Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004115.1 Kokia drynarioides strain JFW-HI SEQ_117300, 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: 33188
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Found at i:42 original size:18 final size:18
Alignment explanation
Indices: 15--49 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5 ATATATGAAA
15 ATGACATAAATAGTTGAG
1 ATGACATAAATAGTTGAG
* *
33 ATGACTTAAATGGTTGA
1 ATGACATAAATAGTTGA
50 ACTTGTCTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (18 bp):
ATGACATAAATAGTTGAG
Found at i:1407 original size:7 final size:7
Alignment explanation
Indices: 1395--1429 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
1385 AATGGAACCC
1395 AATTTTA
1 AATTTTA
1402 AATTTTA
1 AATTTTA
1409 AATTTTA
1 AATTTTA
1416 AATTATTTA
1 AA-T-TTTA
1425 AATTT
1 AATTT
1430 AAAAAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 18 0.69
8 2 0.08
9 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTTA
Found at i:1563 original size:12 final size:12
Alignment explanation
Indices: 1546--1578 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1536 ATGGCCCAAA
1546 CAAACCCAAGTC
1 CAAACCCAAGTC
1558 CAAACCCAAGTC
1 CAAACCCAAGTC
1570 CAAACCCAA
1 CAAACCCAA
1579 TTACAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.45, C:0.42, G:0.06, T:0.06
Consensus pattern (12 bp):
CAAACCCAAGTC
Found at i:1585 original size:12 final size:12
Alignment explanation
Indices: 1545--1585 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1535 AATGGCCCAA
1545 ACAAACCCAAGT
1 ACAAACCCAAGT
*
1557 CCAAACCCAAGT
1 ACAAACCCAAGT
* *
1569 CCAAACCCAATT
1 ACAAACCCAAGT
1581 ACAAA
1 ACAAA
1586 AAGACCCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.49, C:0.37, G:0.05, T:0.10
Consensus pattern (12 bp):
ACAAACCCAAGT
Found at i:3213 original size:60 final size:57
Alignment explanation
Indices: 3128--3319 Score: 240
Period size: 59 Copynumber: 3.2 Consensus size: 57
3118 TATTTTATTT
* * * * *
3128 AAAAATTACATTTGACCCCTAAACTTTGCAAAATTTACATTTTAACCCTTAAACTTCTC
1 AAAAATCACATTTTAACCCTAAACTTTCCAAAA-TTACATTTTAACCC-TAAACTTTTC
*
3187 AAAAATCACATTTTAACCCTCAAACTTCTCCAAAAGTACATTTTAACCCTAAACTTTTC
1 AAAAATCACATTTTAACCCT-AAACTT-TCCAAAATTACATTTTAACCCTAAACTTTTC
* *
3246 CAAAATCACATTTTTCACCCTAAACTTTTCCAAAATTACATTTTAACTCCTAAACTTTTC
1 AAAAATCACA-TTTTAACCCTAAAC-TTTCCAAAATTACATTTTAAC-CCTAAACTTTTC
*
3306 CAAAATCACATTTT
1 AAAAATCACATTTT
3320 GATCACGAAC
Statistics
Matches: 119, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
59 61 0.51
60 52 0.44
61 6 0.05
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.35
Consensus pattern (57 bp):
AAAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTAACCCTAAACTTTTC
Found at i:3287 original size:89 final size:88
Alignment explanation
Indices: 3129--3319 Score: 226
Period size: 89 Copynumber: 2.1 Consensus size: 88
3119 ATTTTATTTA
* * * *
3129 AAAATTACATTTGACCCCTAAACTTTGCAAAATTTACATTTTAACCCTTAAACTTCTCAAAAATC
1 AAAA-TACATTTTAACCCTAAACTTTCCAAAATTCACATTTTAACCCTTAAACTTCTCAAAAATC
3194 ACATTTTAAC-CCTCAAACTTCTCC
65 ACATTTTAACTCCT-AAACTTCTCC
* * *
3218 AAAAGTACATTTTAACCCTAAACTTTTCCAAAA-TCACATTTTTCACCC-TAAACTTTTCCAAAA
1 AAAA-TACATTTTAACCCTAAAC-TTTCCAAAATTCACA-TTTTAACCCTTAAACTTCTCAAAAA
* *
3281 TTACATTTTAACTCCTAAACTTTTCC
63 TCACATTTTAACTCCTAAACTTCTCC
3307 AAAATCACATTTT
1 AAAAT-ACATTTT
3320 GATCACGAAC
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
88 1 0.01
89 68 0.77
90 19 0.22
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.36
Consensus pattern (88 bp):
AAAATACATTTTAACCCTAAACTTTCCAAAATTCACATTTTAACCCTTAAACTTCTCAAAAATCA
CATTTTAACTCCTAAACTTCTCC
Found at i:3331 original size:59 final size:57
Alignment explanation
Indices: 3148--3348 Score: 226
Period size: 59 Copynumber: 3.4 Consensus size: 57
3138 TTTGACCCCT
* * * * *
3148 AAAC-TTTGCAAAATTTACATTTTAACCCTTAAACTTCTCAAAAATCACATTTTAACCCTC
1 AAACTTTTCCAAAA-TTACATTTTAACCC-TAAACTTTTCCAAAATCACATTTT-A-TCAC
* *
3208 AAACTTCTCCAAAAGTACATTTTAACCCTAAACTTTTCCAAAATCACATTTT-TCACCC
1 AAACTTTTCCAAAATTACATTTTAACCCTAAACTTTTCCAAAATCACATTTTATCA--C
3266 TAAACTTTTCCAAAATTACATTTTAACTCCTAAACTTTTCCAAAATCACATTTTGATCAC
1 -AAACTTTTCCAAAATTACATTTTAAC-CCTAAACTTTTCCAAAATCACATTTT-ATCAC
* *
3326 GAACTTTTCCAAAATTGCATTTT
1 AAACTTTTCCAAAATTACATTTT
3349 TTCCCTCGAA
Statistics
Matches: 123, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
56 1 0.01
58 1 0.01
59 67 0.54
60 44 0.36
61 7 0.06
62 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (57 bp):
AAACTTTTCCAAAATTACATTTTAACCCTAAACTTTTCCAAAATCACATTTTATCAC
Found at i:3331 original size:89 final size:90
Alignment explanation
Indices: 3146--3349 Score: 222
Period size: 89 Copynumber: 2.3 Consensus size: 90
3136 CATTTGACCC
* *
3146 CTAAAC-TTTGCAAAATTTACA-TTTTAACCCTTAAACTTCTCAAAAATCACATTTTAACCCTCA
1 CTAAACTTTTCCAAAA-TCACATTTTTAACCCTTAAACTTCTCAAAAATCACATTTTAACCCTCA
*
3209 AACTTCTCCAAAAGTACATTTTAACC
65 AACTTCTCCAAAAGTACATTTTAACA
* * * *
3235 CTAAACTTTTCCAAAATCACATTTTTCACCC-TAAACTTTTCCAAAATTACATTTTAACTCCT-A
1 CTAAACTTTTCCAAAATCACATTTTTAACCCTTAAACTTCTCAAAAATCACATTTTAAC-CCTCA
* *
3298 AACTTTTCCAAAA-TCACATTTTGATCA
65 AACTTCTCCAAAAGT-ACATTTT-AACA
* **
3325 C-GAACTTTTCCAAAATTGCATTTTT
1 CTAAACTTTTCCAAAATCACATTTTT
3350 TCCCTCGAAC
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
88 1 0.01
89 75 0.77
90 22 0.22
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (90 bp):
CTAAACTTTTCCAAAATCACATTTTTAACCCTTAAACTTCTCAAAAATCACATTTTAACCCTCAA
ACTTCTCCAAAAGTACATTTTAACA
Found at i:3346 original size:29 final size:30
Alignment explanation
Indices: 3129--3348 Score: 213
Period size: 30 Copynumber: 7.4 Consensus size: 30
3119 ATTTTATTTA
* * *
3129 AAAATTACA-TTTGACCCCTAAAC-TTTGC
1 AAAATTACATTTTAACTCCTAAACTTTTCC
* *
3157 AAAATTTACATTTTAAC-CCTTAAACTTCTCA
1 AAAA-TTACATTTTAACTCC-TAAACTTTTCC
* *
3188 AAAATCACATTTTAAC-CCTCAAACTTCTCC
1 AAAATTACATTTTAACTCCT-AAACTTTTCC
*
3218 AAAAGTACATTTTAAC-CCTAAACTTTTCC
1 AAAATTACATTTTAACTCCTAAACTTTTCC
* *
3247 AAAATCACATTTTTCAC-CCTAAACTTTTCC
1 AAAATTACA-TTTTAACTCCTAAACTTTTCC
3277 AAAATTACATTTTAACTCCTAAACTTTTCC
1 AAAATTACATTTTAACTCCTAAACTTTTCC
* * *
3307 AAAATCACATTTTGA-TCAC-GAACTTTTCC
1 AAAATTACATTTTAACTC-CTAAACTTTTCC
*
3336 AAAATTGCATTTT
1 AAAATTACATTTT
3349 TTCCCTCGAA
Statistics
Matches: 165, Mismatches: 19, Indels: 15
0.83 0.10 0.08
Matches are distributed among these distances:
28 4 0.02
29 52 0.32
30 103 0.62
31 6 0.04
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTAACTCCTAAACTTTTCC
Found at i:3378 original size:28 final size:28
Alignment explanation
Indices: 3347--3465 Score: 116
Period size: 29 Copynumber: 4.2 Consensus size: 28
3337 AAATTGCATT
* *
3347 TTTTCCCTCGAACATCCAAAAATTACTA
1 TTTTCCCTCGAATATCCAAAAATTACCA
* *
3375 TTTTTCCCTTGAATATCCAAAAATGACCA
1 -TTTTCCCTCGAATATCCAAAAATTACCA
*
3404 TTTT-CCTCCTAGATATCCAAAAATTACCA
1 TTTTCCCT-CGA-ATATCCAAAAATTACCA
* * *
3433 TTTTGCCCTCAAATTTCCAAAAATCA-CA
1 TTTT-CCCTCGAATATCCAAAAATTACCA
3461 TTTTC
1 TTTTC
3466 AACCTTAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
27 4 0.05
28 11 0.14
29 56 0.74
30 2 0.03
31 3 0.04
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (28 bp):
TTTTCCCTCGAATATCCAAAAATTACCA
Found at i:3479 original size:30 final size:30
Alignment explanation
Indices: 3443--3555 Score: 88
Period size: 30 Copynumber: 3.8 Consensus size: 30
3433 TTTTGCCCTC
3443 AAATTTCCAAAAATCACATTTTCAACCTTA
1 AAATTTCCAAAAATCACATTTTCAACCTTA
** * *
3473 AAATTTCCAAAGTTCA-ATTTT-AATCTCA
1 AAATTTCCAAAAATCACATTTTCAACCTTA
* ** * *
3501 AATTTTCCAAAAATTTCAATTTCAATCCCT-
1 AAATTTCCAAAAATCACATTTTCAA-CCTTA
* *
3531 AAATTCCTCAAAAATTACATTTTCA
1 AAATTTC-CAAAAATCACATTTTCA
3556 TCCCAAATTC
Statistics
Matches: 62, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
28 16 0.26
29 9 0.15
30 21 0.34
31 16 0.26
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (30 bp):
AAATTTCCAAAAATCACATTTTCAACCTTA
Found at i:3543 original size:31 final size:29
Alignment explanation
Indices: 3508--3565 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
3498 TCAAATTTTC
*
3508 CAAAAATTTCAATTTCAATCCCTAAATTCCT
1 CAAAAATTACAATTTC-ATCCC-AAATTCCT
*
3539 CAAAAATTACATTTTCATCCCAAATTC
1 CAAAAATTACAATTTCATCCCAAATTC
3566 TCAGAAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.24
30 5 0.20
31 14 0.56
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (29 bp):
CAAAAATTACAATTTCATCCCAAATTCCT
Found at i:15770 original size:39 final size:39
Alignment explanation
Indices: 15727--15861 Score: 132
Period size: 39 Copynumber: 3.5 Consensus size: 39
15717 GAAGATTTTG
*
15727 ATCTCCTACCCCGAGCCTGAGGTAGACCATCATTAGCCA
1 ATCTCTTACCCCGAGCCTGAGGTAGACCATCATTAGCCA
* * * * * *
15766 ATCTCTTACCACAAGCTTGAGGCAGATTGCAGTCATT---CG
1 ATCTCTTACCCCGAGCCTGAGGTAGA--CCA-TCATTAGCCA
* *
15805 ATCTTTTACCCCGAGCCTGAGGTAGACCATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGAGGTAGACCATCATTAGCCA
*
15844 ATCTCTTACCTCGAGCCT
1 ATCTCTTACCCCGAGCCT
15862 AGGGAAGATT
Statistics
Matches: 73, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
36 4 0.05
37 2 0.03
39 60 0.82
41 2 0.03
42 5 0.07
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGAGGTAGACCATCATTAGCCA
Found at i:15871 original size:78 final size:78
Alignment explanation
Indices: 15733--16141 Score: 439
Period size: 78 Copynumber: 5.2 Consensus size: 78
15723 TTTGATCTCC
* * * * * *
15733 TACCCCGAGCCTGAGGTAGACCATCATTAGCCAATCTCTTACCACAAG-CTTGAGGCAGATTGCA
1 TACCCCGAGCCTGAGGCAGATCATCATCAGCCAATCTCTTACCCCGAGCCTAG-GGCAGATTGCA
*
15797 GTCATTCGATCTTT
65 GCCATTCGATCTTT
* * * * *
15811 TACCCCGAGCCTGAGGTAGACCATCATCAGCCAATCTCTTACCTCGAGCCTAGGGAAGATTACAG
1 TACCCCGAGCCTGAGGCAGATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAG
*
15876 CCATTTGATCTTT
66 CCATTCGATCTTT
* * * * * * *
15889 TACCCCGAACCTGGGGCAAATCATCATCAACCATTTGATCTCTTACCCCAAGCTTAGGGTAGATT
1 TACCCCGAGCCTGAGGCAGATCATCATCAGCCA----ATCTCTTACCCCGAGCCTAGGGCAGATT
15954 GCAGCCATTCGATCTTT
62 GCAGCCATTCGATCTTT
* *
15971 TACCCCGAGCCTGTGGCATATCATCATCAGCCAATCTCTTACCCCGAGCCT-GAGGCAGATTGCA
1 TACCCCGAGCCTGAGGCAGATCATCATCAGCCAATCTCTTACCCCGAGCCTAG-GGCAGATTGCA
* *
16035 ACCATTCGATATTT
65 GCCATTCGATCTTT
* * * * *
16049 TACCCCGAG-CTTAGGGCAGATCA-CAATCAACCAATCTCTTACCCTGAGCCTGGGGCAGATTGT
1 TACCCCGAGCCTGA-GGCAGATCATC-ATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGC
*
16112 AGCCATTCAATCTTT
64 AGCCATTCGATCTTT
*
16127 TACCCTGAGCCTGAG
1 TACCCCGAGCCTGAG
16142 CCTGAGCCTG
Statistics
Matches: 281, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
77 4 0.01
78 202 0.72
79 7 0.02
82 68 0.24
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (78 bp):
TACCCCGAGCCTGAGGCAGATCATCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAG
CCATTCGATCTTT
Found at i:15983 original size:160 final size:155
Alignment explanation
Indices: 15763--16141 Score: 456
Period size: 160 Copynumber: 2.4 Consensus size: 155
15753 CCATCATTAG
* * *
15763 CCAATCTCTTACCACAAGCTTGAGGCAGATTGCAGTCATTCGATCTTTTACCCCGAGCCTGAGGT
1 CCAATCTCTTACCCCAAGCTTG-GGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCCTGAGGC
* * * *
15828 AGACCATCATCAGCCAATCTCTTACCTCGAGCCT-AGGGAAGATTACAGCCATTTGATCTTTTAC
65 AGACCATCATCAGCCAATCTCTTACCCCGAGCCTGA-GGAAGATTACAACCATTCGATATTTTAC
*
15892 CCCGAACCTGGGGCAAATCATC-ATCAA
129 CCCGAACCTAGGGCAAATCA-CAATCAA
*
15919 CCATTTGATCTCTTACCCCAAGCTTAGGGTAGATTGCAGCCATTCGATCTTTTACCCCGAGCCTG
1 CCA----ATCTCTTACCCCAAGCTT-GGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCCTG
* * * * *
15984 TGGCATATCATCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATTGCAACCATTCGATATTT
61 AGGCAGACCATCATCAGCCAATCTCTTACCCCGAGCCTGAGGAAGATTACAACCATTCGATATTT
* * *
16049 TACCCCGAGCTTAGGGCAGATCACAATCAA
126 TACCCCGAACCTAGGGCAAATCACAATCAA
** * * * *
16079 CCAATCTCTTACCCTGAGCCTGGGGCAGATTGTAGCCATTCAATCTTTTACCCTGAGCCTGAG
1 CCAATCTCTTACCCCAAG-CTTGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCCTGAG
16142 CCTGAGCCTG
Statistics
Matches: 190, Mismatches: 25, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
156 52 0.27
157 2 0.01
159 1 0.01
160 133 0.70
161 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (155 bp):
CCAATCTCTTACCCCAAGCTTGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCCTGAGGCA
GACCATCATCAGCCAATCTCTTACCCCGAGCCTGAGGAAGATTACAACCATTCGATATTTTACCC
CGAACCTAGGGCAAATCACAATCAA
Found at i:16052 original size:39 final size:39
Alignment explanation
Indices: 15764--16141 Score: 149
Period size: 39 Copynumber: 9.6 Consensus size: 39
15754 CATCATTAGC
* * * * **
15764 CAATCTCTTACCACAAGCTTGAGGCAGATTGCAGTCATT
1 CAATCTTTTACCCCGAGCCTGAGGCAGATTGCAACCATT
* * * * **
15803 CGATCTTTTACCCCGAGCCTGAGGTAGA--CCATCATCAGC
1 CAATCTTTTACCCCGAGCCTGAGGCAGATTGCA--ACCATT
* * * * *
15842 CAATCTCTTACCTCGAGCCT-AGGGAAGATTACAGCCATT
1 CAATCTTTTACCCCGAGCCTGA-GGCAGATTGCAACCATT
** * * * *
15881 TGATCTTTTACCCCGAACCTGGGGCAAATCATCATCAACCATT
1 CAATCTTTTACCCCGAGCCTGAGGCAGAT--T--GCAACCATT
** * * * * *
15924 TGATCTCTTACCCCAAG-CTTAGGGTAGATTGCAGCCATT
1 CAATCTTTTACCCCGAGCCTGA-GGCAGATTGCAACCATT
* * * * **
15963 CGATCTTTTACCCCGAGCCTGTGGCATA-T-CATCATCAGC
1 CAATCTTTTACCCCGAGCCTGAGGCAGATTGCA--ACCATT
*
16002 CAATCTCTTACCCCGAGCCTGAGGCAGATTGCAACCATT
1 CAATCTTTTACCCCGAGCCTGAGGCAGATTGCAACCATT
* * * ** * **
16041 CGATATTTTACCCCGAG-CTTAGGGCAGATCACAATCAAC
1 CAATCTTTTACCCCGAGCCTGA-GGCAGATTGCAACCATT
* * * * *
16080 CAATCTCTTACCCTGAGCCTGGGGCAGATTGTAGCCATT
1 CAATCTTTTACCCCGAGCCTGAGGCAGATTGCAACCATT
*
16119 CAATCTTTTACCCTGAGCCTGAG
1 CAATCTTTTACCCCGAGCCTGAG
16142 CCTGAGCCTG
Statistics
Matches: 241, Mismatches: 80, Indels: 36
0.68 0.22 0.10
Matches are distributed among these distances:
37 4 0.02
38 5 0.02
39 193 0.80
40 5 0.02
41 6 0.02
42 2 0.01
43 26 0.11
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (39 bp):
CAATCTTTTACCCCGAGCCTGAGGCAGATTGCAACCATT
Found at i:16141 original size:6 final size:6
Alignment explanation
Indices: 16130--16167 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
16120 AATCTTTTAC
16130 CCTGAG CCTGAG CCTGAG CCTGAG CCTGAG CCTGAG CC
1 CCTGAG CCTGAG CCTGAG CCTGAG CCTGAG CCTGAG CC
16168 AGATCACCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.37, G:0.32, T:0.16
Consensus pattern (6 bp):
CCTGAG
Found at i:16286 original size:78 final size:77
Alignment explanation
Indices: 16167--16367 Score: 240
Period size: 78 Copynumber: 2.6 Consensus size: 77
16157 GAGCCTGAGC
* * * * * *
16167 CAGATCACCATCAACCAATCTCTTACCACAAGCATGAGGCAGATTGCAGCCATTCGGTCTTTTAC
1 CAGATCACCATCAGCCAATCTCTTACC-CGAGCCTGGGGCAGATTACAGCCATTCGATCTTTTAC
**
16232 CCCGAGCCTAGGG
65 CCCGAGAATAGGG
* *
16245 TAGATCACCATCAGCCAATCTCTTATGCCGAGCCTGGGGCAGATTACAGCCATTCGATCTTTTAC
1 CAGATCACCATCAGCCAATCTCTTA-CCCGAGCCTGGGGCAGATTACAGCCATTCGATCTTTTAC
*
16310 CCCGAGAATGGGG
65 CCCGAGAATAGGG
** **
16323 CAGATCACTGTCAGCCAATCTCTTACCCCGAGCCAAGGGCAGATT
1 CAGATCACCATCAGCCAATCTCTTA-CCCGAGCCTGGGGCAGATT
16368 CCAACCATCC
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
78 103 0.99
79 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.22
Consensus pattern (77 bp):
CAGATCACCATCAGCCAATCTCTTACCCGAGCCTGGGGCAGATTACAGCCATTCGATCTTTTACC
CCGAGAATAGGG
Found at i:16315 original size:39 final size:39
Alignment explanation
Indices: 16204--16327 Score: 106
Period size: 39 Copynumber: 3.2 Consensus size: 39
16194 ACAAGCATGA
* * *
16204 GGCAGATTGCAGCCATTCGGTCTTTTACCCCGAGCCTAG
1 GGCAGATTACAGCCATTCGATCTTTTACCCCGAGCCTGG
* * * ** * * **
16243 GGTAGATCACCA-TCAGCCAATCTCTTATGCCGAGCCTGG
1 GGCAGATTA-CAGCCATTCGATCTTTTACCCCGAGCCTGG
**
16282 GGCAGATTACAGCCATTCGATCTTTTACCCCGAGAATGG
1 GGCAGATTACAGCCATTCGATCTTTTACCCCGAGCCTGG
16321 GGCAGAT
1 GGCAGAT
16328 CACTGTCAGC
Statistics
Matches: 60, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
38 2 0.03
39 56 0.93
40 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (39 bp):
GGCAGATTACAGCCATTCGATCTTTTACCCCGAGCCTGG
Found at i:16349 original size:39 final size:39
Alignment explanation
Indices: 16228--16366 Score: 127
Period size: 39 Copynumber: 3.6 Consensus size: 39
16218 ATTCGGTCTT
* *
16228 TTACCCCGAGCCTAGGGTAGATCACCA-TCAGCCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCA-CAGTCAGCCAATCTC
** * * ** * *
16267 TTATGCCGAGCCTGGGGCAGATTACAGCCATTCGATCTT
1 TTACCCCGAGCCTGGGGCAGATCACAGTCAGCCAATCTC
** *
16306 TTACCCCGAGAATGGGGCAGATCACTGTCAGCCAATCTC
1 TTACCCCGAGCCTGGGGCAGATCACAGTCAGCCAATCTC
**
16345 TTACCCCGAGCCAAGGGCAGAT
1 TTACCCCGAGCCTGGGGCAGAT
16367 TCCAACCATC
Statistics
Matches: 74, Mismatches: 25, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
38 2 0.03
39 72 0.97
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (39 bp):
TTACCCCGAGCCTGGGGCAGATCACAGTCAGCCAATCTC
Found at i:16947 original size:17 final size:17
Alignment explanation
Indices: 16908--16953 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
16898 AACCTAATTT
* *
16908 AATTTAAACTTATTTTG
1 AATTTAAATTTATTTTA
*
16925 AGTTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
16942 AATTTAAATTTA
1 AATTTAAATTTA
16954 ATTAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:18768 original size:59 final size:60
Alignment explanation
Indices: 18572--18795 Score: 249
Period size: 60 Copynumber: 3.7 Consensus size: 60
18562 CTGTTTTATT
* * * * *
18572 TAAAACTTACATATTGACCCTCAAAC--TTCACAAAATTTACATTTTGAGCCCTAAACTTCTC
1 TAAAA-TTACATTTTAACCCTCAAACTTTTC-CAAAA-TCACATTTTAACCCCTAAACTTCTC
* * * * * *
18633 AAAAATCATATTTTAACACTCAAA-ATTTCCAAAAATTACATTTTAACCCCTAAACTTCTC
1 TAAAATTACATTTTAACCCTCAAACTTTTCC-AAAATCACATTTTAACCCCTAAACTTCTC
* * *
18693 CAAAATTACATTTTAACCCTCAAACTTTTCCAAAATCACATTTTCA-CCCTAAACTTTTC
1 TAAAATTACATTTTAACCCTCAAACTTTTCCAAAATCACATTTTAACCCCTAAACTTCTC
*
18752 TAAAATTACATTTTAACCCTCGAACTTTTCCAAAATCACATTTT
1 TAAAATTACATTTTAACCCTCAAACTTTTCCAAAATCACATTTT
18796 GATCTCGAAC
Statistics
Matches: 141, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
59 54 0.38
60 71 0.50
61 16 0.11
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (60 bp):
TAAAATTACATTTTAACCCTCAAACTTTTCCAAAATCACATTTTAACCCCTAAACTTCTC
Found at i:18811 original size:29 final size:30
Alignment explanation
Indices: 18588--18812 Score: 203
Period size: 30 Copynumber: 7.6 Consensus size: 30
18578 TTACATATTG
*
18588 ACCCTCAAAC--TTCACAAAATTTACATTTTGA
1 ACCCTCAAACTTTTC-CAAAA-TCACATTTT-A
* * * *
18619 GCCCT-AAACTTCTCAAAAATCATATTTTA
1 ACCCTCAAACTTTTCCAAAATCACATTTTA
* * *
18648 ACACTCAAA-ATTTCCAAAAATTACATTTTA
1 ACCCTCAAACTTTTCC-AAAATCACATTTTA
* *
18678 ACCC-CTAAACTTCTCCAAAATTACATTTTA
1 ACCCTC-AAACTTTTCCAAAATCACATTTTA
*
18708 ACCCTCAAACTTTTCCAAAATCACATTTTC
1 ACCCTCAAACTTTTCCAAAATCACATTTTA
* *
18738 ACCCT-AAACTTTTCTAAAATTACATTTTA
1 ACCCTCAAACTTTTCCAAAATCACATTTTA
* *
18767 ACCCTCGAACTTTTCCAAAATCACATTTTG
1 ACCCTCAAACTTTTCCAAAATCACATTTTA
* *
18797 A-TCTCGAACTTTTCCA
1 ACCCTCAAACTTTTCCA
18813 TAATTGTATT
Statistics
Matches: 160, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
29 48 0.30
30 97 0.61
31 13 0.08
32 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (30 bp):
ACCCTCAAACTTTTCCAAAATCACATTTTA
Found at i:18835 original size:59 final size:59
Alignment explanation
Indices: 18610--18795 Score: 221
Period size: 59 Copynumber: 3.1 Consensus size: 59
18600 CACAAAATTT
* * * * * * ** *
18610 ACATTTTGAGCCCTAAACTTCTCAAAAATCATATTTTAACACTC-AAAATTTCCAAAAATT
1 ACATTTTCA-CCCTAAACTTTTCCAAAATTACATTTTAACCCTCGAACTTTTCC-AAAATC
* * *
18670 ACATTTTAACCCCTAAACTTCTCCAAAATTACATTTTAACCCTCAAACTTTTCCAAAATC
1 ACATTTTCA-CCCTAAACTTTTCCAAAATTACATTTTAACCCTCGAACTTTTCCAAAATC
*
18730 ACATTTTCACCCTAAACTTTTCTAAAATTACATTTTAACCCTCGAACTTTTCCAAAATC
1 ACATTTTCACCCTAAACTTTTCCAAAATTACATTTTAACCCTCGAACTTTTCCAAAATC
18789 ACATTTT
1 ACATTTT
18796 GATCTCGAAC
Statistics
Matches: 112, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
59 54 0.48
60 51 0.46
61 7 0.06
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (59 bp):
ACATTTTCACCCTAAACTTTTCCAAAATTACATTTTAACCCTCGAACTTTTCCAAAATC
Found at i:18854 original size:28 final size:29
Alignment explanation
Indices: 18822--19031 Score: 196
Period size: 29 Copynumber: 7.3 Consensus size: 29
18812 ATAATTGTAT
*
18822 TTTTGCCTTCGAACATCCAAAAATTACC-
1 TTTTGCCCTCGAACATCCAAAAATTACCA
* *
18850 TTTTGACCTCGAA-ATCCAAAAATTACTA
1 TTTTGCCCTCGAACATCCAAAAATTACCA
* *
18878 TTTTACACAT-GAACATCC-AAAATTACCA
1 TTTTGC-CCTCGAACATCCAAAAATTACCA
* * * *
18906 TTTTGCCCCCGAGCATCTAGAAATTACCA
1 TTTTGCCCTCGAACATCCAAAAATTACCA
* * *
18935 TTTTTCCCCCAAACATCCAAAAATTACCA
1 TTTTGCCCTCGAACATCCAAAAATTACCA
* * * *
18964 TTTTTCCC-CTGAGCATCTAGAAATTACCA
1 TTTTGCCCTC-GAACATCCAAAAATTACCA
* *
18993 TTTTTCCCTCAAACATCCAAAAATTACCA
1 TTTTGCCCTCGAACATCCAAAAATTACCA
*
19022 TTTTTCCCTC
1 TTTTGCCCTC
19032 AAATTTCAAA
Statistics
Matches: 149, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
27 14 0.09
28 39 0.26
29 95 0.64
30 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (29 bp):
TTTTGCCCTCGAACATCCAAAAATTACCA
Found at i:18982 original size:58 final size:58
Alignment explanation
Indices: 18889--19029 Score: 248
Period size: 58 Copynumber: 2.4 Consensus size: 58
18879 TTTACACATG
*
18889 AACATCC-AAAATTACCATTTTGCCCCCGAGCATCTAGAAATTACCATTTTTCCCCCA
1 AACATCCAAAAATTACCATTTTTCCCCCGAGCATCTAGAAATTACCATTTTTCCCCCA
* *
18946 AACATCCAAAAATTACCATTTTTCCCCTGAGCATCTAGAAATTACCATTTTTCCCTCA
1 AACATCCAAAAATTACCATTTTTCCCCCGAGCATCTAGAAATTACCATTTTTCCCCCA
19004 AACATCCAAAAATTACCATTTTTCCC
1 AACATCCAAAAATTACCATTTTTCCC
19030 TCAAATTTCA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
57 7 0.09
58 73 0.91
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.30
Consensus pattern (58 bp):
AACATCCAAAAATTACCATTTTTCCCCCGAGCATCTAGAAATTACCATTTTTCCCCCA
Found at i:19042 original size:28 final size:28
Alignment explanation
Indices: 18926--19065 Score: 115
Period size: 29 Copynumber: 4.9 Consensus size: 28
18916 GAGCATCTAG
* * *
18926 AAATTACCATTTTTCCCCCAAACATCCAA
1 AAATTACCATTTTTCCCTCAAA-TTTCAA
* * * *
18955 AAATTACCATTTTTCCCCTGAGCATCT-AG
1 AAATTACCATTTTT-CCCTCA-AATTTCAA
* *
18984 AAATTACCATTTTTCCCTCAAACATCCAA
1 AAATTACCATTTTTCCCTCAAA-TTTCAA
19013 AAATTACCATTTTTCCCTCAAATTTCAA
1 AAATTACCATTTTTCCCTCAAATTTCAA
*
19041 AAATCA-CA-TTTTCGACCTCAAATTT
1 AAATTACCATTTTTC--CCTCAAATTT
19066 TCCAAAAGTT
Statistics
Matches: 89, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
26 5 0.06
27 3 0.03
28 24 0.27
29 52 0.58
30 4 0.04
31 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (28 bp):
AAATTACCATTTTTCCCTCAAATTTCAA
Found at i:28605 original size:18 final size:18
Alignment explanation
Indices: 28584--28630 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
28574 GAACGTGTGT
28584 CTGCATCTGATTATATGA
1 CTGCATCTGATTATATGA
*
28602 CTGCATCT-AGTTATGTGA
1 CTGCATCTGA-TTATATGA
28620 -TCGCATCTGAT
1 CT-GCATCTGAT
28631 CAGGTTGCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 22 0.88
19 1 0.04
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (18 bp):
CTGCATCTGATTATATGA
Found at i:31443 original size:20 final size:21
Alignment explanation
Indices: 31404--31443 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
31394 AAGATCAAAC
*
31404 AACACTGAGTTATAAAATGCA
1 AACACTAAGTTATAAAATGCA
*
31425 AACACTAAG-TATGAAATGC
1 AACACTAAGTTATAAAATGC
31444 TAAAAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (21 bp):
AACACTAAGTTATAAAATGCA
Done.