Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018893.1 Corchorus olitorius cultivar O-4 contig18926, 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: 48284
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:30 original size:15 final size:15
Alignment explanation
Indices: 6--44 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1 TCTCT
6 CTTTTT-TTTCCTTC
1 CTTTTTCTTTCCTTC
*
20 CTTTTTCTTTCTTTC
1 CTTTTTCTTTCCTTC
*
35 CTTTTCCTTT
1 CTTTTTCTTT
45 TTCTCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
CTTTTTCTTTCCTTC
Found at i:43 original size:21 final size:21
Alignment explanation
Indices: 10--58 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1 TCTCTCTTT
10 TTTTTCC--TTCCTTTTTCT-
1 TTTTTCCTTTTCCTTTTTCTC
28 TTCTTTCCTTTTCCTTTTTCTC
1 TT-TTTCCTTTTCCTTTTTCTC
50 TTTTTCCTT
1 TTTTTCCTT
59 CTATTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.07
19 5 0.19
21 18 0.67
22 2 0.07
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTCCTTTTCCTTTTTCTC
Found at i:220 original size:22 final size:22
Alignment explanation
Indices: 161--221 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
151 ACTGGGCCGC
*
161 GCGCAGGCCCAAGAGGCTAGCA
1 GCGCAGGCCCAAGCGGCTAGCA
*
183 GCGCAGGCCCAGGCGGCTAGCA
1 GCGCAGGCCCAAGCGGCTAGCA
*
205 GCTCAGGCCCAAGCGGC
1 GCGCAGGCCCAAGCGGC
222 CTGGGCTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.21, C:0.36, G:0.38, T:0.05
Consensus pattern (22 bp):
GCGCAGGCCCAAGCGGCTAGCA
Found at i:2296 original size:21 final size:21
Alignment explanation
Indices: 2271--2331 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
2261 CAAGTTGGAT
*
2271 ATGATGCGGACTCAACAGGAC
1 ATGATGCGGACTCAACAAGAC
*
2292 ATGATGCGGACTCAACAAGAT
1 ATGATGCGGACTCAACAAGAC
* * *
2313 ACGATGCGGGCTCAGCAAG
1 ATGATGCGGACTCAACAAG
2332 GCGACTTGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.23, G:0.30, T:0.15
Consensus pattern (21 bp):
ATGATGCGGACTCAACAAGAC
Found at i:5952 original size:13 final size:13
Alignment explanation
Indices: 5934--5958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5924 ATGCGGTTTA
5934 AAAAATAAAAAAT
1 AAAAATAAAAAAT
5947 AAAAATAAAAAA
1 AAAAATAAAAAA
5959 AAATATCGTG
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:10321 original size:22 final size:21
Alignment explanation
Indices: 10296--10399 Score: 91
Period size: 22 Copynumber: 4.8 Consensus size: 21
10286 GGTCATCAAA
*
10296 GAGGTTATCAAAATTTCATTG
1 GAGGTTATCAAAATTTCATAG
* *
10317 CGAGGTTACCATAATTTCATAG
1 -GAGGTTATCAAAATTTCATAG
* *
10339 TGTGATTATCAAAATTTCATAAG
1 -GAGGTTATCAAAATTTCAT-AG
* * *
10362 AAGGTTATTAAAATTTCAAAGG
1 GAGGTTATCAAAATTTCATA-G
*
10384 GAGATTATCAAAATTT
1 GAGGTTATCAAAATTT
10400 AATACTATGG
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 1 0.02
22 61 0.95
23 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (21 bp):
GAGGTTATCAAAATTTCATAG
Found at i:10367 original size:44 final size:44
Alignment explanation
Indices: 10300--10399 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
10290 ATCAAAGAGG
* * * * * *
10300 TTATCAAAATTTCATTGCGAGGTTACCATAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGCAAGGTTACCAAAATTTCAAAGGGAGA
**
10344 TTATCAAAATTTCATAAG-AAGGTTATTAAAATTTCAAAGGGAGA
1 TTATCAAAATTTCAT-AGCAAGGTTACCAAAATTTCAAAGGGAGA
10388 TTATCAAAATTT
1 TTATCAAAATTT
10400 AATACTATGG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 46 0.98
45 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCATAGCAAGGTTACCAAAATTTCAAAGGGAGA
Found at i:10492 original size:22 final size:22
Alignment explanation
Indices: 10467--11134 Score: 247
Period size: 22 Copynumber: 30.3 Consensus size: 22
10457 TAAAAATCTC
*
10467 AATTTCAAAGGGAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
** * * * *
10489 AATTTTGTAGTGTGGTTATTAT
1 AATTTCATAGGGAGGTTATCAA
* *
10511 AATTTCATAAGGAAGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* *
10533 AATATCATAGAGTA-GTTATCAA
1 AATTTCATAG-GGAGGTTATCAA
* * *
10555 AATTTCTTAGAGATCAGATTAT-AA
1 AATTTCATAG-G--GAGGTTATCAA
* *
10579 ATATTTCATAGGAAGGCTATCAA
1 A-ATTTCATAGGGAGGTTATCAA
** *
10602 AATTTCATAGAAAAGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* *
10624 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
*
10646 AATTTCATAGTGG-GATTATCAA
1 AATTTCATAG-GGAGGTTATCAA
* **
10668 AATTTCACA-ATATGGTTATCAA
1 AATTTCATAGGGA-GGTTATCAA
* * *
10690 AATTTTATAGAGAGGTTAACAA
1 AATTTCATAGGGAGGTTATCAA
* *
10712 AATTTCAT-TGTATGGTTATCAA
1 AATTTCATAGGGA-GGTTATCAA
* *
10734 AATTTCATAGGAATGTTATCCAA
1 AATTTCATAGGGAGGTTAT-CAA
** *
10757 AAAAT-ATAGGGAGGTTATTAA
1 AATTTCATAGGGAGGTTATCAA
* * ** * *
10778 AACTTCGTAGAAATGTTATAAA
1 AATTTCATAGGGAGGTTATCAA
* * *
10800 AATTTTATAGCGCA-ATTATCAA
1 AATTTCATAG-GGAGGTTATCAA
* * * * *
10822 AATTTTATAGTGTGCTTATAAA
1 AATTTCATAGGGAGGTTATCAA
** * * *
10844 AATTTTTTAAGGATGTTTATCGA
1 AATTTCATAGGGA-GGTTATCAA
** *
10867 AATTTCATATTGAGGTTATCCA
1 AATTTCATAGGGAGGTTATCAA
* * *
10889 AATTCCATAAGGAGGTTATCAC
1 AATTTCATAGGGAGGTTATCAA
* *
10911 AATTTCATA-GTATGGTTA-CTGA
1 AATTTCATAGGGA-GGTTATC-AA
* * * *
10933 TATTTCGTATGGAGGTAATCAA
1 AATTTCATAGGGAGGTTATCAA
* *
10955 AATTTAATA-GTATGGTTATCAA
1 AATTTCATAGGGA-GGTTATCAA
*
10977 AACTT--TA--GAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* * *
10995 AATTCCATATGGTGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
** *
11017 AATTTTC-TAATTGAGGTTATCGA
1 AA-TTTCAT-AGGGAGGTTATCAA
* **
11040 AATATCAT-GGTGTCGTTATCAA
1 AATTTCATAGG-GAGGTTATCAA
** *
11062 AATTT-ATAATGTGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* * *
11083 ATTTTC-TCTGTGAGGTTATCAA
1 AATTTCAT-AGGGAGGTTATCAA
* * *
11105 AATTACATGAGGAGAGATTATCGA
1 AATTTCAT-AGG-GAGGTTATCAA
11129 AATTTC
1 AATTTC
11135 GTTTTGTAGT
Statistics
Matches: 472, Mismatches: 139, Indels: 68
0.70 0.20 0.10
Matches are distributed among these distances:
18 12 0.03
19 1 0.00
20 4 0.01
21 28 0.06
22 342 0.72
23 54 0.11
24 19 0.04
25 12 0.03
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
AATTTCATAGGGAGGTTATCAA
Found at i:11733 original size:22 final size:22
Alignment explanation
Indices: 11699--12236 Score: 304
Period size: 22 Copynumber: 23.7 Consensus size: 22
11689 TTCATAAAGA
*
11699 TCATAGGGAGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
*
11721 TCATAGTGTGGTTATCAAAGAGGTTATT
1 TCATAGTGAGGTTATC-AA-A----ATT
*
11749 TCATAGTGTGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
** * *
11771 TCATAGCAAGATTATCAGAATT
1 TCATAGTGAGGTTATCAAAATT
**
11793 TCATAGTTTGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
* *
11815 TCGA-AATGAGGTTACTAAAAATT
1 TC-ATAGTGAGGTTA-TCAAAATT
* ** * *
11838 TCATAGGGAACTTACCAAAATC
1 TCATAGTGAGGTTATCAAAATT
* *
11860 TCATATTGTGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
* * *
11882 TAATAGTGTGGTTACCAAAATT
1 TCATAGTGAGGTTATCAAAATT
* * * *
11904 TTATACG-AAAGTTATAAAAATCT
1 TCATA-GTGAGGTTATCAAAAT-T
* *
11927 TAATTTCA-TAAGGTGTTTATCAAAATT
1 TCA--T-AGTGA-G-G-TTATCAAAATT
* * *
11954 TAATAGGGAGGTTATCAATATT
1 TCATAGTGAGGTTATCAAAATT
* * * *
11976 TTATCGTGTGGTTGTCAAAAATT
1 TCATAGTGAGGTTATC-AAAATT
* *
11999 T-ATAAG-GAGGTTATCAGAATC
1 TCAT-AGTGAGGTTATCAAAATT
* **
12020 TCATAGAGTCGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
*
12042 TCATAGAGATCGGATTATC-AAATT
1 TCATAGTGA--GG-TTATCAAAATT
*
12066 TCCATTG-GAAGGTTATCAAAATT
1 T-CATAGTG-AGGTTATCAAAATT
12089 TCATA-TGGAGGTTATCAAAATT
1 TCATAGT-GAGGTTATCAAAATT
* **
12111 TCAAAACGAGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
* *
12133 TCACAGTGTGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
*
12155 TTATAGTGAGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
* *
12177 TCATAGAGAGGTTATCAAATTT
1 TCATAGTGAGGTTATCAAAATT
* *
12199 TCATA-TGGAGGTTCTCGAAATT
1 TCATAGT-GAGGTTATCAAAATT
*
12221 TCTTAAG-GAGGTTATC
1 TCAT-AGTGAGGTTATC
12237 GAAGTTATCA
Statistics
Matches: 399, Mismatches: 82, Indels: 70
0.72 0.15 0.13
Matches are distributed among these distances:
21 7 0.02
22 289 0.72
23 40 0.10
24 11 0.03
25 15 0.04
26 2 0.01
27 7 0.02
28 28 0.07
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
TCATAGTGAGGTTATCAAAATT
Found at i:11895 original size:67 final size:67
Alignment explanation
Indices: 11746--11901 Score: 160
Period size: 67 Copynumber: 2.3 Consensus size: 67
11736 CAAAGAGGTT
* * * * *
11746 ATTTCATAGTGTGGTTA-TCAAAATTTCATAGCAAGATTATCAGAATTTCATAGTTTGGTTATCA
1 ATTTAATAGTGTGGTTACTAAAAATTTCATAGCAAGATTACCAAAATCTCATAGTTTGGTTATCA
11810 AA
66 AA
* * *
11812 ATTTCGAA-A-TGAGGTTACTAAAAATTTCATAGGGAA-CTTACCAAAATCTCATA-TTGTGGTT
1 ATTT--AATAGTGTGGTTACTAAAAATTTCATA-GCAAGATTACCAAAATCTCATAGTT-TGGTT
11873 ATCAAA
62 ATCAAA
*
11879 ATTTAATAGTGTGGTTACCAAAA
1 ATTTAATAGTGTGGTTACTAAAA
11902 TTTTATACGA
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
65 2 0.03
66 14 0.19
67 53 0.73
68 4 0.05
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (67 bp):
ATTTAATAGTGTGGTTACTAAAAATTTCATAGCAAGATTACCAAAATCTCATAGTTTGGTTATCA
AA
Found at i:12123 original size:44 final size:44
Alignment explanation
Indices: 11706--12471 Score: 238
Period size: 44 Copynumber: 16.9 Consensus size: 44
11696 AGATCATAGG
* * **
11706 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAGAGGTTATTTCATAGT
1 GAGGTTATCAAAATTTCATAGAGAGGTTATC-AA-A----ATTTCATAAC
* * * **
11756 GTGGTTATCAAAATTTCATAGCA-AGATTATCAGAATTTCATAGT
1 GAGGTTATCAAAATTTCATAG-AGAGGTTATCAAAATTTCATAAC
** * **
11800 TTGGTTATCAAAATTTCGA-A-ATGAGGTTACTAAAAATTTCATAGG
1 GAGGTTATCAAAATTTC-ATAGA-GAGGTTA-TCAAAATTTCATAAC
** * * ** * * **
11845 GAACTTACCAAAATCTCATATTGTGGTTATCAAAATTTAATAGT
1 GAGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAC
* * * * * *
11889 GTGGTTACCAAAATTTTATACGA-AAGTTATAAAAATCTTAATTTCATAAG
1 GAGGTTATCAAAATTTCATA-GAGAGGTTAT--CAA----AATTTCATAAC
* * * * * * ***
11939 GTGTTTATCAAAATTTAATAGGGAGGTTATCAATATTTTATCGT
1 GAGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAC
* * * *
11983 GTGGTTGTCAAAAATTT-ATA-AGGAGGTTATCAGAATCTCAT-A-
1 GAGGTTATC-AAAATTTCATAGA-GAGGTTATCAAAATTTCATAAC
**
12025 GAGTCGTTATCAAAATTTCATAGAGATCGGATTATC-AAATTTCCAT-TG
1 GAG--GTTATCAAAATTTCATAGAGA--GG-TTATCAAAATTT-CATAAC
*
12073 GAAGGTTATCAAAATTTCATATG-GAGGTTATCAAAATTTCAAAAC
1 G-AGGTTATCAAAATTTCATA-GAGAGGTTATCAAAATTTCATAAC
* * * * **
12118 GAGGTTATCAAAATTTCACAGTGTGGTTATCAAAATTTTATAGT
1 GAGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAC
* **
12162 GAGGTTATCAAAATTTCATAGAGAGGTTATCAAATTTTCATATG
1 GAGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAC
* * * *
12206 GAGGTTCTCGAAATTTCTTAAGGAGGTTATCGAAGTTATCAAAATTTCAT-AT
1 GAGGTTATCAAAATTTCAT-A-GA-G--A--G--GTTATCAAAATTTCATAAC
* * **
12258 GAAGGTTATCAAAATTTCA-AAAGGAGGTTAACAAAATTTCATAGG
1 G-AGGTTATCAAAATTTCATAGA-GAGGTTATCAAAATTTCATAAC
* * ** * ***
12303 GAGGTTAT-GAAATTACATAGTTTA-GTTTTCAAAATTTCATTGG
1 GAGGTTATCAAAATTTCATAG-AGAGGTTATCAAAATTTCATAAC
* ** * *
12346 GAGG-TATCAAAATTTCATAGTG-TCTATATCAAAATTTCGTAAA
1 GAGGTTATCAAAATTTCATAGAGAGGT-TATCAAAATTTCATAAC
* * * ** **
12389 GAGGTTAACAAAATTTTATA-ATGAAGTTATCAAAAAATCATATG
1 GAGGTTATCAAAATTTCATAGA-GAGGTTATCAAAATTTCATAAC
* * *
12433 GTGGTTATCAAAATTTTATA-AGGAGGTTTATAAAAATTT
1 GAGGTTATCAAAATTTCATAGA-GAGG-TTATCAAAATTT
12472 TATAGGAAGT
Statistics
Matches: 544, Mismatches: 121, Indels: 107
0.70 0.16 0.14
Matches are distributed among these distances:
42 8 0.01
43 61 0.11
44 273 0.50
45 60 0.11
46 11 0.02
47 28 0.05
48 6 0.01
49 5 0.01
50 60 0.11
51 2 0.00
52 1 0.00
53 29 0.05
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAC
Found at i:12153 original size:66 final size:65
Alignment explanation
Indices: 11943--12471 Score: 274
Period size: 66 Copynumber: 7.8 Consensus size: 65
11933 CATAAGGTGT
* * * *** * * * *
11943 TTATCAAAATTTAATAGGGAGGTTATCAATATTTTATCGTGTGGTTGTCAAAAATTT-ATAAGGA
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAAAGAGGTTATC-AAAATTTCACATGGA
12007 GG
64 GG
* * *
12009 TTATCAGAATCTCATA-GAGTCGTTATCAAAATTTCATAGAGATCGGATTATC-AAATTTC-CAT
1 TTATCAAAATTTCATAGGAG--GTTATCAAAATTTCATAAAGA--GG-TTATCAAAATTTCACA-
12071 TGGAAGG
60 TGG-AGG
12078 TTATCAAAATTTCATATGGAGGTTATCAAAATTTCA-AAACGAGGTTATCAAAATTTCACA-GTG
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAAA-GAGGTTATCAAAATTTCACATG-G
*
12141 TGG
63 AGG
* * * *
12144 TTATCAAAATTTTATAGTGAGGTTATCAAAATTTCATAGAGAGGTTATCAAATTTTCATATGGAG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTCACATGGAG
12209 G
65 G
* * * *
12210 TTCTCGAAATTTCTTAAGGAGGTTATCGAAGTTATCAAAATTTCAT-ATGAAGGTTATCAAAATT
1 TTATCAAAATTTC---A-TAGG--A--G--GTTATCAAAATTTCATAAAG-AGGTTATCAAAATT
* *
12274 TCAAAAGGAGG
55 TCACATGGAGG
* * * *** * *
12285 TTAACAAAATTTCATAGGGAGGTTAT-GAAATTACATAGTTTA-GTTTTCAAAATTTCA-TTGGG
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTCATA-AAGAGGTTATCAAAATTTCACAT-GG
12347 AGG
63 AGG
** * * * *
12350 -TATCAAAATTTCATAGTG-TCTATATCAAAATTTCGTAAAGAGGTTAACAAAATTTTATAAT-G
1 TTATCAAAATTTCATAG-GAGGT-TATCAAAATTTCATAAAGAGGTTATCAAAATTTCA-CATGG
*
12412 AAG
63 AGG
** * * * *
12415 TTATCAAAAAATCATATGGTGGTTATCAAAATTTTATAAGGAGGTTTATAAAAATTT
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAAAGAGG-TTATCAAAATTT
12472 TATAGGAAGT
Statistics
Matches: 358, Mismatches: 63, Indels: 83
0.71 0.12 0.16
Matches are distributed among these distances:
63 2 0.01
64 22 0.06
65 51 0.14
66 139 0.39
67 34 0.09
68 9 0.03
69 40 0.11
70 3 0.01
71 5 0.01
72 3 0.01
73 1 0.00
74 1 0.00
75 48 0.13
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (65 bp):
TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTCACATGGAGG
Found at i:12273 original size:53 final size:53
Alignment explanation
Indices: 12187--12287 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
12177 TCATAGAGAG
* * * * **
12187 GTTATCAAATTTTCATATGGAGGTTCTCGAAATTTCTTAAGGAGGTTATCGAA
1 GTTATCAAAATTTCATATGAAGGTTATCAAAATTTCAAAAGGAGGTTATCGAA
12240 GTTATCAAAATTTCATATGAAGGTTATCAAAATTTCAAAAGGAGGTTA
1 GTTATCAAAATTTCATATGAAGGTTATCAAAATTTCAAAAGGAGGTTA
12288 ACAAAATTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (53 bp):
GTTATCAAAATTTCATATGAAGGTTATCAAAATTTCAAAAGGAGGTTATCGAA
Found at i:12295 original size:75 final size:75
Alignment explanation
Indices: 12165--12310 Score: 204
Period size: 75 Copynumber: 1.9 Consensus size: 75
12155 TTATAGTGAG
* * * ** * *
12165 GTTATCAAAATTTCATAGAGAGGTTATCAAATTTTCATATGGAGGTTCTCGAAATTTCTTAAGGA
1 GTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCAAAAGGAGGTTAACAAAATTTCATAAGGA
12230 GGTTATCGAA
66 GGTTATCGAA
*
12240 GTTATCAAAATTTCATATGA-AGGTTATCAAAATTTCAAAAGGAGGTTAACAAAATTTCATAGGG
1 GTTATCAAAATTTCATA-GAGAGGTTATCAAAATTTCAAAAGGAGGTTAACAAAATTTCATAAGG
12304 AGGTTAT
65 AGGTTAT
12311 GAAATTACAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 60 0.97
76 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (75 bp):
GTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCAAAAGGAGGTTAACAAAATTTCATAAGGA
GGTTATCGAA
Found at i:12356 original size:21 final size:22
Alignment explanation
Indices: 12240--12477 Score: 151
Period size: 22 Copynumber: 10.9 Consensus size: 22
12230 GGTTATCGAA
* *
12240 GTTATCAAAATTTCATATGAAG
1 GTTATCAAAATTTCATAGGGAG
* *
12262 GTTATCAAAATTTCAAAAGGAG
1 GTTATCAAAATTTCATAGGGAG
*
12284 GTTAACAAAATTTCATAGGGAG
1 GTTATCAAAATTTCATAGGGAG
* * **
12306 GTTAT-GAAATTACATAGTTTA-
1 GTTATCAAAATTTCATAG-GGAG
* *
12327 GTTTTCAAAATTTCATTGGGAG
1 GTTATCAAAATTTCATAGGGAG
* *
12349 G-TATCAAAATTTCATAGTG-T
1 GTTATCAAAATTTCATAGGGAG
* * **
12369 CTATATCAAAATTTCGTAAAGAG
1 GT-TATCAAAATTTCATAGGGAG
* * ** *
12392 GTTAACAAAATTTTATAATGAA
1 GTTATCAAAATTTCATAGGGAG
** * *
12414 GTTATCAAAAAATCATATGGTG
1 GTTATCAAAATTTCATAGGGAG
* *
12436 GTTATCAAAATTTTATAAGGAG
1 GTTATCAAAATTTCATAGGGAG
* *
12458 GTTTATAAAAATTTTATAGG
1 G-TTATCAAAATTTCATAGG
12478 AAGTTAGTGA
Statistics
Matches: 162, Mismatches: 47, Indels: 13
0.73 0.21 0.06
Matches are distributed among these distances:
21 30 0.19
22 115 0.71
23 17 0.10
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAG
Found at i:12378 original size:43 final size:42
Alignment explanation
Indices: 12289--12383 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 42
12279 AGGAGGTTAA
* *
12289 CAAAATTTCATAGGGAGGTTATGAAATTACATAGTTTAGTTTT
1 CAAAATTTCATAGGGAGGTTATAAAATTACATAGTTTAG-TAT
* *
12332 CAAAATTTCATTGGGAGG-TATCAAAATTTCATAGTGTCTA-TAT
1 CAAAATTTCATAGGGAGGTTAT-AAAATTACATAGT-T-TAGTAT
12375 CAAAATTTC
1 CAAAATTTC
12384 GTAAAGAGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
42 3 0.07
43 39 0.87
44 1 0.02
45 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (42 bp):
CAAAATTTCATAGGGAGGTTATAAAATTACATAGTTTAGTAT
Found at i:14375 original size:44 final size:46
Alignment explanation
Indices: 14322--14427 Score: 132
Period size: 44 Copynumber: 2.4 Consensus size: 46
14312 TCCGTAGTAT
* *
14322 GGTTATCAAAATTTCAT-TA-GGAGATTACCAAAATTTCATAGTGA
1 GGTTATCAAAATTTCATATAGGGAGATTAACAAAATTTCATAGAGA
* *
14366 GGTTTTCAAAA-TT-ATATAGGGAGGTTAACAAAATTTCATAGAGA
1 GGTTATCAAAATTTCATATAGGGAGATTAACAAAATTTCATAGAGA
14410 GGTTGA-CAAAATTTCATA
1 GGTT-ATCAAAATTTCATA
14428 AAGAGGTTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
42 2 0.04
43 4 0.08
44 41 0.79
45 2 0.04
46 3 0.06
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (46 bp):
GGTTATCAAAATTTCATATAGGGAGATTAACAAAATTTCATAGAGA
Found at i:14432 original size:22 final size:21
Alignment explanation
Indices: 14322--14472 Score: 112
Period size: 22 Copynumber: 6.9 Consensus size: 21
14312 TCCGTAGTAT
14322 GGTTATCAAAATTTCATTAG-GA
1 GGTTA-CAAAATTTCA-TAGAGA
* *
14344 GATTACCAAAATTTCATAGTGA
1 GGTTA-CAAAATTTCATAGAGA
* *
14366 GGTTTTCAAAATTAT-ATAGGGA
1 GG-TTACAAAATT-TCATAGAGA
14388 GGTTAACAAAATTTCATAGAGA
1 GGTT-ACAAAATTTCATAGAGA
*
14410 GGTTGACAAAATTTCATAAAGA
1 GGTT-ACAAAATTTCATAGAGA
*
14432 GGTT-CATGAAATTGCATAGAGCA
1 GGTTACA--AAATTTCATAGAG-A
*
14455 GGTCT-CAAAACTTCATAG
1 GGT-TACAAAATTTCATAG
14473 TGTTCTTATA
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
20 2 0.02
21 6 0.06
22 89 0.83
23 7 0.07
24 3 0.03
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
GGTTACAAAATTTCATAGAGA
Found at i:14503 original size:22 final size:22
Alignment explanation
Indices: 14478--14525 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
14468 CATAGTGTTC
14478 TTATAAAAATTTCA-TGAGGAGG
1 TTATAAAAATTTCATTG-GGAGG
** *
14500 TTATCGAATTTTCATTGGGAGG
1 TTATAAAAATTTCATTGGGAGG
14522 TTAT
1 TTAT
14526 CGCAACTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (22 bp):
TTATAAAAATTTCATTGGGAGG
Found at i:14535 original size:22 final size:22
Alignment explanation
Indices: 14495--14536 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
14485 AATTTCATGA
*
14495 GGAGGTTATCGAATTTTCATTG
1 GGAGGTTATCGAATCTTCATTG
14517 GGAGGTTATCGCAA-CTTCAT
1 GGAGGTTATCG-AATCTTCAT
14537 AATGTGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (22 bp):
GGAGGTTATCGAATCTTCATTG
Found at i:15925 original size:12 final size:12
Alignment explanation
Indices: 15908--15933 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15898 TCCTCAGCAA
15908 AAAAAAAAAAAG
1 AAAAAAAAAAAG
15920 AAAAAAAAAAAG
1 AAAAAAAAAAAG
15932 AA
1 AA
15934 GAAGAAAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:15926 original size:15 final size:15
Alignment explanation
Indices: 15906--15936 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15896 TATCCTCAGC
15906 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
*
15921 AAAAAAAAAAGAAGA
1 AAAAAAAAAAAAAGA
15936 A
1 A
15937 GAAAGACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:17472 original size:21 final size:21
Alignment explanation
Indices: 17446--17485 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
17436 TATGTCAAAT
17446 ATATACTATATATTATTTTAA
1 ATATACTATATATTATTTTAA
17467 ATATACTATATATTATTTT
1 ATATACTATATATTATTTT
17486 TAATGACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATACTATATATTATTTTAA
Found at i:19941 original size:36 final size:38
Alignment explanation
Indices: 19896--19974 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
19886 GCATCCATAC
19896 CAAAGTCCCT-AA-ACATATAACACAAGGGCAATCTCT
1 CAAAGTCCCTAAACACATATAACACAAGGGCAATCTCT
* * *
19932 CAAAGTCCCTAAACACATGTAACACAAGGGGAATTTCT
1 CAAAGTCCCTAAACACATATAACACAAGGGCAATCTCT
19970 CAAAG
1 CAAAG
19975 GTGATAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 10 0.26
37 2 0.05
38 26 0.68
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (38 bp):
CAAAGTCCCTAAACACATATAACACAAGGGCAATCTCT
Found at i:30296 original size:2 final size:2
Alignment explanation
Indices: 30289--30316 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30279 TATATTTCTT
30289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30317 ATTCGGCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39894 original size:15 final size:16
Alignment explanation
Indices: 39861--39900 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
39851 TTTGTTTGTT
39861 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
39877 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
39892 TTGCTTTCT
1 TTGTTTTCT
39901 TTCAACCTCT
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:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:45368 original size:18 final size:19
Alignment explanation
Indices: 45345--45391 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
45335 GAACAAGGAA
45345 GAGAAGGGGAAGG-AGAGG
1 GAGAAGGGGAAGGAAGAGG
** *
45363 GAGAA-GAAAAGGAAGAGT
1 GAGAAGGGGAAGGAAGAGG
45381 GAGAAGGGGAA
1 GAGAAGGGGAA
45392 TGGGAAGGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
17 5 0.23
18 14 0.64
19 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.02
Consensus pattern (19 bp):
GAGAAGGGGAAGGAAGAGG
Found at i:46917 original size:2 final size:2
Alignment explanation
Indices: 46906--46944 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
46896 ATATATATAT
*
46906 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
46945 AGAAAACATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47247 original size:20 final size:19
Alignment explanation
Indices: 47181--47247 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
47171 ATCATTCAAA
*
47181 GCCCATGGATTTTGGGTTTG
1 GCCCATGGA-TTTGGCTTTG
*
47201 GTCCAATGGACTTTGGCTTTGG
1 G-CCCATGGA-TTTGGCTTT-G
*
47223 GCCCATGGATTTCGCCTTTG
1 GCCCATGGATTT-GGCTTTG
47243 GCCCA
1 GCCCA
47248 ATTATCAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 10 0.26
21 27 0.69
22 2 0.05
ACGTcount: A:0.12, C:0.24, G:0.30, T:0.34
Consensus pattern (19 bp):
GCCCATGGATTTGGCTTTG
Done.