Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016077.1 Corchorus olitorius cultivar O-4 contig16110, 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: 71959
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:480 original size:29 final size:29
Alignment explanation
Indices: 425--483 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
415 AGATTTTAAT
***
425 AAAACTTTGATTCTCTTTGTGTAAAAAAA
1 AAAACTTTGATTCTCTACATGTAAAAAAA
454 AAAACTTTGATTCTCTACATAGTAAAAAAA
1 AAAACTTTGATTCTCTACAT-GTAAAAAAA
484 GAAAGTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAACTTTGATTCTCTACATGTAAAAAAA
Found at i:5133 original size:28 final size:28
Alignment explanation
Indices: 5093--5146 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
5083 ACTTGGTGTC
5093 AACTGTCACGAAACCAAAAAAAAAAAAA
1 AACTGTCACGAAACCAAAAAAAAAAAAA
* * **
5121 AACTGTGATGAAACGGAAAAAAAAAA
1 AACTGTCACGAAACCAAAAAAAAAAA
5147 GTGGTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.65, C:0.13, G:0.13, T:0.09
Consensus pattern (28 bp):
AACTGTCACGAAACCAAAAAAAAAAAAA
Found at i:5943 original size:5 final size:5
Alignment explanation
Indices: 5927--5960 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
5917 TAGTAGTAAG
5927 ATATA TATATA ATATA ATATA ATATA ATATA ATA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATA
5961 GTAAGATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:9955 original size:37 final size:37
Alignment explanation
Indices: 9914--9987 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
9904 ACACCATTAG
* ** *
9914 ATCTAAGCCTAAAGAAAGACTTTTTATCCCCAAACTT
1 ATCTAAGCCTAAACAAAGACTTTGAATCACCAAACTT
*
9951 ATCTAAGCCTAAACAGAGACTTTGAATCACCAAACTT
1 ATCTAAGCCTAAACAAAGACTTTGAATCACCAAACTT
9988 TCTCTTTCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.27
Consensus pattern (37 bp):
ATCTAAGCCTAAACAAAGACTTTGAATCACCAAACTT
Found at i:12965 original size:37 final size:37
Alignment explanation
Indices: 12912--13065 Score: 123
Period size: 37 Copynumber: 4.1 Consensus size: 37
12902 TTTGTGATAG
* * * *
12912 CCCTCTTCATCACAGAGTTCCCCTTACCGTAGTAGCA
1 CCCTCTTCACCGCAGAGCTCCCCTTACCGCAGTAGCA
* * *
12949 CCCTCTTCACCGCAGAGCTCCCTTTATCGCGGTAGCA
1 CCCTCTTCACCGCAGAGCTCCCCTTACCGCAGTAGCA
* * * * * *
12986 CCCTCTTTACCGTAGAACTCTCCTTACTGC-G-ATGACT
1 CCCTCTTCACCGCAGAGCTCCCCTTACCGCAGTA-G-CA
* * *
13023 CCCATCTTCACCGCAGAGCTCTCCTTACTGCGGTAGCA
1 CCC-TCTTCACCGCAGAGCTCCCCTTACCGCAGTAGCA
13061 CCCTC
1 CCCTC
13066 CTTACTGCGG
Statistics
Matches: 93, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
35 1 0.01
36 2 0.02
37 59 0.63
38 28 0.30
39 2 0.02
40 1 0.01
ACGTcount: A:0.18, C:0.40, G:0.16, T:0.27
Consensus pattern (37 bp):
CCCTCTTCACCGCAGAGCTCCCCTTACCGCAGTAGCA
Found at i:13054 original size:38 final size:37
Alignment explanation
Indices: 12944--13065 Score: 133
Period size: 37 Copynumber: 3.3 Consensus size: 37
12934 CTTACCGTAG
*
12944 TAGCACCCTCTTCACCGCAGAGCTC-CCTTTA-TCGCGG
1 TAGCACCCTCTTCACCGCAGAGCTCTCC-TTACT-GCGA
* * *
12981 TAGCACCCTCTTTACCGTAGAACTCTCCTTACTGCGA
1 TAGCACCCTCTTCACCGCAGAGCTCTCCTTACTGCGA
* *
13018 T-GACTCCCATCTTCACCGCAGAGCTCTCCTTACTGCGG
1 TAG-CACCC-TCTTCACCGCAGAGCTCTCCTTACTGCGA
13056 TAGCACCCTC
1 TAGCACCCTC
13066 CTTACTGCGG
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
36 1 0.01
37 35 0.50
38 33 0.47
39 1 0.01
ACGTcount: A:0.18, C:0.39, G:0.16, T:0.26
Consensus pattern (37 bp):
TAGCACCCTCTTCACCGCAGAGCTCTCCTTACTGCGA
Found at i:13068 original size:20 final size:20
Alignment explanation
Indices: 13043--13093 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
13033 CCGCAGAGCT
13043 CTCCTTACTGCGGTAGCACC
1 CTCCTTACTGCGGTAGCACC
13063 CTCCTTACTGCGGTAGCACC
1 CTCCTTACTGCGGTAGCACC
*
13083 CTCTTTACTGC
1 CTCCTTACTGC
13094 AGAGCTCTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.14, C:0.39, G:0.18, T:0.29
Consensus pattern (20 bp):
CTCCTTACTGCGGTAGCACC
Found at i:15609 original size:6 final size:6
Alignment explanation
Indices: 15600--15625 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
15590 ATTTCTTTAC
15600 TTTCAA TTTCAA TTTCAA TTTCAA TT
1 TTTCAA TTTCAA TTTCAA TTTCAA TT
15626 GTGTTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTCAA
Found at i:20708 original size:29 final size:30
Alignment explanation
Indices: 20676--20735 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
20666 AATTGTTAAT
*
20676 TTGAATTGCTA-TATTTTGCTA-TTGATTGA
1 TTGAATTGCAATTA-TTTGCTAGTTGATTGA
*
20705 TTGAATTGCAATTATTTGTTAGTTGATTGA
1 TTGAATTGCAATTATTTGCTAGTTGATTGA
20735 T
1 T
20736 AGATTGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (30 bp):
TTGAATTGCAATTATTTGCTAGTTGATTGA
Found at i:26941 original size:41 final size:40
Alignment explanation
Indices: 26884--27075 Score: 224
Period size: 41 Copynumber: 4.7 Consensus size: 40
26874 AATAATATTG
**
26884 AAAATTACCTTTGACACCAGAAGTTGTTGCTTTGGTAAATT
1 AAAATTA-CTTTGACACCAGAAGTTGTCACTTTGGTAAATT
* * *
26925 AAAATTACTGTTGACACTAGAAGTTGTCGCCTTGGTAAATT
1 AAAATTACT-TTGACACCAGAAGTTGTCACTTTGGTAAATT
*
26966 AAAATTACATTTGACACCAGAAGTTGTCATTTTGGTAAATT
1 AAAATTAC-TTTGACACCAGAAGTTGTCACTTTGGTAAATT
* ***
27007 AAAATTACCTTTGACACCAGAAG-TGTTACTCCAGTAAATT
1 AAAATTA-CTTTGACACCAGAAGTTGTCACTTTGGTAAATT
* *
27047 ATAATTACTGTTGACACCAGAAATTGTCA
1 AAAATTACT-TTGACACCAGAAGTTGTCA
27076 TCTTGAATTA
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.24
41 95 0.73
42 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (40 bp):
AAAATTACTTTGACACCAGAAGTTGTCACTTTGGTAAATT
Found at i:30651 original size:13 final size:14
Alignment explanation
Indices: 30629--30657 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
30619 ACCTTAGACC
30629 TTTTATTCCTTTTT
1 TTTTATTCCTTTTT
30643 TTTTA-TCCTTTTT
1 TTTTATTCCTTTTT
30656 TT
1 TT
30658 CAAGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTCCTTTTT
Found at i:32476 original size:160 final size:160
Alignment explanation
Indices: 32169--32477 Score: 464
Period size: 159 Copynumber: 1.9 Consensus size: 160
32159 CGAAGACGCT
* * *
32169 GCCATATTAATATATGGAGGGAGAGATTTTTTTTTCTCTTTTTTTTGGAGGGAAAAATTTCGTCC
1 GCCATATTAATATATGGAGGGAGAGATATTTTTTTCCCTTTTTTTTGGAGGGAAAAATTTCCTCC
32234 CCACTAAAACAAAGAAAGTTTCCAACTCCACACCTATAATATATAGCGGCGTTTTAACATTAGAC
66 CCACTAAAACAAAGAAAGTTTCCAACTCCACACCTATAATATATAGCGGCGTTTTAACATTAGAC
32299 GCCGCTAATTAGCGGCGTTCTTTCCCAGAC
131 GCCGCTAATTAGCGGCGTTCTTTCCCAGAC
*
32329 GCCATTTTAATATATGGA-GGA-AGATATTTTTTTCCCTTTTTTTTGGAGGGAAAAATTCTCCCT
1 GCCATATTAATATATGGAGGGAGAGATATTTTTTTCCCTTTTTTTTGGAGGGAAAAATT-T-CCT
* * * ** *
32392 CCCC-CTAAAACAAAGAAATTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTCCTTTCCTT
64 CCCCACTAAAACAAAGAAAGTTTCCAACTCCACACCTATAATATATAGCGGCGTTT--TAACATT
32456 -GACGCCGCTAATTAGCGGCGTT
127 AGACGCCGCTAATTAGCGGCGTT
32478 TGGGAAAGGA
Statistics
Matches: 135, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
158 34 0.25
159 52 0.39
160 45 0.33
161 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (160 bp):
GCCATATTAATATATGGAGGGAGAGATATTTTTTTCCCTTTTTTTTGGAGGGAAAAATTTCCTCC
CCACTAAAACAAAGAAAGTTTCCAACTCCACACCTATAATATATAGCGGCGTTTTAACATTAGAC
GCCGCTAATTAGCGGCGTTCTTTCCCAGAC
Found at i:37480 original size:32 final size:32
Alignment explanation
Indices: 37407--37503 Score: 122
Period size: 32 Copynumber: 3.0 Consensus size: 32
37397 AATTGCTGGA
* *
37407 AAATAGCGGCGTCTATTGAAGAAAACGCCCCT
1 AAATAGCGGCGTCTATTGAAGCAAACGCCGCT
**
37439 ATTTAGCGGCGTCTATTGAAGCAAACGCCGCT
1 AAATAGCGGCGTCTATTGAAGCAAACGCCGCT
* * * *
37471 AAATGGCGGCGTTTATTAAACCAAACGCCGCT
1 AAATAGCGGCGTCTATTGAAGCAAACGCCGCT
37503 A
1 A
37504 TATATAATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (32 bp):
AAATAGCGGCGTCTATTGAAGCAAACGCCGCT
Found at i:43189 original size:21 final size:21
Alignment explanation
Indices: 43165--43209 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
43155 GGCGCCCACA
* *
43165 TGGTTGCCTTGAGCACCCATG
1 TGGTTGCCTTGAGAACCCAGG
**
43186 TGGTTTTCTTGAGAACCCAGG
1 TGGTTGCCTTGAGAACCCAGG
43207 TGG
1 TGG
43210 GCAGTGTCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TGGTTGCCTTGAGAACCCAGG
Found at i:43280 original size:76 final size:76
Alignment explanation
Indices: 43143--43293 Score: 173
Period size: 76 Copynumber: 2.0 Consensus size: 76
43133 ACAAGGACCC
* * *
43143 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTTCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
43208 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
43219 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
43281 GATGGGCTGTGTC
63 GATGGGCAGTGTC
43294 TTAGCTCATC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
75 4 0.06
76 53 0.84
77 6 0.10
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:48964 original size:34 final size:34
Alignment explanation
Indices: 48922--48985 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
48912 CAGAAAACTT
*
48922 TTTTTTTTTTCAAAAACGCAGA-ACACAAAACAG
1 TTTTTTTTTTCAAAAACGCAAAGACACAAAACAG
48955 TTTTTTTTTTCAAAAACGCAAAGACACAAAA
1 TTTTTTTTTTCAAAAACGCAAAGACACAAAA
48986 ATTAAAAACG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (34 bp):
TTTTTTTTTTCAAAAACGCAAAGACACAAAACAG
Found at i:50100 original size:18 final size:18
Alignment explanation
Indices: 50063--50100 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
50053 CTAGCCCTAA
*
50063 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAACAAG
50081 AACTAGAAGAGAAAA-AAG
1 AACTAGAAGA-AAAACAAG
50099 AA
1 AA
50101 GAAGAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.66, C:0.08, G:0.18, T:0.08
Consensus pattern (18 bp):
AACTAGAAGAAAAACAAG
Found at i:51412 original size:27 final size:27
Alignment explanation
Indices: 51374--51447 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
51364 GACTGTTGCC
51374 GCAGTGGATCCTCCCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
* *
51401 GCAGTGGATCCTCACACTTCGACCCTA
1 GCAGTGGATCCTCCCACTTCGACCCCA
51428 GCAGTGGATCCTCCCACTTC
1 GCAGTGGATCCTCCCACTTC
51448 ACCTCGGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.19, C:0.41, G:0.19, T:0.22
Consensus pattern (27 bp):
GCAGTGGATCCTCCCACTTCGACCCCA
Found at i:52287 original size:17 final size:17
Alignment explanation
Indices: 52265--52299 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
52255 GAAAAAGTGC
52265 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
*
52282 ATTCTTGTTGGTATATT
1 ATTCTTGTTGGTACATT
52299 A
1 A
52300 ACATTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (17 bp):
ATTCTTGTTGGTACATT
Found at i:54051 original size:20 final size:20
Alignment explanation
Indices: 54026--54065 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
54016 TCTAACTGCT
54026 CCATATGTGGTTATATTACA
1 CCATATGTGGTTATATTACA
54046 CCATATGTGGTTATATTACA
1 CCATATGTGGTTATATTACA
54066 GAGGATATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
CCATATGTGGTTATATTACA
Found at i:54524 original size:32 final size:31
Alignment explanation
Indices: 54476--54660 Score: 199
Period size: 32 Copynumber: 5.7 Consensus size: 31
54466 AGCATGTGTG
* * *
54476 AAAAGAAAACGTCCTTATTTAGCGACGTCTA
1 AAAACAAAACGCCCTTATTTAGCGGCGTCTA
*
54507 CAAAACAAAACGCCCTTATTTGGCGGCGTCTA
1 -AAAACAAAACGCCCTTATTTAGCGGCGTCTA
*
54539 GAGAACAAAACGCCCTTATTTAGCGGCGTCTA
1 -AAAACAAAACGCCCTTATTTAGCGGCGTCTA
* *
54571 AAGAACCAAACGCCCTTATTTAGTGGCGTCTGA
1 AA-AACAAAACGCCCTTATTTAGCGGCGTCT-A
* * * *
54604 AGAACAAAACGTCATTATTTAGCGGCGTCTGC
1 AAAACAAAACGCCCTTATTTAGCGGCGTCT-A
*
54636 AGAACAAAACGCCGCTATATTTAGC
1 AAAACAAAACGCC-CT-TATTTAGC
54661 TGCTTCCAAA
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
31 1 0.01
32 119 0.91
33 3 0.02
34 8 0.06
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (31 bp):
AAAACAAAACGCCCTTATTTAGCGGCGTCTA
Found at i:54549 original size:64 final size:64
Alignment explanation
Indices: 54481--54660 Score: 238
Period size: 64 Copynumber: 2.8 Consensus size: 64
54471 GTGTGAAAAG
* *
54481 AAAACGTCCTTATTTAGCGACGTCTACAAAACAAAACGCCCTTATTTGGCGGCGTCT-AGAGAAC
1 AAAACGTCCTTATTTAGCGGCGTCTACAAAACAAAACGCCCTTATTTAGCGGCGTCTGA-AGAAC
* * *
54545 AAAACGCCCTTATTTAGCGGCGTCTA-AAGAACCAAACGCCCTTATTTAGTGGCGTCTGAAGAAC
1 AAAACGTCCTTATTTAGCGGCGTCTACAA-AACAAAACGCCCTTATTTAGCGGCGTCTGAAGAAC
* * *
54609 AAAACGTCATTATTTAGCGGCGTCTGCAGAACAAAACGCCGCTATATTTAGC
1 AAAACGTCCTTATTTAGCGGCGTCTACAAAACAAAACGCC-CT-TATTTAGC
54661 TGCTTCCAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
63 2 0.02
64 87 0.87
65 4 0.04
66 7 0.07
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (64 bp):
AAAACGTCCTTATTTAGCGGCGTCTACAAAACAAAACGCCCTTATTTAGCGGCGTCTGAAGAAC
Found at i:54622 original size:96 final size:98
Alignment explanation
Indices: 54482--54660 Score: 249
Period size: 96 Copynumber: 1.8 Consensus size: 98
54472 TGTGAAAAGA
* * *
54482 AAACGTCCTTATTTAGCGACGTCTACAAAACAAAACGCCCTTATTTGGCGGCGTCTAG-AGAACA
1 AAACGCCCTTATTTAGCGACGTCTACAAAACAAAACGCCATTATTTAGCGGCGTCT-GCAGAACA
54546 AAACGCC-CT-TATTTAGCGGCGTCTAAAGAACC
65 AAACGCCGCTATATTTAGCGGCGTCTAAAGAACC
* * * *
54578 AAACGCCCTTATTTAGTGGCGTCTGA-AGAACAAAACGTCATTATTTAGCGGCGTCTGCAGAACA
1 AAACGCCCTTATTTAGCGACGTCT-ACAAAACAAAACGCCATTATTTAGCGGCGTCTGCAGAACA
54642 AAACGCCGCTATATTTAGC
65 AAACGCCGCTATATTTAGC
54661 TGCTTCCAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
95 1 0.01
96 60 0.83
97 3 0.04
98 8 0.11
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (98 bp):
AAACGCCCTTATTTAGCGACGTCTACAAAACAAAACGCCATTATTTAGCGGCGTCTGCAGAACAA
AACGCCGCTATATTTAGCGGCGTCTAAAGAACC
Found at i:55843 original size:18 final size:18
Alignment explanation
Indices: 55809--55842 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55799 GAAAAAAATC
55809 TTTTTTTTTGCTTTTTTG
1 TTTTTTTTTGCTTTTTTG
55827 TTTTTTTTTG-TTTTTT
1 TTTTTTTTTGCTTTTTT
55843 TAAAGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTGCTTTTTTG
Found at i:56880 original size:22 final size:22
Alignment explanation
Indices: 56852--56905 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
56842 ACCACACTAT
56852 GAAATTTTGTTAATTTGCTTAC
1 GAAATTTTGTTAATTTGCTTAC
* *
56874 GAAATTTTGTTAATTTTCTTAT
1 GAAATTTTGTTAATTTGCTTAC
56896 GAAATTTTGT
1 GAAATTTTGT
56906 AAACCTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.06, G:0.13, T:0.54
Consensus pattern (22 bp):
GAAATTTTGTTAATTTGCTTAC
Found at i:57151 original size:24 final size:26
Alignment explanation
Indices: 57122--57171 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
57112 AATAGCAATT
57122 AAAAAGAAAAGT-AATT-AATCTAAA
1 AAAAAGAAAAGTAAATTAAATCTAAA
*
57146 AAAAAGCAAAGTAAATTAAATCTAAA
1 AAAAAGAAAAGTAAATTAAATCTAAA
57172 CTATAGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.48
25 4 0.17
26 8 0.35
ACGTcount: A:0.66, C:0.06, G:0.08, T:0.20
Consensus pattern (26 bp):
AAAAAGAAAAGTAAATTAAATCTAAA
Found at i:57896 original size:11 final size:11
Alignment explanation
Indices: 57880--57904 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57870 CCCTCTTCTT
57880 AAACTAGAGAA
1 AAACTAGAGAA
57891 AAACTAGAGAA
1 AAACTAGAGAA
57902 AAA
1 AAA
57905 TAAAAGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAACTAGAGAA
Found at i:58950 original size:22 final size:22
Alignment explanation
Indices: 58922--58965 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
58912 TCAAGCATAT
58922 ATTCATTAATAATATTAGATAA
1 ATTCATTAATAATATTAGATAA
58944 ATTCATTAATAATATTAGATAA
1 ATTCATTAATAATATTAGATAA
58966 GAGCCCGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (22 bp):
ATTCATTAATAATATTAGATAA
Found at i:59558 original size:178 final size:178
Alignment explanation
Indices: 59236--59565 Score: 484
Period size: 178 Copynumber: 1.9 Consensus size: 178
59226 TAAGCCCAAA
* ** * * *
59236 TTATGTAATATTAAGTAGACCGTCTATTTCTGTTAACCGAAACAACTAATTCTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTTCCATTAACCGAAACAACAAATTCTTCGAAAGCATTT
*
59301 TTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAACAAC
66 TTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGAAACAAC
*
59366 CTTTCAAGAGACACTTGAATCATCTCAATTAGACAACTGAAGCAAAAG
131 CTTTCAAGAGACACTTAAATCATCTCAATTAGACAACTGAAGCAAAAG
* *
59414 TTATATAATATTAAGTGGATCGTCTATTTCCATTAACCGAAACAACAAATGT-TTCGAAAGCATT
1 TTATATAATATTAAGTAGACCGTCTATTTCCATTAACCGAAACAACAAAT-TCTTCGAAAGCATT
* * *
59478 TTTTATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATTATGAAACA
65 TTTTATACCTTG-AACAATAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGAAACA
* * *
59542 ATCTTTTAATAGACACTTAAATCA
129 ACCTTTCAAGAGACACTTAAATCA
59566 CCTTAATCGG
Statistics
Matches: 134, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
177 4 0.03
178 129 0.96
179 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTTCCATTAACCGAAACAACAAATTCTTCGAAAGCATTT
TTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGAAACAAC
CTTTCAAGAGACACTTAAATCATCTCAATTAGACAACTGAAGCAAAAG
Found at i:59598 original size:178 final size:177
Alignment explanation
Indices: 59233--59605 Score: 482
Period size: 178 Copynumber: 2.1 Consensus size: 177
59223 CCATAAGCCC
* ** * * *
59233 AAATTATGTAATATTAAGTAGACCGTCTATTTCTGTTAACCGAAACAACTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTTCCATTAACCGAAACAACAAATTCTTCGAAAGCA
*
59298 TTTTTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAAC
66 TTTTTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGAAAC
* * * *
59363 AACCTTTCAAGAGACACTTGAATCATCTCAATTAGACAACTGAAGCA
131 AACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACGGAAGCA
* *
59410 AAAGTTATATAATATTAAGTGGATCGTCTATTTCCATTAACCGAAACAACAAATGT-TTCGAAAG
1 AAA-TTATATAATATTAAGTAGACCGTCTATTTCCATTAACCGAAACAACAAAT-TCTTCGAAAG
* * *
59474 CATTTTTTATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATTATGA
64 CATTTTTTATACCTTG-AACAATAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGA
* * * * * *
59538 AACAATCTTTTAATAGACACTTAAATCACCTTAATCGGATAATCGGAGAG-A
128 AACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAA-CGGA-AGCA
59589 AAATTATATAATATTAA
1 AAATTATATAATATTAA
59606 AATACACCGC
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
177 7 0.04
178 152 0.90
179 8 0.05
180 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATTTCCATTAACCGAAACAACAAATTCTTCGAAAGCA
TTTTTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGAAAC
AACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACGGAAGCA
Found at i:61708 original size:36 final size:36
Alignment explanation
Indices: 61668--61737 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
61658 AATTAAATAA
*
61668 ATTAGAAATGTTTATCGTCAACAATTCAAATATATT
1 ATTAGAAATGCTTATCGTCAACAATTCAAATATATT
61704 ATTAGAAATGCTTATCGTCAACAATTCAAATATA
1 ATTAGAAATGCTTATCGTCAACAATTCAAATATA
61738 ATATATCAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (36 bp):
ATTAGAAATGCTTATCGTCAACAATTCAAATATATT
Found at i:61812 original size:23 final size:24
Alignment explanation
Indices: 61786--61832 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
61776 CAAGTCCTAA
*
61786 TGTATTCAATATA-TTCAATATTG
1 TGTATTCAATATATTTAAATATTG
61809 TGTATTCAATATATTTAAATATTG
1 TGTATTCAATATATTTAAATATTG
61833 AATTGCTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (24 bp):
TGTATTCAATATATTTAAATATTG
Found at i:71213 original size:25 final size:25
Alignment explanation
Indices: 71185--71350 Score: 251
Period size: 25 Copynumber: 6.6 Consensus size: 25
71175 CGCTCATGTT
* *
71185 CTTGTGTTTGGAAAACGAGCCTGTG
1 CTTGCGTTTGGAAAACGAACCTGTG
71210 CTTGCGTTTGGAAAACGAACCTGTG
1 CTTGCGTTTGGAAAACGAACCTGTG
71235 CTTGCGTTTGGAAAACGAACCTGTG
1 CTTGCGTTTGGAAAACGAACCTGTG
* *
71260 TTTGTGTTTGGAAAACGAACCTGTG
1 CTTGCGTTTGGAAAACGAACCTGTG
71285 CTTGCGTTTGGAAAACGAACCTGTG
1 CTTGCGTTTGGAAAACGAACCTGTG
* * * *
71310 CTTGCGTTTGGCAAGCGAGCCTGTA
1 CTTGCGTTTGGAAAACGAACCTGTG
*
71335 CTTGCGTTTAGAAAAC
1 CTTGCGTTTGGAAAAC
71351 ACATAGGCTA
Statistics
Matches: 128, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 128 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (25 bp):
CTTGCGTTTGGAAAACGAACCTGTG
Done.