Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022041.1 Corchorus olitorius cultivar O-4 contig22074, 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: 30574
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3270 original size:54 final size:53
Alignment explanation
Indices: 3185--3333 Score: 130
Period size: 54 Copynumber: 2.8 Consensus size: 53
3175 AATTCAGAGT
* *
3185 AATTAAACTAAAAGGAGTAGAAG-A-AAG-AAACAGTAA-TTAGTTTAATTC-AGA
1 AATTAAACT-AAA-GAGTAAAAGAAGAAGTAAACAG-AAGCTAGTTTAATTCTAGA
* * * *
3236 ACAGTTACATTAAAGAGTAAAAGAAGAAGTAAACA-AAGGCTAGTTTAATTCTTGGT
1 A-A-TTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAA-GCTAGTTTAATTC-TAGA
*
3292 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAAGCTAGT
3334 AATTAAACTA
Statistics
Matches: 79, Mismatches: 9, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
51 9 0.11
52 7 0.09
53 8 0.10
54 51 0.65
55 2 0.03
56 2 0.03
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.23
Consensus pattern (53 bp):
AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAAGCTAGTTTAATTCTAGA
Found at i:3336 original size:42 final size:44
Alignment explanation
Indices: 3290--3415 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 44
3280 TTAATTCTTG
*
3290 GTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG-AGGCT-A
1 GTAATTAAACTAAAGAGTAAAAGAAGAAGAAAACAGTAGGCTGA
* * ** *
3332 GTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAGAGCTTAATTCTGG
1 GTAATTAAACTAAAGAGTAAAAGAAGAAGAAAACAG--T-AGGCTGA
*
3379 GTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGT
1 GTAATTAAACTAAAGAGTAAAAGAAGAAGAAAACAGT
3416 TTAATTCTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
42 33 0.47
45 1 0.01
46 3 0.04
47 33 0.47
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (44 bp):
GTAATTAAACTAAAGAGTAAAAGAAGAAGAAAACAGTAGGCTGA
Found at i:3386 original size:47 final size:47
Alignment explanation
Indices: 3277--3874 Score: 580
Period size: 47 Copynumber: 12.4 Consensus size: 47
3267 AACAAAGGCT
* * *
3277 AGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAG
** * *
3324 AG----AGGCT-AGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAG
* * *
3366 AGCTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAG
* * * *
3413 AGTTTAATTCTTGCTAATTAAATTAAAGAAGTAAACGAAGAAGGAAATAGAGG
1 AGTTTAATTCTGGGTAATTAAACTAAAG-AGTAAAAGAAGAA-G-AA-A-A-G
* *
3466 TTAGTTTAATTCTGGGTAATTAAACTAAAAAGGAAAAGGAA-AA-AAAAG
1 --AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAA-GAAGAAGAAAAG
* * *
3514 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAGGAAGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAG
* *
3561 AATTTAATTCTGGGTAATTAAACCAAAGAGTAAAAGAAGAAGTAAACAGAGG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAG--AA-A-A-G
* * * *
3613 CTAGTTTAATTCTAGGTAATTAAACTAAAAAGCAAGAGAAGAAGAAAAG
1 --AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAG
* * * * * *
3662 AGTTTAATTCGGGGTAATTAAACTGAAGAGCAAGAGAAGAAAAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAG
*
3709 AGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAG--AA-A-A-G
* *
3761 CTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAT
1 --AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAG
* * * * *
3810 AGCTTAATTCCGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAG
*
3857 AGTTTGATTCTGGGTAAT
1 AGTTTAATTCTGGGTAAT
3875 CAAGCTAAGA
Statistics
Matches: 456, Mismatches: 65, Indels: 60
0.78 0.11 0.10
Matches are distributed among these distances:
42 33 0.07
43 3 0.01
45 3 0.01
46 37 0.08
47 232 0.51
48 12 0.03
49 7 0.02
50 7 0.02
51 7 0.02
52 5 0.01
54 83 0.18
55 27 0.06
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.23
Consensus pattern (47 bp):
AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAG
Found at i:3541 original size:101 final size:96
Alignment explanation
Indices: 3246--3874 Score: 535
Period size: 101 Copynumber: 6.5 Consensus size: 96
3236 ACAGTTACAT
*
3246 TAAAG-AGTAAAAGAAGAAGTAAACAAAGGCTAGTTTAATTCTTGGTAATTAAACTAAAGAGTAA
1 TAAAGAAGTAAAAGAAGAAG--AA-AAA-G--AGTTTAATTCTGGGTAATTAAACTAAAGAGTAA
* ** *
3310 AA-GAAGAAGTAAACAG----AGGCT-AGTAATTAAAC
60 AAGGAAGAA-AAAACAGTTTAATTCTGGGTAATTAAAC
* *
3342 TAAA-AAGTAAAAGAAGAAG-AAAAGAGCTTAATTCTGGGTAATTAAACTAAAGAGTAAGA-GAA
1 TAAAGAAGTAAAAGAAGAAGAAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGGAA
* * *
3404 GAAGAAAACAGTTTAATTCTTGCTAATTAAAT
66 GAA-AAAACAGTTTAATTCTGGGTAATTAAAC
* * *
3436 TAAAGAAGTAAACGAAGAAGGAAATAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAAGGAA
1 TAAAGAAGTAAAAGAAGAA-GAAA-A-A-G--AGTTTAATTCTGGGTAATTAAACTAAAGAGTAA
*
3501 AAGGAA-AAAAAAGAGTTTAATTCTGGGTAATTAAAC
60 AAGGAAGAAAAAACAGTTTAATTCTGGGTAATTAAAC
* * *
3537 TAAAG-AGCAAAGGAAGAAGAAAACA-A-TTTAATTCTGGGTAATTAAACCAAAGAGTAAAAGAA
1 TAAAGAAGTAAAAGAAGAAGAAAA-AGAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAG--
* *
3599 GAAGTAAACAGAGGCTAGTTTAATTCTAGGTAATTAAAC
63 GAAG-AAA-A-A-AC-AGTTTAATTCTGGGTAATTAAAC
* * * * * *
3638 TAAA-AAGCAAGAGAAGAAG-AAAAGAGTTTAATTCGGGGTAATTAAACTGAAGAGCAAGA-GAA
1 TAAAGAAGTAAAAGAAGAAGAAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGGAA
*
3700 GAAAAAAACAGTTTAATTCTTGGTAATTAAAC
66 G-AAAAAACAGTTTAATTCTGGGTAATTAAAC
*
3732 TAAAG-AGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAA
1 TAAAGAAGTAAAAGAAGAAG-AAA-A-A-G--AGTTTAATTCTGGGTAATTAAACTAAAGAGTAA
* * *
3796 AA-GAAGAAGAAAATAGCTTAATTCCGGGTAATTAAAC
60 AAGGAAGAA-AAAACAGTTTAATTCTGGGTAATTAAAC
* * * *
3833 TAAAG-AGCAAGAGAAGAAG-AAAACAGTTTGATTCTGGGTAAT
1 TAAAGAAGTAAAAGAAGAAGAAAAAGAGTTTAATTCTGGGTAAT
3875 CAAGCTAAGA
Statistics
Matches: 446, Mismatches: 52, Indels: 72
0.78 0.09 0.13
Matches are distributed among these distances:
89 45 0.10
91 1 0.00
92 3 0.01
93 35 0.08
94 68 0.15
95 17 0.04
96 22 0.05
97 8 0.02
98 13 0.03
99 10 0.02
100 18 0.04
101 170 0.38
102 33 0.07
103 3 0.01
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.23
Consensus pattern (96 bp):
TAAAGAAGTAAAAGAAGAAGAAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGGAA
GAAAAAACAGTTTAATTCTGGGTAATTAAAC
Found at i:3553 original size:148 final size:148
Alignment explanation
Indices: 3332--3874 Score: 831
Period size: 148 Copynumber: 3.7 Consensus size: 148
3322 ACAGAGGCTA
*
3332 GTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAGAGCTTAATTCTGGGTAATTAAACTAAAGAGT
1 GTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAGAGCTTAATTCTGGGTAATTAAACTAAAGAGC
* * * * *
3397 AAGAGAAGAAGAAAACAGTTTAATTCTTGCTAATTAAATTAAAGAAGTAAACGAAGAAGGAAATA
66 AAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAG-AGTAAAAGAAGAAGTAAACA
*
3462 GAGGTTAGTTTAATTCTGG
130 GAGGCTAGTTTAATTCTGG
* *
3481 GTAATTAAACTAAAAAGGAAAAGGAA-AA-AAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAG
1 GTAATTAAACTAAAAAGTAAAA-GAAGAAGAAAAGAGCTTAATTCTGGGTAATTAAACTAAAGAG
* * *
3544 CAA-AGGAAGAAGAAAACAATTTAATTCTGGGTAATTAAACCAAAGAGTAAAAGAAGAAGTAAAC
65 CAAGA-GAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAAC
*
3608 AGAGGCTAGTTTAATTCTAG
129 AGAGGCTAGTTTAATTCTGG
* * * * *
3628 GTAATTAAACTAAAAAGCAAGAGAAGAAGAAAAGAGTTTAATTCGGGGTAATTAAACTGAAGAGC
1 GTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAGAGCTTAATTCTGGGTAATTAAACTAAAGAGC
*
3693 AAGAGAAGAAAAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG
66 AAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG
3758 AGGCTAGTTTAATTCTGG
131 AGGCTAGTTTAATTCTGG
* *
3776 GTAATTAAACTAAAAAGTAAAAGAAGAAGAAAATAGCTTAATTCCGGGTAATTAAACTAAAGAGC
1 GTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAGAGCTTAATTCTGGGTAATTAAACTAAAGAGC
* *
3841 AAGAGAAGAAGAAAACAGTTTGATTCTGGGTAAT
66 AAGAGAAGAAGAAAACAGTTTAATTCTTGGTAAT
3875 CAAGCTAAGA
Statistics
Matches: 358, Mismatches: 31, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
146 3 0.01
147 57 0.16
148 271 0.76
149 24 0.07
150 3 0.01
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (148 bp):
GTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAGAGCTTAATTCTGGGTAATTAAACTAAAGAGC
AAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG
AGGCTAGTTTAATTCTGG
Found at i:3844 original size:195 final size:189
Alignment explanation
Indices: 3332--3874 Score: 619
Period size: 195 Copynumber: 2.8 Consensus size: 189
3322 ACAGAGGCTA
*
3332 GTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAGAGC--TTAATTCTGGGTAATTAAACTAAAGA
1 GTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAGAGCATTTAATTCTGGGTAATTAAACTAAAGA
* * * * * *
3395 GTAAGAGAAGAAGAAAACAGTTTAATTCTTGCTAATTAAATTAAAGAAGTAA-ACGAAGAAGGAA
66 GTAAAAGAAGAAGAAAATAGTTTAATTCTAGGTAATTAAACTAAAG-AGCAAGA-GAAGAA-G-A
* * *
3459 ATAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAAGGAAAAGGAAAAAAAAGAGTTTAATTC
127 A-A-A-G--AGTTTAATTCTGGGTAATTAAACTAAAAAGCAAAAGAAAAAAAAACAGTTTAATTC
3524 TGG
187 TGG
* * * *
3527 GTAATTAAACTAAAGAGCAAAGGAAGAAGAAAACA--ATTTAATTCTGGGTAATTAAACCAAAGA
1 GTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAGAGCATTTAATTCTGGGTAATTAAACTAAAGA
*
3590 GTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCTAGGTAATTAAACTAAAAAGCAAGAGAAGA
66 GTAAAAGAAGAAG--AA-A-A---TAGTTTAATTCTAGGTAATTAAACTAAAGAGCAAGAGAAGA
* * * *
3655 AGAAAAGAGTTTAATTCGGGGTAATTAAACTGAAGAGCAAGAGAAGAAAAAAACAGTTTAATTCT
124 AGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAAAGCAAAAGAA-AAAAAAACAGTTTAATTCT
*
3720 TG
188 GG
3722 GTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCTGGGTAATTAAACT
1 GTAATTAAACTAAAGAGTAAAAGAAGAAG-AAA-AGA-GC-A-TTTAATTCTGGGTAATTAAACT
* * **
3787 AAAAAGTAAAAGAAGAAGAAAATAGCTTAATTCCGGGTAATTAAACTAAAGAGCAAGAGAAGAAG
61 AAAGAGTAAAAGAAGAAGAAAATAGTTTAATTCTAGGTAATTAAACTAAAGAGCAAGAGAAGAAG
* *
3852 AAAACAGTTTGATTCTGGGTAAT
126 AAAAGAGTTTAATTCTGGGTAAT
3875 CAAGCTAAGA
Statistics
Matches: 298, Mismatches: 32, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
194 32 0.11
195 173 0.58
196 4 0.01
197 5 0.02
198 3 0.01
199 4 0.01
200 3 0.01
201 11 0.04
202 63 0.21
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (189 bp):
GTAATTAAACTAAAGAGTAAAAGAAGAAGAAAAGAGCATTTAATTCTGGGTAATTAAACTAAAGA
GTAAAAGAAGAAGAAAATAGTTTAATTCTAGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAG
AGTTTAATTCTGGGTAATTAAACTAAAAAGCAAAAGAAAAAAAAACAGTTTAATTCTGG
Found at i:3898 original size:22 final size:20
Alignment explanation
Indices: 3870--3986 Score: 110
Period size: 22 Copynumber: 5.4 Consensus size: 20
3860 TTGATTCTGG
3870 GTAATCAAGCTAAGAAGAAAGA
1 GTAATCAAG-TAA-AAGAAAGA
*
3892 GTAATCAGAGTAAAAGGAAGA
1 GTAATCA-AGTAAAAGAAAGA
*
3913 GTAATCAAAAGCAAAAGAAAGA
1 GTAATC--AAGTAAAAGAAAGA
*
3935 GTAATC-AGAAACAGAAGAAAGA
1 GTAATCAAG-TA-A-AAGAAAGA
3957 GTAATCAGAAGTAAAAGAAAGA
1 GTAATC--AAGTAAAAGAAAGA
3979 GTAATCAA
1 GTAATCAA
3987 AAGATTAGAG
Statistics
Matches: 81, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.02
20 3 0.04
21 14 0.17
22 55 0.68
23 4 0.05
24 1 0.01
25 2 0.02
ACGTcount: A:0.57, C:0.08, G:0.22, T:0.13
Consensus pattern (20 bp):
GTAATCAAGTAAAAGAAAGA
Found at i:3973 original size:44 final size:43
Alignment explanation
Indices: 3884--3985 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 43
3874 TCAAGCTAAG
* *
3884 AAGAAAGAGTAATCAGAGTAAAAGGAAGAGTAATCAAAAGCAA
1 AAGAAAGAGTAATCAGAGAAAAAGAAAGAGTAATCAAAAGCAA
* *
3927 AAGAAAGAGTAATCAGA-AACAGAAGAAAGAGTAATCAGAAGTAA
1 AAGAAAGAGTAATCAGAGAA-A-AAGAAAGAGTAATCAAAAGCAA
3971 AAGAAAGAGTAATCA
1 AAGAAAGAGTAATCA
3986 AAAGATTAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.02
43 18 0.34
44 34 0.64
ACGTcount: A:0.59, C:0.07, G:0.23, T:0.12
Consensus pattern (43 bp):
AAGAAAGAGTAATCAGAGAAAAAGAAAGAGTAATCAAAAGCAA
Found at i:5179 original size:10 final size:10
Alignment explanation
Indices: 5160--5194 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
5150 TCCATCAGTT
*
5160 TTCAATACGC
1 TTCAACACGC
5170 TTCAACACGC
1 TTCAACACGC
5180 TTCAACACGC
1 TTCAACACGC
5190 TTCAA
1 TTCAA
5195 AACTTGCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.34, G:0.09, T:0.26
Consensus pattern (10 bp):
TTCAACACGC
Found at i:6373 original size:178 final size:178
Alignment explanation
Indices: 6051--6380 Score: 486
Period size: 178 Copynumber: 1.9 Consensus size: 178
6041 TAAGCTCAAA
* * * *
6051 TTATGTAATCTTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTGTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTTGGAAGCATTT
* *
6116 TTTATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGTATGAAAGTTGTAGATCATAGAACAAC
66 TTGATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGAATGAAAGTTGTAGATCATAGAACAAC
*
6181 CTTTCAAGAGACACTTGAATCATCATAATCAGACATCTAGAGCAAAAG
131 CTTTCAAGAGACACTTAAATCATCATAATCAGACATCTAGAGCAAAAG
*
6229 TTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAGCATT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTT-GGAAGCATT
** *
6293 TTTGATA-CTTGAAACATTAAATTTAGTTTTCGTGTCCTT-AATGAAAGTTGTAGATCATGGAAC
65 TTTGATACCTTG-AACATTAAATTTAGTTTTCCAGT-CTTGAATGAAAGTTGTAGATCATAGAAC
* * *
6356 AATCTTTTAATAGACACTTAAATCA
128 AACCTTTCAAGAGACACTTAAATCA
6381 CCTTTATTGG
Statistics
Matches: 135, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
177 7 0.05
178 125 0.93
179 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTTGGAAGCATTT
TTGATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGAATGAAAGTTGTAGATCATAGAACAAC
CTTTCAAGAGACACTTAAATCATCATAATCAGACATCTAGAGCAAAAG
Found at i:6413 original size:178 final size:177
Alignment explanation
Indices: 6048--6425 Score: 458
Period size: 178 Copynumber: 2.1 Consensus size: 177
6038 TCATAAGCTC
* * * *
6048 AAATTATGTAATCTTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTGTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTTGGAAGCA
* *
6113 TTTTTTATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGTATGAAAGTTGTAGATCATAGAAC
66 TTTTTGATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGAATGAAAGTTGTAGATCATAGAAC
* * * * *
6178 AACCTTTCAAGAGACACTTGAATCATCATAATCAGACATCTAGAGCA
131 AACCTTTCAAGAGACACTTAAATCACCATAATCAGAAACCAAGAGCA
*
6225 AAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAG
1 AAA-TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTT-GGAAG
** *
6289 CATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGTGTCCTT-AATGAAAGTTGTAGATCATG
64 CATTTTTGATACCTTG-AACATTAAATTTAGTTTTCCAGT-CTTGAATGAAAGTTGTAGATCATA
* * * * * **
6352 GAACAATCTTTTAATAGACACTTAAATCACCTTTATTGGATAACCAAAGAG-A
127 GAACAACCTTTCAAGAGACACTTAAATCACCATAATCAGA-AACC-AAGAGCA
* *
6404 AAATTATATAATGTTAAATAGA
1 AAATTATATAATATTAAGTAGA
6426 TCGTTTAACC
Statistics
Matches: 170, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
177 10 0.06
178 147 0.86
179 9 0.05
180 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTTGGAAGCA
TTTTTGATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGAATGAAAGTTGTAGATCATAGAAC
AACCTTTCAAGAGACACTTAAATCACCATAATCAGAAACCAAGAGCA
Found at i:6974 original size:2 final size:2
Alignment explanation
Indices: 6962--7003 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
6952 AACCTCAGAG
*
6962 TA TA TA AA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7003 T
1 T
7004 TAATCTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8030 original size:436 final size:436
Alignment explanation
Indices: 7287--8189 Score: 1117
Period size: 436 Copynumber: 2.1 Consensus size: 436
7277 AATTTGTAAA
* * *
7287 GGACAAATAGAACAAAGAAAATAAAAAAATAAAGTGTTAAATCGAGTAAGATAGAATTTGTTAAG
1 GGACAAATAGAA-AAA-AAAATAAAAAAATAAAGTGCTAAATCGAGTAAGAAAGAATTTGTAAAG
* *
7352 AACTAAGTAGCATAAAATAGAAAAGTATAAGGGTGATTTGATAACTAATTCAAATAAGAAAATAT
64 AACTAAGTAGCATAAAATAGAAAAGTATAAGGGTCATTTGATAAATAATTCAAATAAGAAAATAT
* * * *
7417 TTGTTAATTAATGGAGATCTTGAAACATAAAAAATTCCCTTTTGAATCATTCATGAAACTCGTAG
129 TTG---ATTAATGGAGATCTTGAAACATAAAAAATTCCCTTTTAAACCATTAACGAAACTCGTAG
* ** * * *
7482 ATTAAATTAACTTTTGGGTTCTTCATGAAAGTCGTAGATTATACAATAACCTTTTAACCGACACT
191 ATCAAATTAACTTTCAGGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACT
* * * * * * *
7547 TGAATAACTTTAATTGGACATGTGGATCGAAAATTATATGGTATTAAA-TAGACCAACAATC-GA
256 TCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATTA-ACCAACAATCAAA
* * ** **
7610 AACGACCAAATTT-AGGAAGCATTTTTTTGAAT-TGACATAAAAATTTG-CTTTTGAGTCCTTCA
320 AAC-ACAAAATTTCA-GAAGCATTTTTTAGAATAAAACATAAAAA-TTGACTTTTGAGTCCTAAA
* * * *
7672 TGAAAACTGTAGATCATGAAATTACCTTTTAATAGACA-TATGAATCAACTTCATT
382 AGAAAACTATAGATCATGAAATTACCTTTTAATAGACACT-TGAATCAACTTAATC
* *
7727 GGACAAATAGAAAAAAGAATAAAAAAGTAAAGT-CTAAA-CGTCAGATCAAGAAAGAATTTGTAA
1 GGACAAATAGAAAAAAAAATAAAAAAATAAAGTGCTAAATCG--AG-T-AAGAAAGAATTTGTAA
* * *
7790 AGAACTAAGTAGTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATTCAAATAAGAAAAT
62 AGAACTAAGTAGCATAAAATAGAAAAGTATAAGGGTCATTTGATAAATAATTCAAATAAGAAAAT
* *
7855 GTTTG-TTAATGGAGATCTTGAAACAT-AAAAATTCCCTTTTAAACCCTTAACGAAACTCGTAGA
127 ATTTGATTAATGGAGATCTTGAAACATAAAAAATTCCCTTTTAAACCATTAACGAAACTCGTAGA
* * **
7918 TCCAATTTAGCTTTCAGGTCCTTCATGAAAGTCGTAAATCATGTAATAACCTTTTAACCGACACT
192 T-CAAATTAACTTTCAGGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACT
* **
7983 TCAATAACTTCAATCGGAGATGTGGA-CAAAAAATTATACGATATTAAATTAACCGGCAATCAAA
256 TCAATAACTTCAATCGGACATGTGGATC-AAAAATTATACGATATTAAATTAACCAACAATCAAA
* * *
8047 AACACAAAATTTCAGAAGTATTTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTTCTAAAAG
320 AACACAAAATTTCAGAAGCATTTTTTAGAAT-AAAACATAAAAATTGACTTTTGAGTCCTAAAAG
* *
8112 AAAATTATAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATC
384 AAAACTATAGATCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATC
8165 GGACAAATAGAAAAAAAAATAAAAA
1 GGACAAATAGAAAAAAAAATAAAAA
8190 TAAAAGGCAA
Statistics
Matches: 398, Mismatches: 52, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
435 34 0.09
436 146 0.37
437 14 0.04
438 109 0.27
439 5 0.01
440 90 0.23
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (436 bp):
GGACAAATAGAAAAAAAAATAAAAAAATAAAGTGCTAAATCGAGTAAGAAAGAATTTGTAAAGAA
CTAAGTAGCATAAAATAGAAAAGTATAAGGGTCATTTGATAAATAATTCAAATAAGAAAATATTT
GATTAATGGAGATCTTGAAACATAAAAAATTCCCTTTTAAACCATTAACGAAACTCGTAGATCAA
ATTAACTTTCAGGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAAT
AACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATTAACCAACAATCAAAAACACA
AAATTTCAGAAGCATTTTTTAGAATAAAACATAAAAATTGACTTTTGAGTCCTAAAAGAAAACTA
TAGATCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATC
Found at i:11083 original size:26 final size:27
Alignment explanation
Indices: 11034--11091 Score: 91
Period size: 26 Copynumber: 2.1 Consensus size: 27
11024 GAACCCACCA
11034 TAAATTTTCAGAATTTTTTATAGAAAAT
1 TAAATTTTCAG-ATTTTTTATAGAAAAT
*
11062 TAAATTTTCAG-TTTTTTTTAGAAAAT
1 TAAATTTTCAGATTTTTTATAGAAAAT
11088 TAAA
1 TAAA
11092 AAAAAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 18 0.62
28 11 0.38
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (27 bp):
TAAATTTTCAGATTTTTTATAGAAAAT
Found at i:12256 original size:22 final size:24
Alignment explanation
Indices: 12197--12268 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 24
12187 GGAAGAAAAG
*
12197 AGATTTCTTTTTAATTTTTTTTTTAA
1 AGATATCTTTTT-A-TTTTTTTTTAA
*
12223 AGATATCATTTTATTTTTTTTTAA
1 AGATATCTTTTTATTTTTTTTTAA
* * *
12247 A-TTA-CTTTTTCTTATTTTTTAA
1 AGATATCTTTTTATTTTTTTTTAA
12269 TAAAAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 15 0.38
23 2 0.05
24 12 0.30
25 1 0.03
26 10 0.25
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (24 bp):
AGATATCTTTTTATTTTTTTTTAA
Found at i:12403 original size:31 final size:31
Alignment explanation
Indices: 12365--12461 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 31
12355 AATTGGATTT
* * *
12365 AATTGACTCATTCTGGCAAGTATAGGGACTA
1 AATTGACTCATTCTGACAAATAGAGGGACTA
* *
12396 AATTGACTCAATCTTACAAATAGAGGGACTA
1 AATTGACTCATTCTGACAAATAGAGGGACTA
****
12427 AATTGA-TCATT-TTTTTAATAGAGGGACTA
1 AATTGACTCATTCTGACAAATAGAGGGACTA
12456 AATTGA
1 AATTGA
12462 TTTTTATAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 21 0.37
30 4 0.07
31 32 0.56
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (31 bp):
AATTGACTCATTCTGACAAATAGAGGGACTA
Found at i:12475 original size:27 final size:27
Alignment explanation
Indices: 12414--12480 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 27
12404 CAATCTTACA
*
12414 AATAGAGGGACTAAATTGATCATTTTTTT
1 AATAGAGGGACTAAATTGA--ATTTTTAT
12443 AATAGAGGGACTAAATTG-ATTTTTAT
1 AATAGAGGGACTAAATTGAATTTTTAT
12469 AAGTAGAGGGAC
1 AA-TAGAGGGAC
12481 CTCCTAGGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 9 0.25
27 9 0.25
29 18 0.50
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.34
Consensus pattern (27 bp):
AATAGAGGGACTAAATTGAATTTTTAT
Found at i:13371 original size:16 final size:16
Alignment explanation
Indices: 13350--13387 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
13340 CCCCATAATA
13350 GGGTGAGCA-AAGCCTT
1 GGGTGAG-AGAAGCCTT
*
13366 GGGTGAGAGACGCCTT
1 GGGTGAGAGAAGCCTT
13382 GGGTGA
1 GGGTGA
13388 AGGCACTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.21, C:0.16, G:0.45, T:0.18
Consensus pattern (16 bp):
GGGTGAGAGAAGCCTT
Found at i:13858 original size:48 final size:48
Alignment explanation
Indices: 13787--13879 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
13777 AACTCTTGTT
*
13787 TGATCAACCCTATCTTTTACTTTTCACCACCCTTGTTTTTACAAGTTG
1 TGATCAACCCTATCATTTACTTTTCACCACCCTTGTTTTTACAAGTTG
* * *
13835 TGATCAACCTTGTCATTTACTTTTCATCACCCTTGTTTTTACAAG
1 TGATCAACCCTATCATTTACTTTTCACCACCCTTGTTTTTACAAG
13880 GTGTAATCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.22, C:0.26, G:0.09, T:0.44
Consensus pattern (48 bp):
TGATCAACCCTATCATTTACTTTTCACCACCCTTGTTTTTACAAGTTG
Found at i:13868 original size:23 final size:22
Alignment explanation
Indices: 13802--13876 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
13792 AACCCTATCT
* *
13802 TTTACTTTTCACCACCCTTGTT
1 TTTACTTTTCATCACCCTTGTA
* * *
13824 TTTACAAGTTGTGATCAACCTTGTCA
1 TTTAC---TTTTCATCACCCTTGT-A
*
13850 TTTACTTTTCATCACCCTTGTT
1 TTTACTTTTCATCACCCTTGTA
13872 TTTAC
1 TTTAC
13877 AAGGTGTAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
22 10 0.25
23 13 0.32
25 12 0.30
26 5 0.12
ACGTcount: A:0.19, C:0.25, G:0.08, T:0.48
Consensus pattern (22 bp):
TTTACTTTTCATCACCCTTGTA
Found at i:14902 original size:48 final size:48
Alignment explanation
Indices: 14847--14982 Score: 245
Period size: 48 Copynumber: 2.8 Consensus size: 48
14837 ACTCTTGTTA
* * *
14847 GATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTATAAGTTGT
1 GATCAACCTTGTCGTTTACTTTTCATCACCCTTGTTTTTATAAGTTGT
14895 GATCAACCTTGTCGTTTACTTTTCATCACCCTTGTTTTTATAAGTTGT
1 GATCAACCTTGTCGTTTACTTTTCATCACCCTTGTTTTTATAAGTTGT
14943 GATCAACCTTGTCGTTTACTTTTCATCACCCTTGTTTTTA
1 GATCAACCTTGTCGTTTACTTTTCATCACCCTTGTTTTTA
14983 CAAGGTGTAA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 85 1.00
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (48 bp):
GATCAACCTTGTCGTTTACTTTTCATCACCCTTGTTTTTATAAGTTGT
Found at i:14904 original size:25 final size:25
Alignment explanation
Indices: 14871--14954 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
14861 TTTACTTTTC
*
14871 ATCACCCTTGTTTTTATAAGTTGTG
1 ATCAACCTTGTTTTTATAAGTTGTG
** * * *
14896 ATCAACCTTGTCGTT-T-ACTTTTC
1 ATCAACCTTGTTTTTATAAGTTGTG
*
14919 ATCACCCTTGTTTTTATAAGTTGTG
1 ATCAACCTTGTTTTTATAAGTTGTG
14944 ATCAACCTTGT
1 ATCAACCTTGT
14955 CGTTTACTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
23 16 0.36
24 2 0.05
25 26 0.59
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.46
Consensus pattern (25 bp):
ATCAACCTTGTTTTTATAAGTTGTG
Found at i:19543 original size:28 final size:28
Alignment explanation
Indices: 19483--19547 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
19473 TGTGAGCTTA
* * *
19483 AAATGACCAAAATGCCCCTGGATTTTGC
1 AAATGACCAAAATGCCCCTAGATTATCC
19511 AAATGACCAAAATGCCCCTAG-TTGATCC
1 AAATGACCAAAATGCCCCTAGATT-ATCC
*
19539 TAATG-CCAA
1 AAATGACCAA
19548 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.23
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTAGATTATCC
Found at i:20442 original size:65 final size:65
Alignment explanation
Indices: 20333--20475 Score: 259
Period size: 65 Copynumber: 2.2 Consensus size: 65
20323 AAAATCTACT
* * *
20333 TTTCATTGTCTCTCTCCATCAATCTCTCATTTTGTTACTGAAGAATTACCCGATAGGTTTAATGA
1 TTTCATTGTCTCTCTCCATCAATCTCTCAATTTGTTACTCAAGAATTACCCAATAGGTTTAATGA
20398 TTTCATTGTCTCTCTCCATCAATCTCTCAATTTGTTACTCAAGAATTACCCAATAGGTTTAATGA
1 TTTCATTGTCTCTCTCCATCAATCTCTCAATTTGTTACTCAAGAATTACCCAATAGGTTTAATGA
20463 TTTCATTGTCTCT
1 TTTCATTGTCTCT
20476 TTCCTTTTCA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 75 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (65 bp):
TTTCATTGTCTCTCTCCATCAATCTCTCAATTTGTTACTCAAGAATTACCCAATAGGTTTAATGA
Found at i:21386 original size:48 final size:48
Alignment explanation
Indices: 21331--21423 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
21321 AATTCTTGTT
21331 TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAGTTG
1 TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAGTTG
* *
21379 TGATCAACCTTGTCATTTACTTTTCATCACCCTTGTTTTTACAAG
1 TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAG
21424 GTGTAATCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.44
Consensus pattern (48 bp):
TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAGTTG
Found at i:21412 original size:23 final size:23
Alignment explanation
Indices: 21343--21414 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
21333 ATCAACCCTA
21343 TCATTTACTTTTCATCACCCTTG
1 TCATTTACTTTTCATCACCCTTG
* * * *
21366 T-TTTTACAAGTTGTGATCAACCTTG
1 TCATTTAC---TTTTCATCACCCTTG
21391 TCATTTACTTTTCATCACCCTTG
1 TCATTTACTTTTCATCACCCTTG
21414 T
1 T
21415 TTTTACAAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
22 5 0.14
23 14 0.38
25 13 0.35
26 5 0.14
ACGTcount: A:0.19, C:0.25, G:0.08, T:0.47
Consensus pattern (23 bp):
TCATTTACTTTTCATCACCCTTG
Found at i:22452 original size:22 final size:22
Alignment explanation
Indices: 22427--22501 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
22417 CAACCCTATC
22427 TTTTACTTTTCATCACCCTTGT
1 TTTTACTTTTCATCACCCTTGT
* * *
22449 TTTTACAAGTTGTGATCAACCTTGT
1 TTTTAC---TTTTCATCACCCTTGT
** * *
22474 CATCACTTTTCATCACCCTTGA
1 TTTTACTTTTCATCACCCTTGT
22496 TTTTAC
1 TTTTAC
22502 AAGGTGTAAT
Statistics
Matches: 37, Mismatches: 13, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
22 21 0.57
25 16 0.43
ACGTcount: A:0.20, C:0.25, G:0.08, T:0.47
Consensus pattern (22 bp):
TTTTACTTTTCATCACCCTTGT
Found at i:22468 original size:48 final size:47
Alignment explanation
Indices: 22413--22504 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 47
22403 AACTCTTGTT
* * *
22413 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
1 TGATCAACCCTATC-ATCACTTTTCATCACCCTTGATTTTACAAGTTG
* *
22461 TGATCAACCTTGTCATCACTTTTCATCACCCTTGATTTTACAAG
1 TGATCAACCCTATCATCACTTTTCATCACCCTTGATTTTACAAG
22505 GTGTAATCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 27 0.69
48 12 0.31
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.42
Consensus pattern (47 bp):
TGATCAACCCTATCATCACTTTTCATCACCCTTGATTTTACAAGTTG
Found at i:24618 original size:25 final size:25
Alignment explanation
Indices: 24585--24668 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
24575 TTTACTTTTC
*
24585 ATCACCCTTGTTTTTACAAGTTGTG
1 ATCAACCTTGTTTTTACAAGTTGTG
* * *
24610 ATCAACCTTGTCATTTAC---TTTTC
1 ATCAACCTTGT-TTTTACAAGTTGTG
*
24633 ATCACCCTTGTTTTTACAAGTTGTG
1 ATCAACCTTGTTTTTACAAGTTGTG
24658 ATCAACCTTGT
1 ATCAACCTTGT
24669 CATTTACTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 5 0.11
23 13 0.28
25 23 0.50
26 5 0.11
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (25 bp):
ATCAACCTTGTTTTTACAAGTTGTG
Found at i:24631 original size:48 final size:48
Alignment explanation
Indices: 24575--24700 Score: 252
Period size: 48 Copynumber: 2.6 Consensus size: 48
24565 CACCATATCT
24575 TTTACTTTTCATCACCCTTGTTTTTACAAGTTGTGATCAACCTTGTCA
1 TTTACTTTTCATCACCCTTGTTTTTACAAGTTGTGATCAACCTTGTCA
24623 TTTACTTTTCATCACCCTTGTTTTTACAAGTTGTGATCAACCTTGTCA
1 TTTACTTTTCATCACCCTTGTTTTTACAAGTTGTGATCAACCTTGTCA
24671 TTTACTTTTCATCACCCTTGTTTTTACAAG
1 TTTACTTTTCATCACCCTTGTTTTTACAAG
24701 GTGTAATCTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.47
Consensus pattern (48 bp):
TTTACTTTTCATCACCCTTGTTTTTACAAGTTGTGATCAACCTTGTCA
Found at i:30113 original size:20 final size:20
Alignment explanation
Indices: 30090--30131 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
30080 TTGTCCAGCT
30090 TCCACTTTGTTAGATAATTC
1 TCCACTTTGTTAGATAATTC
30110 TCCACTTTGTTAGATAATTC
1 TCCACTTTGTTAGATAATTC
30130 TC
1 TC
30132 TTCTAGGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (20 bp):
TCCACTTTGTTAGATAATTC
Done.