Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009034.1 Corchorus capsularis cultivar CVL-1 contig09055, 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: 38936
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:85 original size:13 final size:13
Alignment explanation
Indices: 67--91 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57 TTTATAACCT
67 CATAAATCATATC
1 CATAAATCATATC
80 CATAAATCATAT
1 CATAAATCATAT
92 TTAATATATA
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
CATAAATCATATC
Found at i:860 original size:124 final size:119
Alignment explanation
Indices: 646--889 Score: 398
Period size: 124 Copynumber: 2.0 Consensus size: 119
636 AGTACAATTT
646 TTTTAAAGAATTCTCTCAAAAAATTTTTTTTAAAGAATTGAAATTTATTTTTTGACTTGGATAGA
1 TTTTAAAGAATTCTCTCAAAAAATTTTTTTTAAAGAATTGAAATTTATTTTTTGACTTGGATAGA
* *
711 CAAACCACATTAAACTTGGCACATTAATTCCTCAAAGTGAACCAAGAATACATA
66 CAAACCACATTAAACTTGGCACATTAATTCCCCAAAGGGAACCAAGAATACATA
*
765 TTTTAAAGAATTTTCTCAAAAAAATTTTTTTTTCAAAGAATTGAAATTTTATTTTTTTGACTTGG
1 TTTTAAAGAATTCTCTC-AAAAAA-TTTTTTTT-AAAGAATTGAAA-TTTA-TTTTTTGACTTGG
* *
830 ATAGACAAACTACATTAAACTTGGCACATTAATTCCCCAAAGGGAGCCAAGAATACATA
61 ATAGACAAACCACATTAAACTTGGCACATTAATTCCCCAAAGGGAACCAAGAATACATA
889 T
1 T
890 ATATATATAT
Statistics
Matches: 115, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
119 16 0.14
120 6 0.05
121 8 0.07
122 12 0.10
123 4 0.03
124 69 0.60
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (119 bp):
TTTTAAAGAATTCTCTCAAAAAATTTTTTTTAAAGAATTGAAATTTATTTTTTGACTTGGATAGA
CAAACCACATTAAACTTGGCACATTAATTCCCCAAAGGGAACCAAGAATACATA
Found at i:893 original size:2 final size:2
Alignment explanation
Indices: 886--913 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
876 CCAAGAATAC
886 AT 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 AT
914 TCACTTCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3147 original size:123 final size:122
Alignment explanation
Indices: 3020--3360 Score: 432
Period size: 123 Copynumber: 2.7 Consensus size: 122
3010 CAGCAAGATT
* *
3020 CATCCCTGACCGAGTATGGGAAATGAAGATGCCCTCTAGGGACCCAACGCCAACAGGCGAGTGAT
1 CATCCCTGACCGAGTATGGGAAATGAAGATGCCCTCAAGGG-CCCAACGCCAACAGGCGAGCGAT
* * * * *
3085 CAAGCAAGGTCGAGGTCGACCTAGTATGGCCATCGACC-GGCAGGCGATCGGCATGAAC
65 CAGGCAAGGCCGAGCTCGACCTAGTATGGCCATCGACCAAG-AGGCGATCGACATGAAC
* * * *
3143 CATCCCTGATCGAGTATGAGAAATGAAGATGCCCTCAAGAGGCCCAACGGCAACAGGCAAGCGAT
1 CATCCCTGACCGAGTATGGGAAATGAAGATGCCCTCAAG-GGCCCAACGCCAACAGGCGAGCGAT
*
3208 CAGGCAAGGCCGAGCTCGACCTAGTATGGCCATCGACCAAGTGGCGATCGACATGAAC
65 CAGGCAAGGCCGAGCTCGACCTAGTATGGCCATCGACCAAGAGGCGATCGACATGAAC
* * * * *
3266 CATCTCTGACCAAGCATGGGAAAAATGATTATGAAGCCCCTCAAAGGGCCCAACGCTAACAGGCG
1 CATCCCTGACCGAGTATGGG--AAATGA--A-GATG-CCCTC-AAGGGCCCAACGCCAACAGGCG
3331 AGCGATCAGGCAAGGCCGAGCTCGACCTAG
59 AGCGATCAGGCAAGGCCGAGCTCGACCTAG
3361 CACGAAAAAT
Statistics
Matches: 188, Mismatches: 21, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
123 121 0.64
124 3 0.02
125 6 0.03
127 1 0.01
128 3 0.02
129 51 0.27
130 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.14
Consensus pattern (122 bp):
CATCCCTGACCGAGTATGGGAAATGAAGATGCCCTCAAGGGCCCAACGCCAACAGGCGAGCGATC
AGGCAAGGCCGAGCTCGACCTAGTATGGCCATCGACCAAGAGGCGATCGACATGAAC
Found at i:3563 original size:21 final size:21
Alignment explanation
Indices: 3472--3667 Score: 96
Period size: 21 Copynumber: 9.4 Consensus size: 21
3462 CCCTCAAAGG
* *
3472 AGAAGAAATGTTCTCCAAAGAT
1 AGAAG-AATGCTCTCCAAAGAA
** *
3494 AGAAGAACACT-TCACAAAGGAG
1 AGAAGAATGCTCTC-CAAA-GAA
* * *
3516 AGGAGAAAGCTC-CCAAAG-G
1 AGAAGAATGCTCTCCAAAGAA
*
3535 AGAGGAATGCTCTCCAAAGAA
1 AGAAGAATGCTCTCCAAAGAA
* * * *
3556 AAAAGAATGCTC-CCTATGAG
1 AGAAGAATGCTCTCCAAAGAA
* * *
3576 AGGATAATGCACTCCAATA-AA
1 AGAAGAATGCTCTCCAA-AGAA
* * * * *
3597 AGGAGAATACTCCCCAAGGAG
1 AGAAGAATGCTCTCCAAAGAA
*
3618 AGAAGAATGCTCCCCAAAGAA
1 AGAAGAATGCTCTCCAAAGAA
* *
3639 AGAAAAATGCTCTCCAAAGAT
1 AGAAGAATGCTCTCCAAAGAA
*
3660 AGGAGAAT
1 AGAAGAAT
3668 ATGATAATAC
Statistics
Matches: 128, Mismatches: 38, Indels: 17
0.70 0.21 0.09
Matches are distributed among these distances:
19 10 0.08
20 22 0.17
21 80 0.62
22 16 0.12
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (21 bp):
AGAAGAATGCTCTCCAAAGAA
Found at i:3585 original size:41 final size:41
Alignment explanation
Indices: 3519--3655 Score: 111
Period size: 42 Copynumber: 3.3 Consensus size: 41
3509 AAAGGAGAGG
*
3519 AGAAAGCTCCCAAAGGAGAG--GAATGCTCTCCAAAGAAAAA
1 AGAATGCTCCC-AAGGAGAGAAGAATGCTCTCCAAAGAAAAA
* * * * * **
3559 AGAATGCTCCCTATGAGAGGATAATGCACTCCAATA-AAAGG
1 AGAATGCTCCCAAGGAGAGAAGAATGCTCTCCAA-AGAAAAA
* *
3600 AGAATACTCCCCAAGGAGAGAAGAATGCTCCCCAAAGAAAGAA
1 AGAATGCT-CCCAAGGAGAGAAGAATGCTCTCCAAAGAAA-AA
3643 A-AATGCTCTCCAA
1 AGAATGCTC-CCAA
3656 AGATAGGAGA
Statistics
Matches: 73, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
39 6 0.08
40 10 0.14
41 23 0.32
42 33 0.45
43 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (41 bp):
AGAATGCTCCCAAGGAGAGAAGAATGCTCTCCAAAGAAAAA
Found at i:3734 original size:21 final size:22
Alignment explanation
Indices: 3686--3804 Score: 60
Period size: 21 Copynumber: 5.7 Consensus size: 22
3676 ACACCCTAAT
* *
3686 GAGAGGAGAATGC-CCCCAAAG
1 GAGAGAAGAATGCTCACCAAAG
3707 GAGAGAA-ATATGCTCACCAAA-
1 GAGAGAAGA-ATGCTCACCAAAG
*
3728 GATAGAAGAATGCTCTA-CAAAG
1 GAGAGAAGAATGCTC-ACCAAAG
* *
3750 GATAGGAGAA-GACTTC-CCAAA-
1 GAGAGAAGAATG-C-TCACCAAAG
*
3771 GAGAG-A-AATGCTCTCCAAA-
1 GAGAGAAGAATGCTCACCAAAG
* *
3790 GAAAGAAAAATGCTC
1 GAGAGAAGAATGCTC
3805 CTTATGAAGA
Statistics
Matches: 80, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
18 2 0.03
19 12 0.15
20 4 0.05
21 38 0.47
22 22 0.28
23 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (22 bp):
GAGAGAAGAATGCTCACCAAAG
Found at i:3759 original size:22 final size:21
Alignment explanation
Indices: 3716--3804 Score: 62
Period size: 21 Copynumber: 4.3 Consensus size: 21
3706 GGAGAGAAAT
3716 ATGCTCACCAAAGATAGAAGA
1 ATGCTCACCAAAGATAGAAGA
*
3737 ATGCTCTA-CAAAGGATAGGAGA
1 ATGCTC-ACCAAA-GATAGAAGA
*
3759 A-GACTTC-CCAAAGAGAG-A-A
1 ATG-C-TCACCAAAGATAGAAGA
* * *
3778 ATGCTCTCCAAAGAAAGAAAA
1 ATGCTCACCAAAGATAGAAGA
3799 ATGCTC
1 ATGCTC
3805 CTTATGAAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
18 2 0.04
19 12 0.21
20 3 0.05
21 22 0.39
22 15 0.27
23 2 0.04
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (21 bp):
ATGCTCACCAAAGATAGAAGA
Found at i:3880 original size:88 final size:88
Alignment explanation
Indices: 3770--3998 Score: 320
Period size: 88 Copynumber: 2.6 Consensus size: 88
3760 GACTTCCCAA
3770 AGAGAGAAATGCTCTCCAAAGAAAGAAAAATGCTCCTTATGAAGAGGATAATGCACTACAATGAA
1 AGAGAGAAATGCTCTCCAAAGAAAGAAAAATGCTCCTTATGAAGAGGATAATGCACTACAATGAA
3835 AGGAGAATACTCACTCCAGAAGG
66 AGGAGAATACTCACTCCAGAAGG
* * * *
3858 AGAGAGAAATGCTCTACAAAGAAAGAAAAATGCTCCCTT-TGAATATGATAATGCACTCCAATGA
1 AGAGAGAAATGCTCTCCAAAGAAAGAAAAATGCT-CCTTATGAAGAGGATAATGCACTACAATGA
**
3922 AAGGAGAATACTCACTCCCTAAGG
65 AAGGAGAATACTCACTCCAGAAGG
* * * * *
3946 AGAGA-ATAATGCTTTCCAAAGAATGAAGAATGCTCCCTACG-AGAGGATAATGC
1 AGAGAGA-AATGCTCTCCAAAGAAAGAAAAATGCTCCTTATGAAGAGGATAATGC
3999 CCCCCGAGGA
Statistics
Matches: 124, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
87 14 0.11
88 106 0.85
89 4 0.03
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (88 bp):
AGAGAGAAATGCTCTCCAAAGAAAGAAAAATGCTCCTTATGAAGAGGATAATGCACTACAATGAA
AGGAGAATACTCACTCCAGAAGG
Found at i:3955 original size:46 final size:46
Alignment explanation
Indices: 3812--3957 Score: 124
Period size: 46 Copynumber: 3.3 Consensus size: 46
3802 CTCCTTATGA
* **
3812 AGAGGATAATGCACTACAATGAAAGGAGAATACTCACTCCAGAAGG
1 AGAGAATAATGCACTACAATGAAAGGAGAATACTCACTCCCTAAGG
* * * * ** *
3858 AGAGAGA-AATGCTCTACAAAGAAA-GA-AA-AAT-GCTCCCTTTGA
1 AGAGA-ATAATGCACTACAATGAAAGGAGAATACTCACTCCCTAAGG
* *
3900 ATATG-ATAATGCACTCCAATGAAAGGAGAATACTCACTCCCTAAGG
1 AGA-GAATAATGCACTACAATGAAAGGAGAATACTCACTCCCTAAGG
3946 AGAGAATAATGC
1 AGAGAATAATGC
3958 TTTCCAAAGA
Statistics
Matches: 72, Mismatches: 20, Indels: 16
0.67 0.19 0.15
Matches are distributed among these distances:
41 1 0.01
42 21 0.29
43 5 0.07
44 4 0.06
45 5 0.07
46 35 0.49
47 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (46 bp):
AGAGAATAATGCACTACAATGAAAGGAGAATACTCACTCCCTAAGG
Found at i:3967 original size:238 final size:233
Alignment explanation
Indices: 3457--3980 Score: 581
Period size: 237 Copynumber: 2.2 Consensus size: 233
3447 ACCTGAGGCA
* **
3457 AATGCCCCTCAAAGGAGA-AGAA-ATGTTCTCCAAAGATAGAAGAACACT-TCACAAAGGAGAGG
1 AATGCCCC-CAAAGGAGAGA-AATATGCTCTCCAAAGATAGAAGAATGCTCTCACAAAGGAGAGG
*
3519 AGAAAGCTCCCAAAGGAGAGGAATGCTCTCCAAAGAAAAAAGAATGCTCCCTATGAGAGGATAAT
64 AGAAAGCTCCCAAAGGAGAGAAATGCTCTCCAAAGAAAAAAGAATGCTCCCTATGAGAGGATAAT
* *
3584 GCACTCCAATAAAAGGAGAATACTCCCCAAGGAGAGAAGAATGCTCCCCAAAGAAAGAAAAATGC
129 GCACTACAATAAAAGGAGAATACTCCCCAAGGAGAGAAGAATGCTCCACAAAGAAAGAAAAATGC
*
3649 TCTCCAAAGATAGGAGAATATGATAATACACCCTAATGAGAGGAG
194 TCTCC----ATA-GAGAATATGATAATACACCCTAATGAAAGGAG
* *
3694 AATGCCCCCAAAGGAGAGAAATATGCTCACCAAAGATAGAAGAATGCTCT-ACAAAGGATAGGAG
1 AATGCCCCCAAAGGAGAGAAATATGCTCTCCAAAGATAGAAGAATGCTCTCACAAAGGAGAGGAG
*
3758 -AAGACTTCCCAAA-GAGAGAAATGCTCTCCAAAGAAAGAAA-AATGCTCCTTATGAAGAGGATA
66 AAAG-C-TCCCAAAGGAGAGAAATGCTCTCCAAAGAAA-AAAGAATGCTCCCTATG-AGAGGATA
* *
3820 ATGCACTACAATGAAAGGAGAATACTCACTCCAGAAGGAGAG-AGAAATGCTCTACAAAGAAAGA
127 ATGCACTACAATAAAAGGAGAATACTC-C-CC--AAGGAGAGAAG-AATGCTCCACAAAGAAAGA
** *
3884 AAAATGCTC-CC-T-TTGAATATGATAATGCACTCC-AATGAAAGGAG
187 AAAATGCTCTCCATAGAGAATATGATAATACAC-CCTAATGAAAGGAG
* * *
3928 AATACTCACTCCCTAAGGAGAG-AATAATGCTTTCCAAAGA-ATGAAGAATGCTC
1 AAT--GC-C-CCCAAAGGAGAGAAAT-ATGCTCTCCAAAGATA-GAAGAATGCTC
3981 CCTACGAGAG
Statistics
Matches: 249, Mismatches: 19, Indels: 37
0.82 0.06 0.12
Matches are distributed among these distances:
234 28 0.11
235 2 0.01
236 16 0.06
237 84 0.34
238 78 0.31
239 1 0.00
240 2 0.01
241 4 0.02
242 34 0.14
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.17
Consensus pattern (233 bp):
AATGCCCCCAAAGGAGAGAAATATGCTCTCCAAAGATAGAAGAATGCTCTCACAAAGGAGAGGAG
AAAGCTCCCAAAGGAGAGAAATGCTCTCCAAAGAAAAAAGAATGCTCCCTATGAGAGGATAATGC
ACTACAATAAAAGGAGAATACTCCCCAAGGAGAGAAGAATGCTCCACAAAGAAAGAAAAATGCTC
TCCATAGAGAATATGATAATACACCCTAATGAAAGGAG
Found at i:4141 original size:98 final size:97
Alignment explanation
Indices: 4028--4497 Score: 591
Period size: 98 Copynumber: 4.8 Consensus size: 97
4018 ACTCGCCGAG
**
4028 CGCCAAACACGAAGCGTGGAACGCTCGTCGAGCGCCAAATGGAGAATGCTCCTCGAGAGCAAGTG
1 CGCCAAATGCGAAGCG-GGAACGCTCGTCGAGCGCCAAATGGAGAATGCTCCTCGAGAGCAAGTG
* *
4093 AAGAAAGCCCGAGATGGCGATAAAGATGACGCT
65 AAGAATGCCCGAGATGGCGAAAAAGATGACGCT
* * * * * *
4126 CACCAAATGCGAAGCGGAGGACGCTCATCGAGCGCCAAATGGAGAATACTCCTTGAGAGCAAATG
1 CGCCAAATGCGAAGCGG-GAACGCTCGTCGAGCGCCAAATGGAGAATGCTCCTCGAGAGCAAGTG
4191 AAGAATGCCCGAGATGGCGAAAAAGATGACGCT
65 AAGAATGCCCGAGATGGCGAAAAAGATGACGCT
* * * * *
4224 CGCCAAACGCAAAACGGAGGACGCTCGTCGAGCGCCGAATGGAGAATGCTCCTCGAGAGCAAGTG
1 CGCCAAATGCGAAGCGG-GAACGCTCGTCGAGCGCCAAATGGAGAATGCTCCTCGAGAGCAAGTG
*
4289 AAGAATGCCCGAGATGGCGAAAAGGATGACGCT
65 AAGAATGCCCGAGATGGCGAAAAAGATGACGCT
** * * * *
4322 CGCCAAATGCGAAATGGAGGACGCTGGTCGAGCGCCAAATGGAGAATGCTCCTTGAGAGAGCAAA
1 CGCCAAATGCGAAGCGG-GAACGCTCGTCGAGCGCCAAATGGAGAATGCTCC-T-CGAGAGCAAG
* *
4387 TGAAGAATGCCCAAGATGGCGAAAAATATGACGCT
63 TGAAGAATGCCCGAGATGGCGAAAAAGATGACGCT
* * *
4422 CGCCAAATGCGAAGCGAAGG-ACGCTCATCGAGCGCCAAAATGGAGAATGATCCTCGAGCGCAAG
1 CGCCAAATGCGAAGCG--GGAACGCTCGTCGAGCGCC-AAATGGAGAATGCTCCTCGAGAGCAAG
* *
4486 TAAAGAAAGCCC
63 TGAAGAATGCCC
4498 AAGGGCGCTT
Statistics
Matches: 326, Mismatches: 40, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
97 1 0.00
98 221 0.68
99 18 0.06
100 69 0.21
101 16 0.05
102 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.30, T:0.13
Consensus pattern (97 bp):
CGCCAAATGCGAAGCGGGAACGCTCGTCGAGCGCCAAATGGAGAATGCTCCTCGAGAGCAAGTGA
AGAATGCCCGAGATGGCGAAAAAGATGACGCT
Found at i:4362 original size:196 final size:197
Alignment explanation
Indices: 4048--4497 Score: 697
Period size: 196 Copynumber: 2.3 Consensus size: 197
4038 GAAGCGTGGA
4048 ACGCTCGTCGAGCGCCAAATGGAGAATGCTCCTCGAGAGCAAGTGAAGAAAGCCCGAGATGGCGA
1 ACGCTCGTCGAGCGCCAAATGGAGAATGCTCCTCGAGAGCAAGTGAAGAAAGCCCGAGATGGCGA
*
4113 TAAAGATGACGCTCACCAAATGCGAAGCGGAGGACGCTCATCGAGCGCCAAATGGAGAATACTCC
66 TAAAGATGACGCTCACCAAATGCGAAACGGAGGACGCTCATCGAGCGCCAAATGGAGAATACTCC
* *
4178 TT-GAGAGCAAATGAAGAATGCCCGAGATGGCGAAAAAGATGACGCTCGCCAAACGCAAAACGGA
131 TTAGAGAGCAAATGAAGAATGCCCAAGATGGCGAAAAAGATGACGCTCGCCAAACGCAAAACGAA
4242 GG
196 GG
* *
4244 ACGCTCGTCGAGCGCCGAATGGAGAATGCTCCTCGAGAGCAAGTGAAGAATGCCCGAGATGGCGA
1 ACGCTCGTCGAGCGCCAAATGGAGAATGCTCCTCGAGAGCAAGTGAAGAAAGCCCGAGATGGCGA
* * ** *
4309 -AAAGGATGACGCTCGCCAAATGCGAAATGGAGGACGCTGGTCGAGCGCCAAATGGAGAATGCTC
66 TAAA-GATGACGCTCACCAAATGCGAAACGGAGGACGCTCATCGAGCGCCAAATGGAGAATACTC
* * * *
4373 CTTGAGAGAGCAAATGAAGAATGCCCAAGATGGCGAAAAATATGACGCTCGCCAAATGCGAAGCG
130 CTT-AGAGAGCAAATGAAGAATGCCCAAGATGGCGAAAAAGATGACGCTCGCCAAACGCAAAACG
4438 AAGG
194 AAGG
* * * *
4442 ACGCTCATCGAGCGCCAAAATGGAGAATGATCCTCGAGCGCAAGTAAAGAAAGCCC
1 ACGCTCGTCGAGCGCC-AAATGGAGAATGCTCCTCGAGAGCAAGTGAAGAAAGCCC
4498 AAGGGCGCTT
Statistics
Matches: 230, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
195 3 0.01
196 120 0.52
198 73 0.32
199 34 0.15
ACGTcount: A:0.34, C:0.23, G:0.30, T:0.13
Consensus pattern (197 bp):
ACGCTCGTCGAGCGCCAAATGGAGAATGCTCCTCGAGAGCAAGTGAAGAAAGCCCGAGATGGCGA
TAAAGATGACGCTCACCAAATGCGAAACGGAGGACGCTCATCGAGCGCCAAATGGAGAATACTCC
TTAGAGAGCAAATGAAGAATGCCCAAGATGGCGAAAAAGATGACGCTCGCCAAACGCAAAACGAA
GG
Found at i:4546 original size:24 final size:24
Alignment explanation
Indices: 4513--4558 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4503 CGCTTAACGG
4513 AGAACGCTCGCTCAA-TGCGAAGCT
1 AGAACGCTCGC-CAAGTGCGAAGCT
*
4537 AGAACTCTCGCCAAGTGCGAAG
1 AGAACGCTCGCCAAGTGCGAAG
4559 AACACCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (24 bp):
AGAACGCTCGCCAAGTGCGAAGCT
Found at i:5082 original size:96 final size:96
Alignment explanation
Indices: 4972--5241 Score: 427
Period size: 95 Copynumber: 2.8 Consensus size: 96
4962 CTTTTACAAG
*
4972 TTCCAAAAAGAAGGGTCGAATGCCCAAAACTGATGATACATCAACAAAAGAAGAAAAAGCCAAGG
1 TTCCAAAAAGAAGGGTCGAATGCCCAAAACTGATGATACATCAACAAAAGAAGAAAAAGCTAAGG
* * *
5037 ACCCTTAGGAGCATCTTGGCTACTTTGCTGC
66 ACCCTAAGGAGCATCCTGGCTACTTTGCTCC
* * *
5068 TTCCAAAAAAAAGGGTCGAAT-ACCAGAACTGATGATACATCAACAAAAGAAGAAAAAGCTAAGG
1 TTCCAAAAAGAAGGGTCGAATGCCCAAAACTGATGATACATCAACAAAAGAAGAAAAAGCTAAGG
* *
5132 ACCCTAAGGAACATCCTGGCTACTTTGTTCC
66 ACCCTAAGGAGCATCCTGGCTACTTTGCTCC
*
5163 TTCCAAAAAGAAGGGTCGAATGCCTAGAAA-TGATGATACATCAACAAAAGAAGAAAAAGCTAAG
1 TTCCAAAAAGAAGGGTCGAATGCCCA-AAACTGATGATACATCAACAAAAGAAGAAAAAGCTAAG
5227 GACCCTAAGGAGCAT
65 GACCCTAAGGAGCAT
5242 TGATCGAGTC
Statistics
Matches: 158, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
95 86 0.54
96 70 0.44
97 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (96 bp):
TTCCAAAAAGAAGGGTCGAATGCCCAAAACTGATGATACATCAACAAAAGAAGAAAAAGCTAAGG
ACCCTAAGGAGCATCCTGGCTACTTTGCTCC
Found at i:10246 original size:45 final size:44
Alignment explanation
Indices: 10180--10303 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 44
10170 GGTTGCAATA
*
10180 TGGCGTGCGACAAGCAAAACAAATCAAAGACTCTCAGACAAAATG
1 TGGCGTGCGACAAG-AAAACAAATCAAAGACTCTCAGACAAAACG
* * * * * *
10225 TGGCGTGCGACATGAACAACAAATCGAAGACCCTCGGTCAACACG
1 TGGCGTGCGACAAGAA-AACAAATCAAAGACTCTCAGACAAAACG
* *
10270 TGGCGTGCGACAAGAATGACAAATCAAAAACTCT
1 TGGCGTGCGACAAGAA-AACAAATCAAAGACTCT
10304 TATCACCAGC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 2 0.03
45 63 0.97
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (44 bp):
TGGCGTGCGACAAGAAAACAAATCAAAGACTCTCAGACAAAACG
Found at i:11212 original size:37 final size:37
Alignment explanation
Indices: 11171--11241 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
11161 TTGCTTGGCG
*
11171 CTCGACAAGTTGACAAAATGTGTCGACCGCCACATCA
1 CTCGACAAGCTGACAAAATGTGTCGACCGCCACATCA
*
11208 CTCGACAAGCTGACAAAATGTGTTGACCGCCACA
1 CTCGACAAGCTGACAAAATGTGTCGACCGCCACA
11242 GGCCACCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (37 bp):
CTCGACAAGCTGACAAAATGTGTCGACCGCCACATCA
Found at i:11362 original size:26 final size:26
Alignment explanation
Indices: 11326--11376 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
11316 GCCAGTTGGC
*
11326 ACTCTACACGTGACCTCCAACGTACG
1 ACTCCACACGTGACCTCCAACGTACG
11352 ACTCCACACGTGACCTCCAACGTAC
1 ACTCCACACGTGACCTCCAACGTAC
11377 AACCCGTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.41, G:0.14, T:0.18
Consensus pattern (26 bp):
ACTCCACACGTGACCTCCAACGTACG
Found at i:11369 original size:13 final size:12
Alignment explanation
Indices: 11333--11374 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
11323 GGCACTCTAC
11333 ACGTGACCTCCA
1 ACGTGACCTCCA
11345 ACGT-ACGACTCCA
1 ACGTGAC--CTCCA
11358 CACGTGACCTCCA
1 -ACGTGACCTCCA
11371 ACGT
1 ACGT
11375 ACAACCCGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 2 0.08
12 8 0.31
13 10 0.38
14 4 0.15
15 2 0.08
ACGTcount: A:0.26, C:0.40, G:0.17, T:0.17
Consensus pattern (12 bp):
ACGTGACCTCCA
Found at i:11989 original size:2 final size:2
Alignment explanation
Indices: 11984--12009 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11974 ACAAAAAAAA
11984 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
12010 TTATTATTAT
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:13660 original size:17 final size:16
Alignment explanation
Indices: 13624--13664 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
13614 TGGGTTCGGG
**
13624 TTTTTTCGGGTTTTGA
1 TTTTTTCGGGTTTAAA
13640 TTTTTTCGGGTTTAAA
1 TTTTTTCGGGTTTAAA
*
13656 CTTTTTCGG
1 TTTTTTCGG
13665 ATTCGGGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.10, G:0.22, T:0.59
Consensus pattern (16 bp):
TTTTTTCGGGTTTAAA
Found at i:13755 original size:13 final size:15
Alignment explanation
Indices: 13730--13770 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
13720 CAGGTCGGGT
13730 TCGGGTTCGGGTTTT-
1 TCGGG-TCGGGTTTTC
13745 TCGGG-CGGGTTTTC
1 TCGGGTCGGGTTTTC
13759 TCGGGTCGGGTT
1 TCGGGTCGGGTT
13771 CATTTTGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.00, C:0.17, G:0.44, T:0.39
Consensus pattern (15 bp):
TCGGGTCGGGTTTTC
Found at i:15543 original size:31 final size:31
Alignment explanation
Indices: 15505--15672 Score: 104
Period size: 31 Copynumber: 5.5 Consensus size: 31
15495 GTAGGCTAAT
15505 TACTCAAATAAGGGTCTAACGTTTGCCAAAA
1 TACTCAAATAAGGGTCTAACGTTTGCCAAAA
* * * * * **
15536 TACTCAAATAAAGATCCGATC-TTT--TAATT
1 TACTCAAATAAGGGT-CTAACGTTTGCCAAAA
15565 TGAC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 T-ACTCAAATAAGGGTCTAACGTTTGCCAAAA
* *
15596 TGCTCAAATAAGGG-CCACATC-TTTG----AA
1 TACTCAAATAAGGGTCTA-A-CGTTTGCCAAAA
* * *
15623 TTCGGCCAAATAAGGGCCTAACGTTTGCCAAAA
1 TAC--TCAAATAAGGGTCTAACGTTTGCCAAAA
15656 TACTCAAATAAGGGTCT
1 TACTCAAATAAGGGTCT
15673 GTCTCGCGCA
Statistics
Matches: 99, Mismatches: 22, Indels: 32
0.65 0.14 0.21
Matches are distributed among these distances:
27 4 0.04
28 4 0.04
29 30 0.30
30 7 0.07
31 46 0.46
32 4 0.04
33 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (31 bp):
TACTCAAATAAGGGTCTAACGTTTGCCAAAA
Found at i:15667 original size:60 final size:59
Alignment explanation
Indices: 15509--15669 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 59
15499 GCTAATTACT
** * * *
15509 CAAATAAGGGTCTAACGTTTGCCAAAATACTCAAATAAAGATCCGATCTTTTAATTTGAC
1 CAAATAAGGGTCTAACGTTTGCCAAAATACTCAAAT-AAGGGCCCATCTTTGAATTCGAC
* *
15569 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCCACATCTTTGAATTCGGC
1 CAAATAAGGGTCTAACGTTTGCCAAAATACTCAAATAAGGGCC-CATCTTTGAATTCGAC
*
15629 CAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGGG
1 CAAATAAGGGTCTAACGTTTGCCAAAATACTCAAATAAGGG
15670 TCTGTCTCGC
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 5 0.05
60 86 0.95
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (59 bp):
CAAATAAGGGTCTAACGTTTGCCAAAATACTCAAATAAGGGCCCATCTTTGAATTCGAC
Found at i:15738 original size:31 final size:30
Alignment explanation
Indices: 15700--15838 Score: 140
Period size: 31 Copynumber: 4.6 Consensus size: 30
15690 AACTGACACC
15700 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTT-GATAACGTT
*
15731 AGGCCCTTATTTGAGCATTTTCGATAACATT
1 AGGCCCTTATTTGAGCATTTT-GATAACGTT
** * *
15762 AGGCCCTTATTTG-GCCAAATT-A-AAAGATC
1 AGGCCCTTATTTGAG-CATTTTGATAACG-TT
* * *
15791 GGGCCCTTATTTGAGCATTTTGACAAATGTT
1 AGGCCCTTATTTGAGCATTTTGA-TAACGTT
15822 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
15839 ATTAGCCTAA
Statistics
Matches: 90, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
28 2 0.02
29 18 0.20
30 3 0.03
31 64 0.71
32 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGATAACGTT
Found at i:18916 original size:30 final size:29
Alignment explanation
Indices: 18849--18920 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
18839 ACACCGAACC
****
18849 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
18878 GCCAAATAAGCCCCTGAACTCTTAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
18907 TGTCAAATAAGCCC
1 -GTCAAATAAGCCC
18921 TGTTGACAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:19418 original size:22 final size:22
Alignment explanation
Indices: 19393--19439 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
19383 TGTACCTGAA
19393 ATATAGTAAAGTATATTGACAC
1 ATATAGTAAAGTATATTGACAC
*
19415 ATATGGTAAAGTATATTGACAC
1 ATATAGTAAAGTATATTGACAC
19437 ATA
1 ATA
19440 CAAATATTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (22 bp):
ATATAGTAAAGTATATTGACAC
Found at i:23561 original size:28 final size:28
Alignment explanation
Indices: 23513--23585 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
23503 CCAGGACATC
*
23513 TCCCTCTGGTATG-ATCAGGCGGAAATTCT
1 TCCCTCT-G-ATGTATCAGGCGGAAAATCT
*
23542 TCCCTTTGATGTATCAGGCGGAAAATCT
1 TCCCTCTGATGTATCAGGCGGAAAATCT
23570 TCCCTCTGATGTATCA
1 TCCCTCTGATGTATCA
23586 CATGGCATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 3 0.08
28 31 0.77
29 6 0.15
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.33
Consensus pattern (28 bp):
TCCCTCTGATGTATCAGGCGGAAAATCT
Found at i:28227 original size:23 final size:23
Alignment explanation
Indices: 28201--28246 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28191 GTACTTCGAT
28201 TTTTTGTTTATATTATTTAGATA
1 TTTTTGTTTATATTATTTAGATA
28224 TTTTTGTTTATATTATTTAGATA
1 TTTTTGTTTATATTATTTAGATA
28247 CTAGAACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (23 bp):
TTTTTGTTTATATTATTTAGATA
Found at i:30935 original size:2 final size:2
Alignment explanation
Indices: 30928--30952 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30918 GTATAAATTT
30928 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 T
30953 GTGAAATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35016 original size:42 final size:42
Alignment explanation
Indices: 34964--35055 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
34954 CTTCTTAGTA
* * ** *
34964 AACCCTAGCTCTAGTTTGGCTATAAATATTTTGTATTCTCAT
1 AACCTTAGCTCTAGTTTGCCTATAAATACGTTGTACTCTCAT
*
35006 TACCTTAGCTCTAGTTTGCCTATAAATACGTTGTACTCTCAT
1 AACCTTAGCTCTAGTTTGCCTATAAATACGTTGTACTCTCAT
35048 AACCTTAG
1 AACCTTAG
35056 TCATCCTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (42 bp):
AACCTTAGCTCTAGTTTGCCTATAAATACGTTGTACTCTCAT
Done.