Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020390.1 Corchorus olitorius cultivar O-4 contig20423, 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: 102310
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:378 original size:84 final size:81
Alignment explanation
Indices: 204--388 Score: 223
Period size: 84 Copynumber: 2.2 Consensus size: 81
194 ATGTTCCTTG
*
204 ACCTCCATAAGATGTCACAAACATAAGTATAAGCCACATATATTTTAAACAATTAAAACATGCCA
1 ACCTCCATAAGATGTCACAAACATAAATATAAGCCACATATA-TTTAAACAATTAAAACATGCCA
*
269 CAAGCAAATTGTAAATTTA
65 CAAGCAAAATGTAAA--TA
* *
288 ACCTCCATAAGATGTCACAAACATAAATATAAGCCACATATA-TTAAACAGTTAGAATATTTATA
1 ACCTCCATAAGATGTCACAAACATAAATATAAGCCACATATATTTAAACAATT--AA-A---ACA
352 TGCCACAAGCAAAATGT-AA-A
60 TGCCACAAGCAAAATGTAAATA
*
372 ATCTCCATAAGATGTCA
1 ACCTCCATAAGATGTCA
389 TAGGCAGAAG
Statistics
Matches: 90, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
82 9 0.10
84 60 0.67
85 1 0.01
87 2 0.02
88 18 0.20
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (81 bp):
ACCTCCATAAGATGTCACAAACATAAATATAAGCCACATATATTTAAACAATTAAAACATGCCAC
AAGCAAAATGTAAATA
Found at i:1777 original size:36 final size:36
Alignment explanation
Indices: 1737--1807 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
1727 GTAAGGTCTC
*
1737 GGGTTCGAGTCTTGTGAATGGAGAAAACCATTATTA
1 GGGTTCGAGTCTTGTGAATAGAGAAAACCATTATTA
1773 GGGTTCGAGTCTTGTGAATAGAGAAAACCATTATT
1 GGGTTCGAGTCTTGTGAATAGAGAAAACCATTATT
1808 GGGAGAGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (36 bp):
GGGTTCGAGTCTTGTGAATAGAGAAAACCATTATTA
Found at i:1902 original size:45 final size:45
Alignment explanation
Indices: 1838--1925 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
1828 ATGGGTCAAT
1838 CCGGCTCGAATAAGGTTAACTTGTAAATATATAAAAAAAAAAAAC
1 CCGGCTCGAATAAGGTTAACTTGTAAATATATAAAAAAAAAAAAC
*
1883 CCGGCTCGAATAAGGTTAACTTGTAAATATATATAAAAAAAAA
1 CCGGCTCGAATAAGGTTAACTTGTAAATATATAAAAAAAAAAA
1926 TACATAGTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (45 bp):
CCGGCTCGAATAAGGTTAACTTGTAAATATATAAAAAAAAAAAAC
Found at i:12095 original size:136 final size:136
Alignment explanation
Indices: 11846--12113 Score: 527
Period size: 136 Copynumber: 2.0 Consensus size: 136
11836 GACTGTTAGA
*
11846 AGATGCTGAAAACTCTAAATGAAAAAACAAGTAATATAAACAGGTTAGGAGAACACTAACTATCT
1 AGATACTGAAAACTCTAAATGAAAAAACAAGTAATATAAACAGGTTAGGAGAACACTAACTATCT
11911 GAGTTGATTAAAGACACATAATGAGCATCGTAAAAGAAGAGGTCTTTGATGAAAATACAGAAAGC
66 GAGTTGATTAAAGACACATAATGAGCATCGTAAAAGAAGAGGTCTTTGATGAAAATACAGAAAGC
11976 ATTAAT
131 ATTAAT
11982 AGATACTGAAAACTCTAAATGAAAAAACAAGTAATATAAACAGGTTAGGAGAACACTAACTATCT
1 AGATACTGAAAACTCTAAATGAAAAAACAAGTAATATAAACAGGTTAGGAGAACACTAACTATCT
12047 GAGTTGATTAAAGACACATAATGAGCATCGTAAAAGAAGAGGTCTTTGATGAAAATACAGAAAGC
66 GAGTTGATTAAAGACACATAATGAGCATCGTAAAAGAAGAGGTCTTTGATGAAAATACAGAAAGC
12112 AT
131 AT
12114 ATAAGCCTCC
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 131 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.22
Consensus pattern (136 bp):
AGATACTGAAAACTCTAAATGAAAAAACAAGTAATATAAACAGGTTAGGAGAACACTAACTATCT
GAGTTGATTAAAGACACATAATGAGCATCGTAAAAGAAGAGGTCTTTGATGAAAATACAGAAAGC
ATTAAT
Found at i:15263 original size:13 final size:13
Alignment explanation
Indices: 15245--15269 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15235 CAAACATATA
15245 TATATATATATTG
1 TATATATATATTG
15258 TATATATATATT
1 TATATATATATT
15270 ATCTATTGTA
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TATATATATATTG
Found at i:19893 original size:13 final size:13
Alignment explanation
Indices: 19837--19894 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
19827 TTATTGAGGT
19837 TTCTATTAGTTGC
1 TTCTATTAGTTGC
*
19850 TTATATTAGTTGC
1 TTCTATTAGTTGC
* *
19863 TTATATTGAG--GT
1 TTCTATT-AGTTGC
19875 TTCTATTAGTTGC
1 TTCTATTAGTTGC
19888 TTCTATT
1 TTCTATT
19895 TAGTATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
11 2 0.05
12 7 0.18
13 27 0.71
14 2 0.05
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (13 bp):
TTCTATTAGTTGC
Found at i:20205 original size:20 final size:19
Alignment explanation
Indices: 20147--20196 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 19
20137 ACAGCGTACT
20147 ATGTTTATTTC-AACATAC
1 ATGTTTATTTCAAACATAC
20165 A----TATTTCAAACATAC
1 ATGTTTATTTCAAACATAC
20180 ATGTTTATTTC-AACATA
1 ATGTTTATTTCAAACATA
20197 TATATGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
18 7 0.26
19 6 0.22
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (19 bp):
ATGTTTATTTCAAACATAC
Found at i:20756 original size:2 final size:2
Alignment explanation
Indices: 20749--20778 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20739 ATCCCCTTGA
20749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20779 GATCAATCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24626 original size:19 final size:19
Alignment explanation
Indices: 24602--24638 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24592 CTGTTTAGCA
24602 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
24621 ACTGTACATATTAGATTA
1 ACTGTACAGATGAGATTA
24639 GGTACTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:27230 original size:30 final size:29
Alignment explanation
Indices: 27178--27238 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
27168 TGAACGGCTT
* * * *
27178 CGTCTTGGATATTGGCACATGAACGACGAA
1 CGTCTTAGACATTGCCAAATGAAC-ACGAA
27208 CGTCTTAGACATTGCCAAATGAACACGAA
1 CGTCTTAGACATTGCCAAATGAACACGAA
27237 CG
1 CG
27239 CCCTGGACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (29 bp):
CGTCTTAGACATTGCCAAATGAACACGAA
Found at i:28164 original size:10 final size:10
Alignment explanation
Indices: 28149--28199 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
28139 GGTATGGCCA
28149 TAAGCTCTAT
1 TAAGCTCTAT
28159 TAAGCTCTAT
1 TAAGCTCTAT
*
28169 TATA-CTCTAAG
1 TA-AGCTCT-AT
*
28180 GAAGCTCTAT
1 TAAGCTCTAT
*
28190 TATGCTCTAT
1 TAAGCTCTAT
28200 GACACTCCAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (10 bp):
TAAGCTCTAT
Found at i:35780 original size:20 final size:21
Alignment explanation
Indices: 35755--35794 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35745 ACTCTACGAT
35755 TTAAAA-CAAAAGAAAGAAAA
1 TTAAAATCAAAAGAAAGAAAA
*
35775 TTAAAATCAAAAGAATGAAA
1 TTAAAATCAAAAGAAAGAAA
35795 GGGATCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.70, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
TTAAAATCAAAAGAAAGAAAA
Found at i:36631 original size:2 final size:2
Alignment explanation
Indices: 36624--36680 Score: 66
Period size: 2 Copynumber: 30.0 Consensus size: 2
36614 AATTTTAAAG
* * *
36624 AT AT AT AT AT AC AT AT AT AT AC AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36666 -T AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT
36681 TATTACATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61845 original size:7 final size:7
Alignment explanation
Indices: 61835--61870 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
61825 AACGGGCAAC
61835 GGCTCAG
1 GGCTCAG
61842 GGCTCAG
1 GGCTCAG
61849 GGCTCAG
1 GGCTCAG
61856 GGCTCAG
1 GGCTCAG
61863 GGCTCAG
1 GGCTCAG
61870 G
1 G
61871 CAACCACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (7 bp):
GGCTCAG
Found at i:65158 original size:24 final size:24
Alignment explanation
Indices: 65126--65174 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
65116 AATAGTTGAA
65126 TGCTTTTAGTTTCAGGGGTTAGGT
1 TGCTTTTAGTTTCAGGGGTTAGGT
65150 TGCTTTTAGTTTCAGGGGTTAGGT
1 TGCTTTTAGTTTCAGGGGTTAGGT
65174 T
1 T
65175 CAATCCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.08, G:0.33, T:0.47
Consensus pattern (24 bp):
TGCTTTTAGTTTCAGGGGTTAGGT
Found at i:66421 original size:2 final size:2
Alignment explanation
Indices: 66414--66440 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
66404 TTCCAGCAGC
66414 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
66441 TCGTCTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68508 original size:21 final size:21
Alignment explanation
Indices: 68482--68541 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
68472 GCTTCTCTAA
*
68482 TAATTTCATCTATACAATACT
1 TAATTTCATCTATACAATACG
* *
68503 TAATTTGATATATACAAT--G
1 TAATTTCATCTATACAATACG
* *
68522 TAATATCATCTGTACAATAC
1 TAATTTCATCTATACAATAC
68542 CTAAACGGAG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 14 0.47
21 16 0.53
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (21 bp):
TAATTTCATCTATACAATACG
Found at i:73077 original size:29 final size:30
Alignment explanation
Indices: 73038--73096 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
73028 TATAAATAAT
* *
73038 ATAATATAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
*
73067 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
73097 CATGGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Found at i:75663 original size:7 final size:7
Alignment explanation
Indices: 75651--75691 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
75641 ATTATATCGG
75651 AATAATC
1 AATAATC
75658 AATAATC
1 AATAATC
75665 AATAATC
1 AATAATC
75672 AATAATC
1 AATAATC
75679 AATAATC
1 AATAATC
75686 AATAAT
1 AATAAT
75692 GGAAGGAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAATC
Found at i:76818 original size:36 final size:36
Alignment explanation
Indices: 76768--76838 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
76758 CTCCTTCCAC
76768 TCCAATAAGAAATAAATCTCTCCTAAACAAAATAAT
1 TCCAATAAGAAATAAATCTCTCCTAAACAAAATAAT
*
76804 TCCAATAATG-AATAAATCTCTCCTAAGCAAAATAA
1 TCCAATAA-GAAATAAATCTCTCCTAAACAAAATAA
76839 ATAATGACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.25
Consensus pattern (36 bp):
TCCAATAAGAAATAAATCTCTCCTAAACAAAATAAT
Found at i:86592 original size:19 final size:20
Alignment explanation
Indices: 86568--86623 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 20
86558 GAGTGGAAAC
86568 GGGTACCAAACAGAGG-GGT
1 GGGTACCAAACAGAGGAGGT
* *
86587 GGGTACCGAATAGAGAGGATGT
1 GGGTACC-AA-ACAGAGGAGGT
*
86609 GGGTACCAAATAGAG
1 GGGTACCAAACAGAG
86624 AATTTTCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 7 0.23
20 7 0.23
21 8 0.26
22 9 0.29
ACGTcount: A:0.34, C:0.12, G:0.39, T:0.14
Consensus pattern (20 bp):
GGGTACCAAACAGAGGAGGT
Found at i:89793 original size:58 final size:61
Alignment explanation
Indices: 89702--89819 Score: 163
Period size: 58 Copynumber: 2.0 Consensus size: 61
89692 TTAAAAAAAG
*
89702 AGGAATACTCTCCGTTTTAGATCTAACCAATGCGTG-T-TCTATGATCGGATGAGTCATAA
1 AGGAATACTCTCCGTTTTAGATCTAACCAATGCGTGCTCTATATGATCGGATGAGTCATAA
***
89761 AGGAATACTC-CTC-TTTTAGATCTAGGTAATGCGTGCTCTATATGATCGGATGAGTCATA
1 AGGAATACTCTC-CGTTTTAGATCTAACCAATGCGTGCTCTATATGATCGGATGAGTCATA
89820 TCTTGATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
58 20 0.38
59 12 0.23
60 20 0.38
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (61 bp):
AGGAATACTCTCCGTTTTAGATCTAACCAATGCGTGCTCTATATGATCGGATGAGTCATAA
Found at i:89857 original size:40 final size:40
Alignment explanation
Indices: 89801--89877 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
89791 GCGTGCTCTA
89801 TATGATCGGATGAGTCATATCTTGATAATTATATGGACAC
1 TATGATCGGATGAGTCATATCTTGATAATTATATGGACAC
* * *
89841 TATGATCTGATTAGTCATATCTTGGTAATTATATGGA
1 TATGATCGGATGAGTCATATCTTGATAATTATATGGA
89878 GTGTTGATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.39
Consensus pattern (40 bp):
TATGATCGGATGAGTCATATCTTGATAATTATATGGACAC
Found at i:92624 original size:198 final size:198
Alignment explanation
Indices: 92286--92725 Score: 835
Period size: 198 Copynumber: 2.2 Consensus size: 198
92276 TGTCTTGTTA
* * *
92286 GTGGAATCCAAAATTTACACCGTCGGTGTATTAAATAATTATCCTAAAAGGCAAATTATACAATA
1 GTGGAATCCAAAATTTACACCGCCGGTGTATCAAATAATTACCCTAAAAGGCAAATTATACAATA
92351 CACCGGCGGTGGAATTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACATGTGTCCTCTAGGG
66 CACCGGCGGTGGAATTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACATGTGTCCTCTAGGG
92416 ACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCG
131 ACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCG
92481 CTT
196 CTT
*
92484 GTGGAATCCAAAATTTACACTGCCGGTGTATCAAATAATTACCCTAAAAGGCAAATTATACAATA
1 GTGGAATCCAAAATTTACACCGCCGGTGTATCAAATAATTACCCTAAAAGGCAAATTATACAATA
*
92549 CACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACATGTGTCCTCTAGGG
66 CACCGGCGGTGGAATTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACATGTGTCCTCTAGGG
92614 ACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCG
131 ACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCG
92679 CTT
196 CTT
92682 GTGGAATCCAAAATTTACACCGCCGGTGTATCAAATAATTACCC
1 GTGGAATCCAAAATTTACACCGCCGGTGTATCAAATAATTACCC
92726 ATAATAAAAT
Statistics
Matches: 236, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 236 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (198 bp):
GTGGAATCCAAAATTTACACCGCCGGTGTATCAAATAATTACCCTAAAAGGCAAATTATACAATA
CACCGGCGGTGGAATTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACATGTGTCCTCTAGGG
ACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCG
CTT
Found at i:95768 original size:21 final size:21
Alignment explanation
Indices: 95744--95790 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
95734 TCTCACAAGG
*
95744 AGGTTATAAAAAATCATAGGA
1 AGGTTACAAAAAATCATAGGA
**
95765 AGGTTACAAAATTTCATAGGA
1 AGGTTACAAAAAATCATAGGA
95786 AGGTT
1 AGGTT
95791 TATTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (21 bp):
AGGTTACAAAAAATCATAGGA
Found at i:95802 original size:23 final size:21
Alignment explanation
Indices: 95757--95805 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 21
95747 TTATAAAAAA
95757 TCATAGGAAGGTTACAAAATT
1 TCATAGGAAGGTTACAAAATT
*
95778 TCATAGGAAGGTTTATTAAAATT
1 TCATAGGAAGG-TTA-CAAAATT
95801 TCATA
1 TCATA
95806 ATTAGGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.44
22 3 0.12
23 11 0.44
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (21 bp):
TCATAGGAAGGTTACAAAATT
Found at i:95873 original size:22 final size:22
Alignment explanation
Indices: 95847--95917 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
95837 TCATAATTAC
* *
95847 AATTTTATAGGTAAATTATCAA
1 AATTTAATAGGTAAGTTATCAA
* *
95869 AATTTCATAGCGT-GGTTATCAA
1 AATTTAATAG-GTAAGTTATCAA
95891 AATTTAATAGG-ATAGTTATCAA
1 AATTTAATAGGTA-AGTTATCAA
95913 AATTT
1 AATTT
95918 CATAAAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 1 0.02
22 38 0.93
23 2 0.05
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (22 bp):
AATTTAATAGGTAAGTTATCAA
Done.