Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016030.1 Corchorus capsularis cultivar CVL-1 contig16051, 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: 71224
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2276 original size:2 final size:2
Alignment explanation
Indices: 2269--2296 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2259 CCTCCACCAA
2269 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2297 CCCGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2604 original size:29 final size:30
Alignment explanation
Indices: 2560--2635 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
2550 CGTCAGAAAA
*
2560 AGGACCGAATTGAGCAGGT-TCAAAGGTTT
1 AGGACCAAATTGAGCAGGTCTCAAAGGTTT
* **
2589 ATGACCAAATTGAGCATTTCGTCAAAGGTTT
1 AGGACCAAATTGAGCAGGTC-TCAAAGGTTT
2620 AGGACCAAATTGAGCA
1 AGGACCAAATTGAGCA
2636 TTTAGCCGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 15 0.38
31 25 0.62
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (30 bp):
AGGACCAAATTGAGCAGGTCTCAAAGGTTT
Found at i:2617 original size:31 final size:31
Alignment explanation
Indices: 2579--2638 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
2569 TTGAGCAGGT
*
2579 TCAAAGGTTTATGACCAAATTGAGCATTTCG
1 TCAAAGGTTTAGGACCAAATTGAGCATTTCG
2610 TCAAAGGTTTAGGACCAAATTGAGCATTT
1 TCAAAGGTTTAGGACCAAATTGAGCATTT
2639 AGCCGATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (31 bp):
TCAAAGGTTTAGGACCAAATTGAGCATTTCG
Found at i:6712 original size:4 final size:4
Alignment explanation
Indices: 6705--6729 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6695 TTTCTCTCTC
6705 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
6730 GTAGAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:8974 original size:7 final size:7
Alignment explanation
Indices: 8962--8986 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8952 AAGGCAAGGT
8962 AATTTTA
1 AATTTTA
8969 AATTTTA
1 AATTTTA
8976 AATTTTA
1 AATTTTA
8983 AATT
1 AATT
8987 GTTGCTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:11553 original size:183 final size:183
Alignment explanation
Indices: 11191--11741 Score: 1059
Period size: 183 Copynumber: 3.0 Consensus size: 183
11181 CAATCCAAGG
* *
11191 TTATGTTCAATGATATACTACACTTAGTTTTTCTTAATATACTTTTGTCTCCATTGATTGGCTCA
1 TTATGTTCAATGATATACTACACTTAGTTTTCCTTAATATACTTTTGTCTCTATTGATTGGCTCA
11256 GCTGTAGTTATCCATATTTTAAGTGAATTAAAATATACTACACTTAGTTTTAGAGTCTTTTAGCC
66 GCTGTAGTTATCCATATTTTAAGTGAATTAAAATATACTACACTTAGTTTTAGAGTCTTTTAGCC
11321 ACCTAGGTGTGATTTCAAGTGAATCAATCTTTACCAAGTATAGAATTGACTGA
131 ACCTAGGTGTGATTTCAAGTGAATCAATCTTTACCAAGTATAGAATTGACTGA
11374 TTATGTTCAATGATATACTACACTTAGTTTTCCTTAATATACTTTTGTCTCTATTGATTGGCTCA
1 TTATGTTCAATGATATACTACACTTAGTTTTCCTTAATATACTTTTGTCTCTATTGATTGGCTCA
11439 GCTGTAGTTATCCATATTTTAAGTGAATTAAAATATACTACACTTAGTTTTAGAGTC-TTTAGCC
66 GCTGTAGTTATCCATATTTTAAGTGAATTAAAATATACTACACTTAGTTTTAGAGTCTTTTAGCC
11503 ACCTAGGTGTGATTTCAAGTGAATCAATCTTTACCAAGTATAGTAATTGACTGA
131 ACCTAGGTGTGATTTCAAGTGAATCAATCTTTACCAAGTATAG-AATTGACTGA
11557 TTATGTTCAATGATATACTACACTTAGTTTTCCTTAATATACTTTTGTCTCTATTGATTGGCTCA
1 TTATGTTCAATGATATACTACACTTAGTTTTCCTTAATATACTTTTGTCTCTATTGATTGGCTCA
11622 GCTGTAGTTATCCATATTTTAAGTGAATTAAAATATACTACACTTAGTTTTAGAGTCTTTTAGCC
66 GCTGTAGTTATCCATATTTTAAGTGAATTAAAATATACTACACTTAGTTTTAGAGTCTTTTAGCC
*
11687 ACCTAGGTGTGGTTTCAAGTGAATCAATCTTTACCAAGTATAGAATTGACTGA
131 ACCTAGGTGTGATTTCAAGTGAATCAATCTTTACCAAGTATAGAATTGACTGA
11740 TT
1 TT
11742 GTACAGACTT
Statistics
Matches: 363, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
182 50 0.14
183 264 0.73
184 49 0.13
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (183 bp):
TTATGTTCAATGATATACTACACTTAGTTTTCCTTAATATACTTTTGTCTCTATTGATTGGCTCA
GCTGTAGTTATCCATATTTTAAGTGAATTAAAATATACTACACTTAGTTTTAGAGTCTTTTAGCC
ACCTAGGTGTGATTTCAAGTGAATCAATCTTTACCAAGTATAGAATTGACTGA
Found at i:16319 original size:30 final size:30
Alignment explanation
Indices: 16283--16360 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
16273 CATCAGAAAA
16283 GGGCTTATTTGGCCTTTTTAA-AGAGTTCAG
1 GGGCTTATTTGGCC-TTTTAATAGAGTTCAG
**
16313 GGGCTTATTTGG-C-TGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTAA-TAGAGTTCAG
16342 GGGCTTATTTGGCCGTTTT
1 GGGCTTATTTGGCC-TTTT
16361 GTGTAAGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
29 22 0.56
30 13 0.33
32 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (30 bp):
GGGCTTATTTGGCCTTTTAATAGAGTTCAG
Found at i:16866 original size:94 final size:92
Alignment explanation
Indices: 16707--16889 Score: 276
Period size: 94 Copynumber: 2.0 Consensus size: 92
16697 GGACCATGTG
* *
16707 TGGAGCCAATATTAAGCACAAATCCATGTATCCATTGTCCTGTTTCGGACCATGTCGTGGCGGGC
1 TGGAGCCAATATTAAGCACAAATCCATGTATCCATTGCCCTGTTTCGGACCATGTCATGGCGGGC
16772 TAAAACGTCTAGCCCACATAATTCCCA
66 TAAAACGTCTAGCCCACATAATTCCCA
* * * *
16799 TGGAGTCAATATTAAGCACGAATCCATATGTATCCATTGCCCTGTTTTGGACCATGTCATTGCGG
1 TGGAGCCAATATTAAGCACAAATCC--ATGTATCCATTGCCCTGTTTCGGACCATGTCATGGCGG
* *
16864 GCTAAAAGGTCTAGCCCACCTAATTC
64 GCTAAAACGTCTAGCCCACATAATTC
16890 AGTTTTAATT
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 23 0.28
94 58 0.72
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (92 bp):
TGGAGCCAATATTAAGCACAAATCCATGTATCCATTGCCCTGTTTCGGACCATGTCATGGCGGGC
TAAAACGTCTAGCCCACATAATTCCCA
Found at i:16993 original size:7 final size:7
Alignment explanation
Indices: 16981--17005 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16971 TGATGAGCAT
16981 TACACAA
1 TACACAA
16988 TACACAA
1 TACACAA
16995 TACACAA
1 TACACAA
17002 TACA
1 TACA
17006 AATCCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (7 bp):
TACACAA
Found at i:35803 original size:31 final size:31
Alignment explanation
Indices: 35768--35833 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
35758 AACTTTATGT
* *
35768 TTTCCGATTGTACCCTTATGTTTAAAACATA
1 TTTCCAATTGTACCCTTATCTTTAAAACATA
* *
35799 TTTCCAATTGTACCCTTTTCTTTAAAATATA
1 TTTCCAATTGTACCCTTATCTTTAAAACATA
35830 TTTC
1 TTTC
35834 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATCTTTAAAACATA
Found at i:36174 original size:19 final size:21
Alignment explanation
Indices: 36142--36184 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
36132 TTCTTTACTA
36142 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
36163 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
36182 TTA
1 TTA
36185 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:36599 original size:22 final size:22
Alignment explanation
Indices: 36574--36724 Score: 83
Period size: 22 Copynumber: 6.8 Consensus size: 22
36564 TCTCTAAGTA
36574 GTTATCAAAATTTCATAAGATG
1 GTTATCAAAATTTCATAAGATG
* * *
36596 GTTATTATAATTTCATGAGGA-G
1 GTTATCAAAATTTCAT-AAGATG
* *
36618 GTTATCAAAATTCCAT-AGTGTG
1 GTTATCAAAATTTCATAAG-ATG
* * *
36640 GTTACCAAAATTTTAT-AGTGTG
1 GTTATCAAAATTTCATAAG-ATG
* *
36662 GTTACCAAAATTTCATATGATCAG
1 GTTATCAAAATTTCATAAGAT--G
* * * * *
36686 GTTATTAAAATGTCTTAGGTTG
1 GTTATCAAAATTTCATAAGATG
**
36708 GTTATTGAAATTTCATA
1 GTTATCAAAATTTCATA
36725 GCGTGGTTAA
Statistics
Matches: 100, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.01
22 79 0.79
23 4 0.04
24 16 0.16
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGATG
Found at i:36817 original size:58 final size:56
Alignment explanation
Indices: 36755--36885 Score: 131
Period size: 56 Copynumber: 2.3 Consensus size: 56
36745 TTTATAGAAA
* *
36755 GGTTATCAAAGAGATT-ATCAAA-ATGTCATAGCGAGGTCATATAAGAATTTCATAGTGT
1 GGTTATCAAA-A-ATTCATCAAATATGTAATAGCGAGGTCAT-CAA-AATTTCATAGTGT
* * * * * *
36813 GGTTAACAAAATTTCATTAAATATTTAATAGGGAGGTCATCAAAATTTTATAGTGT
1 GGTTATCAAAAATTCATCAAATATGTAATAGCGAGGTCATCAAAATTTCATAGTGT
*
36869 GGTTATCAAAATTTCAT
1 GGTTATCAAAAATTCAT
36886 ATGAATGTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
56 30 0.48
57 8 0.13
58 24 0.39
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (56 bp):
GGTTATCAAAAATTCATCAAATATGTAATAGCGAGGTCATCAAAATTTCATAGTGT
Found at i:36860 original size:22 final size:22
Alignment explanation
Indices: 36826--36882 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
36816 TAACAAAATT
*
36826 TCATTAAATATTTAATAGGGAGG
1 TCATCAAA-ATTTAATAGGGAGG
* * *
36849 TCATCAAAATTTTATAGTGTGG
1 TCATCAAAATTTAATAGGGAGG
*
36871 TTATCAAAATTT
1 TCATCAAAATTT
36883 CATATGAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (22 bp):
TCATCAAAATTTAATAGGGAGG
Found at i:36981 original size:22 final size:22
Alignment explanation
Indices: 36912--37183 Score: 145
Period size: 22 Copynumber: 12.5 Consensus size: 22
36902 TAAAAGTCTC
* *
36912 AATTTCATAG-G-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
36932 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* *
36952 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
36974 AATTTCATAGAGATTGGATTATCAA
1 AATTTCATAGAG--T-GATTATCAA
** *
36999 AATTT-ATAGAAAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
*
37020 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
*
37042 AATTTCAAAACGAG-G-TTATCAA
1 AATTTC-ATA-GAGTGATTATCAA
* *
37064 AATTACATA-ATGTGATTATCAG
1 AATTTCATAGA-GTGATTATCAA
* * * *
37086 AATTTCATAGAGAGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * * *
37108 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
37130 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
37152 ATTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
37174 AATTTCATAG
1 AATTTCATAG
37184 TGGTATTTCT
Statistics
Matches: 199, Mismatches: 34, Indels: 35
0.74 0.13 0.13
Matches are distributed among these distances:
19 3 0.02
20 20 0.10
21 28 0.14
22 122 0.61
23 5 0.03
24 8 0.04
25 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:37065 original size:44 final size:45
Alignment explanation
Indices: 36967--37182 Score: 189
Period size: 44 Copynumber: 4.9 Consensus size: 45
36957 CATAGAGTGA
* *
36967 TTATCGAAATTTCATAGAGATTGGATTATCAAAATTT-ATAGAA-AGG
1 TTATCAAAATTTCATAAAG-TT-GATTATCAAAATTTCATA-AAGAGG
**
37013 TTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCA-AAACGAGG
1 TTATCAAAATTTCATAAAGTTGATTATCAAAATTTCATAAA-GAGG
* * * *
37057 TTATCAAAATTACATAATG-TGATTATCAGAATTTCATAGAGAGG
1 TTATCAAAATTTCATAAAGTTGATTATCAAAATTTCATAAAGAGG
* * * * *
37101 TCAACAAAATTTTATAAAG-AGGTTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGTTGATTATCAAAATTTCATAAAGAGG
*
37145 TTATCAAATTTTCA-AAA-TGTGATTA-CAAAAATTTCATA
1 TTATCAAAATTTCATAAAGT-TGATTATC-AAAATTTCATA
37183 GTGGTATTTC
Statistics
Matches: 141, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
42 2 0.01
43 19 0.13
44 99 0.70
45 4 0.03
46 17 0.12
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (45 bp):
TTATCAAAATTTCATAAAGTTGATTATCAAAATTTCATAAAGAGG
Found at i:37096 original size:88 final size:88
Alignment explanation
Indices: 36990--37183 Score: 241
Period size: 88 Copynumber: 2.2 Consensus size: 88
36980 ATAGAGATTG
* * ** **
36990 GATTATCAAAATTT-ATAGAAAGGTTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAAC
1 GATTATCAAAATTTCATAGAAAGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAA-
*
37053 GAGGTTATCAAAATTACATAATGT
65 GAGGTTATCAAAATTACAAAATGT
* * *
37077 GATTATCAGAATTTCATAGAGAGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAAAGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAG
* *
37142 AGGTTATCAAATTTTCAAAATGT
66 AGGTTATCAAAATTACAAAATGT
37165 GATTA-CAAAAATTTCATAG
1 GATTATC-AAAATTTCATAG
37184 TGGTATTTCT
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
87 14 0.15
88 74 0.81
89 3 0.03
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (88 bp):
GATTATCAAAATTTCATAGAAAGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAG
AGGTTATCAAAATTACAAAATGT
Found at i:37158 original size:66 final size:65
Alignment explanation
Indices: 36992--37155 Score: 181
Period size: 66 Copynumber: 2.5 Consensus size: 65
36982 AGAGATTGGA
* ** * *
36992 TTATCAAAATTT-ATAGAA-AGGTTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAACGA
1 TTATCAAAATTTCATA-AAGAGGTTATC-AAATTTCATAGAGAGGTCAACAAAATTTCAAAACGA
37055 GG
64 GG
* * * * *
37057 TTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGAGGTCAACAAAATTTTATAAA-GA
1 TTATCAAAATTTCATAAAGAGGTTATCA-AATTTCATAGAGAGGTCAACAAAATTTCA-AAACGA
37121 GG
64 GG
37123 TTATCAAAATTTCATAAAGAGGTTATCAAATTT
1 TTATCAAAATTTCATAAAGAGGTTATCAAATTT
37156 TCAAAATGTG
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
65 18 0.22
66 60 0.74
67 3 0.04
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (65 bp):
TTATCAAAATTTCATAAAGAGGTTATCAAATTTCATAGAGAGGTCAACAAAATTTCAAAACGAGG
Found at i:37289 original size:20 final size:20
Alignment explanation
Indices: 37264--37314 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
37254 TTATGGAGTA
37264 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
37284 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
37303 ATCAAAATTTCA
1 ATCAAAATTTCA
37315 TATAAAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:37522 original size:45 final size:44
Alignment explanation
Indices: 37470--37576 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 44
37460 AAAATTTGTA
*
37470 GTTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAAG-GAG
1 GTTATCAA-ATTTCATAAGAAGAGTTATCAAAATTTCAT-AGCGAG
* * *
37514 GTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
1 G-TTATC-AAATTTCATAAGAAGAGTTATCAAAATTTCATAGCGAG
37560 GTTATCACAATTTCATA
1 GTTATCA-AATTTCATA
37577 GTGTGATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
44 2 0.04
45 30 0.57
46 21 0.40
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (44 bp):
GTTATCAAATTTCATAAGAAGAGTTATCAAAATTTCATAGCGAG
Found at i:37523 original size:23 final size:21
Alignment explanation
Indices: 37264--37861 Score: 236
Period size: 22 Copynumber: 27.7 Consensus size: 21
37254 TTATGGAGTA
*
37264 ATCAAAATTTCA-AGGAGGAT
1 ATCAAAATTTCATAGGAGGTT
* *
37284 ATCAAAA-TTCA-GGGAGGAT
1 ATCAAAATTTCATAGGAGGTT
**
37303 ATCAAAATTTCATATAAAGGTT
1 ATCAAAATTTCATA-GGAGGTT
*
37325 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG--GAGGTT
* * *
37347 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATAGGA-GGTT
* * *
37369 ATCAAAATTTCATAGTATGTAG
1 ATCAAAATTTCATAGGAGGT-T
*
37391 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATA-GGAGGTT
* * *
37413 AACAAAATTTCATAATGAGATT
1 ATCAAAATTTCAT-AGGAGGTT
* ** *
37435 ATAAAAAAATCATAGAGAGGCT
1 ATCAAAATTTCATAG-GAGGTT
*
37457 ATCAAAA-TT--T-GTA-GTT
1 ATCAAAATTTCATAGGAGGTT
* * *
37473 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCAT-AGGAGGTT
*
37495 ATCAAAATTTTATAAGGAGGTTT
1 ATCAAAATTTCAT-AGGAGG-TT
* *
37518 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGG-AG-GTT
37541 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAG-GAGGTT
* * *
37563 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAG-GAGGTT
* * *
37585 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAG-GAGGTT
37607 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATA-GGAGGTT
* * * * *
37629 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCAT-AGGAGGTT
*
37651 ATCAATATATT-ATATGGAGGTT
1 ATCAAAAT-TTCATA-GGAGGTT
* * * *
37673 ATCAACATCTCATAGTGTTGGTC
1 ATCAAAATTTCATAG-G-AGGTT
* *
37696 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCA-TAGGAGGTT
*
37718 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATA-GGAGGT-T
* * *
37741 -TCAAAATTCCTTAGGGAAGTT
1 ATCAAAATTTCATA-GGAGGTT
* * *
37762 AACCAAATTTCATAAGAAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
** **
37784 AAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* * * * *
37805 CTCGAAATTCCATAGTATCGTT
1 ATCAAAATTTCATAGGA-GGTT
* *
37827 -TTAAAATTTCATTGGAAGGTT
1 ATCAAAATTTCATAGG-AGGTT
37848 ATCAAAATTTCATA
1 ATCAAAATTTCATA
37862 ATGGGATCAT
Statistics
Matches: 431, Mismatches: 106, Indels: 80
0.70 0.17 0.13
Matches are distributed among these distances:
16 8 0.02
17 3 0.01
18 1 0.00
19 20 0.05
20 12 0.03
21 43 0.10
22 279 0.65
23 62 0.14
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:47441 original size:20 final size:20
Alignment explanation
Indices: 47401--47446 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
47391 CTCCCCCTAG
* *
47401 TGTTTGTTTATTTATTTATT
1 TGTTTGTTTATTCATTAATT
*
47421 TGTTTGTTTGTTCATTAATT
1 TGTTTGTTTATTCATTAATT
47441 TAGTTT
1 T-GTTT
47447 TTATTTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.15, C:0.02, G:0.13, T:0.70
Consensus pattern (20 bp):
TGTTTGTTTATTCATTAATT
Found at i:49348 original size:28 final size:28
Alignment explanation
Indices: 49308--49366 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
49298 CTGTATTATT
49308 TATAAGATTGTTTGAATTTGAGGGTTTC
1 TATAAGATTGTTTGAATTTGAGGGTTTC
49336 TATAAGATTGTTTGAATTTGAGGGTTTC
1 TATAAGATTGTTTGAATTTGAGGGTTTC
49364 TAT
1 TAT
49367 GTTTTAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.24, T:0.47
Consensus pattern (28 bp):
TATAAGATTGTTTGAATTTGAGGGTTTC
Found at i:49375 original size:22 final size:22
Alignment explanation
Indices: 49316--49375 Score: 57
Period size: 28 Copynumber: 2.5 Consensus size: 22
49306 TTTATAAGAT
*
49316 TGTTTGAATTTGAGGGTTTCTA
1 TGTTTTAATTTGAGGGTTTCTA
49338 TAAGATTGTTTGAATTTGAGGGTTTCTA
1 T--G--T-TTT-AATTTGAGGGTTTCTA
49366 TGTTTTAATT
1 TGTTTTAATT
49376 CGGAAAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
22 5 0.16
23 3 0.10
24 2 0.06
26 2 0.06
27 2 0.06
28 17 0.55
ACGTcount: A:0.22, C:0.03, G:0.23, T:0.52
Consensus pattern (22 bp):
TGTTTTAATTTGAGGGTTTCTA
Found at i:62953 original size:15 final size:15
Alignment explanation
Indices: 62933--62961 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62923 GTTGGAGTCA
62933 TTCTTAATCAAATTC
1 TTCTTAATCAAATTC
62948 TTCTTAATCAAATT
1 TTCTTAATCAAATT
62962 TTATGAGGTG
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:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (15 bp):
TTCTTAATCAAATTC
Found at i:64631 original size:45 final size:45
Alignment explanation
Indices: 64574--64683 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 45
64564 TTAATCTTCT
*
64574 TATGAAA-TTTGATTAACCTCCCTAAAG-AATTTTGAAGACC-TCAA
1 TATGAAATTTTGA-TAACCTCCC-AAAGAAATTTTGAAGACCAACAA
* * * *
64618 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATGACCAACAC
1 TATGAAATTTTGATAACCTCCCAAAGAAATTTTGAAGACCAACAA
* *
64663 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
64684 ATATGATATA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
43 3 0.05
44 27 0.49
45 25 0.45
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTCCCAAAGAAATTTTGAAGACCAACAA
Found at i:64698 original size:45 final size:45
Alignment explanation
Indices: 64618--64703 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
64608 AAGACCTCAA
* * * *
64618 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATGACCAACAC
1 TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
* *
64663 TATGAGATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCCA-ATGAAATATTGATAACCA
64704 CGTTATGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 3 0.09
45 31 0.91
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
Found at i:64767 original size:22 final size:22
Alignment explanation
Indices: 64618--65023 Score: 114
Period size: 22 Copynumber: 18.6 Consensus size: 22
64608 AAGACCTCAA
64618 TATGAAATTTTGATAACTTC-C-C
1 TATGAAATTTTGATAA--TCACAC
* * *
64640 AATGAAATTTTGATGACCAACAC
1 TATGAAATTTTGATAATC-ACAC
* *
64663 TATGAGATGTTGATAACCTC-CA-
1 TATGAAATTTTGATAA--TCACAC
* * * **
64685 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAATCACAC
* * * *
64707 TATGAAAATTTAAAAACCTACA-
1 TATGAAATTTTGATAATC-ACAC
64729 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAATCACAC
* *
64751 TCTGAAATTTTGATAATCGCAC
1 TATGAAATTTTGATAATCACAC
* * *
64773 TATGAAATTGTGATAATCTCGC
1 TATGAAATTTTGATAATCACAC
*
64795 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AATC-ACAC
* * * * *
64818 TATAAAATGTTGATAAACCTCCC
1 TATGAAATTTTGAT-AATCACAC
* ** *
64841 TATAAAATTTTGATAACTTTC-T
1 TATGAAATTTTGATAA-TCACAC
*
64863 TATGAAATCTTG---AT-A-AC
1 TATGAAATTTTGATAATCACAC
*
64880 TA-CAAATTTTGATAACTTC-C-C
1 TATGAAATTTTGATAA--TCACAC
** * *
64901 TATGATTTTTTGATAATCTCAT
1 TATGAAATTTTGATAATCACAC
* * *
64923 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAATCACAC
* *
64945 TATGAAATTTTGAT-CTACATAC
1 TATGAAATTTTGATAAT-CACAC
* *
64967 TATGAAATTTTGATAA-CCCTC
1 TATGAAATTTTGATAATCACAC
* * *
64988 TTGTGAAATTTTGA-AAACTAAAC
1 -TATGAAATTTTGATAATC-ACAC
65011 TATGAAATTTTGA
1 TATGAAATTTTGA
65024 AATTTTGATT
Statistics
Matches: 287, Mismatches: 64, Indels: 66
0.69 0.15 0.16
Matches are distributed among these distances:
16 7 0.02
17 2 0.01
18 1 0.00
19 2 0.01
20 4 0.01
21 18 0.06
22 190 0.66
23 60 0.21
24 2 0.01
25 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAC
Found at i:64877 original size:45 final size:45
Alignment explanation
Indices: 64755--64878 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
64745 TCACACTCTG
* * * *
64755 AAATTTTGAT-AATC-GCACTATGAAATTGTGAT-AATCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
64799 AAATTTTGATAAATCTTCCTATAAAATGTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAAACCTCCCTATA
* *
64845 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
64879 CTACAAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
44 10 0.15
45 33 0.49
46 24 0.36
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:65209 original size:22 final size:22
Alignment explanation
Indices: 65138--65352 Score: 94
Period size: 22 Copynumber: 9.7 Consensus size: 22
65128 AATCACATTT
* ** *
65138 TGAAAATTTGATAACCTATTTA
1 TGAAATTTTGATAACCCCTCTA
* *
65160 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
65182 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
** * *
65204 TGAAATTCCGATAATCACAT-TA
1 TGAAATTTTGATAA-CCCCTCTA
* * * * *
65226 TGTAATTATGATAACCTCGCTT
1 TGAAATTTTGATAACCCCTCTA
** *
65248 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCCCTCTA
* * **
65270 TGAAATTTTAATAATCTTTCTA
1 TGAAATTTTGATAACCCCTCTA
* *
65292 T-AAAATTTGATAATCCTATCTCTA
1 TGAAATTTTGATAA-CC--CCTCTA
* * *
65316 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCCCTCTA
*
65338 TGAGA-TTTGATAACC
1 TGAAATTTTGATAACC
65353 TTATATCAAA
Statistics
Matches: 142, Mismatches: 45, Indels: 13
0.71 0.22 0.06
Matches are distributed among these distances:
21 19 0.13
22 103 0.73
23 3 0.02
24 7 0.05
25 10 0.07
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:65455 original size:22 final size:22
Alignment explanation
Indices: 65404--65455 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
65394 ATAATCTTCA
65404 CATGAAATTTTGATAACCACAC
1 CATGAAATTTTGATAACCACAC
* * * *
65426 TATAAAATTTTGATAACCTCGC
1 CATGAAATTTTGATAACCACAC
65448 CATGAAAT
1 CATGAAAT
65456 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (22 bp):
CATGAAATTTTGATAACCACAC
Found at i:65658 original size:22 final size:22
Alignment explanation
Indices: 65602--65711 Score: 98
Period size: 22 Copynumber: 5.0 Consensus size: 22
65592 TAACCTGATC
*
65602 CTATGAATTTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
65624 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* * * *
65646 CTTTGGAATTTTGATAACCTC-
1 CTATGAAATTTTGGTAACCACA
* **
65667 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGGTAACCA-CA
* *
65690 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGGTAACCACA
65712 TAGAGACAAG
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.04
22 67 0.93
23 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:66260 original size:31 final size:31
Alignment explanation
Indices: 66225--66290 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
66215 TGATAATTTA
*
66225 GAAATATGTTTTAAAGAA-AAGGGTACAATTG
1 GAAATATGTTTTAAA-AATAAGGGTACAATCG
*
66256 GAAATATGTTTTAAAAATAAGGGTACTATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
66287 GAAA
1 GAAA
66291 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:68496 original size:29 final size:30
Alignment explanation
Indices: 68436--68504 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
68426 ATGGAATGGA
* **
68436 CTTATTTGATCTTTTCTGTAAAGTTGGGGCC
1 CTTATTTGACCTTTTC-GTAAAGTTCAGGCC
68467 CTTATTTGACCTTTTC-TAAAGTTCAGGCC
1 CTTATTTGACCTTTTCGTAAAGTTCAGGCC
68496 CTTATTTGA
1 CTTATTTGA
68505 GATTTATGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 20 0.57
31 15 0.43
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (30 bp):
CTTATTTGACCTTTTCGTAAAGTTCAGGCC
Done.