCAT-CATT-GACAAATTTATT--C
39004749 TAATTTATGACTGCATCATTGACAAATTTATTC
1 TAATTTATGACTGCATCATTGACAAATTTATTC
39004782 TAATT
1 TAATT
39004787 CAATAAGTGT
Statistics
Matches: 51, Mismatches: 12, Indels: 18
0.63 0.15 0.22
Matches are distributed among these distances:
32 5 0.10
33 23 0.45
34 18 0.35
35 5 0.10
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (33 bp):
TAATTTATGACTGCATCATTGACAAATTTATTC
Found at i:39013177 original size:2 final size:2
Alignment explanation
Indices: 39013170--39013204 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
39013160 CACCCACAAG
*
39013170 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
39013205 ACACAAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:39017918 original size:14 final size:14
Alignment explanation
Indices: 39017899--39017926 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39017889 TATGCAATTT
39017899 TGTGCAAATTTGAC
1 TGTGCAAATTTGAC
39017913 TGTGCAAATTTGAC
1 TGTGCAAATTTGAC
39017927 AGTACAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
TGTGCAAATTTGAC
Found at i:39019949 original size:21 final size:23
Alignment explanation
Indices: 39019903--39019948 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 23
39019893 AATTTAAAAA
39019903 TTTAGAAAAATTATAAAATTACT
1 TTTAGAAAAATTATAAAATTACT
*
39019926 TTTA-AAAAA-TA-AAAATTAAT
1 TTTAGAAAAATTATAAAATTACT
39019946 TTT
1 TTT
39019949 TTTTAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 2 0.09
22 5 0.23
23 4 0.18
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TTTAGAAAAATTATAAAATTACT
Found at i:39020415 original size:20 final size:19
Alignment explanation
Indices: 39020387--39020426 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39020377 AAACTATTAG
*
39020387 TTAATTATTAAATTTTTTAT
1 TTAACTATT-AATTTTTTAT
*
39020407 TTAACTATTTATTTTTTAT
1 TTAACTATTAATTTTTTAT
39020426 T
1 T
39020427 AGGCTGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TTAACTATTAATTTTTTAT
Found at i:39025523 original size:20 final size:21
Alignment explanation
Indices: 39025499--39025543 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
39025489 AAAATTACAA
39025499 AAAAATTGAAAAATAATTTTT
1 AAAAATTGAAAAATAATTTTT
*
39025520 AAAAATT-CAAAATAATTTTT
1 AAAAATTGAAAAATAATTTTT
39025540 AAAA
1 AAAA
39025544 TTGGAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAATTGAAAAATAATTTTT
Found at i:39025562 original size:19 final size:19
Alignment explanation
Indices: 39025499--39025562 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
39025489 AAAATTACAA
39025499 AAAAATTGAAAAATAATTTTT
1 AAAAATTG-AAAATAA-TTTT
*
39025520 AAAAATTCAAAATAATTTT
1 AAAAATTGAAAATAATTTT
* *
39025539 TAAAATTGGAAAT-ATTTAT
1 AAAAATTGAAAATAATTT-T
39025558 AAAAA
1 AAAAA
39025563 AATCTAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.11
19 19 0.51
20 7 0.19
21 7 0.19
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAAATTGAAAATAATTTT
Found at i:39025647 original size:29 final size:29
Alignment explanation
Indices: 39025582--39025637 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
39025572 TTTATATTTT
* *
39025582 TAAAAAAT-TATAAAAATTCAAAAAAATC
1 TAAAAAATATATAAAAAGTAAAAAAAATC
39025610 TAAAAAATATATAAAAAGTAAAAAAAAT
1 TAAAAAATATATAAAAAGTAAAAAAAAT
39025638 TAGAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (29 bp):
TAAAAAATATATAAAAAGTAAAAAAAATC
Found at i:39035927 original size:35 final size:35
Alignment explanation
Indices: 39035888--39035958 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
39035878 CATTTGTGTG
39035888 TTTGATTTTCATGTCAAAATTATTATAACTACCAT
1 TTTGATTTTCATGTCAAAATTATTATAACTACCAT
*
39035923 TTTGATTTTCATGTTAAAATTATTATAACTACCAT
1 TTTGATTTTCATGTCAAAATTATTATAACTACCAT
39035958 T
1 T
39035959 GCTGCATAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.48
Consensus pattern (35 bp):
TTTGATTTTCATGTCAAAATTATTATAACTACCAT
Found at i:39039086 original size:2 final size:2
Alignment explanation
Indices: 39039079--39039115 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
39039069 CCAAATACCT
*
39039079 AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
39039116 TATACATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:39039093 original size:10 final size:10
Alignment explanation
Indices: 39039078--39039121 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
39039068 CCCAAATACC
39039078 TACACACACA
1 TACACACACA
39039088 TACACACACA
1 TACACACACA
*
39039098 CACACACACA
1 TACACACACA
* *
39039108 CACACACATA
1 TACACACACA
39039118 TACA
1 TACA
39039122 TATATATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.50, C:0.41, G:0.00, T:0.09
Consensus pattern (10 bp):
TACACACACA
Found at i:39039132 original size:16 final size:16
Alignment explanation
Indices: 39039113--39039145 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39039103 ACACACACAC
*
39039113 ACATATACATATATAT
1 ACATACACATATATAT
39039129 ACATACACATATATAT
1 ACATACACATATATAT
39039145 A
1 A
39039146 TTCAATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (16 bp):
ACATACACATATATAT
Found at i:39046254 original size:43 final size:43
Alignment explanation
Indices: 39046168--39046410 Score: 310
Period size: 43 Copynumber: 5.7 Consensus size: 43
39046158 NNNNNNGACA
* * * **
39046168 CTAAAGAACACGATCTTTAGCGGCG-TTTTTCCTTAAGCGCCG
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCACAAGCGCCG
*
39046210 CTTAAGAACATGTTCTTTAGCGGCGTTTTTTTCACAAGCGCCG
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCACAAGCGCCG
* *
39046253 CTAAAGAACATGTTCTTTAGCGGCATTTTTTTTACAAGCGCCG
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCACAAGCGCCG
* **
39046296 CTAAAGAACATGTTATTTAGCGGCGTTTTTTT-ACAAATGCCG
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCACAAGCGCCG
* * **
39046338 CTAAAGAACATGTTATTTAGCGGCGTTTTTTTTACAAATGCCG
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCACAAGCGCCG
* * *
39046381 CTAAAGAACATATTCTTTAGTGGCGCTTTT
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTT
39046411 ATACAAAAAC
Statistics
Matches: 182, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
42 62 0.34
43 120 0.66
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (43 bp):
CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCACAAGCGCCG
Found at i:39046325 original size:85 final size:85
Alignment explanation
Indices: 39046168--39046410 Score: 319
Period size: 85 Copynumber: 2.9 Consensus size: 85
39046158 NNNNNNGACA
* * * *
39046168 CTAAAGAACACGATCTTTAGCGGCGTTTTTCCTT--AAGCGCCGCTTAAGAACATGTTCTTTAGC
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTT-TTTACAAGCGCCGCTAAAGAACATGTTCTTTAGC
*
39046231 GGCGTTTTTTTCACAAGCGCCG
65 GGCG-TTTTTTCACAAACGCCG
* *
39046253 CTAAAGAACATGTTCTTTAGCGGCATTTTTTTTACAAGCGCCGCTAAAGAACATGTTATTTAGCG
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTACAAGCGCCGCTAAAGAACATGTTCTTTAGCG
* *
39046318 GCGTTTTTTTACAAATGCCG
66 GCGTTTTTTCACAAACGCCG
* ** * *
39046338 CTAAAGAACATGTTATTTAGCGGCGTTTTTTTTACAAATGCCGCTAAAGAACATATTCTTTAGTG
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTACAAGCGCCGCTAAAGAACATGTTCTTTAGCG
*
39046403 GCGCTTTT
66 GCGTTTTT
39046411 ATACAAAAAC
Statistics
Matches: 139, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
84 2 0.01
85 106 0.76
86 31 0.22
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (85 bp):
CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTACAAGCGCCGCTAAAGAACATGTTCTTTAGCG
GCGTTTTTTCACAAACGCCG
Found at i:39070709 original size:42 final size:42
Alignment explanation
Indices: 39070626--39070712 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
39070616 TCATAAGAGT
* **
39070626 TTCAGTTTAACCCTATTGGGTTTCCGTTCGGCTCTTTTGAGC
1 TTCAGATTAACCCTATTGGGTTTCCGTTCAACTCTTTTGAGC
39070668 TTCAGATTAACCCT-TATGGGTTTCCGTTCAACT-TTTATGAGC
1 TTCAGATTAACCCTAT-TGGGTTTCCGTTCAACTCTTT-TGAGC
39070710 TTC
1 TTC
39070713 TGCTCAGCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
41 4 0.10
42 36 0.90
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (42 bp):
TTCAGATTAACCCTATTGGGTTTCCGTTCAACTCTTTTGAGC
Found at i:39072925 original size:27 final size:27
Alignment explanation
Indices: 39072851--39072945 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
39072841 AGTAAATAGA
**
39072851 ATAAAACAATTT-AAAGCAAATAATAT
1 ATAAAACAATTTAAAAATAAATAATAT
* * *
39072877 GTAAGACAAATTT--AAATGAATAATAT
1 ATAAAAC-AATTTAAAAATAAATAATAT
*
39072903 -TCAAAGCAATTTAAAAATAAATAATAT
1 AT-AAAACAATTTAAAAATAAATAATAT
39072930 ATAAAACAATTTAAAA
1 ATAAAACAATTTAAAA
39072946 TAATATGTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
25 6 0.11
26 18 0.33
27 30 0.55
28 1 0.02
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.28
Consensus pattern (27 bp):
ATAAAACAATTTAAAAATAAATAATAT
Found at i:39072929 original size:53 final size:51
Alignment explanation
Indices: 39072863--39073015 Score: 138
Period size: 53 Copynumber: 3.0 Consensus size: 51
39072853 AAAACAATTT
*
39072863 AAAGCAAATAATATGTAAGACAAATTTAAATGAATAATATTCAAAGCAA-TTTAA
1 AAAG-AAATAATATGTAAAACAAATTTAAATGAATAATATTCAAA--AAGTTT-A
* *
39072917 AAATAAATAATATATAAAAC-AATTT-AA--AATAATATGT-AAAAAGTTTA
1 AAAGAAATAATATGTAAAACAAATTTAAATGAATAATAT-TCAAAAAGTTTA
* * * *
39072964 AAAGAAATAATATGTCAAAAGAAATCTGAAATGAATAATATGCAAATAGTTT
1 AAAGAAATAATATGT-AAAACAAAT-TTAAATGAATAATATTCAAAAAGTTT
39073016 TATTATTATT
Statistics
Matches: 81, Mismatches: 9, Indels: 19
0.74 0.08 0.17
Matches are distributed among these distances:
47 16 0.20
48 7 0.09
49 14 0.17
50 2 0.02
51 4 0.05
52 5 0.06
53 30 0.37
54 3 0.04
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (51 bp):
AAAGAAATAATATGTAAAACAAATTTAAATGAATAATATTCAAAAAGTTTA
Found at i:39072963 original size:21 final size:22
Alignment explanation
Indices: 39072921--39072966 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
39072911 ATTTAAAAAT
39072921 AAATAATATATAAAACAATTTA
1 AAATAATATATAAAACAATTTA
* *
39072943 AAATAATATGTAAAA-AGTTTA
1 AAATAATATATAAAACAATTTA
39072964 AAA
1 AAA
39072967 GAAATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATAATATATAAAACAATTTA
Found at i:39072972 original size:22 final size:22
Alignment explanation
Indices: 39072925--39072972 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
39072915 AAAAATAAAT
*
39072925 AATATATAAAACAATTTAAAAT
1 AATATATAAAACAATTTAAAAA
* *
39072947 AATATGTAAAA-AGTTTAAAAGA
1 AATATATAAAACAATTTAAAA-A
39072969 AATA
1 AATA
39072973 ATATGTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (22 bp):
AATATATAAAACAATTTAAAAA
Found at i:39077646 original size:23 final size:23
Alignment explanation
Indices: 39077620--39077718 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
39077610 ATAAGTGCAA
39077620 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
39077643 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
39077666 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
39077689 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
39077712 CACTGAT
1 CACTGAT
39077719 CAATAACACT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:39084287 original size:21 final size:21
Alignment explanation
Indices: 39084257--39084318 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
39084247 GCTTCAGCTT
39084257 AACCCTTATGGGTTTCTGTTC
1 AACCCTTATGGGTTTCTGTTC
* * * * *
39084278 AGCTCTTATGAGCTTCCGTTC
1 AACCCTTATGGGTTTCTGTTC
39084299 AACCCTTATGGGTTTCTGTT
1 AACCCTTATGGGTTTCTGTT
39084319 AGAGGTGATC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (21 bp):
AACCCTTATGGGTTTCTGTTC
Found at i:39084315 original size:42 final size:42
Alignment explanation
Indices: 39084213--39084318 Score: 144
Period size: 42 Copynumber: 2.5 Consensus size: 42
39084203 GAGTTTTAGT
** *
39084213 TTAACCC-TATTGGGTTTCCATTCAGCTCTTTTGAGCTTCAGC
1 TTAACCCTTA-TGGGTTTCTGTTCAGCTCTTATGAGCTTCAGC
*
39084255 TTAACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTTCCG-
1 TTAACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTTCAGC
39084296 TTCAACCCTTATGGGTTTCTGTT
1 TT-AACCCTTATGGGTTTCTGTT
39084319 AGAGGTGATC
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
41 2 0.03
42 54 0.93
43 2 0.03
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (42 bp):
TTAACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTTCAGC
Found at i:39084526 original size:24 final size:24
Alignment explanation
Indices: 39084484--39084543 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
39084474 ATTATATATT
*
39084484 AAATATATTTTTTTTATTTTTAATC
1 AAATATA-TATTTTTATTTTTAATC
39084509 AAATATATATTTTTATTTTTAATC
1 AAATATATATTTTTATTTTTAATC
39084533 AAATATATATT
1 AAATATATATT
39084544 ATATATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 27 0.79
25 7 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (24 bp):
AAATATATATTTTTATTTTTAATC
Found at i:39084554 original size:24 final size:24
Alignment explanation
Indices: 39084484--39084567 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
39084474 ATTATATATT
* * *
39084484 AAATATATTTTTTTTATTTTTAATC
1 AAATATA-TATTTATATTATTAATC
* *
39084509 AAATATATATTTTTATTTTTAATC
1 AAATATATATTTATATTATTAATC
39084533 AAATATATA-TTATATATATTAA--
1 AAATATATATTTATAT-TATTAATC
*
39084555 ATATATATATTTA
1 AAATATATATTTA
39084568 ATATGGGCCG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.15
23 8 0.15
24 30 0.57
25 7 0.13
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATATATATTTATATTATTAATC
Found at i:39090761 original size:29 final size:29
Alignment explanation
Indices: 39090721--39090778 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
39090711 AGTTTACACC
39090721 GGTCACTTAACT-TCAAAAAGTTACTAATT
1 GGTCACTTAACTATCAAAAAGTTA-TAATT
**
39090750 GGTCA-TTCAACTATTTAAAAGTTATAATT
1 GGTCACTT-AACTATCAAAAAGTTATAATT
39090779 TAAGTCATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 2 0.08
29 14 0.56
30 9 0.36
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (29 bp):
GGTCACTTAACTATCAAAAAGTTATAATT
Found at i:39100752 original size:10 final size:11
Alignment explanation
Indices: 39100721--39100753 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
39100711 CGGCCCGCCC
39100721 ATATTAATTTT
1 ATATTAATTTT
*
39100732 ATATTATTTTT
1 ATATTAATTTT
39100743 ATA-TAATTTT
1 ATATTAATTTT
39100753 A
1 A
39100754 AAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:39100919 original size:30 final size:30
Alignment explanation
Indices: 39100875--39100937 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
39100865 ACTTAACAAG
39100875 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
39100905 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
39100935 CAA
1 CAA
39100938 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:39100990 original size:14 final size:14
Alignment explanation
Indices: 39100971--39100997 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39100961 CAAACAATAA
39100971 CAACATAATAGTAG
1 CAACATAATAGTAG
39100985 CAACATAATAGTA
1 CAACATAATAGTA
39100998 AAATGGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
CAACATAATAGTAG
Found at i:39106105 original size:3 final size:3
Alignment explanation
Indices: 39106099--39106131 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
39106089 AAACTACTAT
*
39106099 TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39106132 AATTGCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:39107647 original size:44 final size:44
Alignment explanation
Indices: 39107592--39107704 Score: 138
Period size: 44 Copynumber: 2.6 Consensus size: 44
39107582 GATGCGATCT
* * * *
39107592 GCTCTACTGCAACTTCAGAGAGATAAGATCAA-TCATTTTAACCC
1 GCTCCACTGCAACTTCAGGGAGATAAAATCAACT-ACTTTAACCC
* *
39107636 GCTCCACTGCAACTTCAGGGAGATAAAATCTACTACTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAAATCAACTACTTTAACCC
* *
39107680 GCTCCTCTGTAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
39107705 GGATTATCGG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 59 0.98
45 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAAATCAACTACTTTAACCC
Found at i:39108089 original size:125 final size:125
Alignment explanation
Indices: 39107879--39108106 Score: 393
Period size: 125 Copynumber: 1.8 Consensus size: 125
39107869 GATTCGTCAT
* *
39107879 TGTGGCTTTAATCTTTTTAACTGCAATATCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTG
1 TGTGGCTTTAATCTTTTTAACTGCAATATAGGAGAAACAAGATTCACCAATGTGGCTTTAATCTG
39107944 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTAGGTTTAATCAAGATTTACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTAGGTTTAATCAAGATTTACCGA
* * * * *
39108004 TGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACCGATGTGGTTTTAATCTG
1 TGTGGCTTTAATCTTTTTAACTGCAATATAGGAGAAACAAGATTCACCAATGTGGCTTTAATCTG
39108069 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGT
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGT
39108107 GGCTTCAATC
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 96 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (125 bp):
TGTGGCTTTAATCTTTTTAACTGCAATATAGGAGAAACAAGATTCACCAATGTGGCTTTAATCTG
TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTAGGTTTAATCAAGATTTACCGA
Found at i:39108243 original size:50 final size:50
Alignment explanation
Indices: 39108184--39108711 Score: 495
Period size: 50 Copynumber: 10.7 Consensus size: 50
39108174 TGCATCGCCT
* * *
39108184 GGGAAGTAAGATCCGCTATTGTAGCTTCAATCTTTTTAATTGCAATGTCA
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTCA
** * *
39108234 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGCTCCACTGCAACG-CTA
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTC-A
* * *
39108284 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCA
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTCA
* * *
39108334 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTATTCCACTGCAACG-CTA
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTC-A
* * * *
39108384 GGAAAGTAAGATCCGCTGTTGTAGCTACAATCTTTTTAATTGCAATGTCA
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTCA
* * * *
39108434 GGGAAGTAAGATCCACTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTA
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTC-A
* * * *
39108484 GGAAAGTAAGATCCACTGTTGTAGCTTCAATCTTTTTAACTGC-----CG
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTCA
* * *
39108529 GGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAA--TC-
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTCA
* * * * * * * **
39108576 TGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTGAATTACAATGTTG
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTCA
** * * * ** * *
39108626 GGGAAGCGAGATTCGCTGTCGTAGCTTCAATCTGTTCCGCTGC-ATCGCCT
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAAT-GTCA
* * *
39108676 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTT
1 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTT
39108712 GAATTGCTGC
Statistics
Matches: 388, Mismatches: 78, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
45 37 0.10
46 1 0.00
47 35 0.09
48 1 0.00
49 6 0.02
50 306 0.79
51 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (50 bp):
GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCAACTGCAATGTCA
Found at i:39108311 original size:100 final size:99
Alignment explanation
Indices: 39108008--39108718 Score: 756
Period size: 100 Copynumber: 7.2 Consensus size: 99
39107998 TACCGATGTG
* * * * * * * * *
39108008 GCTTTAATCTTTTTAACTGCAATGT-AGGGGAAGCAAGATTCACCGATGTGGTTTTAATCTGTTC
1 GCTTCAATCTTTTTAATTGCAATGTCA-GGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTC
* *** * * *
39108072 CACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTG
65 CACTGCAACGC-TGGAAAGTAAGATCCGCTGTTGTA
* * * ** * * * * ** *
39108108 GCTTCAATCTTTTGAGTTGCGATGTTGGGGAAGCGAGATTCACCGTCATAGCTTCAAT-TGGTCC
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
* * * *
39108172 GCTGCATCGCCTGGGAAGTAAGATCCGCTATTGTA
66 ACTGCAACG-CTGGAAAGTAAGATCCGCTGTTGTA
* *
39108207 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
39108272 ACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTA
66 ACTGCAACGCT-GGAAAGTAAGATCCGCTGTTGTA
* *
39108307 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTATTCC
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
39108372 ACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTA
66 ACTGCAACGCT-GGAAAGTAAGATCCGCTGTTGTA
* * *
39108407 GCTACAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCACTGTTGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
*
39108472 ACTGCAACGCTAGGAAAGTAAGATCCACTGTTGTA
66 ACTGCAACGCT-GGAAAGTAAGATCCGCTGTTGTA
* *
39108507 GCTTCAATCTTTTTAA---C--TGCCGGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
* * * *
39108567 ACTGCAA-TCTGG-AAGTAAGATTCGCCGTTGTG
66 ACTGCAACGCTGGAAAGTAAGATCCGCTGTTGTA
* * ** * * *
39108599 GCTTCAATCTTTTGAATTACAATGTTGGGGAAGCGAGATTCGCTGTCGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
* * * * * *
39108664 GCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTG
66 ACTGCAACG-CTGGAAAGTAAGATCCGCTGTTGTA
*
39108699 GCTTCAATCTTTTGAATTGC
1 GCTTCAATCTTTTTAATTGC
39108719 TGCAAACTAT
Statistics
Matches: 537, Mismatches: 62, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
92 31 0.06
93 2 0.00
94 2 0.00
95 47 0.09
97 44 0.08
99 85 0.16
100 326 0.61
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (99 bp):
GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
ACTGCAACGCTGGAAAGTAAGATCCGCTGTTGTA
Found at i:39109100 original size:44 final size:44
Alignment explanation
Indices: 39109050--39109138 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
39109040 TTGGCCCCAC
39109050 TGTAAACCTCCAAGTTCAATCCACTGGATGCAAAATTTAAACCA
1 TGTAAACCTCCAAGTTCAATCCACTGGATGCAAAATTTAAACCA
* *
39109094 TGTAAACCTCTAAGTTCAATCCACTGGATGCAAAATTTGAACCA
1 TGTAAACCTCCAAGTTCAATCCACTGGATGCAAAATTTAAACCA
39109138 T
1 T
39109139 CTTTCTCCCG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (44 bp):
TGTAAACCTCCAAGTTCAATCCACTGGATGCAAAATTTAAACCA
Found at i:39109943 original size:43 final size:44
Alignment explanation
Indices: 39109874--39109976 Score: 115
Period size: 43 Copynumber: 2.4 Consensus size: 44
39109864 TGCACCGATC
* * *
39109874 TGAT-CAAAATTTAAGCTGCTCATGATCGCCTTATGCCCCAATT-
1 TGATCCAAAATTTGAGCTGCTCATGATCACCTAATGCCCC-ATTA
*
39109917 TGATCCAAAATTTGAG-TCGCTC-TGATCACCTAATGTCCCATTA
1 TGATCCAAAATTTGAGCT-GCTCATGATCACCTAATGCCCCATTA
*
39109960 TGATCAAAAATTTGAGC
1 TGATCCAAAATTTGAGC
39109977 CGCCCTTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 3 0.06
43 34 0.67
44 14 0.27
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (44 bp):
TGATCCAAAATTTGAGCTGCTCATGATCACCTAATGCCCCATTA
Found at i:39110073 original size:15 final size:15
Alignment explanation
Indices: 39110053--39110091 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
39110043 TGGCCTCTCC
*
39110053 TTTTTCTTTTTTTCT
1 TTTTTCTTTTCTTCT
39110068 TTTTTCTTTTCTTCT
1 TTTTTCTTTTCTTCT
39110083 TTTTT-TTTT
1 TTTTTCTTTT
39110092 GTTTTTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTCTTTTCTTCT
Found at i:39110077 original size:20 final size:19
Alignment explanation
Indices: 39110054--39110096 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
39110044 GGCCTCTCCT
*
39110054 TTTTCTTTTTTTCTTTTTTC
1 TTTTCTTCTTTT-TTTTTTC
*
39110074 TTTTCTTCTTTTTTTTTTG
1 TTTTCTTCTTTTTTTTTTC
39110093 TTTT
1 TTTT
39110097 TTGATCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (19 bp):
TTTTCTTCTTTTTTTTTTC
Found at i:39110098 original size:8 final size:8
Alignment explanation
Indices: 39110053--39110088 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
39110043 TGGCCTCTCC
39110053 TTTTTCTT
1 TTTTTCTT
39110061 TTTTTC-T
1 TTTTTCTT
39110068 TTTTTCTT
1 TTTTTCTT
*
39110076 TTCTTCTT
1 TTTTTCTT
39110084 TTTTT
1 TTTTT
39110089 TTTGTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:39111267 original size:6 final size:6
Alignment explanation
Indices: 39111256--39111304 Score: 73
Period size: 6 Copynumber: 8.0 Consensus size: 6
39111246 TTGACCTCTC
39111256 CTTTTT CTTTTT CTTTTT CTTTTT CTTCTCTT -TTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT-T-TT CTTTTT CTTTTT CTTTTT
39111305 TCTATTTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 2 0.05
6 33 0.82
7 3 0.08
8 2 0.05
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:39111335 original size:8 final size:9
Alignment explanation
Indices: 39111316--39111371 Score: 87
Period size: 9 Copynumber: 6.3 Consensus size: 9
39111306 CTATTTTGAC
39111316 TTTGATTTT
1 TTTGATTTT
39111325 TTTGA-TTT
1 TTTGATTTT
39111333 TTTGATTTT
1 TTTGATTTT
*
39111342 TTGGATTTT
1 TTTGATTTT
*
39111351 TTTTATTTT
1 TTTGATTTT
39111360 TTTGATTTT
1 TTTGATTTT
39111369 TTT
1 TTT
39111372 CTAGTCTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.19
9 34 0.81
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (9 bp):
TTTGATTTT
Found at i:39111338 original size:17 final size:17
Alignment explanation
Indices: 39111316--39111370 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
39111306 CTATTTTGAC
39111316 TTTGATTTTTTTGATTT
1 TTTGATTTTTTTGATTT
*
39111333 TTTGATTTTTTGGATTTT
1 TTTGATTTTTTTGA-TTT
*
39111351 TTTTATTTTTTTGATTT
1 TTTGATTTTTTTGATTT
39111368 TTT
1 TTT
39111371 TCTAGTCTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 19 0.56
18 15 0.44
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (17 bp):
TTTGATTTTTTTGATTT
Found at i:39111341 original size:7 final size:8
Alignment explanation
Indices: 39111316--39111370 Score: 65
Period size: 8 Copynumber: 6.4 Consensus size: 8
39111306 CTATTTTGAC
39111316 TTTGATTTT
1 TTTGA-TTT
39111325 TTTGATTT
1 TTTGATTT
39111333 TTTGATTT
1 TTTGATTT
39111341 TTTGGATTTT
1 TTT-GA-TTT
*
39111351 TTTTATTTT
1 TTTGA-TTT
39111360 TTTGATTT
1 TTTGATTT
39111368 TTT
1 TTT
39111371 TCTAGTCTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
8 20 0.48
9 16 0.38
10 6 0.14
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (8 bp):
TTTGATTT
Found at i:39115254 original size:3 final size:3
Alignment explanation
Indices: 39115248--39115307 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
39115238 AAACTACTAT
39115248 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39115296 TAA TAA TAA TAA
1 TAA TAA TAA TAA
39115308 AATTGCTAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39118536 original size:25 final size:24
Alignment explanation
Indices: 39118507--39118561 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
39118497 AATATGTACC
39118507 AAAAATGTAAATGTAAATGTAAAT
1 AAAAATGTAAATGTAAATGTAAAT
* * * *
39118531 ATAAAATTTATATTTAAATTTAAAT
1 A-AAAATGTAAATGTAAATGTAAAT
39118556 AAAAAT
1 AAAAAT
39118562 AATATATAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (24 bp):
AAAAATGTAAATGTAAATGTAAAT
Found at i:39118567 original size:25 final size:25
Alignment explanation
Indices: 39118520--39118568 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
39118510 AATGTAAATG
*
39118520 TAAATGTAAATATAAAATTTATATT
1 TAAATGTAAATATAAAATATATATT
*
39118545 TAAATTTAAATA-AAAATAATATAT
1 TAAATGTAAATATAAAAT-ATATAT
39118569 AGAAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
TAAATGTAAATATAAAATATATATT
Found at i:39122656 original size:10 final size:10
Alignment explanation
Indices: 39122632--39122669 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
39122622 AATGATGCAA
*
39122632 ATATA-AAAG
1 ATATATAAAT
39122641 ATATATAAAT
1 ATATATAAAT
*
39122651 ATATATATAT
1 ATATATAAAT
39122661 ATATATAAA
1 ATATATAAA
39122670 ATAATGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
9 5 0.20
10 20 0.80
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
ATATATAAAT
Found at i:39124382 original size:22 final size:22
Alignment explanation
Indices: 39124329--39124401 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
39124319 TCTAGGCTTA
*
39124329 TTTGGGTTTA-GTTTGTAATGGG
1 TTTGGGTTTAGGTTTG-AGTGGG
*
39124351 TTTTGAGTTTAGGTTTGAGTGGG
1 -TTTGGGTTTAGGTTTGAGTGGG
39124374 TTTGGGTTTAGGTTT-AGGTGGG
1 TTTGGGTTTAGGTTTGA-GTGGG
39124396 TTTGGG
1 TTTGGG
39124402 CCCGGGCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
21 1 0.02
22 25 0.56
23 14 0.31
24 5 0.11
ACGTcount: A:0.11, C:0.00, G:0.41, T:0.48
Consensus pattern (22 bp):
TTTGGGTTTAGGTTTGAGTGGG
Found at i:39134144 original size:23 final size:23
Alignment explanation
Indices: 39134115--39134165 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
39134105 TAGTATTCAT
*
39134115 TTTTTTTCGAATTATTGATAGTA
1 TTTTTTTCGAATTACTGATAGTA
*
39134138 TTTTTTTCTAATTACTGATAGTA
1 TTTTTTTCGAATTACTGATAGTA
39134161 TTTTT
1 TTTTT
39134166 GCAATTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.61
Consensus pattern (23 bp):
TTTTTTTCGAATTACTGATAGTA
Done.