Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010772.1 Corchorus capsularis cultivar CVL-1 contig10793, 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: 38500
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1822 original size:35 final size:34
Alignment explanation
Indices: 1771--2349 Score: 454
Period size: 35 Copynumber: 16.7 Consensus size: 34
1761 TTCTTACTAA
*
1771 ACTTAATTACCCTGAATTAAGTTACTTATTAACTC
1 ACTTAATTACCCTGAATTAAGTTA-TTACTAACTC
* *
1806 ACTTAATTACCTTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTT-ATTACTAACTC
* * ** *
1841 ACTTAATTACCATGGATTAAGTTGACCAACTGACTC
1 ACTTAATTACCCTGAATTAAGTT-A-TTACTAACTC
* * *
1877 ACTTAATTACCCTGAATTAAGCTA--CCT-ACTG
1 ACTTAATTACCCTGAATTAAGTTATTACTAACTC
* *
1908 ACTTAATTACCCTGAATTAAATTGATTACTAAAC-G
1 ACTTAATTACCCTGAATTAAGTT-ATTACT-AACTC
* * * *
1943 GCTTAATTACCCTGAATTAAATTGATAACTGAA-TT
1 ACTTAATTACCCTGAATTAAGTT-ATTACT-AACTC
* ** *
1978 ACTTAATTACCCTGAATTAAGTTAATTATTTCCTG
1 ACTTAATTACCCTGAATTAAGTT-ATTACTAACTC
* *
2013 ACTTAATTACCCTGAATTAAGTTAATTACTAAATT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTAACTC
*
2048 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTT-ATTACTAACTC
* *
2083 ACTTAATTACCCTGTATTAAGTTGATTACTGAA-TT
1 ACTTAATTACCCTGAATTAAGTT-ATTACT-AACTC
2118 ACTTAATTACCCTGAATTAAG---TTACT---T-
1 ACTTAATTACCCTGAATTAAGTTATTACTAACTC
*
2145 ACTTAATTACCCTGAATTAAGTTTATTCACTGAC-C
1 ACTTAATTACCCTGAATTAAG-TTATT-ACTAACTC
*
2180 TACTTAATTACCCTGAATTAAGTTTATTCACTGAC-C
1 -ACTTAATTACCCTGAATTAAG-TTATT-ACTAACTC
2216 TACTTAATTACCCTGAATTAAGTTTATTCACTAAC-C
1 -ACTTAATTACCCTGAATTAAG-TTATT-ACTAACTC
* * *
2252 TACTTAACTACCCTGAATTAAGTTACTTATTACTGACTT
1 -ACTTAATTACCCTGAATTAAG----TTATTACTAACTC
* ** *
2291 ACTTAATTATCCTGAATTAAGTTACTCGCTGAC-C
1 ACTTAATTACCCTGAATTAAGTTA-TTACTAACTC
* *
2325 TACTTAATTGCCTTGAATTAAGTTA
1 -ACTTAATTACCCTGAATTAAGTTA
2350 CTTATTACTG
Statistics
Matches: 465, Mismatches: 53, Indels: 52
0.82 0.09 0.09
Matches are distributed among these distances:
27 21 0.05
28 1 0.00
31 31 0.07
32 6 0.01
34 5 0.01
35 249 0.54
36 123 0.26
38 24 0.05
39 5 0.01
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.38
Consensus pattern (34 bp):
ACTTAATTACCCTGAATTAAGTTATTACTAACTC
Found at i:1927 original size:14 final size:14
Alignment explanation
Indices: 1879--1927 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
1869 ACTGACTCAC
1879 TTAATTACCCTGAA
1 TTAATTACCCTGAA
* *
1893 TTAAGCTACCTACTGAC
1 TTAA-TTACC--CTGAA
1910 TTAATTACCCTGAA
1 TTAATTACCCTGAA
1924 TTAA
1 TTAA
1928 ATTGATTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 12 0.43
15 4 0.14
16 4 0.14
17 8 0.29
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (14 bp):
TTAATTACCCTGAA
Found at i:2041 original size:105 final size:105
Alignment explanation
Indices: 1771--2314 Score: 553
Period size: 105 Copynumber: 5.2 Consensus size: 105
1761 TTCTTACTAA
* * *
1771 ACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTTAATTACCTTGAATTAAGTTGATTACT
1 ACTTAATTACCCTGAATTAAGTTAATTATTAACTGACTTAATTACCCTGAATTAAGTTGATTACT
* * * * *
1836 -GACTCACTTAATTACCATGGATTAAGTTGACCAACTGACTC
66 AAACT-ACTTAATTACCCTGAATTAAGTTGA-TAACTGACTT
* ** *
1877 ACTTAATTACCCTGAATTAAGCT-A--CCT-ACTGACTTAATTACCCTGAATTAAATTGATTACT
1 ACTTAATTACCCTGAATTAAGTTAATTATTAACTGACTTAATTACCCTGAATTAAGTTGATTACT
** * *
1938 AAACGGCTTAATTACCCTGAATTAAATTGATAACTGAATT
66 AAACTACTTAATTACCCTGAATTAAGTTGATAACTGACTT
** *
1978 ACTTAATTACCCTGAATTAAGTTAATTATTTCCTGACTTAATTACCCTGAATTAAGTTAATTACT
1 ACTTAATTACCCTGAATTAAGTTAATTATTAACTGACTTAATTACCCTGAATTAAGTTGATTACT
* * *
2043 AAATTACTTAATTACCCTGAATTAAGTTGATTACTGACTC
66 AAACTACTTAATTACCCTGAATTAAGTTGATAACTGACTT
* * * *
2083 ACTTAATTACCCTGTATTAAGTTGATTACTGAA-TTACTTAATTACCCTGAATTAA---G-TTAC
1 ACTTAATTACCCTGAATTAAGTTAATTA-TTAACTGACTTAATTACCCTGAATTAAGTTGATTAC
* * *
2143 T----TACTTAATTACCCTGAATTAAGTTTATTCACTGACCT
65 TAAACTACTTAATTACCCTGAATTAAGTTGA-TAACTGACTT
* * * *
2181 ACTTAATTACCCTGAATTAAGTTTATTCACTGACCT-ACTTAATTACCCTGAATTAAGTTTATTC
1 ACTTAATTACCCTGAATTAAGTTAATT-A-TTAACTGACTTAATTACCCTGAATTAAGTTGATT-
* *
2245 ACTAACCTACTTAACTACCCTGAATTAAGTT-ACTTATTACTGACTT
63 ACTAAACTACTTAATTACCCTGAATTAAGTTGA--TA--ACTGACTT
*
2291 ACTTAATTATCCTGAATTAAGTTA
1 ACTTAATTACCCTGAATTAAGTTA
2315 CTCGCTGACC
Statistics
Matches: 368, Mismatches: 49, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
97 25 0.07
98 32 0.09
99 25 0.07
100 1 0.00
101 34 0.09
102 53 0.14
103 5 0.01
104 4 0.01
105 111 0.30
106 23 0.06
107 1 0.00
108 25 0.07
110 29 0.08
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (105 bp):
ACTTAATTACCCTGAATTAAGTTAATTATTAACTGACTTAATTACCCTGAATTAAGTTGATTACT
AAACTACTTAATTACCCTGAATTAAGTTGATAACTGACTT
Found at i:2146 original size:27 final size:27
Alignment explanation
Indices: 2116--2167 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
2106 GATTACTGAA
2116 TTACTTAATTACCCTGAATTAAGTTAC
1 TTACTTAATTACCCTGAATTAAGTTAC
2143 TTACTTAATTACCCTGAATTAAGTT
1 TTACTTAATTACCCTGAATTAAGTT
2168 TATTCACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (27 bp):
TTACTTAATTACCCTGAATTAAGTTAC
Found at i:2185 original size:36 final size:36
Alignment explanation
Indices: 2144--2348 Score: 297
Period size: 36 Copynumber: 5.7 Consensus size: 36
2134 TTAAGTTACT
2144 TACTTAATTACCCTGAATTAAGTTTATTCACTGACC
1 TACTTAATTACCCTGAATTAAGTTTATTCACTGACC
2180 TACTTAATTACCCTGAATTAAGTTTATTCACTGACC
1 TACTTAATTACCCTGAATTAAGTTTATTCACTGACC
*
2216 TACTTAATTACCCTGAATTAAGTTTATTCACTAACC
1 TACTTAATTACCCTGAATTAAGTTTATTCACTGACC
* *
2252 TACTTAACTACCCTGAATTAAGTTACTTATT-ACTGACT
1 TACTTAATTACCCTGAATTAAG-T--TTATTCACTGACC
* * *
2290 TACTTAATTATCCTGAATTAAG-TTACTCGCTGACC
1 TACTTAATTACCCTGAATTAAGTTTATTCACTGACC
* *
2325 TACTTAATTGCCTTGAATTAAGTT
1 TACTTAATTACCCTGAATTAAGTT
2349 ACTTATTACT
Statistics
Matches: 152, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
34 4 0.03
35 24 0.16
36 93 0.61
37 1 0.01
38 25 0.16
39 5 0.03
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (36 bp):
TACTTAATTACCCTGAATTAAGTTTATTCACTGACC
Found at i:2356 original size:73 final size:74
Alignment explanation
Indices: 2141--2360 Score: 331
Period size: 72 Copynumber: 3.0 Consensus size: 74
2131 GAATTAAGTT
2141 ACTTACTTAATTACCCTGAATTAAGTTTATTCACTGACCTACTTAATTACCCTGAATTAAG-T--
1 ACTTACTTAATTACCCTGAATTAAGTTTATTCACTGACCTACTTAATTACCCTGAATTAAGTTAC
2203 TTATTCACTG
66 TTATT-ACTG
* * *
2213 ACCTACTTAATTACCCTGAATTAAGTTTATTCACTAACCTACTTAACTACCCTGAATTAAGTTAC
1 ACTTACTTAATTACCCTGAATTAAGTTTATTCACTGACCTACTTAATTACCCTGAATTAAGTTAC
2278 TTATTACTG
66 TTATTACTG
* * * * *
2287 ACTTACTTAATTATCCTGAATTAAG-TTACTCGCTGACCTACTTAATTGCCTTGAATTAAGTTAC
1 ACTTACTTAATTACCCTGAATTAAGTTTATTCACTGACCTACTTAATTACCCTGAATTAAGTTAC
2351 TTATTACTG
66 TTATTACTG
2360 A
1 A
2361 TTCACCTTTT
Statistics
Matches: 134, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
72 58 0.43
73 44 0.33
74 27 0.20
75 5 0.04
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (74 bp):
ACTTACTTAATTACCCTGAATTAAGTTTATTCACTGACCTACTTAATTACCCTGAATTAAGTTAC
TTATTACTG
Found at i:2931 original size:32 final size:33
Alignment explanation
Indices: 2875--2937 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
2865 ATTTCATCTT
* * *
2875 TTACTTAAAAGATTTAATCTTTATTTACAAAAA
1 TTACTTAAAAGACTCAATCTTTATTCACAAAAA
2908 TTACTTAAAAG-CTCAATCTTTATTCACAAA
1 TTACTTAAAAGACTCAATCTTTATTCACAAA
2938 TTACTCCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (33 bp):
TTACTTAAAAGACTCAATCTTTATTCACAAAAA
Found at i:4707 original size:2 final size:2
Alignment explanation
Indices: 4700--4732 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4690 CGCCATTTGA
4700 AT 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 A
4733 CACCCAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5854 original size:78 final size:78
Alignment explanation
Indices: 5701--5846 Score: 175
Period size: 78 Copynumber: 1.9 Consensus size: 78
5691 CAGGAGGCAA
* * * * *
5701 GTCGACAATAGAAAGCCAAAAGTGGAGATGGCTCATGGTGACCCTATTGAAAAACCTGTATCTGT
1 GTCGACAATAGAAAGCCAAAAGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGAACCTAT
*
5766 TTGCAAAAATCCT
66 TCGCAAAAATCCT
*** * * * *
5779 GTCGACAATAGAAAGCCAGGGGTGGAAATAGCTCGTGGTGGCCCTATTGTAAGACCTGAACCTAT
1 GTCGACAATAGAAAGCCAAAAGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGAACCTAT
5844 TCG
66 TCG
5847 TAGAAATCTT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
78 55 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (78 bp):
GTCGACAATAGAAAGCCAAAAGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGAACCTAT
TCGCAAAAATCCT
Found at i:8672 original size:24 final size:24
Alignment explanation
Indices: 8645--8747 Score: 95
Period size: 24 Copynumber: 4.4 Consensus size: 24
8635 TTTTCTAACA
*
8645 ACCACTATGTGGTCGAATCTCACG
1 ACCACTATGTGGCCGAATCTCACG
*
8669 ACCACCT-TGTGGCCGAATCTCATG
1 ACCA-CTATGTGGCCGAATCTCACG
* * * *
8693 GCCACCA--TGACCGAATCTCAAG
1 ACCACTATGTGGCCGAATCTCACG
* * *
8715 GCTACTATGTGGTCGAATCTCACG
1 ACCACTATGTGGCCGAATCTCACG
8739 ACCACTATG
1 ACCACTATG
8748 ACTTATTCAA
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
22 18 0.29
23 1 0.02
24 41 0.66
25 2 0.03
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (24 bp):
ACCACTATGTGGCCGAATCTCACG
Found at i:15654 original size:25 final size:22
Alignment explanation
Indices: 15596--15682 Score: 97
Period size: 22 Copynumber: 3.9 Consensus size: 22
15586 TTGTTCACCC
*
15596 CTCTATGAAATTCTGATAATCA
1 CTCTATGAAATTTTGATAATCA
*
15618 CAT-TATGTAATTTTGATAATCTGA
1 C-TCTATGAAATTTTGATAATC--A
15642 TCTCTATGAAATTTTGATAATCA
1 -CTCTATGAAATTTTGATAATCA
*
15665 CTCTATGAGA-TTTGATAA
1 CTCTATGAAATTTTGATAA
15683 CCTTCTTTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
21 8 0.14
22 26 0.46
23 2 0.04
24 2 0.04
25 18 0.32
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (22 bp):
CTCTATGAAATTTTGATAATCA
Found at i:15758 original size:22 final size:22
Alignment explanation
Indices: 15729--15854 Score: 105
Period size: 22 Copynumber: 5.7 Consensus size: 22
15719 ATAACCTTCA
15729 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* * *
15751 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * *
15773 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
15794 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCACAC
* **
15817 TATGAAATTCTT-ATAACCTCGT
1 TATGAAATT-TTGATAACCACAC
*
15839 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
15855 TCTTTTTGAT
Statistics
Matches: 83, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
21 4 0.05
22 75 0.90
23 4 0.05
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:15951 original size:24 final size:22
Alignment explanation
Indices: 15890--16051 Score: 105
Period size: 22 Copynumber: 7.3 Consensus size: 22
15880 TTGTGATGAT
* *
15890 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
15912 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
15934 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
15958 TAACC-ACGCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
15980 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
16002 TAACC-TCCTCATCAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * * *
16024 TGACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
16046 TAACCA
1 TAACCA
16052 CATAGAGATA
Statistics
Matches: 113, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.03
22 89 0.79
23 3 0.03
24 18 0.16
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:18183 original size:14 final size:14
Alignment explanation
Indices: 18164--18192 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
18154 ACAAGAGCTT
18164 TTAAAAGGCTTAAA
1 TTAAAAGGCTTAAA
18178 TTAAAAGGCTTAAA
1 TTAAAAGGCTTAAA
18192 T
1 T
18193 ATCGAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (14 bp):
TTAAAAGGCTTAAA
Found at i:21844 original size:3 final size:3
Alignment explanation
Indices: 21836--21869 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
21826 TCCGTTTGTT
21836 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21870 GAAGTATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:24902 original size:47 final size:47
Alignment explanation
Indices: 24828--24929 Score: 186
Period size: 47 Copynumber: 2.2 Consensus size: 47
24818 CAGCTTTTGA
24828 ATATATAATCCCATAATACTAGAAGTCCTTCAACATCAATAGGATGC
1 ATATATAATCCCATAATACTAGAAGTCCTTCAACATCAATAGGATGC
* *
24875 ATATATAATCTCATAATACTAGTAGTCCTTCAACATCAATAGGATGC
1 ATATATAATCCCATAATACTAGAAGTCCTTCAACATCAATAGGATGC
24922 ATATATAA
1 ATATATAA
24930 AAGGATGTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (47 bp):
ATATATAATCCCATAATACTAGAAGTCCTTCAACATCAATAGGATGC
Found at i:26983 original size:19 final size:19
Alignment explanation
Indices: 26942--26984 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
26932 TTGTCTGCCA
*
26942 AAAAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAC
*
26961 AAAAAAAAAAAAAAAAATC
1 AAAAAAAAAAAAAAAAAAC
26980 AAAAA
1 AAAAA
26985 CTAGTCGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.93, C:0.02, G:0.02, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAAAC
Found at i:26984 original size:1 final size:1
Alignment explanation
Indices: 26941--26977 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
26931 TTTGTCTGCC
*
26941 AAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
26978 TCAAAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:29712 original size:11 final size:11
Alignment explanation
Indices: 29696--29724 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
29686 TCTAATTCTC
29696 TTTGAAAAATG
1 TTTGAAAAATG
29707 TTTGAAAAATG
1 TTTGAAAAATG
29718 TTTGAAA
1 TTTGAAA
29725 CATTCCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (11 bp):
TTTGAAAAATG
Found at i:31622 original size:37 final size:37
Alignment explanation
Indices: 31578--31648 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
31568 CTTGATCAAC
* * *
31578 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAAACATAACTTTATGATCA
31615 ATACATGTCTTTCCAAATAAACATAACTTTATGA
1 ATACATGTCTTTCCAAATAAACATAACTTTATGA
31649 ATAATCATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAAACATAACTTTATGATCA
Found at i:31713 original size:31 final size:31
Alignment explanation
Indices: 31677--31736 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
31667 TACCTATTAT
31677 AGACAAATAAGTCTCTTCATAATTGTTCATA
1 AGACAAATAAGTCTCTTCATAATTGTTCATA
*
31708 AGACAAATAAGTCTCTTTATAATTGTTCA
1 AGACAAATAAGTCTCTTCATAATTGTTCA
31737 CTTATGAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (31 bp):
AGACAAATAAGTCTCTTCATAATTGTTCATA
Found at i:34088 original size:37 final size:37
Alignment explanation
Indices: 34044--34114 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
34034 CTTGATCAAC
* * *
34044 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAAACATAACTTTATGATCA
34081 ATACATGTCTTTCCAAATAAACATAACTTTATGA
1 ATACATGTCTTTCCAAATAAACATAACTTTATGA
34115 ATAATCATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAAACATAACTTTATGATCA
Found at i:34179 original size:31 final size:31
Alignment explanation
Indices: 34143--34202 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
34133 TACCTATTAT
34143 AGACAAATAAGTCTCTTCATAATTGTTCATA
1 AGACAAATAAGTCTCTTCATAATTGTTCATA
*
34174 AGACAAATAAGTCTCTTTATAATTGTTCA
1 AGACAAATAAGTCTCTTCATAATTGTTCA
34203 CTTATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (31 bp):
AGACAAATAAGTCTCTTCATAATTGTTCATA
Found at i:34318 original size:12 final size:12
Alignment explanation
Indices: 34301--34325 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34291 CCTCTTCTCT
34301 GTTTATTTCCCC
1 GTTTATTTCCCC
34313 GTTTATTTCCCC
1 GTTTATTTCCCC
34325 G
1 G
34326 CATATGTTGG
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:0.08, C:0.32, G:0.12, T:0.48
Consensus pattern (12 bp):
GTTTATTTCCCC
Done.