Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006587.1 Hibiscus syriacus cultivar Beakdansim tig00016150_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: 103995
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2712 original size:2 final size:2
Alignment explanation
Indices: 2705--2733 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2695 AGTTAGATTT
2705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2734 TTCAATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4166 original size:2 final size:2
Alignment explanation
Indices: 4154--4186 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4144 TCTCCGTTAG
*
4154 CT CT AT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4187 GAACTTCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:16288 original size:30 final size:30
Alignment explanation
Indices: 16217--16355 Score: 100
Period size: 30 Copynumber: 4.6 Consensus size: 30
16207 AACGAGGATA
*
16217 TAATCTCATGCAGATGTCAGAATGTATAAT
1 TAATCTCATGCAGATGTCAGAATGTAAAAT
* * *
16247 CAATCCCATGCAGATGTTAGAATG-AGAAAT
1 TAATCTCATGCAGATGTCAGAATGTA-AAAT
* * * * **
16277 TAATCTAATGCAAATGTCAAAACGGGAAAT
1 TAATCTCATGCAGATGTCAGAATGTAAAAT
* * * * * **
16307 TTATTTCGTACAGAAGTCAGAATGGGAAAT
1 TAATCTCATGCAGATGTCAGAATGTAAAAT
*
16337 TAATCCCATGCAGATGTCA
1 TAATCTCATGCAGATGTCA
16356 AAACGGGGAA
Statistics
Matches: 80, Mismatches: 27, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
29 1 0.01
30 79 0.99
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (30 bp):
TAATCTCATGCAGATGTCAGAATGTAAAAT
Found at i:17097 original size:14 final size:14
Alignment explanation
Indices: 17078--17112 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
17068 AAATAAATTT
17078 TATTTTTAA-AAAA
1 TATTTTTAAGAAAA
17091 TATTTTTAAGAAAA
1 TATTTTTAAGAAAA
17105 TATTTTTA
1 TATTTTTA
17113 GTGTTAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
TATTTTTAAGAAAA
Found at i:18191 original size:28 final size:28
Alignment explanation
Indices: 18151--18216 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
18141 TCCAAACCCG
18151 ACCCGACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
18179 ACCCGACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
*
18207 ACCCAACCCG
1 ACCCGACCCG
18217 CTCGACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.44, C:0.36, G:0.08, T:0.12
Consensus pattern (28 bp):
ACCCGACCCGAATATCACACTTAAAAAA
Found at i:20596 original size:32 final size:32
Alignment explanation
Indices: 20560--20620 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
20550 GACTTGAATA
*
20560 CCTAAAA-GGATAACGTTTGTAGCGTTAGGGTG
1 CCTAAAAGGGA-AACGTTTGTAACGTTAGGGTG
20592 CCTAAAAGGGAAACGTTTGTAACGTTAGG
1 CCTAAAAGGGAAACGTTTGTAACGTTAGG
20621 CACCCTGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (32 bp):
CCTAAAAGGGAAACGTTTGTAACGTTAGGGTG
Found at i:21033 original size:21 final size:21
Alignment explanation
Indices: 21009--21082 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
20999 ACGTTGCATT
*
21009 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
** ** **
21030 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
21050 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
21071 TCGCGTTGCGAT
1 TCGCGTTGCGAT
21083 TTTCCATTTC
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:21050 original size:41 final size:41
Alignment explanation
Indices: 21005--21107 Score: 188
Period size: 41 Copynumber: 2.5 Consensus size: 41
20995 ATTCACGTTG
* *
21005 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
21046 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
21087 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTG
21108 GTCATTTTCG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:21101 original size:20 final size:20
Alignment explanation
Indices: 21030--21102 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
21020 TAGTTGAAAA
*
21030 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
21050 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
21071 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
21091 TCGCGTTGCGAT
1 TCGCGTTGCGAT
21103 AGTTGGTCAT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:21278 original size:17 final size:17
Alignment explanation
Indices: 21256--21289 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21246 AATTTTCTAG
21256 GAATCCGACACTTTGGT
1 GAATCCGACACTTTGGT
21273 GAATCCGACACTTTGGT
1 GAATCCGACACTTTGGT
21290 TCAATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (17 bp):
GAATCCGACACTTTGGT
Found at i:23366 original size:16 final size:18
Alignment explanation
Indices: 23335--23368 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
23325 CAAATAATTA
23335 ATCACATACATTATATTT
1 ATCACATACATTATATTT
23353 ATCA-ATAC-TTATATTT
1 ATCACATACATTATATTT
23369 TGTAAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (18 bp):
ATCACATACATTATATTT
Found at i:23764 original size:37 final size:37
Alignment explanation
Indices: 23713--23788 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
23703 TGTCAATCAA
* *
23713 ACCCGACTCGAAAA-TATACACCATCCACCCGAACTCG
1 ACCCGACCCAAAAATTATACACCATCCACCCG-ACTCG
* * *
23750 ACCCGACCCAAAAATTTTATACCCTCCACCCGACTCG
1 ACCCGACCCAAAAATTATACACCATCCACCCGACTCG
23787 AC
1 AC
23789 ACGAAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 19 0.58
38 14 0.42
ACGTcount: A:0.33, C:0.42, G:0.09, T:0.16
Consensus pattern (37 bp):
ACCCGACCCAAAAATTATACACCATCCACCCGACTCG
Found at i:26101 original size:78 final size:78
Alignment explanation
Indices: 25972--26129 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
25962 TCACGTTATA
25972 CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
1 CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
26037 AAAGACACATAAT
66 AAAGACACATAAT
26050 CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
1 CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
26115 AAAGACACATAAT
66 AAAGACACATAAT
26128 CA
1 CA
26130 GCAAAATTAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.19
Consensus pattern (78 bp):
CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
AAAGACACATAAT
Found at i:28902 original size:17 final size:16
Alignment explanation
Indices: 28880--28912 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
28870 TGTAATTAAT
28880 TAAACTCAAATTCTTTA
1 TAAACTCAAATT-TTTA
28897 TAAACTCAAATTTTTA
1 TAAACTCAAATTTTTA
28913 AAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAACTCAAATTTTTA
Found at i:31069 original size:125 final size:122
Alignment explanation
Indices: 30833--31195 Score: 380
Period size: 125 Copynumber: 3.0 Consensus size: 122
30823 GATGAACAAC
* * * *
30833 AAACTAGACTAATGC-CGGAAA-TTGTGATCCGGCAACAATAATCAGTCTAAATAGCAGCCATGA
1 AAACTAAACTAATGCTC--AAAGTTGTGATCCGACAACAACAATCAGTC-AAATTGCAGCCAT-A
* * * * * *
30896 ATAACTTGAAACGAGATCAAAGAGTTTCCATATCTATTAAACCATGGTCCAGAAAACTATACT
62 AGAACTTGAAACAAGATCAAAGAGTTTCCATATCTATTCAACCATGGTCAAG-AAACAAGA-T
*
30959 AAACTAAACTAATGCTCAAAGTTGTGATCCAACAACAACAATCAGTCAAAATTGCAGCCATAAGA
1 AAACTAAACTAATGCTCAAAGTTGTGATCCGACAACAACAATCAGTC-AAATTGCAGCCATAAGA
**
31024 ACTTGAAACAAGATCAAAGAGTTTCCATATCTATTCAACCATGGTCAAGACTCAAGAT
65 ACTTGAAACAAGATCAAAGAGTTTCCATATCTATTCAACCATGGTCAAGAAACAAGAT
* *** *
31082 -AACTAAACTAATGCTCAAAGTTATGATCCGACATTGACGATCAG-C-AATTAAG-AGCCATAAG
1 AAACTAAACTAATGCTCAAAGTTGTGATCCGACAACAACAATCAGTCAAATT--GCAGCCATAAG
* * * * *
31143 AACTTGAAACAAGATCAAAAAGCTTCCATTTCCATTCAAACC-TGGTTAAGAAA
64 AACTTGAAACAAGATCAAAGAGTTTCCATATCTATTC-AACCATGGTCAAGAAA
31196 ACAGTAACTA
Statistics
Matches: 205, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
119 4 0.02
120 50 0.24
121 6 0.03
122 38 0.19
123 1 0.00
124 4 0.02
125 52 0.25
126 49 0.24
127 1 0.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (122 bp):
AAACTAAACTAATGCTCAAAGTTGTGATCCGACAACAACAATCAGTCAAATTGCAGCCATAAGAA
CTTGAAACAAGATCAAAGAGTTTCCATATCTATTCAACCATGGTCAAGAAACAAGAT
Found at i:31180 original size:120 final size:124
Alignment explanation
Indices: 30865--31198 Score: 376
Period size: 120 Copynumber: 2.7 Consensus size: 124
30855 TGTGATCCGG
* * * *
30865 CAACAATAATCAGTCTAAATAGCAGCCATGAATAACTTGAAACGAGATCAAAGAGTTTCCATATC
1 CAACAACAATCAGTCAAAAT-GCAGCCAT-AAGAACTTGAAACAAGATCAAAGAGTTTCCATATC
* * * * *
30930 TATTAAACCATGGTCCAGAAAACTATACTAAACTAAACTAATGCTCAAAGTTGTGATCCAA
64 TATTCAACCATGGTCAAGAAAACAAGACTAAACTAAACTAATGCTCAAAGTTATGATCCAA
30991 CAACAACAATCAGTCAAAATTGCAGCCATAAGAACTTGAAACAAGATCAAAGAGTTTCCATATCT
1 CAACAACAATCAGTCAAAA-TGCAGCCATAAGAACTTGAAACAAGATCAAAGAGTTTCCATATCT
** *
31056 ATTCAACCATGGTCAAG-ACTCAAGA-T-AACTAAACTAATGCTCAAAGTTATGATCCGA
65 ATTCAACCATGGTCAAGAAAACAAGACTAAACTAAACTAATGCTCAAAGTTATGATCCAA
*** * * * *
31113 CATTGACGATCAG-CAATTAA-G-AGCCATAAGAACTTGAAACAAGATCAAAAAGCTTCCATTTC
1 CAACAACAATCAGTCAA--AATGCAGCCATAAGAACTTGAAACAAGATCAAAGAGTTTCCATATC
* *
31175 CATTCAAACC-TGGTTAAGAAAACA
64 TATTC-AACCATGGTCAAGAAAACA
31199 GTAACTAACA
Statistics
Matches: 180, Mismatches: 23, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
120 49 0.27
121 11 0.06
122 38 0.21
123 3 0.02
124 4 0.02
125 49 0.27
126 25 0.14
127 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (124 bp):
CAACAACAATCAGTCAAAATGCAGCCATAAGAACTTGAAACAAGATCAAAGAGTTTCCATATCTA
TTCAACCATGGTCAAGAAAACAAGACTAAACTAAACTAATGCTCAAAGTTATGATCCAA
Found at i:33002 original size:21 final size:21
Alignment explanation
Indices: 32976--33015 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32966 TCTAATTTTG
32976 CCAATAAACAAGTCACCTTTA
1 CCAATAAACAAGTCACCTTTA
* *
32997 CCAATAATCAATTCACCTT
1 CCAATAAACAAGTCACCTT
33016 GACCGACTTT
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:0.40, C:0.30, G:0.03, T:0.28
Consensus pattern (21 bp):
CCAATAAACAAGTCACCTTTA
Found at i:34741 original size:4 final size:4
Alignment explanation
Indices: 34732--34804 Score: 75
Period size: 4 Copynumber: 19.5 Consensus size: 4
34722 GAAGAAGAAG
34732 AGGA AGGA AGGA AGGA AGGA A-GA AGGA AGGA A-GA AGGA AGGA A-GA
1 AGGA AGGA AGGA AGGA AGGA AGGA AGGA AGGA AGGA AGGA AGGA AGGA
* * * *
34777 A-GA AAGA AAGA AAGA A-GA AGAA AGGA AG
1 AGGA AGGA AGGA AGGA AGGA AGGA AGGA AG
34805 AAAGAATAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
3 15 0.24
4 48 0.76
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (4 bp):
AGGA
Found at i:34756 original size:15 final size:15
Alignment explanation
Indices: 34734--34810 Score: 86
Period size: 15 Copynumber: 5.2 Consensus size: 15
34724 AGAAGAAGAG
34734 GAAGGAAGGAAGGAA
1 GAAGGAAGGAAGGAA
34749 GGAA-GAAGGAAGGAA
1 -GAAGGAAGGAAGGAA
34764 GAAGGAAGGAA-GAA
1 GAAGGAAGGAAGGAA
* * *
34778 GAAAGAAAGAAAGAA
1 GAAGGAAGGAAGGAA
* *
34793 GAAGAAAGGAAGAAA
1 GAAGGAAGGAAGGAA
34808 GAA
1 GAA
34811 TAAGAGGAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
14 15 0.29
15 34 0.65
16 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (15 bp):
GAAGGAAGGAAGGAA
Found at i:34758 original size:11 final size:11
Alignment explanation
Indices: 34719--34810 Score: 102
Period size: 11 Copynumber: 8.5 Consensus size: 11
34709 GAGTGTGTGA
34719 GAAGAA-GAA-
1 GAAGAAGGAAG
34728 GAAG-AGGAAG
1 GAAGAAGGAAG
34738 GAAGGAAGGAAG
1 GAA-GAAGGAAG
34750 GAAGAAGGAAG
1 GAAGAAGGAAG
34761 GAAGAAGGAAG
1 GAAGAAGGAAG
*
34772 GAAGAAGAAAG
1 GAAGAAGGAAG
* *
34783 AAAGAAAGAA-
1 GAAGAAGGAAG
34793 GAAGAAAGGAAG
1 GAAG-AAGGAAG
*
34805 AAAGAA
1 GAAGAA
34811 TAAGAGGAGG
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
8 1 0.01
9 7 0.10
10 6 0.09
11 44 0.63
12 12 0.17
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (11 bp):
GAAGAAGGAAG
Found at i:37362 original size:35 final size:35
Alignment explanation
Indices: 37289--37363 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
37279 CGTCACTAAC
**
37289 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
* *
37324 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
37359 AGTAA
1 AGTAA
37364 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.29, G:0.29, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:37451 original size:24 final size:24
Alignment explanation
Indices: 37424--37534 Score: 82
Period size: 24 Copynumber: 4.7 Consensus size: 24
37414 TATAGCAAAA
*
37424 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
37448 ATCATATCAGAATTCAGGTCATGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
37472 ATCAGATCAGAATCCATGTCAA-T
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
37495 ATCATATCAGAATCCAGGTCAA-T
1 ATCAAAACAGAATTCAAGTCAAGT
*
37518 ATCATAACAGAATTCAA
1 ATCAAAACAGAATTCAA
37535 ATTTGAAATC
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
23 36 0.49
24 37 0.51
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (24 bp):
ATCAAAACAGAATTCAAGTCAAGT
Found at i:37503 original size:23 final size:23
Alignment explanation
Indices: 37441--37530 Score: 117
Period size: 23 Copynumber: 3.8 Consensus size: 23
37431 CATAATTCAA
*
37441 GTCAAGTATCATATCAGAATTCAG
1 GTCAA-TATCATATCAGAATCCAG
* * *
37465 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCATATCAGAATCCAG
37489 GTCAATATCATATCAGAATCCAG
1 GTCAATATCATATCAGAATCCAG
*
37512 GTCAATATCATAACAGAAT
1 GTCAATATCATATCAGAAT
37531 TCAAATTTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 34 0.60
24 23 0.40
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (23 bp):
GTCAATATCATATCAGAATCCAG
Found at i:38616 original size:18 final size:18
Alignment explanation
Indices: 38595--38630 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38585 CTGCCATCCG
*
38595 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
38613 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
38631 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:39940 original size:7 final size:7
Alignment explanation
Indices: 39926--39956 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
39916 TGGTCAACGT
39926 CGGTCAA
1 CGGTCAA
*
39933 CAGTCAA
1 CGGTCAA
39940 CGGTCAA
1 CGGTCAA
39947 CGGTCAA
1 CGGTCAA
39954 CGG
1 CGG
39957 GTCGGGTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:39971 original size:18 final size:18
Alignment explanation
Indices: 39948--40017 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
39938 AACGGTCAAC
39948 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
39966 GGTCAACGGGT----T-G
1 GGTCAACGGGTCGGGTCG
* *
39979 GGTAAACGGGTCAGGTCG
1 GGTCAACGGGTCGGGTCG
39997 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
40015 GGT
1 GGT
40018 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
13 11 0.25
14 1 0.02
17 1 0.02
18 31 0.70
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:39990 original size:31 final size:31
Alignment explanation
Indices: 39952--40012 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
39942 GTCAACGGTC
* *
39952 AACGGGTCGGGTCGGGTCAACGGGTTGGGTA
1 AACGGGTCAGGTCGGGTCAACGGGTCGGGTA
39983 AACGGGTCAGGTCGGGTCAACGGGTCGGGT
1 AACGGGTCAGGTCGGGTCAACGGGTCGGGT
40013 CGGGTTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.18, G:0.48, T:0.18
Consensus pattern (31 bp):
AACGGGTCAGGTCGGGTCAACGGGTCGGGTA
Found at i:44562 original size:156 final size:159
Alignment explanation
Indices: 44366--44666 Score: 468
Period size: 156 Copynumber: 1.9 Consensus size: 159
44356 GCATGTGTTT
*
44366 AAATTTAGTAAAAAAATGAACTTAAAATAAATGACAAATTGAA-AGAATAAGGAGGTTATGAAAA
1 AAATTTAGTAAAAAAATGAACTTAAAATAAATGACAAATTGAAGA-AATAAGGAGATTATGAAAA
* *
44430 ATTGAAGGATTAAATTTAAAAATAAAAAA-TTGTTATCAAAAAGAAGAATTGAAATTACACAT-A
65 ATTGAAGGATTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAAGAATTGAAAATACACATGA
*
44493 TATTTTACTACGGTTTAAGAACATGTGGCTC
130 -ATTATACTACGGTTTAAGAACATGTGGCTC
*
44524 AAATTTGGT-AAAAAATG-ACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATGAAAAA
1 AAATTTAGTAAAAAAATGAACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATGAAAAA
* * *
44587 TTGAAGGATTAAATTGAAAAATAAAAAATTTGTTATTAAAAAGAAGGATTGAAAATATACATGAA
66 TTGAAGGATTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAAGAATTGAAAATACACATGAA
*
44652 TTATACTATGGTTTA
131 TTATACTACGGTTTA
44667 GGATATGCCT
Statistics
Matches: 131, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
156 70 0.53
157 52 0.40
158 9 0.07
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (159 bp):
AAATTTAGTAAAAAAATGAACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATGAAAAA
TTGAAGGATTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAAGAATTGAAAATACACATGAA
TTATACTACGGTTTAAGAACATGTGGCTC
Found at i:45210 original size:24 final size:24
Alignment explanation
Indices: 45178--45235 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
45168 AACATAAATG
* *
45178 AACGAACATAAACGAATGAAA-GTA
1 AACGAACATAAACG-ATCAAACATA
*
45202 AACGAACATAAATGATCAAACATA
1 AACGAACATAAACGATCAAACATA
45226 AACGAACATA
1 AACGAACATA
45236 TTATCGAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.14
Consensus pattern (24 bp):
AACGAACATAAACGATCAAACATA
Found at i:45922 original size:31 final size:31
Alignment explanation
Indices: 45887--45973 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
45877 TACACCGAGG
*
45887 CACCTAGAGTGGTAACGTTTGTAATGTCAGA
1 CACCTAAAGTGGTAACGTTTGTAATGTCAGA
* *
45918 CACCTAAAGTGGTAACGTTTGTAACGTCAGG
1 CACCTAAAGTGGTAACGTTTGTAATGTCAGA
* *
45949 CGCCTAAAGTGGTAACGTTTATAAT
1 CACCTAAAGTGGTAACGTTTGTAAT
45974 TTTGGGAAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (31 bp):
CACCTAAAGTGGTAACGTTTGTAATGTCAGA
Found at i:46651 original size:20 final size:21
Alignment explanation
Indices: 46601--46651 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
46591 ATATACATAT
46601 TATATATA-TTATATATGTAA
1 TATATATATTTATATATGTAA
46621 TAT-TATTATTTAT-TAATG-AA
1 TATATA-TATTTATAT-ATGTAA
46641 TATATATATTT
1 TATATATATTT
46652 TGACATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 9 0.33
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATATTTATATATGTAA
Found at i:47711 original size:16 final size:16
Alignment explanation
Indices: 47681--47710 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47671 AAAAAATAAA
47681 AAAAAATAATGAAAAT
1 AAAAAATAATGAAAAT
47697 AAAAAATAA-GAAAA
1 AAAAAATAATGAAAA
47711 AATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAAAATAATGAAAAT
Found at i:47825 original size:8 final size:8
Alignment explanation
Indices: 47812--47849 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
47802 ACAAAATGTG
47812 TACATATA
1 TACATATA
47820 TACATATA
1 TACATATA
*
47828 TATATATA
1 TACATATA
47836 TA-ATATA
1 TACATATA
47843 -ACATATA
1 TACATATA
47850 AGTGAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:54103 original size:106 final size:105
Alignment explanation
Indices: 53834--54401 Score: 983
Period size: 106 Copynumber: 5.4 Consensus size: 105
53824 AGGTTTTACC
* *
53834 CAGAGCCAATTTCAACCTCCCAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
53899 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
53939 CCGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTCCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
54004 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
54044 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
54109 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
54150 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
54215 ACGAAGGGACCGCTGGTTGTCAACAAACATCTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAT-TTCTCAATTT
* *
54256 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* * *
54321 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* ** *
54362 CAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
54402 GGAACAATAC
Statistics
Matches: 444, Mismatches: 16, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
105 195 0.44
106 247 0.56
107 2 0.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:54199 original size:211 final size:211
Alignment explanation
Indices: 53834--54401 Score: 985
Period size: 211 Copynumber: 2.7 Consensus size: 211
53824 AGGTTTTACC
* *
53834 CAGAGCCAATTTCAACCTCCCAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
53899 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCCGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
53964 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTCCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTCCACGACGAAGGGACCGCTGGTTGTCAACA
54029 AACAT-TTCTCAATCT
196 AACATCTTCTCAATCT
54044 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
54109 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
*
54174 GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
130 GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTCCACGACGAAGGGACCGCTGGTTGTCAAC
*
54239 AAACATCTTCTCAATTT
195 AAACATCTTCTCAATCT
* *
54256 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* * * * **
54321 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGGC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
*
54386 GGAGGATATTGGACTC
130 GAAGGATATTGGACTC
54402 GGAACAATAC
Statistics
Matches: 341, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
210 1 0.00
211 285 0.84
212 55 0.16
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (211 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGTAAGTTCAACTCCACGACGAAGGGACCGCTGGTTGTCAACA
AACATCTTCTCAATCT
Found at i:56537 original size:8 final size:8
Alignment explanation
Indices: 56502--56539 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
56492 TTATTTCACT
56502 TATATGT-
1 TATATGTA
56509 TATAT-TA
1 TATATGTA
*
56516 TATATATA
1 TATATGTA
56524 TATATGTA
1 TATATGTA
56532 TATATGTA
1 TATATGTA
56540 CACATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:56653 original size:15 final size:16
Alignment explanation
Indices: 56633--56664 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56623 TATATATATA
56633 TATTTTC-TTATTTTT
1 TATTTTCATTATTTTT
56648 TATTTTCATTATTTTT
1 TATTTTCATTATTTTT
56664 T
1 T
56665 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (16 bp):
TATTTTCATTATTTTT
Found at i:56659 original size:44 final size:44
Alignment explanation
Indices: 56574--56660 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
56564 CTTTACTTCT
* *
56574 TTATTATTATATTTATTTACATTATTTTTTGTTCTCTATTATTG
1 TTATTATTATATATATTTACATTATTTTTTATTCTCTATTATTG
* *
56618 TTATATATATATATATATTTTC-TTATTTTTTATTTTC-ATTATT
1 TTAT-TAT-TATATATATTTACATTATTTTTTATTCTCTATTATT
56661 TTTTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 10 0.27
45 16 0.43
46 11 0.30
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (44 bp):
TTATTATTATATATATTTACATTATTTTTTATTCTCTATTATTG
Found at i:58469 original size:16 final size:17
Alignment explanation
Indices: 58450--58482 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
58440 ATTATATAAT
58450 TTTTTTA-AAAAAAATA
1 TTTTTTACAAAAAAATA
58466 -TTTTTACAAAAAAATA
1 TTTTTTACAAAAAAATA
58482 T
1 T
58483 AATATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 3
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTTTACAAAAAAATA
Found at i:58643 original size:29 final size:28
Alignment explanation
Indices: 58599--58695 Score: 113
Period size: 31 Copynumber: 3.2 Consensus size: 28
58589 AAATATATAA
58599 TATATAATTTTTAAAATATTTTTGAAAAT
1 TATAT-ATTTTTAAAATATTTTTGAAAAT
* *
58628 TATATGGTTTTAAAAAAATATTTTTGAAAAT
1 TATAT-ATTTT--TAAAATATTTTTGAAAAT
*
58659 TATATATATTTTAAAATATTTTTGGAAATT
1 TATATAT-TTTTAAAATATTTTT-GAAAAT
58689 TATATAT
1 TATATAT
58696 AATTTTTAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
29 20 0.34
30 13 0.22
31 25 0.43
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (28 bp):
TATATATTTTTAAAATATTTTTGAAAAT
Found at i:58751 original size:9 final size:10
Alignment explanation
Indices: 58721--58790 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 10
58711 CGGTTTTAAA
58721 ATATA-TATT
1 ATATATTATT
*
58730 ATATAGTTTTT
1 ATATA-TTATT
58741 ATAT-TTATT
1 ATATATTATT
58750 AT-TATTATT
1 ATATATTATT
* *
58759 ATTTATTATC
1 ATATATTATT
58769 ACTATTATTATT
1 A-TA-TATTATT
58781 A-ATATT-TT
1 ATATATTATT
58789 AT
1 AT
58791 TACTTATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
8 4 0.08
9 22 0.45
10 8 0.16
11 8 0.16
12 7 0.14
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (10 bp):
ATATATTATT
Found at i:58753 original size:3 final size:3
Alignment explanation
Indices: 58745--58798 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
58735 GTTTTTATAT
* * *
58745 TTA TTA TTA TTA TTA TTTA TTA TCA CTA TTA TTA TTA ATA TT- TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58790 TTA CTTA TT
1 TTA -TTA TT
58799 TTCTGTTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:58761 original size:16 final size:16
Alignment explanation
Indices: 58742--58791 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
58732 ATAGTTTTTA
58742 TATTTATTATTATTAT
1 TATTTATTATTATTAT
* *
58758 TATTTATTATCACTAT
1 TATTTATTATTATTAT
*
58774 TA-TTATTAATATT-T
1 TATTTATTATTATTAT
58788 TATT
1 TATT
58792 ACTTATTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 3 0.11
15 9 0.32
16 16 0.57
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATTATTATTAT
Found at i:59071 original size:16 final size:15
Alignment explanation
Indices: 59050--59079 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
59040 CCGGCCGAAA
59050 ATCCCGGGACTGACCC
1 ATCCCGGGA-TGACCC
59066 ATCCCGGGATGACC
1 ATCCCGGGATGACC
59080 GGCCTCAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:60367 original size:26 final size:26
Alignment explanation
Indices: 60313--60375 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
60303 TTGTATTTTA
* *
60313 TTTTGATTATTTTTTTTCTTTTCACT
1 TTTTTATTATTTCTTTTCTTTTCACT
***
60339 TTTATT-TTATTTCTTTTCTTTTTTGT
1 TTT-TTATTATTTCTTTTCTTTTCACT
60365 TTTTTATTATT
1 TTTTTATTATT
60376 AGTCTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 2 0.07
26 27 0.90
27 1 0.03
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (26 bp):
TTTTTATTATTTCTTTTCTTTTCACT
Found at i:60427 original size:9 final size:9
Alignment explanation
Indices: 60393--60430 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
60383 TTTACTAAAT
60393 TTTATTTATA
1 TTTA-TTATA
60403 TTTATT-TA
1 TTTATTATA
*
60411 TCTATTATA
1 TTTATTATA
60420 TTTATTATA
1 TTTATTATA
60429 TT
1 TT
60431 AATTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 14 0.56
10 4 0.16
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATTATA
Found at i:64728 original size:165 final size:161
Alignment explanation
Indices: 64319--65010 Score: 746
Period size: 165 Copynumber: 4.2 Consensus size: 161
64309 TAAACAAACT
* * *
64319 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCA
* * * * * * * *
64384 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACC
*** * * *
64449 TTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
127 CCCGAGTTCGATTACACTCAGCTCAAGGGCACATC
* * *
64484 ATTTGCAGCAT-AGTCTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAACT-TAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTC
* * *
64548 AGCTTCGAGGGCACATCATTTGCAGCATAG-TCTAAGTCAAGAAGGGCTATCTGCCAAAGACCCC
65 AGCTTCCAAGGCACATCATTTGCAGCATAGCT-TAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
64612 CGAGTTCGATTACACTCAGCTTCAAGGGCACATC
129 CGAGTTCGATTACACTCAGC-TCAAGGGCACATC
* * **** * *
64646 ATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTTAGTACGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGACTACA
64711 CTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
62 CTCAGCTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* *
64775 CCCGAATTCGATTACACTCAGCTTCGAGGGCACATC
127 CCCGAGTTCGATTACACTCAGC-TCAAGGGCACATC
* * * * * ***
64811 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAGAAGACCTTTGAGTTCGACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC--TG-CCA-AAGACCCCCGAGTTCGACTACA
*
64876 CTCAGC-T-CAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
62 CTCAGCTTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* *
64939 CCCCGAGTTCGATTACAATCAGCTCTAGGGCACATC
126 CCCCGAGTTCGATTACACTCAGCTCAAGGGCACATC
* * * * * *
64975 ATTTACATCATAGCTCAAGGCAAGAAGGGCTATCTG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG
65011 TCAACAAAAT
Statistics
Matches: 466, Mismatches: 48, Indels: 29
0.86 0.09 0.05
Matches are distributed among these distances:
161 24 0.05
162 45 0.10
163 4 0.01
164 51 0.11
165 315 0.68
166 25 0.05
167 2 0.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (161 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCA
GCTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCG
AGTTCGATTACACTCAGCTCAAGGGCACATC
Found at i:64759 original size:246 final size:246
Alignment explanation
Indices: 64319--64934 Score: 873
Period size: 246 Copynumber: 2.5 Consensus size: 246
64309 TAAACAAACT
* *
64319 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGC-TAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * * **
64384 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGAC
65 GCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAAGAC
*
64448 CTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGTCTAAGTCAAGAAGGG
130 CTTTGAGTACGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGTCTAAGTCAAGAAGGG
*
64513 CTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
195 CTATCTGCCAAAGACCCCCGAATTCGATTACACTCAGCTTCGAGGGCACATC
64565 ATTTGCAGCATAGTCTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAG-CTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
64630 GCTTCAAGGGCACATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGAC
65 GCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAAGAC
* *
64694 CTTTTAGTACGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAG-CTTAAGTCGAGAAG
130 CTTTGAGTACGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGTC-TAAGTCAAGAAG
64757 GGCTATCTGCCAAAGACCCCCGAATTCGATTACACTCAGCTTCGAGGGCACATC
193 GGCTATCTGCCAAAGACCCCCGAATTCGATTACACTCAGCTTCGAGGGCACATC
* * * * * *** *
64811 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAGAAGACCTTTGAGTTCGACTACA
1 ATTTGCAGCATAGCT-AAGTCAAGAAGGGCTATC--TG-CCA-AAGACCCCCGAGTTCGATTACA
* * * *
64876 CTCAGC-TCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
61 CTCAGCTTCAAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
64935 AGACCCCCGA
Statistics
Matches: 333, Mismatches: 28, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
245 3 0.01
246 246 0.74
247 7 0.02
248 2 0.01
249 51 0.15
250 24 0.07
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (246 bp):
ATTTGCAGCATAGCTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAG
CTTCAAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAAGACC
TTTGAGTACGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGTCTAAGTCAAGAAGGGC
TATCTGCCAAAGACCCCCGAATTCGATTACACTCAGCTTCGAGGGCACATC
Found at i:65057 original size:246 final size:243
Alignment explanation
Indices: 64341--65010 Score: 871
Period size: 246 Copynumber: 2.7 Consensus size: 243
64331 GCTTAAGTCG
* *
64341 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
1 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGC
* * *
64406 AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGC
66 AGCATAACTTAAGTCGAGAAGGGTTATC--TGACC-AAAGACCTTTGAGTTCGACTACGCTCAGC
*
64471 TCAACGGCACATCATTTGCAGCATAG-TCTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAG
128 TCAAAGGCACATCATTTGCAGCATAGCTC-AAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAG
* * *
64535 TTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGTCTAAGTCA
192 TTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATACTCTAAGGCA
*
64587 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGT
1 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGC
* *
64652 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTTAGTACGACTACGCTCAGC
66 AGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACCTTTGAGTTCGACTACGCTCAGC
* * * *
64717 TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAAT
128 TCAAAGGCACATCATTTGCAGCATAGCTCAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGT
*
64782 TCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTC-AAGGCT
193 TCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCAT-ACTCTAAGGCA
* *** * *
64833 AGAAGGGTTATCTGTGACCAGAAGACCTTTGAGTTCGACTACACTCAGC-TCAACGGCACATCAT
1 AGAAGGGCTATC--TG-CCA-AAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCAT
* * * *** * **
64897 TTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACAATCAG
62 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAG
* * * * *
64961 CTCTAGGGCACATCATTTACATCATAGCTCAAGGCAAGAAGGGCTATCTG
127 CTCAAAGGCACATCATTTGCAGCATAGCTCAAGTCAAGAAGGGCTATCTG
65011 TCAACAAAAT
Statistics
Matches: 373, Mismatches: 42, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
244 2 0.01
245 65 0.17
246 226 0.61
247 7 0.02
248 2 0.01
249 47 0.13
250 24 0.06
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (243 bp):
AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGC
AGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCA
AAGGCACATCATTTGCAGCATAGCTCAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCG
ATTACACTCAGCTTCGAGGGCACATCATTTACAGCATACTCTAAGGCA
Found at i:65640 original size:38 final size:35
Alignment explanation
Indices: 65569--65818 Score: 159
Period size: 38 Copynumber: 6.6 Consensus size: 35
65559 TATATTTTCG
*
65569 AAAACATTTTG-AAAATATATAATATATAGTTTTT
1 AAAACATTTTGAAAAATATATAATATATAATTTTT
*
65603 AAAACATTTTGAAAACATTTATATATTATATAATTTTTTTTTT
1 AAAACATTTTGAAAA-A--TATATAATATATAA-----TTTTT
** * *
65646 AAAA-ATATTTTTACAA-A-AAAATATAATATATAATTTT
1 AAAACAT-TTTGAAAAATATATAATAT-ATA-AT--TTTT
* *
65683 CAAAACATTTTTGGAAAAATATATATTATATAGTTTTT
1 -AAAACA-TTTT-GAAAAATATATAATATATAATTTTT
65721 AAAACATTTTGAAAATAAATATATAATATATAATTTTTT
1 AAAACATTTTG--AA-AAATATATAATATATAA-TTTTT
65760 GAAAAAACATTTTG-AAAATATATAATATATAATTTTT
1 ---AAAACATTTTGAAAAATATATAATATATAATTTTT
* *
65797 AAAATATTTTTGAAAATTATAT
1 AAAACA-TTTTGAAAAATATAT
65819 GGTTTTAAAA
Statistics
Matches: 170, Mismatches: 17, Indels: 56
0.70 0.07 0.23
Matches are distributed among these distances:
34 16 0.09
35 10 0.06
36 13 0.08
37 17 0.10
38 57 0.34
39 14 0.08
40 6 0.04
41 4 0.02
42 19 0.11
43 14 0.08
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (35 bp):
AAAACATTTTGAAAAATATATAATATATAATTTTT
Found at i:65701 original size:36 final size:35
Alignment explanation
Indices: 65660--65818 Score: 167
Period size: 37 Copynumber: 4.3 Consensus size: 35
65650 ATATTTTTAC
* *
65660 AAAAAAATATAATATATAATTTTCAAAACATTTTTGG
1 AAAAATATATAATATATAATTTTTAAAACA-TTTT-G
* *
65697 AAAAATATATATTATATAGTTTTTAAAACATTTTG
1 AAAAATATATAATATATAATTTTTAAAACATTTTG
65732 AAAATAAATATATAATATATAATTTTTTGAAAAAACATTTTG
1 --AA-AAATATATAATATATAA-TTTTT---AAAACATTTTG
*
65774 -AAAATATATAATATATAATTTTTAAAATATTTTTG
1 AAAAATATATAATATATAATTTTTAAAACA-TTTTG
*
65809 AAAATTATAT
1 AAAAATATAT
65819 GGTTTTAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
34 5 0.05
35 6 0.06
36 12 0.11
37 33 0.31
38 32 0.30
39 6 0.06
42 11 0.10
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (35 bp):
AAAAATATATAATATATAATTTTTAAAACATTTTG
Found at i:65880 original size:30 final size:31
Alignment explanation
Indices: 65784--65892 Score: 127
Period size: 30 Copynumber: 3.5 Consensus size: 31
65774 AAAATATATA
65784 ATATATAATTTTTAAAATATTTTTGAAAATT
1 ATATATAATTTTTAAAATATTTTTGAAAATT
* **
65815 ATATGGT--TTTAAAAAAGTATTTTTGAAAATT
1 ATAT-ATAATTTTTAAAA-TATTTTTGAAAATT
*
65846 ATATAT-A-TTTTAAAATATTTTTGGAAATTT
1 ATATATAATTTTTAAAATATTTTT-GAAAATT
65876 ATATATAATTTTTAAAA
1 ATATATAATTTTTAAAA
65893 GAAACGGTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
29 7 0.11
30 26 0.40
31 23 0.35
32 9 0.14
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (31 bp):
ATATATAATTTTTAAAATATTTTTGAAAATT
Found at i:65939 original size:3 final size:3
Alignment explanation
Indices: 65931--65987 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
65921 GTTTTTATAT
* * *
65931 TTA TTA TTA TTA TTA TTA TTTA TTA TCA CTA TTA TTA TTA ATA TT-
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
65976 TTA TTA CTTA TT
1 TTA TTA -TTA TT
65988 TTCTGTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 37 0.82
4 6 0.13
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:65952 original size:19 final size:19
Alignment explanation
Indices: 65928--65988 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
65918 ATAGTTTTTA
65928 TATTTATTATTATTATTAT
1 TATTTATTATTATTATTAT
* *
65947 TATTTATTATCACTATTAT
1 TATTTATTATTATTATTAT
*
65966 TA-TTAATATT-TTATTACT
1 TATTTATTATTATTATTA-T
65984 TATTT
1 TATTT
65989 TCTGTTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.14
18 9 0.26
19 21 0.60
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTATTATTATTATTAT
Found at i:65988 original size:12 final size:11
Alignment explanation
Indices: 65925--65989 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 11
65915 TATATAGTTT
65925 TTATATTTATTA
1 TTAT-TTTATTA
65937 TTATTATTATTA
1 TTATT-TTATTA
* *
65949 TT-TATTATCA
1 TTATTTTATTA
*
65959 CTATTATTATTA
1 TTATT-TTATTA
*
65971 ATATTTTATTA
1 TTATTTTATTA
65982 CTTATTTT
1 -TTATTTT
65990 CTGTTAAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
10 6 0.14
11 9 0.21
12 27 0.64
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:66258 original size:16 final size:15
Alignment explanation
Indices: 66237--66266 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
66227 CCGGCCGAAA
66237 ATCCCGGGACTGACCC
1 ATCCCGGGA-TGACCC
66253 ATCCCGGGATGACC
1 ATCCCGGGATGACC
66267 GGCCTCAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:67555 original size:26 final size:26
Alignment explanation
Indices: 67501--67563 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
67491 TTGTATTTTA
* *
67501 TTTTGATTATTTTTTTTCTTTTCACT
1 TTTTTATTATTTCTTTTCTTTTCACT
***
67527 TTTATT-TTATTTCTTTTCTTTTTTGT
1 TTT-TTATTATTTCTTTTCTTTTCACT
67553 TTTTTATTATT
1 TTTTTATTATT
67564 AGTCTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 2 0.07
26 27 0.90
27 1 0.03
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (26 bp):
TTTTTATTATTTCTTTTCTTTTCACT
Found at i:67615 original size:9 final size:9
Alignment explanation
Indices: 67581--67618 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
67571 TTTACTAAAT
67581 TTTATTTATA
1 TTTA-TTATA
67591 TTTATT-TA
1 TTTATTATA
*
67599 TCTATTATA
1 TTTATTATA
67608 TTTATTATA
1 TTTATTATA
67617 TT
1 TT
67619 AATTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 14 0.56
10 4 0.16
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATTATA
Found at i:77336 original size:16 final size:17
Alignment explanation
Indices: 77315--77349 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
77305 CATCACATAA
*
77315 ATTAAAATAG-AATTTT
1 ATTAAAAAAGTAATTTT
77331 ATTAAAAAAGTAATTTT
1 ATTAAAAAAGTAATTTT
77348 AT
1 AT
77350 AATAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
ATTAAAAAAGTAATTTT
Found at i:78077 original size:37 final size:36
Alignment explanation
Indices: 78002--78077 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
77992 TTTTTATATT
*
78002 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
78038 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
78075 TTT
1 TTT
78078 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:78259 original size:20 final size:20
Alignment explanation
Indices: 78223--78260 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
78213 ATCCTATTCC
**
78223 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
78243 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
78261 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:82687 original size:21 final size:19
Alignment explanation
Indices: 82637--82687 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
82627 TCATTTTTAG
82637 AATAATTT-ATATTTAAAA
1 AATAATTTAATATTTAAAA
*
82655 ATAAAATATTAATATTATAAATA
1 A-ATAAT-TTAATATT-TAAA-A
82678 AATAATTTAA
1 AATAATTTAA
82688 AATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 1 0.04
19 4 0.15
20 2 0.08
21 9 0.35
22 8 0.31
23 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAATTTAATATTTAAAA
Found at i:83509 original size:33 final size:33
Alignment explanation
Indices: 83467--83531 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
83457 TTCACAATAG
83467 GAAAATCGCAACACGAAAATCGCAACGAGAAAT
1 GAAAATCGCAACACGAAAATCGCAACGAGAAAT
*
83500 GAAATTCGCAACACGAAAATCGCAACGAGAAA
1 GAAAATCGCAACACGAAAATCGCAACGAGAAA
83532 ACTAAAATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.51, C:0.22, G:0.18, T:0.09
Consensus pattern (33 bp):
GAAAATCGCAACACGAAAATCGCAACGAGAAAT
Found at i:83532 original size:14 final size:14
Alignment explanation
Indices: 83467--83525 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 14
83457 TTCACAATAG
83467 GAAAATCGCAACAC
1 GAAAATCGCAACAC
83481 GAAAATCGCAACGA-
1 GAAAATCGCAAC-AC
83495 GAAATGAAATTCGCAACAC
1 G--A--AAA-TCGCAACAC
83514 GAAAATCGCAAC
1 GAAAATCGCAAC
83526 GAGAAAACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
14 20 0.53
15 4 0.11
16 1 0.03
17 1 0.03
18 4 0.11
19 8 0.21
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACAC
Found at i:83579 original size:14 final size:14
Alignment explanation
Indices: 83556--83596 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
83546 GCGAATTTCA
*
83556 TTTCGCGTTGCGAT
1 TTTCGTGTTGCGAT
*
83570 TTTCGTGTTGTGAT
1 TTTCGTGTTGCGAT
*
83584 TTTCCTGTTGCGA
1 TTTCGTGTTGCGA
83597 ATTTAAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.07, C:0.17, G:0.27, T:0.49
Consensus pattern (14 bp):
TTTCGTGTTGCGAT
Found at i:83987 original size:22 final size:22
Alignment explanation
Indices: 83942--83987 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
83932 GATGGAGGGG
* *
83942 GTCGTCGGATATGGGAACGGAT
1 GTCGTCGGAGATGGGAACGAAT
* *
83964 GTCGTCGGAGATGGGGATGAAT
1 GTCGTCGGAGATGGGAACGAAT
83986 GT
1 GT
83988 TGCCGTAGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.11, G:0.43, T:0.24
Consensus pattern (22 bp):
GTCGTCGGAGATGGGAACGAAT
Found at i:84127 original size:19 final size:20
Alignment explanation
Indices: 84105--84142 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
84095 ATATTCGTGT
84105 TTTGAATT-CGAAAATAAAA
1 TTTGAATTGCGAAAATAAAA
**
84124 TTTGCGTTGCGAAAATAAA
1 TTTGAATTGCGAAAATAAA
84143 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (20 bp):
TTTGAATTGCGAAAATAAAA
Found at i:84215 original size:20 final size:20
Alignment explanation
Indices: 84192--84239 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
84182 ATTCATGTTA
84192 CGAATTTGAAAATCACAATG
1 CGAATTTGAAAATCACAATG
* * * **
84212 CGAATCTAAAAATCGCGTTG
1 CGAATTTGAAAATCACAATG
84232 CGAATTTG
1 CGAATTTG
84240 GGAAATCGCG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (20 bp):
CGAATTTGAAAATCACAATG
Found at i:84294 original size:41 final size:42
Alignment explanation
Indices: 84221--84302 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
84211 GCGAATCTAA
** *
84221 AAATCGCGTTGCGAATTTGGGAAATCGCGTTGCGAATTTGGG
1 AAATCGCGTTGCGAATTTCAGAAATCGAGTTGCGAATTTGGG
84263 AAATCGCGTTGCG-ATTTCAGAAA-CTGAGTTGCGAATTTGG
1 AAATCGCGTTGCGAATTTCAGAAATC-GAGTTGCGAATTTGG
84303 AAACTGTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 1 0.03
41 22 0.61
42 13 0.36
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (42 bp):
AAATCGCGTTGCGAATTTCAGAAATCGAGTTGCGAATTTGGG
Found at i:84317 original size:20 final size:21
Alignment explanation
Indices: 84221--84302 Score: 114
Period size: 21 Copynumber: 4.0 Consensus size: 21
84211 GCGAATCTAA
84221 AAATCGCGTTGCGAATTTGGG
1 AAATCGCGTTGCGAATTTGGG
84242 AAATCGCGTTGCGAATTTGGG
1 AAATCGCGTTGCGAATTTGGG
**
84263 AAATCGCGTTGCG-ATTTCAG
1 AAATCGCGTTGCGAATTTGGG
*
84283 AAA-CTGAGTTGCGAATTTGG
1 AAATC-GCGTTGCGAATTTGG
84303 AAACTGTGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.02
20 15 0.28
21 38 0.70
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (21 bp):
AAATCGCGTTGCGAATTTGGG
Found at i:84322 original size:20 final size:20
Alignment explanation
Indices: 84282--84323 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
84272 TGCGATTTCA
*
84282 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTG
*
84302 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
84322 GA
1 GA
84324 GTTCTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:87405 original size:8 final size:8
Alignment explanation
Indices: 87394--87418 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
87384 TATTTATTTA
87394 TTATAATT
1 TTATAATT
87402 TTATAATT
1 TTATAATT
87410 TTATAATT
1 TTATAATT
87418 T
1 T
87419 CACGTCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATAATT
Found at i:88142 original size:21 final size:22
Alignment explanation
Indices: 88116--88156 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
88106 GGAGGGATAT
88116 GAGAGCAAAGTGGTG-GAATTC
1 GAGAGCAAAGTGGTGAGAATTC
*
88137 GAGAGCATAGTGGTGAGAAT
1 GAGAGCAAAGTGGTGAGAAT
88157 ATATTTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.34, C:0.07, G:0.39, T:0.20
Consensus pattern (22 bp):
GAGAGCAAAGTGGTGAGAATTC
Found at i:88805 original size:122 final size:121
Alignment explanation
Indices: 88584--88954 Score: 460
Period size: 122 Copynumber: 3.0 Consensus size: 121
88574 AATCGAAGAT
* * *
88584 TAAATTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATCTATAAGTGAAAGTGA-AGA
1 TAAATTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATATAAGTCAAAGTGACA-A
*
88648 AATGTGTAATTATATCAATTTTATTAAATTTTAAAACTTAAGATGAGATAAAATATA
65 AATGTGTAATTATATCAATTTCATTAAATTTTAAAACTTAAGATGAGATAAAATATA
* * *
88705 TAAATTTAATTTTAATTTTTTAAAATTACGACTAAATTAATAGAATATAAAAGT-ATAAGTGACA
1 TAAA-TTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATATAAGTCA-AAGTGACA
* * * *
88769 AAATAT-AACATTATATCAATTTCATTAAATTTTAAAATTTAAGATGGGGTGAGATAAAAAATA
64 AAATGTGTA-ATTATATCAATTTCATTAAATTTTAAAACTTAAGA-----TGAGATAAAATATA
* * * *** *
88832 TAAAGTAATTTTAATTTATTAAAATTATGATTAAATTGATAGAATATATAAGTCAAACCAACCAA
1 TAAATTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATATAAGTCAAAGTGACAAA
* *
88897 ATGTGTAATTATATCAATTTGATTAAATTTTAAAAGTTAAGATGAGATAAAATATA
66 ATGTGTAATTATATCAATTTCATTAAATTTTAAAACTTAAGATGAGATAAAATATA
88953 TA
1 TA
88955 TTATTTTTTT
Statistics
Matches: 214, Mismatches: 25, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
121 21 0.10
122 88 0.41
123 1 0.00
126 85 0.40
127 19 0.09
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.37
Consensus pattern (121 bp):
TAAATTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATATAAGTCAAAGTGACAAA
ATGTGTAATTATATCAATTTCATTAAATTTTAAAACTTAAGATGAGATAAAATATA
Found at i:88981 original size:126 final size:122
Alignment explanation
Indices: 88588--88960 Score: 414
Period size: 126 Copynumber: 3.0 Consensus size: 122
88578 GAAGATTAAA
* * ** *
88588 TTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATCTATAAGTGAAAGTGAA-GAAATG
1 TTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATATAAGT-AAA-CCAACAAAATG
*
88652 TGTAATTATATCAATTTTATTAAATTTTAAAACTTAAGATGAGATAAAATATATA-AAT
64 TGTAATTATATCAATTTCATTAAATTTTAAAACTTAAGATGAGATAAAATATATATAAT
* * * *** *
88710 TTAATTTTAATTTTTTAAAATTACGACTAAATTAATAGAATATAAAAGTATAAGTGACAAAATAT
1 TTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATATAAGTA-AACCAACAAAATGT
* * *
88775 -AACATTATATCAATTTCATTAAATTTTAAAATTTAAGATGGGGTGAGATAAAA-A-ATATAAA
65 GTA-ATTATATCAATTTCATTAAATTTTAAAACTTAAGA-----TGAGATAAAATATATATAAT
* * * *
88836 GTAATTTTAATTTATTAAAATTATGATTAAATTGATAGAATATATAAGTCAAACCAACCAAATGT
1 TTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATATAAGT-AAACCAACAAAATGT
* * *
88901 GTAATTATATCAATTTGATTAAATTTTAAAAGTTAAGATGAGATAAAATATATATTAT
65 GTAATTATATCAATTTCATTAAATTTTAAAACTTAAGATGAGATAAAATATATATAAT
88959 TT
1 TT
88961 TTTTGTTAGA
Statistics
Matches: 207, Mismatches: 31, Indels: 25
0.79 0.12 0.10
Matches are distributed among these distances:
121 13 0.06
122 85 0.41
123 6 0.03
125 3 0.01
126 88 0.43
127 12 0.06
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.38
Consensus pattern (122 bp):
TTAATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATATAAGTAAACCAACAAAATGTG
TAATTATATCAATTTCATTAAATTTTAAAACTTAAGATGAGATAAAATATATATAAT
Found at i:90922 original size:23 final size:23
Alignment explanation
Indices: 90875--91019 Score: 125
Period size: 23 Copynumber: 6.3 Consensus size: 23
90865 TGAAGTGTCG
90875 CGTAGAATATG-CACCGAAGTG-CCA
1 CGTAGAA-ATGTC-CCGAAG-GACCA
*
90899 CGTAGAAATATCCCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
* * * * * *
90922 CATAGTATTGTTCTGAATGA-CA
1 CGTAGAAATGTCCCGAAGGACCA
*
90944 CGTAGAAATGTCCCAAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
* *
90967 TGTAGAATTGTCCCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
* * *
90990 CGTAGAATTGTCCCAAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCA
91013 CGTAGAA
1 CGTAGAA
91020 CTCTCGACTC
Statistics
Matches: 97, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
22 16 0.16
23 73 0.75
24 8 0.08
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGTCCCGAAGGACCA
Found at i:90963 original size:45 final size:46
Alignment explanation
Indices: 90888--91011 Score: 144
Period size: 45 Copynumber: 2.7 Consensus size: 46
90878 AGAATATGCA
* * * *
90888 CCGAAGTG-CCACGTAGAAATATCCCGAAGGACCACATAGTATTGTT
1 CCGAAG-GACCACGTAGAAATGTCCCAAAGGACCACATAGAATTGTC
* * **
90934 CTGAATGA-CACGTAGAAATGTCCCAAAGGACCATGTAGAATTGTC
1 CCGAAGGACCACGTAGAAATGTCCCAAAGGACCACATAGAATTGTC
*
90979 CCGAAGGACCACGTAGAATTGTCCCAAAGGACC
1 CCGAAGGACCACGTAGAAATGTCCCAAAGGACC
91012 GCGTAGAACT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
45 38 0.58
46 27 0.42
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (46 bp):
CCGAAGGACCACGTAGAAATGTCCCAAAGGACCACATAGAATTGTC
Found at i:94029 original size:16 final size:16
Alignment explanation
Indices: 94010--94067 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
94000 AATATAATTT
94010 AATATTAACATAAAAA
1 AATATTAACATAAAAA
* *
94026 AATAGTAA-ATTAAATA
1 AATATTAACA-TAAAAA
*
94042 AATATT--TAT-AAAA
1 AATATTAACATAAAAA
94055 AATATTAACATAA
1 AATATTAACATAA
94068 TAATCAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
13 9 0.28
14 1 0.03
15 4 0.12
16 18 0.56
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (16 bp):
AATATTAACATAAAAA
Found at i:98913 original size:49 final size:50
Alignment explanation
Indices: 98841--98939 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 50
98831 ATGTCACATA
* *
98841 GATTTATAGTTAAAAAATAAAATAAAAAATTACATTT-TTTAGGTCTTAG
1 GATTTATAATTAAAAAATAAAATAAAAAATTACATTTACTTAGGTCTTAG
98890 GATTTATAATTAAAAAATAAAATAAAAAATTACATTTACTTAGGTCTTAG
1 GATTTATAATTAAAAAATAAAATAAAAAATTACATTTACTTAGGTCTTAG
98940 TATAGTCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 36 0.77
50 11 0.23
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.37
Consensus pattern (50 bp):
GATTTATAATTAAAAAATAAAATAAAAAATTACATTTACTTAGGTCTTAG
Found at i:103558 original size:21 final size:21
Alignment explanation
Indices: 103534--103581 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
103524 CAAAAGGAAA
** *
103534 GATCCCTCGGGAAAAAAGATT
1 GATCCCTCGACAAAAAAGATC
* *
103555 GATCACTCGACAAAAAGGATC
1 GATCCCTCGACAAAAAAGATC
103576 GATCCC
1 GATCCC
103582 AAACTTTCTG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (21 bp):
GATCCCTCGACAAAAAAGATC
Found at i:103591 original size:92 final size:92
Alignment explanation
Indices: 103363--103610 Score: 327
Period size: 92 Copynumber: 2.7 Consensus size: 92
103353 ATCCCTTTTC
** * * * * * *
103363 AAAAAGATCGATTTCTTGACCAAATGATCGATCCCAAACTTTTTATTGTGCAAATGATCAATCCC
1 AAAAAGATCGATCACTCGACAAAAGGATCGATCCCAAACTTTCTGTTGTGCAAATGATCGATCCC
*
103428 TTTTCAAAAGGAACGATCCCTCAGGAA
66 TTTTCAAAAGGAAAGATCCCTCAGGAA
* * *
103455 AAAAAGATCGATCCCTCGACCAAAGGATCGATCCCAAACTTTCTGTTGTGCAAATGATCGATTCC
1 AAAAAGATCGATCACTCGACAAAAGGATCGATCCCAAACTTTCTGTTGTGCAAATGATCGATCCC
*
103520 TTTTCAAAAGGAAAGATCCCTC-GGGA
66 TTTTCAAAAGGAAAGATCCCTCAGGAA
* * * *
103546 AAAAAGATTGATCACTCGACAAAAAGGATCGATCCCAAACTTTCTGTTATGAAAAGGATCGATCC
1 AAAAAGATCGATCACTCGAC-AAAAGGATCGATCCCAAACTTTCTGTTGTGCAAATGATCGATCC
103611 ATTGGGGAAA
Statistics
Matches: 138, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
91 21 0.15
92 117 0.85
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (92 bp):
AAAAAGATCGATCACTCGACAAAAGGATCGATCCCAAACTTTCTGTTGTGCAAATGATCGATCCC
TTTTCAAAAGGAAAGATCCCTCAGGAA
Done.