Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013747.1 Corchorus olitorius cultivar O-4 contig13780, 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: 55544
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2009 original size:27 final size:27
Alignment explanation
Indices: 1946--2010 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1936 AGTGAACTTA
**
1946 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGATGCCC
1973 AAATGACCAAAATGCCCCTGGATGACCC
1 AAATGACCAAAATGCCCCTGGATG-CCC
*
2001 TAATG-CCAAA
1 AAATGACCAAA
2011 TATGGGTGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATGCCC
Found at i:5434 original size:30 final size:31
Alignment explanation
Indices: 5398--5467 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
5388 CAAACAATCT
*
5398 ATCAATCAATTAACA-AATATTTGCAATTC-A
1 ATCAATCAATTAACAGAATA-TGGCAATTCGA
*
5428 ATCAATCAA-TAGCAGAATATGGCAATTCGA
1 ATCAATCAATTAACAGAATATGGCAATTCGA
5458 ATCAAT-AATT
1 ATCAATCAATT
5468 GAAAGATAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 14 0.40
30 21 0.60
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (31 bp):
ATCAATCAATTAACAGAATATGGCAATTCGA
Found at i:10571 original size:18 final size:16
Alignment explanation
Indices: 10539--10574 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
10529 CCTAACACAA
10539 TCCATGCTAATGTGTG
1 TCCATGCTAATGTGTG
*
10555 TCCATGCTAATATGTG
1 TCCATGCTAATGTGTG
10571 TCCA
1 TCCA
10575 AGGTTCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (16 bp):
TCCATGCTAATGTGTG
Found at i:14410 original size:18 final size:18
Alignment explanation
Indices: 14387--14423 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
14377 AAAGGGTAAC
*
14387 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
14405 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
14423 T
1 T
14424 GATAGAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:19028 original size:40 final size:40
Alignment explanation
Indices: 18966--19670 Score: 427
Period size: 40 Copynumber: 17.6 Consensus size: 40
18956 CATTTGTCAA
* *
18966 TTTGCCCTTCCTCATCGTAAGGTGTTTGCAGAATTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTTGTAGAATTCCCAG
* * * *
19006 TTTTCCCTTCCTCATGGGAAGGTGTTGTTTA-CATTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGAATTCCCAG
* * * *
19046 TTTGCCCTTCCTCATCGAAAGGTG-TTGTTGAGTTTCCCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTTGTAGA-ATTCCCAG
* *
19086 TTTGCCCTTCCTCATCAGAAGGTG-TTGTTGAATTTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTTGTAGAA-TTCCCAG
*
19126 TTTGCCCTTCCAT-ATCGGAAGATG--T-T-G---T--CAG
1 TTTGCCCTTCC-TCATCGGAAGGTGTTTGTAGAATTCCCAG
* * *
19157 TTTGCCCTTCCTCATCGGAAGGTGTTGTCTACATTTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGAATTCCCAG
* * * *
19198 TTTGCCTTTCCCCATCGGAAGATG-TTGTCAGAATTACCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTTGT-AGAATTCCCAG
* * *
19238 TTTGCCCTTTCTCATCGGAAGGTGTTGTTAAGTTTACGAGTTTCTCAG
1 TTTGCCCTTCCTCATCGGAAGGTG-T-TT--G--TA-GA-ATTCCCAG
* *
19286 TTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-CATTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGAATTCCCAG
* * * * * * *
19326 TTTGCTCTTCCTCGTCAGAAGATGTTGTTTA-CATTACCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGAATTCCCAG
* * ***
19366 TTTGCTCTTCCTCATCGGAAGGTG-TTGTTA-AGTTTAATAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTTG-TAGA-ATTCCCAG
* * *
19406 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTA-CATTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGAATTCCCAG
* * ** *
19446 TTTGCCCTTTCTCATCGAAAGGTG-TTGTTTATTTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTTGTAGAATTCCCAG
* * * * *
19485 TTTGTCATTCCTCGTCGGAAGGTGTTGTTTA-CATTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGAATTCCCAG
* * *
19525 TTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-CATT--CGG
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGAATTCCCAG
* * *
19563 TTTGCCCTTCCCCATCGGAAGGTG-TTGTTA-AGTTTACCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTTG-TAGA-ATTCCCAG
* * *** *
19603 TTTACCCTTCCTCATCGGAAGGTGTTGTTTATCTTTTCCCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTA-GAATTCCCAG
* *
19645 TCTGTCCTTCCTCATCGGAAGGTGTT
1 TTTGCCCTTCCTCATCGGAAGGTGTT
19671 GTTCCTATTC
Statistics
Matches: 527, Mismatches: 96, Indels: 82
0.75 0.14 0.12
Matches are distributed among these distances:
30 1 0.00
31 24 0.05
33 1 0.00
34 1 0.00
35 1 0.00
36 1 0.00
37 4 0.01
38 33 0.06
39 35 0.07
40 320 0.61
41 35 0.07
42 31 0.06
43 4 0.01
45 1 0.00
46 2 0.00
47 5 0.01
48 28 0.05
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.38
Consensus pattern (40 bp):
TTTGCCCTTCCTCATCGGAAGGTGTTTGTAGAATTCCCAG
Found at i:19068 original size:80 final size:79
Alignment explanation
Indices: 18966--19673 Score: 620
Period size: 80 Copynumber: 8.9 Consensus size: 79
18956 CATTTGTCAA
* * * *
18966 TTTGCCCTTCCTCATCGTAAGGTGTTTGCAGAATTCCCAGTTTTCCCTTCCTCATGGGAAGGTGT
1 TTTGCCCTTCCTCATCGGAAGGTGTTTGTAG-ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGT
19031 TGTTTACATTCCCAG
65 TGTTTACATTCCCAG
* * * *
19046 TTTGCCCTTCCTCATCGAAAGGTG-TTGTTGAGTTTCCCAATTTGCCCTTCCTCATCAGAAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTTG-T-AGATTCCCAGTTTGCCCTTCCTCATCGGAAGGTG
*
19110 TTGTTGA-ATTTCCCAG
64 TTGTTTACA-TTCCCAG
*
19126 TTTGCCCTTCCAT-ATCGGAAGATG--T-T-G--T--CAGTTTGCCCTTCCTCATCGGAAGGTGT
1 TTTGCCCTTCC-TCATCGGAAGGTGTTTGTAGATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGT
*
19182 TGTCTACATTTCCCAG
65 TGTTTACA-TTCCCAG
* * * * *
19198 TTTGCCTTTCCCCATCGGAAGATG-TTGTCAGAATTACCAGTTTGCCCTTTCTCATCGGAAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTTGT-AG-ATTCCCAGTTTGCCCTTCCTCATCGGAA-G-G
*
19262 TTGTTAAGTTTACGAGTTTCTCAG
62 -TGTT--GTTTAC-A--TTCCCAG
* * * * * *
19286 TTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCCAGTTTGCTCTTCCTCGTCAGAAGATGT
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGT
*
19351 TGTTTACATTACCAG
65 TGTTTACATTCCCAG
* * *** *
19366 TTTGCTCTTCCTCATCGGAAGGTG-TTGTTAAGTTTAATAGTTTGCCCTTCCTCACCGGAAGGTG
1 TTTGCCCTTCCTCATCGGAAGGTGTTTG-T-AGATTCCCAGTTTGCCCTTCCTCATCGGAAGGTG
19430 TTGTTTACATTCCCAG
64 TTGTTTACATTCCCAG
* * * * * * *
19446 TTTGCCCTTTCTCATCGAAAGGTGTTGTTTA-TTTCCCAGTTTGTCATTCCTCGTCGGAAGGTGT
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGT
19510 TGTTTACATTCCCAG
65 TGTTTACATTCCCAG
* * * *
19525 TTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATT--CGGTTTGCCCTTCCCCATCGGAAGGTGT
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTAGATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGT
* ** *
19588 TGTTAAGTTTACCAG
65 TGTTTACATTCCCAG
* * ** * * *
19603 TTTACCCTTCCTCATCGGAAGGTGTTGTTTATCTTTTCCCAATCTGTCCTTCCTCATCGGAAGGT
1 TTTGCCCTTCCTCATCGGAAGGTGTT-TGTA--GATTCCCAGTTTGCCCTTCCTCATCGGAAGGT
19668 GTTGTT
63 GTTGTT
19674 CCTATTCCTG
Statistics
Matches: 519, Mismatches: 76, Indels: 64
0.79 0.12 0.10
Matches are distributed among these distances:
71 30 0.06
72 30 0.06
73 2 0.00
74 1 0.00
75 1 0.00
76 1 0.00
77 1 0.00
78 65 0.13
79 78 0.15
80 176 0.34
81 27 0.05
82 30 0.06
83 7 0.01
84 4 0.01
85 4 0.01
86 5 0.01
87 2 0.00
88 51 0.10
89 2 0.00
90 2 0.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (79 bp):
TTTGCCCTTCCTCATCGGAAGGTGTTTGTAGATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTT
GTTTACATTCCCAG
Found at i:19135 original size:120 final size:118
Alignment explanation
Indices: 18966--19673 Score: 704
Period size: 120 Copynumber: 5.9 Consensus size: 118
18956 CATTTGTCAA
** * * *
18966 TTTGCCCTTCCTCATCGTAAGGTGTTTGCAGAATTCCCAGTTTTCCCTTCCTCATGGGAAGGTGT
1 TTTGCCCTTCCTCATCG-AAGGTG-TTGTTGAATTACCAGTTTGCCCTTCCTCATCGGAAGGTGT
* * ** *
19031 TGTTTACATTCCCAGTTTGCCCTTCCTCATCGAAAGGTGTTGTTGAGTTTCCCAA
64 TGTTTACATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCCAG
* *
19086 TTTGCCCTTCCTCATCAGAAGGTGTTGTTGAATTTCCCAGTTTGCCCTTCCAT-ATCGGAAGATG
1 TTTGCCCTTCCTCATC-GAAGGTGTTGTTGAA-TTACCAGTTTGCCCTTCC-TCATCGGAAGGTG
*
19150 TTG-------T--CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTACATTTCCCAG
63 TTGTTTACATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACA-TTCCCAG
* * * * *
19198 TTTGCCTTTCCCCATCGGAAGATGTTGTCAGAATTACCAGTTTGCCCTTTCTCATCGGAAGGTGT
1 TTTGCCCTTCCTCATC-GAAGGTGTTGT-TGAATTACCAGTTTGCCCTTCCTCATCGGAA-G-G-
*
19263 TGTTAAGTTTACGAGTTTCTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCCAG
61 TGTT--GTTTAC-A--TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCCAG
* * * * *
19326 TTTGCTCTTCCTCGTCAGAAGATGTTGTTTACATTACCAGTTTGCTCTTCCTCATCGGAAGGTGT
1 TTTGCCCTTCCTCATC-GAAGGTGTTGTTGA-ATTACCAGTTTGCCCTTCCTCATCGGAAGGTGT
* ** *** *
19391 TGTTAAGTTTAATAGTTTGCCCTTCCTCACCGGAAGGTGTTGTTTACATTCCCAG
64 TGTTTACATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCCAG
* * * * * * *
19446 TTTGCCCTTTCTCATCGAAAGGTGTTGTTTATTTCCCAGTTTGTCATTCCTCGTCGGAAGGTGTT
1 TTTGCCCTTCCTCATCG-AAGGTGTTGTTGAATTACCAGTTTGCCCTTCCTCATCGGAAGGTGTT
*
19511 GTTTACATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATT--CGG
65 GTTTACATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCCAG
* *
19563 TTTGCCCTTCCCCATCGGAAGGTGTTGTT-AAGTTTACCAGTTTACCCTTCCTCATCGGAAGGTG
1 TTTGCCCTTCCTCATC-GAAGGTGTTGTTGAA--TTACCAGTTTGCCCTTCCTCATCGGAAGGTG
* * * *
19627 TTGTTTATCTTTTCCCAATCTGTCCTTCCTCATCGGAAGGTGTTGTT
63 TTGTTTA-C-ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTT
19674 CCTATTCCTG
Statistics
Matches: 492, Mismatches: 66, Indels: 60
0.80 0.11 0.10
Matches are distributed among these distances:
111 32 0.07
112 53 0.11
113 5 0.01
115 4 0.01
116 1 0.00
117 28 0.06
118 34 0.07
119 78 0.16
120 152 0.31
121 2 0.00
123 4 0.01
125 4 0.01
126 1 0.00
127 3 0.01
128 56 0.11
129 35 0.07
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (118 bp):
TTTGCCCTTCCTCATCGAAGGTGTTGTTGAATTACCAGTTTGCCCTTCCTCATCGGAAGGTGTTG
TTTACATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCCAG
Found at i:19161 original size:31 final size:31
Alignment explanation
Indices: 19123--19185 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
19113 TTGAATTTCC
19123 CAGTTTGCCCTTCCAT-ATCGGAAGATGTTGT
1 CAGTTTGCCCTTCC-TCATCGGAAGATGTTGT
*
19154 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
1 CAGTTTGCCCTTCCTCATCGGAAGATGTTGT
19185 C
1 C
19186 TACATTTCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (31 bp):
CAGTTTGCCCTTCCTCATCGGAAGATGTTGT
Found at i:19222 original size:72 final size:71
Alignment explanation
Indices: 19086--19228 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 71
19076 AGTTTCCCAA
*
19086 TTTGCCCTTCCTCATCAGAAGGTGTTGTTGAATTTCCCAGTTTGCCCTTCCATATCGGAAGATGT
1 TTTGCCCTTCCTCATCAGAAGGTGTTGTTGAATTTCCCAGTTTGCCCTTCCACATCGGAAGATGT
19151 TGTCAG
66 TGTCAG
* * *
19157 TTTGCCCTTCCTCATCGGAAGGTGTTGTCT-ACATTTCCCAGTTTGCCTTTCCCCATCGGAAGAT
1 TTTGCCCTTCCTCATCAGAAGGTGTTGT-TGA-ATTTCCCAGTTTGCCCTTCCACATCGGAAGAT
19221 GTTGTCAG
64 GTTGTCAG
19229 AATTACCAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
71 28 0.42
72 38 0.58
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (71 bp):
TTTGCCCTTCCTCATCAGAAGGTGTTGTTGAATTTCCCAGTTTGCCCTTCCACATCGGAAGATGT
TGTCAG
Found at i:19244 original size:112 final size:111
Alignment explanation
Indices: 19043--19265 Score: 290
Period size: 112 Copynumber: 2.0 Consensus size: 111
19033 TTTACATTCC
* * *
19043 CAGTTTGCCCTTCCTCATCGAAAGGTGTTGTTGAGTTTCCCAATTTGCCCTTCCTCATCAGAAGG
1 CAGTTTGCCCTTCCTCATCGAAAGGTGTTGTTGAATTTCCCAATTTGCCCTTCCCCATCAGAAGA
* *
19108 TGTTGTTGAATTTCCCAGTTTGCCCTTCCAT-ATCGGAAGATGTTGT
66 TGTTGTAGAATTTACCAGTTTGCCCTTCC-TCATCGGAAGATGTTGT
* * * *
19154 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCT-ACATTTCCCAGTTTGCCTTTCCCCATCGGAA
1 CAGTTTGCCCTTCCTCATCGAAAGGTGTTGT-TGA-ATTTCCCAATTTGCCCTTCCCCATCAGAA
* *
19218 GATGTTGTCAGAA-TTACCAGTTTGCCCTTTCTCATCGGAAGGTGTTGT
64 GATGTTGT-AGAATTTACCAGTTTGCCCTTCCTCATCGGAAGATGTTGT
19266 TAAGTTTACG
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
111 32 0.33
112 62 0.64
113 3 0.03
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.36
Consensus pattern (111 bp):
CAGTTTGCCCTTCCTCATCGAAAGGTGTTGTTGAATTTCCCAATTTGCCCTTCCCCATCAGAAGA
TGTTGTAGAATTTACCAGTTTGCCCTTCCTCATCGGAAGATGTTGT
Found at i:21848 original size:14 final size:14
Alignment explanation
Indices: 21829--21873 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
21819 ATAGCATTCA
21829 CATTAGTAATTAGG
1 CATTAGTAATTAGG
*
21843 CATTAG-CATTCA--
1 CATTAGTAATT-AGG
21855 CATTAGTAATTAGG
1 CATTAGTAATTAGG
21869 CATTA
1 CATTA
21874 ACAGTTTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 12 0.48
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (14 bp):
CATTAGTAATTAGG
Found at i:21851 original size:26 final size:26
Alignment explanation
Indices: 21820--21873 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
21810 CATTGCCTAA
21820 TAGCATTCACATTAGTAATTAGGCAT
1 TAGCATTCACATTAGTAATTAGGCAT
21846 TAGCATTCACATTAGTAATTAGGCAT
1 TAGCATTCACATTAGTAATTAGGCAT
21872 TA
1 TA
21874 ACAGTTTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (26 bp):
TAGCATTCACATTAGTAATTAGGCAT
Found at i:23048 original size:16 final size:16
Alignment explanation
Indices: 23023--23054 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
23013 CTGATGGGAC
23023 CTCTCCATTTTTTTTT
1 CTCTCCATTTTTTTTT
*
23039 CTCTCGATTTTTTTTT
1 CTCTCCATTTTTTTTT
23055 TCCAGGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.22, G:0.03, T:0.69
Consensus pattern (16 bp):
CTCTCCATTTTTTTTT
Found at i:28086 original size:163 final size:162
Alignment explanation
Indices: 27467--28288 Score: 1270
Period size: 165 Copynumber: 5.0 Consensus size: 162
27457 CGATAGAAAG
* * *
27467 ACGCCGCCATATTAATATATGGAGGGAGAGATTTTTTTTTTCTTTTTTTGGAGGGAAAAATTCCC
1 ACGCCGCCATTTTAATATATGGAGGGAGAGATTTCTTTTTCCTTTTTTTGGAGGGAAAAATTCCC
* * * *
27532 TCCCCCTAAAACAAAGAAAGTTTACAACTCTACGCCTATAATATATAGCGGCGTTCTGGCATCAG
66 TCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGACATCAG
27597 ACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
131 ACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
* * *
27629 ATGCCGCCATTTTAATATATGGAGGGAGATATTTCTTTTTCCTTTTGTTGGAGGG-AAAATTCCC
1 ACGCCGCCATTTTAATATATGGAGGGAGAGATTTCTTTTTCCTTTTTTTGGAGGGAAAAATTCCC
* * *
27693 T-CCCCTAAAACAAAGAAAGTTTCCAACTCTACGGCTATAATAGATAGTAGCGTTTTGACATCAG
66 TCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGACATCAG
27757 ACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
131 ACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
* * * *
27789 ACGCCGCCATTTTAATATATGGAGGGAGGGATTTTATTTATTCCTTTTTTGGGTGGGAAAAATTC
1 ACGCCGCCATTTTAATATATGGAGGGAGAGA-TTTCTTT-TTCCTTTTTTTGGAGGGAAAAATTC
*
27854 CCTCTCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGGCAT
64 CCTC-CCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGACAT
*
27919 CAGACGCCGCTAATTAGTGGCATCTAGAAAAGGAA
128 CAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
*
27954 ACGCTGCCATTTTAATATATGGAGGGAGAGATTTCTTTTTCCTTTTTTTTGGAGGGAAAAATTCC
1 ACGCCGCCATTTTAATATATGGAGGGAGAGATTTCTTTTTCC-TTTTTTTGGAGGGAAAAATTCC
* *
28019 CTCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCTTATAATATATAGCGGCGTTTTGACATCA
65 CTCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGACATCA
*
28084 GACGCCGCTAATTAGTGGCGTCTAGAAGAGGAA
130 GACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
* * * *
28117 ACGCCGCCATTTTAATATATGGAGGGAGGGATTTTCTTTATTCCTTTTTTGGGATGGAAAGATTC
1 ACGCCGCCATTTTAATATATGGAGGGAGAGA-TTTCTTT-TTCCTTTTTTTGGAGGGAAAAATTC
* *
28182 CCTCTCCCCTAAAACAAAGAAAATTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTCACAT
64 CCTC-CCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGACAT
** * *
28247 CAGACGCCTTTAATTAGTGGTGTCTAGGAAAGGAA
128 CAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
28282 ACGCCGC
1 ACGCCGC
28289 TTTGTAAATT
Statistics
Matches: 602, Mismatches: 49, Indels: 15
0.90 0.07 0.02
Matches are distributed among these distances:
160 116 0.19
161 16 0.03
162 63 0.10
163 133 0.22
164 58 0.10
165 216 0.36
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (162 bp):
ACGCCGCCATTTTAATATATGGAGGGAGAGATTTCTTTTTCCTTTTTTTGGAGGGAAAAATTCCC
TCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGACATCAG
ACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
Found at i:28159 original size:328 final size:324
Alignment explanation
Indices: 27467--28288 Score: 1328
Period size: 328 Copynumber: 2.5 Consensus size: 324
27457 CGATAGAAAG
* * * * *
27467 ACGCCGCCATATTAATATATGGAGGGAGAGATTTTTTT-TTTCTTTTTTTGGAGGGAAAAATTCC
1 ACGCCGCCATTTTAATATATGGAGGGAGGGATTTTTTTATTCCTTTTTTGGGTGGGAAAAATTCC
* * *
27531 CTC-CCCCTAAAACAAAGAAAGTTTACAACTCTACGCCTATAATATATAGCGGCGTTCTGGCATC
66 CTCTCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGGCATC
* *
27595 AGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAAATGCCGCCATTTTAATATATGGAGGGAGATA
131 AGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAAACGCCGCCATTTTAATATATGGAGGGAGAGA
27660 TTTCTTTTTCCTTTTGTTGGAGGGAAAATTCCCTCCCCTAAAACAAAGAAAGTTTCCAACTCTAC
196 TTTCTTTTTCCTTTTGTTGGAGGGAAAATTCCCTCCCCTAAAACAAAGAAAGTTTCCAACTCTAC
*
27725 GGCTATAATAGATAGTAGCGTTTTGACATCAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
261 GGCTATAATAGATAGCAGCGTTTTGACATCAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
27789 ACGCCGCCATTTTAATATATGGAGGGAGGGATTTTATTTATTCCTTTTTTGGGTGGGAAAAATTC
1 ACGCCGCCATTTTAATATATGGAGGGAGGGATTTT-TTTATTCCTTTTTTGGGTGGGAAAAATTC
27854 CCTCTCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGGCAT
65 CCTCTCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGGCAT
* *
27919 CAGACGCCGCTAATTAGTGGCATCTAGAAAAGGAAACGCTGCCATTTTAATATATGGAGGGAGAG
130 CAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAAACGCCGCCATTTTAATATATGGAGGGAGAG
*
27984 ATTTCTTTTTCCTTTTTTTTGGAGGGAAAAATTCCCTCCCCCTAAAACAAAGAAAGTTTCCAACT
195 ATTTCTTTTTCC-TTTTGTTGGAGGG-AAAATTCCCT-CCCCTAAAACAAAGAAAGTTTCCAACT
* * *
28049 CTAC-GCTTATAATATATAGCGGCGTTTTGACATCAGACGCCGCTAATTAGTGGCGTCTAGAAGA
257 CTACGGC-TATAATAGATAGCAGCGTTTTGACATCAGACGCCGCTAATTAGTGGCGTCTAGAAAA
28113 GGAA
321 GGAA
*
28117 ACGCCGCCATTTTAATATATGGAGGGAGGGATTTTCTTTATTCCTTTTTTGGGAT-GGAAAGATT
1 ACGCCGCCATTTTAATATATGGAGGGAGGGATTTT-TTTATTCCTTTTTTGGG-TGGGAAAAATT
* **
28181 CCCTCTCCCCTAAAACAAAGAAAATTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTCACA
64 CCCTCTCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGGCA
** * *
28246 TCAGACGCCTTTAATTAGTGGTGTCTAGGAAAGGAAACGCCGC
129 TCAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAAACGCCGC
28289 TTTGTAAATT
Statistics
Matches: 464, Mismatches: 28, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
322 33 0.07
323 3 0.01
324 26 0.06
325 130 0.28
326 12 0.03
327 12 0.03
328 247 0.53
329 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (324 bp):
ACGCCGCCATTTTAATATATGGAGGGAGGGATTTTTTTATTCCTTTTTTGGGTGGGAAAAATTCC
CTCTCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTGGCATC
AGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAAACGCCGCCATTTTAATATATGGAGGGAGAGA
TTTCTTTTTCCTTTTGTTGGAGGGAAAATTCCCTCCCCTAAAACAAAGAAAGTTTCCAACTCTAC
GGCTATAATAGATAGCAGCGTTTTGACATCAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAA
Found at i:28388 original size:32 final size:31
Alignment explanation
Indices: 28347--28421 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
28337 CTAAAACAAT
* *
28347 TAGCGGCGTTTCAGTACAAAAGCGCCACTGAA
1 TAGCGGCGTTTC-CTACAAAAGCGCCACTAAA
** *
28379 TAGCGGCGTTTTCCTACTTAAGTGCCACTAAA
1 TAGCGGCG-TTTCCTACAAAAGCGCCACTAAA
28411 TAGCGGCGTTT
1 TAGCGGCGTTT
28422 TTTTAAGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 3 0.08
32 30 0.81
33 4 0.11
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (31 bp):
TAGCGGCGTTTCCTACAAAAGCGCCACTAAA
Found at i:35133 original size:14 final size:14
Alignment explanation
Indices: 35103--35132 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
35093 ATTTTATTCC
35103 TTCTTTTTGAATTT
1 TTCTTTTTGAATTT
35117 TTCTTGTTTGAATTT
1 TTCTT-TTTGAATTT
35132 T
1 T
35133 CCTTACCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.70
Consensus pattern (14 bp):
TTCTTTTTGAATTT
Found at i:36264 original size:28 final size:27
Alignment explanation
Indices: 36183--36274 Score: 77
Period size: 28 Copynumber: 3.5 Consensus size: 27
36173 TTCTAGCTAT
36183 AGATCAAATTTTTATTCATAATTTACCA
1 AGATCAAATTTTTATTC-TAATTTACCA
* * **
36211 AGATCTAA-TCTT-TTCT-AGCTA--A
1 AGATCAAATTTTTATTCTAATTTACCA
36233 AGATCAAATTTTTATTCTTAATTTACCA
1 AGATCAAATTTTTATTC-TAATTTACCA
*
36261 AGATCTAATCTTTT
1 AGATCAAAT-TTTT
36275 TAGGCCTGAG
Statistics
Matches: 48, Mismatches: 9, Indels: 13
0.69 0.13 0.19
Matches are distributed among these distances:
22 8 0.17
23 3 0.06
24 6 0.12
25 2 0.04
26 6 0.12
27 3 0.06
28 16 0.33
29 4 0.08
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (27 bp):
AGATCAAATTTTTATTCTAATTTACCA
Found at i:36287 original size:50 final size:50
Alignment explanation
Indices: 36152--36274 Score: 210
Period size: 50 Copynumber: 2.5 Consensus size: 50
36142 TTTTATTACC
* * *
36152 AATTTACCAAGACCTAACCTTTTCTAGCTATAGATCAAATTTTTATTCAT
1 AATTTACCAAGATCTAATCTTTTCTAGCTAAAGATCAAATTTTTATTCAT
*
36202 AATTTACCAAGATCTAATCTTTTCTAGCTAAAGATCAAATTTTTATTCTT
1 AATTTACCAAGATCTAATCTTTTCTAGCTAAAGATCAAATTTTTATTCAT
36252 AATTTACCAAGATCTAATCTTTT
1 AATTTACCAAGATCTAATCTTTT
36275 TAGGCCTGAG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (50 bp):
AATTTACCAAGATCTAATCTTTTCTAGCTAAAGATCAAATTTTTATTCAT
Found at i:37851 original size:10 final size:12
Alignment explanation
Indices: 37827--37866 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
37817 TCTAGAAGGG
37827 GAGAAGGAAAGA
1 GAGAAGGAAAGA
37839 GAGAAGGAAAGA
1 GAGAAGGAAAGA
37851 GAGAGAGGAAA-A
1 GAGA-AGGAAAGA
37863 GAGA
1 GAGA
37867 GTAAAGAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 21 0.78
13 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
GAGAAGGAAAGA
Found at i:42609 original size:10 final size:12
Alignment explanation
Indices: 42585--42624 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
42575 TCCAGAAGGG
42585 GAGAAGGAAAGA
1 GAGAAGGAAAGA
42597 GAGAAGGAAAGA
1 GAGAAGGAAAGA
42609 GAGAGAGGAAA-A
1 GAGA-AGGAAAGA
42621 GAGA
1 GAGA
42625 GTAAAGAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 21 0.78
13 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
GAGAAGGAAAGA
Found at i:44471 original size:41 final size:41
Alignment explanation
Indices: 44419--44499 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
44409 GTAAGAAAAA
*
44419 TATTTTTGTTTATATTTTTGTGTGAAAATATTTAAAAAATG
1 TATTTTTGTTTATATTTTTGTATGAAAATATTTAAAAAATG
44460 TATTTTTGTTTATATTTTTGTATGAAAATATTTAAAAAAT
1 TATTTTTGTTTATATTTTTGTATGAAAATATTTAAAAAAT
44500 ACATTGGTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (41 bp):
TATTTTTGTTTATATTTTTGTATGAAAATATTTAAAAAATG
Found at i:46297 original size:19 final size:18
Alignment explanation
Indices: 46252--46323 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 18
46242 ACAACAGGTG
* *
46252 GTATTATGTATTATTAGT
1 GTATTATTTATTATTAAT
*
46270 CGTAGTATTTATTATTAAT
1 -GTATTATTTATTATTAAT
46289 GTTATTA-TTATTTATTAAT
1 G-TATTATTTA-TTATTAAT
46308 GTATTCATTTATTATT
1 GTATT-ATTTATTATT
46324 TCCGCAGGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.18
19 34 0.76
20 3 0.07
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (18 bp):
GTATTATTTATTATTAAT
Done.