Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013378.1 Corchorus capsularis cultivar CVL-1 contig13399, 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: 147859
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1713 original size:2 final size:2
Alignment explanation
Indices: 1708--1732 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1698 TTTTTTTTTA
1708 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1733 ATAAGAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1793 original size:52 final size:52
Alignment explanation
Indices: 1733--1834 Score: 186
Period size: 52 Copynumber: 2.0 Consensus size: 52
1723 TATATATATA
*
1733 ATAAGAGTTCTAATGATTGATGAAATGATATTAATACACAATTTAATTCAAT
1 ATAAGAGTTCTAATGATTAATGAAATGATATTAATACACAATTTAATTCAAT
*
1785 ATAAGAGTTCTAATGATTAATGAAATGATCTTAATACACAATTTAATTCA
1 ATAAGAGTTCTAATGATTAATGAAATGATATTAATACACAATTTAATTCA
1835 TATTTTTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (52 bp):
ATAAGAGTTCTAATGATTAATGAAATGATATTAATACACAATTTAATTCAAT
Found at i:2183 original size:2 final size:2
Alignment explanation
Indices: 2176--2204 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2166 TATCAGCAAA
2176 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2205 ATTAATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8227 original size:453 final size:449
Alignment explanation
Indices: 7379--8277 Score: 1645
Period size: 453 Copynumber: 2.0 Consensus size: 449
7369 AAGGTTATAA
*
7379 CATCAGGCTTGACCCTAAATTCTTCCATCAAACTAAGCACCTGCAGATCAAAGCTTTGCATGAAT
1 CATCAGGCTTGACCCTAAATTCATCCATCAAACTAAGCACCTGCAGATCAAAGCTTTGCATGAAT
7444 TAATGAATCAAAACAAGCAAAATCACTGCCCTAAAACTGCAGGAGTTATAGAATCCAGTATATGA
66 TAATGAATCAAAACAAGCAAAATCACTGCCCTAAAACTGCAGGAGTTATAGAATCCAGTATATGA
7509 TTGCTTAAAAGAAAATAACTGGAAATAGTAATCATTGGTCTAACCTCATCAACCCCATCCCTGTC
131 TTGCTTAAAAGAAAATAACTGGAAATAGTAATCATTGGTCTAACCTCATCAACCCCATCCCTGTC
7574 CATGATGTCAACAAAAGATTTGATCAGTGAGTTAAAAATCACAAGATCAGGACGCACCCCAAGTT
196 CATGATGTCAACAAAAGATTTGATCAGTGAGTTAAAAATCACAAGATCAGGACGCACCCCAAGTT
* *
7639 CCTTCATCCTATACACAAACCTCAAGGCTTCCTTTATCCGACCTTCTTTACGATATCCACTGACA
261 CCTTCATCCTATACACAAACCTCAAGGCTTCCTTTATCCGACCTTCTTTACAATATCCAATGACA
* **
7704 ATGATGCCACAAGTTAGCTCATTAGGCTGCACGCCATTTTTCTGCATCTCTGAAATCATTGCTTC
326 ATGATGCCACAAGTTAGCTCATTAGGCTGCACCCCATTTTTCTGCATCTCTGAAATCATTGCGAC
* *
7769 AGCTCGATCAGTCTCATCATTTTGTGAATAAGCTGTTGCTCTGGTATTATAAGTAAATT
391 AGCTCGATCAGTCTCATCATTTTGTGAATAAGCTGTTGCTATGGTAGTATAAGTAAATT
* *
7828 CATCAGGTTTGACCCTAAATTCATCCATCAAAGTAAGCACCTGCAGATCAAAGCTTTGCATGAAT
1 CATCAGGCTTGACCCTAAATTCATCCATCAAACTAAGCACCTGCAGATCAAAGCTTTGCATGAAT
7893 TAATGAATCAAAACAAGCAAAATCACTGCCCTAAAACTGCAGGAGTTATAGAATCCAGTATATGA
66 TAATGAATCAAAACAAGCAAAATCACTGCCCTAAAACTGCAGGAGTTATAGAATCCAGTATATGA
*
7958 TTGCTTAAAAGAAAATAATTGGAAATAGTAATCATTGGTCTAACTCACCTCATCAACCCCATCCC
131 TTGCTTAAAAGAAAATAACTGGAAATAGTAATCATTGGTCT-A---ACCTCATCAACCCCATCCC
*
8023 TGTCCATGATGTCAACAAAAGATTTGATCAGTGAGTTAAAAATCACAAGATTAGGACGCACCCCA
192 TGTCCATGATGTCAACAAAAGATTTGATCAGTGAGTTAAAAATCACAAGATCAGGACGCACCCCA
8088 AGTTCCTTCATCCTATACACAAACCTCAAGGCTTCCTTTATCCGACCTTCTTTACAATATCCAAT
257 AGTTCCTTCATCCTATACACAAACCTCAAGGCTTCCTTTATCCGACCTTCTTTACAATATCCAAT
*
8153 GATAATGATGCCACAAGTTAGCTCATTAGGCTGCACCCCATTTTTCTGCATCTCTGAAATCATTG
322 GACAATGATGCCACAAGTTAGCTCATTAGGCTGCACCCCATTTTTCTGCATCTCTGAAATCATTG
8218 CGACAGCTCGATCAGTCTCATCATTTTGTGAATAAGCTGTTGCTATGGTAGTATAAGTAA
387 CGACAGCTCGATCAGTCTCATCATTTTGTGAATAAGCTGTTGCTATGGTAGTATAAGTAA
8278 CAACATCCGG
Statistics
Matches: 433, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
449 167 0.39
450 1 0.00
453 265 0.61
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (449 bp):
CATCAGGCTTGACCCTAAATTCATCCATCAAACTAAGCACCTGCAGATCAAAGCTTTGCATGAAT
TAATGAATCAAAACAAGCAAAATCACTGCCCTAAAACTGCAGGAGTTATAGAATCCAGTATATGA
TTGCTTAAAAGAAAATAACTGGAAATAGTAATCATTGGTCTAACCTCATCAACCCCATCCCTGTC
CATGATGTCAACAAAAGATTTGATCAGTGAGTTAAAAATCACAAGATCAGGACGCACCCCAAGTT
CCTTCATCCTATACACAAACCTCAAGGCTTCCTTTATCCGACCTTCTTTACAATATCCAATGACA
ATGATGCCACAAGTTAGCTCATTAGGCTGCACCCCATTTTTCTGCATCTCTGAAATCATTGCGAC
AGCTCGATCAGTCTCATCATTTTGTGAATAAGCTGTTGCTATGGTAGTATAAGTAAATT
Found at i:13103 original size:12 final size:12
Alignment explanation
Indices: 13086--13110 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13076 GAGTTCTGGA
13086 AAAAAAAAACAC
1 AAAAAAAAACAC
13098 AAAAAAAAACAC
1 AAAAAAAAACAC
13110 A
1 A
13111 GAAACTTAAT
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAC
Found at i:24178 original size:12 final size:12
Alignment explanation
Indices: 24161--24185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24151 TATGGTAGTA
24161 GCTTTGTCAATG
1 GCTTTGTCAATG
24173 GCTTTGTCAATG
1 GCTTTGTCAATG
24185 G
1 G
24186 AGCGATCCAT
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:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (12 bp):
GCTTTGTCAATG
Found at i:42686 original size:1 final size:1
Alignment explanation
Indices: 42680--42705 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
42670 AATTTAAGCC
42680 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
42706 GAAGAAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44861 original size:197 final size:197
Alignment explanation
Indices: 44526--44919 Score: 788
Period size: 197 Copynumber: 2.0 Consensus size: 197
44516 CTCTAAGGAC
44526 CGGACCGGCCGGTCCGGTCCGGTTTTTAAAACAATGGTTTATACCTCAATTTACAATTGAAGATA
1 CGGACCGGCCGGTCCGGTCCGGTTTTTAAAACAATGGTTTATACCTCAATTTACAATTGAAGATA
44591 AATTGGTCTTTGCTTAAAGTAAATTAAGATGTGTGGTCAGGATTTAATCAAAAATCTTGATGATA
66 AATTGGTCTTTGCTTAAAGTAAATTAAGATGTGTGGTCAGGATTTAATCAAAAATCTTGATGATA
44656 CTTAGTTTCTGCACCACCCTAATTCTATCTGAATCAGGAAAAATCTTATAATTAATTAATTAAAG
131 CTTAGTTTCTGCACCACCCTAATTCTATCTGAATCAGGAAAAATCTTATAATTAATTAATTAAAG
44721 GT
196 GT
44723 CGGACCGGCCGGTCCGGTCCGGTTTTTAAAACAATGGTTTATACCTCAATTTACAATTGAAGATA
1 CGGACCGGCCGGTCCGGTCCGGTTTTTAAAACAATGGTTTATACCTCAATTTACAATTGAAGATA
44788 AATTGGTCTTTGCTTAAAGTAAATTAAGATGTGTGGTCAGGATTTAATCAAAAATCTTGATGATA
66 AATTGGTCTTTGCTTAAAGTAAATTAAGATGTGTGGTCAGGATTTAATCAAAAATCTTGATGATA
44853 CTTAGTTTCTGCACCACCCTAATTCTATCTGAATCAGGAAAAATCTTATAATTAATTAATTAAAG
131 CTTAGTTTCTGCACCACCCTAATTCTATCTGAATCAGGAAAAATCTTATAATTAATTAATTAAAG
44918 GT
196 GT
44920 AAAAATTAAT
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 197 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (197 bp):
CGGACCGGCCGGTCCGGTCCGGTTTTTAAAACAATGGTTTATACCTCAATTTACAATTGAAGATA
AATTGGTCTTTGCTTAAAGTAAATTAAGATGTGTGGTCAGGATTTAATCAAAAATCTTGATGATA
CTTAGTTTCTGCACCACCCTAATTCTATCTGAATCAGGAAAAATCTTATAATTAATTAATTAAAG
GT
Found at i:45883 original size:155 final size:154
Alignment explanation
Indices: 45498--45871 Score: 422
Period size: 155 Copynumber: 2.4 Consensus size: 154
45488 TCTCAAATAG
* * * *
45498 ACTTAGAATGAAAAACTTAAGCAAGTTTTTCAGTTAAGGACAGTTTGAGGTGAGAAGT-CAGCTC
1 ACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAAGTCCAGTTC
* * * * * *
45562 ACTATCAAGGGGAGTTCGGTTTTATTTATATTTTTACCCATAGCTTTATGGAGATAATCTAAGCC
66 ACCATCAAGGGGAGCTCAGTTTTACTTAAATTTTTA-CCATAGCTTTATGGAGAGAATCTAAGCC
**
45627 TACTGGTGGAAAATCAGCTTCATTGG
130 TACT-GTGGAAAATCAGCTTCATTAA
**
45653 ACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTT-AGG-GAGAGAAACCTAGT
1 ACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGA-AGTCC-AGT
* *
45716 TCACCATCAAGGGGAGCTCAGTTTTACTTAGAATTTTT-CCATAG-TTTCGTGGGGAGAATCTAA
64 TCACCATCAAGGGGAGCTCAGTTTTACTTA-AATTTTTACCATAGCTTT-ATGGAGAGAATCTAA
* *
45779 GTCT-CT-TGGCAAAGTTTCAGC-TCATTCAA
127 GCCTACTGTGG-AAA--ATCAGCTTCATT-AA
* *
45808 ACTTAGAATGAAAAACTTATTCTAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAAGTCCAGTT
1 ACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAAGTCCAGTT
45872 TGCCATGAAG
Statistics
Matches: 186, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
152 3 0.02
153 7 0.04
154 14 0.08
155 119 0.64
156 34 0.18
157 9 0.05
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (154 bp):
ACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAAGTCCAGTTC
ACCATCAAGGGGAGCTCAGTTTTACTTAAATTTTTACCATAGCTTTATGGAGAGAATCTAAGCCT
ACTGTGGAAAATCAGCTTCATTAA
Found at i:46244 original size:17 final size:17
Alignment explanation
Indices: 46196--46237 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
46186 TAATACAACA
*
46196 CATGCTACCTGGTACCT
1 CATGCTACCTAGTACCT
46213 CATGCTACCTAGTACCT
1 CATGCTACCTAGTACCT
46230 CATGCTAC
1 CATGCTAC
46238 ATTGTACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (17 bp):
CATGCTACCTAGTACCT
Found at i:46945 original size:2 final size:2
Alignment explanation
Indices: 46938--46972 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
46928 TTGACACAAC
46938 AT AT AT AT AT AT AT AT AT AT AT AT -T AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
46973 GGAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57142 original size:20 final size:21
Alignment explanation
Indices: 57117--57159 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
57107 GTCTTGGGTT
57117 TTACTCTCACGGAA-TGTGAG
1 TTACTCTCACGGAATTGTGAG
57137 TTACTCTCACGGAATTGTGAG
1 TTACTCTCACGGAATTGTGAG
57158 TT
1 TT
57160 TTCTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
TTACTCTCACGGAATTGTGAG
Found at i:57946 original size:6 final size:6
Alignment explanation
Indices: 57935--57969 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
57925 TTTTGAAACC
57935 CAAATA CAAATA CAAATA CAAATA CAAATA CAAAT
1 CAAATA CAAATA CAAATA CAAATA CAAATA CAAAT
57970 GTAGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CAAATA
Found at i:60061 original size:2 final size:2
Alignment explanation
Indices: 60054--60083 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60044 TTAATCATAC
60054 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
60084 GAATTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61254 original size:2 final size:2
Alignment explanation
Indices: 61247--61276 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
61237 ATTAATTATC
61247 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
61277 AAAATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61618 original size:15 final size:15
Alignment explanation
Indices: 61598--61631 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
61588 AGATAAAGAA
61598 TAAGAAAACAATTAT
1 TAAGAAAACAATTAT
*
61613 TAAGAAAACAATTTT
1 TAAGAAAACAATTAT
61628 TAAG
1 TAAG
61632 CCATCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (15 bp):
TAAGAAAACAATTAT
Found at i:67738 original size:13 final size:13
Alignment explanation
Indices: 67720--67744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67710 AATATATACA
67720 ATAACTACTATAT
1 ATAACTACTATAT
67733 ATAACTACTATA
1 ATAACTACTATA
67745 AGCAATTATT
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAACTACTATAT
Found at i:67841 original size:2 final size:2
Alignment explanation
Indices: 67836--67863 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
67826 GAGAGAGAAC
67836 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
67864 TAATGTATAT
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):
AT
Found at i:69258 original size:1 final size:1
Alignment explanation
Indices: 69252--69286 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
69242 AAGGTGAAGG
69252 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
69287 GCATGGCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:71926 original size:63 final size:63
Alignment explanation
Indices: 71833--72023 Score: 229
Period size: 63 Copynumber: 3.0 Consensus size: 63
71823 GGGTGGTGGC
* * * * * * * *
71833 GTAAACGTGAACACAGGAAAAGGGAAGCCCAGCGGCACTTCGGTGAACGTTGGAAAAGGTGGA
1 GTAAATGTAAACACAGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGAAAAGGCGGA
* * * *
71896 GTGAATGTAAACACCGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGGAAAGGCGGT
1 GTAAATGTAAACACAGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGAAAAGGCGGA
* * * * *
71959 GTAAATGTAAATACTGGGAAAGGAAAGCCCGGGGGAACTTCTGTTAATGTTGGAAAAGGCGGA
1 GTAAATGTAAACACAGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGAAAAGGCGGA
72022 GT
1 GT
72024 TGGAGTGAAC
Statistics
Matches: 108, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 108 1.00
ACGTcount: A:0.33, C:0.15, G:0.34, T:0.18
Consensus pattern (63 bp):
GTAAATGTAAACACAGGGAAAGGAAAGCCCAGCGGCACTTCTGTTAATGTTGGAAAAGGCGGA
Found at i:96408 original size:2 final size:2
Alignment explanation
Indices: 96396--96425 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
96386 TTGTACCGAG
96396 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
96426 TAGTCTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:104084 original size:15 final size:15
Alignment explanation
Indices: 104045--104089 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
104035 TCTAGCTATT
*
104045 GAAGAAGAAGATGAG
1 GAAGAAGAAGAAGAG
*
104060 GAAGAGGAAGAAGAG
1 GAAGAAGAAGAAGAG
*
104075 GATGAAGAAGAAGAG
1 GAAGAAGAAGAAGAG
104090 CACCATCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.04
Consensus pattern (15 bp):
GAAGAAGAAGAAGAG
Found at i:115144 original size:5 final size:6
Alignment explanation
Indices: 115129--115168 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
115119 GATGTAAGCT
*
115129 TTTTTA TTTTTA TTTTTA TTTTTAA TTTTAA TTTTT- TTTT
1 TTTTTA TTTTTA TTTTTA TTTTT-A TTTTTA TTTTTA TTTT
115169 CCTTTGCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 4 0.13
6 22 0.71
7 5 0.16
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:115152 original size:18 final size:18
Alignment explanation
Indices: 115128--115168 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
115118 AGATGTAAGC
*
115128 TTTTTT-ATTTTTATTTT
1 TTTTTTAATTTTAATTTT
115145 TATTTTTAATTTTAATTTT
1 T-TTTTTAATTTTAATTTT
115164 TTTTT
1 TTTTT
115169 CCTTTGCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 9 0.43
19 11 0.52
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTAATTTTAATTTT
Found at i:129067 original size:31 final size:31
Alignment explanation
Indices: 128981--129068 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 31
128971 ACGGTGTCTG
* **
128981 ACGTGGCATGCCACATGTACCAAAAAGTGAC
1 ACGTGACATGCCACATGTGTCAAAAAGTGAC
* * * *
129012 ACATGTCA--CCTCACGTGTACCAAAAAGTGAC
1 ACGTGACATGCCACATGTGT--CAAAAAGTGAC
129043 ACGTGACATGCCACATGTGTCAAAAA
1 ACGTGACATGCCACATGTGTCAAAAA
129069 ATGGCAAAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
29 6 0.14
31 29 0.67
33 8 0.19
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (31 bp):
ACGTGACATGCCACATGTGTCAAAAAGTGAC
Found at i:132358 original size:21 final size:22
Alignment explanation
Indices: 132335--132391 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 22
132325 CAAAGCGATT
132335 GAAGAACAATAAAAATAAATTGAA
1 GAAGAACAATAAAAATAAATT--A
132359 GGAAGAACAATAAAAATAAATTA
1 -GAAGAACAATAAAAATAAATTA
*
132382 AAAGGAACAA
1 GAA-GAACAA
132392 AAACAAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 2 0.07
23 7 0.23
25 21 0.70
ACGTcount: A:0.67, C:0.05, G:0.14, T:0.14
Consensus pattern (22 bp):
GAAGAACAATAAAAATAAATTA
Found at i:140614 original size:41 final size:39
Alignment explanation
Indices: 140558--140643 Score: 136
Period size: 41 Copynumber: 2.2 Consensus size: 39
140548 TCTCCGCGAG
*
140558 TTTTTCTTCACTTTCAGCATCGTCTCAGGACGTTAAAACAT
1 TTTTTTTTCACTTTCAGCATCGTCTCAGGACGTT-AAAC-T
*
140599 TTTTTTTTTACTTTCAGCATCGTCTCAGGACGTTAAACT
1 TTTTTTTTCACTTTCAGCATCGTCTCAGGACGTTAAACT
140638 TTTTTT
1 TTTTTT
140644 ACTTTCTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 7 0.16
40 4 0.09
41 32 0.74
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (39 bp):
TTTTTTTTCACTTTCAGCATCGTCTCAGGACGTTAAACT
Found at i:140991 original size:3 final size:3
Alignment explanation
Indices: 140983--141056 Score: 91
Period size: 3 Copynumber: 24.7 Consensus size: 3
140973 ATGTTAACTA
*
140983 ATT ATT ATT -TT ATAT ATT -TGT ACT ATCT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT
141028 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
141057 ATAAAGATCG
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
2 5 0.08
3 53 0.84
4 5 0.08
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:141217 original size:22 final size:22
Alignment explanation
Indices: 141191--141235 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
141181 GTTCCTATTT
* *
141191 TTTAGGTCTAAGAGAGGGTTTA
1 TTTAGGTCCAAAAGAGGGTTTA
141213 TTTAGGTCCAAAAGAGGGTTTA
1 TTTAGGTCCAAAAGAGGGTTTA
141235 T
1 T
141236 ATATAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (22 bp):
TTTAGGTCCAAAAGAGGGTTTA
Found at i:142384 original size:45 final size:45
Alignment explanation
Indices: 142333--142422 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
142323 TAATAGAGTA
142333 GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATGAACTGG
1 GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATGAACTGG
* * *
142378 GTGGAATTACTAAAAGATCCCTACCCCGGATTAGTGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATGAACTGG
142423 AGAACTAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATGAACTGG
Found at i:143771 original size:21 final size:21
Alignment explanation
Indices: 143742--143781 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
143732 CAAAAAAAAA
* * *
143742 TTAATTAAATTAATTTATCAT
1 TTAAATAAATAAATATATCAT
143763 TTAAATAAATAAATATATC
1 TTAAATAAATAAATATATC
143782 CTACGGCTTG
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:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAATAAATAAATATATCAT
Found at i:144595 original size:2 final size:2
Alignment explanation
Indices: 144590--144619 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
144580 CTATATATAG
*
144590 GT GT GT GT GT GT GT GT GA GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
144620 ATGTAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (2 bp):
GT
Found at i:147441 original size:1 final size:1
Alignment explanation
Indices: 147435--147461 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
147425 ATGCAAGAAG
147435 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
147462 AAGGCTAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.