Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015717.1 Corchorus capsularis cultivar CVL-1 contig15738, 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: 98835
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3215 original size:19 final size:18
Alignment explanation
Indices: 3182--3217 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3172 TTGAAATAAT
3182 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
3200 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
3218 GAAATCTTCA
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:6915 original size:31 final size:31
Alignment explanation
Indices: 6821--7087 Score: 373
Period size: 31 Copynumber: 8.7 Consensus size: 31
6811 AATCTCCAAA
*
6821 TGACACCAGAAGTTGTC-ATGATCTTATAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
6851 TGACACCAGAAGTTGTC-ATGATCTTACAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
* *
6881 TGACACCAGAAGTTGTCAATGTTCTTGCAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
* *
6912 TGACACCAGAAGTTGTCAATGTTCTTGCAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
* *
6943 TGACACCAGAAGTTGTCAATGTTCTTGCAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
* * *
6974 TGACACCATAAGTTATC-ATGATCTTGCAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
7004 TGACACCAGAAGTTGTCAAT-AGTCTTACAAT
1 TGACACCAGAAGTTGTCAATGA-TCTTACAAT
* *
7035 TGACACCAGAAGTTGTCAATGGTCTTACAGT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
*
7066 TGACACAAGAAGTTGTC-ATGAT
1 TGACACCAGAAGTTGTCAATGAT
7088 AAATTTCCAA
Statistics
Matches: 220, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
30 78 0.35
31 142 0.65
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
TGACACCAGAAGTTGTCAATGATCTTACAAT
Found at i:6999 original size:92 final size:91
Alignment explanation
Indices: 6821--7087 Score: 394
Period size: 92 Copynumber: 2.9 Consensus size: 91
6811 AATCTCCAAA
*
6821 TGACACCAGAAGTTGTC-ATGATCTTATAATTGACACCAGAAGTTGTC-ATGATCTTACAATTGA
1 TGACACCAGAAGTTGTCAATG-TCTTACAATTGACACCAGAAGTTGTCAATGATCTTACAATTGA
*
6884 CACCAGAAGTTGTCAATGTTCTTGCAAT
65 CACCAGAAGTTGTC-ATGATCTTGCAAT
* * *
6912 TGACACCAGAAGTTGTCAATGTTCTTGCAATTGACACCAGAAGTTGTCAATGTTCTTGCAATTGA
1 TGACACCAGAAGTTGTCAATG-TCTTACAATTGACACCAGAAGTTGTCAATGATCTTACAATTGA
* *
6977 CACCATAAGTTATCATGATCTTGCAAT
65 CACCAGAAGTTGTCATGATCTTGCAAT
* *
7004 TGACACCAGAAGTTGTCAATAGTCTTACAATTGACACCAGAAGTTGTCAATGGTCTTACAGTTGA
1 TGACACCAGAAGTTGTCAAT-GTCTTACAATTGACACCAGAAGTTGTCAATGATCTTACAATTGA
*
7069 CACAAGAAGTTGTCATGAT
65 CACCAGAAGTTGTCATGAT
7088 AAATTTCCAA
Statistics
Matches: 158, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
91 17 0.11
92 114 0.72
93 27 0.17
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (91 bp):
TGACACCAGAAGTTGTCAATGTCTTACAATTGACACCAGAAGTTGTCAATGATCTTACAATTGAC
ACCAGAAGTTGTCATGATCTTGCAAT
Found at i:7007 original size:123 final size:123
Alignment explanation
Indices: 6821--7087 Score: 405
Period size: 123 Copynumber: 2.2 Consensus size: 123
6811 AATCTCCAAA
* *
6821 TGACACCAGAAGTTGTC-ATGATCTTATAATTGACACCAGAAGTTGTCATGATCTTACAATTGAC
1 TGACACCAGAAGTTGTCAATGATCTTACAATTGACACCAGAAGTTATCATGATCTTACAATTGAC
* * *
6885 ACCAGAAGTTGTCAAT-GTTCTTGCAATTGACACCAGAAGTTGTCAATGTTCTTGCAAT
66 ACCAGAAGTTGTCAATAG-TCTTACAATTGACACCAGAAGTTGTCAATGGTCTTACAAT
* * * *
6943 TGACACCAGAAGTTGTCAATGTTCTTGCAATTGACACCATAAGTTATCATGATCTTGCAATTGAC
1 TGACACCAGAAGTTGTCAATGATCTTACAATTGACACCAGAAGTTATCATGATCTTACAATTGAC
*
7008 ACCAGAAGTTGTCAATAGTCTTACAATTGACACCAGAAGTTGTCAATGGTCTTACAGT
66 ACCAGAAGTTGTCAATAGTCTTACAATTGACACCAGAAGTTGTCAATGGTCTTACAAT
*
7066 TGACACAAGAAGTTGTC-ATGAT
1 TGACACCAGAAGTTGTCAATGAT
7088 AAATTTCCAA
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
122 21 0.16
123 109 0.83
124 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (123 bp):
TGACACCAGAAGTTGTCAATGATCTTACAATTGACACCAGAAGTTATCATGATCTTACAATTGAC
ACCAGAAGTTGTCAATAGTCTTACAATTGACACCAGAAGTTGTCAATGGTCTTACAAT
Found at i:8912 original size:53 final size:53
Alignment explanation
Indices: 8850--8997 Score: 156
Period size: 53 Copynumber: 2.8 Consensus size: 53
8840 CGGTATTTTC
* * * *
8850 GAATTTATCACGTGGGACTCTCATTTTTCATGGAGGAGATC-AGCAGTGTGCAT
1 GAATATATCATGTGGGACTCTCATTCTTCATAGAGGAGATCGA-CAGTGTGCAT
* ** * *
8903 GAATATATCATATAAGACTCTCATTGTTCATATG-GGAGATCGACAGTGTGTAT
1 GAATATATCATGTGGGACTCTCATTCTTCATA-GAGGAGATCGACAGTGTGCAT
* * *
8956 AAATATATCATGTGGGACTCTCGTTCTTCATATAGGAGATCG
1 GAATATATCATGTGGGACTCTCATTCTTCATAGAGGAGATCG
8998 GCGATTTTCA
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
53 75 0.97
54 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (53 bp):
GAATATATCATGTGGGACTCTCATTCTTCATAGAGGAGATCGACAGTGTGCAT
Found at i:9265 original size:19 final size:20
Alignment explanation
Indices: 9241--9279 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
9231 GATCTTCGTT
9241 CTTCATAGT-GAAGATCATC
1 CTTCATAGTAGAAGATCATC
* *
9260 CTTCATGGTAGATGATCATC
1 CTTCATAGTAGAAGATCATC
9280 ACACTTGCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (20 bp):
CTTCATAGTAGAAGATCATC
Found at i:9385 original size:184 final size:183
Alignment explanation
Indices: 9077--9450 Score: 721
Period size: 184 Copynumber: 2.0 Consensus size: 183
9067 GACTAACGAT
9077 CTTCATGGTAGATGATCATCACACTTGCCAATTTGATTTCGCCTCTTCTATGATCTTCGTTTAGG
1 CTTCATGGTAGATGATCATCACACTTGCCAATTTGATTTCGCCTCTTCTATGATCTTCGTTTAGG
*
9142 TGCCCGTCATGCTTGCAAACTTCCATTTAATATCTATGATCTTCGCTTAGACGATCATCACACAC
66 TACCCGTCATGCTTGCAAACTTCCATTTAATATCTATGATCTTCGCTTAGACGATCATCACACAC
9207 GCATTTAGGAAATCGACGATCTATGATCTTCGTTCTTCATAGTGAAGATCATC
131 GCATTTAGGAAATCGACGATCTATGATCTTCGTTCTTCATAGTGAAGATCATC
9260 CTTCATGGTAGATGATCATCACACTTGCCAACTTTGATTTCGCCTCTTCTATGATCTTCGTTTAG
1 CTTCATGGTAGATGATCATCACACTTGCCAA-TTTGATTTCGCCTCTTCTATGATCTTCGTTTAG
9325 GTACCCGTCATGCTTGCAAACTTCCATTTAATATCTATGATCTTCGCTTAGACGATCATCACACA
65 GTACCCGTCATGCTTGCAAACTTCCATTTAATATCTATGATCTTCGCTTAGACGATCATCACACA
*
9390 TGCATTTAGGAAATCGACGATCTATGATCTTCGTTCTTCATAGTGAAGATCATC
130 CGCATTTAGGAAATCGACGATCTATGATCTTCGTTCTTCATAGTGAAGATCATC
9444 CTTCATG
1 CTTCATG
9451 TAGGAGACAG
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
183 31 0.16
184 157 0.84
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (183 bp):
CTTCATGGTAGATGATCATCACACTTGCCAATTTGATTTCGCCTCTTCTATGATCTTCGTTTAGG
TACCCGTCATGCTTGCAAACTTCCATTTAATATCTATGATCTTCGCTTAGACGATCATCACACAC
GCATTTAGGAAATCGACGATCTATGATCTTCGTTCTTCATAGTGAAGATCATC
Found at i:9687 original size:37 final size:37
Alignment explanation
Indices: 9629--9700 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
9619 TTCCATCCCA
* *
9629 ACGAGGGAGTCTCTTGCTGAGAAGAACATGTAACCCG
1 ACGAGGGAGTCTCGTGCTGAGAAGAACATGCAACCCG
* *
9666 ACGAGGGAGTCTCGTGGTGAGACGAACATGCAACC
1 ACGAGGGAGTCTCGTGCTGAGAAGAACATGCAACC
9701 TTGGCGTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.32, T:0.17
Consensus pattern (37 bp):
ACGAGGGAGTCTCGTGCTGAGAAGAACATGCAACCCG
Found at i:9766 original size:54 final size:54
Alignment explanation
Indices: 9666--9957 Score: 201
Period size: 54 Copynumber: 5.6 Consensus size: 54
9656 ATGTAACCCG
* * ** **
9666 ACGAGGGAGTCTCGTGGTGAGACGAACATGCAACCTTGGCGTTCTTCTGTCCAA
1 ACGAGGGAGTCTCTTGGTGAGACGAACATGCAACCCTGGCACTCTTCCATCCAA
* * * *
9720 ACGTGGGAGTCTCTTGGTGGGACGAACGTGC-ACTCCTGGCACTCTTCCATCCCA
1 ACGAGGGAGTCTCTTGGTGAGACGAACATGCAAC-CCTGGCACTCTTCCATCCAA
* * * * * * **
9774 ATGAGGGAGTCTCTTGGTGAGACGAATATGAAACCTTTGCGCTCCGCCATCC--
1 ACGAGGGAGTCTCTTGGTGAGACGAACATGCAACCCTGGCACTCTTCCATCCAA
* * ** **
9826 -CGA--GTGTCTCTTGGTGAGACGAACATGCAACCTTGGCGTTCTTCTGTCCAA
1 ACGAGGGAGTCTCTTGGTGAGACGAACATGCAACCCTGGCACTCTTCCATCCAA
* * * * * * *
9877 ACGTGGGAGTCTCCTGGTGAGACAAACGTGC-ACTCTTGGCATTCTTCCATCCCA
1 ACGAGGGAGTCTCTTGGTGAGACGAACATGCAAC-CCTGGCACTCTTCCATCCAA
*
9931 AC----GAGTCTCTTGGAGAGACGAACATGC
1 ACGAGGGAGTCTCTTGGTGAGACGAACATGC
9958 GCTCTTCCGT
Statistics
Matches: 186, Mismatches: 44, Indels: 20
0.74 0.18 0.08
Matches are distributed among these distances:
49 37 0.20
50 21 0.11
51 2 0.01
52 2 0.01
53 4 0.02
54 118 0.63
55 2 0.01
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (54 bp):
ACGAGGGAGTCTCTTGGTGAGACGAACATGCAACCCTGGCACTCTTCCATCCAA
Found at i:9979 original size:41 final size:41
Alignment explanation
Indices: 9919--9998 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
9909 CTCTTGGCAT
*
9919 TCTTCCATCCCAACGAGTCTCTTGGAGAGACGAACATGCGC
1 TCTTCCATCCCAACCAGTCTCTTGGAGAGACGAACATGCGC
*
9960 TCTTCCGTCCCAACCAGTCTCTTGGAGAGACGAACATGC
1 TCTTCCATCCCAACCAGTCTCTTGGAGAGACGAACATGC
9999 ATCCCGACGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.23
Consensus pattern (41 bp):
TCTTCCATCCCAACCAGTCTCTTGGAGAGACGAACATGCGC
Found at i:10253 original size:75 final size:75
Alignment explanation
Indices: 10130--10350 Score: 352
Period size: 75 Copynumber: 2.9 Consensus size: 75
10120 GAGTGAAACT
* * * *
10130 GGTGGCGTCTGCTTGGACGCTAGGCCTCGCTAAGAGTTATACGGGGGCGCCAGTTTAGGCGCTTA
1 GGTGGCGTCTGCTTGGACGCTCGGCCTCGCTGAGAGTTATACGGGGGCGCCAGTCTAGGCGCTCA
10195 GCCGTCTGCG
66 GCCGTCTGCG
* * *
10205 GGTGGCGTCTGCTTGGACGCTCGGCCTTGCTGAGATTTATATGGGGGCGCCAGTCTAGGCGCTCA
1 GGTGGCGTCTGCTTGGACGCTCGGCCTCGCTGAGAGTTATACGGGGGCGCCAGTCTAGGCGCTCA
10270 GCCGTCTGCG
66 GCCGTCTGCG
* * *
10280 GGTGGCGTCTGCTTGGACGCTCGGCCTCGCTGAGAGTTATACGGGGGCACTAGTCTAGGCACTCA
1 GGTGGCGTCTGCTTGGACGCTCGGCCTCGCTGAGAGTTATACGGGGGCGCCAGTCTAGGCGCTCA
10345 GCCGTC
66 GCCGTC
10351 ATAGACGAAG
Statistics
Matches: 133, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 133 1.00
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.24
Consensus pattern (75 bp):
GGTGGCGTCTGCTTGGACGCTCGGCCTCGCTGAGAGTTATACGGGGGCGCCAGTCTAGGCGCTCA
GCCGTCTGCG
Found at i:10692 original size:28 final size:27
Alignment explanation
Indices: 10629--10704 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 27
10619 TTCACGGCAG
*
10629 AAGGCTGATGAACATGCAAGTGTTCCT
1 AAGGCTGACGAACATGCAAGTGTTCCT
* *
10656 TAGGTTGACGAACATGCAATGTGTTCCT
1 AAGGCTGACGAACATGCAA-GTGTTCCT
10684 AAGGCTGACGAACTATG-AAGT
1 AAGGCTGACGAAC-ATGCAAGT
10705 TGGGGGTGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 18 0.43
28 21 0.50
29 3 0.07
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (27 bp):
AAGGCTGACGAACATGCAAGTGTTCCT
Found at i:13845 original size:27 final size:27
Alignment explanation
Indices: 13795--13846 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
13785 ATGGAGGAGA
*
13795 GTGAAGAAGACGAGAGAGAAAGAAATC
1 GTGAAGAAGACGAGAGAAAAAGAAATC
*
13822 GTGAGGAAGA-GAGAGAAAAGAGAAA
1 GTGAAGAAGACGAGAGAAAA-AGAAA
13847 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.54, C:0.04, G:0.37, T:0.06
Consensus pattern (27 bp):
GTGAAGAAGACGAGAGAAAAAGAAATC
Found at i:17044 original size:32 final size:35
Alignment explanation
Indices: 16989--17052 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
16979 GGGTTTCCAA
*
16989 TTAAAAATATATATTTATATTTTCTG-TTTTTCCT
1 TTAAAAAAATATATTTATATTTTCTGCTTTTTCCT
*
17023 TTAAAAAAATAT-TTTCT-TTTTCTGCTTTTT
1 TTAAAAAAATATATTTATATTTTCTGCTTTTT
17053 ATTTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 9 0.33
34 11 0.41
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.59
Consensus pattern (35 bp):
TTAAAAAAATATATTTATATTTTCTGCTTTTTCCT
Found at i:19474 original size:19 final size:19
Alignment explanation
Indices: 19450--19519 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
19440 AAAAGAAAGA
*
19450 GAATTTTTATCAAGCATGG
1 GAATTTTTACCAAGCATGG
* *
19469 GAATTTTTACCAAGAATGA
1 GAATTTTTACCAAGCATGG
19488 GAATTTTTACCAAGCAT-G
1 GAATTTTTACCAAGCATGG
19506 GAATTTTTATCCAA
1 GAATTTTTA-CCAA
19520 ATCCCGTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
18 9 0.20
19 36 0.80
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (19 bp):
GAATTTTTACCAAGCATGG
Found at i:19493 original size:38 final size:38
Alignment explanation
Indices: 19442--19519 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
19432 TCAACAACAA
*
19442 AAGAAAGAGAATTTTTATCAAGCATGGGAATTTTTA-CC
1 AAGAAAGAGAATTTTTACCAAGCAT-GGAATTTTTATCC
*
19480 AAGAATGAGAATTTTTACCAAGCATGGAATTTTTATCC
1 AAGAAAGAGAATTTTTACCAAGCATGGAATTTTTATCC
19518 AA
1 AA
19520 ATCCCGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 10 0.27
38 27 0.73
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (38 bp):
AAGAAAGAGAATTTTTACCAAGCATGGAATTTTTATCC
Found at i:22995 original size:32 final size:31
Alignment explanation
Indices: 22959--23022 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
22949 TTGACTCTAG
* * *
22959 ATCTAAGACTATTAGATTAGGACTAATAAATT
1 ATCTAAAACTAATAAATTA-GACTAATAAATT
* *
22991 ATCTAAAATTAATAAATTAGACTACTAAATT
1 ATCTAAAACTAATAAATTAGACTAATAAATT
23022 A
1 A
23023 CCCCCCCCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.34
Consensus pattern (31 bp):
ATCTAAAACTAATAAATTAGACTAATAAATT
Found at i:30534 original size:5 final size:5
Alignment explanation
Indices: 30518--30550 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
30508 TTAAAAAAAT
*
30518 TAAAC TAGAC TAAAC TAAAC TAAAC TAAAC TAA
1 TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAA
30551 GAGAAAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (5 bp):
TAAAC
Found at i:30805 original size:20 final size:20
Alignment explanation
Indices: 30748--30807 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
30738 TAAACTAATG
*
30748 AAATCAAAT-AAAGATAACTA
1 AAAT-AAATGAAAGATAATTA
30768 AAATAAATTGAAAG-TAATTA
1 AAATAAA-TGAAAGATAATTA
30788 AAATAGAA-GAAAGATAATTA
1 AAATA-AATGAAAGATAATTA
30808 TGAGAAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 8 0.23
20 21 0.60
21 6 0.17
ACGTcount: A:0.63, C:0.03, G:0.10, T:0.23
Consensus pattern (20 bp):
AAATAAATGAAAGATAATTA
Found at i:33276 original size:20 final size:21
Alignment explanation
Indices: 33235--33278 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
33225 ACTTCGCTTA
33235 CTCCTGATATACTTGTACAACT
1 CTCCTGATATACTTGTA-AACT
*
33257 CTCCTTATATACTTGT-AACT
1 CTCCTGATATACTTGTAAACT
33277 CT
1 CT
33279 TAATGCTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
22 15 0.71
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (21 bp):
CTCCTGATATACTTGTAAACT
Found at i:34768 original size:20 final size:21
Alignment explanation
Indices: 34727--34770 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
34717 ACTTCGCTTA
34727 CTCCTGATATACTTGTACAACT
1 CTCCTGATATACTTGTA-AACT
34749 CTCCTGATATACTTGT-AACT
1 CTCCTGATATACTTGTAAACT
34769 CT
1 CT
34771 TAATGCTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.27
22 16 0.73
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (21 bp):
CTCCTGATATACTTGTAAACT
Found at i:36194 original size:18 final size:19
Alignment explanation
Indices: 36171--36208 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
36161 GAAATAGGAT
36171 TTCAAATTCAACAGA-AGA
1 TTCAAATTCAACAGATAGA
36189 TTCAAATTCAACAGATAGA
1 TTCAAATTCAACAGATAGA
36208 T
1 T
36209 AAGATAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
TTCAAATTCAACAGATAGA
Found at i:42097 original size:15 final size:14
Alignment explanation
Indices: 42077--42115 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
42067 CTAACCCATA
42077 ATTTTTCTTTGTTTT
1 ATTTTTCTTT-TTTT
42092 ATTTTTCTTTTTTT
1 ATTTTTCTTTTTTT
*
42106 CTTTTT-TTTT
1 ATTTTTCTTTT
42116 AGGATTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.17
14 9 0.39
15 10 0.43
ACGTcount: A:0.05, C:0.08, G:0.03, T:0.85
Consensus pattern (14 bp):
ATTTTTCTTTTTTT
Found at i:49397 original size:18 final size:19
Alignment explanation
Indices: 49374--49411 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
49364 GAAATAGGAT
49374 TTCAAATCCAACAGA-AGA
1 TTCAAATCCAACAGATAGA
*
49392 TTCAAATTCAACAGATAGA
1 TTCAAATCCAACAGATAGA
49411 T
1 T
49412 AGGATAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATCCAACAGATAGA
Found at i:49788 original size:2 final size:2
Alignment explanation
Indices: 49781--49808 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
49771 TTTAGTTAAT
49781 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49809 ATAAAACAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62355 original size:22 final size:22
Alignment explanation
Indices: 62329--62375 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
62319 TTTCTGACTC
62329 GACCCCGA-AAAGGGTCGAACTG
1 GACCCCGAGAAA-GGTCGAACTG
* *
62351 GACCCTGAGGAAGGTCGAACTG
1 GACCCCGAGAAAGGTCGAACTG
62373 GAC
1 GAC
62376 AAGGGGAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.30, C:0.26, G:0.34, T:0.11
Consensus pattern (22 bp):
GACCCCGAGAAAGGTCGAACTG
Found at i:70772 original size:12 final size:11
Alignment explanation
Indices: 70750--70791 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
70740 GACCACCAAG
70750 AAAAG-AAAAA
1 AAAAGAAAAAA
*
70760 AAATGAAAAAA
1 AAAAGAAAAAA
70771 AAAGAGAAAAAA
1 AAA-AGAAAAAA
70783 GAAAAGAAA
1 -AAAAGAAA
70792 GAAGAAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.15
11 8 0.30
12 12 0.44
13 3 0.11
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:70796 original size:12 final size:11
Alignment explanation
Indices: 70747--70803 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 11
70737 TGCGACCACC
70747 AAGAAAAGAAA
1 AAGAAAAGAAA
*
70758 AA-AAATGAAA
1 AAGAAAAGAAA
*
70768 AAAAAAGAGAAAA
1 AAGAAA-AG-AAA
70781 AAGAAAAGAAA
1 AAGAAAAGAAA
70792 GAAGAAACAGAA
1 -AAGAAA-AGAA
70804 TTTCAAAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 9 0.24
11 8 0.21
12 9 0.24
13 12 0.32
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:70797 original size:19 final size:19
Alignment explanation
Indices: 70750--70798 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
70740 GACCACCAAG
70750 AAAAGAA-AAAAAATGAAA
1 AAAAGAAGAAAAAATGAAA
*
70768 AAAA-AAGAGAAAAAAGAAA
1 AAAAGAAGA-AAAAATGAAA
70787 AGAAAGAAGAAA
1 A-AAAGAAGAAA
70799 CAGAATTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
18 5 0.19
19 10 0.38
20 5 0.19
21 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAGAAGAAAAAATGAAA
Found at i:70803 original size:25 final size:22
Alignment explanation
Indices: 70747--70803 Score: 53
Period size: 25 Copynumber: 2.5 Consensus size: 22
70737 TGCGACCACC
*
70747 AAGAAAAG-AAAAAAAATGAAA
1 AAGAAAAGAAAAAAAAAAGAAA
*
70768 AAAAAAGAGAAAAAAGAAAAGAAA
1 AAGAAA-AGAAAAAA-AAAAGAAA
70792 GAAGAAACAGAA
1 -AAGAAA-AGAA
70804 TTTCAAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 5 0.18
22 2 0.07
23 5 0.18
24 7 0.25
25 9 0.32
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (22 bp):
AAGAAAAGAAAAAAAAAAGAAA
Found at i:85207 original size:12 final size:12
Alignment explanation
Indices: 85168--85199 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
85158 GACGAGGAGG
85168 AAGAAAAGAAGAA
1 AAGAAAAGAA-AA
85181 AAGAAAAGAAAA
1 AAGAAAAGAAAA
85193 AAGAAAA
1 AAGAAAA
85200 TATAAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAGAAAAGAAAA
Found at i:86094 original size:35 final size:34
Alignment explanation
Indices: 86014--86528 Score: 587
Period size: 35 Copynumber: 14.9 Consensus size: 34
86004 GTAAATCAGT
*
86014 AGTAATCAACCTAATTCA-GGTAATTAAGTGAA-TC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGT-AATTC
* *
86048 AATAATCAACTTAATTCAGGGTAATTAAGTATTTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTAATTC
* *
86083 AGTTAGTAACTTAATTCAGGGTAATTAAGTAGTTC
1 AG-TAATAACTTAATTCAGGGTAATTAAGTAATTC
* *
86118 A--ACT--C-TAATTCAGGGTAATTAAGTGAGTT-
1 AGTAATAACTTAATTCAGGGTAATTAAGT-AATTC
* *
86147 AATAAGTAACTTAATTCAGGGTAATTAAGTAGTTC
1 AGTAA-TAACTTAATTCAGGGTAATTAAGTAATTC
* * * *
86182 AATGAGTAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGT-AATAACTTAATTCAGGGTAATTAAGTAATTC
* *
86217 GGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTAATTC
* *
86252 AGTAATCAATTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTAATTC
86287 AGTAATCAACTTAATTCAGGGTAATTAAGTAATTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTAATTC
*
86322 TGTAATTAACTTAATTCAGGGTAATTAAGTAATTC
1 AGTAA-TAACTTAATTCAGGGTAATTAAGTAATTC
86357 AGTAATCAACTTAATTCAGGGTAATTAAGTAATTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTAATTC
86392 AGTAATTAACTTAATTCAGGGTAATTAAGTAATTC
1 AGTAA-TAACTTAATTCAGGGTAATTAAGTAATTC
* *
86427 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTAATTC
** *
86462 AGTAATCAACTTTAATTTGGGGGTAATTAAGTAGTTC
1 AGTAAT-AAC-TTAA-TTCAGGGTAATTAAGTAATTC
* *
86499 AATAAGTAACTTAATTCAGGGCAATTAAGT
1 AGTAA-TAACTTAATTCAGGGTAATTAAGT
86529 TTAGTAAGCA
Statistics
Matches: 428, Mismatches: 33, Indels: 39
0.86 0.07 0.08
Matches are distributed among these distances:
29 20 0.05
30 5 0.01
31 1 0.00
32 3 0.01
34 26 0.06
35 335 0.78
36 14 0.03
37 23 0.05
38 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (34 bp):
AGTAATAACTTAATTCAGGGTAATTAAGTAATTC
Found at i:86126 original size:29 final size:29
Alignment explanation
Indices: 86090--86183 Score: 109
Period size: 29 Copynumber: 3.1 Consensus size: 29
86080 TTCAGTTAGT
86090 AACT-TAATTCAGGGTAATTAAGTAGTTC
1 AACTCTAATTCAGGGTAATTAAGTAGTTC
*
86118 AACTCTAATTCAGGGTAATTAAGTGAGTTAAT
1 AACTCTAATTCAGGGTAATTAAGT-AGTT--C
*
86150 AAGTAACTTAATTCAGGGTAATTAAGTAGTTC
1 AACT--C-TAATTCAGGGTAATTAAGTAGTTC
86182 AA
1 AA
86184 TGAGTAACTT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
28 4 0.07
29 19 0.34
30 4 0.07
32 5 0.09
34 5 0.09
35 19 0.34
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (29 bp):
AACTCTAATTCAGGGTAATTAAGTAGTTC
Found at i:86320 original size:8 final size:8
Alignment explanation
Indices: 86307--86432 Score: 63
Period size: 8 Copynumber: 14.6 Consensus size: 8
86297 TTAATTCAGG
86307 GTAATTAA
1 GTAATTAA
**
86315 GTAATTCT
1 GTAATTAA
86323 GTAATTAA
1 GTAATTAA
* *
86331 CTTAATTCAGG
1 -GTAATT-A-A
86342 GTAATTAA
1 GTAATTAA
*
86350 GTAATTCA
1 GTAATTAA
*
86358 GTAATCAA
1 GTAATTAA
* *
86366 CTTAATTCAGG
1 -GTAATT-A-A
86377 GTAATTAA
1 GTAATTAA
*
86385 GTAATTCA
1 GTAATTAA
86393 GTAATTAA
1 GTAATTAA
* *
86401 CTTAATTCAGG
1 -GTAATT-A-A
86412 GTAATTAA
1 GTAATTAA
*
86420 GTAATTCA
1 GTAATTAA
86428 GTAAT
1 GTAAT
86433 CAACTTAATT
Statistics
Matches: 86, Mismatches: 23, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
8 51 0.59
9 17 0.20
10 18 0.21
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (8 bp):
GTAATTAA
Found at i:95651 original size:25 final size:25
Alignment explanation
Indices: 95621--95669 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
95611 CATACATAGC
95621 ACAACAATGCCTACAAGCTAGATCA
1 ACAACAATGCCTACAAGCTAGATCA
95646 ACAACAATGCCTACAAGCTAGATC
1 ACAACAATGCCTACAAGCTAGATC
95670 TTCCTAGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.29, G:0.12, T:0.16
Consensus pattern (25 bp):
ACAACAATGCCTACAAGCTAGATCA
Done.