Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015868.1 Corchorus olitorius cultivar O-4 contig15901, 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: 38589
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:8667 original size:25 final size:25
Alignment explanation
Indices: 8634--8701 Score: 127
Period size: 25 Copynumber: 2.7 Consensus size: 25
8624 CTTATTTTTT
*
8634 CTCAAGCCCTGCGCCACTTCCTTTC
1 CTCAGGCCCTGCGCCACTTCCTTTC
8659 CTCAGGCCCTGCGCCACTTCCTTTC
1 CTCAGGCCCTGCGCCACTTCCTTTC
8684 CTCAGGCCCTGCGCCACT
1 CTCAGGCCCTGCGCCACT
8702 CTCTTCTCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.10, C:0.49, G:0.16, T:0.25
Consensus pattern (25 bp):
CTCAGGCCCTGCGCCACTTCCTTTC
Found at i:8715 original size:25 final size:25
Alignment explanation
Indices: 8631--8720 Score: 114
Period size: 25 Copynumber: 3.6 Consensus size: 25
8621 GTGCTTATTT
*
8631 TTTC-TCAAGCCCTGCGCCACTTCC
1 TTTCATCAGGCCCTGCGCCACTTCC
*
8655 TTTCCTCAGGCCCTGCGCCACTTCC
1 TTTCATCAGGCCCTGCGCCACTTCC
*
8680 TTTCCTCAGGCCCTGCGCCAC-TCTC
1 TTTCATCAGGCCCTGCGCCACTTC-C
8705 TTCTCAT-AGGCCCTGC
1 TT-TCATCAGGCCCTGC
8721 ACCATCCTCT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
24 6 0.10
25 52 0.85
26 3 0.05
ACGTcount: A:0.10, C:0.46, G:0.16, T:0.29
Consensus pattern (25 bp):
TTTCATCAGGCCCTGCGCCACTTCC
Found at i:12340 original size:22 final size:22
Alignment explanation
Indices: 12273--12346 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
12263 TGTCTTTTTC
* * * *
12273 AAATTTTGATAATCACACGATCA
1 AAATTTTGATAACCATACAAT-G
* *
12296 AAATTTTGATAACC-TTCGTATG
1 AAATTTTGATAACCATAC-AATG
12318 AAATTTTGATAACCATACAATG
1 AAATTTTGATAACCATACAATG
12340 -AATTTTG
1 AAATTTTG
12347 TCAACCTCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 7 0.17
22 18 0.43
23 17 0.40
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCATACAATG
Found at i:17707 original size:22 final size:22
Alignment explanation
Indices: 17675--17799 Score: 93
Period size: 22 Copynumber: 5.8 Consensus size: 22
17665 CGTCCTTGAT
* *
17675 ACTATGTAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACATC
17697 ACTATGAAA-TTTGATAACAT-
1 ACTATGAAATTTTGATAACATC
*
17717 ATCTATGAACTTTTGATAATC-TC
1 A-CTATGAAATTTTGATAA-CATC
* *
17740 ACAATGAAATTTT-ACTGACATC
1 ACTATGAAATTTTGA-TAACATC
*
17762 -CTTATGAAATTTTG-TTA-ATC
1 AC-TATGAAATTTTGATAACATC
* *
17782 TCTATGAAGTTTTGATAA
1 ACTATGAAATTTTGATAA
17800 TCACACCATA
Statistics
Matches: 83, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
20 15 0.18
21 25 0.30
22 41 0.49
23 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACATC
Found at i:17711 original size:21 final size:21
Alignment explanation
Indices: 17675--17751 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
17665 CGTCCTTGAT
*
17675 ACTATGTAATTTTGATAACCTC
1 ACTATG-AAATTTGATAACCTC
*
17697 ACTATGAAATTTGATAACAT-
1 ACTATGAAATTTGATAACCTC
* *
17717 ATCTATGAACTTTTGATAATCTC
1 A-CTATGAA-ATTTGATAACCTC
*
17740 ACAATGAAATTT
1 ACTATGAAATTT
17752 TACTGACATC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 22 0.49
22 21 0.47
23 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ACTATGAAATTTGATAACCTC
Found at i:17781 original size:44 final size:43
Alignment explanation
Indices: 17676--17783 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
17666 GTCCTTGATA
* * *
17676 CTATGTAATTTTGATAACCTCACTATGAAATTTGATAACATAT
1 CTATGAAATTTTGATAATCTCACAATGAAATTTGATAACATAT
* * * *
17719 CTATGAACTTTTGATAATCTCACAATGAAATTTTACTGACAT-C
1 CTATGAAATTTTGATAATCTCACAATGAAATTTGA-TAACATAT
*
17762 CTTATGAAATTTTGTTAATCTC
1 C-TATGAAATTTTGATAATCTC
17784 TATGAAGTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
43 31 0.57
44 23 0.43
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (43 bp):
CTATGAAATTTTGATAATCTCACAATGAAATTTGATAACATAT
Found at i:17886 original size:19 final size:21
Alignment explanation
Indices: 17862--17918 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
17852 ACAATCTCAC
17862 TATGAAATTT-GAATAA-C-AT
1 TATGAAATTTCG-ATAATCGAT
17881 TATGAAATTTCGATAATCGTAT
1 TATGAAATTTCGATAATCG-AT
*
17903 TATGAAATTTTGATAA
1 TATGAAATTTCGATAA
17919 ATTTTCTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 14 0.42
20 2 0.06
22 17 0.52
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (21 bp):
TATGAAATTTCGATAATCGAT
Found at i:17932 original size:22 final size:23
Alignment explanation
Indices: 17902--17961 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
17892 GATAATCGTA
17902 TTATG-AAATTTTGATAA-ATTT
1 TTATGAAAATTTTGATAACATTT
*
17923 TCTAT-AAAATTTTG-TAACCTTT
1 T-TATGAAAATTTTGATAACATTT
17945 TTATGAAAA-TTTGATAA
1 TTATGAAAATTTTGATAA
17962 TTACACCATG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
21 11 0.33
22 22 0.67
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.48
Consensus pattern (23 bp):
TTATGAAAATTTTGATAACATTT
Found at i:18984 original size:19 final size:19
Alignment explanation
Indices: 18960--18997 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18950 GAGAAAATAA
18960 GCGTGGAGCTTAGTTTTTT
1 GCGTGGAGCTTAGTTTTTT
18979 GCGTGGAGCTTAGTTTTTT
1 GCGTGGAGCTTAGTTTTTT
18998 CCGCGGAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.32, T:0.47
Consensus pattern (19 bp):
GCGTGGAGCTTAGTTTTTT
Found at i:19005 original size:19 final size:19
Alignment explanation
Indices: 18964--19006 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
18954 AAATAAGCGT
* *
18964 GGAGCTTAGTTTTTTGCGT
1 GGAGCTTAGTTTTTTCCGC
18983 GGAGCTTAGTTTTTTCCGC
1 GGAGCTTAGTTTTTTCCGC
19002 GGAGC
1 GGAGC
19007 AAGTTTGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.12, C:0.16, G:0.33, T:0.40
Consensus pattern (19 bp):
GGAGCTTAGTTTTTTCCGC
Found at i:19011 original size:18 final size:19
Alignment explanation
Indices: 18964--19012 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
18954 AAATAAGCGT
* * *
18964 GGAGCTTAGTTTTTTGCGT
1 GGAGCTAAGTTTTTTCCGC
*
18983 GGAGCTTAGTTTTTTCCGC
1 GGAGCTAAGTTTTTTCCGC
19002 GGAGC-AAGTTT
1 GGAGCTAAGTTT
19013 GTAGCTGTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.41
Consensus pattern (19 bp):
GGAGCTAAGTTTTTTCCGC
Found at i:22251 original size:15 final size:15
Alignment explanation
Indices: 22231--22260 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22221 CTGTTTTATT
22231 AATATGATTTACAAA
1 AATATGATTTACAAA
22246 AATATGATTTACAAA
1 AATATGATTTACAAA
22261 TTGTTTTATT
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:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
AATATGATTTACAAA
Found at i:24638 original size:8 final size:9
Alignment explanation
Indices: 24598--24630 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
24588 TATAATATAT
24598 TTTAATAATA
1 TTTAA-AATA
24608 TTTAAAATA
1 TTTAAAATA
24617 TTTAAAATA
1 TTTAAAATA
24626 TTTAA
1 TTTAA
24631 TAATTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAAAATA
Found at i:25386 original size:22 final size:22
Alignment explanation
Indices: 25358--25404 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
25348 TAGTAGTTGA
25358 ATTTTTGCATGGCACCTTTTGC
1 ATTTTTGCATGGCACCTTTTGC
*
25380 ATTTTTGCATGGCATCTTTTGC
1 ATTTTTGCATGGCACCTTTTGC
25402 ATT
1 ATT
25405 CATCCTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.49
Consensus pattern (22 bp):
ATTTTTGCATGGCACCTTTTGC
Found at i:26724 original size:85 final size:86
Alignment explanation
Indices: 26624--26802 Score: 306
Period size: 88 Copynumber: 2.1 Consensus size: 86
26614 TGGGAAATGC
26624 TGCATTTCAATCATCCATTAAACATCTTCAGAGCACTC-TTTTACACAACAGCACGTATATGAAT
1 TGCATTTCAATCATCCATTAAACATCTTCAGAGCACTCATTTTACACAACAGCACGTATATGAAT
26688 TCTCATATTTATACACTACAT
66 TCTCATATTTATACACTACAT
* *
26709 TGCATTTCAATCATCCATTAAACATCTTCAGAGCACTCATATTTTACACATCAGCACGTATATGC
1 TGCATTTCAATCATCCATTAAACATCTTCAGAGCACTC--ATTTTACACAACAGCACGTATATGA
*
26774 ATTCTCATATTTATACATTACAT
64 ATTCTCATATTTATACACTACAT
26797 TGCATT
1 TGCATT
26803 CAAATTGCAG
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
85 38 0.43
88 50 0.57
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (86 bp):
TGCATTTCAATCATCCATTAAACATCTTCAGAGCACTCATTTTACACAACAGCACGTATATGAAT
TCTCATATTTATACACTACAT
Found at i:29749 original size:15 final size:14
Alignment explanation
Indices: 29731--29807 Score: 52
Period size: 15 Copynumber: 5.4 Consensus size: 14
29721 AATTCGAGGA
29731 AGTAAAAGAATAAT
1 AGTAAAAGAATAAT
29745 CAGTAAAA-AAGTAAT
1 -AGTAAAAGAA-TAAT
** *
29760 AGTAATCCGTAA-AAG
1 AGTAA-AAG-AATAAT
29775 AGTAAAA-AATAAT
1 AGTAAAAGAATAAT
*
29788 CAGTAAAAGAGTAAT
1 -AGTAAAAGAATAAT
29803 AGTAA
1 AGTAA
29808 TCAGTAAAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 19 0.40
15 23 0.48
17 2 0.04
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (14 bp):
AGTAAAAGAATAAT
Found at i:29771 original size:21 final size:21
Alignment explanation
Indices: 29741--30082 Score: 237
Period size: 21 Copynumber: 16.3 Consensus size: 21
29731 AGTAAAAGAA
*
29741 TAATCAGTAAAAAAGTAATAG
1 TAATCAGTAAAAGAGTAATAG
* * *
29762 TAATCCGTAAAAGAGTAAAAAA
1 TAATCAGTAAAAGAGT-AATAG
29784 TAATCAGTAAAAGAGTAATAG
1 TAATCAGTAAAAGAGTAATAG
*
29805 TAATCAGT-AAAGAGTAAAGAG
1 TAATCAGTAAAAGAGT-AATAG
*
29826 TAATCAAG-AAATG-GTAA-AG
1 TAATC-AGTAAAAGAGTAATAG
*
29845 ATTAATCAG-AAAAGGGTAATAG
1 --TAATCAGTAAAAGAGTAATAG
* * *
29867 TAGTTAGT-AAAGAGTAAAGAG
1 TAATCAGTAAAAGAGT-AATAG
* *
29888 TAATCAGGAAATG-GTAA-AG
1 TAATCAGTAAAAGAGTAATAG
*
29907 ATTAATCAG-AAAAGGGTAATAG
1 --TAATCAGTAAAAGAGTAATAG
* * *
29929 TAGTTAGT-AAAGAGTAAAGAG
1 TAATCAGTAAAAGAGT-AATAG
* *
29950 TAATCAGGAAAAGAGAAATAG
1 TAATCAGTAAAAGAGTAATAG
*
29971 TAATCAGTAAAAGAGTAAAGAG
1 TAATCAGTAAAAGAGT-AATAG
* *
29993 TAATCA--AGGAAGGGTAATAG
1 TAATCAGTA-AAAGAGTAATAG
*
30013 TAATCAGTAAAAGAGTAAACAG
1 TAATCAGTAAAAGAGT-AATAG
30035 TGAA-CAGTAAAATGA-TAATAG
1 T-AATCAGTAAAA-GAGTAATAG
*
30056 TAATCAGT-AAAGAGTAAATGG
1 TAATCAGTAAAAGAGT-AATAG
30077 TAATCA
1 TAATCA
30083 ATAATTAAAA
Statistics
Matches: 254, Mismatches: 39, Indels: 56
0.73 0.11 0.16
Matches are distributed among these distances:
19 6 0.02
20 60 0.24
21 123 0.48
22 61 0.24
23 4 0.02
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.21
Consensus pattern (21 bp):
TAATCAGTAAAAGAGTAATAG
Found at i:29876 original size:62 final size:62
Alignment explanation
Indices: 29784--29960 Score: 309
Period size: 62 Copynumber: 2.8 Consensus size: 62
29774 GAGTAAAAAA
* * * *
29784 TAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAATCAAGAAATGGTAAAGAT
1 TAATCAG-AAAAGGGTAATAGTAGTTAGTAAAGAGTAAAGAGTAATCAGGAAATGGTAAAGAT
29847 TAATCAGAAAAGGGTAATAGTAGTTAGTAAAGAGTAAAGAGTAATCAGGAAATGGTAAAGAT
1 TAATCAGAAAAGGGTAATAGTAGTTAGTAAAGAGTAAAGAGTAATCAGGAAATGGTAAAGAT
29909 TAATCAGAAAAGGGTAATAGTAGTTAGTAAAGAGTAAAGAGTAATCAGGAAA
1 TAATCAGAAAAGGGTAATAGTAGTTAGTAAAGAGTAAAGAGTAATCAGGAAA
29961 AGAGAAATAG
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 103 0.94
63 7 0.06
ACGTcount: A:0.50, C:0.04, G:0.24, T:0.22
Consensus pattern (62 bp):
TAATCAGAAAAGGGTAATAGTAGTTAGTAAAGAGTAAAGAGTAATCAGGAAATGGTAAAGAT
Found at i:29975 original size:62 final size:63
Alignment explanation
Indices: 29760--30082 Score: 302
Period size: 62 Copynumber: 5.1 Consensus size: 63
29750 AAAAAGTAAT
* * * * * *
29760 AGTAATCCGTAAAAGAGTAAAAAATAATCAGTAAAAGAGTAATAGTAATCAGTAAAGAGTAAAG
1 AGTAATCAGGAAAAG-GTAAAGATTAATCAGTAAAAGAGTAATAGTAGTTAGTAAAGAGTAAAG
* * *
29824 AGTAATCAAGAAATGGTAAAGATTAATCAG-AAAAGGGTAATAGTAGTTAGTAAAGAGTAAAG
1 AGTAATCAGGAAAAGGTAAAGATTAATCAGTAAAAGAGTAATAGTAGTTAGTAAAGAGTAAAG
* *
29886 AGTAATCAGGAAATGGTAAAGATTAATCAG-AAAAGGGTAATAGTAGTTAGTAAAGAGTAAAG
1 AGTAATCAGGAAAAGGTAAAGATTAATCAGTAAAAGAGTAATAGTAGTTAGTAAAGAGTAAAG
* * * * * * *
29948 AGTAATCAGGAAAAGAG-AAATAGTAATCAGTAAAAGAGTAAAGAGTAATCAAG-GAAGGGT-AA
1 AGTAATCAGGAAAAG-GTAAAGATTAATCAGTAAAAGAGT-AATAGTAGT-TAGTAAAGAGTAAA
*
30010 T
63 G
* * * * *
30011 AGTAATCAGTAAAAGAGTAAACAGTGAA-CAGTAAAATGA-TAATAGTAATCAGTAAAGAGTAAA
1 AGTAATCAGGAAAAG-GTAAAGA-TTAATCAGTAAAA-GAGTAATAGTAGTTAGTAAAGAGTAAA
30074 TG
63 -G
30076 -GTAATCA
1 AGTAATCA
30083 ATAATTAAAA
Statistics
Matches: 220, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
62 117 0.53
63 52 0.24
64 45 0.20
65 6 0.03
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (63 bp):
AGTAATCAGGAAAAGGTAAAGATTAATCAGTAAAAGAGTAATAGTAGTTAGTAAAGAGTAAAG
Found at i:30208 original size:35 final size:34
Alignment explanation
Indices: 30120--30224 Score: 153
Period size: 35 Copynumber: 3.1 Consensus size: 34
30110 GTAAAAAGCT
* *
30120 TAAAAAGAGTAAAAATAGTATTCAGTAATTAAAA
1 TAAAAAGAGTAAAAATGGTATTCAGTAATTAAAG
*
30154 T-AAAA-A-TTAAAATGGTATTCAGTAATTAAAG
1 TAAAAAGAGTAAAAATGGTATTCAGTAATTAAAG
30185 TAAAGAAGAGTAAAAATGGTATTCAGTAATTAAAG
1 TAAA-AAGAGTAAAAATGGTATTCAGTAATTAAAG
30220 TAAAA
1 TAAAA
30225 CATGCAAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
31 23 0.37
32 3 0.05
33 6 0.10
34 3 0.05
35 28 0.44
ACGTcount: A:0.55, C:0.03, G:0.14, T:0.28
Consensus pattern (34 bp):
TAAAAAGAGTAAAAATGGTATTCAGTAATTAAAG
Found at i:30235 original size:35 final size:33
Alignment explanation
Indices: 30130--30255 Score: 127
Period size: 35 Copynumber: 3.8 Consensus size: 33
30120 TAAAAAGAGT
* *
30130 AAAAATAGTATTCAGTAATTAAAATAAAAAT--
1 AAAAATGGTATTCAGTAATTAAAGTAAAAATGA
*
30161 TAAAATGGTATTCAGTAATTAAAGTAAAGAA-GA
1 AAAAATGGTATTCAGTAATTAAAGTAAA-AATGA
30194 GTAAAAATGGTATTCAGTAATTAAAGTAAAACATGCA
1 --AAAAATGGTATTCAGTAATTAAAGTAAAA-ATG-A
* *
30231 AAAAATGGAAGTCAGTAA--AAAGTAA
1 AAAAATGGTATTCAGTAATTAAAGTAA
30256 GAAAATTGTA
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
31 25 0.31
32 2 0.02
33 7 0.09
34 1 0.01
35 44 0.54
36 1 0.01
37 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (33 bp):
AAAAATGGTATTCAGTAATTAAAGTAAAAATGA
Found at i:30282 original size:27 final size:26
Alignment explanation
Indices: 30230--30310 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 26
30220 TAAAACATGC
30230 AAAAAA-TGG-AAGTCAGTAAAAA-GT
1 AAAAAATTGGTAA-TCAGTAAAAAGGT
*
30254 AAGAAAATT-GTAATGAGTAAAAAGGGT
1 AA-AAAATTGGTAATCAGTAAAAA-GGT
30281 AAAAAATTGGTAATCAGTAAAAAGAGT
1 AAAAAATTGGTAATCAGTAAAAAG-GT
30308 AAA
1 AAA
30311 GGTAATCAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
24 2 0.04
25 14 0.29
26 10 0.21
27 22 0.46
ACGTcount: A:0.57, C:0.02, G:0.21, T:0.20
Consensus pattern (26 bp):
AAAAAATTGGTAATCAGTAAAAAGGT
Found at i:30394 original size:17 final size:17
Alignment explanation
Indices: 30372--30404 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30362 AAGAGGAGAA
*
30372 AAGTAAACAAGGGTAAT
1 AAGTAAAAAAGGGTAAT
30389 AAGTAAAAAAGGGTAA
1 AAGTAAAAAAGGGTAA
30405 GAAAAAGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.24, T:0.15
Consensus pattern (17 bp):
AAGTAAAAAAGGGTAAT
Found at i:32216 original size:26 final size:26
Alignment explanation
Indices: 32176--32229 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
32166 GATGATACTG
*
32176 TAAAAATTGATTTTTTCTAAATAAAA
1 TAAAAATTGAATTTTTCTAAATAAAA
32202 TAAAAATTGAATTTTTCTAAATAAAA
1 TAAAAATTGAATTTTTCTAAATAAAA
32228 TA
1 TA
32230 TTTTAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
TAAAAATTGAATTTTTCTAAATAAAA
Found at i:32404 original size:26 final size:27
Alignment explanation
Indices: 32351--32416 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
32341 AAAAGTACAC
* *
32351 AAAATTATATTTTAATAGTGTCATAATT
1 AAAA-TATATTTTAATAATGGCATAATT
*
32379 AAAATATTTTTTAATAATGGCA-AATT
1 AAAATATATTTTAATAATGGCATAATT
32405 AGAAATATATTT
1 A-AAATATATTT
32417 GGAAAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 5 0.15
27 24 0.73
28 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (27 bp):
AAAATATATTTTAATAATGGCATAATT
Found at i:33585 original size:27 final size:27
Alignment explanation
Indices: 33530--33591 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
33520 TATAAATTTC
*
33530 TATTATTTTAATGATGAAATAATTAAAA
1 TATTATTTTAATAATGAAAT-ATTAAAA
33558 TATT-TTTTAATAATGATAAT-TTAGAAA
1 TATTATTTTAATAATGA-AATATTA-AAA
33585 TA-TATTT
1 TATTATTT
33592 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 4 0.13
27 19 0.63
28 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (27 bp):
TATTATTTTAATAATGAAATATTAAAA
Found at i:34019 original size:5 final size:5
Alignment explanation
Indices: 34009--34061 Score: 70
Period size: 5 Copynumber: 9.8 Consensus size: 5
33999 TAGAACCCCT
34009 TATAA TATAA TAATAA TATAA TATAA TATAA TATAA TAATATA TATATA
1 TATAA TATAA T-ATAA TATAA TATAA TATAA TATAA T-ATA-A TATA-A
34058 TATA
1 TATA
34062 CAAGCTAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
5 26 0.58
6 17 0.38
7 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:34023 original size:8 final size:9
Alignment explanation
Indices: 34009--34061 Score: 69
Period size: 8 Copynumber: 6.2 Consensus size: 9
33999 TAGAACCCCT
34009 TATAATATA
1 TATAATATA
34018 -ATAATA-A
1 TATAATATA
34025 TATAATATAA
1 TATAATAT-A
34035 TATAATATA
1 TATAATATA
34044 -ATAATATA
1 TATAATATA
34052 TAT-ATATA
1 TATAATATA
34060 TA
1 TA
34062 CAAGCTAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
7 1 0.03
8 27 0.68
9 3 0.08
10 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TATAATATA
Found at i:35657 original size:6 final size:6
Alignment explanation
Indices: 35646--35675 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35636 ATTGTGTTGT
*
35646 CTGAGA CTGAGA CTGAGA CTGAGA ATGAGA
1 CTGAGA CTGAGA CTGAGA CTGAGA CTGAGA
35676 GAGATGGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.33, T:0.17
Consensus pattern (6 bp):
CTGAGA
Done.