Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004742.1 Hibiscus syriacus cultivar Beakdansim tig00010703_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: 109929
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:789 original size:15 final size:15
Alignment explanation
Indices: 769--797 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
759 ATTGAAACAA
769 TTAAATAGTTTAATG
1 TTAAATAGTTTAATG
784 TTAAATAGTTTAAT
1 TTAAATAGTTTAAT
798 AGTCTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
TTAAATAGTTTAATG
Found at i:3528 original size:24 final size:25
Alignment explanation
Indices: 3482--3530 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
3472 GGTTTCGATT
3482 TTTTCGGTTATCGGTTTTTTGGATCAG
1 TTTTCGGTTAT--GTTTTTTGGATCAG
3509 TTTTCGGTTAT-TTTTTTGGATC
1 TTTTCGGTTATGTTTTTTGGATC
3531 GGATTGGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.50
27 11 0.50
ACGTcount: A:0.10, C:0.10, G:0.22, T:0.57
Consensus pattern (25 bp):
TTTTCGGTTATGTTTTTTGGATCAG
Found at i:9032 original size:97 final size:98
Alignment explanation
Indices: 8705--9545 Score: 998
Period size: 98 Copynumber: 8.6 Consensus size: 98
8695 CTGGAACTGG
* * *
8705 GAAATTGTTTTGTTGACAGTCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGCTGTCTTGGGTC
1 GAAATTG-TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
**
8770 CAATATCCTTCATTGTGAAGTTGAAATTGGC-CC
65 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCC
** * * *
8803 TGAAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTC
1 -GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* *
8867 CAATA----T--CTGTAAAGTTGAGATTGGCTCC
65 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCC
* * * * *
8895 AAAACTGTTTGTTGACAGTCAGCCGCCCATTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCC
* *
8960 AATATACTTCGTTGTGAAGTTGAAATTGGC-CC
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCC
** * * * *
8992 TGAAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTC
1 -GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* *
9056 CAATA----T--CTGTGAAGTTGAGATTGACTCC
65 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCC
* * * *
9084 AAAACTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCC
9149 AATATCCTTCGCTGTGAAGTTGAAATTGGC-CC
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCC
** * * * *
9181 TGAAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTC
1 -GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
*
9245 CAATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
65 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCC
*** *
9279 GAAATTGTTTGTTGACAGTCAATTGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCC
1 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCC
*
9344 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCC
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCC
*
9377 GAAATTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCC
1 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCC
*
9442 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCC
* * * * *
9475 GAAATTGGGAAATTTGTTGTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTATTGTC
1 GAAATT--G-----T-TTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
9540 TTGAGT
58 TTGAGT
9546 GGTACGATAT
Statistics
Matches: 630, Mismatches: 84, Indels: 49
0.83 0.11 0.06
Matches are distributed among these distances:
91 42 0.07
92 110 0.17
93 2 0.00
96 2 0.00
97 194 0.31
98 222 0.35
99 7 0.01
100 1 0.00
105 1 0.00
106 49 0.08
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (98 bp):
GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCC
AATATCCTTCGCTGTGAAGTTGAAATTGGCTCC
Found at i:9033 original size:189 final size:189
Alignment explanation
Indices: 8713--9447 Score: 1202
Period size: 189 Copynumber: 3.9 Consensus size: 189
8703 GGGAAATTGT
*
8713 TTTGTTGACAGTCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCC
1 TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCC
*
8778 TTCATTGTGAAGTTGAAATTGGCCCTGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAA
66 TTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAA
* *
8843 GTTGAACTTGTGTTGTCTTGAGTCCAATATCTGTAAAGTTGAGATTGGCTCCAAAACTG
131 GTTGAACTTGTGTTGTCTCGAGTCCAATATCTGTGAAGTTGAGATTGGCTCCAAAACTG
* *
8902 TTTGTTGACAGTCAGCCGCCCATTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATAC
1 TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCC
8967 TTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAA
66 TTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAA
*
9032 GTTGAACTTGTGTTGTCTCGAGTCCAATATCTGTGAAGTTGAGATTGACTCCAAAACTG
131 GTTGAACTTGTGTTGTCTCGAGTCCAATATCTGTGAAGTTGAGATTGGCTCCAAAACTG
9091 TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCC
1 TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCC
*
9156 TTCGCTGTGAAGTTGAAATTGGCCCTGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAA
66 TTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAA
* *
9221 GTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTG
131 GTTGAACTTGTGTTGTCTCGAGTCCAATA----T--CTGTGAAGTTGAGATTGGCTCCAAAACTG
*** *
9286 TTTGTTGACAGTCAATTGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCC
1 TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCC
** * * *
9351 TTCGTTGTGAAGTTGAAATTGGCTCC-GAAATTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTG
66 TTCGTTGTGAAGTTGAAATTGGC-CCTGAAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTG
* *
9415 AAGTTGAGCTTGTGTTGTCTTGAGTCCAATATC
129 AAGTTGAACTTGTGTTGTCTCGAGTCCAATATC
9448 CTTCGCTGTG
Statistics
Matches: 513, Mismatches: 25, Indels: 15
0.93 0.05 0.03
Matches are distributed among these distances:
189 338 0.66
190 1 0.00
192 1 0.00
193 1 0.00
195 116 0.23
196 56 0.11
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.35
Consensus pattern (189 bp):
TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCC
TTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAA
GTTGAACTTGTGTTGTCTCGAGTCCAATATCTGTGAAGTTGAGATTGGCTCCAAAACTG
Found at i:17435 original size:20 final size:20
Alignment explanation
Indices: 17410--17451 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17400 TAATAACGTG
17410 AAAATAAATA-AATATAATAA
1 AAAATAAATACAATA-AATAA
*
17430 AAAATATATACAATAAATAA
1 AAAATAAATACAATAAATAA
17450 AA
1 AA
17452 CGAGGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAATACAATAAATAA
Found at i:17436 original size:12 final size:13
Alignment explanation
Indices: 17412--17448 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17402 ATAACGTGAA
17412 AATAAATAAATAT
1 AATAAATAAATAT
17425 AATAAA-AAATAT
1 AATAAATAAATAT
17437 -ATACAATAAATA
1 AATA-AATAAATA
17449 AAACGAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.14
12 8 0.36
13 11 0.50
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
AATAAATAAATAT
Found at i:20041 original size:29 final size:29
Alignment explanation
Indices: 19986--20042 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
19976 TTTTCACCTA
*
19986 ACTAAATTGATGTAAGCAATGACATCAAT
1 ACTAAATTGATGTAAGCAATGAAATCAAT
* *
20015 ACTAACTTGATGTAAGCAATTAAATCAA
1 ACTAAATTGATGTAAGCAATGAAATCAA
20043 ATTAATTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (29 bp):
ACTAAATTGATGTAAGCAATGAAATCAAT
Found at i:20673 original size:22 final size:22
Alignment explanation
Indices: 20645--20721 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
20635 GAAAATATCT
*
20645 GCAACTCGAATACGTCAATTTC
1 GCAACTCGAATTCGTCAATTTC
20667 GCAACTCGAATTCGTCAATTTC
1 GCAACTCGAATTCGTCAATTTC
* *
20689 ACAACTCGAATTCGCCAATTTC
1 GCAACTCGAATTCGTCAATTTC
*
20711 GTAACTC-AATT
1 GCAACTCGAATT
20722 ACCGATGTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 4 0.08
22 46 0.92
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (22 bp):
GCAACTCGAATTCGTCAATTTC
Found at i:20958 original size:62 final size:59
Alignment explanation
Indices: 20892--21021 Score: 152
Period size: 62 Copynumber: 2.2 Consensus size: 59
20882 CGAATTCGTA
* * * *
20892 TTGCGAATTTGAAAATTGAGTTGTGAATTTGGGAAATTCGTGTTGCGAATTCCAAATTCGCG
1 TTGCGAATTTGAAAACTGAGTTGCGAAATT-GG-AATTCGTGTTACGAATTCCAAA-TCGCG
* * * **
20954 TTGCGAATTTGGAAACTGTGTTGCGAAATTGGAGTTCGTGTTACGAATTTGAAATCGCG
1 TTGCGAATTTGAAAACTGAGTTGCGAAATTGGAATTCGTGTTACGAATTCCAAATCGCG
21013 TTGCGAATT
1 TTGCGAATT
21022 CGTTGGTTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 14 0.24
60 18 0.31
61 2 0.03
62 25 0.42
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (59 bp):
TTGCGAATTTGAAAACTGAGTTGCGAAATTGGAATTCGTGTTACGAATTCCAAATCGCG
Found at i:20962 original size:42 final size:42
Alignment explanation
Indices: 20863--20980 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
20853 TTATATCAGT
* * *
20863 AATTGAGTTGCGAAATTGGCG-AATTCGTATTGCGAATTTGAA
1 AATTGAGTTGCGAATTTGG-GAAATTCGTGTTGCGAATTTCAA
* *
20905 AATTGAGTTGTGAATTTGGGAAATTCGTGTTGCGAA-TTCCA
1 AATTGAGTTGCGAATTTGGGAAATTCGTGTTGCGAATTTCAA
* *
20946 AATTCGCGTTGCGAATTT-GGAAACT-GTGTTGCGAA
1 AATT-GAGTTGCGAATTTGGGAAATTCGTGTTGCGAA
20981 ATTGGAGTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
40 10 0.15
41 14 0.21
42 42 0.64
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (42 bp):
AATTGAGTTGCGAATTTGGGAAATTCGTGTTGCGAATTTCAA
Found at i:20976 original size:20 final size:21
Alignment explanation
Indices: 20869--21021 Score: 120
Period size: 20 Copynumber: 7.5 Consensus size: 21
20859 CAGTAATTGA
* *
20869 GTTGCGAAATTGGCGAATTCGT
1 GTTGCGAATTTGG-AAATTCGT
* * *
20891 ATTGCGAATTTGAAAATT-GA
1 GTTGCGAATTTGGAAATTCGT
*
20911 GTTGTGAATTTGGGAAATTCGT
1 GTTGCGAATTT-GGAAATTCGT
** *
20933 GTTGCGAA-TTCCAAATTCGC
1 GTTGCGAATTTGGAAATTCGT
*
20953 GTTGCGAATTTGGAAACT-GT
1 GTTGCGAATTTGGAAATTCGT
* *
20973 GTTGCGAAATTGG-AGTTCGT
1 GTTGCGAATTTGGAAATTCGT
* *
20993 GTTACGAATTT-GAAA-TCGC
1 GTTGCGAATTTGGAAATTCGT
21012 GTTGCGAATT
1 GTTGCGAATT
21022 CGTTGGTTAT
Statistics
Matches: 101, Mismatches: 25, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.15
20 50 0.50
21 18 0.18
22 18 0.18
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (21 bp):
GTTGCGAATTTGGAAATTCGT
Found at i:30642 original size:22 final size:22
Alignment explanation
Indices: 30609--30650 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
30599 ATTAATCACG
30609 TCAATTTTAAATATGATAAAATT
1 TCAATTTTAAAT-TGATAAAATT
*
30632 TCAA-TTTAAATTTATAAAA
1 TCAATTTTAAATTGATAAAA
30651 CAACGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
TCAATTTTAAATTGATAAAATT
Found at i:42044 original size:21 final size:21
Alignment explanation
Indices: 42018--42057 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42008 CAGAACCCCA
*
42018 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
42039 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
42058 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:57190 original size:6 final size:6
Alignment explanation
Indices: 57181--57217 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
57171 TTAACTTTCA
57181 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT A
57218 TATTAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:58372 original size:23 final size:24
Alignment explanation
Indices: 58346--58390 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
58336 AGATTTGATT
58346 TTTTTTAGTTTT-TTTAAAATATA
1 TTTTTTAGTTTTATTTAAAATATA
* *
58369 TTTTTTATTTTTATTTTAAATA
1 TTTTTTAGTTTTATTTAAAATA
58391 AAAATTCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTTTAGTTTTATTTAAAATATA
Found at i:60551 original size:2 final size:2
Alignment explanation
Indices: 60544--60575 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
60534 TTTAATTTTA
60544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60576 GACATAATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66786 original size:21 final size:21
Alignment explanation
Indices: 66749--66831 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
66739 TTTTGGTGCA
*
66749 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
66769 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
66790 GAAGGGGAACCGATTCCCCCCACT
1 G-A-GGGAACCGATTCCCCCCA-T
* *
66814 G-GGGAATCGATACCCCCC
1 GAGGGAACCGATTCCCCCC
66832 TGGGGTTCTG
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
20 10 0.19
21 23 0.44
22 1 0.02
23 16 0.31
24 2 0.04
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:70321 original size:20 final size:20
Alignment explanation
Indices: 70284--70333 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
70274 CTCAAAATCA
*
70284 TTTTTCAAAA-CTTCATTTT
1 TTTTTCAAAATCTTAATTTT
70303 GTTTTTCAAAATC-TAATTTT
1 -TTTTTCAAAATCTTAATTTT
*
70323 ATTTTCAAAAT
1 TTTTTCAAAAT
70334 AAAATCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 10 0.37
20 16 0.59
21 1 0.04
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTTCAAAATCTTAATTTT
Found at i:80692 original size:3 final size:3
Alignment explanation
Indices: 80673--80749 Score: 117
Period size: 3 Copynumber: 26.7 Consensus size: 3
80663 CCATTAACTC
80673 TCT TCT T-T TC- TCTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
80717 TCT TCT TCT TCT TCT TCT TCT TCT T-T TC- TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
80750 CTCCTCGACA
Statistics
Matches: 69, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 8 0.12
3 59 0.86
4 2 0.03
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:81348 original size:19 final size:19
Alignment explanation
Indices: 81321--81378 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
81311 ATTTCATTTG
*
81321 TTTGATTTATTATTATTAT
1 TTTGTTTTATTATTATTAT
*
81340 TTTGTTTTAATATTATTAT
1 TTTGTTTTATTATTATTAT
* * *
81359 TATATTATATTATTATTAT
1 TTTGTTTTATTATTATTAT
81378 T
1 T
81379 AAATAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTGTTTTATTATTATTAT
Found at i:81353 original size:22 final size:22
Alignment explanation
Indices: 81328--81379 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
81318 TTGTTTGATT
* * *
81328 TATTATTATTATTTTGTTTTAA
1 TATTATTATTATATTATATTAA
*
81350 TATTATTATTATATTATATTAT
1 TATTATTATTATATTATATTAA
81372 TATTATTA
1 TATTATTA
81380 AATAAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTATTATTATATTATATTAA
Found at i:81399 original size:3 final size:3
Alignment explanation
Indices: 81327--81379 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
81317 TTTGTTTGAT
* *
81327 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
81371 TTA TTA TTA
1 TTA TTA TTA
81380 AATAAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:85255 original size:8 final size:7
Alignment explanation
Indices: 85231--85272 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
85221 TTTTCATACA
85231 TGCA-TT
1 TGCATTT
85237 TGCATTT
1 TGCATTT
85244 TGCATCTT
1 TGCAT-TT
85252 TGCATTT
1 TGCATTT
* *
85259 TTCATTG
1 TGCATTT
85266 TGCATTT
1 TGCATTT
85273 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:85255 original size:15 final size:14
Alignment explanation
Indices: 85231--85272 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
85221 TTTTCATACA
85231 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
85244 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
85259 TTCATTGTGCATTT
1 TGCATTTTGCATTT
85273 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:85363 original size:27 final size:27
Alignment explanation
Indices: 85332--85387 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
85322 CGTTCACATA
85332 TTTACATTTGCAATTACATTTGCATTT
1 TTTACATTTGCAATTACATTTGCATTT
* * * *
85359 TTTACGTTTGTATTTACATTTTCATTT
1 TTTACATTTGCAATTACATTTGCATTT
85386 TT
1 TT
85388 ATATAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.59
Consensus pattern (27 bp):
TTTACATTTGCAATTACATTTGCATTT
Found at i:87017 original size:2 final size:2
Alignment explanation
Indices: 87010--87055 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
87000 ATCCTTTTAA
87010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87052 AT AT
1 AT AT
87056 CATTTGTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87374 original size:14 final size:14
Alignment explanation
Indices: 87355--87423 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
87345 GCAAAGAAAG
87355 AAGAAGAAGAAAAA
1 AAGAAGAAGAAAAA
87369 AAGAAGAA-AAATAA
1 AAGAAGAAGAAA-AA
* *
87383 AAGAAAAATAAAAA
1 AAGAAGAAGAAAAA
* * *
87397 AACAAAAAGGAAAA
1 AAGAAGAAGAAAAA
87411 AA-AAGAAGGAAAA
1 AAGAAGAA-GAAAA
87424 TTGAATCAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
13 7 0.15
14 36 0.78
15 3 0.07
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (14 bp):
AAGAAGAAGAAAAA
Found at i:87389 original size:20 final size:22
Alignment explanation
Indices: 87364--87417 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
87354 GAAGAAGAAG
*
87364 AAAAAAAGAAGAAA-AATAAAAGA
1 AAAAAAAGAA-AAACAA-AAAGGA
*
87387 AAAATAA-AAAAACAAAAAGGA
1 AAAAAAAGAAAAACAAAAAGGA
87408 AAAAAAAGAA
1 AAAAAAAGAA
87418 GGAAAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 14 0.54
22 6 0.23
23 6 0.23
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.04
Consensus pattern (22 bp):
AAAAAAAGAAAAACAAAAAGGA
Found at i:87394 original size:11 final size:10
Alignment explanation
Indices: 87347--87417 Score: 63
Period size: 11 Copynumber: 6.6 Consensus size: 10
87337 CTCATCCAGC
87347 AAAGAAAGAAGA
1 AAAGAAA-AA-A
87359 AGAAGAAAAAA
1 A-AAGAAAAAA
87370 AGAAGAAAAATA
1 A-AAGAAAAA-A
87382 AAAGAAAAATA
1 AAAGAAAAA-A
*
87393 AAA-AAACAA
1 AAAGAAAAAA
*
87402 AAAGGAAAAA
1 AAAGAAAAAA
87412 AAAGAA
1 AAAGAA
87418 GGAAAATTGA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
9 4 0.08
10 13 0.25
11 24 0.46
12 5 0.10
13 6 0.12
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:89900 original size:114 final size:114
Alignment explanation
Indices: 89700--89916 Score: 371
Period size: 114 Copynumber: 1.9 Consensus size: 114
89690 CACGTTCTCG
* * *
89700 TAGTAGAAATAAGGAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGATTC
* *
89765 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATAAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATAAATTTGCTCA
*
89814 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGATTC
*
89879 GGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGAT
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGAT
89917 GAACTGCATG
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGATTC
GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATAAATTTGCTCA
Found at i:90139 original size:31 final size:31
Alignment explanation
Indices: 90097--90159 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
90087 GCACATATAA
* *
90097 AATCTGGCAACTCTGCACTTGATGAATTCAG
1 AATCTGGCAACTCTGCAATTAATGAATTCAG
*
90128 AATCTGTCAACTCTGCAATTAATGAATTCAG
1 AATCTGGCAACTCTGCAATTAATGAATTCAG
90159 A
1 A
90160 CCACATCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (31 bp):
AATCTGGCAACTCTGCAATTAATGAATTCAG
Found at i:92521 original size:22 final size:22
Alignment explanation
Indices: 92493--92567 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
92483 ATCTACACTC
92493 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
92515 TCCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
92537 TTTAAAGATAATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
92559 TTCAAAGAT
1 TTCAAAGAT
92568 AAAAGCTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:93641 original size:76 final size:76
Alignment explanation
Indices: 93513--93762 Score: 396
Period size: 76 Copynumber: 3.3 Consensus size: 76
93503 CTATTTCCCA
* *
93513 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGGTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
93578 AACCTTAGGGT
66 AACCTTAGGGT
93589 CATCTGTAAGTCCTACAGTGCATGATGGTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGGTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
93654 AGCCTTAGGGT
66 AACCTTAGGGT
* *
93665 CATCTATAAGTCCTACAGTGCATGAT-GTGTCGAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGGT-TCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* *
93729 AAACCTTCGAGT
65 AAACCTTAGGGT
*
93741 CAGT-TGTAAGCCCTACAGTGCA
1 CA-TCTGTAAGTCCTACAGTGCA
93763 GAATGTTTTT
Statistics
Matches: 162, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
75 2 0.01
76 159 0.98
77 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGGTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGT
Found at i:93987 original size:113 final size:113
Alignment explanation
Indices: 93789--94515 Score: 1117
Period size: 113 Copynumber: 6.4 Consensus size: 113
93779 TTCTTAAAAA
*
93789 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAG
1 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* *
93854 AAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTTGATGGATCAGC
66 AAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTTGATGGATCAAC
93902 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGTTCATAATGA
1 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGA
* * * *
93966 GAAGAACTTGTTTAACCTTTTG-TTCAAATCCATCACTTGATGGATCAAC
65 GAAGAACTTGTTCAACTTTTTGCTT-GAATTCATCACTTGATGGATCAAC
*
94015 ATTTCCAGGTAGAGTTCATAATGATAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
94080 AAGAACTTGTTCAACTTTTTGCTTGAATTCATCA-TTCGATGGATCAAC
66 AAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTT-GATGGATCAAC
* * * *
94128 ATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAACTTCATAATAAG
1 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * *
94192 AAGAACTTGTTTAACCTTTTGTTTAAATTCATCACTTGATGGATCAAC
66 AAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTTGATGGATCAAC
*
94240 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAG
1 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* *
94305 AAGAACTTGTTCAACTTTTTGTTTGAATTCATCA-TTCGATGGATCATC
66 AAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTT-GATGGATCAAC
* * * * *
94353 ATTACCAGGTAGAATCCCA-AAGGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGA
1 ATTTCCAGGTAGAGT-TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
94417 GAAGAACTTGTTCAACTTTTTGCTCGAATTCATCACTTGATGGATCAAC
65 GAAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTTGATGGATCAAC
*
94466 TTTTCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 ATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
94516 CTTGCGCAAT
Statistics
Matches: 558, Mismatches: 44, Indels: 24
0.89 0.07 0.04
Matches are distributed among these distances:
112 109 0.20
113 440 0.79
114 9 0.02
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACTTTTTGCTTGAATTCATCACTTGATGGATCAAC
Found at i:94415 original size:338 final size:338
Alignment explanation
Indices: 93789--94514 Score: 1154
Period size: 338 Copynumber: 2.1 Consensus size: 338
93779 TTCTTAAAAA
* * *
93789 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAG
1 ATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAACTTCATAATAAG
* * * *
93854 AAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTTGATGGATCAGCATTTCCAGGTAGAGTTC
65 AAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACATTTCCAGGTAGAGTTC
*
93919 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAGAACTTGTTTAACCT
130 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAGAACTTGTTCAACCT
* * * * *
93984 TTTGTTCAAATCCATCACTTGATGGATCAACATTTCCAGGTAGAGTTCATAATGATAAGAACTCA
195 TTTGTTCAAATCCATCACTTGATGGATCAACATTACCAGGTAGAATCCATAAGGAGAAGAACTCA
*
94049 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCA
260 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCA
94114 -TTCGATGGATCAAC
325 CTT-GATGGATCAAC
94128 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAACTTCATAATAAGA
1 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAACTTCATAATAAGA
* *
94193 AGAACTTGTTTAACCTTTTGTTTAAATTCATCACTTGATGGATCAACATTTCCAGGTAGAGTTCA
66 AGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACATTTCCAGGTAGAGTTCA
* *
94258 TAATGAGAAGAACTCATCTGAAGAATGAAGA-AGAAGTTCATAATGAGAAGAACTTGTTCAACTT
131 TAATGAGAAGAACTCATCTGAAGAAGGAAGAGA-AAGTTCATAATGAGAAGAACTTGTTCAACCT
** * *
94322 TTTGTTTGAATTCATCA-TTCGATGGATCATCATTACCAGGTAGAATCCCA-AAGGAGAAGAACT
195 TTTGTTCAAATCCATCACTT-GATGGATCAACATTACCAGGTAGAAT-CCATAAGGAGAAGAACT
*
94385 CATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCAT
258 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCAT
94450 CACTTGATGGATCAAC
323 CACTTGATGGATCAAC
*
94466 TTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 ATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
94515 ACTTGCGCAA
Statistics
Matches: 358, Mismatches: 24, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
337 3 0.01
338 305 0.85
339 50 0.14
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (338 bp):
ATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAACTTCATAATAAGA
AGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACATTTCCAGGTAGAGTTCA
TAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAGAACTTGTTCAACCTT
TTGTTCAAATCCATCACTTGATGGATCAACATTACCAGGTAGAATCCATAAGGAGAAGAACTCAT
CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCAC
TTGATGGATCAAC
Found at i:94789 original size:22 final size:22
Alignment explanation
Indices: 94753--94816 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
94743 TTTTATTTCA
94753 TTTGTTTTATTTATTATTAATAT
1 TTTGTTTTA-TTATTATTAATAT
* *
94776 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTATTATTATTAATAT
* * *
94798 ATTATATTATTATTATTAA
1 TTTGTTTTATTATTATTAA
94817 ATAAATAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 25 0.74
23 9 0.26
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (22 bp):
TTTGTTTTATTATTATTAATAT
Found at i:94835 original size:3 final size:3
Alignment explanation
Indices: 94763--94815 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
94753 TTTGTTTTAT
* * *
94763 TTA TTA TTA ATA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
94807 TTA TTA TTA
1 TTA TTA TTA
94816 AATAAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 8 0.19
3 34 0.81
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:95264 original size:19 final size:19
Alignment explanation
Indices: 95242--95280 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
95232 CGAATCCTGC
*
95242 AAAATGAAAAAAAAGAGAA
1 AAAATGAAAAAAAACAGAA
*
95261 AAAATGAAGAAAAACAGAA
1 AAAATGAAAAAAAACAGAA
95280 A
1 A
95281 CGAGAGCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAATGAAAAAAAACAGAA
Found at i:101356 original size:31 final size:31
Alignment explanation
Indices: 101321--101418 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
101311 TATTCAATTT
*
101321 TCATTTTTAATAATTTGATAAAATTTAATGA
1 TCATTTTTAATAATTTGATAAAATTTAATAA
* * *
101352 TCATTTATAACAATTTGATAAAATATAATAA
1 TCATTTTTAATAATTTGATAAAATTTAATAA
* *
101383 CCA-TTTTAACT-ATTAGAT-AAATTTAATAA
1 TCATTTTTAA-TAATTTGATAAAATTTAATAA
*
101412 TTATTTT
1 TCATTTT
101419 GTAAGTTTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
29 11 0.20
30 14 0.26
31 29 0.54
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (31 bp):
TCATTTTTAATAATTTGATAAAATTTAATAA
Found at i:101977 original size:15 final size:16
Alignment explanation
Indices: 101944--101981 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
101934 CCAACCATAA
101944 AAAAATAAATTAAAAC
1 AAAAATAAATTAAAAC
* *
101960 AAAAATCAATT-AACC
1 AAAAATAAATTAAAAC
101975 AAAAATA
1 AAAAATA
101982 TGCCATAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAATAAATTAAAAC
Found at i:107011 original size:11 final size:10
Alignment explanation
Indices: 106972--107010 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
106962 GGAAAAAAAT
106972 AAATAAAGAGA
1 AAATAAAG-GA
*
106983 AAATAAAGTA
1 AAATAAAGGA
106993 AAATAAAAGGA
1 AAAT-AAAGGA
107004 AAATAAA
1 AAATAAA
107011 ATGCTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (10 bp):
AAATAAAGGA
Found at i:107058 original size:13 final size:13
Alignment explanation
Indices: 107041--107071 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
107031 AAAAATGAAA
107041 AAAAATATAAAGAT
1 AAAAATA-AAAGAT
107055 AAAAATAAAAGAT
1 AAAAATAAAAGAT
107068 AAAA
1 AAAA
107072 CAAAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAGAT
Found at i:107117 original size:20 final size:21
Alignment explanation
Indices: 107084--107123 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
107074 AAATGAAAAT
*
107084 ATGAAATATAATATGATAATG
1 ATGAAATATAATATAATAATG
*
107105 ATGAAGTAT-ATATAATAAT
1 ATGAAATATAATATAATAAT
107124 AGTAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (21 bp):
ATGAAATATAATATAATAATG
Found at i:107301 original size:24 final size:24
Alignment explanation
Indices: 107227--107301 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
107217 GTAAAGAAAT
* * * *
107227 ATAAAATATACATATATATAAATA
1 ATAAAAAATAAATATAAATAAAAA
107251 ATAAAACAA-AAATA-AAATAAAATA
1 ATAAAA-AATAAATATAAATAAAA-A
* *
107275 ATAAAAAATATATATACATAAAAA
1 ATAAAAAATAAATATAAATAAAAA
107299 ATA
1 ATA
107302 TGCTTTGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
23 8 0.20
24 25 0.61
25 8 0.20
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (24 bp):
ATAAAAAATAAATATAAATAAAAA
Found at i:109084 original size:32 final size:34
Alignment explanation
Indices: 109006--109084 Score: 112
Period size: 32 Copynumber: 2.4 Consensus size: 34
108996 CGAAGGTTTG
*
109006 GTGTTTCAAGAGAAACATTTTCAAAGGTTTCCTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTCCTT
*
109040 -T-TTTCAAGAGAAACAATTTCAAAGGTTT-TTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTCCTT
109071 GTGTTTCAA-AGAAA
1 GTGTTTCAAGAGAAA
109085 ATGTCTCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 2 0.05
32 32 0.78
33 7 0.17
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (34 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTCCTT
Found at i:109215 original size:36 final size:36
Alignment explanation
Indices: 109155--109600 Score: 217
Period size: 36 Copynumber: 13.0 Consensus size: 36
109145 TTGGTGCTTC
* *
109155 AAGAGGAACTGTCTCAAGAGAGACAAAACTTGTTTT
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
* * *
109191 AAGGGAAATTGTTTCAAGAGAGACAAAATTTG-TTT
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
* *
109226 CAGAGAAA-TGTCTC-A-AGAGACAAAACTCAGTTTT
1 AAGAGAAATTGTCTCAAGAGAGACAAAACT-TGTTTT
* * * * *
109260 AAAAGAAATTGTCTCGAGAGAGACGAAATTTGTTTA
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
* ** *
109296 AAG-GAAAATAGAT-TC-A-A-AG----ATTTTG-TTC
1 AAGAG-AAATTG-TCTCAAGAGAGACAAAACTTGTTTT
* * * * *
109324 AAGGGAAACTGTCTCAAGTGAGACAAAATTTGTTTC
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
* * * **
109360 AAGAGAAACTGTCTCAAAAGAGACAAAATTTAGTTCC
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTT-GTTTT
* * * ** * *
109397 AAAAGAAACTGTCTCGAGAGAGATGAAATTTGTTTA
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
* * * *
109433 AAG-GAAACATAT-TC-A-A-AG-----ATTTGTTTC
1 AAGAGAAA-TTGTCTCAAGAGAGACAAAACTTGTTTT
* *
109460 AAGGGAAACTGTCTCAAGAGAGACAAAA-TTG-TTT
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
* * ****
109494 AAGAGAAAATGTCTCAAGGGAGACAAAAAAACTTTT
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
* * *
109530 AAGAAAAAATGTCTCAAGACAGACAAAA-TTGTTTT
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
*
109565 AAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTT
1 AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
109601 GAGATAAACC
Statistics
Matches: 321, Mismatches: 57, Indels: 64
0.73 0.13 0.14
Matches are distributed among these distances:
27 14 0.04
28 17 0.05
29 8 0.02
30 1 0.00
31 4 0.01
32 13 0.04
33 5 0.02
34 43 0.13
35 60 0.19
36 115 0.36
37 41 0.13
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (36 bp):
AAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTT
Found at i:109224 original size:21 final size:20
Alignment explanation
Indices: 109168--109231 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
109158 AGGAACTGTC
109168 TCAAGAGAGACAAAACTTGTT
1 TCAAGAGAGACAAAA-TTGTT
*
109189 TTAAG-G-G---AAATTGTT
1 TCAAGAGAGACAAAATTGTT
109204 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAA-TTGTT
109225 TC-AGAGA
1 TCAAGAGA
109232 AATGTCTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 13
0.70 0.04 0.26
Matches are distributed among these distances:
15 9 0.26
16 4 0.11
17 1 0.03
19 1 0.03
20 9 0.26
21 11 0.31
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (20 bp):
TCAAGAGAGACAAAATTGTT
Found at i:109268 original size:69 final size:70
Alignment explanation
Indices: 109164--109600 Score: 211
Period size: 73 Copynumber: 6.4 Consensus size: 70
109154 CAAGAGGAAC
* ** *
109164 TGTCTCAAGAGAGACAAAACTTGTTTTAAGGGAAATTGTTTCAAGAGAGACAAAATTTGTTTCAG
1 TGTCTCAAGAGAGACAAAACTAGTTTTAAAAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAG
109229 AGAAA
66 AGAAA
* *
109234 TGTCTC-A-AGAGACAAAACTCAGTTTTAAAAGAAATTGTCTCGAGAGAGACGAAATTTGTTT-A
1 TGTCTCAAGAGAGACAAAACT-AGTTTTAAAAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCA
* *
109296 AAGGAA
65 GAGAAA
* ** * ** * *
109302 ------AATAGATTCAAAGA-T-TTTGTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTTT
1 TGTCTCAAGAGAGACAAA-ACTAGTT-TT-AAAAGAAATTGTCTCAAGAGAGACAAAATTTGTTT
109359 CAAGAGAAA
63 C-AGAGAAA
* * ** * * **
109368 CTGTCTCAAAAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCGAGAGAGATGAAATTTGTTT-
1 -TGTCTCAAGAGAGACAAAA-CTAGTTTTAAAAGAAATTGTCTCAAGAGAGACAAAATTTGTTTC
*
109432 AAAGGAAACA
64 AGA-G-AA-A
* * * * ** * *
109442 TAT-TC-A-A-AG-----ATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTGTTTAAG
1 TGTCTCAAGAGAGACAAAACTAGTTTTAAAAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAG
109497 AGAAAA
66 AG-AAA
* ** * * * *
109503 TGTCTCAAGGGAGACAAAAAAACTTTTAAGAA-AAAATGTCTCAAGACAGACAAAA-TTGTTTTA
1 TGTCTCAAGAGAGACAAAACTAGTTTTAA-AAGAAATTGTCTCAAGAGAGACAAAATTTG-TTTC
109566 AGAGAAA
64 AGAGAAA
*
109573 CTGTCTCAAGAGAGACAAAACTTGTTTT
1 -TGTCTCAAGAGAGACAAAACTAGTTTT
109601 GAGATAAACC
Statistics
Matches: 276, Mismatches: 57, Indels: 67
0.69 0.14 0.17
Matches are distributed among these distances:
61 3 0.01
62 14 0.05
63 35 0.13
64 38 0.14
65 3 0.01
66 5 0.02
68 17 0.06
69 38 0.14
70 40 0.14
71 33 0.12
72 4 0.01
73 42 0.15
74 2 0.01
75 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (70 bp):
TGTCTCAAGAGAGACAAAACTAGTTTTAAAAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAG
AGAAA
Found at i:109433 original size:137 final size:135
Alignment explanation
Indices: 109184--109521 Score: 474
Period size: 137 Copynumber: 2.5 Consensus size: 135
109174 GAGACAAAAC
* * *
109184 TTGTTTTAAGGGAAATTGTTTCAAGAGAGACAAAATTTGTTTC-AGAGAAATGTCTC--AAGAGA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATGTCTCAAAAGAGA
** *
109246 CAAAACTCAGTTTTAAAAGAAATTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAA-ATAGATT
66 CAAAACTCAGTTCCAAAAGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAACAT--ATT
109310 CAAAGAT
129 CAAAGAT
*
109317 TT-TGTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGA
1 TTGT-TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA-TGTCTCAAAAGA
* * *
109381 GACAAAATTTAGTTCCAAAAGAAACTGTCTCGAGAGAGATGAAATTTGTTTAAAGGAAACATATT
64 GACAAAACTCAGTTCCAAAAGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAACATATT
109446 CAAAGAT
129 CAAAGAT
**
109453 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTGTTT-AAGAGAAAATGTCTCAAGGGAG
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAG-AAATGTCTCAAAAGAG
109516 ACAAAA
65 ACAAAA
109522 AAACTTTTAA
Statistics
Matches: 184, Mismatches: 13, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
132 1 0.01
133 37 0.20
134 29 0.16
135 15 0.08
136 42 0.23
137 58 0.32
138 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (135 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATGTCTCAAAAGAGA
CAAAACTCAGTTCCAAAAGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAACATATTCA
AAGAT
Found at i:109565 original size:35 final size:35
Alignment explanation
Indices: 109453--109600 Score: 181
Period size: 35 Copynumber: 4.2 Consensus size: 35
109443 ATTCAAAGAT
* * *
109453 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
*
109488 TTG-TTTAAGAGAAAATGTCTCAAGGGAGACAAAAA
1 TTGTTTTAAGAGAAAATGTCTCAAGAGAGAC-AAAA
*** * *
109523 AACTTTTAAGAAAAAATGTCTCAAGACAGACAAAA
1 TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
*
109558 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
109593 CTTGTTTT
1 -TTGTTTT
109601 GAGATAAACC
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
34 23 0.24
35 40 0.43
36 31 0.33
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
Found at i:109616 original size:36 final size:35
Alignment explanation
Indices: 109453--109617 Score: 107
Period size: 36 Copynumber: 4.7 Consensus size: 35
109443 ATTCAAAGAT
* * ** *
109453 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTTAAGAGAAACCATCTCAAGACAGACAAAA
*** **
109488 TTG-TTTAAGAGAAAATGTCTCAAGGGAGACAAAAA
1 TTGTTTTAAGAGAAACCATCTCAAGACAGAC-AAAA
*** * ***
109523 AACTTTTAAGAAAAAATGTCTCAAGACAGACAAAA
1 TTGTTTTAAGAGAAACCATCTCAAGACAGACAAAA
** *
109558 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTTAAGAGAAACCATCTCAAGACAGACAAAA
* *
109593 CTTGTTTTGAGATAAACCATCTCAA
1 -TTGTTTTAAGAGAAACCATCTCAA
109618 AGGTGATCAA
Statistics
Matches: 107, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
34 23 0.21
35 40 0.37
36 44 0.41
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (35 bp):
TTGTTTTAAGAGAAACCATCTCAAGACAGACAAAA
Done.