Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 9 of 143
Found at i:2622749 original size:8 final size:9
Alignment explanation
Indices: 2622736--2623045 Score: 90
Period size: 8 Copynumber: 36.3 Consensus size: 9
2622726 ATATATGTTC
2622736 TAATTAT-T
1 TAATTATAT
2622744 TAATTATAT
1 TAATTATAT
* *
2622753 TAAAGTA-AA
1 T-AATTATAT
2622762 TAATTATAT
1 TAATTATAT
2622771 TGAATTAAATATT
1 T-AATT--ATA-T
2622784 TAATTAT-T
1 TAATTATAT
2622792 TAATTATAT
1 TAATTATAT
** * *
2622801 TAAAGAGAA
1 TAATTATAT
2622810 TAATTATAT
1 TAATTATAT
2622819 TAAATTAAATATT
1 T-AATT--ATA-T
2622832 TAATTAT-T
1 TAATTATAT
2622840 TAATTATAT
1 TAATTATAT
* *
2622849 TAAAGTA-AA
1 T-AATTATAT
2622858 TAATTATAT
1 TAATTATAT
2622867 TAAGTTA-A-
1 TAA-TTATAT
*
2622875 -AA-GAT-T
1 TAATTATAT
2622881 TAATTAT-T
1 TAATTATAT
2622889 TAATTATAT
1 TAATTATAT
* *
2622898 TAAAGTA-AA
1 T-AATTATAT
2622907 TAATTATAT
1 TAATTATAT
2622916 TAAGTTA-A-
1 TAA-TTATAT
*
2622924 -AA-GAT-T
1 TAATTATAT
2622930 TAATTAT-T
1 TAATTATAT
*
2622938 TAATTATGT
1 TAATTATAT
* *
2622947 TAAAGTA-AA
1 T-AATTATAT
2622956 TAATTATAT
1 TAATTATAT
2622965 TAATT-TA-
1 TAATTATAT
*
2622972 -AA-GAT-T
1 TAATTATAT
2622978 TAATTAT-T
1 TAATTATAT
2622986 TAATTATAT
1 TAATTATAT
* *
2622995 TAAGTA-AA
1 TAATTATAT
2623003 TAATTATAT
1 TAATTATAT
2623012 TAAGTTA-A-
1 TAA-TTATAT
*
2623020 -AA-GAT-T
1 TAATTATAT
2623026 TAATTAT-T
1 TAATTATAT
2623034 TAATTATAT
1 TAATTATAT
2623043 TAA
1 TAA
2623046 AGTAAATAAT
Statistics
Matches: 222, Mismatches: 37, Indels: 85
0.65 0.11 0.25
Matches are distributed among these distances:
5 3 0.01
6 3 0.01
7 14 0.06
8 87 0.39
9 60 0.27
10 37 0.17
12 14 0.06
13 4 0.02
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (9 bp):
TAATTATAT
Found at i:2622901 original size:49 final size:49
Alignment explanation
Indices: 2622736--2623185 Score: 736
Period size: 49 Copynumber: 9.3 Consensus size: 49
2622726 ATATATGTTC
*
2622736 TAATTATTTAATTATATTAAAGTAAATAATTATATTGAA-TT-AAATATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATT-AAGTTAAAAGATT
* *
2622784 TAATTATTTAATTATATTAAAG-AGAATAATTATATTAAATT-AAATATT
1 TAATTATTTAATTATATTAAAGTA-AATAATTATATTAAGTTAAAAGATT
2622832 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
2622881 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
* *
2622930 TAATTATTTAATTATGTTAAAGTAAATAATTATATTAA-TTTAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
2622978 TAATTATTTAATTATATT-AAGTAAATAATTATATTAAGTTAAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
*
2623026 TAATTATTTAATTATATTAAAGTAAATAATTATATGAAAG-T-AAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATAT-TAAGTTAAAAGATT
* *
2623074 TAATTACTAAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
*
2623123 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAATATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
2623172 TAATTATTTAATTA
1 TAATTATTTAATTA
2623186 ATAAAAACAG
Statistics
Matches: 380, Mismatches: 13, Indels: 17
0.93 0.03 0.04
Matches are distributed among these distances:
47 25 0.07
48 175 0.46
49 177 0.47
50 3 0.01
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (49 bp):
TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
Found at i:2623114 original size:242 final size:242
Alignment explanation
Indices: 2622736--2623185 Score: 789
Period size: 242 Copynumber: 1.9 Consensus size: 242
2622726 ATATATGTTC
*
2622736 TAATTATTTAATTATATTAAAGTAAATAATTATATTGAATTAAATATTTAATTATTTAATTATAT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTGAATTAAAGATTTAATTATTTAATTATAT
* * * * *
2622801 TAAAGAGAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTATA
66 TAAAGAGAATAATTATATGAAAGTAAAGATTTAATTACTAAATTATATTAAAGTAAATAATTATA
2622866 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
131 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
2622931 AATTATTTAATTATGTTAAAGTAAATAATTATATTAATTTAAAGATT
196 AATTATTTAATTATGTTAAAGTAAATAATTATATTAATTTAAAGATT
2622978 TAATTATTTAATTATATT-AAGTAAATAATTATATT-AAGTTAAAAGATTTAATTATTTAATTAT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTGAA-TT-AAAGATTTAATTATTTAATTAT
2623041 ATTAAAGTA-AATAATTATATGAAAGTAAAGATTTAATTACTAAATTATATTAAAGTAAATAATT
64 ATTAAAG-AGAATAATTATATGAAAGTAAAGATTTAATTACTAAATTATATTAAAGTAAATAATT
*
2623105 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAATA
128 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGA
2623170 TTTAATTATTTAATTA
193 TTTAATTATTTAATTA
2623186 ATAAAAACAG
Statistics
Matches: 198, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
240 2 0.01
241 19 0.10
242 176 0.89
243 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (242 bp):
TAATTATTTAATTATATTAAAGTAAATAATTATATTGAATTAAAGATTTAATTATTTAATTATAT
TAAAGAGAATAATTATATGAAAGTAAAGATTTAATTACTAAATTATATTAAAGTAAATAATTATA
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
AATTATTTAATTATGTTAAAGTAAATAATTATATTAATTTAAAGATT
Found at i:2628811 original size:66 final size:66
Alignment explanation
Indices: 2628705--2628861 Score: 217
Period size: 66 Copynumber: 2.4 Consensus size: 66
2628695 CAAATTGCTC
*
2628705 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
2628769 AA
65 AA
* ** *
2628771 AACTTAAAGAGGAGGTTGCATTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
2628836 C
66 A
* * *
2628837 AACTTAAAGTGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAACGAG
2628862 GCAAGCGGAG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 1 0.01
66 78 0.99
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:2628873 original size:21 final size:21
Alignment explanation
Indices: 2628847--2628889 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2628837 AACTTAAAGT
2628847 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
*
2628868 GGAGGCAGCAGCTAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
2628889 G
1 G
2628890 AAGAAAGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.47, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGGCAAGC
Found at i:2628898 original size:21 final size:21
Alignment explanation
Indices: 2628853--2628899 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2628843 AAGTGGAGGC
* **
2628853 AGCAGCGAGGCAAGCGGAGGC
1 AGCAGCGAGGCAAGCGAAGAA
*
2628874 AGCAGCTAGGCAAGCGAAGAA
1 AGCAGCGAGGCAAGCGAAGAA
2628895 AGCAG
1 AGCAG
2628900 AGGCTACAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.40, T:0.02
Consensus pattern (21 bp):
AGCAGCGAGGCAAGCGAAGAA
Found at i:2629273 original size:43 final size:43
Alignment explanation
Indices: 2629215--2629381 Score: 307
Period size: 43 Copynumber: 3.9 Consensus size: 43
2629205 GCGCTTTATC
* *
2629215 AAAAGCGCCGTTAAAGAACATGGCCTTCAGCGGCACTTGTGGA
1 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
2629258 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
1 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
2629301 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
1 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
*
2629344 AAATGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTT
1 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTT
2629382 TTTCCATAAA
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 121 1.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
Found at i:2629396 original size:86 final size:85
Alignment explanation
Indices: 2629201--2629399 Score: 301
Period size: 86 Copynumber: 2.3 Consensus size: 85
2629191 CTGTTATATT
*
2629201 AGCGGCGCTTTATCAAAAGCGCCGTTAAAGAACATGGCCTTCAGCGGCACTTGTGGAAAAAGCGC
1 AGCGGCGCTTTATCAAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCACTTGTGGAAAAAGCGC
2629266 CGCTAAAGAACATGGCCTTC
66 CGCTAAAGAACATGGCCTTC
*** * *
2629286 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGAAAATGCG
1 AGCGGCGCTT-TATCAAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCACTTGTGGAAAAAGCG
2629351 CCGCTAAAGAACATGGCCTTC
65 CCGCTAAAGAACATGGCCTTC
*
2629372 AGCGGCGCTTTTTCCATAAA-CGCCGCTA
1 AGCGGCGCTTTAT-CA-AAAGCGCCGCTA
2629400 TTTTTTGCGG
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
85 11 0.11
86 88 0.86
87 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (85 bp):
AGCGGCGCTTTATCAAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCACTTGTGGAAAAAGCGC
CGCTAAAGAACATGGCCTTC
Found at i:2629569 original size:16 final size:16
Alignment explanation
Indices: 2629548--2629582 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2629538 TATATGTGTT
2629548 TATATATGTATATATA
1 TATATATGTATATATA
*
2629564 TATATATGTATGTATA
1 TATATATGTATATATA
2629580 TAT
1 TAT
2629583 TTGTTTACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (16 bp):
TATATATGTATATATA
Found at i:2632834 original size:8 final size:9
Alignment explanation
Indices: 2632801--2632834 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2632791 TAAAAAAATT
*
2632801 TATTTAGAA
1 TATTTAAAA
2632810 TATTTAAAA
1 TATTTAAAA
2632819 TATTTAAAA
1 TATTTAAAA
2632828 T-TTTAAA
1 TATTTAAA
2632835 TTAGTAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
TATTTAAAA
Found at i:2632900 original size:29 final size:31
Alignment explanation
Indices: 2632846--2632910 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
2632836 TAGTAAAGAT
*
2632846 AAAATTATATTTTGATTTCTTTAAAATGATA
1 AAAATTATATTTTAATTTCTTTAAAATGATA
*
2632877 AAAATTA-A-TTTAATTT-TTTAAAAATTATA
1 AAAATTATATTTTAATTTCTTT-AAAATGATA
2632906 AAAAT
1 AAAAT
2632911 ATAAACTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 3 0.10
29 20 0.65
30 1 0.03
31 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (31 bp):
AAAATTATATTTTAATTTCTTTAAAATGATA
Found at i:2649044 original size:1 final size:1
Alignment explanation
Indices: 2649038--2649067 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2649028 TAGAAAATAC
2649038 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2649068 GGAGAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2650036 original size:15 final size:16
Alignment explanation
Indices: 2650005--2650040 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2649995 AATACTCATA
*
2650005 TTAATCGAATTAAAAT
1 TTAATCGAATAAAAAT
2650021 TTAATCG-ATAAAAAT
1 TTAATCGAATAAAAAT
2650036 TTAAT
1 TTAAT
2650041 ATAATTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TTAATCGAATAAAAAT
Found at i:2650887 original size:115 final size:115
Alignment explanation
Indices: 2650740--2650970 Score: 462
Period size: 115 Copynumber: 2.0 Consensus size: 115
2650730 TTGCGAAACA
2650740 TCTAGCATCATGCGAGTTTGGTATGCAAGCTAAATCCTGCGAACCATGCAAAATTCAGCCTAGAC
1 TCTAGCATCATGCGAGTTTGGTATGCAAGCTAAATCCTGCGAACCATGCAAAATTCAGCCTAGAC
2650805 CCATGGGTCTACTCGGGTTGTCGGTCGGTAATAGTAAGTATCATAACAAG
66 CCATGGGTCTACTCGGGTTGTCGGTCGGTAATAGTAAGTATCATAACAAG
2650855 TCTAGCATCATGCGAGTTTGGTATGCAAGCTAAATCCTGCGAACCATGCAAAATTCAGCCTAGAC
1 TCTAGCATCATGCGAGTTTGGTATGCAAGCTAAATCCTGCGAACCATGCAAAATTCAGCCTAGAC
2650920 CCATGGGTCTACTCGGGTTGTCGGTCGGTAATAGTAAGTATCATAACAAG
66 CCATGGGTCTACTCGGGTTGTCGGTCGGTAATAGTAAGTATCATAACAAG
2650970 T
1 T
2650971 TGTTATTATC
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (115 bp):
TCTAGCATCATGCGAGTTTGGTATGCAAGCTAAATCCTGCGAACCATGCAAAATTCAGCCTAGAC
CCATGGGTCTACTCGGGTTGTCGGTCGGTAATAGTAAGTATCATAACAAG
Found at i:2651859 original size:30 final size:30
Alignment explanation
Indices: 2651825--2651889 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
2651815 ACTTATTTTA
*
2651825 TTGTTAATTTTGTCATTATTTTAGAGGCAT
1 TTGTTAATTTTGTCATTATTTTAGAGACAT
*
2651855 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTCATTATTTTAGAGACAT
2651885 TTGTT
1 TTGTT
2651890 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTCATTATTTTAGAGACAT
Found at i:2656004 original size:23 final size:23
Alignment explanation
Indices: 2655978--2656035 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
2655968 TACTATTTTG
2655978 TTGTTATTATTTGGA-TATTAATT
1 TTGTTATTATTT-GATTATTAATT
* *
2656001 TTGTTACTATTTTATTATTAATT
1 TTGTTATTATTTGATTATTAATT
*
2656024 TTGCTATTATTT
1 TTGTTATTATTT
2656036 TAAAGGCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.64
Consensus pattern (23 bp):
TTGTTATTATTTGATTATTAATT
Found at i:2656031 original size:12 final size:11
Alignment explanation
Indices: 2655947--2656036 Score: 56
Period size: 12 Copynumber: 7.6 Consensus size: 11
2655937 TGTTTAATTG
2655947 TTATTTTGTTAA
1 TTATTTTGTT-A
*
2655959 TTATATTGCTACTA
1 TTATTTTG-T--TA
2655973 TT-TTGTTGTTA
1 TTATT-TTGTTA
* *
2655984 TTATTTGGATA
1 TTATTTTGTTA
2655995 TTAATTTTGTTA
1 TT-ATTTTGTTA
* *
2656007 CTATTTTATTA
1 TTATTTTGTTA
*
2656018 TTAATTTTGCTA
1 TT-ATTTTGTTA
2656030 TTATTTT
1 TTATTTT
2656037 AAAGGCATTT
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
11 24 0.40
12 26 0.43
13 3 0.05
14 6 0.10
15 1 0.02
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.63
Consensus pattern (11 bp):
TTATTTTGTTA
Found at i:2658693 original size:8 final size:8
Alignment explanation
Indices: 2658675--2658724 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
2658665 TTACATAAAA
2658675 AAAATTTAT
1 AAAA-TTAT
2658684 AAAATTAT
1 AAAATTAT
2658692 AAAGA-TAT
1 AAA-ATTAT
2658700 -AAATTATT
1 AAAATTA-T
*
2658708 AAAATAAT
1 AAAATTAT
2658716 AAAATTAT
1 AAAATTAT
2658724 A
1 A
2658725 TTTTAATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
6 1 0.03
7 4 0.11
8 20 0.57
9 10 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (8 bp):
AAAATTAT
Found at i:2661057 original size:12 final size:12
Alignment explanation
Indices: 2661042--2661083 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
2661032 CTGAAAGGGA
2661042 AGAAGAAAAAAG
1 AGAAGAAAAAAG
2661054 AGAAG--AAAA-
1 AGAAGAAAAAAG
*
2661063 TGAAGAAAAAAG
1 AGAAGAAAAAAG
2661075 AGAAGAAAA
1 AGAAGAAAA
2661084 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 4 0.16
10 4 0.16
11 4 0.16
12 13 0.52
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (12 bp):
AGAAGAAAAAAG
Found at i:2661090 original size:12 final size:11
Alignment explanation
Indices: 2661041--2661097 Score: 61
Period size: 10 Copynumber: 5.5 Consensus size: 11
2661031 GCTGAAAGGG
2661041 AAGAAGAA-AA
1 AAGAAGAAGAA
2661051 AAG-AGAAGAA
1 AAGAAGAAGAA
2661061 AATGAAGAA-AA
1 AA-GAAGAAGAA
2661072 AAG-AGAAGAA
1 AAGAAGAAGAA
2661082 AATGAAGAA-AA
1 AA-GAAGAAGAA
2661093 AAGAA
1 AAGAA
2661098 AAAATGATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 8 0.20
10 15 0.37
11 10 0.24
12 8 0.20
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.04
Consensus pattern (11 bp):
AAGAAGAAGAA
Found at i:2661107 original size:21 final size:21
Alignment explanation
Indices: 2661043--2661096 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2661033 TGAAAGGGAA
2661043 GAAGAAAAAAGAGAAGAAAAT
1 GAAGAAAAAAGAGAAGAAAAT
2661064 GAAGAAAAAAGAGAAGAAAAT
1 GAAGAAAAAAGAGAAGAAAAT
2661085 GAAGAAAAAAGA
1 GAAGAAAAAAGA
2661097 AAAAATGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (21 bp):
GAAGAAAAAAGAGAAGAAAAT
Found at i:2669869 original size:16 final size:17
Alignment explanation
Indices: 2669848--2669880 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2669838 AATGTTAGAG
2669848 CATATA-AATTTAAAAC
1 CATATATAATTTAAAAC
*
2669864 CATATATATTTTAAAAC
1 CATATATAATTTAAAAC
2669881 TTTAAAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (17 bp):
CATATATAATTTAAAAC
Found at i:2706140 original size:20 final size:21
Alignment explanation
Indices: 2706108--2706146 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2706098 AAAAGTATAA
2706108 AATATATTTAAAA-TAATTTT
1 AATATATTTAAAATTAATTTT
2706128 AATAT-TTTAAAAATTAATT
1 AATATATTT-AAAATTAATT
2706147 AAATGCTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 9 0.53
21 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATATTTAAAATTAATTTT
Found at i:2723770 original size:2 final size:2
Alignment explanation
Indices: 2723763--2723800 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2723753 ATTAAATTTT
2723763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2723801 ATTACATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2727407 original size:5 final size:6
Alignment explanation
Indices: 2727390--2727416 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2727380 GGAGGGACAT
2727390 GAGGGG GAGGGG GAGGGG GAGGGG GAG
1 GAGGGG GAGGGG GAGGGG GAGGGG GAG
2727417 AGAAGGATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (6 bp):
GAGGGG
Found at i:2727751 original size:2 final size:2
Alignment explanation
Indices: 2727744--2727773 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2727734 TACTTTTTAC
2727744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2727774 TATTTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2730959 original size:24 final size:24
Alignment explanation
Indices: 2730927--2730981 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
2730917 AACAGGTACT
* *
2730927 GGTGCTACTGATGCTATTACAACA
1 GGTGTTACTGATGCTACTACAACA
2730951 GGTGTTACTGATGCTACTACAACA
1 GGTGTTACTGATGCTACTACAACA
2730975 GGTGTTA
1 GGTGTTA
2730982 GTGCTAGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (24 bp):
GGTGTTACTGATGCTACTACAACA
Found at i:2733047 original size:29 final size:30
Alignment explanation
Indices: 2733000--2733063 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
2732990 ACGTGTGGTA
* *
2733000 CCTAAATTGCAGAATTTTTAT-TTTGGGTG
1 CCTAAAATGCAGAATTTTTATAGTTGGGTG
2733029 CCTAAAATG-AGAATTTTTTATAGTTGGGTG
1 CCTAAAATGCAGAA-TTTTTATAGTTGGGTG
*
2733059 ACTAA
1 CCTAA
2733064 CTGTGTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 15 0.50
30 11 0.37
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (30 bp):
CCTAAAATGCAGAATTTTTATAGTTGGGTG
Found at i:2739641 original size:2 final size:2
Alignment explanation
Indices: 2739634--2739667 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2739624 GTGGCTATGC
*
2739634 CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2739668 ATATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2739672 original size:2 final size:2
Alignment explanation
Indices: 2739667--2739699 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2739657 TCTCTCTCTC
2739667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2739700 CTCAGAGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2742466 original size:8 final size:8
Alignment explanation
Indices: 2742453--2742478 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2742443 ACGTCTCAAC
2742453 TTATGAAT
1 TTATGAAT
2742461 TTATGAAT
1 TTATGAAT
2742469 TTATGAAT
1 TTATGAAT
2742477 TT
1 TT
2742479 TTCTCATACT
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:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (8 bp):
TTATGAAT
Found at i:2743814 original size:80 final size:80
Alignment explanation
Indices: 2743681--2743841 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
2743671 ACCAATTTAA
*
2743681 CGGTCTCACTATTGTACAAAGACTAAATCACTTTCCCACTAAACTTTCCCCTTAAAAGCTGAATT
1 CGGTCTCACTATTGTACAAAGACTAAATCACTTTCCCACTAAACTTCCCCCTTAAAAGCTGAATT
2743746 GTAAAGATTTATTTT
66 GTAAAGATTTATTTT
2743761 CGGTCTCACTATTGTACAAAGACTAAATCACTTTCCCACTAAACTTCCCCCTTAAAAGCTGAATT
1 CGGTCTCACTATTGTACAAAGACTAAATCACTTTCCCACTAAACTTCCCCCTTAAAAGCTGAATT
2743826 GTAAAGATTTATTTT
66 GTAAAGATTTATTTT
2743841 C
1 C
2743842 AAGATCAAGT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (80 bp):
CGGTCTCACTATTGTACAAAGACTAAATCACTTTCCCACTAAACTTCCCCCTTAAAAGCTGAATT
GTAAAGATTTATTTT
Found at i:2748199 original size:30 final size:29
Alignment explanation
Indices: 2748165--2748230 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
2748155 ATGATTTGTG
*
2748165 AAAATTGAATTAAATCAAAATTTCATGAAT
1 AAAATTGAATAAAATCAAAA-TTCATGAAT
* ** *
2748195 AAAATCGTGTAAAATCAAAATTCATGTAT
1 AAAATTGAATAAAATCAAAATTCATGAAT
*
2748224 AACATTG
1 AAAATTG
2748231 CACTTTGAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (29 bp):
AAAATTGAATAAAATCAAAATTCATGAAT
Found at i:2750168 original size:20 final size:20
Alignment explanation
Indices: 2750139--2750178 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2750129 TGAGGTATTA
*
2750139 GTGCTTGTAAATTATTCGAG
1 GTGCTCGTAAATTATTCGAG
2750159 GTGCTCGTAAATTATTCGAG
1 GTGCTCGTAAATTATTCGAG
2750179 TTTAAGTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (20 bp):
GTGCTCGTAAATTATTCGAG
Found at i:2762461 original size:11 final size:11
Alignment explanation
Indices: 2762445--2762473 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2762435 ATATATATTC
2762445 AAAAATTATAA
1 AAAAATTATAA
2762456 AAAAA-TATAA
1 AAAAATTATAA
2762466 AAAAATTA
1 AAAAATTA
2762474 ATACGGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:2772436 original size:24 final size:24
Alignment explanation
Indices: 2772378--2772437 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2772368 ACTAATAATT
*
2772378 GTTTAACTCAAACAAATAAACAAA
1 GTTTAACTGAAACAAATAAACAAA
* * * *
2772402 GTTTAATTGAAACAATTAAATAGA
1 GTTTAACTGAAACAAATAAACAAA
2772426 GTTTAACTGAAA
1 GTTTAACTGAAA
2772438 TATTATTTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (24 bp):
GTTTAACTGAAACAAATAAACAAA
Found at i:2796684 original size:17 final size:17
Alignment explanation
Indices: 2796627--2796708 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
2796617 TTATATATAC
*
2796627 TATTTATATTATTAAAT
1 TATTTATATTATTGAAT
* * *
2796644 TAAAATTTATATTTTTGTAC
1 T---ATTTATATTATTGAAT
2796664 TATTTATATTATTGAAT
1 TATTTATATTATTGAAT
*
2796681 TATTTA-ATCATATT-AAA
1 TATTTATAT--TATTGAAT
2796698 TATTTATATTA
1 TATTTATATTA
2796709 AAATTGAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
16 4 0.08
17 28 0.55
18 6 0.12
20 13 0.25
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTGAAT
Found at i:2796796 original size:6 final size:6
Alignment explanation
Indices: 2796787--2796854 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
2796777 TTTTAATTTT
*
2796787 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
2796835 CTTTGA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
2796855 AAAAATTAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 8 0.15
6 39 0.74
8 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:2796808 original size:17 final size:16
Alignment explanation
Indices: 2796778--2796851 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
2796768 AAATTGATTT
*
2796778 TTTAATTTTATTTAAA
1 TTTAAATTTATTTAAA
2796794 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
2796811 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
2796825 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTTAAA
2796842 TTTAAATTTA
1 TTTAAATTTA
2796852 AATAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.22
15 2 0.04
16 11 0.22
17 27 0.53
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:2796831 original size:31 final size:31
Alignment explanation
Indices: 2796793--2796852 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2796783 TTTTATTTAA
*
2796793 ATTTAAATTTATTTTAAATTTAAATTTAATT
1 ATTTAAATTTACTTTAAATTTAAATTTAATT
*
2796824 ATTTAAATTTACTTTGAATTTAAATTTAA
1 ATTTAAATTTACTTTAAATTTAAATTTAA
2796853 ATAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTTAAATTTACTTTAAATTTAAATTTAATT
Found at i:2797571 original size:3 final size:3
Alignment explanation
Indices: 2797563--2797596 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2797553 TGAAAGACAT
2797563 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2797597 GAAAAAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2798710 original size:166 final size:159
Alignment explanation
Indices: 2798396--2798743 Score: 468
Period size: 166 Copynumber: 2.1 Consensus size: 159
2798386 TTCTGATTGC
* *
2798396 TTTACAATTTAGTCCTTTGACTGTTTGACTGCACCAGAGGTCGCCACGTGTCTTTTTGGATTATT
1 TTTACAAATTAGTCCTTTGACTGTTTGACAGCACCAGAGGTCGCCACGTGTCTTTTTGGATTATT
* *
2798461 ATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAAT
66 ATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTCATTTAAT
** * *
2798526 TACGAAATTAGTCCAAGAATTTTCCATGG
131 TACGAAATTACCCCAAGAATTTTCCAAGA
* *
2798555 TTTATAAATTAGTCCTTTGACTGTTTGACAGCACCAG-GGGCTGCCACGTGTCATTTTTTTGGAT
1 TTTACAAATTAGTCCTTTGACTGTTTGACAGCACCAGAGGTC-GCCACGTGTC---TTTTTGGAT
2798619 TATTTATGCATTTAGTCCTTTTTTATTTTAATATATTT-TTTTAATTTAATCCCCAAATCAA-TT
62 TA-TTATGCATTTAGTCC-TTTTTATTTT--TA-ATTTGTTTTAATTTAATCCCCAAATCAACTT
*
2798682 TGCATTTAATTACGAAATTACCCCAAGAATTTTTCAAGA
122 T-CATTTAATTACGAAATTACCCCAAGAATTTTCCAAGA
* *
2798721 TTTACAACTTAATCCTTTGACTG
1 TTTACAAATTAGTCCTTTGACTG
2798744 CTGGATGCCT
Statistics
Matches: 165, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
158 3 0.02
159 44 0.27
162 11 0.07
163 15 0.09
164 10 0.06
165 3 0.02
166 75 0.45
167 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (159 bp):
TTTACAAATTAGTCCTTTGACTGTTTGACAGCACCAGAGGTCGCCACGTGTCTTTTTGGATTATT
ATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTCATTTAAT
TACGAAATTACCCCAAGAATTTTCCAAGA
Found at i:2798886 original size:30 final size:30
Alignment explanation
Indices: 2798823--2799041 Score: 268
Period size: 30 Copynumber: 7.4 Consensus size: 30
2798813 CAGAAATTCT
* *
2798823 ATTTTGACCCTAAAACTTTTCC-AAATTAT
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
2798852 ATTTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
* *
2798882 ATTTTAACCCCAAAACTTTTCCAAAATCAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
* * *
2798912 ATTTTAACCCCATAACTTTTCCAAAATTAT
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
*
2798942 ATTTTG-CCCCTAAAACTTTTCCAAAATTAT
1 ATTTTGACCCC-AAAACTTTTCCAAAATTAC
* *
2798972 ATTTTGACCTCAAAACTTTTCCAAAATCAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
**
2799002 ATTTTGACCCTGAAAC-TTT-CAAAATTTACC
1 ATTTTGACCCCAAAACTTTTCCAAAA-TTA-C
2799032 ATTTT-ACCCC
1 ATTTTGACCCC
2799042 CGAAACTTCT
Statistics
Matches: 168, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
28 5 0.03
29 34 0.20
30 126 0.75
31 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (30 bp):
ATTTTGACCCCAAAACTTTTCCAAAATTAC
Found at i:2799019 original size:90 final size:90
Alignment explanation
Indices: 2798823--2799027 Score: 310
Period size: 90 Copynumber: 2.3 Consensus size: 90
2798813 CAGAAATTCT
2798823 ATTTTGACCCTAAAACTTTTCC-AAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
1 ATTTTGACCCTAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
2798887 AACCCCAAAACTTTTCCAAAATCAC
66 AACCCCAAAACTTTTCCAAAATCAC
* * * *
2798912 ATTTTAACCCCATAACTTTTCCAAAATTATATTTTG-CCCCTAAAACTTTTCCAAAATTATATTT
1 ATTTTGACCCTAAAACTTTTCCAAAATTATATTTTGACCCC-AAAACTTTTCCAAAATTACATTT
* *
2798976 TGACCTCAAAACTTTTCCAAAATCAC
65 TAACCCCAAAACTTTTCCAAAATCAC
*
2799002 ATTTTGACCCTGAAAC-TTT-CAAAATT
1 ATTTTGACCCTAAAACTTTTCCAAAATT
2799028 TACCATTTTA
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
88 7 0.07
89 26 0.25
90 71 0.68
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (90 bp):
ATTTTGACCCTAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
AACCCCAAAACTTTTCCAAAATCAC
Found at i:2799047 original size:30 final size:28
Alignment explanation
Indices: 2798859--2799123 Score: 80
Period size: 30 Copynumber: 8.9 Consensus size: 28
2798849 TATATTTTGA
* * *
2798859 CCCCAAAACTTTTCCAAAATTACATTTTAA
1 CCCCGAAACTTT--CAAAATTCCATTTTAC
* *
2798889 CCCCAAAACTTTTCCAAAA-TCACATTTTAA
1 CCCCGAAAC-TTT-CAAAATTC-CATTTTAC
** *
2798919 CCCC-ATAACTTTTCCAAAATTATATTTTGC
1 CCCCGA-AAC-TTT-CAAAATTCCATTTTAC
** **
2798949 CCCTAAAACTTTTCCAAAATTATATTTTGA-
1 CCCCGAAAC-TTT-CAAAATTCCATTTT-AC
* *
2798979 CCTCAAAACTTTTCCAAAA-TCACATTTTGA-
1 CCCCGAAAC-TTT-CAAAATTC-CATTTT-AC
*
2799009 CCCTGAAACTTTCAAAATTTACCATTTTAC
1 CCCCGAAACTTTCAAAA-TT-CCATTTTAC
*
2799039 CCCCGAAAC-TTCTAAAATTCCATTTTTAA
1 CCCCGAAACTTTC-AAAATTCCA-TTTTAC
2799068 CCCCG--A-TTTCACCGAAAATTACCATTTTAC
1 CCCCGAAACTTT---C-AAAATT-CCATTTTAC
* * *
2799098 CCTCGAATCTTTTAAAATTCCATTTT
1 CCCCGAAACTTTCAAAATTCCATTTT
2799124 TAAACTCGAT
Statistics
Matches: 193, Mismatches: 21, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.02
28 15 0.08
29 28 0.15
30 135 0.70
31 9 0.05
33 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (28 bp):
CCCCGAAACTTTCAAAATTCCATTTTAC
Found at i:2799048 original size:90 final size:89
Alignment explanation
Indices: 2798823--2799071 Score: 299
Period size: 90 Copynumber: 2.8 Consensus size: 89
2798813 CAGAAATTCT
*
2798823 ATTTTGACCCTAAAACTTTTCCAAATTATATTTTGA-CCCCAAAACTTTTCCAAAATTACATTTT
1 ATTTTGACCCTAAAACTTTTCAAAATTATATTTT-ACCCCCAAAACTTTTCCAAAATTACATTTT
2798887 AACCCCAAAACTTTTCCAAAATCAC
65 AACCCCAAAACTTTTCCAAAATCAC
* * * * * *
2798912 ATTTTAACCCCATAACTTTTCCAAAATTATATTTTGCCCCTAAAACTTTTCCAAAATTATATTTT
1 ATTTTGACCCTAAAACTTTT-CAAAATTATATTTTACCCCCAAAACTTTTCCAAAATTACATTTT
* *
2798977 GACCTCAAAACTTTTCCAAAATCAC
65 AACCCCAAAACTTTTCCAAAATCAC
* * * * *
2799002 ATTTTGACCCTGAAAC-TTTCAAAATTTACCATTTTACCCCCGAAAC--TTCTAAAATTCCATTT
1 ATTTTGACCCTAAAACTTTTCAAAA-TTA-TATTTTACCCCCAAAACTTTTCCAAAATTACA-TT
2799064 TTAACCCC
63 TTAACCCC
2799072 GATTTCACCG
Statistics
Matches: 133, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
88 15 0.11
89 31 0.23
90 87 0.65
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (89 bp):
ATTTTGACCCTAAAACTTTTCAAAATTATATTTTACCCCCAAAACTTTTCCAAAATTACATTTTA
ACCCCAAAACTTTTCCAAAATCAC
Found at i:2799066 original size:29 final size:29
Alignment explanation
Indices: 2799033--2799243 Score: 144
Period size: 29 Copynumber: 7.2 Consensus size: 29
2799023 AAATTTACCA
*
2799033 TTTTACCCCCGAAACTTCTAAAATTCCAT
1 TTTTACCCCCGAATCTTCTAAAATTCCAT
* * ** *
2799062 TTTTAACCCCGATTTCACCGAAAATTACCA-
1 TTTTACCCCCGA-ATCTTCTAAAATT-CCAT
* *
2799092 TTTTACCCTCGAATCTTTTAAAATTCCAT
1 TTTTACCCCCGAATCTTCTAAAATTCCAT
** * * * *
2799121 TTTTAAACTCGATTTCATCGAAAATTACCAT
1 TTTTACCCCCGA-ATCTTCTAAAATT-CCAT
* *
2799152 TTTT-CCCTCGAAGCTTCTAAAATTCCAT
1 TTTTACCCCCGAATCTTCTAAAATTCCAT
* *
2799180 TTTTAACCCCG-AT-TTCACTGAAATTTACCA-
1 TTTTACCCCCGAATCTT--CT-AAAATT-CCAT
*
2799210 TTTTACCCCCGAATCTTTTAAAATTCCAT
1 TTTTACCCCCGAATCTTCTAAAATTCCAT
2799239 TTTTA
1 TTTTA
2799244 ACCCTGATTA
Statistics
Matches: 137, Mismatches: 32, Indels: 26
0.70 0.16 0.13
Matches are distributed among these distances:
27 2 0.01
28 15 0.11
29 54 0.39
30 48 0.35
31 16 0.12
32 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTTACCCCCGAATCTTCTAAAATTCCAT
Found at i:2799097 original size:59 final size:59
Alignment explanation
Indices: 2799022--2799277 Score: 352
Period size: 59 Copynumber: 4.3 Consensus size: 59
2799012 TGAAACTTTC
*
2799022 AAAATTTACCATTTTACCCCCGAAACTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAA-TTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * * *
2799082 AAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAAACTCGATTTCATCG
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * *
2799141 AAAATTACCATTTTTCCCTCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACTG
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * *
2799200 AAATTTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTACACC-
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* *
2799258 AAAATTGCCATTTTGCCCCC
1 AAAATTACCATTTTACCCCC
2799278 CCCGGTATCC
Statistics
Matches: 172, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
58 17 0.10
59 151 0.88
60 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.37
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:2811368 original size:69 final size:69
Alignment explanation
Indices: 2811236--2811994 Score: 1328
Period size: 69 Copynumber: 11.0 Consensus size: 69
2811226 CTGCAAGTCT
* * *
2811236 CAACGTCATCCCCTCGAAATTGAAG-AGGAG-TGGATATCAAG-CCTCATCTCTGAAATTGAAGT
1 CAACGTCATCCTCTTGAAATTGAAGTA-GAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGT
2811298 AAGAG
65 AAGAG
2811303 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811368 AGAG
66 AGAG
2811372 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811437 AGAG
66 AGAG
*
2811441 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGCCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811506 AGAG
66 AGAG
2811510 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811575 AGAG
66 AGAG
2811579 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811644 AGAG
66 AGAG
*
2811648 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811713 AGAG
66 AGAG
* *
2811717 CAACGTCATCCTCCTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811782 AGAG
66 AGAG
* *
2811786 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGAATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811851 AGAG
66 AGAG
* *
2811855 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811920 AGAG
66 AGAG
* * * * * *
2811924 CAACGTCATCCCCTCGAAATTGAAATAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
2811988 AGAG
66 AGAG
2811992 CAA
1 CAA
2811995 GATCATTTCC
Statistics
Matches: 672, Mismatches: 17, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
67 26 0.04
68 51 0.08
69 595 0.89
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (69 bp):
CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTCATCTCTGAAATTGAAGTA
AGAG
Found at i:2812357 original size:6 final size:6
Alignment explanation
Indices: 2812348--2812415 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
2812338 TTTTAATTTT
*
2812348 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
2812396 CTTTGA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
2812416 AAAAATTAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 8 0.15
6 39 0.74
8 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:2812369 original size:17 final size:16
Alignment explanation
Indices: 2812339--2812412 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
2812329 AAATTGATTT
*
2812339 TTTAATTTTATTTAAA
1 TTTAAATTTATTTAAA
2812355 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
2812372 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
2812386 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTTAAA
2812403 TTTAAATTTA
1 TTTAAATTTA
2812413 AATAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.22
15 2 0.04
16 11 0.22
17 27 0.53
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:2812392 original size:31 final size:31
Alignment explanation
Indices: 2812354--2812413 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2812344 TTTTATTTAA
*
2812354 ATTTAAATTTATTTTAAATTTAAATTTAATT
1 ATTTAAATTTACTTTAAATTTAAATTTAATT
*
2812385 ATTTAAATTTACTTTGAATTTAAATTTAA
1 ATTTAAATTTACTTTAAATTTAAATTTAA
2812414 ATAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTTAAATTTACTTTAAATTTAAATTTAATT
Found at i:2813130 original size:3 final size:3
Alignment explanation
Indices: 2813122--2813158 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2813112 TGAAAGACAT
2813122 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2813159 GAAAAAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2813899 original size:30 final size:33
Alignment explanation
Indices: 2813863--2813926 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2813853 CTTAATGGTC
*
2813863 TATTTGCGT-AA-TTGGTCC-TTCCGCATTTTT
1 TATTTGCGTAAATTTAGTCCTTTCCGCATTTTT
* *
2813893 TATTTGCTTAAATTTAGTCCTTTCTGCATTTTT
1 TATTTGCGTAAATTTAGTCCTTTCCGCATTTTT
2813926 T
1 T
2813927 TAATTCTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 8 0.29
31 2 0.07
32 6 0.21
33 12 0.43
ACGTcount: A:0.16, C:0.17, G:0.12, T:0.55
Consensus pattern (33 bp):
TATTTGCGTAAATTTAGTCCTTTCCGCATTTTT
Found at i:2814153 original size:162 final size:161
Alignment explanation
Indices: 2813963--2814308 Score: 523
Period size: 162 Copynumber: 2.1 Consensus size: 161
2813953 TTCTGATTGC
* * * *
2813963 TTTACAATTTAGTCCTTTGACTGTTTGACTGCACCAGGGGCCGCCACGTGTCTTTTTTTGGATTA
1 TTTACAAATTAGTCCTTTGACTGTTTGACAGCACCAGGGGCCACCACGTGTCATTTTTTGGATTA
* * *
2814028 TTTATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTT-TATT
66 TTTATGCATTTAGTCCTTTTTATTTTTAATAT-ATTTAATTTAATCCCCAAATCAA-TTTGCATT
** * *
2814092 TAATTACGAAATTAGTCCAAGAATTTTCCATGG
129 TAATTACGAAATTACCCCAAGAATTTTCCAAGA
* *
2814125 TTTATAAATTAGTCCTTTGACTGTTTGACAGCACCAGGGGCTACCACGTGTCATTTTTTGGATTA
1 TTTACAAATTAGTCCTTTGACTGTTTGACAGCACCAGGGGCCACCACGTGTCATTTTTTGGATTA
2814190 TTTATGCATTTAGTCCTTTTTATTTTTAATATATTTAATTTAATCCCCAAATCAATTTGCATTTA
66 TTTATGCATTTAGTCCTTTTTATTTTTAATATATTTAATTTAATCCCCAAATCAATTTGCATTTA
*
2814255 ATTACGAAATTACCCCAAGAATTTTTCAAGA
131 ATTACGAAATTACCCCAAGAATTTTCCAAGA
* *
2814286 TTTACAACTTAATCCTTTGACTG
1 TTTACAAATTAGTCCTTTGACTG
2814309 CTGGATGCCT
Statistics
Matches: 166, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
160 3 0.02
161 73 0.44
162 90 0.54
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (161 bp):
TTTACAAATTAGTCCTTTGACTGTTTGACAGCACCAGGGGCCACCACGTGTCATTTTTTGGATTA
TTTATGCATTTAGTCCTTTTTATTTTTAATATATTTAATTTAATCCCCAAATCAATTTGCATTTA
ATTACGAAATTACCCCAAGAATTTTCCAAGA
Found at i:2814416 original size:30 final size:30
Alignment explanation
Indices: 2814377--2814674 Score: 372
Period size: 30 Copynumber: 10.0 Consensus size: 30
2814367 CCCCGAACAA
* **
2814377 TCCAGAAATTATATTTTGACCTTAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
2814408 TCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
2814438 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
2814468 TCCAAAATTA-TTTTTGACCCCGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
2814497 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
2814527 TCCAAAATCACATTTTAACCCCACAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
2814557 TCTAAAATTATATTTTG-CCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
2814586 TCCAAAATTACATTTTAACCTCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* **
2814616 TCCAAAATCACATTTTGACCCTGAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
2814645 T-CAAAATTTACCATTTT-ACCCCTAAAACTT
1 TCCAAAA-TTA-CATTTTGACCCC-AAAACTT
2814675 CTAAAATTCC
Statistics
Matches: 233, Mismatches: 28, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
28 5 0.02
29 61 0.26
30 162 0.70
31 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:2814512 original size:59 final size:60
Alignment explanation
Indices: 2814377--2814674 Score: 381
Period size: 59 Copynumber: 5.0 Consensus size: 60
2814367 CCCCGAACAA
** * *
2814377 TCCAGAAATTATATTTTGACCTTAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
* * *
2814438 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTA-TTTTTGACCCCGAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
* * *
2814497 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATCACATTTTAACCCCACAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
* *
2814557 TCTAAAATTATATTTTG-CCCCAAAACTTTTCCAAAATTACATTTTAACCTCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
* * **
2814616 TCCAAAATCACATTTTGACCCTGAAAC-TTT-CAAAATTTACCATTTT-ACCCCTAAAACTT
1 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAA-TTA-CATTTTAACCCC-AAAACTT
2814675 CTAAAATTCC
Statistics
Matches: 210, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
58 5 0.02
59 117 0.56
60 84 0.40
61 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (60 bp):
TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
Found at i:2814542 original size:89 final size:90
Alignment explanation
Indices: 2814377--2814674 Score: 399
Period size: 89 Copynumber: 3.3 Consensus size: 90
2814367 CCCCGAACAA
** *
2814377 TCCAGAAATTATATTTTGACCTTAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCA
1 TCCA-AAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
* *
2814442 AAATTATATTTTGACCCCAAAACTTT
65 AAATCACATTTTGACCCCAAAACTTT
*
2814468 TCCAAAATTAT-TTTTGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAA
1 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAA
* *
2814532 AATCACATTTTAACCCCACAACTTT
66 AATCACATTTTGACCCCAAAACTTT
* * *
2814557 TCTAAAATTATATTTTG-CCCCAAAACTTTTCCAAAATTACATTTTAACCTCAAAACTTTTCCAA
1 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAA
**
2814621 AATCACATTTTGACCCTGAAAC-TT
66 AATCACATTTTGACCCCAAAACTTT
*
2814645 T-CAAAATTTACCATTTT-ACCCCTAAAACTT
1 TCCAAAA-TTA-TATTTTGACCCC-AAAACTT
2814675 CTAAAATTCC
Statistics
Matches: 184, Mismatches: 18, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
87 4 0.02
88 6 0.03
89 151 0.82
90 19 0.10
91 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (90 bp):
TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAA
AATCACATTTTGACCCCAAAACTTT
Found at i:2814665 original size:29 final size:28
Alignment explanation
Indices: 2814401--2814748 Score: 97
Period size: 30 Copynumber: 11.8 Consensus size: 28
2814391 TTTGACCTTA
* * *
2814401 AAACTTTTCCAAAATTACATTTTGACCCTA
1 AAAC-TTT-CAAAATTCCATTTTAACCCTG
** * **
2814431 AAACTTTTCCAAAATTATATTTTGACCCCA
1 AAAC-TTT-CAAAATTCCATTTTAACCCTG
* *
2814461 AAACTTTTCCAAAATT--ATTTTTGACCCCG
1 AAAC-TTT-CAAAATTCCA-TTTTAACCCTG
* * **
2814490 AAACTTTTCCAAAATTACATTTTGACCCCA
1 AAAC-TTT-CAAAATTCCATTTTAACCCTG
*
2814520 AAACTTTTCCAAAA-TCACATTTTAACCC-C
1 AAAC-TTT-CAAAATTC-CATTTTAACCCTG
** * **
2814549 ACAACTTTTCTAAAATTATATTTT-GCCCCA
1 A-AAC-TTTC-AAAATTCCATTTTAACCCTG
* *
2814579 AAACTTTTCCAAAATTACATTTTAA-CCTCA
1 AAAC-TTT-CAAAATTCCATTTTAACCCT-G
*
2814609 AAACTTTTCCAAAA-TCACATTTTGACCCTG
1 AAAC-TTT-CAAAATTC-CATTTTAACCCTG
* *
2814639 AAACTTTCAAAATTTACCATTTTACCCCTA
1 AAACTTTCAAAA-TT-CCATTTTAACCCTG
2814669 AAAC-TTCTAAAATTCCATTTTTAACCCTG
1 AAACTTTC-AAAATTCCA-TTTTAACCCTG
*
2814698 --ATTTCATCGAAAATTACCATTTT-ACCCTCG
1 AAACTT--TC-AAAATT-CCATTTTAACCCT-G
* *
2814728 AATCTTTTAAAATTCCATTTT
1 AAACTTTCAAAATTCCATTTT
2814749 TAAACCCGAT
Statistics
Matches: 266, Mismatches: 27, Indels: 52
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.00
28 17 0.06
29 82 0.31
30 155 0.58
31 9 0.03
32 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (28 bp):
AAACTTTCAAAATTCCATTTTAACCCTG
Found at i:2814722 original size:59 final size:59
Alignment explanation
Indices: 2814647--2814903 Score: 354
Period size: 59 Copynumber: 4.4 Consensus size: 59
2814637 TGAAACTTTC
** * * *
2814647 AAAATTTACCATTTTACCCCTAAAACTTCTAAAATTCCATTTTTAACCCTGATTTCATCG
1 AAAA-TTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * *
2814707 AAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAAACCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * *
2814766 AAAATTACCATTTTGCCCCCGAAGCTTCTAAAATTCCGTTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * *
2814825 AAATTTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACC-
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* *
2814883 AAAATTGCCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
2814904 GGTATCCATA
Statistics
Matches: 174, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
58 18 0.10
59 152 0.87
60 4 0.02
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:2814797 original size:118 final size:117
Alignment explanation
Indices: 2814646--2814903 Score: 390
Period size: 118 Copynumber: 2.2 Consensus size: 117
2814636 CTGAAACTTT
* ** * *
2814646 CAAAATTTACCATTTTACCCCTAAAACTTCTAAAATTCCATTTTTAACCCTGATTTCATCGAAAA
1 CAAAA-TTACCATTTTGCCCCCGAAACTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAA
* *
2814711 TTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAAACCCGATTTCAC
65 TTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAAACCCGATTACAC
* * *
2814764 CGAAAATTACCATTTTGCCCCCGAAGCTTCTAAAATTCCGTTTTTAACCCCGATTTCACCGAAAT
1 C-AAAATTACCATTTTGCCCCCGAAACTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAA
*
2814829 TTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACAC
65 TTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAAACCCGATTACAC
*
2814882 CAAAATTGCCATTTTGCCCCCG
1 CAAAATTACCATTTTGCCCCCG
2814904 GGTATCCATA
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
117 20 0.16
118 103 0.81
119 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.35
Consensus pattern (117 bp):
CAAAATTACCATTTTGCCCCCGAAACTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAAT
TACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAAACCCGATTACAC
Found at i:2814886 original size:29 final size:30
Alignment explanation
Indices: 2814677--2814896 Score: 86
Period size: 29 Copynumber: 7.5 Consensus size: 30
2814667 TAAAACTTCT
* * *
2814677 AAAATT-CCATTTTTAACCCTGATTTCATCG
1 AAAATTACCATTTTTAACCCCGATTACA-CC
* ***
2814707 AAAATTACCA-TTTT-ACCCTCGAAT-CTTTT
1 AAAATTACCATTTTTAACCC-CGATTAC-ACC
* *
2814736 AAAATT-CCATTTTTAAACCCGATTTCACC
1 AAAATTACCATTTTTAACCCCGATTACACC
** * *
2814765 GAAAATTACCA-TTTTGCCCCCGA--AGCTTCT
1 -AAAATTACCATTTTTAACCCCGATTA-C-ACC
* *
2814795 AAAATT-CCGTTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTTAACCCCGATTACACC
* * * ***
2814824 GAAATTTACCA-TTTTACCCCCGAAT-CTTTT
1 -AAAATTACCATTTTTAACCCCGATTAC-ACC
2814854 AAAATT-CCATTTTTAACCCCGATTACACC
1 AAAATTACCATTTTTAACCCCGATTACACC
*
2814883 AAAATTGCCATTTT
1 AAAATTACCATTTT
2814897 GCCCCCGGGT
Statistics
Matches: 136, Mismatches: 35, Indels: 38
0.65 0.17 0.18
Matches are distributed among these distances:
28 8 0.06
29 61 0.45
30 59 0.43
31 8 0.06
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTTAACCCCGATTACACC
Found at i:2814925 original size:58 final size:59
Alignment explanation
Indices: 2814674--2814938 Score: 231
Period size: 59 Copynumber: 4.5 Consensus size: 59
2814664 CCCTAAAACT
* * * * * *
2814674 TCTA-AAATTCCATTTTTAACCCTGATTTCATCGAAAATTACCATTTTACCCTC--GAA
1 TCTATAAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTGCCCCCGGGTA
* * * *
2814730 TCTTTTAAAATTCCATTTTTAAACCCGATTTCACCGAAAATTACCATTTTGCCCCCGAAGCT-
1 TC-TAT-AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTGCCCCCG--GGTA
* * *
2814792 TCTA-AAATTCCGTTTTTAACCCCGATTTCACCGAAATTTACCATTTTACCCCC--GAA
1 TCTATAAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTGCCCCCGGGTA
* * * *
2814848 TCTTTTAAAATTCCATTTTTAACCCCGATTACACC-AAAATTGCCATTTTGCCCCCGGGTA
1 TC-TAT-AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTGCCCCCGGGTA
* * * *
2814908 TCCATAAGTCCCGTTTTTTACCCCGATTTCA
1 TCTATAAATTCCGTTTTTAACCCCGATTTCA
2814939 TCATTTATCA
Statistics
Matches: 167, Mismatches: 29, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
56 4 0.02
57 2 0.01
58 38 0.23
59 116 0.69
60 4 0.02
61 1 0.01
62 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (59 bp):
TCTATAAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTGCCCCCGGGTA
Found at i:2814926 original size:118 final size:117
Alignment explanation
Indices: 2814672--2814938 Score: 358
Period size: 118 Copynumber: 2.3 Consensus size: 117
2814662 ACCCCTAAAA
* * * * * *
2814672 CTTCTAAAATTCCATTTTTAACCCTGATTTCATCGAAAATTACCATTTTACCCTCGAATCTTTTA
1 CTTCCAAAATCCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTA
*
2814737 AAATTCCATTTTTAAACCCGATTTCACCGAAAATTACCATTTTGCCCCCGAAG
66 AAATTCCATTTTTAAACCCGATTACACCGAAAATTACCATTTTGCCCCCG-AG
* * *
2814790 CTTCTAAAATTCCGTTTTTAACCCCGATTTCACCGAAATTTACCATTTTACCCCCGAATCTTTTA
1 CTTCCAAAATCCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTA
* *
2814855 AAATTCCATTTTTAACCCCGATTACACC-AAAATTGCCATTTTGCCCCCG-G
66 AAATTCCATTTTTAAACCCGATTACACCGAAAATTACCATTTTGCCCCCGAG
* * *
2814905 GTATCCATAAGTCCCGTTTTTTACCCCGATTTCA
1 CT-TCCA-AAATCCCGTTTTTAACCCCGATTTCA
2814939 TCATTTATCA
Statistics
Matches: 134, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
115 2 0.01
116 3 0.02
117 43 0.32
118 86 0.64
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (117 bp):
CTTCCAAAATCCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTA
AAATTCCATTTTTAAACCCGATTACACCGAAAATTACCATTTTGCCCCCGAG
Found at i:2820693 original size:18 final size:18
Alignment explanation
Indices: 2820670--2820707 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2820660 ATACATCACA
2820670 GTGATTTCCCATTTTTTG
1 GTGATTTCCCATTTTTTG
2820688 GTGATTTCCCATTTTTTG
1 GTGATTTCCCATTTTTTG
2820706 GT
1 GT
2820708 TTCTCTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.18, T:0.55
Consensus pattern (18 bp):
GTGATTTCCCATTTTTTG
Found at i:2824830 original size:29 final size:30
Alignment explanation
Indices: 2824786--2824874 Score: 108
Period size: 31 Copynumber: 3.0 Consensus size: 30
2824776 TTGATTTAAT
2824786 GTGCAATTGTATACATG-AACTTTAATTTG
1 GTGCAATTGTATACATGAAACTTTAATTTG
* * *
2824815 GTGCAATTATACACATGAAACTCTAATTGTG
1 GTGCAATTGTATACATGAAACTTTAATT-TG
* * *
2824846 GTTCAAATGTATACTTGAAACTTTAATTT
1 GTGCAATTGTATACATGAAACTTTAATTT
2824875 TGATTTAATC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 15 0.31
30 10 0.20
31 24 0.49
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (30 bp):
GTGCAATTGTATACATGAAACTTTAATTTG
Found at i:2828893 original size:21 final size:21
Alignment explanation
Indices: 2828850--2828893 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2828840 ACGTGATAAT
* * *
2828850 ATTTTTTTTTTTTAAATTGAG
1 ATTTTATTTTTATAAATTAAG
*
2828871 ATTTTATTTTTATAGATTAAG
1 ATTTTATTTTTATAAATTAAG
2828892 AT
1 AT
2828894 ACTACGAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (21 bp):
ATTTTATTTTTATAAATTAAG
Found at i:2832548 original size:35 final size:35
Alignment explanation
Indices: 2832509--2832596 Score: 167
Period size: 35 Copynumber: 2.5 Consensus size: 35
2832499 AAAAGGTTCA
2832509 TAAAATAAATTTTCCTATTTACATTATTTCAAAAT
1 TAAAATAAATTTTCCTATTTACATTATTTCAAAAT
2832544 TAAAATAAATTTTCCTATTTACATTATTTCAAAAT
1 TAAAATAAATTTTCCTATTTACATTATTTCAAAAT
*
2832579 TAAAATAAATATTCCTAT
1 TAAAATAAATTTTCCTAT
2832597 ATAATTTATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (35 bp):
TAAAATAAATTTTCCTATTTACATTATTTCAAAAT
Found at i:2833564 original size:18 final size:19
Alignment explanation
Indices: 2833530--2833567 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2833520 AAATTACAAA
2833530 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
2833549 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
2833567 A
1 A
2833568 TTTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:2833593 original size:8 final size:9
Alignment explanation
Indices: 2833574--2833626 Score: 61
Period size: 10 Copynumber: 5.4 Consensus size: 9
2833564 TATATTTTTG
2833574 AAAAATTAA
1 AAAAATTAA
2833583 AAAAATTAA
1 AAAAATTAA
*
2833592 AAAATTCTAA
1 AAAAAT-TAA
2833602 AAAATATGTAA
1 AAAA-AT-TAA
2833613 AAAAAGTTAA
1 AAAAA-TTAA
2833623 AAAA
1 AAAA
2833627 TTTCTAGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
9 14 0.37
10 15 0.39
11 9 0.24
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (9 bp):
AAAAATTAA
Found at i:2838183 original size:4 final size:4
Alignment explanation
Indices: 2838167--2838225 Score: 109
Period size: 4 Copynumber: 14.8 Consensus size: 4
2838157 TTTGACTCAT
*
2838167 ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2838215 ATAC ATAC ATA
1 ATAC ATAC ATA
2838226 GGAGCTTTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:2841689 original size:29 final size:28
Alignment explanation
Indices: 2841626--2841698 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
2841616 TAGCATATAT
* *
2841626 TTTTATAATTTTTAAAGGATTAAATCAAA
1 TTTTATTATTTTT-AAGGATGAAATCAAA
*
2841655 TATTATTATTTTTAAGGATCGAAATGC-AA
1 TTTTATTATTTTTAAGGAT-GAAAT-CAAA
2841684 TTTTATT-TTTATTAA
1 TTTTATTATTT-TTAA
2841699 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
28 9 0.24
29 27 0.73
30 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.49
Consensus pattern (28 bp):
TTTTATTATTTTTAAGGATGAAATCAAA
Found at i:2844797 original size:6 final size:7
Alignment explanation
Indices: 2844777--2844803 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2844767 CAGTGTAACC
2844777 AATAAAA
1 AATAAAA
2844784 AATAAAA
1 AATAAAA
2844791 AATAAAA
1 AATAAAA
2844798 AATAAA
1 AATAAA
2844804 TTCAGCTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AATAAAA
Found at i:2866022 original size:43 final size:43
Alignment explanation
Indices: 2865969--2866064 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
2865959 TAATTATTTG
**
2865969 TATATAATTTTAATTAATATAATAATAAATTT-AATTTTTATATT
1 TATAT-ATTTT-ATTAATATAATAATAAATTTGAAAATTTATATT
* * * *
2866013 TATATATTTTATTAATTTAATATTCATTTTGAAAATTTATATT
1 TATATATTTTATTAATATAATAATAAATTTGAAAATTTATATT
2866056 TATATATTT
1 TATATATTT
2866065 ACAAAAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 16 0.36
43 24 0.53
44 5 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (43 bp):
TATATATTTTATTAATATAATAATAAATTTGAAAATTTATATT
Found at i:2866035 original size:16 final size:15
Alignment explanation
Indices: 2865996--2866036 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2865986 TATAATAATA
2865996 AATTTAAT-TTTTAT
1 AATTTAATATTTTAT
2866010 -ATTTATATATTTTATT
1 AATTTA-ATATTTTA-T
2866026 AATTTAATATT
1 AATTTAATATT
2866037 CATTTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.22
14 2 0.09
15 5 0.22
16 6 0.26
17 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTAATATTTTAT
Found at i:2866713 original size:68 final size:71
Alignment explanation
Indices: 2866598--2866729 Score: 173
Period size: 68 Copynumber: 1.9 Consensus size: 71
2866588 TGGGAAGAAT
2866598 AAAAATGTAAACTTTTTATTTAACCAACAACTAGAAAAGATTAAATTAAATTA-TAAT-TTTAAA
1 AAAAATGTAAACTTTTTATTTAACCAACAACTAGAAAAGATTAAATTAAATTATTAATATTTAAA
2866661 GGGATC
66 GGGATC
**** * *
2866667 AAAAATGTAAA-TTTTTATTTAACCAGTGGCTTA-AAAGGATTTAATTAAATTATTAATATTTAA
1 AAAAATGTAAACTTTTTATTTAACCAACAAC-TAGAAAAGATTAAATTAAATTATTAATATTTAA
2866730 GAGAAATTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
68 32 0.59
69 17 0.31
70 5 0.09
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (71 bp):
AAAAATGTAAACTTTTTATTTAACCAACAACTAGAAAAGATTAAATTAAATTATTAATATTTAAA
GGGATC
Found at i:2867513 original size:18 final size:17
Alignment explanation
Indices: 2867490--2867532 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2867480 TAATATATAA
*
2867490 ATAAATAATTAAAATTTT
1 ATAAATAATTAAAA-TAT
*
2867508 ATAAATTTATTAAAATAT
1 ATAAA-TAATTAAAATAT
2867526 ATAAATA
1 ATAAATA
2867533 TATAAACGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 12 0.57
19 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATAATTAAAATAT
Found at i:2868382 original size:12 final size:13
Alignment explanation
Indices: 2868342--2868388 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
2868332 TTAGGGGAAA
2868342 TTATTTTCAATTAAT
1 TTATTTT-AATT-AT
*
2868357 TTAATTTAATTAT
1 TTATTTTAATTAT
2868370 TTATTTTAA-TA-
1 TTATTTTAATTAT
2868381 TTATTTTA
1 TTATTTTA
2868389 CTTTTAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 10 0.33
14 4 0.13
15 6 0.20
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTTAATTAT
Found at i:2874523 original size:18 final size:18
Alignment explanation
Indices: 2874500--2874542 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2874490 GTTCAAGGGG
2874500 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
2874518 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
2874536 TAATTAA
1 TAATTAA
2874543 AAACCTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:2876451 original size:32 final size:28
Alignment explanation
Indices: 2876385--2876454 Score: 72
Period size: 32 Copynumber: 2.4 Consensus size: 28
2876375 AAAATTTATA
*
2876385 TATTTATATCATATTTATATTTTTTTGC
1 TATTTATATTATATTTATATTTTTTTGC
2876413 TA-TTATATTATATTTTAATTACTTTTTATTG-
1 TATTTATATTATA-TTT-A-TA-TTTTT-TTGC
2876444 TATTTATATTA
1 TATTTATATTA
2876455 AGAAATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
27 9 0.26
28 5 0.14
29 1 0.03
30 2 0.06
31 7 0.20
32 11 0.31
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (28 bp):
TATTTATATTATATTTATATTTTTTTGC
Found at i:2876534 original size:17 final size:17
Alignment explanation
Indices: 2876512--2876544 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2876502 CTAAAAAGAT
2876512 GATATACATAT-AAATTA
1 GATATA-ATATCAAATTA
2876529 GATATAATATCAAATT
1 GATATAATATCAAATT
2876545 TAACTCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
GATATAATATCAAATTA
Found at i:2877466 original size:31 final size:31
Alignment explanation
Indices: 2877406--2877466 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2877396 TTATTTTTCG
* *
2877406 AGTTAAATTTGATCTTGAATTTTTTAAAAAT
1 AGTTAAATTTGATCTTGAACTTTTAAAAAAT
*
2877437 AGTTGAATTTGATCATT-AACTTTTAAAAAA
1 AGTTAAATTTGATC-TTGAACTTTTAAAAAA
2877467 AATAGTCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTAAATTTGATCTTGAACTTTTAAAAAAT
Found at i:2878321 original size:16 final size:15
Alignment explanation
Indices: 2878300--2878329 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2878290 ATTCGTTTGG
2878300 TATAT-TTAAATATT
1 TATATATTAAATATT
2878314 TATATATTAAATATT
1 TATATATTAAATATT
2878329 T
1 T
2878330 TTTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATTAAATATT
Found at i:2890095 original size:2 final size:2
Alignment explanation
Indices: 2890088--2890112 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2890078 AGATAAAGAG
2890088 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2890113 GGATTCGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2903015 original size:30 final size:29
Alignment explanation
Indices: 2902981--2903038 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2902971 AATTTAAAAG
*
2902981 AATTAAATC-AAATCAAAATTTTATGTATAA
1 AATTAAA-CAAAATC-AAAGTTTATGTATAA
*
2903011 AATTATACAAAATCAAAGTTTATGTATA
1 AATTAAACAAAATCAAAGTTTATGTATA
2903039 TGATTGCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (29 bp):
AATTAAACAAAATCAAAGTTTATGTATAA
Found at i:2903387 original size:22 final size:22
Alignment explanation
Indices: 2903349--2903393 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2903339 ATTTTAAAAA
*
2903349 AATATTTATATTATTTTAATTT
1 AATATTTATAATATTTTAATTT
*
2903371 AATATTTAATAAT-TTTTTATTT
1 AATATTT-ATAATATTTTAATTT
2903393 A
1 A
2903394 TTGAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATATTTATAATATTTTAATTT
Found at i:2904840 original size:28 final size:28
Alignment explanation
Indices: 2904811--2904870 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
2904801 AAATAGAAAT
2904811 AAATATATGAAAAATTTAAAATATATATA
1 AAATATA-GAAAAATTTAAAATATATATA
* **
2904840 AAATCTAGAAAAAAATAAAATATATATA
1 AAATATAGAAAAATTTAAAATATATATA
2904868 AAA
1 AAA
2904871 ATAAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (28 bp):
AAATATAGAAAAATTTAAAATATATATA
Found at i:2904841 original size:11 final size:10
Alignment explanation
Indices: 2904788--2904873 Score: 58
Period size: 10 Copynumber: 8.8 Consensus size: 10
2904778 ATATACACAT
*
2904788 TAAAAAAATA
1 TAAAAATATA
*
2904798 TAAAAATAGA
1 TAAAAATATA
2904808 -AATAAATATA
1 TAA-AAATATA
2904818 TGAAAAAT-T-
1 T-AAAAATATA
2904827 T-AAAATATA
1 TAAAAATATA
*
2904836 TATAAAATCTA
1 TA-AAAATATA
*
2904847 GAAAAA-A-A
1 TAAAAATATA
2904855 TAAAATATATA
1 TAAAA-ATATA
2904866 TAAAAATA
1 TAAAAATA
2904874 AAATTTATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
7 5 0.08
8 6 0.10
9 5 0.08
10 23 0.39
11 18 0.31
12 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (10 bp):
TAAAAATATA
Found at i:2904859 original size:17 final size:17
Alignment explanation
Indices: 2904837--2904888 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
2904827 TAAAATATAT
* *
2904837 ATAAAATCTAGAAAAAA
1 ATAAAATATATAAAAAA
*
2904854 ATAAAATATATATAAAA
1 ATAAAATATATAAAAAA
*
2904871 ATAAAATTTATAAAAAA
1 ATAAAATATATAAAAAA
2904888 A
1 A
2904889 ATACGATAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
ATAAAATATATAAAAAA
Found at i:2910003 original size:17 final size:17
Alignment explanation
Indices: 2909981--2910019 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2909971 ACATTAAATT
2909981 TTCATACCTTGTAATCA
1 TTCATACCTTGTAATCA
2909998 TTCATACCTTGTAATCA
1 TTCATACCTTGTAATCA
2910015 TTCAT
1 TTCAT
2910020 GTTTTCACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (17 bp):
TTCATACCTTGTAATCA
Found at i:2916941 original size:6 final size:6
Alignment explanation
Indices: 2916930--2916963 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2916920 ACACCTCTCT
*
2916930 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCT TCTT
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTT
2916964 TTTTGATTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (6 bp):
TCTTCA
Found at i:2923340 original size:23 final size:23
Alignment explanation
Indices: 2923306--2923349 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2923296 GAATTCTAAT
2923306 AATTTTATATTT-GAATTATTTCA
1 AATTTTATATTTAG-ATTATTTCA
2923329 AATTATTA-ATTTAGATTATTT
1 AATT-TTATATTTAGATTATTT
2923350 TAAGTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (23 bp):
AATTTTATATTTAGATTATTTCA
Found at i:2930334 original size:27 final size:28
Alignment explanation
Indices: 2930272--2930334 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 28
2930262 ATTAATTCAA
* *
2930272 AAAAATTAATTAATTACGTAAATGATTT
1 AAAATTTAATTAATTACGTAAATGACTT
*** *
2930300 ATTTTTTATTTAA-TACGTAAATGACTT
1 AAAATTTAATTAATTACGTAAATGACTT
2930327 AAAATTTA
1 AAAATTTA
2930335 CAGTAAAAGT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (28 bp):
AAAATTTAATTAATTACGTAAATGACTT
Found at i:2932439 original size:13 final size:13
Alignment explanation
Indices: 2932423--2932447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2932413 ACTTATATAC
2932423 ATCAAAACTTTAT
1 ATCAAAACTTTAT
2932436 ATCAAAACTTTA
1 ATCAAAACTTTA
2932448 ATTAATTATT
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
ATCAAAACTTTAT
Found at i:2936619 original size:22 final size:25
Alignment explanation
Indices: 2936576--2936620 Score: 60
Period size: 22 Copynumber: 1.9 Consensus size: 25
2936566 TATTTTAATC
*
2936576 TTATAACTATTTTTATATATTTTGA
1 TTATAACTATTTTTATAAATTTTGA
2936601 TTATAA-T-TTTTTA-AAATTTT
1 TTATAACTATTTTTATAAATTTT
2936621 TTAAGACTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 1 0.05
25 6 0.32
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATAACTATTTTTATAAATTTTGA
Found at i:2939705 original size:16 final size:16
Alignment explanation
Indices: 2939684--2939715 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2939674 ATGATTCTCT
2939684 TTCAACTTACTTTGTG
1 TTCAACTTACTTTGTG
2939700 TTCAACTTACTTTGTG
1 TTCAACTTACTTTGTG
2939716 ACATACATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (16 bp):
TTCAACTTACTTTGTG
Found at i:2940483 original size:2 final size:2
Alignment explanation
Indices: 2940476--2940508 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2940466 CCTGCATGTG
2940476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2940509 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2947935 original size:31 final size:31
Alignment explanation
Indices: 2947897--2947999 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 31
2947887 GCTAAGTGCC
*
2947897 TCACCATCTCGCAAAGTGATTCCATCACGCT
1 TCACCATCTCGCAAAGTGATACCATCACGCT
* * * * * *
2947928 TCACCATCTAGCTAAGTGATCCCATAACACC
1 TCACCATCTCGCAAAGTGATACCATCACGCT
* * * *
2947959 TAATCATCTCGCGAAGTGATACCGTCACG-T
1 TCACCATCTCGCAAAGTGATACCATCACGCT
2947989 CTCACCATCTC
1 -TCACCATCTC
2948000 ATAAGTTGAT
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (31 bp):
TCACCATCTCGCAAAGTGATACCATCACGCT
Found at i:2948025 original size:49 final size:49
Alignment explanation
Indices: 2947963--2948064 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 49
2947953 AACACCTAAT
* *
2947963 CATCTCGCGAAGTGATACC-GTCACGTCTCACCATCTCATAAGTTGATCC
1 CATCTCGCGAAGTGAT-CCTGTCACGCCTCACCATCTCATAAGATGATCC
** * * *
2948012 CATCTCGTTAAGTGATCCTGTCATGCCTCACCATCTCGTGAGATGATCC
1 CATCTCGCGAAGTGATCCTGTCACGCCTCACCATCTCATAAGATGATCC
2948061 CATC
1 CATC
2948065 ATGCTCCACC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 2 0.04
49 43 0.96
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (49 bp):
CATCTCGCGAAGTGATCCTGTCACGCCTCACCATCTCATAAGATGATCC
Found at i:2948123 original size:31 final size:31
Alignment explanation
Indices: 2948087--2948252 Score: 165
Period size: 31 Copynumber: 5.4 Consensus size: 31
2948077 CTCATTAAGT
* *
2948087 GCCTCACCATCTCGCTAACTGATCCCATCAC
1 GCCTCACCATCTCGCTAAGTGATCCTATCAC
* * * *
2948118 ACCTCACCAACTCGCGAAGTGA--CTATCAT
1 GCCTCACCATCTCGCTAAGTGATCCTATCAC
** *
2948147 GCCTCGTCATCTCGCTAAGTGATCTTATCAC
1 GCCTCACCATCTCGCTAAGTGATCCTATCAC
* * * *
2948178 GGCTCACCACCTCACGAAGTGATCCTATCAC
1 GCCTCACCATCTCGCTAAGTGATCCTATCAC
* * * *
2948209 TCCTCACCACCTCACTAAGTGATCCTGTCAC
1 GCCTCACCATCTCGCTAAGTGATCCTATCAC
2948240 GCCTCACCATCTC
1 GCCTCACCATCTC
2948253 ATGAGGTGAT
Statistics
Matches: 107, Mismatches: 26, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.21
31 85 0.79
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.24
Consensus pattern (31 bp):
GCCTCACCATCTCGCTAAGTGATCCTATCAC
Found at i:2948184 original size:60 final size:61
Alignment explanation
Indices: 2948088--2948253 Score: 183
Period size: 60 Copynumber: 2.7 Consensus size: 61
2948078 TCATTAAGTG
* * * *
2948088 CCTCACCATCTCGCTAACTGATCCCATCACACCTCACCAACTCGCGAAGTGA-CTATCA-T
1 CCTCACCATCTCGCTAAGTGATCCTATCACGCCTCACCAACTCACGAAGTGACCTATCACT
** * * *
2948147 GCCTCGTCATCTCGCTAAGTGATCTTATCACGGCTCACCACCTCACGAAGTGATCCTATCACT
1 -CCTCACCATCTCGCTAAGTGATCCTATCACGCCTCACCAACTCACGAAGTGA-CCTATCACT
* * * *
2948210 CCTCACCACCTCACTAAGTGATCCTGTCACGCCTCACCATCTCA
1 CCTCACCATCTCGCTAAGTGATCCTATCACGCCTCACCAACTCA
2948254 TGAGGTGATC
Statistics
Matches: 86, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
60 43 0.50
62 42 0.49
63 1 0.01
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.24
Consensus pattern (61 bp):
CCTCACCATCTCGCTAAGTGATCCTATCACGCCTCACCAACTCACGAAGTGACCTATCACT
Found at i:2948262 original size:31 final size:31
Alignment explanation
Indices: 2948163--2948270 Score: 128
Period size: 31 Copynumber: 3.5 Consensus size: 31
2948153 TCATCTCGCT
* * *
2948163 AAGTGATCTTATCACGGCTCACCACCTCACG
1 AAGTGATCCTATCACGCCTCACCACCTCATG
*
2948194 AAGTGATCCTATCACTCCTCACCACCTCACT-
1 AAGTGATCCTATCACGCCTCACCACCTCA-TG
* *
2948225 AAGTGATCCTGTCACGCCTCACCATCTCATG
1 AAGTGATCCTATCACGCCTCACCACCTCATG
* *
2948256 AGGTGATCCCATCAC
1 AAGTGATCCTATCAC
2948271 ACCTTGCAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.02
31 64 0.98
ACGTcount: A:0.25, C:0.37, G:0.14, T:0.24
Consensus pattern (31 bp):
AAGTGATCCTATCACGCCTCACCACCTCATG
Found at i:2948954 original size:18 final size:18
Alignment explanation
Indices: 2948931--2948983 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
2948921 CCGATTCCCG
2948931 ACCGAATTAATTCGATTA
1 ACCGAATTAATTCGATTA
*
2948949 ACCGAATTCAA-TCGGTTA
1 ACCGAATT-AATTCGATTA
*
2948967 ACCAAATTAATTCGATT
1 ACCGAATTAATTCGATT
2948984 TTACCCGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (18 bp):
ACCGAATTAATTCGATTA
Found at i:2954951 original size:21 final size:24
Alignment explanation
Indices: 2954899--2954946 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2954889 TATAATTTTT
* *
2954899 ATATTTTATTATTTTAAATAAAAA
1 ATATATTATTATTATAAATAAAAA
2954923 ATATATTATT-TTATAAATAAAAA
1 ATATATTATTATTATAAATAAAAA
2954946 A
1 A
2954947 AATTAAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATATTATTATTATAAATAAAAA
Found at i:2955638 original size:14 final size:14
Alignment explanation
Indices: 2955619--2955656 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
2955609 TACATTATCT
2955619 TTTTAATAAATAAG
1 TTTTAATAAATAAG
2955633 TTTTAATAAATAAG
1 TTTTAATAAATAAG
2955647 TTTTAATAAA
1 TTTTAATAAA
2955657 ATATAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (14 bp):
TTTTAATAAATAAG
Found at i:2986200 original size:3 final size:3
Alignment explanation
Indices: 2986194--2986226 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2986184 CAACAACTAT
2986194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2986227 AATTTAGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3000649 original size:2 final size:2
Alignment explanation
Indices: 3000642--3000675 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3000632 TTTCTAAACC
* *
3000642 AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3000676 TTTTAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:3000680 original size:14 final size:14
Alignment explanation
Indices: 3000642--3000697 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
3000632 TTTCTAAACC
*
3000642 ATATATATATATAT
1 ATATATATTTATAT
3000656 ATATATATTTATAT
1 ATATATATTTATAT
* * *
3000670 TTATATTTTTAAAT
1 ATATATATTTATAT
*
3000684 -TAT-TGTTTATAT
1 ATATATATTTATAT
3000696 AT
1 AT
3000698 TTTTATCTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
12 7 0.20
13 4 0.11
14 24 0.69
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
ATATATATTTATAT
Found at i:3020869 original size:3 final size:3
Alignment explanation
Indices: 3020861--3020896 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3020851 TATCAAAATC
3020861 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3020897 GCTGAGCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3028465 original size:21 final size:21
Alignment explanation
Indices: 3028439--3028479 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3028429 TGTAGGTGGA
3028439 AATTAAAACCTGAGTGCTCAG
1 AATTAAAACCTGAGTGCTCAG
3028460 AATTAAAACCTGAGTGCTCA
1 AATTAAAACCTGAGTGCTCA
3028480 TAGTTGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (21 bp):
AATTAAAACCTGAGTGCTCAG
Found at i:3036528 original size:16 final size:17
Alignment explanation
Indices: 3036507--3036539 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3036497 ATAATTTTAC
*
3036507 TTTTAATAA-TTTAAAA
1 TTTTAAAAATTTTAAAA
3036523 TTTTAAAAATTTTAAAA
1 TTTTAAAAATTTTAAAA
3036540 AGCCTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAAAATTTTAAAA
Found at i:3040987 original size:60 final size:60
Alignment explanation
Indices: 3040919--3041039 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
3040909 AGCCAACAGT
*
3040919 TAGAATTGGAAAAAGATTTTAAATTTTACGGAGCTTACAATAGCCTCTGTTATGAGTTAC
1 TAGAATTGGAAAAAGATTTTAAATCTTACGGAGCTTACAATAGCCTCTGTTATGAGTTAC
3040979 TAGAATTGGAAAAAGATTTTAAATCTTACGGAGCTTACAATAGCCTCTGTTATGAGTTAC
1 TAGAATTGGAAAAAGATTTTAAATCTTACGGAGCTTACAATAGCCTCTGTTATGAGTTAC
3041039 T
1 T
3041040 CTATAGGGAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (60 bp):
TAGAATTGGAAAAAGATTTTAAATCTTACGGAGCTTACAATAGCCTCTGTTATGAGTTAC
Found at i:3043026 original size:22 final size:23
Alignment explanation
Indices: 3042989--3043033 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3042979 TATATTTAAA
*
3042989 AAATAATATATTAAAATTATATT
1 AAATAATATATTAAAATCATATT
3043012 AAATAATA-ATTAAAATCATATT
1 AAATAATATATTAAAATCATATT
3043034 TATAGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATAATATATTAAAATCATATT
Found at i:3046026 original size:18 final size:18
Alignment explanation
Indices: 3046003--3046037 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3045993 CTCCTCGGCT
3046003 CTCGAGACCGCTCCTCTG
1 CTCGAGACCGCTCCTCTG
* *
3046021 CTCGAGATCTCTCCTCT
1 CTCGAGACCGCTCCTCT
3046038 TCCCGAAGCA
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:0.11, C:0.43, G:0.17, T:0.29
Consensus pattern (18 bp):
CTCGAGACCGCTCCTCTG
Found at i:3052356 original size:3 final size:3
Alignment explanation
Indices: 3052337--3052371 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3052327 AAGAGATGGA
* *
3052337 GCT GTT GCT GAT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
3052372 AAGTGTAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.29, G:0.34, T:0.34
Consensus pattern (3 bp):
GCT
Found at i:3056980 original size:44 final size:45
Alignment explanation
Indices: 3056891--3056983 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
3056881 TAATTTTTGT
3056891 ATTGTAATTTTAAAATTTGTTTTCATATAAAAAATAACCTAAAAA
1 ATTGTAATTTTAAAATTTGTTTTCATATAAAAAATAACCTAAAAA
* * *
3056936 ATTGTATTTTTAAAATTTGTTTTCGTATAAAAAATAACTTAAAAA
1 ATTGTAATTTTAAAATTTGTTTTCATATAAAAAATAACCTAAAAA
3056981 ATT
1 ATT
3056984 ATTACAGTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (45 bp):
ATTGTAATTTTAAAATTTGTTTTCATATAAAAAATAACCTAAAAA
Found at i:3060180 original size:19 final size:21
Alignment explanation
Indices: 3060142--3060199 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
3060132 TAAATATGTA
3060142 AAAATATTAAAAAATAATAAT
1 AAAATATTAAAAAATAATAAT
*
3060163 AAAAT-TTAAAATATATAATGTAT
1 AAAATATTAAAA-A-ATAAT-AAT
3060186 AAAA-ATTCAAAAAA
1 AAAATATT-AAAAAA
3060200 ATAGCATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 6 0.19
21 6 0.19
22 6 0.19
23 9 0.29
24 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATATTAAAAAATAATAAT
Found at i:3060278 original size:81 final size:81
Alignment explanation
Indices: 3060193--3060357 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 81
3060183 TATAAAAATT
3060193 CAAAAAAATAGCATGAAATACTTGTGGATTTCCATGTTTAAAAATTTAATATTTTAGTTGGTATT
1 CAAAAAAATAGCATGAAATACTTGTGGATTTCCATGTTTAAAAATTTAATATTTTAGTTGGTATT
3060258 TTAGTTAAAAAAGCAA
66 TTAGTTAAAAAAGCAA
*
3060274 CAAAAAAATAGCATGAAATACTTGTGGATTTTCATGTTTAAAAATTTAATATTTTAGTTGGTATT
1 CAAAAAAATAGCATGAAATACTTGTGGATTTCCATGTTTAAAAATTTAATATTTTAGTTGGTATT
3060339 TTAGTTAAAAAAGCAA
66 TTAGTTAAAAAAGCAA
3060355 CAA
1 CAA
3060358 TTTAGCTCCA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (81 bp):
CAAAAAAATAGCATGAAATACTTGTGGATTTCCATGTTTAAAAATTTAATATTTTAGTTGGTATT
TTAGTTAAAAAAGCAA
Found at i:3061622 original size:12 final size:11
Alignment explanation
Indices: 3061584--3061645 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 11
3061574 TTTAAAATTT
*
3061584 AAAATTTAT-T
1 AAAATTTATAA
3061594 AAAATATTAT--
1 AAAAT-TTATAA
3061604 AAAATTTATAA
1 AAAATTTATAA
3061615 ACAAATTTTATAA
1 A-AAA-TTTATAA
*
3061628 TAAA-TTATAA
1 AAAATTTATAA
3061638 AAAATTTA
1 AAAATTTA
3061646 AATTATAAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
9 4 0.09
10 19 0.43
11 8 0.18
12 6 0.14
13 7 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATTTATAA
Found at i:3061653 original size:23 final size:24
Alignment explanation
Indices: 3061599--3061653 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
3061589 TTATTAAAAT
*
3061599 ATTATAAAATTTATAAACAAATTTT
1 ATTAT-AAATTTATAAACAAATTTA
*
3061624 ATAATAAA-TTATAAA-AAATTTAA
1 ATTATAAATTTATAAACAAATTT-A
3061647 ATTATAA
1 ATTATAA
3061654 GTTTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 6 0.23
23 13 0.50
24 3 0.12
25 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
ATTATAAATTTATAAACAAATTTA
Done.