Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009385.1 Corchorus capsularis cultivar CVL-1 contig09406, 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: 102935
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:388 original size:13 final size:13
Alignment explanation
Indices: 370--426 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
360 AATACCAAAT
370 TACTAAATGAAAA
1 TACTAAATGAAAA
*
383 TACTAATTGAAAA
1 TACTAAATGAAAA
* * *
396 CACCATAATGCCAAA
1 TACTA-AATG-AAAA
411 TCACTAAATGAAAA
1 T-ACTAAATGAAAA
425 TA
1 TA
427 TGCAAAAACT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
13 16 0.48
14 7 0.21
15 7 0.21
16 3 0.09
ACGTcount: A:0.54, C:0.16, G:0.07, T:0.23
Consensus pattern (13 bp):
TACTAAATGAAAA
Found at i:580 original size:27 final size:28
Alignment explanation
Indices: 526--595 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
516 AGATGAACTT
* *
526 AAAAATGACTAAAATGCCCCCGAGTGC-
1 AAAAATGACCAAAATGCCCCAGAGTGCA
553 AAAAATGACCAAAATGCCCCTAGA-TGCA
1 AAAAATGACCAAAATGCCCC-AGAGTGCA
*
581 AAAAATGATCAAAAT
1 AAAAATGACCAAAAT
596 ACCCTTGGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCAGAGTGCA
Found at i:4930 original size:195 final size:197
Alignment explanation
Indices: 4578--4947 Score: 516
Period size: 195 Copynumber: 1.9 Consensus size: 197
4568 ATTTGGCAGG
* * * * *
4578 AATGATACTTTTTGTGGCAAAACCTATATTGGTCACTATAAGTTTCATTTGTTTGTGACAAAAAA
1 AATGATAATTTTTGTGGCAAAACCTATATTGGTCACTACAAATCTCATTTGTCTGTGACAAAAAA
* * * *
4643 AGTACCTCGTCACATTTGTGTGTAACATTTTTTGACGACAAGTTGTGTCACTAACAATTTAATTA
66 AGTACCTCATCACATTTGTGTGTAACATTTTGTGACGACAAGTTGTGTCACTAACAATTCAACTA
*
4708 ATTAGTGACTACAAAATAATGTCACAAAAACA-TTAGCCATTTTGGCGCCAAACATGAATATGGC
131 ATTAGTGACTACAAAATAATATCACAAAAA-AGTTAGCCATTTTGGCGCCAAACATGAATATGGC
4772 GAA
195 GAA
* *
4775 AATGATAATTTTTGTGGCCAAACCTATATTGGTCACTACAAATCTCATATT-TCTGTGAC-GAAA
1 AATGATAATTTTTGTGGCAAAACCTATATTGGTCACTACAAATCTCAT-TTGTCTGTGACAAAAA
* * *
4838 AAGTACCTCATCACTTTTGTGTGTAATA-TTTGTGACGGCAAGTTGTGTCACTAACAATTCAACT
65 AAGTACCTCATCACATTTGTGTGTAACATTTTGTGACGACAAGTTGTGTCACTAACAATTCAACT
* * *
4902 AATTAGTGGCTACGAAGT-ATCATCACAAAAAAGTTAGCCATTTTGG
130 AATTAGTGACTACAAAATAAT-ATCACAAAAAAGTTAGCCATTTTGG
4948 TATGGGATCC
Statistics
Matches: 152, Mismatches: 18, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
194 3 0.02
195 69 0.45
196 28 0.18
197 50 0.33
198 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (197 bp):
AATGATAATTTTTGTGGCAAAACCTATATTGGTCACTACAAATCTCATTTGTCTGTGACAAAAAA
AGTACCTCATCACATTTGTGTGTAACATTTTGTGACGACAAGTTGTGTCACTAACAATTCAACTA
ATTAGTGACTACAAAATAATATCACAAAAAAGTTAGCCATTTTGGCGCCAAACATGAATATGGCG
AA
Found at i:5510 original size:29 final size:29
Alignment explanation
Indices: 5454--5518 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
5444 TAAGGGAAAT
*
5454 AAAGAATTATGGATAATTTTTCTAAAAAA
1 AAAGAATTATGGATAATTTATCTAAAAAA
*
5483 AAAGAATTATGGATAA-TTATCGTTAAAAA
1 AAAGAATTATGGATAATTTATC-TAAAAAA
*
5512 TAAGAAT
1 AAAGAAT
5519 AAGGTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.32
Consensus pattern (29 bp):
AAAGAATTATGGATAATTTATCTAAAAAA
Found at i:7238 original size:56 final size:55
Alignment explanation
Indices: 7138--7248 Score: 186
Period size: 56 Copynumber: 2.0 Consensus size: 55
7128 TAATGAATCT
* *
7138 GGTGGCATTCACAATGTTGGTTTAACTGAGCGTGACATTTAGAATTATTTGAGAA
1 GGTGGCATTCACAATGTTGGTTTAACTGAGCATGACATTCAGAATTATTTGAGAA
*
7193 GGTGGCGTTCACAATGTTGGTTTTAACTGAGCATGACATTCAGAATTATTTGAGAA
1 GGTGGCATTCACAATGTTGG-TTTAACTGAGCATGACATTCAGAATTATTTGAGAA
7249 ATTAAAGACA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 19 0.37
56 33 0.63
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (55 bp):
GGTGGCATTCACAATGTTGGTTTAACTGAGCATGACATTCAGAATTATTTGAGAA
Found at i:30304 original size:21 final size:21
Alignment explanation
Indices: 30280--30328 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
30270 ATAATTTAGA
*
30280 TTTAATTTAGTTTGC-TTTATT
1 TTTAATTTA-ATTGCTTTTATT
* *
30301 TTTAGTTTAATTGCTTTTCTT
1 TTTAATTTAATTGCTTTTATT
30322 TTTAATT
1 TTTAATT
30329 GTTCTATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTAATTTAATTGCTTTTATT
Found at i:35059 original size:6 final size:6
Alignment explanation
Indices: 35050--35077 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
35040 CTTTTCCTTA
35050 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
35078 CGTTTTAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:35083 original size:18 final size:18
Alignment explanation
Indices: 35050--35084 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35040 CTTTTCCTTA
*
35050 TTTTATTTTTATTTTTAT
1 TTTTATTTTTAGTTTTAT
*
35068 TTTTATTTTTCGTTTTA
1 TTTTATTTTTAGTTTTA
35085 GTGCTAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTATTTTTAGTTTTAT
Found at i:36248 original size:35 final size:35
Alignment explanation
Indices: 36202--36858 Score: 1030
Period size: 35 Copynumber: 18.7 Consensus size: 35
36192 CTTAATTACC
*
36202 CTTACCTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
36237 CTCACTTAATTATCCC-GAATTAAGTTGATTACTGA
1 CTTACTTAATTA-CCCTGAATTAAGTTGATTACTGA
* * *
36272 ATTACTTAATTACCCTTAATTAAGTTTATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
36307 CTGACTTAATTACCCTGAATTAAGTTGATTACTGG
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
36342 CTGACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
36377 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
36412 CTCACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
36447 CTCACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
36482 CTCACTTAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
36517 ATTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
36552 CTAACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
36587 CTTACTTAATTATCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
36622 ATTACTTAATTACCCTGAATTAAGTT-ACTAACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGA-TTACTGA
36657 CTTTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 C-TTACTTAATTACCCTGAATTAAGTTGATTACTGA
* * *
36693 ATTACTTAATTACCCTGAATTAAGTTTATTACTTA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
36728 ATTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* * *
36763 ATTACTTAATTACCCTGAATTAAGTTTATTACTTA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
36798 ATTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
36833 ATTACTTAATTACCCTGAATTAAGTT
1 CTTACTTAATTACCCTGAATTAAGTT
36859 ACTTATTACT
Statistics
Matches: 579, Mismatches: 38, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
34 4 0.01
35 540 0.93
36 34 0.06
37 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (35 bp):
CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
Found at i:40012 original size:22 final size:22
Alignment explanation
Indices: 39984--40027 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39974 TGTTATATTA
39984 TACTAAATG-CAAGAAGTGAATT
1 TACTAAATGCCAA-AAGTGAATT
40006 TACTAAATGCCAAAAGTGAATT
1 TACTAAATGCCAAAAGTGAATT
40028 AGAAAATGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (22 bp):
TACTAAATGCCAAAAGTGAATT
Found at i:57299 original size:9 final size:9
Alignment explanation
Indices: 57281--57314 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
57271 TTCCTAAATT
*
57281 AATTATGGA
1 AATTAAGGA
57290 AATTAAGGA
1 AATTAAGGA
*
57299 AAATAAGGA
1 AATTAAGGA
57308 AATTAAG
1 AATTAAG
57315 TATTTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (9 bp):
AATTAAGGA
Found at i:63856 original size:35 final size:34
Alignment explanation
Indices: 63812--64046 Score: 249
Period size: 35 Copynumber: 6.7 Consensus size: 34
63802 CAGTAATAAG
* *
63812 TAACTTAATTCAGGGTAATTAAGTAGGTTAGTGAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGT-AA
* * *
63847 TAATTTAATTCAGGGTAATCAATTAAGTCAGTAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
63881 GTAGCTTAATTCAGGGTAATTAAGTAAAGTCAGTTAG
1 -TAACTTAATTCAGGGTAATTAAGT-AAGTCAG-TAA
* *
63918 TAACTTAATTCAGGGAAATTAAGTAATTCAGTAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
63952 TCAACTTAATCCACGGTAATTAAGTAAGTCCA-TAA
1 T-AACTTAATTCAGGGTAATTAAGTAAGT-CAGTAA
* *
63987 GTAACTTAATTCAGGATAATTAAGTAAGTCA-TGGA
1 -TAACTTAATTCAGGGTAATTAAGTAAGTCAGT-AA
*
64022 TCGACTTAATTCAGGGTAATTAAGT
1 T-AACTTAATTCAGGGTAATTAAGT
64047 TTAGTAAGAA
Statistics
Matches: 168, Mismatches: 24, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
34 9 0.05
35 125 0.74
36 32 0.19
37 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (34 bp):
TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
Found at i:63932 original size:106 final size:103
Alignment explanation
Indices: 63810--64046 Score: 282
Period size: 106 Copynumber: 2.3 Consensus size: 103
63800 ATCAGTAATA
* * * * *
63810 AGTAACTTAATTCAGGGTAATTAAGTAGGTT-AGTGAAT-AATTTAATTCAGGGTAATCAATTAA
1 AGTAACTTAATTCAGGGTAATTAAGTA-ATTCAGT-AATCAACTTAATCCACGGTAATCAAGTAA
* *
63873 GT-CAGTAAGTAGCTTAATTCAGGGTAATTAAGTAAAGTCAGTT
64 GTCCA-TAAGTAACTTAATTCAGGATAATTAAGT-AAGTCA--T
* *
63916 AGTAACTTAATTCAGGGAAATTAAGTAATTCAGTAATCAACTTAATCCACGGTAATTAAGTAAGT
1 AGTAACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATCCACGGTAATCAAGTAAGT
63981 CCATAAGTAACTTAATTCAGGATAATTAAGTAAGTCAT
66 CCATAAGTAACTTAATTCAGGATAATTAAGTAAGTCAT
* *
64019 GGATCGACTTAATTCAGGGTAATTAAGT
1 AG-T-AACTTAATTCAGGGTAATTAAGT
64047 TTAGTAAGAA
Statistics
Matches: 114, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
103 2 0.02
104 1 0.01
105 32 0.28
106 77 0.68
107 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (103 bp):
AGTAACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATCCACGGTAATCAAGTAAGT
CCATAAGTAACTTAATTCAGGATAATTAAGTAAGTCAT
Found at i:88222 original size:4 final size:4
Alignment explanation
Indices: 88213--88449 Score: 83
Period size: 4 Copynumber: 61.0 Consensus size: 4
88203 ATAAAAATTA
* ** * * *
88213 AAAT AAAT AAAT AAGT AGGT AAGT GAA- AAAT AAAT AAAT AGAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
88260 -AAT AAA- AGAT AAACT ATAAT AAAT AAAT AGAT -AAT -AAT AATATT
1 AAAT AAAT AAAT AAA-T A-AAT AAAT AAAT AAAT AAAT AAAT AA-A-T
* * ** *
88304 ACAT AGAT -AAT AGGGT AAAT AAAT -AAT -AAT -AAT -AAT AAAT AGAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
88348 AAGA- AAGT AAAT -AAT AAAT ACAAT -AAT AAAT AGAT AAAAT AAAA AAAT
1 AA-AT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT -AAAT AAAT AAAT
* * * * * *
88396 AAGT AGAT AGAT -AAT -AAT AAAT AAAT AGAT AAAGA AAAT AACT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT
88442 AAAT AAAT
1 AAAT AAAT
88450 TTAATAAAAA
Statistics
Matches: 176, Mismatches: 37, Indels: 40
0.70 0.15 0.16
Matches are distributed among these distances:
3 40 0.23
4 114 0.65
5 18 0.10
6 4 0.02
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:88271 original size:7 final size:8
Alignment explanation
Indices: 88240--88428 Score: 61
Period size: 7 Copynumber: 26.4 Consensus size: 8
88230 GGTAAGTGAA
*
88240 AAATAAAT
1 AAATAGAT
88248 AAATAGAT
1 AAATAGAT
88256 AAATA-AT
1 AAATAGAT
88263 AAA-AGAT
1 AAATAGAT
88270 AAACT--AT
1 AAA-TAGAT
*
88277 -AATAAAT
1 AAATAGAT
88284 AAATAGAT
1 AAATAGAT
88292 -AATA-AT
1 AAATAGAT
*
88298 -AATA-TT
1 AAATAGAT
*
88304 ACATAGAT
1 AAATAGAT
*
88312 -AATAGGGT
1 AAATA-GAT
*
88320 AAATAAAT
1 AAATAGAT
88328 -AATA-AT
1 AAATAGAT
88334 -AATA-AT
1 AAATAGAT
88340 AAATAGAT
1 AAATAGAT
*
88348 AAGAAAG-T
1 AA-ATAGAT
88356 AAATA-AT
1 AAATAGAT
88363 AAAT--A-
1 AAATAGAT
*
88368 CAATA-AT
1 AAATAGAT
88375 AAATAGAT
1 AAATAGAT
88383 AAAATA-A-
1 -AAATAGAT
88390 AAA-A-AT
1 AAATAGAT
*
88396 AAGTAGAT
1 AAATAGAT
*
88404 AGATA-AT
1 AAATAGAT
*
88411 -AATAAAT
1 AAATAGAT
88418 AAATAGAT
1 AAATAGAT
88426 AAA
1 AAA
88429 GAAAATAACT
Statistics
Matches: 140, Mismatches: 18, Indels: 46
0.69 0.09 0.23
Matches are distributed among these distances:
5 6 0.04
6 28 0.20
7 48 0.34
8 46 0.33
9 12 0.09
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (8 bp):
AAATAGAT
Found at i:88364 original size:39 final size:39
Alignment explanation
Indices: 88321--88447 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 39
88311 TAATAGGGTA
*
88321 AATAAATAATAATAATAATAAATAGATAAGAAAGTAAAT
1 AATAAATAATAATAATAATAAATAGATAAGAAAATAAAT
* * *
88360 AAT--A-AAT-ACAATAATAAATAGATAAAATAAAAAAAT
1 AATAAATAATAATAATAATAAATAGATAAGA-AAATAAAT
* *
88396 AAGTAGATAGATAATAATAAATAAATAGATAAAGAAAATAACT
1 AA-TAAATA-ATAATAAT-AATAAATAGAT-AAGAAAATAAAT
*
88439 AAAAAATAA
1 AATAAATAA
88448 ATTTAATAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
35 18 0.26
36 11 0.16
37 2 0.03
39 4 0.06
40 1 0.01
41 3 0.04
42 8 0.12
43 19 0.28
44 3 0.04
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.23
Consensus pattern (39 bp):
AATAAATAATAATAATAATAAATAGATAAGAAAATAAAT
Found at i:88377 original size:51 final size:51
Alignment explanation
Indices: 88321--88443 Score: 125
Period size: 51 Copynumber: 2.4 Consensus size: 51
88311 TAATAGGGTA
88321 AATAAATAATAATAATAATAAATAGATAAG-A-A-AG-TAAATAATAAATACAAT
1 AATAAATAATAATAATAA-AAATA-ATAAGTAGATAGAT-AATAATAAATA-AAT
88372 AATAAATAGATAA-AATAAAAA-AATAAGTAGATAGATAATAATAAATAAAT
1 AATAAATA-ATAATAATAAAAATAATAAGTAGATAGATAATAATAAATAAAT
*
88422 AGATAAAGAA-AATAACTAAAAA
1 A-ATAAATAATAATAA-TAAAAA
88444 ATAAATTTAA
Statistics
Matches: 63, Mismatches: 1, Indels: 16
0.79 0.01 0.20
Matches are distributed among these distances:
48 5 0.08
49 4 0.06
50 11 0.17
51 38 0.60
52 5 0.08
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (51 bp):
AATAAATAATAATAATAAAAATAATAAGTAGATAGATAATAATAAATAAAT
Found at i:88862 original size:16 final size:16
Alignment explanation
Indices: 88840--88877 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
88830 TTTAAAAAAT
88840 AAATTAATTAT-TAAAC
1 AAATTAA-TATCTAAAC
*
88856 CAATTAATATCTAAAC
1 AAATTAATATCTAAAC
88872 AAATTA
1 AAATTA
88878 TGAAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATTAATATCTAAAC
Found at i:89955 original size:54 final size:55
Alignment explanation
Indices: 89840--90049 Score: 268
Period size: 54 Copynumber: 3.9 Consensus size: 55
89830 ACAGAAACCT
* * * *
89840 TTCTTGGAATGACCGCATTGGATCAAAT-TGAAGATCAACTCCGATCATC-AAAAAC
1 TTCTTGGAATGACCGCACTGGATC--ATCTGAGGGTCAACTCTGATCATCTAAAAAC
* *
89895 TTCTTGGAATGACTGCACTGGATCATCCGAGGGTCAACTCTGATC-TCTAAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGAGGGTCAACTCTGATCATCTAAAAAC
*
89949 TTCTTGGAATGACCGCACTGGATCATCTG-GGGATCAACTCTGATCAT-TGAAAAC
1 TTCTTGGAATGACCGCACTGGATCATCTGAGGG-TCAACTCTGATCATCTAAAAAC
* * *
90003 TTCTTGGGATGACCGCACTGGATCATCTAAGGGTCAACTTTGATCAT
1 TTCTTGGAATGACCGCACTGGATCATCTGAGGGTCAACTCTGATCAT
90050 TTGAACATCA
Statistics
Matches: 138, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
53 7 0.05
54 105 0.76
55 26 0.19
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (55 bp):
TTCTTGGAATGACCGCACTGGATCATCTGAGGGTCAACTCTGATCATCTAAAAAC
Found at i:91763 original size:19 final size:19
Alignment explanation
Indices: 91741--91777 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
91731 CACATTTTCT
91741 TTTTTCATTTT-TTTTCTTG
1 TTTTTC-TTTTGTTTTCTTG
91760 TTTTTCTTTTGTTTTCTT
1 TTTTTCTTTTGTTTTCTT
91778 TTGCTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.03, C:0.11, G:0.05, T:0.81
Consensus pattern (19 bp):
TTTTTCTTTTGTTTTCTTG
Found at i:91780 original size:10 final size:9
Alignment explanation
Indices: 91740--91779 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
91730 TCACATTTTC
91740 TTTTTTCATT
1 TTTTTTC-TT
91750 TTTTTTCTT
1 TTTTTTCTT
*
91759 GTTTTTCTT
1 TTTTTTCTT
91768 TTGTTTTCTT
1 TT-TTTTCTT
91778 TT
1 TT
91780 GCTAATTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 11 0.41
10 16 0.59
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.82
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:97223 original size:20 final size:20
Alignment explanation
Indices: 97180--97221 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
97170 TGAAATTATC
*
97180 AATTAAAAAGAAAGCAATTA
1 AATTAAAAAGAAAGCAAGTA
*
97200 AATTAAAAATAAAGCAAAGTA
1 AATTAAAAAGAAAGC-AAGTA
97221 A
1 A
97222 TTCAAATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (20 bp):
AATTAAAAAGAAAGCAAGTA
Done.