Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020375.1 Corchorus olitorius cultivar O-4 contig20408, 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: 159064
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1962 original size:29 final size:31
Alignment explanation
Indices: 1930--1994 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
1920 TATGGGATTT
1930 ATTTGT-CCAAAA-AAAAAGTTAAGGGGCCA
1 ATTTGTCCCAAAATAAAAAGTTAAGGGGCCA
** * *
1959 ATTTGTCCCAAAATGGATAGTTAAGGGGCTA
1 ATTTGTCCCAAAATAAAAAGTTAAGGGGCCA
1990 ATTTG
1 ATTTG
1995 GGTATTAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 6 0.20
30 6 0.20
31 18 0.60
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (31 bp):
ATTTGTCCCAAAATAAAAAGTTAAGGGGCCA
Found at i:6485 original size:31 final size:31
Alignment explanation
Indices: 6430--6495 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
6420 ATGATTATAC
*
6430 ATATTATTATATATATAATTT-TATATCTTTA
1 ATATTATTATATATATAATTTATATAT-ATTA
6461 ATATTATTATATATATTTAA-TTATATATATTA
1 ATATTATTATATATA--TAATTTATATATATTA
6493 ATA
1 ATA
6496 AACGGTCGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 15 0.48
32 8 0.26
33 8 0.26
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (31 bp):
ATATTATTATATATATAATTTATATATATTA
Found at i:8989 original size:13 final size:13
Alignment explanation
Indices: 8971--8995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8961 TTGGAATTTC
8971 AAATAATATTTAT
1 AAATAATATTTAT
8984 AAATAATATTTA
1 AAATAATATTTA
8996 CAATTTACAA
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:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:12581 original size:14 final size:14
Alignment explanation
Indices: 12562--12609 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
12552 ATGAAAAATG
*
12562 ATAAAATGGTAAAA
1 ATAAAATGATAAAA
* *
12576 ATAAAAT-TTTAAA
1 ATAAAATGATAAAA
*
12589 TTAAAATGATAAAA
1 ATAAAATGATAAAA
12603 ATAAAAT
1 ATAAAAT
12610 AATTATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
ATAAAATGATAAAA
Found at i:26508 original size:18 final size:18
Alignment explanation
Indices: 26487--26526 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
26477 ACATTTATCT
26487 TATTACTATTACTTATA-A
1 TATTACTATTA-TTATATA
*
26505 TATTATTATTATTATATA
1 TATTACTATTATTATATA
26523 TATT
1 TATT
26527 GTTGTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTACTATTATTATATA
Found at i:29917 original size:110 final size:110
Alignment explanation
Indices: 29723--29935 Score: 336
Period size: 110 Copynumber: 1.9 Consensus size: 110
29713 TCTGACTAAT
** * * * * *
29723 CCAGATTCAACTTGGGTCGCGCATCTGGATTTGGTGGGTGAGTTTACCAATGGGGACGGCTGCGT
1 CCAGATTCAACCCGGGTCGCGCACCTGAATTTGGTGGGTGAATCTACCAATAGGGACGGCTGCGT
*
29788 ACATAAGATCTCGAGCCTGAAACCTGTTTAAGTTGGAAGAAGCCG
66 ACATAAGATCTCGAACCTGAAACCTGTTTAAGTTGGAAGAAGCCG
*
29833 CCAGATTCAACCCGGGTTGCGCACCTGAATTTGGTGGGTGAATCTACCAATAGGGACGGCTGCGT
1 CCAGATTCAACCCGGGTCGCGCACCTGAATTTGGTGGGTGAATCTACCAATAGGGACGGCTGCGT
*
29898 ACGTAAGATCTCGAACCTGAAACCTGTTTAAGTTGGAA
66 ACATAAGATCTCGAACCTGAAACCTGTTTAAGTTGGAA
29936 TAAACCGCTT
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 93 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (110 bp):
CCAGATTCAACCCGGGTCGCGCACCTGAATTTGGTGGGTGAATCTACCAATAGGGACGGCTGCGT
ACATAAGATCTCGAACCTGAAACCTGTTTAAGTTGGAAGAAGCCG
Found at i:44958 original size:20 final size:22
Alignment explanation
Indices: 44919--44970 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
44909 GCAAAAATCC
44919 AAGCTCCGTGCTTATTTTCTCA
1 AAGCTCCGTGCTTATTTTCTCA
*
44941 AAGCTCCGTGCTT-TTTCTCTGA
1 AAGCTCCGTGCTTATTT-TCTCA
*
44963 AATCTCCG
1 AAGCTCCG
44971 CGATTTCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.17, C:0.29, G:0.15, T:0.38
Consensus pattern (22 bp):
AAGCTCCGTGCTTATTTTCTCA
Found at i:70105 original size:11 final size:11
Alignment explanation
Indices: 70089--70118 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
70079 TTCCCACGGC
70089 AAGAAGGCTAG
1 AAGAAGGCTAG
70100 AAGAAGGCTAG
1 AAGAAGGCTAG
70111 AAGAAGGC
1 AAGAAGGC
70119 ACTGACTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.37, T:0.07
Consensus pattern (11 bp):
AAGAAGGCTAG
Found at i:70137 original size:12 final size:12
Alignment explanation
Indices: 70120--70144 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
70110 GAAGAAGGCA
70120 CTGACTTAGTTG
1 CTGACTTAGTTG
70132 CTGACTTAGTTG
1 CTGACTTAGTTG
70144 C
1 C
70145 CTATATAAAG
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:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (12 bp):
CTGACTTAGTTG
Found at i:70988 original size:17 final size:17
Alignment explanation
Indices: 70968--71004 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
70958 GATCACCGGC
70968 GATTTTTGATTATTGAT
1 GATTTTTGATTATTGAT
* *
70985 GATTTTTTATTATTGGT
1 GATTTTTGATTATTGAT
71002 GAT
1 GAT
71005 CTTGGGGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (17 bp):
GATTTTTGATTATTGAT
Found at i:72602 original size:4 final size:4
Alignment explanation
Indices: 72593--72619 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
72583 CTCACACGCA
72593 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
72620 AGAAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:72625 original size:4 final size:4
Alignment explanation
Indices: 72618--72642 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
72608 TAAATAAATA
72618 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
72643 TCTTTACCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:75431 original size:19 final size:18
Alignment explanation
Indices: 75394--75430 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
75384 ATAAAAGTTA
75394 TACATGTTTGAGTTTTTT
1 TACATGTTTGAGTTTTTT
75412 TACATGTTTGAGTTTTTT
1 TACATGTTTGAGTTTTTT
75430 T
1 T
75431 TTCATCGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.16, T:0.62
Consensus pattern (18 bp):
TACATGTTTGAGTTTTTT
Found at i:79020 original size:25 final size:25
Alignment explanation
Indices: 78977--79027 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
78967 ATATAAATTT
78977 TTATATATAATTATGATTTCTTAAAAA
1 TTATATATAATTATGA-TT-TTAAAAA
*
79004 TTATATGT-ATTAT-ATTTTAAAAA
1 TTATATATAATTATGATTTTAAAAA
79027 T
1 T
79028 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 5 0.22
27 7 0.30
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
TTATATATAATTATGATTTTAAAAA
Found at i:80772 original size:13 final size:12
Alignment explanation
Indices: 80750--80784 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
80740 AAGACATTGA
80750 AATAGTATTAAT
1 AATAGTATTAAT
80762 AATAGTAATTAAT
1 AATAGT-ATTAAT
*
80775 AATAATATTA
1 AATAGTATTA
80785 TTACTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (12 bp):
AATAGTATTAAT
Found at i:85075 original size:21 final size:21
Alignment explanation
Indices: 85051--85117 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
85041 AATTCTCTGT
85051 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
85072 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
85093 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
85114 AAAT
1 AAAT
85118 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:85097 original size:42 final size:42
Alignment explanation
Indices: 85038--85118 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
85028 TCTAAGTCTT
85038 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
85080 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
85119 CTGATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:85259 original size:56 final size:56
Alignment explanation
Indices: 85184--85297 Score: 174
Period size: 56 Copynumber: 2.0 Consensus size: 56
85174 TTTATTTTGT
*
85184 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGGGAA
* * * * *
85240 AGAATAATTAAGTATAGATATGGGGATATGATTTATTTTAATATTTATTGTGGGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGGGAA
85296 AG
1 AG
85298 GAAATGAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.37
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGGGAA
Found at i:85490 original size:2 final size:2
Alignment explanation
Indices: 85483--85509 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
85473 TAATATGTAG
85483 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
85510 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:96055 original size:33 final size:33
Alignment explanation
Indices: 96013--96093 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
96003 CTGTTGCTGT
*
96013 CCGTGAACTTCATTGTAAAGGCGTGATGAAGGC
1 CCGTGAACTTCATTGTAAAGGCGTGAAGAAGGC
* **
96046 CCGTGAACTTCATTGGAACTGCGTGAAGAAGGC
1 CCGTGAACTTCATTGTAAAGGCGTGAAGAAGGC
96079 CCGT-AACTTCATTGT
1 CCGTGAACTTCATTGT
96094 TTGTAAGAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 10 0.23
33 33 0.77
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (33 bp):
CCGTGAACTTCATTGTAAAGGCGTGAAGAAGGC
Found at i:106806 original size:27 final size:27
Alignment explanation
Indices: 106776--106827 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
106766 TTATGTCCTT
*
106776 AAATGACAGATAAAAATGGACAAAGAA
1 AAATGACAGATAAAAAGGGACAAAGAA
106803 AAATGACAGATAAAAAGGGACAAAG
1 AAATGACAGATAAAAAGGGACAAAG
106828 GGAGTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.62, C:0.08, G:0.21, T:0.10
Consensus pattern (27 bp):
AAATGACAGATAAAAAGGGACAAAGAA
Found at i:106817 original size:13 final size:13
Alignment explanation
Indices: 106776--106818 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
106766 TTATGTCCTT
106776 AAATGACAGATAA
1 AAATGACAGATAA
* *
106789 AAATGGACAAAGAA
1 AAAT-GACAGATAA
106803 AAATGACAGATAA
1 AAATGACAGATAA
106816 AAA
1 AAA
106819 GGGACAAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.65, C:0.07, G:0.16, T:0.12
Consensus pattern (13 bp):
AAATGACAGATAA
Found at i:109566 original size:43 final size:44
Alignment explanation
Indices: 109474--109597 Score: 119
Period size: 43 Copynumber: 2.8 Consensus size: 44
109464 TAACCACACC
* ** *
109474 ATGAAATTATGATAACCTCGTTATTAAATTCTGATAAGCTCCCT
1 ATGAAATTATGATAACCACACTATTAAATTCTGATAACCTCCCT
* *
109518 ATGAAATTTTGATAACCACACTA-TATAATT-TGATAACCTCCTT
1 ATGAAATTATGATAACCACACTATTA-AATTCTGATAACCTCCCT
** * *
109561 ATGAAATTAAAATAACCAC-CTTATGAAATTTTGATAA
1 ATGAAATTATGATAACCACAC-TATTAAATTCTGATAA
109598 TCACCCAATG
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
42 1 0.02
43 35 0.53
44 30 0.45
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (44 bp):
ATGAAATTATGATAACCACACTATTAAATTCTGATAACCTCCCT
Found at i:109586 original size:65 final size:66
Alignment explanation
Indices: 109451--109597 Score: 172
Period size: 65 Copynumber: 2.2 Consensus size: 66
109441 ATGAAATTCG
* * * * *** * *
109451 TATGTAATTTCGATAACCACACCATGAAATTATGATAACCTCGTTATTAAATTCTGATAAGCTCC
1 TATGAAATTTTGATAACCACACCATGAAATTATGATAACCTCCTTATGAAATTAAAATAACCACC
109516 C
66 C
*
109517 TATGAAATTTTGATAACCACACTAT-ATAATT-TGATAACCTCCTTATGAAATTAAAATAACCAC
1 TATGAAATTTTGATAACCACACCATGA-AATTATGATAACCTCCTTATGAAATTAAAATAACCAC
*
109580 CT
65 CC
109582 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
109598 TCACCCAATG
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
65 43 0.62
66 26 0.38
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (66 bp):
TATGAAATTTTGATAACCACACCATGAAATTATGATAACCTCCTTATGAAATTAAAATAACCACC
C
Found at i:109597 original size:22 final size:22
Alignment explanation
Indices: 109451--109621 Score: 107
Period size: 22 Copynumber: 7.8 Consensus size: 22
109441 ATGAAATTCG
* *
109451 TATGTAATTTCGATAACCACAC-
1 TATGAAATTTTGATAACCAC-CT
* * * *
109473 CATGAAATTATGATAACCTCGT
1 TATGAAATTTTGATAACCACCT
* * * * *
109495 TATTAAATTCTGATAAGCTCCC
1 TATGAAATTTTGATAACCACCT
109517 TATGAAATTTTGATAACCACAC-
1 TATGAAATTTTGATAACCAC-CT
*
109539 TAT-ATAA-TTTGATAACCTCCT
1 TATGA-AATTTTGATAACCACCT
***
109560 TATGAAATTAAAATAACCACCT
1 TATGAAATTTTGATAACCACCT
* *
109582 TATGAAATTTTGATAATCACCC
1 TATGAAATTTTGATAACCACCT
* * *
109604 AATGGAATTTTGACAACC
1 TATGAAATTTTGATAACC
109622 TTCACTATAA
Statistics
Matches: 113, Mismatches: 30, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.01
21 17 0.15
22 94 0.83
23 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCT
Found at i:109613 original size:87 final size:88
Alignment explanation
Indices: 109474--109636 Score: 202
Period size: 87 Copynumber: 1.9 Consensus size: 88
109464 TAACCACACC
** * * * * * *
109474 ATGAAATTATGATAACCTCGTTATTAAATTCTGATAAGCTCCCTATGAAATTTTGATAACC-ACA
1 ATGAAATTAAAATAACCACCTTATGAAATTCTGATAAGCACCCAATGAAATTTTGACAACCTACA
*
109538 CTATATAATTTGATAACCTCCTT
66 CTATAAAATTTGATAACCTCCTT
* * * *
109561 ATGAAATTAAAATAACCACCTTATGAAATTTTGATAATCACCCAATGGAATTTTGACAACCTTCA
1 ATGAAATTAAAATAACCACCTTATGAAATTCTGATAAGCACCCAATGAAATTTTGACAACCTACA
109626 CTATAAAATTT
66 CTATAAAATTT
109637 TGTTAACTTC
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
87 50 0.81
88 12 0.19
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (88 bp):
ATGAAATTAAAATAACCACCTTATGAAATTCTGATAAGCACCCAATGAAATTTTGACAACCTACA
CTATAAAATTTGATAACCTCCTT
Found at i:109678 original size:22 final size:22
Alignment explanation
Indices: 109627--109679 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
109617 CAACCTTCAC
* *
109627 TATAAAATTTTGTTAACTTCTG
1 TATAAAATTGTGATAACTTCTG
* *
109649 TATGAAATTGTGATAATTTCCT-
1 TATAAAATTGTGATAACTT-CTG
109671 TATAAAATT
1 TATAAAATT
109680 TAAACAATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (22 bp):
TATAAAATTGTGATAACTTCTG
Found at i:109790 original size:17 final size:17
Alignment explanation
Indices: 109768--109801 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
109758 CTATGAGCTA
109768 TGACTGTAATGGTATTC
1 TGACTGTAATGGTATTC
109785 TGACTGTAATGGTATTC
1 TGACTGTAATGGTATTC
109802 AGAAATGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (17 bp):
TGACTGTAATGGTATTC
Found at i:113229 original size:12 final size:12
Alignment explanation
Indices: 113212--113236 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
113202 CAAAAATATC
113212 AGTTATGTTTTT
1 AGTTATGTTTTT
113224 AGTTATGTTTTT
1 AGTTATGTTTTT
113236 A
1 A
113237 ATTCTAGTTA
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:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (12 bp):
AGTTATGTTTTT
Found at i:115449 original size:22 final size:23
Alignment explanation
Indices: 115403--115450 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
115393 TTATTCATCA
**
115403 TTTTTTAAACTAATTAAGTTAAT
1 TTTTTTAAAAAAATTAAGTTAAT
*
115426 TTTTTTAAAAAAATTTAGTT-AT
1 TTTTTTAAAAAAATTAAGTTAAT
115448 TTT
1 TTT
115451 GATTGACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTTTAAAAAAATTAAGTTAAT
Found at i:116564 original size:11 final size:11
Alignment explanation
Indices: 116540--116595 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
116530 TTGACATTGT
116540 AACAAAAACAA
1 AACAAAAACAA
* *
116551 AACTAAAACGA
1 AACAAAAACAA
116562 AACAAAAACAA
1 AACAAAAACAA
*
116573 AA-AAACAGAAAA
1 AACAAA-A-ACAA
116585 AACAAAAACAA
1 AACAAAAACAA
116596 CACCAAACGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.08
11 24 0.67
12 6 0.17
13 3 0.08
ACGTcount: A:0.79, C:0.16, G:0.04, T:0.02
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:120647 original size:24 final size:21
Alignment explanation
Indices: 120594--120646 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
120584 GAGGAGTTGA
120594 CGTCGCCGCCGGAAGTGGAGG
1 CGTCGCCGCCGGAAGTGGAGG
*
120615 CGTCGCCGCCGGCAGTGGAGG
1 CGTCGCCGCCGGAAGTGGAGG
*
120636 CGTTGCCGCCG
1 CGTCGCCGCCG
120647 CAGCCGCGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.09, C:0.34, G:0.45, T:0.11
Consensus pattern (21 bp):
CGTCGCCGCCGGAAGTGGAGG
Found at i:120847 original size:14 final size:14
Alignment explanation
Indices: 120824--120858 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
120814 CTCAAGTTTT
* *
120824 TTTTTTTTTTTCTC
1 TTTTTCTTTTTCTA
120838 TTTTTCTTTTTCTA
1 TTTTTCTTTTTCTA
120852 TTTTTCT
1 TTTTTCT
120859 CCTAGACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTTTTTCTA
Found at i:137931 original size:20 final size:19
Alignment explanation
Indices: 137906--137945 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
137896 TTCAAAATAG
*
137906 ATTAAAAGGAATTTATTAAA
1 ATTAAAAGGAAATT-TTAAA
*
137926 ATTAAAATGAAATTTTAAA
1 ATTAAAAGGAAATTTTAAA
137945 A
1 A
137946 ATATAGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (19 bp):
ATTAAAAGGAAATTTTAAA
Done.