Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020233.1 Corchorus olitorius cultivar O-4 contig20266, 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: 110511
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:178 original size:15 final size:15
Alignment explanation
Indices: 155--203 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
145 AAGTAACCCT
* *
155 TTTCCTTCCTTCCCC
1 TTTCTTTCCTTCCCA
*
170 TTTCTTTCC-TCCCT
1 TTTCTTTCCTTCCCA
184 TCTTCTTTCCTTCCCA
1 T-TTCTTTCCTTCCCA
200 TTTC
1 TTTC
204 CTTCATACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 5 0.17
15 19 0.66
16 5 0.17
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTCTTTCCTTCCCA
Found at i:2208 original size:56 final size:57
Alignment explanation
Indices: 2102--2215 Score: 180
Period size: 56 Copynumber: 2.0 Consensus size: 57
2092 AGTTTCTCTC
*
2102 AAATCTCTCTCTTTTTCTATCCAAAATACCAACAAGATTATCTCCAATAACTTCCAT
1 AAATCTCTCTCTTTCTCTATCCAAAATACCAACAAGATTATCTCCAATAACTTCCAT
2159 AAATCTCTC-CGTTTCTCTATCCAAAACT-CC-ACAAGATTATCTCCAATAACTTCCAT
1 AAATCTCTCTC-TTTCTCTATCCAAAA-TACCAACAAGATTATCTCCAATAACTTCCAT
2215 A
1 A
2216 CTATGCCTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
56 28 0.52
57 25 0.46
58 1 0.02
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (57 bp):
AAATCTCTCTCTTTCTCTATCCAAAATACCAACAAGATTATCTCCAATAACTTCCAT
Found at i:4279 original size:20 final size:20
Alignment explanation
Indices: 4254--4292 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4244 CGTTGTTAGT
4254 CGTGTTATCCATGTCAACAA
1 CGTGTTATCCATGTCAACAA
**
4274 CGTGTTATCTGTGTCAACA
1 CGTGTTATCCATGTCAACA
4293 CGTTTAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (20 bp):
CGTGTTATCCATGTCAACAA
Found at i:13980 original size:42 final size:44
Alignment explanation
Indices: 13895--14016 Score: 185
Period size: 42 Copynumber: 2.8 Consensus size: 44
13885 CTTTTTTAAA
*
13895 TTTTTAATGGCTGCAAGATTGGATCTTTTTTGTTCTTAGTTTAG
1 TTTTTAATGGCTGCAAGATTGGATCTTTTTTGTTCTTACTTTAG
* *
13939 TTTTTAATGGCTACAAGATTTGAT-TTTTTT-TTCTTACTTTAG
1 TTTTTAATGGCTGCAAGATTGGATCTTTTTTGTTCTTACTTTAG
*
13981 TTTTTAATGGCTGCAAGATTGGATCTGTTCTTGTTC
1 TTTTTAATGGCTGCAAGATTGGATCT-TTTTTGTTC
14017 ATGATTCATG
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
42 33 0.48
43 7 0.10
44 26 0.38
45 3 0.04
ACGTcount: A:0.19, C:0.11, G:0.18, T:0.52
Consensus pattern (44 bp):
TTTTTAATGGCTGCAAGATTGGATCTTTTTTGTTCTTACTTTAG
Found at i:20417 original size:34 final size:34
Alignment explanation
Indices: 20379--20443 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
20369 CAGTAGTCAC
20379 ATTAAAATCCGATAAATTTAGAAACGACTTATAT
1 ATTAAAATCCGATAAATTTAGAAACGACTTATAT
20413 ATTAAAATCCGATAAATTTAGAAACGACTTA
1 ATTAAAATCCGATAAATTTAGAAACGACTTA
20444 CATAGAATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (34 bp):
ATTAAAATCCGATAAATTTAGAAACGACTTATAT
Found at i:21145 original size:30 final size:30
Alignment explanation
Indices: 21104--21185 Score: 146
Period size: 30 Copynumber: 2.7 Consensus size: 30
21094 ACCATAAATT
* *
21104 GGAATGTAATAGTGAATGTCCTTTTTTTGA
1 GGAAAGTAATAGTAAATGTCCTTTTTTTGA
21134 GGAAAGTAATAGTAAATGTCCTTTTTTTGA
1 GGAAAGTAATAGTAAATGTCCTTTTTTTGA
21164 GGAAAGTAATAGTAAATGTCCT
1 GGAAAGTAATAGTAAATGTCCT
21186 AAACTAAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (30 bp):
GGAAAGTAATAGTAAATGTCCTTTTTTTGA
Found at i:32502 original size:4 final size:4
Alignment explanation
Indices: 32424--32488 Score: 130
Period size: 4 Copynumber: 16.2 Consensus size: 4
32414 ATCTTGAGAG
32424 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
32472 ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT A
32489 AACTAGACAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:45007 original size:2 final size:2
Alignment explanation
Indices: 45000--45047 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
44990 CTCATAAATT
* * * *
45000 TA TA TA TA TA TA TA TC TA TA TC TA TA TA TA TA TA GA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45042 TA TA TA
1 TA TA TA
45048 AACTACTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:47886 original size:42 final size:43
Alignment explanation
Indices: 47806--47891 Score: 147
Period size: 42 Copynumber: 2.0 Consensus size: 43
47796 ATTTAAGCCA
47806 AAAACTAATCCCCTATCAATATCTTTTCTAGTTTTCTTCATCT
1 AAAACTAATCCCCTATCAATATCTTTTCTAGTTTTCTTCATCT
* *
47849 AAAACTAATCCTCTATCCATAT-TTTTCTAGTTTTCTTCATCT
1 AAAACTAATCCCCTATCAATATCTTTTCTAGTTTTCTTCATCT
47891 A
1 A
47892 GGGACATTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 21 0.51
43 20 0.49
ACGTcount: A:0.28, C:0.24, G:0.02, T:0.45
Consensus pattern (43 bp):
AAAACTAATCCCCTATCAATATCTTTTCTAGTTTTCTTCATCT
Found at i:48597 original size:22 final size:21
Alignment explanation
Indices: 48561--48611 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
48551 CTTACAAGAT
*
48561 TACTAAAATTTTAATAAAGGC
1 TACTAAAATTGTAATAAAGGC
* *
48582 TACTAACAATTGTAATAAGGGT
1 TACTAA-AATTGTAATAAAGGC
48604 TACTAAAA
1 TACTAAAA
48612 CGTTCAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (21 bp):
TACTAAAATTGTAATAAAGGC
Found at i:48748 original size:28 final size:28
Alignment explanation
Indices: 48704--48758 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
48694 TTCATATAAT
* * *
48704 ATTATTGAAATGCTTAATGAGGTTATTG
1 ATTATTGAAAGGCTTAATAAGGGTATTG
*
48732 ATTATTGAAAGGTTTAATAAGGGTATT
1 ATTATTGAAAGGCTTAATAAGGGTATT
48759 AAAAAACTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.42
Consensus pattern (28 bp):
ATTATTGAAAGGCTTAATAAGGGTATTG
Found at i:48944 original size:20 final size:21
Alignment explanation
Indices: 48884--48944 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 21
48874 GTTATTAAAA
*
48884 AAAATCTTCACAAGGTTACTAT
1 AAAATCTT-ACAAGGTAACTAT
* * *
48906 AAAAT-TCATAAGTTAACTAT
1 AAAATCTTACAAGGTAACTAT
*
48926 -AAATCTTACAAGGTCACTA
1 AAAATCTTACAAGGTAACTA
48945 AATAAAAACT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
19 4 0.13
20 20 0.67
21 1 0.03
22 5 0.17
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.31
Consensus pattern (21 bp):
AAAATCTTACAAGGTAACTAT
Found at i:49089 original size:87 final size:86
Alignment explanation
Indices: 48991--49170 Score: 306
Period size: 87 Copynumber: 2.1 Consensus size: 86
48981 TAAGATCACT
48991 AAAAATCTTAAACGAGGTGATTAAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAAT
1 AAAAATCTTAAACGAGGTGATTAAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAAT
*
49056 GAAAAGTTTATAAGCTTACCA
66 GAAAAATTTATAAGCTTACCA
* *
49077 AAAAACTCTTAAACGAGGTGATTGAATAAATTTAAGAAAATTATTTAAAAAGCTTTTAAGTTTAA
1 AAAAA-TCTTAAACGAGGTGATTAAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAA
*
49142 TGAAAAATTTATAAGCTTGCCA
65 TGAAAAATTTATAAGCTTACCA
49164 AGAAAAT
1 A-AAAAT
49171 TTACAAGGTT
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
86 5 0.06
87 79 0.90
88 4 0.05
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (86 bp):
AAAAATCTTAAACGAGGTGATTAAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAAT
GAAAAATTTATAAGCTTACCA
Found at i:52144 original size:2 final size:2
Alignment explanation
Indices: 52132--52187 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
52122 ATATGAGAAG
*
52132 AT AT AT TT AT AT AT AT -T AT AT AT -T AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52171 AT -T AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT A
52188 AAACACTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
1 5 0.11
2 42 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:52153 original size:7 final size:7
Alignment explanation
Indices: 52141--52179 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
52131 GATATATTTA
52141 TATATAT
1 TATATAT
52148 TATATA-
1 TATATAT
52154 T-TATA-
1 TATATAT
52159 TATATAT
1 TATATAT
52166 TATATAT
1 TATATAT
52173 TATATAT
1 TATATAT
52180 ATAATATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 5 0.17
7 20 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:52160 original size:18 final size:18
Alignment explanation
Indices: 52132--52187 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
52122 ATATGAGAAG
52132 ATATATT-TATATATATT
1 ATATATTATATATATATT
52149 ATATATTATATATATATT
1 ATATATTATATATATATT
*
52167 ATATATTATATATATAAT
1 ATATATTATATATATATT
52185 ATA
1 ATA
52188 AAACACTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
17 7 0.19
18 30 0.81
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATTATATATATATT
Found at i:52456 original size:22 final size:22
Alignment explanation
Indices: 52430--52526 Score: 62
Period size: 22 Copynumber: 4.5 Consensus size: 22
52420 CTAAAAGTCA
52430 AAACCCCAAATCATCGATGTGC
1 AAACCCCAAATCATCGATGTGC
** *
52452 AAACCATAAAT-AT-GAAAGT-C
1 AAACCCCAAATCATCG-ATGTGC
**
52472 AAACCCCAAAT-ATTAATG-GTC
1 AAACCCCAAATCATCGATGTG-C
* *
52493 AAACCCCAAAGCATCCATTGTG-
1 AAACCCCAAATCATCGA-TGTGC
52515 AAACCCCAAATC
1 AAACCCCAAATC
52527 TTAATGGTCG
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
20 15 0.26
21 16 0.28
22 23 0.40
23 2 0.04
24 1 0.02
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (22 bp):
AAACCCCAAATCATCGATGTGC
Found at i:52482 original size:20 final size:20
Alignment explanation
Indices: 52423--52502 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 20
52413 TCTAAATCTA
52423 AAAGTCAAAACCCCAAATCATCG
1 AAAGTC-AAACCCCAAAT-AT-G
* **
52446 -ATGTGCAAACCATAAATATG
1 AAAGT-CAAACCCCAAATATG
*
52466 AAAGTCAAACCCCAAATATT
1 AAAGTCAAACCCCAAATATG
*
52486 AATGGTCAAACCCCAAA
1 AA-AGTCAAACCCCAAA
52503 GCATCCATTG
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 15 0.33
21 18 0.39
22 12 0.26
23 1 0.02
ACGTcount: A:0.47, C:0.25, G:0.10, T:0.17
Consensus pattern (20 bp):
AAAGTCAAACCCCAAATATG
Found at i:52495 original size:21 final size:21
Alignment explanation
Indices: 52469--52535 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
52459 AAATATGAAA
52469 GTCAAACCCCAAATATTAATG
1 GTCAAACCCCAAATATTAATG
* ** *
52490 GTCAAACCCCAAAGCATCCATT
1 GTCAAACCCCAAA-TATTAATG
* *
52512 GTGAAACCCCAAATCTTAATG
1 GTCAAACCCCAAATATTAATG
52533 GTC
1 GTC
52536 GAACTACAAA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.22
Consensus pattern (21 bp):
GTCAAACCCCAAATATTAATG
Found at i:52640 original size:23 final size:22
Alignment explanation
Indices: 52577--52644 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
52567 AGCATGATTA
*
52577 GTCAAACCCCTACTA-GTAATGG
1 GTCAAACCCCTAATATGTAAT-G
* *
52599 GATCAAACCTCAAAT-TGTAATG
1 G-TCAAACCCCTAATATGTAATG
52621 GTCAAACCCCTAATCATGT-ATG
1 GTCAAACCCCTAAT-ATGTAATG
52643 GT
1 GT
52645 GAAATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
21 11 0.30
22 8 0.22
23 18 0.49
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (22 bp):
GTCAAACCCCTAATATGTAATG
Found at i:52690 original size:87 final size:86
Alignment explanation
Indices: 52564--52874 Score: 410
Period size: 87 Copynumber: 3.6 Consensus size: 86
52554 GGTCAAACTG
* * * * *
52564 TAAAGCATGATTAGTCAAACCCCTACTAGTAATGGGATCAAACCTCAAATTGTAATGGTCAAACC
1 TAAAACATGATTAGGCAAA-CCCTACTAGTAATGGGATCAAACCCCAAATCGTAATAGTCAAACC
*
52629 CCTAATCATGTATGGTGAAATT
65 CCTAATCATGTATAGTGAAATT
* * *
52651 TAAAACATGATTAGGCAAACCCTTACTAATATTAGGATCAAACCCCAAATCGTAATAGTCAAA-C
1 TAAAACATGATTAGGCAAACCC-TACTAGTAATGGGATCAAACCCCAAATCGTAATAGTCAAACC
*
52715 CATAAATCATGTATAGTGAAATT
65 CCT-AATCATGTATAGTGAAATT
*
52738 TAAAGA-ATGATTAGGCAAACCCATACTAGTAATGGGATCAAACCCCAAATCATAATAGTCAAAC
1 TAAA-ACATGATTAGGCAAACCC-TACTAGTAATGGGATCAAACCCCAAATCGTAATAGTCAAAC
* *
52802 CCCAAATCATGTATAGTGAAAAT
64 CCCTAATCATGTATAGTGAAATT
* * *
52825 TAAAGCATGATTAGACAAACTCCTACTAGTAATGGGATAAAACCCCAAAT
1 TAAAACATGATTAGGCAAAC-CCTACTAGTAATGGGATCAAACCCCAAAT
52875 TAGGTGGGTG
Statistics
Matches: 197, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
86 6 0.03
87 186 0.94
88 5 0.03
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (86 bp):
TAAAACATGATTAGGCAAACCCTACTAGTAATGGGATCAAACCCCAAATCGTAATAGTCAAACCC
CTAATCATGTATAGTGAAATT
Found at i:52801 original size:174 final size:175
Alignment explanation
Indices: 52515--52874 Score: 472
Period size: 174 Copynumber: 2.1 Consensus size: 175
52505 ATCCATTGTG
* * * * * * *
52515 AAACCCCAAATCTTAATGGTCGAACTACAAATCATGTACGGTCAAACTGTAAAGCATGATTAGTC
1 AAACCCCAAATCGTAATAGTCAAACCACAAATCATGTACAGTCAAACTGTAAAGAATGATTAGGC
* * ** * * *
52580 AAACCCCTACTAGTAATGGGATCAAACCTCAAATTGTAATGGTCAAACCCCTAATCATGTATGGT
66 AAACCCATACTAGTAATGGGATCAAACCCCAAATCATAATAGTCAAACCCCAAATCATGTATAGT
* * * *
52645 GAAATTTAAAACATGATTAGGCAAAC-CCTTACTAATATTAGGATC
131 GAAAATTAAAACATGATTAGACAAACTCC-TACTAATAATAGGATA
* * * *
52690 AAACCCCAAATCGTAATAGTCAAACCATAAATCATGTATAGTGAAA-TTTAAAGAATGATTAGGC
1 AAACCCCAAATCGTAATAGTCAAACCACAAATCATGTACAGTCAAACTGTAAAGAATGATTAGGC
52754 AAACCCATACTAGTAATGGGATCAAACCCCAAATCATAATAGTCAAACCCCAAATCATGTATAGT
66 AAACCCATACTAGTAATGGGATCAAACCCCAAATCATAATAGTCAAACCCCAAATCATGTATAGT
* * *
52819 GAAAATTAAAGCATGATTAGACAAACTCCTACTAGTAATGGGATA
131 GAAAATTAAAACATGATTAGACAAACTCCTACTAATAATAGGATA
52864 AAACCCCAAAT
1 AAACCCCAAAT
52875 TAGGTGGGTG
Statistics
Matches: 159, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
174 119 0.75
175 40 0.25
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (175 bp):
AAACCCCAAATCGTAATAGTCAAACCACAAATCATGTACAGTCAAACTGTAAAGAATGATTAGGC
AAACCCATACTAGTAATGGGATCAAACCCCAAATCATAATAGTCAAACCCCAAATCATGTATAGT
GAAAATTAAAACATGATTAGACAAACTCCTACTAATAATAGGATA
Found at i:52995 original size:20 final size:21
Alignment explanation
Indices: 52958--53025 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 21
52948 TTTAACGTGG
**
52958 TTTGACTATTAAGTTTTG-GA
1 TTTGACTATTAAACTTTGAGA
*
52978 TTTGATTATTAAACTTTGAGA
1 TTTGACTATTAAACTTTGAGA
* * *
52999 TTTGCCTATCAAA-TTTTATGA
1 TTTGACTATTAAACTTTGA-GA
53020 TTTGAC
1 TTTGAC
53026 ATGTACAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 19 0.50
21 19 0.50
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (21 bp):
TTTGACTATTAAACTTTGAGA
Found at i:59217 original size:2 final size:2
Alignment explanation
Indices: 59205--59238 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
59195 CTTCTTGCAT
59205 TA TA T- TA 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 TA TA TA TA T
59239 TAATATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:64639 original size:169 final size:166
Alignment explanation
Indices: 64363--64681 Score: 410
Period size: 169 Copynumber: 1.9 Consensus size: 166
64353 GATTTATGGG
** * * * *
64363 TAATTATTTGATACATTGGCGGTATAAATTTTGGATTCTACGGGTTGTGAAGTTGATACATGTCT
1 TAATTATTTGATACACCGGCGGTATAAATTTTGGACTCCACGGGTTGTGAAGTTGACACATGTCA
* *
64428 ATTTTCTGAATTAATTACATTTTAAATATTTCAATCTAGTCCCT-ATGGACACATATCACCCTTC
66 ATTTTCTGAATCAATTACATTTTAAATATTTCAATCTAGTCCCTAAAGGACACATATCACCCTTC
* *
64492 AAGATCTGTTTGTGCAGTCTATATTATATATATGAT
131 AAGATCCGCTTGTGCAGTCTATATTATATATATGAT
* *
64528 TAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAATGGGTTGTGGAGTTGACACAT
1 TAATTATTTGATACACCGGCGGTATAAATTTTGGACTCCAC----GGGTTGTGAAGTTGACACAT
* * * *
64593 GTCCAATTTT-TTAATCAATTA-AGTTTTAAATATTTCAATTTAGTCCCTAAAGGACACGTGTCA
62 GT-CAATTTTCTGAATCAATTACA-TTTTAAATATTTCAATCTAGTCCCTAAAGGACACATATCA
*
64656 CCCTTCAAGATCCGCTTGTGTAGTCT
125 CCCTTCAAGATCCGCTTGTGCAGTCT
64682 GCTAAACTCC
Statistics
Matches: 130, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
165 36 0.28
168 1 0.01
169 53 0.41
170 40 0.31
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (166 bp):
TAATTATTTGATACACCGGCGGTATAAATTTTGGACTCCACGGGTTGTGAAGTTGACACATGTCA
ATTTTCTGAATCAATTACATTTTAAATATTTCAATCTAGTCCCTAAAGGACACATATCACCCTTC
AAGATCCGCTTGTGCAGTCTATATTATATATATGAT
Found at i:87116 original size:12 final size:12
Alignment explanation
Indices: 87099--87125 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
87089 GTATTAAAAA
87099 AAAAGGAAATTG
1 AAAAGGAAATTG
87111 AAAAGGAAATTG
1 AAAAGGAAATTG
87123 AAA
1 AAA
87126 TGTCCATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (12 bp):
AAAAGGAAATTG
Found at i:89160 original size:13 final size:13
Alignment explanation
Indices: 89142--89171 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
89132 AGGAAATTTT
*
89142 TTATTTTTTTTAA
1 TTATTTTTTATAA
89155 TTATTTTTTATAA
1 TTATTTTTTATAA
89168 TTAT
1 TTAT
89172 ATTGAATCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTTTTTATAA
Found at i:90400 original size:17 final size:16
Alignment explanation
Indices: 90347--90396 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
90337 TCACCCCCCG
90347 GATCACTAGTGATCTAA
1 GATCACTAGTGATC-AA
*
90364 GATCACCAGTGATGCAA
1 GATCACTAGTGAT-CAA
*
90381 GATCACTGGTGATCAA
1 GATCACTAGTGATCAA
90397 AGATTACATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (16 bp):
GATCACTAGTGATCAA
Found at i:92251 original size:79 final size:79
Alignment explanation
Indices: 92090--92288 Score: 274
Period size: 79 Copynumber: 2.5 Consensus size: 79
92080 TTGGGTTTGG
* ** *
92090 GATCCGAAATGGGCCTTGAAATGTGTTCATTTATTG-ATTATCCATGATGGGGTCTGATGTCCAA
1 GATCCGAAATGGGCCTTGAAATGGGTTCATTCCTTGTTTTATCCATGATGGGGTCTGATGTCCAA
*
92154 AAAATAATCCGATG
66 AAAATAATCCGATA
* * * * * **
92168 GATCCGAAATGGGACTTGAAATGGGTTCATTCCTTGTTTTATCCATTATTGGGTTTGGTGTCCGC
1 GATCCGAAATGGGCCTTGAAATGGGTTCATTCCTTGTTTTATCCATGATGGGGTCTGATGTCCAA
92233 AAAATAATCCGATA
66 AAAATAATCCGATA
*
92247 GATCCAAAATGGGCCTTGAAATGGGTTCATTCCTTGTTTTAT
1 GATCCGAAATGGGCCTTGAAATGGGTTCATTCCTTGTTTTAT
92289 GATTATCCAC
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
78 32 0.30
79 74 0.70
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (79 bp):
GATCCGAAATGGGCCTTGAAATGGGTTCATTCCTTGTTTTATCCATGATGGGGTCTGATGTCCAA
AAAATAATCCGATA
Done.