Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009562.1 Corchorus capsularis cultivar CVL-1 contig09583, 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: 121833
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:12043 original size:26 final size:27
Alignment explanation
Indices: 11953--12043 Score: 96
Period size: 26 Copynumber: 3.3 Consensus size: 27
11943 TTTCTTTCTG
* *
11953 TTTTTACTGAATACCACTTTTTACTC-
1 TTTTTACTTAATACCATTTTTTACTCT
*
11979 TTTTTACTTAATTACCATTTTTTTGCTCTCCT
1 TTTTTACTTAA-TACCA-TTTTTT--ACT-CT
12011 TTTTTACTTAATACCA-TTTTTACTCT
1 TTTTTACTTAATACCATTTTTTACTCT
12037 TTTTTAC
1 TTTTTAC
12044 AATTTTTATC
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
26 19 0.35
27 7 0.13
28 5 0.09
29 5 0.09
30 2 0.04
31 6 0.11
32 11 0.20
ACGTcount: A:0.20, C:0.21, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTTACTTAATACCATTTTTTACTCT
Found at i:13060 original size:26 final size:25
Alignment explanation
Indices: 13031--13087 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
13021 ATTTCTACAT
*
13031 AAATTTAGTAAC-CTCACATTCTTAGA
1 AAATTTAGAAACACT-ACATTCTTA-A
13057 AAATTTAGAAACACTACATTCTTAA
1 AAATTTAGAAACACTACATTCTTAA
13082 AAATTT
1 AAATTT
13088 CAGGTTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 7 0.24
26 20 0.69
27 2 0.07
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (25 bp):
AAATTTAGAAACACTACATTCTTAA
Found at i:15316 original size:45 final size:45
Alignment explanation
Indices: 15260--15349 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
15250 ATTTACTTCT
*
15260 CCAGCTCATCATTAATCCGAGGTAGGGATCTTTTAATAATTCCAC
1 CCAGCTCATCATTAATCCGAGGTAGAGATCTTTTAATAATTCCAC
* * * *
15305 CCAGCTTATCATTAATTCGGGGTAGAGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGAGGTAGAGATCTTTTAATAATTCCAC
15350 TACTTTATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGAGGTAGAGATCTTTTAATAATTCCAC
Found at i:16006 original size:73 final size:70
Alignment explanation
Indices: 15913--16112 Score: 233
Period size: 73 Copynumber: 2.8 Consensus size: 70
15903 TCGACTCTTA
* * * * *
15913 ATTACTGATCACCTTAACTCTTAATTATCGATTTACTGATTGCTA-TTTTTACCTTGACTCTTTT
1 ATTACT-ATTACCTTGACTCTTAATTATCAATTTACTGATTACTACTTTTTA-CTTGACTC-TTG
15977 AATTACTG
63 AATTACTG
* *
15985 ATTAATCTCTTACCTTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTACTTGATTCTTG
1 ATT-A-CTATTACCTTGACTCTTAATTATCAATTTACTGATTACTA-CTTTTTACTTGACTCTTG
*
16050 ATTTACTG
63 AATTACTG
*
16058 ATTACTATTACCTTGACTCTTAATCATCAATTTACTGATTAATCT-CTTTTTACTT
1 ATTACTATTACCTTGACTCTTAATTATCAATTTACTGATT-A-CTACTTTTTACTT
16113 AATTACTGAT
Statistics
Matches: 112, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
71 44 0.39
72 5 0.04
73 48 0.43
74 9 0.08
75 6 0.05
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.49
Consensus pattern (70 bp):
ATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTACTACTTTTTACTTGACTCTTGAAT
TACTG
Found at i:16038 original size:18 final size:17
Alignment explanation
Indices: 16016--16065 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
16006 TTAATTATCA
*
16016 ATTTACTGATTACTATCT
1 ATTTACTGATTACTAT-G
*
16034 TTTTACTTGATT-CT-TG
1 ATTTAC-TGATTACTATG
16050 ATTTACTGATTACTAT
1 ATTTACTGATTACTAT
16066 TACCTTGACT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
15 5 0.19
16 7 0.27
17 2 0.08
18 7 0.27
19 5 0.19
ACGTcount: A:0.24, C:0.14, G:0.08, T:0.54
Consensus pattern (17 bp):
ATTTACTGATTACTATG
Found at i:16087 original size:71 final size:72
Alignment explanation
Indices: 15913--16112 Score: 244
Period size: 71 Copynumber: 2.8 Consensus size: 72
15903 TCGACTCTTA
* * * *
15913 ATTACTGATCACCTTAACTCTTAATTATCGATTTACTGATTGCTA--TTTTTACCTTGACTCTTT
1 ATTACT-ATTACCTTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTA-CTTGACTCTTT
*
15976 TAATTACTG
64 GAATTACTG
* *
15985 ATTAATCTCTTACCTTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTACTTGATTC-TT
1 ATT-A-CTATTACCTTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTACTTGACTCTTT
*
16049 GATTTACTG
64 GAATTACTG
* * *
16058 ATTACTATTACCTTGACTCTTAATCATCAATTTACTGATTAATCTCTTTTTACTT
1 ATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTACTT
16113 AATTACTGAT
Statistics
Matches: 112, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
71 47 0.42
72 4 0.04
73 46 0.41
74 9 0.08
75 6 0.05
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.49
Consensus pattern (72 bp):
ATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTACTTGACTCTTTGA
ATTACTG
Found at i:19993 original size:174 final size:174
Alignment explanation
Indices: 19703--20222 Score: 941
Period size: 174 Copynumber: 3.0 Consensus size: 174
19693 CCTATTGATC
19703 TTTCTCGAGGAAAAGAAATTGCTCCTGAAGAAGCACACAATCCTATTCAAGGAGAGCATATTGTC
1 TTTCTCGAGGAAAAGAAATTGCTCCTGAAGAAGCACACAATCCTATTCAAGGAGAGCATATTGTC
* *
19768 CCAGAAACGGCACAAACCCATGAAAAGATCACCAACCCCGGGAATACTGAAATTTCCATGAACTA
66 CTAGAAGCGGCACAAACCCATGAAAAGATCACCAACCCCGGGAATACTGAAATTTCCATGAACTA
19833 TTATAATGAAATATGGGATCGGAATGAGATAATCATCAATGAAA
131 TTATAATGAAATATGGGATCGGAATGAGATAATCATCAATGAAA
* *
19877 TTTCTCGAGGAAAAGAAATTGCTCTTGAAGAAGCACACGATCCTATTCAAGGAGAGCATATTGTC
1 TTTCTCGAGGAAAAGAAATTGCTCCTGAAGAAGCACACAATCCTATTCAAGGAGAGCATATTGTC
19942 CTAGAAGCGGCACAAACCCATGAAAAGATCACCAACCCCGGGAATACTGAAATTTCCATGAACTA
66 CTAGAAGCGGCACAAACCCATGAAAAGATCACCAACCCCGGGAATACTGAAATTTCCATGAACTA
* *
20007 TTACAATGAAATATGGGATCCGAATGAGATAATCATCAATGAAA
131 TTATAATGAAATATGGGATCGGAATGAGATAATCATCAATGAAA
* *
20051 TTTCTCGAGCAAAAGAAATTGCTCCTGAAGAAGCACACAATCCTATTCAAGGAGAGCATATTGGC
1 TTTCTCGAGGAAAAGAAATTGCTCCTGAAGAAGCACACAATCCTATTCAAGGAGAGCATATTGTC
* **
20116 CTAGAAGCGGCACAAATCCATGAAAAGATCACCAACCTTGGGAATACTGAAATTTCCATGAACTA
66 CTAGAAGCGGCACAAACCCATGAAAAGATCACCAACCCCGGGAATACTGAAATTTCCATGAACTA
20181 TTATAATGAAATATGGGATCGGAATGAGATAATCATCAATGA
131 TTATAATGAAATATGGGATCGGAATGAGATAATCATCAATGA
20223 TGCATTTGCT
Statistics
Matches: 331, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 331 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (174 bp):
TTTCTCGAGGAAAAGAAATTGCTCCTGAAGAAGCACACAATCCTATTCAAGGAGAGCATATTGTC
CTAGAAGCGGCACAAACCCATGAAAAGATCACCAACCCCGGGAATACTGAAATTTCCATGAACTA
TTATAATGAAATATGGGATCGGAATGAGATAATCATCAATGAAA
Found at i:25859 original size:51 final size:51
Alignment explanation
Indices: 25804--25939 Score: 162
Period size: 44 Copynumber: 2.8 Consensus size: 51
25794 CTTGGATCTT
* *
25804 CTTTGATAATAATCCTCTACATACGT-GACTTTTCTTTCAATCATCTTTGGA
1 CTTTGATAATAATCCTCCACATACGTGGA-TCTTCTTTCAATCATCTTTGGA
* *
25855 CTTTGATAATAATCCTCCACATATGTGGATCTTGTTTC-A--ATC-TT---
1 CTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCAATCATCTTTGGA
*
25899 CTTTGATAATCATCCTCCACATACGTGGATCTTCTTTCAAT
1 CTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCAAT
25940 AATCCTCACT
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
44 35 0.47
45 1 0.01
47 2 0.03
48 3 0.04
50 1 0.01
51 31 0.41
52 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (51 bp):
CTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCAATCATCTTTGGA
Found at i:31083 original size:19 final size:21
Alignment explanation
Indices: 31059--31098 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31049 ATCCTTTTAA
*
31059 AATTTT-AA-GAAAAATAAAT
1 AATTTTGAACGAAAAAAAAAT
31078 AATTTTGAACGAAAAAAAAAT
1 AATTTTGAACGAAAAAAAAAT
31099 CAACCCCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (21 bp):
AATTTTGAACGAAAAAAAAAT
Found at i:38830 original size:7 final size:7
Alignment explanation
Indices: 38814--38848 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
38804 CATCATTATT
38814 GCCTAAA
1 GCCTAAA
*
38821 GCCCAAA
1 GCCTAAA
38828 GCCTAAA
1 GCCTAAA
38835 GCCTAAA
1 GCCTAAA
38842 GCCTAAA
1 GCCTAAA
38849 TCCATGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.43, C:0.31, G:0.14, T:0.11
Consensus pattern (7 bp):
GCCTAAA
Found at i:40766 original size:28 final size:28
Alignment explanation
Indices: 40734--40797 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
40724 CAGGACGTCA
*
40734 CCCTCTGGTATATCAGGCGGAAAATCTT
1 CCCTCTGATATATCAGGCGGAAAATCTT
* *
40762 CCCTCTGATATGTTAGGCGGAAAATCTT
1 CCCTCTGATATATCAGGCGGAAAATCTT
40790 CCCTCTGA
1 CCCTCTGA
40798 CTGGTCACAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (28 bp):
CCCTCTGATATATCAGGCGGAAAATCTT
Found at i:41507 original size:155 final size:155
Alignment explanation
Indices: 41112--41507 Score: 526
Period size: 156 Copynumber: 2.5 Consensus size: 155
41102 TTGCTGGGTT
* * ** *
41112 CGAGCCCTCCTTCATGGTGAACTAGGTTTCACATTCCAAACTGTCCTTAAATGAAAAACGTGCAT
1 CGAGCTCTCCTTCATGGTGAACT-GGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACGTGCAT
* ** ** **
41177 AAATTTTTCATCCTAAGTCTGATTGAGATGAAATTTCGTCAAGGGACTTAGATTATCTCCATAAG
65 AAATTTTTCATCTTAAGTCCAATAAAGATGAAATTTCCACAAGGGACTTAGATTATCTCCATAAG
* *
41242 ACTATGGAAAAATTTATAAGTAAAAC
130 ACTATGGAAAAAATTATAAGTAAAAA
* * * * *
41268 CGAACTCTCCTTCATAGTGAAGTTGGTTTCTCACCCCAAATTGTCATTAACTGAAAAACGTGCAT
1 CGAGCTCTCCTTCATGGTGAA-CTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACGTGCAT
* * *
41333 AAGTTTTTCATCTTAAGTCCAATAAAGCT-AAATTTCCACCAGTAGG-CTTAGATTATCTCCATA
65 AAATTTTTCATCTTAAGTCCAATAAAGATGAAATTTCCACAAG--GGACTTAGATTATCTCCATA
41396 AGACTATGGAAAAAATTATAAGTAAAAA
128 AGACTATGGAAAAAATTATAAGTAAAAA
* *
41424 TGAGCTCTCCTTCATGGTGAACTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACATGCATA
1 CGAGCTCTCCTTCATGGTGAACTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACGTGCATA
41489 AATTTTTCATCTTAAGTCC
66 AATTTTTCATCTTAAGTCC
41508 GTTTGAGATG
Statistics
Matches: 207, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
155 68 0.33
156 136 0.66
157 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (155 bp):
CGAGCTCTCCTTCATGGTGAACTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACGTGCATA
AATTTTTCATCTTAAGTCCAATAAAGATGAAATTTCCACAAGGGACTTAGATTATCTCCATAAGA
CTATGGAAAAAATTATAAGTAAAAA
Found at i:42459 original size:26 final size:26
Alignment explanation
Indices: 42413--42465 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
42403 ATTTTAATGC
42413 TTAAATTTTATTTTTTATTAA-AAAA
1 TTAAATTTTATTTTTTATTAAGAAAA
42438 TTAAATTATTATTTTATT-TTAAGAAAA
1 TTAAATT-TTATTTT-TTATTAAGAAAA
42465 T
1 T
42466 ATGGGCGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 7 0.28
26 11 0.44
27 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TTAAATTTTATTTTTTATTAAGAAAA
Found at i:47839 original size:132 final size:132
Alignment explanation
Indices: 47700--47959 Score: 414
Period size: 131 Copynumber: 2.0 Consensus size: 132
47690 TAAGAAATAT
* * *
47700 TTTAAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTCGTAAAATGGTAAAAATAAAATAGG
1 TTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGG
47765 TATAAGGATATTAGATTTAATTAAACAAAAA-TAGAGTTTCTAGCTAAGTAAAACTATAAAAGTA
66 TATAAGGATATTAGATTTAATTAAACAAAAATTAGAGTTTCTAGCTAAGTAAAACTATAAAAGTA
47829 TA
131 TA
* *
47831 TTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGT
1 TTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGG
* * * * * *
47896 TATAAGGATATTAGATTTAATTAAATAAAAATTGGAGTTTTTAGTTGAGTAAAATTATAAAAGT
66 TATAAGGATATTAGATTTAATTAAACAAAAATTAGAGTTTCTAGCTAAGTAAAACTATAAAAGT
47960 TTAAACAATG
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
131 90 0.77
132 27 0.23
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.37
Consensus pattern (132 bp):
TTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGG
TATAAGGATATTAGATTTAATTAAACAAAAATTAGAGTTTCTAGCTAAGTAAAACTATAAAAGTA
TA
Found at i:52573 original size:30 final size:30
Alignment explanation
Indices: 52537--52858 Score: 407
Period size: 30 Copynumber: 10.6 Consensus size: 30
52527 CATGGTGTAT
52537 ATGACAACTTCTGGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
52567 ATGACAACTTCTGGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* *
52597 ATGAAAACTTCTGGTGTCAGTTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
*
52627 ATGACAACTTCCGGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* * *
52657 ATGACAA-TT-T-CTGTCAATTGTAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* * *
52684 ATGATAACTTCTGGTGCCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* *
52714 ATGACAACTTCTGGTGTCAATTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* * *
52744 ATGACAGCTTCTGGTGTCAATTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* * *
52774 ACTGACAACTTCTGATGTCAATTGTAAGACC
1 A-TGACAACTTCTGGTGTCAATTGCAAGATC
*
52805 ATTGACAACTTCTGGTGTCAATCAATTGTAAGATC
1 A-TGACAACTTCTGGTG----TCAATTGCAAGATC
52840 ATGACAACTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
52859 TCTTTGAATA
Statistics
Matches: 260, Mismatches: 24, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
27 20 0.08
28 2 0.01
29 3 0.01
30 164 0.63
31 42 0.16
34 15 0.06
35 14 0.05
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAGATC
Found at i:52760 original size:117 final size:121
Alignment explanation
Indices: 52538--52858 Score: 416
Period size: 117 Copynumber: 2.6 Consensus size: 121
52528 ATGGTGTATA
* * * *
52538 TGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGATCATGAAA
1 TGACAACTTCTGATGTCAATTGTAAGATCATGACAACTTCTGGTGCCAATTGCAAGATCATGACA
* * *
52603 ACTTCTGGTGTCAGTTGCAAGATCATGACAACTTCCGGTGTCAATTGCAAGATCA-
66 ACTTCTGGTGTCAATTGCAAGACCATGACAACTTCCGGTGTCAATTGCAAGACCAC
* * * *
52658 TGACAA-TT-T-CTGTCAATTGTAAAATCATGATAACTTCTGGTGCCAATTGCAAAATCATGACA
1 TGACAACTTCTGATGTCAATTGTAAGATCATGACAACTTCTGGTGCCAATTGCAAGATCATGACA
* * * *
52720 ACTTCTGGTGTCAATTGTAAGACCATGACAGCTTCTGGTGTCAATTGTAAGACCAC
66 ACTTCTGGTGTCAATTGCAAGACCATGACAACTTCCGGTGTCAATTGCAAGACCAC
* *
52776 TGACAACTTCTGATGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATCAATTGTAAGATCA
1 TGACAACTTCTGATGTCAATTGTAAGATCA-TGACAACTTCTGGTG-C---CAATTGCAAGATCA
52841 TGACAACTTCTGGTGTCA
61 TGACAACTTCTGGTGTCA
52859 TCTTTGAATA
Statistics
Matches: 172, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
117 94 0.55
118 7 0.04
119 4 0.02
120 7 0.04
121 15 0.09
122 14 0.08
123 1 0.01
126 30 0.17
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (121 bp):
TGACAACTTCTGATGTCAATTGTAAGATCATGACAACTTCTGGTGCCAATTGCAAGATCATGACA
ACTTCTGGTGTCAATTGCAAGACCATGACAACTTCCGGTGTCAATTGCAAGACCAC
Found at i:52930 original size:25 final size:25
Alignment explanation
Indices: 52902--52953 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
52892 TGATTGAGTT
52902 TAGAATTATGCCAATGATGTTTGGC
1 TAGAATTATGCCAATGATGTTTGGC
52927 TAGAATTATGCCAATGATGTTTGGC
1 TAGAATTATGCCAATGATGTTTGGC
52952 TA
1 TA
52954 TTCGGCAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.37
Consensus pattern (25 bp):
TAGAATTATGCCAATGATGTTTGGC
Found at i:54034 original size:20 final size:20
Alignment explanation
Indices: 54009--54049 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
53999 AAAAATGGAG
*
54009 TTTTTAATAGAGTAAAACTA
1 TTTTTAATAGAGGAAAACTA
*
54029 TTTTTAGTAGAGGAAAACTA
1 TTTTTAATAGAGGAAAACTA
54049 T
1 T
54050 AACAGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (20 bp):
TTTTTAATAGAGGAAAACTA
Found at i:54400 original size:9 final size:9
Alignment explanation
Indices: 54388--54417 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
54378 ACATTATAAT
54388 TAATATAGA
1 TAATATAGA
54397 TAATATAGA
1 TAATATAGA
54406 TATATATAGA
1 TA-ATATAGA
54416 TA
1 TA
54418 TAATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (9 bp):
TAATATAGA
Found at i:54434 original size:9 final size:9
Alignment explanation
Indices: 54420--54444 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54410 TATAGATATA
54420 ATAATAATC
1 ATAATAATC
54429 ATAATAATC
1 ATAATAATC
54438 ATAATAA
1 ATAATAA
54445 AGACAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAATAATC
Found at i:54801 original size:17 final size:16
Alignment explanation
Indices: 54779--54812 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
54769 TAAGAGAGAG
54779 AAAAAGGAAGGAAAAAA
1 AAAAAGGAA-GAAAAAA
54796 AAAAAGGAAGAAAAAA
1 AAAAAGGAAGAAAAAA
54812 A
1 A
54813 GAGCAAGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAGGAAGAAAAAA
Found at i:56030 original size:62 final size:62
Alignment explanation
Indices: 55953--56138 Score: 320
Period size: 62 Copynumber: 3.0 Consensus size: 62
55943 AGCAACATAA
*
55953 GTTATTGTTCCACATGAAACATACAAATAAAGAAACATACTTTAGCATTTGTGTATATCTGT
1 GTTATTGTTCCACATGAAATATACAAATAAAGAAACATACTTTAGCATTTGTGTATATCTGT
*
56015 GTTATTGTTCCACATGAAATATACAAATAAAGCAACATACTTTAGCATTTGTGTATATCTGT
1 GTTATTGTTCCACATGAAATATACAAATAAAGAAACATACTTTAGCATTTGTGTATATCTGT
* * *
56077 GTTATTGTTCCACAAGAAATATACAAA-AAAAAAACATACTTAAGCATTTGTGTATATCTGT
1 GTTATTGTTCCACATGAAATATACAAATAAAGAAACATACTTTAGCATTTGTGTATATCTGT
56138 G
1 G
56139 CATGTGAGTT
Statistics
Matches: 118, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
61 32 0.27
62 86 0.73
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (62 bp):
GTTATTGTTCCACATGAAATATACAAATAAAGAAACATACTTTAGCATTTGTGTATATCTGT
Found at i:61022 original size:6 final size:6
Alignment explanation
Indices: 61006--61037 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
60996 GGGAAGTGGG
61006 AATTG- AATTGA AATTGA AATTGA AATTGA AAT
1 AATTGA AATTGA AATTGA AATTGA AATTGA AAT
61038 GAGAGCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
AATTGA
Found at i:71219 original size:12 final size:12
Alignment explanation
Indices: 71187--71225 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
71177 ATGGAATTAA
71187 ATATCCGTCG--
1 ATATCCGTCGAT
71197 ATAT-C-TCGAT
1 ATATCCGTCGAT
71207 ATATCCGTCGAT
1 ATATCCGTCGAT
71219 ATATCCG
1 ATATCCG
71226 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 1 0.04
10 8 0.32
11 1 0.04
12 12 0.48
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:71349 original size:10 final size:10
Alignment explanation
Indices: 71336--71371 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
71326 ACATCTCGAT
71336 ATATCCGTAA
1 ATATCCGTAA
*
71346 ATATCCATAA
1 ATATCCGTAA
71356 ATATCCGTAA
1 ATATCCGTAA
71366 ATATCC
1 ATATCC
71372 ATATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:71359 original size:20 final size:20
Alignment explanation
Indices: 71336--71374 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
71326 ACATCTCGAT
71336 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
71356 ATATCCGTAAATATCCATA
1 ATATCCGTAAATATCCATA
71375 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:72225 original size:9 final size:10
Alignment explanation
Indices: 72200--72224 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
72190 TTCGCAGCAC
72200 AAAAAATAAA
1 AAAAAATAAA
72210 AAAAAATAAA
1 AAAAAATAAA
72220 AAAAA
1 AAAAA
72225 TGTCTACATA
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:72415 original size:13 final size:12
Alignment explanation
Indices: 72385--72427 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
72375 CATCGATACC
72385 TCGATATATCCG
1 TCGATATATCCG
72397 TCGATATATCCG
1 TCGATATATCCG
*
72409 TTCGATATATTCG
1 -TCGATATATCCG
72422 TCGATA
1 TCGATA
72428 CCTGTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:74512 original size:12 final size:12
Alignment explanation
Indices: 74495--74520 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
74485 ACACGTTTAT
74495 ACGACACGAAAC
1 ACGACACGAAAC
74507 ACGACACGAAAC
1 ACGACACGAAAC
74519 AC
1 AC
74521 AAATTACCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.35, G:0.15, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Found at i:81783 original size:2 final size:2
Alignment explanation
Indices: 81778--81802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
81768 AAAAATCAGA
81778 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
81803 AAGACTTTGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:87525 original size:16 final size:16
Alignment explanation
Indices: 87504--87534 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
87494 CAAATCGGGC
87504 GGAAATAAAACCCAAT
1 GGAAATAAAACCCAAT
*
87520 GGAAATTAAACCCAA
1 GGAAATAAAACCCAA
87535 ACAATCTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (16 bp):
GGAAATAAAACCCAAT
Found at i:94495 original size:1 final size:1
Alignment explanation
Indices: 94489--94515 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
94479 TTTGAGTTAA
94489 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
94516 AAAAAGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:102740 original size:24 final size:24
Alignment explanation
Indices: 102712--102759 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
102702 GAAATCGTTT
*
102712 CCAAGCTCCTCCATCCGGAAATGC
1 CCAAGCTCCTCCATCCAGAAATGC
*
102736 CCAAGCTCCTCCCTCCAGAAATGC
1 CCAAGCTCCTCCATCCAGAAATGC
102760 AACCATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.25, C:0.44, G:0.15, T:0.17
Consensus pattern (24 bp):
CCAAGCTCCTCCATCCAGAAATGC
Found at i:104379 original size:2 final size:2
Alignment explanation
Indices: 104372--104414 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
104362 CAAAAATTAA
*
104372 AC AC AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
104414 A
1 A
104415 TATATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:104816 original size:114 final size:114
Alignment explanation
Indices: 104516--104866 Score: 540
Period size: 115 Copynumber: 3.0 Consensus size: 114
104506 ACTACAATTG
* * * *
104516 AAGATAGCAGCGTCTGAGGTCCAAAACGCCGCTAAATGGAGGCGTCTGAACCTCAAGACGCCGCC
1 AAGATAGCGGCGTCTGGGGT-CAAGACGCCGCTAAATGGAGGCGTCTGAACCTCAAGACGCCGCG
*
104581 ATCTTTAATTTTTCTCCGAGAAAGGCAAATTGGGTAAAAATGAAGGCTAA
65 ATCTTTAATTTTTCTCCGAGAAAGGCAAATTGGGAAAAAATGAAGGCTAA
* * *
104631 AAGATAACGACGTCTGGGGGTCAAGACGCCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCG
1 AAGATAGCGGCGTCT-GGGGTCAAGACGCCGCTAAATGGAGGCGTCTGAACCTCAAGACGCCGCG
*
104696 ATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGAAAAAATGAAGGCTAA
65 ATCTTTAATTTTTCTCCGAGAAAGGCAAATTGGGAAAAAATGAAGGCTAA
* * *
104746 AAGATAGCGGCGTCTGGGGTCAAGACGCCACTAAATGGAGGCGTCTGAACCACAAAACGCCGCGA
1 AAGATAGCGGCGTCTGGGGTCAAGACGCCGCTAAATGGAGGCGTCTGAACCTCAAGACGCCGCGA
**
104811 TCTTTAATTTTTCTCCGAGAAAGGCAAATTGGGTAAAATTGTGAAGGCTAA
66 TCTTTAATTTTTCTCCGAGAAAGGCAAATTGGG-AAAA-AATGAAGGCTAA
104862 AAGAT
1 AAGAT
104867 GTCAGAGTGT
Statistics
Matches: 215, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
114 78 0.36
115 118 0.55
116 19 0.09
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (114 bp):
AAGATAGCGGCGTCTGGGGTCAAGACGCCGCTAAATGGAGGCGTCTGAACCTCAAGACGCCGCGA
TCTTTAATTTTTCTCCGAGAAAGGCAAATTGGGAAAAAATGAAGGCTAA
Found at i:114341 original size:21 final size:21
Alignment explanation
Indices: 114302--114350 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
114292 TCAATGCTTT
**
114302 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
114324 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
114345 A-GAAGC
1 AGGAAGC
114351 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.