Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019228.1 Corchorus olitorius cultivar O-4 contig19261, 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: 97673
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:762 original size:13 final size:13
Alignment explanation
Indices: 744--843 Score: 71
Period size: 13 Copynumber: 7.5 Consensus size: 13
734 AAAGTCAACA
744 GATGACGTGGCAG
1 GATGACGTGGCAG
757 GATGAC-TGGTCAACG
1 GATGACGTGG-C-A-G
* *
772 GGTGACGTGGCAA
1 GATGACGTGGCAG
*
785 GATGATGTGGCAG
1 GATGACGTGGCAG
*
798 GATGAC-TAGTCAACG
1 GATGACGT-GGC-A-G
*
813 GGTGACGTGGCA-
1 GATGACGTGGCAG
825 GATGACGTGGCAG
1 GATGACGTGGCAG
*
838 GTTGAC
1 GATGAC
844 TCGGTCAACA
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
12 15 0.22
13 29 0.43
14 4 0.06
15 15 0.22
16 4 0.06
ACGTcount: A:0.24, C:0.16, G:0.41, T:0.19
Consensus pattern (13 bp):
GATGACGTGGCAG
Found at i:788 original size:41 final size:40
Alignment explanation
Indices: 742--852 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 40
732 TCAAAGTCAA
742 CAGATGACGTGGCAGGATGACTGGTCAACGGGTGACGTGG
1 CAGATGACGTGGCAGGATGACTGGTCAACGGGTGACGTGG
* *
782 CAAGATGATGTGGCAGGATGACTAGTCAACGGGTGACGTGG
1 C-AGATGACGTGGCAGGATGACTGGTCAACGGGTGACGTGG
*
823 CAGATGACGTGGCAGGTTGACTCGGTCAAC
1 CAGATGACGTGGCAGGATGACT-GGTCAAC
853 AGTCAACACG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 20 0.31
41 44 0.69
ACGTcount: A:0.24, C:0.18, G:0.39, T:0.19
Consensus pattern (40 bp):
CAGATGACGTGGCAGGATGACTGGTCAACGGGTGACGTGG
Found at i:10066 original size:2 final size:2
Alignment explanation
Indices: 10059--10083 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10049 TTATTTTACT
10059 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 T
10084 GTATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11207 original size:24 final size:24
Alignment explanation
Indices: 11148--11216 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
11138 TTTTTCTGAA
* * *
11148 AAATAAATATAGTTATCAAATTAT
1 AAATATATATATTTATCAAATCAT
*
11172 AAATATAAATATTTATCAAATCAT
1 AAATATATATATTTATCAAATCAT
* * *
11196 ATATATATATATATATTAAAT
1 AAATATATATATTTATCAAAT
11217 ATAGTTATCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (24 bp):
AAATATATATATTTATCAAATCAT
Found at i:14706 original size:9 final size:9
Alignment explanation
Indices: 14676--14709 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
14666 GAGATCGAAG
*
14676 AGAGAGAAA
1 AGAGAGAGA
*
14685 AGAAAGAGA
1 AGAGAGAGA
14694 AGAGAGAGA
1 AGAGAGAGA
14703 AGAGAGA
1 AGAGAGA
14710 AACTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (9 bp):
AGAGAGAGA
Found at i:15000 original size:31 final size:29
Alignment explanation
Indices: 14932--15010 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
14922 GATCATTTAT
* * *
14932 AAAACGTTTGGTACTAAATTAGACGAAAT
1 AAAAGGTTTGGTACCAAATTAGACGAAAC
**
14961 AAAAGGTTTGGTACCAAATTAGTATTAAAC
1 AAAAGGTTTGGTACCAAATTAG-ACGAAAC
14991 ATAAAGGTTTGGTACCAAAT
1 A-AAAGGTTTGGTACCAAAT
15011 CGAAATTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 20 0.47
30 5 0.12
31 18 0.42
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (29 bp):
AAAAGGTTTGGTACCAAATTAGACGAAAC
Found at i:15673 original size:12 final size:12
Alignment explanation
Indices: 15656--15680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15646 TTTGCAAGTG
15656 AATAAATTTTCA
1 AATAAATTTTCA
15668 AATAAATTTTCA
1 AATAAATTTTCA
15680 A
1 A
15681 CTTTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAAATTTTCA
Found at i:18752 original size:169 final size:169
Alignment explanation
Indices: 18473--18808 Score: 629
Period size: 169 Copynumber: 2.0 Consensus size: 169
18463 GATTGAAAAT
* *
18473 CAAACAGACTGTACATGTCTAAACAATCATATAAACTGTACACTCAAAATATCATCAAAGAATTT
1 CAAACAGACTGTACATGTCTAAACAATCATACAAACTGTACACTCAAAATATCATCAAAGAATCT
18538 AATACTGTATATATGTATATATGAAGGAAACCTCTTTCATCTATTTGAATGTATACATGG-TCTC
66 AATACTGTATATATGTATATATGAAGGAAACCTCTTTCATCTATTTGAATGTATACA-GGCTCTC
*
18602 TATACTGCTGTTTTGGCAACTCTTTTGATTTCAAAGTAAC
130 TATACTGCAGTTTTGGCAACTCTTTTGATTTCAAAGTAAC
18642 CAAACAGACTGTACATGTCTAAACAATCATACAAACTGTACACTCAAAATATCATCAAAGAATCT
1 CAAACAGACTGTACATGTCTAAACAATCATACAAACTGTACACTCAAAATATCATCAAAGAATCT
18707 AATACTGTATATATGTATATATGAAGGAAACCTCTTTCATCTATTTGAATGTATACAGGCTCTCT
66 AATACTGTATATATGTATATATGAAGGAAACCTCTTTCATCTATTTGAATGTATACAGGCTCTCT
18772 ATACTGCAGTTTTGGCAACTCTTTTGATTTCAAAGTA
131 ATACTGCAGTTTTGGCAACTCTTTTGATTTCAAAGTA
18809 CCTGATTTGT
Statistics
Matches: 163, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
168 2 0.01
169 161 0.99
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (169 bp):
CAAACAGACTGTACATGTCTAAACAATCATACAAACTGTACACTCAAAATATCATCAAAGAATCT
AATACTGTATATATGTATATATGAAGGAAACCTCTTTCATCTATTTGAATGTATACAGGCTCTCT
ATACTGCAGTTTTGGCAACTCTTTTGATTTCAAAGTAAC
Found at i:19029 original size:44 final size:44
Alignment explanation
Indices: 18979--19066 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
18969 ATATAAAGAT
18979 AAACAAAAAATAAAAGGATGTGAGAGAGAGGAAAATACTGAATC
1 AAACAAAAAATAAAAGGATGTGAGAGAGAGGAAAATACTGAATC
19023 AAACAAAAAATAAAAGGATGTGAGAGAGAGGAAAATACTGAATC
1 AAACAAAAAATAAAAGGATGTGAGAGAGAGGAAAATACTGAATC
19067 TCTATACGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.57, C:0.07, G:0.23, T:0.14
Consensus pattern (44 bp):
AAACAAAAAATAAAAGGATGTGAGAGAGAGGAAAATACTGAATC
Found at i:19914 original size:28 final size:28
Alignment explanation
Indices: 19883--19940 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
19873 AAGATAAGAA
19883 ACTAGATAAGAAAATGATCAGAGAATTT
1 ACTAGATAAGAAAATGATCAGAGAATTT
*
19911 ACTAGATAAGAAAATTATCAGAGAATTT
1 ACTAGATAAGAAAATGATCAGAGAATTT
19939 AC
1 AC
19941 CTCCTCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.26
Consensus pattern (28 bp):
ACTAGATAAGAAAATGATCAGAGAATTT
Found at i:20596 original size:18 final size:18
Alignment explanation
Indices: 20573--20609 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20563 GAAGGACAGA
20573 GCATCCAGTTCAGTAAGT
1 GCATCCAGTTCAGTAAGT
20591 GCATCCAGTTCAGTAAGT
1 GCATCCAGTTCAGTAAGT
20609 G
1 G
20610 TAAGTTCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (18 bp):
GCATCCAGTTCAGTAAGT
Found at i:21199 original size:17 final size:18
Alignment explanation
Indices: 21163--21205 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
21153 AAGTTTCCAG
21163 AAACAAATGAATCACACAA
1 AAACAAATGAAT-ACACAA
21182 AAACAAATGAAT-CACAA
1 AAACAAATGAATACACAA
*
21199 ACACAAA
1 AAACAAA
21206 CACAAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.48
19 12 0.52
ACGTcount: A:0.65, C:0.21, G:0.05, T:0.09
Consensus pattern (18 bp):
AAACAAATGAATACACAA
Found at i:24417 original size:31 final size:30
Alignment explanation
Indices: 24382--24466 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
24372 GGGAGGTCCA
* * *
24382 TGTACTCTACAAAAATGTTCAATTTCATCTC
1 TGTACTC-ACAAAAATGGTCAATTTAATCCC
*
24413 TGTACTCA-AAAAGTGGTCAATTTAATCCC
1 TGTACTCACAAAAATGGTCAATTTAATCCC
* *
24442 TGTATTCACAAAATTGGGTCAATTT
1 TGTACTCACAAAAAT-GGTCAATTT
24467 CGTTCTTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 24 0.52
30 6 0.13
31 16 0.35
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (30 bp):
TGTACTCACAAAAATGGTCAATTTAATCCC
Found at i:32441 original size:23 final size:23
Alignment explanation
Indices: 32415--32460 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
32405 CTGTTTTTAC
*
32415 CCAATTCTCTATTAAAATAGTGG
1 CCAATTCTCTATTAAAACAGTGG
*
32438 CCAATTCTGTATTAAAACAGTGG
1 CCAATTCTCTATTAAAACAGTGG
32461 ATGGATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (23 bp):
CCAATTCTCTATTAAAACAGTGG
Found at i:35693 original size:78 final size:78
Alignment explanation
Indices: 35602--35762 Score: 286
Period size: 78 Copynumber: 2.1 Consensus size: 78
35592 AGATTTATAG
* *
35602 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
*
35667 TACCATTTTACTA
66 TACCATTTAACTA
*
35680 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATTTAATATCTTTATAACTATTTCAGTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
35745 TACCATTTAACTA
66 TACCATTTAACTA
35758 TTTTA
1 TTTTA
35763 ACTAGAAAAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.51
Consensus pattern (78 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
TACCATTTAACTA
Found at i:36321 original size:23 final size:23
Alignment explanation
Indices: 36295--36352 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
36285 GTCGAGTCAA
36295 TTGGATTTTTCGTCATTTGGGTT
1 TTGGATTTTTCGTCATTTGGGTT
36318 TTGGATTTTTCGTCATTTGGGTT
1 TTGGATTTTTCGTCATTTGGGTT
36341 TTGGATTTTTCG
1 TTGGATTTTTCG
36353 AGTCAATTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.09, C:0.09, G:0.26, T:0.57
Consensus pattern (23 bp):
TTGGATTTTTCGTCATTTGGGTT
Found at i:37164 original size:4 final size:4
Alignment explanation
Indices: 37155--37216 Score: 124
Period size: 4 Copynumber: 15.5 Consensus size: 4
37145 GAAGAAGAGG
37155 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
37203 ATGT ATGT ATGT AT
1 ATGT ATGT ATGT AT
37217 AGGACAAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:39633 original size:22 final size:22
Alignment explanation
Indices: 39605--39648 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
39595 TCGATTTAGT
39605 GTCTTATTCTTCCAAATCTCCA
1 GTCTTATTCTTCCAAATCTCCA
39627 GTCTTATTCTTCCAAATCTCCA
1 GTCTTATTCTTCCAAATCTCCA
39649 ATCCTCTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.41
Consensus pattern (22 bp):
GTCTTATTCTTCCAAATCTCCA
Found at i:56735 original size:32 final size:32
Alignment explanation
Indices: 56699--56759 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
56689 ATATTTTAAA
* * *
56699 GGGCTTGGACAAGAATTTTAAGCCCGTTTGAT
1 GGGCTTGGACAAAAATATCAAGCCCGTTTGAT
*
56731 GGGCTTTGACAAAAATATCAAGCCCGTTT
1 GGGCTTGGACAAAAATATCAAGCCCGTTT
56760 ATTAAATGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (32 bp):
GGGCTTGGACAAAAATATCAAGCCCGTTTGAT
Found at i:57029 original size:14 final size:13
Alignment explanation
Indices: 56993--57031 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
56983 ATTTTATATT
*
56993 TATAATTATATTTA
1 TATAATTA-ATTAA
57007 TATAATTAATTAA
1 TATAATTAATTAA
57020 TATAATTTAATT
1 TATAA-TTAATT
57032 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATAATTAATTAA
Found at i:57915 original size:11 final size:10
Alignment explanation
Indices: 57894--57932 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
57884 CCCTTTCCTA
*
57894 TATATATAAT
1 TATAAATAAT
57904 TATCAAATAAT
1 TAT-AAATAAT
57915 TATAAATTAAT
1 TATAAA-TAAT
57926 TATAAAT
1 TATAAAT
57933 TTGTTATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (10 bp):
TATAAATAAT
Found at i:57939 original size:11 final size:11
Alignment explanation
Indices: 57900--57933 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
57890 CCTATATATA
57900 TAATTATCAAA-
1 TAATTAT-AAAT
57911 TAATTATAAAT
1 TAATTATAAAT
57922 TAATTATAAAT
1 TAATTATAAAT
57933 T
1 T
57934 TGTTATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:58654 original size:2 final size:2
Alignment explanation
Indices: 58641--58688 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
58631 ACAACTATTA
* *
58641 AT AT AGT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT GT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58684 AT AT A
1 AT AT A
58689 ACAAATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59866 original size:437 final size:434
Alignment explanation
Indices: 58912--59930 Score: 1216
Period size: 437 Copynumber: 2.3 Consensus size: 434
58902 TCAAAATCAT
** * *
58912 AAAATTTCAAAAGCATTTTTTAGAATTGAAATATAAAAATT-AGCTTTTGAGTCTTTCATGAAAG
1 AAAATTTCGGAAGCATTTTTTAGAATTGAAACATAAAAATTGA-CTTTTGAGT-TCTCATGAAAG
* * * *
58976 TTGTAGATCATAAAATTACCTTTTAATAGACACATGAGTTACCTTAATTGGACAAATAGAACAAA
64 TTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAA-AAA
* * *
59041 AAAATAAAAAAATTGAAGTGTTAAATCGAGTAAGATAGAATTTGAAAAGGACTAAGTAGCATAAA
128 AAAATAAAAAAA-TAAAGTCTTAAAGCGAGTAAGATAGAATTTGAAAAGGACTAAGTAGCATAAA
* * * * *
59106 ATAGAAAAGTATGAGGGTGATTTGATAACTAATTCAAATAAGAAAATATTTGTTAATGGAGATCT
192 ATAGAAAAGAATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATATGTTAATGGAGATCT
* *
59171 TAAAACATAAAAATTCTCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGATTC
257 TAAAACATAAAAATTCTCTTTTGAACCCTTCAAGAAACTCGTAGATCAAATTAACTTTCGGATCC
** * * * *
59236 TTCATGAAAATCGTGGATTATACAGTAACCTTTTAACCGACAATTGAATAACTTTAATTGGACAT
322 TTCATGAAAATCGTAAATCATACAATAACCTTTTAACCGACAATTCAATAACTTCAATTGGACAT
* * * * * *
59301 TTGGATCGAAAATTATATGGTATTAAATAGACCAACAATCGAAATAAAC
387 GTGGAACAAAAATTATACGATAATAAATAGACCAACAATC-AAATAAAC
* * * *
59350 -AAATTTAGGAAGCATATTTTT-GAATTGAAACATAAAAATCTG-CTCTTGAATCCTTCATGAAA
1 AAAATTTCGGAAGCAT-TTTTTAGAATTGAAACATAAAAAT-TGACTTTTGAGTTC-TCATGAAA
* *
59412 GTTATAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAAAAA
63 GTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAAAAA
* * * * *
59477 AGAATAAAAAAATAAAG-CTT-AAGCGTTAGATTAAGATAGAATTTGTAAATGACTAAGTTGTAT
128 AAAATAAAAAAATAAAGTCTTAAAGCG--AG--TAAGATAGAATTTGAAAAGGACTAAGTAGCAT
* *
59540 AAAGTAGAAAAGAATGA-GGTCATTTGATAAATAATCCAAATAAGAAAATGTATGTTAATGGAGA
189 AAAATAGAAAAGAATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATATGTTAATGGAGA
* *
59604 TCTTGAAACATAAAAATT-TCCTTTTTGAACCCTTCAAGAAACTCGTAGATCAAAATTAGCTTTC
254 TCTTAAAACATAAAAATTCT-C-TTTTGAACCCTTCAAGAAACTCGTAGATC-AAATTAACTTTC
* * * * * *
59668 GGGTCCTTCATGGAAGTTGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCAATT
316 GGATCCTTCATGAAAATCGTAAATCATACAATAACCTTTTAACCGACAATTCAATAACTTCAATT
**
59733 GGACATGT-GAACAAAAAATTATACGATAATAAATTA-ACCGGCAAT-AAA-AACCAC
381 GGACATGTGGAAC-AAAAATTATACGATAATAAA-TAGACCAACAATCAAATAA--AC
** * * *
59787 AAAATTTCGGAAGCATTTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTTCTAATGAAAATT
1 AAAATTTCGGAAGCATTTTTTAGAATTGAAACATAAAAATTGACTTTTGAGTTCTCATGAAAGTT
* * *
59852 GTAGATCGTGAAATTATCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAAAAAAAA
66 GTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAG-AAAAAAA
*
59917 AATACAAAAATAAA
130 AATAAAAAAATAAA
59931 AGGCAACGCG
Statistics
Matches: 493, Mismatches: 69, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
433 4 0.01
434 2 0.00
435 9 0.02
436 77 0.16
437 244 0.49
438 155 0.31
439 2 0.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (434 bp):
AAAATTTCGGAAGCATTTTTTAGAATTGAAACATAAAAATTGACTTTTGAGTTCTCATGAAAGTT
GTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAAAAAAAA
ATAAAAAAATAAAGTCTTAAAGCGAGTAAGATAGAATTTGAAAAGGACTAAGTAGCATAAAATAG
AAAAGAATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATATGTTAATGGAGATCTTAAA
ACATAAAAATTCTCTTTTGAACCCTTCAAGAAACTCGTAGATCAAATTAACTTTCGGATCCTTCA
TGAAAATCGTAAATCATACAATAACCTTTTAACCGACAATTCAATAACTTCAATTGGACATGTGG
AACAAAAATTATACGATAATAAATAGACCAACAATCAAATAAAC
Found at i:61374 original size:22 final size:21
Alignment explanation
Indices: 61349--61408 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 21
61339 AAAATGATAT
*
61349 GGCACGACACGACCCACGTGTC
1 GGCAC-ACACGACCCACGTGCC
61371 GGCACAGCACGACCCACGTGCC
1 GGCACA-CACGACCCACGTGCC
61393 GACGCA-ACACGACCCA
1 G--GCACACACGACCCA
61409 TTTTTAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 1 0.03
22 29 0.85
23 1 0.03
24 3 0.09
ACGTcount: A:0.27, C:0.43, G:0.25, T:0.05
Consensus pattern (21 bp):
GGCACACACGACCCACGTGCC
Found at i:73227 original size:21 final size:21
Alignment explanation
Indices: 73201--73240 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
73191 TTATGTTCTA
* *
73201 ATAATCTCATTTGTACAGTAC
1 ATAATCTAATCTGTACAGTAC
73222 ATAATCTAATCTGTACAGT
1 ATAATCTAATCTGTACAGT
73241 GTAATTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
ATAATCTAATCTGTACAGTAC
Found at i:73257 original size:17 final size:17
Alignment explanation
Indices: 73235--73275 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
73225 ATCTAATCTG
73235 TACAGTGTAATTTCATC
1 TACAGTGTAATTTCATC
73252 TACAGTGTAATTTCATC
1 TACAGTGTAATTTCATC
73269 TGACAGT
1 T-ACAGT
73276 TGCTAAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (17 bp):
TACAGTGTAATTTCATC
Found at i:75516 original size:60 final size:60
Alignment explanation
Indices: 75445--75591 Score: 179
Period size: 60 Copynumber: 2.4 Consensus size: 60
75435 AATATTTGTT
* **
75445 AAAATGCTTAAATAAGGACCTGA-TCTTTTAATTTGGCCAAATAAGGCCCTAATGTTTACC
1 AAAATGCTTAAATAAGG-CCTGAGTCTTTTAATTTGGCCAAATAAGGACCTAACATTTACC
* * * * *
75505 AAAATACTTAAATAAGGGCTCAGTCTTTTAATTTGGCCAAATAAGGATCTAACATTTGCC
1 AAAATGCTTAAATAAGGCCTGAGTCTTTTAATTTGGCCAAATAAGGACCTAACATTTACC
*
75565 AAAATGCTCAAATAAGGGCCTGGAGTC
1 AAAATGCTTAAATAA-GGCCT-GAGTC
75592 GAAAATAATT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
59 3 0.04
60 61 0.85
61 4 0.06
62 4 0.06
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (60 bp):
AAAATGCTTAAATAAGGCCTGAGTCTTTTAATTTGGCCAAATAAGGACCTAACATTTACC
Found at i:76621 original size:60 final size:60
Alignment explanation
Indices: 76518--76679 Score: 227
Period size: 60 Copynumber: 2.7 Consensus size: 60
76508 ACTAATGACA
* *
76518 GGCCCTTATTTGAGCATTTTCGATAACATTAGACCCTTGTTTGGCCAAATAAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACACTAGACCCTTATTTGGCCAAATAAAAAGATCG
* * * *
76578 GGCCCTTATTTGAGCATTTTCGATAACGCTAGGCCTTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACACTAGACCCTTATTTGGCCAAATAAAAAGATCG
* ***
76638 GGCCCTTATTTGAGCATTTT-GGTAATGTTAGACCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCGATAACACTAGACCCTTATTTG
76680 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 17 0.19
60 74 0.81
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACACTAGACCCTTATTTGGCCAAATAAAAAGATCG
Found at i:76646 original size:29 final size:29
Alignment explanation
Indices: 76551--76649 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 29
76541 TAACATTAGA
* *
76551 CCCTTGTTTGGCCAAATAAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
** * * *
76580 CCCTTATTTGAG-CATTTTCGATAACGCT-AGG
1 CCCTTATTTG-GCCAAATT--A-AAAGATCGGG
*
76611 CCTTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
76640 CCCTTATTTG
1 CCCTTATTTG
76650 AGCATTTTGG
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
28 4 0.08
29 24 0.48
30 2 0.04
31 16 0.32
32 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCGGG
Found at i:79448 original size:18 final size:18
Alignment explanation
Indices: 79414--79456 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
79404 AGCTGATGAG
*
79414 CAGGGTGGTGCTGCTGAT
1 CAGGGTGGTGCTACTGAT
79432 CAGGGTGGCT-CTACTGAT
1 CAGGGTGG-TGCTACTGAT
*
79450 CAAGGTG
1 CAGGGTG
79457 TGGCCCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.16, C:0.19, G:0.40, T:0.26
Consensus pattern (18 bp):
CAGGGTGGTGCTACTGAT
Found at i:79946 original size:25 final size:25
Alignment explanation
Indices: 79912--79960 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
79902 AACTTTTGCT
79912 AGTTGAATCAAACTACTGACATCTG
1 AGTTGAATCAAACTACTGACATCTG
*
79937 AGTTGAATCAAACTATTGACATCT
1 AGTTGAATCAAACTACTGACATCT
79961 TCGGTCGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (25 bp):
AGTTGAATCAAACTACTGACATCTG
Found at i:88466 original size:149 final size:150
Alignment explanation
Indices: 88272--88547 Score: 482
Period size: 149 Copynumber: 1.8 Consensus size: 150
88262 GCAATATTAC
* *
88272 CATTAGCACTAGCAGCACCTAGTTGTCTCTTATGTCACCATCTAAAAGTTAATGAGCATTACCCT
1 CATTACCACTAGCAGCACCTAGTTGTCTCTTATGTCACCATCTAAAAGTTAATGAGCATAACCCT
88337 ATACACATTTATATGCTAAATCATGGACATGAAGTTTAAAACTACCATTTTTCATCA-AAAACAC
66 ATACACATTTATATGCTAAATCATGGACATGAAGTTTAAAACTACCATTTTTCATCACAAAACAC
88401 ACTGAATTAAAGCAGTGCAA
131 ACTGAATTAAAGCAGTGCAA
* **
88421 CATTACCATTAGCAGCACCTAGTTGTCTCTTATGTCACTGTCTAAAAGTTAATGAGCATAACCCT
1 CATTACCACTAGCAGCACCTAGTTGTCTCTTATGTCACCATCTAAAAGTTAATGAGCATAACCCT
* *
88486 ATACATATTTATATGCTAAATCGTGGACATGAAGTTTAAAACTACCATTTTTCATCACAAAA
66 ATACACATTTATATGCTAAATCATGGACATGAAGTTTAAAACTACCATTTTTCATCACAAAA
88548 AAAAAAAAAA
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
149 115 0.97
150 4 0.03
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (150 bp):
CATTACCACTAGCAGCACCTAGTTGTCTCTTATGTCACCATCTAAAAGTTAATGAGCATAACCCT
ATACACATTTATATGCTAAATCATGGACATGAAGTTTAAAACTACCATTTTTCATCACAAAACAC
ACTGAATTAAAGCAGTGCAA
Done.