Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012070.1 Corchorus olitorius cultivar O-4 contig12103, 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: 40585
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Found at i:1827 original size:40 final size:40
Alignment explanation
Indices: 1767--1862 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
1757 TTTCAATATG
**
1767 GTTTTTAATTGGTTTGATTTCATCCCTGATTAAGGGCAAT
1 GTTTTTAATTGGTTCAATTTCATCCCTGATTAAGGGCAAT
* **
1807 GTTTTTAATTGGTTCAATTTCATCCCTGATTGAGGTTAAT
1 GTTTTTAATTGGTTCAATTTCATCCCTGATTAAGGGCAAT
*
1847 ATTTATTAATTGGTTC
1 GTTT-TTAATTGGTTC
1863 GATATAGTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 38 0.78
41 11 0.22
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (40 bp):
GTTTTTAATTGGTTCAATTTCATCCCTGATTAAGGGCAAT
Found at i:3843 original size:30 final size:30
Alignment explanation
Indices: 3809--3868 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3799 GTCGTCTCGG
*
3809 CAGGGTTCCCCGGACCCGAACGTTTCGACA
1 CAGGGTTCCCCGGACACGAACGTTTCGACA
3839 CAGGGTTCCCCGGACACGAACGTTTCGACA
1 CAGGGTTCCCCGGACACGAACGTTTCGACA
3869 GCTTGGCGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.17
Consensus pattern (30 bp):
CAGGGTTCCCCGGACACGAACGTTTCGACA
Found at i:3961 original size:5 final size:5
Alignment explanation
Indices: 3951--3988 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
3941 AAATGGTTGC
*
3951 TTTGT TTTGT TTTGG TTTGT TTTGT TTTG- TTTGT TTTG
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTG
3989 ATGTTTTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (5 bp):
TTTGT
Found at i:3971 original size:15 final size:14
Alignment explanation
Indices: 3951--3988 Score: 67
Period size: 15 Copynumber: 2.6 Consensus size: 14
3941 AAATGGTTGC
3951 TTTGTTTTGTTTTGG
1 TTTGTTTTGTTTT-G
3966 TTTGTTTTGTTTTG
1 TTTGTTTTGTTTTG
3980 TTTGTTTTG
1 TTTGTTTTG
3989 ATGTTTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (14 bp):
TTTGTTTTGTTTTG
Found at i:16149 original size:50 final size:49
Alignment explanation
Indices: 16089--16266 Score: 248
Period size: 50 Copynumber: 3.6 Consensus size: 49
16079 GGATATCCAG
*
16089 AAGAGCGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTT
1 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAC-GTCCTTTT
*
16139 AAGAGTGAATTGGAAGACAGTTTAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAC-GTCCTTTT
* *
16189 GAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGATCCTTTT
1 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACG-TCCTTTT
* * * *
16239 TATATTTGAATTGGAAGACAATTCAAAG
1 AAGA-GTGAATTGGAAGACAGTTCAAAG
16267 AAGTTGATCG
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 94 0.81
51 21 0.18
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (49 bp):
AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGTCCTTTT
Found at i:16176 original size:23 final size:23
Alignment explanation
Indices: 16100--16179 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 23
16090 AGAGCGAATT
*
16100 GGAAGACAGTTCAAAGGATAAGC
1 GGAAGACAGTTTAAAGGATAAGC
* **
16123 GGAAGACAGTCCTTTTAA-GAGTGAATT
1 GGAAGACAG---TTTAAAGGA-T-AAGC
16150 GGAAGACAGTTTAAAGGATAAGC
1 GGAAGACAGTTTAAAGGATAAGC
16173 GGAAGAC
1 GGAAGAC
16180 GGTCCTTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
23 18 0.41
24 6 0.14
25 4 0.09
26 5 0.11
27 11 0.25
ACGTcount: A:0.40, C:0.11, G:0.30, T:0.19
Consensus pattern (23 bp):
GGAAGACAGTTTAAAGGATAAGC
Found at i:16526 original size:28 final size:28
Alignment explanation
Indices: 16483--16627 Score: 236
Period size: 28 Copynumber: 5.2 Consensus size: 28
16473 TTTACTTCTT
16483 ATTTTGGTCATTTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
* *
16511 ATTTTGGTCATCTTGCATGTCCAGGGGT
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
16539 ATTTTGGTCATTTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
*
16567 ATTTTGGTCATTTTGCATGTCCAGGGGT
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
** *
16595 ATTTTGGTCATTTTGCACATCCAGGGGA
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
16623 ATTTT
1 ATTTT
16628 TGTCGTTTCA
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 109 1.00
ACGTcount: A:0.16, C:0.17, G:0.27, T:0.41
Consensus pattern (28 bp):
ATTTTGGTCATTTTGCATGTCCAGGGGC
Found at i:20645 original size:21 final size:23
Alignment explanation
Indices: 20614--20662 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
20604 TAAAATGGGA
20614 ATTTTCAAAAACA-AAGTAAAAG
1 ATTTTCAAAAACAGAAGTAAAAG
20636 ATTTT-AAAAACAGAAGTAAAAG
1 ATTTTCAAAAACAGAAGTAAAAG
20658 ATTTT
1 ATTTT
20663 GACACATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (23 bp):
ATTTTCAAAAACAGAAGTAAAAG
Found at i:23256 original size:13 final size:13
Alignment explanation
Indices: 23240--23275 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
23230 CGGCATTTGG
*
23240 TGGCACTCGGCCT
1 TGGCACTCGGCAT
*
23253 TGGCACTGGGCAT
1 TGGCACTCGGCAT
23266 TGGCACTCGG
1 TGGCACTCGG
23276 GACTTGCCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.11, C:0.31, G:0.36, T:0.22
Consensus pattern (13 bp):
TGGCACTCGGCAT
Found at i:23323 original size:33 final size:33
Alignment explanation
Indices: 23286--24150 Score: 695
Period size: 33 Copynumber: 25.3 Consensus size: 33
23276 GACTTGCCGA
23286 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
* * *
23319 TGGCACTCGGGACTTGCCAATGGCACACAGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
** *
23352 TGGCACTCGGGACTTGTTGATGGCACTCTGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTC--G----GCC-T
*
23392 TGGCACTCGGGACTTGCCGATGGCACTCAGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
*
23425 TGGCACTCGGGACTTGCCGATGGCACTCGACAC-
1 TGGCACTCGGGACTTGCCGATGGCACTCGGC-CT
* * *
23458 TAGCACTCGGCACTTGCCGATAGCACTCGGCACTT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGC-C-T
23493 GCCGATGGCACTCGGGACTTGCCGATGGCACTCGGCCT
1 -----TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
* *
23531 TGGCACTAGGGACTTGCCGATGGCACTCGACAC-
1 TGGCACTCGGGACTTGCCGATGGCACTCGGC-CT
* * *
23564 TAGCACTCGGCACTTGCCGATGGCACTCTGGGCTTGCCAA
1 TGGCACTCGGGACTTGCCGATGGCACTC---G---GCC-T
23604 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
* *
23637 TGGCACTCGGGACTTGCCAATGGCACTCGGTCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
* * * * * *
23670 TGGCAGTCGGGCCTTGGC-ACTCGGGACT-TGCCGA
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCC-T
* * *
23704 TGGCACTCGGCACTTGCCGGTGGCACTCGGGACTTGTT
1 TGGCACTCGGGACTTGCCGATGGCACTC-GG-C---CT
** * * * *
23742 GATGGCACTC-GTCCTTGGCAC-TTGGGACT-TGCCGA
1 --TGGCACTCGGGACTT-GC-CGATGGCACTCGGCC-T
* * *
23777 TGGCACTCGGCACTTGCCAATGGCACTCAGGACT
1 TGGCACTCGGGACTTGCCGATGGCACTC-GGCCT
* ** * * * *
23811 TGTCGGT-GGTACTCGACC-TTGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTG-CCGATGGCACTC--G----GCC-T
*
23850 TGGCAC-CGGGACTTGTCGATGGCACT-GGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
23881 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
* *
23914 TGGCACTCGGGACTTGCTGATGGCACACGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
* * *
23947 TGGCACTCGGGACTTGTCGACTTG---TC-G--A
1 TGGCACTCGGGACTTGCCGA-TGGCACTCGGCCT
23975 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
24008 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
24041 TGGCACTCGGGACTTGCCGATGGCACTCGGCAC-
1 TGGCACTCGGGACTTGCCGATGGCACTCGGC-CT
* *
24074 TAGCACTCGGCACTTGCCGATGGCACTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
**
24107 TGGCACTCGGGACTTGCCGATGGTGCTCGGCCT
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
*
24140 TGGCGCTCGGG
1 TGGCACTCGGG
24151 GGGTGCTAAT
Statistics
Matches: 671, Mismatches: 98, Indels: 126
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.00
28 19 0.03
30 3 0.00
31 8 0.01
32 25 0.04
33 436 0.65
34 42 0.06
35 3 0.00
36 3 0.00
37 2 0.00
38 6 0.01
39 25 0.04
40 96 0.14
41 1 0.00
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (33 bp):
TGGCACTCGGGACTTGCCGATGGCACTCGGCCT
Found at i:23333 original size:53 final size:53
Alignment explanation
Indices: 23253--24129 Score: 514
Period size: 53 Copynumber: 16.7 Consensus size: 53
23243 CACTCGGCCT
* *
23253 TGGCACTGGGCATTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
1 TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* * * * *
23306 TGGCACTCGGCCTTGGCACTCGGGACTTGCCAATGGCACAC-AGCCTTGGC-A
1 TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* * **** *
23357 CTCGGGACTTGTTGATGGCACTCTGGACTTGCCGATGGCACTCGGGACTTGCCGA
1 -T-GGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* ** *
23412 TGGCACTCAGCCTTGGCACTCGGGACTTGCCGATGGCACTCGACACTAG-C-A
1 TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* * * *
23463 CTCGGCACT-TGCCGATAGCACTCGGCACTTGCCGATGGCACTCGGGACTTGCCGA
1 -T-GGCACTCGGCC-TTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* ** *
23518 TGGCACTCGGCCTTGGCACTAGGGACTTGCCGATGGCACTCGACACTAG-C-A
1 TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* * *
23569 CTCGGCACT-TGCCGATGGCACTCTGGG-CTTGCCAATGGCACTCGGGACTTGCCGA
1 -T-GGCACTCGGCC-TTGGCACTC-GGGACTTGCCGATGGCACTCGGGACTTGCCGA
* *
23624 TGGCACTCGGCCTTGGCACTCGGGACTTGCCAATGGCACTC-GG---T--C-T
1 TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* * *
23670 TGGCAGTCGGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGCACTTGCCGG
1 TGGCACTC-GGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* * * * *
23724 TGGCACTCGGGACTTGTTG-A-T-GGCACTCGTCC-TTGGCACTTGGGACTTGCCGA
1 TGGCACTC-GGCCTTG--GCACTCGGGACTTG-CCGATGGCACTCGGGACTTGCCGA
* * * * *
23777 TGGCACTCGGCACTTGCCAATGGCACTCAGGACTTGTCGGTGGTACTC--GACCTTGGC-A
1 TGGCACTCGGC-C-T-----TGGCACTCGGGACTTGCCGATGGCACTCGGGA-CTTGCCGA
* * * * *
23835 CTCGGGACT-TGCCGATGGCAC-CGGGACTTGTCGATGGCACT---G----GCC-T
1 -T-GGCACTCGGCC-TTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* * * * * *
23881 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCC-TTGGCACTCGGGACTTGCTGA
1 TGGCACTC-GGCCTTGGC-ACTCGGGACT-TGCCGATGGCACTCGGGACTTGCCGA
*
23934 TGGCACACGGCCTTGGCACTCGGGACTTGTCGACTTGTCGATGGCACTCGGGACTTGCCGA
1 TGGCACTCGGCCTTGGCACTCGGGAC-T-T-G-C----CGATGGCACTCGGGACTTGCCGA
* *
23995 TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTC-GGCCTTGGC-A
1 TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
* * * * *
24046 CTCGGGACT-TGCCGATGGCACTCGGCAC-T----A--GCACTCGGCACTTGCCGA
1 -T-GGCACTCGGCC-TTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
24094 TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGG
1 TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGG
24130 TGCTCGGCCT
Statistics
Matches: 627, Mismatches: 118, Indels: 158
0.69 0.13 0.17
Matches are distributed among these distances:
44 5 0.01
45 16 0.03
46 37 0.06
47 44 0.07
48 4 0.01
49 1 0.00
51 8 0.01
52 63 0.10
53 320 0.51
54 39 0.06
55 5 0.01
56 2 0.00
57 2 0.00
58 6 0.01
59 13 0.02
60 18 0.03
61 44 0.07
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (53 bp):
TGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
Found at i:23400 original size:73 final size:68
Alignment explanation
Indices: 23286--24129 Score: 545
Period size: 73 Copynumber: 12.3 Consensus size: 68
23276 GACTTGCCGA
* * *
23286 TGGCACTCGGGACTTGCCGATGGCACTCG--GCCTTGGCACTCGGGACTTGCCAATGGCACACAG
1 TGGCACTCGGGACTTGCCGATGGCACTCGACGCCATGGCACTCGGGACTTGCCGATGGCACTCAG
23349 CCT
66 CCT
**
23352 TGGCACTCGGGACTTGTTGATGGCACTCTGGACTTGCCGATGGCACTCGGGACTTGCCGATGGCA
1 TGGCACTCGGGACTTGCCGATGGCACTC--GAC--GCC-ATGGCACTCGGGACTTGCCGATGGCA
23417 CTCAGCCT
61 CTCAGCCT
* * * *
23425 TGGCACTCGGGACTTGCCGATGGCACTCGAC-AC-TAGCACTCGGCACTTGCCGATAGCACTCGG
1 TGGCACTCGGGACTTGCCGATGGCACTCGACGCCATGGCACTCGGGACTTGCCGATGGCACT---
*
23488 CACTTGCCGA
63 CA---GCC-T
* *
23498 TGGCACTCGGGACTTGCCGATGGCACTCG--GCCTTGGCACTAGGGACTTGCCGATGGCACTC-G
1 TGGCACTCGGGACTTGCCGATGGCACTCGACGCCATGGCACTCGGGACTTGCCGATGGCACTCAG
23560 ACAC-
66 -C-CT
* * *
23564 TAGCACTCGGCACTTGCCGATGGCACTCTGGGCTTGCCAATGGCACTCGGGACTTGCCGATGGCA
1 TGGCACTCGGGACTTGCCGATGGCACTC--GAC--GCC-ATGGCACTCGGGACTTGCCGATGGCA
*
23629 CTCGGCCT
61 CTCAGCCT
* * * * * * *
23637 TGGCACTCGGGACTTGCCAATGGCACTCG--GTCTTGGCAGTCGGGCCTTGGC-ACTCGGGACT-
1 TGGCACTCGGGACTTGCCGATGGCACTCGACGCCATGGCACTCGGGACTTGCCGA-T-GGCACTC
* *
23698 TGCCGA
64 AGCC-T
* * ** ** *
23704 TGGCACTCGGCACTTGCCGGTGGCACTCGGGACTTGTTGATGGCACTC-GTCCTTGGCAC-TTGG
1 TGGCACTCGGGACTTGCCGATGGCACTC--GAC--G-CCATGGCACTCGGGACTT-GC-CGATGG
* * *
23767 GACT-TGCCGA
59 CACTCAGCC-T
* * ** * *
23777 TGGCACTCGGCACTTGCCAATGGCACTCAGGACTTGTCGGTGGTACTC--GACCTTGGC-ACTCG
1 TGGCACTCGGGACTTGCCGATGGCACTC--GAC--G-CCATGGCACTCGGGA-CTTGCCGA-T-G
* * *
23839 GGACT-TGCCGA
58 GCACTCAGCC-T
* * *
23850 TGGCAC-CGGGACTTGTCGATGGCACT-G--GCCTTGGCACTCGGGACTTGCCGATGGCACTCGG
1 TGGCACTCGGGACTTGCCGATGGCACTCGACGCCATGGCACTCGGGACTTGCCGATGGCACTCAG
23911 CCT
66 CCT
* * * * *
23914 TGGCACTCGGGACTTGCTGATGGCACACG--GCCTTGGCACTCGGGACTTGTCGACTTG---TC-
1 TGGCACTCGGGACTTGCCGATGGCACTCGACGCCATGGCACTCGGGACTTGCCGA-TGGCACTCA
*
23973 G--A
65 GCCT
* *
23975 TGGCACTCGGGACTTGCCGATGGCACTCG--GCCTTGGCACTCGGGACTTGCCGATGGCACTCGG
1 TGGCACTCGGGACTTGCCGATGGCACTCGACGCCATGGCACTCGGGACTTGCCGATGGCACTCAG
24038 CCT
66 CCT
* * *
24041 TGGCACTCGGGACTTGCCGATGGCACTCG--G-CACTAGCACTCGGCACTTGCCGATGGCACTCG
1 TGGCACTCGGGACTTGCCGATGGCACTCGACGCCA-TGGCACTCGGGACTTGCCGATGGCACTCA
24103 GCCT
65 GCCT
24107 TGGCACTCGGGACTTGCCGATGG
1 TGGCACTCGGGACTTGCCGATGG
24130 TGCTCGGCCT
Statistics
Matches: 647, Mismatches: 75, Indels: 112
0.78 0.09 0.13
Matches are distributed among these distances:
60 2 0.00
61 50 0.08
63 3 0.00
64 22 0.03
65 29 0.04
66 207 0.32
67 35 0.05
68 4 0.01
69 4 0.01
70 1 0.00
71 5 0.01
72 30 0.05
73 243 0.38
74 11 0.02
75 1 0.00
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (68 bp):
TGGCACTCGGGACTTGCCGATGGCACTCGACGCCATGGCACTCGGGACTTGCCGATGGCACTCAG
CCT
Found at i:23687 original size:14 final size:14
Alignment explanation
Indices: 23657--23699 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
23647 GACTTGCCAA
*
23657 TGGCACTC-GGTCT
1 TGGCACTCGGGACT
* *
23670 TGGCAGTCGGGCCT
1 TGGCACTCGGGACT
23684 TGGCACTCGGGACT
1 TGGCACTCGGGACT
23698 TG
1 TG
23700 CCGATGGCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (14 bp):
TGGCACTCGGGACT
Found at i:23861 original size:19 final size:20
Alignment explanation
Indices: 23266--24070 Score: 382
Period size: 20 Copynumber: 44.5 Consensus size: 20
23256 CACTGGGCAT
23266 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
23286 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23306 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
*
23319 TGGCACTCGGGACTTGCCAA
1 TGGCACTCGGGACTTGCCGA
* *
23339 TGGCA--C---AC-AGCC-T
1 TGGCACTCGGGACTTGCCGA
**
23352 TGGCACTCGGGACTTGTTGA
1 TGGCACTCGGGACTTGCCGA
*
23372 TGGCACTCTGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
23392 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23412 TGGCACTC---A---GCC-T
1 TGGCACTCGGGACTTGCCGA
23425 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23445 TGGCACTC--GAC---AC--
1 TGGCACTCGGGACTTGCCGA
* *
23458 TAGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
23478 TAGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
23498 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23518 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
*
23531 TGGCACTAGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23551 TGGCACTC--GAC---AC--
1 TGGCACTCGGGACTTGCCGA
* *
23564 TAGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23584 TGGCACTCTGGG-CTTGCCAA
1 TGGCACTC-GGGACTTGCCGA
23604 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23624 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
*
23637 TGGCACTCGGGACTTGCCAA
1 TGGCACTCGGGACTTGCCGA
* *
23657 TGGCACTC-GGTCTTGGCAGTCGGGCCT
1 TGGCACTCGGGACTT-GC---C--G--A
23684 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
23704 TGGCACTCGGCACTTGCCGG
1 TGGCACTCGGGACTTGCCGA
**
23724 TGGCACTCGGGACTTGTTGA
1 TGGCACTCGGGACTTGCCGA
*
23744 TGGCACTC--G---T-CC-T
1 TGGCACTCGGGACTTGCCGA
*
23757 TGGCACTTGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
23777 TGGCACTCGGCACTTGCCAA
1 TGGCACTCGGGACTTGCCGA
* * *
23797 TGGCACTCAGGACTTGTCGG
1 TGGCACTCGGGACTTGCCGA
* *
23817 TGGTACTC--GA----CC-T
1 TGGCACTCGGGACTTGCCGA
23830 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23850 TGGCAC-CGGGACTTGTCGA
1 TGGCACTCGGGACTTGCCGA
*
23869 TGGCACT---G----GCC-T
1 TGGCACTCGGGACTTGCCGA
23881 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23901 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
*
23914 TGGCACTCGGGACTTGCTGA
1 TGGCACTCGGGACTTGCCGA
* * *
23934 TGGCACAC-GGCCTTGGC-A
1 TGGCACTCGGGACTTGCCGA
* * * *
23952 CTCGGGACTTGTCGACTTGTCGA
1 -T-GGCACTCG-GGACTTGCCGA
23975 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
23995 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
24008 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
24028 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
24041 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
24061 TGGCACTCGG
1 TGGCACTCGG
24071 CACTAGCACT
Statistics
Matches: 588, Mismatches: 88, Indels: 218
0.66 0.10 0.24
Matches are distributed among these distances:
12 7 0.01
13 90 0.15
14 25 0.04
15 20 0.03
16 1 0.00
17 2 0.00
18 22 0.04
19 61 0.10
20 326 0.55
21 8 0.01
22 8 0.01
23 2 0.00
24 1 0.00
27 10 0.02
28 5 0.01
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (20 bp):
TGGCACTCGGGACTTGCCGA
Found at i:24081 original size:13 final size:13
Alignment explanation
Indices: 24063--24087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24053 CTTGCCGATG
24063 GCACTCGGCACTA
1 GCACTCGGCACTA
24076 GCACTCGGCACT
1 GCACTCGGCACT
24088 TGCCGATGGC
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:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (13 bp):
GCACTCGGCACTA
Found at i:28307 original size:41 final size:41
Alignment explanation
Indices: 28237--28382 Score: 197
Period size: 41 Copynumber: 3.6 Consensus size: 41
28227 AAAATAAAAT
** * *
28237 TCTAAATCCGGGAC-AAATTGAATCAATAAATAAGTATTAC
1 TCTAAATTAGGGACAAAATTGAATTAATAAATAAATATTAC
28277 TCTAAATTAGGGACAAAATTGAATTAATAAATAAATATTAC
1 TCTAAATTAGGGACAAAATTGAATTAATAAATAAATATTAC
**
28318 TCTAAATTAGGGACAAAATTGAATTAATAAATAAATAACAGC
1 TCTAAATTAGGGACAAAATTGAATTAATAAATAAATATTA-C
**
28360 -CTAAATTAGGGACCCAATTGAAT
1 TCTAAATTAGGGACAAAATTGAAT
28383 GAAATCACAC
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
40 12 0.12
41 83 0.86
42 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (41 bp):
TCTAAATTAGGGACAAAATTGAATTAATAAATAAATATTAC
Found at i:32772 original size:18 final size:18
Alignment explanation
Indices: 32738--32807 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
32728 TGGCCACCCT
32738 TTTTATAATTGACTTAAAAA
1 TTTT-TAATT-ACTTAAAAA
***
32758 TTTTTAATTACTTAATTT
1 TTTTTAATTACTTAAAAA
*
32776 TTTTTAATT--TTGAAAA
1 TTTTTAATTACTTAAAAA
32792 TATTTTAATTACTTAA
1 T-TTTTAATTACTTAA
32808 TTTTTGAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
16 4 0.10
17 8 0.21
18 15 0.38
19 8 0.21
20 4 0.10
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTTTAATTACTTAAAAA
Found at i:32984 original size:30 final size:31
Alignment explanation
Indices: 32948--33024 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
32938 TTTTTGTAAT
*
32948 GTTATATCCTGAATTGTCA-CCTCA-TCAAAC
1 GTTATATCCTGAATTG-CATCCTCAGGCAAAC
* * **
32978 GTTATATCCTTAATTGGATTTTCAGGCAAAC
1 GTTATATCCTGAATTGCATCCTCAGGCAAAC
33009 GTTATATCCTGAATTG
1 GTTATATCCTGAATTG
33025 ATCATTTAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 1 0.03
30 18 0.46
31 20 0.51
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (31 bp):
GTTATATCCTGAATTGCATCCTCAGGCAAAC
Done.