Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023851.1 Corchorus olitorius cultivar O-4 contig23884, 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: 128041
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:34 original size:2 final size:2
Alignment explanation
Indices: 27--79 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
17 TACTATTTAG
*
27 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69 TA CTA TA TA TA
1 TA -TA TA TA TA
80 AGAGTACGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:167 original size:27 final size:26
Alignment explanation
Indices: 136--219 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 26
126 TTTTTTAAAC
*
136 ATATTTCTAAATTGACATTATTAAAAT
1 ATATTT-TAAATTGCCATTATTAAAAT
*
163 ATATTTTAATTATGCCATTATTATTAAA-
1 ATATTTTAAAT-TGCCATTATTA--AAAT
* *
191 ATATATAAAATTGCCATTATTAAAAT
1 ATATTTTAAATTGCCATTATTAAAAT
217 ATA
1 ATA
220 AAGTCCTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
25 3 0.06
26 7 0.15
27 27 0.56
28 8 0.17
29 3 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATTTTAAATTGCCATTATTAAAAT
Found at i:1092 original size:24 final size:21
Alignment explanation
Indices: 1002--1142 Score: 72
Period size: 22 Copynumber: 6.3 Consensus size: 21
992 AATGATATAT
* *
1002 AATTTCATAGAGAGATTATCGA
1 AATTTCATAGA-AGGTTATCAA
* *
1024 AATTTCATACTATGG-TATCAAA
1 AATTTCATA-GAAGGTTATC-AA
* *
1046 AATTT-ATAGGGAGATTAAT-AA
1 AATTTCATA-GAAGGTT-ATCAA
1067 AATTTCATAGAGAGGGTTATCAAA
1 AATTTCATAGA-A-GGTTATC-AA
**
1091 AAAATCATATGAAGGTTATCAA
1 AATTTCATA-GAAGGTTATCAA
* *
1113 AATTTCATAGAAAAGTTTATTAA
1 AATTTCATAG--AAGGTTATCAA
1136 AATTTCA
1 AATTTCA
1143 ATGTTAAGTT
Statistics
Matches: 90, Mismatches: 17, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
21 17 0.19
22 32 0.36
23 29 0.32
24 10 0.11
25 2 0.02
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (21 bp):
AATTTCATAGAAGGTTATCAA
Found at i:1120 original size:22 final size:22
Alignment explanation
Indices: 1002--1232 Score: 63
Period size: 22 Copynumber: 10.4 Consensus size: 22
992 AATGATATAT
* *
1002 AATTTCATA-GAGAGATTATCGA
1 AATTTCATATGA-AGGTTATCAA
*
1024 AATTTCATACT-ATGG-TATCAAA
1 AATTTCATA-TGAAGGTTATC-AA
* * *
1046 AATTT-ATAGGGAGATTAAT-AA
1 AATTTCATATGAAGGTT-ATCAA
1067 AATTTCATA-GAGAGGGTTATCAAA
1 AATTTCATATGA-A-GGTTATC-AA
**
1091 AAAATCATATGAAGGTTATCAA
1 AATTTCATATGAAGGTTATCAA
* *
1113 AATTTCATA-GAAAAGTTTATTAA
1 AATTTCATATG--AAGGTTATCAA
*
1136 AATTTCA-ATGTTAA-GTTATCAG
1 AATTTCATATG--AAGGTTATCAA
* * * *
1158 TATTTCAT-TGGGAGTTTATCAC
1 AATTTCATAT-GAAGGTTATCAA
* ** *
1180 AATTTCATA-AAATAATCATCAA
1 AATTTCATATGAA-GGTTATCAA
* *
1202 AATTTCATAGTG-TGTTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
1224 AATTTCATA
1 AATTTCATA
1233 AAAATATTTA
Statistics
Matches: 151, Mismatches: 36, Indels: 44
0.65 0.16 0.19
Matches are distributed among these distances:
21 19 0.13
22 87 0.58
23 33 0.22
24 10 0.07
25 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:15673 original size:19 final size:19
Alignment explanation
Indices: 15649--15688 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
15639 TATGATCAAA
15649 CATCTAAATGAGAAATGAC
1 CATCTAAATGAGAAATGAC
15668 CATCTAAATGAGAAATGAC
1 CATCTAAATGAGAAATGAC
15687 CA
1 CA
15689 GATGAACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (19 bp):
CATCTAAATGAGAAATGAC
Found at i:19538 original size:4 final size:4
Alignment explanation
Indices: 19529--19562 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
19519 TTCTAAACAT
*
19529 AATA AATA AACA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
19563 CTCAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:19546 original size:12 final size:12
Alignment explanation
Indices: 19522--19563 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
19512 CCATCATTTC
19522 TAAACATAATAAA
1 TAAACA-AATAAA
19535 TAAACAAATAAA
1 TAAACAAATAAA
*
19547 TAAATAAATAAA
1 TAAACAAATAAA
19559 TAAAC
1 TAAAC
19564 TCAGAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 21 0.78
13 6 0.22
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAACAAATAAA
Found at i:26781 original size:7 final size:7
Alignment explanation
Indices: 26771--26800 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
26761 TCGTTTTCGT
26771 TTTTTTG
1 TTTTTTG
26778 TTTTTTG
1 TTTTTTG
26785 TTTTTTG
1 TTTTTTG
26792 -TTTTTG
1 TTTTTTG
26798 TTT
1 TTT
26801 CGTTTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTTTG
Found at i:26788 original size:14 final size:13
Alignment explanation
Indices: 26771--26800 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
26761 TCGTTTTCGT
26771 TTTTTTGTTTTTTG
1 TTTTTTG-TTTTTG
26785 TTTTTTGTTTTTG
1 TTTTTTGTTTTTG
26798 TTT
1 TTT
26801 CGTTTTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (13 bp):
TTTTTTGTTTTTG
Found at i:26812 original size:22 final size:23
Alignment explanation
Indices: 26787--26835 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
26777 GTTTTTTGTT
* *
26787 TTTTGTTTTTGTTTCGTTTTC-A
1 TTTTGTTTTTGTTGCGTTGTCAA
26809 TTTTGTTTTTGTTGCGTTGTCAA
1 TTTTGTTTTTGTTGCGTTGTCAA
26832 TTTT
1 TTTT
26836 TGAAAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.06, C:0.08, G:0.16, T:0.69
Consensus pattern (23 bp):
TTTTGTTTTTGTTGCGTTGTCAA
Found at i:27114 original size:137 final size:135
Alignment explanation
Indices: 26836--27122 Score: 396
Period size: 137 Copynumber: 2.1 Consensus size: 135
26826 TGTCAATTTT
26836 TGAAAACAAAAACATGTTTGGATATACATTTTGGTTATATGTTTTTAAATAAAAAAATTTAAAAA
1 TGAAAACAAAAACATGTTTGGATATACATTTTGGTTATATGTTTTTAAATAAAAAAATTTAAAAA
**** *
26901 AAAGGTTAAAAAGCATGTGAGTTACTGTTCATCATTGTGTTTTTATTTTGTTTTTGTTGCGTTGT
66 AAAGGTTAAAAAGCATGTGAGTTACTGTTCATCATTGTGTTTTTATTTTGAAAGTGTT--GTTGG
* ****
26966 CAATTTT
129 AAAAACA
* *
26973 TGAAAACAAAAACATGTTTGGATATACATTTTGGTTGTATGTTTTTAAATAAAAAAGTTTTAAAA
1 TGAAAACAAAAACATGTTTGGATATACATTTTGGTTATATGTTTTTAAATAAAAAA-ATTTAAAA
*
27038 AAAAGGTTAAAAAGCATGTGAGTTACTGTTCATCATTGTGTTTCTGTGTTTTGAAAGTGTT-TTG
65 AAAAGGTTAAAAAGCATGTGAGTTACTGTTCATCATTGTGTTT-T-TATTTTGAAAGTGTTGTTG
27102 GAAAAACA
128 GAAAAACA
27110 TGAAAACACAAAA
1 TGAAAACA-AAAA
27123 TTCTTGCTTC
Statistics
Matches: 133, Mismatches: 13, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
137 68 0.51
138 54 0.41
139 1 0.01
140 10 0.08
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.39
Consensus pattern (135 bp):
TGAAAACAAAAACATGTTTGGATATACATTTTGGTTATATGTTTTTAAATAAAAAAATTTAAAAA
AAAGGTTAAAAAGCATGTGAGTTACTGTTCATCATTGTGTTTTTATTTTGAAAGTGTTGTTGGAA
AAACA
Found at i:30872 original size:244 final size:244
Alignment explanation
Indices: 30427--30890 Score: 694
Period size: 244 Copynumber: 1.9 Consensus size: 244
30417 TTTCTTACAA
*
30427 GTACATTTGGAGATGTTAGAAATTAAAGCGATTTCGTCAAGTTTTAAGAAATAATGTGAAGAACT
1 GTACATTTGGAGATGTTAGAAATTAAAGCGATTTCGTCAAGTTTTAAGAAATAATGTGAAGAACC
* * * *
30492 GAATCTCGGAACATGACCACGAGTGGACGACCTTTCTAGACGCAATTGGAACATAAAACGAGGCA
66 GAATCTCAGAACATGACCACGAGTGGACAACCTTCCTAGACGCAATTGGAACACAAAACGAGGCA
** * * * * * * * *
30557 AAATGATGGGGATGTAGCTTCTGAGGATTGAGGCTTGCCGTCGCAGGAAGGCCGTGCGCGGCTAG
131 AAACAACGAGGATGTAGCTTCTGAGGACTGAGGCTTGCCATCGCAGGAAGGCCATGCACGACTAA
30622 CCCCCTGGACGAGAACAAACCATCTAATTGCTTTATTTTTGCCTTATAT
196 CCCCCTGGACGAGAACAAACCATCTAATTGCTTTATTTTTGCCTTATAT
*
30671 GTACATTTGGAGATGTTAGAAATTAAAGCGATTTCGTCAAGTTTTAAGAACTAATGTGAAGAACC
1 GTACATTTGGAGATGTTAGAAATTAAAGCGATTTCGTCAAGTTTTAAGAAATAATGTGAAGAACC
** * * * * * *
30736 GAATCTCAGAACATGACTGCTAGTGGACAATCTTCCTAGATGCAATTGGAACACAATATGAGTCA
66 GAATCTCAGAACATGACCACGAGTGGACAACCTTCCTAGACGCAATTGGAACACAAAACGAGGCA
*
30801 AAACAACGAGGATGTAGCTTCTGAGGACTGAGGCTTGTCATCGCAGGAAGGCCATGCACGACTAA
131 AAACAACGAGGATGTAGCTTCTGAGGACTGAGGCTTGCCATCGCAGGAAGGCCATGCACGACTAA
*
30866 CCCCCTGGACGAGACCAAACCATCT
196 CCCCCTGGACGAGAACAAACCATCT
30891 GAGGCTTGTC
Statistics
Matches: 194, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
244 194 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (244 bp):
GTACATTTGGAGATGTTAGAAATTAAAGCGATTTCGTCAAGTTTTAAGAAATAATGTGAAGAACC
GAATCTCAGAACATGACCACGAGTGGACAACCTTCCTAGACGCAATTGGAACACAAAACGAGGCA
AAACAACGAGGATGTAGCTTCTGAGGACTGAGGCTTGCCATCGCAGGAAGGCCATGCACGACTAA
CCCCCTGGACGAGAACAAACCATCTAATTGCTTTATTTTTGCCTTATAT
Found at i:36011 original size:31 final size:31
Alignment explanation
Indices: 35973--36036 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
35963 AATTTTGGCT
*
35973 AAATGCTCAATTTGTTACCAAACCTTTCAAG
1 AAATGCTCAATTTGATACCAAACCTTTCAAG
36004 AAATGCTCAATTTGATACCAAACCTTTCAAG
1 AAATGCTCAATTTGATACCAAACCTTTCAAG
36035 AA
1 AA
36037 TGTTGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (31 bp):
AAATGCTCAATTTGATACCAAACCTTTCAAG
Found at i:53860 original size:24 final size:24
Alignment explanation
Indices: 53804--53860 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
53794 AAATTGACTT
53804 CTGCAGCTGTTGCAATAGCAGCAG
1 CTGCAGCTGTTGCAATAGCAGCAG
* * *
53828 CAGCTGCTGTTGCAA-AGGCTGCAG
1 CTGCAGCTGTTGCAATA-GCAGCAG
53852 CTGCAGCTG
1 CTGCAGCTG
53861 CCAATGTAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (24 bp):
CTGCAGCTGTTGCAATAGCAGCAG
Found at i:57948 original size:39 final size:40
Alignment explanation
Indices: 57905--57985 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
57895 TCTTCAAAGA
* *
57905 ACCAAAACAATTTATATCCAATCACTC-AAAGACAATTTT
1 ACCAAAAAAATTTATATCCAATCACTCAAAACACAATTTT
57944 ACCAAAAAAATTTATATCCAATCACTCGAAAACACAATTTT
1 ACCAAAAAAATTTATATCCAATCACTC-AAAACACAATTTT
57985 A
1 A
57986 TATTGGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 26 0.68
41 12 0.32
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.27
Consensus pattern (40 bp):
ACCAAAAAAATTTATATCCAATCACTCAAAACACAATTTT
Found at i:82762 original size:21 final size:21
Alignment explanation
Indices: 82738--82777 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
82728 GCAAATTGTT
82738 TATAACAAAAATATAATAATA
1 TATAACAAAAATATAATAATA
* * *
82759 TATAATAATAGTATAATAA
1 TATAACAAAAATATAATAA
82778 CATGAAATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
TATAACAAAAATATAATAATA
Found at i:82763 original size:10 final size:10
Alignment explanation
Indices: 82748--82777 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
82738 TATAACAAAA
82748 ATATAATAAT
1 ATATAATAAT
82758 ATATAATAAT
1 ATATAATAAT
82768 AGTATAATAA
1 A-TATAATAA
82778 CATGAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
ATATAATAAT
Found at i:87039 original size:25 final size:25
Alignment explanation
Indices: 86989--87039 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
86979 ATTGTGGTGC
** **
86989 TCACATTGTTGATTCTTTTTTTTTT
1 TCACATTGTTGATTCAATTTGGTTT
87014 TCACATTGTTGATTCAATTTGGTTT
1 TCACATTGTTGATTCAATTTGGTTT
87039 T
1 T
87040 TTCTGTAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.61
Consensus pattern (25 bp):
TCACATTGTTGATTCAATTTGGTTT
Found at i:95550 original size:20 final size:20
Alignment explanation
Indices: 95513--95550 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
95503 ATTCAAAATA
*
95513 AAATAAAAATTACCCATTTT
1 AAATAAAAATCACCCATTTT
*
95533 AAATAAAAATCACTCATT
1 AAATAAAAATCACCCATT
95551 GATAAATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAAAAATCACCCATTTT
Found at i:95556 original size:21 final size:20
Alignment explanation
Indices: 95513--95558 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
95503 ATTCAAAATA
* *
95513 AAATAAAAATTACCCATTTT
1 AAATAAAAATCACCCATTAT
*
95533 AAATAAAAATCACTCATTGAT
1 AAATAAAAATCACCCATT-AT
95554 AAATA
1 AAATA
95559 TGATATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (20 bp):
AAATAAAAATCACCCATTAT
Found at i:95725 original size:90 final size:90
Alignment explanation
Indices: 95615--95796 Score: 337
Period size: 90 Copynumber: 2.0 Consensus size: 90
95605 AAAAAAAACC
* * *
95615 GTCATAAACTACTTATATAGTGAGTGCCCTGTGTCTTTAAAATAAAAGTAGTTGTTGTGCAAAGT
1 GTCATAAACCACTTACATAGTGAGTGCCCTGTGTCTTTAAAATAAAAGTAGTTGTTGTGCAAAAT
95680 TATTAAATAGTTCCATCCTAACAAA
66 TATTAAATAGTTCCATCCTAACAAA
95705 GTCATAAACCACTTACATAGTGAGTGCCCTGTGTCTTTAAAATAAAAGTAGTTGTTGTGCAAAAT
1 GTCATAAACCACTTACATAGTGAGTGCCCTGTGTCTTTAAAATAAAAGTAGTTGTTGTGCAAAAT
95770 TATTAAATAGTTCCATCCTAACAAA
66 TATTAAATAGTTCCATCCTAACAAA
95795 GT
1 GT
95797 TATTGTATTA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (90 bp):
GTCATAAACCACTTACATAGTGAGTGCCCTGTGTCTTTAAAATAAAAGTAGTTGTTGTGCAAAAT
TATTAAATAGTTCCATCCTAACAAA
Found at i:122661 original size:23 final size:23
Alignment explanation
Indices: 122634--122687 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
122624 TATTTTTGAT
* *
122634 TTTTTGATGGGTCATTGTGTATA
1 TTTTTGACGGGTCATTGAGTATA
122657 TTTTTGACGGGTCATTGAGTATA
1 TTTTTGACGGGTCATTGAGTATA
122680 TTTTTGAC
1 TTTTTGAC
122688 ATGATTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.50
Consensus pattern (23 bp):
TTTTTGACGGGTCATTGAGTATA
Found at i:127029 original size:11 final size:11
Alignment explanation
Indices: 127015--127045 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
127005 ATCCTTTTCC
127015 TTTTGTTTTTT
1 TTTTGTTTTTT
127026 TTTTGTTTTTT
1 TTTTGTTTTTT
127037 TTTT-TTTTT
1 TTTTGTTTTT
127046 CCTCTGCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:127045 original size:16 final size:16
Alignment explanation
Indices: 127015--127044 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
127005 ATCCTTTTCC
127015 TTTTGTTTTTTTTTTG
1 TTTTGTTTTTTTTTTG
127031 TTTT-TTTTTTTTTT
1 TTTTGTTTTTTTTTT
127045 TCCTCTGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (16 bp):
TTTTGTTTTTTTTTTG
Found at i:127144 original size:26 final size:26
Alignment explanation
Indices: 127106--127356 Score: 416
Period size: 26 Copynumber: 9.7 Consensus size: 26
127096 TTCATTTTCT
**
127106 AGTAGGGAACATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTC
127132 AGTAGGGGTCATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTC
127158 AGTAGGGGTCATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTC
127184 AGTAGGGGTCATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTC
*
127210 AGTAGGGGTCATGTAGTTGCATATTT
1 AGTAGGGGTCATGTAGTTGCATATTC
*
127236 AGTAGGGGACATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTC
* *
127262 AGTAGGGGACATGTAGTTGCATATTT
1 AGTAGGGGTCATGTAGTTGCATATTC
*
127288 AGTAGGGGACATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTC
127314 AGTA-GGGTCATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTC
*
127339 CGTA-GGGTCATGTAGTTG
1 AGTAGGGGTCATGTAGTTG
127357 TCATGTAGTT
Statistics
Matches: 216, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
25 37 0.17
26 179 0.83
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.34
Consensus pattern (26 bp):
AGTAGGGGTCATGTAGTTGCATATTC
Found at i:127184 original size:52 final size:52
Alignment explanation
Indices: 127106--127492 Score: 528
Period size: 52 Copynumber: 7.3 Consensus size: 52
127096 TTCATTTTCT
**
127106 AGTAGGGAACATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTC
127158 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTC
* *
127210 AGTAGGGGTCATGTAGTTGCATATTTAGTAGGGGACATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTC
* * *
127262 AGTAGGGGACATGTAGTTGCATATTTAGTAGGGGACATGTAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTC
*
127314 AGTA-GGGTCATGTAGTTGCATATTCCGTA-GGGTCATGTAGTTGTCATGTAGTTCC
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTG-CA--TA-TT-C
* * * *
127369 ATATTCAGTAGGGACATGTAGTTGCATAATCAG-AGGGGTCATGTAGTTGTATATTC
1 --AGT-AG--GGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTC
* *
127425 AGTAGGGGTCATGTAGTTGTATATTCAGTAGGGGTCATGCAGTTGCATATTC
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTC
*
127477 AGTAGGGGTGATGTAG
1 AGTAGGGGTCATGTAG
127493 AAATTAATTA
Statistics
Matches: 301, Mismatches: 21, Indels: 26
0.86 0.06 0.07
Matches are distributed among these distances:
50 13 0.04
51 44 0.15
52 191 0.63
53 4 0.01
54 4 0.01
55 1 0.00
56 1 0.00
57 4 0.01
58 3 0.01
60 2 0.01
61 34 0.11
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (52 bp):
AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTC
Found at i:127240 original size:78 final size:78
Alignment explanation
Indices: 127106--127492 Score: 528
Period size: 78 Copynumber: 4.9 Consensus size: 78
127096 TTCATTTTCT
**
127106 AGTAGGGAACATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATG
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATG
127171 TAGTTGCATATTC
66 TAGTTGCATATTC
* *
127184 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTTAGTAGGGGACATG
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATG
127249 TAGTTGCATATTC
66 TAGTTGCATATTC
* * *
127262 AGTAGGGGACATGTAGTTGCATATTTAGTAGGGGACATGTAGTTGCATATTCAGTA-GGGTCATG
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATG
127326 TAGTTGCATATTC
66 TAGTTGCATATTC
* * * *
127339 CGTA-GGGTCATGTAGTTGTCATGTAGTTCCATATTCAGTAGGGACATGTAGTTGCATAATCAG-
1 AGTAGGGGTCATGTAGTTG-CA--TA-TT-C--AGT-AG--GGGTCATGTAGTTGCATATTCAGT
*
127402 AGGGGTCATGTAGTTGTATATTC
56 AGGGGTCATGTAGTTGCATATTC
* * *
127425 AGTAGGGGTCATGTAGTTGTATATTCAGTAGGGGTCATGCAGTTGCATATTCAGTAGGGGTGATG
1 AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATG
127490 TAG
66 TAG
127493 AAATTAATTA
Statistics
Matches: 274, Mismatches: 22, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
76 13 0.05
77 45 0.16
78 138 0.50
79 4 0.01
80 4 0.01
82 1 0.00
83 4 0.01
84 4 0.01
85 1 0.00
86 46 0.17
87 14 0.05
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (78 bp):
AGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATGTAGTTGCATATTCAGTAGGGGTCATG
TAGTTGCATATTC
Found at i:127372 original size:36 final size:36
Alignment explanation
Indices: 127320--127392 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
127310 ATTCAGTAGG
* * *
127320 GTCATGTAGTTGCATATTCCGTAGGGTCATGTAGTT
1 GTCATGTAGTTCCATATTCAGTAGGGACATGTAGTT
127356 GTCATGTAGTTCCATATTCAGTAGGGACATGTAGTT
1 GTCATGTAGTTCCATATTCAGTAGGGACATGTAGTT
127392 G
1 G
127393 CATAATCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (36 bp):
GTCATGTAGTTCCATATTCAGTAGGGACATGTAGTT
Found at i:127392 original size:61 final size:61
Alignment explanation
Indices: 127297--127418 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 61
127287 TAGTAGGGGA
* * * *
127297 CATGTAGTTGCATATTCAGTAGGGTCATGTAGTTGCATATTCCGTA-GGGTCATGTAGTTGT
1 CATGTAGTTCCATATTCAGTAGGGACATGTAGTTGCATAATCAG-AGGGGTCATGTAGTTGT
127358 CATGTAGTTCCATATTCAGTAGGGACATGTAGTTGCATAATCAGAGGGGTCATGTAGTTGT
1 CATGTAGTTCCATATTCAGTAGGGACATGTAGTTGCATAATCAGAGGGGTCATGTAGTTGT
127419 ATATTCAGTA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
60 1 0.02
61 55 0.98
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (61 bp):
CATGTAGTTCCATATTCAGTAGGGACATGTAGTTGCATAATCAGAGGGGTCATGTAGTTGT
Found at i:127417 original size:86 final size:88
Alignment explanation
Indices: 127271--127444 Score: 273
Period size: 86 Copynumber: 2.0 Consensus size: 88
127261 CAGTAGGGGA
* * *
127271 CATGTAGTTGCATATTTAGTAGGGGACATGTAGTTGCATATTCAGTAGGGTCATGTAGTTGCATA
1 CATGTAGTTCCATATTCAGTAGGGGACATGTAGTTGCATAATCAGTAGGGTCATGTAGTTGCATA
*
127336 TTCCGTA-GGGTCATGTAGTTGT
66 TTCAGTAGGGGTCATGTAGTTGT
*
127358 CATGTAGTTCCATATTCAGTA-GGGACATGTAGTTGCATAATCAG-AGGGGTCATGTAGTTGTAT
1 CATGTAGTTCCATATTCAGTAGGGGACATGTAGTTGCATAATCAGTA-GGGTCATGTAGTTGCAT
127421 ATTCAGTAGGGGTCATGTAGTTGT
65 ATTCAGTAGGGGTCATGTAGTTGT
127445 ATATTCAGTA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
85 1 0.01
86 45 0.56
87 34 0.43
ACGTcount: A:0.24, C:0.11, G:0.29, T:0.36
Consensus pattern (88 bp):
CATGTAGTTCCATATTCAGTAGGGGACATGTAGTTGCATAATCAGTAGGGTCATGTAGTTGCATA
TTCAGTAGGGGTCATGTAGTTGT
Found at i:127438 original size:26 final size:26
Alignment explanation
Indices: 127356--127492 Score: 197
Period size: 26 Copynumber: 5.3 Consensus size: 26
127346 TCATGTAGTT
*
127356 GTCATGTAGTTCCATATTCAGTA-GG
1 GTCATGTAGTTGCATATTCAGTAGGG
* *
127381 GACATGTAGTTGCATAATCAG-AGGG
1 GTCATGTAGTTGCATATTCAGTAGGG
*
127406 GTCATGTAGTTGTATATTCAGTAGGG
1 GTCATGTAGTTGCATATTCAGTAGGG
*
127432 GTCATGTAGTTGTATATTCAGTAGGG
1 GTCATGTAGTTGCATATTCAGTAGGG
*
127458 GTCATGCAGTTGCATATTCAGTAGGG
1 GTCATGTAGTTGCATATTCAGTAGGG
*
127484 GTGATGTAG
1 GTCATGTAG
127493 AAATTAATTA
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
24 1 0.01
25 38 0.38
26 61 0.61
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.34
Consensus pattern (26 bp):
GTCATGTAGTTGCATATTCAGTAGGG
Done.