Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold39
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: 4724573
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 178835 characters in sequence are not A, C, G, or T
File 18 of 27
Found at i:3065329 original size:21 final size:20
Alignment explanation
Indices: 3065299--3065337 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3065289 CACATTTTTA
3065299 TCTAAATGTATCGATACATT
1 TCTAAATGTATCGATACATT
3065319 TCTAGAATGTATCGATACA
1 TCTA-AATGTATCGATACA
3065338 AGGTCCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATCGATACATT
Found at i:3070248 original size:21 final size:23
Alignment explanation
Indices: 3070207--3070248 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3070197 TATTTATTTT
*
3070207 AATATGAAAAGAAAAGCACAAAA
1 AATATGAAAAAAAAAGCACAAAA
3070230 AATAT-AAAAAAAAAG-ACAA
1 AATATGAAAAAAAAAGCACAA
3070249 GAATACAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (23 bp):
AATATGAAAAAAAAAGCACAAAA
Found at i:3071736 original size:19 final size:20
Alignment explanation
Indices: 3071692--3071782 Score: 132
Period size: 19 Copynumber: 4.7 Consensus size: 20
3071682 TTGCTAGTTT
**
3071692 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
3071712 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
**
3071731 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
3071751 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
3071770 CATGTATCGATAC
1 CATGTATCGATAC
3071783 CATGTATCGA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
19 32 0.50
20 32 0.50
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:3071741 original size:39 final size:39
Alignment explanation
Indices: 3071692--3071782 Score: 182
Period size: 39 Copynumber: 2.3 Consensus size: 39
3071682 TTGCTAGTTT
3071692 CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
1 CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
3071731 CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
1 CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
3071770 CATGTATCGATAC
1 CATGTATCGATAC
3071783 CATGTATCGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (39 bp):
CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
Found at i:3071788 original size:13 final size:13
Alignment explanation
Indices: 3071770--3071795 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3071760 ATACAATGAA
3071770 CATGTATCGATAC
1 CATGTATCGATAC
3071783 CATGTATCGATAC
1 CATGTATCGATAC
3071796 AAAGCATAAT
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:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
CATGTATCGATAC
Found at i:3071792 original size:32 final size:33
Alignment explanation
Indices: 3071751--3071815 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
3071741 TACAATTGTG
*
3071751 CATGTATCGATACAATG-A-ACATGTATCGATAC
1 CATGTATCGATACAAAGCATA-ATGTATCGATAC
3071783 CATGTATCGATACAAAGCATAATGTATCGATAC
1 CATGTATCGATACAAAGCATAATGTATCGATAC
3071816 ATCTGGATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 16 0.53
33 13 0.43
34 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (33 bp):
CATGTATCGATACAAAGCATAATGTATCGATAC
Found at i:3078774 original size:30 final size:30
Alignment explanation
Indices: 3078738--3078814 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
3078728 TGAATAGTAC
3078738 ATGTATCGATACATTTTATTTTCTACCCAG
1 ATGTATCGATACATTTTATTTTCTACCCAG
* *
3078768 ATGTATCGATACATTCTGTTTTCTACCCAG
1 ATGTATCGATACATTTTATTTTCTACCCAG
*
3078798 ACGTATCGATACATTTT
1 ATGTATCGATACATTTT
3078815 TCAATGTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (30 bp):
ATGTATCGATACATTTTATTTTCTACCCAG
Found at i:3078825 original size:20 final size:20
Alignment explanation
Indices: 3078800--3078872 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
3078790 CTACCCAGAC
3078800 GTATCGATACATTTTTCAAT
1 GTATCGATACATTTTTCAAT
***
3078820 GTATCGATACATTTTGTTTTT
1 GTATCGATACATTTT-TCAAT
* *
3078841 TTACCGATACATTTTTCAAT
1 GTATCGATACATTTTTCAAT
*
3078861 TTATCGATACAT
1 GTATCGATACAT
3078873 CTAGTTAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (20 bp):
GTATCGATACATTTTTCAAT
Found at i:3094107 original size:26 final size:26
Alignment explanation
Indices: 3094055--3094126 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
3094045 CAAGAAATGG
*
3094055 TTGTCAAGAAAT-TATCGTCA-AGAACTT
1 TTGTCAAGAAATGT-TTGTCAGA-AAC-T
*
3094082 TTGTCGAG-AATGTTTGTCAGAAACT
1 TTGTCAAGAAATGTTTGTCAGAAACT
*
3094107 TTGTCAAGAAATTTTTGTCA
1 TTGTCAAGAAATGTTTGTCA
3094127 ATATAACCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 8 0.21
26 21 0.55
27 9 0.24
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (26 bp):
TTGTCAAGAAATGTTTGTCAGAAACT
Found at i:3094125 original size:14 final size:14
Alignment explanation
Indices: 3094040--3094127 Score: 76
Period size: 14 Copynumber: 6.6 Consensus size: 14
3094030 TAATTCGCCA
*
3094040 TTTGTCAAGAAATG
1 TTTGTCAAGAAATT
*
3094054 GTTGTCAAGAAATT
1 TTTGTCAAGAAATT
* * *
3094068 ATCGTCAAG-AACT
1 TTTGTCAAGAAATT
* *
3094081 TTTGTCGAG-AATG
1 TTTGTCAAGAAATT
*
3094094 TTTGTC-AGAAA-C
1 TTTGTCAAGAAATT
3094106 TTTGTCAAGAAATT
1 TTTGTCAAGAAATT
3094120 TTTGTCAA
1 TTTGTCAA
3094128 TATAACCCTT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
12 8 0.14
13 24 0.41
14 27 0.46
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (14 bp):
TTTGTCAAGAAATT
Found at i:3094235 original size:29 final size:28
Alignment explanation
Indices: 3094138--3094610 Score: 518
Period size: 28 Copynumber: 16.4 Consensus size: 28
3094128 TATAACCCTT
3094138 TTTCAAAAGCCCACAAGTCAGTGGCACCC
1 TTTC-AAAGCCCACAAGTCAGTGGCACCC
* *
3094167 TTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
3094195 TTTCAAAGCCCACAAGTTAGTGGCAACCC
1 TTTCAAAGCCCACAAGTCAGTGGC-ACCC
*
3094224 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
3094252 TTTCAAAGCTCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
3094280 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
3094308 TTTCAAAAGCCCACGAGTCAGTGGCATCC
1 TTTC-AAAGCCCACAAGTCAGTGGCACCC
* * * *
3094337 TTTCAAAAGCCCACGAGTCAGGGGCATCT
1 TTTC-AAAGCCCACAAGTCAGTGGCACCC
* *
3094366 TTTCAAAAGCCCACGAGTCAGTAGCACCC
1 TTTC-AAAGCCCACAAGTCAGTGGCACCC
*
3094395 TTTCAAAACCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* **
3094423 TTTCAAAGCCCACGAGTCAGTGGCATTCTT
1 TTTCAAAGCCCACAAGTCAGTGGCA--CCC
* *
3094453 TTTCAAAGCCCATAAGTCAGTGGCACCTT
1 TTTCAAAGCCCACAAGTCAGTGGCACC-C
* *
3094482 TTTCAAAGCCCACAAGTCAATGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
3094510 TTTCAAAGCCC-CTAAGTCAGTGGCATCT
1 TTTCAAAGCCCAC-AAGTCAGTGGCACCC
3094538 TTTCAAAGCCCACAAGTC-GATGGCAACCC
1 TTTCAAAGCCCACAAGTCAG-TGGC-ACCC
* * ** *
3094567 TTCTAAAACCCACACAAGTTGGTGGCAACC
1 TT-TCAAAGCC-CACAAGTCAGTGGCACCC
3094597 TTCTCTAAAGCCCA
1 TT-TC-AAAGCCCA
3094611 TACGAGTTGG
Statistics
Matches: 395, Mismatches: 36, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
27 2 0.01
28 196 0.50
29 141 0.36
30 39 0.10
31 16 0.04
32 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:3094286 original size:85 final size:84
Alignment explanation
Indices: 3094138--3094610 Score: 572
Period size: 85 Copynumber: 5.5 Consensus size: 84
3094128 TATAACCCTT
* *
3094138 TTTCAAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAG
1 TTTC-AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAG
*
3094203 CCCACAAGTTAGTGGCAACCC
65 CCCACAAGTCAGTGGC-ACCC
* * * *
3094224 TTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCTCACAAGTTAGTGGCATCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGC
*
3094289 CCACAAGTCAGTGGCATCC
66 CCACAAGTCAGTGGCACCC
* * * *
3094308 TTTCAAAAGCCCACGAGTCAGTGGCATCCTTTCAAAAGCCCACGAGTCAGGGGCATCTTTTCAAA
1 TTTC-AAAGCCCACAAGTCAGTGGCACCCTTTC-AAAGCCCACAAGTCAGTGGCATCTTTTC-AA
* *
3094373 AGCCCACGAGTCAGTAGCACCC
63 AGCCCACAAGTCAGTGGCACCC
* *
3094395 TTTCAAAACCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCAGTGGCATTCTTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-TC-TTTTCAAA
* *
3094460 GCCCATAAGTCAGTGGCACCTT
64 GCCCACAAGTCAGTGGCACC-C
* *
3094482 TTTCAAAGCCCACAAGTCAATGGCACCTTTTCAAAGCCC-CTAAGTCAGTGGCATCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC-AAGTCAGTGGCATCTTTTCAAAG
3094546 CCCACAAGTC-GATGGCAACCC
65 CCCACAAGTCAG-TGGC-ACCC
* * ** *
3094567 TTCTAAAACCCACACAAGTTGGTGGCAACCTTCTCTAAAGCCCA
1 TT-TCAAAGCC-CACAAGTCAGTGGCACCCTT-TC-AAAGCCCA
3094611 TACGAGTTGG
Statistics
Matches: 337, Mismatches: 36, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
84 8 0.02
85 142 0.42
86 86 0.26
87 92 0.27
88 2 0.01
89 7 0.02
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (84 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGC
CCACAAGTCAGTGGCACCC
Found at i:3094583 original size:31 final size:31
Alignment explanation
Indices: 3094548--3094636 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 31
3094538 TTTCAAAGCC
* *
3094548 CACAAGTCGATGGCAACCCTTCTAAAACCCA
1 CACAAGTTGGTGGCAACCCTTCTAAAACCCA
* *
3094579 CACAAGTTGGTGGCAACCTTCTCTAAAGCCCA
1 CACAAGTTGGTGGCAACCCT-TCTAAAACCCA
* *
3094611 TACGAGTTGGTGGCAACCCTTCTAAA
1 CACAAGTTGGTGGCAACCCTTCTAAA
3094637 CTTATTGTCG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 23 0.46
32 27 0.54
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (31 bp):
CACAAGTTGGTGGCAACCCTTCTAAAACCCA
Found at i:3095506 original size:30 final size:29
Alignment explanation
Indices: 3095472--3095558 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 29
3095462 AGATGCATAT
3095472 ATACATTCTATTTTCTACCCAGATGTATCG
1 ATACATTCT-TTTTCTACCCAGATGTATCG
3095502 ATACA---TTTTT-T----A-ATGTATCG
1 ATACATTCTTTTTCTACCCAGATGTATCG
*
3095522 ATACATTCTGTTTCCTACCCAGATGTATCG
1 ATACATTCT-TTTTCTACCCAGATGTATCG
3095552 ATACATT
1 ATACATT
3095559 TTTCAATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 20
0.69 0.01 0.30
Matches are distributed among these distances:
20 13 0.28
21 1 0.02
23 1 0.02
24 3 0.07
25 2 0.04
26 4 0.09
27 1 0.02
29 1 0.02
30 20 0.43
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (29 bp):
ATACATTCTTTTTCTACCCAGATGTATCG
Found at i:3095540 original size:50 final size:50
Alignment explanation
Indices: 3095472--3095627 Score: 242
Period size: 50 Copynumber: 3.1 Consensus size: 50
3095462 AGATGCATAT
* *
3095472 ATACATTCTATTTTCTACCCAGATGTATCGATACATTTTTTAATGTATCG
1 ATACATTCTGTTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCG
*
3095522 ATACATTCTGTTTCCTACCCAGATGTATCGATACATTTTTCAAT-TATCG
1 ATACATTCTGTTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCG
* * *
3095571 ATACATTTTGTTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCA
1 ATACATTCTG-TTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCG
3095622 ATACAT
1 ATACAT
3095628 CTAGTTAATT
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
49 14 0.14
50 73 0.75
51 10 0.10
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.44
Consensus pattern (50 bp):
ATACATTCTGTTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCG
Found at i:3095733 original size:78 final size:78
Alignment explanation
Indices: 3095601--3095755 Score: 292
Period size: 78 Copynumber: 2.0 Consensus size: 78
3095591 CAGATGTATC
*
3095601 GATACATTTTTCAATGTATCAATACATCTAGTTAATTTTGAGCATTTCGGGTTTTTTTCAACCTT
1 GATACATTTTTCAATGTATCAATACATCTAGTTAATTTTGAGCATTTCGAGTTTTTTTCAACCTT
3095666 GGCCCATGGGACT
66 GGCCCATGGGACT
3095679 GATACATTTTTCAATGTATCAATACATCTAGTTAATTTTGAGCATTTCGAGTTTTTTTCAACCTT
1 GATACATTTTTCAATGTATCAATACATCTAGTTAATTTTGAGCATTTCGAGTTTTTTTCAACCTT
*
3095744 GGCTCATGGGAC
66 GGCCCATGGGAC
3095756 CTAATGTCAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (78 bp):
GATACATTTTTCAATGTATCAATACATCTAGTTAATTTTGAGCATTTCGAGTTTTTTTCAACCTT
GGCCCATGGGACT
Found at i:3096636 original size:20 final size:20
Alignment explanation
Indices: 3096598--3096636 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3096588 TAGCCTTTGA
**
3096598 TCATGCATTTTTATTATGTT
1 TCATGCATTTTTAACATGTT
3096618 TCATGCATTTTTAACATGT
1 TCATGCATTTTTAACATGT
3096637 CTGGCATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (20 bp):
TCATGCATTTTTAACATGTT
Found at i:3113275 original size:18 final size:18
Alignment explanation
Indices: 3113244--3113278 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3113234 AGAATTGTCA
*
3113244 ATTTTTCTTATTTGTTTG
1 ATTTTGCTTATTTGTTTG
*
3113262 ATTTTGCTTTTTTGTTT
1 ATTTTGCTTATTTGTTT
3113279 TATGAATTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.11, T:0.74
Consensus pattern (18 bp):
ATTTTGCTTATTTGTTTG
Found at i:3113833 original size:2 final size:2
Alignment explanation
Indices: 3113826--3113850 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3113816 ATTACTTGCA
3113826 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3113851 AAAAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3114256 original size:3 final size:3
Alignment explanation
Indices: 3114248--3114276 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3114238 GGTATTCTCT
3114248 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3114277 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3115252 original size:13 final size:14
Alignment explanation
Indices: 3115234--3115265 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
3115224 AGGCCTTGAG
3115234 AAAAAGAAAAAA-A
1 AAAAAGAAAAAAGA
3115247 AAAAAGAAAAAAGA
1 AAAAAGAAAAAAGA
3115261 AAAAA
1 AAAAA
3115266 AGAAGCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:3120123 original size:22 final size:22
Alignment explanation
Indices: 3120075--3120126 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
3120065 ATTAAAATTT
* * *
3120075 TAAATTATAATAATATTAAATAA
1 TAAATT-TAAAAATATAAAAAAA
3120098 -AAATTTAAAAATATAAAAAAA
1 TAAATTTAAAAATATAAAAAAA
3120119 TAAATTTA
1 TAAATTTA
3120127 TTTTTGTCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAATTTAAAAATATAAAAAAA
Found at i:3120277 original size:34 final size:31
Alignment explanation
Indices: 3120226--3120289 Score: 76
Period size: 34 Copynumber: 2.0 Consensus size: 31
3120216 ATATTACAAG
*
3120226 AAAAATAATATCAATTTAATTAATATAAATACAT
1 AAAAATAAAATCAATTT-ATT-ATA-AAATACAT
3120260 AAAAATAAAAT-ATATTTATTATAAAATACA
1 AAAAATAAAATCA-ATTTATTATAAAATACA
3120290 AAATTAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 7 0.25
32 3 0.11
33 4 0.14
34 14 0.50
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAAATAAAATCAATTTATTATAAAATACAT
Found at i:3121300 original size:17 final size:16
Alignment explanation
Indices: 3121240--3121304 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
3121230 TTGGCGAGGA
*
3121240 ATTTTTTATTTAATTT
1 ATTTTTTATTTATTTT
* *
3121256 ATTTTATATTT-TTAT
1 ATTTTTTATTTATTTT
**
3121271 ATATTTAAATTTATTTT
1 AT-TTTTTATTTATTTT
3121288 ATTTTTTAATTTATTTT
1 ATTTTTT-ATTTATTTT
3121305 TTTGAAAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 4 0.10
16 21 0.54
17 14 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTATTTATTTT
Found at i:3121302 original size:27 final size:26
Alignment explanation
Indices: 3121244--3121303 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
3121234 CGAGGAATTT
3121244 TTTATTTAATTTATTTTATATTTTTA
1 TTTATTTAATTTATTTTATATTTTTA
*
3121270 TATATTTAAATTTATTTTAT-TTTTTAA
1 TTTATTT-AATTTATTTTATATTTTT-A
3121297 TTTATTT
1 TTTATTT
3121304 TTTTGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 11 0.37
27 19 0.63
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTATTTAATTTATTTTATATTTTTA
Found at i:3121319 original size:37 final size:39
Alignment explanation
Indices: 3121278--3121352 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 39
3121268 TATATATTTA
3121278 AATTTATTTT-ATTTTTTAATT-TATTT-TTTTGAAAAAG
1 AATTT-TTTTCATTTTTTAATTCTATTTCTTTTGAAAAAG
**
3121315 AATTTTTTTCATTTTTTTCTTCTATTTCTTTTGAAAAA
1 AATTTTTTTCATTTTTTAATTCTATTTCTTTTGAAAAA
3121353 TCAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 4 0.12
37 14 0.42
38 5 0.15
39 10 0.30
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (39 bp):
AATTTTTTTCATTTTTTAATTCTATTTCTTTTGAAAAAG
Found at i:3123327 original size:13 final size:13
Alignment explanation
Indices: 3123309--3123336 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3123299 TATTATTCAA
3123309 TGTATCGATACAT
1 TGTATCGATACAT
3123322 TGTATCGATACAT
1 TGTATCGATACAT
3123335 TG
1 TG
3123337 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3123331 original size:33 final size:33
Alignment explanation
Indices: 3123289--3123354 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3123279 GCCAAGGAAA
*
3123289 TGTATCGATATATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
3123322 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
3123355 CTGGGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:3124302 original size:20 final size:20
Alignment explanation
Indices: 3124257--3124302 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3124247 GTTAACAACC
*
3124257 CATGATTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
3124277 CTATGTTTCATGCA-TTTGCAG
1 C-ATGTTTCATGCATTTTG-AG
3124298 CATGT
1 CATGT
3124303 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Found at i:3133381 original size:51 final size:51
Alignment explanation
Indices: 3133322--3133437 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
3133312 TGAACAGTAC
3133322 ATGTATCGATACATTATAG-TTTTTTACCCAGATGTATCAATACATTTCTCA
1 ATGTATCGATACATTAT-GTTTTTTTACCCAGATGTATCAATACATTTCTCA
* * * *
3133373 ATGTATCGATACATTATGTTTTTTTACCTAGATGTATCGATACATTTTTTA
1 ATGTATCGATACATTATGTTTTTTTACCCAGATGTATCAATACATTTCTCA
3133424 ATGTATCGATACAT
1 ATGTATCGATACAT
3133438 CTAGTTAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 1 0.02
51 59 0.98
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (51 bp):
ATGTATCGATACATTATGTTTTTTTACCCAGATGTATCAATACATTTCTCA
Found at i:3134175 original size:19 final size:19
Alignment explanation
Indices: 3134139--3134176 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3134129 GAACTTTGAT
*
3134139 TATTAAATAGTAAAAAAAA
1 TATTAAATAGGAAAAAAAA
3134158 TATTAAA-AGGAAACAAAAA
1 TATTAAATAGGAAA-AAAAA
3134177 AAGGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (19 bp):
TATTAAATAGGAAAAAAAA
Found at i:3134903 original size:23 final size:23
Alignment explanation
Indices: 3134860--3134917 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3134850 TATGGGTAGG
3134860 AAGAAGAAAGAAGAAGAAAAAGAA
1 AAGAAGAAA-AAGAAGAAAAAGAA
* * *
3134884 AGGAAGAAAAGGAAGTAAAAGAA
1 AAGAAGAAAAAGAAGAAAAAGAA
*
3134907 AAAAAGAAAAA
1 AAGAAGAAAAA
3134918 AATATGAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (23 bp):
AAGAAGAAAAAGAAGAAAAAGAA
Found at i:3142135 original size:20 final size:20
Alignment explanation
Indices: 3142110--3142162 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
3142100 TCCCGTAGCC
3142110 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
3142130 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
3142150 ATGTATCGATACA
1 ATGTATCGATACA
3142163 TTGGTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:3142240 original size:33 final size:33
Alignment explanation
Indices: 3142202--3142268 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
3142192 GTTACAAGCT
3142202 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTATAC--CATGTATCGATACA
3142235 ATGTATCGATACATTATACCATGTATCGATACA
1 ATGTATCGATACATTATACCATGTATCGATACA
3142268 A
1 A
3142269 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTATACCATGTATCGATACA
Found at i:3142253 original size:20 final size:20
Alignment explanation
Indices: 3142230--3142267 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3142220 TCATGTATCG
3142230 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
*
3142250 ATACCATGTATCGATACA
1 ATACAATGTATCGATACA
3142268 AATAGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:3142266 original size:13 final size:13
Alignment explanation
Indices: 3142222--3142247 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3142212 ACATTTCTTC
3142222 ATGTATCGATACA
1 ATGTATCGATACA
3142235 ATGTATCGATACA
1 ATGTATCGATACA
3142248 TTATACCATG
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:3142342 original size:19 final size:21
Alignment explanation
Indices: 3142297--3142348 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
3142287 CTGCCAATTT
**
3142297 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
3142318 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
3142337 CATGTATCGATA
1 CATGTATCGATA
3142349 TAATGTATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 15 0.52
20 1 0.03
21 13 0.45
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:3142360 original size:32 final size:33
Alignment explanation
Indices: 3142319--3142381 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
3142309 CAATTTGTCC
**
3142319 ATGTATCGATACATTG-AACATGTATCGATATA
1 ATGTATCGATACAAGGTAACATGTATCGATATA
*
3142351 ATGTATCGATACAAGGTAGCATGTATCGATA
1 ATGTATCGATACAAGGTAACATGTATCGATA
3142382 CATTCAAGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAGGTAACATGTATCGATATA
Found at i:3142926 original size:22 final size:22
Alignment explanation
Indices: 3142898--3142967 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
3142888 CCCTTAAAAA
3142898 TTCTCCCCCTTAAACAATTATC
1 TTCTCCCCCTTAAACAATTATC
*** **
3142920 TTCTCCCCCTTTATGTAA--AAA
1 TTCTCCCCC-TTAAACAATTATC
3142941 TTCTCCCCCTTAAACAATTATC
1 TTCTCCCCCTTAAACAATTATC
3142963 TTCTC
1 TTCTC
3142968 AATAAATTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
20 5 0.14
21 10 0.29
22 15 0.43
23 5 0.14
ACGTcount: A:0.26, C:0.34, G:0.01, T:0.39
Consensus pattern (22 bp):
TTCTCCCCCTTAAACAATTATC
Found at i:3151531 original size:13 final size:13
Alignment explanation
Indices: 3151513--3151538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3151503 CAATTTTTTG
3151513 TGTATCGATACAT
1 TGTATCGATACAT
3151526 TGTATCGATACAT
1 TGTATCGATACAT
3151539 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:3152227 original size:38 final size:40
Alignment explanation
Indices: 3152161--3152240 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 40
3152151 TTTTATTTCT
*
3152161 CCCTTAATCAAAATAAATTTAACAAATTTGTACATTCTCC
1 CCCTTAATCAAAATAAATTTAACAAATTTATACATTCTCC
* *
3152201 CCCTTAAT-AAAAT-AATTGTAGC-AATTTATGCATTCTCC
1 CCCTTAATCAAAATAAATT-TAACAAATTTATACATTCTCC
3152239 CC
1 CC
3152241 TTTATCTCCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 20 0.56
39 8 0.22
40 8 0.22
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (40 bp):
CCCTTAATCAAAATAAATTTAACAAATTTATACATTCTCC
Found at i:3152286 original size:21 final size:21
Alignment explanation
Indices: 3152245--3152288 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3152235 CTCCCCTTTA
* *
3152245 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
3152266 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
3152287 TC
1 TC
3152289 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:3156205 original size:15 final size:15
Alignment explanation
Indices: 3156185--3156215 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3156175 ATTTCGTTTG
*
3156185 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3156200 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3156215 G
1 G
3156216 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:3158048 original size:21 final size:21
Alignment explanation
Indices: 3158019--3158063 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3158009 AAGTTTTCAT
*
3158019 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3158039 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3158061 TTT
1 TTT
3158064 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:3160855 original size:16 final size:16
Alignment explanation
Indices: 3160836--3160869 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3160826 ATAGCCATGT
*
3160836 ATCGACATAATTCATA
1 ATCGACACAATTCATA
*
3160852 ATCGATACAATTCATA
1 ATCGACACAATTCATA
3160868 AT
1 AT
3160870 GTATCGATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (16 bp):
ATCGACACAATTCATA
Found at i:3160945 original size:33 final size:33
Alignment explanation
Indices: 3160900--3160966 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
3160890 GTTACAAGCT
* *
3160900 ATGTATCGATACATT-TCCTCATGTATCGATACA
1 ATGTATCAATACATTGTAC-CATGTATCGATACA
3160933 ATGTATCAATACATTGTACCATGTATCGATACA
1 ATGTATCAATACATTGTACCATGTATCGATACA
3160966 A
1 A
3160967 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (33 bp):
ATGTATCAATACATTGTACCATGTATCGATACA
Found at i:3161033 original size:64 final size:64
Alignment explanation
Indices: 3160933--3161093 Score: 281
Period size: 64 Copynumber: 2.5 Consensus size: 64
3160923 TATCGATACA
* *
3160933 ATGTATCAATAC-A-TTGTACCATGTATCGATACAAATAGTGATAGGGTAGCTACTGCCAATTTC
1 ATGTATCGATACAATTTGT-CCATGTATCGATACAAATAATGATAGGGTAGCTACTGCCAATTTC
3160996 ATGTATCGATACAATTTGTCCATGTATCGATACAAATAATGATAGGGTAGCTACTGCCAATTTC
1 ATGTATCGATACAATTTGTCCATGTATCGATACAAATAATGATAGGGTAGCTACTGCCAATTTC
3161060 ATGTATCGATACAATTTGTCCATGTATCGATACA
1 ATGTATCGATACAATTTGTCCATGTATCGATACA
3161094 TTGAACATGT
Statistics
Matches: 94, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
63 11 0.12
64 79 0.84
65 4 0.04
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (64 bp):
ATGTATCGATACAATTTGTCCATGTATCGATACAAATAATGATAGGGTAGCTACTGCCAATTTC
Found at i:3161104 original size:19 final size:19
Alignment explanation
Indices: 3161059--3161115 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
3161049 CTGCCAATTT
**
3161059 CATGTATCGATACAATTTGTC
1 CATGTATCGATAC-A-TTGAA
3161080 CATGTATCGATACATTGAA
1 CATGTATCGATACATTGAA
3161099 CATGTATCGATACATTG
1 CATGTATCGATACATTG
3161116 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 20 0.59
20 1 0.03
21 13 0.38
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
CATGTATCGATACATTGAA
Found at i:3161119 original size:13 final size:13
Alignment explanation
Indices: 3161101--3161125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3161091 ACATTGAACA
3161101 TGTATCGATACAT
1 TGTATCGATACAT
3161114 TGTATCGATACA
1 TGTATCGATACA
3161126 AGGCAGCATG
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:3161141 original size:33 final size:32
Alignment explanation
Indices: 3161082--3161146 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
3161072 AATTTGTCCA
**
3161082 TGTATCGATACATTGAACATGTATCGATACAT
1 TGTATCGATACAAGGAACATGTATCGATACAT
*
3161114 TGTATCGATACAAGGCAGCATGTATCGATACAT
1 TGTATCGATACAAGG-AACATGTATCGATACAT
3161147 CTGAGTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAGGAACATGTATCGATACAT
Found at i:3162253 original size:209 final size:209
Alignment explanation
Indices: 3161893--3162312 Score: 840
Period size: 209 Copynumber: 2.0 Consensus size: 209
3161883 CTCCTCGATA
3161893 CTTCCTTGTCGAGTGCTTACCCAATTCACTAAAAGAATTGATTACCTTTAAGGCAAAGGTATAAC
1 CTTCCTTGTCGAGTGCTTACCCAATTCACTAAAAGAATTGATTACCTTTAAGGCAAAGGTATAAC
3161958 CTTACAATCCTTATCTTTTAAAGGCTAAGATAGCAACCTCTTAATCTCTTCAAGAACTATACCCT
66 CTTACAATCCTTATCTTTTAAAGGCTAAGATAGCAACCTCTTAATCTCTTCAAGAACTATACCCT
3162023 AGGTTCCTAAGAGATTAACACTTTTCGGTTGAACACAACCTCAACAAAAACAAAGAATGTTTACA
131 AGGTTCCTAAGAGATTAACACTTTTCGGTTGAACACAACCTCAACAAAAACAAAGAATGTTTACA
3162088 AACGACAATTGCCT
196 AACGACAATTGCCT
3162102 CTTCCTTGTCGAGTGCTTACCCAATTCACTAAAAGAATTGATTACCTTTAAGGCAAAGGTATAAC
1 CTTCCTTGTCGAGTGCTTACCCAATTCACTAAAAGAATTGATTACCTTTAAGGCAAAGGTATAAC
3162167 CTTACAATCCTTATCTTTTAAAGGCTAAGATAGCAACCTCTTAATCTCTTCAAGAACTATACCCT
66 CTTACAATCCTTATCTTTTAAAGGCTAAGATAGCAACCTCTTAATCTCTTCAAGAACTATACCCT
3162232 AGGTTCCTAAGAGATTAACACTTTTCGGTTGAACACAACCTCAACAAAAACAAAGAATGTTTACA
131 AGGTTCCTAAGAGATTAACACTTTTCGGTTGAACACAACCTCAACAAAAACAAAGAATGTTTACA
3162297 AACGACAATTGCCT
196 AACGACAATTGCCT
3162311 CT
1 CT
3162313 AATTAGGCTT
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 211 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.29
Consensus pattern (209 bp):
CTTCCTTGTCGAGTGCTTACCCAATTCACTAAAAGAATTGATTACCTTTAAGGCAAAGGTATAAC
CTTACAATCCTTATCTTTTAAAGGCTAAGATAGCAACCTCTTAATCTCTTCAAGAACTATACCCT
AGGTTCCTAAGAGATTAACACTTTTCGGTTGAACACAACCTCAACAAAAACAAAGAATGTTTACA
AACGACAATTGCCT
Found at i:3162692 original size:13 final size:13
Alignment explanation
Indices: 3162674--3162699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3162664 ACATTTTGGG
3162674 ATGTATCGATACA
1 ATGTATCGATACA
3162687 ATGTATCGATACA
1 ATGTATCGATACA
3162700 TAATATGTGT
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:3162807 original size:20 final size:20
Alignment explanation
Indices: 3162782--3162845 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
3162772 TTCTTTATAA
3162782 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAT
3162802 GTATCGATACA-------AT
1 GTATCGATACATTTGGTCAT
3162815 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAT
3162835 GTATCGATACA
1 GTATCGATACA
3162846 ATGTATCGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 13 0.35
20 24 0.65
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (20 bp):
GTATCGATACATTTGGTCAT
Found at i:3162818 original size:13 final size:12
Alignment explanation
Indices: 3162799--3162857 Score: 63
Period size: 13 Copynumber: 5.1 Consensus size: 12
3162789 TACATTTGGT
3162799 CATGTATCGATA
1 CATGTATCGATA
3162811 CAATGTATCGATA
1 C-ATGTATCGATA
*
3162824 CAT-T-T-GGT-
1 CATGTATCGATA
3162832 CATGTATCGATA
1 CATGTATCGATA
3162844 CAATGTATCGATA
1 C-ATGTATCGATA
3162857 C
1 C
3162858 TGTGCAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 2 0.05
11 3 0.08
12 4 0.10
13 24 0.62
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:3162824 original size:33 final size:33
Alignment explanation
Indices: 3162782--3162857 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
3162772 TTCTTTATAA
3162782 GTATCGATACATTTGGTCATGTATCGATACAAT
1 GTATCGATACATTTGGTCATGTATCGATACAAT
3162815 GTATCGATACATTTGGTCATGTATCGATACAAT
1 GTATCGATACATTTGGTCATGTATCGATACAAT
3162848 GTATCGATAC
1 GTATCGATAC
3162858 TGTGCAATCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (33 bp):
GTATCGATACATTTGGTCATGTATCGATACAAT
Found at i:3162871 original size:33 final size:33
Alignment explanation
Indices: 3162782--3162878 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 33
3162772 TTCTTTATAA
* *
3162782 GTATCGATACATTTGGTCATGTATCGATACAAT
1 GTATCGATACATGTGATCATGTATCGATACAAT
* *
3162815 GTATCGATACATTTGGTCATGTATCGATACAAT
1 GTATCGATACATGTGATCATGTATCGATACAAT
3162848 GTATCGATAC-TGTGCAATC-TGTATCGATACA
1 GTATCGATACATGTG--ATCATGTATCGATACA
3162879 TTTGAAGGTG
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
32 3 0.05
33 55 0.92
34 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (33 bp):
GTATCGATACATGTGATCATGTATCGATACAAT
Found at i:3165340 original size:13 final size:13
Alignment explanation
Indices: 3165322--3165357 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
3165312 ATAAACCCTT
*
3165322 TGTATCGATACAC
1 TGTATCGATACAA
3165335 TGTATCGATACAA
1 TGTATCGATACAA
3165348 TGTATCGATA
1 TGTATCGATA
3165358 TAGAGAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3165575 original size:8 final size:8
Alignment explanation
Indices: 3165562--3165587 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3165552 AACATCATTC
3165562 ATCACAAA
1 ATCACAAA
3165570 ATCACAAA
1 ATCACAAA
3165578 ATCACAAA
1 ATCACAAA
3165586 AT
1 AT
3165588 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:3167676 original size:22 final size:23
Alignment explanation
Indices: 3167637--3167684 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
3167627 TAACAAAGGA
*
3167637 TTGAATAAAACCAGAAATTAT-TT
1 TTGAATAAAACCA-AAAATATGTT
*
3167660 TTGAA-AATACCAAAAATATGTT
1 TTGAATAAAACCAAAAATATGTT
3167682 TTG
1 TTG
3167685 TTCAATCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 11 0.50
23 5 0.23
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.35
Consensus pattern (23 bp):
TTGAATAAAACCAAAAATATGTT
Found at i:3168017 original size:13 final size:13
Alignment explanation
Indices: 3167999--3168024 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3167989 TACACCAAGT
3167999 ATGTATCGATACA
1 ATGTATCGATACA
3168012 ATGTATCGATACA
1 ATGTATCGATACA
3168025 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:3168022 original size:32 final size:33
Alignment explanation
Indices: 3167981--3168044 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3167971 TAGCCAAACT
* **
3167981 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3168013 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3168045 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3170281 original size:21 final size:21
Alignment explanation
Indices: 3170248--3170297 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
3170238 TTGCAAGTTG
*
3170248 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3170270 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
3170291 AAATAAA
1 AAATAAA
3170298 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3172115 original size:15 final size:15
Alignment explanation
Indices: 3172095--3172125 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3172085 TAAAAATGTC
*
3172095 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3172110 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3172125 C
1 C
3172126 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:3174225 original size:13 final size:13
Alignment explanation
Indices: 3174207--3174245 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
3174197 ACATTTTTCT
3174207 TTGTATCGATACA
1 TTGTATCGATACA
3174220 TTGTATCGATACA
1 TTGTATCGATACA
3174233 TTGTATCGATACA
1 TTGTATCGATACA
3174246 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3176101 original size:45 final size:46
Alignment explanation
Indices: 3176037--3176127 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 46
3176027 AAAGGGGGAG
3176037 AGAATAGATGTATGTATGTGCAAATAAA-TTTTTGATATTACCTTA
1 AGAATAGATGTATGTATGTGCAAATAAATTTTTTGATATTACCTTA
3176082 AGAATAGATGTATGTATGTGCAAATAAATTTTTTGATATTACCTTA
1 AGAATAGATGTATGTATGTGCAAATAAATTTTTTGATATTACCTTA
3176128 TTAAGGGGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 28 0.62
46 17 0.38
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (46 bp):
AGAATAGATGTATGTATGTGCAAATAAATTTTTTGATATTACCTTA
Found at i:3176888 original size:13 final size:13
Alignment explanation
Indices: 3176870--3176895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3176860 TACACCAAGT
3176870 ATGTATCGATACA
1 ATGTATCGATACA
3176883 ATGTATCGATACA
1 ATGTATCGATACA
3176896 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:3176888 original size:32 final size:33
Alignment explanation
Indices: 3176852--3176915 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3176842 TATCCAAACT
* **
3176852 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3176884 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3176916 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3184417 original size:70 final size:70
Alignment explanation
Indices: 3184267--3184408 Score: 221
Period size: 70 Copynumber: 2.0 Consensus size: 70
3184257 AGGTTTAACA
* ** * *
3184267 AAAAAGTTTTGTGACTGATCGAGATTGTACGGAGACATTTGAGTGCCTTGGGATGAAACTCGAGA
1 AAAAAGTTTTGTGACTAATCGAGATTGTACGGAGACATCCGAGTACCTTGGGATGAAACCCGAGA
3184332 AAATG
66 AAATG
* *
3184337 AAAAAGTTTTGTGACTAATCGGGATTGTACGGAGACATCCGAGTACCTTGGGATGAAACCCGGGA
1 AAAAAGTTTTGTGACTAATCGAGATTGTACGGAGACATCCGAGTACCTTGGGATGAAACCCGAGA
3184402 AAATG
66 AAATG
3184407 AA
1 AA
3184409 CTAATTTTGA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (70 bp):
AAAAAGTTTTGTGACTAATCGAGATTGTACGGAGACATCCGAGTACCTTGGGATGAAACCCGAGA
AAATG
Found at i:3186465 original size:20 final size:20
Alignment explanation
Indices: 3186403--3186459 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
3186393 AATTTGCCTA
*
3186403 CATGTATCGATATCATTGAAA
1 CATGTATCGATA-CATTGAAT
* *
3186424 AATGTATTGATACATTGAAT
1 CATGTATCGATACATTGAAT
3186444 CATGTATCGATACATT
1 CATGTATCGATACATT
3186460 ATATCAATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 21 0.68
21 10 0.32
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:3187260 original size:52 final size:50
Alignment explanation
Indices: 3187130--3187470 Score: 234
Period size: 52 Copynumber: 6.8 Consensus size: 50
3187120 GGTGATAAAA
* * * * * *
3187130 ATGCCAATATGCTAATTCAGGGCCAGCGATATTGGGCTTAAAGATGCGAAG
1 ATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTT-AAGATGCGAAG
* * * * *
3187181 AATGTCAATGTGCTGATTCACA-ACTAGCAACATTAGACTTGAAGATGAGAAG
1 -ATGCCAATGTGCTGATTCA-AGGCTAGCGACATTGGACTT-AAGATGCGAAG
* * *
3187233 AATGCTAATGTGCTGATTCAAGGCTAGCGACATTGGGCTTAGGAATGGCGAAG
1 -ATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAG-AT-GCGAAG
* * *
3187286 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAG
1 ATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTT-AAGATGCGAAG
* * * * *
3187335 GTGCCAATGTGCTGATTCAAAGCCAGCGATATTGGACTTAAAGATGGCAAAG
1 ATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTT-AAGAT-GCGAAG
* * * * * *
3187387 GTGCTAATATGTTGATTCAAGGCCAGCGATATTGGACTT-A-A----AAG
1 ATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAGATGCGAAG
* * * *
3187431 -TGCCAATATGCTGATTCAAGGATAGCAATATTGGACTTAA
1 ATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAA
3187471 AGGTGCCAAT
Statistics
Matches: 241, Mismatches: 39, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
43 33 0.14
44 4 0.02
49 47 0.20
50 1 0.00
51 3 0.01
52 146 0.61
53 7 0.03
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (50 bp):
ATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAGATGCGAAG
Found at i:3187382 original size:101 final size:100
Alignment explanation
Indices: 3187131--3187472 Score: 322
Period size: 101 Copynumber: 3.4 Consensus size: 100
3187121 GTGATAAAAA
* * * * *
3187131 TGCCAATATGCTAATTCAGGGCCAGCGATATTGGGCTTAAAGAT-GCGAAGAATGTCAATGTGCT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGGCGAAG-ATGCCAATATGCT
* * * * * *
3187195 GATTCACA-ACTAGCAACATTAGACTTGAAGATGAGAAGAA
65 GATTCA-AGGCCAGCGATATTGGACTT-AAGAT--GAAG-G
* * * * * *
3187235 TGCTAATGTGCTGATTCAAGGCTAGCGACATTGGGCTT-AGGAATGGCGAAGATGCCAATATGCT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-ATGGCGAAGATGCCAATATGCT
3187299 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
65 GATTCAAGGCCAGCGATATTGGACTT-AAGATGAAGG
* * * * * *
3187336 TGCCAATGTGCTGATTCAAAGCCAGCGATATTGGACTTAAAGATGGCAAAGGTGCTAATATGTTG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGGCGAAGATGCCAATATGCTG
3187401 ATTCAAGGCCAGCGATATTGGACTT-A-A--AA-G
66 ATTCAAGGCCAGCGATATTGGACTTAAGATGAAGG
** *
3187431 TGCCAATATGCTGATTCAAGGATAGCAATATTGGACTTAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
3187473 GTGCCAATGT
Statistics
Matches: 203, Mismatches: 31, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
95 38 0.19
96 2 0.01
98 1 0.00
99 1 0.00
101 77 0.38
102 6 0.03
103 3 0.01
104 69 0.34
105 6 0.03
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (100 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGGCGAAGATGCCAATATGCTG
ATTCAAGGCCAGCGATATTGGACTTAAGATGAAGG
Found at i:3187507 original size:43 final size:43
Alignment explanation
Indices: 3187383--3187517 Score: 144
Period size: 43 Copynumber: 3.1 Consensus size: 43
3187373 TAAAGATGGC
* * *
3187383 AAAGGTGCTAATATGTTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT
* * ** *
3187426 AAAAGTGCCAATATGCTGATTCAAGGATAGCAATATTGGACTT
1 AAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT
* * * * *
3187469 AAAGGTGCCAATGTGCTAATTTAAGGCCAGTGACATTGGGCTT
1 AAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT
3187512 AGAAGG
1 A-AAGG
3187518 AAATGCCACC
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
43 71 0.95
44 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT
Found at i:3187559 original size:32 final size:31
Alignment explanation
Indices: 3187521--3187766 Score: 305
Period size: 32 Copynumber: 7.7 Consensus size: 31
3187511 TAGAAGGAAA
3187521 TGCCACCAACTTGTGTGGGCTTTCAAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-AAAAGGGT
* *
3187553 TGCCACCAACTTATGTGGGCTTTAAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAAA-AGGGT
*
3187585 TGCCATCAACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTA-AAAGGGT
**
3187617 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAG-GGT
* * *
3187649 TTCCACTAACTTATGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTA-AAAGGGT
**
3187681 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAG-GGT
* *
3187713 TGTCACCAACTTGTGTGGGCTTT-GAAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAG-GGT
*
3187744 TGCAACCAACTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTT
3187767 GAAGAAGGTT
Statistics
Matches: 188, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
31 38 0.20
32 145 0.77
33 5 0.03
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
Found at i:3187605 original size:64 final size:64
Alignment explanation
Indices: 3187521--3187776 Score: 369
Period size: 64 Copynumber: 4.0 Consensus size: 64
3187511 TAGAAGGAAA
* *
3187521 TGCCACCAACTTGTGTGGGCTTTCA-AAAGGGTTGCCACCAACTTATGTGGGC-TTTAAAGAAGG
1 TGCCACCAACTTGTGTGGGCTTT-AGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAG-AGG
3187584 T
64 T
*
3187585 TGCCATCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAGGT
* * *
3187649 TTCCACTAACTTATGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAGGT
* *
3187713 TGTCACCAACTTGTGTGGGCTTT-G-AAGAGGTTGCAACCAACTTGTGTGGGC-TTTGAAGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAGAAAG-GGTTGCCACCAACTTGTGTGGGCTTTTGAAG-AGG
3187775 T
64 T
3187776 T
1 T
3187777 TCTTCAATGA
Statistics
Matches: 176, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
62 10 0.06
63 29 0.16
64 131 0.74
65 6 0.03
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (64 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAGGT
Found at i:3187630 original size:96 final size:95
Alignment explanation
Indices: 3187521--3187776 Score: 338
Period size: 96 Copynumber: 2.7 Consensus size: 95
3187511 TAGAAGGAAA
3187521 TGCCACCAACTTGTGTGGGCTTTCAAAAGGGTTGCCACCAACTTATGTGGGCTTTAAAGAAGGTT
1 TGCCACCAACTTGTGTGGGCTTT-AAAAGGGTTGCCACCAACTTATGTGGGCTTTAAAGAAGGTT
*
3187586 GCCATCAACTTGTGTGGGCTTTAGAA-AGGGT
65 GCCACCAACTTGTGTGGGCTTTAGAAGA-GGT
** * * *
3187617 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGTTTCCACTAACTTATGTGGGCTTTAGAA-AGGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAG-GGTTGCCACCAACTTATGTGGGCTTTA-AAGAAGGT
*
3187681 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGT
64 TGCCACCAACTTGTGTGGGCTTTAGAAGAGGT
* * * * *
3187713 TGTCACCAACTTGTGTGGGCTTT-GAAGAGGTTGCAACCAACTTGTGTGGGCTTTGAAGAAGGTT
1 TGCCACCAACTTGTGTGGGCTTTAAAAG-GGTTGCCACCAACTTATGTGGGCTTTAAAGAAGGTT
3187777 TCTTCAATGA
Statistics
Matches: 142, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
94 2 0.01
95 35 0.25
96 102 0.72
97 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (95 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGGTTGCCACCAACTTATGTGGGCTTTAAAGAAGGTTG
CCACCAACTTGTGTGGGCTTTAGAAGAGGT
Found at i:3188041 original size:27 final size:28
Alignment explanation
Indices: 3188003--3188172 Score: 104
Period size: 27 Copynumber: 5.9 Consensus size: 28
3187993 CTTTGAGAAG
3188003 AAAAAGGTGCCACGA-AGTTGTGGACTT
1 AAAAAGGTGCCACGAGAGTTGTGGACTT
* * *
3188030 AAAAGGGTGCCAC-AGAGTTATGGACTAAAAAA
1 AAAAAGGTGCCACGAGAGTTGTGGACT-----T
*
3188062 AAAAAGGTGCCACG-GAGTTGTGAACTT
1 AAAAAGGTGCCACGAGAGTTGTGGACTT
*
3188089 AAAAAGGTGCCA--ACGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGA-GAGTTGTGGAC-TT
*
3188117 GAAAAGAAAAAGGTGCCA-TAGAGTTGTGGACTT
1 ------AAAAAGGTGCCACGAGAGTTGTGGACTT
3188150 -AAAAGAGTGCCAC-AGAGTTGTGG
1 AAAAAG-GTGCCACGAGAGTTGTGG
3188173 GCTTTGAAAA
Statistics
Matches: 114, Mismatches: 10, Indels: 38
0.70 0.06 0.23
Matches are distributed among these distances:
26 6 0.05
27 59 0.52
28 2 0.02
32 22 0.19
33 2 0.02
34 22 0.19
35 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (28 bp):
AAAAAGGTGCCACGAGAGTTGTGGACTT
Found at i:3188271 original size:97 final size:101
Alignment explanation
Indices: 3188150--3188718 Score: 341
Period size: 98 Copynumber: 5.9 Consensus size: 101
3188140 TTGTGGACTT
* *
3188150 AAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAAGAAAAAGCTACCATAGAGTTGTGGACTT-AA
1 AAAAGAGTGCCACAGAGTTATGGGCTTTGAAAAAGAAAAAGCTACCACAGAGTTGTGGACTTAAA
3188214 AAG-A-GTGCCACGGAGTTGTGGGCTTTGAAAAAGA
66 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAAGA
* * *
3188248 AAAAG-GTGCCACGGAGTTATGGGCTTTGAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAA
1 AAAAGAGTGCCACAGAGTTATGGGCTTTGAAAAAGAAAAAGCTACCACAGAGTTGTGGACTTAAA
* *
3188312 AAGAAAAGGTGCCACGGAGTTGTGGAC-TT---AGAG-
66 AAG--AAGGTGCCACGGAGTTGTGGGCTTTGAAAAAGA
* * * * * * * *
3188345 AAGAGA-TGCCACTGAGTTGTGGGC-TT--AAAAGGAAAAGGTGCCACAAAGTTATGGACTTAAA
1 AAAAGAGTGCCACAGAGTTATGGGCTTTGAAAAAGAAAAAGCTACCACAGAGTTGTGGACTTAAA
* * *
3188406 GGAAAAAGGTGCCACGGAGTTATGGAC-TT-----A-A
66 --AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAAGA
* * * * * * *
3188437 AAAAG-GTACCACAAAGTTGTGGAC-TT-AAAAGGGAAAAAGATGCCAC-GAAGTTGTGGACTTA
1 AAAAGAGTGCCACAGAGTTATGGGCTTTGAAAA-AGAAAAAGCTACCACAG-AGTTGTGGACTTA
* * *
3188498 AAAAGAAAAGGTGCAACGGAGTTGTGGAC-TT--AAAAGG
64 AAAAG--AAGGTGCCACGGAGTTGTGGGCTTTGAAAAAGA
* * * * * * **
3188535 AAAA-ATTGTCACGGAGTTATGGAC-TT-AAAAAG-AAAAGGTGCCATGGAGTTGTGGACTTAAA
1 AAAAGAGTGCCACAGAGTTATGGGCTTTGAAAAAGAAAAAGCTACCACAGAGTTGTGGACTTAAA
* * *
3188596 AGGGAAAAGGGTACCACGGAGTTGTGGAC-TT-AAAAAG-
66 A---AGAA-GGTGCCACGGAGTTGTGGGCTTTGAAAAAGA
* * * * * *
3188633 AAAAG-GTGTCACAGAGTTGTGGAC-TT-AAAAAG-AAAAGGTGCCATAGAGTTGTGGACTTAAA
1 AAAAGAGTGCCACAGAGTTATGGGCTTTGAAAAAGAAAAAGCTACCACAGAGTTGTGGACTTAAA
3188694 AAGAAAAGGTGCCACGGAGTTGTGG
66 AAG--AAGGTGCCACGGAGTTGTGG
3188719 ACTTAAAAGG
Statistics
Matches: 395, Mismatches: 47, Indels: 60
0.79 0.09 0.12
Matches are distributed among these distances:
92 23 0.06
93 3 0.01
94 103 0.26
95 1 0.00
96 47 0.12
97 78 0.20
98 113 0.29
99 6 0.02
101 3 0.01
102 18 0.05
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (101 bp):
AAAAGAGTGCCACAGAGTTATGGGCTTTGAAAAAGAAAAAGCTACCACAGAGTTGTGGACTTAAA
AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAAGA
Found at i:3188575 original size:64 final size:64
Alignment explanation
Indices: 3188036--3188794 Score: 650
Period size: 62 Copynumber: 11.9 Consensus size: 64
3188026 ACTTAAAAGG
* * * * * *
3188036 GTGCCACAGAGTTATGGACTAAAAAAAAAAAGGTGCCACGGAGTTGTGAACTT---A--AAAAG
1 GTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * **
3188095 GTGCCAAC-GAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCATAGAGTTGTGGACTTAAAA-G---
1 GTGCC-ACGGAGTTGTGGAC-TTAAAAAG-AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAA
3188155 -A
63 AA
* * * * **
3188156 GTGCCACAGAGTTGTGGGCTTTGAAAAAGAAAAAGCTACCATAGAGTTGTGGACTTAAAA-G---
1 GTGCCACGGAGTTGTGGAC-TT-AAAAAG-AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAA
3188217 -A
63 AA
* * * *
3188218 GTGCCACGGAGTTGTGGGCTTTGAAAAAGAAAAAGGTGCCACGGAGTTATGGGCTTTGAAAAAGA
1 GTGCCACGGAGTTGTGGAC-TT-AAAAAG-AAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGA
3188283 AAAA
61 AAAA
* * *
3188287 GGTGCCACAGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTT-AGA-G-AAGA
1 -GTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * * ** *
3188349 GATGCCACTGAGTTGTGGGCTTAAAAGGAAAAGGTGCCACAAAGTTATGGACTT-AAAGGAAAAA
1 G-TGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * **
3188413 GGTGCCACGGAGTTATGGACTT---AA-AAAAGGTACCACAAAGTTGTGGACTTAAAAGGGAAAA
1 -GTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAA-GGAAAA
3188474 A
64 A
* *
3188475 GATGCCACGAAGTTGTGGACTTAAAAAGAAAAGGTGCAACGGAGTTGTGGACTTAAAAGGAAAAA
1 G-TGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * * *
3188540 TTGTCACGGAGTTATGGACTTAAAAAGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGGAAAAG
1 GTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAA-GGAAAA-
*
3188605 G
64 A
* * * * *
3188606 GTACCACGGAGTTGTGGACTTAAAAAGAAAAGGTGTCACAGAGTTGTGGACTTAAAAAGAAAAG
1 GTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
** ** *
3188670 GTGCCATAGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGAAG
1 GTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAA-GGAAAAA
* * * *
3188735 GATGCCGCAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCAC-TAGGTTGTGGACTTAAAA
1 G-TGCCACGGAGTTGTGGACTTAAAAAG-AAAAG-GTGCCACGGA-GTTGTGGACTTAAAA
3188795 AAAAAAAGGA
Statistics
Matches: 593, Mismatches: 72, Indels: 61
0.82 0.10 0.08
Matches are distributed among these distances:
59 14 0.02
60 33 0.06
61 48 0.08
62 159 0.27
63 4 0.01
64 131 0.22
65 27 0.05
66 101 0.17
67 28 0.05
68 28 0.05
69 3 0.01
70 17 0.03
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.21
Consensus pattern (64 bp):
GTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
Found at i:3188626 original size:130 final size:131
Alignment explanation
Indices: 3188004--3188824 Score: 759
Period size: 130 Copynumber: 6.5 Consensus size: 131
3187994 TTTGAGAAGA
*
3188004 AAAAGGTGCCAC-GAAGTTGTGGACTT-AAAAG-----GGTGCCACAGAGTTATGGACTAAAAAA
1 AAAAGGTGCCACAG-AGTTGTGGACTTAAAAAGAAAAAGGTGCCACAGAGTTATGGACTTAAAAA
* * * *
3188062 AAAAAGGTGCCACGGAGTTGTGAACTT---A---AAAAGG-TGCCAAC-GAGTTGTGGGCTTTGA
65 GAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGATGCC-ACGGAGTTGTGGAC-TTAA
3188119 AAAG
128 AAAG
* * *
3188123 AAAAAGGTGCCATAGAGTTGTGGACTT-AAAAG----A-GTGCCACAGAGTTGTGGGCTTTGAAA
1 -AAAAGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACAGAGTTATGGAC-TT-AAA
* * ** *
3188182 AAGAAAAAGCTACCATAGAGTTGTGGACTTAAAA--G---A-G-TGCCACGGAGTTGTGGGCTTT
63 AAG-AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGATGCCACGGAGTTGTGGAC-TT
3188240 GAAAAAG
126 -AAAAAG
* * * *
3188247 AAAAAGGTGCCACGGAGTTATGGGCTTTGAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAA
1 -AAAAGGTGCCACAGAGTTGTGGAC-TT-AAAAAGAAAAAGGTGCCACAGAGTTATGGACTTAAA
* * * *
3188312 AAGAAAAGGTGCCACGGAGTTGTGGACTT---AGAGAAGA-GATGCCACTGAGTTGTGGGCTTAA
63 AAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGATGCCACGGAGTTGTGGACTTAA
*
3188373 AAGG
128 AAAG
* * * *
3188377 AAAAGGTGCCACAAAGTTATGGACTT-AAAGGAAAAAGGTGCCACGGAGTTATGGACTT---AA-
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACAGAGTTATGGACTTAAAAAG
* ** * *
3188437 AAAAGGTACCACAAAGTTGTGGACTTAAAAGGGAAAAAGATGCCACGAAGTTGTGGACTTAAAAA
66 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGATGCCACGGAGTTGTGGACTTAAAAA
3188502 G
131 G
* * * * * *
3188503 AAAAGGTGCAACGGAGTTGTGGACTTAAAAGGAAAAA-TTGTCACGGAGTTATGGACTTAAAAAG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACAGAGTTATGGACTTAAAAAG
* * *
3188567 AAAAGGTGCCATGGAGTTGTGGACTTAAAAGGGAAAAGGGTACCACGGAGTTGTGGACTTAAAAA
66 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGATGCCACGGAGTTGTGGACTTAAAAA
3188632 G
131 G
* * *
3188633 AAAAGGTGTCACAGAGTTGTGGACTTAAAAAG-AAAAGGTGCCATAGAGTTGTGGACTTAAAAAG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACAGAGTTATGGACTTAAAAAG
** * * *
3188697 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGAAGGATGCCGCAGAGTTGTGGACTTAAAAG
66 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGATGCCACGGAGTTGTGGACTTAAAAA
3188762 G
131 G
* * *
3188763 AAAAAGAGTGCCACTAG-GTTGTGGACTTAAAAAAAAAAAGGATGCCACTGAGTCATGGACTT
1 -AAAAG-GTGCCAC-AGAGTTGTGGACTTAAAAAGAAAAAGG-TGCCACAGAGTTATGGACTT
3188825 TGGGAAGGGT
Statistics
Matches: 587, Mismatches: 74, Indels: 66
0.81 0.10 0.09
Matches are distributed among these distances:
120 45 0.08
121 2 0.00
122 30 0.05
123 42 0.07
124 27 0.05
125 8 0.01
126 96 0.16
127 15 0.03
128 3 0.01
129 49 0.08
130 177 0.30
131 12 0.02
132 57 0.10
133 8 0.01
134 16 0.03
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.21
Consensus pattern (131 bp):
AAAAGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACAGAGTTATGGACTTAAAAAG
AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGATGCCACGGAGTTGTGGACTTAAAAA
G
Found at i:3188753 original size:34 final size:32
Alignment explanation
Indices: 3188004--3188824 Score: 669
Period size: 32 Copynumber: 25.8 Consensus size: 32
3187994 TTTGAGAAGA
3188004 AAAAGGTGCCAC-GAAGTTGTGGACTT-AAAAG
1 AAAAGGTGCCACAG-AGTTGTGGACTTAAAAAG
* * *
3188035 ----GGTGCCACAGAGTTATGGACTAAAAAAA
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
* *
3188063 AAAAGGTGCCACGGAGTTGTGAACTT----A-
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
* *
3188090 AAAAGGTGCCA-ACGAGTTGTGGGCTTTGAAAAG
1 AAAAGGTGCCACA-GAGTTGTGGAC-TTAAAAAG
*
3188123 AAAAAGGTGCCATAGAGTTGTGGACTT-AAAAG
1 -AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
*
3188155 ---A-GTGCCACAGAGTTGTGGGCTTTGAAAAAG
1 AAAAGGTGCCACAGAGTTGTGGAC-TT-AAAAAG
* * *
3188185 AAAAAGCTACCATAGAGTTGTGGACTT-AAAAG
1 -AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
* *
3188217 ---A-GTGCCACGGAGTTGTGGGCTTTGAAAAAG
1 AAAAGGTGCCACAGAGTTGTGGAC-TT-AAAAAG
* * *
3188247 AAAAAGGTGCCACGGAGTTATGGGCTTTGAAAAAG
1 -AAAAGGTGCCACAGAGTTGTGGAC-TT-AAAAAG
3188282 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
1 -AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
* *
3188315 AAAAGGTGCCACGGAGTTGTGGACTT--AGAG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
* * * * *
3188345 AAGAGATGCCACTGAGTTGTGGGCTTAAAAGG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
* * *
3188377 AAAAGGTGCCACAAAGTTATGGACTT-AAAGG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
* *
3188408 AAAAAGGTGCCACGGAGTTATGGACTT---AA-
1 -AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
* * *
3188437 AAAAGGTACCACAAAGTTGTGGACTTAAAAGGG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAA-AG
*
3188470 AAAAAGATGCCAC-GAAGTTGTGGACTTAAAAAG
1 -AAAAGGTGCCACAG-AGTTGTGGACTTAAAAAG
* * *
3188503 AAAAGGTGCAACGGAGTTGTGGACTTAAAAGG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
** * * *
3188535 AAAAATTGTCACGGAGTTATGGACTTAAAAAG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
** *
3188567 AAAAGGTGCCATGGAGTTGTGGACTTAAAAGGG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAA-AG
* *
3188600 AAAAGGGTACCACGGAGTTGTGGACTTAAAAAG
1 AAAA-GGTGCCACAGAGTTGTGGACTTAAAAAG
*
3188633 AAAAGGTGTCACAGAGTTGTGGACTTAAAAAG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
*
3188665 AAAAGGTGCCATAGAGTTGTGGACTTAAAAAG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
* *
3188697 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAA-AG
** * *
3188730 TGAAGGATGCCGCAGAGTTGTGGACTTAAAAGG
1 AAAAGG-TGCCACAGAGTTGTGGACTTAAAAAG
*
3188763 AAAAAGAGTGCCACTAG-GTTGTGGACTTAAAAAAA
1 -AAAAG-GTGCCAC-AGAGTTGTGGACTT-AAAAAG
* **
3188798 AAAAGGATGCCACTGAGTCATGGACTT
1 AAAAGG-TGCCACAGAGTTGTGGACTT
3188825 TGGGAAGGGT
Statistics
Matches: 648, Mismatches: 90, Indels: 101
0.77 0.11 0.12
Matches are distributed among these distances:
27 69 0.11
28 36 0.06
30 36 0.06
31 6 0.01
32 261 0.40
33 29 0.04
34 138 0.21
35 73 0.11
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.21
Consensus pattern (32 bp):
AAAAGGTGCCACAGAGTTGTGGACTTAAAAAG
Found at i:3190085 original size:15 final size:15
Alignment explanation
Indices: 3190067--3190117 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
3190057 ACTTTTGCAC
3190067 TTTTTGTTTTTGTTT
1 TTTTTGTTTTTGTTT
* * *
3190082 TTTTTATTGTTGTTA
1 TTTTTGTTTTTGTTT
3190097 TTTTTGTTTTTGTTGT
1 TTTTTGTTTTTGTT-T
3190113 TTTTT
1 TTTTT
3190118 TTCTTTCTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.04, C:0.00, G:0.14, T:0.82
Consensus pattern (15 bp):
TTTTTGTTTTTGTTT
Found at i:3190100 original size:18 final size:16
Alignment explanation
Indices: 3190067--3190119 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 16
3190057 ACTTTTGCAC
*
3190067 TTTTTGTTTTTGTTTTT
1 TTTTTGTTGTT-TTTTT
3190084 TTTATTGTTGTTATTTTT
1 TTT-TTGTTGTT-TTTTT
3190102 GTTTTTGTTGTTTTTTT
1 -TTTTTGTTGTTTTTTT
3190119 T
1 T
3190120 CTTTCTTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 1 0.03
17 8 0.25
18 20 0.62
19 3 0.09
ACGTcount: A:0.04, C:0.00, G:0.13, T:0.83
Consensus pattern (16 bp):
TTTTTGTTGTTTTTTT
Found at i:3191191 original size:20 final size:20
Alignment explanation
Indices: 3191168--3191214 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3191158 TGCAGAAGAA
3191168 TCTAGAACACTTTGGAAAGT
1 TCTAGAACACTTTGGAAAGT
*** *
3191188 TCTAGAATGTTTTGGAATGT
1 TCTAGAACACTTTGGAAAGT
3191208 TCTAGAA
1 TCTAGAA
3191215 TATCGTGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (20 bp):
TCTAGAACACTTTGGAAAGT
Found at i:3191215 original size:10 final size:10
Alignment explanation
Indices: 3191186--3191255 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
3191176 ACTTTGGAAA
3191186 GTTCTAGAAT
1 GTTCTAGAAT
* *
3191196 GTTTTGGAAT
1 GTTCTAGAAT
3191206 GTTCTAGAAT
1 GTTCTAGAAT
* * *
3191216 -ATCGTGGAAG
1 GTTC-TAGAAT
*
3191226 GCTCTAGAA-
1 GTTCTAGAAT
3191235 GATTCTAGAAT
1 G-TTCTAGAAT
3191246 GTTCTAGAAT
1 GTTCTAGAAT
3191256 AATGTGGAAG
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
9 3 0.07
10 40 0.87
11 3 0.07
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (10 bp):
GTTCTAGAAT
Found at i:3191215 original size:20 final size:20
Alignment explanation
Indices: 3191178--3191255 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
3191168 TCTAGAACAC
*
3191178 TTTGGAAAGTTCTAGAATGT
1 TTTGGAATGTTCTAGAATGT
*
3191198 TTTGGAATGTTCTAGAATAT
1 TTTGGAATGTTCTAGAATGT
** * *
3191218 CGTGGAAGGCTCTAGAA-GAT
1 TTTGGAATGTTCTAGAATG-T
* *
3191238 TCTAGAATGTTCTAGAAT
1 TTTGGAATGTTCTAGAAT
3191256 AATGTGGAAG
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (20 bp):
TTTGGAATGTTCTAGAATGT
Found at i:3191224 original size:40 final size:40
Alignment explanation
Indices: 3191180--3191270 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
3191170 TAGAACACTT
* * *
3191180 TGGAAAGTTCTAGAATG-TTTTGGAATGTTCTAGAAT-ATCG
1 TGGAAGGTTCTAGAA-GATTCTAGAATGTTCTAGAATAAT-G
*
3191220 TGGAAGGCTCTAGAAGATTCTAGAATGTTCTAGAATAATG
1 TGGAAGGTTCTAGAAGATTCTAGAATGTTCTAGAATAATG
3191260 TGGAAGGTTCT
1 TGGAAGGTTCT
3191271 GGAACTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 1 0.02
40 41 0.93
41 2 0.05
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (40 bp):
TGGAAGGTTCTAGAAGATTCTAGAATGTTCTAGAATAATG
Found at i:3191269 original size:20 final size:20
Alignment explanation
Indices: 3191180--3191270 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
3191170 TAGAACACTT
* ** *
3191180 TGGAAAGTTCTAGAATGTTT
1 TGGAAGGTTCTAGAATAATG
*
3191200 TGGAATGTTCTAGAAT-ATCG
1 TGGAAGGTTCTAGAATAAT-G
* * * *
3191220 TGGAAGGCTCTAGAAGATTC
1 TGGAAGGTTCTAGAATAATG
* *
3191240 TAGAATGTTCTAGAATAATG
1 TGGAAGGTTCTAGAATAATG
3191260 TGGAAGGTTCT
1 TGGAAGGTTCT
3191271 GGAACTTTAT
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
19 1 0.02
20 51 0.96
21 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (20 bp):
TGGAAGGTTCTAGAATAATG
Found at i:3200538 original size:14 final size:14
Alignment explanation
Indices: 3200515--3200547 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3200505 TGCGGGGCCT
3200515 GAATGACCCAAATA
1 GAATGACCCAAATA
*
3200529 GAATGGCCCAAATA
1 GAATGACCCAAATA
3200543 GAATG
1 GAATG
3200548 CATTTTGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (14 bp):
GAATGACCCAAATA
Found at i:3202205 original size:20 final size:20
Alignment explanation
Indices: 3202180--3202252 Score: 105
Period size: 20 Copynumber: 3.6 Consensus size: 20
3202170 TTGTAAAACA
3202180 TATCGATACATTGAATCATG
1 TATCGATACATTGAATCATG
3202200 TATCGATACATTGAATCATG
1 TATCGATACATTGAATCATG
*
3202220 TATCGATACA-T-AAGTTATG
1 TATCGATACATTGAA-TCATG
3202239 TATCGGATACATTG
1 TATC-GATACATTG
3202253 TATTGATACA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
18 2 0.04
19 9 0.19
20 36 0.75
21 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
TATCGATACATTGAATCATG
Found at i:3213239 original size:20 final size:21
Alignment explanation
Indices: 3213214--3213261 Score: 89
Period size: 20 Copynumber: 2.3 Consensus size: 21
3213204 AATATCAAAG
3213214 ATGTTTTAGAGTTAAGTAT-A
1 ATGTTTTAGAGTTAAGTATAA
3213234 ATGTTTTAGAGTTAAGTATAA
1 ATGTTTTAGAGTTAAGTATAA
3213255 ATGTTTT
1 ATGTTTT
3213262 CCAAGCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (21 bp):
ATGTTTTAGAGTTAAGTATAA
Found at i:3213402 original size:20 final size:21
Alignment explanation
Indices: 3213367--3213405 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3213357 AGGTTAAAAC
*
3213367 CCTAGAAAGTATCGATACAGA
1 CCTAGAAAGAATCGATACAGA
3213388 CCTAG-AAGAATCGATACA
1 CCTAGAAAGAATCGATACA
3213406 TATTGCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (21 bp):
CCTAGAAAGAATCGATACAGA
Found at i:3213432 original size:13 final size:13
Alignment explanation
Indices: 3213414--3213438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3213404 CATATTGCTT
3213414 TGTATCGATACAC
1 TGTATCGATACAC
3213427 TGTATCGATACA
1 TGTATCGATACA
3213439 TGATCTTAGT
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:3213456 original size:32 final size:33
Alignment explanation
Indices: 3213397--3213458 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
3213387 ACCTAGAAGA
*
3213397 ATCGATACATATTGCTTTGTATCGATACACTGT
1 ATCGATACATATTGCTTAGTATCGATACACTGT
3213430 ATCGATACATGA-T-CTTAGTATCGATACAC
1 ATCGATACAT-ATTGCTTAGTATCGATACAC
3213459 AGCGAATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 15 0.56
33 11 0.41
34 1 0.04
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (33 bp):
ATCGATACATATTGCTTAGTATCGATACACTGT
Found at i:3215206 original size:13 final size:13
Alignment explanation
Indices: 3215188--3215213 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3215178 TACAACAAGT
3215188 ATGTATCGATACA
1 ATGTATCGATACA
3215201 ATGTATCGATACA
1 ATGTATCGATACA
3215214 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:3219268 original size:15 final size:15
Alignment explanation
Indices: 3219248--3219278 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3219238 TAAAAATGTC
*
3219248 CAAAATGACGAAGCT
1 CAAAATGAAGAAGCT
3219263 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3219278 C
1 C
3219279 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:0.19, G:0.19, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3221362 original size:21 final size:21
Alignment explanation
Indices: 3221333--3221372 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3221323 CATCTGGAAA
3221333 TTCAATGTATCGATACATTTT
1 TTCAATGTATCGATACATTTT
*
3221354 TTCATTGTATCGATACATT
1 TTCAATGTATCGATACATT
3221373 GTATCGATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
TTCAATGTATCGATACATTTT
Found at i:3221374 original size:13 final size:13
Alignment explanation
Indices: 3221356--3221396 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
3221346 TACATTTTTT
3221356 CATTGTATCGATA
1 CATTGTATCGATA
3221369 CATTGTATCGATA
1 CATTGTATCGATA
3221382 CATTGTATCGATA
1 CATTGTATCGATA
3221395 CA
1 CA
3221397 GGGTGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:3225554 original size:21 final size:22
Alignment explanation
Indices: 3225528--3225578 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
3225518 GATGTGCTTA
3225528 AAAAGAAAGAAGA-AGAATTAG
1 AAAAGAAAGAAGACAGAATTAG
* *
3225549 AAAAGAAA-ATGACTGAATTAG
1 AAAAGAAAGAAGACAGAATTAG
3225570 AAAA-AAAGA
1 AAAAGAAAGA
3225579 TAATTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.12
Consensus pattern (22 bp):
AAAAGAAAGAAGACAGAATTAG
Found at i:3225586 original size:21 final size:21
Alignment explanation
Indices: 3225542--3225588 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3225532 GAAAGAAGAA
*
3225542 GAATTAGAAAAGAAAATGACT
1 GAATTAGAAAAGAAAATAACT
*
3225563 GAATTAGAAAA-AAAGATAATT
1 GAATTAGAAAAGAAA-ATAACT
3225584 GAATT
1 GAATT
3225589 GCAAAATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.23
Consensus pattern (21 bp):
GAATTAGAAAAGAAAATAACT
Found at i:3228419 original size:13 final size:13
Alignment explanation
Indices: 3228401--3228425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3228391 ATTACTCAAA
3228401 TGTATCGATACAT
1 TGTATCGATACAT
3228414 TGTATCGATACA
1 TGTATCGATACA
3228426 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3238140 original size:52 final size:52
Alignment explanation
Indices: 3238062--3238179 Score: 200
Period size: 52 Copynumber: 2.3 Consensus size: 52
3238052 CGAAATATGA
* * *
3238062 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
*
3238114 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
3238166 AAATTTGCCTGCAT
1 AAATTTGCCTGCAT
3238180 AAAATGTATC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
Found at i:3238195 original size:37 final size:37
Alignment explanation
Indices: 3238145--3238216 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
3238135 TACATTTTAT
3238145 AATGTATCAATACATCTGGGCAAATTTGCCTGCATAA
1 AATGTATCAATACATCTGGGCAAATTTGCCTGCATAA
*
3238182 AATGTATCGATACATCTGGGCAAATTTGCCTGCAT
1 AATGTATCAATACATCTGGGCAAATTTGCCTGCAT
3238217 GTATCGATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (37 bp):
AATGTATCAATACATCTGGGCAAATTTGCCTGCATAA
Found at i:3238224 original size:32 final size:33
Alignment explanation
Indices: 3238145--3238227 Score: 114
Period size: 37 Copynumber: 2.4 Consensus size: 33
3238135 TACATTTTAT
*
3238145 AATGTATCAATACATCTGGGCAAATTTGCCTGC
1 AATGTATCGATACATCTGGGCAAATTTGCCTGC
3238178 ATAAAATGTATCGATACATCTGGGCAAATTTGCCTGC
1 ----AATGTATCGATACATCTGGGCAAATTTGCCTGC
3238215 -ATGTATCGATACA
1 AATGTATCGATACA
3238228 AAGATCAGTG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
32 13 0.29
37 32 0.71
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (33 bp):
AATGTATCGATACATCTGGGCAAATTTGCCTGC
Found at i:3238254 original size:13 final size:13
Alignment explanation
Indices: 3238236--3238260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3238226 CAAAGATCAG
3238236 TGTATCGATACAA
1 TGTATCGATACAA
3238249 TGTATCGATACA
1 TGTATCGATACA
3238261 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3238338 original size:33 final size:33
Alignment explanation
Indices: 3238301--3238367 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3238291 CGTAGCTTAA
3238301 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3238334 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3238367 A
1 A
3238368 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3238341 original size:13 final size:13
Alignment explanation
Indices: 3238323--3238347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3238313 CAAAAAAATA
3238323 TGTATCGATACAT
1 TGTATCGATACAT
3238336 TGTATCGATACA
1 TGTATCGATACA
3238348 ACACTTTATG
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:3239096 original size:55 final size:53
Alignment explanation
Indices: 3239013--3239385 Score: 215
Period size: 55 Copynumber: 6.8 Consensus size: 53
3239003 GAAGAGCGAT
* * * *
3239013 AAAAGGA--CCAATACGTTGATTCACGGCCAACGATATTGGGTTGAAAGATGAG
1 AAAAGGATGCCAATATGCTGATTCAAGGCCAACTATATTGGGTT-AAAGATGAG
* * * * **
3239065 AAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAG
1 -AAAAGGATGCCAATATGCTGATTCAAGGCCAACTATATTG-GGTTAAAGATGAG
* * *
3239120 AAAA--ATGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATG
1 AAAAGGATGCCAATATGCTGATTCAAGGCCAACTATATTGGG--TTAAAGATGA-G
* * * *
3239174 --AAGG-TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTGAAAAATGAAGATGAG
1 AAAAGGATGCCAATATGCTGATTCAAGGCCAACTATATTGG---G----TTAAAGATGAG
* * * *
3239231 AAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAG
1 AAAAG-GAT---G--CC-AATATGCTGATTCAAGGCCAACTATATTGGG-TTAAAGATGAG
* ** * * * **
3239292 AAAAATGATGTTAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G
1 -AAAAGGATGCCAATATGCTGATTCAAGGCCAACTATATTG-GGTTAAAGATGAG
3239346 AAAAGG-TGCCAATATGCTGATTCAAGGCCAACTATATTGG
1 AAAAGGATGCCAATATGCTGATTCAAGGCCAACTATATTGG
3239386 ACTTAAAGGT
Statistics
Matches: 247, Mismatches: 48, Indels: 52
0.71 0.14 0.15
Matches are distributed among these distances:
52 61 0.25
53 53 0.21
54 6 0.02
55 64 0.26
56 3 0.01
57 1 0.00
58 9 0.04
59 3 0.01
60 1 0.00
61 13 0.05
62 4 0.02
64 2 0.01
66 1 0.00
67 26 0.11
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (53 bp):
AAAAGGATGCCAATATGCTGATTCAAGGCCAACTATATTGGGTTAAAGATGAG
Found at i:3239190 original size:53 final size:53
Alignment explanation
Indices: 3239056--3239212 Score: 174
Period size: 53 Copynumber: 2.9 Consensus size: 53
3239046 TATTGGGTTG
* *
3239056 AAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATT-GAACTT
1 AAAGATGAG-AAAA--ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAACTT
* ***
3239111 AAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTT
1 AAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAACTT
** * *
3239164 AAAGATGATG-AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGA
1 AAAGATGA-GAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGA
3239213 CTGAAAAATG
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
52 30 0.34
53 44 0.50
54 5 0.06
55 9 0.10
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (53 bp):
AAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAACTT
Found at i:3239408 original size:43 final size:43
Alignment explanation
Indices: 3239347--3239436 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
3239337 TAAAGATGGA
*
3239347 AAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACTACATTGGACTT
* *
3239390 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACTACATTGGACTT
3239433 AAAG
1 AAAG
3239437 AAGAAGAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAACTACATTGGACTT
Found at i:3239604 original size:49 final size:49
Alignment explanation
Indices: 3239539--3239661 Score: 201
Period size: 49 Copynumber: 2.5 Consensus size: 49
3239529 ATATGCGGCT
* * *
3239539 AGCGATATTGGGCTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
*
3239588 AGCGACATTGGACTTAAAGATGAAGTTGCCAATGTGCTGAGTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
*
3239637 AGCGACATTGGACTTGAAGATGAAG
1 AGCGACATTGGACTTAAAGATGAAG
3239662 ATGAGAAAAG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (49 bp):
AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
Found at i:3239676 original size:218 final size:220
Alignment explanation
Indices: 3238948--3239867 Score: 1009
Period size: 227 Copynumber: 4.2 Consensus size: 220
3238938 GACTTGCAGT
* * * * * * * * * * *
3238948 GTGCCACTGTGCAGATTCAAGGCCTGCCACACTAGACTTAAATGATGACGAGGATGAAGAGCGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTGAA-GATGAAGATGA-GAAAAGTGAT
3239013 AAA-AGGACCAATACGTTGATTCACGGCCAACGATATTGGG-TTGAAAGATGAGAAAAAGGATGT
64 AAAGAGG-CCAATACGTTGATTCACGGCCAACGATATTGGGCTT-AAAGATGAGAAAAAGGATGT
* **
3239076 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAGAAAAATGCCAATGTGCTGATT
127 AAATGTGCTGATTC-AGGCCAGCTACATTGAACTTAAAGATG-GAAAGGTGCCAATGTGCTGATT
**
3239141 CAAGGCCAACAACATTGGGTTTTAAAGATGATGAA
190 CAAGGCCAACAACATT-GGACTT-AA-A-GATGAA
* * *
3239176 GGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGAC-TGAAAAATGAAGATGAGAAAAGTGAT
1 -GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTG-AAGATGAAGATGAGAAAAGTGAT
* * * *
3239240 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAATGATGTTA
64 AAAGAGGCCAATACGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTAA
*
3239305 ATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCA
129 ATGTGCTGATTC-AGGCCAGCTACATTGAACTTAAAGATGG-AAAGGTGCCAATGTGCTGATTCA
* *
3239370 AGGCCAACTATATTGGACTT-AA-A-G--
192 AGGCCAACAACATTGGACTTAAAGATGAA
* * * * *
3239394 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGAGGATGAAGAGTGATA
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTGAAGATGAAGATGA-GAAAAGTGATA
*
3239459 AA-AGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGA--TAA
65 AAGAGG-CCAATACGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTAA
* * * * * * **
3239521 AAGAGTCAAT-ATGC-GGCTAGCGATATTGGGCTTAAAGAT-G-AAGGTGCCAATGTGCTGATTC
129 ATGTG-C--TGATTCAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATGTGCTGATTC
* *
3239582 AAGGCCAGCGACATTGGACTTAAAGATGAA
191 AAGGCCAACAACATTGGACTTAAAGATGAA
* *
3239612 GTTGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGACTTGAAGATGAAGATGAGAAAAGTGATA
1 G-TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTGAAGATGAAGATGAGAAAAGTGATA
* * *
3239677 AAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAA
65 AAGAGGCCAATACGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTAAA
* *
3239742 TGTGCTGATTCAAGGCCA-CTACATTGAACTTAAAGATGGAATAGGTGCCGATATGCTGATTCAA
130 TGTGCTGATTC-AGGCCAGCTACATTGAACTTAAAGATGGAA-AGGTGCCAATGTGCTGATTCAA
* * *
3239806 GGCCAGCTATATTGGACTT-AA-A-G--
193 GGCCAACAACATTGGACTTAAAGATGAA
* *
3239829 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTT
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTT
3239868 AAAGGTGAGG
Statistics
Matches: 591, Mismatches: 75, Indels: 63
0.81 0.10 0.09
Matches are distributed among these distances:
213 38 0.06
214 2 0.00
215 2 0.00
216 61 0.10
217 49 0.08
218 133 0.23
219 67 0.11
220 12 0.02
221 4 0.01
222 37 0.06
223 1 0.00
224 1 0.00
226 5 0.01
227 135 0.23
228 13 0.02
229 31 0.05
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (220 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTGAAGATGAAGATGAGAAAAGTGATAA
AGAGGCCAATACGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTAAAT
GTGCTGATTCAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATGTGCTGATTCAAGGC
CAACAACATTGGACTTAAAGATGAA
Found at i:3239952 original size:49 final size:49
Alignment explanation
Indices: 3239739--3240434 Score: 901
Period size: 49 Copynumber: 14.7 Consensus size: 49
3239729 AAAAGGATGT
*
3239739 CAATGTGCTGATTCAAGGCCA-CTACATTGAACTTAAAGATGGAATAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-A-AGGTGC
* * *
3239790 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3239833 CAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGGTG-AGGTG-
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
3239880 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3239929 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3239978 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3240021 CAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3240069 TAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3240118 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3240167 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3240210 CAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
3240258 TAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
3240307 CAATATGCTGATTCAGGGCCAGCAATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
3240350 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
3240399 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
3240435 GAAGGGATGC
Statistics
Matches: 566, Mismatches: 50, Indels: 60
0.84 0.07 0.09
Matches are distributed among these distances:
43 153 0.27
44 1 0.00
45 3 0.01
47 41 0.07
48 100 0.18
49 238 0.42
51 19 0.03
52 11 0.02
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:3240103 original size:140 final size:139
Alignment explanation
Indices: 3239730--3240439 Score: 806
Period size: 140 Copynumber: 5.0 Consensus size: 139
3239720 AAGATGAGAA
* * *
3239730 AAAGGATGTCAATGTGCTGATTCAAGGCCA-CTACATTGAACTTAAAGATGGAATAGGTGCCGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG-T-G---AGGTGCCAAT
* *
3239794 ATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCC
60 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
*
3239853 AGCTACATTAGACTT
125 AGCTACATTGGACTT
*
3239868 AAAGGTGAGGTGCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAAT
1 AAAGGT---G-CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG-TG-AGGTGCCAAT
* *
3239933 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
60 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
*
3239998 AGCTATATTGGACTT
125 AGCTACATTGGACTT
* *
3240013 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGGTGAGGTGCTAATGTGCT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-GTGAGGTGCCAATGTGCT
* *
3240078 GATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTA
65 GATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTA
3240143 CATTGGACTTAAAGAT
130 CATTGGAC-T-----T
* *
3240159 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA---AGGTGCCAATGTGCTG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTGAGGTGCCAATGTGCTG
* * * *
3240220 ATTCAAGGCCAGCTACATTAGACTTAAAGGT-GAGGTGCTAATGTGCTGATTCAAGGCCAGCTAC
66 ATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
*
3240284 ATTGGATTT
131 ATTGGACTT
* * * *
3240293 AAAGATGAAGGTGCCAATATGCTGATTCAGGGCCAGCAATATTGGACTT-AA---AGGTGCCAAT
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTGAGGTGCCAAT
*
3240354 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGCTGATTCAAGGC
60 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATGTGCTGATTCAAGGC
* *
3240418 CAGCTATATTGGGCTT
124 CAGCTACATTGGACTT
3240434 AGAAGG
1 A-AAGG
3240440 GATGCCACCG
Statistics
Matches: 508, Mismatches: 38, Indels: 54
0.85 0.06 0.09
Matches are distributed among these distances:
134 1 0.00
136 5 0.01
137 2 0.00
138 6 0.01
139 36 0.07
140 206 0.41
141 142 0.28
142 20 0.04
145 49 0.10
146 41 0.08
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (139 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTGAGGTGCCAATGTGCTG
ATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
ATTGGACTT
Found at i:3240165 original size:189 final size:189
Alignment explanation
Indices: 3239739--3240423 Score: 1125
Period size: 189 Copynumber: 3.6 Consensus size: 189
3239729 AAAAGGATGT
* * *
3239739 CAATGTGCTGATTCAAGGCCA-CTACATTGAACTTAAAGATGGAATAGGTGCCGATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT--AA-AGGTGCCAATATGCTGATT
3239803 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTT
63 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTT
3239868 AAAGGTGAGGTGC-AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
128 AAAGGTGAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
3239929 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
3239994 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAA
66 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAA
3240059 GGTGAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
131 GGTGAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
3240118 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
3240183 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAA
66 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAA
*
3240248 GGTGAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGATGAAGGTGC
131 GGTGAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * * *
3240307 CAATATGCTGATTCAGGGCCAGCAATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* *
3240366 GGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
66 GGCCAGCTATATTGGACTT-----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTA
3240424 TATTGGGCTT
Statistics
Matches: 475, Mismatches: 12, Indels: 17
0.94 0.02 0.03
Matches are distributed among these distances:
183 42 0.09
188 98 0.21
189 297 0.63
190 20 0.04
191 18 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (189 bp):
CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAA
GGTGAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:3240479 original size:33 final size:32
Alignment explanation
Indices: 3240427--3240658 Score: 326
Period size: 33 Copynumber: 7.2 Consensus size: 32
3240417 CCAGCTATAT
*
3240427 TGGGC-TTAGA-AGGGATGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* * *
3240457 TAGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
3240490 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* *
3240522 TGGGCTTTAGAAGAAGGTTGCCACCGACTTATG
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTG
* * *
3240555 TGGGCTTTGAAAGAAGGTTGCCACCAACTTGTG
1 TGGGCTTT-AGAGAGGGTTGCCACCGACTTGTG
3240588 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
3240620 TGGGCTTT-GAGAGGGTTGCCATCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
3240651 TGGGCTTT
1 TGGGCTTT
3240659 GAAAAGAAAA
Statistics
Matches: 181, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
30 4 0.02
31 35 0.19
32 57 0.31
33 84 0.46
34 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (32 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Found at i:3240518 original size:65 final size:64
Alignment explanation
Indices: 3240427--3240658 Score: 335
Period size: 65 Copynumber: 3.6 Consensus size: 64
3240417 CCAGCTATAT
* * *
3240427 TGGGC-TTAGA-AGGGATGCCACCGACTTGTGTAGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCGACTTGTG
*
3240490 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCGACTTATG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAG-AGAAGGTTGCCACCGACTTGTG
* * * *
3240555 TGGGCTTTGAAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTT-AGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTG
*
3240620 TGGGCTTT-GAGAGGGTTGCCATCGACTTGTGTGGGCTTT
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTT
3240659 GAAAAGAAAA
Statistics
Matches: 152, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
63 32 0.21
64 5 0.03
65 80 0.53
66 35 0.23
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (64 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTG
Found at i:3240611 original size:98 final size:98
Alignment explanation
Indices: 3240427--3240662 Score: 367
Period size: 98 Copynumber: 2.4 Consensus size: 98
3240417 CCAGCTATAT
* * *
3240427 TGGGC-TTAGAAG-GGATGCCACCGACTTGTGTAGGCTTT-AGAGAATGGTTGCCACCAACTTGT
1 TGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGAATGGTTGCCACCAACTTGT
3240489 GTGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
66 GTGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
3240522 TGGGCTTTAGAAGAAGGTTGCCACCGACTTATGTGGGCTTTGAAAGAA-GGTTGCCACCAACTTG
1 TGGGCTTTAGAAG-AGGTTGCCACCGACTTGTGTGGGCTTTGAAAGAATGGTTGCCACCAACTTG
3240586 TGTGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
65 TGTGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
3240620 TGGGCTTT-G-AGAGGGTTGCCATCGACTTGTGTGGGCTTTGAAA
1 TGGGCTTTAGAAGA-GGTTGCCACCGACTTGTGTGGGCTTTGAAA
3240663 AGAAAAAGGT
Statistics
Matches: 130, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
95 6 0.05
96 37 0.28
97 1 0.01
98 81 0.62
99 5 0.04
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (98 bp):
TGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGAATGGTTGCCACCAACTTGT
GTGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Found at i:3240692 original size:34 final size:34
Alignment explanation
Indices: 3240649--3241182 Score: 643
Period size: 34 Copynumber: 15.5 Consensus size: 34
3240639 CATCGACTTG
3240649 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
* *
3240683 TGTGGGCTTTAAAAAGAAAAATGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
* *
3240717 TGTGGGCTTTGAAAGGAACAAGGTGCCAC-GAGGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGA-GT
** * * *
3240751 CATGGAC-TTAAAAAG-AAAAGGTGCCACAGAGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
* *
3240783 GGTGGGCTTT-AAAAAAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
*
3240816 TGTGGGCTTTGAAAAGGGAAAATGAGTGCCACGGAGT
1 TGTGGGCTTTGAAAA--GAAAAAG-GTGCCACGGAGT
*
3240853 TGTGGGCTTT-AGAAAGAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTGA-AAAGAAAAAGGTGCCACGGAGT
*
3240887 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGAAGT
1 TGTGGGCTTTGAAAA--GAAAAAG-GTGCCACGGAGT
*
3240924 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
*
3240958 TGTGGGCTTTTAAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGC-TTT-GAAAAGAAAAAGGTGCCACGGAGT
* * *
3240994 TGTGGGCTTTGAAAGGAACAAGGTGCCACGGGGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
* * *
3241028 CGTGGAC-TTAAAAAG-AAAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
* *
3241060 GGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
3241094 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGAAAA--GAAAAAG-GTGCCACGGAGT
*
3241131 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCATGGAGT
1 TGTGGGCTTTGAAAA-GAAAAAG-GTGCCACGGAGT
*
3241166 TGTGGGCTTTGGAAAGA
1 TGTGGGCTTTGAAAAGA
3241183 GATGCCACTG
Statistics
Matches: 437, Mismatches: 42, Indels: 41
0.84 0.08 0.08
Matches are distributed among these distances:
32 41 0.09
33 51 0.12
34 165 0.38
35 51 0.12
36 57 0.13
37 72 0.16
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (34 bp):
TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
Found at i:3240886 original size:71 final size:70
Alignment explanation
Indices: 3240649--3241181 Score: 639
Period size: 71 Copynumber: 7.7 Consensus size: 70
3240639 CATCGACTTG
* *
3240649 TGTGGGCTTT-GAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAAAAATGTGCCA
1 TGTGGGCTTTAG-AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGGTGCCA
3240711 CGGAGT
65 CGGAGT
* ** * *
3240717 TGTGGGCTTT-GAAAGGAACAAGGTGCCAC-GAGGTCATGGAC-TT-AAAA-AG-AAAAGGTGCC
1 TGTGGGCTTTAGAAA-GAAAAAGGTGCCACGGA-GTTGTGGGCTTTGAAAAGGGAAAAAGGTGCC
*
3240776 ACAGAGT
64 ACGGAGT
* * *
3240783 GGTGGGCTTTA-AAAAAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAATGAGTGCCA
1 TGTGGGCTTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAG-GTGCCA
3240847 CGGAGT
65 CGGAGT
*
3240853 TGTGGGCTTTAGAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAG-GTGCCA
*
3240918 CGAAGT
65 CGGAGT
* * **
3240924 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTTAAAAAAGAAAAAGGTGCCAC
1 TGTGGGCTTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGGTGCCAC
3240989 GGAGT
66 GGAGT
* * * * *
3240994 TGTGGGCTTT-GAAAGGAACAAGGTGCCACGGGGTCGTGGAC-TT-AAAA-AG-AAAAGGTGCCA
1 TGTGGGCTTTAGAAA-GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGGTGCCA
3241054 CGGAGT
65 CGGAGT
* *
3241060 GGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAG-GTGCCA
3241125 CGGAGT
65 CGGAGT
* *
3241131 TGTGGGCTTTA-AAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTTGGAAAG
1 TGTGGGCTTTAGAAA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAG
3241182 AGATGCCACT
Statistics
Matches: 405, Mismatches: 41, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
65 18 0.04
66 79 0.20
67 24 0.06
68 39 0.10
69 10 0.02
70 72 0.18
71 137 0.34
72 26 0.06
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (70 bp):
TGTGGGCTTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGGTGCCAC
GGAGT
Found at i:3241056 original size:207 final size:209
Alignment explanation
Indices: 3240649--3241175 Score: 718
Period size: 207 Copynumber: 2.6 Consensus size: 209
3240639 CATCGACTTG
* *
3240649 TGTGGGCTTT-GAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAAAAA-TGTGCC
1 TGTGGGCTTTAG-AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCC
* * ** *
3240710 ACGGAGTTGTGGGCTTTGAAAGGAACAAGGTGCCAC-GAGGTCATGGAC--TTAAAAAGAAAAGG
65 ACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGA-GTTGTGGGCTTTTAAAAAGAAAAGG
* * *
3240772 TGCCACAGAGTGGTGGGCTTTAAAAAAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAA
129 TGCCACAGAGTGGTGGGCTTTAAAAAAAAAAGGTGCCACGGAGTCGTGGACTTTGAAAAGAGAAA
3240837 ATGAGTGCCACGGAGT
194 ATGAGTGCCACGGAGT
*
3240853 TGTGGGCTTTAGAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
* *
3240918 CGAAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTTAAAAAAGAAAAAGG
66 CGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTT-AAAAAG-AAAAGG
* * ** * *
3240983 TGCCACGGAGTTGTGGGCTTTGAAAGGAACAAGGTGCCACGGGGTCGTGGAC-TT-AAAA-AGAA
129 TGCCACAGAGTGGTGGGCTTT-AAAAAAAAAAGGTGCCACGGAGTCGTGGACTTTGAAAAGAGAA
3241045 AA-G-GTGCCACGGAGT
193 AATGAGTGCCACGGAGT
* *
3241060 GGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
*
3241125 CGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTT
66 CGGAGTTGTGGGCTTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTT
3241176 GGAAAGAGAT
Statistics
Matches: 287, Mismatches: 25, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
204 41 0.14
205 5 0.02
206 6 0.02
207 143 0.50
208 24 0.08
209 7 0.02
210 10 0.03
211 27 0.09
212 24 0.08
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (209 bp):
TGTGGGCTTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
CGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTTAAAAAGAAAAGGTG
CCACAGAGTGGTGGGCTTTAAAAAAAAAAGGTGCCACGGAGTCGTGGACTTTGAAAAGAGAAAAT
GAGTGCCACGGAGT
Done.