Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016733.1 Corchorus olitorius cultivar O-4 contig16766, 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: 59192
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:24 original size:15 final size:15
Alignment explanation
Indices: 4--33 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1 TGA
4 TTGATTTCAATTAAT
1 TTGATTTCAATTAAT
19 TTGATTTCAATTAAT
1 TTGATTTCAATTAAT
34 AGATTGGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTGATTTCAATTAAT
Found at i:2263 original size:21 final size:22
Alignment explanation
Indices: 2237--2277 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
2227 TAATTAAATG
2237 CAATTTGATCCCTG-TTTTATT
1 CAATTTGATCCCTGATTTTATT
2258 CAATTTGATCCCTGATTTTA
1 CAATTTGATCCCTGATTTTA
2278 GAAATTATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CAATTTGATCCCTGATTTTATT
Found at i:2283 original size:21 final size:21
Alignment explanation
Indices: 2238--2283 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2228 AATTAAATGC
**
2238 AATTTGATCCCTGTTTTATTC
1 AATTTGATCCCTGTTTTATGA
2259 AATTTGATCCCTGATTTTA-GA
1 AATTTGATCCCTG-TTTTATGA
2280 AATT
1 AATT
2284 ATGCTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (21 bp):
AATTTGATCCCTGTTTTATGA
Found at i:3337 original size:16 final size:16
Alignment explanation
Indices: 3290--3337 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
3280 CAAAGTTGAA
** *
3290 GAAAAAATTAAAAAAA
1 GAAAAAATGGAAAAAT
* *
3306 GAAGAAAGGGAAAAAT
1 GAAAAAATGGAAAAAT
3322 GAAAAAATGGAAAAAT
1 GAAAAAATGGAAAAAT
3338 CAGAAAATTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (16 bp):
GAAAAAATGGAAAAAT
Found at i:6925 original size:19 final size:18
Alignment explanation
Indices: 6892--6927 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6882 TTGAGATAAT
6892 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
6910 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
6928 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:16776 original size:7 final size:6
Alignment explanation
Indices: 16750--16794 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
16740 ATAGAGTAAT
16750 AAAAGA AAAAG- -AAAGA AAAAGGA AAAAGA AAAAG- AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAAG
16795 TTAGGATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 20 0.57
7 6 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:16776 original size:17 final size:15
Alignment explanation
Indices: 16750--16794 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 15
16740 ATAGAGTAAT
16750 AAAAGAAAAAGAAAGA
1 AAAAGAAAAAGAAA-A
16766 AAAAGGAAAAAGAAAAA
1 AAAA-GAAAAAG-AAAA
16783 GAAAAGAAAAAG
1 -AAAAGAAAAAG
16795 TTAGGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.15
17 15 0.58
18 7 0.27
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:16779 original size:23 final size:24
Alignment explanation
Indices: 16750--16794 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
16740 ATAGAGTAAT
16750 AAAAGAAAAAG-AAAGAAAAAGGA
1 AAAAGAAAAAGAAAAGAAAAAGGA
16773 AAAAGAAAAAGAAAAGAAAAAG
1 AAAAGAAAAAGAAAAGAAAAAG
16795 TTAGGATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAGAAAAAGAAAAGAAAAAGGA
Found at i:18289 original size:15 final size:14
Alignment explanation
Indices: 18269--18298 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
18259 ATTGGTTGCC
18269 TTGTTTTGTTTCGTT
1 TTGTTTTGTTT-GTT
18284 TTGTTTTGTTTGTT
1 TTGTTTTGTTTGTT
18298 T
1 T
18299 GATGTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.03, G:0.20, T:0.77
Consensus pattern (14 bp):
TTGTTTTGTTTGTT
Found at i:22052 original size:73 final size:75
Alignment explanation
Indices: 21965--22109 Score: 188
Period size: 75 Copynumber: 2.0 Consensus size: 75
21955 TTATATGGAC
* * *
21965 TGTGAGCAAAGGAATGGC-GAGTTTCAATCAAAA-A-GTTTTCAAAAGCAGTTTTAATCAAAGCT
1 TGTGAGCAAAGGAATGACGGAGTTTCAATCAAAAGATG-TTTCAAAAGCAGTTTTAATCAAAACA
22027 ATGATTTCAGT
65 ATGATTTCAGT
* * * **
22038 TGTGAGCAAAGGAATGACGGTGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTCGTCAAAACAA
1 TGTGAGCAAAGGAATGACGGAGTTTCAATCAAAAGATGTTTCAAAAGCAGTTTTAATCAAAACAA
22103 TGATTTC
66 TGATTTC
22110 GAGGTGACTG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
73 17 0.28
74 13 0.21
75 30 0.49
76 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (75 bp):
TGTGAGCAAAGGAATGACGGAGTTTCAATCAAAAGATGTTTCAAAAGCAGTTTTAATCAAAACAA
TGATTTCAGT
Found at i:23012 original size:23 final size:23
Alignment explanation
Indices: 22986--23030 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
22976 AAGAAAAGAA
22986 AAAAGAGAAATTCAAAAAAAAAG
1 AAAAGAGAAATTCAAAAAAAAAG
23009 AAAAGAGAAATTCAAAAAAAAA
1 AAAAGAGAAATTCAAAAAAAAA
23031 TCAAAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.76, C:0.04, G:0.11, T:0.09
Consensus pattern (23 bp):
AAAAGAGAAATTCAAAAAAAAAG
Found at i:23042 original size:14 final size:13
Alignment explanation
Indices: 23025--23082 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
23015 GAAATTCAAA
23025 AAAAAATCAAAATC
1 AAAAAATC-AAATC
23039 AAAAAATCAAATC
1 AAAAAATCAAATC
* * **
23052 AAAGTCAATGAAAGA
1 AAA--AAATCAAATC
23067 AAAAAATCAAATC
1 AAAAAATCAAATC
23080 AAA
1 AAA
23083 CCAAAATCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
13 17 0.50
14 8 0.24
15 9 0.26
ACGTcount: A:0.69, C:0.12, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAATCAAATC
Found at i:23929 original size:50 final size:50
Alignment explanation
Indices: 23854--24003 Score: 203
Period size: 50 Copynumber: 3.0 Consensus size: 50
23844 AGTTTTACAA
* *
23854 TAAAATT-CTTTTTCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGC-TTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
*
23904 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * * * * *
23954 TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAGATTCGTTTTTTAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
24004 GACATCGAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 88 0.99
51 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:24751 original size:50 final size:50
Alignment explanation
Indices: 24598--25084 Score: 807
Period size: 50 Copynumber: 9.8 Consensus size: 50
24588 CGAATGCTCA
* *
24598 GGCTTTTCCATAAGCCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAG-CCAAACTCGTTTCCATACGAGTCAATTATCAACATG
* **
24649 GGC-TTTCCACAAGCCAAACTCGTTT-CATACGAGTCAATTATAAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
*
24697 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
* * *
24747 GGCTTTTCCACAAGCCGAACTCATTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
24797 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
*
24847 GGCTTTTCCACAAGCCAAACTGGTTTCCATACGAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
* * *
24897 GGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCAATTATCAACGTA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
24947 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
**
24997 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAATGTG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
*
25047 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
25085 GTTTAAACAT
Statistics
Matches: 411, Mismatches: 23, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
48 24 0.06
49 33 0.08
50 351 0.85
51 3 0.01
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
Found at i:32989 original size:50 final size:49
Alignment explanation
Indices: 32926--33066 Score: 201
Period size: 50 Copynumber: 2.8 Consensus size: 49
32916 GTTTTACAAT
* *
32926 AAAATTGCTTTCCATTTGTGAGTTCATGATCAAAATTCGTTTTTCAAAAG
1 AAAATTGCTTTCCATTTGTGAG-TCAAGATCAAAATTCGCTTTTCAAAAG
* * *
32976 AAAAATGCTTTCCATTTGTGTGCCCAAGATCAAAATTCGCTTTTCAAAAG
1 AAAATTGCTTTCCATTTGTGAG-TCAAGATCAAAATTCGCTTTTCAAAAG
*
33026 AAAATTGCTTTCCAGTTGTGAGTCTAAGATCAAAATTCGCT
1 AAAATTGCTTTCCATTTGTGAGTC-AAGATCAAAATTCGCT
33067 CTTCGAGAGG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 1 0.01
50 79 0.99
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (49 bp):
AAAATTGCTTTCCATTTGTGAGTCAAGATCAAAATTCGCTTTTCAAAAG
Found at i:34063 original size:69 final size:69
Alignment explanation
Indices: 33969--34536 Score: 893
Period size: 69 Copynumber: 8.2 Consensus size: 69
33959 AATGTTTTGA
* * *
33969 CTTTTCTATAAGCCAAACTCGTTTCCATACGAGTAAATTTAAGCCTTGGTTCCATCCAAGCCACA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
34034 TAGG
66 TAGG
* *
34038 CTTTTCTATAAGCCAAACTCATTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
34103 TAGG
66 TAGG
34107 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
34172 TAGG
66 TAGG
34176 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
34241 TAGG
66 TAGG
* * * *
34245 CTTCTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGTCTTGGTTACATCCAAGCCACA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
34310 TAGG
66 TAGG
* * * * * *
34314 CTATTCCACAAGGCAAACTCGTTTCCATACGAGTCAATTTAAGCATTGGTTTCATCCAAGCCACA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
34379 TAGG
66 TAGG
* * *
34383 CTTTTCCACAAGCCAAACTCGTTTCCGTACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCATA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
34448 TAGG
66 TAGG
* * * * * * *
34452 CCTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTGAAGCCTTGGTTCCACCCAAGCGAAA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
**
34517 GGGG
66 TAGG
34521 CTTTTCCATAAGCCAA
1 CTTTTCCATAAGCCAA
34537 GTTCAATTCC
Statistics
Matches: 465, Mismatches: 34, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 465 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (69 bp):
CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCACA
TAGG
Found at i:34647 original size:69 final size:68
Alignment explanation
Indices: 34571--34847 Score: 333
Period size: 69 Copynumber: 4.0 Consensus size: 68
34561 TTCCAAGACT
* *
34571 AAACTCGTTTCCATATGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCATGTGCTTTTCCATA
1 AAACTCGTTTCCTTACGAGTCAGTTCAAGCCTTGGTTCCATCCAA-CAGCATGTGCTTTTCCATA
34636 AGCC
65 AGCC
34640 AAACTCGTTTCCTTACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCATGTGCTTTTCCATA
1 AAACTCGTTTCCTTACGAGTCAGTTCAAGCCTTGGTTCCATCCAA-CAGCATGTGCTTTTCCATA
34705 AGCC
65 AGCC
* * ** ** *
34709 GAACTCGTTTCCTTACGAGTCAGTTTAAGCCTCAGTTCCATCCGAA-TTC-TTTGACTTTTCCAT
1 AAACTCGTTTCCTTACGAGTCAGTTCAAGCCTTGGTTCCATCC-AACAGCATGTG-CTTTTCCAT
*
34772 AAGTC
64 AAGCC
* * * * * * * *
34777 AAACTCGCTTCCGTGCGAGTCAGTTTAAGCATTGGTTCCTTCCATACAGCAGGGGCTTTTCCATA
1 AAACTCGTTTCCTTACGAGTCAGTTCAAGCCTTGGTTCCATCCA-ACAGCATGTGCTTTTCCATA
34842 AGCC
65 AGCC
34846 AA
1 AA
34848 GTTAAACAAG
Statistics
Matches: 179, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
67 4 0.02
68 50 0.28
69 122 0.68
70 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.31
Consensus pattern (68 bp):
AAACTCGTTTCCTTACGAGTCAGTTCAAGCCTTGGTTCCATCCAACAGCATGTGCTTTTCCATAA
GCC
Found at i:35597 original size:27 final size:25
Alignment explanation
Indices: 35542--35613 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 25
35532 GGTCACCTAT
* *
35542 GGGCATTTCGGTCATTTTTGCACTTAG
1 GGGCATTTTGGTCA--TTTGCACTCAG
35569 GGGCATTTTGGTCATTTGCACAGTCAG
1 GGGCATTTTGGTCATTTGCAC--TCAG
35596 GGAGCATTTTGGTCATTT
1 GG-GCATTTTGGTCATTT
35614 TAAGTTCACT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.17
27 18 0.45
28 15 0.38
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (25 bp):
GGGCATTTTGGTCATTTGCACTCAG
Found at i:35863 original size:34 final size:34
Alignment explanation
Indices: 35825--35893 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
35815 TCCCTTGTTA
35825 TTAAGTTTGTCCAATTTAGTTGATCGCATTCATT
1 TTAAGTTTGTCCAATTTAGTTGATCGCATTCATT
*
35859 TTAAGTTTGTCCAATTTAGTTGATCTCATTCATT
1 TTAAGTTTGTCCAATTTAGTTGATCGCATTCATT
35893 T
1 T
35894 CCCATTAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.49
Consensus pattern (34 bp):
TTAAGTTTGTCCAATTTAGTTGATCGCATTCATT
Found at i:44957 original size:10 final size:10
Alignment explanation
Indices: 44942--44968 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
44932 TCTGATGCAA
44942 AAAAAAAAAG
1 AAAAAAAAAG
44952 AAAAAAAAAG
1 AAAAAAAAAG
44962 AAAAAAA
1 AAAAAAA
44969 GAATAAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:46236 original size:58 final size:58
Alignment explanation
Indices: 46137--46246 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
46127 ATTAATCAAA
*
46137 TATCAAGTGACATGTTCTTTATTAGATGCATAAAGAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAGAAAGACGTTTTAGGACCAAGACT
* * * *
46195 TATCGAGTGACGTGTTTTTTTATTAGATGTC-TAAA-ATAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATG-CATAAAGAAAGACGTTTTAGGACC
46247 GAGGCATGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
58 27 0.60
59 17 0.38
60 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAGAAAGACGTTTTAGGACCAAGACT
Found at i:47580 original size:36 final size:36
Alignment explanation
Indices: 47526--47595 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
47516 TTCAATAACC
*
47526 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTGATTTTGATTATCATATTTCTTA
*
47562 TTACAT-TTTTTTGAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTG-ATTTTGATTATCATATTTCT
47596 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTGATTTTGATTATCATATTTCTTA
Found at i:48490 original size:204 final size:201
Alignment explanation
Indices: 48109--48515 Score: 760
Period size: 204 Copynumber: 2.0 Consensus size: 201
48099 GCTTAATAAC
48109 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
48174 GATACAACACATTATTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
48239 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
48304 CGATTTA
195 CGATTTA
48311 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
48376 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATAT--AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGT
*
48441 TGGTTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
48506 CCGATTTA
194 CCGATTTA
48514 TT
1 TT
48516 AATTATTAAG
Statistics
Matches: 200, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
202 91 0.46
203 15 0.08
204 94 0.47
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Found at i:48623 original size:24 final size:23
Alignment explanation
Indices: 48591--48636 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
48581 ACGTTTGCAC
48591 AAATACCTAAGAATTTGAATTAAA
1 AAATACCTAAGAATTT-AATTAAA
48615 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
48637 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (23 bp):
AAATACCTAAGAATTTAATTAAA
Found at i:48686 original size:39 final size:40
Alignment explanation
Indices: 48627--48707 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
48617 ATACCTAAGA
* *
48627 ATTTAATTAATGTAAGTATTTTAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
48666 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
48706 AT
1 AT
48708 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
Found at i:48702 original size:18 final size:18
Alignment explanation
Indices: 48643--48703 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
48633 TTAATGTAAG
48643 TATTTTAGTTATTATAGTA
1 TATTTTAGTTATTATA-TA
* * * * *
48662 TTACATTTAATTAATGTAAA
1 -TA-TTTTAGTTATTATATA
48682 TATTTTAGTTATTATATA
1 TATTTTAGTTATTATATA
48700 TATT
1 TATT
48704 ACATAGGAAT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 15 0.50
19 2 0.07
20 3 0.10
21 10 0.33
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (18 bp):
TATTTTAGTTATTATATA
Found at i:50826 original size:52 final size:52
Alignment explanation
Indices: 50748--50854 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
50738 AAATTATTAA
50748 GAAGGTAATTTAGTTAAAGATCAGTTTGCACCTTGGATAGTTGCAAAATCAG
1 GAAGGTAATTTAGTTAAAGATCAGTTTGCACCTTGGATAGTTGCAAAATCAG
50800 GAAGGTAATTTAGTTAAAGATCAGTTTGCACCTTGGATAGTTGCAAAATCAG
1 GAAGGTAATTTAGTTAAAGATCAGTTTGCACCTTGGATAGTTGCAAAATCAG
50852 GAA
1 GAA
50855 TTCTTGCTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (52 bp):
GAAGGTAATTTAGTTAAAGATCAGTTTGCACCTTGGATAGTTGCAAAATCAG
Found at i:53686 original size:4 final size:4
Alignment explanation
Indices: 53669--53780 Score: 206
Period size: 4 Copynumber: 28.0 Consensus size: 4
53659 GAGACCTCTG
*
53669 CATA CATG CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
53717 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA TATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53765 CATA CATA CATA CATA
1 CATA CATA CATA CATA
53781 TGTATAATTT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 104 1.00
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:54056 original size:42 final size:42
Alignment explanation
Indices: 53997--54101 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
53987 TCGTTCGAGT
*
53997 CCGAACCTGAAATTACCCGAGTTGACCATAAAAGTCAACGTC
1 CCGAACCCGAAATTACCCGAGTTGACCATAAAAGTCAACGTC
*
54039 CCGAACCCAAAATTACCCGAGTTGACCATAAAAGTCAACGTC
1 CCGAACCCGAAATTACCCGAGTTGACCATAAAAGTCAACGTC
*
54081 CCGAACCCGAAATTATCCGAG
1 CCGAACCCGAAATTACCCGAG
54102 CCCGAAAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.17
Consensus pattern (42 bp):
CCGAACCCGAAATTACCCGAGTTGACCATAAAAGTCAACGTC
Found at i:54838 original size:22 final size:23
Alignment explanation
Indices: 54798--54850 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
54788 ATCAAAGTCA
*
54798 AACCCGAACCCGATCCGAGCCCG
1 AACCCGAACCCGATCCGAGACCG
*
54821 -ACCCGAACCCTA-CTCGAGACCG
1 AACCCGAACCCGATC-CGAGACCG
54843 AACCCGAA
1 AACCCGAA
54851 AATACCCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 18 0.69
23 7 0.27
ACGTcount: A:0.30, C:0.45, G:0.19, T:0.06
Consensus pattern (23 bp):
AACCCGAACCCGATCCGAGACCG
Found at i:54865 original size:16 final size:16
Alignment explanation
Indices: 54840--54897 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
54830 CTACTCGAGA
54840 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
* *
54856 CCGGACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
54872 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
54888 TCGAACCCGA
1 CCGAACCCGA
54898 CTTAACCCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 3 0.09
16 29 0.83
17 3 0.09
ACGTcount: A:0.38, C:0.40, G:0.16, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:54876 original size:32 final size:32
Alignment explanation
Indices: 54840--54941 Score: 113
Period size: 32 Copynumber: 3.2 Consensus size: 32
54830 CTACTCGAGA
*
54840 CCGAACCCGAAAATACCCGGACCCGACATAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
* *
54872 CCGAACCCGAAAATACTCGAACCCGACTTAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
*
54904 CC-AAGCCCGAAAA-ACCCCAAACCCGA-AGT-AC
1 CCGAA-CCCGAAAATA-CCCGAACCCGACA-TAAC
54935 CCGAACC
1 CCGAACC
54942 TGAACCCGCC
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
31 9 0.15
32 51 0.85
ACGTcount: A:0.38, C:0.41, G:0.14, T:0.07
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:56234 original size:16 final size:16
Alignment explanation
Indices: 56213--56243 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56203 CCAAAAAACC
56213 CAAAACCCGAATGACA
1 CAAAACCCGAATGACA
*
56229 CAAAACCCGAGTGAC
1 CAAAACCCGAATGAC
56244 CTGAGGCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.32, G:0.16, T:0.06
Consensus pattern (16 bp):
CAAAACCCGAATGACA
Found at i:57040 original size:94 final size:93
Alignment explanation
Indices: 56904--57074 Score: 270
Period size: 94 Copynumber: 1.8 Consensus size: 93
56894 TAGTAATATC
* * *
56904 GTAAAAATAAAATAGGTATAAGGATATTAGATTTGATTAAATAAAAATAAAGTTTTTAGTTGAGT
1 GTAAAAATAAAATAGGTATAAGGATATTAGATTTAATAAAATAAAAATAAAGTTTTTAGTTGACT
56969 AAAACTATAAAAGTAAAATGGTAAAATG
66 AAAACTATAAAAGTAAAATGGTAAAATG
* * * *
56997 GTAAAATTAAAATAGTTTATATGGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTGAC
1 GTAAAAATAAAATAG-GTATAAGGATATTAGATTTAATAAAATAAAAATAAAGTTTTTAGTTGAC
57062 TAAAACTATAAAA
65 TAAAACTATAAAA
57075 ATTTAAACAA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 14 0.20
94 56 0.80
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (93 bp):
GTAAAAATAAAATAGGTATAAGGATATTAGATTTAATAAAATAAAAATAAAGTTTTTAGTTGACT
AAAACTATAAAAGTAAAATGGTAAAATG
Found at i:58488 original size:22 final size:22
Alignment explanation
Indices: 58462--58625 Score: 131
Period size: 22 Copynumber: 7.5 Consensus size: 22
58452 TCTCATACTT
*
58462 ACTATGAAATTTTGATAATCTC
1 ACTATGAAATTTTGATAACCTC
* *
58484 GCTAT-ATTATTTTGATAACCTC
1 ACTATGA-AATTTTGATAACCTC
* * *
58506 CCTAAGAAATTGTGATAACCTC
1 ACTATGAAATTTTGATAACCTC
* * *
58528 CCTGTGAAACTTTGATAACCAT-
1 ACTATGAAATTTTGATAACC-TC
*
58550 ACTATGAAGTTTTGAT-ACCATC
1 ACTATGAAATTTTGATAACC-TC
*
58572 -CTATGAAATTTTGATAACCAC
1 ACTATGAAATTTTGATAACCTC
* * *
58593 ACTATAAAATTGTGATAAACTC
1 ACTATGAAATTTTGATAACCTC
58615 TA-TATGAAATT
1 -ACTATGAAATT
58626 AATTTTGATG
Statistics
Matches: 113, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
21 21 0.19
22 89 0.79
23 3 0.03
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCTC
Found at i:58609 original size:43 final size:43
Alignment explanation
Indices: 58492--58609 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
58482 TCGCTATATT
* * *
58492 ATTTTGATAACCTCCCTA-AGAAATTGTGATAACCTCCCTGTGAA
1 ATTTTGATAACCACACTATA-AAATTGTGAT-ACCTCCCTATGAA
* * * * *
58536 ACTTTGATAACCATACTATGAAGTTTTGATACCAT-CCTATGAA
1 ATTTTGATAACCACACTATAAAATTGTGATACC-TCCCTATGAA
58579 ATTTTGATAACCACACTATAAAATTGTGATA
1 ATTTTGATAACCACACTATAAAATTGTGATA
58610 AACTCTATAT
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
43 36 0.61
44 23 0.39
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (43 bp):
ATTTTGATAACCACACTATAAAATTGTGATACCTCCCTATGAA
Found at i:58715 original size:22 final size:22
Alignment explanation
Indices: 58690--58731 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58680 GATTTGGTAC
58690 ACTATGAAATTTGGATAACCAT
1 ACTATGAAATTTGGATAACCAT
* *
58712 ACTATGAACTTTTGATAACC
1 ACTATGAAATTTGGATAACC
58732 TTCCTATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
ACTATGAAATTTGGATAACCAT
Found at i:58738 original size:22 final size:21
Alignment explanation
Indices: 58691--58756 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
58681 ATTTGGTACA
* * *
58691 CTATGAAATTTGGATAACCATA
1 CTATG-AATTTTGATAACCTTC
58713 CTATGAACTTTTGATAACCTTC
1 CTATGAA-TTTTGATAACCTTC
*
58735 CTATGGAATGTTGATAA-CTTC
1 CTAT-GAATTTTGATAACCTTC
58756 C
1 C
58757 CTACAGAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 7 0.18
22 28 0.74
23 3 0.08
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
CTATGAATTTTGATAACCTTC
Found at i:58765 original size:22 final size:22
Alignment explanation
Indices: 58723--58765 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
58713 CTATGAACTT
**
58723 TTGATAACCTTCCTATGGAATG
1 TTGATAACCTTCCTACAGAATG
58745 TTGATAA-CTTCCCTACAGAAT
1 TTGATAACCTT-CCTACAGAAT
58766 TTCGTTAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (22 bp):
TTGATAACCTTCCTACAGAATG
Found at i:59051 original size:6 final size:6
Alignment explanation
Indices: 59031--59080 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
59021 TGCTTCCGTT
* *
59031 TTTTTG TTTTATG TTTTTG -TTTCG TTTTTG -TTTTG CTTTTG -TTTTG
1 TTTTTG TTTT-TG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
59077 TTTT
1 TTTT
59081 CAATTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 14 0.37
6 18 0.47
7 6 0.16
ACGTcount: A:0.02, C:0.04, G:0.16, T:0.78
Consensus pattern (6 bp):
TTTTTG
Found at i:59059 original size:11 final size:11
Alignment explanation
Indices: 59031--59080 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
59021 TGCTTCCGTT
59031 TTTTTGTTTTATG
1 TTTTTG-TTT-TG
*
59044 TTTTTGTTTCG
1 TTTTTGTTTTG
59055 TTTTTGTTTTG
1 TTTTTGTTTTG
*
59066 CTTTTGTTTTG
1 TTTTTGTTTTG
59077 TTTT
1 TTTT
59081 CAATTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 24 0.73
12 3 0.09
13 6 0.18
ACGTcount: A:0.02, C:0.04, G:0.16, T:0.78
Consensus pattern (11 bp):
TTTTTGTTTTG
Done.