Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000272.1 Hibiscus syriacus cultivar Beakdansim tig00000506_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: 97149
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:4780 original size:46 final size:46
Alignment explanation
Indices: 4704--5283 Score: 612
Period size: 46 Copynumber: 12.6 Consensus size: 46
4694 TGCATCAACA
* * *
4704 CATCCATTCATACA-TTTAGTTATGGTATCCTTTCAAGCCTTAATG
1 CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
* *
4749 CATCTGTTCATGCATTTTAGTTATGGCATCCTGTCAAGCCTTAATG
1 CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
*
4795 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
1 CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
* * *
4841 CATCCGTTCATGCATTTTTATTTATGACATCCTTTCATA-CCTTAGTG
1 CATCCGTTCATGCA-TTTTAGTTATGGCATCCTTTCA-AGCCTTAATG
** *
4888 CATCTATTCATGCACTTTAGTTATGGCATCCTTTCATA-CCTTAATG
1 CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCA-AGCCTTAATG
* * * * * *
4934 CATCCGTTCATGCATTTTTATTTATGGAATCCTTTGATGCCTTAGTA
1 CATCCGTTCATGCA-TTTTAGTTATGGCATCCTTTCAAGCCTTAATG
* * * * *
4981 TATCCGTTCATGCACTTTAGTTATGGCATCATTTCATGCCTTAATA
1 CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
* * * ** * *
5027 CACCCGTCCATGTATTTTTTTTATGGCATCCTTTCATGCCTTAGTG
1 CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
* * * *
5073 CATTCGTTCATGCACTTTAGTTATGGCATCATTTCATGCCTTAATG
1 CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
* * * *
5119 CATCCATTCATGAATTTTTATTTATGGCATCCTTTCATA-CCTTAGTG
1 CATCCGTTCATGCA-TTTTAGTTATGGCATCCTTTCA-AGCCTTAATG
* * ** *
5166 CATCCGTTCATTCACTTTAGTTATGTAATCCTTTCATGCCTTAATG
1 CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
* * * * *
5212 CATTCGTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAGTA
1 CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
**
5258 CATATGTTCATGCACTTTT-GTTATGG
1 CATCCGTTCATGCA-TTTTAGTTATGG
5284 TATAGTCAAT
Statistics
Matches: 445, Mismatches: 81, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
45 11 0.02
46 316 0.71
47 117 0.26
48 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (46 bp):
CATCCGTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATG
Found at i:4845 original size:20 final size:20
Alignment explanation
Indices: 4774--4850 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 20
4764 TTTAGTTATG
*
4774 GCATCCTGTCAAGCCTTAAT
1 GCATCCTTTCAAGCCTTAAT
* *
4794 GCATCCTTTCATGCATTTTAGTTAT
1 GCATCCTTTCAAGC--CTTA---AT
4819 GGCATCCTTTCAAGCCTTAAT
1 -GCATCCTTTCAAGCCTTAAT
*
4840 GCATCCGTTCA
1 GCATCCTTTCA
4851 TGCATTTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 22 0.49
21 2 0.04
22 3 0.07
24 3 0.07
25 2 0.04
26 13 0.29
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.36
Consensus pattern (20 bp):
GCATCCTTTCAAGCCTTAAT
Found at i:4938 original size:20 final size:20
Alignment explanation
Indices: 4868--4944 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
4858 TTATTTATGA
*
4868 CATCCTTTCATACCTTAGTG
1 CATCCTTTCATACCTTAATG
*
4888 CAT-CTATTCATGCACTTTAGTTATGG
1 CATCCT-TTCAT--ACCTTA---AT-G
4914 CATCCTTTCATACCTTAATG
1 CATCCTTTCATACCTTAATG
*
4934 CATCCGTTCAT
1 CATCCTTTCAT
4945 GCATTTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
19 2 0.04
20 19 0.42
21 2 0.04
22 5 0.11
24 5 0.11
25 1 0.02
26 9 0.20
27 2 0.04
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.40
Consensus pattern (20 bp):
CATCCTTTCATACCTTAATG
Found at i:5059 original size:185 final size:185
Alignment explanation
Indices: 4704--5283 Score: 772
Period size: 185 Copynumber: 3.1 Consensus size: 185
4694 TGCATCAACA
* * * *
4704 CATCCATTCATACA-TTTAGTTATGGTATCCTTTCA-AGCCTTAATGCATCTGTTCATGCA-TTT
1 CATCTATTCATGCACTTTAGTTATGGCATCCTTTCATA-CCTTAATGCATCCGTTCATGCATTTT
* * * * * *
4766 TAGTTATGGCATCCTGTCAAGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCA
65 TATTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCA
* * *
4831 AGCCTTAATGCATCCGTTCATGCATTTTTATTTATGACATCCTTTCATACCTTAGTG
130 TGCCTTAATGCATCCGTTCATGCATTTTT-TTTATGGCATCCTTTCATGCCTTAGTG
4888 CATCTATTCATGCACTTTAGTTATGGCATCCTTTCATACCTTAATGCATCCGTTCATGCATTTTT
1 CATCTATTCATGCACTTTAGTTATGGCATCCTTTCATACCTTAATGCATCCGTTCATGCATTTTT
* * ** *
4953 ATTTATGGAATCCTTTGATGCCTTAGTATATCCGTTCATGCACTTTAGTTATGGCATCATTTCAT
66 ATTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCAT
* * * *
5018 GCCTTAATACACCCGTCCATGTATTTTTTTTATGGCATCCTTTCATGCCTTAGTG
131 GCCTTAATGCATCCGTTCATGCATTTTTTTTATGGCATCCTTTCATGCCTTAGTG
* * * * *
5073 CAT-TCGTTCATGCACTTTAGTTATGGCATCATTTCATGCCTTAATGCATCCATTCATGAATTTT
1 CATCT-ATTCATGCACTTTAGTTATGGCATCCTTTCATACCTTAATGCATCCGTTCATGCATTTT
* * **
5137 TATTTATGGCATCCTTTCATACCTTAGTGCATCCGTTCATTCACTTTAGTTATGTAATCCTTTCA
65 TATTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCA
* * *
5202 TGCCTTAATGCATTCGTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAGTA
130 TGCCTTAATGCATCCGTTCATGCATTTTTTTTATGGCATCCTTTCATGCCTTAGTG
* * *
5258 CATATGTTCATGCACTTTTGTTATGG
1 CATCTATTCATGCACTTTAGTTATGG
5284 TATAGTCAAT
Statistics
Matches: 347, Mismatches: 44, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
184 13 0.04
185 251 0.72
186 83 0.24
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (185 bp):
CATCTATTCATGCACTTTAGTTATGGCATCCTTTCATACCTTAATGCATCCGTTCATGCATTTTT
ATTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCAT
GCCTTAATGCATCCGTTCATGCATTTTTTTTATGGCATCCTTTCATGCCTTAGTG
Found at i:5268 original size:139 final size:139
Alignment explanation
Indices: 4718--5283 Score: 670
Period size: 139 Copynumber: 4.1 Consensus size: 139
4708 CATTCATACA
* * * *
4718 TTTAGTTATGGTATCCTTTCA-AGCCTTAATGCATCTGTTCATGCATTTTAGTTATGGCATCCTG
1 TTTAGTTATGGCATCCTTTCATA-CCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCCTT
* * * *
4782 TCAAGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCAAGCCTTAATGCATCCG
65 TCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCCG
4847 TTCATGCATT
130 TTCATGCATT
* * * **
4857 TTTATTTATGACATCCTTTCATACCTTAGTGCATCTATTCATGCACTTTAGTTATGGCATCCTTT
1 TTTAGTTATGGCATCCTTTCATACCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCCTTT
* * * * * *
4922 CATACCTTAATGCATCCGTTCATGCATTTTTATTTATGGAATCCTTTGATGCCTTAGTATATCCG
66 CATGCCTTAATGCATCCGTTCATGCA-TTTTAGTTATGGCATCCTTTCATGCCTTAATACATCCG
*
4987 TTCATGCA-C
130 TTCATGCATT
* * * * * * * **
4996 TTTAGTTATGGCATCATTTCATGCCTTAATACACCCGTCCATGTATTTTTTTTATGGCATCCTTT
1 TTTAGTTATGGCATCCTTTCATACCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCCTTT
* * * * * *
5061 CATGCCTTAGTGCATTCGTTCATGCACTTTAGTTATGGCATCATTTCATGCCTTAATGCATCCAT
66 CATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCCGT
*
5126 TCATGAATT
131 TCATGCATT
* * * **
5135 TTTATTTATGGCATCCTTTCATACCTTAGTGCATCCGTTCATTCACTTTAGTTATGTAATCCTTT
1 TTTAGTTATGGCATCCTTTCATACCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCCTTT
* * * **
5200 CATGCCTTAATGCATTCGTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAGTACATATGT
66 CATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCCGT
*
5265 TCATGCACT
131 TCATGCATT
5274 TTT-GTTATGG
1 TTTAGTTATGG
5284 TATAGTCAAT
Statistics
Matches: 352, Mismatches: 72, Indels: 7
0.82 0.17 0.02
Matches are distributed among these distances:
138 42 0.12
139 270 0.77
140 40 0.11
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (139 bp):
TTTAGTTATGGCATCCTTTCATACCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCCTTT
CATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCCGT
TCATGCATT
Found at i:5714 original size:74 final size:74
Alignment explanation
Indices: 5632--5794 Score: 213
Period size: 74 Copynumber: 2.2 Consensus size: 74
5622 ACTACTACCC
* * * *
5632 TGGTATCGATACTTCTATACTATGGTATCGATAC-CCCTTTCAATATCAATATCATTTCT-ATAT
1 TGGTATCGATACTTCTACACTATGGTACCGATACTCCCTTTCAATATCAATACCATTT-TGACAT
* *
5695 TCTGTGTTGCA
65 TCTG-GATCCA
* * *
5706 TGGTATCGATACTACTACACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTTGACATT
1 TGGTATCGATACTTCTACACTATGGTACCGATACTCCCTTTCAATATCAATACCATTTTGACATT
5771 CTGGATCCA
66 CTGGATCCA
5780 TGGTATCGATACTTC
1 TGGTATCGATACTTC
5795 CCTTAGTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
74 50 0.65
75 27 0.35
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (74 bp):
TGGTATCGATACTTCTACACTATGGTACCGATACTCCCTTTCAATATCAATACCATTTTGACATT
CTGGATCCA
Found at i:9255 original size:59 final size:58
Alignment explanation
Indices: 9184--9330 Score: 201
Period size: 58 Copynumber: 2.5 Consensus size: 58
9174 TGCAAAATGT
*
9184 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGG-AACTTCGTGTGCTAACATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCAACTT-GTGTGCTAA-AGGA
** * *
9243 TAAGAAATTCATACTAAGTGTAT-AATTTATGTATTGGGCACCTTGTGTGCTAAAGGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCAACTTGTGTGCTAAAGGA
9300 TAAGGAAA-TCATACTAAGTGTATGAATTTCC
1 TAA-GAAATTCATACTAAGTGTATGAATTTCC
9331 ATATGAGAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
57 21 0.27
58 30 0.38
59 27 0.35
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (58 bp):
TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCAACTTGTGTGCTAAAGGA
Found at i:9899 original size:68 final size:68
Alignment explanation
Indices: 9702--9908 Score: 283
Period size: 68 Copynumber: 3.0 Consensus size: 68
9692 AAAAGATCAA
* *
9702 GAGGCCTAACTGTGCATAT-AATAGAAAGGTGTTATTTATACCAGTTAGATGAAAC-ACTAAGTG
1 GAGGCCTAACTGTGCATATGAA-AGAAAGGTGTCATTTATGCCAGTTAGATG-AACGACTAAGTG
9765 TCTTT
64 TCTTT
* * * *
9770 GAGGCCTAACTGTGCATATGAAAGAAATGTGTCATTTAAGTCAGTTAGATGAAAGACTAAGTGTC
1 GAGGCCTAACTGTGCATATGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAACGACTAAGTGTC
9835 TTT
66 TTT
* * * *
9838 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGAATAAGTATC
1 GAGGCCTAACTGTGCATATGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAACGACTAAGTGTC
*
9903 ATT
66 TTT
9906 GAG
1 GAG
9909 TAAAAGAATA
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
67 2 0.02
68 118 0.97
69 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (68 bp):
GAGGCCTAACTGTGCATATGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAACGACTAAGTGTC
TTT
Found at i:10009 original size:81 final size:80
Alignment explanation
Indices: 9840--10137 Score: 454
Period size: 80 Copynumber: 3.7 Consensus size: 80
9830 GTGTCTTTGA
* ** *
9840 GGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGAATAAGTATCAT
1 GGCCTAACTGTGCAT-TGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCAT
9905 TGAGTAAAAGAATAAT
65 TGAGTAAAAGAATAAT
*
9921 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTACCATT
1 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCATT
*
9986 GAGTAAAAAAAATAAT
66 GAGT-AAAAGAATAAT
*
10002 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAATTAGATGAACGGTTAAGTACCATT
1 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCATT
*
10067 AAGTAAAAGAATAAT
66 GAGTAAAAGAATAAT
* * * * *
10082 GGCCTAACTGTACATTAGTAGAAAGGTGTCAATTATGTCAGTTAGACGAAC-GTTAA
1 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAA
10138 ACCCTGTTGA
Statistics
Matches: 200, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
79 5 0.03
80 104 0.52
81 91 0.46
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (80 bp):
GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCATT
GAGTAAAAGAATAAT
Found at i:12430 original size:26 final size:26
Alignment explanation
Indices: 12401--12452 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12391 TTTGAAAAAC
*
12401 CTGAGAGCATCGATGCATCAAATGCA
1 CTGAGAGCATCGATGCATAAAATGCA
*
12427 CTGAGTGCATCGATGCATAAAATGCA
1 CTGAGAGCATCGATGCATAAAATGCA
12453 TTCGATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (26 bp):
CTGAGAGCATCGATGCATAAAATGCA
Found at i:12496 original size:20 final size:20
Alignment explanation
Indices: 12471--12509 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12461 TTGAAAAATT
12471 AATTGGTGCATCGATGCATG
1 AATTGGTGCATCGATGCATG
*
12491 AATTGGTGCATCGGTGCAT
1 AATTGGTGCATCGATGCAT
12510 CACTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
AATTGGTGCATCGATGCATG
Found at i:14670 original size:13 final size:13
Alignment explanation
Indices: 14642--14680 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
14632 TGGGCAAGGT
*
14642 TTTGAAAA-ACTA
1 TTTGAAAATAATA
14654 TTTGAAAATAATA
1 TTTGAAAATAATA
*
14667 TTTGTAAATAATA
1 TTTGAAAATAATA
14680 T
1 T
14681 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:21162 original size:45 final size:46
Alignment explanation
Indices: 21074--21164 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
21064 TTTGAAAAAC
* * *
21074 CTGAGTGCGTCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
21120 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
21165 TTCGATGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:21209 original size:20 final size:20
Alignment explanation
Indices: 21184--21221 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
21174 TGAAAAATTA
21184 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
21204 ATTGGTGCATCGATGCAT
1 ATTGGTGCATCGATGCAT
21222 CACTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:27644 original size:20 final size:20
Alignment explanation
Indices: 27607--27657 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
27597 CAAAATAATC
* *
27607 CAATTT-AACATTCTAACAT
1 CAATTTCAACACTCAAACAT
27626 CAATTTCAACACTCAAACAT
1 CAATTTCAACACTCAAACAT
*
27646 TAATTTACAACA
1 CAATTT-CAACA
27658 TAGTACATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.22
20 16 0.59
21 5 0.19
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (20 bp):
CAATTTCAACACTCAAACAT
Found at i:29201 original size:39 final size:39
Alignment explanation
Indices: 29063--29238 Score: 172
Period size: 39 Copynumber: 4.4 Consensus size: 39
29053 CATAACAACC
* *
29063 TGCGGTAAGGACTTACCCTGTGCACAAAGCGTAGAGGAGCA
1 TGCGGTAAGGACTTACCCTGAGCACAAA--GTCGAGGAGCA
* * * * * * * *
29104 TGTGGTAAAGAATTACCCTGTGCACAGAGTGCATATGAGCC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGT-C-GAGGAGCA
* *
29145 TACGATAAGGACTTACCCTGAGCACAAAGTCGAGGAGCA
1 TGCGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCA
* * *
29184 TGCGGTAAGGACTTACCCTGAGCACTAAGCCGAGGAGCC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCA
*
29223 TGAGGTAAGGACTTAC
1 TGCGGTAAGGACTTAC
29239 AAGTTATAGA
Statistics
Matches: 109, Mismatches: 24, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
39 56 0.51
40 1 0.01
41 52 0.48
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.19
Consensus pattern (39 bp):
TGCGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCA
Found at i:29636 original size:20 final size:20
Alignment explanation
Indices: 29613--29651 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29603 GTTCGTTTCA
29613 GGTTGGACT-AGGTCGGGTCG
1 GGTTGG-CTCAGGTCGGGTCG
*
29633 GGTTGGGTCAGGTCGGGTC
1 GGTTGGCTCAGGTCGGGTC
29652 AGATAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.08, C:0.15, G:0.51, T:0.26
Consensus pattern (20 bp):
GGTTGGCTCAGGTCGGGTCG
Found at i:33975 original size:30 final size:30
Alignment explanation
Indices: 33914--33975 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
33904 AATTTGAATC
* *
33914 CAAATTTAATCAAAATTTCACTTTGGCCCT
1 CAAATTTAATCAAAATTTCAATTTAGCCCT
* * *
33944 CAAATTTAATTAAGATTTCAATTTAGTCCT
1 CAAATTTAATCAAAATTTCAATTTAGCCCT
33974 CA
1 CA
33976 GAAAAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (30 bp):
CAAATTTAATCAAAATTTCAATTTAGCCCT
Found at i:38205 original size:14 final size:14
Alignment explanation
Indices: 38186--38213 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38176 CAATACCGTC
38186 AATCTCAAACAAAA
1 AATCTCAAACAAAA
38200 AATCTCAAACAAAA
1 AATCTCAAACAAAA
38214 TGTTAATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
AATCTCAAACAAAA
Found at i:41514 original size:30 final size:31
Alignment explanation
Indices: 41453--41521 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
41443 ACGTCATCGC
* * *
41453 TTTGGACATATTGTAAATGACATATCATCAT
1 TTTGGACATATGGTAAATGACACACCATCAT
*
41484 TTTGGACATATGGT-AATGTCACACCATCAT
1 TTTGGACATATGGTAAATGACACACCATCAT
41514 TTTGGACA
1 TTTGGACA
41522 CGTATCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.62
31 13 0.38
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTGGACATATGGTAAATGACACACCATCAT
Found at i:42856 original size:21 final size:22
Alignment explanation
Indices: 42830--42874 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42820 GAATGCAAAT
42830 AGGGAATCG-GTACCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
* *
42851 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
42873 AG
1 AG
42875 TACTGCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (22 bp):
AGGGAATCGAGTACCCTGCTAC
Found at i:43503 original size:23 final size:23
Alignment explanation
Indices: 43433--43518 Score: 104
Period size: 23 Copynumber: 3.7 Consensus size: 23
43423 TCATATAAAT
43433 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
43456 TTTGTC-CCAAAG-GACCGCGTAGAA
1 -TTG-CACCGAAGTG-CCACGTAGAA
43480 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
43503 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
43519 TATAATACGT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
22 1 0.02
23 33 0.62
24 18 0.34
25 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:43793 original size:30 final size:30
Alignment explanation
Indices: 43759--43821 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
43749 TCATATCGCG
* *
43759 TAGACATATTATTTCCATACCTTTATCACA
1 TAGACATATCATTTACATACCTTTATCACA
43789 TAGACATATCATTTACATACCTTTATCACA
1 TAGACATATCATTTACATACCTTTATCACA
43819 TAG
1 TAG
43822 CTCATATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (30 bp):
TAGACATATCATTTACATACCTTTATCACA
Found at i:45990 original size:31 final size:31
Alignment explanation
Indices: 45947--46011 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
45937 AAGATATTAC
*
45947 CACTTTCGTTTTTATTTAATTAAAATGTGGT
1 CACTTTCATTTTTATTTAATTAAAATGTGGT
*
45978 CACTTTCATTTTTATTTAATTAAGATGTGGT
1 CACTTTCATTTTTATTTAATTAAAATGTGGT
46009 CAC
1 CAC
46012 CCGAGTTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.49
Consensus pattern (31 bp):
CACTTTCATTTTTATTTAATTAAAATGTGGT
Found at i:47025 original size:6 final size:6
Alignment explanation
Indices: 47014--47665 Score: 1234
Period size: 6 Copynumber: 110.3 Consensus size: 6
47004 CACTTAATTT
47014 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47062 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47110 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47158 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47206 TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47252 TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47298 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATAC-
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47345 -ATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47392 TATACA TATACA TATACA TATAC- -ATACA TATACA TATAC- -ATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47436 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47484 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47532 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47580 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
47628 TATACA TATACA TATACA TATACA TATACA TATACA TA
1 TATACA TATACA TATACA TATACA TATACA TATACA TA
47666 CGCATACGCA
Statistics
Matches: 636, Mismatches: 0, Indels: 20
0.97 0.00 0.03
Matches are distributed among these distances:
4 20 0.03
6 616 0.97
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:50820 original size:22 final size:22
Alignment explanation
Indices: 50792--50835 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
50782 CGCTTCCCAA
*
50792 TACTTTTGTTATGGGTATCACT
1 TACTTTTGTTATGGGCATCACT
50814 TACTTTTGTTATGGGCATCACT
1 TACTTTTGTTATGGGCATCACT
50836 CTCTTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (22 bp):
TACTTTTGTTATGGGCATCACT
Found at i:59627 original size:20 final size:22
Alignment explanation
Indices: 59600--59675 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 22
59590 AGAACCCGTA
59600 GAGGGTATCGGTACCC-TCAAG
1 GAGGGTATCGGTACCCATCAAG
*
59621 G-GGGTATCGATACCCATTCAAG
1 GAGGGTATCGGTACCCA-TCAAG
*
59643 GATGGTATCGGTACCCATGCAAAG
1 GAGGGTATCGGTACCCAT-C-AAG
*
59667 GGGGGTATC
1 GAGGGTATC
59676 AATACCTAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 13 0.29
21 1 0.02
22 7 0.16
23 14 0.31
24 10 0.22
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (22 bp):
GAGGGTATCGGTACCCATCAAG
Found at i:65430 original size:21 final size:21
Alignment explanation
Indices: 65382--65444 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 21
65372 AAATTGTCAT
65382 GGGGGTATCGGTACCATCTGAG
1 GGGGGTA-CGGTACCATCTGAG
65404 GGGGGTACGGGTACCATCTGA-
1 GGGGGTAC-GGTACCATCTGAG
65425 GGGGGTACCGGTACCATCTG
1 GGGGGTA-CGGTACCATCTG
65445 GGCAATCTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
21 19 0.49
22 20 0.51
ACGTcount: A:0.17, C:0.21, G:0.41, T:0.21
Consensus pattern (21 bp):
GGGGGTACGGTACCATCTGAG
Found at i:70023 original size:20 final size:20
Alignment explanation
Indices: 69990--70035 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
69980 AATGATTTTC
* * *
69990 TTTTG-AAAGGAAAATTAGA
1 TTTTGAAAAGAAAAATGAAA
70009 TTTTGAAAAGAAAAATGAAA
1 TTTTGAAAAGAAAAATGAAA
70029 TTTTGAA
1 TTTTGAA
70036 GAATGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (20 bp):
TTTTGAAAAGAAAAATGAAA
Found at i:71204 original size:3 final size:3
Alignment explanation
Indices: 71196--71252 Score: 53
Period size: 3 Copynumber: 17.7 Consensus size: 3
71186 TAAAATTTAA
71196 ATT ATT ATT ATT ATT ATT ATT A-T ATAT ATAT ATAT ATAT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T AT-T AT-T AT-T ATT
*
71242 ACT ATT ATT AT
1 ATT ATT ATT AT
71253 ATAAATAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 29 0.58
4 19 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:71255 original size:2 final size:2
Alignment explanation
Indices: 71216--71240 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71206 TTATTATTAT
71216 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 T
71241 TACTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72638 original size:12 final size:13
Alignment explanation
Indices: 72613--72641 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
72603 TATAGTTTTT
72613 TTTATTTCATTTA
1 TTTATTTCATTTA
72626 TTTATTT-ATTTA
1 TTTATTTCATTTA
72638 TTTA
1 TTTA
72642 CAATGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTCATTTA
Found at i:76004 original size:21 final size:22
Alignment explanation
Indices: 75959--76031 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
75949 CATACATGCA
*
75959 TTTACATTTTGTATCTGTTCAT
1 TTTACATTTTGTATCTGTACAT
*
75981 TTT-CATTTTGTATTCT-TACTT
1 TTTACATTTTGTA-TCTGTACAT
* *
76002 TTTACATCTTTGAAT-TGCACAT
1 TTTACAT-TTTGTATCTGTACAT
*
76024 TTTGCATT
1 TTTACATT
76032 CTTATTTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 17 0.41
22 19 0.46
23 5 0.12
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (22 bp):
TTTACATTTTGTATCTGTACAT
Found at i:78594 original size:15 final size:15
Alignment explanation
Indices: 78574--78624 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 15
78564 AAGAAAGAAG
78574 AAGGAAAAAAACAAA
1 AAGGAAAAAAACAAA
78589 AAGG---AAAA-AAA
1 AAGGAAAAAAACAAA
78600 AAGGAAAAAAACAAA
1 AAGGAAAAAAACAAA
78615 AA-GAAAAAAA
1 AAGGAAAAAAA
78625 GGGGAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 7 0.22
12 4 0.12
14 12 0.38
15 9 0.28
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (15 bp):
AAGGAAAAAAACAAA
Found at i:78607 original size:10 final size:11
Alignment explanation
Indices: 78581--78610 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
78571 AAGAAGGAAA
78581 AAAACAAAAAGG
1 AAAA-AAAAAGG
78593 AAAAAAAAAGG
1 AAAAAAAAAGG
78604 AAAAAAA
1 AAAAAAA
78611 CAAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:78621 original size:25 final size:25
Alignment explanation
Indices: 78563--78624 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 25
78553 CTCATCCAGC
* *
78563 AAAGAAAGAAGAAGGAAAAAAACAA
1 AAAGAAAAAAAAAGGAAAAAAACAA
78588 AAAGGAAAAAAAAAGGAAAAAAACAA
1 AAA-GAAAAAAAAAGGAAAAAAACAA
78614 AAAGAAAAAAA
1 AAAGAAAAAAA
78625 GGGGAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 11 0.32
26 23 0.68
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (25 bp):
AAAGAAAAAAAAAGGAAAAAAACAA
Found at i:83370 original size:22 final size:22
Alignment explanation
Indices: 83344--83420 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
83334 ATCTACACTC
83344 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
83366 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
83388 TTTAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
83410 TTCAAAGATGA
1 TTCAAAGATGA
83421 AAGCTTTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:84224 original size:76 final size:76
Alignment explanation
Indices: 84098--85041 Score: 1701
Period size: 76 Copynumber: 12.4 Consensus size: 76
84088 CTATTTCCCA
84098 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
84163 AGGCTTAGGGT
66 AGCCTTAGGGT
**
84174 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
84239 AGCCTTAGGGT
66 AGCCTTAGGGT
84250 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
84315 AAGCCTTAGGGT
65 AAGCCTTAGGGT
* * *
84327 CATCTGTATGTCCTACAGTGCATGATGTTTCCAAAAAACTTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
84392 AGCCTTAGGGT
66 AGCCTTAGGGT
84403 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
84468 AGCCTTAGGGT
66 AGCCTTAGGGT
*
84479 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAAC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
84543 AGCCTTAGGGT
66 AGCCTTAGGGT
84554 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
84619 AAAGCCTTAGGGT
64 AAAGCCTTAGGGT
*
84632 CATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
84697 AGCCATAGGGT
66 AGCCTTAGGGT
84708 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
84773 AGCCTTAGGGT
66 AGCCTTAGGGT
*
84784 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
84849 AGCCTTAGGGT
66 AGCCTTAGGGT
*
84860 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
84925 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
84936 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAACCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
85001 AACCTTAGGGT
66 AGCCTTAGGGT
**
85012 CATCTGTAAGTCCTTTAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
85042 TCAACATTTC
Statistics
Matches: 841, Mismatches: 23, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
75 58 0.07
76 635 0.76
77 91 0.11
78 57 0.07
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:84649 original size:305 final size:305
Alignment explanation
Indices: 84098--85041 Score: 1730
Period size: 305 Copynumber: 3.1 Consensus size: 305
84088 CTATTTCCCA
84098 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
84163 AGGCTTAGGGTCATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
84228 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
*
84293 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTATGTCCTACAGTGCATGATGTTTC
196 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
*
84358 CAAAAAACTTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
261 CAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
84403 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
84468 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAAC-TTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
84532 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAAGCCT
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAAGCCT
84597 TCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
195 TCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
* * *
84662 CTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCATAGGGT
260 CCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
84708 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
84773 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
84838 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAAGCCTT
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
*
84902 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTC
196 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
* *
84967 CAAAAAACCTTCGGGAGATTTTTGATGTTTTCAAAACCTTAGGGT
261 CAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
**
85012 CATCTGTAAGTCCTTTAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
85042 TCAACATTTC
Statistics
Matches: 617, Mismatches: 20, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
304 200 0.32
305 360 0.58
306 57 0.09
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (305 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
CAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:85192 original size:3 final size:3
Alignment explanation
Indices: 85176--85221 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
85166 TAAAATTAAA
*
85176 ATT ATT -TT -TT ATT ATT ATT ATT AAT ATAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
85220 AT
1 AT
85222 ATAAATAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:85222 original size:19 final size:19
Alignment explanation
Indices: 85185--85224 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
85175 AATTATTTTT
85185 TATTATTATTATTAATATA
1 TATTATTATTATTAATATA
*
85204 TATTATTATTATTATTATA
1 TATTATTATTATTAATATA
85223 TA
1 TA
85225 AATAAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTATTATTAATATA
Found at i:94034 original size:22 final size:23
Alignment explanation
Indices: 94008--94056 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
93998 CATACTCGTG
94008 AGCTACAATGCAC-TCTATAAGA
1 AGCTACAATGCACATCTATAAGA
94030 AGCTACAATGCACATCTATAAGA
1 AGCTACAATGCACATCTATAAGA
94053 AGCT
1 AGCT
94057 CTCACTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (23 bp):
AGCTACAATGCACATCTATAAGA
Found at i:96438 original size:18 final size:16
Alignment explanation
Indices: 96409--96486 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 16
96399 AATCTACGTT
96409 TGATAATGTAAAACATC
1 TGATAATGT-AAACATC
96426 TGATAACTGTAAACATC
1 TGATAA-TGTAAACATC
*
96443 TTATAAT-TGAAA-ATC
1 TGATAATGT-AAACATC
* *
96458 AT-ATAACTTTAAATATC
1 -TGATAA-TGTAAACATC
96475 TGATAATGTAAA
1 TGATAATGTAAA
96487 TATTTAGAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
15 8 0.15
16 15 0.29
17 26 0.50
18 3 0.06
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (16 bp):
TGATAATGTAAACATC
Done.