Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008839.1 Corchorus capsularis cultivar CVL-1 contig08860, 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: 44044
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:49 original size:14 final size:15
Alignment explanation
Indices: 20--61 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
10 GGCTCAGTGT
*
20 AAAAGTGTAAAAAGGGT
1 AAAAGTGT--AAAGGGC
37 AAAAG-GTAAAGGGC
1 AAAAGTGTAAAGGGC
51 AAAAGTGTAAA
1 AAAAGTGTAAA
62 AAGTAGGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.48
15 5 0.22
16 2 0.09
17 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.29, T:0.14
Consensus pattern (15 bp):
AAAAGTGTAAAGGGC
Found at i:1759 original size:6 final size:6
Alignment explanation
Indices: 1748--1773 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1738 ATATCAGAAT
1748 AATGAA AATGAA AATGAA AATGAA AA
1 AATGAA AATGAA AATGAA AATGAA AA
1774 AGAAGAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AATGAA
Found at i:11632 original size:41 final size:41
Alignment explanation
Indices: 11585--11726 Score: 164
Period size: 41 Copynumber: 3.4 Consensus size: 41
11575 AAAATTCAAC
* *
11585 TCATGGTAATTAAGAAAGTCAAACACAATCAAGGTCTTAAT
1 TCATGGTAATTAAGAAAGTCAAACACAGTCAAAGTCTTAAT
*
11626 TCATGGTAATTAAGAAGAG-CAAATACAGTCAAAGTCTTAAT
1 TCATGGTAATTAAGAA-AGTCAAACACAGTCAAAGTCTTAAT
* * *
11667 TCATGGTAAGTAAGGAAAAGT-AAACACAGTTAATGTCTTAAT
1 TCATGGTAATTAA-G-AAAGTCAAACACAGTCAAAGTCTTAAT
*
11709 TCACAGG-AATTAAGAAAG
1 TCA-TGGTAATTAAGAAAG
11727 GTGATCACAG
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
40 4 0.05
41 48 0.55
42 31 0.36
43 4 0.05
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (41 bp):
TCATGGTAATTAAGAAAGTCAAACACAGTCAAAGTCTTAAT
Found at i:11813 original size:41 final size:41
Alignment explanation
Indices: 11767--12251 Score: 534
Period size: 41 Copynumber: 11.5 Consensus size: 41
11757 AAGTAGAAAC
11767 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
11808 AGTAAAGCAAAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
11849 AG-ACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTA-AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* *
11890 AG-ACAAGCACAGACTTAATTTCAAGGAAGGAAATCAGAAGGAAGGAAA
1 AGTA-AAGCACAGACTTAATTTCAAGGAAGGAAAT-------TAGGTAA
* * * * ** * ** ** *
11938 TTAGGTAAAGTAAAGCAC-AAACTT-AATTTCAAGG-GAGGAAATTA
1 --A-GTAAAGCACAG-ACTTAATTTCAA--GGAAGGAAATTAGGTAA
* *
11982 GGTAAAAAATAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAA
1 AGT--A--A-AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
12028 AG-ACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTA-AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* *
12069 AGTAAAGCACAGACTTAATTTCAAGGAATGAAACTAGGTAA
1 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
12110 AGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* *
12151 AGAAAAGCACATACTTAA-TTCAAGGAAGGAAATTAGGTAA
1 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
12191 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
12232 AGTAAAGCACAGACTTAATT
1 AGTAAAGCACAGACTTAATT
12252 CAGGGTAATT
Statistics
Matches: 379, Mismatches: 40, Indels: 50
0.81 0.09 0.11
Matches are distributed among these distances:
40 39 0.10
41 283 0.75
42 2 0.01
43 2 0.01
44 2 0.01
45 8 0.02
46 14 0.04
47 2 0.01
48 5 0.01
50 3 0.01
51 12 0.03
52 7 0.02
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (41 bp):
AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
Found at i:11903 original size:123 final size:123
Alignment explanation
Indices: 11771--12251 Score: 698
Period size: 123 Copynumber: 3.8 Consensus size: 123
11761 AGAAACAGTA
11771 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCAAAGACTTAATTTCAAGGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCAAAGACTTAATTTCAAGGAA
*
11836 GGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
66 GGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
11894 AAGCACAGACTTAATTTCAAGGAAGGAAATCAGAAGGAAGGAAATTAGGTAAAGTAAAGCACAA-
1 AAGCACAGACTTAA-TT------------TC--AAGGAAGGAAATTAGGTAAAGTAAAGCA-AAG
* *
11958 ACTTAATTTCAAGGGAGGAAATTAGGTAAA-AAATAGCACAGACTTAATTTCAATGAAGGAAATT
50 ACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAA-AGCACAGACTTAATTTCAAGGAAGGAAATT
12022 AGGTAAAGAC
114 AGGTAAAGAC
*
12032 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAAGGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCAAAGACTTAATTTCAAGGAA
* * *
12097 TGAAACTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
66 GGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
* *
12155 AAGCACATACTTAA-TTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAAGGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCAAAGACTTAATTTCAAGGAA
*
12219 GGAAATTAGGTAAAGTAAAGCACAGACTTAATT
66 GGAAATTAGGTAAAGAAAAGCACAGACTTAATT
12252 CAGGGTAATT
Statistics
Matches: 326, Mismatches: 13, Indels: 39
0.86 0.03 0.10
Matches are distributed among these distances:
122 81 0.25
123 120 0.37
124 5 0.02
125 2 0.01
136 2 0.01
137 4 0.01
138 110 0.34
139 2 0.01
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (123 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCAAAGACTTAATTTCAAGGAA
GGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
Found at i:11956 original size:56 final size:56
Alignment explanation
Indices: 11871--11979 Score: 184
Period size: 56 Copynumber: 1.9 Consensus size: 56
11861 ACTTAATTTC
*
11871 AAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATCAG
1 AAGGAAGGAAATTAGGTAAAGACAAGCACAAACTTAATTTCAAGGAAGGAAATCAG
*
11927 AAGGAAGGAAATTAGGTAAAGTA-AAGCACAAACTTAATTTCAAGGGAGGAAAT
1 AAGGAAGGAAATTAGGTAAAG-ACAAGCACAAACTTAATTTCAAGGAAGGAAAT
11980 TAGGTAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
56 49 0.98
57 1 0.02
ACGTcount: A:0.49, C:0.09, G:0.25, T:0.17
Consensus pattern (56 bp):
AAGGAAGGAAATTAGGTAAAGACAAGCACAAACTTAATTTCAAGGAAGGAAATCAG
Found at i:11996 original size:97 final size:97
Alignment explanation
Indices: 11830--12020 Score: 314
Period size: 97 Copynumber: 2.0 Consensus size: 97
11820 ACTTAATTTC
* *
11830 AAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACA
1 AAGGAAGGAAATTAGGTAAAGACAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAA
11895 AGCACAGACTTAATTTCAAGGAAGGAAATCAG
66 AGCACAGACTTAATTTCAAGGAAGGAAATCAG
*
11927 AAGGAAGGAAATTAGGTAAAGTA-AAGCACAAACTTAATTTCAAGGGAGGAAATTAGGTAAA-AA
1 AAGGAAGGAAATTAGGTAAAG-ACAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
*
11990 ATAGCACAGACTTAATTTCAATGAAGGAAAT
65 A-AGCACAGACTTAATTTCAAGGAAGGAAAT
12021 TAGGTAAAGA
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
96 2 0.02
97 85 0.97
98 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (97 bp):
AAGGAAGGAAATTAGGTAAAGACAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAA
AGCACAGACTTAATTTCAAGGAAGGAAATCAG
Found at i:12037 original size:138 final size:135
Alignment explanation
Indices: 11787--12251 Score: 606
Period size: 138 Copynumber: 3.6 Consensus size: 135
11777 AGACTTAATT
11787 TCAAGGAAGGAAATTAGGTAAAGTAAAGCA-AAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG
1 TCAAGGAAGGAAATTAGGTAAAGTAAAGCACAA-ACTTAATTTCAAGGAAGGAAATTAGGTAAAG
*
11851 ACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
65 AAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAA-TTCAAGG
11916 AAGGAAA
129 AAGGAAA
*
11923 TCAGAAGGAAGGAAATTAGGTAAAGTAAAGCACAAACTTAATTTCAAGGGAGGAAATTAGGTAAA
1 TC--AAGGAAGGAAATTAGGTAAAGTAAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAA
*
11988 -AAATAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATT----
64 GAAA-AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAAG
12048 --------
128 GAAGGAAA
* * *
12048 TCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAAGGAATGAAACTAGGTAAAGA
1 TCAAGGAAGGAAATTAGGTAAAGTAAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGA
* *
12113 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACATACTTAA-T-------
66 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAAGGAA
12170 -----
131 GGAAA
* *
12170 TCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT
1 TCAAGGAAGGAAATTAGGTAAAGTAAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGA
12235 AAAGCACAGACTTAATT
66 AAAGCACAGACTTAATT
12252 CAGGGTAATT
Statistics
Matches: 311, Mismatches: 13, Indels: 24
0.89 0.04 0.07
Matches are distributed among these distances:
122 80 0.26
123 108 0.35
124 3 0.01
125 2 0.01
136 2 0.01
137 4 0.01
138 110 0.35
139 2 0.01
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.21
Consensus pattern (135 bp):
TCAAGGAAGGAAATTAGGTAAAGTAAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGA
AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAAGGAA
GGAAA
Found at i:12418 original size:36 final size:37
Alignment explanation
Indices: 12244--12418 Score: 186
Period size: 37 Copynumber: 4.9 Consensus size: 37
12234 TAAAGCACAG
* *
12244 ACTTAATTCAGGGTAATTAAGTAGAGTC-----AAGA
1 ACTTAATTCAGGGAAATTAAGTGGAGTCAATAAAAGA
* *
12276 ACTTAATTCAGGGCAAA-TAAGTGGATTCAGTAAAAGA
1 ACTTAATTCAGGG-AAATTAAGTGGAGTCAATAAAAGA
*
12313 ACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAAGA
1 ACTTAATTCAGGGAAATTAAGTGGAGTCAATAAAAGA
*
12350 ACTTAATTCAGGGAAATTAAGTAGAGTCAATAAAAG-
1 ACTTAATTCAGGGAAATTAAGTGGAGTCAATAAAAGA
* * * *
12386 GCTTAATTC-GGAGCAATTAAGTGGCGTTAATAA
1 ACTTAATTCAGG-GAAATTAAGTGGAGTCAATAA
12419 GGAATTTAAT
Statistics
Matches: 122, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
32 22 0.18
33 2 0.02
35 2 0.02
36 27 0.22
37 69 0.57
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (37 bp):
ACTTAATTCAGGGAAATTAAGTGGAGTCAATAAAAGA
Found at i:14050 original size:2 final size:2
Alignment explanation
Indices: 14043--14072 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
14033 GATTTTACAA
*
14043 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14073 TGGAGTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21215 original size:82 final size:82
Alignment explanation
Indices: 21112--21269 Score: 219
Period size: 82 Copynumber: 1.9 Consensus size: 82
21102 TTTCACTAAT
* * *
21112 GTTTCAAAAAATGTCTTTATTACTCGTCGCAAGAACTGTCTCTACCTAAAAACATAATCTGAGAC
1 GTTTCAAAAAATGTCTCTATTACTCGTCGCAACAACTGTCTCTA-CTAAAAACAGAATCTGAGAC
*
21177 -GTATTATTGGCGGGAAC
65 AGTACTATTGGCGGGAAC
* * ** *
21194 GTTTTAAAAAATGTCTCTATTACTCGTCTCTCCAACTGTCTCTACTAGAAACAGAATCTGAGACA
1 GTTTCAAAAAATGTCTCTATTACTCGTCGCAACAACTGTCTCTACTAAAAACAGAATCTGAGACA
21259 GTACTATTGGC
66 GTACTATTGGC
21270 CTCAAGTGTC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (82 bp):
GTTTCAAAAAATGTCTCTATTACTCGTCGCAACAACTGTCTCTACTAAAAACAGAATCTGAGACA
GTACTATTGGCGGGAAC
Found at i:26811 original size:18 final size:18
Alignment explanation
Indices: 26788--26825 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
26778 GGCTTAATCT
26788 ATAATATATAGAAATACA
1 ATAATATATAGAAATACA
*
26806 ATAATATTTAGAAATACA
1 ATAATATATAGAAATACA
26824 AT
1 AT
26826 TGTTAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
ATAATATATAGAAATACA
Found at i:26977 original size:16 final size:18
Alignment explanation
Indices: 26945--26990 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
26935 ACCCTTTTTT
26945 CTATATCTATAATTCTATA
1 CTATATCTA-AATTCTATA
26964 -TATATCTAAA-TCTATA
1 CTATATCTAAATTCTATA
*
26980 CTATATGTAAA
1 CTATATCTAAA
26991 AGCACCAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 11 0.44
18 8 0.32
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.43
Consensus pattern (18 bp):
CTATATCTAAATTCTATA
Found at i:28508 original size:22 final size:22
Alignment explanation
Indices: 28483--28524 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
28473 TTTGAGAATT
28483 TTCT-TATGAAATTTTGTTTAAC
1 TTCTCTATGAAATTTT-TTTAAC
28505 TTCTCTATGAAATTTTTTTA
1 TTCTCTATGAAATTTTTTTA
28525 TCCTCCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (22 bp):
TTCTCTATGAAATTTTTTTAAC
Found at i:28536 original size:22 final size:23
Alignment explanation
Indices: 28488--28538 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
28478 GAATTTTCTT
* * *
28488 ATGAAATTTTGTTTAACTTCTCT
1 ATGAAATTTTGTTTAACCTCCCC
*
28511 ATGAAATTTT-TTTATCCTCCCC
1 ATGAAATTTTGTTTAACCTCCCC
28533 ATGAAA
1 ATGAAA
28539 CGTTGAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (23 bp):
ATGAAATTTTGTTTAACCTCCCC
Found at i:28566 original size:22 final size:21
Alignment explanation
Indices: 28541--28629 Score: 60
Period size: 22 Copynumber: 4.2 Consensus size: 21
28531 CCATGAAACG
28541 TTGAAAACATTACTATGAAATT
1 TTGAAAACATT-CTATGAAATT
* * *
28563 TTGATAACTACTCTACGAAATT
1 TTGAAAAC-ATTCTATGAAATT
* *
28585 TTGATAAGC--TCAATG-AATT
1 TTGA-AAACATTCTATGAAATT
28604 CTTGAAAACATTCCTAT-AAATT
1 -TTGAAAACATT-CTATGAAATT
28626 TTGA
1 TTGA
28630 TAATCTTCTA
Statistics
Matches: 51, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
19 7 0.14
20 8 0.16
21 5 0.10
22 27 0.53
23 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (21 bp):
TTGAAAACATTCTATGAAATT
Found at i:28733 original size:66 final size:68
Alignment explanation
Indices: 28663--28855 Score: 169
Period size: 69 Copynumber: 2.9 Consensus size: 68
28653 AAACACATTG
* * *
28663 TGAAATTTTAATAATCTCCCTATAAAATATTGATAATC-ACACTATGAACTTTCGGTAACC-A-C
1 TGAAATTTTAATAACCTCCCTATAAAATATTGATAA-CGACACTATGAAATTTCGATAACCGATC
28725 ACTA
65 ACTA
* * * * * * *
28729 TGAAATTGTAATAACCTCCTTATTAAATTTTTATAACGGCACTATGAAATTTTGATAACCTGATC
1 TGAAATTTTAATAACCTCCCTATAAAATATTGATAACGACACTATGAAATTTCGATAACC-GATC
*
28794 CCTA
65 ACTA
* * * * * * *
28798 TGAAATTTTAATAACCTCTCTGTGAAATTTTGGTAACCACGA-TATGAAATTTGGATAA
1 TGAAATTTTAATAACCTCCCTATAAAATATTGATAACGAC-ACTATGAAATTTCGATAA
28856 TCTCCTTATA
Statistics
Matches: 101, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
65 1 0.01
66 48 0.48
68 1 0.01
69 50 0.50
70 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (68 bp):
TGAAATTTTAATAACCTCCCTATAAAATATTGATAACGACACTATGAAATTTCGATAACCGATCA
CTA
Found at i:28743 original size:22 final size:22
Alignment explanation
Indices: 28663--28849 Score: 99
Period size: 22 Copynumber: 8.4 Consensus size: 22
28653 AAACACATTG
* * *
28663 TGAAATTTTAATAATCTCCCTA
1 TGAAATTTTAATAACCACACTA
* * * *
28685 TAAAATATTGATAATCACACTA
1 TGAAATTTTAATAACCACACTA
* ***
28707 TGAACTTTCGGTAACCACACTA
1 TGAAATTTTAATAACCACACTA
* *
28729 TGAAATTGTAATAACCTC-CTTA
1 TGAAATTTTAATAACCACAC-TA
* * **
28751 TTAAATTTTTATAACGGCACTA
1 TGAAATTTTAATAACCACACTA
* *
28773 TGAAATTTTGATAACCTGATCCCTA
1 TGAAATTTTAATAACC--A-CACTA
* * *
28798 TGAAATTTTAATAACCTCTCTG
1 TGAAATTTTAATAACCACACTA
**
28820 TGAAATTTTGGTAACCACGA-TA
1 TGAAATTTTAATAACCAC-ACTA
28842 TGAAATTT
1 TGAAATTT
28850 GGATAATCTC
Statistics
Matches: 123, Mismatches: 36, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
21 1 0.01
22 102 0.83
23 1 0.01
25 19 0.15
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
TGAAATTTTAATAACCACACTA
Found at i:29651 original size:20 final size:21
Alignment explanation
Indices: 29610--29652 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
29600 ATGATCATAC
* *
29610 ATGGTTCCCCTCATGTACTTG
1 ATGGTTCACCACATGTACTTG
29631 ATGGTTCACCACATG-ACTTG
1 ATGGTTCACCACATGTACTTG
29651 AT
1 AT
29653 TTCACCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (21 bp):
ATGGTTCACCACATGTACTTG
Found at i:29658 original size:18 final size:20
Alignment explanation
Indices: 29621--29658 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29611 TGGTTCCCCT
29621 CATGTACTTGATGGTTCACCA
1 CATGTACTTGAT-GTTCACCA
29642 CATG-ACTTGAT-TTCACC
1 CATGTACTTGATGTTCACC
29659 TTGATGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (20 bp):
CATGTACTTGATGTTCACCA
Found at i:39375 original size:24 final size:24
Alignment explanation
Indices: 39306--39373 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
39296 GAAAGCAAAA
* *
39306 GAGCAGCAGAAAAAGAAAAAGAGT
1 GAGCAACAGAAAAAGAAAAAGAAT
*
39330 GAGCAACA-ACAGAAGAAAAAGAAT
1 GAGCAACAGA-AAAAGAAAAAGAAT
39354 GAGCAACAGGAAAAAGAAAA
1 GAGCAACA-GAAAAAGAAAA
39374 GACTGTTAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 1 0.03
24 27 0.73
25 8 0.22
26 1 0.03
ACGTcount: A:0.62, C:0.10, G:0.25, T:0.03
Consensus pattern (24 bp):
GAGCAACAGAAAAAGAAAAAGAAT
Found at i:40317 original size:2 final size:2
Alignment explanation
Indices: 40273--40300 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40263 TGTTATTGCT
40273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40301 CACACACACA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43541 original size:38 final size:40
Alignment explanation
Indices: 43464--43545 Score: 132
Period size: 38 Copynumber: 2.1 Consensus size: 40
43454 ATTCTATTAA
43464 AAACTCTATTTTTATTTAATTAATAAATTCAATACTTTTAT
1 AAACTCTATTTTTATTTAATT-ATAAATTCAATACTTTTAT
*
43505 AAACTCTATTTTTATTTAA-T-TAAATTCAATATTTTTAT
1 AAACTCTATTTTTATTTAATTATAAATTCAATACTTTTAT
43543 AAA
1 AAA
43546 TATTTCATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 20 0.50
40 1 0.03
41 19 0.47
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (40 bp):
AAACTCTATTTTTATTTAATTATAAATTCAATACTTTTAT
Found at i:43545 original size:17 final size:17
Alignment explanation
Indices: 43486--43546 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
43476 TATTTAATTA
*
43486 ATAAATTCAATACTTTT
1 ATAAATTCAATATTTTT
* * *
43503 ATAAACTCTATTTTTATTT
1 ATAAATTC-AATATT-TTT
43522 AATTAAATTCAATATTTTT
1 -A-TAAATTCAATATTTTT
43541 ATAAAT
1 ATAAAT
43547 ATTTCATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
17 12 0.36
18 4 0.12
19 6 0.18
20 5 0.15
21 6 0.18
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAAATTCAATATTTTT
Done.