Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012921.1 Corchorus capsularis cultivar CVL-1 contig12942, 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: 19532
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:5568 original size:8 final size:8
Alignment explanation
Indices: 5529--5616 Score: 65
Period size: 8 Copynumber: 10.8 Consensus size: 8
5519 ATTTCCCAGC
*
5529 AAAAAAAG
1 AAAAGAAG
*
5537 AAGAGAA-
1 AAAAGAAG
5544 AAACAGAAAG
1 AAA-AG-AAG
*
5554 AAGAAGAAT
1 AA-AAGAAG
5563 AAAAG-AG
1 AAAAGAAG
*
5570 AAAA-AAA
1 AAAAGAAG
5577 AAAGAGAGAG
1 AAA-AGA-AG
5587 AAAAGAAG
1 AAAAGAAG
5595 AAAAGAAG
1 AAAAGAAG
5603 AAAAGAAG
1 AAAAGAAG
*
5611 AGAAGA
1 AAAAGA
5617 TAAAATTGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
7 11 0.17
8 34 0.53
9 10 0.16
10 8 0.12
11 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.01
Consensus pattern (8 bp):
AAAAGAAG
Found at i:5588 original size:17 final size:19
Alignment explanation
Indices: 5532--5616 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 19
5522 TCCCAGCAAA
* *
5532 AAAAGAAGAGAAAAACAGA-
1 AAAAGAAGA-AAAGAGAGAG
5551 AAGAAGAAGAATAA-A-AGAG
1 AA-AAGAAGAA-AAGAGAGAG
5570 AAAA-AA-AAAAGAGAGAG
1 AAAAGAAGAAAAGAGAGAG
5587 AAAAGAAG-AAA-AGA-AG
1 AAAAGAAGAAAAGAGAGAG
*
5603 AAAAGAAGAGAAGA
1 AAAAGAAGAAAAGA
5617 TAAAATTGAT
Statistics
Matches: 56, Mismatches: 1, Indels: 19
0.74 0.01 0.25
Matches are distributed among these distances:
15 2 0.04
16 13 0.23
17 15 0.27
18 11 0.20
19 6 0.11
20 9 0.16
ACGTcount: A:0.73, C:0.01, G:0.25, T:0.01
Consensus pattern (19 bp):
AAAAGAAGAAAAGAGAGAG
Found at i:5593 original size:32 final size:34
Alignment explanation
Indices: 5542--5606 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
5532 AAAAGAAGAG
*
5542 AAAAACAGAAAGAAGAAGAATAAAAG-AGAAAAA
1 AAAAACAGAAAGAAGAAGAAGAAAAGAAGAAAAA
* *
5575 AAAAAGAGAGAGAA-AAGAAGAAAAGAAGAAAA
1 AAAAACAGAAAGAAGAAGAAGAAAAGAAGAAAA
5607 GAAGAGAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (34 bp):
AAAAACAGAAAGAAGAAGAAGAAAAGAAGAAAAA
Found at i:5601 original size:43 final size:42
Alignment explanation
Indices: 5529--5666 Score: 138
Period size: 43 Copynumber: 3.2 Consensus size: 42
5519 ATTTCCCAGC
5529 AAAAAAAGAAGAGAAAA-ACAGAAAGAAGAAGAATAAAAGAGAAA
1 AAAAAAAGAAGAGAAAAGA-AG-AAGAAGAAGAA-AAAAGAGAAA
5573 AAAAAAAGAGAGAGAAAAGAAGAA-AAGAAGAAAAGAAGAGAAGA
1 AAAAAAAGA-AGAGAAAAGAAGAAGAAGAAGAAAA-AAGAGAA-A
* ** * * *
5617 TAAAATTGATGA-AAAAGAAAAAGAAAAAGAAAAAAGAGAAA
1 AAAAAAAGAAGAGAAAAGAAGAAGAAGAAGAAAAAAGAGAAA
5658 CAAAAAAAG
1 -AAAAAAAG
5667 CAATAATGGT
Statistics
Matches: 79, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
41 1 0.01
42 23 0.29
43 26 0.33
44 18 0.23
45 10 0.13
46 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.04
Consensus pattern (42 bp):
AAAAAAAGAAGAGAAAAGAAGAAGAAGAAGAAAAAAGAGAAA
Found at i:5615 original size:13 final size:13
Alignment explanation
Indices: 5532--5616 Score: 66
Period size: 13 Copynumber: 6.1 Consensus size: 13
5522 TCCCAGCAAA
5532 AAAAGAAGAGAA-
1 AAAAGAAGAGAAG
5544 AAACAGAAAGAAGAAG
1 AAA-AG-AAG-AGAAG
*
5560 AATAA-AAGAGAAA
1 AA-AAGAAGAGAAG
*
5573 AAAAAAAGAGAGAG
1 AAAAGAAGAGA-AG
5587 AAAAGAAGAAAAGAAG
1 AAAAGAAG---AGAAG
5603 AAAAGAAGAGAAG
1 AAAAGAAGAGAAG
5616 A
1 A
5617 TAAAATTGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
12 5 0.08
13 20 0.33
14 14 0.23
15 4 0.07
16 13 0.22
17 4 0.07
ACGTcount: A:0.73, C:0.01, G:0.25, T:0.01
Consensus pattern (13 bp):
AAAAGAAGAGAAG
Found at i:5650 original size:13 final size:13
Alignment explanation
Indices: 5550--5664 Score: 65
Period size: 13 Copynumber: 8.2 Consensus size: 13
5540 AGAAAAACAG
*
5550 AAAGAAGAAGAATA
1 AAAGAAAAAGAA-A
5564 AAAGAGAAAA-AAA
1 AAAGA-AAAAGAAA
* *
5577 AAAGAGAGAGAAA
1 AAAGAAAAAGAAA
5590 AGAAG-AAAAGAAGA
1 A-AAGAAAAAGAA-A
5604 AAAGAAGAGAAGATAA
1 AAAGAA-A-AAGA-AA
5620 AATTGATGAAAAAG-AA
1 AA---A-GAAAAAGAAA
5636 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
* *
5649 AAAGAGAAACAAA
1 AAAGAAAAAGAAA
5662 AAA
1 AAA
5665 AGCAATAATG
Statistics
Matches: 81, Mismatches: 7, Indels: 27
0.70 0.06 0.23
Matches are distributed among these distances:
12 9 0.11
13 35 0.43
14 13 0.16
15 4 0.05
16 11 0.14
17 1 0.01
18 3 0.04
19 2 0.02
20 3 0.04
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.04
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:5818 original size:48 final size:48
Alignment explanation
Indices: 5681--5819 Score: 188
Period size: 48 Copynumber: 2.9 Consensus size: 48
5671 AATGGTTTTC
* * * * **
5681 AAAAAGAGTCATGGTTTTTAAAAGATTTTGATAAAATAATTTTTCAAA
1 AAAAAAAGTCATGGTTTTCAAAAGGTTTTAATAAAATGGTTTTTCAAA
* *
5729 AAAAAAAGTCATGGTTTTCAAAAGGTGTTAATAAAATGGTTTTTTAAA
1 AAAAAAAGTCATGGTTTTCAAAAGGTTTTAATAAAATGGTTTTTCAAA
* *
5777 AAAAATAGTCATGGTTTTCAAAAGGTTTTAATAAAAGGGTTTT
1 AAAAAAAGTCATGGTTTTCAAAAGGTTTTAATAAAATGGTTTT
5820 CCCAAAGTTG
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (48 bp):
AAAAAAAGTCATGGTTTTCAAAAGGTTTTAATAAAATGGTTTTTCAAA
Found at i:7114 original size:121 final size:122
Alignment explanation
Indices: 6896--7145 Score: 484
Period size: 121 Copynumber: 2.0 Consensus size: 122
6886 ACAAAACCAC
6896 ATCATTGGCAAGATTTGACAAGAAAAAACTTCTTGGCCTACTAATGGATATGTACTTGGCTTTTT
1 ATCATTGGCAAGATTTGACAAGAAAAAACTTCTTGGCCTACTAATGGA-ATGTACTTGGCTTTTT
6961 GTTTCTTAACTCTAAGCCTACAATTATATACTCTATTTATTTATTTAAATATACAAAG
65 GTTTCTTAACTCTAAGCCTACAATTATATACTCTATTTATTTATTTAAATATACAAAG
7019 ATCATTGGCAAGATTTGACAAGAAAAAACTTCTTGGCCTACTAATGG-ATGTACTTGGCTTTTTG
1 ATCATTGGCAAGATTTGACAAGAAAAAACTTCTTGGCCTACTAATGGAATGTACTTGGCTTTTTG
7083 TTTCTTAACTCTAAGCCTACAATTATATACTCTATTTATTTATTTAAATATACAAAG
66 TTTCTTAACTCTAAGCCTACAATTATATACTCTATTTATTTATTTAAATATACAAAG
7140 ATCATT
1 ATCATT
7146 TGTTTCAAGT
Statistics
Matches: 127, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
121 80 0.63
123 47 0.37
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (122 bp):
ATCATTGGCAAGATTTGACAAGAAAAAACTTCTTGGCCTACTAATGGAATGTACTTGGCTTTTTG
TTTCTTAACTCTAAGCCTACAATTATATACTCTATTTATTTATTTAAATATACAAAG
Found at i:9718 original size:14 final size:14
Alignment explanation
Indices: 9697--9730 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9687 ACTGATGAAC
*
9697 AAATTTGTGACAGA
1 AAATTTGTAACAGA
*
9711 ATATTTGTAACAGA
1 AAATTTGTAACAGA
9725 AAATTT
1 AAATTT
9731 TCCCGATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (14 bp):
AAATTTGTAACAGA
Found at i:10261 original size:9 final size:9
Alignment explanation
Indices: 10247--10299 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 9
10237 TTTTTCAAGT
*
10247 AAAAAAGGA
1 AAAAAAGAA
10256 AAAAAAGAA
1 AAAAAAGAA
10265 AGAAAAAGAA
1 A-AAAAAGAA
10275 GAAAATAA-AA
1 -AAAA-AAGAA
10285 ATAAAAAGAA
1 A-AAAAAGAA
10295 AAAAA
1 AAAAA
10300 GAATGAAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 16 0.42
10 19 0.50
11 3 0.08
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:10271 original size:12 final size:12
Alignment explanation
Indices: 10254--10313 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
10244 AGTAAAAAAG
10254 GAAAAAAAGAAA
1 GAAAAAAAGAAA
10266 GAAAAAGAAGAAA
1 GAAAAA-AAGAAA
*
10279 -ATAAAAATAAAAA
1 GA-AAAAA-AGAAA
*
10292 GAAAAAAAGAAT
1 GAAAAAAAGAAA
*
10304 GAAGAAAAGA
1 GAAAAAAAGA
10314 GGCTCTAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 20 0.50
13 19 0.47
14 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (12 bp):
GAAAAAAAGAAA
Found at i:10271 original size:13 final size:13
Alignment explanation
Indices: 10250--10299 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
10240 TTCAAGTAAA
*
10250 AAAGGAAAAAAAG
1 AAAGAAAAAAAAG
*
10263 AAAGAAAAAGAAG
1 AAAGAAAAAAAAG
10276 AAA-ATAAAAATAA-
1 AAAGA-AAAAA-AAG
10289 AAAGAAAAAAA
1 AAAGAAAAAAA
10300 GAATGAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 2 0.06
13 26 0.84
14 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:10279 original size:20 final size:18
Alignment explanation
Indices: 10248--10299 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
10238 TTTTCAAGTA
*
10248 AAAAAGGAAAAAAAGAAAG
1 AAAAA-GAAAAAAAAAAAG
*
10267 AAAAAGAAGAAAATAAAAAT
1 AAAAAGAA-AAAA-AAAAAG
10287 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
10300 GAATGAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 4 0.14
19 13 0.45
20 12 0.41
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAAG
Found at i:10311 original size:20 final size:19
Alignment explanation
Indices: 10247--10313 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 19
10237 TTTTTCAAGT
*
10247 AAAAAAGGAAAAAAAGAAAG
1 AAAAAA-GAAAAAAAGAATG
10267 AAAAAGAAGAAAATAAA-AAT-
1 -AAAA-AAGAAAA-AAAGAATG
10287 -AAAAAGAAAAAAAGAATG
1 AAAAAAGAAAAAAAGAATG
10305 AAGAAAAGA
1 AA-AAAAGA
10314 GGCTCTAGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
16 3 0.08
17 10 0.26
18 3 0.08
19 1 0.03
20 6 0.15
21 11 0.28
22 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAAAAGAAAAAAAGAATG
Found at i:10818 original size:21 final size:22
Alignment explanation
Indices: 10794--10868 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 22
10784 TACTCTCCTT
10794 TTTTC-CTTATACTGATTACCA
1 TTTTCTCTTATACTGATTACCA
*
10815 TTTTACTCTTTGAATTACTGATCACCA
1 TTTT-CTC-TT--A-TACTGATTACCA
* *
10842 TTTACTCTT-TACTGATTACTA
1 TTTTCTCTTATACTGATTACCA
10863 TTTTCT
1 TTTTCT
10869 GCTCCTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
21 19 0.44
22 1 0.02
23 1 0.02
24 2 0.05
25 2 0.05
26 4 0.09
27 14 0.33
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTCTCTTATACTGATTACCA
Found at i:10903 original size:22 final size:22
Alignment explanation
Indices: 10875--11108 Score: 137
Period size: 22 Copynumber: 10.7 Consensus size: 22
10865 TTCTGCTCCT
10875 TTTTTACTGATTACTCTTTTAC
1 TTTTTACTGATTACTCTTTTAC
* *
10897 TTTTTACTGATT-GTCTTTTGC
1 TTTTTACTGATTACTCTTTTAC
10918 TTTTTACTGATTAC-CTTTTTA-
1 TTTTTACTGATTACTC-TTTTAC
* *
10939 TTTCTTGCTGATTAGCTTTTTTTAC
1 TTT-TTACTGATTA-C-TCTTTTAC
* * *
10964 TCTTTACTAATCA-TCTTCTTAC
1 TTTTTACTGATTACTCTT-TTAC
* *
10986 -TCTTACTGATT-TTACTTTTAC
1 TTTTTACTGATTACT-CTTTTAC
* * *
11007 TTCTTACTTATTACCTTTTTTAC
1 TTTTTACTGATTA-CTCTTTTAC
** *
11030 -TCATACTGATTACTATTTTAC
1 TTTTTACTGATTACTCTTTTAC
** * *
11051 TTTTTACTGCCTATTATTTTAC
1 TTTTTACTGATTACTCTTTTAC
*
11073 TCTTGT--TGATTAC-CTTCTTAC
1 T-TTTTACTGATTACTCTT-TTAC
11094 TTTTTACTGATTACT
1 TTTTTACTGATTACT
11109 AATTACCATT
Statistics
Matches: 161, Mismatches: 32, Indels: 37
0.70 0.14 0.16
Matches are distributed among these distances:
20 5 0.03
21 55 0.34
22 76 0.47
23 10 0.06
24 13 0.08
25 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTTACTGATTACTCTTTTAC
Found at i:10904 original size:43 final size:43
Alignment explanation
Indices: 10843--10936 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
10833 TGATCACCAT
*
10843 TTACTC-TTTACTGATTACT-ATTTTCTGCTCCTTTTTTACTGA
1 TTACTCTTTTACTGATTACTGATTGTCTGCTCC-TTTTTACTGA
** ** *
10885 TTACTCTTTTACTTTTTACTGATTGTCTTTTGCTTTTTACTGA
1 TTACTCTTTTACTGATTACTGATTGTCTGCTCCTTTTTACTGA
10928 TTAC-CTTTT
1 TTACTCTTTT
10937 TATTTCTTGC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 11 0.25
43 25 0.57
44 8 0.18
ACGTcount: A:0.15, C:0.19, G:0.07, T:0.59
Consensus pattern (43 bp):
TTACTCTTTTACTGATTACTGATTGTCTGCTCCTTTTTACTGA
Found at i:11401 original size:55 final size:54
Alignment explanation
Indices: 11340--11567 Score: 288
Period size: 55 Copynumber: 4.3 Consensus size: 54
11330 CATTTTAACT
*
11340 CTTAATTATCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTTTTTTTA
1 CTTAATTA-CGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * *
11395 CTTAATTACTTATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTAC-GATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * *
11450 CTTAATTACCGATTTACTGATTTCTATTACTTTGACTCTGATTAATTTCTTTTTA
1 CTTAATTA-CGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * *
11505 CTTAATTAC----TGCT--TTACTATTACCTTAACTCTGATTAATCTCTTCTTA
1 CTTAATTACGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
11553 CTTAATTACTGATTT
1 CTTAATTAC-GATTT
11568 GCCCTTGATG
Statistics
Matches: 152, Mismatches: 14, Indels: 16
0.84 0.08 0.09
Matches are distributed among these distances:
48 39 0.26
50 3 0.02
53 1 0.01
54 2 0.01
55 106 0.70
56 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (54 bp):
CTTAATTACGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
Found at i:11451 original size:29 final size:29
Alignment explanation
Indices: 11419--11506 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
11409 TACTGATTAC
11419 TACTACTTTGACTCTGATTAATCTCTTTT
1 TACTACTTTGACTCTGATTAATCTCTTTT
* * * *
11448 TACTTA-ATT-AC-C-GATTTA-CTGATTTC
1 TAC-TACTTTGACTCTGATTAATCT-CTTTT
* *
11474 TATTACTTTGACTCTGATTAATTTCTTTT
1 TACTACTTTGACTCTGATTAATCTCTTTT
11503 TACT
1 TACT
11507 TAATTACTGC
Statistics
Matches: 41, Mismatches: 11, Indels: 14
0.62 0.17 0.21
Matches are distributed among these distances:
25 4 0.10
26 12 0.29
27 3 0.07
28 3 0.07
29 16 0.39
30 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.52
Consensus pattern (29 bp):
TACTACTTTGACTCTGATTAATCTCTTTT
Found at i:15017 original size:24 final size:24
Alignment explanation
Indices: 14989--15035 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
14979 TACTAATGCT
*
14989 AAATTACTAATTAAAAATATTCTA
1 AAATTACTAATTAAAAACATTCTA
15013 AAATTACTAATTAAAAACATTCT
1 AAATTACTAATTAAAAACATTCT
15036 TGTGTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATTACTAATTAAAAACATTCTA
Found at i:15830 original size:29 final size:29
Alignment explanation
Indices: 15788--15848 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
15778 GATCAGTAAA
15788 AGAATCTTTCAAAGCATACTATTCAAGTC
1 AGAATCTTTCAAAGCATACTATTCAAGTC
15817 AGAATCTTTCAAAGCATACTATTCAAGTC
1 AGAATCTTTCAAAGCATACTATTCAAGTC
15846 AGA
1 AGA
15849 TCTAGGGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (29 bp):
AGAATCTTTCAAAGCATACTATTCAAGTC
Found at i:16187 original size:70 final size:69
Alignment explanation
Indices: 16091--16455 Score: 398
Period size: 70 Copynumber: 5.3 Consensus size: 69
16081 CGAATGCTTC
* **
16091 GGCTTTTCCATAAGCCAAACTGGTTTCCACACGAGTCAGATCCAGCCTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGT-AGATCCAGATTTGGTTCCATCCAAGCAT
16156 TCAAG
65 TCAAG
* * * *
16161 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTTGGTTCCATCCAAACA-
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGT-AGATCCAGATTTGGTTCCATCCAAGCAT
16225 --AGAG
65 TCA-AG
** * * * *
16229 AGGCTTTTCCATAAGCCAAACTCACTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGTA
1 -GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAG-TAGATCCAGATTTGGTTCCATCCAAGCA
*
16294 TTCAGG
64 TTCAAG
* * * * *
16300 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTAGATCCAGCTTCGGTTCCATCCAGGCAAG
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTAGATCCAGATTTGGTTCCATCCAAGC-AT
*
16365 T-GA-
65 TCAAG
* * * **
16368 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAAGATTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAG-TAGATCCAGATTTGGTTCCATCCAAGCAT
*
16433 TCAGG
65 TCAAG
16438 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCATAAGCCAA
16456 GTTCAGTGAG
Statistics
Matches: 244, Mismatches: 41, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
67 1 0.00
68 36 0.15
69 94 0.39
70 111 0.45
71 1 0.00
72 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (69 bp):
GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTAGATCCAGATTTGGTTCCATCCAAGCATT
CAAG
Found at i:16402 original size:138 final size:139
Alignment explanation
Indices: 16091--16455 Score: 554
Period size: 138 Copynumber: 2.6 Consensus size: 139
16081 CGAATGCTTC
* * * * * **
16091 GGCTTTTCCATAAGCCAAACTGGTTTCCACACGAG-TCAGATCCAGCCTTGGTTCCATCCAAGCA
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTCAGATTTGGTTCCATCCAAGCA
* * *
16155 TTCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTTGGTTCCATCC
65 TTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCC
16220 AAACAAGAGA
130 AAACAAGAGA
* *
16230 GGCTTTTCCATAAGCCAAACTCACTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGTAT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGCAT
16295 TCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGT-AGATCCAGCTTCGGTTCCATCCA
66 TCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCA
** *
16359 GGCAAGTGA
131 AACAAGAGA
*
16368 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAAGATTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGCAT
*
16433 TCAGGGGCTTTTCCATAAGCCAA
66 TCAGGGGCTTTTCCACAAGCCAA
16456 GTTCAGTGAG
Statistics
Matches: 206, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
138 111 0.54
139 94 0.46
140 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (139 bp):
GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGCAT
TCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCA
AACAAGAGA
Found at i:16638 original size:47 final size:47
Alignment explanation
Indices: 16565--16701 Score: 211
Period size: 47 Copynumber: 2.9 Consensus size: 47
16555 ATCCAGGCAA
* * *
16565 TCTTCTCTTGCTTCCACGCGGGTTTTCAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
16612 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* * * *
16659 TCTTTTCTCGCTTCCATGCGAGTCTGCAATTTAGTCACCAAAG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAG
16702 TAGGTCAACG
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 83 1.00
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
Found at i:17613 original size:20 final size:20
Alignment explanation
Indices: 17588--17626 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17578 AAATACAAGG
17588 CATTTGATTTACAAATTGGA
1 CATTTGATTTACAAATTGGA
*
17608 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
17627 TGCTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:18196 original size:19 final size:19
Alignment explanation
Indices: 18172--18210 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
18162 ACTTTGCAGC
18172 ATGGATTTTACAATAGGAG
1 ATGGATTTTACAATAGGAG
18191 ATGGATTTTACAATAGGAG
1 ATGGATTTTACAATAGGAG
18210 A
1 A
18211 AAAGGGGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (19 bp):
ATGGATTTTACAATAGGAG
Done.