Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000024.1 Hibiscus syriacus cultivar Beakdansim tig00000042_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: 74730
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:3381 original size:101 final size:99
Alignment explanation
Indices: 3206--3406 Score: 350
Period size: 101 Copynumber: 2.0 Consensus size: 99
3196 ACGTGATTCT
*
3206 TATAGTATCCCTTAACAAGGAATGGTGAAGAAATCATCATCAGATGTGAGGTATGACCTTGACTT
1 TATAGTATCCCTTAACAAGAAATGGTGAAGAAATCATCATCAGATGT-AGGTATGACCTTGACTT
3271 CTTGCCCAGTTTACATATTGTTTCTTTCCTCCAAAG
65 CTTGCCCAGTTTACATATTG-TTCTTTCCTCCAAAG
3307 TATAGTATCCCTTAACAAGAAAATGGTGAAGAAATCATCATCAGATGT-GGTATTGACCTTGACT
1 TATAGTATCCCTTAACAAG-AAATGGTGAAGAAATCATCATCAGATGTAGGTA-TGACCTTGACT
3371 TCTTGCCCAGTTTACATATTGTTCTTTCCTCCAAAG
64 TCTTGCCCAGTTTACATATTGTTCTTTCCTCCAAAG
3407 CTATCATAGT
Statistics
Matches: 97, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
100 19 0.20
101 51 0.53
102 27 0.28
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (99 bp):
TATAGTATCCCTTAACAAGAAATGGTGAAGAAATCATCATCAGATGTAGGTATGACCTTGACTTC
TTGCCCAGTTTACATATTGTTCTTTCCTCCAAAG
Found at i:5313 original size:23 final size:22
Alignment explanation
Indices: 5287--5333 Score: 85
Period size: 23 Copynumber: 2.1 Consensus size: 22
5277 TGTTACATTC
5287 CATGAACCAACCAAACACTCCCT
1 CATGAACCAACCAAACAC-CCCT
5310 CATGAACCAACCAAACACCCCT
1 CATGAACCAACCAAACACCCCT
5332 CA
1 CA
5334 AGTACATCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.40, C:0.45, G:0.04, T:0.11
Consensus pattern (22 bp):
CATGAACCAACCAAACACCCCT
Found at i:9357 original size:7 final size:7
Alignment explanation
Indices: 9345--9392 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
9335 TTAGAATTAT
9345 AATTTTA
1 AATTTTA
9352 AATTTTA
1 AATTTTA
9359 AATTTTA
1 AATTTTA
*
9366 AATTATA
1 AATTTTA
*
9373 AATTATAA
1 AATT-TTA
9381 AATTTTA
1 AATTTTA
9388 AATTT
1 AATTT
9393 ATATAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
7 31 0.86
8 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AATTTTA
Found at i:9374 original size:14 final size:14
Alignment explanation
Indices: 9334--9392 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
9324 GATATTAAGA
9334 TTTAGAATTAT-AAT
1 TTTA-AATTATAAAT
*
9348 TTTAAATTTTAAAT
1 TTTAAATTATAAAT
9362 TTTAAATTATAAAT
1 TTTAAATTATAAAT
* *
9376 TATAAAATTTTAAAT
1 T-TTAAATTATAAAT
9391 TT
1 TT
9393 ATATAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 5 0.13
14 22 0.56
15 12 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TTTAAATTATAAAT
Found at i:9401 original size:21 final size:22
Alignment explanation
Indices: 9358--9409 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
9348 TTTAAATTTT
*
9358 AAATTTTAAATTATAAATTATA
1 AAATTTTAAATTATAAATAATA
*
9380 AAATTTTAAATT-TATATAATA
1 AAATTTTAAATTATAAATAATA
9401 AATATTTTA
1 AA-ATTTTA
9410 TCATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATTTTAAATTATAAATAATA
Found at i:21185 original size:23 final size:23
Alignment explanation
Indices: 21159--21244 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
21149 ATTATTATAT
* *
21159 GGCACTTCGGTGCATTTCTATTC
1 GGCACTACGGTGCATTTCTACTC
*
21182 GGCACTACGGTGCATTTCTACAC
1 GGCACTACGGTGCATTTCTACTC
*
21205 GGCACTACGGTGCAATTCTACGT-
1 GGCACTACGGTGCATTTCTAC-TC
**
21228 GGCACTTTGGTGCATTT
1 GGCACTACGGTGCATTT
21245 ATACGAGCTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACTC
Found at i:23932 original size:16 final size:16
Alignment explanation
Indices: 23911--23953 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
23901 GAAAATTAAA
23911 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
23927 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
23944 GAGTGATAAG
1 GATTGATAAG
23954 AACTGATGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:24849 original size:22 final size:22
Alignment explanation
Indices: 24823--24865 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24813 TTCTGGGCTA
*
24823 GGGGAATCGGTACCCATTCAAG
1 GGGGAATCGATACCCATTCAAG
*
24845 GGGGAATCGATACCCCTTCAA
1 GGGGAATCGATACCCATTCAA
24866 ACGAACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (22 bp):
GGGGAATCGATACCCATTCAAG
Found at i:26299 original size:23 final size:23
Alignment explanation
Indices: 26273--26363 Score: 119
Period size: 23 Copynumber: 4.0 Consensus size: 23
26263 ATTATTATAT
*
26273 GGCACTTCGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
*
26296 GGCACTACGGTGCATTTCTACAC
1 GGCACTACGGTGCATTTCTACGC
* *
26319 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
** *
26342 GGCACTTTGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
26364 AGCTGTGGTG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:26617 original size:20 final size:21
Alignment explanation
Indices: 26594--26633 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
26584 AAATGATTGT
26594 ATATAA-ATATGTATGTTTTG
1 ATATAAGATATGTATGTTTTG
*
26614 ATATAATGATATGTGTGTTT
1 ATATAA-GATATGTATGTTT
26634 CTCGTGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (21 bp):
ATATAAGATATGTATGTTTTG
Found at i:29052 original size:16 final size:16
Alignment explanation
Indices: 29031--29073 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
29021 GAAAATTAAA
29031 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
29047 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
29064 GAGTGATAAG
1 GATTGATAAG
29074 AACTGATGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:29972 original size:22 final size:22
Alignment explanation
Indices: 29946--29988 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29936 TTCTGGGCTA
* *
29946 GGGGAATCGGTACCCATTCAAG
1 GGGGAACCGATACCCATTCAAG
*
29968 GGGGAACCGATACCCCTTCAA
1 GGGGAACCGATACCCATTCAA
29989 ACGAACAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (22 bp):
GGGGAACCGATACCCATTCAAG
Found at i:31439 original size:23 final size:23
Alignment explanation
Indices: 31406--31496 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 23
31396 ATTATTATAT
*
31406 GGCACTTCGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
*
31429 GGTACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * * *
31452 GGCAGTACAGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
* *
31475 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
31497 AGCTGTGGTG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:31751 original size:20 final size:21
Alignment explanation
Indices: 31728--31767 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
31718 AAATGATTGT
31728 ATATAA-ATATGTATGTTTTG
1 ATATAAGATATGTATGTTTTG
*
31748 ATATAATGATATGTGTGTTT
1 ATATAA-GATATGTATGTTT
31768 CTCGTGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (21 bp):
ATATAAGATATGTATGTTTTG
Found at i:36540 original size:11 final size:12
Alignment explanation
Indices: 36514--36646 Score: 53
Period size: 13 Copynumber: 10.9 Consensus size: 12
36504 AGTAAGTAAA
36514 AAAATAAATAAT
1 AAAATAAATAAT
36526 AAAATATATATAA-
1 AAAATA-A-ATAAT
* *
36539 AAAAGAAA-AAG
1 AAAATAAATAAT
*
36550 AAAATAAATAAA
1 AAAATAAATAAT
*
36562 ACAAATAAACAA-
1 A-AAATAAATAAT
*
36574 AATAAT-AATAAC
1 AA-AATAAATAAT
* *
36586 AAAGT-AAGAAT
1 AAAATAAATAAT
* *
36597 AATATATATATAT
1 AAAATAAATA-AT
*
36610 ATAATAAATAA-
1 AAAATAAATAAT
36621 AAAAGTAAATATAT
1 AAAA-TAAATA-AT
*
36635 ATAAATTAATAA
1 A-AAATAAATAA
36647 ATTAAATGAC
Statistics
Matches: 91, Mismatches: 17, Indels: 25
0.68 0.13 0.19
Matches are distributed among these distances:
10 2 0.02
11 25 0.27
12 25 0.27
13 26 0.29
14 10 0.11
15 3 0.03
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:36613 original size:29 final size:27
Alignment explanation
Indices: 36515--36637 Score: 72
Period size: 24 Copynumber: 4.9 Consensus size: 27
36505 GTAAGTAAAA
*
36515 AAATAAATAA-TAAA-ATATATATAA-
1 AAATAAAAAAGTAAATATATATATAAC
* *
36539 AAA-AGAAAAAG-AAA-ATAAATAAAAC
1 AAATA-AAAAAGTAAATATATATATAAC
*
36564 AAAT-AAACA--AAATA-ATA-ATAAC
1 AAATAAAAAAGTAAATATATATATAAC
* *
36586 AAAGTAAGAATAA-TATATATATATATAAT
1 AAA-TAA-AA-AAGTAAATATATATATAAC
36615 AAATAAAAAAGTAAATATATATA
1 AAATAAAAAAGTAAATATATATA
36638 AATTAATAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
22 7 0.09
23 7 0.09
24 24 0.32
25 5 0.07
26 3 0.04
27 17 0.22
28 6 0.08
29 7 0.09
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (27 bp):
AAATAAAAAAGTAAATATATATATAAC
Found at i:36928 original size:2 final size:2
Alignment explanation
Indices: 36872--36910 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
36862 TTTGTGTAGA
36872 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36911 ATAGTAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37103 original size:2 final size:2
Alignment explanation
Indices: 37096--37136 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
37086 AAACATACGC
37096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37137 AAAATAATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37264 original size:12 final size:12
Alignment explanation
Indices: 37247--37289 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
37237 GAATAAAAGG
37247 AAAATAATAGTA
1 AAAATAATAGTA
*
37259 AAAATAATAATA
1 AAAATAATAGTA
*
37271 AATATAATAGTA
1 AAAATAATAGTA
*
37283 ATAATAA
1 AAAATAA
37290 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (12 bp):
AAAATAATAGTA
Found at i:37309 original size:59 final size:58
Alignment explanation
Indices: 37192--37318 Score: 129
Period size: 59 Copynumber: 2.2 Consensus size: 58
37182 AGAAAAATAT
*
37192 ATAATAATAAAATATAAAAATATACATATATAATATAAATAAGTAGAATAAAAGGAAA
1 ATAATAATAAAATATAAAAATATACATATATAATATAAATAAGTAAAATAAAAGGAAA
* * *
37250 ATAATAGTAAAAATAATAATAAATATA-ATA-GTAATAATAAA-AATTAAAATGAAAA-GAAA
1 ATAATAAT-AAAAT-ATAA-AAATATACATATATAAT-ATAAATAAGTAAAAT-AAAAGGAAA
*
37309 AGAA-AATAAA
1 ATAATAATAAA
37319 TAAATATATA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
57 3 0.05
58 9 0.16
59 23 0.40
60 16 0.28
61 7 0.12
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.24
Consensus pattern (58 bp):
ATAATAATAAAATATAAAAATATACATATATAATATAAATAAGTAAAATAAAAGGAAA
Found at i:37902 original size:37 final size:37
Alignment explanation
Indices: 37861--37965 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
37851 GTGCTTGTGG
* *
37861 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
37898 ATCCTATTTTTAGGAGTTTAAATCCTAGAAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
37935 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
37966 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:39021 original size:106 final size:106
Alignment explanation
Indices: 38696--39777 Score: 1579
Period size: 106 Copynumber: 10.3 Consensus size: 106
38686 GCATTGTTCT
* * * * *** *
38696 GAGTCCAATATCCTCCGTCGTGAAGTTGTAATTGGCTCTGGAACCAGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
38761 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
38802 GAGTCCAATATCCTTCGCTATGAAGTTAAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
38861 TCAGCCG-CCTCTTCGTCGTAAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
38903 G-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
38967 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
39008 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGCCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
39073 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
39114 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
39179 CCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
39220 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
39285 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
39326 GAGTCCAATATTCTTCGTTGTAAAGTTGAAATCGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
39391 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
39432 GAGTCCAATATCCTACATTGTGAAGTTGAATTTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
39497 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
39538 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
39603 CCAACGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
39644 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGATAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
39709 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
39750 GAGTCCAATATCCTTCGTTGTGAAGTTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTG
39778 TTTGTTGACA
Statistics
Matches: 882, Mismatches: 83, Indels: 22
0.89 0.08 0.02
Matches are distributed among these distances:
99 3 0.00
100 72 0.08
101 5 0.01
102 4 0.00
104 3 0.00
105 5 0.01
106 788 0.89
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:39820 original size:186 final size:188
Alignment explanation
Indices: 39585--39965 Score: 662
Period size: 186 Copynumber: 2.0 Consensus size: 188
39575 CTGAAATTGA
39585 GAAGTTGTTTGTTGACAACCAACGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAGTTGTTTGTTGACAACCAACGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
39650 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGG-AAGTTGTTTATTGATAACCAGC
66 AATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATT-GGAAAGTTGTTTATTGACAACCAGC
39714 GGTCCCTTCGTCGTGAAGTTGAACTTGCG-T-TGTCTGGAGTCCAATATCCTTCGTTGT
130 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTGTCTGGAGTCCAATATCCTTCGTTGT
* *
39771 GAAGTTGTTTGTTGACAACCAGCGGTCCCTT-TTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
1 GAAGTTGTTTGTTGACAACCAACGGTCCCTTCGTT-GTGAAGTTGAACTTGCGTTGTCTGGAGTC
39835 CAATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTGGAAAGTTGTTTATTGACAACCAGC
65 CAATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTGGAAAGTTGTTTATTGACAACCAGC
*
39900 GGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTGTCTGGAGTCCAATATCCTTCGTTGT
130 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTGTCTGGAGTCCAATATCCTTCGTTGT
39959 GAAGTTG
1 GAAGTTG
39966 AAATTAGATC
Statistics
Matches: 185, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
185 4 0.02
186 146 0.79
187 1 0.01
188 34 0.18
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (188 bp):
GAAGTTGTTTGTTGACAACCAACGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTGGAAAGTTGTTTATTGACAACCAGCG
GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTGTCTGGAGTCCAATATCCTTCGTTGT
Found at i:39824 original size:80 final size:80
Alignment explanation
Indices: 39691--39857 Score: 280
Period size: 80 Copynumber: 2.1 Consensus size: 80
39681 CTGAAATTAG
*
39691 GAAGTTGTTTATTGATAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
**
39756 AATATCCTTCGTTGT
66 AATATCCTTCACTGT
* **
39771 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTTTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
39836 AATATCCTTCACTGT
66 AATATCCTTCACTGT
39851 GAAGTTG
1 GAAGTTG
39858 AAATTGGCTC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (80 bp):
GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCACTGT
Found at i:39993 original size:108 final size:108
Alignment explanation
Indices: 39772--40040 Score: 400
Period size: 108 Copynumber: 2.5 Consensus size: 108
39762 CTTCGTTGTG
* ** *
39772 AAGTTGTTTGTTGACAACCAGCGGTCCCTTTTTCGTGAAGTTGAACTTGCG-T-TGTCTGGAGTC
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTGTCTGGAGTC
* *
39835 CAATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTGGA
66 CAATATCCTTCACTGTGAAGTTGAAATTAGATCTAAAATTGGA
39878 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTGTCTGGAGTC
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTGTCTGGAGTC
** *
39943 CAATATCCTTCGTTGTGAAGTTGAAATTAGATCTGAAATTGGGA
66 CAATATCCTTCACTGTGAAGTTGAAATTAGATCTAAAATT-GGA
* * *
39987 AA-TTGTTTATTGATAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
40041 CTTGAGTGGC
Statistics
Matches: 148, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
106 47 0.32
107 1 0.01
108 95 0.64
109 5 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (108 bp):
AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTGTCTGGAGTC
CAATATCCTTCACTGTGAAGTTGAAATTAGATCTAAAATTGGA
Found at i:40898 original size:22 final size:22
Alignment explanation
Indices: 40872--40941 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
40862 TTATGTTTGG
40872 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
40894 TCAAAGGTTTGGCATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
40916 TCATAA-GTTTGGCATTTGATGC
1 TCA-AAGGTTTGGCATTTGATGC
40938 TCAA
1 TCAA
40942 CAGTTTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 1 0.02
22 42 0.93
23 2 0.04
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:41581 original size:14 final size:14
Alignment explanation
Indices: 41564--41632 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 14
41554 TTCTTTTTGA
41564 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
41578 TTTTTGTTC-TTCT
1 TTTTTGTTCTTTCT
41591 TTTTTGCTTCTTTTCT
1 TTTTTG-TTC-TTTCT
*
41607 TTTTTGTT-TTTGCCC
1 TTTTTGTTCTTT--CT
41622 TTTTTGTTCTT
1 TTTTTGTTCTT
41633 CGCACTTGGC
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
13 13 0.27
14 12 0.25
15 11 0.23
16 12 0.25
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:44997 original size:19 final size:19
Alignment explanation
Indices: 44964--45000 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
44954 TGCAGATAAT
44964 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
44983 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
45001 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:46184 original size:11 final size:12
Alignment explanation
Indices: 46158--46212 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
46148 AGTAAGTAAA
46158 AAAATAAATAAT
1 AAAATAAATAAT
*
46170 AAAATATAT-AT
1 AAAATAAATAAT
* *
46181 AAAA-AAAAAAG
1 AAAATAAATAAT
*
46192 AAAATAAATAAA
1 AAAATAAATAAT
46204 ACAAATAAA
1 A-AAATAAA
46213 CAAATAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 2 0.06
11 11 0.32
12 14 0.41
13 7 0.21
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:46197 original size:27 final size:28
Alignment explanation
Indices: 46132--46199 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 28
46122 TAAAATGAAG
46132 AAAGCAAAGATAAAATAGTAAGTAAAAAAA
1 AAAG-AAA-ATAAAATAGTAAGTAAAAAAA
* *
46162 TAA-ATAATAAAATA-TATA-TAAAAAAA
1 AAAGAAAATAAAATAGTA-AGTAAAAAAA
46188 AAAGAAAATAAA
1 AAAGAAAATAAA
46200 TAAAACAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
26 12 0.38
27 16 0.50
28 2 0.06
30 2 0.06
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (28 bp):
AAAGAAAATAAAATAGTAAGTAAAAAAA
Found at i:46266 original size:35 final size:31
Alignment explanation
Indices: 46216--46288 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 31
46206 AAATAAACAA
*
46216 ATAAT-AATAACAAAGTACGAATATATATATATAT
1 ATAATAAATAAAAAAGTA--AATATATATA-A-AT
46250 ATAATAAATAAAAAAGTAAATATATATAAAT
1 ATAATAAATAAAAAAGTAAATATATATAAAT
46281 -TAATAAAT
1 ATAATAAAT
46289 TAAATGACGA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 8 0.22
31 2 0.05
32 1 0.03
33 10 0.27
34 5 0.14
35 11 0.30
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (31 bp):
ATAATAAATAAAAAAGTAAATATATATAAAT
Found at i:46293 original size:35 final size:34
Alignment explanation
Indices: 46216--46280 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
46206 AAATAAACAA
* *
46216 ATAAT-AATAACAAAGTACGAATATATATATATAT
1 ATAATAAATAAAAAAGTAC-AATATATATAAATAT
46250 ATAATAAATAAAAAAGTA-AATATATATAAAT
1 ATAATAAATAAAAAAGTACAATATATATAAAT
46281 TAATAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 12 0.43
34 5 0.18
35 11 0.39
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (34 bp):
ATAATAAATAAAAAAGTACAATATATATAAATAT
Found at i:46564 original size:2 final size:2
Alignment explanation
Indices: 46518--46548 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46508 TTTGTGTAGA
46518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46549 GTAAAATGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46621 original size:23 final size:22
Alignment explanation
Indices: 46595--46662 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
46585 AAAATAAAAT
46595 AAATATAATATAATGATAATAAA
1 AAATATAATATAAT-ATAATAAA
*
46618 AAATATAA-AAAAT-TAATAGAA
1 AAATATAATATAATATAATA-AA
* *
46639 AAATATATGTATAATATTATAAA
1 AAATATA-ATATAATATAATAAA
46662 A
1 A
46663 TATAGCACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 5 0.14
21 9 0.24
22 4 0.11
23 15 0.41
24 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
AAATATAATATAATATAATAAA
Found at i:46797 original size:12 final size:11
Alignment explanation
Indices: 46769--46809 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
46759 TAACAAAATA
* *
46769 AATAATATAAA
1 AATAATACAAG
46780 AATAATACAAG
1 AATAATACAAG
46791 TAATAATACAAG
1 -AATAATACAAG
46803 AATAATA
1 AATAATA
46810 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:46855 original size:27 final size:28
Alignment explanation
Indices: 46826--46878 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
46816 AAGAGAAAGA
46826 AAAAAATTATA-ATA-ATAATA-AAATAT
1 AAAAAA-TATACATATATAATATAAATAT
46852 AAAAAATATACATATATAATATAAATA
1 AAAAAATATACATATATAATATAAATA
46879 AGTAGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 4 0.17
26 9 0.38
27 6 0.25
28 5 0.21
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAAAATATACATATATAATATAAATAT
Found at i:46915 original size:12 final size:12
Alignment explanation
Indices: 46893--46947 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
46883 GAATAAAAGG
*
46893 AAAATATAATAGT
1 AAAA-ATAATAAT
46906 AAAAATAATAAT
1 AAAAATAATAAT
* *
46918 AAATATAATAGT
1 AAAAATAATAAT
* *
46930 AATAATAAAAAT
1 AAAAATAATAAT
46942 AAAAAT
1 AAAAAT
46948 GCAAAGAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
12 30 0.88
13 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:46921 original size:24 final size:24
Alignment explanation
Indices: 46894--46944 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
46884 AATAAAAGGA
*
46894 AAATATAATAGTAAAAATAATAAT
1 AAATATAATAGTAAAAATAAAAAT
*
46918 AAATATAATAGTAATAATAAAAAT
1 AAATATAATAGTAAAAATAAAAAT
46942 AAA
1 AAA
46945 AATGCAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (24 bp):
AAATATAATAGTAAAAATAAAAAT
Found at i:47531 original size:37 final size:37
Alignment explanation
Indices: 47490--47587 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 37
47480 GTGCTTGTGG
* *
47490 ATCCTATTTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAAGAGTTTAAATCATAGAAAAACTCT
* * *
47527 ATCCTATTTTTAGGAGTTTAAATAATAGAAAAATTCT
1 ATCCTATTTTTAAGAGTTTAAATCATAGAAAAACTCT
* *
47564 ATCCTATTTTTAAAAGTTTGAATC
1 ATCCTATTTTTAAGAGTTTAAATC
47588 CTTATAGGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTAAATCATAGAAAAACTCT
Found at i:49779 original size:15 final size:14
Alignment explanation
Indices: 49759--49866 Score: 55
Period size: 13 Copynumber: 7.6 Consensus size: 14
49749 CAATAATTAA
*
49759 AATAATGTATTTTAT
1 AATAATATA-TTTAT
49774 AATAATATATTTAT
1 AATAATATATTTAT
* *
49788 AATTATTTA-TTAT
1 AATAATATATTTAT
* *
49801 ATTTAA-ATTTTTA-
1 A-ATAATATATTTAT
49814 AATTAATATATTTTTAT
1 AA-TAATATA--TTTAT
** *
49831 AATTTTAATAATTA-
1 AATAAT-ATATTTAT
49845 AATAATATATTT-T
1 AATAATATATTTAT
49858 AATAATATA
1 AATAATATA
49867 AAATAAAAAT
Statistics
Matches: 69, Mismatches: 15, Indels: 20
0.66 0.14 0.19
Matches are distributed among these distances:
13 24 0.35
14 23 0.33
15 11 0.16
16 6 0.09
17 5 0.07
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (14 bp):
AATAATATATTTAT
Found at i:49818 original size:19 final size:19
Alignment explanation
Indices: 49779--49813 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49769 TTTATAATAA
49779 TATATTTATAATTATTTAT
1 TATATTTATAATTATTTAT
49798 TATATTTA-AATT-TTTA
1 TATATTTATAATTATTTA
49814 AATTAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTTATAATTATTTAT
Found at i:49864 original size:43 final size:44
Alignment explanation
Indices: 49750--49866 Score: 109
Period size: 43 Copynumber: 2.7 Consensus size: 44
49740 AATATTTTAC
*
49750 AATAATTAAAATAATGTATTTT-ATAATAATATATTTATAATTATT
1 AATAATT-AAATAATATATTTTAATAAT-ATATATTTATAATTATT
* * ** *
49795 TATTA-TATTTAA-AT-TTTTAAATTAATATATTTTTATAATT-TT
1 AATAATTAAATAATATATTTT-AA-TAATATATATTTATAATTATT
49837 AATAATTAAATAATATATTTTAATAATATA
1 AATAATTAAATAATATATTTTAATAATATA
49867 AAATAAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
41 4 0.07
42 6 0.11
43 30 0.54
44 9 0.16
45 7 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (44 bp):
AATAATTAAATAATATATTTTAATAATATATATTTATAATTATT
Found at i:49903 original size:2 final size:2
Alignment explanation
Indices: 49892--49920 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
49882 AAATATTAAT
49892 TA TA -A 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
49921 AAATATCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:52798 original size:22 final size:21
Alignment explanation
Indices: 52761--52801 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
52751 AATATTTAAT
*
52761 ATTTTTTGGTTTATTCGGTTA
1 ATTTTTTGGTTGATTCGGTTA
52782 ATTTTGTTGGTTGATTCGGT
1 ATTTT-TTGGTTGATTCGGT
52802 AAAAACCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.05, G:0.24, T:0.59
Consensus pattern (21 bp):
ATTTTTTGGTTGATTCGGTTA
Found at i:52843 original size:2 final size:2
Alignment explanation
Indices: 52836--52871 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52826 AAGCTAAATA
52836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52872 CGGTTAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57648 original size:225 final size:223
Alignment explanation
Indices: 57252--57695 Score: 748
Period size: 225 Copynumber: 2.0 Consensus size: 223
57242 AGACATAGTG
* *
57252 TTGAGTTAATCGATCGACGGAATCGGCCAAGAGGGGGGGTGAATTGGCAATTAAAATTTTGGTGG
1 TTGAGTTAATCGATCGACGGAATCGGCCAAGAGAGGGGGTGAATTGGCAATTAAAAATTTGGTGG
57317 AAGCTTTTGCAGAAAATTGAAAGTAATTGCACAGCGATTTAGAGTGGTTCGACTTTCTCAATCAA
66 AAGCTTTTGCAGAAAATTGAAAGTAATTGCACAGCGATTTAGAGTGGTTCGACTTTCTCAATCAA
* * *
57382 AGTTTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCTAACAAATTCACTAATTTATTCT
131 AGTCTACGTCCACTACCTTAGCTATCCACACTAAAGATTTTC-AACAAATTCACTAATTT-GTCT
*
57447 TTCTTTTGAGGCCAAAGAGATAACCTTCCTA
194 TTCTTTTGAGGACAAAGAG-TAACCTTCCTA
*
57478 TTGAGTTAATCGATTGACGGAATCGGCCAAGA-AGGGGGTGAATTGGCAATTAAAAATTTGGTGG
1 TTGAGTTAATCGATCGACGGAATCGGCCAAGAGAGGGGGTGAATTGGCAATTAAAAATTTGGTGG
57542 AAGCTTTTGCAGAAAATTGAAAGTAATTGCACAGCGATTTAGAGTGGTTCGACTTTCTCAA-CAA
66 AAGCTTTTGCAGAAAATTGAAAGTAATTGCACAGCGATTTAGAGTGGTTCGACTTTCTCAATC-A
* * *
57606 AAGTCTATGTCCACTACCTTAGCTATCCACACTAAAGATTTTCCATAAATTCACTAATTTGTCTT
130 AAGTCTACGTCCACTACCTTAGCTATCCACACTAAAGATTTTCAACAAATTCACTAATTTGTCTT
57671 TCTTTTGAGGACAAAGAGTAACCTT
195 TCTTTTGAGGACAAAGAGTAACCTT
57696 ACAAACCCTC
Statistics
Matches: 207, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
222 7 0.03
223 21 0.10
224 16 0.08
225 132 0.64
226 31 0.15
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (223 bp):
TTGAGTTAATCGATCGACGGAATCGGCCAAGAGAGGGGGTGAATTGGCAATTAAAAATTTGGTGG
AAGCTTTTGCAGAAAATTGAAAGTAATTGCACAGCGATTTAGAGTGGTTCGACTTTCTCAATCAA
AGTCTACGTCCACTACCTTAGCTATCCACACTAAAGATTTTCAACAAATTCACTAATTTGTCTTT
CTTTTGAGGACAAAGAGTAACCTTCCTA
Found at i:57971 original size:17 final size:17
Alignment explanation
Indices: 57949--57991 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
57939 TCTCTCTTGA
57949 TTCTAGTTGCTTGTTGT
1 TTCTAGTTGCTTGTTGT
*
57966 TTCTAGTTTCTTGTTGT
1 TTCTAGTTGCTTGTTGT
*
57983 TTCTTGTTG
1 TTCTAGTTG
57992 TTGATCAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.05, C:0.12, G:0.21, T:0.63
Consensus pattern (17 bp):
TTCTAGTTGCTTGTTGT
Found at i:59268 original size:18 final size:19
Alignment explanation
Indices: 59247--59284 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
59237 GATCCTCTGG
59247 TTGTGCTTGTTCCT-TTGC
1 TTGTGCTTGTTCCTCTTGC
59265 TTGTGCTTGTTCCTCTTGC
1 TTGTGCTTGTTCCTCTTGC
59284 T
1 T
59285 GTTCTGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.00, C:0.24, G:0.21, T:0.55
Consensus pattern (19 bp):
TTGTGCTTGTTCCTCTTGC
Found at i:59294 original size:18 final size:18
Alignment explanation
Indices: 59247--59294 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
59237 GATCCTCTGG
*
59247 TTGTGCTTGTTCCTTTGC
1 TTGTGCTGGTTCCTTTGC
*
59265 TTGTGCTTGTTCCTCTTGC
1 TTGTGCTGGTTCCT-TTGC
*
59284 -TGTTCTGGTTC
1 TTGTGCTGGTTC
59295 ATCGTCGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.00, C:0.23, G:0.23, T:0.54
Consensus pattern (18 bp):
TTGTGCTGGTTCCTTTGC
Found at i:60919 original size:22 final size:22
Alignment explanation
Indices: 60845--60925 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
60835 TGAACCCTTG
*
60845 GGGGGTATCGATTCCCC-T-AA
1 GGGGGAATCGATTCCCCTTCAA
*
60865 GGGGGAATC-AGTTCCCATTCAAA
1 GGGGGAATCGA-TTCCCCTTC-AA
* *
60888 GGGGGAATCGGTTCCCCTTCAT
1 GGGGGAATCGATTCCCCTTCAA
*
60910 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
60926 TCTGCCCTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.02
20 13 0.27
21 1 0.02
22 15 0.31
23 19 0.39
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:67081 original size:22 final size:21
Alignment explanation
Indices: 67039--67078 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
67029 GAGTTTATTT
*
67039 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
67060 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
67079 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:69043 original size:18 final size:18
Alignment explanation
Indices: 69020--69056 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
69010 GTGCACTAAG
69020 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGTTTCA
69038 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGTTTCA
69056 A
1 A
69057 AATAGCCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (18 bp):
AGTGCATTCGATGTTTCA
Found at i:69112 original size:64 final size:63
Alignment explanation
Indices: 69021--69231 Score: 194
Period size: 65 Copynumber: 3.3 Consensus size: 63
69011 TGCACTAAGA
** * * *
69021 GTGCATTCGATGTTTCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATACATGGCTG
1 GTGCA-TCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
** * *
69086 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATAGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
69150 T
63 G
* ** *
69151 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--
69214 TG
62 TG
69216 GTGCATCGATGCATCA
1 GTGCATCGATGCATCA
69232 CTTTGATAAA
Statistics
Matches: 118, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 39 0.33
65 70 0.59
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:69657 original size:22 final size:22
Alignment explanation
Indices: 69629--69676 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
69619 GTTCCATAAT
69629 TTTTAACCTT-GAAATTTTAAAA
1 TTTTAA-CTTCGAAATTTTAAAA
69651 TTTTAACTTCGAAATTTTAAAA
1 TTTTAACTTCGAAATTTTAAAA
69673 TTTT
1 TTTT
69677 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTTAACTTCGAAATTTTAAAA
Found at i:70539 original size:22 final size:22
Alignment explanation
Indices: 70511--70559 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
70501 AAAGATTAGA
70511 CAATCGTAAATGTCTATTTTGC
1 CAATCGTAAATGTCTATTTTGC
70533 CAATCGTAAATGTCTATTTTGC
1 CAATCGTAAATGTCTATTTTGC
70555 CAATC
1 CAATC
70560 ATATATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (22 bp):
CAATCGTAAATGTCTATTTTGC
Done.