Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011947.1 Corchorus capsularis cultivar CVL-1 contig11968, 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: 55968
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3550 original size:19 final size:18
Alignment explanation
Indices: 3517--3553 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3507 TTGAAATAAT
3517 TCTTCAATAATCTTCAAG
1 TCTTCAATAATCTTCAAG
*
3535 TCTTCAAATTATCTTCAAG
1 TCTTC-AATAATCTTCAAG
3554 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAG
Found at i:11268 original size:14 final size:14
Alignment explanation
Indices: 11244--11289 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
11234 AGGAGGCTTG
11244 GAAGAATTGAAATT
1 GAAGAATTGAAATT
11258 GAA-ACATTG-AATT
1 GAAGA-ATTGAAATT
11271 CGAAGAATTGAAATT
1 -GAAGAATTGAAATT
11286 GAAG
1 GAAG
11290 CAATGGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 5 0.18
14 18 0.64
15 5 0.18
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (14 bp):
GAAGAATTGAAATT
Found at i:11366 original size:14 final size:15
Alignment explanation
Indices: 11344--11385 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
11334 ACATTGACAT
11344 TTGGAATTTGAAGAA
1 TTGGAATTTGAAGAA
*
11359 TTGG-ATTTGAAGCA
1 TTGGAATTTGAAGAA
*
11373 TTGAAATATTGAA
1 TTGGAAT-TTGAA
11386 ATTTTTTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.52
15 6 0.26
16 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (15 bp):
TTGGAATTTGAAGAA
Found at i:11430 original size:22 final size:22
Alignment explanation
Indices: 11405--11470 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
11395 CCAAAAAAAA
*
11405 GAAATATTGAAATTGAAACATT
1 GAAAAATTGAAATTGAAACATT
11427 GAAAAATTGAAATTGAAACATT
1 GAAAAATTGAAATTGAAACATT
** *
11449 GAAGGATTGAAATTGAAGCATT
1 GAAAAATTGAAATTGAAACATT
11471 AGCATTTGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (22 bp):
GAAAAATTGAAATTGAAACATT
Found at i:11464 original size:36 final size:36
Alignment explanation
Indices: 11415--12091 Score: 213
Period size: 36 Copynumber: 17.8 Consensus size: 36
11405 GAAATATTGA
*
11415 AATTGAAACATTGAAAAATTGAAATTGAAACATTGAAG
1 AATTG-AA-ATTGAAGAATTGAAATTGAAACATTGAAG
* * * * * *
11453 GATTGAAATTGAAGCATTAGCATTTGGAA-TTTGAAG
1 AATTGAAATTGAAGAATT-GAAATTGAAACATTGAAG
* * **
11489 AATTGAAATTGAAGTATTGAAATTGAAGCGCTGAAG
1 AATTGAAATTGAAGAATTGAAATTGAAACATTGAAG
*
11525 AATTGAAATTGAAGCATTGAAGAATTG-AAC--TGAAG
1 AATTGAAATTGAAGAATTG-A-AATTGAAACATTGAAG
* *
11560 --TTGAAGAATTGAAATAATTGAGGAATTGAAGCATTGAAG
1 AATTG-A-AATTG-AAGAATTGA--AATTGAAACATTGAAG
** *** * * *
11599 AACTTGAAGAAAGATCACCCTGGATCATTGAAGTAAATTGAAG
1 AA-TTGAA-ATTGA--AGAATTGA-AATTGAA--ACATTGAAG
* * * **
11642 CATTGAATTATTGAAGAATTGGAGCATTGGATGATTGAAG
1 AATTGAA--ATTGAAGAATT-GA-AATTGAAACATTGAAG
** *
11682 AATTGAAGAAAGATA-AATTGAAGCATCG--A-ATTGAAG
1 AATTGAA-ATTGA-AGAATTGAA--ATTGAAACATTGAAG
* * *
11718 GATTGAACTTGAAGCATTGAAATTGAAAC--TGAAG
1 AATTGAAATTGAAGAATTGAAATTGAAACATTGAAG
* * *
11752 CATTGAAATATTG-A-AATTGAAGAATTGAAA-AATGGA-
1 AATTG-AA-ATTGAAGAATTG-A-AATTGAAACATTGAAG
*
11788 AATTGAAGTATTGAAGAAGTGAAATTGAAGCATTGGCATTTGGAATTTG
1 AATTGAA--ATTGAAGAATTGAAATTGAA--A----CA-TT-GAA---G
* *
11837 AAATTGAAGCATTGAAGGATTGAATTTGAAGA-ATTG-A-
1 -AATTGAA--ATTGAAGAATTGAAATTGAA-ACATTGAAG
*
11874 AATTGAAACATTGAAGAATTGAAATTAAAACATTGAAG
1 AATTG-AA-ATTGAAGAATTGAAATTGAAACATTGAAG
* ***
11912 GATTGGGTTTGAAGAATTGAAATTGAAATTGAGCTATTGAAG
1 AATTGAAATTGAAGAATTGAAATTG-AA---A-C-ATTGAAG
* *
11954 AATTGGAATTGAAGAATTGAAATTGAAGCATTGAAG
1 AATTGAAATTGAAGAATTGAAATTGAAACATTGAAG
* * * **
11990 GATTGAATTTGAAGAATTGACATTGAAGGATTGAAG
1 AATTGAAATTGAAGAATTGAAATTGAAACATTGAAG
* * **
12026 AATTGAATTTGAAGAATTGACATTGAAGGATTGAAG
1 AATTGAAATTGAAGAATTGAAATTGAAACATTGAAG
*
12062 AATTGAAATTGAAGTATTGAAGAATTGAAA
1 AATTGAAATTGAAGAATTG-A-AATTGAAA
12092 TTGACCAACT
Statistics
Matches: 486, Mismatches: 90, Indels: 126
0.69 0.13 0.18
Matches are distributed among these distances:
33 6 0.01
34 15 0.03
35 33 0.07
36 239 0.49
37 26 0.05
38 26 0.05
39 15 0.03
40 17 0.03
41 15 0.03
42 50 0.10
43 14 0.03
44 2 0.00
45 2 0.00
49 1 0.00
50 25 0.05
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.29
Consensus pattern (36 bp):
AATTGAAATTGAAGAATTGAAATTGAAACATTGAAG
Found at i:11502 original size:14 final size:14
Alignment explanation
Indices: 11483--11516 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
11473 CATTTGGAAT
11483 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
*
11497 TTGAAGTATTGAAA
1 TTGAAGAATTGAAA
11511 TTGAAG
1 TTGAAG
11517 CGCTGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (14 bp):
TTGAAGAATTGAAA
Found at i:11523 original size:22 final size:22
Alignment explanation
Indices: 11498--11574 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
11488 GAATTGAAAT
* *
11498 TGAAGTATTGAAATTGAAGCGC
1 TGAAGAATTGAAATTGAAGCAC
*
11520 TGAAGAATTGAAATTGAAGCAT
1 TGAAGAATTGAAATTGAAGCAC
* *
11542 TGAAGAATTG-AACTGAAG--T
1 TGAAGAATTGAAATTGAAGCAC
11561 TGAAGAATTGAAAT
1 TGAAGAATTGAAAT
11575 AATTGAGGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 11 0.22
20 2 0.04
21 7 0.14
22 29 0.59
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (22 bp):
TGAAGAATTGAAATTGAAGCAC
Found at i:11571 original size:8 final size:8
Alignment explanation
Indices: 11483--12090 Score: 168
Period size: 8 Copynumber: 81.6 Consensus size: 8
11473 CATTTGGAAT
11483 TTGAAGAA
1 TTGAAGAA
11491 TTG-A-AA
1 TTGAAGAA
*
11497 TTGAAGTA
1 TTGAAGAA
11505 TTG-A-AA
1 TTGAAGAA
**
11511 TTGAAGCG
1 TTGAAGAA
*
11519 CTGAAGAA
1 TTGAAGAA
11527 TTG-A-AA
1 TTGAAGAA
*
11533 TTGAAGCA
1 TTGAAGAA
11541 TTGAAGAA
1 TTGAAGAA
11549 TTGAACTGAA
1 TTGAA--GAA
11559 GTTGAAGAA
1 -TTGAAGAA
*
11568 TTGAAATAA
1 TTG-AAGAA
*
11577 TTGAGGAA
1 TTGAAGAA
*
11585 TTGAAGCA
1 TTGAAGAA
11593 TTGAAGAA
1 TTGAAGAA
11601 CTTGAAGAA
1 -TTGAAGAA
* ** *
11610 -AGATCACC
1 TTGAAGA-A
* * **
11618 CTGGATCA
1 TTGAAGAA
11626 TTGAAGTAAA
1 TTGAAG--AA
*
11636 TTGAAGCA
1 TTGAAGAA
**
11644 TTGAATTA
1 TTGAAGAA
11652 TTGAAGAA
1 TTGAAGAA
* *
11660 TTGGAGCA
1 TTGAAGAA
*
11668 TTGGATG-A
1 TT-GAAGAA
11676 TTGAAGAA
1 TTGAAGAA
11684 TTGAAGAA
1 TTGAAGAA
*
11692 -AGATA-AA
1 TTGA-AGAA
*
11699 TTGAAGCA
1 TTGAAGAA
*
11707 -T--CGAA
1 TTGAAGAA
*
11712 TTGAAGGA
1 TTGAAGAA
*
11720 TTG-A-AC
1 TTGAAGAA
*
11726 TTGAAGCA
1 TTGAAGAA
11734 TTG-A-AA
1 TTGAAGAA
11740 TTG-A-AA
1 TTGAAGAA
* *
11746 CTGAAGCA
1 TTGAAGAA
11754 TTGAA-ATA
1 TTGAAGA-A
11762 TTG-A-AA
1 TTGAAGAA
11768 TTGAAGAA
1 TTGAAGAA
11776 TTGAA-AA
1 TTGAAGAA
* *
11783 ATGGA-AA
1 TTGAAGAA
*
11790 TTGAAGTA
1 TTGAAGAA
11798 TTGAAGAA
1 TTGAAGAA
*
11806 GTG-A-AA
1 TTGAAGAA
*
11812 TTGAAGCA
1 TTGAAGAA
*
11820 TTG--GCAT
1 TTGAAG-AA
11827 TTG--GAA
1 TTGAAGAA
11833 TTTG-A-AA
1 -TTGAAGAA
*
11840 TTGAAGCA
1 TTGAAGAA
*
11848 TTGAAGGA
1 TTGAAGAA
*
11856 TTG-A-AT
1 TTGAAGAA
11862 TTGAAGAA
1 TTGAAGAA
11870 TTG-A-AA
1 TTGAAGAA
11876 TTGAA-ACA
1 TTGAAGA-A
11884 TTGAAGAA
1 TTGAAGAA
11892 TTG-A-AA
1 TTGAAGAA
*
11898 TT-AAAACA
1 TTGAAGA-A
*
11906 TTGAAGGA
1 TTGAAGAA
**
11914 TTG--GGT
1 TTGAAGAA
11920 TTGAAGAA
1 TTGAAGAA
11928 TTG-A-AA
1 TTGAAGAA
11934 TTG-A-AA
1 TTGAAGAA
*
11940 TTG-AGCTA
1 TTGAAG-AA
11948 TTGAAGAA
1 TTGAAGAA
11956 TTG--GAA
1 TTGAAGAA
11962 TTGAAGAA
1 TTGAAGAA
11970 TTG-A-AA
1 TTGAAGAA
*
11976 TTGAAGCA
1 TTGAAGAA
*
11984 TTGAAGGA
1 TTGAAGAA
*
11992 TTG-A-AT
1 TTGAAGAA
11998 TTGAAGAA
1 TTGAAGAA
*
12006 TTG-A-CA
1 TTGAAGAA
*
12012 TTGAAGGA
1 TTGAAGAA
12020 TTGAAGAA
1 TTGAAGAA
*
12028 TTG-A-AT
1 TTGAAGAA
12034 TTGAAGAA
1 TTGAAGAA
*
12042 TTG-A-CA
1 TTGAAGAA
*
12048 TTGAAGGA
1 TTGAAGAA
12056 TTGAAGAA
1 TTGAAGAA
12064 TTG-A-AA
1 TTGAAGAA
*
12070 TTGAAGTA
1 TTGAAGAA
12078 TTGAAGAA
1 TTGAAGAA
12086 TTGAA
1 TTGAA
12091 ATTGACCAAC
Statistics
Matches: 439, Mismatches: 95, Indels: 132
0.66 0.14 0.20
Matches are distributed among these distances:
5 2 0.00
6 101 0.23
7 67 0.15
8 228 0.52
9 26 0.06
10 10 0.02
11 5 0.01
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (8 bp):
TTGAAGAA
Found at i:11667 original size:24 final size:24
Alignment explanation
Indices: 11625--12090 Score: 99
Period size: 22 Copynumber: 20.6 Consensus size: 24
11615 ACCCTGGATC
*
11625 ATTGAAGTAAATTGAAGCATTGAATT
1 ATTGAAG--AATTGAAGCATTGAATG
* *
11651 ATTGAAGAATTGGAGCATTGGATG
1 ATTGAAGAATTGAAGCATTGAATG
** *
11675 ATTGAAGAATTGAAG-AAAG-ATAA
1 ATTGAAGAATTGAAGCATTGAAT-G
* * *
11698 ATTGAAGCATCG-A--ATTGAAGG
1 ATTGAAGAATTGAAGCATTGAATG
*
11719 ATTG-A-ACTTGAAGCATTGAAATTG
1 ATTGAAGAATTGAAGCATTG-AA-TG
* * **
11743 AAACTGAAGCATTGAAATATTGAA--
1 --ATTGAAGAATTGAAGCATTGAATG
** *
11767 ATTGAAGAATTGAAAAATGGAA--
1 ATTGAAGAATTGAAGCATTGAATG
* * *
11789 ATTGAAGTATTGAAGAAGTGAA--
1 ATTGAAGAATTGAAGCATTGAATG
*
11811 ATTGAAGCATTG--GCATTTGGAAT-
1 ATTGAAGAATTGAAGCA-TT-GAATG
*
11834 -TTG-A-AATTGAAGCATTGAAGG
1 ATTGAAGAATTGAAGCATTGAATG
* *
11855 ATTG-A-ATTTGAAGAATTGAA--
1 ATTGAAGAATTGAAGCATTGAATG
*
11875 ATTGAA-ACATTGAAGAATTGAA--
1 ATTGAAGA-ATTGAAGCATTGAATG
* * *
11897 ATT-AAAACATTGAAGGATTG--GG
1 ATTGAAGA-ATTGAAGCATTGAATG
*
11919 TTTGAAGAATTGAA--ATTGAAATTGAG
1 ATTGAAGAATTGAAGCATTG-AA-T--G
*
11945 CTATTGAAGAATTG--GAATTGAA-G
1 --ATTGAAGAATTGAAGCATTGAATG
*
11968 AATTG-A-AATTGAAGCATTGAAGG
1 -ATTGAAGAATTGAAGCATTGAATG
* * *
11991 ATTG-A-ATTTGAAGAATTG-A-C
1 ATTGAAGAATTGAAGCATTGAATG
* *
12011 ATTGAAGGATTGAAGAATTGAAT-
1 ATTGAAGAATTGAAGCATTGAATG
*
12034 -TTGAAGAATTG-A-CATTGAAGG
1 ATTGAAGAATTGAAGCATTGAATG
12055 ATTGAAGAATTGAA--ATTGAA-G
1 ATTGAAGAATTGAAGCATTGAATG
12076 TATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
12091 ATTGACCAAC
Statistics
Matches: 342, Mismatches: 53, Indels: 94
0.70 0.11 0.19
Matches are distributed among these distances:
19 2 0.01
20 34 0.10
21 19 0.06
22 197 0.58
23 21 0.06
24 29 0.08
26 11 0.03
27 5 0.01
28 24 0.07
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.29
Consensus pattern (24 bp):
ATTGAAGAATTGAAGCATTGAATG
Found at i:11731 original size:14 final size:13
Alignment explanation
Indices: 11697--11744 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
11687 AAGAAAGATA
*
11697 AATTGAAGCATCG
1 AATTGAAGCATTG
*
11710 AATTGAAGGATTG
1 AATTGAAGCATTG
11723 AACTTGAAGCATTG
1 AA-TTGAAGCATTG
11737 AAATTGAA
1 -AATTGAA
11745 ACTGAAGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 13 0.43
14 15 0.50
15 2 0.07
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (13 bp):
AATTGAAGCATTG
Found at i:11738 original size:22 final size:22
Alignment explanation
Indices: 11711--12045 Score: 141
Period size: 22 Copynumber: 15.2 Consensus size: 22
11701 GAAGCATCGA
* *
11711 ATTGAAGGATTGAACTTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
*
11733 ATTG-A-AATTGAAACTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
*
11753 ATTGAA-ATATTGAAATTGAAGA
1 ATTGAAGA-ATTGAAATTGAAGC
* * *
11775 ATTGAAAAATGGAAATTGAAGT
1 ATTGAAGAATTGAAATTGAAGC
*
11797 ATTGAAGAAGTGAAATTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
*
11819 ATTGGCATTTGGAATTTGAAATTGAAGC
1 ATT-G-A---AGAA-TTGAAATTGAAGC
* * *
11847 ATTGAAGGATTGAATTTGAAGA
1 ATTGAAGAATTGAAATTGAAGC
*
11869 ATTG-A-AATTGAAACATTGAAGA
1 ATTGAAGAATTG-AA-ATTGAAGC
* *
11891 ATTG-A-AATTAAAACATTGAAGG
1 ATTGAAGAATT-GAA-ATTGAAGC
**
11913 ATTG--GGTTTGAAGAATTGAA--
1 ATTGAAGAATTG-A-AATTGAAGC
* *
11933 ATTG-A-AATTGAGCTATTGAAGA
1 ATTGAAGAATTGA--AATTGAAGC
11955 ATTG--GAATTGAAGAATTGAA--
1 ATTGAAGAATTG-A-AATTGAAGC
*
11975 ATTGAAGCATTGAAGGATTGAA--
1 ATTGAAGAATTGAA--ATTGAAGC
* * *
11997 TTTGAAGAATTGACATTGAAGG
1 ATTGAAGAATTGAAATTGAAGC
* *
12019 ATTGAAGAATTGAATTTGAAGA
1 ATTGAAGAATTGAAATTGAAGC
12041 ATTGA
1 ATTGA
12046 CATTGAAGGA
Statistics
Matches: 248, Mismatches: 38, Indels: 54
0.73 0.11 0.16
Matches are distributed among these distances:
19 1 0.00
20 44 0.18
21 7 0.03
22 169 0.68
23 6 0.02
24 1 0.00
26 1 0.00
27 4 0.02
28 15 0.06
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.30
Consensus pattern (22 bp):
ATTGAAGAATTGAAATTGAAGC
Found at i:11770 original size:14 final size:14
Alignment explanation
Indices: 11726--12095 Score: 149
Period size: 14 Copynumber: 25.3 Consensus size: 14
11716 AGGATTGAAC
*
11726 TTGAAGCATTGAAA
1 TTGAAGAATTGAAA
*
11740 TTG-A-AACTGAAGCA
1 TTGAAGAATTGAA--A
11754 TTGAA-ATATTGAAA
1 TTGAAGA-ATTGAAA
11768 TTGAAGAATTGAAAA
1 TTGAAGAATTG-AAA
* *
11783 ATGGA-AATTGAAGTA
1 TTGAAGAATTGAA--A
*
11798 TTGAAGAAGTGAAA
1 TTGAAGAATTGAAA
* * *
11812 TTGAAGCATTGGCAT
1 TTGAAGAATT-GAAA
11827 TTGGAATTTGAAATTGAAGCA
1 TT-GAA---G-AATTGAA--A
* *
11848 TTGAAGGATTGAAT
1 TTGAAGAATTGAAA
11862 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
11876 TTGAA-ACATTGAAGAA
1 TTGAAGA-ATTG-A-AA
*
11892 TTG-A-AATTAAAACA
1 TTGAAGAATT-GAA-A
* ***
11906 TTGAAGGATTGGGT
1 TTGAAGAATTGAAA
11920 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
*
11934 TTG-A-AATTGAGCTA
1 TTGAAGAATTGA--AA
*
11948 TTGAAGAATTGGAA
1 TTGAAGAATTGAAA
11962 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
*
11976 TTGAAGCATTGAAGGA
1 TTGAAGAATTGAA--A
*
11992 TTG-A-ATTTGAAGAA
1 TTGAAGAATTG-A-AA
*
12006 TTG-A-CATTGAAGGA
1 TTGAAGAATTGAA--A
*
12020 TTGAAGAATTGAAT
1 TTGAAGAATTGAAA
*
12034 TTGAAGAATTGACA
1 TTGAAGAATTGAAA
*
12048 TTGAAGGATTGAAGAA
1 TTGAAGAATTG-A-AA
12064 TTG-A-AATTGAAGTA
1 TTGAAGAATTGAA--A
12078 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
12092 TTGA
1 TTGA
12096 CCAACTGTCA
Statistics
Matches: 269, Mismatches: 45, Indels: 84
0.68 0.11 0.21
Matches are distributed among these distances:
12 13 0.05
13 8 0.03
14 153 0.57
15 28 0.10
16 55 0.20
17 1 0.00
19 3 0.01
20 6 0.02
21 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.30
Consensus pattern (14 bp):
TTGAAGAATTGAAA
Found at i:12522 original size:70 final size:70
Alignment explanation
Indices: 12287--12624 Score: 529
Period size: 70 Copynumber: 4.8 Consensus size: 70
12277 CCATGTTGCT
* *
12287 TGGATGGAACCAATGCTTGAACTGACTCGTATGGAAACGAGTTT-GCTTGTGGAAACGCCCTTGA
1 TGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCTTGA
12351 ATGCC
66 ATGCC
* *
12356 TGGATGGAACCAAAGCTTGAACTGATTCGTATGGAAACGAGTTTGGCTTGTGGAAAAAGCCCCT-
1 TGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGG-AAAAGCCCTTG
*
12420 AGATGCT
65 A-ATGCC
12427 TGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCTTGA
1 TGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCTTGA
12492 ATGCC
66 ATGCC
*
12497 TGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCTCC-TG
1 TGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGC-CCTTG
*
12561 AATGCT
65 AATGCC
* * * *
12567 TGAATGGAACCAATGTTTGAACTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAG
1 TGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
12625 TCAAAGTGTT
Statistics
Matches: 249, Mismatches: 15, Indels: 9
0.91 0.05 0.03
Matches are distributed among these distances:
69 42 0.17
70 140 0.56
71 67 0.27
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (70 bp):
TGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCTTGA
ATGCC
Found at i:12566 original size:140 final size:141
Alignment explanation
Indices: 12283--12624 Score: 582
Period size: 140 Copynumber: 2.4 Consensus size: 141
12273 AAGTCCATGT
*
12283 TGCTTGGATGGAACCAATGCTTGAACTGACTCGTATGGAAACGAGTTT-GCTTGTGGAAACGCCC
1 TGCTTGGATGGAACCAATGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
* *
12347 TTGAATGCCTGGATGGAACCAAAGCTTGAACTGATTCGTATGGAAACGAGTTTGGCTTGTGGAAA
66 TTGAATGCCTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAA
12412 AAGCCCCTAGA
131 AAGCCCCTAGA
*
12423 TGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
1 TGCTTGGATGGAACCAATGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
12488 TTGAATGCCTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGG-AA
66 TTGAATGCCTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAA
*
12552 AAGCTCCT-GAA
131 AAGCCCCTAG-A
* * *
12563 TGCTTGAATGGAACCAATGTTTGAACTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAG
1 TGCTTGGATGGAACCAATGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
12625 TCAAAGTGTT
Statistics
Matches: 191, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
139 1 0.01
140 115 0.60
141 75 0.39
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (141 bp):
TGCTTGGATGGAACCAATGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
TTGAATGCCTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAA
AAGCCCCTAGA
Found at i:13240 original size:50 final size:50
Alignment explanation
Indices: 13147--13242 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
13137 TTGAATAGCA
* *
13147 AATTTTGGTCTTAGACTCACAAATGGAATGCAATATTATTATAAAAAATG
1 AATTTTGGTCTTAGACTCACAAATGGAATACAATATTACTATAAAAAATG
* * *
13197 AATTTTGGTCTTGGACTCACAAATTGAATACAATCTTACTATAAAA
1 AATTTTGGTCTTAGACTCACAAATGGAATACAATATTACTATAAAA
13243 CTTCTTGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (50 bp):
AATTTTGGTCTTAGACTCACAAATGGAATACAATATTACTATAAAAAATG
Found at i:14335 original size:45 final size:44
Alignment explanation
Indices: 14276--14386 Score: 152
Period size: 43 Copynumber: 2.5 Consensus size: 44
14266 AAAACATAAC
* * *
14276 TTTGGAAAATCATTTTATCAAAACCTTTTGAAAACCATGACTTTT
1 TTTGAAAAACCATTTTATCAAAA-CTTTTGAAAACCATGACTCTT
14321 TTTGAAAAACCATTTTATC-AAACTTTTGAAAACCATGACTCTT
1 TTTGAAAAACCATTTTATCAAAACTTTTGAAAACCATGACTCTT
* * *
14364 TTTGAAAAGCTATTTTACCAAAA
1 TTTGAAAAACCATTTTATCAAAA
14387 TCATGATTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
43 36 0.61
44 6 0.10
45 17 0.29
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (44 bp):
TTTGAAAAACCATTTTATCAAAACTTTTGAAAACCATGACTCTT
Found at i:14438 original size:23 final size:21
Alignment explanation
Indices: 14412--14453 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
14402 AAAACCACCG
14412 TTGCACTTTTTCTTTCTTTTTTT
1 TTGCAC-TTTTC-TTCTTTTTTT
*
14435 TTGCTCTTTTCTTCTTTTT
1 TTGCACTTTTCTTCTTTTT
14454 CCTTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 5 0.28
23 5 0.28
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (21 bp):
TTGCACTTTTCTTCTTTTTTT
Found at i:15136 original size:3 final size:3
Alignment explanation
Indices: 15128--15154 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
15118 TTTTATTCCT
15128 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
15155 AACAAACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:22413 original size:22 final size:23
Alignment explanation
Indices: 22388--22431 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
22378 TTTTTTTTGC
*
22388 TTTTTCCCTTTCCTTT-TCTTTT
1 TTTTTCCATTTCCTTTCTCTTTT
*
22410 TTTTTCTATTTCCTTTCTCTTT
1 TTTTTCCATTTCCTTTCTCTTT
22432 CTTGTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTCCATTTCCTTTCTCTTTT
Found at i:22434 original size:27 final size:28
Alignment explanation
Indices: 22378--22431 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
22368 GTGCCTTTAA
*
22378 TTTTTTTTGCTTTTTCCCTTTCCTTTTC
1 TTTTTTTTGCTATTTCCCTTTCCTTTTC
*
22406 TTTTTTTTTCTATTT-CCTTTCTCTTT
1 TTTTTTTTGCTATTTCCCTTTC-CTTT
22432 CTTGTTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTTTTTTGCTATTTCCCTTTCCTTTTC
Found at i:22444 original size:22 final size:22
Alignment explanation
Indices: 22397--22446 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
22387 CTTTTTCCCT
* * *
22397 TTCCTTTTCTTTTTTTTTCTAT
1 TTCCTTTTCTTTCTTGTTCTAC
22419 TTCCTTTCTCTTTCTTGTT-TAC
1 TTCCTTT-TCTTTCTTGTTCTAC
22441 TTCCTT
1 TTCCTT
22447 CCCCAAGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.04, C:0.24, G:0.02, T:0.70
Consensus pattern (22 bp):
TTCCTTTTCTTTCTTGTTCTAC
Found at i:25757 original size:6 final size:6
Alignment explanation
Indices: 25746--25773 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
25736 TTGTGAATTA
25746 TTTCTT TTTCTT TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC
25774 AAATTAGATT
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:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:31474 original size:23 final size:21
Alignment explanation
Indices: 31442--31485 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31432 AGGGCTATTT
31442 TTGAACAAGCAAAAGTCGACTAG
1 TTGAACAAGC--AAGTCGACTAG
*
31465 TTGAAGAAGCAAGTCGACTAG
1 TTGAACAAGCAAGTCGACTAG
31486 CCTACAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (21 bp):
TTGAACAAGCAAGTCGACTAG
Found at i:32483 original size:21 final size:21
Alignment explanation
Indices: 32430--32489 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
32420 TTTGGATCAA
*
32430 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * *
32451 GTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTAG
32472 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
32490 CAAGATATGC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATATTCCAATCGATTCTAG
Found at i:34344 original size:9 final size:10
Alignment explanation
Indices: 34311--34346 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
34301 AGTTATATTG
34311 AAAAATATCAA
1 AAAAATAT-AA
34322 AAAAATATAA
1 AAAAATATAA
34332 AAAAATA-AA
1 AAAAATATAA
34341 AAAAAT
1 AAAAAT
34347 TCGACCAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 8 0.32
10 9 0.36
11 8 0.32
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAATATAA
Found at i:34940 original size:17 final size:17
Alignment explanation
Indices: 34918--34953 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
34908 AGGCCTAGTG
34918 AAGCTAGTAAAAGGCAT
1 AAGCTAGTAAAAGGCAT
34935 AAGCTAGTAAAAGGCAT
1 AAGCTAGTAAAAGGCAT
34952 AA
1 AA
34954 TCTTGTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.22, T:0.17
Consensus pattern (17 bp):
AAGCTAGTAAAAGGCAT
Found at i:48153 original size:24 final size:24
Alignment explanation
Indices: 48121--48180 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
48111 CATATACACC
48121 TCTAGACGCCGCCAAATAGTGGCG
1 TCTAGACGCCGCCAAATAGTGGCG
*
48145 TCTAGACGCCGCCAAATAGTGGTG
1 TCTAGACGCCGCCAAATAGTGGCG
48169 TCTAGACGCCGC
1 TCTAGACGCCGC
48181 TATGTTTTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.18
Consensus pattern (24 bp):
TCTAGACGCCGCCAAATAGTGGCG
Found at i:53187 original size:13 final size:13
Alignment explanation
Indices: 53169--53198 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
53159 TGGAAAAATC
53169 CTGTCTCAACCTG
1 CTGTCTCAACCTG
53182 CTGTCTCAACCTG
1 CTGTCTCAACCTG
53195 CTGT
1 CTGT
53199 TAGTGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.37, G:0.17, T:0.33
Consensus pattern (13 bp):
CTGTCTCAACCTG
Found at i:55606 original size:14 final size:14
Alignment explanation
Indices: 55589--55622 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55579 TGTTTTGAAC
*
55589 TTTTTGTTAATTAG
1 TTTTTGTTAATTAA
*
55603 TTTTTTTTAATTAA
1 TTTTTGTTAATTAA
55617 TTTTTG
1 TTTTTG
55623 CATATTTCAT
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:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (14 bp):
TTTTTGTTAATTAA
Done.