Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020720.1 Corchorus olitorius cultivar O-4 contig20753, 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: 106056
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:267 original size:14 final size:15
Alignment explanation
Indices: 250--278 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
240 TTGTTTTACT
250 TGATTGA-TTTTGAA
1 TGATTGAGTTTTGAA
264 TGATTGAGTTTTGAA
1 TGATTGAGTTTTGAA
279 AGTTTGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (15 bp):
TGATTGAGTTTTGAA
Found at i:500 original size:18 final size:18
Alignment explanation
Indices: 473--521 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 18
463 GCATCCTCAG
473 GGGGCGCCTCACCGTGGC
1 GGGGCGCCTCACCGTGGC
*
491 GGGGCACCTCCCACCGTGGC
1 GGGGCGCCT--CACCGTGGC
511 GGGGCGCCTCA
1 GGGGCGCCTCA
522 TGGGGACGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 10 0.37
20 17 0.63
ACGTcount: A:0.08, C:0.41, G:0.41, T:0.10
Consensus pattern (18 bp):
GGGGCGCCTCACCGTGGC
Found at i:548 original size:33 final size:33
Alignment explanation
Indices: 497--560 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
487 TGGCGGGGCA
*
497 CCTCCCACCGTGGCGGGGCGCCTCATGGGGACG
1 CCTCCCACCGTGGCGGGGCGCCCCATGGGGACG
* * *
530 CCTCTCACCGTGGTGGGGCGCCCCCTGGGGA
1 CCTCCCACCGTGGCGGGGCGCCCCATGGGGA
561 TACCTCCGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.08, C:0.39, G:0.39, T:0.14
Consensus pattern (33 bp):
CCTCCCACCGTGGCGGGGCGCCCCATGGGGACG
Found at i:1027 original size:30 final size:32
Alignment explanation
Indices: 971--1029 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
961 AAAATGTCTT
**
971 AATTTGGAAATTTCAAGGTCCAAAATATCCCG
1 AATTTGGAAATTTCAAGGGACAAAATATCCCG
1003 AATTTGG-AATTTC-AGGGACAAAATATC
1 AATTTGGAAATTTCAAGGGACAAAATATC
1030 TTGATTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.48
31 6 0.24
32 7 0.28
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (32 bp):
AATTTGGAAATTTCAAGGGACAAAATATCCCG
Found at i:20183 original size:13 final size:13
Alignment explanation
Indices: 20162--20195 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
20152 AAAAATTAGT
20162 AAAAT-AAAAACA
1 AAAATGAAAAACA
*
20174 AAAATGAAAAATA
1 AAAATGAAAAACA
20187 AAAATGAAA
1 AAAATGAAA
20196 TAAAAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAATGAAAAACA
Found at i:24908 original size:10 final size:10
Alignment explanation
Indices: 24887--24915 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
24877 TTTCGTTGCT
24887 TTCTTC-TCC
1 TTCTTCATCC
24896 TTCTTCATCC
1 TTCTTCATCC
24906 TTCTTCATCC
1 TTCTTCATCC
24916 CTTTTATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (10 bp):
TTCTTCATCC
Found at i:25715 original size:38 final size:38
Alignment explanation
Indices: 25664--25771 Score: 189
Period size: 38 Copynumber: 2.8 Consensus size: 38
25654 TTTGAACTAA
*
25664 TGCTGGATCATAATCATAAAAAACATTCATTGAGCAAT
1 TGCTGGATCATAATCACAAAAAACATTCATTGAGCAAT
* *
25702 TGCTGGATCATAATCACAAAAAACATTCATTAAGCAGT
1 TGCTGGATCATAATCACAAAAAACATTCATTGAGCAAT
25740 TGCTGGATCATAATCACAAAAAACATTCATTG
1 TGCTGGATCATAATCACAAAAAACATTCATTG
25772 GACACAAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.28
Consensus pattern (38 bp):
TGCTGGATCATAATCACAAAAAACATTCATTGAGCAAT
Found at i:26302 original size:12 final size:12
Alignment explanation
Indices: 26268--26302 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
26258 TGAGCTAGAT
26268 GCAGGGCCAGAG
1 GCAGGGCCAGAG
26280 GCAGAGG-CAGAG
1 GCAG-GGCCAGAG
26292 GCAGGGCCAGA
1 GCAGGGCCAGA
26303 TCCATAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.29, C:0.23, G:0.49, T:0.00
Consensus pattern (12 bp):
GCAGGGCCAGAG
Found at i:29097 original size:30 final size:30
Alignment explanation
Indices: 29061--29172 Score: 197
Period size: 30 Copynumber: 3.7 Consensus size: 30
29051 TCAACAGCTA
* *
29061 CATCTATACCATCACCATTACCTACACCAC
1 CATCTATGCCTTCACCATTACCTACACCAC
29091 CATCTATGCCTTCACCATTACCTACACCAC
1 CATCTATGCCTTCACCATTACCTACACCAC
29121 CATCTATGCCTTCACCATTACCTACACCAC
1 CATCTATGCCTTCACCATTACCTACACCAC
*
29151 CATCTATGCCTTCACCTTTACC
1 CATCTATGCCTTCACCATTACC
29173 AGGAAGAGCT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.27, C:0.43, G:0.03, T:0.28
Consensus pattern (30 bp):
CATCTATGCCTTCACCATTACCTACACCAC
Found at i:29106 original size:18 final size:18
Alignment explanation
Indices: 29085--29166 Score: 62
Period size: 15 Copynumber: 5.2 Consensus size: 18
29075 CCATTACCTA
29085 CACCACCATCTATGCCTT
1 CACCACCATCTATGCCTT
*
29103 ---CACCAT-TA--CCTA
1 CACCACCATCTATGCCTT
29115 CACCACCATCTATGCCTT
1 CACCACCATCTATGCCTT
*
29133 ---CACCAT-TA--CCTA
1 CACCACCATCTATGCCTT
29145 CACCACCATCTATGCCTT
1 CACCACCATCTATGCCTT
29163 CACC
1 CACC
29167 TTTACCAGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 24
0.63 0.05 0.32
Matches are distributed among these distances:
12 6 0.12
14 4 0.08
15 24 0.50
16 4 0.08
18 10 0.21
ACGTcount: A:0.26, C:0.45, G:0.04, T:0.26
Consensus pattern (18 bp):
CACCACCATCTATGCCTT
Found at i:29194 original size:21 final size:21
Alignment explanation
Indices: 29170--29229 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
29160 CTTCACCTTT
*
29170 ACCAGGAAGAGCTTCTCCACC
1 ACCAGGATGAGCTTCTCCACC
29191 ACCAGGATGAGCTTCTCCACC
1 ACCAGGATGAGCTTCTCCACC
29212 ACCAGGATGAGCTTCTCC
1 ACCAGGATGAGCTTCTCC
29230 TTCCACATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.25, C:0.37, G:0.20, T:0.18
Consensus pattern (21 bp):
ACCAGGATGAGCTTCTCCACC
Found at i:29326 original size:21 final size:21
Alignment explanation
Indices: 29302--29344 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29292 CTACATCATT
*
29302 CCCACCATCATGAATAGCATC
1 CCCACCACCATGAATAGCATC
*
29323 CCCACCACCATGAATATCATC
1 CCCACCACCATGAATAGCATC
29344 C
1 C
29345 ACAGCTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.42, G:0.07, T:0.19
Consensus pattern (21 bp):
CCCACCACCATGAATAGCATC
Found at i:30413 original size:31 final size:29
Alignment explanation
Indices: 30378--30443 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
30368 CGTCCAAAAT
*
30378 TATCC-TTATTTGACGCTTTTGGGTAACGTTA
1 TATCCTTTA-TTGACG-TTTT-GGAAACGTTA
*
30409 TATCCTTTATTGACGTTTTTGAAACGTTA
1 TATCCTTTATTGACGTTTTGGAAACGTTA
30438 TATCCT
1 TATCCT
30444 GAATTGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 14 0.44
30 4 0.12
31 11 0.34
32 3 0.09
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.47
Consensus pattern (29 bp):
TATCCTTTATTGACGTTTTGGAAACGTTA
Found at i:64912 original size:18 final size:18
Alignment explanation
Indices: 64889--64923 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
64879 CTACCGACCG
64889 AATAATATATATATATAA
1 AATAATATATATATATAA
*
64907 AATAATATATATTTATA
1 AATAATATATATATATA
64924 TATATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAATATATATATATAA
Found at i:64930 original size:26 final size:25
Alignment explanation
Indices: 64894--64945 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
64884 GACCGAATAA
64894 TATATATATATAAAATAATATATATT
1 TATATATATAT-AAATAATATATATT
*
64920 TATATATATATAAATAATATTTATT
1 TATATATATATAAATAATATATATT
64945 T
1 T
64946 TTAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATATATATATAAATAATATATATT
Found at i:65704 original size:70 final size:70
Alignment explanation
Indices: 65630--65790 Score: 322
Period size: 70 Copynumber: 2.3 Consensus size: 70
65620 GTGGCTGACC
65630 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
1 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
65695 GGTTG
66 GGTTG
65700 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
1 AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
65765 GGTTG
66 GGTTG
65770 AATTTGTTTTCTTATTTTCTT
1 AATTTGTTTTCTTATTTTCTT
65791 CAATTCTCTG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 91 1.00
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (70 bp):
AATTTGTTTTCTTATTTTCTTATTTATGTTACTGAGTTGAATTTGTTTAAATCAGAAATCTTCAT
GGTTG
Found at i:73921 original size:7 final size:7
Alignment explanation
Indices: 73900--73933 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
73890 ATGGTATATA
73900 TATTGACC
1 TATTG-CC
73908 TATTGCC
1 TATTGCC
*
73915 GATTGCC
1 TATTGCC
73922 TATTGCC
1 TATTGCC
73929 TATTG
1 TATTG
73934 GGAAGTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (7 bp):
TATTGCC
Found at i:77061 original size:32 final size:32
Alignment explanation
Indices: 77020--77095 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
77010 AAAAAAAGCA
77020 ACGTGACAATGCCATGTCAGCAGTATAGTCCG
1 ACGTGACAATGCCATGTCAGCAGTATAGTCCG
*
77052 ACGTGACAATGCCATGTCAGCAGTATGGTCCG
1 ACGTGACAATGCCATGTCAGCAGTATAGTCCG
*
77084 ACGTGTCAATGC
1 ACGTGACAATGC
77096 GACATCAGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.22
Consensus pattern (32 bp):
ACGTGACAATGCCATGTCAGCAGTATAGTCCG
Found at i:77104 original size:32 final size:32
Alignment explanation
Indices: 77020--77104 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 32
77010 AAAAAAAGCA
**
77020 ACGTGACAATGCCATGTCAGCAGTATAGTCCG
1 ACGTGACAATGCCACATCAGCAGTATAGTCCG
** *
77052 ACGTGACAATGCCATGTCAGCAGTATGGTCCG
1 ACGTGACAATGCCACATCAGCAGTATAGTCCG
* *
77084 ACGTGTCAATGCGACATCAGC
1 ACGTGACAATGCCACATCAGC
77105 GGCATGACGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (32 bp):
ACGTGACAATGCCACATCAGCAGTATAGTCCG
Found at i:79774 original size:12 final size:12
Alignment explanation
Indices: 79757--79788 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
79747 TACCCTATGT
79757 AAACACGACACG
1 AAACACGACACG
79769 AAACACGACACG
1 AAACACGACACG
*
79781 AAATACGA
1 AAACACGA
79789 ATTACCAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.28, G:0.16, T:0.03
Consensus pattern (12 bp):
AAACACGACACG
Found at i:82561 original size:12 final size:12
Alignment explanation
Indices: 82546--82570 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
82536 AAAAGGGTTA
82546 AAATTTGATACT
1 AAATTTGATACT
82558 AAATTTGATACT
1 AAATTTGATACT
82570 A
1 A
82571 TTTATATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
AAATTTGATACT
Found at i:85822 original size:178 final size:179
Alignment explanation
Indices: 85498--85828 Score: 520
Period size: 178 Copynumber: 1.9 Consensus size: 179
85488 TATCCATAGA
* *
85498 AAAGTTAAAGGGCTTAATGAAGTAAAATAAAATAGTTAAAGGACTAAATAGTATAAATTAAAAAT
1 AAAGTTAAAGGGCTTAATAAAGTAAAATAAAATAGTTAAAGGACTAAATAATATAAATTAAAAAT
* * * ** * * **
85563 GTCGGGGGACTACTTTGTTAATATGCCATTATATGGCATGACATGTGTACCTCAACCAAGGGGGA
66 ATCGGGAGACTACTTTGTAAATATGCCATTATATGGCATGACAACTATACCTCAACCAAGAGAAA
85628 CAATTGTTGATAAATCCTTAGGGTTGCATCATTATAAATAAGCATATAT
131 CAATTGTTGATAAATCCTTAGGGTTGCATCATTATAAATAAGCATATAT
*
85677 AAAGTTAAAGGGCTTAATAAATTAAAATAAAATAGTTAAAGGACTAAATAATATAAATTAAAAAT
1 AAAGTTAAAGGGCTTAATAAAGTAAAATAAAATAGTTAAAGGACTAAATAATATAAATTAAAAAT
* *
85742 AT-TGGAGACTACTTTGTAAATATGCCATTATATGGCATGACAACTATCCCTCAACCAAGAGAAA
66 ATCGGGAGACTACTTTGTAAATATGCCATTATATGGCATGACAACTATACCTCAACCAAGAGAAA
*
85806 CACTTGTTGATAAATCCTTAGGG
131 CAATTGTTGATAAATCCTTAGGG
85829 GTTTATCATA
Statistics
Matches: 137, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
178 74 0.54
179 63 0.46
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (179 bp):
AAAGTTAAAGGGCTTAATAAAGTAAAATAAAATAGTTAAAGGACTAAATAATATAAATTAAAAAT
ATCGGGAGACTACTTTGTAAATATGCCATTATATGGCATGACAACTATACCTCAACCAAGAGAAA
CAATTGTTGATAAATCCTTAGGGTTGCATCATTATAAATAAGCATATAT
Found at i:88393 original size:17 final size:17
Alignment explanation
Indices: 88371--88404 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
88361 CTAAAAAAAA
88371 TAGGGATTTATTTGTCC
1 TAGGGATTTATTTGTCC
88388 TAGGGATTTATTTGTCC
1 TAGGGATTTATTTGTCC
88405 CAAAAGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (17 bp):
TAGGGATTTATTTGTCC
Found at i:89554 original size:23 final size:23
Alignment explanation
Indices: 89489--89554 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
89479 GCTTAATTAA
*
89489 CTCTCTTTCTCTTTCTCTCTCTCT
1 CTCTCTTTTTC-TTCTCTCTCTCT
* *
89513 CTCTCTTTTTTTTGGCTCTCTTTCT
1 CTCTCTTTTTCTT--CTCTCTCTCT
89538 CTC-CTGTTTTCTTCTCT
1 CTCTCT-TTTTCTTCTCT
89555 GAGCAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
23 6 0.17
24 11 0.31
25 18 0.51
ACGTcount: A:0.00, C:0.35, G:0.05, T:0.61
Consensus pattern (23 bp):
CTCTCTTTTTCTTCTCTCTCTCT
Found at i:90678 original size:17 final size:17
Alignment explanation
Indices: 90656--90691 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
90646 ATTTTGCACC
90656 ATCAAATCAAATTATAT
1 ATCAAATCAAATTATAT
90673 ATCAAATCAAATTATAT
1 ATCAAATCAAATTATAT
90690 AT
1 AT
90692 GCGTGTAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (17 bp):
ATCAAATCAAATTATAT
Found at i:91137 original size:21 final size:21
Alignment explanation
Indices: 91111--91155 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
91101 CTAAACTGAA
91111 TTGCTAAATACCGCC-CCATTT
1 TTGCTAAATACCGCCTCC-TTT
**
91132 TTGCTAGTTACCGCCTCCTTT
1 TTGCTAAATACCGCCTCCTTT
91153 TTG
1 TTG
91156 ACACTTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.16, C:0.31, G:0.13, T:0.40
Consensus pattern (21 bp):
TTGCTAAATACCGCCTCCTTT
Found at i:96083 original size:23 final size:22
Alignment explanation
Indices: 96053--96112 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 22
96043 AAGAGTTGCT
96053 AAGCATCAAAATGCTTTTGATCA
1 AAGCATCAAAATGCTTTTGAT-A
*
96076 AAGCATCAAAA---TTTTGATT
1 AAGCATCAAAATGCTTTTGATA
96095 AAGCATCAAAATGCTTTT
1 AAGCATCAAAATGCTTTT
96113 TTATAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 11 0.33
20 7 0.21
22 4 0.12
23 11 0.33
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (22 bp):
AAGCATCAAAATGCTTTTGATA
Found at i:99476 original size:19 final size:18
Alignment explanation
Indices: 99448--99487 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
99438 CAATATATAA
99448 TAAAAATAATTAATTAAC
1 TAAAAATAATTAATTAAC
* *
99466 TAAAGAATAATTTATTTAC
1 TAAA-AATAATTAATTAAC
99485 TAA
1 TAA
99488 GAAGACCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAAATAATTAATTAAC
Found at i:101895 original size:23 final size:23
Alignment explanation
Indices: 101859--101902 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
101849 TCTTTCTCCC
*
101859 CCAATCGTTCAAACTAGAAAAGA
1 CCAATCGTTCAAACAAGAAAAGA
* *
101882 CCAATTGTTGAAACAAGAAAA
1 CCAATCGTTCAAACAAGAAAA
101903 AGGATCAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (23 bp):
CCAATCGTTCAAACAAGAAAAGA
Found at i:102391 original size:23 final size:22
Alignment explanation
Indices: 102365--102436 Score: 53
Period size: 23 Copynumber: 3.2 Consensus size: 22
102355 AGTATTAATA
102365 AATACAACATTATAAATAAACAT
1 AATACAACATTAT-AATAAACAT
*
102388 AATA-ATACA-TATTAAT-AATAT
1 AATACA-ACATTA-TAATAAACAT
102409 AAATATC-ACATTAGTAATAAACAT
1 -AATA-CAACATTA-TAATAAACAT
102433 AATA
1 AATA
102437 TATATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
21 4 0.10
22 13 0.33
23 18 0.46
24 4 0.10
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.31
Consensus pattern (22 bp):
AATACAACATTATAATAAACAT
Found at i:102392 original size:13 final size:14
Alignment explanation
Indices: 102360--102396 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
102350 TGTATAGTAT
102360 TAATAAATACAACA
1 TAATAAATACAACA
*
102374 TTATAAATA-AACA
1 TAATAAATACAACA
102387 TAAT-AATACA
1 TAATAAATACA
102397 TATTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (14 bp):
TAATAAATACAACA
Found at i:102802 original size:11 final size:11
Alignment explanation
Indices: 102786--102812 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
102776 GAAGAAGAAG
102786 AAAAAAAAACT
1 AAAAAAAAACT
102797 AAAAAAAAACT
1 AAAAAAAAACT
102808 AAAAA
1 AAAAA
102813 TGAGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAAAACT
Found at i:103108 original size:13 final size:13
Alignment explanation
Indices: 103090--103114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
103080 TGTAACATAG
103090 TTATTATTATTAA
1 TTATTATTATTAA
103103 TTATTATTATTA
1 TTATTATTATTA
103115 TTAAGAGTAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:105794 original size:2 final size:2
Alignment explanation
Indices: 105787--105818 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
105777 TATAATTAGC
105787 AT AT 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 AT AT
105819 TGCCTTCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.