Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022526.1 Corchorus olitorius cultivar O-4 contig22559, 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: 110340
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:751 original size:12 final size:12
Alignment explanation
Indices: 734--759 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
724 CATTCATCAA
734 AAGAAATGGTTG
1 AAGAAATGGTTG
746 AAGAAATGGTTG
1 AAGAAATGGTTG
758 AA
1 AA
760 AGATCAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (12 bp):
AAGAAATGGTTG
Found at i:1647 original size:41 final size:41
Alignment explanation
Indices: 1462--1636 Score: 219
Period size: 41 Copynumber: 4.2 Consensus size: 41
1452 TCTCTCTCCC
* * *
1462 CCAAAGTCCCCAAGCACATATATAACACAAGGGGCAACTTTCTTTA
1 CCAAAGTCCTCAAGCACATATATAACAC-AGAGGC-A---TCTATA
* *
1508 --AAACTCCTCAAGCACATATATAACACAGAGGCATCCATA
1 CCAAAGTCCTCAAGCACATATATAACACAGAGGCATCTATA
1547 CCAAAGTCCTCAAGCACATATATAACACAGAGGCATCTATA
1 CCAAAGTCCTCAAGCACATATATAACACAGAGGCATCTATA
* * *
1588 TCAAAGTCCTCAAGCACATATATAACACAAAGGAATCTATA
1 CCAAAGTCCTCAAGCACATATATAACACAGAGGCATCTATA
1629 CCAAAGTC
1 CCAAAGTC
1637 TCTAAACACA
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
39 4 0.03
41 82 0.71
42 1 0.01
43 5 0.04
44 24 0.21
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (41 bp):
CCAAAGTCCTCAAGCACATATATAACACAGAGGCATCTATA
Found at i:3880 original size:2 final size:2
Alignment explanation
Indices: 3826--3860 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3816 TCTTCATTCA
*
3826 AT AT AT AT AT AT AC 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 A
3861 AACAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4716 original size:2 final size:2
Alignment explanation
Indices: 4709--4741 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4699 GTCCTCATGG
*
4709 GT GT GT GT GT GT GT GT GT GT GT GT GT TT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
4742 ATAGTTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
GT
Found at i:7308 original size:11 final size:11
Alignment explanation
Indices: 7292--7339 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
7282 GAACTTCATG
7292 TTTGAAGACTA
1 TTTGAAGACTA
7303 TTTGAAGA-TAA
1 TTTGAAGACT-A
7314 TTTGAAGAC--
1 TTTGAAGACTA
7323 -TTGAAGACTA
1 TTTGAAGACTA
7333 -TTGAAGA
1 TTTGAAGA
7340 ATTATTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.24
10 8 0.24
11 17 0.52
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (11 bp):
TTTGAAGACTA
Found at i:11651 original size:11 final size:10
Alignment explanation
Indices: 11637--11708 Score: 81
Period size: 11 Copynumber: 6.8 Consensus size: 10
11627 ACAGGCCACT
11637 ACCGGCCATTC
1 ACCGGCCA-TC
*
11648 ACCGAGCCACC
1 ACCG-GCCATC
11659 ACCGGCCATC
1 ACCGGCCATC
*
11669 ACCGTGCCACC
1 ACCG-GCCATC
11680 ACCGGCCATC
1 ACCGGCCATC
*
11690 ACCGTGCCATT
1 ACCG-GCCATC
11701 ACCGGCCA
1 ACCGGCCA
11709 AATGCTTTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
10 22 0.42
11 27 0.51
12 4 0.08
ACGTcount: A:0.21, C:0.49, G:0.19, T:0.11
Consensus pattern (10 bp):
ACCGGCCATC
Found at i:11672 original size:21 final size:21
Alignment explanation
Indices: 11631--11708 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
11621 CCATTAACAG
* *
11631 GCCACTACCGGCCATTCACCGA
1 GCCACCACCGGCCA-TCACCGT
11653 GCCACCACCGGCCATCACCGT
1 GCCACCACCGGCCATCACCGT
11674 GCCACCACCGGCCATCACCGT
1 GCCACCACCGGCCATCACCGT
**
11695 GCCATTACCGGCCA
1 GCCACCACCGGCCA
11709 AATGCTTTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 39 0.75
22 13 0.25
ACGTcount: A:0.21, C:0.49, G:0.19, T:0.12
Consensus pattern (21 bp):
GCCACCACCGGCCATCACCGT
Found at i:13584 original size:11 final size:11
Alignment explanation
Indices: 13568--13615 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
13558 GAAGTTCGTG
13568 TTTGAAGACTA
1 TTTGAAGACTA
13579 TTTGAAGA-TAA
1 TTTGAAGACT-A
13590 TTTGAAGAC--
1 TTTGAAGACTA
13599 -TTGAAGACTA
1 TTTGAAGACTA
13609 -TTGAAGA
1 TTTGAAGA
13616 ATTATTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.24
10 8 0.24
11 17 0.52
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (11 bp):
TTTGAAGACTA
Found at i:22644 original size:27 final size:24
Alignment explanation
Indices: 22614--22662 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
22604 TAATAGATCG
22614 TTTATATTATATTATATATATAATAAT
1 TTTAT-TTATATT-TATATA-AATAAT
*
22641 TTTATTTTTATTTATATAAATA
1 TTTATTTATATTTATATAAATA
22663 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 6 0.29
26 6 0.29
27 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTATTTATATTTATATAAATAAT
Found at i:25029 original size:21 final size:21
Alignment explanation
Indices: 24989--25034 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
24979 TTAAAATAAT
*
24989 TAAAAATAAAAGCAATTAAAC
1 TAAAAATAAAAGCAAGTAAAC
*
25010 TAAAAAT-AAAGCAAAGTAAAT
1 TAAAAATAAAAGC-AAGTAAAC
25031 TAAA
1 TAAA
25035 TCTAAACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (21 bp):
TAAAAATAAAAGCAAGTAAAC
Found at i:27737 original size:19 final size:19
Alignment explanation
Indices: 27713--27758 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
27703 TCAATGAATA
27713 AAGCATTCTTAAAAATTCT
1 AAGCATTCTTAAAAATTCT
27732 AAGCATTCTTAAAAATTCT
1 AAGCATTCTTAAAAATTCT
27751 AAGCATTC
1 AAGCATTC
27759 ATCAATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (19 bp):
AAGCATTCTTAAAAATTCT
Found at i:28133 original size:21 final size:21
Alignment explanation
Indices: 28109--28172 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
28099 AAGAAATACA
*
28109 AATAACTAATTCAAATCAAGG
1 AATAACTAATTCAAATCAAGC
28130 AATAGAC-AA-T-AAATCAAAGC
1 AATA-ACTAATTCAAATC-AAGC
*
28150 AATAA-TCATTCAAATCAATGC
1 AATAACTAATTCAAATCAA-GC
28171 AA
1 AA
28173 GGAAAAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
19 7 0.20
20 11 0.31
21 15 0.43
22 2 0.06
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.22
Consensus pattern (21 bp):
AATAACTAATTCAAATCAAGC
Found at i:41736 original size:182 final size:183
Alignment explanation
Indices: 41504--41898 Score: 625
Period size: 183 Copynumber: 2.2 Consensus size: 183
41494 AAGTGAATTC
* * *
41504 TTTTGAGTCCCACCAGGCGTGCCAAAAA-AGATGTTTTGGTATGACCGAAGTGGGAGG-AAACAT
1 TTTTGTGTCCCACCGGGCGTGCCAAAAAGAGATGTTTTGGTATGACCGAAGTGGAAGGAAAACAT
*
41567 TGGTGTGGG-CTTGGCCTAGGCGGACACCAGATCTGCGAAAATGAAAAGAAAAGTCGAGGATCGC
66 TGGTGCGGGTC-TGGCCTAGGCGGACACCAGATCTGCGAAAATGAAAAGAAAAGTCGAGGATCGC
*
41631 CAACTTGAGAAAAAATTGAAGAAGATTTGACGACGCAGAGTGAGAAGACAATAA
130 CAACTTGAGAAAAAATTGAAAAAGATTTGACGACGCAGAGTGAGAAGACAATAA
* * * *
41685 TTTTGTGTCCCACTGGGCGTGGCAAAAAGAGATGTTTTGGTATGGCCGAAGTGGAAGGAAAACGT
1 TTTTGTGTCCCACCGGGCGTGCCAAAAAGAGATGTTTTGGTATGACCGAAGTGGAAGGAAAACAT
* *
41750 TGGTGCGGGTCTGGCCTAGGCGGACACCAGATCTGCGAAAATTAAAAGAAGAGTCGAGGATCGCC
66 TGGTGCGGGTCTGGCCTAGGCGGACACCAGATCTGCGAAAATGAAAAGAAAAGTCGAGGATCGCC
* * * *
41815 GACTTGAGAAAAAATTGAAAAAGATTTGACGATGTAGAGTGAGAAGACAATCA
131 AACTTGAGAAAAAATTGAAAAAGATTTGACGACGCAGAGTGAGAAGACAATAA
41868 TTTTGTGTCCCACCGGGCGTGCCAAAAAGAG
1 TTTTGTGTCCCACCGGGCGTGCCAAAAAGAG
41899 GTTGCGCCAA
Statistics
Matches: 194, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
181 24 0.12
182 27 0.14
183 142 0.73
184 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (183 bp):
TTTTGTGTCCCACCGGGCGTGCCAAAAAGAGATGTTTTGGTATGACCGAAGTGGAAGGAAAACAT
TGGTGCGGGTCTGGCCTAGGCGGACACCAGATCTGCGAAAATGAAAAGAAAAGTCGAGGATCGCC
AACTTGAGAAAAAATTGAAAAAGATTTGACGACGCAGAGTGAGAAGACAATAA
Found at i:43975 original size:2 final size:2
Alignment explanation
Indices: 43968--44005 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
43958 ATTTTAAAGC
*
43968 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44006 GTGCTGCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:44246 original size:135 final size:134
Alignment explanation
Indices: 43996--44249 Score: 472
Period size: 135 Copynumber: 1.9 Consensus size: 134
43986 TATATATTTA
43996 TATATATATAGTGCTGCTATTATGATCTGCCACATGAATCTGAATTTTTGTTGGAGGATATAATA
1 TATATATATAGTGCTGCTATTATGATCTGCCACATGAATCTGAATTTTTGTTGGAGGATATAATA
44061 TTCGAATCTCATTACAATCATGGATATTTTCGAACCATCCAAATGAGAAAGCGATCATAATAGCA
66 TTCGAATCTCATTACAATCATGGATATTTTCGAACCATCCAAATGAGAAAGCGATCATAATAGCA
44126 GCAC
131 GCAC
*
44130 TATATATATAGTGCTGCTATTATGATCTGTCACATGAATCTGAATTTTTGTTGGAGGAATATAAT
1 TATATATATAGTGCTGCTATTATGATCTGCCACATGAATCTGAATTTTTGTTGGAGG-ATATAAT
* *
44195 ATTTGAATCTCATTACAATCATTGATATTTTCGAACCATCCAAATGAGAAAGCGA
65 ATTCGAATCTCATTACAATCATGGATATTTTCGAACCATCCAAATGAGAAAGCGA
44250 ATAACAAACT
Statistics
Matches: 116, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
134 56 0.48
135 60 0.52
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (134 bp):
TATATATATAGTGCTGCTATTATGATCTGCCACATGAATCTGAATTTTTGTTGGAGGATATAATA
TTCGAATCTCATTACAATCATGGATATTTTCGAACCATCCAAATGAGAAAGCGATCATAATAGCA
GCAC
Found at i:45327 original size:22 final size:22
Alignment explanation
Indices: 45302--45385 Score: 91
Period size: 23 Copynumber: 3.9 Consensus size: 22
45292 ATAAACTCCA
* *
45302 TATGAAACTTTGATAACCTAAC
1 TATGAAATTTTGATAACCTTAC
* *
45324 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTAC
*
45347 TATGAAATTTTG-TAATCTTAC
1 TATGAAATTTTGATAACCTTAC
*
45368 TATG-ATTTTTGATAACCT
1 TATGAAATTTTGATAACCT
45386 CCCTGTGAGA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.12
21 15 0.29
22 13 0.25
23 17 0.33
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTAC
Found at i:46750 original size:11 final size:11
Alignment explanation
Indices: 46734--46763 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
46724 AATAAGCAAT
46734 CGTAGCTAGCC
1 CGTAGCTAGCC
*
46745 CGTAGCTAGTC
1 CGTAGCTAGCC
46756 CGTAGCTA
1 CGTAGCTA
46764 AATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (11 bp):
CGTAGCTAGCC
Found at i:48510 original size:2 final size:2
Alignment explanation
Indices: 48503--48546 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
48493 AAAGCCACAC
*
48503 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA GTA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
48545 TA
1 TA
48547 AATAAGAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:49627 original size:22 final size:22
Alignment explanation
Indices: 49558--49726 Score: 82
Period size: 22 Copynumber: 7.7 Consensus size: 22
49548 TGACTATTTT
*
49558 TATGAAATTTTGATAA-CTACCC
1 TATGAAATTTTGATAATTTA-CC
** *
49580 TATTCAATTTTGAT-ATTTACGT
1 TATGAAATTTTGATAATTTAC-C
*
49602 TATGGAATTTTGATAATTTACC
1 TATGAAATTTTGATAATTTACC
* **
49624 TATGAAATTGTGATAAACT-CC
1 TATGAAATTTTGATAATTTACC
* ** **
49645 ATATGAAACTTTGATAACCTAAT
1 -TATGAAATTTTGATAATTTACC
* *
49668 TATGAAATTTTAATAAACCTT-CC
1 TATGAAATTTTGAT-AA-TTTACC
*
49691 TATGAAATTTTG-TAACCTT-CC
1 TATGAAATTTTGATAA-TTTACC
*
49712 TATG-ATTTTTGATAA
1 TATGAAATTTTGATAA
49727 CCTCTCTGTG
Statistics
Matches: 116, Mismatches: 23, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
20 6 0.05
21 19 0.16
22 70 0.60
23 19 0.16
24 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAATTTACC
Found at i:49709 original size:21 final size:22
Alignment explanation
Indices: 49602--49729 Score: 111
Period size: 22 Copynumber: 5.9 Consensus size: 22
49592 ATATTTACGT
* *
49602 TATGGAATTTTGATAA-TTTACC
1 TATGAAATTTTGATAACCTT-CC
* *
49624 TATGAAATTGTGATAAAC-TCC
1 TATGAAATTTTGATAACCTTCC
* ***
49645 ATATGAAACTTTGATAACCTAAT
1 -TATGAAATTTTGATAACCTTCC
*
49668 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
49691 TATGAAATTTTG-TAACCTTCC
1 TATGAAATTTTGATAACCTTCC
*
49712 TATG-ATTTTTGATAACCT
1 TATGAAATTTTGATAACCT
49730 CTCTGTGAGA
Statistics
Matches: 85, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
20 6 0.07
21 20 0.24
22 43 0.51
23 16 0.19
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:53703 original size:37 final size:37
Alignment explanation
Indices: 53636--53737 Score: 104
Period size: 37 Copynumber: 2.8 Consensus size: 37
53626 ACTTAAAATT
*
53636 AAATCATAAGTAAATA-ATATA-TATATATATAGTA-GA
1 AAATCATAAGTAAATATATATAGTCTA-ATATA-TACGA
** * *
53672 AATATTTTTAG-AAATATATATAGTCTAATATATACGT
1 AA-ATCATAAGTAAATATATATAGTCTAATATATACGA
53709 AAATCATAAGTAAATATATATAGTCTAAT
1 AAATCATAAGTAAATATATATAGTCTAAT
53738 TTTAAGTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
36 14 0.26
37 36 0.68
38 3 0.06
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (37 bp):
AAATCATAAGTAAATATATATAGTCTAATATATACGA
Found at i:54332 original size:18 final size:17
Alignment explanation
Indices: 54309--54342 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54299 ATTGACCGAA
54309 TCCTTATAACCAAAAATT
1 TCCTTA-AACCAAAAATT
*
54327 TCCTTAACCCAAAAAT
1 TCCTTAAACCAAAAAT
54343 GACCTAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (17 bp):
TCCTTAAACCAAAAATT
Found at i:60788 original size:2 final size:2
Alignment explanation
Indices: 60781--60813 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
60771 TAATACTAAT
60781 TA TA TA TA 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 TA T
60814 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62923 original size:4 final size:4
Alignment explanation
Indices: 62916--62955 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
62906 TTTCAAAAAA
62916 AAAG AAAG AAAG AAAG AAA- AAAG AAAG AAA- AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
62956 AAGAAGAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 9 0.27
4 24 0.73
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:62937 original size:19 final size:18
Alignment explanation
Indices: 62913--62956 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 18
62903 ATTTTTCAAA
62913 AAAAAAGAAAGAAAGAAAG
1 AAAAAAGAAAGAAA-AAAG
62932 AAAAAAGAAAGAAAAAAG
1 AAAAAAGAAAGAAAAAAG
62950 AAGAAAA
1 AA-AAAA
62957 AGAAGAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAAG
Found at i:62940 original size:11 final size:11
Alignment explanation
Indices: 62910--62957 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
62900 TCAATTTTTC
62910 AAAAAA-AAAG
1 AAAAAAGAAAG
62920 AAAGAAAGAAAG
1 AAA-AAAGAAAG
62932 AAAAAAGAAAG
1 AAAAAAGAAAG
62943 AAAAAAG-AAG
1 AAAAAAGAAAG
62953 AAAAA
1 AAAAA
62958 GAAGAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 11 0.31
11 18 0.50
12 7 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:62962 original size:19 final size:22
Alignment explanation
Indices: 62910--62964 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
62900 TCAATTTTTC
*
62910 AAAAAAAAAGAAAGAAAGAAAG
1 AAAAAAGAAGAAAGAAAGAAAG
62932 AAAAAAGAAAGAAA-AAAG-AAG
1 AAAAAAG-AAGAAAGAAAGAAAG
62953 -AAAAAGAAGAAA
1 AAAAAAGAAGAAA
62965 CAAAATAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 6 0.19
20 6 0.19
21 3 0.10
22 10 0.32
23 6 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAGAAAGAAAGAAAG
Found at i:64925 original size:9 final size:9
Alignment explanation
Indices: 64893--64949 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
64883 TTATTTTTGT
*
64893 TTATAATAA
1 TTATTATAA
* *
64902 TAATAATAA
1 TTATTATAA
*
64911 TAATTATAA
1 TTATTATAA
*
64920 TTATTATTA
1 TTATTATAA
*
64929 TTATTATTA
1 TTATTATAA
64938 TTA-TATAA
1 TTATTATAA
64946 TTAT
1 TTAT
64950 ATTTTTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
8 7 0.17
9 35 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTATTATAA
Found at i:69479 original size:20 final size:22
Alignment explanation
Indices: 69456--69502 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
69446 TCATTCTCAC
*
69456 CTCACCAT-TATAAT-TCTAAT
1 CTCACCATATATAATAACTAAT
*
69476 CTCA-CATATATACTAACTAAT
1 CTCACCATATATAATAACTAAT
69497 CTCACC
1 CTCACC
69503 TTCAATCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 9 0.41
22 1 0.05
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (22 bp):
CTCACCATATATAATAACTAAT
Found at i:72781 original size:23 final size:25
Alignment explanation
Indices: 72754--72810 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
72744 GCTTAAAAAG
72754 GGGTAGTTCTTTCAGAAA-A-GAGT
1 GGGTAGTTCTTTCAGAAAGAGGAGT
*
72777 GGGTAG-T-TTTCATAAAGAGGAGT
1 GGGTAGTTCTTTCAGAAAGAGGAGT
*
72800 GGATAGTTCTT
1 GGGTAGTTCTT
72811 AAAAAAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 8 0.29
22 2 0.07
23 15 0.54
24 1 0.04
25 2 0.07
ACGTcount: A:0.28, C:0.07, G:0.32, T:0.33
Consensus pattern (25 bp):
GGGTAGTTCTTTCAGAAAGAGGAGT
Found at i:75800 original size:42 final size:42
Alignment explanation
Indices: 75741--75825 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
75731 CATTTCAGGG
* ** *
75741 AAACCTCATTCATCAAGAAAATGTGGAACTCTATAAGAAGGT
1 AAACCTAATTCATCAAGAAAACATGGAACTATATAAGAAGGT
* *
75783 AAACCTAATTCGTCAAGAAAACATGGAATTATATAAGAAGGT
1 AAACCTAATTCATCAAGAAAACATGGAACTATATAAGAAGGT
75825 A
1 A
75826 TAAATTTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (42 bp):
AAACCTAATTCATCAAGAAAACATGGAACTATATAAGAAGGT
Found at i:77191 original size:16 final size:16
Alignment explanation
Indices: 77170--77201 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
77160 CAATAACCAA
77170 GATACACAGTTACCGT
1 GATACACAGTTACCGT
77186 GATACACAGTTACCGT
1 GATACACAGTTACCGT
77202 AGCAATGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (16 bp):
GATACACAGTTACCGT
Found at i:88489 original size:42 final size:42
Alignment explanation
Indices: 88430--88511 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
88420 TTTAATTGGG
88430 CGGGCTTGGGCATAAGTTAAGGCCCGTTTAGTCGGGCCGGAC
1 CGGGCTTGGGCATAAGTTAAGGCCCGTTTAGTCGGGCCGGAC
*
88472 CGGGCTTGGGCATAAGTTAAGGCTCGTTTAGTCGGGCCGG
1 CGGGCTTGGGCATAAGTTAAGGCCCGTTTAGTCGGGCCGG
88512 CCATGTAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.16, C:0.22, G:0.39, T:0.23
Consensus pattern (42 bp):
CGGGCTTGGGCATAAGTTAAGGCCCGTTTAGTCGGGCCGGAC
Found at i:92964 original size:102 final size:102
Alignment explanation
Indices: 92788--92980 Score: 368
Period size: 102 Copynumber: 1.9 Consensus size: 102
92778 TCTTTACTAT
92788 CTTGAAACAATCCCCATTTGAATTCTCATCACTACTTTGCTGAAGAAAAGCTGACAGGCTCTTTC
1 CTTGAAACAATCCCCATTTGAATTCTCATCACTACTTTGCTGAAGAAAAGCTGACAGGCTCTTTC
92853 CGCATAACTCTGTTGGAATAACCGCCTTTTTAATCTC
66 CGCATAACTCTGTTGGAATAACCGCCTTTTTAATCTC
* *
92890 CTTGAAACAATCCCCATTTGAATTCTTATCACTACTTTGCTGAAGAAAAGCTGGCAGGCTCTTTC
1 CTTGAAACAATCCCCATTTGAATTCTCATCACTACTTTGCTGAAGAAAAGCTGACAGGCTCTTTC
92955 CGCATAACTCTGTTGGAATAACCGCC
66 CGCATAACTCTGTTGGAATAACCGCC
92981 GCCTTAATTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (102 bp):
CTTGAAACAATCCCCATTTGAATTCTCATCACTACTTTGCTGAAGAAAAGCTGACAGGCTCTTTC
CGCATAACTCTGTTGGAATAACCGCCTTTTTAATCTC
Found at i:106763 original size:20 final size:19
Alignment explanation
Indices: 106739--106789 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
106729 TTTGGCTAAG
*
106739 ATTTCATATATATTCTATTA
1 ATTTCATATAT-TGCTATTA
*
106759 GTTTCATATACTTGCTATTA
1 ATTTCATATA-TTGCTATTA
106779 ATTTCATATAT
1 ATTTCATATAT
106790 CCAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (19 bp):
ATTTCATATATTGCTATTA
Found at i:107653 original size:12 final size:12
Alignment explanation
Indices: 107636--107660 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
107626 GAAAATTCAA
107636 GGCTCGAGCTCG
1 GGCTCGAGCTCG
107648 GGCTCGAGCTCG
1 GGCTCGAGCTCG
107660 G
1 G
107661 CCGAGCTTTC
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:0.44, T:0.16
Consensus pattern (12 bp):
GGCTCGAGCTCG
Found at i:107707 original size:16 final size:16
Alignment explanation
Indices: 107686--107726 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
107676 CCTGCTCGAG
107686 CTCGAGCTCGAACGAA
1 CTCGAGCTCGAACGAA
107702 CTCGAGCTCGAACGAA
1 CTCGAGCTCGAACGAA
107718 CTCGAGCTC
1 CTCGAGCTC
107727 TACTCGAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.27, C:0.34, G:0.24, T:0.15
Consensus pattern (16 bp):
CTCGAGCTCGAACGAA
Done.