Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
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: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 1 of 21
Found at i:260 original size:13 final size:13
Alignment explanation
Indices: 242--291 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
232 TATATTGTAC
242 TTTATATAATATA
1 TTTATATAATATA
255 TTTATATAATA-A
1 TTTATATAATATA
267 TTTA-A-AATTATA
1 TTTATATAA-TATA
**
279 TAAATATAATATA
1 TTTATATAATATA
292 ACATATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 2 0.06
11 3 0.10
12 8 0.26
13 16 0.52
14 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTATATAATATA
Found at i:6258 original size:19 final size:19
Alignment explanation
Indices: 6225--6263 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6215 TAATTATATT
6225 TAAATAATTAATATTTATA
1 TAAATAATTAATATTTATA
6244 TAAAT-ATTAATTATTTATA
1 TAAATAATTAA-TATTTATA
6263 T
1 T
6264 TATATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAATAATTAATATTTATA
Found at i:6513 original size:18 final size:20
Alignment explanation
Indices: 6481--6521 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
6471 AAAGAATATC
6481 ATATATTATATTTTTAAATT
1 ATATATTATATTTTTAAATT
*
6501 ATATA-TATATTTTTAATTT
1 ATATATTATATTTTTAAATT
6520 AT
1 AT
6522 CTAGTCTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATATTATATTTTTAAATT
Found at i:6865 original size:2 final size:2
Alignment explanation
Indices: 6858--6914 Score: 84
Period size: 2 Copynumber: 29.5 Consensus size: 2
6848 ACTAATACTA
6858 AT AT AT AT AT AT AT AT AT AT ACT A- AT AT AT AT AT AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
6898 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
6915 ATGGCATATT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 46 0.90
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6884 original size:24 final size:22
Alignment explanation
Indices: 6850--6914 Score: 98
Period size: 24 Copynumber: 3.0 Consensus size: 22
6840 CAAAGTTTAC
6850 TAATACTAATATATATATATAT
1 TAATACTAATATATATATATAT
6872 ATATATACTAATATATATATATAT
1 -TA-ATACTAATATATATATATAT
6896 TAATA-T-ATATATATATATA
1 TAATACTAATATATATATATA
6915 ATGGCATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.32
21 1 0.02
22 3 0.07
23 4 0.10
24 20 0.49
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATACTAATATATATATATAT
Found at i:6923 original size:18 final size:16
Alignment explanation
Indices: 6847--6910 Score: 89
Period size: 16 Copynumber: 4.1 Consensus size: 16
6837 AACCAAAGTT
6847 TACTAATACTA-ATATA
1 TACTAATA-TATATATA
6863 TA-T-ATATATATATA
1 TACTAATATATATATA
6877 TACTAATATATATATA
1 TACTAATATATATATA
*
6893 TATTAATATATATATA
1 TACTAATATATATATA
6909 TA
1 TA
6911 TATAATGGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
13 2 0.05
14 10 0.23
15 2 0.05
16 30 0.68
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TACTAATATATATATA
Found at i:8081 original size:132 final size:131
Alignment explanation
Indices: 7569--8143 Score: 757
Period size: 132 Copynumber: 4.4 Consensus size: 131
7559 GTCAGTTAGT
* * * * *
7569 TTGTTTCCTACACCAGGACTTGGACCAGAATCCTTAATGCCTTCAAGATTGAAGCTATCTGTTAG
1 TTGTTTCCTACA-CAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAG
* * ** *
7634 CTCGTTTCCGGTACCATTGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGT-T
65 CCCGTTTCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTATCTGTAT
7698 ATC
130 A-C
**
7701 CCGTTTCCCGTAC-CAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTA
1 TTGTTT-CC-TACACAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTA
*
7765 GCCCGTTTCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGT-
64 GCCCGTTTCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTATCTGTA
7829 TAGC
129 TA-C
**
7833 CCGTTTCCCGTAC-CAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTA
1 TTGTTT-CC-TACACAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTA
*
7897 GCCCGTTTCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGT-TGAT
64 GCCCGTTTCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTATCTG-T
7961 ATAC
128 ATAC
*
7965 TTGTTTCCTACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCGGTTAG
1 TTGTTTCCTACAC-AGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAG
* * * * * * * * *
8030 CCTGTTTCCCGTACCAGGGCTCGGGCCGGAATCCTTAATGCCACCACGAGTGGAGCTGTCGGTAA
65 CCCGTTTCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTATCTGTAT
8095 AC
130 AC
* *
8097 TTGTTTCCTACACTAGGGCTC-GAGCCAGAGTTCTTAATGCCTCCAAG
1 TTGTTTCCTACAC-AGGGCTCGGA-CCGGAGTCCTTAATGCCTCCAAG
8144 GGTTTGACTA
Statistics
Matches: 408, Mismatches: 27, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
130 3 0.01
131 7 0.02
132 390 0.96
133 5 0.01
134 3 0.01
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (131 bp):
TTGTTTCCTACACAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGC
CCGTTTCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTATCTGTATA
C
Found at i:8092 original size:66 final size:66
Alignment explanation
Indices: 7580--8071 Score: 758
Period size: 66 Copynumber: 7.5 Consensus size: 66
7570 TGTTTCCTAC
* * * * * * *
7580 ACCAGGACTTGGACCAGAATCCTTAATGCCTTCAAGATTGAAGCTATCTGTTAGCTCGTTTCCGG
1 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCCCG
7645 T
66 T
** *
7646 ACCATTGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTATCCCGTTTCCCG
1 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCCCG
7711 T
66 T
7712 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCCCG
1 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCCCG
7777 T
66 T
7778 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCCCG
1 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCCCG
7843 T
66 T
7844 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCCCG
1 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCCCG
7909 T
66 T
* * **
7910 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGT-TGATATA-CTTGTTT-C
1 ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTG-T-TAGCCCGTTTCC
7972 C-T
64 CGT
* *
7974 ACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCGGTTAGCCTGTTTCC
1 AC-C-AGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCC
8039 CGT
64 CGT
* *
8042 ACCAGGGCTCGGGCCGGAATCCTTAATGCC
1 ACCAGGGCTCGGACCGGAGTCCTTAATGCC
8072 ACCACGAGTG
Statistics
Matches: 395, Mismatches: 23, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
64 3 0.01
65 7 0.02
66 376 0.95
67 6 0.02
68 3 0.01
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (66 bp):
ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTTTCCCG
T
Found at i:8115 original size:66 final size:66
Alignment explanation
Indices: 7569--8143 Score: 429
Period size: 66 Copynumber: 8.7 Consensus size: 66
7559 GTCAGTTAGT
* * * * * * * * * * *
7569 TTGTTTCCTACACCAGGACTTGGACCAGAATCCTTAATGCCTTCAAGATTGAAGCTATCTGTTAG
1 TTGTTTCCTACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTCGGTAAA
7634 C
66 C
* ** * * * *
7635 TCGTTTCCGGTAC-C-ATTGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTT
1 TTGTTTCC--TACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTCGGTA
*
7698 ATC
64 AAC
** * * * *
7701 CCGTTTCCCGTAC-C-AGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTT
1 TTGTTT-CC-TACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTCGGTA
*
7764 AGC
64 AAC
** * * * *
7767 CCGTTTCCCGTAC-C-AGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTT
1 TTGTTT-CC-TACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTCGGTA
*
7830 AGC
64 AAC
** * * * *
7833 CCGTTTCCCGTAC-C-AGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTT
1 TTGTTT-CC-TACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTCGGTA
*
7896 AGC
64 AAC
** * *
7899 CCGTTTCCCGTAC-C-AGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTTGATA
1 TTGTTT-CC-TACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTCGGTA
*
7962 TAC
64 AAC
* * * *
7965 TTGTTTCCTACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCGGTTAG
1 TTGTTTCCTACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTCGGTAAA
8030 C
66 C
* * * * * *
8031 CTGTTTCCCGTAC-C-AGGGCTCGGGCCGGAATCCTTAATGCCACCACGAGTGGAGCTGTCGGTA
1 TTGTTT-CC-TACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTCGGTA
8094 AAC
64 AAC
* *
8097 TTGTTTCCTACACTAGGGCTC-GAGCCAGAGTTCTTAATGCCTCCAAG
1 TTGTTTCCTACACTAGGGCTCGGA-CCGGAGTCCTTAATGCCTCCAAG
8144 GGTTTGACTA
Statistics
Matches: 452, Mismatches: 47, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
64 6 0.01
65 7 0.02
66 427 0.94
67 6 0.01
68 6 0.01
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (66 bp):
TTGTTTCCTACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTCGGTAAA
C
Found at i:8183 original size:198 final size:198
Alignment explanation
Indices: 7575--8203 Score: 661
Period size: 198 Copynumber: 3.2 Consensus size: 198
7565 TAGTTTGTTT
* * * * * * *
7575 CCTACACCAGGACTTGGACCAGAATCCTTAATGCCTTCAAGATTGAAGCTATCTGTTAGCTCGTT
1 CCTACACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCGGTTAGCCCGTT
* ** * * * * * *
7640 TCCGGTACCATTGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTATCCCGT
66 TCCCGTACCAGGGCTCGGACCGGAATCCTTAATGCCACCAAGAGTGAAGCTATCGGTAAACCCGT
* * **
7705 TTCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGT-TAGCCC
131 TTCCCGTACCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGTGAAGCTATCAATATA---C
7769 GTT-TCC
193 -TTGTCC
* *
7775 CGT--ACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGTT
1 CCTACACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCGGTTAGCCCGTT
* * * * * *
7838 TCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCTGTTAGCCCGT
66 TCCCGTACCAGGGCTCGGACCGGAATCCTTAATGCCACCAAGAGTGAAGCTATCGGTAAACCCGT
* * **
7903 TTCCCGTACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGAGTGAAGCTGTTGATATACTTG
131 TTCCCGTACCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGTGAAGCTATCAATATACTTG
**
7968 TTT
196 TCC
* *
7971 CCTACACTAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCGGTTAGCCTGTT
1 CCTACACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCGGTTAGCCCGTT
* * * * **
8036 TCCCGTACCAGGGCTCGGGCCGGAATCCTTAATGCCACCACGAGTGGAGCTGTCGGTAAACTTGT
66 TCCCGTACCAGGGCTCGGACCGGAATCCTTAATGCCACCAAGAGTGAAGCTATCGGTAAACCCGT
* *
8101 TT-CC-TACACTAGGGCTC-GAGCCAGAGTTCTTAATGCCTCCAAGGGTTTG-A-CTATCAATGA
131 TTCCCGTAC-C-AGGGCTCGGA-CCAGAGTCCTTAATGCCTCCAAGAG--TGAAGCTATCAAT-A
8161 -ACTTGTGCC
190 TACTTGT-CC
*
8170 CCT-CACCAGGGCTC-GACCCGGAGTTCTTAATGCC
1 CCTACACCAGGGCTCGGA-CCGGAGTCCTTAATGCC
8204 CCCGAGGGTG
Statistics
Matches: 373, Mismatches: 44, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
195 2 0.01
196 7 0.02
197 7 0.02
198 346 0.93
199 7 0.02
200 4 0.01
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (198 bp):
CCTACACCAGGGCTCGGACCGGAGTCCTTAATGCCTCCAAGATTGAAGCTATCGGTTAGCCCGTT
TCCCGTACCAGGGCTCGGACCGGAATCCTTAATGCCACCAAGAGTGAAGCTATCGGTAAACCCGT
TTCCCGTACCAGGGCTCGGACCAGAGTCCTTAATGCCTCCAAGAGTGAAGCTATCAATATACTTG
TCC
Found at i:8904 original size:22 final size:24
Alignment explanation
Indices: 8877--8931 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
8867 ATCATTTAAA
8877 TAATATTTAAAATA-TTTTAT-AT
1 TAATATTTAAAATATTTTTATAAT
**
8899 TAATATTT-TTATATTTTTATAAT
1 TAATATTTAAAATATTTTTATAAT
8922 TAA-ATTTAAA
1 TAATATTTAAA
8932 TAAAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 3 0.12
22 18 0.69
23 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TAATATTTAAAATATTTTTATAAT
Found at i:9538 original size:18 final size:19
Alignment explanation
Indices: 9503--9539 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
9493 TTAAATTGAT
9503 ATAATTTGAATTAATATTTA
1 ATAATTTGAA-TAATATTTA
9523 ATAATTTGAA-AATATTT
1 ATAATTTGAATAATATTT
9540 TTATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
ATAATTTGAATAATATTTA
Found at i:9575 original size:22 final size:22
Alignment explanation
Indices: 9545--9611 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 22
9535 TATTTTTATT
9545 TAAAT-TTAATTATAAAATATAA
1 TAAATATTAATTATAAAA-ATAA
9567 -AAATATTAA-TATAAAAATAA
1 TAAATATTAATTATAAAAATAA
* *
9587 TTTATTATTAATTATAAATAATAA
1 -TAAATATTAATTATAAA-AATAA
9611 T
1 T
9612 TACAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 4 0.11
21 11 0.29
22 11 0.29
23 7 0.18
24 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATATTAATTATAAAAATAA
Found at i:9770 original size:18 final size:17
Alignment explanation
Indices: 9727--9793 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 17
9717 GATTATATAA
9727 ATATAATAT-AAAAAAT
1 ATATAATATAAAAAAAT
*
9743 ACTTAAAATATAAAATAAAT
1 A--TATAATATAAAA-AAAT
**
9763 ATATAATATATTAAAATTT
1 ATATAATATA--AAAAAAT
9782 ATATAATATAAA
1 ATATAATATAAA
9794 TTATTAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
16 1 0.02
17 2 0.05
18 15 0.37
19 15 0.37
20 8 0.20
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAATATAAAAAAAT
Found at i:9784 original size:17 final size:17
Alignment explanation
Indices: 9759--9816 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
9749 AATATAAAAT
*
9759 AAATATATAATATATTA
1 AAATTTATAATATATTA
9776 AAATTTAT-ATA-A-TA
1 AAATTTATAATATATTA
9790 TAAA-TTATTAATATATTA
1 -AAATTTA-TAATATATTA
9808 AAATTTATA
1 AAATTTATA
9817 TTTATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
14 5 0.15
15 5 0.15
16 6 0.18
17 13 0.38
18 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTATAATATATTA
Found at i:9790 original size:37 final size:37
Alignment explanation
Indices: 9749--9846 Score: 109
Period size: 32 Copynumber: 2.8 Consensus size: 37
9739 AAATACTTAA
9749 AATATAAAATAAATATATAATATATTAAAATTTATAT
1 AATATAAAATAAATATATAATATATTAAAATTTATAT
9786 AATAT-AAAT---TAT-TAATATATTAAAATTTATAT
1 AATATAAAATAAATATATAATATATTAAAATTTATAT
* * * *
9818 -TTATATATATAAATATAAAATATTTTAAA
1 AATATA-AAATAAATATATAATATATTAAA
9847 TATAATTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
31 3 0.06
32 20 0.39
33 6 0.12
36 7 0.14
37 15 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (37 bp):
AATATAAAATAAATATATAATATATTAAAATTTATAT
Found at i:9793 original size:32 final size:32
Alignment explanation
Indices: 9750--9834 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 32
9740 AATACTTAAA
*
9750 ATATAAAATAAATATATAATATATTAAAATTT
1 ATATAATATAAATATATAATATATTAAAATTT
9782 ATATAATATAAAT-TATTAATATATTAAAATTT
1 ATATAATATAAATATA-TAATATATTAAAATTT
* *
9814 ATAT-TTATATATATA-AATATA
1 ATATAATATAAATATATAATATA
9835 AAATATTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.12
31 8 0.17
32 34 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
ATATAATATAAATATATAATATATTAAAATTT
Found at i:9834 original size:18 final size:18
Alignment explanation
Indices: 9778--9834 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 18
9768 ATATATTAAA
9778 ATTTATATAATATAAAT-T
1 ATTTATAT-ATATAAATAT
*
9796 ATTAATATAT-TAAAATTTAT
1 ATTTATATATAT-AAA--TAT
9816 ATTTATATATATAAATAT
1 ATTTATATATATAAATAT
9834 A
1 A
9835 AAATATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
16 1 0.03
17 5 0.16
18 11 0.34
19 1 0.03
20 13 0.41
21 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTATATATATAAATAT
Found at i:10328 original size:22 final size:21
Alignment explanation
Indices: 10303--10344 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
10293 ATATATTAAA
10303 ATATTATTAT-ATTAATATTTAT
1 ATATT-TTATAATTAA-ATTTAT
10325 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
10345 ATTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:10787 original size:16 final size:16
Alignment explanation
Indices: 10754--10848 Score: 74
Period size: 16 Copynumber: 6.2 Consensus size: 16
10744 AATTTAATAG
*
10754 TTAAATTT--AATTAC
1 TTAAATTTAAAATAAC
*
10768 TTAAAATTAAAATAAC
1 TTAAATTTAAAATAAC
* *
10784 TTAAACTTAAAATAAT
1 TTAAATTTAAAATAAC
*
10800 TTTAATTTAAAA-AA-
1 TTAAATTTAAAATAAC
*
10814 TTAAATTTAAATTAA-
1 TTAAATTTAAAATAAC
* *
10829 TTTAATGTAAAATTAAC
1 TTAAATTTAAAA-TAAC
10846 TTA
1 TTA
10849 TCTAATTGAA
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
14 17 0.27
15 13 0.20
16 32 0.50
17 2 0.03
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAAATAAC
Found at i:10824 original size:30 final size:31
Alignment explanation
Indices: 10774--10848 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 31
10764 TTACTTAAAA
10774 TTAAAATAACTTAAACTTAAAATAATTTTAAT
1 TTAAAATAACTTAAACTTAAAATAA-TTTAAT
* *
10806 TTAAAA-AA-TTAAATTTAAATTAATTTAAT
1 TTAAAATAACTTAAACTTAAAATAATTTAAT
*
10835 GTAAAATTAACTTA
1 TTAAAA-TAACTTA
10849 TCTAATTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 11 0.30
30 13 0.35
31 4 0.11
32 9 0.24
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (31 bp):
TTAAAATAACTTAAACTTAAAATAATTTAAT
Found at i:11735 original size:10 final size:11
Alignment explanation
Indices: 11717--11749 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
11707 ATTTTTTATT
11717 TTATAATTTTA
1 TTATAATTTTA
11728 TT-TAATTTTA
1 TTATAATTTTA
*
11738 TTATATTTTTA
1 TTATAATTTTA
11749 T
1 T
11750 CAATTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATAATTTTA
Found at i:12024 original size:14 final size:15
Alignment explanation
Indices: 12005--12036 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
11995 ATTAAATACG
12005 AATATATTTAA-TAA
1 AATATATTTAATTAA
12019 AATATATTTAATTAA
1 AATATATTTAATTAA
12034 AAT
1 AAT
12037 TTTAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATATTTAATTAA
Found at i:17020 original size:14 final size:15
Alignment explanation
Indices: 17001--17030 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
16991 ACCATGCAAG
17001 AGCTGAAA-ATCGAA
1 AGCTGAAACATCGAA
17015 AGCTGAAACATCGAA
1 AGCTGAAACATCGAA
17030 A
1 A
17031 ACAGCTGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
AGCTGAAACATCGAA
Found at i:18162 original size:15 final size:15
Alignment explanation
Indices: 18144--18220 Score: 50
Period size: 15 Copynumber: 4.9 Consensus size: 15
18134 TAAATTATTA
18144 AAATTTATATAAAAT
1 AAATTTATATAAAAT
*
18159 AAATTATTAATATATAA-
1 AAA-T-TT-ATATAAAAT
18176 AAATTTATAT-AAAT
1 AAATTTATATAAAAT
* * *
18190 ATATATTATTTTAAAT
1 AAAT-TTATATAAAAT
*
18206 AAAATTATGATAAAA
1 AAATTTAT-ATAAAA
18221 AATATAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
13 2 0.04
14 7 0.15
15 14 0.30
16 12 0.26
17 5 0.11
18 7 0.15
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (15 bp):
AAATTTATATAAAAT
Found at i:18177 original size:31 final size:30
Alignment explanation
Indices: 18142--18220 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 30
18132 TTTAAATTAT
*
18142 TAAAATTTATATAAAATAAATTATTAATATA
1 TAAAATTTATATAAAATAAATTATT-ATAAA
* *
18173 TAAAAATTTATATAAATATATATTATTTTAAA
1 T-AAAATTTATATAAA-ATAAATTATTATAAA
18205 TAAAA-TTATGATAAAA
1 TAAAATTTAT-ATAAAA
18221 AATATAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 5 0.12
31 10 0.24
32 18 0.43
33 9 0.21
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
TAAAATTTATATAAAATAAATTATTATAAA
Found at i:18208 original size:32 final size:32
Alignment explanation
Indices: 18143--18209 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
18133 TTAAATTATT
*
18143 AAAATTTATATAAAATAAATTATTAATATATA
1 AAAATTTATATAAAATAAATTATTAATAAATA
* *
18175 AAAATTTATATAAATATATATTATT-TTAAATA
1 AAAATTTATATAAA-ATAAATTATTAATAAATA
18207 AAA
1 AAA
18210 TTATGATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 22 0.71
33 9 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAATTTATATAAAATAAATTATTAATAAATA
Found at i:22661 original size:30 final size:30
Alignment explanation
Indices: 22627--22687 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
22617 TTTAAATAAT
*
22627 TTTAA-AAATTAATTATATTAAAAATTTATA
1 TTTAATAAATTAATAATA-TAAAAATTTATA
** *
22657 TTTAATTTATTAATAATATATAAATTTATA
1 TTTAATAAATTAATAATATAAAAATTTATA
22687 T
1 T
22688 ATTTATACGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAATAAATTAATAATATAAAAATTTATA
Found at i:22678 original size:22 final size:23
Alignment explanation
Indices: 22635--22678 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
22625 ATTTTAAAAA
*
22635 TTAATTATATTAAAAATTTATAT
1 TTAATTATATTAAAAATATATAT
*
22658 TTAATT-TATTAATAATATATA
1 TTAATTATATTAAAAATATATA
22679 AATTTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATTATATTAAAAATATATAT
Found at i:22872 original size:2 final size:2
Alignment explanation
Indices: 22865--22933 Score: 63
Period size: 2 Copynumber: 35.5 Consensus size: 2
22855 AATAATCACA
* * *
22865 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AA AT -T AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
22906 A- AT GT ACT CT AT AT AT AT AT AT AT -T AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A
22934 CTATTAATGA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
1 3 0.06
2 49 0.92
3 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22950 original size:31 final size:31
Alignment explanation
Indices: 22884--22950 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
22874 CATATATATA
*
22884 TATATATATATAAATTATATTTAATGTACTC
1 TATATATATATAAATTATATTTAATGTAATC
*
22915 TATATATATATATATTATACTATTAATG-AAT-
1 TATATATATATAAATTATA-T-TTAATGTAATC
22946 TATAT
1 TATAT
22951 TATGTCACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 23 0.72
32 3 0.09
33 6 0.19
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (31 bp):
TATATATATATAAATTATATTTAATGTAATC
Found at i:23723 original size:11 final size:11
Alignment explanation
Indices: 23707--23766 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
23697 AATAATAAAA
23707 AATTTAAATTT
1 AATTTAAATTT
23718 AATTTAAATTT
1 AATTTAAATTT
23729 AA-TTAAATTT
1 AATTTAAATTT
* *
23739 TATTT---TTAA
1 AATTTAAATT-T
23748 AATTTAAATTT
1 AATTTAAATTT
23759 AATTTAAA
1 AATTTAAA
23767 ATAAAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
8 2 0.05
9 4 0.10
10 9 0.22
11 23 0.57
12 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:23755 original size:7 final size:6
Alignment explanation
Indices: 23706--23795 Score: 62
Period size: 6 Copynumber: 15.0 Consensus size: 6
23696 AAATAATAAA
**
23706 AAATTT AAATTT -AATTT AAATTT -AA-TT AAATTTT ATTTTT AAAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAA-TTT AAATTT -AAATTT
* * * *
23753 AAATTT -AATTT AAAATA AAAATT AAATTATT AAATTT TAATTT
1 AAATTT AAATTT AAATTT AAATTT AAA-T-TT AAATTT AAATTT
23796 GACTAAACTC
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
4 2 0.03
5 14 0.21
6 38 0.57
7 8 0.12
8 5 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:25448 original size:19 final size:18
Alignment explanation
Indices: 25414--25485 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 18
25404 ATGTAATGTC
*
25414 ATTATTATA-CTATCATT
1 ATTATTATATTTATCATT
*
25431 ATTATTAATATTTATCATA
1 ATTATT-ATATTTATCATT
*
25450 ATTAATTATATTAAT-ATT
1 ATT-ATTATATTTATCATT
*
25468 A--ATTATATTTATAATT
1 ATTATTATATTTATCATT
25484 AT
1 AT
25486 AATATATGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 10 0.22
16 4 0.09
17 6 0.13
18 6 0.13
19 16 0.36
20 3 0.07
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATTATATTTATCATT
Found at i:26355 original size:3 final size:3
Alignment explanation
Indices: 26347--26386 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
26337 GGGAAAAGAG
26347 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
26387 ATGAAGGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:26780 original size:83 final size:81
Alignment explanation
Indices: 26685--26858 Score: 278
Period size: 83 Copynumber: 2.1 Consensus size: 81
26675 TAAAAGAGTA
26685 ACCTAATAATTAAATCTTATTATTATTATCCAAATTTTAACTTTTTTTATTTATATAAATTTTTA
1 ACCTAATAATTAAATCTTATTATTATTATCCAAATTTTAAC-TTTTTTATTTATATAAA-TTTTA
*
26750 AATATTTATGTAGTATTG
64 AATATTTATATAGTATTG
* * *
26768 ACCTAATAATTAAATTTTATTATTTTTATCTAAATTTTAACTTTTTTATTTATATAAATTTTAAA
1 ACCTAATAATTAAATCTTATTATTATTATCCAAATTTTAACTTTTTTATTTATATAAATTTTAAA
26833 TATTTATATAGTATTG
66 TATTTATATAGTATTG
*
26849 ACATAA-AATT
1 ACCTAATAATT
26859 TTGCAAGACT
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
80 4 0.05
81 27 0.31
82 17 0.20
83 38 0.44
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (81 bp):
ACCTAATAATTAAATCTTATTATTATTATCCAAATTTTAACTTTTTTATTTATATAAATTTTAAA
TATTTATATAGTATTG
Found at i:27776 original size:30 final size:27
Alignment explanation
Indices: 27738--27803 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
27728 AGATAAAAAA
27738 TTACGAATATTTGAATTTAAATTTTATAT
1 TTACGAATATTT-AATTTAAATTTT-TAT
* *
27767 TTACTGAATATTTACTTTGAATTTTTAT
1 TTAC-GAATATTTAATTTAAATTTTTAT
*
27795 TTACAAATA
1 TTACGAATA
27804 ATACATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.12
28 7 0.21
29 14 0.42
30 8 0.24
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (27 bp):
TTACGAATATTTAATTTAAATTTTTAT
Found at i:27967 original size:3 final size:3
Alignment explanation
Indices: 27959--27987 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
27949 CTCTTAAATG
27959 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27988 TTCATTTGGA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28237 original size:3 final size:3
Alignment explanation
Indices: 28229--28265 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
28219 TGTGTTTAGT
28229 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28266 AAGTATTGTG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:30492 original size:17 final size:18
Alignment explanation
Indices: 30470--30511 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
30460 AAAAAATCTA
30470 AAAATTTACA-TTTTTGC
1 AAAATTTACATTTTTTGC
**
30487 AAAATTTTTATTTTTTGC
1 AAAATTTACATTTTTTGC
30505 AAAATTT
1 AAAATTT
30512 TTATACTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (18 bp):
AAAATTTACATTTTTTGC
Found at i:30501 original size:18 final size:18
Alignment explanation
Indices: 30480--30515 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
30470 AAAATTTACA
30480 TTTTTGCAAAATTTTTAT
1 TTTTTGCAAAATTTTTAT
30498 TTTTTGCAAAATTTTTAT
1 TTTTTGCAAAATTTTTAT
30516 ACTACATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTTTGCAAAATTTTTAT
Found at i:32248 original size:18 final size:17
Alignment explanation
Indices: 32225--32276 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
32215 CTAGATATTT
32225 AAATAATTATTTTTAATA
1 AAATAATTATTTTTAA-A
* *
32243 AAATAATAAAATTTTAAA
1 AAATAAT-TATTTTTAAA
*
32261 AAATAA-TATTTATAAA
1 AAATAATTATTTTTAAA
32277 TTTTAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 7 0.25
18 14 0.50
19 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATAATTATTTTTAAA
Found at i:32271 original size:15 final size:17
Alignment explanation
Indices: 32240--32276 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
32230 ATTATTTTTA
32240 ATAAAATAATAAAATTT
1 ATAAAATAATAAAATTT
*
32257 -TAAAA-AATAATATTT
1 ATAAAATAATAAAATTT
32272 ATAAA
1 ATAAA
32277 TTTTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAATAATAAAATTT
Found at i:32328 original size:29 final size:30
Alignment explanation
Indices: 32269--32328 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
32259 AAAAATAATA
*
32269 TTTATAAATTTTAATTTTTATAATGTATTT
1 TTTATAAATTTTAATTTTAATAATGTATTT
32299 TTTA-AAATTTTAA-TTTAAT-ATGATATTT
1 TTTATAAATTTTAATTTTAATAATG-TATTT
32327 TT
1 TT
32329 AAATACTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.11
28 12 0.43
29 9 0.32
30 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTATAAATTTTAATTTTAATAATGTATTT
Found at i:33234 original size:21 final size:20
Alignment explanation
Indices: 33207--33246 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
33197 ATATTAAAAA
33207 TTAT-TTTTAT-ATTAATATT
1 TTATATTTTATAATTAA-ATT
33226 TTATATTTTATAATTAAATT
1 TTATATTTTATAATTAAATT
33246 T
1 T
33247 AAATGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATATTTTATAATTAAATT
Found at i:34906 original size:39 final size:40
Alignment explanation
Indices: 34836--34911 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 40
34826 ACAAATCATC
* *
34836 TTAAAATTAAATATAATATTATCTTTAATATT-ATTAAAT
1 TTAAAATTAAAAATAATATTATATTTAATATTGATTAAAT
* * * *
34875 TTAAGATTAAAAATAATTTTTTATTTTATATTGATTA
1 TTAAAATTAAAAATAATATTATATTTAATATTGATTA
34912 TGATTATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
39 26 0.87
40 4 0.13
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (40 bp):
TTAAAATTAAAAATAATATTATATTTAATATTGATTAAAT
Found at i:37031 original size:17 final size:17
Alignment explanation
Indices: 37000--37044 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
36990 TTTTATGTTA
*
37000 ATTAATAATTTTTTAATT
1 ATTAATAAATTTTT-ATT
*
37018 -TTATTAAATTTTTATT
1 ATTAATAAATTTTTATT
37034 ATTAATAAATT
1 ATTAATAAATT
37045 AAATTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTAATAAATTTTTATT
Found at i:37046 original size:22 final size:22
Alignment explanation
Indices: 37020--37061 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
37010 TTTTAATTTT
* *
37020 ATTAAATTTTTATTATTAATAA
1 ATTAAATTATTAATATTAATAA
37042 ATTAAATTATTAATATTAAT
1 ATTAAATTATTAATATTAAT
37062 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTAAATTATTAATATTAATAA
Found at i:37072 original size:16 final size:16
Alignment explanation
Indices: 37012--37072 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 16
37002 TAATAATTTT
37012 TTAATTTTATTAAAT-
1 TTAATTTTATTAAATA
*
37027 TT--TTATTATTAATAAA
1 TTAATT-TTATTAA-ATA
*
37043 TTAA-ATTATT-AATA
1 TTAATTTTATTAAATA
37057 TTAATTTTATTAAATA
1 TTAATTTTATTAAATA
37073 ATTTTAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
13 2 0.06
14 13 0.37
15 9 0.26
16 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTTTATTAAATA
Found at i:37082 original size:23 final size:24
Alignment explanation
Indices: 37012--37083 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 24
37002 TAATAATTTT
37012 TTAATTTTATTAAAT--TTTTATTA
1 TTAATTTTATTAAATAATTTTA-TA
** * *
37035 TTAA-TAAATTAAATTA-TTAATA
1 TTAATTTTATTAAATAATTTTATA
37057 TTAATTTTATTAAATAATTTTA-A
1 TTAATTTTATTAAATAATTTTATA
37080 TTAA
1 TTAA
37084 AAATTGACTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 14 0.37
23 21 0.55
24 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAATTTTATTAAATAATTTTATA
Found at i:37084 original size:14 final size:13
Alignment explanation
Indices: 37013--37088 Score: 50
Period size: 13 Copynumber: 5.4 Consensus size: 13
37003 AATAATTTTT
37013 TAATTTTATTAAA
1 TAATTTTATTAAA
37026 T--TTTTATTATTAA
1 TAATTTTATTA--AA
37039 TAAATTAAATTATTAATA
1 T-AATT---TTATTAA-A
37057 TTAATTTTATTAAA
1 -TAATTTTATTAAA
37071 TAATTTTAATTAAA
1 TAATTTT-ATTAAA
37085 -AATT
1 TAATT
37089 GACTTAAGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 22
0.70 0.00 0.30
Matches are distributed among these distances:
11 8 0.15
13 15 0.29
14 7 0.13
15 7 0.13
16 2 0.04
17 1 0.02
18 5 0.10
19 7 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATTTTATTAAA
Found at i:37227 original size:30 final size:30
Alignment explanation
Indices: 37191--37249 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
37181 TACACTTGAG
37191 TGATATAATTT-ATTAAAAATAAAAATTTAA
1 TGATATAATTTGA-TAAAAATAAAAATTTAA
* *
37221 TGATATAATTTGATAAAATTTAAAATTTA
1 TGATATAATTTGATAAAAATAAAAATTTA
37250 TAAATTACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (30 bp):
TGATATAATTTGATAAAAATAAAAATTTAA
Found at i:38595 original size:2 final size:2
Alignment explanation
Indices: 38584--38617 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
38574 TGTTTTGCTT
38584 TA TA -A 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 TA T
38618 TTGCAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40055 original size:2 final size:2
Alignment explanation
Indices: 40048--40094 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
40038 GATTACTTCA
40048 AT AT AT AT AT AT 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 AT AT AT AT AT AT
40090 AT AT A
1 AT AT A
40095 CCTAATTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40167 original size:2 final size:2
Alignment explanation
Indices: 40160--40186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40150 AAATATTGTC
40160 AT 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 AT A
40187 GTTAAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41009 original size:16 final size:16
Alignment explanation
Indices: 40988--41030 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
40978 AAATTTTAAA
*
40988 ATATTATTTATATTAT
1 ATATTATATATATTAT
*
41004 ATATTATATATTTTAT
1 ATATTATATATATTAT
41020 ACGTATTATAT
1 A--TATTATAT
41031 TTATATAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
18 8 0.35
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
ATATTATATATATTAT
Found at i:42020 original size:91 final size:91
Alignment explanation
Indices: 41919--42101 Score: 330
Period size: 91 Copynumber: 2.0 Consensus size: 91
41909 TAACTTTGAA
* *
41919 TATATTATTTTAATATTACAACTAACCTACTTGAATTTAAAATATAAAATTTAATCTATTTATTT
1 TATATTATTTTAATATTACAACTAACCCACTTGAATTTAAAATATAAAATTTAATCTATATATTT
*
41984 AATATAATATTCAAGTATAGTATAAC
66 AATATAATATTCAAGTATAATATAAC
42010 TATATTATTTTAATATTACAACTAACCCACTTGAATTTAAAATATAAAATTTAATCTATATATTT
1 TATATTATTTTAATATTACAACTAACCCACTTGAATTTAAAATATAAAATTTAATCTATATATTT
*
42075 AATATAATATTTAAGTATAATATAAC
66 AATATAATATTCAAGTATAATATAAC
42101 T
1 T
42102 CTTAATGAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (91 bp):
TATATTATTTTAATATTACAACTAACCCACTTGAATTTAAAATATAAAATTTAATCTATATATTT
AATATAATATTCAAGTATAATATAAC
Found at i:42076 original size:13 final size:12
Alignment explanation
Indices: 42050--42097 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
42040 TTGAATTTAA
*
42050 AATATAAAATTT
1 AATATAATATTT
*
42062 AATCTATATATTT
1 AATATA-ATATTT
42075 AATATAATATTT
1 AATATAATATTT
42087 AAGTATAATAT
1 AA-TATAATAT
42098 AACTCTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 13 0.42
13 18 0.58
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (12 bp):
AATATAATATTT
Found at i:43182 original size:11 final size:11
Alignment explanation
Indices: 43166--43190 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43156 TAATTAATAC
43166 ATTAAATTAAA
1 ATTAAATTAAA
43177 ATTAAATTAAA
1 ATTAAATTAAA
43188 ATT
1 ATT
43191 TTTATATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAAATTAAA
Found at i:45569 original size:22 final size:23
Alignment explanation
Indices: 45542--45586 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
45532 TCAAAACATA
45542 AAACTTGT-AATTTTACTGTTTT
1 AAACTTGTCAATTTTACTGTTTT
* *
45564 AAACTTGTCATTTTTATTGTTTT
1 AAACTTGTCAATTTTACTGTTTT
45587 TTGTCCCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (23 bp):
AAACTTGTCAATTTTACTGTTTT
Found at i:49352 original size:17 final size:17
Alignment explanation
Indices: 49330--49364 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
49320 TAGAGGTGTA
*
49330 TATAAAATATTTATATT
1 TATAAAATATTTAAATT
49347 TATAAAATATTTAAATT
1 TATAAAATATTTAAATT
49364 T
1 T
49365 GATGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAAAATATTTAAATT
Found at i:49437 original size:19 final size:19
Alignment explanation
Indices: 49392--49431 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
49382 TTGACTCCAT
49392 AATTATTAAATTAAATTTA
1 AATTATTAAATTAAATTTA
49411 AATTATTAAA-TAAA-TTA
1 AATTATTAAATTAAATTTA
49428 AATT
1 AATT
49432 TTATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.33
18 4 0.19
19 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTATTAAATTAAATTTA
Found at i:52827 original size:2 final size:2
Alignment explanation
Indices: 52820--52855 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
52810 ATTAAAAGTT
52820 TA TA TA TA -A 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 TA TA T
52856 CCAGTGCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53325 original size:26 final size:24
Alignment explanation
Indices: 53289--53361 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 24
53279 TAATAATTAT
53289 ATTTAAAATATTATAAATTTATATA
1 ATTT-AAATATTATAAATTTATATA
*
53314 ATTTTAATATATTA-ATAATTTATATT
1 A-TTTAA-ATATTATA-AATTTATATA
* *
53340 ATATAAATATTATATATTTATA
1 ATTTAAATATTATAAATTTATA
53362 ATTATCAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
24 13 0.32
25 9 0.22
26 19 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTAAATATTATAAATTTATATA
Found at i:53333 original size:17 final size:18
Alignment explanation
Indices: 53311--53348 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53301 ATAAATTTAT
*
53311 ATAATTT-TAATATATTA
1 ATAATTTATAATATATAA
*
53328 ATAATTTATATTATATAA
1 ATAATTTATAATATATAA
53346 ATA
1 ATA
53349 TTATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAATTTATAATATATAA
Found at i:53371 original size:24 final size:24
Alignment explanation
Indices: 53294--53373 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 24
53284 ATTATATTTA
*
53294 AAATATTATAAATTTATATAATT-TT
1 AAATATTATATA-TT-TATAATTATT
53319 AATATATTA-ATAATTTAT-ATTATAT
1 AA-ATATTATAT-ATTTATAATTAT-T
*
53344 AAATATTATATATTTATAATTATC
1 AAATATTATATATTTATAATTATT
53368 AAATAT
1 AAATAT
53374 AATTAATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
23 3 0.06
24 22 0.47
25 15 0.32
26 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATATTATATATTTATAATTATT
Found at i:53373 original size:50 final size:48
Alignment explanation
Indices: 53279--53380 Score: 120
Period size: 50 Copynumber: 2.1 Consensus size: 48
53269 TTATTTTTTA
*
53279 TAATAATTATATTTAAAATATTATAAATTTATATAATTTTAATAT-AT
1 TAATAATTATATTTAAAATATTATAAATTTATATAATTTAAATATAAT
*
53326 TAATAATTTATATTATATAAATATTATATA-TT-TATAATTATCAAATATAAT
1 TAATAA-TTATATT-TA-AAATATTATAAATTTATATAATT-T-AAATATAAT
53377 TAAT
1 TAAT
53381 TTTAAAAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
47 6 0.13
48 14 0.30
49 5 0.11
50 16 0.34
51 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (48 bp):
TAATAATTATATTTAAAATATTATAAATTTATATAATTTAAATATAAT
Found at i:53382 original size:24 final size:23
Alignment explanation
Indices: 53277--53382 Score: 67
Period size: 24 Copynumber: 4.5 Consensus size: 23
53267 TATTATTTTT
53277 TATAATAA-TTATATT-TA-AAA
1 TATAATAATTTATATTATACAAA
* * **
53297 TATTATAAATTTATATAATTTTAATA
1 TATAAT-AATTTATATTA-TACAA-A
*
53323 TATTAATAATTTATATTATATAAA
1 TA-TAATAATTTATATTATACAAA
*
53347 TATTATATATTTATAATTAT-CAAA
1 TATAATA-ATTTAT-ATTATACAAA
53371 TATAATTAATTT
1 TATAA-TAATTT
53383 TAAAAAACAT
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
20 5 0.07
21 2 0.03
22 6 0.09
23 4 0.06
24 21 0.31
25 13 0.19
26 13 0.19
27 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAATAATTTATATTATACAAA
Found at i:53841 original size:18 final size:17
Alignment explanation
Indices: 53775--53927 Score: 71
Period size: 18 Copynumber: 8.4 Consensus size: 17
53765 CGATAGTTTT
*
53775 AAATATAAAAAAATTATA
1 AAATATAAATAAA-TATA
53793 AAATATAAATATAATATA
1 AAATATAAATA-AATATA
53811 AAA-ATTAAAATAAATATA
1 AAATA-T-AAATAAATATA
*
53829 AAATATCACAT-AATA-A
1 AAATAT-AAATAAATATA
*
53845 AAAAATAATATAGAAATATA
1 AAATATAA-AT--AAATATA
**
53865 AATATATTAAATTTATATA
1 AA-ATA-TAAATAAATATA
* *
53884 ATAATAATTATTAATATATAA
1 A-AAT-ATAAATAA-ATAT-A
*
53905 AAATTTATAA-AAATATA
1 AAATATA-AATAAATATA
53922 AAATAT
1 AAATAT
53928 TTAAATATAA
Statistics
Matches: 103, Mismatches: 16, Indels: 33
0.68 0.11 0.22
Matches are distributed among these distances:
15 1 0.01
16 8 0.08
17 11 0.11
18 35 0.34
19 26 0.25
20 13 0.13
21 6 0.06
22 3 0.03
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (17 bp):
AAATATAAATAAATATA
Found at i:53881 original size:17 final size:17
Alignment explanation
Indices: 53861--53936 Score: 63
Period size: 17 Copynumber: 4.6 Consensus size: 17
53851 AATATAGAAA
*
53861 TATAAATATATTAAATT
1 TATAAATATATAAAATT
53878 TAT--ATA-ATAATAA-T
1 TATAAATATATAA-AATT
*
53892 TATTAATATATAAAAATT
1 TATAAATATAT-AAAATT
*
53910 TATAAAAATATAAAATAT
1 TATAAATATATAAAAT-T
53928 T-TAAATATA
1 TATAAATATA
53937 ATTATGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
14 7 0.15
15 5 0.10
16 3 0.06
17 19 0.40
18 14 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAAATATATAAAATT
Found at i:54939 original size:22 final size:22
Alignment explanation
Indices: 54911--54958 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
54901 TGTTAAAAAG
* *
54911 GGTTATGGTTCTTTTCTCTTTT
1 GGTTATGGTTCTTTCCTCCTTT
54933 GGTTATGGTTCTTTCCTCCTTT
1 GGTTATGGTTCTTTCCTCCTTT
54955 GGTT
1 GGTT
54959 TACTTACCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.04, C:0.17, G:0.21, T:0.58
Consensus pattern (22 bp):
GGTTATGGTTCTTTCCTCCTTT
Found at i:55473 original size:18 final size:18
Alignment explanation
Indices: 55450--55484 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55440 TTAAAAAATT
*
55450 ATTTTTATATGTTGAAAG
1 ATTTTTATATCTTGAAAG
*
55468 ATTTTTTTATCTTGAAA
1 ATTTTTATATCTTGAAA
55485 ATAATATTAA
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:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (18 bp):
ATTTTTATATCTTGAAAG
Found at i:55726 original size:18 final size:18
Alignment explanation
Indices: 55692--55726 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55682 AATTTACGTG
* *
55692 TTTATATTTATATTATTT
1 TTTATATTTAAAATATTT
55710 TTTATATTTAAAATATT
1 TTTATATTTAAAATATT
55727 ATATTTTTTA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATATTTAAAATATTT
Found at i:56291 original size:11 final size:12
Alignment explanation
Indices: 56256--56293 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
56246 TTTTCGTATC
56256 ATATTGATTTTTT
1 ATATT-ATTTTTT
*
56269 ATATTATGTTTT
1 ATATTATTTTTT
56281 A-ATTATTTTTT
1 ATATTATTTTTT
56292 AT
1 AT
56294 TAAATGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 7 0.32
13 5 0.23
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:56317 original size:23 final size:20
Alignment explanation
Indices: 56262--56317 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 20
56252 TATCATATTG
56262 ATTTTTTATATTATGTTTTA
1 ATTTTTTATATTATGTTTTA
* *
56282 ATTATTTTTTATTAAATGTTTTT
1 ATT-TTTTATATT--ATGTTTTA
56305 ATTTTTATATATT
1 ATTTTT-TATATT
56318 TAAAATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 3 0.10
21 8 0.28
22 3 0.10
23 15 0.52
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
ATTTTTTATATTATGTTTTA
Found at i:56923 original size:16 final size:14
Alignment explanation
Indices: 56896--56934 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
56886 TTTAAAGTAT
*
56896 TATAAATTTATATA
1 TATATATTTATATA
56910 -ATAT-TTTATATA
1 TATATATTTATATA
56922 TATATATTTATAT
1 TATATATTTATAT
56935 GTTTTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 8 0.36
13 7 0.32
14 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATATTTATATA
Found at i:57002 original size:21 final size:22
Alignment explanation
Indices: 56959--57006 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
56949 GTCATATTCA
* *
56959 TTTTTATATTATGTTTTAATTAT
1 TTTTTATATCATGATTT-ATTAT
56982 TTTTTATATCATGATTT-TTAT
1 TTTTTATATCATGATTTATTAT
57003 TTTT
1 TTTT
57007 CGTATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
23 15 0.65
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTTTATATCATGATTTATTAT
Found at i:57353 original size:695 final size:682
Alignment explanation
Indices: 56113--57384 Score: 1601
Period size: 695 Copynumber: 1.9 Consensus size: 682
56103 AGATGGAAAG
* * *
56113 AAAAAAGAAAAGAAAGAAAAGGAAAGAACGAAATAAAAAAATTTAATATGTTTATATTTATGTTT
1 AAAAAAGAAAAGAAAGAAAAGGAAAGAACGAAATAAAAAAATTTAACATGTTTATATTTATATTC
*
56178 GTATTATTTTTTATTGTTTAAATTATTATAAATTTATATAATTGTATACATATATATTAATAGTT
66 GTATTATTTTTTATTGTTTAAAGTATTATAAATTTATATAATTGTATACATATATATTAATAGTT
* * *
56243 TTTTTTTCGTATCATATTGATTTTTTATATTATGTTTTAATTATTTTTTATTAAATGTTTTTATT
131 TTTTATTCATATCATATTCATTTTTTATATTATGTTTTAATTATTTTTTATTAAATGTTTTTATT
*
56308 TTTATATATTTAAAATAATATAAATTTATATAAATTTTTACACATTAATTATTTGTATATGTATA
196 TTTATATATTTAAAATAATATAAATTTATATAAATTTTTACACATTAATTATTTATATATGTATA
* * * *
56373 TTTTGACATATTAGTGTAATTAAATAATATATTTAAAATGATGAATTCTTAAGTCGATGTACTAT
261 -TTTGACACATTAGTGTAATTAAATAATATATTTAAAATAATGAATTCATAAGTCAATGTACTAT
* *
56438 CTATTTAAAATTCATACCCTATTCTAAATATAAATTTAAATAAATAAATAAATATTATTTAATAA
325 CGATTTAAAATTCATACCCTACTCTAAATATAAATTT--ATAAATAAAT-AATATTATTTAATAA
*
56503 AATTTAGTTTTTATTAAAAATAATTAAAATATAAAAAATTAAAAATATCATTATTTATTTTATTT
387 AATTTAATTTTTATTAAAAATAATTAAAATAT-----ATTAAAAATATCATTATTTATTTTATTT
* * *** *
56568 TTAAATGATGTGTTTAAAGTAATAAATTTTTGTGTTAACTCACAAAAAATTTAAATTTTATTTTT
447 TTAAATGATATATTTAAAGTAATAAATTTTTAAATTAACTCACAAAAAATTTAAATTTTATTTTA
*
56633 AATTTTAAATACATAATTATTATTT-AATAAAATTTATTTTATAATTAATTTTTTATTAATAATA
512 AATTTTAAAAACATAATTATTATTTAAATAAAATTTATTTTATAATTAATTTTTTATTAATAATA
56697 TAAAATTAACTATATAAATAAATCTGATGTTAATATATGTCTTGCTTTTGAGTTTTTTTTCACAG
577 TAAAATTAACTATATAAATAAATCTGATGTTAATATATGTCTTGCTTTTGAGTTTTTTTTCACAG
56762 GCCATGGGAGAAGGAAAAATGCAAAAAATAAAAGAAAAAAT
642 GCCATGGGAGAAGGAAAAATGCAAAAAATAAAAGAAAAAAT
* * *
56803 AAAAAATAAAAGAAAGAAAATGAGAGAGA-GAAATAAAAGAAAATTTAACATGTTTATATTTATA
1 AAAAAAGAAAAGAAAGAAAAGGAAAGA-ACGAAAT-AAA-AAAATTTAACATGTTTATATTTATA
* * * *
56867 TTCGTGTTATTTTTTATTGTTTAAAGTATTATAAATTTATATAATATTTTATATATATATATTTA
63 TTCGTATTATTTTTTATTGTTTAAAGTATTATAAATTTATAT-A-ATTGTATACATATATATTAA
* *
56932 TATGTTTTTATATTCATGTCATATTCA-TTTTTATATTATGTTTTAATTATTTTTTA-TATCATG
126 TA-GTTTTT-TATTCATATCATATTCATTTTTTATATTATGTTTTAATTATTTTTTATTA-AATG
* * * *
56995 ATTTTTATTTTTCGTATATTTAAAGTAATATAAATTTATATAAATTTTTATATATTAATTATTTA
188 -TTTTTATTTTT-ATATATTTAAAATAATATAAATTTATATAAATTTTTACACATTAATTATTTA
* * *
57060 TTTATGTATA-TTGATACGTTAGTGTAATTAAATAATATATTTAAAATAAT-AGATCTGCAT-A-
251 TATATGTATATTTGACACATTAGTGTAATTAAATAATATATTTAAAATAATGA-AT-T-CATAAG
* * ** *
57121 TTAATGTA-TGATCGATTTAAAATTTATA-TTTACTCTAAATA-CAA-TT-T-AATAAAT-ATAT
313 TCAATGTACT-ATCGATTTAAAATTCATACCCTACTCTAAATATAAATTTATAAATAAATAATAT
*
57179 TA-TTAATAAAATTTAATTTTTATTAAAAATAATTAAAAT-T-TTAAAAATATTATTA-TTATTT
377 TATTTAATAAAATTTAATTTTTATTAAAAATAATTAAAATATATTAAAAATATCATTATTTATTT
* * *
57240 TATTTTTAAATGATATATTTAATAAGTAATGAATTTTTAAATT-A-T-A-ATAAAATTT-ATTTT
442 TATTTTTAAATGATATATTT-A-AAGTAATAAATTTTTAAATTAACTCACAAAAAATTTAAATTT
*
57300 CTAATTTTAAATATAAAATTAAAAACATAATTATTATTT-AATAAAATTTA-TTTA-AA-TAACA
505 -T-ATTTTAAAT-T----TTAAAAACATAATTATTATTTAAATAAAATTTATTTTATAATTAA-T
57361 TTTTTATTAATAATAATTAAAATT
562 TTTTTATTAATAAT-A-TAAAATT
57385 TATAAATAAA
Statistics
Matches: 508, Mismatches: 48, Indels: 61
0.82 0.08 0.10
Matches are distributed among these distances:
674 4 0.01
675 9 0.02
676 9 0.02
677 26 0.05
678 19 0.04
679 32 0.06
680 5 0.01
681 38 0.07
684 1 0.00
685 36 0.07
686 6 0.01
688 7 0.01
689 1 0.00
690 29 0.06
691 4 0.01
692 64 0.13
693 3 0.01
694 33 0.06
695 98 0.19
696 26 0.05
697 58 0.11
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (682 bp):
AAAAAAGAAAAGAAAGAAAAGGAAAGAACGAAATAAAAAAATTTAACATGTTTATATTTATATTC
GTATTATTTTTTATTGTTTAAAGTATTATAAATTTATATAATTGTATACATATATATTAATAGTT
TTTTATTCATATCATATTCATTTTTTATATTATGTTTTAATTATTTTTTATTAAATGTTTTTATT
TTTATATATTTAAAATAATATAAATTTATATAAATTTTTACACATTAATTATTTATATATGTATA
TTTGACACATTAGTGTAATTAAATAATATATTTAAAATAATGAATTCATAAGTCAATGTACTATC
GATTTAAAATTCATACCCTACTCTAAATATAAATTTATAAATAAATAATATTATTTAATAAAATT
TAATTTTTATTAAAAATAATTAAAATATATTAAAAATATCATTATTTATTTTATTTTTAAATGAT
ATATTTAAAGTAATAAATTTTTAAATTAACTCACAAAAAATTTAAATTTTATTTTAAATTTTAAA
AACATAATTATTATTTAAATAAAATTTATTTTATAATTAATTTTTTATTAATAATATAAAATTAA
CTATATAAATAAATCTGATGTTAATATATGTCTTGCTTTTGAGTTTTTTTTCACAGGCCATGGGA
GAAGGAAAAATGCAAAAAATAAAAGAAAAAAT
Found at i:57402 original size:20 final size:20
Alignment explanation
Indices: 57363--57402 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
57353 AAATAACATT
* * *
57363 TTTATTAATAATAATTAAAA
1 TTTATAAATAAAAATAAAAA
57383 TTTATAAATAAAAATAAAAA
1 TTTATAAATAAAAATAAAAA
57403 CTCCCGCATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTATAAATAAAAATAAAAA
Found at i:59523 original size:3 final size:3
Alignment explanation
Indices: 59515--59560 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
59505 TATCTAACAG
59515 TAA TAA TAA 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 TAA TAA TAA T
59561 TAAAACGTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:60042 original size:15 final size:15
Alignment explanation
Indices: 60022--60052 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
60012 ATTTTGTAAC
*
60022 ATAAATCTTTACCCA
1 ATAAATCTTTAACCA
60037 ATAAATCTTTAACCA
1 ATAAATCTTTAACCA
60052 A
1 A
60053 ATAAGTCTGG
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:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAATCTTTAACCA
Found at i:60325 original size:15 final size:15
Alignment explanation
Indices: 60305--60335 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
60295 TATCCATATT
60305 CAAATAAGCGTCAGA
1 CAAATAAGCGTCAGA
60320 CAAATAAGCGTCAGA
1 CAAATAAGCGTCAGA
60335 C
1 C
60336 TAAAGTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (15 bp):
CAAATAAGCGTCAGA
Found at i:64291 original size:26 final size:27
Alignment explanation
Indices: 64248--64301 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
64238 ATCATCTTAA
*
64248 AAATTAATTTAAATTA-TTTATTAAAT
1 AAATTAATTTAAATTATTTTAATAAAT
64274 AAATTAAATTTAAA-TATTTTAATAAAT
1 AAATT-AATTTAAATTATTTTAATAAAT
64301 A
1 A
64302 TGAGCAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATTAATTTAAATTATTTTAATAAAT
Found at i:64680 original size:24 final size:26
Alignment explanation
Indices: 64618--64680 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
64608 TTTAAAATAG
* *
64618 TATA-TATTTAATTTTTATATTATAT
1 TATATTATTTTATTTTTATATCATAT
64643 TATATT-TTAATTATTTTTATATCATA-
1 TATATTATT--TTATTTTTATATCATAT
64669 TA-ATTATTTTAT
1 TATATTATTTTAT
64681 AATCAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
24 4 0.12
25 9 0.28
26 5 0.16
27 14 0.44
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TATATTATTTTATTTTTATATCATAT
Found at i:64685 original size:19 final size:18
Alignment explanation
Indices: 64650--64693 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
64640 TATTATATTT
64650 TAATTATTTTTATATCATA
1 TAATTATTTTTATATCA-A
64669 TAATTA-TTTTATAATCAA
1 TAATTATTTTTAT-ATCAA
64687 -AATTATT
1 TAATTATT
64694 AAATCAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 8 0.35
19 10 0.43
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTATTTTTATATCAA
Found at i:65387 original size:23 final size:25
Alignment explanation
Indices: 65359--65414 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
65349 AGTTTTTTTT
65359 AAATAAATAAAA-TTAT-AAT-TTAA
1 AAATAAA-AAAATTTATAAATATTAA
65382 AAATAAAAAAATTTATAAATATTAA
1 AAATAAAAAAATTTATAAATATTAA
*
65407 AATTAAAA
1 AAATAAAA
65415 TTTATTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.14
23 11 0.38
24 3 0.10
25 11 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAAAAAAATTTATAAATATTAA
Found at i:65436 original size:20 final size:20
Alignment explanation
Indices: 65408--65445 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
65398 AAATATTAAA
65408 ATTAAAATT-TATTAAATATC
1 ATTAAAATTATA-TAAATATC
*
65428 ATTATAATTATATAAATA
1 ATTAAAATTATATAAATA
65446 GATGAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAAATTATATAAATATC
Found at i:68610 original size:15 final size:15
Alignment explanation
Indices: 68577--68616 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
68567 TAATAATTTT
68577 TTAAATATA-AAACA
1 TTAAATATATAAACA
* *
68591 TTAAATATATTAATA
1 TTAAATATATAAACA
68606 TTAAATATATA
1 TTAAATATATA
68617 TTTATATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAATATATAAACA
Found at i:68617 original size:17 final size:17
Alignment explanation
Indices: 68595--68630 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
68585 AAAACATTAA
68595 ATATATTAATATTAAAT
1 ATATATTAATATTAAAT
* *
68612 ATATATTTATATTTAAT
1 ATATATTAATATTAAAT
68629 AT
1 AT
68631 TTATATTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATTAATATTAAAT
Found at i:69902 original size:2 final size:2
Alignment explanation
Indices: 69891--69921 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
69881 ATAAAGATAG
69891 TA TA -A 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
69922 CATTTATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:70964 original size:32 final size:33
Alignment explanation
Indices: 70888--70964 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 33
70878 ATAATAAAAA
*
70888 ATTAAAATATTATATAATATAAAAATATGAACAT
1 ATTAAAAT-TTATATAACATAAAAATATGAACAT
* * * * *
70922 ATCAAAATTTATATAACGT-AAATTATTAAGAT
1 ATTAAAATTTATATAACATAAAAATATGAACAT
70954 ATTAAAATTTA
1 ATTAAAATTTA
70965 AAAATATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 20 0.56
33 9 0.25
34 7 0.19
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (33 bp):
ATTAAAATTTATATAACATAAAAATATGAACAT
Found at i:71554 original size:2 final size:2
Alignment explanation
Indices: 71549--71589 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
71539 CGTTGAAAAA
*
71549 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
71590 GTAGATAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:73846 original size:2 final size:2
Alignment explanation
Indices: 73834--73864 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
73824 ATTTTCCTTT
*
73834 TA TA AA 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 T
73865 TTCAGATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:75087 original size:3 final size:3
Alignment explanation
Indices: 75079--75111 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
75069 AAATTTTTAT
75079 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
75112 AAGAATTTGT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:75658 original size:24 final size:25
Alignment explanation
Indices: 75604--75659 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
75594 TTAATATTTT
75604 TTATTAATTTAATTTTTAAAAATTAC
1 TTATT-ATTTAATTTTTAAAAATTAC
*
75630 -AATTATTTAATTTTTAAAAA-TAC
1 TTATTATTTAATTTTTAAAAATTAC
75653 TTATTAT
1 TTATTAT
75660 ATATTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 3 0.11
24 21 0.78
25 3 0.11
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATTATTTAATTTTTAAAAATTAC
Found at i:76027 original size:21 final size:20
Alignment explanation
Indices: 75995--76035 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
75985 TAGAAAATAT
*
75995 TTTTATAAAAAAAATCATAA
1 TTTTAAAAAAAAAATCATAA
*
76015 TTTTAAAATAAAAAATTATAA
1 TTTTAAAA-AAAAAATCATAA
76036 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTTAAAAAAAAAATCATAA
Found at i:76550 original size:3 final size:3
Alignment explanation
Indices: 76542--76574 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
76532 ATTGTTTGAC
76542 AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
76575 TTTCATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:76767 original size:22 final size:23
Alignment explanation
Indices: 76735--76790 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
76725 TTTATTTCTT
*
76735 TATTCGATTAA-ATTCATAAACA
1 TATTCGTTTAATATTCATAAACA
*
76757 TATTCGTTTAATATTTATAAACA
1 TATTCGTTTAATATTCATAAACA
* *
76780 AATTCATTTAA
1 TATTCGTTTAA
76791 GTGAGCCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (23 bp):
TATTCGTTTAATATTCATAAACA
Found at i:77350 original size:19 final size:20
Alignment explanation
Indices: 77328--77366 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
77318 TATTTATTAC
77328 TTAAT-TTTAAAATTATTTT
1 TTAATATTTAAAATTATTTT
77347 TTAATATTTAAAATTATTTT
1 TTAATATTTAAAATTATTTT
77367 AATCTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATATTTAAAATTATTTT
Found at i:78119 original size:19 final size:19
Alignment explanation
Indices: 78073--78128 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
78063 TCTCCGTCCC
*
78073 CTTTCCTTTCCTTTCCTTT
1 CTTTCCTTTCTTTTCCTTT
* *
78092 CTTTTCTTTACTTTTTCTTT
1 CTTTCCTTT-CTTTTCCTTT
*
78112 -TTTCCTTTCTTTCCCTT
1 CTTTCCTTTCTTTTCCTT
78129 CCCGCTTACA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 7 0.23
19 15 0.50
20 8 0.27
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTCCTTTCTTTTCCTTT
Found at i:79658 original size:28 final size:27
Alignment explanation
Indices: 79627--79694 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
79617 TTTTATAATT
*
79627 ATATTT-ATAATATTATATATTTATATAA
1 ATATTTAAT-ATATTATATA-CTATATAA
*
79655 ATATTTAATATATTATGTACTATATAA
1 ATATTTAATATATTATATACTATATAA
79682 AT-TTTAATATATT
1 ATATTTAATATATT
79695 TTTATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 11 0.30
27 9 0.24
28 15 0.41
29 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
ATATTTAATATATTATATACTATATAA
Found at i:79834 original size:2 final size:2
Alignment explanation
Indices: 79827--79856 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
79817 AGAGATAAGC
79827 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
79857 GTATGTGAAA
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:79968 original size:8 final size:8
Alignment explanation
Indices: 79955--80059 Score: 56
Period size: 9 Copynumber: 12.2 Consensus size: 8
79945 CACTTTTGAT
*
79955 ATTAAATA
1 ATTAAAAA
79963 ATTAAAAA
1 ATTAAAAA
*
79971 ATAAAAATA
1 ATTAAAA-A
79980 ATTAAAAA
1 ATTAAAAA
79988 ATTTAAAAAA
1 A-TT-AAAAA
79998 ATT--AAA
1 ATTAAAAA
80004 ATT-AAAA
1 ATTAAAAA
80011 A-TAAATAA
1 ATTAAA-AA
80019 ATTCTAAAAA
1 A-T-TAAAAA
*
80029 TTCTAAAAAAA
1 AT-T--AAAAA
80040 ATTTAAAAA
1 A-TTAAAAA
80049 ATCTAAAAA
1 AT-TAAAAA
80058 AT
1 AT
80060 AGAAAATTCA
Statistics
Matches: 79, Mismatches: 5, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
6 7 0.09
7 6 0.08
8 19 0.24
9 28 0.35
10 8 0.10
11 10 0.13
12 1 0.01
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (8 bp):
ATTAAAAA
Found at i:79980 original size:17 final size:17
Alignment explanation
Indices: 79958--80019 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
79948 TTTTGATATT
79958 AAATAATTAAAAAATAA
1 AAATAATTAAAAAATAA
79975 AAATAATTAAAAAATTTAA
1 AAATAATTAAAAAA--TAA
*
79994 AAA-AATT-AAAATTAA
1 AAATAATTAAAAAATAA
*
80009 AAATAAATAAA
1 AAATAATTAAA
80020 TTCTAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 6 0.15
16 3 0.08
17 20 0.51
18 4 0.10
19 6 0.15
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAATTAAAAAATAA
Found at i:80026 original size:17 final size:16
Alignment explanation
Indices: 79982--80029 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
79972 TAAAAATAAT
79982 TAAA-AAATTTAAAAA
1 TAAATAAATTTAAAAA
* *
79997 -AATTAAAATTAAAAA
1 TAAATAAATTTAAAAA
80012 TAAATAAATTCTAAAAA
1 TAAATAAATT-TAAAAA
80029 T
1 T
80030 TCTAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 10 0.38
16 7 0.27
17 7 0.27
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAATAAATTTAAAAA
Found at i:80046 original size:20 final size:21
Alignment explanation
Indices: 80017--80058 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
80007 AAAAATAAAT
*
80017 AAATTCTAAAAATTCTAAAAA
1 AAATTCTAAAAAATCTAAAAA
80038 AAATT-TAAAAAATCTAAAAA
1 AAATTCTAAAAAATCTAAAAA
80058 A
1 A
80059 TAGAAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATTCTAAAAAATCTAAAAA
Found at i:80549 original size:16 final size:16
Alignment explanation
Indices: 80530--80565 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
80520 AATATGATAT
80530 ATATAAAATAATAAAA
1 ATATAAAATAATAAAA
* *
80546 ATATAATATAATATAA
1 ATATAAAATAATAAAA
80562 ATAT
1 ATAT
80566 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAAATAATAAAA
Found at i:80586 original size:34 final size:34
Alignment explanation
Indices: 80547--80611 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
80537 ATAATAAAAA
80547 TATAATATAATATAAAT-ATTTATTAAAATTTTTT
1 TATAATATAA-ATAAATAATTTATTAAAATTTTTT
* *
80581 TATAATATAAATTATTAATTTATTAAAATTT
1 TATAATATAAATAAATAATTTATTAAAATTT
80612 ATAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TATAATATAAATAAATAATTTATTAAAATTTTTT
Found at i:81045 original size:28 final size:28
Alignment explanation
Indices: 81004--81066 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
80994 TAATTTTTTT
*
81004 ATATTTTAATTTTTAATTAAT-TTAAAAA
1 ATATATTAATTTTT-ATTAATATTAAAAA
* *
81032 ATATATTATTTTTTATTATTATTAAAAA
1 ATATATTAATTTTTATTAATATTAAAAA
*
81060 ATTTATT
1 ATATATT
81067 TTGATCAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATATATTAATTTTTATTAATATTAAAAA
Found at i:81244 original size:2 final size:2
Alignment explanation
Indices: 81232--81273 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
81222 TTGTATTATT
*
81232 TA TA TA CA 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 TA TA
81274 AGATAGAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:83631 original size:2 final size:2
Alignment explanation
Indices: 83624--83655 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
83614 AATTCGAATT
83624 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
83656 AAATGTAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84495 original size:102 final size:102
Alignment explanation
Indices: 84300--84483 Score: 226
Period size: 102 Copynumber: 1.8 Consensus size: 102
84290 TGTTATTTAG
* * * *
84300 TCTATACTAATATTAAATTCTTTTATTGAGTTCGTATTATAAATTAATTAGATATTAACTCAATT
1 TCTATACTAATATTAAATTCTTTTATTAAGTTCATATTATAAATTAATGAGATACTAACTCAATT
* **
84365 AATAAATTTATTATGAAGTATAATTAAATGAATTCAA
66 AATAAATTTACTAAAAAGTATAATTAAATGAATTCAA
* * * * * * *
84402 TCTATATTAATGTTAAATTTTTTTATTAAGTTCATATTATAAGTTAACTGA-ATACTCATTTAAT
1 TCTATACTAATATTAAATTCTTTTATTAAGTTCATATTATAAATTAA-TGAGATACTAACTCAAT
84466 TAATAAATTTACTAAAAA
65 TAATAAATTTACTAAAAA
84484 TTTAAATTAA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
102 65 0.97
103 2 0.03
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (102 bp):
TCTATACTAATATTAAATTCTTTTATTAAGTTCATATTATAAATTAATGAGATACTAACTCAATT
AATAAATTTACTAAAAAGTATAATTAAATGAATTCAA
Found at i:85745 original size:18 final size:19
Alignment explanation
Indices: 85722--85759 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
85712 CGAAGTAATA
85722 TATTTTA-TTTGATAAATT
1 TATTTTATTTTGATAAATT
*
85740 TATTTTATTTTGATTAATT
1 TATTTTATTTTGATAAATT
85759 T
1 T
85760 TTAAATATAA
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:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TATTTTATTTTGATAAATT
Found at i:85809 original size:20 final size:20
Alignment explanation
Indices: 85784--85831 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
85774 TATTTATGTA
85784 TTTAAATTAATTAATTTAA-T
1 TTTAAATTAA-TAATTTAACT
* *
85804 TTTAAAATAATATTTTAACT
1 TTTAAATTAATAATTTAACT
85824 TTTAAATT
1 TTTAAATT
85832 TAATCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAATTAATAATTTAACT
Found at i:85830 original size:19 final size:19
Alignment explanation
Indices: 85784--85830 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
85774 TATTTATGTA
85784 TTTAAATTAATTAATTTAAT
1 TTTAAA-TAATTAATTTAAT
*
85804 TTTAAAATAA-TATTTTAACT
1 TTT-AAATAATTAATTTAA-T
85824 TTTAAAT
1 TTTAAAT
85831 TTAATCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 11 0.46
20 10 0.42
21 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAAATAATTAATTTAAT
Found at i:85994 original size:9 final size:9
Alignment explanation
Indices: 85980--86024 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
85970 TATTATATTA
85980 TATTTTAAT
1 TATTTTAAT
85989 TATTTTAAT
1 TATTTTAAT
85998 TATTTTAAT
1 TATTTTAAT
*
86007 TA-TATAAT
1 TATTTTAAT
86015 TATATTTAAT
1 TAT-TTTAAT
86025 ATTAATAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
8 7 0.22
9 20 0.62
10 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TATTTTAAT
Found at i:86001 original size:18 final size:17
Alignment explanation
Indices: 85971--86024 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
85961 ATATATTTAT
*
85971 ATTATATTA-TATTTTA
1 ATTATATAATTATTTTA
*
85987 ATTATTTTAATTATTTTA
1 ATTA-TATAATTATTTTA
86005 ATTATATAATTATATTTA
1 ATTATATAATTAT-TTTA
86023 AT
1 AT
86025 ATTAATAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 4 0.12
17 11 0.34
18 17 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATAATTATTTTA
Found at i:86254 original size:14 final size:14
Alignment explanation
Indices: 86235--86278 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
86225 TTCTCTTTCA
86235 ATAAATATTTAAAT
1 ATAAATATTTAAAT
*
86249 ATAAATA-TAAAAT
1 ATAAATATTTAAAT
**
86262 ATATTTATTTAAAT
1 ATAAATATTTAAAT
86276 ATA
1 ATA
86279 TATAAAACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAAATATTTAAAT
Found at i:86296 original size:27 final size:26
Alignment explanation
Indices: 86235--86307 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
86225 TTCTCTTTCA
86235 ATAAA-TATTTAAATATAAATATAAAAT
1 ATAAATTATTTAAATAT--ATATAAAAT
*
86262 AT-ATTTATTTAAATATATATAAAACT
1 ATAAATTATTTAAATATATATAAAA-T
* *
86288 TTAAATTATATAAATATATA
1 ATAAATTATTTAAATATATA
86308 CACTCATGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 8 0.21
26 3 0.08
27 28 0.72
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAAATTATTTAAATATATATAAAAT
Found at i:86521 original size:15 final size:16
Alignment explanation
Indices: 86495--86524 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
86485 ATTAAAATGA
86495 TTATATAAATATAATT
1 TTATATAAATATAATT
86511 TTATA-AAATATAAT
1 TTATATAAATATAAT
86525 AAGTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATATAAATATAATT
Done.