Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014988.1 Corchorus capsularis cultivar CVL-1 contig15009, 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: 107958
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:162 original size:2 final size:2
Alignment explanation
Indices: 155--182 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
145 CTTGGAGTAT
155 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
183 ATTGACATTT
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):
TA
Found at i:1647 original size:29 final size:30
Alignment explanation
Indices: 1592--1652 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
1582 ATATTTATCT
* *
1592 TATAATGGGTAGTTTTTTTTCTAAAATTGG
1 TATAATGGGTAGTTTTTTATCTAAAATGGG
1622 TATAATGGGTAG-TTTTTATCTAAAATGGG
1 TATAATGGGTAGTTTTTTATCTAAAATGGG
1651 TA
1 TA
1653 GTTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (30 bp):
TATAATGGGTAGTTTTTTATCTAAAATGGG
Found at i:7020 original size:16 final size:16
Alignment explanation
Indices: 6999--7029 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6989 CATTGCTGAG
6999 ATGTACATCACATGAT
1 ATGTACATCACATGAT
7015 ATGTACATCACATGA
1 ATGTACATCACATGA
7030 AACTAGTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (16 bp):
ATGTACATCACATGAT
Found at i:10137 original size:17 final size:17
Alignment explanation
Indices: 10115--10147 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10105 GTGAGTATAA
*
10115 AATTTCATCTATATTAG
1 AATTTCATCCATATTAG
10132 AATTTCATCCATATTA
1 AATTTCATCCATATTA
10148 ATGTATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTTCATCCATATTAG
Found at i:10418 original size:109 final size:108
Alignment explanation
Indices: 10205--10419 Score: 328
Period size: 109 Copynumber: 2.0 Consensus size: 108
10195 ATTAATCGGA
* * *
10205 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTTTAAGGCTGGGATACTCGGA
1 TATATTAATTATTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATACTCGGA
*
10270 AAAAAGAAAACCAAAAAATTGATTTAAGGATATTTTTAATTAAT
66 AAAAAGAAAACAAAAAAATTGA-TTAAGGATATTTTTAATTAAT
* * *
10314 TATATTAATTATTGAACAAAATAATTCGACTTTACATTATAAATTATAAGGCTGAGATATTC-GA
1 TATATTAATTATTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATACTCGGA
*
10378 AAAAA-AAAACAAAAAAATTGA-TAAGGATATTGTTAATTAAT
66 AAAAAGAAAACAAAAAAATTGATTAAGGATATTTTTAATTAAT
10419 T
1 T
10420 TTTACATTAT
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
105 20 0.20
107 15 0.15
108 7 0.07
109 56 0.57
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.34
Consensus pattern (108 bp):
TATATTAATTATTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATACTCGGA
AAAAAGAAAACAAAAAAATTGATTAAGGATATTTTTAATTAAT
Found at i:11189 original size:31 final size:31
Alignment explanation
Indices: 11154--11212 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
11144 GTTAGATAAG
** *
11154 TAAGGATATAATAGGTATTTTAAAAGTTAAA
1 TAAGGATATAATAGACATTTCAAAAGTTAAA
*
11185 TAAGGGTATAATAGACATTTCAAAAGTT
1 TAAGGATATAATAGACATTTCAAAAGTT
11213 TCTCAAAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (31 bp):
TAAGGATATAATAGACATTTCAAAAGTTAAA
Found at i:11673 original size:26 final size:25
Alignment explanation
Indices: 11634--11689 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
11624 CTATTTCACA
* *
11634 ATTATTACTGATAATTTTTATATATT
1 ATTATTAATGATAATTTTTA-ATATG
*
11660 ATTATTAATTATAATTTTTAATATG
1 ATTATTAATGATAATTTTTAATATG
11685 ATTAT
1 ATTAT
11690 AGGTCAGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
ATTATTAATGATAATTTTTAATATG
Found at i:32643 original size:27 final size:27
Alignment explanation
Indices: 32613--32665 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
32603 CATACTTTCC
32613 CACTACATTGCACGAACCAAACACAAT
1 CACTACATTGCACGAACCAAACACAAT
*
32640 CACTACATTGCATGAACCAAACACAA
1 CACTACATTGCACGAACCAAACACAA
32666 CCTAAAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.32, G:0.08, T:0.15
Consensus pattern (27 bp):
CACTACATTGCACGAACCAAACACAAT
Found at i:33049 original size:29 final size:29
Alignment explanation
Indices: 32986--33056 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
32976 AGCATTTGAT
32986 CGTTTTGTCCCTTGAACTTCAATTTTGGA
1 CGTTTTGTCCCTTGAACTTCAATTTTGGA
* *
33015 CATTTTGTCGC-TGAACTTCAATTTTGGGA
1 CGTTTTGTCCCTTGAACTTCAATTTT-GGA
* *
33044 TGTTTTGCCCCTT
1 CGTTTTGTCCCTT
33057 TAACCTAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 14 0.41
29 19 0.56
30 1 0.03
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (29 bp):
CGTTTTGTCCCTTGAACTTCAATTTTGGA
Found at i:41999 original size:22 final size:23
Alignment explanation
Indices: 41969--42018 Score: 93
Period size: 22 Copynumber: 2.2 Consensus size: 23
41959 TTTTTCTGTT
41969 TTGTCATTGTTCTTCCTGCTCAG
1 TTGTCATTGTTCTTCCTGCTCAG
41992 TTGT-ATTGTTCTTCCTGCTCAG
1 TTGTCATTGTTCTTCCTGCTCAG
42014 TTGTC
1 TTGTC
42019 GTCTTGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.08, C:0.24, G:0.18, T:0.50
Consensus pattern (23 bp):
TTGTCATTGTTCTTCCTGCTCAG
Found at i:50463 original size:5 final size:6
Alignment explanation
Indices: 50447--50473 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
50437 ATTTTTGCAC
50447 CTTTTT CTTTTT CTTTTT CTTTTT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT
50474 ATTTTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:51845 original size:23 final size:23
Alignment explanation
Indices: 51819--51888 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
51809 GAATTGTTAG
51819 TAATCACACTCTTGAAATTTTGA
1 TAATCACACTCTTGAAATTTTGA
* *
51842 TAATCACACT-ATGAAATTGTGA
1 TAATCACACTCTTGAAATTTTGA
* *
51864 TAA-C-CTCGCTATGAAATTTTGA
1 TAATCACACTCT-TGAAATTTTGA
51886 TAA
1 TAA
51889 ATCTTCCTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 2 0.05
21 1 0.03
22 26 0.67
23 10 0.26
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (23 bp):
TAATCACACTCTTGAAATTTTGA
Found at i:51859 original size:22 final size:22
Alignment explanation
Indices: 51831--52060 Score: 142
Period size: 22 Copynumber: 10.6 Consensus size: 22
51821 ATCACACTCT
*
51831 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAATCTCACTA
* * *
51853 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAATCTCACTA
51875 TGAAATTTTGATAAATCTTC-CTA
1 TGAAATTTTGAT-AATC-TCACTA
* * *
51898 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AATCTCACTA
* * *
51921 TAAAATTTTGATAACTTTC-TTA
1 TGAAATTTTGATAA-TCTCACTA
51943 TGAAATTTTGATAA-CT-AC--
1 TGAAATTTTGATAATCTCACTA
*
51961 --AAATTTTGATAA-CATCCCTA
1 TGAAATTTTGATAATC-TCACTA
** * *
51981 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAATCTCACTA
* *
52003 TGAATTTTTGTTAATCTC-CATA
1 TGAAATTTTGATAATCTCAC-TA
*
52025 TGAAATTTTGAT-CTACAT-ACTA
1 TGAAATTTTGATAAT-C-TCACTA
52047 TGAAATTTTGATAA
1 TGAAATTTTGATAA
52061 CCCTCTTGTG
Statistics
Matches: 164, Mismatches: 27, Indels: 33
0.73 0.12 0.15
Matches are distributed among these distances:
16 13 0.08
17 1 0.01
18 1 0.01
20 1 0.01
21 1 0.01
22 104 0.63
23 41 0.25
24 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCACTA
Found at i:51903 original size:23 final size:23
Alignment explanation
Indices: 51872--51956 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
51862 GATAACCTCG
*
51872 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
51895 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
51918 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* *
51940 TTATGAAATTTTGATAA
1 CTATAAAATTTTGATAA
51957 CTACAAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
22 17 0.31
23 37 0.69
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:51950 original size:45 final size:46
Alignment explanation
Indices: 51833--51956 Score: 148
Period size: 45 Copynumber: 2.8 Consensus size: 46
51823 CACACTCTTG
* * * *
51833 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATTTTGATAAACCTCCCTATA
*
51877 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCTCCCTATA
* *
51923 AAATTTTGATAACT-TTCTTATGAAATTTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAA
51957 CTACAAATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
44 10 0.14
45 35 0.51
46 24 0.35
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (46 bp):
AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCTCCCTATA
Found at i:51983 original size:38 final size:38
Alignment explanation
Indices: 51923--51995 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
51913 CCTCCCTATA
* * *
51923 AAATTTTGATAACTTTCTTATGAAATTTTGATAACTAC
1 AAATTTTGATAACATCCCTATGAAATTTTGATAACTAC
**
51961 AAATTTTGATAACATCCCTATGATTTTTTGATAAC
1 AAATTTTGATAACATCCCTATGAAATTTTGATAAC
51996 CTCATTATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (38 bp):
AAATTTTGATAACATCCCTATGAAATTTTGATAACTAC
Found at i:52072 original size:22 final size:22
Alignment explanation
Indices: 52047--52122 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
52037 CTACATACTA
*
52047 TGAAATTTTGATAACCCTCTTG
1 TGAAATTTTGATAACCATCTTG
* * ** *
52069 TGAAATTTTGAAAACTAAATTA
1 TGAAATTTTGATAACCATCTTG
* * *
52091 TGAAATTTTGATGACCTTCATG
1 TGAAATTTTGATAACCATCTTG
52113 TGAAATTTTG
1 TGAAATTTTG
52123 GGCTAATTGT
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCATCTTG
Found at i:52073 original size:44 final size:43
Alignment explanation
Indices: 52025--52122 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 43
52015 AATCTCCATA
* *
52025 TGAAATTTTG-ATCTACATACTATGAAATTTTGATAACCCTCTTG
1 TGAAATTTTGAAACTA-A-ACTATGAAATTTTGATAACCCTCATG
* * *
52069 TGAAATTTTGAAAACTAAATTATGAAATTTTGATGACCTTCATG
1 TGAAATTTTG-AAACTAAACTATGAAATTTTGATAACCCTCATG
52113 TGAAATTTTG
1 TGAAATTTTG
52123 GGCTAATTGT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 42 0.89
45 1 0.02
46 4 0.09
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (43 bp):
TGAAATTTTGAAACTAAACTATGAAATTTTGATAACCCTCATG
Found at i:52171 original size:31 final size:30
Alignment explanation
Indices: 52133--52297 Score: 108
Period size: 31 Copynumber: 5.5 Consensus size: 30
52123 GGCTAATTGT
52133 TCAAATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTT-CCAAAATGC
* * * **
52164 TCAAATAAGGGCCCGATC-TTT-TAATTTGGC
1 TCAAATAAGGG-CCTAACGTTTCCAAAAT-GC
*
52194 T-AAATAAGGGCCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCTAACGTT-TCCAAAATGC
* * * **
52224 TCAAATAAGGGCATGATC-TTT-TAATTTGAC
1 TCAAATAAGGGCCT-AACGTTTCCAAAATG-C
* *
52254 -CAAATAAGGGTCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCTAACGTT-TCCAAAATGC
52284 TCAAATAAGGGCCT
1 TCAAATAAGGGCCT
52298 GGTGTCAGTT
Statistics
Matches: 100, Mismatches: 22, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
28 6 0.06
29 31 0.31
30 11 0.11
31 46 0.46
32 6 0.06
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (30 bp):
TCAAATAAGGGCCTAACGTTTCCAAAATGC
Found at i:52228 original size:60 final size:60
Alignment explanation
Indices: 52134--52296 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
52124 GCTAATTGTT
* *
52134 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* **
52194 TAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCATGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
*
52254 CAAATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
52297 TGGTGTCAGT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 93 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:52362 original size:31 final size:30
Alignment explanation
Indices: 52327--52492 Score: 139
Period size: 31 Copynumber: 5.5 Consensus size: 30
52317 CGTGAGACAT
52327 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTT-GCAAACGTTAG
** **
52358 GCCCTTATTTG-GCCAAATT-CAAA-GATGGG
1 GCCCTTATTTGAG-CATTTTGCAAACG-TTAG
52387 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTT-GCAAACGTTAG
* * * *
52418 GCCCTTATTTG-GCCGA-ATT--AAAAGATCG
1 GCCCTTATTTGAG-C-ATTTTGCAAACGTTAG
52446 GACCCTTATTTGAGCATTTTGACAAACGTTAG
1 G-CCCTTATTTGAGCATTTTG-CAAACGTTAG
52478 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
52493 ATTAGCCGAA
Statistics
Matches: 105, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
28 9 0.09
29 34 0.32
30 4 0.04
31 49 0.47
32 9 0.09
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (30 bp):
GCCCTTATTTGAGCATTTTGCAAACGTTAG
Found at i:52400 original size:60 final size:60
Alignment explanation
Indices: 52327--52488 Score: 279
Period size: 60 Copynumber: 2.7 Consensus size: 60
52317 CGTGAGACAT
* *
52327 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
*
52387 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCGAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
* *
52447 ACCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
52489 AGCAATTAGC
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
Found at i:52528 original size:19 final size:20
Alignment explanation
Indices: 52504--52549 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
52494 TTAGCCGAAT
*
52504 TTTTGATATCCTCCCTG-AA
1 TTTTGATATCCTCCATGAAA
*
52523 TTTTGATATTCTCCATGAAA
1 TTTTGATATCCTCCATGAAA
52543 TTTTGAT
1 TTTTGAT
52550 TACTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (20 bp):
TTTTGATATCCTCCATGAAA
Found at i:52676 original size:22 final size:22
Alignment explanation
Indices: 52651--52897 Score: 127
Period size: 22 Copynumber: 11.3 Consensus size: 22
52641 AATCACATTT
*
52651 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
52673 TGAAATTTTGATAATCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * *
52695 T-AAGATTTTGTTGACCCCTTTA
1 TGAA-ATTTTGATAACCTCTTTA
* * * *
52717 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
52739 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
52761 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
* *
52783 TGAAATTTTGATAA-TTTTTCTA
1 TGAAATTTTGATAACCTCTT-TA
*
52805 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* *
52829 TAAAATTTCGATAA--TCATTCTA
1 TGAAATTTTGATAACCTC-TT-TA
* *
52851 TGAGA-TTTGATAACCT-TATA
1 TGAAATTTTGATAACCTCTTTA
* * *
52871 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
52891 TGAAATT
1 TGAAATT
52898 GAGACTTTTA
Statistics
Matches: 167, Mismatches: 42, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.01
20 16 0.10
21 29 0.17
22 99 0.59
23 5 0.03
24 3 0.02
25 13 0.08
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:52677 original size:44 final size:44
Alignment explanation
Indices: 52627--52819 Score: 166
Period size: 44 Copynumber: 4.4 Consensus size: 44
52617 GAAATATCAC
*
52627 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTTTGAAATTTTGATAACCTCTT
* * * *
52671 TATGAAATTTTGATAATCTC-TTTAT-AAGATTTTGTTGACCCCTT
1 TATGAAATTTTGATAATCACATTT-TGAA-ATTTTGATAACCTCTT
* * * *
52715 TATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTTTGAAATTTTGATAACCTC-TT
* * * *
52760 T-TGAAATTTTGATAA-CAACACTATGAAATTTTGATAA-TTTTT
1 TATGAAATTTTGATAATC-ACATTTTGAAATTTTGATAACCTCTT
52802 CTAT-AAATTTTGATAATC
1 -TATGAAATTTTGATAATC
52820 CGATCTCTAT
Statistics
Matches: 120, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
42 1 0.01
43 25 0.21
44 89 0.74
45 5 0.04
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.45
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTTTGAAATTTTGATAACCTCTT
Found at i:52791 original size:88 final size:88
Alignment explanation
Indices: 52627--52792 Score: 196
Period size: 88 Copynumber: 1.9 Consensus size: 88
52617 GAAATATCAC
* * * * *
52627 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAATCTCT
1 TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAATCACA
*
52692 TTATAAGATTTTGTTGACCCCTT
66 CTATAAGATTTTGTTGACCCCTT
* *
52715 TATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAA-CA
1 TATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAATC-
52777 ACACTATGAA-ATTTTG
63 ACACTAT-AAGATTTTG
52793 ATAATTTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
87 5 0.08
88 57 0.86
89 4 0.06
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (88 bp):
TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAATCACA
CTATAAGATTTTGTTGACCCCTT
Found at i:53100 original size:22 final size:22
Alignment explanation
Indices: 53068--53132 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
53058 TTGTGATAAT
*
53068 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTCAA
* ** *
53090 TAACCAACCTAAGAGGTTTTAA
1 TAACCAACCTATGAAATTTCAA
53112 TAACCTAATCCTATGAAATTT
1 TAACC-AA-CCTATGAAATTT
53133 TGGCAACCAC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 22 0.67
23 2 0.06
24 9 0.27
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.31
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTCAA
Found at i:53162 original size:22 final size:22
Alignment explanation
Indices: 53122--53209 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
53112 TAACCTAATC
**
53122 CTATGAAATTTTGGCAACCACA
1 CTATGAAATTTTGATAACCACA
* *
53144 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * *
53165 CTCATTAAATTATAATAACCATCA
1 CT-ATGAAATTTTGATAACCA-CA
53189 -TATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
53210 TAGAGACAAG
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
21 4 0.08
22 45 0.88
23 2 0.04
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:56184 original size:8 final size:8
Alignment explanation
Indices: 56171--56210 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
56161 TTTTTTGGTA
*
56171 ACATATGT
1 ACATATAT
56179 ACATATAT
1 ACATATAT
*
56187 ACATACAT
1 ACATATAT
*
56195 ACATACAT
1 ACATATAT
56203 ACATATAT
1 ACATATAT
56211 GCATGTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (8 bp):
ACATATAT
Found at i:56194 original size:4 final size:4
Alignment explanation
Indices: 56178--56207 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
56168 GTAACATATG
*
56178 TACA TATA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
56208 TATGCATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (4 bp):
TACA
Found at i:56195 original size:12 final size:12
Alignment explanation
Indices: 56178--56210 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
56168 GTAACATATG
56178 TACATATATACA
1 TACATATATACA
*
56190 TACATACATACA
1 TACATATATACA
56202 TACATATAT
1 TACATATAT
56211 GCATGTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (12 bp):
TACATATATACA
Found at i:59867 original size:6 final size:6
Alignment explanation
Indices: 59856--59885 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
59846 TTAGTTTCTT
*
59856 TTTTTC TTTTTC ATTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
59886 AAATTAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:62079 original size:14 final size:17
Alignment explanation
Indices: 62049--62085 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
62039 TAATAACATA
62049 GAATTTGTAAGAAGTTT
1 GAATTTGTAAGAAGTTT
62066 -AATTTGT-A-AAGTTT
1 GAATTTGTAAGAAGTTT
62080 GAATTT
1 GAATTT
62086 TTTTGACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.32
15 6 0.32
16 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (17 bp):
GAATTTGTAAGAAGTTT
Found at i:65795 original size:2 final size:2
Alignment explanation
Indices: 65778--65849 Score: 63
Period size: 2 Copynumber: 40.5 Consensus size: 2
65768 CGTTTAGTTA
* *
65778 AT AT AT A- AT -T AA AT AT AT TT AT AT AT AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65816 -T AT AT AT AT A- AT -T AT AT AT AT A- AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65850 ATTATTAAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
1 9 0.16
2 48 0.84
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:66165 original size:34 final size:34
Alignment explanation
Indices: 66104--66180 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
66094 CATTCTCAAT
* *
66104 GGTAA-TTACAAGGGCTTTCTTGTATATTCTTCA
1 GGTAACTTGCAAGGGCTTTCTCGTATATTCTTCA
* *
66137 GGTAAACTTGCAAGGGCTTTGTCG-ATATTCTTGA
1 GGT-AACTTGCAAGGGCTTTCTCGTATATTCTTCA
66171 GGTAACTTGC
1 GGTAACTTGC
66181 TATTCAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 10 0.26
34 14 0.37
35 14 0.37
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (34 bp):
GGTAACTTGCAAGGGCTTTCTCGTATATTCTTCA
Found at i:70092 original size:21 final size:21
Alignment explanation
Indices: 70040--70092 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
70030 TTTAAATGTC
*
70040 TCATTATGAACCCGCAACTCA
1 TCATTATGAGCCCGCAACTCA
*
70061 TCA-TATTGAGCCCGCATCTCA
1 TCATTA-TGAGCCCGCAACTCA
*
70082 TCATTAAGAGC
1 TCATTATGAGC
70093 ATCAGTGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.26
Consensus pattern (21 bp):
TCATTATGAGCCCGCAACTCA
Found at i:84171 original size:14 final size:14
Alignment explanation
Indices: 84152--84179 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
84142 ATAGTATAGA
84152 TATAGATTAATTAT
1 TATAGATTAATTAT
84166 TATAGATTAATTAT
1 TATAGATTAATTAT
84180 GAGTGGTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TATAGATTAATTAT
Found at i:89715 original size:21 final size:21
Alignment explanation
Indices: 89691--89731 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
89681 TACTTTCCTT
*
89691 GTAAAGAGTTT-TCCTTCATTA
1 GTAAA-AGTTTATACTTCATTA
89712 GTAAAAGTTTATACTTCATT
1 GTAAAAGTTTATACTTCATT
89732 TCATTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
GTAAAAGTTTATACTTCATTA
Found at i:95518 original size:55 final size:55
Alignment explanation
Indices: 95434--95541 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
95424 CTTACTTGGC
* *
95434 GCAATGTCCACAGCAATGAATTGATTCAAATTTCTTTGGCATAACGAGAGCTAAT
1 GCAATGTCCACAGCAATGAATTGATTCAAAGTTCTTTGGCATAACAAGAGCTAAT
* *
95489 GCAATGTCCACAGTAATGAATTTATTCAAAGTTCTTTGGCATAACAAGAGCTA
1 GCAATGTCCACAGCAATGAATTGATTCAAAGTTCTTTGGCATAACAAGAGCTA
95542 TCTGACACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (55 bp):
GCAATGTCCACAGCAATGAATTGATTCAAAGTTCTTTGGCATAACAAGAGCTAAT
Done.