Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014826.1 Corchorus capsularis cultivar CVL-1 contig14847, 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: 137463
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:17227 original size:28 final size:28
Alignment explanation
Indices: 17190--17265 Score: 116
Period size: 28 Copynumber: 2.7 Consensus size: 28
17180 AAATGGACTC
17190 AAAATGACCAAAATGCCCCTTGAATGCA
1 AAAATGACCAAAATGCCCCTTGAATGCA
* * **
17218 AAAATCACCAAAATGCCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTTGAATGCA
17246 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
17266 GTATGACCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.42, C:0.28, G:0.13, T:0.17
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTTGAATGCA
Found at i:18508 original size:77 final size:77
Alignment explanation
Indices: 18427--18636 Score: 312
Period size: 77 Copynumber: 2.7 Consensus size: 77
18417 TTAAACTACC
* * * **
18427 GTCCTCGTATAAGTTAAAATGGAACGAACGTCTCCCAATAGATCGTACCATTGAAACAGCTGAAC
1 GTCCTCGTATAAGTTAAAATGGAACGAACGTCTCCCAAGAGACCGTACCATTAAAACAGCCAAAC
18492 GCCTAAACTGGA
66 GCCTAAACTGGA
*
18504 GTCCTCGTATAAGTTATAATGGAACGAACGTCTCCCAAGAGACCGTACCATTAAAACAGCCAAAC
1 GTCCTCGTATAAGTTAAAATGGAACGAACGTCTCCCAAGAGACCGTACCATTAAAACAGCCAAAC
*
18569 GCCTAAACTGGC
66 GCCTAAACTGGA
* * * **
18581 GTCCCCGTATAAGTTAAAATGGAACGAACATCACCCCGGAGACCGTACCATTAAAA
1 GTCCTCGTATAAGTTAAAATGGAACGAACGTCTCCCAAGAGACCGTACCATTAAAA
18637 TGACAGAACG
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 120 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (77 bp):
GTCCTCGTATAAGTTAAAATGGAACGAACGTCTCCCAAGAGACCGTACCATTAAAACAGCCAAAC
GCCTAAACTGGA
Found at i:24720 original size:2 final size:2
Alignment explanation
Indices: 24713--24770 Score: 75
Period size: 2 Copynumber: 28.5 Consensus size: 2
24703 CCATTTTTGG
24713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA GT- TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA T-A
24757 TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA T
24771 TGAAATGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.04
2 46 0.90
3 2 0.04
4 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:26035 original size:13 final size:13
Alignment explanation
Indices: 26017--26042 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26007 CCCATGTTAA
26017 ACTGAAAGGTAAT
1 ACTGAAAGGTAAT
26030 ACTGAAAGGTAAT
1 ACTGAAAGGTAAT
26043 GATTCAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (13 bp):
ACTGAAAGGTAAT
Found at i:26070 original size:5 final size:5
Alignment explanation
Indices: 26060--26084 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
26050 AACATACCTG
26060 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
26085 TGTTTGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:28086 original size:2 final size:2
Alignment explanation
Indices: 28079--28104 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28069 TCTAAATAAG
28079 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28105 CTACATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32351 original size:37 final size:37
Alignment explanation
Indices: 32306--32437 Score: 158
Period size: 37 Copynumber: 3.6 Consensus size: 37
32296 GTGGTTTGTA
* *
32306 AGGAGAGCTCTGCAGTAAAGAGGGCGCTACCACAGTG
1 AGGAGAGCTCTGCGGTAAAGAGGGTGCTACCACAGTG
* * ** *
32343 AGGCGAGCTCTGCGGTGAAGAGGGTGCTACCATTGTA
1 AGGAGAGCTCTGCGGTAAAGAGGGTGCTACCACAGTG
* * *
32380 AGGAGAGCTCTACGGTAAAGAAGGTGCCACCACAGTG
1 AGGAGAGCTCTGCGGTAAAGAGGGTGCTACCACAGTG
*
32417 AGGAGAGCTCTG-GGTGAAGAG
1 AGGAGAGCTCTGCGGTAAAGAG
32438 TGCTATCGCA
Statistics
Matches: 77, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
36 7 0.09
37 70 0.91
ACGTcount: A:0.28, C:0.19, G:0.37, T:0.16
Consensus pattern (37 bp):
AGGAGAGCTCTGCGGTAAAGAGGGTGCTACCACAGTG
Found at i:32398 original size:74 final size:73
Alignment explanation
Indices: 32301--32437 Score: 211
Period size: 74 Copynumber: 1.9 Consensus size: 73
32291 TGGCAGTGGT
* * * *
32301 TTGTAAGGAGAGCTCTGCAGTAAAGAGGGCGCTACCACAGTGAGGCGAGCTCTGCGGTGAAGAGG
1 TTGTAAGGAGAGCTCTACAGTAAAGAAGGCGCCACCACAGTGAGGAGAGCTCTG-GGTGAAGAGG
32366 GTGCTACCA
65 GTGCTACCA
* *
32375 TTGTAAGGAGAGCTCTACGGTAAAGAAGGTGCCACCACAGTGAGGAGAGCTCTGGGTGAAGAG
1 TTGTAAGGAGAGCTCTACAGTAAAGAAGGCGCCACCACAGTGAGGAGAGCTCTGGGTGAAGAG
32438 TGCTATCGCA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
73 9 0.16
74 48 0.84
ACGTcount: A:0.28, C:0.18, G:0.36, T:0.18
Consensus pattern (73 bp):
TTGTAAGGAGAGCTCTACAGTAAAGAAGGCGCCACCACAGTGAGGAGAGCTCTGGGTGAAGAGGG
TGCTACCA
Found at i:32697 original size:91 final size:91
Alignment explanation
Indices: 32565--32744 Score: 297
Period size: 91 Copynumber: 2.0 Consensus size: 91
32555 CGCAAAAGTG
* *
32565 GAAGACGAGAACAACTATGTTCACCTCTGTTTTTCAAATCCATGAACAGGGGAAGAGATGAAACT
1 GAAGACGAGAACAACTACGTTCACCTCTGTTTTTCAAATCCAAGAACAGGGGAAGAGATGAAACT
*
32630 CATAAATAAAGAGAATAGCTCCACCT
66 CATAAATAAAGAAAATAGCTCCACCT
* * * *
32656 GAAGACGAGAACATCTCCGTTCACCTTTGTTTTTCAAATCCAAGAATAGGGGAAGAGATGAAACT
1 GAAGACGAGAACAACTACGTTCACCTCTGTTTTTCAAATCCAAGAACAGGGGAAGAGATGAAACT
32721 CATAAATAAAGAAAATAGCTCCAC
66 CATAAATAAAGAAAATAGCTCCAC
32745 TTTTCTTCAT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Consensus pattern (91 bp):
GAAGACGAGAACAACTACGTTCACCTCTGTTTTTCAAATCCAAGAACAGGGGAAGAGATGAAACT
CATAAATAAAGAAAATAGCTCCACCT
Found at i:33877 original size:18 final size:19
Alignment explanation
Indices: 33851--33889 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
33841 GTGGGGAAGC
*
33851 CTTGTTGTCATGTGA-GGT
1 CTTGATGTCATGTGATGGT
*
33869 CTTGATGTCGTGTGATGGT
1 CTTGATGTCATGTGATGGT
33888 CT
1 CT
33890 AACGTACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.10, C:0.13, G:0.33, T:0.44
Consensus pattern (19 bp):
CTTGATGTCATGTGATGGT
Found at i:34923 original size:17 final size:17
Alignment explanation
Indices: 34901--34933 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
34891 CCACAGTGTA
34901 TCAAATAATAACCCATT
1 TCAAATAATAACCCATT
34918 TCAAATAATAACCCAT
1 TCAAATAATAACCCAT
34934 AATATAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (17 bp):
TCAAATAATAACCCATT
Found at i:38511 original size:35 final size:35
Alignment explanation
Indices: 38472--39045 Score: 396
Period size: 35 Copynumber: 16.6 Consensus size: 35
38462 TTAAGTCGAT
* * *
38472 CTTAATTACCCTGAATTAAGCTAACTACTGACTCA
1 CTTAATTACCCTGAATTAAGCTTACTACTTACTTA
* * *
38507 CTTAATTACCCTGAATTAAGTTACTTATTGACTGATTTA
1 CTTAATTACCCTGAATTAAG---CTTACT-ACTTACTTA
* * *
38546 CTTAATTACCCTGAATTAAG-TTAATTACTGACTGA
1 CTTAATTACCCTGAATTAAGCTT-ACTACTTACTTA
* *
38581 CTTAATTATCCTGAATTAA-ATTACTTA-TTACTTA
1 CTTAATTACCCTGAATTAAGCTTAC-TACTTACTTA
*
38615 CTTAATTACCCTGAATTAAGTCACTGACTTACTTACTTA
1 CTTAATTACCCTGAATTAAG---CTTAC-TACTTACTTA
* *
38654 CTTCATTACCCTCAATTAAG-TTACTGACTTACTTTA
1 CTTAATTACCCTGAATTAAGCTTACT-ACTTAC-TTA
* ** * * *
38690 CTTAATTAACCAAAATCAA-ATTACTAGCTGACTTA
1 CTTAATTACCCTGAATTAAGCTTACTA-CTTACTTA
* *
38725 CTTAATTACCCTGAATTAAG----CTGCTTACTGA
1 CTTAATTACCCTGAATTAAGCTTACTACTTACTTA
38756 CTTAATTACCCTGAATTAAG-TTACGTA-TTACTTA
1 CTTAATTACCCTGAATTAAGCTTAC-TACTTACTTA
* * * * *
38790 CTTAATTACCCCGAAATAAG-TTATTCACTGACCTA
1 CTTAATTACCCTGAATTAAGCTTACT-ACTTACTTA
*
38825 CTTAATTACCCTGAATTAAGC-TACTAACTAACTTA
1 CTTAATTACCCTGAATTAAGCTTACT-ACTTACTTA
38860 CTTAATTACCCTGAATTAAGC-TA-T--TTA-TTGA
1 CTTAATTACCCTGAATTAAGCTTACTACTTACTT-A
38891 CTTAATTACCCTGAATTAAG--T--TACTTA-TTGA
1 CTTAATTACCCTGAATTAAGCTTACTACTTACTT-A
*
38922 CTTAATTACCCTGAATTAAG-TTGC--C-TA-TTA
1 CTTAATTACCCTGAATTAAGCTTACTACTTACTTA
* * * *
38952 CTTAATTACCTTGAATTAGGTCACTGACTTACTAACTTA
1 CTTAATTACCCTGAATTAAG---CTTAC-TACTTACTTA
* * *
38991 CTTAATTACCCTGAATTAAG-TTATTCACTAACCTA
1 CTTAATTACCCTGAATTAAGCTTACT-ACTTACTTA
* *
39026 CTTAATTATCCTAAATTAAG
1 CTTAATTACCCTGAATTAAG
39046 TTATTTATTG
Statistics
Matches: 444, Mismatches: 55, Indels: 80
0.77 0.09 0.14
Matches are distributed among these distances:
29 1 0.00
30 22 0.05
31 80 0.18
32 4 0.01
33 1 0.00
34 58 0.13
35 164 0.37
36 29 0.07
37 1 0.00
38 11 0.02
39 73 0.16
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.38
Consensus pattern (35 bp):
CTTAATTACCCTGAATTAAGCTTACTACTTACTTA
Found at i:39029 original size:39 final size:39
Alignment explanation
Indices: 38945--39029 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
38935 AATTAAGTTG
* * * *
38945 CCTA-TTACTTAATTACCTTGAATTAGGTCACTGACTTA
1 CCTACTTACTTAATTACCCTGAATTAAGTCACTCACTAA
* *
38983 -CTAACTTACTTAATTACCCTGAATTAAGTTATTCACTAA
1 CCT-ACTTACTTAATTACCCTGAATTAAGTCACTCACTAA
39022 CCTACTTA
1 CCTACTTA
39030 ATTATCCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.05
38 1 0.03
39 33 0.87
40 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (39 bp):
CCTACTTACTTAATTACCCTGAATTAAGTCACTCACTAA
Found at i:39985 original size:16 final size:16
Alignment explanation
Indices: 39964--40001 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
39954 AAAACTCGAG
39964 AAAGAAGGAA-AAGAAA
1 AAAGAA-GAAGAAGAAA
39980 AAAGAAGAAGAAGAAA
1 AAAGAAGAAGAAGAAA
39996 AAAGAA
1 AAAGAA
40002 CGAATCAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGAAGAAGAAGAAA
Found at i:40345 original size:13 final size:14
Alignment explanation
Indices: 40327--40359 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40317 TCTTGTGATT
*
40327 TGTGTGCTAA-CAG
1 TGTGTGCAAATCAG
40340 TGTGTGCAAATCAG
1 TGTGTGCAAATCAG
40354 TGTGTG
1 TGTGTG
40360 AAACTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.21, C:0.12, G:0.33, T:0.33
Consensus pattern (14 bp):
TGTGTGCAAATCAG
Found at i:41456 original size:8 final size:8
Alignment explanation
Indices: 41443--41487 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
41433 AGAACAAAGA
*
41443 TTTATTTT
1 TTTATTAT
41451 TTTATTAT
1 TTTATTAT
*
41459 TTTATCAT
1 TTTATTAT
41467 TATTATTAT
1 T-TTATTAT
41476 TATTATTAT
1 T-TTATTAT
41485 TTT
1 TTT
41488 TAACTTTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 17 0.52
9 16 0.48
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTATTAT
Found at i:41458 original size:3 final size:3
Alignment explanation
Indices: 41452--41485 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
41442 ATTTATTTTT
*
41452 TTA TTA TT- TTA TCA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41486 TTTAACTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41752 original size:18 final size:18
Alignment explanation
Indices: 41726--41762 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
41716 ACAAGTCGAT
*
41726 ATAAGAATTACTAATTGA
1 ATAAAAATTACTAATTGA
41744 ATAAAAATTACTAATTGA
1 ATAAAAATTACTAATTGA
41762 A
1 A
41763 ATCATGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
ATAAAAATTACTAATTGA
Found at i:42330 original size:36 final size:36
Alignment explanation
Indices: 42215--42330 Score: 121
Period size: 36 Copynumber: 3.2 Consensus size: 36
42205 TAAAATAAGT
* *
42215 AACTGAAGAAAGACCACCATGGATCATTCT-GACACA
1 AACTGAAGAAAGACCACCCTGGATCATTCTGGAC-TA
* * * * *
42251 AATTGAAGAAAGACCACCCTGGGTCA-GCTGAATTA
1 AACTGAAGAAAGACCACCCTGGATCATTCTGGACTA
*
42286 AACTGAAGAACA-ACCACCCTCGATCATTCTGGACTA
1 AACTGAAGAA-AGACCACCCTGGATCATTCTGGACTA
42322 AACTGAAGA
1 AACTGAAGA
42331 GACTACAGGA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
35 24 0.38
36 40 0.62
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (36 bp):
AACTGAAGAAAGACCACCCTGGATCATTCTGGACTA
Found at i:42355 original size:21 final size:21
Alignment explanation
Indices: 42326--42376 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
42316 GGACTAAACT
42326 GAAGAGACTACAGGAATTGATG
1 GAAG-GACTACAGGAATTGATG
42348 GAAGGACTACAGGAATTGATG
1 GAAGGACTACAGGAATTGATG
42369 GAAGGACT
1 GAAGGACT
42377 CGAATGCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.39, C:0.10, G:0.33, T:0.18
Consensus pattern (21 bp):
GAAGGACTACAGGAATTGATG
Found at i:42989 original size:16 final size:16
Alignment explanation
Indices: 42964--42999 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42954 GAAATCTCAG
42964 GGCAACAATGCAACAA
1 GGCAACAATGCAACAA
* *
42980 GGCAATAATGCAGCAA
1 GGCAACAATGCAACAA
42996 GGCA
1 GGCA
43000 GAGCAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.08
Consensus pattern (16 bp):
GGCAACAATGCAACAA
Found at i:44787 original size:21 final size:21
Alignment explanation
Indices: 44748--44787 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
44738 TAATTAAGAG
*
44748 TTTTTAATATTTAAACAGAAA
1 TTTTTAATATTCAAACAGAAA
44769 TTTTTAA-ATTCAAATCAGA
1 TTTTTAATATTCAAA-CAGA
44788 CTTAGTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TTTTTAATATTCAAACAGAAA
Found at i:50490 original size:48 final size:48
Alignment explanation
Indices: 50419--50513 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
50409 AGTTGAATGA
*
50419 TAAGTTTAGTCTTAACCATAGGACCTAAGCTTAATTTCATGTAGATAT
1 TAAGTTTAATCTTAACCATAGGACCTAAGCTTAATTTCATGTAGATAT
50467 TAAGTTTAATCTTAACCATAGGACCTAAGCTTAATTTCATGTAGATA
1 TAAGTTTAATCTTAACCATAGGACCTAAGCTTAATTTCATGTAGATA
50514 GAGTATGGCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (48 bp):
TAAGTTTAATCTTAACCATAGGACCTAAGCTTAATTTCATGTAGATAT
Found at i:50501 original size:25 final size:25
Alignment explanation
Indices: 50419--50501 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 25
50409 AGTTGAATGA
* *
50419 TAAGTTTAGTCTTAACCATAGGACC
1 TAAGCTTAATCTTAACCATAGGACC
* ** **
50444 TAAGCTTAAT-TTCA-TGTA-GATAT
1 TAAGCTTAATCTTAACCATAGGA-CC
*
50467 TAAGTTTAATCTTAACCATAGGACC
1 TAAGCTTAATCTTAACCATAGGACC
50492 TAAGCTTAAT
1 TAAGCTTAAT
50502 TTCATGTAGA
Statistics
Matches: 40, Mismatches: 14, Indels: 8
0.65 0.23 0.13
Matches are distributed among these distances:
22 2 0.05
23 11 0.28
24 6 0.15
25 19 0.47
26 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (25 bp):
TAAGCTTAATCTTAACCATAGGACC
Found at i:51030 original size:22 final size:22
Alignment explanation
Indices: 51004--51045 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
50994 AATGAAGAAC
51004 AACTTCTGCCCAGAACTTGGAG
1 AACTTCTGCCCAGAACTTGGAG
*
51026 AACTTCTGCCTAGAACTTGG
1 AACTTCTGCCCAGAACTTGG
51046 TCTGTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (22 bp):
AACTTCTGCCCAGAACTTGGAG
Found at i:58571 original size:15 final size:15
Alignment explanation
Indices: 58551--58582 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
58541 GATGGCGGTG
58551 AATATTATTATGTTA
1 AATATTATTATGTTA
58566 AATATTATTATGTTA
1 AATATTATTATGTTA
58581 AA
1 AA
58583 AAAATGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
AATATTATTATGTTA
Found at i:63544 original size:18 final size:18
Alignment explanation
Indices: 63509--63542 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
63499 CTCCTCTTTC
63509 ATGAAAACACTTCTTTTT
1 ATGAAAACACTTCTTTTT
63527 ATGAAAA-ACTT-TTTTT
1 ATGAAAACACTTCTTTTT
63543 TTTGCTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (18 bp):
ATGAAAACACTTCTTTTT
Found at i:74311 original size:235 final size:235
Alignment explanation
Indices: 73900--74370 Score: 942
Period size: 235 Copynumber: 2.0 Consensus size: 235
73890 TTGATTTAAA
73900 TTAATTCATTTCTTATTTGGCATTAGGGTCGCCCAGGGGTATTTTGGTCATTTTCACGTCCAGGG
1 TTAATTCATTTCTTATTTGGCATTAGGGTCGCCCAGGGGTATTTTGGTCATTTTCACGTCCAGGG
73965 GGGCATTTTGGTCATTTTGTATTTAGGGGGCATCTTGGGTCATTTTAAGCTCACTCGCAATTAAG
66 GGGCATTTTGGTCATTTTGTATTTAGGGGGCATCTTGGGTCATTTTAAGCTCACTCGCAATTAAG
74030 ATTAACTAATTCATTTCAGATCGCGTTGAAAATAACAATCTTAATTTGTAATTCAGTAATTTGGT
131 ATTAACTAATTCATTTCAGATCGCGTTGAAAATAACAATCTTAATTTGTAATTCAGTAATTTGGT
74095 TTTGTTGCACTTTAGTAATTTAGTAAGTTATGCATATTGT
196 TTTGTTGCACTTTAGTAATTTAGTAAGTTATGCATATTGT
74135 TTAATTCATTTCTTATTTGGCATTAGGGTCGCCCAGGGGTATTTTGGTCATTTTCACGTCCAGGG
1 TTAATTCATTTCTTATTTGGCATTAGGGTCGCCCAGGGGTATTTTGGTCATTTTCACGTCCAGGG
74200 GGGCATTTTGGTCATTTTGTATTTAGGGGGCATCTTGGGTCATTTTAAGCTCACTCGCAATTAAG
66 GGGCATTTTGGTCATTTTGTATTTAGGGGGCATCTTGGGTCATTTTAAGCTCACTCGCAATTAAG
74265 ATTAACTAATTCATTTCAGATCGCGTTGAAAATAACAATCTTAATTTGTAATTCAGTAATTTGGT
131 ATTAACTAATTCATTTCAGATCGCGTTGAAAATAACAATCTTAATTTGTAATTCAGTAATTTGGT
74330 TTTGTTGCACTTTAGTAATTTAGTAAGTTATGCATATTGT
196 TTTGTTGCACTTTAGTAATTTAGTAAGTTATGCATATTGT
74370 T
1 T
74371 CATTTAGTAA
Statistics
Matches: 236, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
235 236 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (235 bp):
TTAATTCATTTCTTATTTGGCATTAGGGTCGCCCAGGGGTATTTTGGTCATTTTCACGTCCAGGG
GGGCATTTTGGTCATTTTGTATTTAGGGGGCATCTTGGGTCATTTTAAGCTCACTCGCAATTAAG
ATTAACTAATTCATTTCAGATCGCGTTGAAAATAACAATCTTAATTTGTAATTCAGTAATTTGGT
TTTGTTGCACTTTAGTAATTTAGTAAGTTATGCATATTGT
Found at i:74461 original size:67 final size:67
Alignment explanation
Indices: 74375--74508 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
74365 ATTGTTCATT
*
74375 TAGTAACTTAGTTTTGTTGCACTTTAATCATATAGCTTAATCACCTTTAGTAATAGGTTTAGTTT
1 TAGTAACTTAGTTTTGTTGCACTTTAATCATATAGCTTAATCACCTTTAGTAATAGATTTAGTTT
74440 TC
66 TC
*
74442 TAGTAATTTAGTTTTGTTGCACTTTAATCATATAGCTTAATCACCTTTAGTAATAGATTTAGTTT
1 TAGTAACTTAGTTTTGTTGCACTTTAATCATATAGCTTAATCACCTTTAGTAATAGATTTAGTTT
74507 TC
66 TC
74509 GATTGTGATT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (67 bp):
TAGTAACTTAGTTTTGTTGCACTTTAATCATATAGCTTAATCACCTTTAGTAATAGATTTAGTTT
TC
Found at i:77307 original size:50 final size:48
Alignment explanation
Indices: 77224--77366 Score: 137
Period size: 51 Copynumber: 2.9 Consensus size: 48
77214 TGTAAATAAG
* ** *
77224 AGATTGAAGCTTTAAGTAATTAGTAGGTAAAAATGTCATCTTT-AGGTAAA
1 AGATTGAATCTTTAAGT-ATTAGTAAAT-AAAATGTCACCTTTGA-GTAAA
* * *
77274 AGATTGAATCTTTAGAGTGATTAGTAAATAAAATTTTAACCTTTGATTAAA
1 AGATTGAATCTTTA-AGT-ATTAGTAAATAAAA-TGTCACCTTTGAGTAAA
* *
77325 AGATTGAATTTTTAAGT-TTAGTAAATAAAATGTCACATTTGA
1 AGATTGAATCTTTAAGTATTAGTAAATAAAATGTCACCTTTGA
77367 ATTAGAAGTT
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
47 9 0.12
48 13 0.17
50 20 0.26
51 35 0.45
52 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (48 bp):
AGATTGAATCTTTAAGTATTAGTAAATAAAATGTCACCTTTGAGTAAA
Found at i:77380 original size:48 final size:48
Alignment explanation
Indices: 77270--77386 Score: 121
Period size: 48 Copynumber: 2.4 Consensus size: 48
77260 CATCTTTAGG
* *
77270 TAAAAGATTGAA-TCTTTAGAGTGATTAGTAAATAAAATTTTAACCTTTGAT
1 TAAAAGATTGAACT-TTTA-AGT--TTAGTAAATAAAATTGTAACATTTGAT
* *
77321 TAAAAGATTGAATTTTTAAGTTTAGTAAATAAAA-TGTCACATTTGAAT
1 TAAAAGATTGAACTTTTAAGTTTAGTAAATAAAATTGTAACATTTG-AT
* *
77369 TAGAAGTTTGAACTTTTA
1 TAAAAGATTGAACTTTTA
77387 GGCCGTTAGT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
47 8 0.14
48 30 0.52
50 3 0.05
51 16 0.28
52 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (48 bp):
TAAAAGATTGAACTTTTAAGTTTAGTAAATAAAATTGTAACATTTGAT
Found at i:78700 original size:50 final size:49
Alignment explanation
Indices: 78637--78975 Score: 285
Period size: 51 Copynumber: 6.8 Consensus size: 49
78627 TGTAAATAAG
* **
78637 AGATTGAAGCTTTA-AGTAATTAGTAGGTGAAAATGTCATCTTTAGGTAAA
1 AGATTGAATCTTTAGAGTAATTAGTAAAT-AAAATGTCATCTTT-GGTAAA
* * * * *
78687 AGATTGAATCTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTGAATAAA
1 AGATTGAATCTTTAGAGTAATTAGTAAATAAAA-TGTCATCTTTG-GTAAA
* **
78738 AGATTGAAGCTTTA-AGTAATTAGTAGGTAAAAATGTCATCTTTAGGTAAA
1 AGATTGAATCTTTAGAGTAATTAGTAAAT-AAAATGTCATCTTT-GGTAAA
* * * * *
78788 AGATTGAATCTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTGAATAAA
1 AGATTGAATCTTTAGAGTAATTAGTAAATAAAA-TGTCATCTTTG-GTAAA
* * *
78839 AGATTGAATTTTTTTA-AGTAGTTCGTAAATAAAATGTCATCTTTGGGTAAA
1 AGATTGAA--TCTTTAGAGTAATTAGTAAATAAAATGTCATCTTT-GGTAAA
* * * * * *
78890 AGATTGATTCTTTAGAGTGATTAGTAAATAAAATTTTAACCTTTGATTAAA
1 AGATTGAATCTTTAGAGTAATTAGTAAATAAAA-TGTCATCTTTG-GTAAA
*
78941 AGATTGAATTTTTA-AGT--TTAGTAAATAAAATGTCA
1 AGATTGAATCTTTAGAGTAATTAGTAAATAAAATGTCA
78976 CATTTGAATT
Statistics
Matches: 230, Mismatches: 45, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
47 3 0.01
48 13 0.06
49 5 0.02
50 77 0.33
51 111 0.48
52 16 0.07
53 5 0.02
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (49 bp):
AGATTGAATCTTTAGAGTAATTAGTAAATAAAATGTCATCTTTGGTAAA
Found at i:78741 original size:51 final size:50
Alignment explanation
Indices: 78683--78971 Score: 300
Period size: 51 Copynumber: 5.7 Consensus size: 50
78673 CATCTTTAGG
78683 TAAAAGATTGAATCTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTGAA
1 TAAAAGATTGAATCTTTA-AGTGATTAGTAAATAAAATTTTAAGCTTTGAA
* * ** * * * * *
78734 TAAAAGATTGAAGCTTTAAGTAATTAGTAGGTAAAAATGTCATCTTT-AGG
1 TAAAAGATTGAATCTTTAAGTGATTAGTAAATAAAATTTTAAGCTTTGA-A
78784 TAAAAGATTGAATCTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTGAA
1 TAAAAGATTGAATCTTTA-AGTGATTAGTAAATAAAATTTTAAGCTTTGAA
* * * * * **
78835 TAAAAGATTGAATTTTTTTAAGT-AGTTCGTAAATAAAA-TGTCATCTTTGGG
1 TAAAAGATTGAA--TCTTTAAGTGA-TTAGTAAATAAAATTTTAAGCTTTGAA
* * *
78886 TAAAAGATTGATTCTTTAGAGTGATTAGTAAATAAAATTTTAACCTTTGAT
1 TAAAAGATTGAATCTTTA-AGTGATTAGTAAATAAAATTTTAAGCTTTGAA
*
78937 TAAAAGATTGAATTTTTAAGT--TTAGTAAATAAAAT
1 TAAAAGATTGAATCTTTAAGTGATTAGTAAATAAAAT
78972 GTCACATTTG
Statistics
Matches: 194, Mismatches: 35, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
48 14 0.07
49 6 0.03
50 57 0.29
51 96 0.49
52 16 0.08
53 5 0.03
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.38
Consensus pattern (50 bp):
TAAAAGATTGAATCTTTAAGTGATTAGTAAATAAAATTTTAAGCTTTGAA
Found at i:78806 original size:101 final size:100
Alignment explanation
Indices: 78631--78975 Score: 505
Period size: 101 Copynumber: 3.4 Consensus size: 100
78621 GTAACTTGTA
*
78631 AATAAGAGATTGAAGCTTTAAGTAATTAGTAGGTGAAAATGTCATCTTTAGGTAAAAGATTGAAT
1 AATAAAAGATTGAAGCTTTAAGTAATTAGTAGGT-AAAATGTCATCTTTAGGTAAAAGATTGAAT
78696 CTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTG
65 CTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTG
78732 AATAAAAGATTGAAGCTTTAAGTAATTAGTAGGTAAAAATGTCATCTTTAGGTAAAAGATTGAAT
1 AATAAAAGATTGAAGCTTTAAGTAATTAGTAGGT-AAAATGTCATCTTTAGGTAAAAGATTGAAT
78797 CTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTG
65 CTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTG
** * * ** * *
78833 AATAAAAGATTGAATTTTTTTAAGTAGTTCGTAAATAAAATGTCATCTTTGGGTAAAAGATTGAT
1 AATAAAAGATTGAA--GCTTTAAGTAATTAGTAGGTAAAATGTCATCTTTAGGTAAAAGATTGAA
*
78898 TCTTTAGAGTGATTAGTAAATAAAATTTTAACCTTTG
64 TCTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTG
* ** **
78935 ATTAAAAGATTGAATTTTTAAGT--TTAGTAAATAAAATGTCA
1 AATAAAAGATTGAAGCTTTAAGTAATTAGTAGGTAAAATGTCA
78976 CATTTGAATT
Statistics
Matches: 229, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
98 17 0.07
100 9 0.04
101 113 0.49
102 76 0.33
103 14 0.06
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (100 bp):
AATAAAAGATTGAAGCTTTAAGTAATTAGTAGGTAAAATGTCATCTTTAGGTAAAAGATTGAATC
TTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTG
Found at i:79778 original size:26 final size:26
Alignment explanation
Indices: 79694--79778 Score: 64
Period size: 26 Copynumber: 3.1 Consensus size: 26
79684 AGTAAATAAT
*
79694 TAAAAAGAGATTAATCAGAGTTAAAGG
1 TAAAAAAAGATTAATCAGAGTT-AAGG
* * * * *
79721 TAATAGTAATGAGTAAATCATTAATTAA-G
1 TAA-A-AAAAGA-TTAATCA-GAGTTAAGG
79750 TAAAAAAAGATTAATCAGAGTTAAGG
1 TAAAAAAAGATTAATCAGAGTTAAGG
79776 TAA
1 TAA
79779 TAGTGATCAG
Statistics
Matches: 42, Mismatches: 11, Indels: 11
0.66 0.17 0.17
Matches are distributed among these distances:
25 5 0.12
26 10 0.24
27 7 0.17
28 2 0.05
29 7 0.17
30 8 0.19
31 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.18, T:0.27
Consensus pattern (26 bp):
TAAAAAAAGATTAATCAGAGTTAAGG
Found at i:79801 original size:55 final size:55
Alignment explanation
Indices: 79649--79918 Score: 326
Period size: 55 Copynumber: 4.9 Consensus size: 55
79639 AGTAAATTGA
* * ** * * *
79649 TAATCAAGAGTCAAGATAATAGTAAGAAGAAAATCAGTAAATAATTAAAAAGAGAT
1 TAATC-AGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* * *
79705 TAATCAGAGTTAAAGGTAATAGTAATGAGTAAATCATTAATTAAGTAAAAAAAGAT
1 TAATCAGAGTT-AAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* * *
79761 TAATCAGAGTTAAGGTAATAGTGATCAGTAAATCAGTAATTAAGT-GAAAGAGGT
1 TAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* * * ** * *
79815 AAATCAGAGTCAAAGTAGCAGTAATCAGTAAATCAGTAAATAATTAAAAAGAGAT
1 TAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
*
79870 TAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAA
1 TAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
79919 GATAGTAATC
Statistics
Matches: 179, Mismatches: 33, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
54 43 0.24
55 84 0.47
56 52 0.29
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (55 bp):
TAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
Found at i:79870 original size:109 final size:110
Alignment explanation
Indices: 79649--79920 Score: 339
Period size: 109 Copynumber: 2.5 Consensus size: 110
79639 AGTAAATTGA
* * ** * * * *
79649 TAATCAAGAGTCAAGATAATAGTAAGAAGAAAATCAGTAAATAATTAAAAAGAGATTAATCAGAG
1 TAATC-AGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGATAAATCAGAG
* * * * *
79714 TTAAAGGTAATAGTAATGAGTAAATCATTAATTAAGTAAAAAAAGAT
64 TCAAAGGTAACAGTAATCAGTAAATCAGTAAATAAGTAAAAAAAGAT
* * *
79761 TAATCAGAGTTAAGGTAATAGTGATCAGTAAATCAGTAATTAAGTGAAAGAGGTAAATCAGAGTC
1 TAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATAAATCAGAGTC
* * *
79826 AAA-GTAGCAGTAATCAGTAAATCAGTAAATAATTAAAAAGAGAT
66 AAAGGTAACAGTAATCAGTAAATCAGTAAATAAGTAAAAAAAGAT
*
79870 TAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAGA
1 TAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGA
79921 TAGTAATCAG
Statistics
Matches: 138, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
109 82 0.59
110 19 0.14
111 32 0.23
112 5 0.04
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (110 bp):
TAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATAAATCAGAGTC
AAAGGTAACAGTAATCAGTAAATCAGTAAATAAGTAAAAAAAGAT
Found at i:79940 original size:18 final size:17
Alignment explanation
Indices: 79887--79941 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
79877 AGTTAAGGTA
79887 ATAGTAATCAGTAAAT-
1 ATAGTAATCAGTAAATG
* *
79903 -CAGTAATCAAGTAAAAG
1 ATAGTAATC-AGTAAATG
79920 ATAGTAATCAGTAAATTG
1 ATAGTAATCAGTAAA-TG
79938 ATAG
1 ATAG
79942 GCAAGGTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 7 0.23
16 6 0.19
17 6 0.19
18 12 0.39
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.27
Consensus pattern (17 bp):
ATAGTAATCAGTAAATG
Found at i:79997 original size:34 final size:33
Alignment explanation
Indices: 79913--79997 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 33
79903 CAGTAATCAA
* *
79913 GTAAAAGATAGTAATCAGTAAATTGATAGGCAAG
1 GTAAAAGAT-GTAATCAGTAAATTGAGAGCCAAG
*
79947 GTAAGAGAT-TAATCAGT-AATTAGAGAGCCAAG
1 GTAAAAGATGTAATCAGTAAATT-GAGAGCCAAG
*
79979 GTAAAAAATGGTAATCAGT
1 GTAAAAGAT-GTAATCAGT
79998 GAATCGATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 4 0.09
32 23 0.53
34 16 0.37
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.24
Consensus pattern (33 bp):
GTAAAAGATGTAATCAGTAAATTGAGAGCCAAG
Found at i:80030 original size:22 final size:24
Alignment explanation
Indices: 79995--80038 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
79985 AATGGTAATC
79995 AGTGAATCGATAATCAAGAGTTAA
1 AGTGAATCGATAATCAAGAGTTAA
*
80019 AGTG-ATC-ATAATTAAGAGTT
1 AGTGAATCGATAATCAAGAGTT
80039 GAGTGGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 3 0.16
24 4 0.21
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (24 bp):
AGTGAATCGATAATCAAGAGTTAA
Found at i:80278 original size:22 final size:21
Alignment explanation
Indices: 80196--80296 Score: 82
Period size: 21 Copynumber: 4.9 Consensus size: 21
80186 AATAGCATTC
*
80196 AATCAGTAAAAAGTAAAAAGT
1 AATCAGTAAAAAGTAAAAGGT
* **
80217 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAAAGTAAAA-GGT
* *
80237 AATTAGT-AAGAGTAAAAGGT
1 AATCAGTAAAAAGTAAAAGGT
* *
80257 TATCATTAAAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAA-AAGGT
*
80279 AATCAGTAAAGAGTAAAA
1 AATCAGTAAAAAGTAAAA
80297 TCAGTGAAGA
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
19 9 0.15
20 13 0.21
21 21 0.34
22 18 0.30
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (21 bp):
AATCAGTAAAAAGTAAAAGGT
Found at i:80298 original size:16 final size:16
Alignment explanation
Indices: 80279--80318 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
80269 GTAAGAAGGT
80279 AATCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
*
80295 AATCAGTGAAGAGTAA
1 AATCAGTAAAGAGTAA
80311 AAT-AGTAA
1 AATCAGTAA
80319 TCAGTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (16 bp):
AATCAGTAAAGAGTAA
Found at i:80335 original size:14 final size:15
Alignment explanation
Indices: 80306--80339 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
80296 ATCAGTGAAG
*
80306 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
80321 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
80335 AGTAA
1 AGTAA
80340 GAGTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:80543 original size:29 final size:29
Alignment explanation
Indices: 80482--80545 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
80472 GTGGTAATAA
**
80482 ATAAAAGAGAGCAAGAAAAGAGTAATTAG
1 ATAAAAGAGAGCAAGAAAAGAGTAAAAAG
*
80511 -TAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAGCAAGAAAAGAGTAAAAA-G
80539 ATAAAAG
1 ATAAAAG
80546 TAGCAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 6 0.21
29 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.14
Consensus pattern (29 bp):
ATAAAAGAGAGCAAGAAAAGAGTAAAAAG
Found at i:88209 original size:19 final size:18
Alignment explanation
Indices: 88176--88212 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
88166 TTGAAATAAT
88176 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
88194 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
88213 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:89079 original size:12 final size:12
Alignment explanation
Indices: 89057--89095 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
89047 CATGACCGGC
*
89057 CAACACATGGAG
1 CAACGCATGGAG
*
89069 CATCGCATGGAG
1 CAACGCATGGAG
*
89081 CAACGCATGGGG
1 CAACGCATGGAG
89093 CAA
1 CAA
89096 ACGGCCACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.26, G:0.31, T:0.10
Consensus pattern (12 bp):
CAACGCATGGAG
Found at i:91144 original size:15 final size:16
Alignment explanation
Indices: 91124--91156 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
91114 AATTATAAAG
*
91124 AAAATAATA-AAACTA
1 AAAATAAAACAAACTA
91139 AAAATAAAACAAACTA
1 AAAATAAAACAAACTA
91155 AA
1 AA
91157 TTAAATCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAATAAAACAAACTA
Found at i:91569 original size:153 final size:152
Alignment explanation
Indices: 91367--91672 Score: 558
Period size: 153 Copynumber: 2.0 Consensus size: 152
91357 AAGCTCTTGA
*
91367 TCCAGTGTGAATTATCACTTTTATTCTTTAAACAATTAACTCTTGATCCAGTGTGGTAATTGGCT
1 TCCAGTGTGAATTATCACTTTTATTCTTTAAACAATTAACTCTTGATCCAGTGTGATAATTGGCT
*
91432 AAGAAAAAAGCACTAAGAACAATTATAATTATTCACGCATGCATAGCAAGTATAACCAAACTTAT
66 AAGAAAAAAGCACTAAGAACAATTATAATTATTCACACATGCATAGCAAGTATAACCAAACTTAT
91497 TAAAATAAGGTTTATTAATCCCT
131 T-AAATAAGGTTTATTAATCCCT
* *
91520 TCCAGTGTGAATTGTCCCTTTTATTCTTTAAACAATTAACTCTTGATCCAGTGTGATAATTGGCT
1 TCCAGTGTGAATTATCACTTTTATTCTTTAAACAATTAACTCTTGATCCAGTGTGATAATTGGCT
*
91585 AAGAAAAAAGCATTAAGAACAATTATAATTATTCACACATGCATAGCAAGTATAACCAAACTTAT
66 AAGAAAAAAGCACTAAGAACAATTATAATTATTCACACATGCATAGCAAGTATAACCAAACTTAT
91650 TAAATAAGGTTTATTAATCCCT
131 TAAATAAGGTTTATTAATCCCT
91672 T
1 T
91673 GGAAGGAAGA
Statistics
Matches: 148, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
152 22 0.15
153 126 0.85
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (152 bp):
TCCAGTGTGAATTATCACTTTTATTCTTTAAACAATTAACTCTTGATCCAGTGTGATAATTGGCT
AAGAAAAAAGCACTAAGAACAATTATAATTATTCACACATGCATAGCAAGTATAACCAAACTTAT
TAAATAAGGTTTATTAATCCCT
Found at i:92231 original size:363 final size:361
Alignment explanation
Indices: 91568--92654 Score: 1996
Period size: 363 Copynumber: 3.0 Consensus size: 361
91558 ACTCTTGATC
* *
91568 CAGTGTGATAATTGGCTAAGAAAAAAGCATTAAGAACAATTATAATTATTCACACATGCATAGCA
1 CAGTGTGATAATTGGCTAAGAACAAAGCATTAAGAACAATTATAATTATTCACGCATGCATAGCA
* *
91633 AGTATAACCAAACTTATTAAATAAGGTTTATTAATCCCTTGGAAGGAAGATCTCTCGCTTCCAAT
66 AGTATAACCAAACTTATAAAATAAGGTTTATTAATCCCTTGGAAGGAAGATCCCTCGCTTCCAAT
91698 TGTTACCAAACAATCATGCCCGAAGATCCTTCAAAGCTTGATTTAACAATAGATCTATCAAATCA
131 TGTTACCAAACAATCATGCCCGAAGATCCTTCAAAGCTTGATTTAACAATAGATCTATCAAATCA
*
91763 TATCAATAGCTGCAGTTCTAAATCAACAATCATCAAGATCATAAAATAAAACAGAGATTAAAAAC
196 TATCAATAGCTGCAATTCTAAATCAACAATCATCAAGATCATAAAATAAAACAGAGATTAAAAAC
*
91828 TATCAATTAAGAACAAATACCAAATTATAAGCACACAAATCTCACCATAATTAATTGATTAAATT
261 TATCAATTAAGAACAAATATCAAATTATAAGCACACAAATCTCACCATAATTAATTGATTAAATT
91893 CACCAAAGGATAAGAACTATTAAGAATTTAGCTACT
326 CACCAAAGGATAAGAACTATTAAGAATTTAGCTACT
*
91929 CAGTGTGATAATTGGCTAAGAACAAAGCATTAAGAACAATTATAGTTATTCACGCATGCATAGCA
1 CAGTGTGATAATTGGCTAAGAACAAAGCATTAAGAACAATTATAATTATTCACGCATGCATAGCA
*
91994 AGTATAACCAAACTTATGAAAATAAGGTTTATTAATCTCTTGGAAGGAAGATCCCTCGCTTCCAA
66 AGTATAACCAAACTTAT-AAAATAAGGTTTATTAATCCCTTGGAAGGAAGATCCCTCGCTTCCAA
* *
92059 TTTATTACCAAACAATCATGCCCGAAGATCCTTCAAAGCTTGATTTAACAATATATCTATCAAAT
130 -TTGTTACCAAACAATCATGCCCGAAGATCCTTCAAAGCTTGATTTAACAATAGATCTATCAAAT
*
92124 CATATCAATAGCTGCAATTCTAAATCAACAATCATCAAGATCATAAAATAAAAAAGAGATTAAAA
194 CATATCAATAGCTGCAATTCTAAATCAACAATCATCAAGATCATAAAATAAAACAGAGATTAAAA
92189 ACTATCAATTAAGAACAAATATCAAATTATAAGCACACAAATCTCACCATAATTAATTGATTAAA
259 ACTATCAATTAAGAACAAATATCAAATTATAAGCACACAAATCTCACCATAATTAATTGATTAAA
92254 TTCACCAAAGGATAAGAACTATTAAGAATTTAGCTACT
324 TTCACCAAAGGATAAGAACTATTAAGAATTTAGCTACT
*
92292 CATTGTGATAATTGGCTAAGAACAAAGCATTAAGAACAATTATAATTATTCACGCATGCATAGCA
1 CAGTGTGATAATTGGCTAAGAACAAAGCATTAAGAACAATTATAATTATTCACGCATGCATAGCA
92357 AGTATAACCAAACTTATTAAAATAAGGTTTATTAATCCCTTGGAAGGAAGATCCCTCGCTTCCAA
66 AGTATAACCAAACTTA-TAAAATAAGGTTTATTAATCCCTTGGAAGGAAGATCCCTCGCTTCCAA
92422 TTGTTACCAAACAATCATGCCCGAAGATCCTTCAAAGCTTGATTTAACAATAGATCTATCAAATC
130 TTGTTACCAAACAATCATGCCCGAAGATCCTTCAAAGCTTGATTTAACAATAGATCTATCAAATC
*
92487 ATATCAATAGCTGCAATTCTAAATCAAC-ATCATCAAGATCATAAAATAAAACAGAGTTTAAAAA
195 ATATCAATAGCTGCAATTCTAAATCAACAATCATCAAGATCATAAAATAAAACAGAGATTAAAAA
**
92551 CTATCAATTAAGAACAAATATCAAATTATAATTACACAAATCTCACCATAATTAATTGATTAAAT
260 CTATCAATTAAGAACAAATATCAAATTATAAGCACACAAATCTCACCATAATTAATTGATTAAAT
*
92616 TCACCAAAGGATAGGAACTATTAAGAATTTAGCTACT
325 TCACCAAAGGATAAGAACTATTAAGAATTTAGCTACT
92653 CA
1 CA
92655 TGGATTTGGA
Statistics
Matches: 702, Mismatches: 21, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
361 214 0.30
362 135 0.19
363 352 0.50
364 1 0.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.28
Consensus pattern (361 bp):
CAGTGTGATAATTGGCTAAGAACAAAGCATTAAGAACAATTATAATTATTCACGCATGCATAGCA
AGTATAACCAAACTTATAAAATAAGGTTTATTAATCCCTTGGAAGGAAGATCCCTCGCTTCCAAT
TGTTACCAAACAATCATGCCCGAAGATCCTTCAAAGCTTGATTTAACAATAGATCTATCAAATCA
TATCAATAGCTGCAATTCTAAATCAACAATCATCAAGATCATAAAATAAAACAGAGATTAAAAAC
TATCAATTAAGAACAAATATCAAATTATAAGCACACAAATCTCACCATAATTAATTGATTAAATT
CACCAAAGGATAAGAACTATTAAGAATTTAGCTACT
Found at i:94465 original size:35 final size:35
Alignment explanation
Indices: 94426--94544 Score: 184
Period size: 35 Copynumber: 3.4 Consensus size: 35
94416 AGCCATTAAA
*
94426 TGATTTACTTAATTACACCGAATTAAGCTAATTAC
1 TGATTTACTTAATTACACCGAATTAAGTTAATTAC
* * *
94461 TGATTTACTTAACTACACCGAATTAAGTTGACTAC
1 TGATTTACTTAATTACACCGAATTAAGTTAATTAC
94496 TGATTTACTTAATTACACCGAATTAAGTTAATTAC
1 TGATTTACTTAATTACACCGAATTAAGTTAATTAC
**
94531 CAATTTACTTAATT
1 TGATTTACTTAATT
94545 TACCAGTTTA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 75 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (35 bp):
TGATTTACTTAATTACACCGAATTAAGTTAATTAC
Found at i:94549 original size:17 final size:17
Alignment explanation
Indices: 94498--94634 Score: 84
Period size: 17 Copynumber: 7.7 Consensus size: 17
94488 TTGACTACTG
*
94498 ATTTACTTAATTACACCGA
1 ATTTACTTAATT-TACC-A
* *
94517 ATTAAGTTAA-TTACCA
1 ATTTACTTAATTTACCA
94533 ATTTACTTAATTTACCA
1 ATTTACTTAATTTACCA
* *
94550 GTTTACTTAATTGCACCGA
1 ATTTACTTAATT-TACC-A
* *
94569 ATTAAGTTAA-TTACCAA
1 ATTTACTTAATTTACC-A
94586 ACTACTTAACTTAA-TTACCA
1 A-T--TT-ACTTAATTTACCA
94606 GA-TTACTTAATTTACCA
1 -ATTTACTTAATTTACCA
*
94623 GTTTACTTAATT
1 ATTTACTTAATT
94635 GCATCGAATT
Statistics
Matches: 93, Mismatches: 15, Indels: 22
0.72 0.12 0.17
Matches are distributed among these distances:
16 15 0.16
17 43 0.46
18 6 0.06
19 16 0.17
20 2 0.02
21 11 0.12
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (17 bp):
ATTTACTTAATTTACCA
Found at i:94559 original size:52 final size:55
Alignment explanation
Indices: 94499--94617 Score: 174
Period size: 52 Copynumber: 2.2 Consensus size: 55
94489 TGACTACTGA
94499 TTTACTTAATTACACCGAATTAAGTTAATTACC-AA-T-TT-ACTTAATTTACCAG
1 TTTACTTAATTACACCGAATTAAGTTAATTACCAAACTATTAACTTAA-TTACCAG
*
94551 TTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTACTTAACTTAATTACCAG
1 TTTACTTAATTACACCGAATTAAGTTAATTACCAAACTA-TTAACTTAATTACCAG
*
94607 ATTACTTAATT
1 TTTACTTAATT
94618 TACCAGTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
52 32 0.53
53 2 0.03
54 1 0.02
56 19 0.32
57 6 0.10
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (55 bp):
TTTACTTAATTACACCGAATTAAGTTAATTACCAAACTATTAACTTAATTACCAG
Found at i:94599 original size:21 final size:21
Alignment explanation
Indices: 94570--94615 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
94560 TTGCACCGAA
*
94570 TTAAGTTAATTACCAAACTAC
1 TTAACTTAATTACCAAACTAC
* *
94591 TTAACTTAATTACCAGATTAC
1 TTAACTTAATTACCAAACTAC
94612 TTAA
1 TTAA
94616 TTTACCAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.37
Consensus pattern (21 bp):
TTAACTTAATTACCAAACTAC
Found at i:94612 original size:73 final size:73
Alignment explanation
Indices: 94518--94691 Score: 278
Period size: 73 Copynumber: 2.4 Consensus size: 73
94508 TTACACCGAA
*
94518 TTAAGTTAATTACCAATTTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTAC
1 TTAACTTAATTACCAATTTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTAC
94583 CAAACTAC
66 CAAACTAC
* *
94591 TTAACTTAATTACCAGA-TTACTTAATTTACCAGTTTACTTAATTGCATCGAATTAAGTTGATTA
1 TTAACTTAATTACCA-ATTTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTA
* *
94655 TCAAATTAC
65 CCAAACTAC
*
94664 TTAATTTAATTACCAATTTACTTAATTT
1 TTAACTTAATTACCAATTTACTTAATTT
94692 CACCGAATTA
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
72 1 0.01
73 91 0.98
74 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (73 bp):
TTAACTTAATTACCAATTTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTAC
CAAACTAC
Found at i:94667 original size:21 final size:21
Alignment explanation
Indices: 94643--94688 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
94633 TTGCATCGAA
* *
94643 TTAAGTTGATTATCAAATTAC
1 TTAAGTTAATTACCAAATTAC
* *
94664 TTAATTTAATTACCAATTTAC
1 TTAAGTTAATTACCAAATTAC
94685 TTAA
1 TTAA
94689 TTTCACCGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAAGTTAATTACCAAATTAC
Found at i:94686 original size:56 final size:56
Alignment explanation
Indices: 94612--95053 Score: 374
Period size: 56 Copynumber: 8.0 Consensus size: 56
94602 ACCAGATTAC
* * * *
94612 TTAATTTACCAGTTTACTTAATTGCATCGAATTAAGTTGATTATCAAATTACTTAAT
1 TTAA-TTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
*
94669 TTAATTACCAATTTACTTAATTTCACCGAATTAAGTTGATTACCAAATTAC-TAA-
1 TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
* * * * * * * ** *
94723 TT-A-CACCGAATTAAGTTGATT--ACCAAATT-ACTTAATTACACCGA--A-TTAAG
1 TTAATTACC-AATTTACTTAATTACACCGAATTAAGTTGATTAC-CAAATTACTTAAT
* * * * * * * *
94773 TTGATTACCAAATTACTTAATTTAATTACC-AGTTTACTTAATTGCACCGAATTA---AA-
1 TTAATTACCAATTTACTTAA-TT-A-CACCGAATTAAGTTGATT--ACCAAATTACTTAAT
* *
94829 TTGATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
1 TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
* * * * * *
94885 TTAATTACCAAATTACTTAATTACACCGGATTAAGCTGATTATCGAATTGCTTAAT
1 TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
* * *
94941 TTAATTTCCAATTTACTTAATCACACCGAATTAAGTTGATTACCCAATTACTTAAT
1 TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
** *
94997 CCAATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAAT
1 TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
95053 T
1 T
95054 ACACCGAATT
Statistics
Matches: 316, Mismatches: 48, Indels: 43
0.78 0.12 0.11
Matches are distributed among these distances:
49 4 0.01
50 10 0.03
51 17 0.05
52 16 0.05
53 14 0.04
54 12 0.04
55 10 0.03
56 222 0.70
57 8 0.03
58 2 0.01
59 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (56 bp):
TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
Found at i:94689 original size:21 final size:21
Alignment explanation
Indices: 94651--94691 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
94641 AATTAAGTTG
*
94651 ATTATCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
94672 ATTACCAATTTACTTAATTT
1 ATTACCAAATTACTTAATTT
94692 CACCGAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:94730 original size:34 final size:35
Alignment explanation
Indices: 94672--94794 Score: 221
Period size: 35 Copynumber: 3.5 Consensus size: 35
94662 ACTTAATTTA
* *
94672 ATTACCAATTTACTTAATTTCACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
94707 ATTACCAAATTAC-TAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
94741 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
94776 ATTACCAAATTACTTAATT
1 ATTACCAAATTACTTAATT
94795 TAATTACCAG
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
34 33 0.39
35 52 0.61
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (35 bp):
ATTACCAAATTACTTAATTACACCGAATTAAGTTG
Found at i:94747 original size:125 final size:126
Alignment explanation
Indices: 94428--94885 Score: 579
Period size: 125 Copynumber: 3.7 Consensus size: 126
94418 CCATTAAATG
* * ** * * *
94428 ATTTACTTAATTACACCGAATTAAGCTAATTACTGATTTACTTAACTACACCGAATTAAGTTGAC
1 ATTTACTTAATTGCACCGAATTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
** * * *
94493 TACTGATTTACTTAATTACACCGAATTAAGTTAATTACCAATTTACTTAA--T--TTACCA
66 TACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
* * * *
94550 GTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTACTTAACTTAATTACC-AGATT-ACT
1 ATTTACTTAATTGCACCGAATTAAGTTAATTACCAAATTACTTAA-TT-A-CACCGA-ATTAAGT
* ** * * *
94613 TAATTTACCAGTTTACTTAATTGCATCGAATTAAGTTGATTATCAAATTACTTAATTTAATTACC
62 TGA-TTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACC
94678 A
126 A
* *
94679 ATTTACTTAATTTCACCGAATTAAGTTGATTACCAAATTAC-TAATTACACCGAATTAAGTTGAT
1 ATTTACTTAATTGCACCGAATTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
94743 TACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
66 TACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
* * *
94804 GTTTACTTAATTGCACCGAATTAAATTGATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
1 ATTTACTTAATTGCACCGAATTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
94869 TACCAAATTACTTAATT
66 TACCAAATTACTTAATT
94886 TAATTACCAA
Statistics
Matches: 289, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
122 38 0.13
123 1 0.00
124 6 0.02
125 149 0.52
126 46 0.16
127 3 0.01
128 3 0.01
129 43 0.15
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (126 bp):
ATTTACTTAATTGCACCGAATTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
TACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
Found at i:94800 original size:21 final size:21
Alignment explanation
Indices: 94776--94815 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
94766 AATTAAGTTG
94776 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
**
94797 ATTACCAGTTTACTTAATT
1 ATTACCAAATTACTTAATT
94816 GCACCGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:94836 original size:35 final size:35
Alignment explanation
Indices: 94797--94885 Score: 142
Period size: 35 Copynumber: 2.5 Consensus size: 35
94787 ACTTAATTTA
** *
94797 ATTACCAGTTTACTTAATTGCACCGAATTAAATTG
1 ATTACCAAATTACTTAATTACACCGAATTAAATTG
*
94832 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTACACCGAATTAAATTG
94867 ATTACCAAATTACTTAATT
1 ATTACCAAATTACTTAATT
94886 TAATTACCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (35 bp):
ATTACCAAATTACTTAATTACACCGAATTAAATTG
Found at i:94838 original size:91 final size:91
Alignment explanation
Indices: 94707--94941 Score: 382
Period size: 91 Copynumber: 2.6 Consensus size: 91
94697 AATTAAGTTG
94707 ATTACCAAATTAC-TAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTA
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTA
94771 AGTTGATTACCAAATTACTTAATTTA
66 AGTTGATTACCAAATTACTTAATTTA
** * *
94797 ATTACCAGTTTACTTAATTGCACCGAATTAAATTGATTACCAAATTACTTAATTACACCGAATTA
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTA
94862 AGTTGATTACCAAATTACTTAATTTA
66 AGTTGATTACCAAATTACTTAATTTA
* * * * *
94888 ATTACCAAATTACTTAATTACACCGGATTAAGCTGATTATCGAATTGCTTAATT
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATT
94942 TAATTTCCAA
Statistics
Matches: 131, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 11 0.08
91 120 0.92
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (91 bp):
ATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTA
AGTTGATTACCAAATTACTTAATTTA
Found at i:94891 original size:21 final size:21
Alignment explanation
Indices: 94867--94906 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
94857 AATTAAGTTG
94867 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
94888 ATTACCAAATTACTTAATT
1 ATTACCAAATTACTTAATT
94907 ACACCGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:94984 original size:91 final size:90
Alignment explanation
Indices: 94591--94941 Score: 342
Period size: 91 Copynumber: 3.9 Consensus size: 90
94581 ACCAAACTAC
* ** * *
94591 TTAACTTAATTACCAGATTACTTAA--T--TTACCAGTTTACTTAATTGCATCGAATTAAGTTGA
1 TTAACTTAATTACCA-AATACTTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTGA
* *
94652 TTATCAAATTACTTAATTTAATTACC-AA
65 TTACCAAATTACTTAA-TT-A-CACCGAA
* * *
94680 TTTACTTAATTTCACC-GA-A-TTAAGTTGATTACCAAATTAC-TAATTACACCGAATTAAGTTG
1 TTAACTTAA-TT-ACCAAATACTTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTG
94741 ATTACCAAATTACTTAATTACACCGAA
64 ATTACCAAATTACTTAATTACACCGAA
* * * ** * *
94768 TTAAGTTGATTACCAAATTACTTAATTTAATTACCAGTTTACTTAATTGCACCGAATTAAATTGA
1 TTAACTTAATTACCAAA-TACTTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTGA
94833 TTACCAAATTACTTAATTACACCGAA
65 TTACCAAATTACTTAATTACACCGAA
* * * * *
94859 TTAAGTTGATTACCAAATTACTTAATTTAATTACCAAATTACTTAATTACACCGGATTAAGCTGA
1 TTAACTTAATTACCAAA-TACTTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTGA
* * *
94924 TTATCGAATTGCTTAATT
65 TTACCAAATTACTTAATT
94942 TAATTTCCAA
Statistics
Matches: 222, Mismatches: 28, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
86 3 0.01
87 10 0.05
88 10 0.05
89 12 0.05
90 54 0.24
91 133 0.60
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (90 bp):
TTAACTTAATTACCAAATACTTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
TACCAAATTACTTAATTACACCGAA
Found at i:95040 original size:35 final size:35
Alignment explanation
Indices: 95000--95084 Score: 134
Period size: 35 Copynumber: 2.4 Consensus size: 35
94990 ACTTAATCCA
*
95000 ATTACCAATTTACTTAATTACACCGAATTAAGTTG
1 ATTACCAATTTACTTAATTACACCGAATTAAGTAG
* *
95035 TTTACCAAATTACTTAATTACACCGAATTAAGTAG
1 ATTACCAATTTACTTAATTACACCGAATTAAGTAG
*
95070 ATTACAAATTTACTT
1 ATTACCAATTTACTT
95085 TTTCTTACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (35 bp):
ATTACCAATTTACTTAATTACACCGAATTAAGTAG
Found at i:95075 original size:19 final size:19
Alignment explanation
Indices: 95016--95075 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
95006 AATTTACTTA
*
95016 ATTACACCGAATTAAGTTG
1 ATTACACCGAATTAAGTAG
* * **
95035 -TT-TACCAAATTACTTA-
1 ATTACACCGAATTAAGTAG
95051 ATTACACCGAATTAAGTAG
1 ATTACACCGAATTAAGTAG
95070 ATTACA
1 ATTACA
95076 AATTTACTTT
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
17 11 0.38
18 12 0.41
19 6 0.21
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (19 bp):
ATTACACCGAATTAAGTAG
Found at i:98834 original size:23 final size:23
Alignment explanation
Indices: 98808--98859 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
98798 CTAAATGGAG
98808 ATGCAACAATACCAAATTACTAA
1 ATGCAACAATACCAAATTACTAA
** *
98831 ATGCAGTAATACCAAGTTACTAA
1 ATGCAACAATACCAAATTACTAA
98854 ATGCAA
1 ATGCAA
98860 ATATGCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (23 bp):
ATGCAACAATACCAAATTACTAA
Found at i:99010 original size:28 final size:28
Alignment explanation
Indices: 98968--99059 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 28
98958 ACGTAAAGAT
* * * *
98968 TGACCAGAATGCCCCCTGAGTGTCAAAA
1 TGACCAAAATACCCCCTGAATGCCAAAA
*
98996 TGACCAAAATA-CCCCTGAATGCCAGAA
1 TGACCAAAATACCCCCTGAATGCCAAAA
* * *
99023 TGACCAAAATA-CTCCTAAATGCAAAAA
1 TGACCAAAATACCCCCTGAATGCCAAAA
*
99050 AGACCAAAAT
1 TGACCAAAAT
99060 GCTAATTCGA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 45 0.83
28 9 0.17
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.16
Consensus pattern (28 bp):
TGACCAAAATACCCCCTGAATGCCAAAA
Found at i:99024 original size:27 final size:27
Alignment explanation
Indices: 98980--99059 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 27
98970 ACCAGAATGC
* *
98980 CCCCTGAGTGTCAAAATGACCAAAATA
1 CCCCTGAATGCCAAAATGACCAAAATA
*
99007 CCCCTGAATGCCAGAATGACCAAAATA
1 CCCCTGAATGCCAAAATGACCAAAATA
* * * *
99034 CTCCTAAATGCAAAAAAGACCAAAAT
1 CCCCTGAATGCCAAAATGACCAAAAT
99060 GCTAATTCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.16
Consensus pattern (27 bp):
CCCCTGAATGCCAAAATGACCAAAATA
Found at i:117950 original size:41 final size:41
Alignment explanation
Indices: 117905--118128 Score: 333
Period size: 41 Copynumber: 5.4 Consensus size: 41
117895 CATATGCATT
117905 AAGTAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAA
1 AAGTAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAA
117946 AAGTAAACACAGTCAAAAGTCTTAATTCAGGGTAATTAAGAA
1 AAGTAAACACAGTC-AAAGTCTTAATTCAGGGTAATTAAGAA
* ** *
117988 AA-TCAAACACAGTCAAAGTCTTAATCCAGGGTGGTTGAGAA
1 AAGT-AAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAA
*
118029 AAGTAAACACAGTCAAAGTCTTAATTCAGGGTGATTAAGAA
1 AAGTAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAA
*
118070 AGGTAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAA
1 AAGTAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAA
** * *
118111 GGGTAAATACGGTCAAAG
1 AAGTAAACACAGTCAAAG
118129 AACTTAAAAA
Statistics
Matches: 168, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
41 128 0.76
42 40 0.24
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (41 bp):
AAGTAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAA
Found at i:118231 original size:40 final size:37
Alignment explanation
Indices: 118136--118258 Score: 165
Period size: 37 Copynumber: 3.1 Consensus size: 37
118126 AAGAACTTAA
118136 AAAGAACTTAATTAAGGGTAATTAAGTAAAATCAGTC
1 AAAGAACTTAATTAAGGGTAATTAAGTAAAATCAGTC
118173 AAAGAACTTAATTAAGGGTAATTAAGTAAAATCAGTC
1 AAAGAACTTAATTAAGGGTAATTAAGTAAAATCAGTC
*
118210 AATAAAGAACTTAATTCAGGGTAATTCAGAAAGTAAAATCAGTC
1 ---AAAGAACTTAATTAAGGGTAATT----AAGTAAAATCAGTC
*
118254 CAAGA
1 AAAGA
118259 CCCTGGTAGT
Statistics
Matches: 77, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
37 37 0.48
40 22 0.29
41 4 0.05
44 14 0.18
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (37 bp):
AAAGAACTTAATTAAGGGTAATTAAGTAAAATCAGTC
Found at i:127867 original size:1 final size:1
Alignment explanation
Indices: 127861--127894 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
127851 TTCCATAAGC
127861 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
127895 TCTTCAAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:131554 original size:12 final size:13
Alignment explanation
Indices: 131513--131557 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
131503 AATTATTGTT
131513 TGCTTTATTAATC
1 TGCTTTATTAATC
*
131526 TGCTTTATTAATT
1 TGCTTTATTAATC
131539 TGCTTTA-TAATC
1 TGCTTTATTAATC
131551 TGCTTTA
1 TGCTTTA
131558 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:131926 original size:37 final size:38
Alignment explanation
Indices: 131856--131934 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 38
131846 TAGTTTTTGA
*
131856 TTTTCCGTTTTTTCTAAAAAAAAAAAAGTTTTTTCCGAT
1 TTTTCCGGTTTTTCTAAAAAAAAAAAAG-TTTTTCCGAT
*
131895 TTTTCCGGTTTTTCTAAAAAAAAAATA-TTTTTCCGAT
1 TTTTCCGGTTTTTCTAAAAAAAAAAAAGTTTTTCCGAT
131932 TTT
1 TTT
131935 AAAATTAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 13 0.34
39 25 0.66
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.48
Consensus pattern (38 bp):
TTTTCCGGTTTTTCTAAAAAAAAAAAAGTTTTTCCGAT
Found at i:132034 original size:36 final size:36
Alignment explanation
Indices: 131958--132034 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
131948 CCAATTTTTA
* *
131958 TTTAAAAAAAATTAATTTTTCTTTTTCCGTTTTTCC
1 TTTAAAAAAAATTAATTTTTATTTTTCCGTTTTGCC
* *
131994 TTTAAAAAAAA-T-ATATTTTATTTTTCTGTTTCTGCT
1 TTTAAAAAAAATTAAT-TTTTATTTTTCCGTTT-TGCC
132030 TTTAA
1 TTTAA
132035 TTTTTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 2 0.06
35 15 0.43
36 18 0.51
ACGTcount: A:0.30, C:0.10, G:0.04, T:0.56
Consensus pattern (36 bp):
TTTAAAAAAAATTAATTTTTATTTTTCCGTTTTGCC
Done.