Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004979.1 Hibiscus syriacus cultivar Beakdansim tig00011177_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: 105977
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6776 original size:29 final size:29
Alignment explanation
Indices: 6734--6790 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
6724 TGAAGCACTC
*
6734 AAAAGAAGACAAAAATTCAAGCACTCAAA
1 AAAAGAAAACAAAAATTCAAGCACTCAAA
* * * *
6763 AAAAGAAAAGAAAAGTTGAAGTACTCAA
1 AAAAGAAAACAAAAATTCAAGCACTCAA
6791 CAACAATTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.61, C:0.12, G:0.14, T:0.12
Consensus pattern (29 bp):
AAAAGAAAACAAAAATTCAAGCACTCAAA
Found at i:9528 original size:13 final size:12
Alignment explanation
Indices: 9510--9539 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
9500 TAACCAAAGA
9510 TGAAAAGGTATG
1 TGAAAAGGTATG
9522 TTGAAAAGGTATG
1 -TGAAAAGGTATG
9535 TGAAA
1 TGAAA
9540 GATGCTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAAAGGTATG
Found at i:18387 original size:22 final size:22
Alignment explanation
Indices: 18361--18404 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18351 TGGTTAAAAT
18361 AGAAAAATAAGAATTAAATAAA
1 AGAAAAATAAGAATTAAATAAA
*
18383 AGAAAAATAATAATTAAATAAA
1 AGAAAAATAAGAATTAAATAAA
18405 CAAATTAAAG
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:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (22 bp):
AGAAAAATAAGAATTAAATAAA
Found at i:19137 original size:75 final size:78
Alignment explanation
Indices: 19045--19192 Score: 221
Period size: 76 Copynumber: 1.9 Consensus size: 78
19035 ATACCAAAAA
* * *
19045 AAAATATAATATTCTAAATCCTAATTGAAATACT-AAAACCTATTTAAACTAAAATAAAAAGAT-
1 AAAATATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATG
19108 AAAGATAAAATAT
66 AAAGATAAAATAT
* *
19121 AAAA-ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATG
1 AAAATATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATG
*
19185 AAATATAA
66 AAAGATAA
19193 TGTTTAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 25 0.39
76 32 0.50
77 7 0.11
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (78 bp):
AAAATATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATG
AAAGATAAAATAT
Found at i:21954 original size:17 final size:18
Alignment explanation
Indices: 21923--21957 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21913 AAGATATATT
21923 AAAAT-AAAATAAATAAA
1 AAAATAAAAATAAATAAA
21940 AAAATAAAAATAATATAA
1 AAAATAAAAATAA-ATAA
21958 TAATAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAAATAAATAAA
Found at i:22053 original size:21 final size:22
Alignment explanation
Indices: 22020--22060 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
22010 GGTTAAAATA
22020 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
22042 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
22061 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:22776 original size:64 final size:70
Alignment explanation
Indices: 22651--22842 Score: 220
Period size: 64 Copynumber: 2.7 Consensus size: 70
22641 TAAAACATCT
*
22651 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCAAA-A-AAAT-AAT----AT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATA-CAAAGATAAATAAATAAAAAT
*
22708 AATATTC
64 AATATCC
22715 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGAT-AA-AT--AA-ATAAA
22780 AATAATATCC
61 AATAATATCC
* *
22790 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA
1 TAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAA
22843 ATACAATGTT
Statistics
Matches: 110, Mismatches: 4, Indels: 18
0.83 0.03 0.14
Matches are distributed among these distances:
63 9 0.08
64 36 0.33
66 2 0.02
67 2 0.02
70 1 0.01
71 2 0.02
74 1 0.01
75 28 0.25
76 29 0.26
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (70 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAATAAATAAAAATAA
TATCC
Found at i:22839 original size:76 final size:75
Alignment explanation
Indices: 22706--22869 Score: 240
Period size: 76 Copynumber: 2.2 Consensus size: 75
22696 AAAAAATAAT
* *
22706 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-ATA
22771 AAAT-ATAAAA
65 AAATGATAAAA
*
22781 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 ATAATATCCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAATA
* * *
22846 CAATGTTTAAA
65 AAATGATAAAA
*
22857 ATATTATCCTAAA
1 ATAATATCCTAAA
22870 TTTGAATTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
75 32 0.40
76 48 0.60
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (75 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAA
AATGATAAAA
Found at i:23879 original size:15 final size:15
Alignment explanation
Indices: 23861--23890 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23851 CAACAAAAAG
*
23861 AAAAATAAAGAAGAA
1 AAAAATAAAAAAGAA
23876 AAAAATAAAAAAGAA
1 AAAAATAAAAAAGAA
23891 GAAGAAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAAATAAAAAAGAA
Found at i:23880 original size:21 final size:21
Alignment explanation
Indices: 23855--23898 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23845 GTGCTGCAAC
23855 AAAAAGAAAAATA-AAGAAGAA
1 AAAAAGAAAAA-AGAAGAAGAA
*
23876 AAAAATAAAAAAGAAGAAGAA
1 AAAAAGAAAAAAGAAGAAGAA
23897 AA
1 AA
23899 GAACTCCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAAAGAAAAAAGAAGAAGAA
Found at i:32655 original size:17 final size:18
Alignment explanation
Indices: 32635--32672 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
32625 AGTTTTTTAG
32635 TTTTTT-GG-TTTTTCTT
1 TTTTTTCGGCTTTTTCTT
32651 TTTTTTCGGCCTTTTTCTT
1 TTTTTTCGG-CTTTTTCTT
32670 TTT
1 TTT
32673 AAAAAATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
19 11 0.58
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.76
Consensus pattern (18 bp):
TTTTTTCGGCTTTTTCTT
Found at i:33510 original size:45 final size:46
Alignment explanation
Indices: 33434--33538 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 46
33424 ATAACTAATG
* *
33434 AATAAAATAATAATAAACAAACATGTCTTAA-C-T-C-TAATTCCT
1 AATAAAATAATAATAAAAAAAAATGTCTTAACCATCCTTAATTCCT
*
33476 AATAAAATAATAATAATTAAAAATAATGTTTTAACTCATCCTTAATTCCT
1 AATAAAATAATAATAA--AAAAA-AATGTCTTAAC-CATCCTTAATTCCT
33526 AATAAAATAATAA
1 AATAAAATAATAA
33539 ATCTAATCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
42 16 0.31
44 4 0.08
45 8 0.15
47 1 0.02
48 1 0.02
49 1 0.02
50 21 0.40
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (46 bp):
AATAAAATAATAATAAAAAAAAATGTCTTAACCATCCTTAATTCCT
Found at i:36131 original size:19 final size:19
Alignment explanation
Indices: 36107--36145 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
36097 TCGAATGCAT
36107 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
36126 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
36145 T
1 T
36146 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:36162 original size:65 final size:64
Alignment explanation
Indices: 36044--36252 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
36034 TATTCAAAGG
* *
36044 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
36105 ATTC
61 ATTT
36109 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
36174 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
36238 CATGCATCGATGCAC
1 CATGCACCGATGCAC
36253 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.41
65 65 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:36270 original size:64 final size:65
Alignment explanation
Indices: 36093--36255 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
36083 GAATTAATTG
* * * *
36093 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
36158 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
36221 A
65 A
36222 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
36256 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:39440 original size:35 final size:35
Alignment explanation
Indices: 39396--39505 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 35
39386 AAGGGAATTA
* **
39396 TGATTATATAGGCGTGAAATGGTGATATAAGATGG
1 TGATCATATAGGCGTGAAATGGTGATGGAAGATGG
* *
39431 TGATCATATAGGCGTGTAATGTTGATGGAAGATGG
1 TGATCATATAGGCGTGAAATGGTGATGGAAGATGG
**
39466 TGATGTTATAGGCGTGAAAATGGTGATGGAAGATGG
1 TGATCATATAGGCGTG-AAATGGTGATGGAAGATGG
39502 TGAT
1 TGAT
39506 GAACAAATAG
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 44 0.68
36 21 0.32
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.31
Consensus pattern (35 bp):
TGATCATATAGGCGTGAAATGGTGATGGAAGATGG
Found at i:49517 original size:13 final size:12
Alignment explanation
Indices: 49501--49542 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
49491 GTGCAAAAAG
49501 AAAGAAAATCAGA
1 AAAGAAAATCA-A
*
49514 AAAGAAAA-GAA
1 AAAGAAAATCAA
49525 AAAGAAAATTCAA
1 AAAGAAAA-TCAA
49538 AAAGA
1 AAAGA
49543 GAAAGCAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.74, C:0.05, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAGAAAATCAA
Found at i:49532 original size:24 final size:25
Alignment explanation
Indices: 49501--49547 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
49491 GTGCAAAAAG
49501 AAAGAAAA-TCAGAAAAGA-AAAGAA
1 AAAGAAAATTCA-AAAAGAGAAAGAA
49525 AAAGAAAATTCAAAAAGAGAAAG
1 AAAGAAAATTCAAAAAGAGAAAG
49548 CAAGCCAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.06
Consensus pattern (25 bp):
AAAGAAAATTCAAAAAGAGAAAGAA
Found at i:56740 original size:15 final size:14
Alignment explanation
Indices: 56720--56770 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
56710 TTTGATATCA
56720 TTTCTTTCCATTTTC
1 TTTCTTT-CATTTTC
56735 TTTCTTATCATTTTC
1 TTTCTT-TCATTTTC
*
56750 TTTCTTAACATTTTC
1 TTTCTT-TCATTTTC
56765 TTTCTT
1 TTTCTT
56771 CTTCCATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
15 33 0.97
16 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTCTTTCATTTTC
Found at i:56995 original size:10 final size:9
Alignment explanation
Indices: 56979--57022 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
56969 GTGCTGGAAC
56979 AAAAGAAAA
1 AAAAGAAAA
56988 AGAAAGAAAA
1 A-AAAGAAAA
*
56998 AAAACAAAA
1 AAAAGAAAA
57007 AAAAGAAAA
1 AAAAGAAAA
57016 GAAAAGA
1 -AAAAGA
57023 CTCCTACAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 16 0.52
10 15 0.48
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:72006 original size:6 final size:6
Alignment explanation
Indices: 71995--72028 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
71985 CTACTACAAC
*
71995 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAA
72029 GGAAAAGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:72014 original size:13 final size:12
Alignment explanation
Indices: 71992--72028 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
71982 AAACTACTAC
71992 AACAAAAAGAAA
1 AACAAAAAGAAA
*
72004 AAGAAAGAAGAAA
1 AACAAA-AAGAAA
72017 AACAAAAAGAAA
1 AACAAAAAGAAA
72029 GGAAAAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (12 bp):
AACAAAAAGAAA
Found at i:76484 original size:13 final size:12
Alignment explanation
Indices: 76468--76509 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
76458 GTGCAAAAAG
76468 AAAGAAAATCAGA
1 AAAGAAAATCA-A
76481 AAAGAAAAT-AA
1 AAAGAAAATCAA
*
76492 AAAGGAAATTCAA
1 AAA-GAAAATCAA
76505 AAAGA
1 AAAGA
76510 GAAAGCAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 4 0.15
12 8 0.31
13 14 0.54
ACGTcount: A:0.71, C:0.05, G:0.14, T:0.10
Consensus pattern (12 bp):
AAAGAAAATCAA
Found at i:82673 original size:20 final size:19
Alignment explanation
Indices: 82626--82675 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
82616 GGCCAAGAGC
* *
82626 ATGTATTTTCATTAAAGTT
1 ATGTATTTTCATTAAAATA
* *
82645 GTATATTTTCATTAACAATA
1 ATGTATTTTCATTAA-AATA
82665 ATGTATTTTCA
1 ATGTATTTTCA
82676 AAGAGATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (19 bp):
ATGTATTTTCATTAAAATA
Found at i:87061 original size:31 final size:32
Alignment explanation
Indices: 87000--87065 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
86990 TATTCCTTCT
* *
87000 TTTCTTTCATTCATTTTGCTTTTAACCATTTC
1 TTTCTTTCATTCATTTTGCCTTAAACCATTTC
87032 TTTCTTTTCATTCA-TTT-CCTTAAACCATTTC
1 TTTC-TTTCATTCATTTTGCCTTAAACCATTTC
87063 TTT
1 TTT
87066 ATCTTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 15 0.48
32 7 0.23
33 9 0.29
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.59
Consensus pattern (32 bp):
TTTCTTTCATTCATTTTGCCTTAAACCATTTC
Found at i:87072 original size:33 final size:32
Alignment explanation
Indices: 86996--87082 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
86986 CACCTATTCC
* *
86996 TTCTTTTC-TTTCATTCATTTTGCTTTTAACCAT
1 TTCTTTTCTTTTCATTCA-TTT-CCTTAAACCAT
87029 TTC-TTTCTTTTCATTCATTTCCTTAAACCAT
1 TTCTTTTCTTTTCATTCATTTCCTTAAACCAT
* *
87060 TTCTTTATCTTTTTATTCTTTTC
1 TTCTTT-TCTTTTCATTCATTTC
87083 TTCTTATATC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 12 0.26
32 9 0.19
33 26 0.55
ACGTcount: A:0.15, C:0.22, G:0.01, T:0.62
Consensus pattern (32 bp):
TTCTTTTCTTTTCATTCATTTCCTTAAACCAT
Found at i:87996 original size:20 final size:22
Alignment explanation
Indices: 87958--88013 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
87948 GGAAGATGAT
87958 TAATAAAGGAAGAATAAATGAAA
1 TAATAAA-GAAGAATAAATGAAA
87981 TAATAAAGAA-AA-AAATGAAA
1 TAATAAAGAAGAATAAATGAAA
88001 TGAAATAAAGAAG
1 T--AATAAAGAAG
88014 GGATAGAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 12 0.40
23 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (22 bp):
TAATAAAGAAGAATAAATGAAA
Found at i:88077 original size:17 final size:18
Alignment explanation
Indices: 88046--88079 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
88036 GATGGTCTTG
*
88046 ATGGATGATGTTGATGAA
1 ATGGATGATGGTGATGAA
88064 ATGGA-GATGGTGATGA
1 ATGGATGATGGTGATGA
88080 TGTTGTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (18 bp):
ATGGATGATGGTGATGAA
Found at i:91279 original size:15 final size:14
Alignment explanation
Indices: 91252--91286 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
91242 TATAAAATCG
91252 ATATATTCATCTAT
1 ATATATTCATCTAT
91266 ATATATTACATCTAT
1 ATATATT-CATCTAT
*
91281 AGATAT
1 ATATAT
91287 GATGATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (14 bp):
ATATATTCATCTAT
Found at i:93053 original size:30 final size:30
Alignment explanation
Indices: 93017--93099 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 30
93007 CTAAACCTTC
93017 TTTTCTTTCATTCCTTTTCTTAAAATC-A-TT
1 TTTTCTTTCATT-CTTTTCTTAAAA-CAATTT
*
93047 TTTTCTTTTCATTCATTTCTT-AAACAATTT
1 TTTTC-TTTCATTCTTTTCTTAAAACAATTT
93077 TTTATCTTTCCATTCTTTTCTTA
1 TTT-TCTTT-CATTCTTTTCTTA
93100 TTCTATATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
28 1 0.02
29 4 0.09
30 20 0.44
31 20 0.44
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTCTTTCATTCTTTTCTTAAAACAATTT
Found at i:93060 original size:31 final size:31
Alignment explanation
Indices: 93017--93099 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
93007 CTAAACCTTC
93017 TTTTC-TTTCATTCCTTTTCTTAAAATC-A-TT
1 TTTTCTTTTCATT-CTTTTCTTAAAA-CAATTT
*
93047 TTTTCTTTTCATTCATTTCTT-AAACAATTT
1 TTTTCTTTTCATTCTTTTCTTAAAACAATTT
*
93077 TTTATCTTTCCATTCTTTTCTTA
1 TTT-TCTTTTCATTCTTTTCTTA
93100 TTCTATATAC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 1 0.02
29 4 0.09
30 17 0.38
31 23 0.51
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTCTTTTCATTCTTTTCTTAAAACAATTT
Found at i:96923 original size:9 final size:10
Alignment explanation
Indices: 96896--96922 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
96886 TGAAAGAACA
96896 AAAAAAAATT
1 AAAAAAAATT
96906 AAAAAAAATT
1 AAAAAAAATT
96916 AAAAAAA
1 AAAAAAA
96923 TATTCTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAAATT
Done.