Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022744.1 Corchorus olitorius cultivar O-4 contig22777, 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: 39627
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:8680 original size:14 final size:14
Alignment explanation
Indices: 8646--8673 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8636 AGCAAGAGAG
8646 TAGTCGACTTAAGC
1 TAGTCGACTTAAGC
8660 TAGTCGACTTAAGC
1 TAGTCGACTTAAGC
8674 ACGTCGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
TAGTCGACTTAAGC
Found at i:9916 original size:21 final size:22
Alignment explanation
Indices: 9891--9937 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
9881 CCAATTTAGC
*
9891 TTTAGATTTAA-ATTTCTTGTT
1 TTTAGATTTAAGATTTATTGTT
*
9912 TTTAGATTTAAGATTTATTTTT
1 TTTAGATTTAAGATTTATTGTT
9934 TTTA
1 TTTA
9938 TGCATCTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTAGATTTAAGATTTATTGTT
Found at i:15689 original size:23 final size:22
Alignment explanation
Indices: 15663--15710 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
15653 GATCTTTCCC
15663 TGAATTGAAAACTTTGAAAAACT
1 TGAATTGAAAACTTTG-AAAACT
* *
15686 TGAATTGGATACTTTGAAAACT
1 TGAATTGAAAACTTTGAAAACT
15708 TGA
1 TGA
15711 TGGGATCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (22 bp):
TGAATTGAAAACTTTGAAAACT
Found at i:15702 original size:61 final size:61
Alignment explanation
Indices: 15605--15755 Score: 239
Period size: 61 Copynumber: 2.5 Consensus size: 61
15595 TTGAAAAACT
* * * *
15605 TTGAAAACTTCTAAAAAACTTGAATTGAATATTTTGAAAATTTGATGGGATCTTTCCCTGAA
1 TTGAAAACTT-TGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAA
*
15667 TTGAAAACTTTGAAAAACTTGAATTGGATACTTTGAAAACTTGATGGGATCTTTCCCTAAA
1 TTGAAAACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAA
*
15728 TTGAAAACTTTGAAAGACTTGAATTGAA
1 TTGAAAACTTTGAAAAACTTGAATTGAA
15756 ATTCTTTTTG
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
61 72 0.88
62 10 0.12
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (61 bp):
TTGAAAACTTTGAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAA
Found at i:19300 original size:8 final size:8
Alignment explanation
Indices: 19287--19353 Score: 66
Period size: 8 Copynumber: 8.4 Consensus size: 8
19277 AATGATGCAC
19287 TGAAGAAT
1 TGAAGAAT
19295 TGAAGAAT
1 TGAAGAAT
* *
19303 TGGAGTAT
1 TGAAGAAT
* *
19311 TAAATAAT
1 TGAAGAAT
19319 TGAAGAAT
1 TGAAGAAT
19327 TGAA-ACAT
1 TGAAGA-AT
19335 TGAATG-AT
1 TGAA-GAAT
19343 TGAAGAAT
1 TGAAGAAT
19351 TGA
1 TGA
19354 TGGAGAAAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
7 2 0.04
8 45 0.96
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.30
Consensus pattern (8 bp):
TGAAGAAT
Found at i:19319 original size:24 final size:24
Alignment explanation
Indices: 19292--19353 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
19282 TGCACTGAAG
* **
19292 AATTGAAGAATTGGAGTATTAAAT
1 AATTGAAGAATTGAAACATTAAAT
*
19316 AATTGAAGAATTGAAACATTGAAT
1 AATTGAAGAATTGAAACATTAAAT
*
19340 GATTGAAGAATTGA
1 AATTGAAGAATTGA
19354 TGGAGAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.31
Consensus pattern (24 bp):
AATTGAAGAATTGAAACATTAAAT
Found at i:19422 original size:58 final size:58
Alignment explanation
Indices: 19317--19702 Score: 493
Period size: 58 Copynumber: 6.7 Consensus size: 58
19307 GTATTAAATA
* * * *
19317 ATTGAAG--AATTGAAACATTGAATGATTGAAGAATTGATGGAGAAAGACCATCCTGGATC
1 ATTGAAGTAAATTGAAGCATGGAATAATTGAAGAATTGA---AGAAAGACCACCCTGGATC
* ** * *
19376 ATTGAAGTAAATTAAAGCATCAAATAATGGAAGAATTAAAGAAAGACCACCCTGGATC
1 ATTGAAGTAAATTGAAGCATGGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
*
19434 ATTGAAGTAAATTGAAGCATGGAATAATTGAAGAATTGAAGAAAGATCACCCTGGATC
1 ATTGAAGTAAATTGAAGCATGGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
*
19492 ATTGAAGTAAATTGAAGCATGGAATAATTGAAGAATTGAAGAAAGATCACCCTGGATC
1 ATTGAAGTAAATTGAAGCATGGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
* * *
19550 ATTGAAGTAAATTG-AGCCATTGAAGAATTG-A-AATTGAAGAAAAACCACCCTGGATC
1 ATTGAAGTAAATTGAAG-CATGGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
* * *
19606 ATTGAAGTAAATTGATGCATTGAATAATTG-A-AATTGAAGAAAGAGCACCCTGGATC
1 ATTGAAGTAAATTGAAGCATGGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
* * *
19662 GTTGAAGTAAATTGATGCATTGAATAATTG-A-AATTGAAGAA
1 ATTGAAGTAAATTGAAGCATGGAATAATTGAAGAATTGAAGAA
19703 TTGAAGTATT
Statistics
Matches: 300, Mismatches: 23, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
56 113 0.38
57 4 0.01
58 153 0.51
59 7 0.02
61 23 0.08
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (58 bp):
ATTGAAGTAAATTGAAGCATGGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
Found at i:19691 original size:8 final size:8
Alignment explanation
Indices: 19680--20567 Score: 285
Period size: 8 Copynumber: 118.1 Consensus size: 8
19670 AAATTGATGC
*
19680 ATTGAATA
1 ATTGAAGA
19688 ATTG-A-A
1 ATTGAAGA
19694 ATTGAAGA
1 ATTGAAGA
*
19702 ATTGAAGT
1 ATTGAAGA
19710 ATTG-A-A
1 ATTGAAGA
*
19716 ATTGAAGC
1 ATTGAAGA
*
19724 ATTCAAGA
1 ATTGAAGA
19732 ATTG-A-A
1 ATTGAAGA
*
19738 ATTGAAGC
1 ATTGAAGA
19746 ATTGAAGA
1 ATTGAAGA
19754 ATTG-A-A
1 ATTGAAGA
*
19760 ATTGAAGC
1 ATTGAAGA
19768 ATTGAAGA
1 ATTGAAGA
19776 ATTG-A-A
1 ATTGAAGA
19782 ATTGAA-A
1 ATTGAAGA
19789 CATTGAAGA
1 -ATTGAAGA
19798 ATTG-A-A
1 ATTGAAGA
19804 ATTG-AGA
1 ATTGAAGA
*
19811 CATTGACA-T
1 -ATTGA-AGA
19820 ATT-AA-A
1 ATTGAAGA
19826 ATTGAA-A
1 ATTGAAGA
*
19833 CATTGAAGG
1 -ATTGAAGA
19842 ATTG-A-A
1 ATTGAAGA
*
19848 TTTGAAGA
1 ATTGAAGA
19856 ATTG-A-A
1 ATTGAAGA
*
19862 ATTGAAGC
1 ATTGAAGA
19870 ATTGAA-A
1 ATTGAAGA
19877 TATTG-A-A
1 -ATTGAAGA
19884 ATTGAA-A
1 ATTGAAGA
*
19891 CATTGAAGG
1 -ATTGAAGA
19900 ATT---GA
1 ATTGAAGA
*
19905 ATCTGGAGA
1 AT-TGAAGA
*
19914 ATTGACA-T
1 ATTGA-AGA
19922 ATT-AA-A
1 ATTGAAGA
19928 ATTGAA-A
1 ATTGAAGA
*
19935 CATTGAAGG
1 -ATTGAAGA
19944 ATTG-A-A
1 ATTGAAGA
*
19950 TTTGAAGA
1 ATTGAAGA
19958 ATTG-A-A
1 ATTGAAGA
*
19964 ATTGAAGC
1 ATTGAAGA
19972 ATTGAA-A
1 ATTGAAGA
19979 TATTG-A-A
1 -ATTGAAGA
19986 ATTGAA-A
1 ATTGAAGA
19993 CATTGAAGA
1 -ATTGAAGA
20002 ATTG-A-A
1 ATTGAAGA
* *
20008 TTTGAAGG
1 ATTGAAGA
20016 ATTGAA-A
1 ATTGAAGA
20023 TATTG-A-A
1 -ATTGAAGA
20030 ATTGAA-A
1 ATTGAAGA
20037 CATTGAAGA
1 -ATTGAAGA
20046 ATATG-A-A
1 AT-TGAAGA
* *
20053 TTTGAAGC
1 ATTGAAGA
20061 ATTGAA-A
1 ATTGAAGA
*
20068 TATT-TA-A
1 -ATTGAAGA
20075 ATTGAA-A
1 ATTGAAGA
*
20082 CATTGAAAA
1 -ATTGAAGA
20091 ATTG-A-A
1 ATTGAAGA
* *
20097 TTTGAAGC
1 ATTGAAGA
*
20105 ATTGAA-T
1 ATTGAAGA
20112 ATTG-A-A
1 ATTGAAGA
*
20118 ATTGAAGC
1 ATTGAAGA
20126 ATTGAAGA
1 ATTGAAGA
20134 ATTG-A-A
1 ATTGAAGA
* *
20140 ATTTAAGC
1 ATTGAAGA
*
20148 ATTGAAAA
1 ATTGAAGA
20156 ATTG-A-A
1 ATTGAAGA
*
20162 ATTGAAGT
1 ATTGAAGA
20170 ATTGAA-A
1 ATTGAAGA
20177 TATTG-A-A
1 -ATTGAAGA
20184 ATTG-A-A
1 ATTGAAGA
*
20190 ATTAAAGA
1 ATTGAAGA
20198 ATTG-A-A
1 ATTGAAGA
* *
20204 ATTAAAGC
1 ATTGAAGA
20212 ATTG-A-A
1 ATTGAAGA
*
20218 TTTGAA-A
1 ATTGAAGA
20225 CATTGAAGA
1 -ATTGAAGA
20234 ATTG--GA
1 ATTGAAGA
*
20240 ATTGAAGC
1 ATTGAAGA
**
20248 ATTGAATT
1 ATTGAAGA
20256 ATTG-A-A
1 ATTGAAGA
* *
20262 ATAGAAAA
1 ATTGAAGA
20270 ATTG-A-A
1 ATTGAAGA
*
20276 ATTGAAGC
1 ATTGAAGA
20284 ATTGAAGTA
1 ATTGAAG-A
*
20293 TTTG-A-A
1 ATTGAAGA
** *
20299 ATTGCCGC
1 ATTGAAGA
20307 ATTGAAGA
1 ATTGAAGA
20315 ATTG-A-A
1 ATTGAAGA
*
20321 ATTGAAGC
1 ATTGAAGA
20329 ATTGAAGA
1 ATTGAAGA
* *
20337 ATTAAAAA
1 ATTGAAGA
*
20345 AAT--AGA
1 ATTGAAGA
*
20351 TCATTCCGGAATAA
1 --ATT---GAA-GA
*
20365 ATTGAAGC
1 ATTGAAGA
20373 ATTGAAGA
1 ATTGAAGA
20381 ATTGAAGA
1 ATTGAAGA
* * *
20389 TTTGAGGC
1 ATTGAAGA
*
20397 ATTGAATA
1 ATTGAAGA
*
20405 ATTGAAGG
1 ATTGAAGA
* *
20413 ATTGGAGC
1 ATTGAAGA
*
20421 ATTGAATA
1 ATTGAAGA
20429 ATTGAAGA
1 ATTGAAGA
20437 ATTGGAA-A
1 ATT-GAAGA
*
20445 CATTGAATA
1 -ATTGAAGA
20454 ATTGAAGA
1 ATTGAAGA
**
20462 ATTGGGGA
1 ATTGAAGA
*
20470 ATTGAATA
1 ATTGAAGA
20478 ATTGAAGCA
1 ATTGAAG-A
*
20487 CA-T-AATA
1 -ATTGAAGA
20494 ATTTGAAGA
1 A-TTGAAGA
*
20503 ATTGAATA
1 ATTGAAGA
20511 ATTGAAGA
1 ATTGAAGA
* *
20519 GTTGAAGC
1 ATTGAAGA
*
20527 ATTGAATA
1 ATTGAAGA
*
20535 ATTGAAAA
1 ATTGAAGA
20543 ATTGAAGA
1 ATTGAAGA
20551 ATTGAAGA
1 ATTGAAGA
20559 ATTGAAGA
1 ATTGAAGA
20567 A
1 A
20568 AGAGATCATT
Statistics
Matches: 662, Mismatches: 120, Indels: 196
0.68 0.12 0.20
Matches are distributed among these distances:
5 3 0.00
6 136 0.21
7 76 0.11
8 409 0.62
9 31 0.05
10 2 0.00
12 3 0.00
13 1 0.00
14 1 0.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (8 bp):
ATTGAAGA
Found at i:19726 original size:44 final size:44
Alignment explanation
Indices: 19670--20567 Score: 480
Period size: 44 Copynumber: 20.8 Consensus size: 44
19660 TCGTTGAAGT
* * *
19670 AAATTGATGCATTGAATAATTGAAATTGAAGAATTGAAGTATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGAATTG
* *
19714 AAATTGAAGCATTCAAGAATTGAAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGAATTG
19758 AAATTGAAGCATTGAAGAATTGAAATTGAA-ACATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGA-ATTGAAGAATTG
* *
19802 AAATTG-AGACATTGACA-TATTAAAATTGAA-ACATTGAAG----G
1 AAATTGAAG-CATTGA-AGAATTGAAATTGAAGA-ATTGAAGAATTG
* *
19842 --ATTGAA--TTTGAAGAATTGAAATTGAAGCATTGAA-ATATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGA-ATTG
* * * * *
19882 AAATTGAAACATTGAAGGATTG-AATCTGGAGAATTGACA-TATTA
1 AAATTGAAGCATTGAAGAATTGAAAT-TGAAGAATTGA-AGAATTG
* *
19926 AAATTGAAACATTGAAG----G--ATTG-A-ATTTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGAATTG
19962 AAATTGAAGCATTGAA-ATATTGAAATTGAA-ACATTGAAGAATTG
1 AAATTGAAGCATTGAAGA-ATTGAAATTGAAGA-ATTGAAGAATTG
* *
20006 AATTTGAAGGATTGAA-ATATTGAAATTGAA-ACATTGAAGAATATG
1 AAATTGAAGCATTGAAGA-ATTGAAATTGAAGA-ATTGAAGAAT-TG
* * *
20051 AATTTGAAGCATTGAA-ATATTTAAATTGAA-ACATTGAAAAATTG
1 AAATTGAAGCATTGAAGA-ATTGAAATTGAAGA-ATTGAAGAATTG
* * *
20095 AATTTGAAGCATTGAA-TATTGAAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGAATTG
* * *
20138 AAATTTAAGCATTGAAAAATTGAAATTGAAGTATTGAA-ATATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGA-ATTG
* *
20182 AAATTGAA--ATT--A-AA--G-AATTG-A-AATTAAAGCATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGAATTG
* * * * **
20216 AATTTGAAACATTGAAGAATTGGAATTGAAGCATTGAATTATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGAATTG
* ** * *
20260 AAATAGAAAAATT---G-A----AATTGAAGCATTGAAGTATTTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAG-AATTG
** * *
20297 AAATTGCCGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTAAA
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGAATT--G
* * *** *
20343 AAAAT-AGATCATTCCGGAA-T-AAATTGAAGCATTGAAGAATTG
1 AAATTGA-AGCATTGAAGAATTGAAATTGAAGAATTGAAGAATTG
* * * * *
20385 AAGATTTGAGGCATTGAATAATTGAAGGATTGGAGCATTGAATAATTG
1 AA-A-TTGAAGCATTGAAGAATTGAA--ATTGAAGAATTGAAGAATTG
* * ** *
20433 AAGAATTGGAAACATTGAATAATTGAAGAATTGGGGAATTGAATAATTG
1 -A-AATT-GAAGCATTGAAGAATTG-A-AATTGAAGAATTGAAGAATTG
* ** * *
20482 AAGCACAT-AATAATTTGAAGAATTGAATAATTGAAGAGTTGAAGCATTG
1 AA--A-TTGAAGCA-TTGAAGAATTG-A-AATTGAAGAATTGAAGAATTG
**
20531 AATAATTGAAAAATTGAAGAATTGAAGAATTGAAGAA
1 -A-AATTGAAGCATTGAAGAATTG-A-AATTGAAGAA
20568 AGAGATCATT
Statistics
Matches: 687, Mismatches: 94, Indels: 142
0.74 0.10 0.15
Matches are distributed among these distances:
34 16 0.02
35 3 0.00
36 67 0.10
37 13 0.02
38 7 0.01
39 7 0.01
40 7 0.01
41 3 0.00
42 20 0.03
43 46 0.07
44 300 0.44
45 62 0.09
46 13 0.02
47 1 0.00
48 47 0.07
49 69 0.10
50 4 0.01
51 2 0.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (44 bp):
AAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGAATTG
Found at i:19874 original size:22 final size:22
Alignment explanation
Indices: 19849--19963 Score: 92
Period size: 22 Copynumber: 5.2 Consensus size: 22
19839 AGGATTGAAT
19849 TTGAAGAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
*
19871 TTGAA-ATATTGAAATTGAAACA
1 TTGAAGA-ATTGAAATTGAAGCA
* * *
19893 TTGAAGGATTG-AATCTGGAGAA
1 TTGAAGAATTGAAAT-TGAAGCA
* * *
19915 TTGACA-TATTAAAATTGAAACA
1 TTGA-AGAATTGAAATTGAAGCA
* * *
19937 TTGAAGGATTGAATTTGAAGAA
1 TTGAAGAATTGAAATTGAAGCA
19959 TTGAA
1 TTGAA
19964 ATTGAAGCAT
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
21 5 0.07
22 63 0.88
23 4 0.06
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.30
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAGCA
Found at i:19976 original size:22 final size:21
Alignment explanation
Indices: 19951--20217 Score: 295
Period size: 22 Copynumber: 12.2 Consensus size: 21
19941 AGGATTGAAT
19951 TTGAAGAATTGAAATTGAAGCA
1 TTGAA-AATTGAAATTGAAGCA
*
19973 TTGAAATATTGAAATTGAAACA
1 TTGAAA-ATTGAAATTGAAGCA
* *
19995 TTGAAGAATTGAATTTGAAGGA
1 TTGAA-AATTGAAATTGAAGCA
*
20017 TTGAAATATTGAAATTGAAACA
1 TTGAAA-ATTGAAATTGAAGCA
*
20039 TTGAAGAATATGAATTTGAAGCA
1 TTGAA-AAT-TGAAATTGAAGCA
* *
20062 TTGAAATATTTAAATTGAAACA
1 TTGAAA-ATTGAAATTGAAGCA
*
20084 TTGAAAAATTGAATTTGAAGCA
1 TTG-AAAATTGAAATTGAAGCA
*
20106 TTGAATATTGAAATTGAAGCA
1 TTGAAAATTGAAATTGAAGCA
*
20127 TTGAAGAATTGAAATTTAAGCA
1 TTGAA-AATTGAAATTGAAGCA
*
20149 TTGAAAAATTGAAATTGAAGTA
1 TTG-AAAATTGAAATTGAAGCA
20171 TTGAAATATTGAAATTGAA--A
1 TTGAAA-ATTGAAATTGAAGCA
* *
20191 TTAAAGAATTGAAATTAAAGCA
1 TTGAA-AATTGAAATTGAAGCA
20213 TTGAA
1 TTGAA
20218 TTTGAAACAT
Statistics
Matches: 208, Mismatches: 24, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
20 16 0.08
21 27 0.13
22 140 0.67
23 25 0.12
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (21 bp):
TTGAAAATTGAAATTGAAGCA
Found at i:20287 original size:14 final size:14
Alignment explanation
Indices: 19680--20334 Score: 279
Period size: 14 Copynumber: 46.0 Consensus size: 14
19670 AAATTGATGC
*
19680 ATTGAATAATTGAA
1 ATTGAAGAATTGAA
19694 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
19708 GTATTG-A-AATTGAA
1 --ATTGAAGAATTGAA
*
19722 GCATTCAAGAATTGAA
1 --ATTGAAGAATTGAA
*
19738 ATTGAAGCATTGAAGA
1 ATTGAAGAATTG-A-A
19754 ATTG-A-AATTGAA
1 ATTGAAGAATTGAA
19766 GCATTGAAGAATTGAA
1 --ATTGAAGAATTGAA
*
19782 ATT---GAA---AC
1 ATTGAAGAATTGAA
19790 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
19804 ATTG-AGACATTGACA
1 ATTGAAGA-ATTGA-A
19819 TATT-AA-AATTGAAA
1 -ATTGAAGAATTG-AA
*
19833 CATTGAAGGATTGAA
1 -ATTGAAGAATTGAA
*
19848 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
19862 ATTGAAGCATTGAAA
1 ATTGAAGAATTG-AA
19877 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
*
19891 CATTGAAGGATTG-A
1 -ATTGAAGAATTGAA
*
19905 ATCTGGAGAATTGACA
1 AT-TGAAGAATTGA-A
19921 TATT-AA-AATTGAAA
1 -ATTGAAGAATTG-AA
*
19935 CATTGAAGGATTGAA
1 -ATTGAAGAATTGAA
*
19950 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
19964 ATTGAAGCATTGAAA
1 ATTGAAGAATTG-AA
19979 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
19993 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
* *
20008 TTTGAAGGATTGAAA
1 ATTGAAGAATTG-AA
20023 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
20037 CATTGAAGAATATGAA
1 -ATTGAAGAAT-TGAA
* *
20053 TTTGAAGCATTGAA
1 ATTGAAGAATTGAA
**
20067 ATATTTA-AATTGAAA
1 AT-TGAAGAATTG-AA
*
20082 CATTGAAAAATTGAA
1 -ATTGAAGAATTGAA
* *
20097 TTTGAAGCATTGAA
1 ATTGAAGAATTGAA
20111 TATTG-A-AATTGAA
1 -ATTGAAGAATTGAA
20124 GCATTGAAGAATTGAA
1 --ATTGAAGAATTGAA
* *
20140 ATTTAAGCATTG--
1 ATTGAAGAATTGAA
20152 A---AA-AATTGAA
1 ATTGAAGAATTGAA
*
20162 ATTGAAGTATTGAAA
1 ATTGAAGAATTG-AA
20177 TATTG-A-AATTGAA
1 -ATTGAAGAATTGAA
*
20190 ATTAAAGAATTGAA
1 ATTGAAGAATTGAA
* *
20204 ATTAAAGCATTGAA
1 ATTGAAGAATTGAA
*
20218 TTTGAA-ACATTGAAGA
1 ATTGAAGA-ATTG-A-A
20234 ATTG--GAATTGAA
1 ATTGAAGAATTGAA
**
20246 GCATTGAATTATTGAA
1 --ATTGAAGAATTGAA
* *
20262 ATAGAAAAATTGAA
1 ATTGAAGAATTGAA
*
20276 ATTGAAGCATTGAA
1 ATTGAAGAATTGAA
**
20290 GTATTTG-A-AATTGCCGC
1 --A-TTGAAGAATTG--AA
20307 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
20321 ATTGAAGCATTGAA
1 ATTGAAGAATTGAA
20335 GAATTAAAAA
Statistics
Matches: 493, Mismatches: 72, Indels: 152
0.69 0.10 0.21
Matches are distributed among these distances:
8 8 0.02
9 2 0.00
10 1 0.00
11 6 0.01
12 6 0.01
13 18 0.04
14 285 0.58
15 63 0.13
16 97 0.20
17 7 0.01
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:20339 original size:22 final size:22
Alignment explanation
Indices: 19670--19861 Score: 244
Period size: 22 Copynumber: 8.7 Consensus size: 22
19660 TCGTTGAAGT
* *
19670 AAATTGATGCATTGAATAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
19692 AAATTGAAGAATTGAAGTATTG
1 AAATTGAAGCATTGAAGAATTG
*
19714 AAATTGAAGCATTCAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
19736 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
19758 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
*
19780 AAATTGAAACATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
19802 AAATTG-AGACATTGACA-TATTA
1 AAATTGAAG-CATTGA-AGAATTG
* *
19824 AAATTGAAACATTGAAGGATTG
1 AAATTGAAGCATTGAAGAATTG
* *
19846 AATTTGAAGAATTGAA
1 AAATTGAAGCATTGAA
19862 ATTGAAGCAT
Statistics
Matches: 148, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
21 2 0.01
22 144 0.97
23 2 0.01
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.30
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGAATTG
Found at i:20482 original size:57 final size:57
Alignment explanation
Indices: 20408--20564 Score: 110
Period size: 57 Copynumber: 2.8 Consensus size: 57
20398 TTGAATAATT
* * *
20408 GAAGGATTGG-AGCATTGAATAATTGAAGAATTGGAA-ACATTGAATAATTGAAGAATT
1 GAAGAATTGGAAGAATTGAATAATTGAAGAATT-GAAGA-ATTGAATAATTGAAAAATT
** * * * * *
20465 GGGGAATT-GAATAATTGAAGCACA-T-AATAATTTGAAGAATTGAATAATTGAAGAGTT
1 GAAGAATTGGAAGAATTGAA-TA-ATTGAAGAA-TTGAAGAATTGAATAATTGAAAAATT
* * *
20522 GAAGCATT-GAATAATTGAAAAATTGAAGAATTGAAGAATTGAA
1 GAAGAATTGGAAGAATTGAATAATTGAAGAATTGAAGAATTGAA
20565 GAAAGAGATC
Statistics
Matches: 80, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
55 1 0.01
56 16 0.20
57 57 0.71
58 5 0.06
59 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (57 bp):
GAAGAATTGGAAGAATTGAATAATTGAAGAATTGAAGAATTGAATAATTGAAAAATT
Found at i:28542 original size:19 final size:18
Alignment explanation
Indices: 28509--28544 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28499 TTTAGATAAT
28509 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
28527 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
28545 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:28552 original size:11 final size:10
Alignment explanation
Indices: 28504--28556 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
28494 GCCTCTTTAG
28504 ATAATTCTTCA
1 ATAA-TCTTCA
28515 ATAATCTTC-
1 ATAATCTTCA
28524 A-AATCTTCAA
1 ATAATCTTC-A
*
28534 ATTATCTTCA
1 ATAATCTTCA
28544 ATAAGTCTTCA
1 ATAA-TCTTCA
28555 AT
1 AT
28557 CACAGAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 10 0.28
11 18 0.50
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42
Consensus pattern (10 bp):
ATAATCTTCA
Found at i:32309 original size:22 final size:22
Alignment explanation
Indices: 32284--32387 Score: 113
Period size: 22 Copynumber: 4.7 Consensus size: 22
32274 TGTAGTCAAC
*
32284 CTAAAACAATTTTAAATGTAAG
1 CTAAAACAATTTCAAATGTAAG
*
32306 CTAAAACAA-CTCAAA-GTTAAG
1 CTAAAACAATTTCAAATG-TAAG
* *
32327 CTAAAACAATATCAAAAGGTAAG
1 CTAAAACAATTTC-AAATGTAAG
*
32350 CTAAAACAGTTTCAAATGTAAG
1 CTAAAACAATTTCAAATGTAAG
* *
32372 CCAAAACAGTTTCAAA
1 CTAAAACAATTTCAAA
32388 GTTAAGATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
20 1 0.01
21 17 0.24
22 34 0.48
23 18 0.25
24 1 0.01
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (22 bp):
CTAAAACAATTTCAAATGTAAG
Found at i:32393 original size:22 final size:22
Alignment explanation
Indices: 32284--32446 Score: 107
Period size: 22 Copynumber: 7.2 Consensus size: 22
32274 TGTAGTCAAC
* *
32284 CTAAAACAATTTTAAA-TGTAAG
1 CTAAAACAGTTTCAAAGT-TAAG
**
32306 CTAAAACA-ACTCAAAGTTAAG
1 CTAAAACAGTTTCAAAGTTAAG
* * *
32327 CTAAAACAATATCAAAAGGTAAG
1 CTAAAACAGTTTC-AAAGTTAAG
32350 CTAAAACAGTTTCAAA-TGTAAG
1 CTAAAACAGTTTCAAAGT-TAAG
*
32372 CCAAAACAGTTTCAAAGTTAAG
1 CTAAAACAGTTTCAAAGTTAAG
* * * *
32394 ATAAAATAGTTCCAAACAAAAGGTAAG
1 CTAAAACAGTT----TC-AAAGTTAAG
* *
32421 CTAAAACATTTTCAAAGGTAAG
1 CTAAAACAGTTTCAAAGTTAAG
32443 CTAA
1 CTAA
32447 CACAACCTAT
Statistics
Matches: 112, Mismatches: 19, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
21 16 0.14
22 58 0.52
23 21 0.19
26 1 0.01
27 16 0.14
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.23
Consensus pattern (22 bp):
CTAAAACAGTTTCAAAGTTAAG
Found at i:34570 original size:34 final size:34
Alignment explanation
Indices: 34527--34624 Score: 180
Period size: 34 Copynumber: 2.9 Consensus size: 34
34517 TCATTAAAGA
34527 AAATCAAAAGCCAAAAATGAAAATCACATAATGC
1 AAATCAAAAGCCAAAAATGAAAATCACATAATGC
*
34561 AAATCAAAAGGCAAAAATGAAAATCACATAATGC
1 AAATCAAAAGCCAAAAATGAAAATCACATAATGC
34595 AAATCAAAAGCC-AAAATGAAAATCACATAA
1 AAATCAAAAGCCAAAAATGAAAATCACATAA
34625 AGGATCATTG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 18 0.29
34 44 0.71
ACGTcount: A:0.60, C:0.16, G:0.09, T:0.14
Consensus pattern (34 bp):
AAATCAAAAGCCAAAAATGAAAATCACATAATGC
Found at i:36381 original size:51 final size:51
Alignment explanation
Indices: 36322--36424 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
36312 CAGCGGCCAT
* * *
36322 TGTATCTTTAACTTATAGATTTGAC-CTATCTCTACCCTTGATGTAGAGTGG
1 TGTATCTTTAACTTATACATTTGACTC-ATCTCTACCATTGATGTAAAGTGG
*
36373 TGTATCTTTAACTTATACATTTGACTCGTCTCTACCATTGATGTAAAGTGG
1 TGTATCTTTAACTTATACATTTGACTCATCTCTACCATTGATGTAAAGTGG
36424 T
1 T
36425 TTTGATAGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
51 46 0.98
52 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (51 bp):
TGTATCTTTAACTTATACATTTGACTCATCTCTACCATTGATGTAAAGTGG
Found at i:37747 original size:31 final size:30
Alignment explanation
Indices: 37704--37765 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
37694 TATAAAAGGG
* * *
37704 AAATATATATTAATAGTATCTTACATATAT
1 AAATATACATTAACAATATCTTACATATAT
37734 AAATAGTACATTAACAATATCTTACATATAT
1 AAATA-TACATTAACAATATCTTACATATAT
37765 A
1 A
37766 TTTATATCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (30 bp):
AAATATACATTAACAATATCTTACATATAT
Found at i:38314 original size:21 final size:20
Alignment explanation
Indices: 38275--38319 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
38265 AAATAACAAT
* *
38275 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
38295 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
38316 TAAA
1 TAAA
38320 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Done.