Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004265.1 Hibiscus syriacus cultivar Beakdansim tig00009346_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: 80673
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:858 original size:25 final size:24
Alignment explanation
Indices: 830--917 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 24
820 AAAAATAATA
830 TAAAACTAGATATATAACATTAAAT
1 TAAAACTA-ATATATAACATTAAAT
*
855 TAAAACATAATAT-TAATCA-TAAAC
1 TAAAAC-TAATATATAA-CATTAAAT
* *
879 TAAATA-TAAAATATAACATTCAAT
1 TAAA-ACTAATATATAACATTAAAT
903 TAAAAACATAATATA
1 T-AAAAC-TAATATA
918 AAAACTAACG
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
23 7 0.14
24 19 0.38
25 16 0.32
26 8 0.16
ACGTcount: A:0.59, C:0.09, G:0.01, T:0.31
Consensus pattern (24 bp):
TAAAACTAATATATAACATTAAAT
Found at i:915 original size:24 final size:24
Alignment explanation
Indices: 841--918 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
831 AAAACTAGAT
841 ATATAACATTAAATT-AAAACATA
1 ATATAACATTAAATTAAAAACATA
* * * *
864 ATATTAATCA-TAAACTAAATATAAA
1 ATA-TAA-CATTAAATTAAAAACATA
*
889 ATATAACATTCAATTAAAAACATA
1 ATATAACATTAAATTAAAAACATA
913 ATATAA
1 ATATAA
919 AAACTAACGA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
23 5 0.12
24 27 0.64
25 10 0.24
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (24 bp):
ATATAACATTAAATTAAAAACATA
Found at i:5699 original size:3 final size:3
Alignment explanation
Indices: 5691--5717 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5681 AAATCTTTAC
5691 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
5718 CAAATCTTGA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10165 original size:18 final size:18
Alignment explanation
Indices: 10142--10184 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
10132 GTAGACCTCG
*
10142 AGAAGAAGAAC-GAGACAA
1 AGAAGAAG-ACGGAGAAAA
10160 AGAAGAAGACGGAGAAAA
1 AGAAGAAGACGGAGAAAA
10178 AGAAGAA
1 AGAAGAA
10185 TGTTGGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.63, C:0.07, G:0.30, T:0.00
Consensus pattern (18 bp):
AGAAGAAGACGGAGAAAA
Found at i:14959 original size:18 final size:20
Alignment explanation
Indices: 14938--14982 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
14928 AATAAAAAAA
14938 TGTTTTGT-TTTAAAT-TGT
1 TGTTTTGTATTTAAATATGT
* *
14956 TGTTTTTTATTTAATTATGT
1 TGTTTTGTATTTAAATATGT
14976 TGTTTTG
1 TGTTTTG
14983 AAGACTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 9 0.41
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.69
Consensus pattern (20 bp):
TGTTTTGTATTTAAATATGT
Found at i:27364 original size:31 final size:31
Alignment explanation
Indices: 27286--27356 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
27276 TCGATATAAC
27286 AATTGAATTTACAAAATGGTTTTTGGACTTG
1 AATTGAATTTACAAAATGGTTTTTGGACTTG
27317 AATTGAATTTACAAAAT-GTTTTTGGACTT-
1 AATTGAATTTACAAAATGGTTTTTGGACTTG
27346 AATTGAATTTA
1 AATTGAATTTA
27357 TTCAAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 11 0.28
30 12 0.30
31 17 0.43
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (31 bp):
AATTGAATTTACAAAATGGTTTTTGGACTTG
Found at i:27561 original size:21 final size:21
Alignment explanation
Indices: 27535--27576 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27525 ATTTGAATAT
*
27535 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
27556 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
27577 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:27643 original size:20 final size:22
Alignment explanation
Indices: 27605--27644 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
27595 TTTGAGTATA
27605 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
27627 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
27645 ATATACGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:30793 original size:31 final size:31
Alignment explanation
Indices: 30715--30785 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
30705 TCGATATAAC
30715 AATTGAATTTACAAAATGGTTTTTGGACTTG
1 AATTGAATTTACAAAATGGTTTTTGGACTTG
30746 AATTGAATTTACAAAAT-GTTTTTGGACTT-
1 AATTGAATTTACAAAATGGTTTTTGGACTTG
30775 AATTGAATTTA
1 AATTGAATTTA
30786 TTCAAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 11 0.28
30 12 0.30
31 17 0.43
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (31 bp):
AATTGAATTTACAAAATGGTTTTTGGACTTG
Found at i:30997 original size:21 final size:21
Alignment explanation
Indices: 30971--31012 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
30961 ATTTGAATAT
*
30971 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
30992 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
31013 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:31079 original size:20 final size:22
Alignment explanation
Indices: 31041--31080 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
31031 TTTGAGTATA
31041 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
31063 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
31081 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:31334 original size:34 final size:32
Alignment explanation
Indices: 31295--31364 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
31285 TTTTGTAAAG
* *
31295 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
31329 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
31361 GGGA
1 GGGA
31365 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:32605 original size:2 final size:2
Alignment explanation
Indices: 32598--32625 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32588 TGCAAAATGA
32598 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
32626 GCCATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39795 original size:166 final size:168
Alignment explanation
Indices: 39520--39855 Score: 640
Period size: 166 Copynumber: 2.0 Consensus size: 168
39510 TAAAAATCTC
39520 CAAATGGAGGACCATATCAGTTTAACAAAGAATCTTGCATGGTCCACGAGCTAGCTTCACCAGGC
1 CAAATGGAGGACCATATCAGTTTAACAAAGAATCTTGCATGGTCCACGAGCTAGCTTCACCAGGC
39585 AAGTGGAGAAGTACACATTCTTCTCTTTTGAGTTTCTTATGCCCTTAAT-AAGACCCAGGAGTTT
66 AAGTGGAGAAGTACACATTCTTCTCTTTTGAGTTTCTTATGCCCTTAATAAAGACCCAGGAGTTT
39649 CCTAATCTGGATCATTTAGAAATAAACTTGCCTTCTAT
131 CCTAATCTGGATCATTTAGAAATAAACTTGCCTTCTAT
39687 CAAATGGAGGACCATATCA-TTTAACAAAGAATCTTGCATGGTCCACGAGCTAGCTTCACCAGGC
1 CAAATGGAGGACCATATCAGTTTAACAAAGAATCTTGCATGGTCCACGAGCTAGCTTCACCAGGC
39751 AAGTGGAGAAGTACACATTCTTCTCTTTTGAGTTTCTTATGCCCTTAATAAGAAGACCCAGGAGT
66 AAGTGGAGAAGTACACATTCTTCTCTTTTGAGTTTCTTATGCCCTTAAT-A-AAGACCCAGGAGT
39816 TTCCTAATCTGGATCATTTAGAAATAAACTTGCCTTCTAT
129 TTCCTAATCTGGATCATTTAGAAATAAACTTGCCTTCTAT
39856 TTAGGCTAGT
Statistics
Matches: 166, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
166 94 0.57
167 19 0.11
169 53 0.32
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (168 bp):
CAAATGGAGGACCATATCAGTTTAACAAAGAATCTTGCATGGTCCACGAGCTAGCTTCACCAGGC
AAGTGGAGAAGTACACATTCTTCTCTTTTGAGTTTCTTATGCCCTTAATAAAGACCCAGGAGTTT
CCTAATCTGGATCATTTAGAAATAAACTTGCCTTCTAT
Found at i:42557 original size:20 final size:20
Alignment explanation
Indices: 42532--42659 Score: 123
Period size: 20 Copynumber: 6.3 Consensus size: 20
42522 TTTTCCTAAT
42532 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
42552 TCGCAACGCGAATTTGAAAAA
1 TCGCAATGCGAATACG-TAAA
*
42573 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
42593 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
42614 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
42634 TCGCAATGCGTAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
42654 TCGCAA
1 TCGCAA
42660 CGAGATTCTG
Statistics
Matches: 84, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
19 1 0.01
20 53 0.63
21 30 0.36
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:42578 original size:41 final size:41
Alignment explanation
Indices: 42532--42639 Score: 198
Period size: 41 Copynumber: 2.6 Consensus size: 41
42522 TTTTCCTAAT
*
42532 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGAAAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATTTGAAAAA
*
42573 TCGCAATGCGATTACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATTTGAAAAA
42614 TCGCAATGCGATTACGTAAATCGCAA
1 TCGCAATGCGATTACGTAAATCGCAA
42640 TGCGTATCTG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGATTACGTAAATCGCAACGCGAATTTGAAAAA
Found at i:43574 original size:24 final size:24
Alignment explanation
Indices: 43521--43567 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
43511 GTATTCGAAA
43521 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
43545 TTTGATCTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
43568 TTGTGATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:46031 original size:20 final size:20
Alignment explanation
Indices: 46006--46094 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
45996 CAACGCGGAA
46006 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAATATGACT
* * *
46026 ATCGCAACACGAAAATGAAT
1 ATCGCAACGCGAATATGACT
46046 ATCGCAACATG-GAAT-TGACT
1 ATCGCAAC--GCGAATATGACT
46066 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGC-GAATATGACT
46086 ATCGCAACG
1 ATCGCAACG
46095 AGAGAATCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.02
20 54 0.93
21 3 0.05
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:46065 original size:40 final size:41
Alignment explanation
Indices: 46016--46093 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
46006 ATCGCAACGC
46016 GAATATGACTATCGCAACACGAAAATGAATATCGCAACATG
1 GAATATGACTATCGCAACACGAAAATGAATATCGCAACATG
* * *
46057 GAAT-TGACTATCGCAACGCGGAAATGACTATCGCAAC
1 GAATATGACTATCGCAACACGAAAATGAATATCGCAAC
46094 GAGAGAATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (41 bp):
GAATATGACTATCGCAACACGAAAATGAATATCGCAACATG
Found at i:46123 original size:19 final size:19
Alignment explanation
Indices: 46099--46185 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 19
46089 GCAACGAGAG
46099 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
46118 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
46137 AAGCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
46151 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
46171 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
46186 CTAATTTCGC
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 7 0.12
16 5 0.09
17 2 0.04
18 3 0.05
19 29 0.51
20 11 0.19
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:46135 original size:52 final size:53
Alignment explanation
Indices: 46066--46185 Score: 179
Period size: 52 Copynumber: 2.3 Consensus size: 53
46056 GGAATTGACT
** *
46066 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGC-GAAATGAAAAGCGCAACGAGAGAATCGCAATGCGAAAATGAAA
* *
46119 ATCGCAATGCGAAATGAAAAGCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGCGAAATGAAAAGCGCAACGAGAGAATCGCAATGCGAAAATGAAA
46172 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
46186 CTAATTTCGC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 30 0.50
53 30 0.50
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (53 bp):
ATCGCAACGCGAAATGAAAAGCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:46215 original size:20 final size:19
Alignment explanation
Indices: 46189--46257 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 19
46179 CGCGAAACTA
46189 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
46208 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
46226 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
46242 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
46258 CTCTCGTTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
14 6 0.14
16 7 0.17
17 3 0.07
18 4 0.10
19 9 0.21
20 13 0.31
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:46240 original size:34 final size:34
Alignment explanation
Indices: 46197--46290 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 34
46187 TAATTTCGCA
46197 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
*
46231 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
** * *
46264 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
46291 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
Found at i:47867 original size:42 final size:42
Alignment explanation
Indices: 47788--47878 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
47778 CCTCTTCAAC
* * *
47788 GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAAGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
47830 GATGATAAGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAAGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
47872 GATGACA
1 GATGACA
47879 GGTGAGTCGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (42 bp):
GATGACAAGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:48417 original size:33 final size:33
Alignment explanation
Indices: 48357--48440 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
48347 TCTAAAACTT
** * *
48357 AAAATCGCAACGCGAAAATGACTATCGCAACGAG
1 AAAATCGCAACGCG-AAATGAAAATCGCAACAAC
* *
48391 AGAATCGCAATGCGAAATGAAAATCGCAACAAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACAAC
48424 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
48441 ATGACTATCG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 30 0.71
34 12 0.29
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACAAC
Found at i:48452 original size:20 final size:20
Alignment explanation
Indices: 48427--48478 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
48417 CAACAACAAA
*
48427 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
48447 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
48467 ATCGCAATGCGA
1 ATCGCAATGCGA
48479 TTTTCATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:48531 original size:20 final size:20
Alignment explanation
Indices: 48506--48649 Score: 210
Period size: 20 Copynumber: 7.5 Consensus size: 20
48496 GATTCTTTCG
48506 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
48526 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
48546 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
48566 TTGTGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
48586 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
48600 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
48620 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
48640 TTGCGATAGT
1 TTGCGATAGT
48650 AAACTATTCT
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
14 7 0.06
16 5 0.05
18 6 0.05
20 93 0.84
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:48551 original size:40 final size:40
Alignment explanation
Indices: 48468--48649 Score: 210
Period size: 40 Copynumber: 4.9 Consensus size: 40
48458 AAAATGACTA
* **
48468 TCGCAATGCGATTTTCATTTT-GCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
48503 TCG--TTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
48541 TCGCATTGCGATAGTCATTTTCGCATTGTGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* *
48581 TTGCATTGCGAT--TC--TCTCG--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
48615 TCGCGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
48650 AAACTATTCT
Statistics
Matches: 124, Mismatches: 10, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
33 13 0.10
34 34 0.27
35 3 0.02
36 8 0.06
38 11 0.09
40 55 0.44
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:48604 original size:54 final size:57
Alignment explanation
Indices: 48506--48647 Score: 200
Period size: 54 Copynumber: 2.5 Consensus size: 57
48496 GATTCTTTCG
*
48506 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCATTGCGATA-TCA-TCTCG-ATTGCGATAGTCATTTTCGCA
* * *
48566 TTGTGATAGTCATTTTTGCATTGCGAT-TC-TCTCG-TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCATTGCGATATCATCTCGATTGCGATAGTCATTTTCGCA
48620 TTGCGATAGTCATTTTCGCATTGCGATA
1 TTGCGATAGTCATTTTCGCATTGCGATA
48648 GTAAACTATT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
54 44 0.59
56 4 0.05
58 2 0.03
60 25 0.33
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (57 bp):
TTGCGATAGTCATTTTCGCATTGCGATATCATCTCGATTGCGATAGTCATTTTCGCA
Found at i:50600 original size:20 final size:20
Alignment explanation
Indices: 50542--50611 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
50532 AAAACTTTAA
** **
50542 ATCGCAACATGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
50562 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
50582 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
50602 ATCGCAACGC
1 ATCGCAACGC
50612 AAGAATCGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:50650 original size:33 final size:34
Alignment explanation
Indices: 50582--50654 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
50572 GAAAATGACT
* **
50582 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
50616 ATCGCAACGCGAA-ATGAAAATCGCAACG-ATAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCA-AGA
50649 ATCGCA
1 ATCGCA
50655 TTGCGATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 21 0.60
34 13 0.37
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
Found at i:51041 original size:22 final size:22
Alignment explanation
Indices: 50980--51051 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 22
50970 TGACCGTGAA
* * *
50980 TGATTTCGCCGGAGATGGAGAC
1 TGATATCGTCGGAGATGGGGAC
*
51002 TGATATCTTC---G-TGGGGAC
1 TGATATCGTCGGAGATGGGGAC
*
51020 TGATTTCGTCGGAGATGGGGAC
1 TGATATCGTCGGAGATGGGGAC
*
51042 GGATATCGTC
1 TGATATCGTC
51052 TTAGAGAGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 14 0.37
19 1 0.03
21 1 0.03
22 22 0.58
ACGTcount: A:0.19, C:0.17, G:0.36, T:0.28
Consensus pattern (22 bp):
TGATATCGTCGGAGATGGGGAC
Found at i:51242 original size:20 final size:20
Alignment explanation
Indices: 51217--51290 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
51207 GCACTATGTA
51217 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* **
51237 AATCGCATTGCGATTTTCCA
1 AATCGCATTGCGATTTACGT
* *
51257 AATTCGCGTTGCGATTTATGT
1 AA-TCGCATTGCGATTTACGT
*
51278 ATTCGCATTGCGA
1 AATCGCATTGCGA
51291 ATTTGGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:57422 original size:18 final size:18
Alignment explanation
Indices: 57369--57411 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
57359 TCTTCTTATT
*
57369 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATTGCTTTTA
57388 TTTATTTAATTGCTTTTA
1 TTTATTTAATTGCTTTTA
57406 -TTATTT
1 TTTATTT
57412 TAATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTAATTGCTTTTA
Found at i:58280 original size:15 final size:15
Alignment explanation
Indices: 58260--58353 Score: 86
Period size: 18 Copynumber: 6.0 Consensus size: 15
58250 AATATAAGTT
58260 TATATATAAACTATA
1 TATATATAAACTATA
58275 TTTATATTATAAACTATA
1 --TATA-TATAAACTATA
58293 TAATTATTATAAGA-TATA
1 T-A-TA-TATAA-ACTATA
58311 TATATATAAAC--TA
1 TATATATAAACTATA
*
58324 TGTATATAAACTATA
1 TATATATAAACTATA
*
58339 TATGTATAAACTATA
1 TATATATAAACTATA
58354 AAAAATATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
13 12 0.18
14 1 0.01
15 20 0.30
16 3 0.04
17 6 0.09
18 24 0.36
19 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:58287 original size:18 final size:17
Alignment explanation
Indices: 58242--58324 Score: 75
Period size: 18 Copynumber: 4.8 Consensus size: 17
58232 AAAAATTATA
*
58242 ATATATAAAATATAAGTTT
1 ATATATAAACTAT-A-TTT
58261 ATATATAAACTATATTT
1 ATATATAAACTATATTT
58278 ATATTATAAACTATATAATT
1 ATA-TATAAACTATAT--TT
58298 AT-TATAAGA-TATA--T
1 ATATATAA-ACTATATTT
58312 ATATATAAACTAT
1 ATATATAAACTAT
58325 GTATATAAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
14 4 0.07
15 8 0.14
17 6 0.11
18 22 0.39
19 13 0.23
20 4 0.07
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
ATATATAAACTATATTT
Found at i:58329 original size:13 final size:13
Alignment explanation
Indices: 58309--58353 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
58299 TTATAAGATA
58309 TATATATATAAAC
1 TATATATATAAAC
*
58322 TATGTATATAAAC
1 TATATATATAAAC
58335 TATATATGTATAAAC
1 TATATA--TATAAAC
58350 TATA
1 TATA
58354 AAAAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.61
15 11 0.39
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:58386 original size:25 final size:24
Alignment explanation
Indices: 58306--58379 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 24
58296 TTATTATAAG
*
58306 ATATATATATATAAACTATGTATATAAA
1 ATATATATGTATAAACTA--TA-A-AAA
*
58334 CTATATATGTATAAACTATAAAAA
1 ATATATATGTATAAACTATAAAAA
*
58358 ATATATAGTTTATAAACTATAA
1 ATATATA-TGTATAAACTATAA
58380 TTTATATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 9 0.22
25 14 0.34
26 2 0.05
28 16 0.39
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATATATGTATAAACTATAAAAA
Found at i:58414 original size:52 final size:51
Alignment explanation
Indices: 58358--58472 Score: 128
Period size: 52 Copynumber: 2.3 Consensus size: 51
58348 ACTATAAAAA
* * *
58358 ATATATAGTTTATAAACTATAATTTAT-ATTAATATAGTATATATA-TGTATGT
1 ATATATACTATATAAACTATAAATTATAATT--TATAGTA-ATATAGTGTATGT
* * *
58410 ATATAAACTATATAAACTATAAATTATAATTTATATTAATATAGTGTGTGT
1 ATATATACTATATAAACTATAAATTATAATTTATAGTAATATAGTGTATGT
58461 ATATATA-TATAT
1 ATATATACTATAT
58473 GTATGTATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
50 10 0.19
51 18 0.33
52 23 0.43
53 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (51 bp):
ATATATACTATATAAACTATAAATTATAATTTATAGTAATATAGTGTATGT
Found at i:58781 original size:35 final size:36
Alignment explanation
Indices: 58711--58784 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
58701 ACAATAGTTA
* *
58711 ATATATGTAACATATAGTATATGTATACATGTAAACT
1 ATATATGTAACATATAGTACATGTATA-ATATAAACT
* *
58748 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACATATAGTACATGTATAATATAAACT
58783 AT
1 AT
58785 GTATAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.27
37 24 0.73
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (36 bp):
ATATATGTAACATATAGTACATGTATAATATAAACT
Found at i:58793 original size:20 final size:20
Alignment explanation
Indices: 58770--58833 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
58760 TATAGTACAT
* *
58770 GTATGTATAAACTATGTATA
1 GTATATATAAACTATATATA
58790 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
* * *
58810 TATATATATAAACCATATAAA
1 -GTATATATAAACTATATATA
58831 GTA
1 GTA
58834 AATTACTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:58817 original size:21 final size:20
Alignment explanation
Indices: 58775--58828 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
58765 TACATGTATG
* *
58775 TATAAACTATGTATAGTATA
1 TATAAACTATATATAATATA
58795 TATAAACTATATATATATATA
1 TATAAACTATATATA-ATATA
*
58816 TATAAACCATATA
1 TATAAACTATATA
58829 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (20 bp):
TATAAACTATATATAATATA
Found at i:58894 original size:2 final size:2
Alignment explanation
Indices: 58889--58976 Score: 51
Period size: 2 Copynumber: 44.0 Consensus size: 2
58879 AATAATAAAG
* * *
58889 TA TA TA TA TA TA TA TA TA TA TA TA AA GT- TT TA GTA TA AA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA
* *
58931 TA TA TA CA TA TA TA -A TA -A TA TA AA GTA TA -A GTA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
58971 TA TA TA
1 TA TA TA
58977 AAGTATAATT
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
1 5 0.07
2 57 0.85
3 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (2 bp):
TA
Found at i:58973 original size:40 final size:39
Alignment explanation
Indices: 58889--59049 Score: 138
Period size: 40 Copynumber: 4.1 Consensus size: 39
58879 AATAATAAAG
* * *
58889 TATATATATATATATAT-AT-ATATAAAGTTTTAGTATA
1 TATATATATAAATATATAATAATATAAAGTATAAGTATA
* *
58926 AAGTATATATACATATATAATAATATAAAGTATAAGTATA
1 TA-TATATATAAATATATAATAATATAAAGTATAAGTATA
*
58966 TTATATATATAAAGTATAATTATAATGACTAAAGTATATAAGTATA
1 -TATATATATAAA-TAT-ATAATAAT-A-TAAAG--TATAAGTATA
*
59012 TA-ATATA-AAATATATAATTAT-TAAA-TAT-AGTATA
1 TATATATATAAATATATAATAATATAAAGTATAAGTATA
59046 TATA
1 TATA
59050 CATACATGCA
Statistics
Matches: 104, Mismatches: 9, Indels: 24
0.76 0.07 0.18
Matches are distributed among these distances:
34 8 0.08
35 4 0.04
37 1 0.01
38 18 0.17
39 2 0.02
40 25 0.24
41 10 0.10
42 10 0.10
43 4 0.04
44 10 0.10
45 2 0.02
46 10 0.10
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (39 bp):
TATATATATAAATATATAATAATATAAAGTATAAGTATA
Found at i:58980 original size:24 final size:23
Alignment explanation
Indices: 58939--59016 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 23
58929 TATATATACA
58939 TATATAATAATATAAAGTATAAG
1 TATATAATAATATAAAGTATAAG
*
58962 TATATTATATATATAAAGTATAA-
1 TATATAATA-ATATAAAGTATAAG
* *
58985 T-TATAATGA-CTAAAGTATATAAG
1 TATATAATAATATAAAG--TATAAG
59008 TATATAATA
1 TATATAATA
59017 TAAAATATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
20 5 0.11
21 1 0.02
22 10 0.22
23 10 0.22
24 19 0.42
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (23 bp):
TATATAATAATATAAAGTATAAG
Found at i:59000 original size:20 final size:19
Alignment explanation
Indices: 58959--59003 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
58949 TATAAAGTAT
58959 AAGTAT-ATTATATATATA
1 AAGTATAATTATATATATA
58977 AAGTATAATTATA-ATGACTA
1 AAGTATAATTATATAT-A-TA
58997 AAGTATA
1 AAGTATA
59004 TAAGTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
19 7 0.29
20 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (19 bp):
AAGTATAATTATATATATA
Found at i:59020 original size:22 final size:21
Alignment explanation
Indices: 58893--59205 Score: 114
Period size: 22 Copynumber: 14.9 Consensus size: 21
58883 ATAAAGTATA
58893 TATATATATATATATATATAAAG
1 TATATA-ATATATA-ATATAAAG
* * *
58916 T-TTTAGTATA-AAGTATATA-
1 TATATAATATATAA-TATAAAG
*
58935 TACAT-ATATAATAATATAAAG
1 TATATAATAT-ATAATATAAAG
58956 TATA-AGTATATTATATATATAAAG
1 TATATA--ATA-TATA-ATATAAAG
58980 --TATAAT-TATAATGACTAAAG
1 TATATAATATATAAT-A-TAAAG
*
59000 TATATAAGTATATAATATAAAA
1 TATATAA-TATATAATATAAAG
*
59022 TATATAAT-TATTAA-ATATAG
1 TATATAATATA-TAATATAAAG
* *
59042 TATAT-ATACATACATGCATACA-
1 TATATAATATATA-AT--ATAAAG
* * * * *
59064 CACA-CATATAT-ATACACATG
1 TATATAATATATAATATA-AAG
59084 TATATAATA-AT-ATA-AAA-
1 TATATAATATATAATATAAAG
59101 TATATAAGTATATAATATAAAG
1 TATATAA-TATATAATATAAAG
*
59123 TACATAAGTAT-TAA-ATATAAG
1 TATATAA-TATATAATATA-AAG
59144 TATATAA-ATATTAAATATAAAG
1 TATATAATATA-T-AATATAAAG
*
59166 TATATAA-ATATATCTATAAAG
1 TATATAATATATA-ATATAAAG
59187 TATA-AAGTATATATATATA
1 TATATAA-TATATA-ATATA
59206 CTTTATATTA
Statistics
Matches: 223, Mismatches: 27, Indels: 81
0.67 0.08 0.24
Matches are distributed among these distances:
17 7 0.03
18 7 0.03
19 19 0.09
20 49 0.22
21 46 0.21
22 63 0.28
23 17 0.08
24 15 0.07
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.37
Consensus pattern (21 bp):
TATATAATATATAATATAAAG
Found at i:59112 original size:15 final size:15
Alignment explanation
Indices: 59085--59178 Score: 63
Period size: 15 Copynumber: 6.4 Consensus size: 15
59075 ATACACATGT
59085 ATATAATAA-TATAAA
1 ATAT-ATAAGTATAAA
*
59100 ATATATAAGTATATA
1 ATATATAAGTATAAA
*
59115 ATATA-AAGTACATAA
1 ATATATAAGTATA-AA
* *
59130 GTAT-TAAATAT-AA
1 ATATATAAGTATAAA
* * *
59143 GTATATAAATATTAA
1 ATATATAAGTATAAA
59158 ATATA-AAGTATATAA
1 ATATATAAGTATA-AA
59173 ATATAT
1 ATATAT
59179 CTATAAAGTA
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
13 6 0.10
14 22 0.35
15 35 0.56
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (15 bp):
ATATATAAGTATAAA
Found at i:59150 original size:21 final size:22
Alignment explanation
Indices: 59092--59205 Score: 119
Period size: 22 Copynumber: 5.3 Consensus size: 22
59082 TGTATATAAT
*
59092 AATATAAAATATATAAGTA-TA
1 AATATAAAGTATATAAGTATTA
*
59113 TAATATAAAGTACATAAGTATTA
1 -AATATAAAGTATATAAGTATTA
*
59136 AATAT-AAGTATATAAATATTA
1 AATATAAAGTATATAAGTATTA
*
59157 AATATAAAGTATATAAATA-TA
1 AATATAAAGTATATAAGTATTA
**
59178 TCTATAAAGTATA-AAGTATATA
1 AATATAAAGTATATAAGTAT-TA
*
59200 TATATA
1 AATATA
59206 CTTTATATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.05
21 32 0.40
22 42 0.52
23 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (22 bp):
AATATAAAGTATATAAGTATTA
Found at i:59171 original size:30 final size:28
Alignment explanation
Indices: 59092--59205 Score: 92
Period size: 28 Copynumber: 4.0 Consensus size: 28
59082 TGTATATAAT
*
59092 AATATAAAATATATAAGTATAT-AATATA
1 AATATAAAGTATA-AAGTATATAAATATA
* *
59120 AAGTACATAAGTATTAAA-TATA-AGTATATA
1 AA-TATA-AAGTA-TAAAGTATATA-AATATA
59150 AATATTAAA-TATAAAGTATATAAATATA
1 AATA-TAAAGTATAAAGTATATAAATATA
** *
59178 TCTATAAAGTATAAAGTATATATATATA
1 AATATAAAGTATAAAGTATATAAATATA
59206 CTTTATATTA
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
27 8 0.12
28 33 0.48
29 12 0.17
30 14 0.20
31 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (28 bp):
AATATAAAGTATAAAGTATATAAATATA
Found at i:59172 original size:9 final size:8
Alignment explanation
Indices: 59092--59178 Score: 64
Period size: 7 Copynumber: 11.9 Consensus size: 8
59082 TGTATATAAT
59092 AATATA-A
1 AATATATA
59099 AATATATA
1 AATATATA
*
59107 AGTATAT-
1 AATATATA
59114 AATATA-A
1 AATATATA
* *
59121 AGTACATA
1 AATATATA
*
59129 AGTAT-T-
1 AATATATA
59135 AA-ATATA
1 AATATATA
*
59142 AGTATATA
1 AATATATA
59150 AATAT-TA
1 AATATATA
59157 AATATA-A
1 AATATATA
*
59164 AGTATATA
1 AATATATA
59172 AATATAT
1 AATATAT
59179 CTATAAAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 30 0.48
8 28 0.45
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (8 bp):
AATATATA
Found at i:59188 original size:43 final size:42
Alignment explanation
Indices: 59093--59205 Score: 113
Period size: 43 Copynumber: 2.6 Consensus size: 42
59083 GTATATAATA
* * *
59093 ATATAAAATATATAAGTATATAATATAAAGTACATAAGTATT
1 ATATAAAGTATATAAATATATAATATAAAGTACATAAATATT
* *
59135 AAATATAAGTATATAAATAT-TAAATATAAAGTATATAAATATAT
1 ATATA-AAGTATATAAATATAT-AATATAAAGTACATAAATAT-T
* *
59179 CTATAAAGTATA-AAGTATATATATATA
1 ATATAAAGTATATAAATATATA-ATATA
59206 CTTTATATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
42 11 0.19
43 43 0.74
44 4 0.07
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (42 bp):
ATATAAAGTATATAAATATATAATATAAAGTACATAAATATT
Found at i:59212 original size:22 final size:21
Alignment explanation
Indices: 59192--59362 Score: 70
Period size: 20 Copynumber: 8.9 Consensus size: 21
59182 TAAAGTATAA
59192 AGTATATA-TATATACTTTAT
1 AGTATATACTATATACTTTAT
*
59212 ATTATATACTTATATACTTTAT
1 AGTATATAC-TATATACTTTAT
* * * * *
59234 TGT-TATACTCTCT-CTCTCT
1 AGTATATACTATATACTTTAT
* *
59253 A-TATATA-TATAT--GTAAT
1 AGTATATACTATATACTTTAT
59270 A-TATATACT-TATACTTTAT
1 AGTATATACTATATACTTTAT
* * *
59289 ATTATTATA-TATGTA-TATAT
1 AGTA-TATACTATATACTTTAT
* * *
59309 ACTTTATACTA-AAAC-TT-T
1 AGTATATACTATATACTTTAT
59327 A-TATATA-TATATACTTTAT
1 AGTATATACTATATACTTTAT
*
59346 AGTTTATA-TATATACTT
1 AGTATATACTATATACTT
59363 ATACACTTTA
Statistics
Matches: 110, Mismatches: 26, Indels: 30
0.66 0.16 0.18
Matches are distributed among these distances:
16 2 0.02
17 19 0.17
18 9 0.08
19 20 0.18
20 35 0.32
21 12 0.11
22 13 0.12
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.51
Consensus pattern (21 bp):
AGTATATACTATATACTTTAT
Found at i:59224 original size:8 final size:8
Alignment explanation
Indices: 59200--59514 Score: 109
Period size: 8 Copynumber: 41.1 Consensus size: 8
59190 AAAGTATATA
59200 TATATACT
1 TATATACT
59208 T-TATA-T
1 TATATACT
59214 TATATACT
1 TATATACT
59222 TATATACT
1 TATATACT
**
59230 T-TATTGT
1 TATATACT
59237 TATACT-CT
1 TATA-TACT
* *
59245 CTCTCT-CT
1 -TATATACT
59253 ATATATA-T
1 -TATATACT
* *
59261 ATATGTAAT
1 -TATATACT
59270 ATATATAC-
1 -TATATACT
59278 T-TATACTT
1 TATATAC-T
59286 TATATTA-T
1 TATA-TACT
*
59294 TATATATGT
1 TATATA-CT
59303 ATATATACT
1 -TATATACT
59312 T-TATAC-
1 TATATACT
*
59318 TA-AAACTT
1 TATATAC-T
59326 TATATA-T
1 TATATACT
59333 ATATATACT
1 -TATATACT
*
59342 T-TATAGT
1 TATATACT
59349 T-TATA--
1 TATATACT
59354 TATATACT
1 TATATACT
*
59362 TATACACTT
1 TATATAC-T
59371 TATATTA-T
1 TATA-TACT
*
59379 TATATATGT
1 TATATA-CT
59388 ATATATACT
1 -TATATACT
*
59397 T-TATATT
1 TATATACT
59404 TA-ATACT
1 TATATACT
59411 TATATACT
1 TATATACT
59419 TATAT--T
1 TATATACT
* *
59425 T-GATGCT
1 TATATACT
59432 TATATACT
1 TATATACT
*
59440 TATATATTT
1 TATATA-CT
59449 TATAATA-T
1 TAT-ATACT
59457 TATATA-T
1 TATATACT
59464 GTATATA--
1 -TATATACT
59471 TATATA--
1 TATATACT
59477 TATATA-T
1 TATATACT
59484 TATAT--T
1 TATATACT
59490 TATATACT
1 TATATACT
59498 TATATACT
1 TATATACT
59506 TATATACT
1 TATATACT
59514 T
1 T
59515 TAGTCTTTAT
Statistics
Matches: 244, Mismatches: 24, Indels: 78
0.71 0.07 0.23
Matches are distributed among these distances:
5 3 0.01
6 35 0.14
7 57 0.23
8 103 0.42
9 28 0.11
10 18 0.07
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (8 bp):
TATATACT
Found at i:59257 original size:2 final size:2
Alignment explanation
Indices: 59252--59558 Score: 75
Period size: 2 Copynumber: 155.0 Consensus size: 2
59242 TCTCTCTCTC
* *
59252 TA TA TA TA TA TA TG TA -A TA TA TA TA CT- TA TA CTT TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * * *
59293 T- TA TA TA TG TA TA TA TA CTT TA TA CTA -A AA CTT 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
* * * *
59334 TA TA TA CTT TA TA GTT TA TA TA TA TA CT- TA TA CA CTT TA TA T-
1 TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
* * *
59376 TA T- TA TA TA TG TA TA TA TA CTT TA TA TT TA -A TA CT- 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
* * *
59417 CT- TA TA TT TGA TGC T- TA TA TA CT- TA TA TA T- TT TA TA -A TA
1 -TA TA TA TA T-A T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
59456 T- TA TA TA TG TA TA TA TA TA TA TA TA TA T- TA TA TT 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
* * *
59496 CT- TA TA TA CT- TA TA TA CTT TA GTC TT TA TA -A T- TA TA CTA TA
1 -TA TA TA TA -TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA -TA TA
*
59537 TA TA TA TA T- TA -A TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
59559 ATGTAGACAT
Statistics
Matches: 223, Mismatches: 40, Indels: 84
0.64 0.12 0.24
Matches are distributed among these distances:
1 23 0.10
2 179 0.80
3 21 0.09
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59423 original size:21 final size:21
Alignment explanation
Indices: 59389--59510 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 21
59379 TATATATGTA
59389 TATATACTTTATATTTAATACT
1 TATATAC-TTATATTTAATACT
* *
59411 TATATACTTATATTTGATGCT
1 TATATACTTATATTTAATACT
59432 TATATACTTATATATTTTATAATA-T
1 TATATAC-T-TATA--TT-TAATACT
*
59457 TATATA-TGTATATAT-ATA-T
1 TATATACT-TATATTTAATACT
59476 ATATATA-TTATATTTATATACT
1 -TATATACTTATATTTA-ATACT
59498 TATATACTTATAT
1 TATATACTTATAT
59511 ACTTTAGTCT
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
19 10 0.12
20 8 0.10
21 29 0.35
22 15 0.18
23 9 0.11
25 9 0.11
26 3 0.04
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (21 bp):
TATATACTTATATTTAATACT
Found at i:59468 original size:25 final size:24
Alignment explanation
Indices: 59431--59511 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 24
59421 TATTTGATGC
59431 TTATATACTTATATATTTTATAATA
1 TTATATA-TTATATATTTTATAATA
*
59456 TTATATATGTATATATATATATATATA
1 TTATATAT-TATATAT-TTTATA-ATA
*
59483 TTATAT-TTATATA-CTTAT-ATA
1 TTATATATTATATATTTTATAATA
59504 CTTATATA
1 -TTATATA
59512 CTTTAGTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
21 3 0.06
22 6 0.12
23 3 0.06
24 1 0.02
25 20 0.42
26 6 0.12
27 9 0.19
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (24 bp):
TTATATATTATATATTTTATAATA
Found at i:59525 original size:16 final size:17
Alignment explanation
Indices: 59354--59516 Score: 104
Period size: 17 Copynumber: 10.1 Consensus size: 17
59344 ATAGTTTATA
*
59354 TATATACTTATACACTT
1 TATATACTTATATACTT
59371 TATATTA-TTATATA-TGT
1 TATA-TACTTATATACT-T
59388 ATATATACTT-TATA-TT
1 -TATATACTTATATACTT
59404 TA-ATACTTATATAC-T
1 TATATACTTATATACTT
* *
59419 TATAT--TT-GATGC-T
1 TATATACTTATATACTT
*
59432 TATATACTTATATATTT
1 TATATACTTATATACTT
*
59449 TATAATA-TTATATA-TG
1 TAT-ATACTTATATACTT
*
59465 TATATA-TATATATA-TA
1 TATATACT-TATATACTT
*
59481 TATTATATTTATATAC-T
1 TA-TATACTTATATACTT
59498 TATATACTTATATACTT
1 TATATACTTATATACTT
59515 TA
1 TA
59517 GTCTTTATAA
Statistics
Matches: 119, Mismatches: 10, Indels: 34
0.73 0.06 0.21
Matches are distributed among these distances:
13 9 0.08
14 8 0.07
15 15 0.13
16 31 0.26
17 44 0.37
18 12 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (17 bp):
TATATACTTATATACTT
Found at i:59588 original size:17 final size:17
Alignment explanation
Indices: 59566--59602 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
59556 ATAATGTAGA
*
59566 CATGTATGTATGTCTAT
1 CATGTATATATGTCTAT
59583 CATGTATATATGTCTAT
1 CATGTATATATGTCTAT
59600 CAT
1 CAT
59603 ACATACATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (17 bp):
CATGTATATATGTCTAT
Found at i:59595 original size:8 final size:8
Alignment explanation
Indices: 59453--59595 Score: 50
Period size: 8 Copynumber: 17.8 Consensus size: 8
59443 ATATTTTATA
59453 ATAT-TAT
1 ATATGTAT
59460 ATATGTAT
1 ATATGTAT
*
59468 ATATATAT
1 ATATGTAT
*
59476 ATATATATT
1 ATATGTA-T
*
59485 ATATTTAT
1 ATATGTAT
59493 ATACT-TAT
1 ATA-TGTAT
59501 ATACT-TAT
1 ATA-TGTAT
59509 ATACT-T-T
1 ATA-TGTAT
* *
59516 AGTCTTTAT
1 A-TATGTAT
59525 A-AT-TAT
1 ATATGTAT
*
59531 ACTATATAT
1 A-TATGTAT
*
59540 ATATATTAAT
1 ATAT-GT-AT
59550 ATATGTAT
1 ATATGTAT
*
59558 A-ATGTAG
1 ATATGTAT
*
59565 ACATGTAT
1 ATATGTAT
* *
59573 GTATGTCT
1 ATATGTAT
59581 ATCATGTAT
1 AT-ATGTAT
59590 ATATGT
1 ATATGT
59596 CTATCATACA
Statistics
Matches: 110, Mismatches: 13, Indels: 25
0.74 0.09 0.17
Matches are distributed among these distances:
6 4 0.04
7 14 0.13
8 63 0.57
9 23 0.21
10 6 0.05
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:59633 original size:24 final size:25
Alignment explanation
Indices: 59601--59663 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
59591 TATGTCTATC
59601 ATACATACATACATGCATCAAA-AT
1 ATACATACATACATGCATCAAATAT
* * *
59625 ATACATACATATATGTATTAAATAT
1 ATACATACATACATGCATCAAATAT
* *
59650 ATATATATATACAT
1 ATACATACATACAT
59664 ACCATGCATG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 19 0.59
25 13 0.41
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (25 bp):
ATACATACATACATGCATCAAATAT
Found at i:59749 original size:20 final size:19
Alignment explanation
Indices: 59700--59751 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
59690 ATATACATGC
*
59700 ATATATGTATGATATATGT
1 ATATATGCATGATATATGT
*
59719 AT-TATTACATGCATATATGT
1 ATATA-TGCATG-ATATATGT
59739 ATATATGCATGAT
1 ATATATGCATGAT
59752 GTGTGTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.07
19 8 0.30
20 15 0.56
21 2 0.07
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (19 bp):
ATATATGCATGATATATGT
Found at i:59986 original size:22 final size:22
Alignment explanation
Indices: 59953--59994 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
59943 GTATGATACA
59953 TATGTTATATGCATATATTATG
1 TATGTTATATGCATATATTATG
*
59975 TATG-TATGATGCATGTATTA
1 TATGTTAT-ATGCATATATTA
59995 AAATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (22 bp):
TATGTTATATGCATATATTATG
Found at i:61527 original size:7 final size:7
Alignment explanation
Indices: 61515--61618 Score: 74
Period size: 7 Copynumber: 14.7 Consensus size: 7
61505 GTACTGTATA
61515 TATAAAG
1 TATAAAG
61522 TATAAAG
1 TATAAAG
61529 TATATAA-
1 TATA-AAG
*
61536 TATAAAC
1 TATAAAG
*
61543 TATTAAAC
1 TA-TAAAG
61551 TATATAA-
1 TATA-AAG
61558 TAT-AAG
1 TATAAAG
61564 TATTAAA-
1 TA-TAAAG
61571 TATAAAG
1 TATAAAG
61578 TATTAAAG
1 TA-TAAAG
*
61586 TATATAAA
1 TATA-AAG
61594 TAT-AAG
1 TATAAAG
* *
61600 TATTAAT
1 TATAAAG
61607 TATAAAG
1 TATAAAG
61614 TATAA
1 TATAA
61619 TTTATTAATT
Statistics
Matches: 81, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
5 2 0.02
6 13 0.16
7 41 0.51
8 25 0.31
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.37
Consensus pattern (7 bp):
TATAAAG
Found at i:61554 original size:22 final size:21
Alignment explanation
Indices: 61514--61597 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 21
61504 GGTACTGTAT
61514 ATATAAAGTA-TAAAGTATATA
1 ATATAAAGTATTAAA-TATATA
*
61535 ATATAAACTATTAAACTATATA
1 ATATAAAGTATTAAA-TATATA
61557 ATAT-AAGTATTAAATATA-A
1 ATATAAAGTATTAAATATATA
61576 AGTATTAAAGTATATAAATATA
1 A-TA-TAAAGTAT-TAAATATA
61598 AGTATTAATT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
19 2 0.04
20 6 0.11
21 19 0.35
22 20 0.36
23 8 0.15
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (21 bp):
ATATAAAGTATTAAATATATA
Found at i:61573 original size:35 final size:36
Alignment explanation
Indices: 61513--61612 Score: 132
Period size: 35 Copynumber: 2.8 Consensus size: 36
61503 TGGTACTGTA
61513 TATATAAAGTATAAAGTA-TATAATATAAACTATTAAAC
1 TATATAAA-TAT-AAGTATTA-AATATAAACTATTAAAC
* *
61551 TATAT-AATATAAGTATTAAATATAAAGTATTAAAG
1 TATATAAATATAAGTATTAAATATAAACTATTAAAC
*
61586 TATATAAATATAAGTATTAATTATAAA
1 TATATAAATATAAGTATTAAATATAAA
61613 GTATAATTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
35 25 0.44
36 25 0.44
37 2 0.04
38 5 0.09
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (36 bp):
TATATAAATATAAGTATTAAATATAAACTATTAAAC
Found at i:61596 original size:36 final size:36
Alignment explanation
Indices: 61513--61616 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
61503 TGGTACTGTA
*
61513 TATATAAAGTATAAAGTA-TATAATATAAACTATTAAAC
1 TATATAAA-TAT-AAGTATTA-AATATAAAGTATTAAAC
*
61551 TATAT-AATATAAGTATTAAATATAAAGTATTAAAG
1 TATATAAATATAAGTATTAAATATAAAGTATTAAAC
*
61586 TATATAAATATAAGTATTAATTATAAAGTAT
1 TATATAAATATAAGTATTAAATATAAAGTAT
61617 AATTTATTAA
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
35 25 0.41
36 29 0.48
37 2 0.03
38 5 0.08
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (36 bp):
TATATAAATATAAGTATTAAATATAAAGTATTAAAC
Found at i:61624 original size:21 final size:19
Alignment explanation
Indices: 61567--61628 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 19
61557 ATATAAGTAT
61567 TAAATATAAAGTATTAAAGTATA
1 TAAATAT-AAGTATT-AA-T-TA
61590 TAAATATAAGTATTAATTA
1 TAAATATAAGTATTAATTA
*
61609 TAAAGTATAATTTATTAATT
1 TAAA-TATAA-GTATTAATT
61629 TAATTATCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 6 0.17
20 6 0.17
21 10 0.28
22 7 0.19
23 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (19 bp):
TAAATATAAGTATTAATTA
Found at i:61869 original size:16 final size:16
Alignment explanation
Indices: 61820--61870 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
61810 TCATTTACAG
*
61820 GTCAGGTTGAAAACATA
1 GTCAAGTTGAAAACA-A
* * *
61837 -TCAAGTTCATAATAA
1 GTCAAGTTGAAAACAA
61852 GTCAAGTTGAAAACAA
1 GTCAAGTTGAAAACAA
61868 GTC
1 GTC
61871 GGGTAATATC
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (16 bp):
GTCAAGTTGAAAACAA
Found at i:62959 original size:3 final size:3
Alignment explanation
Indices: 62953--63049 Score: 176
Period size: 3 Copynumber: 32.3 Consensus size: 3
62943 TACCCATATC
62953 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
63001 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
63049 A
1 A
63050 AATATATTAA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:63093 original size:22 final size:21
Alignment explanation
Indices: 63048--63093 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
63038 TTATTATTAT
* * *
63048 TAAATATATTAAATACATATA
1 TAAATATATTAAAAAAATAAA
63069 TAAATATTATTAAAAAAATAAA
1 TAAATA-TATTAAAAAAATAAA
63091 TAA
1 TAA
63094 TAAAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATATTAAAAAAATAAA
Found at i:64455 original size:19 final size:19
Alignment explanation
Indices: 64419--64454 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
64409 TAATTTAGTT
64419 ATTTATTTTATATGTTTTC
1 ATTTATTTTATATGTTTTC
64438 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
64455 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTC
Found at i:65250 original size:19 final size:19
Alignment explanation
Indices: 65210--65254 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
65200 TTTTCAATTA
*
65210 TTTATTTATTTATAATATT
1 TTTATTTATTTACAATATT
*
65229 TTTATTTATTTGCAAGTA-T
1 TTTATTTATTTACAA-TATT
65248 TTTATTT
1 TTTATTT
65255 CATGTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTATTTATTTACAATATT
Found at i:72253 original size:19 final size:19
Alignment explanation
Indices: 72215--72253 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
72205 GTTATCTTGT
*
72215 AAAAGAAATTATGTTAAAA
1 AAAAGAAATTATCTTAAAA
*
72234 AAAAGAAATTTTCTTTAAAA
1 AAAAGAAATTATC-TTAAAA
72254 TTTTCAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (19 bp):
AAAAGAAATTATCTTAAAA
Found at i:75777 original size:1 final size:1
Alignment explanation
Indices: 75763--75857 Score: 109
Period size: 1 Copynumber: 95.0 Consensus size: 1
75753 ATGCTTGAAG
* * * * * *
75763 AAAAAGAAAGAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAGAAAAGAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
75828 AAAAAAAAGAAAAAAAAAGAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
75858 GAGAAAGGGG
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:75798 original size:22 final size:22
Alignment explanation
Indices: 75763--75859 Score: 149
Period size: 22 Copynumber: 4.3 Consensus size: 22
75753 ATGCTTGAAG
75763 AAAAAGAAAGAAAAAAAAAAAAA
1 AAAAAGAAA-AAAAAAAAAAAAA
75786 AAAAAGAAAAAAAAAAAAAAAA
1 AAAAAGAAAAAAAAAAAAAAAA
*
75808 AAAAAGAAAAGAAAAAAAAGAAA
1 AAAAAGAAAA-AAAAAAAAAAAA
* *
75831 AAAAAGAAAAAAAAAGAAGAAA
1 AAAAAGAAAAAAAAAAAAAAAA
75853 AAAAAGA
1 AAAAAGA
75860 GAAAGGGGGT
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
22 41 0.58
23 30 0.42
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAAAAAAA
Found at i:75813 original size:45 final size:48
Alignment explanation
Indices: 75763--75864 Score: 158
Period size: 45 Copynumber: 2.2 Consensus size: 48
75753 ATGCTTGAAG
75763 AAAAAGAAAGA-AAAAAAAAAAAAAAAAAGAAAAAAAAA-AA-AAAAA
1 AAAAAGAAAGAGAAAAAAAAAAAAAAAAAGAAAAAAAAAGAAGAAAAA
*
75808 AAAAAGAAA-AGAAAAAAAAGAAAAAAAAGAAAAAAAAAGAAGAAAAA
1 AAAAAGAAAGAGAAAAAAAAAAAAAAAAAGAAAAAAAAAGAAGAAAAA
*
75855 AAAGAGAAAG
1 AAAAAGAAAG
75865 GGGGTCAAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
44 1 0.02
45 35 0.69
46 2 0.04
47 13 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (48 bp):
AAAAAGAAAGAGAAAAAAAAAAAAAAAAAGAAAAAAAAAGAAGAAAAA
Found at i:78087 original size:111 final size:112
Alignment explanation
Indices: 77781--78303 Score: 970
Period size: 111 Copynumber: 4.7 Consensus size: 112
77771 AAGATTCAAA
77781 TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
77846 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAA-
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTA-CTGAAT
77893 TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
77958 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTA-TGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTGAAT
78004 TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
78069 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTA-TGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTGAAT
78115 TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAG-AGAACTCATCTGAAGAAGG
1 TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
78179 AAG-AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTGAAT
* *
78225 TCATCA-TTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
78288 AAGAAGAAGTTCATAA
66 AAGAAGAAGTTCATAA
78304 GAAGAATTTC
Statistics
Matches: 405, Mismatches: 2, Indels: 10
0.97 0.00 0.02
Matches are distributed among these distances:
108 14 0.03
109 80 0.20
110 49 0.12
111 156 0.39
112 106 0.26
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
TCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTGAAT
Found at i:78640 original size:3 final size:3
Alignment explanation
Indices: 78634--78706 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
78624 TACCCATATC
*
78634 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
78682 ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
78707 AATATTAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:80051 original size:21 final size:21
Alignment explanation
Indices: 80025--80077 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
80015 TAGATTTAGT
80025 TTTATTTTTTATAATTAGTTA
1 TTTATTTTTTATAATTAGTTA
* ** *
80046 TTTATTTTATATGTTTATTTA
1 TTTATTTTTTATAATTAGTTA
*
80067 TTTATGTTTTA
1 TTTATTTTTTA
80078 AATATATTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.70
Consensus pattern (21 bp):
TTTATTTTTTATAATTAGTTA
Done.