Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016895.1 Corchorus olitorius cultivar O-4 contig16928, 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: 29622
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:2697 original size:14 final size:14
Alignment explanation
Indices: 2678--2724 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2668 TTTTATAATT
*
2678 ATTTTATTTTTACC
1 ATTTTATTTTTAAC
* *
2692 ATTTTA-ATTTAAA
1 ATTTTATTTTTAAC
*
2705 ATTTTATTTTTAGC
1 ATTTTATTTTTAAC
2719 ATTTTA
1 ATTTTA
2725 CTATTTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (14 bp):
ATTTTATTTTTAAC
Found at i:6546 original size:8 final size:8
Alignment explanation
Indices: 6525--6555 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
6515 AAGTTAAAAC
6525 TAATATAGA
1 TAATATA-A
6534 TAATATAA
1 TAATATAA
6542 TAATATAA
1 TAATATAA
6550 TAATAT
1 TAATAT
6556 GGAAAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
TAATATAA
Found at i:6752 original size:2 final size:2
Alignment explanation
Indices: 6747--6771 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6737 TTTAGGTCAT
6747 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
6772 GTATGTGTGT
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:11830 original size:26 final size:26
Alignment explanation
Indices: 11794--11846 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
11784 AATCCTGCTA
11794 CATCGCGATCCTCTTTCTCTTCTTTG
1 CATCGCGATCCTCTTTCTCTTCTTTG
11820 CATCGCGATCCTCTTTCTCTTCTTTG
1 CATCGCGATCCTCTTTCTCTTCTTTG
11846 C
1 C
11847 GATTTATGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.08, C:0.36, G:0.11, T:0.45
Consensus pattern (26 bp):
CATCGCGATCCTCTTTCTCTTCTTTG
Found at i:13146 original size:22 final size:22
Alignment explanation
Indices: 13121--13716 Score: 212
Period size: 22 Copynumber: 26.8 Consensus size: 22
13111 GTGTTGTCAC
*
13121 CAAAATTTGATAGGGAGATTAT
1 CAAAATTTCATAGGGAGATTAT
* * * *
13143 CAAAATTTTAAATTGTGAGGTTAT
1 CAAAA-TTT-CATAGGGAGATTAT
* * *
13167 CAAAATTTTATAGAGAGTTTAT
1 CAAAATTTCATAGGGAGATTAT
* * * * *
13189 TAAACTTTCATAGTGTGGTTAT
1 CAAAATTTCATAGGGAGATTAT
* * * *
13211 CAAAATTT--T--GTAAAGTAG
1 CAAAATTTCATAGGGAGATTAT
** *
13229 CAAAATTTCATATAGTGATTAT
1 CAAAATTTCATAGGGAGATTAT
* *
13251 CAAAATTTTATATGGATTAGATTAT
1 CAAAATTTCATA-GG--GAGATTAT
* *
13276 TAAAATTTCATAGGAAGATTAT
1 CAAAATTTCATAGGGAGATTAT
* * * * *
13298 CAAAATTTTATTGTGTGGTTAT
1 CAAAATTTCATAGGGAGATTAT
*
13320 CAAAATTTAATAGGGA-AGTTAT
1 CAAAATTTCATAGGGAGA-TTAT
* *
13342 CAAAATTTCATAGCGAGGTTAT
1 CAAAATTTCATAGGGAGATTAT
* * *
13364 CAGAATTTCATA-AGAAAGTTAT
1 CAAAATTTCATAGGGAGA-TTAT
* * *
13386 CAAAAGTTGATAGCGA-AGTTAT
1 CAAAATTTCATAGGGAGA-TTAT
* * *
13408 CAAAATTTCATAATGGTGGTTAT
1 CAAAATTTCAT-AGGGAGATTAT
13431 CAAAATTTCAT-GAGGACG-TTAT
1 CAAAATTTCATAG-GGA-GATTAT
* * * * *
13453 TAGAATTTCATAAGGAGGTTGT
1 CAAAATTTCATAGGGAGATTAT
* * * *
13475 CAAAAATTTCATAGTGTGCTTAC
1 C-AAAATTTCATAGGGAGATTAT
* * *
13498 CAAAATTTTATAGGTAGGTTAT
1 CAAAATTTCATAGGGAGATTAT
* * * *
13520 AAAAATTTCATAGAGTGGTTAT
1 CAAAATTTCATAGGGAGATTAT
* * *
13542 AAAAATTTCATAAGGATCAGGTTAT
1 CAAAATTTCAT-AGG--GAGATTAT
** *
13567 CAAAATTTCATCTGAAGGA-TAT
1 CAAAATTTCATAGGGA-GATTAT
* * * *
13589 CCAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATAGGGAGATTAT
* * *
13611 CAAAATTTCTTAGCGAGGTTAT
1 CAAAATTTCATAGGGAGATTAT
* *
13633 CAAAATTTCAT-GATGAGGTTAT
1 CAAAATTTCATAG-GGAGATTAT
* *
13655 CAACATTAT-ATAAGGG-G-GTAT
1 CAAAATT-TCAT-AGGGAGATTAT
* * *
13676 CAAAATTTCATAGTGAGCTCAT
1 CAAAATTTCATAGGGAGATTAT
13698 CAAAATTTTTCATAGGGAG
1 CAAAA--TTTCATAGGGAG
13717 TTTACCATAG
Statistics
Matches: 420, Mismatches: 120, Indels: 66
0.69 0.20 0.11
Matches are distributed among these distances:
18 10 0.02
20 6 0.01
21 17 0.04
22 279 0.66
23 46 0.11
24 30 0.07
25 32 0.08
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGATTAT
Found at i:13342 original size:44 final size:44
Alignment explanation
Indices: 13229--13687 Score: 281
Period size: 44 Copynumber: 10.3 Consensus size: 44
13219 TGTAAAGTAG
* * *
13229 CAAAATTTCATATAGTG-A-TTATCAAAATTTTATATGGATTAGATTAT
1 CAAAATTTCATA-AG-GAAGTTATCAAAATTTCATA--GAGT-GGTTAT
* * * *
13276 TAAAATTTCAT-AGGAAGATTATCAAAATTTTATTGTGTGGTTAT
1 CAAAATTTCATAAGGAAG-TTATCAAAATTTCATAGAGTGGTTAT
* * * *
13320 CAAAATTTAATAGGGAAGTTATCAAAATTTCATAGCGAGGTTAT
1 CAAAATTTCATAAGGAAGTTATCAAAATTTCATAGAGTGGTTAT
* * * * * **
13364 CAGAATTTCATAAGAAAGTTATCAAAAGTTGATAGCGAAGTTAT
1 CAAAATTTCATAAGGAAGTTATCAAAATTTCATAGAGTGGTTAT
**
13408 CAAAATTTCATAATGGTGGTTATCAAAATTTCAT-GAG-GACGTTAT
1 CAAAATTTCATAA-GGAAGTTATCAAAATTTCATAGAGTG--GTTAT
* * * * * * *
13453 TAGAATTTCATAAGGAGGTTGTCAAAAATTTCATAGTGTGCTTAC
1 CAAAATTTCATAAGGAAGTTATC-AAAATTTCATAGAGTGGTTAT
* * *
13498 CAAAATTTTAT-AGGTAGGTTATAAAAATTTCATAGAGTGGTTAT
1 CAAAATTTCATAAGG-AAGTTATCAAAATTTCATAGAGTGGTTAT
* * * *
13542 AAAAATTTCATAAGGATCAGGTTATCAAAATTTCATCTGA-AGGATAT
1 CAAAATTTCATAAGGA--A-GTTATCAAAATTTCAT-AGAGTGGTTAT
* ** * * *
13589 CCAAATTTCAT-AGTGTGGTTATCAAAATTTCTTAGCGAGGTTAT
1 CAAAATTTCATAAG-GAAGTTATCAAAATTTCATAGAGTGGTTAT
* * * * * *
13633 CAAAATTTCATGATGAGGTTATCAACATTAT-ATA-AGGGGGTAT
1 CAAAATTTCATAAGGAAGTTATCAAAATT-TCATAGAGTGGTTAT
13676 CAAAATTTCATA
1 CAAAATTTCATA
13688 GTGAGCTCAT
Statistics
Matches: 326, Mismatches: 66, Indels: 44
0.75 0.15 0.10
Matches are distributed among these distances:
43 18 0.06
44 173 0.53
45 73 0.22
46 4 0.01
47 56 0.17
48 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (44 bp):
CAAAATTTCATAAGGAAGTTATCAAAATTTCATAGAGTGGTTAT
Found at i:13371 original size:66 final size:64
Alignment explanation
Indices: 13121--13705 Score: 295
Period size: 66 Copynumber: 8.8 Consensus size: 64
13111 GTGTTGTCAC
* * * * * *
13121 CAAAATTTGATAGGG-AGATTATCAAAATTTTAAATTGTGAGGTTATCAAAATTTTATAGAGAGT
1 CAAAATTTCATAGGGAAG-TTATCAAAA-TTT-CATAG-GAGGTTATCAAAATTTCATTG-GAGG
13185 TTAT
61 TTAT
* * * ** ** * * * * *
13189 TAAACTTTCATAGTGTGGTTATCAAAATTTTGTA--AAG-TAGCAAAATTTCATATAGTGATTAT
1 CAAAATTTCATAGGGAAGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCAT-TGGAGGTTAT
* * * * * *
13251 CAAAATTTTATATGGATTAGATTATTAAAATTTCATAGGAAGATTATCAAAATTTTATTGTGTGG
1 CAAAATTTCATAGGGA--AG-TTATCAAAATTTCATAGG-AGGTTATCAAAATTTCATTG-GAGG
13316 TTAT
61 TTAT
* * * * *
13320 CAAAATTTAATAGGGAAGTTATCAAAATTTCATAGCGAGGTTATCAGAATTTCATAAGAAAGTTA
1 CAAAATTTCATAGGGAAGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCAT-TGGAGGTTA
13385 T
64 T
* * * * * *
13386 CAAAAGTTGATAGCGAAGTTATCAAAATTTCATAATGGTGGTTATCAAAATTTCATGAGGACGTT
1 CAAAATTTCATAGGGAAGTTATCAAAATTTCAT-A-GGAGGTTATCAAAATTTCAT-TGGAGGTT
13451 AT
63 AT
* * * * * * * * * *
13453 TAGAATTTCATAAGGAGGTTGTCAAAAATTTCATAGTGTGCTTACCAAAATTTTATAGGTAGGTT
1 CAAAATTTCATAGGGAAGTTATC-AAAATTTCATAG-GAGGTTATCAAAATTTCATTGG-AGGTT
13518 AT
63 AT
* * ** * *
13520 AAAAATTTCATAGAGTGGTTATAAAAATTTCATAAGGATCAGGTTATCAAAATTTCATCTGAAGG
1 CAAAATTTCATAGGGAAGTTATCAAAATTTCAT-AGG---AGGTTATCAAAATTTCAT-TGGAGG
*
13585 ATAT
61 TTAT
* * ** *
13589 CCAAATTTCATAGTGTGGTTATCAAAATTTCTTAGCGAGGTTATCAAAATTTCA-TGATGAGGTT
1 CAAAATTTCATAGGGAAGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATTG--GAGGTT
13653 AT
63 AT
* * * *
13655 CAACATTAT-ATAAGGG--GGTATCAAAATTTCATAGTGAGCTCATCAAAATTT
1 CAAAATT-TCAT-AGGGAAGTTATCAAAATTTCATAG-GAGGTTATCAAAATTT
13706 TTCATAGGGA
Statistics
Matches: 400, Mismatches: 90, Indels: 57
0.73 0.16 0.10
Matches are distributed among these distances:
62 28 0.07
63 2 0.00
64 3 0.01
65 43 0.11
66 112 0.28
67 93 0.23
68 35 0.09
69 83 0.21
70 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (64 bp):
CAAAATTTCATAGGGAAGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATTGGAGGTTAT
Found at i:13478 original size:67 final size:67
Alignment explanation
Indices: 13315--13643 Score: 215
Period size: 67 Copynumber: 4.9 Consensus size: 67
13305 TTATTGTGTG
* * * * * * *
13315 GTTATCAAAATTTAATAGGGAAGTTATCAAAATTTCAT-A-GCGAGGTTATCAGAATTTCATAAG
1 GTTATAAAAATTTCATAGAGAGGTTATCAAAATTTCATAATG-GTGGTTATCAAAATTTCATAGG
* *
13378 AAA
65 TAC
* * * * *
13381 GTTATCAAAAGTTGATAGCGAAGTTATCAAAATTTCATAATGGTGGTTATCAAAATTTCATGAGG
1 GTTATAAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGGTGGTTATCAAAATTTCAT-AGG
13446 -AC
65 TAC
* * * * * * *
13448 GTTATTAGAATTTCATA-AGGAGGTTGTCAAAAATTTCATAGT-GTGCTTACCAAAATTTTATAG
1 GTTATAAAAATTTCATAGA-GAGGTTATC-AAAATTTCATAATGGTGGTTATCAAAATTTCATAG
*
13511 GTAG
64 GTAC
* * *
13515 GTTATAAAAATTTCATAGAGTGGTTATAAAAATTTCATAA-GGATCAGGTTATCAAAATTTCATC
1 GTTATAAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGG-T--GGTTATCAAAATTTCATA
* * *
13579 TGAAG
63 GGTAC
* ** * * * *
13584 GATATCCAAATTTCATAGTGTGGTTATCAAAATTTC-TTA-GCGAGGTTATCAAAATTTCAT
1 GTTATAAAAATTTCATAGAGAGGTTATCAAAATTTCATAATG-GTGGTTATCAAAATTTCAT
13644 GATGAGGTTA
Statistics
Matches: 213, Mismatches: 38, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
66 67 0.31
67 78 0.37
68 19 0.09
69 49 0.23
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (67 bp):
GTTATAAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGGTGGTTATCAAAATTTCATAGGT
AC
Found at i:13478 original size:89 final size:88
Alignment explanation
Indices: 13315--13643 Score: 234
Period size: 89 Copynumber: 3.7 Consensus size: 88
13305 TTATTGTGTG
*
13315 GTTATCAAAATTTAATAGGGAAGTTATCAAAATTTCATAGCGAGGTTATCAGAATTTCATAAGAA
1 GTTATCAAAATTTAATAGGGAAGTTATCAAAATTTCATAGCGACGTTATCAGAATTTCATAAGAA
13380 AGTTATCAAAAGTTGATAGCGAA
66 AGTTATCAAAAGTTGATAGCGAA
* * ** *
13403 GTTATCAAAATTTCATAATGGTGGTTATCAAAATTTCATGAG-GACGTTATTAGAATTTCATAAG
1 GTTATCAAAATTTAAT-AGGGAAGTTATCAAAATTTCAT-AGCGACGTTATCAGAATTTCATAAG
* * * * * * *
13467 GAGGTTGTCAAAAATTTCATAGTG-T
64 AAAGTTATC-AAAAGTTGATAGCGAA
* * * * * * ** * *
13492 GCTTACCAAAATTTTATAGGTAGGTTATAAAAATTTCATAGAGTGGTTATAAAAATTTCATAAGG
1 G-TTATCAAAATTTAATAGGGAAGTTATCAAAATTTCATAGCGACGTTATCAGAATTTCATAA-G
* * *
13557 ATCAGGTTATCAAAATTTCAT--CTGAA
64 A--AAGTTATCAAAAGTTGATAGC-GAA
* * * * ** * * *
13583 GGATATCCAAATTTCATAGTGTGGTTATCAAAATTTCTTAGCGAGGTTATCAAAATTTCAT
1 -GTTATCAAAATTTAATAGGGAAGTTATCAAAATTTCATAGCGACGTTATCAGAATTTCAT
13644 GATGAGGTTA
Statistics
Matches: 191, Mismatches: 39, Indels: 19
0.77 0.16 0.08
Matches are distributed among these distances:
88 17 0.09
89 81 0.42
90 28 0.15
91 57 0.30
92 8 0.04
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (88 bp):
GTTATCAAAATTTAATAGGGAAGTTATCAAAATTTCATAGCGACGTTATCAGAATTTCATAAGAA
AGTTATCAAAAGTTGATAGCGAA
Found at i:13798 original size:22 final size:21
Alignment explanation
Indices: 13731--13798 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
13721 CCATAGTGTA
*
13731 ATTACCAAAATTTTATAAAGAG
1 ATTAACAAAATTTTAT-AAGAG
* * *
13753 GTTAACAAAATTTCATAGGAAG
1 ATTAACAAAATTTTATAAG-AG
* *
13775 ATTATCGAAATTTTATATAGAG
1 ATTAACAAAATTTTATA-AGAG
13797 AT
1 AT
13799 AATAAAAAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 2 0.06
22 32 0.91
23 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (21 bp):
ATTAACAAAATTTTATAAGAG
Found at i:13944 original size:22 final size:22
Alignment explanation
Indices: 13859--13944 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
13849 GGAAGGTTAT
* * *
13859 CAAAATTTCATAGTGTA-TTTAC
1 CAAAATTTCATAGTG-AGGTAAA
* * *
13881 CAAAATTTCATTGTGGGGTAAT
1 CAAAATTTCATAGTGAGGTAAA
*
13903 CAAAATTTCATAGTAAGGTAAA
1 CAAAATTTCATAGTGAGGTAAA
* *
13925 CAAAATTTTATAGTGTGGTA
1 CAAAATTTCATAGTGAGGTA
13945 TTTTATATTT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTAAA
Found at i:16636 original size:15 final size:16
Alignment explanation
Indices: 16611--16649 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16601 GAGATTGAAA
16611 AAAAGCAATTAAAC-AG
1 AAAA-CAATTAAACTAG
*
16627 AAAACAATTATACTAG
1 AAAACAATTAAACTAG
16643 AAAACAA
1 AAAACAA
16650 AACAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (16 bp):
AAAACAATTAAACTAG
Found at i:19932 original size:21 final size:21
Alignment explanation
Indices: 19908--19980 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
19898 GGCTTGGAAT
19908 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATGGCC
* * **
19929 GGTGGTGGCACGGGCTTAACC
1 GGTGATGGCACGGGCATGGCC
* * *
19950 GGTGGTGGTACGGTGAATGGCC
1 GGTGATGGCACGG-GCATGGCC
*
19972 GGTAATGGC
1 GGTGATGGC
19981 TTGGTAGTGG
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
21 29 0.74
22 10 0.26
ACGTcount: A:0.15, C:0.19, G:0.47, T:0.19
Consensus pattern (21 bp):
GGTGATGGCACGGGCATGGCC
Found at i:20923 original size:24 final size:24
Alignment explanation
Indices: 20891--20948 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
20881 GGATTATATC
20891 ACCATCGAATTCCATGGTCAATGA
1 ACCATCGAATTCCATGGTCAATGA
20915 ACCATCGAATTCCATGGTCAATGA
1 ACCATCGAATTCCATGGTCAATGA
20939 ACCATCGAAT
1 ACCATCGAAT
20949 ACATCGATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (24 bp):
ACCATCGAATTCCATGGTCAATGA
Found at i:23183 original size:23 final size:24
Alignment explanation
Indices: 23136--23187 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
23126 TAAAAAAAAA
23136 TTTTATGACGCAGAGACGAAATTTT
1 TTTTATGACGCAGAGAC-AAATTTT
23161 TTTTATGACGCAGA-A-AAACTTTT
1 TTTTATGACGCAGAGACAAA-TTTT
23184 TTTT
1 TTTT
23188 TTCTTTCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.12
23 8 0.31
24 1 0.04
25 14 0.54
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (24 bp):
TTTTATGACGCAGAGACAAATTTT
Found at i:23313 original size:48 final size:50
Alignment explanation
Indices: 23229--23323 Score: 133
Period size: 48 Copynumber: 1.9 Consensus size: 50
23219 TTTTTCAAAA
23229 ACGCAACACAAAAAATTTAAAAACGCAAAAATCAAAAATTTTCTTTTATG
1 ACGCAACACAAAAAATTTAAAAACGCAAAAATCAAAAATTTTCTTTTATG
* * *
23279 ACGCAA-ACACAAAA-TTAAAAACGGACAAAA-CAAAAATTTTTTTTT
1 ACGCAACACAAAAAATTTAAAAACGCA-AAAATCAAAAATTTTCTTTT
23324 TAGGTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
48 24 0.59
49 11 0.27
50 6 0.15
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25
Consensus pattern (50 bp):
ACGCAACACAAAAAATTTAAAAACGCAAAAATCAAAAATTTTCTTTTATG
Found at i:23671 original size:15 final size:16
Alignment explanation
Indices: 23647--23686 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
23637 AGAGATTGAA
*
23647 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
23662 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
23678 AGAAAACAA
1 AGAAAACAA
23687 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:27634 original size:111 final size:110
Alignment explanation
Indices: 27437--27711 Score: 389
Period size: 111 Copynumber: 2.5 Consensus size: 110
27427 GGGTTTCAAT
* *
27437 ATTTGAGATTTACCCTTTTAAAAAATAAAACA-ACTTTATAATTGGGGCTAAACC-T-TATTTAT
1 ATTTAAGATTTACCC--TTAAAAAATAAAACATA-TTTATAATTGGGGCTAAACCTTATATTTAA
* * **
27499 AAGTGTTCAAACTTATTTTTCTAAAACCCTAAGATAGTGGATCTTACC
63 AAGTGTTCAAACTTATTTTTCTAAAACCCTAAAATAATGGATCTTAAA
* *
27547 ATTTAAGATTTACCCTTGAAAAAATAAAACATATTT-TAGTTGGGACTAAACCTTATAATTTAAA
1 ATTTAAGATTTACCCTT-AAAAAATAAAACATATTTATAATTGGGGCTAAACCTTAT-ATTTAAA
27611 AGTGTTCAAACTTATTTTTCTAAAACCCTAAAATAATGGATCTTAAA
64 AGTGTTCAAACTTATTTTTCTAAAACCCTAAAATAATGGATCTTAAA
*
27658 ATTTAAGATTTACCCTT-AAAAATAAAACATATTTATAATTGGGGCTTAACCTTA
1 ATTTAAGATTTACCCTTAAAAAATAAAACATATTTATAATTGGGGCTAAACCTTA
27712 ATTATTGTTA
Statistics
Matches: 148, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
108 16 0.11
109 34 0.23
110 32 0.22
111 66 0.45
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (110 bp):
ATTTAAGATTTACCCTTAAAAAATAAAACATATTTATAATTGGGGCTAAACCTTATATTTAAAAG
TGTTCAAACTTATTTTTCTAAAACCCTAAAATAATGGATCTTAAA
Found at i:28619 original size:36 final size:39
Alignment explanation
Indices: 28548--28620 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
28538 CCTGCTTGTG
28548 CAGGCCCAGGCACGCGGGCCTAGCGCAGGCCCAGGCGTGC
1 CAGGCCCAGGCACGCGGGCCTA-CGCAGGCCCAGGCGTGC
28588 CAGG-CCAGGCACGCGGGCC-A-GCAGGCCCAGGCG
1 CAGGCCCAGGCACGCGGGCCTACGCAGGCCCAGGCG
28621 CACGGGCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 13 0.39
38 1 0.03
39 15 0.45
40 4 0.12
ACGTcount: A:0.16, C:0.40, G:0.41, T:0.03
Consensus pattern (39 bp):
CAGGCCCAGGCACGCGGGCCTACGCAGGCCCAGGCGTGC
Found at i:28635 original size:24 final size:24
Alignment explanation
Indices: 28588--28664 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
28578 CCAGGCGTGC
*
28588 CAGG-CCAGGCACGCGGGCC-A-G
1 CAGGCCCAGGCGCGCGGGCCAACG
*
28609 CAGGCCCAGGCGCACGGGCCAACG
1 CAGGCCCAGGCGCGCGGGCCAACG
*
28633 CAGGCTCAGGCGCGCGGGCCAACG
1 CAGGCCCAGGCGCGCGGGCCAACG
28657 CAGGCCCA
1 CAGGCCCA
28665 ACGGCCTGGC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.08
22 13 0.27
23 1 0.02
24 30 0.62
ACGTcount: A:0.19, C:0.40, G:0.39, T:0.01
Consensus pattern (24 bp):
CAGGCCCAGGCGCGCGGGCCAACG
Found at i:28766 original size:14 final size:15
Alignment explanation
Indices: 28747--28778 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28737 CCAAAAGAAG
28747 AAAAAGAA-GAAAAA
1 AAAAAGAAGGAAAAA
28761 AAAAAGAAGGAAAAA
1 AAAAAGAAGGAAAAA
28776 AAA
1 AAA
28779 GAAATAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGGAAAAA
Found at i:28791 original size:13 final size:11
Alignment explanation
Indices: 28739--28782 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
28729 GGCCTGGCCC
28739 AAAAGAAGAAAA
1 AAAAGAA-AAAA
*
28751 AGAAGAAAAAA
1 AAAAGAAAAAA
28762 AAAAGAAGGAAAA
1 AAAAGAA--AAAA
28775 AAAAGAAA
1 AAAAGAAA
28783 TAAAGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 11 0.39
12 6 0.21
13 11 0.39
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Done.