Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007911.1 Corchorus capsularis cultivar CVL-1 contig07932, 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: 67530
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:1825 original size:12 final size:12
Alignment explanation
Indices: 1808--1832 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1798 GCATATCAAA
1808 AAAATTACCATT
1 AAAATTACCATT
1820 AAAATTACCATT
1 AAAATTACCATT
1832 A
1 A
1833 TAAGGATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTACCATT
Found at i:1862 original size:15 final size:15
Alignment explanation
Indices: 1839--1868 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1829 ATTATAAGGA
*
1839 TCATTATAAAAAATT
1 TCATAATAAAAAATT
1854 TCATAATAAAAAATT
1 TCATAATAAAAAATT
1869 CCCATTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
TCATAATAAAAAATT
Found at i:1881 original size:20 final size:21
Alignment explanation
Indices: 1853--1891 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1843 TATAAAAAAT
*
1853 TTCATAATAAAA-AATTCCCA
1 TTCAAAATAAAACAATTCCCA
1873 TTCAAAATAAAACAATTCC
1 TTCAAAATAAAACAATTCC
1892 TATGTTTCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (21 bp):
TTCAAAATAAAACAATTCCCA
Found at i:3991 original size:2 final size:2
Alignment explanation
Indices: 3978--4008 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
3968 TATTAGGATG
3978 TA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
4009 AAAAGTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13619 original size:20 final size:20
Alignment explanation
Indices: 13581--13629 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
13571 TTTTAAATCA
**
13581 TAAATGAAA-TGTATTAAAT
1 TAAATGAAATTGTAAGAAAT
13600 TAAATGAAATTGTAAGAAAT
1 TAAATGAAATTGTAAGAAAT
*
13620 TGAATGAAAT
1 TAAATGAAAT
13630 GCTCAAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (20 bp):
TAAATGAAATTGTAAGAAAT
Found at i:13854 original size:13 final size:13
Alignment explanation
Indices: 13836--13860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13826 AGAGAAACCG
13836 AATGTAAGTAAAT
1 AATGTAAGTAAAT
13849 AATGTAAGTAAA
1 AATGTAAGTAAA
13861 AATACCATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (13 bp):
AATGTAAGTAAAT
Found at i:15000 original size:2 final size:2
Alignment explanation
Indices: 14993--15018 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14983 ATCTATAAAC
14993 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
15019 GTATTCTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16684 original size:21 final size:21
Alignment explanation
Indices: 16660--16703 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
16650 GTAAAGGCTC
*
16660 ATATTAAAGATGA-ATATGAAG
1 ATATGAAAGATGATAT-TGAAG
*
16681 ATATGAAATATGATATTGAAG
1 ATATGAAAGATGATATTGAAG
16702 AT
1 AT
16704 TAATAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (21 bp):
ATATGAAAGATGATATTGAAG
Found at i:21220 original size:5 final size:6
Alignment explanation
Indices: 21203--21228 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21193 ATGTATAGAG
21203 ACAAAA ACAAAA ACAAAA ACAAAA AC
1 ACAAAA ACAAAA ACAAAA ACAAAA AC
21229 TCACCAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:30774 original size:24 final size:25
Alignment explanation
Indices: 30747--30803 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 25
30737 GAAAGCAAGC
* *
30747 GAGCAACAGA-AGAAGAAAAAGAGT
1 GAGCAACAGACAGAACAAAAAGAAT
30771 GAGCAACA-ACAGAACAAAAAGAAT
1 GAGCAACAGACAGAACAAAAAGAAT
30795 GAGCAACAG
1 GAGCAACAG
30804 GAAAAGGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.58, C:0.14, G:0.25, T:0.04
Consensus pattern (25 bp):
GAGCAACAGACAGAACAAAAAGAAT
Found at i:36172 original size:5 final size:5
Alignment explanation
Indices: 36150--36184 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
36140 GCTTTAAAAT
36150 AATAA TAATAA TAATAA AATAA AATAA AATAA AAT
1 AATAA -AATAA -AATAA AATAA AATAA AATAA AAT
36185 TCCATTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
AATAA
Found at i:36311 original size:26 final size:25
Alignment explanation
Indices: 36278--36326 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
36268 GTCCCTCTTG
* *
36278 AAAAAAAATGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGAGTTAGTAACCTC
*
36303 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAA-AAAAAGAGAGTTAGTAACC
36327 CCTAAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.18
Consensus pattern (25 bp):
AAAAAAAAAGAGAGTTAGTAACCTC
Found at i:38989 original size:2 final size:2
Alignment explanation
Indices: 38982--39014 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
38972 GAAAATCCTT
*
38982 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39015 GTTGTGGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41185 original size:3 final size:3
Alignment explanation
Indices: 41177--41208 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41167 TTTATTTTCT
41177 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
41209 GGTATACGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:44281 original size:41 final size:41
Alignment explanation
Indices: 44224--44301 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
44214 AGTCCCAATC
*
44224 TTTTTTCTTTATGCTCTTCTCTGCCTCCATAGTTAGGTTTT
1 TTTTTTCTTTATGCTCTTCTCTACCTCCATAGTTAGGTTTT
*
44265 TTTTTTCTTTCA-GCTCTTGTCTACCTCCATAGTTAGG
1 TTTTTTCTTT-ATGCTCTTCTCTACCTCCATAGTTAGG
44302 GTTTCAAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 33 0.97
42 1 0.03
ACGTcount: A:0.12, C:0.23, G:0.13, T:0.53
Consensus pattern (41 bp):
TTTTTTCTTTATGCTCTTCTCTACCTCCATAGTTAGGTTTT
Found at i:47577 original size:16 final size:16
Alignment explanation
Indices: 47556--47588 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
47546 ACCCTCGATC
*
47556 ATAATTGAAATATTGA
1 ATAATTGAAAAATTGA
47572 ATAATTGAAAAATTGA
1 ATAATTGAAAAATTGA
47588 A
1 A
47589 GCAAGACCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (16 bp):
ATAATTGAAAAATTGA
Found at i:47630 original size:8 final size:8
Alignment explanation
Indices: 47617--47697 Score: 67
Period size: 8 Copynumber: 10.1 Consensus size: 8
47607 ATTTAAGTAG
*
47617 ATTGAAGC
1 ATTGAAGA
*
47625 ATTGAATA
1 ATTGAAGA
* *
47633 GTTGAAGG
1 ATTGAAGA
*
47641 ATTGAAGT
1 ATTGAAGA
*
47649 ATTGAATA
1 ATTGAAGA
47657 ATTGAAGA
1 ATTGAAGA
*
47665 ATTTG-AGC
1 A-TTGAAGA
47673 ATTGAATG-
1 ATTGAA-GA
47681 ATTGAAGA
1 ATTGAAGA
47689 ATTGAAGA
1 ATTGAAGA
47697 A
1 A
47698 AGACCACCCT
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
7 4 0.07
8 50 0.86
9 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.31
Consensus pattern (8 bp):
ATTGAAGA
Found at i:47630 original size:50 final size:50
Alignment explanation
Indices: 47575--47887 Score: 229
Period size: 50 Copynumber: 6.0 Consensus size: 50
47565 ATATTGAATA
* * * *
47575 ATTGAAAAATTGAAGCAAGACCACCCTGGATCATTTAAGTAGATTGAAGC
1 ATTGAATAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGC
* ** *** * * *
47625 ATTGAATAGTTGAAGGATTGA--AGTATTGAATAATTGAAG-AATTTG-AGC
1 ATTGAATAATTGAA-GAAAGACCA-CCCTGGATCATTGAAGTAAATTGAAGC
* * * *
47673 ATTGAATGATTGAAGAATTGAAGAAAGACCACCCTGTATCTTTGAATTAAATTGAAGC
1 ATTGAATAATT---GAA--G-A-A-AGACCACCCTGGATCATTGAAGTAAATTGAAGC
* *
47731 ATTAAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTTAAGC
1 ATTGAATAATT---G-A----AGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGC
*
47789 ATTGAATAATTGAAGAAAGACCACCCTGGATAATTGAAGTAAATTGAAGC
1 ATTGAATAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGC
* * *
47839 ACTGAATAATTGATGAAAGACCACCCTGGATCGTTGAAGTAAATTGAAG
1 ATTGAATAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAG
47888 TAAATTGAAG
Statistics
Matches: 206, Mismatches: 39, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
48 12 0.06
49 5 0.02
50 102 0.50
51 6 0.03
52 1 0.00
53 1 0.00
54 1 0.00
55 3 0.01
56 9 0.04
57 6 0.03
58 55 0.27
59 2 0.01
60 1 0.00
61 1 0.00
63 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (50 bp):
ATTGAATAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGC
Found at i:47652 original size:24 final size:24
Alignment explanation
Indices: 47617--47695 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
47607 ATTTAAGTAG
*
47617 ATTGAAGCATTGAATAGTTGAAGG
1 ATTGAAGCATTGAATAGTTGAAGA
* *
47641 ATTGAAGTATTGAATAATTGAAGA
1 ATTGAAGCATTGAATAGTTGAAGA
47665 ATTTG-AGCATTGAAT-GATTGAAGA
1 A-TTGAAGCATTGAATAG-TTGAAGA
47689 ATTGAAG
1 ATTGAAG
47696 AAAGACCACC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
23 3 0.06
24 41 0.87
25 3 0.06
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.32
Consensus pattern (24 bp):
ATTGAAGCATTGAATAGTTGAAGA
Found at i:47743 original size:58 final size:58
Alignment explanation
Indices: 47657--47887 Score: 246
Period size: 50 Copynumber: 4.3 Consensus size: 58
47647 GTATTGAATA
* * *
47657 ATTGAAG-AATTTG-AGCATTGAATGATTGAAGAATTGAAGAAAGACCACCCTGTATC
1 ATTGAAGTAAATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
* * *
47713 TTTGAATTAAATTGAAGCATTAAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
1 ATTGAAGTAAATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
* *
47771 ATTGAAGTAAATTTAAGCATTG---AA-T----AATTGAAGAAAGACCACCCTGGATA
1 ATTGAAGTAAATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
*
47821 ATTGAAGTAAATTGAAGCACTGAATAATT---G-A-T---GAAAGACCACCCTGGATC
1 ATTGAAGTAAATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
*
47871 GTTGAAGTAAATTGAAG
1 ATTGAAGTAAATTGAAG
47888 TAAATTGAAG
Statistics
Matches: 153, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
50 77 0.50
53 3 0.02
54 3 0.02
55 2 0.01
56 5 0.03
57 5 0.03
58 58 0.38
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (58 bp):
ATTGAAGTAAATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATC
Found at i:47774 original size:24 final size:24
Alignment explanation
Indices: 47746--47869 Score: 81
Period size: 24 Copynumber: 5.0 Consensus size: 24
47736 ATAATTGAAG
47746 AATTGAAGAAAGACCACCCTGGAT
1 AATTGAAGAAAGACCACCCTGGAT
* **** ** *
47770 CATTGAAGTAAATTTAAGCATTGAAT
1 AATTGAAG-AAAGACCA-CCCTGGAT
47796 AATTGAAGAAAGACCACCCTGGAT
1 AATTGAAGAAAGACCACCCTGGAT
* *
47820 AATTGAAGTAAATTGA--AGCACTGAAT
1 AATTGAAG-AAA--GACCA-CCCTGGAT
*
47846 AATTGATGAAAGACCACCCTGGAT
1 AATTGAAGAAAGACCACCCTGGAT
47870 CGTTGAAGTA
Statistics
Matches: 71, Mismatches: 21, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
23 2 0.03
24 26 0.37
25 16 0.23
26 25 0.35
27 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (24 bp):
AATTGAAGAAAGACCACCCTGGAT
Found at i:47887 original size:10 final size:10
Alignment explanation
Indices: 47872--47897 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
47862 CCCTGGATCG
47872 TTGAAGTAAA
1 TTGAAGTAAA
47882 TTGAAGTAAA
1 TTGAAGTAAA
47892 TTGAAG
1 TTGAAG
47898 CATTGACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (10 bp):
TTGAAGTAAA
Found at i:47916 original size:22 final size:20
Alignment explanation
Indices: 47889--48075 Score: 125
Period size: 22 Copynumber: 9.1 Consensus size: 20
47879 AAATTGAAGT
47889 AAATTGAAGCATTGACATATTG
1 AAATTGAAGCATTGA-A-ATTG
*
47911 AAATTGAAACATTG-AA--G
1 AAATTGAAGCATTGAAATTG
*
47928 -AATTGAA--TTTGAAGAATTG
1 AAATTGAAGCATTG-A-AATTG
47947 AAATTGAAGCATTGAAATTG
1 AAATTGAAGCATTGAAATTG
*
47967 AAATTGAAGCATTGAAGAACTG
1 AAATTGAAGCATTG-A-AATTG
** *
47989 AAATTGAAGCACAGAAGAATCG
1 AAATTGAAGCATTG-A-AATTG
*
48011 AAATTGAAGCATTGACATTTGG
1 AAATTGAAGCATTGA-AATT-G
* *
48033 AATTTGAAGAATTGAAATTG
1 AAATTGAAGCATTGAAATTG
* *
48053 AAGCATTGAAGGATTGAATTTG
1 AA--ATTGAAGCATTGAAATTG
48075 A
1 A
48076 GGAATTGAAA
Statistics
Matches: 133, Mismatches: 19, Indels: 26
0.75 0.11 0.15
Matches are distributed among these distances:
14 3 0.02
16 7 0.05
17 3 0.02
19 2 0.02
20 30 0.23
21 8 0.06
22 80 0.60
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.28
Consensus pattern (20 bp):
AAATTGAAGCATTGAAATTG
Found at i:47918 original size:6 final size:6
Alignment explanation
Indices: 47907--47974 Score: 55
Period size: 6 Copynumber: 10.0 Consensus size: 6
47897 GCATTGACAT
*
47907 ATTGAA ATTGAAA CATTGAAGA ATTGAA TTTGAAGA ATTGAA ATTGAA
1 ATTGAA ATTG-AA -ATTG-A-A ATTGAA ATTG-A-A ATTGAA ATTGAA
47955 GCATTGAA ATTGAA ATTGAA
1 --ATTGAA ATTGAA ATTGAA
47975 GCATTGAAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
6 27 0.51
7 5 0.09
8 20 0.38
9 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (6 bp):
ATTGAA
Found at i:47947 original size:36 final size:36
Alignment explanation
Indices: 47907--48169 Score: 172
Period size: 36 Copynumber: 6.9 Consensus size: 36
47897 GCATTGACAT
*
47907 ATTGAAATTGAAACATTGAAGAATTGAATTTGAAGA
1 ATTGAAATTGAAACATTGAAGAATTGAAATTGAAGA
*
47943 ATTGAAATTGAAGCATTGAAATTGAAATTGAAGCATTGAAGA
1 ATTGAAATTGAAACATTG-AA--G-AATTGAA--ATTGAAGA
* * ** * *
47985 ACTGAAATTGAAGCACAGAAGAATCGAAATTGAAGC
1 ATTGAAATTGAAACATTGAAGAATTGAAATTGAAGA
* * * *
48021 ATTGACATTTGGAA-TTTGAAGAATTGAAATTGAAGC
1 ATTGA-AATTGAAACATTGAAGAATTGAAATTGAAGA
* *
48057 ATTGAAGGATTG-AA-TTTGAGGAATTGAAATTGAAGCATTGAAA
1 ATTGAA--ATTGAAACATTGAAGAATTGAAATTG-A--A--G--A
* * * *
48100 TATTGAAATTGAAACATTAAAGATTTGAATTTTAAGA
1 -ATTGAAATTGAAACATTGAAGAATTGAAATTGAAGA
* *
48137 ATTGCAATTGAAACATGGAAGAATTGAAATTGA
1 ATTGAAATTGAAACATTGAAGAATTGAAATTGA
48170 CCAACTGTCA
Statistics
Matches: 178, Mismatches: 30, Indels: 38
0.72 0.12 0.15
Matches are distributed among these distances:
35 1 0.01
36 97 0.54
37 12 0.07
38 6 0.03
39 4 0.02
40 7 0.04
41 4 0.02
42 26 0.15
43 3 0.02
44 18 0.10
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.29
Consensus pattern (36 bp):
ATTGAAATTGAAACATTGAAGAATTGAAATTGAAGA
Found at i:47997 original size:14 final size:14
Alignment explanation
Indices: 47889--48148 Score: 102
Period size: 14 Copynumber: 18.6 Consensus size: 14
47879 AAATTGAAGT
*
47889 AAATTGAAGCATTG
1 AAATTGAAGAATTG
47903 ACATATTG-A-AATTG
1 A-A-ATTGAAGAATTG
47917 AAACATTGAAGAATTG
1 -AA-ATTGAAGAATTG
*
47933 AATTTGAAGAATTG
1 AAATTGAAGAATTG
*
47947 AAATTGAAGCATTG
1 AAATTGAAGAATTG
47961 AAATTG-A-AATTG
1 AAATTGAAGAATTG
*
47973 AAGCATTGAAGAACTG
1 AA--ATTGAAGAATTG
*
47989 AAATTGAAG----C
1 AAATTGAAGAATTG
* *
47999 ACA--GAAGAATCG
1 AAATTGAAGAATTG
*
48011 AAATTGAAGCATTG
1 AAATTGAAGAATTG
*
48025 ACATTTG--GAATTTG
1 A-AATTGAAGAA-TTG
48039 AAGAATTG-A-AATTG
1 -A-AATTGAAGAATTG
*
48053 AAGCATTGAAGGATTG
1 AA--ATTGAAGAATTG
* *
48069 AATTTGAGGAATTG
1 AAATTGAAGAATTG
*
48083 AAATTGAAGCATTG
1 AAATTGAAGAATTG
48097 AAATATTG-A-AATTG
1 -AA-ATTGAAGAATTG
* *
48111 AAACATTAAAGATTTG
1 -AA-ATTGAAGAATTG
* *
48127 AATTTTAAGAATTG
1 AAATTGAAGAATTG
*
48141 CAATTGAA
1 AAATTGAA
48149 ACATGGAAGA
Statistics
Matches: 185, Mismatches: 34, Indels: 54
0.68 0.12 0.20
Matches are distributed among these distances:
8 4 0.02
10 2 0.01
12 9 0.05
13 4 0.02
14 112 0.61
15 25 0.14
16 29 0.16
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (14 bp):
AAATTGAAGAATTG
Found at i:48083 original size:58 final size:59
Alignment explanation
Indices: 47907--48169 Score: 210
Period size: 58 Copynumber: 4.6 Consensus size: 59
47897 GCATTGACAT
* * * *
47907 ATTGA-AATTGAAACATTGAAGAATTGAATTTGAAGAATTGAA--ATTGAAGCATTG-A-A
1 ATTGACAATTGGAACATTGAAGAATTGAAATTGAAGCATTGAAGGATTGAA--TTTGAAGA
* ** * * * *
47963 ATTGA-AATT-GAAGCATTGAAGAACTGAAATTGAAGCACAGAAGAATCGAAATTGAAGC
1 ATTGACAATTGGAA-CATTGAAGAATTGAAATTGAAGCATTGAAGGATTGAATTTGAAGA
* * *
48021 ATTGACATTTGGAA-TTTGAAGAATTGAAATTGAAGCATTGAAGGATTGAATTTGAGGA
1 ATTGACAATTGGAACATTGAAGAATTGAAATTGAAGCATTGAAGGATTGAATTTGAAGA
* * *
48079 ATTGA-AATT-GAAGCATTGAA-ATATTGAAATTGAAACATT-AAAGATTTGAATTTTAAGA
1 ATTGACAATTGGAA-CATTGAAGA-ATTGAAATTGAAGCATTGAAGGA-TTGAATTTGAAGA
* *
48137 ATTG-CAATTGAAACATGGAAGAATTGAAATTGA
1 ATTGACAATTGGAACATTGAAGAATTGAAATTGA
48170 CCAACTGTCA
Statistics
Matches: 167, Mismatches: 26, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
55 2 0.01
56 40 0.24
57 9 0.05
58 107 0.64
59 6 0.04
60 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.29
Consensus pattern (59 bp):
ATTGACAATTGGAACATTGAAGAATTGAAATTGAAGCATTGAAGGATTGAATTTGAAGA
Found at i:48097 original size:22 final size:21
Alignment explanation
Indices: 48072--48117 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
48062 AGGATTGAAT
48072 TTGAGGAATTGAAATTGAAGCA
1 TTGA-GAATTGAAATTGAAGCA
* *
48094 TTGAAATATTGAAATTGAAACA
1 TTGAGA-ATTGAAATTGAAGCA
48116 TT
1 TT
48118 AAAGATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (21 bp):
TTGAGAATTGAAATTGAAGCA
Found at i:48127 original size:22 final size:22
Alignment explanation
Indices: 48079--48128 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
48069 AATTTGAGGA
* *
48079 ATTGAAATTGAAGCATTGAAAT
1 ATTGAAATTGAAACATTAAAAT
48101 ATTGAAATTGAAACATTAAAGAT
1 ATTGAAATTGAAACATTAAA-AT
48124 -TTGAA
1 ATTGAA
48129 TTTTAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (22 bp):
ATTGAAATTGAAACATTAAAAT
Found at i:48519 original size:69 final size:70
Alignment explanation
Indices: 48405--49123 Score: 927
Period size: 70 Copynumber: 10.3 Consensus size: 70
48395 AACCCATGTG
* * *
48405 GCTTGGATGGAACCAATGCTTGAATTGACTCGTATGGAAACGAGTTTGGCATGTGGAAAAGCCCC
1 GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCC
*
48470 TAAAT
66 TGAAT
* *
48475 GCTTAGATGGAACCAAAGCTTAAACT-AC-CATGTAT-GAAACGAGTTTGGCTTGTGGAAAAGCC
1 GCTTGGATGGAACCAAAGCTTGAACTGACTC--GTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
*
48537 CTTGAAT
64 CCTGAAT
* * * *
48544 GCTTGGATGGAACTAGAGCTTGATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCA
1 GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCC
**
48609 TGTCT
66 TGAAT
* * * **
48614 -CTTGGATGGAACCAATGCTGGAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCC
48678 TG--T
66 TGAAT
* *
48681 CGCTTGGATGGAACCAATGCTTGAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
1 -GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
*
48746 CTAAAT
65 CTGAAT
* *
48752 GCTTTGATGGAACCAAAGCTTAAACT-ACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
1 GCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
*
48816 TTGAAT
65 CTGAAT
* * *
48822 GCTTGGATAGAACTAAAGC-TGATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCC
1 GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCC
*
48886 TAAAT
66 TGAAT
* * * *
48891 GTTTTGATGGAACCAAAGCTT-AAATTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
1 GCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
48955 CTGAAT
65 CTGAAT
* * * * *
48961 GCTTGGATGGAACTAAAGCTTGATCTGACTCATATGGAAATGAGTTTGGCTTGTGGAAAAGCCCT
1 GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCC
49026 TGAAT
66 TGAAT
* * * * *
49031 GCTTGGAT-GAAACAAACGCTTTAACTGAGTCGTATAGAATCGAGTTTGGCTTGTGGAAAAGCCC
1 GCTTGGATGGAACCAAA-GCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
49095 CTGAAT
65 CTGAAT
*
49101 GATTGGATGGAACCAAAGCTTGA
1 GCTTGGATGGAACCAAAGCTTGA
49124 GCTGGAACGA
Statistics
Matches: 564, Mismatches: 69, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
67 1 0.00
68 1 0.00
69 248 0.44
70 302 0.54
71 12 0.02
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (70 bp):
GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCC
TGAAT
Found at i:48653 original size:139 final size:139
Alignment explanation
Indices: 48405--49123 Score: 945
Period size: 139 Copynumber: 5.2 Consensus size: 139
48395 AACCCATGTG
* *
48405 GCTTGGATGGAACCAATGCTTGAAT-TGACTCGTATGGAAACGAGTTTGGCATGTGGAAAAGCCC
1 GCTTGGATGGAACCAAAGCTTG-ATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
* * *
48469 CTAAATGCTTAGATGGAACCAAAGCTTAAACTAC-CATGTAT-GAAACGAGTTTGGCTTGTGGAA
65 ATGAATGCTTGGATGGAACCAAAGCTTAAACTACTC--GTATGGAAACGAGTTTGGCTTGTGGAA
48532 AAGCCCTTGAAT
128 AAGCCCTTGAAT
* *
48544 GCTTGGATGGAACTAGAGCTTGATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCA
1 GCTTGGATGGAACCAAAGCTTGATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCA
** * ** *
48609 TGTCT-CTTGGATGGAACCAATGCTGGAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
66 TGAATGCTTGGATGGAACCAAAGCTTAAACT-ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
48673 G-CCTATG--T
130 GCCCT-TGAAT
*
48681 CGCTTGGATGGAACCAATGCTTGAAT-TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 -GCTTGGATGGAACCAAAGCTTG-ATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
* * *
48745 CCTAAATGCTTTGATGGAACCAAAGCTTAAACTACCTCGTATGGAAACGAGTTTGGCTTGTGGAA
64 CATGAATGCTTGGATGGAACCAAAGCTTAAACTA-CTCGTATGGAAACGAGTTTGGCTTGTGGAA
48810 AAGCCCTTGAAT
128 AAGCCCTTGAAT
* * *
48822 GCTTGGATAGAACTAAAGC-TGATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCC
1 GCTTGGATGGAACCAAAGCTTGATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCA
* * * *
48886 TAAATGTTTTGATGGAACCAAAGCTTAAATTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
66 TGAATGCTTGGATGGAACCAAAGCTTAAACTA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
*
48951 GCCCCTGAAT
130 GCCCTTGAAT
* * * *
48961 GCTTGGATGGAACTAAAGCTTGATCTGACTCATATGGAAATGAGTTTGGCTTGTGGAAAAGCCCT
1 GCTTGGATGGAACCAAAGCTTGATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCA
* * * * *
49026 TGAATGCTTGGAT-GAAACAAACGCTTTAACTGAGTCGTATAGAATCGAGTTTGGCTTGTGGAAA
66 TGAATGCTTGGATGGAACCAAA-GCTTAAACT-ACTCGTATGGAAACGAGTTTGGCTTGTGGAAA
*
49090 AGCCCCTGAAT
129 AGCCCTTGAAT
*
49101 GATTGGATGGAACCAAAGCTTGA
1 GCTTGGATGGAACCAAAGCTTGA
49124 GCTGGAACGA
Statistics
Matches: 518, Mismatches: 46, Indels: 31
0.87 0.08 0.05
Matches are distributed among these distances:
137 1 0.00
138 92 0.18
139 284 0.55
140 139 0.27
141 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (139 bp):
GCTTGGATGGAACCAAAGCTTGATCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCA
TGAATGCTTGGATGGAACCAAAGCTTAAACTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
CCCTTGAAT
Found at i:49709 original size:50 final size:50
Alignment explanation
Indices: 49655--49756 Score: 179
Period size: 50 Copynumber: 2.0 Consensus size: 50
49645 CTAAAATGCC
*
49655 TTTTGAAAAGT-GAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 TTTTGAAAA-TCGAATTTTGATATTGGACTCACAAATGGAATGCAATCTTA
49705 TTTTGAAAATCGAATTTTGATATTGGACTCACAAATGGAATGCAATCTTA
1 TTTTGAAAATCGAATTTTGATATTGGACTCACAAATGGAATGCAATCTTA
49755 TT
1 TT
49757 ATAGAACTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 1 0.02
50 49 0.98
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (50 bp):
TTTTGAAAATCGAATTTTGATATTGGACTCACAAATGGAATGCAATCTTA
Found at i:49870 original size:14 final size:14
Alignment explanation
Indices: 49851--49877 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49841 CGGGAAAATC
49851 TTCTGTTACAAAAA
1 TTCTGTTACAAAAA
49865 TTCTGTTACAAAA
1 TTCTGTTACAAAA
49878 CTTGGCCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
TTCTGTTACAAAAA
Found at i:52018 original size:2 final size:2
Alignment explanation
Indices: 52011--52036 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52001 GATGATCTGT
52011 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
52037 CATTTAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54534 original size:19 final size:18
Alignment explanation
Indices: 54510--54545 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
54500 TGAAGATTTC
54510 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
54529 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
54546 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:55847 original size:15 final size:16
Alignment explanation
Indices: 55827--55860 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
55817 GATTGCTCTC
*
55827 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
55842 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
55858 TTA
1 TTA
55861 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:59946 original size:52 final size:52
Alignment explanation
Indices: 59898--60010 Score: 181
Period size: 52 Copynumber: 2.2 Consensus size: 52
59888 GCTTGAATGT
** *
59898 TTTGAAAACTTGATGGGAACTTTCCCACTTTAAAAAGACCTAAATTGAACAC
1 TTTGAAAACCAGATGGGAACTTTCCCACTTCAAAAAGACCTAAATTGAACAC
*
59950 TTTGAAAACCAGATGGGAACTTTCCCACTTCGAAAAGACCTAAATTGAACAC
1 TTTGAAAACCAGATGGGAACTTTCCCACTTCAAAAAGACCTAAATTGAACAC
*
60002 CTTGAAAAC
1 TTTGAAAAC
60011 TTTGAATGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (52 bp):
TTTGAAAACCAGATGGGAACTTTCCCACTTCAAAAAGACCTAAATTGAACAC
Done.