Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008017.1 Hibiscus syriacus cultivar Beakdansim tig00110483_pilon, whole genome shotgun sequence
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: 3132588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 15
Found at i:875736 original size:23 final size:23
Alignment explanation
Indices: 875705--875769 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
875695 CTCGAGACTC
* *
875705 GAGCTCGATTGAAGCTTGATTCT
1 GAGCTCGATTCAAGCTCGATTCT
*
875728 TAGCTCGATTCAAGCTCGATTCT
1 GAGCTCGATTCAAGCTCGATTCT
875751 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTCAAGCTCGA
875770 CATTGCCCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGATTCT
Found at i:875743 original size:11 final size:11
Alignment explanation
Indices: 875706--875769 Score: 74
Period size: 11 Copynumber: 5.6 Consensus size: 11
875696 TCGAGACTCG
*
875706 AGCTCGATTGA
1 AGCTCGATTCA
* *
875717 AGCTTGATTCTT
1 AGCTCGATTC-A
875729 AGCTCGATTCA
1 AGCTCGATTCA
*
875740 AGCTCGATTCTG
1 AGCTCGATTC-A
875752 AGCTCGATTCA
1 AGCTCGATTCA
875763 AGCTCGA
1 AGCTCGA
875770 CATTGCCCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 25 0.57
12 19 0.43
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:877389 original size:105 final size:105
Alignment explanation
Indices: 877275--877555 Score: 298
Period size: 113 Copynumber: 2.6 Consensus size: 105
877265 TACTTCGCTC
* * * *
877275 TGTTAAAGGCTCAGTTTTTCTACGTATGCGGGTTCGTATTGGGTGGATCTCTGATATTTCCCATG
1 TGTTAAAGGCACAGTTTTTCAACGTAAGCGGGTTCGTATTGGGTGGATCTCTGACATTTCCCATG
* * *
877340 AAAATTCTCCGA-GTGGTATTGGTCACTGGTCCATTTACTT
66 AAAATTCTCC-ATGTGGTATTGGTAACCGGTCAATTTACTT
* * *
877380 TGTTAAAGGCACAGTTTTTCAACGTAAGCGGGTTGGTATTGGCCTATTGGGTGGATCTTTGACAC
1 TGTTAAAGGCACAGTTTTTCAACGTAAGC--G--GG--TT--CGTATTGGGTGGATCTCTGACAT
* * *
877445 TTCCCATGTAAATTTTCCATTTGGTATTGGTAACCGGTCAATTTACTT
58 TTCCCATGAAAATTCTCCATGTGGTATTGGTAACCGGTCAATTTACTT
* * * * *
877493 TGTTAAA-G-ACAGTTTTTCAACTTAAGTGGGTTGGTTTTGGGTGGATCTCTTACATTTCCCATG
1 TGTTAAAGGCACAGTTTTTCAACGTAAGCGGGTTCGTATTGGGTGGATCTCTGACATTTCCCATG
877556 CAGTTCCTCT
Statistics
Matches: 146, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
103 25 0.17
105 28 0.19
107 3 0.02
109 3 0.02
111 19 0.13
112 2 0.01
113 66 0.45
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (105 bp):
TGTTAAAGGCACAGTTTTTCAACGTAAGCGGGTTCGTATTGGGTGGATCTCTGACATTTCCCATG
AAAATTCTCCATGTGGTATTGGTAACCGGTCAATTTACTT
Found at i:885756 original size:2 final size:2
Alignment explanation
Indices: 885749--885783 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
885739 TTGATTCAGT
885749 TA 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 TA T
885784 GATTTCAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:895365 original size:8 final size:8
Alignment explanation
Indices: 895352--895392 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
895342 CTCATTTTCA
895352 GAGAATTT
1 GAGAATTT
895360 GAGAATTT
1 GAGAATTT
*
895368 -AGAGTTT
1 GAGAATTT
*
895375 GGGAATTT
1 GAGAATTT
895383 GAGAATTT
1 GAGAATTT
895391 GA
1 GA
895393 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:895691 original size:128 final size:128
Alignment explanation
Indices: 895463--895835 Score: 728
Period size: 128 Copynumber: 2.9 Consensus size: 128
895453 AAATCGGAGT
*
895463 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
895528 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
895591 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
895656 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
895719 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
895784 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
895836 AATAAGGTAA
Statistics
Matches: 242, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 242 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:896109 original size:14 final size:14
Alignment explanation
Indices: 896090--896119 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
896080 CATAAGTTGA
*
896090 TTTTAATGTATATG
1 TTTTAATATATATG
896104 TTTTAATATATATG
1 TTTTAATATATATG
896118 TT
1 TT
896120 AATGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTTAATATATATG
Found at i:896296 original size:33 final size:34
Alignment explanation
Indices: 896235--896334 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
896225 AAATTTAATG
*
896235 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* * * *
896269 TTAAA-TTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
*
896302 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
896335 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:896944 original size:21 final size:21
Alignment explanation
Indices: 896856--896949 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
896846 TATGGTATAA
*
896856 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
896877 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
896898 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
896919 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
896940 AACCCTGCGG
1 AACCCTGCGG
896950 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:896979 original size:21 final size:21
Alignment explanation
Indices: 896953--897000 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
896943 CCTGCGGAGA
*
896953 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
896974 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
896995 GGGCAT
1 TGGCAT
897001 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:898759 original size:30 final size:30
Alignment explanation
Indices: 898725--898808 Score: 78
Period size: 33 Copynumber: 2.7 Consensus size: 30
898715 AATAATTCTA
* *
898725 AATAAATAATAATTATATAAATATTATTTT
1 AATAAATAATAATTATATAAATATTAATAT
* *
898755 AATAAAAAAATAATATTACATAAATATTAATAT
1 AAT-AAATAAT-A-ATTATATAAATATTAATAT
* * *
898788 AAAAAATAATAACTATTTAAA
1 AATAAATAATAATTATATAAA
898809 AAAATACTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
30 10 0.24
31 7 0.17
32 7 0.17
33 18 0.43
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
AATAAATAATAATTATATAAATATTAATAT
Found at i:900141 original size:16 final size:16
Alignment explanation
Indices: 900120--900160 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
900110 TCGGGGTCCG
900120 TAAATTATTTTTTAAT
1 TAAATTATTTTTTAAT
900136 TAAATTATTTTTTAAT
1 TAAATTATTTTTTAAT
900152 TAAATTATT
1 TAAATTATT
900161 ATGATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAAATTATTTTTTAAT
Found at i:900385 original size:5 final size:5
Alignment explanation
Indices: 900371--900698 Score: 486
Period size: 5 Copynumber: 67.6 Consensus size: 5
900361 AGTATATAAA
* *
900371 TATAT ATATAT TATAA TATAA TATAT T-TAT TATA- TAT-T TATA- T-TAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
900417 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA-
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
900466 T-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
900515 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
900565 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
900615 TATAT TATAT TATAT TATAT TATA- TATAT ATATAT TATTT TATACAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TATAT TATAT TAT--AT
*
900662 AATAT T-TAT TATAT TAT-T TAT-T TA-AT TA-AT TA-AT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
900699 TCAGATCCAA
Statistics
Matches: 302, Mismatches: 6, Indels: 29
0.90 0.02 0.09
Matches are distributed among these distances:
3 4 0.01
4 40 0.13
5 245 0.81
6 10 0.03
7 3 0.01
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:901991 original size:11 final size:12
Alignment explanation
Indices: 901977--902032 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
901967 TTGAATTTTC
901977 CTTTT-TTTATT
1 CTTTTATTTATT
901988 CTTTTATTTATT
1 CTTTTATTTATT
902000 -TATTTATTTATT
1 CT-TTTATTTATT
*
902012 -ATTTATTTATT
1 CTTTTATTTATT
902023 -TTATTATTTA
1 CTT-TTATTTA
902033 ACATTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 17 0.43
12 23 0.57
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (12 bp):
CTTTTATTTATT
Found at i:901999 original size:4 final size:4
Alignment explanation
Indices: 901990--902032 Score: 63
Period size: 4 Copynumber: 11.0 Consensus size: 4
901980 TTTTTATTCT
901990 TTTA TTTA TTTA TTTA TTTA -TTA TTTA TTTA TTT- TATTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
902033 ACATTAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 4 0.11
4 31 0.86
5 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:902018 original size:23 final size:23
Alignment explanation
Indices: 901990--902050 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
901980 TTTTTATTCT
**
901990 TTTATTTATTTATTTATTTATTA
1 TTTATTTATTTATTTATTTAACA
902013 TTTATTTATTT-TATTATTTAACA
1 TTTATTTATTTAT-TTATTTAACA
*
902036 TTAATTTGATTTATT
1 TTTATTT-ATTTATT
902051 CTTTAGGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 1 0.03
23 25 0.78
24 5 0.16
25 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTTATTTATTTATTTAACA
Found at i:905702 original size:24 final size:24
Alignment explanation
Indices: 905675--905741 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
905665 TCAAAGGGAC
905675 TCATCTACTGCAAAAGCACAAGCT
1 TCATCTACTGCAAAAGCACAAGCT
* * *
905699 TCATCTGCTGTAAAA-CTGCAAGCT
1 TCATCTACTGCAAAAGC-ACAAGCT
*
905723 TCGTCTACTGCAAAAGCAC
1 TCATCTACTGCAAAAGCAC
905742 TGGCCTCTGT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 1 0.03
24 32 0.94
25 1 0.03
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (24 bp):
TCATCTACTGCAAAAGCACAAGCT
Found at i:910558 original size:21 final size:22
Alignment explanation
Indices: 910518--910559 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
910508 TTATAATAGG
* *
910518 GGAATCGATTTCCCTTCTACAA
1 GGAATCGATTACCCTGCTACAA
910540 GGAATCGA-TACCCTGCTACA
1 GGAATCGATTACCCTGCTACA
910560 GTACGGCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (22 bp):
GGAATCGATTACCCTGCTACAA
Found at i:911328 original size:24 final size:23
Alignment explanation
Indices: 911301--911352 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
911291 TGTACCGTAA
*
911301 TGCCACATAGAATTTGCACTGAAG
1 TGCCACATAGAA-ATGCACTGAAG
* * *
911325 TGCCGCGTAGAAATGCACTGTAG
1 TGCCACATAGAAATGCACTGAAG
911348 TGCCA
1 TGCCA
911353 TATAAGATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCCACATAGAAATGCACTGAAG
Found at i:915015 original size:18 final size:18
Alignment explanation
Indices: 914988--915022 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
914978 CCACTATGAA
*
914988 ATGTCTTGAAGGACCACT
1 ATGTCCTGAAGGACCACT
915006 ATGTCCTGAAGGACCAC
1 ATGTCCTGAAGGACCAC
915023 GTAGAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (18 bp):
ATGTCCTGAAGGACCACT
Found at i:917343 original size:31 final size:31
Alignment explanation
Indices: 917274--917349 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
917264 ATCTTTCGAG
* *
917274 ACATATTGACAGTTTACCTATGTTCTAAGGA
1 ACATATGGACAGTTTACCTAGGTTCTAAGGA
* ** *
917305 ACATATGGCCAGTTTACCTAGGTTCTTCGGG
1 ACATATGGACAGTTTACCTAGGTTCTAAGGA
*
917336 ACCTATGGACAGTT
1 ACATATGGACAGTT
917350 GCCGAGGTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (31 bp):
ACATATGGACAGTTTACCTAGGTTCTAAGGA
Found at i:917993 original size:6 final size:6
Alignment explanation
Indices: 917982--918010 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
917972 AAACGTACTT
917982 ATGTAA ATGTAA ATGTAA ATGTAA ATGTA
1 ATGTAA ATGTAA ATGTAA ATGTAA ATGTA
918011 TAGTTATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
ATGTAA
Found at i:920646 original size:23 final size:23
Alignment explanation
Indices: 920620--920664 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
920610 CACCACAGCT
*
920620 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
920643 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
920665 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:922285 original size:21 final size:21
Alignment explanation
Indices: 922261--922301 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
922251 TGTTGTTCGT
* *
922261 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
922282 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
922302 TTGCCCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:929533 original size:23 final size:23
Alignment explanation
Indices: 929504--929568 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
929494 CATATGAATT
* * * *
929504 TGTCCCGAATGACTATTATGAAA
1 TGTCCCGAAGGACCACTATAAAA
929527 TGTCCCGAAGGACCACTATAAAA
1 TGTCCCGAAGGACCACTATAAAA
*
929550 TGTCCCGAAAGACCACTAT
1 TGTCCCGAAGGACCACTAT
929569 GTCCCGAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (23 bp):
TGTCCCGAAGGACCACTATAAAA
Found at i:929572 original size:18 final size:18
Alignment explanation
Indices: 929549--929583 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
929539 CCACTATAAA
929549 ATGTCCCGAAAGACCACT
1 ATGTCCCGAAAGACCACT
*
929567 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAAGACCAC
929584 GTAGAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.34, G:0.20, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAAGACCACT
Found at i:933308 original size:2 final size:2
Alignment explanation
Indices: 933295--933610 Score: 191
Period size: 2 Copynumber: 166.0 Consensus size: 2
933285 GACCTTTTAC
* * *
933295 AT AT AT ACT AT AT AGT AT AT AT AGC GT AT AGC AT AT AT AT -T AT
1 AT AT AT A-T AT AT A-T AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* * *
933338 -T AT A- AA AT AT -T AT AT AGT AT -T AT AT -T TT AT AT AT GT -T
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
933375 AT AT AT -T AT AT -T AT AT AGT AT AT AT AT AT AT AT AT GT -T AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
933415 AGT AC A- AT ACT AT AT AGT AT AT AT AT AT AT -T AT AT -T AT AT
1 A-T AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
933455 AT TT AT AT -T AT AT AT A- AT AT AT AT A- AT AT AT -T 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
* * *
933493 TT AT AT -T AT AT AT AT AT AT AT AT -T TT AT AT -T AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** *
933532 AT -T AT AT AT AT AT AT AT AT AT AT TT GC AT -T GT AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
933570 AT AT AGT AT -T AT AT -T AT AT AGC AT AT AT AT AT -T AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
933611 TATTTATTTA
Statistics
Matches: 250, Mismatches: 26, Indels: 76
0.71 0.07 0.22
Matches are distributed among these distances:
1 27 0.11
2 205 0.82
3 18 0.07
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:933440 original size:71 final size:68
Alignment explanation
Indices: 933365--933555 Score: 217
Period size: 71 Copynumber: 2.7 Consensus size: 68
933355 TATTATATTT
*
933365 TATATATGTTATATATTATATTATATAGTATATATATATATATATGTTATAGTA-CAATACTATA
1 TATATAT-TTATATATTATATTATATA-TATATATATATATATATATTATA-TATCAATACTATA
933429 TAGTATA
63 TA-TATA
** *
933436 TATATATATTATAT-TATATATTTATATTATATATAATATATATAATATATTATATATTTATATT
1 TATATAT-TTATATAT-TATA-TTATA-TATATAT-ATATATAT-ATATATTATATATCAATACT
933500 ATATATATA
60 ATATATATA
933509 TATATATTT-TATATTATATTTATATTATATATATATATATATATATT
1 TATATATTTATATATTATA-TTATA-TATATATATATATATATATATT
933556 TGCATTGTAT
Statistics
Matches: 108, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
69 7 0.06
70 9 0.08
71 38 0.35
72 13 0.12
73 23 0.21
74 18 0.17
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (68 bp):
TATATATTTATATATTATATTATATATATATATATATATATATATTATATATCAATACTATATAT
ATA
Found at i:933615 original size:98 final size:101
Alignment explanation
Indices: 933374--933615 Score: 275
Period size: 98 Copynumber: 2.4 Consensus size: 101
933364 TTATATATGT
* **
933374 TATATATTATATTATATAGTATATATATA-TATATATGTTATAGTACAATACTATATAGTATATA
1 TATATATTATATTATATAGTATATATATATTATATATATTATTTTACAATACTATATAGTATATA
*
933438 TATATATTATATTATATATTTATATTATATATAATA
66 TATATATTATATTATATATTTACATTATATATAATA
* * * * *
933474 TATATAATATATTATATA-TTTATAT-TATATATATATATATATTTTATATTA-TATTTA-TAT-
1 TATATATTATATTATATAGTATATATATAT-TATATATAT-TATTTTACAATACTATATAGTATA
* * *
933534 TATATATA-TATATATATATATTTGCATTGTAT-TATTA
64 TATATATATTATAT-TATATATTTACATTATATATAATA
*
933571 TATAGTATTATATTATATAGCATATATATATTATATATATTATTT
1 TATA-TATTATATTATATAGTATATATATATTATATATATTATTT
933616 ATTTAATTAA
Statistics
Matches: 120, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
97 13 0.11
98 43 0.36
99 23 0.19
100 33 0.28
101 8 0.07
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (101 bp):
TATATATTATATTATATAGTATATATATATTATATATATTATTTTACAATACTATATAGTATATA
TATATATTATATTATATATTTACATTATATATAATA
Found at i:933617 original size:13 final size:13
Alignment explanation
Indices: 933425--933617 Score: 119
Period size: 13 Copynumber: 14.1 Consensus size: 13
933415 AGTACAATAC
* *
933425 TATATAGTATATA
1 TATATATTATTTA
933438 TATATATTATATTA
1 TATATATTAT-TTA
933452 TATAT-TTATATTA
1 TATATATTAT-TTA
* *
933465 TATATAATATATA
1 TATATATTATTTA
*
933478 TAATATATTATATA
1 T-ATATATTATTTA
* *
933492 TTTATATTATATA
1 TATATATTATTTA
933505 TATATATATATTT-
1 TATATAT-TATTTA
933518 TATAT-TATATTTA
1 TATATAT-TATTTA
*
933531 TAT-TATATATATA
1 TATATAT-TATTTA
933544 TATATATATATTTGCA
1 TATATAT-TATTT--A
*
933560 T-TGTATTA-TTA
1 TATATATTATTTA
933571 TATAGTATTATATTA
1 TATA-TATTAT-TTA
933586 TATAGCATATATATATTA
1 TAT---ATAT-TAT-TTA
933604 TATATATTATTTA
1 TATATATTATTTA
933617 T
1 T
933618 TTAATTAATT
Statistics
Matches: 151, Mismatches: 12, Indels: 34
0.77 0.06 0.17
Matches are distributed among these distances:
11 2 0.01
12 9 0.06
13 71 0.47
14 39 0.26
15 14 0.09
16 2 0.01
17 3 0.02
18 11 0.07
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (13 bp):
TATATATTATTTA
Found at i:934912 original size:18 final size:18
Alignment explanation
Indices: 934878--934912 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
934868 TTTTATTCTT
* *
934878 TTATTTAATATTTATTTA
1 TTATTTAACATTAATTTA
934896 TTATTTAACATTAATTT
1 TTATTTAACATTAATTT
934913 GATTTATTTT
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:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTTAACATTAATTTA
Found at i:937227 original size:15 final size:17
Alignment explanation
Indices: 937196--937227 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
937186 ATGTATTTTT
937196 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
937213 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
937228 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:937376 original size:16 final size:16
Alignment explanation
Indices: 937355--937393 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
937345 AAGAAAGTAA
937355 AAAAAATAACAAAAAT
1 AAAAAATAACAAAAAT
* *
937371 AAAAAATCAGAAAAAT
1 AAAAAATAACAAAAAT
937387 AACAAAA
1 AA-AAAA
937394 CATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.79, C:0.08, G:0.03, T:0.10
Consensus pattern (16 bp):
AAAAAATAACAAAAAT
Found at i:938252 original size:29 final size:29
Alignment explanation
Indices: 938210--938272 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
938200 CAAATACTAA
938210 TAATTATAAAATTATTAGTTATTTATTAT
1 TAATTATAAAATTATTAGTTATTTATTAT
938239 TAATTATAAAATTATTAGTTATTTATTAT
1 TAATTATAAAATTATTAGTTATTTATTAT
938268 TAATT
1 TAATT
938273 TAGGCAAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
TAATTATAAAATTATTAGTTATTTATTAT
Found at i:944564 original size:37 final size:37
Alignment explanation
Indices: 944523--944599 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
944513 ATTTTTTTAT
944523 ATTAGTCGTTCATTTTACTAAAGGTAACTATCTTAAA
1 ATTAGTCGTTCATTTTACTAAAGGTAACTATCTTAAA
944560 ATTAGTCGTTCATTTTACTAAAGGTAACTATCTTAAA
1 ATTAGTCGTTCATTTTACTAAAGGTAACTATCTTAAA
944597 ATT
1 ATT
944600 TTATTTTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (37 bp):
ATTAGTCGTTCATTTTACTAAAGGTAACTATCTTAAA
Found at i:947033 original size:31 final size:31
Alignment explanation
Indices: 946998--947068 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
946988 CTGAAGAACC
* *
946998 TAGGTAAACTATCCATATGTCTC-ATAGAATA
1 TAGGTAAACTATCCATATGTCTCGAAAG-ACA
* *
947029 TAGGTAAAATGTCCATATGTCTCGAAAGACA
1 TAGGTAAACTATCCATATGTCTCGAAAGACA
947060 TAGGTAAAC
1 TAGGTAAAC
947069 CCTCGACTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (31 bp):
TAGGTAAACTATCCATATGTCTCGAAAGACA
Found at i:947829 original size:64 final size:64
Alignment explanation
Indices: 947744--947931 Score: 163
Period size: 64 Copynumber: 2.9 Consensus size: 64
947734 GTACCAATCC
*
947744 ATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCATTTCATGCATCGATGCACATACT
1 ATGCACCGATGCACCATGAATTAAA-TGAAACATCGAATGCATTTCATGCATCGATGCACATACT
* ** * *
947808 ATGCACCGATGCACTGA-GAATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCA-G
1 ATGCACCGATGCAC-CATGAATTAAATG-AAACATCGAATGCATTTCATGCATCGATGCA-CATA
*
947871 CC
63 CT
* * * * *
947873 ATGCATCGATGCACTC-TGGCTATT--TTGAAACATCGAATGCACTTGATGCATCGATGCAC
1 ATGCACCGATGCAC-CAT-G-AATTAAATGAAACATCGAATGCATTTCATGCATCGATGCAC
947932 TAAGGGTCCA
Statistics
Matches: 105, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
63 3 0.03
64 49 0.47
65 47 0.45
66 3 0.03
67 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
ATGCACCGATGCACCATGAATTAAATGAAACATCGAATGCATTTCATGCATCGATGCACATACT
Found at i:947844 original size:65 final size:63
Alignment explanation
Indices: 947722--947931 Score: 201
Period size: 65 Copynumber: 3.3 Consensus size: 63
947712 TTTTTCAGAG
* * * **
947722 TGATGCACCGATGTACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCA-GAA-TATTTTGAAACATCGAATGCA
947785 TT
62 TT
* * *
947787 TCATGCATCGATGCACATACTATGCACCGATGCACTGAGAAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGAATATTT-TG-AAACATCGAATGCAT
947851 T
63 T
* * * ** *
947852 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGAATATTTTGAAACATCGAATGCATT
947916 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
947932 TAAGGGTCCA
Statistics
Matches: 121, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 49 0.40
65 62 0.51
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGAATATTTTGAAACATCGAATGCATT
Found at i:950100 original size:34 final size:32
Alignment explanation
Indices: 950038--950107 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
950028 CCTTACAAAC
* *
950038 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
950070 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
950104 TCCC
1 TCCC
950108 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:950416 original size:21 final size:21
Alignment explanation
Indices: 950390--950431 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
950380 CCAGAATGGG
*
950390 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
950411 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
950432 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:950561 original size:19 final size:19
Alignment explanation
Indices: 950537--950603 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
950527 GAGCCTCGGG
*
950537 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
950556 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
950575 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
950594 TTACTATTCA
1 TTACTGTTCA
950604 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:950715 original size:30 final size:31
Alignment explanation
Indices: 950668--950758 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
950658 AAATTTTGAA
950668 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
950697 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
950728 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
950759 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:953622 original size:34 final size:32
Alignment explanation
Indices: 953560--953629 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
953550 CCTTACAAAC
* *
953560 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
953592 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
953626 TCCC
1 TCCC
953630 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:953699 original size:31 final size:31
Alignment explanation
Indices: 953660--953732 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
953650 AGTAAACAAG
953660 AAAA-CATTTTGTAAATTCAATTCAAGTCCA
1 AAAACCATTTTGTAAATTCAATTCAAGTCCA
953690 AAAACCATTTTGTAAATTCAATTCAAGTCCA
1 AAAACCATTTTGTAAATTCAATTCAAGTCCA
953721 AAAACCATTTTG
1 AAAACCATTTTG
953733 CCTTAAATTG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 4 0.10
31 38 0.90
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
AAAACCATTTTGTAAATTCAATTCAAGTCCA
Found at i:954051 original size:23 final size:21
Alignment explanation
Indices: 954002--954051 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
953992 TATGACAAAC
*
954002 TTAATAGAAAATATTAAAAAA
1 TTAATAGAAAACATTAAAAAA
*
954023 TATAATATGAAAACATTTTAAAAA
1 T-TAATA-GAAAACA-TTAAAAAA
954047 TTAAT
1 TTAAT
954052 CCTAAACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 5 0.21
23 10 0.42
24 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (21 bp):
TTAATAGAAAACATTAAAAAA
Found at i:954141 original size:14 final size:14
Alignment explanation
Indices: 954122--954154 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
954112 GACATACTTA
954122 AAAAT-AATCAAAAT
1 AAAATAAAT-AAAAT
954136 AAAATAAATAAAAT
1 AAAATAAATAAAAT
954150 AAAAT
1 AAAAT
954155 GATATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:959632 original size:28 final size:28
Alignment explanation
Indices: 959600--959655 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
959590 TAATTTAACT
*
959600 GTACATTTTCAATGCTCATTAATGCAAA
1 GTACATTTTCAATACTCATTAATGCAAA
959628 GTACATTTTCAATACTCATTAATGCAAA
1 GTACATTTTCAATACTCATTAATGCAAA
959656 CAAGTAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (28 bp):
GTACATTTTCAATACTCATTAATGCAAA
Found at i:962063 original size:70 final size:70
Alignment explanation
Indices: 961950--962087 Score: 249
Period size: 70 Copynumber: 2.0 Consensus size: 70
961940 CAGACACGGC
*
961950 TACTTAGAGAAAAATGTAGAGTCCGAGAAACATAGATCTTAAGCACAAGGACCTTACATCATCAA
1 TACTTAGAGAAAAATGTAGAGTCCGAGAAACATAGATCTTAAGCACAAGGACCCTACATCATCAA
962015 AGTAG
66 AGTAG
* *
962020 TACTTAGTGAAAAATGTAGAGTCCGAGCAACATAGATCTTAAGCACAAGGACCCTACATCATCAA
1 TACTTAGAGAAAAATGTAGAGTCCGAGAAACATAGATCTTAAGCACAAGGACCCTACATCATCAA
962085 AGT
66 AGT
962088 GAATTCAGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (70 bp):
TACTTAGAGAAAAATGTAGAGTCCGAGAAACATAGATCTTAAGCACAAGGACCCTACATCATCAA
AGTAG
Found at i:974527 original size:17 final size:17
Alignment explanation
Indices: 974505--974537 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
974495 TCTTTAAGGT
974505 ATATTTTATTA-TATTTA
1 ATATTTT-TTAGTATTTA
974522 ATATTTTTTAGTATTT
1 ATATTTTTTAGTATTT
974538 TATTTAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
ATATTTTTTAGTATTTA
Found at i:974565 original size:28 final size:29
Alignment explanation
Indices: 974505--974573 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 29
974495 TCTTTAAGGT
974505 ATATTTTA-TT-ATATTTAATATTTTTTA
1 ATATTTTATTTAATATTTAATATTTTTTA
*
974532 GTATTTTATTTAACTATTT-AT-TTTTTTA
1 ATATTTTATTTAA-TATTTAATATTTTTTA
974560 ATATTTTATTTAAT
1 ATATTTTATTTAAT
974574 TAATTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 8 0.22
28 21 0.57
29 3 0.08
30 5 0.14
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (29 bp):
ATATTTTATTTAATATTTAATATTTTTTA
Found at i:974567 original size:16 final size:17
Alignment explanation
Indices: 974533--974570 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
974523 TATTTTTTAG
974533 TATTTTATTTAACTATT
1 TATTTTATTTAACTATT
974550 TATTTT-TTTAA-TATTT
1 TATTTTATTTAACTA-TT
974566 TATTT
1 TATTT
974571 AATTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.10
16 12 0.60
17 6 0.30
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTATTTAACTATT
Found at i:974582 original size:27 final size:27
Alignment explanation
Indices: 974505--974584 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
974495 TCTTTAAGGT
* *
974505 ATATTTTATTATATTTAA-TATTTTTTA
1 ATATTTTATT-TAATTAATTTTTTTTTA
* * *
974532 GTATTTTATTTAACTATTTATTTTTTTA
1 ATATTTTATTTAATTAATT-TTTTTTTA
974560 ATATTTTATTTAATTAATTTTTTTT
1 ATATTTTATTTAATTAATTTTTTTT
974585 GCAGTTATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 4 0.09
27 16 0.37
28 23 0.53
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (27 bp):
ATATTTTATTTAATTAATTTTTTTTTA
Found at i:976659 original size:32 final size:31
Alignment explanation
Indices: 976586--976661 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
976576 ACGATCGACT
* *
976586 ATGACCGTTGACCGGTGTTGACCACTGTTGA
1 ATGACCTTTGACCGGCGTTGACCACTGTTGA
* *
976617 CTAGAACTTTGACCGGCGTTGACCAGGC-GTTGA
1 AT-GACCTTTGACCGGCGTTGACCA--CTGTTGA
976650 ATGACCTTTGAC
1 ATGACCTTTGAC
976662 TTTTATCGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
31 1 0.03
32 28 0.78
33 6 0.17
34 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (31 bp):
ATGACCTTTGACCGGCGTTGACCACTGTTGA
Found at i:982213 original size:40 final size:40
Alignment explanation
Indices: 982148--982228 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
982138 TAAGAGAATG
*
982148 TTCAGGAAAACAATTAACTATATGATCTCTAAATTATAGT
1 TTCAAGAAAACAATTAACTATATGATCTCTAAATTATAGT
*
982188 TTCAAGAAAGCAATTAACTATATGATCTCTAAATTATAGT
1 TTCAAGAAAACAATTAACTATATGATCTCTAAATTATAGT
982228 T
1 T
982229 ATTTTTTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (40 bp):
TTCAAGAAAACAATTAACTATATGATCTCTAAATTATAGT
Found at i:990432 original size:20 final size:20
Alignment explanation
Indices: 990395--990433 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
990385 CTCGATGGTT
* *
990395 TTTTTATATATTTTTTTATA
1 TTTTTATATACTTGTTTATA
*
990415 TTTTTATTTACTTGTTTAT
1 TTTTTATATACTTGTTTAT
990434 TGGAATTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTATATACTTGTTTATA
Found at i:990544 original size:13 final size:13
Alignment explanation
Indices: 990526--990550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
990516 TTGTTGGACT
990526 TTTTGTTAATTTA
1 TTTTGTTAATTTA
990539 TTTTGTTAATTT
1 TTTTGTTAATTT
990551 TGTTTATTAC
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTGTTAATTTA
Found at i:995030 original size:21 final size:21
Alignment explanation
Indices: 995004--995045 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
994994 TTACAAATAT
995004 TATTTAATTGTAATTCTATAA
1 TATTTAATTGTAATTCTATAA
995025 TATTTAATTGTAATTCTATAA
1 TATTTAATTGTAATTCTATAA
995046 ATTAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
TATTTAATTGTAATTCTATAA
Found at i:995057 original size:21 final size:21
Alignment explanation
Indices: 995012--995057 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
995002 ATTATTTAAT
* *
995012 TGTAATTCTATAATATTTAAT
1 TGTAATTCTATAATATTAAAA
995033 TGTAATTCTATAA-ATTAAAAA
1 TGTAATTCTATAATATT-AAAA
995054 TGTA
1 TGTA
995058 TCATATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (21 bp):
TGTAATTCTATAATATTAAAA
Found at i:995397 original size:17 final size:17
Alignment explanation
Indices: 995377--995419 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
995367 CTAAATAACA
995377 TAAATTAAAATTTAATG
1 TAAATTAAAATTTAATG
995394 TAAATTAAAATTTAATG
1 TAAATTAAAATTTAATG
995411 TAAATTAAA
1 TAAATTAAA
995420 TTTCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
TAAATTAAAATTTAATG
Found at i:996723 original size:22 final size:23
Alignment explanation
Indices: 996677--996720 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
996667 TATATAAAAT
996677 TATTTTCTATTAAATATTTTTAA
1 TATTTTCTATTAAATATTTTTAA
*
996700 TATTTT-TATTTAAT-TTTTTAA
1 TATTTTCTATTAAATATTTTTAA
996721 ATAATTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTTCTATTAAATATTTTTAA
Found at i:998502 original size:42 final size:42
Alignment explanation
Indices: 998447--998536 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
998437 TTATGTTGAT
*
998447 TTTA-TTTAGACTTATTAAGACTTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTAAGACTTAATAGTGTTATGGTGTTA
* *
998488 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTAAGACTTAATAGTGTTATGGTGTTA
998530 TTTATTT
1 TTTATTT
998537 ACTTGTTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 41 0.91
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.53
Consensus pattern (42 bp):
TTTATTTTAGACTTATTAAGACTTAATAGTGTTATGGTGTTA
Found at i:998681 original size:17 final size:18
Alignment explanation
Indices: 998659--998692 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
998649 TTTTTTTTTA
998659 GTGTTATGG-TGTTATTG
1 GTGTTATGGTTGTTATTG
998676 GTGTTATGGTTGTTATT
1 GTGTTATGGTTGTTATT
998693 TAAAATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (18 bp):
GTGTTATGGTTGTTATTG
Found at i:1000280 original size:11 final size:11
Alignment explanation
Indices: 1000266--1000290 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1000256 TTAAGACATG
1000266 ATTAATTTATT
1 ATTAATTTATT
1000277 ATTAATTTATT
1 ATTAATTTATT
1000288 ATT
1 ATT
1000291 TAGTTATTTA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTAATTTATT
Found at i:1001102 original size:24 final size:25
Alignment explanation
Indices: 1001061--1001107 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1001051 AAAAAAATAA
*
1001061 AAAAAAAAACAAAAAAAGGCAAAAT
1 AAAAAAAAACAAAAAAAGCCAAAAT
1001086 AAAAAAAAAC-AAAAAAGCCAAA
1 AAAAAAAAACAAAAAAAGCCAAA
1001108 TTTTCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.81, C:0.11, G:0.06, T:0.02
Consensus pattern (25 bp):
AAAAAAAAACAAAAAAAGCCAAAAT
Found at i:1005581 original size:117 final size:117
Alignment explanation
Indices: 1005375--1005608 Score: 450
Period size: 117 Copynumber: 2.0 Consensus size: 117
1005365 TGTTTCCAGA
*
1005375 ACCTAAAAAAAACTTTAAGAACCCTACTTGCTGCCGCCACCTTCCCCTATTCATTCCCCATTGTT
1 ACCTAAAAAAAACTTTAAGAACCCTACTTGCTGCCGCCACCTTCCCCTATTCATTCCCCATTATT
1005440 CTTCATCAAGTCTAGAGCTTTCTAGGTTTGATTATTCAACAAGAGCAATGTT
66 CTTCATCAAGTCTAGAGCTTTCTAGGTTTGATTATTCAACAAGAGCAATGTT
*
1005492 ACCTAAAAAAAACTTTAAGAACCCTACTTGTTGCCGCCACCTTCCCCTATTCATTCCCCATTATT
1 ACCTAAAAAAAACTTTAAGAACCCTACTTGCTGCCGCCACCTTCCCCTATTCATTCCCCATTATT
1005557 CTTCATCAAGTCTAGAGCTTTCTAGGTTTGATTATTCAACAAGAGCAATGTT
66 CTTCATCAAGTCTAGAGCTTTCTAGGTTTGATTATTCAACAAGAGCAATGTT
1005609 CATTAACCCG
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (117 bp):
ACCTAAAAAAAACTTTAAGAACCCTACTTGCTGCCGCCACCTTCCCCTATTCATTCCCCATTATT
CTTCATCAAGTCTAGAGCTTTCTAGGTTTGATTATTCAACAAGAGCAATGTT
Found at i:1006056 original size:29 final size:29
Alignment explanation
Indices: 1006021--1006082 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1006011 TCTTATTCAT
1006021 GTTTTTGGCTTTTACAGAGATATCATTGA
1 GTTTTTGGCTTTTACAGAGATATCATTGA
1006050 GTTTTTGGCTTTTACAGAGATATCATTGA
1 GTTTTTGGCTTTTACAGAGATATCATTGA
1006079 GTTT
1 GTTT
1006083 CCACACATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.47
Consensus pattern (29 bp):
GTTTTTGGCTTTTACAGAGATATCATTGA
Found at i:1009384 original size:29 final size:29
Alignment explanation
Indices: 1009318--1009406 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
1009308 CCCGAAGGAC
* * * *
1009318 CTATCCATATGTTCCGAAGAACATAGGTAA
1 CTATCCATATGTCCCAAAGGACAT-TGTAA
* *
1009348 TTGTCCATATGTCCCAAAGGACATTGTAA
1 CTATCCATATGTCCCAAAGGACATTGTAA
1009377 CTATCCATATGTCCCAAAGGACATTGTAA
1 CTATCCATATGTCCCAAAGGACATTGTAA
1009406 C
1 C
1009407 ACCCCAACCC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 32 0.63
30 19 0.37
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (29 bp):
CTATCCATATGTCCCAAAGGACATTGTAA
Found at i:1010333 original size:31 final size:30
Alignment explanation
Indices: 1010298--1010400 Score: 109
Period size: 31 Copynumber: 3.3 Consensus size: 30
1010288 GTTTTGTAGA
*
1010298 ACATAGGTAACCTGTCCATATGTCTGGAAAG
1 ACATAGGTAAACTGTCCATATGTCT-GAAAG
* * * *
1010329 ACATAGATAAATTGTTCATATGTCTCAAAGG
1 ACATAGGTAAACTGTCCATATGTCTGAAA-G
*
1010360 ACATAGGTAAACTGTCCATATGTCCCG-AAG
1 ACATAGGTAAACTGTCCATATGT-CTGAAAG
1010390 TACATAGGTAA
1 -ACATAGGTAA
1010401 CCCTCAACTC
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
30 4 0.07
31 54 0.92
32 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (30 bp):
ACATAGGTAAACTGTCCATATGTCTGAAAG
Found at i:1011847 original size:21 final size:19
Alignment explanation
Indices: 1011823--1011880 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
1011813 ATATTTAATG
1011823 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
*
1011842 ACAAAAGAATATCAATTGTT-
1 A-AAAAG-ATACCAATTGTTA
1011862 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
1011881 TCAATTGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 11 0.32
19 6 0.18
20 6 0.18
21 11 0.32
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:1012348 original size:19 final size:18
Alignment explanation
Indices: 1012319--1012367 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1012309 ACCACATGCA
*
1012319 TAAACATTCAAAT-TTAGG
1 TAAAAATTCAAATATT-GG
*
1012337 TCAAAAATTCAAATATTTG
1 T-AAAAATTCAAATATTGG
1012356 TAAAAATTCAAA
1 TAAAAATTCAAA
1012368 ATAAAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.44
19 13 0.48
20 2 0.07
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (18 bp):
TAAAAATTCAAATATTGG
Found at i:1014123 original size:25 final size:25
Alignment explanation
Indices: 1014091--1014154 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
1014081 CCCCCTTACT
1014091 TTAACACTTCTCCCATTTAAAACAC
1 TTAACACTTCTCCCATTTAAAACAC
1014116 TTAACACTTCTCCCATTTAAAACAC
1 TTAACACTTCTCCCATTTAAAACAC
1014141 TTAACACTTCTCCC
1 TTAACACTTCTCCC
1014155 CCTTTTTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.33, C:0.34, G:0.00, T:0.33
Consensus pattern (25 bp):
TTAACACTTCTCCCATTTAAAACAC
Found at i:1015324 original size:20 final size:21
Alignment explanation
Indices: 1015272--1015332 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
1015262 TTCCCCTGTG
1015272 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
1015295 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
1015315 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1015333 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1019416 original size:117 final size:117
Alignment explanation
Indices: 1019194--1019417 Score: 317
Period size: 117 Copynumber: 1.9 Consensus size: 117
1019184 AACTTTCAAA
* *
1019194 TCGAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTTTTCAATAT
1 TCGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTTTTCAACAT
*
1019259 TTCATTTTGATTTTCAAAATCCATTTTAATTTCTAGAAGAAGTTTGTTTAAT
66 TTCATTTTGATTTTCAAAATCCATTTTAATTTCTAAAAGAAGTTTGTTTAAT
* * * *
1019311 TCGAAAATTTCTTTTTCAA-AGTTTTCATATTTCATTTTTGAAAGCTCTAACTCTTTTTTCAACA
1 TCGAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTTTTCAACA
* * * *
1019375 TTTCATTTTGATTTTCCAAGTCTATTTTAGCTTTC-AAAAGAAG
65 TTTCATTTTGATTTTCAAAATCCATTTTA-ATTTCTAAAAGAAG
1019418 ATCATTTTTA
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
116 1 0.01
117 89 0.95
118 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.49
Consensus pattern (117 bp):
TCGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTTTTCAACAT
TTCATTTTGATTTTCAAAATCCATTTTAATTTCTAAAAGAAGTTTGTTTAAT
Found at i:1021900 original size:16 final size:16
Alignment explanation
Indices: 1021879--1021909 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1021869 TAATAAATAA
1021879 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1021895 ACGAACATAAACGAA
1 ACGAACATAAACGAA
1021910 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1022000 original size:16 final size:16
Alignment explanation
Indices: 1021976--1022009 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1021966 CATTTAATAA
1021976 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
* *
1021992 ATAAGCGAACATAAAC
1 ATAAACGAACACAAAC
1022008 AT
1 AT
1022010 TGGACACCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.12
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:1023145 original size:14 final size:14
Alignment explanation
Indices: 1023128--1023157 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1023118 AATGAACATA
1023128 AACGAACATAACCG
1 AACGAACATAACCG
1023142 AACGAACATAACCG
1 AACGAACATAACCG
1023156 AA
1 AA
1023158 TGTTCACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.27, G:0.13, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1032957 original size:20 final size:22
Alignment explanation
Indices: 1032932--1032971 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1032922 AGTCGTATAT
1032932 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1032952 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1032972 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1033173 original size:20 final size:20
Alignment explanation
Indices: 1033150--1033192 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1033140 TTCAAACAGT
1033150 ATCGATACTGTTTAAACAAC
1 ATCGATACTGTTTAAACAAC
* *
1033170 ATCGGTACTGTTTAAACAGC
1 ATCGATACTGTTTAAACAAC
1033190 ATC
1 ATC
1033193 ATGACTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATCGATACTGTTTAAACAAC
Found at i:1037068 original size:83 final size:83
Alignment explanation
Indices: 1036919--1037077 Score: 248
Period size: 83 Copynumber: 1.9 Consensus size: 83
1036909 GAATTTCGAG
* * * *
1036919 AGAGCTTTACTCCAACTAAATCTCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAA
1 AGAGCTTTACTCCAACCAAATATCTTTTAATATCTAAATTTAAACAAATAATAATATATTTAAAA
1036984 TTTAAAATATTGAACCTA
66 TTTAAAATATTGAACCTA
* *
1037002 AGAGTTTTACTCC-ACCAAGATATCTTTTAATATCTAAATTTAAACAGATAATAATATATTTAAA
1 AGAGCTTTACTCCAACCAA-ATATCTTTTAATATCTAAATTTAAACAAATAATAATATATTTAAA
1037066 ATTTAAAATATT
65 ATTTAAAATATT
1037078 AAATAGATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
82 4 0.06
83 65 0.94
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (83 bp):
AGAGCTTTACTCCAACCAAATATCTTTTAATATCTAAATTTAAACAAATAATAATATATTTAAAA
TTTAAAATATTGAACCTA
Found at i:1040994 original size:8 final size:8
Alignment explanation
Indices: 1040981--1041007 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1040971 ACTGTTTAGC
1040981 TATGTATT
1 TATGTATT
1040989 TATGTATT
1 TATGTATT
1040997 TATGTATT
1 TATGTATT
1041005 TAT
1 TAT
1041008 TTATACATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (8 bp):
TATGTATT
Found at i:1041665 original size:7 final size:7
Alignment explanation
Indices: 1041653--1041681 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1041643 ACAGAGGAAT
1041653 GAGTGAG
1 GAGTGAG
1041660 GAGTGAG
1 GAGTGAG
1041667 GAGTGAG
1 GAGTGAG
1041674 GAGTGAG
1 GAGTGAG
1041681 G
1 G
1041682 GCCATCACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.59, T:0.14
Consensus pattern (7 bp):
GAGTGAG
Found at i:1042731 original size:31 final size:31
Alignment explanation
Indices: 1042691--1042791 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
1042681 ATAAATAGTA
*
1042691 ATAAATTTAATAATTATTTTGTAATAATTTG
1 ATAAATTTAATGATTATTTTGTAATAATTTG
* * *
1042722 ATAAGTTTAATGATTATTTTATAATAATTCG
1 ATAAATTTAATGATTATTTTGTAATAATTTG
* *
1042753 ATAAATTAAATGATTATTATGTAAT-ATTTG
1 ATAAATTTAATGATTATTTTGTAATAATTTG
*
1042783 A-AAGTTTAA
1 ATAAATTTAA
1042792 GGATCAAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 6 0.10
30 5 0.08
31 48 0.81
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.48
Consensus pattern (31 bp):
ATAAATTTAATGATTATTTTGTAATAATTTG
Found at i:1042998 original size:24 final size:24
Alignment explanation
Indices: 1042970--1043015 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1042960 CCATTATAAT
1042970 ATTTTTT-ATTAACAAATTTAAAGA
1 ATTTTTTAATTAA-AAATTTAAAGA
*
1042994 ATTTTTTAATTTAAAATTTAAA
1 ATTTTTTAATTAAAAATTTAAA
1043016 TTGATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTTTTAATTAAAAATTTAAAGA
Found at i:1052845 original size:13 final size:13
Alignment explanation
Indices: 1052802--1052848 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1052792 TATATTTGTC
1052802 TAAATTAAATATT
1 TAAATTAAATATT
* *
1052815 TAAA-GAATTATTTT
1 TAAATTAA--ATATT
1052829 TAAATTAAATATT
1 TAAATTAAATATT
1052842 TAAATTA
1 TAAATTA
1052849 TTCCTTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.07
13 15 0.56
14 8 0.30
15 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
TAAATTAAATATT
Found at i:1058324 original size:15 final size:15
Alignment explanation
Indices: 1058306--1058337 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1058296 TATATATGTT
1058306 TTTATTGTTTTATTA
1 TTTATTGTTTTATTA
*
1058321 TTTATTGTTTTTTTA
1 TTTATTGTTTTATTA
1058336 TT
1 TT
1058338 GTTTCTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTATTGTTTTATTA
Found at i:1058482 original size:23 final size:24
Alignment explanation
Indices: 1058448--1058502 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
1058438 CATAATGAAA
*
1058448 AATTAAATATTG-ATTTTAAAGTAT
1 AATTAAATATTGAATATTAAA-TAT
*
1058472 AATTAAA-ATTGAATATTGAATAT
1 AATTAAATATTGAATATTAAATAT
1058495 AATTAAAT
1 AATTAAAT
1058503 TATTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (24 bp):
AATTAAATATTGAATATTAAATAT
Found at i:1060741 original size:3 final size:3
Alignment explanation
Indices: 1060733--1060769 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1060723 AGCCTAAGCT
1060733 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
1060770 TCCCCTACTT
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:1061332 original size:3 final size:3
Alignment explanation
Indices: 1061324--1061350 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1061314 TAAAAAGGTT
1061324 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1061351 TATATTAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1064341 original size:27 final size:28
Alignment explanation
Indices: 1064310--1064374 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
1064300 TATAGAAATC
*
1064310 AAATTTGTTAATATAATGATCATAATT-
1 AAATTTGTTAATATAATAATCATAATTA
* * *
1064337 AAATTTATTAATCTAATAATTATAATTA
1 AAATTTGTTAATATAATAATCATAATTA
1064365 ATAATTTGTT
1 A-AATTTGTT
1064375 TTATATTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 23 0.74
28 1 0.03
29 7 0.23
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (28 bp):
AAATTTGTTAATATAATAATCATAATTA
Found at i:1065373 original size:3 final size:3
Alignment explanation
Indices: 1065367--1065392 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1065357 AAACTAAAAA
1065367 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1065393 AAAAGCAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1074619 original size:21 final size:21
Alignment explanation
Indices: 1074562--1074619 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
1074552 GAAATAAATG
*
1074562 AAATAAATAATAAT-AAACATA
1 AAATAAATAA-AATGAAACAAA
***
1074583 AAAT-AATTGGATGAAACAAA
1 AAATAAATAAAATGAAACAAA
1074603 AAATAAATAAAATGAAA
1 AAATAAATAAAATGAAA
1074620 TTGAATAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 2 0.07
20 13 0.46
21 13 0.46
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (21 bp):
AAATAAATAAAATGAAACAAA
Found at i:1075046 original size:2 final size:2
Alignment explanation
Indices: 1074913--1075029 Score: 72
Period size: 2 Copynumber: 61.5 Consensus size: 2
1074903 TGAAGTAAGA
*
1074913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AC AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
1074953 AGG A- AA AT AGT AA AA AT AGT AA AT AG AT A- AA AT A- AT A- AT
1 A-T AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
1074992 A- AT A- AT A- AT AT 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 AT AT AT AT AT AT AT A
1075030 GGAAAATAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
1 9 0.10
2 79 0.85
3 5 0.05
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (2 bp):
AT
Found at i:1076511 original size:106 final size:106
Alignment explanation
Indices: 1076327--1077512 Score: 1872
Period size: 106 Copynumber: 11.2 Consensus size: 106
1076317 GCATTGTTCC
* * * * * *
1076327 GAGTCCAATATCCTCCATCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1076392 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1076433 GAGTCCAATATCCTTTGTTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1076498 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1076539 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1076604 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1076645 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1076710 CAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1076751 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1076816 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1076857 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTAGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1076922 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1076963 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1077028 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1077069 GAGTCCAATATCGTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1077134 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1077175 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1077240 CCAACGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1077281 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATAT--GAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT-TGGGAAGTTGTTTGTTGACA
1077344 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1077386 GAGTACAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * *
1077451 CCAGCGGTCCTTTCATCATGAAGTTGAATTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1077492 GAGTCCAATATCCTTCGTTGT
1 GAGTCCAATATCCTTCGTTGT
1077513 TTGTTGACAA
Statistics
Matches: 999, Mismatches: 78, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
104 1 0.00
105 97 0.10
106 900 0.90
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1078537 original size:22 final size:22
Alignment explanation
Indices: 1078511--1078565 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1078501 TTGTGTTTGG
1078511 TCAAAGGTTTGGAATTTGATGC
1 TCAAAGGTTTGGAATTTGATGC
*
1078533 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGAATTTGATGC
1078555 TCAAAGGTTTG
1 TCAAAGGTTTG
1078566 ATGGGGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGAATTTGATGC
Found at i:1079194 original size:23 final size:21
Alignment explanation
Indices: 1079158--1079231 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 21
1079148 TGCATGTGCT
* *
1079158 TTTTTGTCCCTTTTTCTTTTTG
1 TTTTTGT-TCTTTTTTTTTTTG
*
1079180 ATTTTTGTTCTTTTTTTTTCTTCT
1 -TTTTTGTTCTTTTTTTTT-TT-G
*
1079204 TTTTTGCTTCTTTTCTTTTTTG
1 TTTTTG-TTCTTTTTTTTTTTG
1079226 TTTTTG
1 TTTTTG
1079232 CCCTTTTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 15 0.35
23 17 0.40
24 11 0.26
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.77
Consensus pattern (21 bp):
TTTTTGTTCTTTTTTTTTTTG
Found at i:1083712 original size:42 final size:42
Alignment explanation
Indices: 1083666--1083754 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
1083656 GCAAAGAAAC
*
1083666 TAAAAATATA-ATGAAAATA-AATAAATAGTATAAATAAAATAA
1 TAAAAATATATATAAAAATATAA-AAAT-GTATAAATAAAATAA
** *
1083708 TAAAAATATATATAAAAATATAAAAATGTATGTATAATATAA
1 TAAAAATATATATAAAAATATAAAAATGTATAAATAAAATAA
1083750 TAAAA
1 TAAAA
1083755 TACTAAATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 27 0.66
43 12 0.29
44 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.29
Consensus pattern (42 bp):
TAAAAATATATATAAAAATATAAAAATGTATAAATAAAATAA
Found at i:1083719 original size:22 final size:22
Alignment explanation
Indices: 1083667--1083795 Score: 76
Period size: 21 Copynumber: 6.1 Consensus size: 22
1083657 CAAAGAAACT
1083667 AAAA-ATAT-AATGAAAATAA-A
1 AAAATATATAAAT-AAAATAATA
*
1083687 TAAATAGTATAAATAAAATAATA
1 AAAATA-TATAAATAAAATAATA
*
1083710 AAAATATATATA-AAAAT-ATA
1 AAAATATATAAATAAAATAATA
* ** *
1083730 AAAATGTATGTATAATATAAT-
1 AAAATATATAAATAAAATAATA
* *
1083751 AAAATA-CTAAATAGTAATAATA
1 AAAATATATAAATA-AAATAATA
* * *
1083773 ATAATAAATAAATGAAA-AATA
1 AAAATATATAAATAAAATAATA
1083794 AA
1 AA
1083796 TATACATATA
Statistics
Matches: 83, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
20 20 0.24
21 25 0.30
22 24 0.29
23 14 0.17
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.28
Consensus pattern (22 bp):
AAAATATATAAATAAAATAATA
Found at i:1084474 original size:37 final size:37
Alignment explanation
Indices: 1084433--1084525 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
1084423 ATGCTTGTGG
* * *
1084433 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
1084470 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
1084507 ATCATATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
1084526 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:1108287 original size:24 final size:20
Alignment explanation
Indices: 1108277--1108346 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
1108267 AAATATTCAA
1108277 AAAAATAAATATTAAAATATT
1 AAAAATAAATATT-AAATATT
*
1108298 AAAAATAAATATTAAATTACT
1 AAAAATAAATATTAAA-TATT
* *
1108319 AAAAACTTGAATA-TACATATT
1 AAAAA--TAAATATTAAATATT
1108340 AAAAATA
1 AAAAATA
1108347 CTAAAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 29 0.71
22 3 0.07
23 5 0.12
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (20 bp):
AAAAATAAATATTAAATATT
Found at i:1108303 original size:21 final size:21
Alignment explanation
Indices: 1108259--1108323 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
1108249 TATAAATATA
*
1108259 AAATATTCAAATATTCAAAAAAAT
1 AAATATTAAAATATT---AAAAAT
1108283 AAATATTAAAATATTAAAAAT
1 AAATATTAAAATATTAAAAAT
* *
1108304 AAATATTAAATTACTAAAAA
1 AAATATTAAAATATTAAAAA
1108324 CTTGAATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.63
24 14 0.37
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATATTAAAATATTAAAAAT
Found at i:1108304 original size:9 final size:8
Alignment explanation
Indices: 1108247--1108313 Score: 54
Period size: 8 Copynumber: 8.8 Consensus size: 8
1108237 ATTATTTTAA
1108247 ATTATAAAT
1 ATTA-AAAT
1108256 A-TAAAAT
1 ATTAAAAT
*
1108263 ATTCAAAT
1 ATTAAAAT
*
1108271 ATTCAAAAA
1 ATT-AAAAT
*
1108280 AAT-AAAT
1 ATTAAAAT
1108287 ATTAAAAT
1 ATTAAAAT
1108295 ATTAAAA-
1 ATTAAAAT
1108302 A-T-AAAT
1 ATTAAAAT
1108308 ATTAAA
1 ATTAAA
1108314 TTACTAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
5 3 0.07
6 2 0.04
7 12 0.26
8 23 0.50
9 6 0.13
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (8 bp):
ATTAAAAT
Found at i:1108531 original size:19 final size:19
Alignment explanation
Indices: 1108507--1108554 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1108497 TAAACTATTC
1108507 TTACTAAATTAATCGAGAA
1 TTACTAAATTAATCGAGAA
1108526 TTACTAAATTAATCGAGAA
1 TTACTAAATTAATCGAGAA
*
1108545 TTACAAAATT
1 TTACTAAATT
1108555 TAAATCAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.33
Consensus pattern (19 bp):
TTACTAAATTAATCGAGAA
Found at i:1114815 original size:23 final size:23
Alignment explanation
Indices: 1114774--1114819 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1114764 ATATAATGTA
1114774 TGTGATATATATATGTGTGTGTTT
1 TGTGATATATATA-GTGTGTGTTT
1114798 TGTGATATGATATA-TGTGTGTT
1 TGTGATAT-ATATAGTGTGTGTT
1114820 AGTGCTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 8 0.38
25 5 0.24
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (23 bp):
TGTGATATATATAGTGTGTGTTT
Found at i:1115458 original size:25 final size:25
Alignment explanation
Indices: 1115420--1115478 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
1115410 AAAAAACATA
* *
1115420 GTAAGTTTCGACTAATCTAAAATTT
1 GTAAGTCTCAACTAATCTAAAATTT
* * *
1115445 GTAAGTCTCAACTATTTTAAATTTT
1 GTAAGTCTCAACTAATCTAAAATTT
*
1115470 GTAATTCTC
1 GTAAGTCTC
1115479 GATTAATCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (25 bp):
GTAAGTCTCAACTAATCTAAAATTT
Found at i:1115692 original size:18 final size:18
Alignment explanation
Indices: 1115648--1115697 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
1115638 TCTTTAATAT
1115648 GTATATTTAATTTTTTTTA
1 GTATATTTAA-TTTTTTTA
1115667 GTA-ATTTAATTTTTTTA
1 GTATATTTAATTTTTTTA
*
1115684 GTATTTTTATATTT
1 GTATATTTA-ATTT
1115698 AATTATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 11 0.39
18 10 0.36
19 7 0.25
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (18 bp):
GTATATTTAATTTTTTTA
Found at i:1115721 original size:24 final size:25
Alignment explanation
Indices: 1115668--1115721 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
1115658 TTTTTTTTAG
* * **
1115668 TAATTTAATTTTTTTAGTATTTTTA
1 TAATTTAATTTATTTAATATTTGAA
1115693 T-ATTTAA-TTATTTAATATTTGAA
1 TAATTTAATTTATTTAATATTTGAA
1115716 TAATTT
1 TAATTT
1115722 TATATTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 13 0.54
24 10 0.42
25 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (25 bp):
TAATTTAATTTATTTAATATTTGAA
Found at i:1115856 original size:21 final size:21
Alignment explanation
Indices: 1115830--1115870 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1115820 TATTAATCAC
1115830 CGTGGACTGTCACGTCAATAA
1 CGTGGACTGTCACGTCAATAA
*
1115851 CGTGGATTGTCACGTCAATA
1 CGTGGACTGTCACGTCAATA
1115871 CCATAACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
CGTGGACTGTCACGTCAATAA
Found at i:1117457 original size:30 final size:31
Alignment explanation
Indices: 1117391--1117457 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
1117381 TATTCAAATT
1117391 TTTTAATATTTAATTTTTAAGAATATTAATAA
1 TTTT-ATATTTAATTTTTAAGAATATTAATAA
1117423 TTTTATATTTGAA-TTTTAA-AATAATT-ATAA
1 TTTTATATTT-AATTTTTAAGAAT-ATTAATAA
1117453 TTTTA
1 TTTTA
1117458 AAAAATAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 12 0.36
31 15 0.45
32 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TTTTATATTTAATTTTTAAGAATATTAATAA
Found at i:1118592 original size:4 final size:4
Alignment explanation
Indices: 1118576--1118607 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1118566 AGATCAAAAC
*
1118576 AGAA AGAA GGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1118608 TTACTCGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1123024 original size:13 final size:13
Alignment explanation
Indices: 1122999--1123032 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1122989 GACCCTACCC
1122999 GACTCGA-CCGTT
1 GACTCGACCCGTT
1123011 GACTCGACCCGTT
1 GACTCGACCCGTT
*
1123024 GACCCGACC
1 GACTCGACC
1123033 TGACCGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.18, C:0.41, G:0.24, T:0.18
Consensus pattern (13 bp):
GACTCGACCCGTT
Found at i:1123053 original size:14 final size:14
Alignment explanation
Indices: 1123034--1123066 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1123024 GACCCGACCT
1123034 GACCGTTGATCGTA
1 GACCGTTGATCGTA
*
1123048 GACCGTTGATCGTT
1 GACCGTTGATCGTA
1123062 GACCG
1 GACCG
1123067 GGTGCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.27
Consensus pattern (14 bp):
GACCGTTGATCGTA
Found at i:1123101 original size:29 final size:29
Alignment explanation
Indices: 1123067--1123227 Score: 216
Period size: 29 Copynumber: 5.6 Consensus size: 29
1123057 TCGTTGACCG
* * *
1123067 GGTGCTATTTTAGTAATAAATTTGAAATG
1 GGTGCTATTTTAGTAATTAATTCGAAATA
1123096 GGTGCTATTTTAGTAATTAATTCGAAATA
1 GGTGCTATTTTAGTAATTAATTCGAAATA
*
1123125 GGTGCTATTTTAGTAATTAATTCAAAATA
1 GGTGCTATTTTAGTAATTAATTCGAAATA
*
1123154 GGTGCTATTTAAGTAATTAATTCGAAATA
1 GGTGCTATTTTAGTAATTAATTCGAAATA
* ** *
1123183 GGTGATATTTTAGTAATT-ATTTTAAAAA
1 GGTGCTATTTTAGTAATTAATTCGAAATA
*
1123211 GGGTGCTATTTTTGTAA
1 -GGTGCTATTTTAGTAA
1123228 AATGGTTGAT
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
28 7 0.06
29 111 0.94
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (29 bp):
GGTGCTATTTTAGTAATTAATTCGAAATA
Found at i:1130123 original size:29 final size:28
Alignment explanation
Indices: 1130085--1130139 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
1130075 CGACCCGACC
*
1130085 GACTGTTGACCCAACTCGACCGTTGACT
1 GACTGTTGACCCAACCCGACCGTTGACT
* *
1130113 GACTCGTTGACCCGACCCGATCGTTGA
1 GACT-GTTGACCCAACCCGACCGTTGA
1130140 TCGTTGACCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.24
Consensus pattern (28 bp):
GACTGTTGACCCAACCCGACCGTTGACT
Found at i:1130310 original size:29 final size:29
Alignment explanation
Indices: 1130150--1130304 Score: 240
Period size: 29 Copynumber: 5.3 Consensus size: 29
1130140 TCGTTGACCG
*
1130150 GGTGCTATTTTAGTAATTAATTCGAAATA
1 GGTGCTATTTTAGTAATTAATTCAAAATA
*
1130179 GGTGCTATTTTAGTAATTAATTCGAAATA
1 GGTGCTATTTTAGTAATTAATTCAAAATA
*
1130208 GGTGCTATTTTTGTAATTAATTCAAAATA
1 GGTGCTATTTTAGTAATTAATTCAAAATA
1130237 GGTGCTATTTTAGTAATTAATTCAAAATA
1 GGTGCTATTTTAGTAATTAATTCAAAATA
* * *
1130266 GGTACTATTTTAGTAATT-ATTTAAAAAA
1 GGTGCTATTTTAGTAATTAATTCAAAATA
1130294 GTGTGCTATTT
1 G-GTGCTATTT
1130305 CTGTAAAATG
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
28 9 0.08
29 109 0.92
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTAGTAATTAATTCAAAATA
Found at i:1139389 original size:15 final size:15
Alignment explanation
Indices: 1139369--1139454 Score: 93
Period size: 15 Copynumber: 5.8 Consensus size: 15
1139359 GGTTTTCCGA
1139369 AATTTGAATTACTGG
1 AATTTGAATTACTGG
* *
1139384 AATTTGAATTATTGA
1 AATTTGAATTACTGG
*
1139399 AATTTGAATTTCTGG
1 AATTTGAATTACTGG
**
1139414 AAAATGAATTACTGG
1 AATTTGAATTACTGG
*
1139429 AATTTAAATT-CTGG
1 AATTTGAATTACTGG
**
1139443 AAAATGAATTAC
1 AATTTGAATTAC
1139455 ATTTCTGGAA
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
14 11 0.20
15 45 0.80
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (15 bp):
AATTTGAATTACTGG
Found at i:1139401 original size:30 final size:29
Alignment explanation
Indices: 1139367--1139454 Score: 113
Period size: 30 Copynumber: 3.0 Consensus size: 29
1139357 TTGGTTTTCC
** *
1139367 GAAATTTGAATTACTGGAATTTGAATTATT
1 GAAATTTGAATT-CTGGAAAATGAATTACT
1139397 GAAATTTGAATTTCTGGAAAATGAATTACT
1 GAAATTTGAA-TTCTGGAAAATGAATTACT
* *
1139427 GGAATTTAAATTCTGGAAAATGAATTAC
1 GAAATTTGAATTCTGGAAAATGAATTAC
1139455 ATTTCTGGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 18 0.35
30 32 0.62
31 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (29 bp):
GAAATTTGAATTCTGGAAAATGAATTACT
Found at i:1139460 original size:20 final size:20
Alignment explanation
Indices: 1139437--1139486 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1139427 GGAATTTAAA
*
1139437 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATAAATTACAT
1139457 TTCTGGAAAATAAATTACAT
1 TTCTGGAAAATAAATTACAT
1139477 TTCTGGAAAA
1 TTCTGGAAAA
1139487 CGTTTTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATAAATTACAT
Found at i:1139574 original size:18 final size:17
Alignment explanation
Indices: 1139551--1139584 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1139541 GTTTTTTAAA
1139551 AATTATTATAATATAATT
1 AATTATT-TAATATAATT
*
1139569 AATTATTTTATATAAT
1 AATTATTTAATATAAT
1139585 ATTAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTATTTAATATAATT
Found at i:1139598 original size:31 final size:32
Alignment explanation
Indices: 1139560--1139647 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 32
1139550 AAATTATTAT
1139560 AATATAATTAATTATTTTATATAATATTAA-A
1 AATATAATTAATTATTTTATATAATATTAATA
*
1139591 AATATAA-T-ATTATATTATTATAAATATTAATA
1 AATATAATTAATTATTTTA-TAT-AATATTAATA
* *
1139623 AATATATTTTAAATATTTTA-ATAAT
1 AATATA-ATTAATTATTTTATATAAT
1139648 TAATATTTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
29 8 0.17
30 4 0.09
31 15 0.32
32 10 0.21
33 2 0.04
34 1 0.02
35 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
AATATAATTAATTATTTTATATAATATTAATA
Found at i:1139601 original size:26 final size:26
Alignment explanation
Indices: 1139563--1139656 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 26
1139553 TTATTATAAT
1139563 ATAAT-TAATTATTTTATATAATATTA
1 ATAATATAA-TATTTTATATAATATTA
*
1139589 AAAATATAATATTATATTATTATAAATATTA
1 ATAATATAATA-T-T-TTA-TAT-AATATTA
* *
1139620 ATAA-AT-ATATTTTAAAT-ATTTTA
1 ATAATATAATATTTTATATAATATTA
1139643 ATAAT-TAATATTTT
1 ATAATATAATATTTT
1139657 GATGAAAATG
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
23 10 0.18
24 7 0.12
25 2 0.04
26 9 0.16
27 5 0.09
28 2 0.04
29 6 0.11
30 5 0.09
31 10 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATAATATAATATTTTATATAATATTA
Done.