Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018904.1 Corchorus olitorius cultivar O-4 contig18937, 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: 109109
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4427 original size:2 final size:2
Alignment explanation
Indices: 4420--4450 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4410 ATCATACATC
4420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4451 ATGATAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6371 original size:38 final size:38
Alignment explanation
Indices: 6329--6406 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
6319 TTAAGTAAAA
6329 TTAATGAGTATTTGAATTTATGTACTCTATTACTTTTT
1 TTAATGAGTATTTGAATTTATGTACTCTATTACTTTTT
6367 TTAATGAGTATTTGAATTTATGTACTCTATTACTTTTT
1 TTAATGAGTATTTGAATTTATGTACTCTATTACTTTTT
6405 TT
1 TT
6407 TGAAGCTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (38 bp):
TTAATGAGTATTTGAATTTATGTACTCTATTACTTTTT
Found at i:10040 original size:20 final size:21
Alignment explanation
Indices: 9998--10040 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
9988 CTAAGTTATA
**
9998 TATTGAAAAGTTCTATATGGT
1 TATTGAAAAGTTCTATAAAGT
10019 TATTGAAAAGTT-TATAAAGT
1 TATTGAAAAGTTCTATAAAGT
10039 TA
1 TA
10041 AAAACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (21 bp):
TATTGAAAAGTTCTATAAAGT
Found at i:10164 original size:20 final size:20
Alignment explanation
Indices: 10127--10165 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10117 ACAAAGCAAT
* * *
10127 CTTAATAAAGTTATTAAAAG
1 CTTAACAAAATTACTAAAAG
10147 CTTAACAAAATTACTAAAA
1 CTTAACAAAATTACTAAAA
10166 AAGCGTAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (20 bp):
CTTAACAAAATTACTAAAAG
Found at i:10274 original size:20 final size:22
Alignment explanation
Indices: 10210--10275 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 22
10200 AAAAAATGAC
* * *
10210 AAAAAAGTTTAATA-AATCACT
1 AAAAGAGTTTAAGATAATTACT
10231 AAAAGAGTTTAAGATAATTA-T
1 AAAAGAGTTTAAGATAATTACT
10252 AAAA-AGTTT-AGA-AGATTACT
1 AAAAGAGTTTAAGATA-ATTACT
10272 AAAA
1 AAAA
10276 TTTTAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.03
19 7 0.18
20 10 0.26
21 17 0.44
22 4 0.10
ACGTcount: A:0.56, C:0.05, G:0.11, T:0.29
Consensus pattern (22 bp):
AAAAGAGTTTAAGATAATTACT
Found at i:10315 original size:22 final size:22
Alignment explanation
Indices: 10267--10318 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
10257 GTTTAGAAGA
*
10267 TTACT-AAAATTTTAATAAAGG
1 TTACTAAAAATTGTAATAAAGG
** *
10288 CGACTAAAAATTGTAATAAGGG
1 TTACTAAAAATTGTAATAAAGG
10310 TTACTAAAA
1 TTACTAAAA
10319 CGTTTAGTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (22 bp):
TTACTAAAAATTGTAATAAAGG
Found at i:10777 original size:199 final size:199
Alignment explanation
Indices: 10424--11248 Score: 1161
Period size: 199 Copynumber: 4.2 Consensus size: 199
10414 TGACAGCGTG
* * * *
10424 TTGTATAATAATCCTATAAGAAAAATTATATAATACACCGTCAGTGGATTTTAGCAGACTGTACG
1 TTGTATAATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACG
* * * *
10489 TGCGGGGTTTAAAGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATTTTAAATATTTAATTA
66 TGCAGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTA
* * * ** * * *
10554 ATCATGAAATGAAGTATGTGTCAACTTCTTAACGTGCTTATGGAGTTCAAAATTTACATTAATAG
131 ATTATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACATTAACAA
10619 TGTA
196 TGTA
* *
10623 TTGTATGATAATCCTATAAGAACAATTATACAGTACACCGTCAGTGGAGTTTAGCAGACTGCACG
1 TTGTATAATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACG
10688 TGCAGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTA
66 TGCAGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTA
* * * *
10753 ATTATAAAATGGGGTATATGTCAACTTTTTAACCCGCTTATAGAGTTCAAAATTTACATTGACAA
131 ATTATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACATTAACAA
10818 TGTA
196 TGTA
* * *
10822 TTGTATAATAATCCTATAAGAACAATTATACAATAGACCGCCAGTGAAGTTTAG-AGACTGCACG
1 TTGTATAATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACG
* *
10886 TGCAGGGTTTAAGGGTTGACATGTGTC-CCATTAGGCAATATGTATTAATATTAAATATTTTATT
66 TGCAGGGTTTAAGGGTTGACATGTGTCTCC-TTAGGGAATATGTATTAATATTAAATATTTAATT
* *
10950 AATTATGAAATGGGGTATATGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTACA-TAGAC
130 AATTATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACATTA-AC
*
11014 AGTGTA
194 AATGTA
* **
11020 TTGTATGATAATCCTATAAGAACAATTATACAATACATTGTCAGTGGAGTTTAGCAGACTGCACG
1 TTGTATAATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACG
** * *
11085 TGCAGGGTTTAAGCATTGACATGTGTCTCATTAGGGAATATGTATTAATATTATATATTTAATTA
66 TGCAGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTA
* * * * * * * * * * *
11150 ATGATGAAATGAGATTTGTGTCAACCTCTTAAGCCGCTTATAGAATCCAAAATTTGCACTGACAA
131 ATTATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACATTAACAA
11215 TGTA
196 TGTA
* *
11219 TTATATAATAATCCTATAAGAAAAATTATA
1 TTGTATAATAATCCTATAAGAACAATTATA
11249 TAAAGTGAAT
Statistics
Matches: 559, Mismatches: 62, Indels: 10
0.89 0.10 0.02
Matches are distributed among these distances:
197 3 0.01
198 180 0.32
199 374 0.67
200 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (199 bp):
TTGTATAATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACG
TGCAGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTA
ATTATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACATTAACAA
TGTA
Found at i:11066 original size:397 final size:398
Alignment explanation
Indices: 10424--11248 Score: 1258
Period size: 397 Copynumber: 2.1 Consensus size: 398
10414 TGACAGCGTG
* * * * *
10424 TTGTATAATAATCCTATAAGAAAAATTATATAATACACCGTCAGTGGATTTTAGCAGACTGTACG
1 TTGTATAATAATCCTATAAGAAAAATTATACAATACACCGCCAGTGAAGTTTAGCAGACTGCACG
* * * *
10489 TGCGGGGTTTAAAGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATTTTAAATATTTAATTA
66 TGCAGGGTTTAAAGGTTGACATGTGTCCCATTAGGCAATATGTATTAATATTAAATATTTAATTA
* ** *
10554 ATCATGAAATGAAGTATGTGTCAACTTCTTAACGTGCTTATGGAGTTCAAAATTTACATTAATAG
131 ATCATGAAATGAAGTATATGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTACATTAACAG
*
10619 TGTATTGTATGATAATCCTATAAGAACAATTATACAGTACACCGTCAGTGGAGTTTAGCAGACTG
196 TGTATTGTATGATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTG
** *
10684 CACGTGCAGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGAATATGTATTAATATTAAATATTTA
261 CACGTGCAGGGTTTAAGCATTGACATGTGTCTCATTAGGGAATATGTATTAATATTAAATATTTA
* * * * * * * *
10749 ATTAATTATAAAATGGGGTATATGTCAACTTTTTAACCCGCTTATAGAGTTCAAAATTTACATTG
326 ATTAATGATAAAATGAGATATATGTCAACCTCTTAACCCGCTTATAGAATCCAAAATTTACACTG
10814 ACAATGTA
391 ACAATGTA
* *
10822 TTGTATAATAATCCTATAAGAACAATTATACAATAGACCGCCAGTGAAGTTTAG-AGACTGCACG
1 TTGTATAATAATCCTATAAGAAAAATTATACAATACACCGCCAGTGAAGTTTAGCAGACTGCACG
* *
10886 TGCAGGGTTTAAGGGTTGACATGTGTCCCATTAGGCAATATGTATTAATATTAAATATTTTATTA
66 TGCAGGGTTTAAAGGTTGACATGTGTCCCATTAGGCAATATGTATTAATATTAAATATTTAATTA
* **
10951 ATTATGAAATGGGGTATATGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTACA-TAGACA
131 ATCATGAAATGAAGTATATGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTACATTA-ACA
**
11015 GTGTATTGTATGATAATCCTATAAGAACAATTATACAATACATTGTCAGTGGAGTTTAGCAGACT
195 GTGTATTGTATGATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
*
11080 GCACGTGCAGGGTTTAAGCATTGACATGTGTCTCATTAGGGAATATGTATTAATATTATATATTT
260 GCACGTGCAGGGTTTAAGCATTGACATGTGTCTCATTAGGGAATATGTATTAATATTAAATATTT
* * * * *
11145 AATTAATGATGAAATGAGATTTGTGTCAACCTCTTAAGCCGCTTATAGAATCCAAAATTTGCACT
325 AATTAATGATAAAATGAGATATATGTCAACCTCTTAACCCGCTTATAGAATCCAAAATTTACACT
11210 GACAATGTA
390 GACAATGTA
*
11219 TTATATAATAATCCTATAAGAAAAATTATA
1 TTGTATAATAATCCTATAAGAAAAATTATA
11249 TAAAGTGAAT
Statistics
Matches: 384, Mismatches: 42, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
396 2 0.01
397 334 0.87
398 48 0.12
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (398 bp):
TTGTATAATAATCCTATAAGAAAAATTATACAATACACCGCCAGTGAAGTTTAGCAGACTGCACG
TGCAGGGTTTAAAGGTTGACATGTGTCCCATTAGGCAATATGTATTAATATTAAATATTTAATTA
ATCATGAAATGAAGTATATGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTACATTAACAG
TGTATTGTATGATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTG
CACGTGCAGGGTTTAAGCATTGACATGTGTCTCATTAGGGAATATGTATTAATATTAAATATTTA
ATTAATGATAAAATGAGATATATGTCAACCTCTTAACCCGCTTATAGAATCCAAAATTTACACTG
ACAATGTA
Found at i:14626 original size:2 final size:2
Alignment explanation
Indices: 14619--14679 Score: 68
Period size: 2 Copynumber: 27.5 Consensus size: 2
14609 ATTGTTATCA
14619 AT AT AT AT AT AT AT AT GAT AT AT AT GAT AT AT AT GAT AT GAT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT AT -AT AT -AT AT
14663 AT GAT AT AT GAT AT AT A
1 AT -AT AT AT -AT AT AT A
14680 ATACTAATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 41 0.77
3 12 0.23
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (2 bp):
AT
Found at i:14641 original size:7 final size:6
Alignment explanation
Indices: 14619--14679 Score: 68
Period size: 7 Copynumber: 9.2 Consensus size: 6
14609 ATTGTTATCA
14619 ATATAT ATATAT ATATGAT ATATAT GATATAT ATGATAT GATATAT GATATAT
1 ATATAT ATATAT ATAT-AT ATATAT -ATATAT AT-ATAT -ATATAT -ATATAT
14672 GATATAT A
1 -ATATAT A
14680 ATACTAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
6 15 0.29
7 34 0.67
8 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:14641 original size:9 final size:9
Alignment explanation
Indices: 14619--14679 Score: 90
Period size: 9 Copynumber: 6.8 Consensus size: 9
14609 ATTGTTATCA
14619 ATATATAT-
1 ATATATATG
14627 ATATATATG
1 ATATATATG
14636 ATATATATG
1 ATATATATG
14645 ATATATATG
1 ATATATATG
14654 ATATGATAT-
1 ATAT-ATATG
14663 ATGATATATG
1 AT-ATATATG
14673 ATATATA
1 ATATATA
14680 ATACTAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.16
9 33 0.67
10 8 0.16
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (9 bp):
ATATATATG
Found at i:15026 original size:98 final size:98
Alignment explanation
Indices: 14919--15113 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
14909 TATAATGAAT
* *
14919 ATTATAATTAATTAGAGACACGTGTCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATT
1 ATTAGAATTAATTAGAGACACGTGTCGAGATTTGGAGGCCTCAACATTTAAAGAATTTCCATATT
*
14984 TGTAGTGTACATTGTTATCATTATATATATATG
66 TATAGTGTACATTGTTATCATTATATATATATG
*
15017 ATTAGAATTAATTAGAGACACGTGTCGAGATTTGGAGGCCTCAATATTTAAAGAATTTCCATATT
1 ATTAGAATTAATTAGAGACACGTGTCGAGATTTGGAGGCCTCAACATTTAAAGAATTTCCATATT
15082 TATAGTGTACATTGTTATCATTATATATATAT
66 TATAGTGTACATTGTTATCATTATATATATAT
15114 ATATATGATA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (98 bp):
ATTAGAATTAATTAGAGACACGTGTCGAGATTTGGAGGCCTCAACATTTAAAGAATTTCCATATT
TATAGTGTACATTGTTATCATTATATATATATG
Found at i:15126 original size:7 final size:7
Alignment explanation
Indices: 15103--15138 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
15093 TTGTTATCAT
15103 TATAT-A
1 TATATGA
15109 TATAT-A
1 TATATGA
15115 TATATGA
1 TATATGA
15122 TATATGA
1 TATATGA
15129 TATATGA
1 TATATGA
15136 TAT
1 TAT
15139 TTCATTGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (7 bp):
TATATGA
Found at i:18084 original size:45 final size:45
Alignment explanation
Indices: 18026--18155 Score: 208
Period size: 45 Copynumber: 2.9 Consensus size: 45
18016 CTAAATTCTA
* *
18026 CTCCATCTT-TAGGTAATTCATCAAAATAAAACTAATATTATACTC
1 CTCCAT-TTCTAGGTAATTCATCAAAATAAAGCTAATATTACACTC
*
18071 CTCCATTTCTAGGTAATTCATCAAAATAAAGCTAATATTCCACTC
1 CTCCATTTCTAGGTAATTCATCAAAATAAAGCTAATATTACACTC
*
18116 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
1 CTCCATTTCTAGGTAATTCATCAAAATAAAGCTAATATTA
18156 GTTGTTGCTT
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 2 0.03
45 77 0.97
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (45 bp):
CTCCATTTCTAGGTAATTCATCAAAATAAAGCTAATATTACACTC
Found at i:23528 original size:12 final size:12
Alignment explanation
Indices: 23511--23542 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
23501 TCATGCAAAG
23511 CACTCTTAATCT
1 CACTCTTAATCT
23523 CACTCTTAATCT
1 CACTCTTAATCT
23535 CACTCTTA
1 CACTCTTA
23543 GTAGCTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (12 bp):
CACTCTTAATCT
Found at i:25373 original size:2 final size:2
Alignment explanation
Indices: 25362--25422 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
25352 GAAAAATCCT
25362 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
25403 CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA
25423 ATTGTTTACC
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:27123 original size:13 final size:13
Alignment explanation
Indices: 27105--27131 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27095 TGTCTCATTA
27105 GGTAAGCTTAATG
1 GGTAAGCTTAATG
27118 GGTAAGCTTAATG
1 GGTAAGCTTAATG
27131 G
1 G
27132 ATCAAATGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (13 bp):
GGTAAGCTTAATG
Found at i:33263 original size:2 final size:2
Alignment explanation
Indices: 33256--33289 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33246 ATTTAAAAAG
33256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33290 TCATAAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36058 original size:21 final size:22
Alignment explanation
Indices: 36017--36067 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
36007 CATAAATTAA
36017 ATAAATGATTCTAAAAAAAGCC
1 ATAAATGATTCTAAAAAAAGCC
* * *
36039 ATAAATTATTC-AAAATAAGCA
1 ATAAATGATTCTAAAAAAAGCC
*
36060 ATCAATGA
1 ATAAATGA
36068 AGGATACAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (22 bp):
ATAAATGATTCTAAAAAAAGCC
Found at i:37491 original size:24 final size:24
Alignment explanation
Indices: 37459--37507 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
37449 TATATTCTTC
37459 ACACATTCCCAAATCACAATGGAA
1 ACACATTCCCAAATCACAATGGAA
37483 ACACATTCCCAAATCACAATGGAA
1 ACACATTCCCAAATCACAATGGAA
37507 A
1 A
37508 GGGAAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.29, G:0.08, T:0.16
Consensus pattern (24 bp):
ACACATTCCCAAATCACAATGGAA
Found at i:39425 original size:2 final size:2
Alignment explanation
Indices: 39418--39449 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39408 TAATATTTAG
39418 TA TA 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 TA TA
39450 CCCTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49120 original size:16 final size:16
Alignment explanation
Indices: 49101--49154 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
49091 AAATTGTTTG
49101 GAAAAGAATTTTGATT
1 GAAAAGAATTTTGATT
* *
49117 GAAAAAGAA-ATTGTTT
1 G-AAAAGAATTTTGATT
*
49133 GGAAAATAATTTTGATT
1 -GAAAAGAATTTTGATT
49150 GAAAA
1 GAAAA
49155 AGTTAGTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (16 bp):
GAAAAGAATTTTGATT
Found at i:49124 original size:17 final size:17
Alignment explanation
Indices: 49102--49156 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
49092 AATTGTTTGG
49102 AAAAGAATTTTGATTGA
1 AAAAGAATTTTGATTGA
* * *
49119 AAAAGAA-ATTGTTTGG
1 AAAAGAATTTTGATTGA
*
49135 AAAATAATTTTGATTGA
1 AAAAGAATTTTGATTGA
49152 AAAAG
1 AAAAG
49157 TTAGTTGAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (17 bp):
AAAAGAATTTTGATTGA
Found at i:49131 original size:33 final size:33
Alignment explanation
Indices: 49089--49156 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
49079 GTGGCGATGG
49089 AGAAATTGTTTGGAAAAGAATTTTGATTGAAAA
1 AGAAATTGTTTGGAAAAGAATTTTGATTGAAAA
*
49122 AGAAATTGTTTGGAAAATAATTTTGATTGAAAA
1 AGAAATTGTTTGGAAAAGAATTTTGATTGAAAA
49155 AG
1 AG
49157 TTAGTTGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.34
Consensus pattern (33 bp):
AGAAATTGTTTGGAAAAGAATTTTGATTGAAAA
Found at i:54893 original size:20 final size:20
Alignment explanation
Indices: 54868--54907 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
54858 TTAAGTTCAA
54868 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
54888 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
54908 GTTTATTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CTCTCACGGAATGTGAGTTT
Found at i:56410 original size:2 final size:2
Alignment explanation
Indices: 56405--56429 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56395 GTATTGAGTA
56405 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
56430 ATAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57429 original size:30 final size:30
Alignment explanation
Indices: 57393--57472 Score: 160
Period size: 30 Copynumber: 2.7 Consensus size: 30
57383 GTTTTTGTTC
57393 AAAAAAAGAAGTAAGAACCGTTATCTCAAA
1 AAAAAAAGAAGTAAGAACCGTTATCTCAAA
57423 AAAAAAAGAAGTAAGAACCGTTATCTCAAA
1 AAAAAAAGAAGTAAGAACCGTTATCTCAAA
57453 AAAAAAAGAAGTAAGAACCG
1 AAAAAAAGAAGTAAGAACCG
57473 AACCTCTTGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.14
Consensus pattern (30 bp):
AAAAAAAGAAGTAAGAACCGTTATCTCAAA
Found at i:57676 original size:38 final size:38
Alignment explanation
Indices: 57615--57691 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
57605 TATAAGTACT
* * *
57615 ATGATTTTGGAAGTTTGACTTTCGAATCAATGGAAGGA
1 ATGAATTTGAAAGTTTGACTTTCGAACCAATGGAAGGA
57653 ATGAATTTGAAAGTTTGACTTTCGAACCAATGGAAGGA
1 ATGAATTTGAAAGTTTGACTTTCGAACCAATGGAAGGA
57691 A
1 A
57692 GTGAGGGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.31
Consensus pattern (38 bp):
ATGAATTTGAAAGTTTGACTTTCGAACCAATGGAAGGA
Found at i:59114 original size:17 final size:17
Alignment explanation
Indices: 59092--59128 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
59082 ATCTGAAGCG
59092 TCTCCATGGTGCTCTGC
1 TCTCCATGGTGCTCTGC
59109 TCTCCATGGTGCTCTGC
1 TCTCCATGGTGCTCTGC
59126 TCT
1 TCT
59129 TCTTTCGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.35, G:0.22, T:0.38
Consensus pattern (17 bp):
TCTCCATGGTGCTCTGC
Found at i:70131 original size:6 final size:6
Alignment explanation
Indices: 70092--70130 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
70082 CAACACTCTA
70092 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT- TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
70131 TAAATTAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (6 bp):
TTTTTG
Found at i:79278 original size:30 final size:30
Alignment explanation
Indices: 79244--79321 Score: 156
Period size: 30 Copynumber: 2.6 Consensus size: 30
79234 GTAACGAAAT
79244 AAGAACCACCTCTAGCAATTTATCAAAAAA
1 AAGAACCACCTCTAGCAATTTATCAAAAAA
79274 AAGAACCACCTCTAGCAATTTATCAAAAAA
1 AAGAACCACCTCTAGCAATTTATCAAAAAA
79304 AAGAACCACCTCTAGCAA
1 AAGAACCACCTCTAGCAA
79322 GACATCTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.18
Consensus pattern (30 bp):
AAGAACCACCTCTAGCAATTTATCAAAAAA
Found at i:87626 original size:25 final size:25
Alignment explanation
Indices: 87592--87653 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
87582 CTAATACTCG
87592 GTCGAGCTCGAGCTCGAATTTTTGA
1 GTCGAGCTCGAGCTCGAATTTTTGA
87617 GTCGAGCTCGAGCTCGAATTTTTGA
1 GTCGAGCTCGAGCTCGAATTTTTGA
*
87642 GTCAAGCTCGAG
1 GTCGAGCTCGAG
87654 TAGCTCACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (25 bp):
GTCGAGCTCGAGCTCGAATTTTTGA
Found at i:89504 original size:16 final size:16
Alignment explanation
Indices: 89463--89518 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
89453 AAGCAATTCA
*
89463 AATTAAACAGAAAA-C
1 AATTAAATAGAAAAGC
*
89478 ATGTTAAATAG-AAAGC
1 A-ATTAAATAGAAAAGC
89494 AATTAAGATAGAAAAGC
1 AATTAA-ATAGAAAAGC
89511 AA-TAAATA
1 AATTAAATA
89519 ATAAACACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 11 0.32
16 16 0.47
17 7 0.21
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (16 bp):
AATTAAATAGAAAAGC
Found at i:89511 original size:17 final size:15
Alignment explanation
Indices: 89481--89518 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
89471 AGAAAACATG
89481 TTAAATAGAAAGCAA
1 TTAAATAGAAAGCAA
89496 TTAAGATAGAAAAGCAA
1 TTAA-ATAG-AAAGCAA
89513 -TAAATA
1 TTAAATA
89519 ATAAACACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 7 0.33
17 7 0.33
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (15 bp):
TTAAATAGAAAGCAA
Found at i:94524 original size:16 final size:16
Alignment explanation
Indices: 94482--94525 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
94472 AAATATTGTG
**
94482 TATACATATAAAAAAA
1 TATACATATATTAAAA
* *
94498 TATAAAGATATTAAAA
1 TATACATATATTAAAA
94514 TATACATATATT
1 TATACATATATT
94526 GCATTATATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (16 bp):
TATACATATATTAAAA
Found at i:96835 original size:10 final size:10
Alignment explanation
Indices: 96820--96844 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
96810 TTCAATTTAA
96820 TTTAATCGGT
1 TTTAATCGGT
96830 TTTAATCGGT
1 TTTAATCGGT
96840 TTTAA
1 TTTAA
96845 AATAGGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (10 bp):
TTTAATCGGT
Found at i:96976 original size:11 final size:11
Alignment explanation
Indices: 96960--97073 Score: 67
Period size: 11 Copynumber: 10.8 Consensus size: 11
96950 AAAAAATTTG
96960 TTATATATATT
1 TTATATATATT
*
96971 TTATATATATC
1 TTATATATATT
* * *
96982 ATAAATATA-A
1 TTATATATATT
96992 TT-TATATATT
1 TTATATATATT
* *
97002 TTACATGTATT
1 TTATATATATT
97013 TTATATATA--
1 TTATATATATT
* * *
97022 TCATAAATA-A
1 TTATATATATT
*
97032 TTAAATATATT
1 TTATATATATT
*
97043 TTATATATATC
1 TTATATATATT
* *
97054 ATAAATATATT
1 TTATATATATT
*
97065 TGATATATA
1 TTATATATA
97074 ATAGCATAAT
Statistics
Matches: 74, Mismatches: 25, Indels: 8
0.69 0.23 0.07
Matches are distributed among these distances:
9 12 0.16
10 9 0.12
11 53 0.72
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (11 bp):
TTATATATATT
Found at i:98022 original size:23 final size:23
Alignment explanation
Indices: 97996--98043 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
97986 TGAAAGTACA
* *
97996 ATAGAATTGATGTTATAATAATT
1 ATAGAATTGATGTTACAAAAATT
98019 ATAGAATTGATGTTACAAAAATT
1 ATAGAATTGATGTTACAAAAATT
98042 AT
1 AT
98044 CAAGATATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (23 bp):
ATAGAATTGATGTTACAAAAATT
Found at i:106824 original size:21 final size:22
Alignment explanation
Indices: 106800--106840 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
106790 GTTTATAATA
*
106800 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
106821 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
106841 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:108674 original size:132 final size:134
Alignment explanation
Indices: 108435--108700 Score: 473
Period size: 132 Copynumber: 2.0 Consensus size: 134
108425 TATTAAAAAA
* *
108435 TACATATTTTTGTAAAACTTCTGAATCGCCCGTTATATTCTTACTTTTTTAATATATTTCTTAAA
1 TACATACTATTGTAAAACTTCTGAATCGCCCGTTATATTCTTACTTTTTTAATATATTTCTTAAA
* *
108500 TGTCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATATA
66 TGCCATTGTTTAGACTTTTATAATTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATATA
108565 ATAT
131 ATAT
*
108569 TACATACTATTGTAAAACTTCTGAATCGCCCGTTATA-TCTT-TTTTTTTAATATATTTCTTAAA
1 TACATACTATTGTAAAACTTCTGAATCGCCCGTTATATTCTTACTTTTTTAATATATTTCTTAAA
108632 TGCCATTGTTTAGACTTTTATAATTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATATA
66 TGCCATTGTTTAGACTTTTATAATTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATATA
108697 ATAT
131 ATAT
108701 CCTTATGACT
Statistics
Matches: 127, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
132 88 0.69
133 4 0.03
134 35 0.28
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.48
Consensus pattern (134 bp):
TACATACTATTGTAAAACTTCTGAATCGCCCGTTATATTCTTACTTTTTTAATATATTTCTTAAA
TGCCATTGTTTAGACTTTTATAATTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATATA
ATAT
Done.