Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022529.1 Corchorus olitorius cultivar O-4 contig22562, 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: 66599
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4042 original size:31 final size:31
Alignment explanation
Indices: 4004--4064 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3994 CCTGAGGTTA
* *
4004 AAACCCGA-ACCTGTATGACCCTAAACCCAGC
1 AAACCCGAGACCCGAATGA-CCTAAACCCAGC
*
4035 AAACCCGAGACCCGAATGACCTGAACCCAG
1 AAACCCGAGACCCGAATGACCTAAACCCAG
4065 ATGAGCCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.36, C:0.38, G:0.16, T:0.10
Consensus pattern (31 bp):
AAACCCGAGACCCGAATGACCTAAACCCAGC
Found at i:4084 original size:16 final size:15
Alignment explanation
Indices: 4044--4086 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
4034 CAAACCCGAG
*
4044 ACCCGAATGACCTGA
1 ACCCGAATGACCGGA
4059 ACCC-AGATGAGCCGGA
1 ACCCGA-ATGA-CCGGA
4075 ACCCGAATGACC
1 ACCCGAATGACC
4087 CACGAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 1 0.04
15 10 0.42
16 12 0.50
17 1 0.04
ACGTcount: A:0.33, C:0.35, G:0.23, T:0.09
Consensus pattern (15 bp):
ACCCGAATGACCGGA
Found at i:9668 original size:2 final size:2
Alignment explanation
Indices: 9661--9700 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
9651 GAGAGCACTC
9661 AT AT AT AT A- AT 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 AT AT AT AT AT AT A
9701 ATCGATCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10345 original size:10 final size:10
Alignment explanation
Indices: 10330--10359 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
10320 AATAAAACAA
10330 AAATTGAAAT
1 AAATTGAAAT
10340 AAATTGAAAT
1 AAATTGAAAT
10350 AAATTGAAAT
1 AAATTGAAAT
10360 GTTGCTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (10 bp):
AAATTGAAAT
Found at i:12915 original size:36 final size:36
Alignment explanation
Indices: 12861--12941 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
12851 CGTTCAGGAG
12861 CAGGAGGAGATGGCTGATCAGAT-TGAGGCTGCACAA
1 CAGGAGGAGATGGCTGATCAG-TCTGAGGCTGCACAA
* * * * *
12897 CAGGAGGTGGTGGTTGATCAGTCTGATGCTGCTCAA
1 CAGGAGGAGATGGCTGATCAGTCTGAGGCTGCACAA
*
12933 CTGGAGGAG
1 CAGGAGGAG
12942 GATGTCGCTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
35 1 0.03
36 36 0.97
ACGTcount: A:0.25, C:0.16, G:0.38, T:0.21
Consensus pattern (36 bp):
CAGGAGGAGATGGCTGATCAGTCTGAGGCTGCACAA
Found at i:14967 original size:17 final size:21
Alignment explanation
Indices: 14893--14959 Score: 134
Period size: 21 Copynumber: 3.2 Consensus size: 21
14883 CTTTTAACCA
14893 ATTTATGTTGATTGTTTGTGG
1 ATTTATGTTGATTGTTTGTGG
14914 ATTTATGTTGATTGTTTGTGG
1 ATTTATGTTGATTGTTTGTGG
14935 ATTTATGTTGATTGTTTGTGG
1 ATTTATGTTGATTGTTTGTGG
14956 ATTT
1 ATTT
14960 TTTATGTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (21 bp):
ATTTATGTTGATTGTTTGTGG
Found at i:15719 original size:13 final size:13
Alignment explanation
Indices: 15690--15719 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
15680 CTTAAATTAA
15690 TTTTTGAAAATTG
1 TTTTTGAAAATTG
15703 TTTTT-AAAATTG
1 TTTTTGAAAATTG
15715 TTTTT
1 TTTTT
15720 AGAACTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (13 bp):
TTTTTGAAAATTG
Found at i:18666 original size:76 final size:76
Alignment explanation
Indices: 18516--18659 Score: 175
Period size: 76 Copynumber: 1.9 Consensus size: 76
18506 ACAAGGACCC
* * *
18516 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
18581 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * * **
18592 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGTGTTTTGCCTGATCACCCAG
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTTGCCTGAGAACCCAG
18655 ATGGG
64 ATGGG
18660 TTGTGTCTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
76 51 0.89
77 6 0.11
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:27469 original size:29 final size:29
Alignment explanation
Indices: 27427--27484 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
27417 TGTATTTAAG
27427 CCTTGCCATGATAGTATTAGTTTTTTTTT
1 CCTTGCCATGATAGTATTAGTTTTTTTTT
27456 CCTTGCCATGATAGTATTAGTTTTTTTTT
1 CCTTGCCATGATAGTATTAGTTTTTTTTT
27485 ATGCAGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (29 bp):
CCTTGCCATGATAGTATTAGTTTTTTTTT
Found at i:28718 original size:13 final size:13
Alignment explanation
Indices: 28689--28718 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
28679 CTTAAATTAA
28689 TTTTTGAAAATTG
1 TTTTTGAAAATTG
28702 TTTTT-AAAATTG
1 TTTTTGAAAATTG
28714 TTTTT
1 TTTTT
28719 AGAACTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (13 bp):
TTTTTGAAAATTG
Found at i:31822 original size:106 final size:108
Alignment explanation
Indices: 31635--31850 Score: 355
Period size: 106 Copynumber: 2.0 Consensus size: 108
31625 ACATTTCCAC
* *
31635 ATGCAAAACCATAATTCATAAACATATATTGAAAATTTCCTTAATTTATATAATTAATTATAAGT
1 ATGCAAAACCATAATTCATAAACATAAACTGAAAATTTCCTTAATTTATATAATTAATTATAAGT
*
31700 CCAAATTAAAACTCATAGGTTTACAAACAAGCTGCTACATTTA
66 CCAAATTAAAACTCATAGGCTTACAAACAAGCTGCTACATTTA
* *
31743 ATGCAAAACCATAATTTATAAACATAAACTG-AAATTTCCTTAATTTAT-TCATTAATTATAAGT
1 ATGCAAAACCATAATTCATAAACATAAACTGAAAATTTCCTTAATTTATATAATTAATTATAAGT
* *
31806 CCAAATTAAAACTCATAGGCTTACCAAGAAGCTGCTACATTTA
66 CCAAATTAAAACTCATAGGCTTACAAACAAGCTGCTACATTTA
31849 AT
1 AT
31851 AGGCATCATT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
106 56 0.55
107 17 0.17
108 28 0.28
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.34
Consensus pattern (108 bp):
ATGCAAAACCATAATTCATAAACATAAACTGAAAATTTCCTTAATTTATATAATTAATTATAAGT
CCAAATTAAAACTCATAGGCTTACAAACAAGCTGCTACATTTA
Found at i:35263 original size:165 final size:165
Alignment explanation
Indices: 34984--35362 Score: 582
Period size: 165 Copynumber: 2.3 Consensus size: 165
34974 GATCCTGAAA
*
34984 GGCATGAGCCTATCAACGCAGTGCAACCCTTCCAAGTGAACCCCCAATCCGACAAATGCGGTCAC
1 GGCATGAGCCTATCAACGCAGTGCAACCCTTCCAAGTGAACCCCCAATCGGACAAATGCGGTCAC
* * * *
35049 CGAGTATTCGAGTTAAATTGACAAAGTGTAGAACTGACGAGCATCTCCCACGGAGACCTCCACCT
66 CAAGTATTCGAGTTAAATTGACAAAATGTAGAACTAACGAGCATCTCCCACAGAGACCTCCACCT
* * *
35114 CCGCGAAACACCAACCTGGGGCGGGACACTTGACG
131 CCGCGAAACACCAACATGGGGCAGGACACCTGACG
35149 GGCATGAGCCTATCAACGCAGTGCAACCCTTCCAAGTGAACCCCCAATCGGACAAATGCGGTCAC
1 GGCATGAGCCTATCAACGCAGTGCAACCCTTCCAAGTGAACCCCCAATCGGACAAATGCGGTCAC
* * *
35214 CAAGTATTCGAGTTAAATTGACAAAATGTAGAGCTAACGAGCGTCTCCCACAGAGACCTCCGCCT
66 CAAGTATTCGAGTTAAATTGACAAAATGTAGAACTAACGAGCATCTCCCACAGAGACCTCCACCT
* * **
35279 CGGCGAAACACCGACATGGGGCAGGACACCTGGGG
131 CCGCGAAACACCAACATGGGGCAGGACACCTGACG
* *
35314 GGCAAGAGCCTATCAACGCATTGCAA-CCTTCCCAAGTGAA-CCCCAATCG
1 GGCATGAGCCTATCAACGCAGTGCAACCCTT-CCAAGTGAACCCCCAATCG
35363 AACGAATACG
Statistics
Matches: 196, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
164 13 0.07
165 183 0.93
ACGTcount: A:0.30, C:0.31, G:0.23, T:0.16
Consensus pattern (165 bp):
GGCATGAGCCTATCAACGCAGTGCAACCCTTCCAAGTGAACCCCCAATCGGACAAATGCGGTCAC
CAAGTATTCGAGTTAAATTGACAAAATGTAGAACTAACGAGCATCTCCCACAGAGACCTCCACCT
CCGCGAAACACCAACATGGGGCAGGACACCTGACG
Found at i:35600 original size:151 final size:149
Alignment explanation
Indices: 35253--35624 Score: 537
Period size: 150 Copynumber: 2.5 Consensus size: 149
35243 AGAGCTAACG
* *
35253 AGCGTCTCCCACAGAGACCTCCGCCTCGGCGAAACACCGACATGGGGCAGGACACCTGGGGGGCA
1 AGCGTCTCCCACGGAGACCTCCGCCTCGGCGAAACACCGACATGGGGCAGGACA-CTTGGGGGCA
* *
35318 AGAGCCTATCAACGCATTGCAACCTTCCCAAGTGAACCCCAATCGAACGAATACGGCCGCCTAAC
65 AGAGCCTATCAACGCATTGCAACCGTCCCAAGTGAACCCCAATCGAACGAATACGGCCGACTAAC
* * *
35383 AATTCGGTCACAAGTTGACG
130 AATTCAGTCACAAGCTGACA
* * * * *
35403 AGCATCTCCCATGGAGACCTCCGCCTTGGCGAAACAACGACCTGGGGCAGGACACTTGGGAGGCA
1 AGCGTCTCCCACGGAGACCTCCGCCTCGGCGAAACACCGACATGGGGCAGGACACTTGGG-GGCA
* * * *
35468 TGAGCCTATCAACGCATTGCAACCGTCCTAAGTGAACCCCGAGTCGAACGAATTCGGCCGACTAA
65 AGAGCCTATCAACGCATTGCAACCGTCCCAAGTGAACCCC-AATCGAACGAATACGGCCGACTAA
35533 CAATTCAGTCACAAGCTGACA
129 CAATTCAGTCACAAGCTGACA
* * * *
35554 AGCGTCTCTCACGGAGACCTCCGCCTCAGCGAGACACCGATATGGGGCAGGACACTTGGGGGCAA
1 AGCGTCTCCCACGGAGACCTCCGCCTCGGCGAAACACCGACATGGGGCAGGACACTTGGGGGCAA
35619 GAGCCT
66 GAGCCT
35625 GACAACACAA
Statistics
Matches: 194, Mismatches: 26, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
149 5 0.03
150 99 0.51
151 90 0.46
ACGTcount: A:0.27, C:0.32, G:0.26, T:0.15
Consensus pattern (149 bp):
AGCGTCTCCCACGGAGACCTCCGCCTCGGCGAAACACCGACATGGGGCAGGACACTTGGGGGCAA
GAGCCTATCAACGCATTGCAACCGTCCCAAGTGAACCCCAATCGAACGAATACGGCCGACTAACA
ATTCAGTCACAAGCTGACA
Found at i:35923 original size:76 final size:76
Alignment explanation
Indices: 35797--36201 Score: 413
Period size: 76 Copynumber: 5.4 Consensus size: 76
35787 CCTGTCTCCC
* * * * *
35797 ACGGCTGAGTGCCTAAATTGGCACCGCCGTCCCTCAGTGAGGCTGAGCGTCCATGCAGATGCCAC
1 ACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCGTCCATGCAGACGCCAC
35862 TCACTCATCCA
66 TCACTCATCCA
* * * * *
35873 ACGGCTGAGTGCCAATACTGGCACCCCCGTCCCTTAGTGAGGCAGAGCGTCCATGCAGATGCAAC
1 ACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCGTCCATGCAGACGCCAC
35938 TCACTCATCCA
66 TCACTCATCCA
* * * *
35949 ACGGCTGAGTGTCTAGACTGGCACCCCCGT--CTCAGAATGAGGCTGAGCGTCGAT--TGACGCC
1 ACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAG--TGAGGCAGAGCGTCCATGCAGACGCC
*
36010 ACTCA-TC--CTA
64 ACTCACTCATCCA
* **
36020 A-GGCTGAGTGCCTAGACTAGCACCCCCGTCCCTCAGTGAGGCAGAGCGTCCATGCAGAAACCAC
1 ACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCGTCCATGCAGACGCCAC
*
36084 TCACTCATCCG
66 TCACTCATCCA
* * * * *
36095 ACGGCTTAGTGCCTAGACTGGCGCCCCCGTTTCTCTCAATGAGGCTA-AGCGTCCAAGCAGACG-
1 ACGGCTGAGTGCCTAGACTGGCACCCCCG--TCCCTCAGTGAGGC-AGAGCGTCCATGCAGACGC
*
36158 --C-CACTCATCCG
63 CACTCACTCATCCA
* * **
36169 ACGGATGAGTGCCTAGACTTGCGTCCCCGTCCC
1 ACGGCTGAGTGCCTAGACTGGCACCCCCGTCCC
36202 ACTCTCAATG
Statistics
Matches: 277, Mismatches: 39, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
70 41 0.15
71 3 0.01
72 17 0.06
73 4 0.01
74 48 0.17
75 3 0.01
76 135 0.49
78 25 0.09
79 1 0.00
ACGTcount: A:0.21, C:0.34, G:0.25, T:0.19
Consensus pattern (76 bp):
ACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCGTCCATGCAGACGCCAC
TCACTCATCCA
Found at i:36067 original size:146 final size:148
Alignment explanation
Indices: 35797--36201 Score: 431
Period size: 146 Copynumber: 2.7 Consensus size: 148
35787 CCTGTCTCCC
* * * * * * * * *
35797 ACGGCTGAGTGCCTAAATTGGCACCGCCG-TCCCTCAGTGAGGCTGAGCGTCCATGCAGATGCCA
1 ACGGCTGAGTGCCTAGACTGGCACCCCCGTTCTCACAATGAGGCTAAGCGTCCAAGCAGA---CG
* * * *
35861 CTCACTCATCCAACGGCTGAGTGCCAATACTGGCACCCCCGTCCCTTAGTGAGGCAGAGCGTCCA
63 C-CACTCATCCAA-GGCTGAGTGCCTAGACTAGCACCCCCGTCCCTCAGTGAGGCAGAGCGTCCA
**
35926 TGCAGATGCAACTCACTCATCCA
126 TGCAGAAACAACTCACTCATCCA
* * * * **
35949 ACGGCTGAGTGTCTAGACTGGCACCCCCG-TCTCAGAATGAGGCTGAGCGT-CGA-TTGACGCCA
1 ACGGCTGAGTGCCTAGACTGGCACCCCCGTTCTCACAATGAGGCTAAGCGTCCAAGCAGACGCCA
36011 CTCATCCTAAGGCTGAGTGCCTAGACTAGCACCCCCGTCCCTCAGTGAGGCAGAGCGTCCATGCA
66 CTCATCC-AAGGCTGAGTGCCTAGACTAGCACCCCCGTCCCTCAGTGAGGCAGAGCGTCCATGCA
* *
36076 GAAACCACTCACTCATCCG
130 GAAACAACTCACTCATCCA
* * *
36095 ACGGCTTAGTGCCTAGACTGGCGCCCCCGTTTCTCTCAATGAGGCTAAGCGTCCAAGCAGACGCC
1 ACGGCTGAGTGCCTAGACTGGCACCCCCG-TTCTCACAATGAGGCTAAGCGTCCAAGCAGACGCC
* * * **
36160 ACTCATCCGACGGATGAGTGCCTAGACTTGCGTCCCCGTCCC
65 ACTCATCC-AAGGCTGAGTGCCTAGACTAGCACCCCCGTCCC
36202 ACTCTCAATG
Statistics
Matches: 212, Mismatches: 36, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
146 101 0.48
147 4 0.02
148 18 0.08
149 2 0.01
150 44 0.21
151 1 0.00
152 42 0.20
ACGTcount: A:0.21, C:0.34, G:0.25, T:0.19
Consensus pattern (148 bp):
ACGGCTGAGTGCCTAGACTGGCACCCCCGTTCTCACAATGAGGCTAAGCGTCCAAGCAGACGCCA
CTCATCCAAGGCTGAGTGCCTAGACTAGCACCCCCGTCCCTCAGTGAGGCAGAGCGTCCATGCAG
AAACAACTCACTCATCCA
Found at i:38890 original size:13 final size:13
Alignment explanation
Indices: 38872--38897 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38862 TAAAATTTAG
38872 ACACAATTTTAAT
1 ACACAATTTTAAT
38885 ACACAATTTTAAT
1 ACACAATTTTAAT
38898 GTAAGGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ACACAATTTTAAT
Found at i:39270 original size:19 final size:18
Alignment explanation
Indices: 39246--39281 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
39236 TGCAATCTTT
39246 CTTGATTCTCTCATTAATG
1 CTTGATTCTCTC-TTAATG
39265 CTTGATTCTCTCTTAAT
1 CTTGATTCTCTCTTAAT
39282 TCCAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.19, C:0.22, G:0.08, T:0.50
Consensus pattern (18 bp):
CTTGATTCTCTCTTAATG
Found at i:41655 original size:20 final size:20
Alignment explanation
Indices: 41630--41669 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41620 AAATATAATA
41630 TTTAAATTTATTTATATCAT
1 TTTAAATTTATTTATATCAT
41650 TTTAAATTTATTTATATCAT
1 TTTAAATTTATTTATATCAT
41670 AAACCACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAAATTTATTTATATCAT
Found at i:42380 original size:5 final size:5
Alignment explanation
Indices: 42366--42400 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
42356 AATTAAAGCA
42366 GCAA- GCAAG GCAAG GCAAG GCAAG GCAAAG GCAAG
1 GCAAG GCAAG GCAAG GCAAG GCAAG GC-AAG GCAAG
42401 AACAAACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.43, C:0.20, G:0.37, T:0.00
Consensus pattern (5 bp):
GCAAG
Found at i:42390 original size:15 final size:16
Alignment explanation
Indices: 42366--42400 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
42356 AATTAAAGCA
42366 GCAA-GCAAGGC-AAG
1 GCAAGGCAAGGCAAAG
42380 GCAAGGCAAGGCAAAG
1 GCAAGGCAAGGCAAAG
42396 GCAAG
1 GCAAG
42401 AACAAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 7 0.37
16 8 0.42
ACGTcount: A:0.43, C:0.20, G:0.37, T:0.00
Consensus pattern (16 bp):
GCAAGGCAAGGCAAAG
Found at i:47689 original size:26 final size:26
Alignment explanation
Indices: 47652--47726 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 26
47642 ATCTAAAGAT
*
47652 TAATAATTTTAATTTATAATTTATATA
1 TAATATTTTTAATTTATAATTTAT-TA
47679 TAA-ATTTTTAATTT-TAATGTT-TTA
1 TAATATTTTTAATTTATAAT-TTATTA
47703 TAATATTTTATATATTTAT-ATTTA
1 TAATATTTT-TA-ATTTATAATTTA
47727 ACATTTAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
24 5 0.12
25 10 0.24
26 16 0.39
27 9 0.22
28 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (26 bp):
TAATATTTTTAATTTATAATTTATTA
Found at i:54197 original size:44 final size:44
Alignment explanation
Indices: 54127--54218 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
54117 TAAGATGACT
* *
54127 TTAACATGTTAGCTCCCGACTCAAAAGAGATTAGTCTCAGGCTA
1 TTAACATGTTAGCCCCCCACTCAAAAGAGATTAGTCTCAGGCTA
* * *
54171 TTAACCTGTTAGCCCCCCACGT-AAAAGAGATTAGTCTTAGGTTA
1 TTAACATGTTAGCCCCCCAC-TCAAAAGAGATTAGTCTCAGGCTA
54215 TTAA
1 TTAA
54219 GACTTGGATG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (44 bp):
TTAACATGTTAGCCCCCCACTCAAAAGAGATTAGTCTCAGGCTA
Found at i:62725 original size:16 final size:17
Alignment explanation
Indices: 62691--62726 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
62681 CTATGGTGAT
62691 AATTATAAAGATATTTA
1 AATTATAAAGATATTTA
*
62708 AATTATAAA-ATCTTTA
1 AATTATAAAGATATTTA
62724 AAT
1 AAT
62727 AATTAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
AATTATAAAGATATTTA
Found at i:66088 original size:22 final size:22
Alignment explanation
Indices: 66060--66101 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
66050 TTAAATCGAC
*
66060 TCAAAT-CTAAATATCTTGAACA
1 TCAAATCCAAAAT-TCTTGAACA
66082 TCAAATCCAAAATTCTTGAA
1 TCAAATCCAAAATTCTTGAA
66102 TTGAAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (22 bp):
TCAAATCCAAAATTCTTGAACA
Done.