Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011552.1 Corchorus capsularis cultivar CVL-1 contig11573, 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: 88373
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:206 original size:2 final size:2
Alignment explanation
Indices: 194--227 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
184 CCACCATGAT
194 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
228 TTCTAACTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:850 original size:3 final size:3
Alignment explanation
Indices: 842--876 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
832 AAAACTTACA
*
842 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTT TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
877 TGAATGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:935 original size:86 final size:86
Alignment explanation
Indices: 790--1018 Score: 415
Period size: 86 Copynumber: 2.7 Consensus size: 86
780 GCGAAGAAAC
790 TTGAATGAGATCAAACAAATTAAGGATGGAGACAATTACATGAAAACTTACATTGTTGTTGTTGT
1 TTGAATGAGATCAAACAAATTAAGGATGGAGACAATTACATGAAAACTTACATTGTTGTTGTTGT
855 TGTTGTTGTTGTTGTTTTT-GT
66 TGTT-TTGTTGTTGTTTTTGGT
876 TTGAATGAGATCAAACAAATTAAGGATGGAGACAATTACATGAAAACTTACATTGTTGTTGTTGT
1 TTGAATGAGATCAAACAAATTAAGGATGGAGACAATTACATGAAAACTTACATTGTTGTTGTTGT
* * *
941 TGTTTTTTTTTTTTTTTTGGT
66 TGTTTTGTTGTTGTTTTTGGT
962 TTGAATGAGATCAAACAAATTAAGGATGGAGACAATTACATGAAAACTTACATTGTT
1 TTGAATGAGATCAAACAAATTAAGGATGGAGACAATTACATGAAAACTTACATTGTT
1019 TTTTTTTTTT
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
85 11 0.08
86 128 0.92
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (86 bp):
TTGAATGAGATCAAACAAATTAAGGATGGAGACAATTACATGAAAACTTACATTGTTGTTGTTGT
TGTTTTGTTGTTGTTTTTGGT
Found at i:1114 original size:13 final size:14
Alignment explanation
Indices: 1091--1125 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
1081 CGTGTGTATA
1091 TATATATATTATACT
1 TATATA-ATTATACT
1106 T-TATAATTATACT
1 TATATAATTATACT
1119 TATATAA
1 TATATAA
1126 ATTTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.47
14 9 0.47
15 1 0.05
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATAATTATACT
Found at i:4903 original size:22 final size:21
Alignment explanation
Indices: 4868--4950 Score: 62
Period size: 22 Copynumber: 3.8 Consensus size: 21
4858 CACATGGCCA
*
4868 AGCACTTGA-CCGGCCACACC
1 AGCACATGACCCGGCCACACC
**
4888 AGCTACATGACCCGGCCATGCC
1 AGC-ACATGACCCGGCCACACC
4910 GATCGCACATG-CCCGGCCACACC
1 -A--GCACATGACCCGGCCACACC
* *
4933 GGCCACATGACCTGGCCA
1 AG-CACATGACCCGGCCA
4951 TGCCCATGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
20 4 0.08
21 11 0.22
22 16 0.33
23 11 0.22
24 5 0.10
25 2 0.04
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.11
Consensus pattern (21 bp):
AGCACATGACCCGGCCACACC
Found at i:4941 original size:45 final size:44
Alignment explanation
Indices: 4877--4962 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 44
4867 AAGCACTTGA
* *
4877 CCGGCCACACCAGCTACATGACCCGGCCATGCCGATCGCACATGC
1 CCGGCCACACCAGCCACATGACCCGGCCATGCCCAT-GCACATGC
* *
4922 CCGGCCACACCGGCCACATGACCTGGCCATGCCCATGCACA
1 CCGGCCACACCAGCCACATGACCCGGCCATGCCCATGCACA
4963 ACCGGCCGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 5 0.14
45 32 0.86
ACGTcount: A:0.22, C:0.45, G:0.22, T:0.10
Consensus pattern (44 bp):
CCGGCCACACCAGCCACATGACCCGGCCATGCCCATGCACATGC
Found at i:7254 original size:33 final size:33
Alignment explanation
Indices: 7217--7289 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
7207 CGCCAAGCGA
*
7217 TGGCCGGTTG-TGGCCGGACATGTCC-ATGTCGCG
1 TGGCCGG-TGATGGCCGGACATCTCCGA-GTCGCG
* *
7250 TGGCCAGTGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
7283 TGGCCGG
1 TGGCCGG
7290 GCTTCTCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
32 2 0.06
33 31 0.91
34 1 0.03
ACGTcount: A:0.10, C:0.29, G:0.41, T:0.21
Consensus pattern (33 bp):
TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
Found at i:7290 original size:23 final size:23
Alignment explanation
Indices: 7259--7312 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
7249 GTGGCCAGTG
*
7259 ATGGCCGGGCATCTCCGAGTCGC
1 ATGGCCGGGCATCTCCAAGTCGC
* *
7282 GTGGCCGGGCTTCTCCAAGTCGC
1 ATGGCCGGGCATCTCCAAGTCGC
7305 ATGGCCGG
1 ATGGCCGG
7313 TCACTCGCGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.11, C:0.33, G:0.37, T:0.19
Consensus pattern (23 bp):
ATGGCCGGGCATCTCCAAGTCGC
Found at i:12662 original size:6 final size:5
Alignment explanation
Indices: 12630--12664 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
12620 TTCTGGTCGA
12630 ATTTT -TTTT ATTTT ATTTT ATTTT ATTTAT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T ATTTT
12665 TCGATATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:12760 original size:17 final size:17
Alignment explanation
Indices: 12738--12771 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12728 GAATCGGCTA
12738 TGAATTTTTGAAGTTTC
1 TGAATTTTTGAAGTTTC
*
12755 TGAATTTTTGAATTTTC
1 TGAATTTTTGAAGTTTC
12772 AAGAAGGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
TGAATTTTTGAAGTTTC
Found at i:13798 original size:33 final size:33
Alignment explanation
Indices: 13756--13840 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 33
13746 GCCGGACATG
*
13756 TCCATGTCGCGTGGCCGGTGATGACCGGGAATC
1 TCCAAGTCGCGTGGCCGGTGATGACCGGGAATC
* * * * **
13789 TCCGAGTCGCGTGGCCAGTGTTGGCCGGGCTTC
1 TCCAAGTCGCGTGGCCGGTGATGACCGGGAATC
*
13822 TCCAAGTCGCATGGCCGGT
1 TCCAAGTCGCGTGGCCGGT
13841 CACTCGAGCC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.12, C:0.29, G:0.36, T:0.22
Consensus pattern (33 bp):
TCCAAGTCGCGTGGCCGGTGATGACCGGGAATC
Found at i:18760 original size:35 final size:34
Alignment explanation
Indices: 18684--19218 Score: 557
Period size: 35 Copynumber: 15.7 Consensus size: 34
18674 TTCTAACTAA
* *
18684 ACTTAATTACCCTGAATTAAATTGCTTA-T---T
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACT
*
18714 ACTTAATTACCCTGAATTAAGTTGATTACTGATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACT
*
18748 GACTTAATTACCCTGATTTAAGTTGATTACTGACT
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGACT
*
18783 CACTTAATTACCCTGAATTAAGTTGATTACTGATT
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGACT
*
18818 GACTTAATTACCCTGATTTAAGTTGATTACTGACT
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGACT
18853 CACTTAATTACCCTGAATTAAGGTTGATTACTGACTT
1 -ACTTAATTACCCTGAATTAA-GTTGATTACTGAC-T
* *
18890 ACTTAATTACCCTGAATTAAGTTGCTTACCGACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACT
* *
18924 CACTTAATTATCCTGAATTAA---G-TTACTGCCTT
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGAC-T
* ** * * *
18956 ACTTAGTTTTCCTGAACTAAGTT-ACTAACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTG-ACT
18991 ACTTAATTACCCTGAATTAAGGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAA-GTTGATTACTGAC-T
* *
19027 ACTTAATTACCCTGAATTAAGTTGCTTACCGACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACT
*
19061 CACTTAATTACCCTGAATTAAGTT-ACT-CGTTGAACT
1 -ACTTAATTACCCTGAATTAAGTTGATTAC--TG-ACT
* *
19097 ACTTAATTACCCTGAATTAAGTT-ACTTATTAACT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACT
19131 CACTTAATTACCCTGAATTAGAGTTG---A---ACT
1 -ACTTAATTACCCTGAATTA-AGTTGATTACTGACT
* *
19161 ACTTAATTACCCCGAATTAAGTTGATTGCTGACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACT
19195 CACTTAATTACCCTGAATTAAGTT
1 -ACTTAATTACCCTGAATTAAGTT
19219 ACTCATTAAC
Statistics
Matches: 431, Mismatches: 40, Indels: 63
0.81 0.07 0.12
Matches are distributed among these distances:
28 5 0.01
29 18 0.04
30 29 0.07
31 24 0.06
32 2 0.00
33 2 0.00
34 10 0.02
35 269 0.62
36 70 0.16
37 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (34 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACT
Found at i:18798 original size:70 final size:69
Alignment explanation
Indices: 18684--19218 Score: 613
Period size: 70 Copynumber: 7.8 Consensus size: 69
18674 TTCTAACTAA
* *
18684 ACTTAATTACCCTGAATTAAATTGCTTA-T---T-ACTTAATTACCCTGAATTAAGTTGATTACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
18744 GATT
66 GATT
*
18748 GACTTAATTACCCTGATTTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTAC
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTAC
18813 TGATT
65 TGATT
*
18818 GACTTAATTACCCTGATTTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGGTTGATTA
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAA-GTTGATTA
18883 CTGACTT
64 CTGA-TT
* * *
18890 ACTTAATTACCCTGAATTAAGTTGCTTACCGACTCACTTAATTATCCTGAATTAA---G-TTACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
*
18951 GCCTT
66 G-ATT
* ** * * * *
18956 ACTTAGTTTTCCTGAACTAAGTT-ACTAACTGAATTACTTAATTACCCTGAATTAAGGTTGATTA
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTCACTTAATTACCCTGAATTAA-GTTGATTA
19020 CTGACTT
64 CTGA-TT
* * *
19027 ACTTAATTACCCTGAATTAAGTTGCTTACCGACTCACTTAATTACCCTGAATTAAGTT-ACT-CG
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTAC-
*
19090 TTGAACT
65 -TG-ATT
* *
19097 ACTTAATTACCCTGAATTAAGTT-ACTTATTAACTCACTTAATTACCCTGAATTAGAGTTGA--A
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTCACTTAATTACCCTGAATTA-AGTTGATTA
19159 C----T
64 CTGATT
* *
19161 ACTTAATTACCCCGAATTAAGTTGATTGCTGACTCACTTAATTACCCTGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTT
19219 ACTCATTAAC
Statistics
Matches: 408, Mismatches: 38, Indels: 50
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.01
64 49 0.12
65 26 0.06
66 53 0.13
67 1 0.00
68 1 0.00
69 3 0.01
70 146 0.36
71 122 0.30
72 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (69 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
GATT
Found at i:19013 original size:137 final size:138
Alignment explanation
Indices: 18714--19225 Score: 615
Period size: 137 Copynumber: 3.7 Consensus size: 138
18704 ATTGCTTATT
*
18714 ACTTAATTACCCTGAATTAA-GTTGATTACTGA-TTGACTTAATTACCCTGATTTAAGTTGATTA
1 ACTTAATTACCCTGAATTAAGGTTGATTACTGACTT-ACTTAATTACCCTGAATTAAGTTGATTA
* ** *
18777 CTGACTCACTTAATTACCCTGAATTAAGTTGATTACTG-ATTGACTTAATTACCCTGATTTAAGT
65 CCGACTCACTTAATTACCCTGAATTAA---G-TTACTGCATTGACTTAATTTTCCTGAATTAAGT
*
18841 TGA-TTACTGACTC
126 T-ACTTACTGAATC
*
18854 ACTTAATTACCCTGAATTAAGGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGCTTAC
1 ACTTAATTACCCTGAATTAAGGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTAC
* * * * *
18919 CGACTCACTTAATTATCCTGAATTAAGTTACTGCCTT-ACTTAGTTTTCCTGAACTAAGTTACTA
66 CGACTCACTTAATTACCCTGAATTAAGTTACTGCATTGACTTAATTTTCCTGAATTAAGTTACTT
*
18983 ACTGAATT
131 ACTGAATC
*
18991 ACTTAATTACCCTGAATTAAGGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGCTTAC
1 ACTTAATTACCCTGAATTAAGGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTAC
* **
19056 CGACTCACTTAATTACCCTGAATTAAGTTACT-CGTTGAACTACTTAATTACCCTGAATTAAGTT
66 CGACTCACTTAATTACCCTGAATTAAGTTACTGCATTG----ACTTAATTTTCCTGAATTAAGTT
*
19120 ACTTA-TTAACTC
127 ACTTACTGAA-TC
* *
19132 ACTTAATTACCCTGAATT-AGAGTTG---A---AC-TACTTAATTACCCCGAATTAAGTTGATTG
1 ACTTAATTACCCTGAATTAAG-GTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTA
*
19189 CTGACTCACTTAATTACCCTGAATTAAGTTACT-CATT
65 CCGACTCACTTAATTACCCTGAATTAAGTTACTGCATT
19226 AACCGATTCA
Statistics
Matches: 334, Mismatches: 27, Indels: 28
0.86 0.07 0.07
Matches are distributed among these distances:
134 61 0.18
135 2 0.01
136 4 0.01
137 127 0.38
138 4 0.01
140 25 0.07
141 109 0.33
142 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (138 bp):
ACTTAATTACCCTGAATTAAGGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTAC
CGACTCACTTAATTACCCTGAATTAAGTTACTGCATTGACTTAATTTTCCTGAATTAAGTTACTT
ACTGAATC
Found at i:19163 original size:64 final size:64
Alignment explanation
Indices: 19026--19218 Score: 255
Period size: 64 Copynumber: 2.9 Consensus size: 64
19016 ATTACTGACT
* *
19026 TACTTAATTACCCTGAATTAAGTTGCTTACCGACTCACTTAATTACCCTGAATTAAGTTACTCGT
1 TACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTTAATTACCCTGAATT-AG--A---GT
19091 TGAAC
60 TGAAC
* *
19096 TACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCCTGAATTAGAGTTGAAC
1 TACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTTAATTACCCTGAATTAGAGTTGAAC
* *
19160 TACTTAATTACCCCGAATTAAGTTGA-TTGCTGACTCACTTAATTACCCTGAATTA-AGTT
1 TACTTAATTACCCTGAATTAAGTT-ACTTACTGACTCACTTAATTACCCTGAATTAGAGTT
19219 ACTCATTAAC
Statistics
Matches: 114, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
63 4 0.04
64 56 0.49
65 1 0.01
67 1 0.01
69 2 0.02
70 50 0.44
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (64 bp):
TACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTTAATTACCCTGAATTAGAGTTGAAC
Found at i:36596 original size:24 final size:25
Alignment explanation
Indices: 36550--36597 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
36540 ATTGGAGTAT
**
36550 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTAATTAATTTTA
*
36575 TTATTT-TCTTGTTAATTTATTTT
1 TTATTTATCTTGTTAATTAATTTT
36598 TATTGTTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATTTATCTTGTTAATTAATTTTA
Found at i:39012 original size:12 final size:12
Alignment explanation
Indices: 38997--39031 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
38987 CCTGACCGGT
38997 CATCGCATGGGC
1 CATCGCATGGGC
39009 CATCGCATGGGC
1 CATCGCATGGGC
39021 CATCGCATGGG
1 CATCGCATGGG
39032 GCAACCGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.34, T:0.17
Consensus pattern (12 bp):
CATCGCATGGGC
Found at i:39052 original size:30 final size:30
Alignment explanation
Indices: 39018--39082 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
39008 CCATCGCATG
39018 GGCCATCGCATGGGGCAACCG-GCCACAACC
1 GGCCATCGCATGGGGCAACCGCG-CACAACC
* *
39048 GGCCATTGCATGGGGCATCCGCGCACAACC
1 GGCCATCGCATGGGGCAACCGCGCACAACC
39078 GGCCA
1 GGCCA
39083 ATGGACCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.22, C:0.38, G:0.31, T:0.09
Consensus pattern (30 bp):
GGCCATCGCATGGGGCAACCGCGCACAACC
Found at i:39657 original size:12 final size:12
Alignment explanation
Indices: 39627--39660 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
39617 CGCATGGGAC
39627 CATGACCGGCCA
1 CATGACCGGCCA
39639 -A-GACCGGCCA
1 CATGACCGGCCA
39649 CATGACCGGCCA
1 CATGACCGGCCA
39661 TTGCTTGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.26, C:0.41, G:0.26, T:0.06
Consensus pattern (12 bp):
CATGACCGGCCA
Found at i:46548 original size:30 final size:30
Alignment explanation
Indices: 46514--46578 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
46504 TCATCGCATG
46514 GGCCATCGCATGAGGCAACCG-GCCACAACC
1 GGCCATCGCATGAGGCAACCGCG-CACAACC
* * *
46544 GGCCATCGCATGGGGCATCCGCGCACAATC
1 GGCCATCGCATGAGGCAACCGCGCACAACC
46574 GGCCA
1 GGCCA
46579 ACGGACCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.09
Consensus pattern (30 bp):
GGCCATCGCATGAGGCAACCGCGCACAACC
Found at i:47654 original size:21 final size:21
Alignment explanation
Indices: 47629--47670 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
47619 TATGACTCAT
47629 ATGCTATGAA-TGCTATGATTG
1 ATGCTATGAATTGCT-TGATTG
*
47650 ATGCTTTGAATTGCTTGATTG
1 ATGCTATGAATTGCTTGATTG
47671 GGTCGACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (21 bp):
ATGCTATGAATTGCTTGATTG
Found at i:55267 original size:2 final size:2
Alignment explanation
Indices: 55226--55255 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55216 AACATACGAC
55226 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
55256 GAATCAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55739 original size:22 final size:23
Alignment explanation
Indices: 55714--55765 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
55704 ATAAACTCCA
*
55714 TATGAAACTTTGAT-AACCTAAC
1 TATGAAACTTTAATAAACCTAAC
* **
55736 TATGAAATTTTAATAAACCTTCC
1 TATGAAACTTTAATAAACCTAAC
55759 TATGAAA
1 TATGAAA
55766 TTTCGTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (23 bp):
TATGAAACTTTAATAAACCTAAC
Found at i:58736 original size:58 final size:58
Alignment explanation
Indices: 58646--58763 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
58636 AGTTTTCATG
*
58646 ATTTTAGCTTCATTAGATTTATGATTTATTCGACTTTAATTGTATATTTGTATCTCTC
1 ATTTTAGCTTCATTAGATTTATGATTTATTCGACTTTAATTGTATATTTGTACCTCTC
58704 ATTTTAGCTTCATTAGATTTATGATTTATTCGACTTTAATTGTATATTTGTACCTCTC
1 ATTTTAGCTTCATTAGATTTATGATTTATTCGACTTTAATTGTATATTTGTACCTCTC
58762 AT
1 AT
58764 GCTTTAAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.53
Consensus pattern (58 bp):
ATTTTAGCTTCATTAGATTTATGATTTATTCGACTTTAATTGTATATTTGTACCTCTC
Found at i:59637 original size:18 final size:18
Alignment explanation
Indices: 59616--59652 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
59606 AACTTTCAAC
59616 ACTGCCCCTACCCCAGCA
1 ACTGCCCCTACCCCAGCA
* *
59634 ACTGCCCCTGCCCTAGCA
1 ACTGCCCCTACCCCAGCA
59652 A
1 A
59653 GAAGGCCCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.51, G:0.14, T:0.14
Consensus pattern (18 bp):
ACTGCCCCTACCCCAGCA
Found at i:61000 original size:72 final size:73
Alignment explanation
Indices: 60880--61053 Score: 260
Period size: 73 Copynumber: 2.4 Consensus size: 73
60870 TGGAAAATGG
* * *
60880 ACCATTTCAGTCGACTTAAACAGAAGTTGAAAACGCCCTACCTGTTGTG-CCATTCTGTATGAAT
1 ACCATTTCAGTCGACTTAAATAGAAGTTGAAAACGCCCTACCTATTGTGCCCATTCTGTATGAAC
60944 AGTAAATT
66 AGTAAATT
** *
60952 ACCATTTCAGTCGACTTAAATAGAAGTTGAAAACGCCCTGGCTATTGTGCCCATTTTGTATGAAC
1 ACCATTTCAGTCGACTTAAATAGAAGTTGAAAACGCCCTACCTATTGTGCCCATTCTGTATGAAC
61017 AGTAAATT
66 AGTAAATT
* * *
61025 GCCATTTCAGTCGACTGAAATTGAAGTTG
1 ACCATTTCAGTCGACTTAAATAGAAGTTG
61054 GAATGGCCCG
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 45 0.49
73 47 0.51
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (73 bp):
ACCATTTCAGTCGACTTAAATAGAAGTTGAAAACGCCCTACCTATTGTGCCCATTCTGTATGAAC
AGTAAATT
Found at i:61366 original size:18 final size:18
Alignment explanation
Indices: 61343--61379 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
61333 GACAAAATAA
61343 AATTAAGATAATAATTAT
1 AATTAAGATAATAATTAT
61361 AATTAAGATAATAATTAT
1 AATTAAGATAATAATTAT
61379 A
1 A
61380 GAAGAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTAAGATAATAATTAT
Found at i:64084 original size:192 final size:192
Alignment explanation
Indices: 63757--64135 Score: 749
Period size: 192 Copynumber: 2.0 Consensus size: 192
63747 ACTCCAAAAA
*
63757 GAAGGTGGGGTTCTTATACATTTTATGTTTAACTTAGTCATTTGATTATGCTTTTTTGATCCTTT
1 GAAGGTGGGGTTCTTATACACTTTATGTTTAACTTAGTCATTTGATTATGCTTTTTTGATCCTTT
63822 TCTCTTATTGCTTGAGTTTATGATAGGAGTTAGATAAGGTAATATTTTTCATAAATAAACTAAAT
66 TCTCTTATTGCTTGAGTTTATGATAGGAGTTAGATAAGGTAATATTTTTCATAAATAAACTAAAT
63887 TTGTAGGTTATGATTTGTGGAGGTATAGCCTTGATGATTGCTTTGTAACTCTAAATAGCCTT
131 TTGTAGGTTATGATTTGTGGAGGTATAGCCTTGATGATTGCTTTGTAACTCTAAATAGCCTT
63949 GAAGGTGGGGTTCTTATACACTTTATGTTTAACTTAGTCATTTGATTATGCTTTTTTGATCCTTT
1 GAAGGTGGGGTTCTTATACACTTTATGTTTAACTTAGTCATTTGATTATGCTTTTTTGATCCTTT
64014 TCTCTTATTGCTTGAGTTTATGATAGGAGTTAGATAAGGTAATATTTTTCATAAATAAACTAAAT
66 TCTCTTATTGCTTGAGTTTATGATAGGAGTTAGATAAGGTAATATTTTTCATAAATAAACTAAAT
64079 TTGTAGGTTATGATTTGTGGAGGTATAGCCTTGATGATTGCTTTGTAACTCTAAATA
131 TTGTAGGTTATGATTTGTGGAGGTATAGCCTTGATGATTGCTTTGTAACTCTAAATA
64136 AGTTTGATCA
Statistics
Matches: 186, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
192 186 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (192 bp):
GAAGGTGGGGTTCTTATACACTTTATGTTTAACTTAGTCATTTGATTATGCTTTTTTGATCCTTT
TCTCTTATTGCTTGAGTTTATGATAGGAGTTAGATAAGGTAATATTTTTCATAAATAAACTAAAT
TTGTAGGTTATGATTTGTGGAGGTATAGCCTTGATGATTGCTTTGTAACTCTAAATAGCCTT
Found at i:69856 original size:31 final size:31
Alignment explanation
Indices: 69787--69949 Score: 155
Period size: 31 Copynumber: 5.5 Consensus size: 31
69777 TCCTTTTGTG
* * * **
69787 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
69818 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
69849 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
69880 CA--T---GTGCCAC--G--ACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* * *
69902 CATGTGGCGTGCCACATGTCACTTTTTAGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
69933 CACGTGGCGTGCCACGT
1 CACGTGGCGTGCCACGT
69950 CGGACACCGT
Statistics
Matches: 109, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
22 13 0.12
24 2 0.02
26 5 0.05
27 7 0.06
29 2 0.02
31 80 0.73
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.33
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:71428 original size:72 final size:72
Alignment explanation
Indices: 71338--71529 Score: 206
Period size: 85 Copynumber: 2.5 Consensus size: 72
71328 TATTGACATA
* *
71338 ATTGGAGACAATTTTTGCAGGGATTCCTTCATAATTTGGCTTTCTCTTCATCCAATGAGTCATCT
1 ATTGGAGACAATTTTTGCAGAGATTCCTTCATAATTTGGCTTTCTCTTCATCCAATGAGTCAGCT
71403 TTGCATT
66 TTGCATT
* *
71410 ATTGGAGACAATTTTTGCAGAGATTCTTTATGATAACTTTGCAGACCATTGGCTTTCTCTTCATC
1 ATTGGAGACAATTTTTGCAGAGATTC-CT-TCATAA---T--------TTGGCTTTCTCTTCATC
*
71475 TAATGAGTCAGCTTTGCATT
53 CAATGAGTCAGCTTTGCATT
*
71495 ATTGGAGACAATTTTTGCAGAGATT-CTTTATAATT
1 ATTGGAGACAATTTTTGCAGAGATTCCTTCATAATT
71530 GGGATAACTT
Statistics
Matches: 100, Mismatches: 7, Indels: 27
0.75 0.05 0.20
Matches are distributed among these distances:
71 1 0.01
72 25 0.25
73 1 0.01
74 5 0.05
77 1 0.01
79 1 0.01
82 5 0.05
83 1 0.01
85 60 0.60
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (72 bp):
ATTGGAGACAATTTTTGCAGAGATTCCTTCATAATTTGGCTTTCTCTTCATCCAATGAGTCAGCT
TTGCATT
Found at i:71563 original size:21 final size:21
Alignment explanation
Indices: 71537--71582 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
71527 ATTGGGATAA
71537 CTTTGCAGACCATTATTTTTC
1 CTTTGCAGACCATTATTTTTC
71558 CTTTGCAGACCATTATTTTTC
1 CTTTGCAGACCATTATTTTTC
71579 CTTT
1 CTTT
71583 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.24, G:0.09, T:0.50
Consensus pattern (21 bp):
CTTTGCAGACCATTATTTTTC
Found at i:74655 original size:18 final size:18
Alignment explanation
Indices: 74632--74667 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
74622 CCTATGAAAT
*
74632 TCCAAAAAATTTTCAAAA
1 TCCAAAAAATCTTCAAAA
74650 TCCAAAAAATCTTCAAAA
1 TCCAAAAAATCTTCAAAA
74668 AAACATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (18 bp):
TCCAAAAAATCTTCAAAA
Found at i:81901 original size:27 final size:26
Alignment explanation
Indices: 81828--81902 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
81818 GCATTAGGGT
*
81828 CACA-TAAGGGCATTTTGGTCATTTT
1 CACACTAAGGGCATTTTGGTCATTTG
* *
81853 CACACTAAGGGCATTCTAGTCATTTG
1 CACACTAAGGGCATTTTGGTCATTTG
* * *
81879 CATATTCAGGGGCATTTTGGTCAT
1 CACACT-AAGGGCATTTTGGTCAT
81903 CTTAAGTCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 4 0.10
26 22 0.55
27 14 0.35
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (26 bp):
CACACTAAGGGCATTTTGGTCATTTG
Found at i:85556 original size:22 final size:23
Alignment explanation
Indices: 85529--85579 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
85519 AGATTTGAAG
85529 AAAAAAGCAAAA-AAAAAAAAAA
1 AAAAAAGCAAAAGAAAAAAAAAA
* * *
85551 AAAAAAGGAAAAGGAAAAAATAA
1 AAAAAAGCAAAAGAAAAAAAAAA
85574 AAAAAA
1 AAAAAA
85580 TGGAAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (23 bp):
AAAAAAGCAAAAGAAAAAAAAAA
Found at i:87876 original size:2 final size:2
Alignment explanation
Indices: 87869--87899 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
87859 TTACTAAAGT
87869 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
87900 GATCAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.