Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023464.1 Corchorus olitorius cultivar O-4 contig23497, 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: 68664
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:13601 original size:25 final size:27
Alignment explanation
Indices: 13566--13616 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
13556 AATAGCAATT
13566 ATAAAGAAAAGC-AATTAAA-CTAAAA
1 ATAAAGAAAAGCAAATTAAATCTAAAA
*
13591 ATAAAGCAAAGCAAATTAAATCTAAA
1 ATAAAGAAAAGCAAATTAAATCTAAA
13617 CTATTACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
26 7 0.30
27 5 0.22
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.18
Consensus pattern (27 bp):
ATAAAGAAAAGCAAATTAAATCTAAAA
Found at i:15843 original size:29 final size:29
Alignment explanation
Indices: 15792--15856 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
15782 GTGTTCATGA
* *
15792 TTTGGGGTTACTAACTCATTTTT-TTTTAT
1 TTTGAGGTTACTAACACATTTTTGTTTT-T
15821 TTTGAGGTTACTAACAC-TCTTTTGTTTTT
1 TTTGAGGTTACTAACACAT-TTTTGTTTTT
*
15850 TTAGAGG
1 TTTGAGG
15857 GACAATACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 26 0.84
30 4 0.13
ACGTcount: A:0.18, C:0.11, G:0.17, T:0.54
Consensus pattern (29 bp):
TTTGAGGTTACTAACACATTTTTGTTTTT
Found at i:26514 original size:22 final size:20
Alignment explanation
Indices: 26463--26515 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
26453 GCTTCTTGAG
26463 ATAATTCTTC-AATCATCTTC
1 ATAA-TCTTCAAATCATCTTC
*
26483 A-AATCTTCAAATTATCTTC
1 ATAATCTTCAAATCATCTTC
26502 AATAAGTCTTCAAA
1 -ATAA-TCTTCAAA
26516 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAATCTTCAAATCATCTTC
Found at i:31683 original size:19 final size:18
Alignment explanation
Indices: 31650--31685 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31640 TTGAGATAAT
31650 TCTTCAATCATCTTCAAA
1 TCTTCAATCATCTTCAAA
*
31668 TCTTCAAATTATCTTCAA
1 TCTTC-AATCATCTTCAA
31686 TAAGGCTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATCATCTTCAAA
Found at i:36773 original size:2 final size:2
Alignment explanation
Indices: 36766--36794 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36756 AAATAATAAA
36766 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 A
36795 AAGCCCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36924 original size:21 final size:21
Alignment explanation
Indices: 36899--36941 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
36889 CATCATATTC
36899 GCATAATAAAAAGAAGCACTT
1 GCATAATAAAAAGAAGCACTT
* *
36920 GCATAATAAAAAGGAGTACTT
1 GCATAATAAAAAGAAGCACTT
36941 G
1 G
36942 GGCTGAGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (21 bp):
GCATAATAAAAAGAAGCACTT
Found at i:40069 original size:47 final size:47
Alignment explanation
Indices: 40008--40463 Score: 684
Period size: 47 Copynumber: 9.7 Consensus size: 47
39998 ACAATCAAAT
* * *
40008 GTTTAAATC-AGGTAATTAAACTAAATAATGAAAGAAGAAGAGATTA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATTA
*
40054 GTTTAATTCTAGGTAATTAAAATAAATAGTAAAAGAAGAAGAGATTA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATTA
* * *
40101 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAGGAAGAGGTCA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATTA
*
40148 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGGTTA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATTA
40195 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATTA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATTA
* * *
40242 GTTTAATTCTAGGTGATTAAACTAAATACTAAAAGAAAAAGAGATTA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATTA
* * * * *
40289 GTTTAATGCTAGGTAATTAAACTAAGTAGTAAGAGAAGAATAGTTTA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATTA
* * *
40336 GTTTAATTTTGGGTAATTAAACTAAATAGTAAAAGAAG-AGAAGGTTA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAG-AGATTA
*
40383 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGATG-TTA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGA-GATTA
*
40430 GTTTAATTCTAGGTAATTAAACTAAAGAGTAAAA
1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAA
40464 AAGGAAGTAA
Statistics
Matches: 374, Mismatches: 32, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
46 9 0.02
47 362 0.97
48 3 0.01
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.30
Consensus pattern (47 bp):
GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATTA
Found at i:45549 original size:19 final size:18
Alignment explanation
Indices: 45512--45551 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
45502 TTCTTGAAAT
*
45512 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
45530 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
45549 AAT
1 AAT
45552 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:46254 original size:55 final size:55
Alignment explanation
Indices: 46173--46283 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
46163 GATTTTCTTC
46173 TTAGTTTTATATTACAATAGCATATCATATTTTGCATTGCACAATAGAAGAGAGT
1 TTAGTTTTATATTACAATAGCATATCATATTTTGCATTGCACAATAGAAGAGAGT
* *
46228 TTAGTTTTATATTAGAGTAGCATATCATATTTTGCATTGCACAATAGAAGAGAGT
1 TTAGTTTTATATTACAATAGCATATCATATTTTGCATTGCACAATAGAAGAGAGT
46283 T
1 T
46284 AAGCGCTTGG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (55 bp):
TTAGTTTTATATTACAATAGCATATCATATTTTGCATTGCACAATAGAAGAGAGT
Found at i:46416 original size:27 final size:27
Alignment explanation
Indices: 46353--46422 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
46343 TAGGTTGGTT
* *
46353 TTGGACTTGCACTTGGACATTTTAGCT
1 TTGGACTTGCATTTGGACATTTTAGCC
* *
46380 TTTGACTTGCATTTGGACCTTTTAGCC
1 TTGGACTTGCATTTGGACATTTTAGCC
* *
46407 TTGGATTTGCTTTTGG
1 TTGGACTTGCATTTGG
46423 GCCATAATGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (27 bp):
TTGGACTTGCATTTGGACATTTTAGCC
Found at i:49784 original size:35 final size:35
Alignment explanation
Indices: 49743--49915 Score: 222
Period size: 35 Copynumber: 4.9 Consensus size: 35
49733 TCAGAGTAAT
* *
49743 TAAAGAGTAATAAGTAAAATGGTAACGGTAAAGAG
1 TAAAGAGTAATCAGTAAAATGGTAATGGTAAAGAG
* **
49778 TAAAGAGTAATCAGTAAAATGGTAATGATGTCATCAG
1 TAAAGAGTAATCAGTAAAATGGTAATG--GTAAAGAG
*
49815 TAAAGAGTAATCAGTAAAATGGTAATAGTAATA-AG
1 TAAAGAGTAATCAGTAAAATGGTAATGGTAA-AGAG
* *
49850 TAAAGAGTAATCAGTGAAATGGTAATGGCAAAGAG
1 TAAAGAGTAATCAGTAAAATGGTAATGGTAAAGAG
* *
49885 TAAAGAGTAATTAGTAAAATGGTAATAGTAA
1 TAAAGAGTAATCAGTAAAATGGTAATGGTAA
49916 TCAATAAAAG
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
34 1 0.01
35 87 0.73
37 31 0.26
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.24
Consensus pattern (35 bp):
TAAAGAGTAATCAGTAAAATGGTAATGGTAAAGAG
Found at i:49853 original size:72 final size:70
Alignment explanation
Indices: 49743--49994 Score: 249
Period size: 72 Copynumber: 3.6 Consensus size: 70
49733 TCAGAGTAAT
**
49743 TAAAGAGTAATAAGTAAAATGGTAACGGTAA-AGAGTAAAGAGTAATCAGTAAAATGGTAATGAT
1 TAAAGAGTAATAAGTAAAATGGTAATAGTAATA-AGTAAAGAGTAATCAGTAAAATGGTAATG--
*
49807 GTC-ATCAG
63 G-CAAACAG
* *
49815 TAAAGAGTAATCAGTAAAATGGTAATAGTAATAAGTAAAGAGTAATCAGTGAAATGGTAATGGCA
1 TAAAGAGTAATAAGTAAAATGGTAATAGTAATAAGTAAAGAGTAATCAGTAAAATGGTAATGGCA
*
49880 AAGAG
66 AACAG
* *
49885 TAAAGAGTAATTAGTAAAATGGTAATAGTAATCAA-TAAA-AG-----AGT-AAA-GAGTAATAG
1 TAAAGAGTAATAAGTAAAATGGTAATAGTAAT-AAGTAAAGAGTAATCAGTAAAATG-GTAATGG
*
49941 CAATCAG
64 CAAACAG
*
49948 TAAAGAGTAA-AGAGTAAAAATGGTAATAGTAATCAGTAAAAGAGTAA
1 TAAAGAGTAATA-AGT-AAAATGGTAATAGTAATAAGT-AAAGAGTAA
49995 AGAGTAATCA
Statistics
Matches: 156, Mismatches: 12, Indels: 27
0.80 0.06 0.14
Matches are distributed among these distances:
62 1 0.01
63 28 0.18
64 21 0.13
65 3 0.02
66 2 0.01
69 3 0.02
70 39 0.25
71 2 0.01
72 56 0.36
73 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.22, T:0.23
Consensus pattern (70 bp):
TAAAGAGTAATAAGTAAAATGGTAATAGTAATAAGTAAAGAGTAATCAGTAAAATGGTAATGGCA
AACAG
Found at i:49934 original size:7 final size:7
Alignment explanation
Indices: 49922--50050 Score: 72
Period size: 7 Copynumber: 18.3 Consensus size: 7
49912 GTAATCAATA
49922 AAAGAGT
1 AAAGAGT
49929 AAAGAGT
1 AAAGAGT
* *
49936 -AATAGC
1 AAAGAGT
**
49942 AATCAGT
1 AAAGAGT
49949 AAAGAGT
1 AAAGAGT
49956 AAAGAGT
1 AAAGAGT
*
49963 AAAAATGGT
1 AAAGA--GT
*
49972 -AATAGT
1 AAAGAGT
**
49978 AATCAGT
1 AAAGAGT
49985 AAAAGAGT
1 -AAAGAGT
49993 AAAGAGT
1 AAAGAGT
*
50000 AATCAGA-A
1 AA--AGAGT
50008 AAAGAGT
1 AAAGAGT
50015 AATAGTAGT
1 AA-AG-AGT
50024 --A-AGT
1 AAAGAGT
50028 AAAGAGT
1 AAAGAGT
50035 AAAGAGT
1 AAAGAGT
50042 AAAGAGT
1 AAAGAGT
50049 AA
1 AA
50051 TCAGTAAAAT
Statistics
Matches: 94, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
4 3 0.03
6 11 0.12
7 60 0.64
8 12 0.13
9 8 0.09
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.19
Consensus pattern (7 bp):
AAAGAGT
Found at i:49960 original size:27 final size:28
Alignment explanation
Indices: 49906--49964 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
49896 TAGTAAAATG
*
49906 GTAATAGTAATCAATAAAAGAGTAAAGA
1 GTAATAGCAATCAATAAAAGAGTAAAGA
*
49934 GTAATAGCAATCAGT-AAAGAGTAAAGA
1 GTAATAGCAATCAATAAAAGAGTAAAGA
49961 GTAA
1 GTAA
49965 AAATGGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.20
Consensus pattern (28 bp):
GTAATAGCAATCAATAAAAGAGTAAAGA
Found at i:49988 original size:64 final size:63
Alignment explanation
Indices: 49883--50002 Score: 204
Period size: 64 Copynumber: 1.9 Consensus size: 63
49873 AATGGCAAAG
**
49883 AGTAAAGAGTAATTAGTAAAATGGTAATAGTAATCAATAAAAGAGTAAAGAGTAATAGCAATC
1 AGTAAAGAGTAAAGAGTAAAATGGTAATAGTAATCAATAAAAGAGTAAAGAGTAATAGCAATC
*
49946 AGTAAAGAGTAAAGAGTAAAAATGGTAATAGTAATCAGTAAAAGAGTAAAGAGTAAT
1 AGTAAAGAGTAAAGAGT-AAAATGGTAATAGTAATCAATAAAAGAGTAAAGAGTAAT
50003 CAGAAAAAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 15 0.28
64 38 0.72
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.23
Consensus pattern (63 bp):
AGTAAAGAGTAAAGAGTAAAATGGTAATAGTAATCAATAAAAGAGTAAAGAGTAATAGCAATC
Found at i:49990 original size:107 final size:104
Alignment explanation
Indices: 49743--50059 Score: 311
Period size: 107 Copynumber: 3.0 Consensus size: 104
49733 TCAGAGTAAT
* * * * *
49743 TAAAGAGTAATAAGTAAAATGGTAACGGTAAAGAGTAAAGAGTAATCAGTAAAATGGTAATGATG
1 TAAAGAGTAAAAAGTGAAATAGTAATGGAAAAGAGTAAAGAGTAATCAGTAAAATGGTAAT-A-G
* * ** *
49808 TCATCAGTAAAGAGTAATCAGTAAAATGGTAAT-AGTAATAAG
64 TAATCAATAAAGAGTAAAGAGT-AAATAGTAATCAGTAA-AAG
** * * *
49850 TAAAGAGTAATCAGTGAAATGGTAATGGCAAAGAGTAAAGAGTAATTAGTAAAATGGTAATAGTA
1 TAAAGAGTAAAAAGTGAAATAGTAATGGAAAAGAGTAAAGAGTAATCAGTAAAATGGTAATAGTA
*
49915 ATCAATAAAAGAGTAAAGAGT-AATAGCAATCAGTAAAGAG
66 ATCAAT-AAAGAGTAAAGAGTAAATAGTAATCAGTAAA-AG
* * *
49955 TAAAGAGTAAAAA-TGGTAATAGTAATCAGTAAAAGAGTAAAGAGTAATCAG-AAAAAGAGTAAT
1 TAAAGAGTAAAAAGT-GAAATAGTAAT--GGAAAAGAGTAAAGAGTAATCAGTAAAATG-GTAAT
* *
50018 AGTAGT-AAGTAAAGAGTAAAGAGTAAAGAGTAATCAGTAAAA
62 AGTAATCAA-TAAAGAGTAAAGAGTAAATAGTAATCAGTAAAA
50060 TGGTAATAGT
Statistics
Matches: 179, Mismatches: 22, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
104 9 0.05
105 34 0.19
106 35 0.20
107 101 0.56
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.22
Consensus pattern (104 bp):
TAAAGAGTAAAAAGTGAAATAGTAATGGAAAAGAGTAAAGAGTAATCAGTAAAATGGTAATAGTA
ATCAATAAAGAGTAAAGAGTAAATAGTAATCAGTAAAAG
Found at i:50019 original size:43 final size:43
Alignment explanation
Indices: 49946--50159 Score: 234
Period size: 43 Copynumber: 4.8 Consensus size: 43
49936 AATAGCAATC
**
49946 AGTAAAGAGTAAAGAGTAAAAATGGTAATAGTAATCAGTAAAAG
1 AGTAAAGAGTAATCAGT-AAAATGGTAATAGTAATCAGTAAAAG
* * *
49990 AGTAAAGAGTAATCAG-AAAAAGAGTAATAGTAGTAAGTAAAGAGTAAAG
1 AGTAAAGAGTAATCAGTAAAATG-GTAATAGTAATCAGT----A--AAAG
50039 AGTAAAGAGTAATCAGTAAAATGGTAATAGTAATCAGTAAAAG
1 AGTAAAGAGTAATCAGTAAAATGGTAATAGTAATCAGTAAAAG
* * * * *
50082 AATAAAGAGTAAACAGTAAAATGGTATTACTAATCGGT-AAAG
1 AGTAAAGAGTAATCAGTAAAATGGTAATAGTAATCAGTAAAAG
* *
50124 AGTAAAGAGTAATCTGTAAAATGGTAATGGTAATCA
1 AGTAAAGAGTAATCAGTAAAATGGTAATAGTAATCA
50160 ATAATTAAAA
Statistics
Matches: 142, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
42 38 0.27
43 50 0.35
44 14 0.10
45 1 0.01
47 1 0.01
49 33 0.23
50 5 0.04
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.22
Consensus pattern (43 bp):
AGTAAAGAGTAATCAGTAAAATGGTAATAGTAATCAGTAAAAG
Found at i:50036 original size:35 final size:34
Alignment explanation
Indices: 49743--50036 Score: 204
Period size: 35 Copynumber: 8.3 Consensus size: 34
49733 TCAGAGTAAT
* ** *
49743 TAAAGAGTAATAAGTAAAATGGTAACGGTAAAGAG
1 TAAAGAGTAATCAGTAAAATGGTAATAGTATA-AG
*
49778 TAAAGAGTAATCAGTAAAATGGTAATGATGTCATCAG
1 TAAAGAGTAATCAGTAAAATGGTAAT-A-GT-ATAAG
49815 TAAAGAGTAATCAGTAAAATGGTAATAGTAATAAG
1 TAAAGAGTAATCAGTAAAATGGTAATAGT-ATAAG
* * * *
49850 TAAAGAGTAATCAGTGAAATGGTAATGGCAAAGAG
1 TAAAGAGTAATCAGTAAAATGGTAATAGTATA-AG
*
49885 TAAAGAGTAATTAGTAAAATGGTAATAGTAATCAA-
1 TAAAGAGTAATCAGTAAAATGGTAATAGT-AT-AAG
** * * *
49920 TAAAAGAGTAAAGAGT--AATAGCAATCAGTAAAGAG
1 T-AAAGAGTAATCAGTAAAATGGTAAT-AGTATA-AG
** * *
49955 TAAAGAGTAAAAATGGT--AATAGTAATCAGTAAAAGAG
1 TAAAGAGTAATCA--GTAAAATGGTAAT-AGT-ATA-AG
*
49992 TAAAGAGTAATCAG-AAAAAGAGTAATAGTAGTAAG
1 TAAAGAGTAATCAGTAAAATG-GTAATAGTA-TAAG
50027 TAAAGAGTAA
1 TAAAGAGTAA
50037 AGAGTAAAGA
Statistics
Matches: 214, Mismatches: 28, Indels: 34
0.78 0.10 0.12
Matches are distributed among these distances:
33 1 0.00
34 22 0.10
35 102 0.48
36 35 0.16
37 53 0.25
38 1 0.00
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.22
Consensus pattern (34 bp):
TAAAGAGTAATCAGTAAAATGGTAATAGTATAAG
Found at i:50056 original size:14 final size:14
Alignment explanation
Indices: 50025--50101 Score: 52
Period size: 14 Copynumber: 5.4 Consensus size: 14
50015 AATAGTAGTA
*
50025 AGTAAAGAGTAAAG
1 AGTAAAGAGTAAAC
*
50039 AGTAAAGAGTAATC
1 AGTAAAGAGTAAAC
*
50053 AGTAAA-ATGGT-AAT
1 AGTAAAGA--GTAAAC
**
50067 AGTAATCAGTAAA-
1 AGTAAAGAGTAAAC
50080 AGAATAAAGAGTAAAC
1 AG--TAAAGAGTAAAC
50096 AGTAAA
1 AGTAAA
50102 ATGGTATTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
13 5 0.10
14 30 0.61
15 12 0.24
16 2 0.04
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (14 bp):
AGTAAAGAGTAAAC
Found at i:50122 original size:92 final size:93
Alignment explanation
Indices: 49946--50135 Score: 267
Period size: 92 Copynumber: 2.1 Consensus size: 93
49936 AATAGCAATC
* * *
49946 AGTAAAGAGTAAAGAGTAAAAATGGTAATAGTAATCAGTAAAAGAGTAAAGAGTAATCAGAAAAA
1 AGTAAAGAGTAAACAGTAAAAATGGTAATAGTAATCAGTAAAAGAATAAAGAGTAAACAGAAAAA
* *
50011 GAGTAATAGTAGTAAGTAAAGAGTAAAG
66 GAGTAATACTAATAAGTAAAGAGTAAAG
*
50039 AGTAAAGAGTAATCAGT-AAAATGGTAATAGTAATCAGTAAAAGAATAAAGAGTAAACAGTAAAA
1 AGTAAAGAGTAAACAGTAAAAATGGTAATAGTAATCAGTAAAAGAATAAAGAGTAAACAG-AAAA
* * **
50103 TG-GTATTACTAATCGGTAAAGAGTAAAG
65 AGAGTAATACTAATAAGTAAAGAGTAAAG
50131 AGTAA
1 AGTAA
50136 TCTGTAAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
92 66 0.77
93 20 0.23
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (93 bp):
AGTAAAGAGTAAACAGTAAAAATGGTAATAGTAATCAGTAAAAGAATAAAGAGTAAACAGAAAAA
GAGTAATACTAATAAGTAAAGAGTAAAG
Found at i:50156 original size:21 final size:21
Alignment explanation
Indices: 50047--50159 Score: 79
Period size: 21 Copynumber: 5.3 Consensus size: 21
50037 AGAGTAAAGA
*
50047 GTAATCAGTAAAATGGTAATA
1 GTAATCAGTAAAATGGTAATG
* *
50068 GTAATCAGTAAAA-GAATAAAG
1 GTAATCAGTAAAATG-GTAATG
* * *
50089 AGTAAACAGTAAAATGGTATTA
1 -GTAATCAGTAAAATGGTAATG
* * *
50111 CTAATCGGT-AAA-GAGTAAAG
1 GTAATCAGTAAAATG-GTAATG
*
50131 AGTAATCTGTAAAATGGTAATG
1 -GTAATCAGTAAAATGGTAATG
50153 GTAATCA
1 GTAATCA
50160 ATAATTAAAA
Statistics
Matches: 67, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
19 1 0.01
20 7 0.10
21 35 0.52
22 22 0.33
23 2 0.03
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (21 bp):
GTAATCAGTAAAATGGTAATG
Found at i:50242 original size:35 final size:35
Alignment explanation
Indices: 50199--50309 Score: 195
Period size: 35 Copynumber: 3.1 Consensus size: 35
50189 AAAAAGATTT
*
50199 AAAAGAGTAAAAATGGTATTCAGCAATTAAAGTAA
1 AAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAA
50234 AAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAAA
1 AAAAGAGTAAAAATGGTATTCAGTAATTAAAGT-AA
*
50270 AAAAAAGTAAAAATGGTATTCAGTAATTAAAGTAA
1 AAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAA
50305 AAAAG
1 AAAAG
50310 GCAAAAAATG
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
35 38 0.53
36 34 0.47
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.23
Consensus pattern (35 bp):
AAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAA
Found at i:50279 original size:36 final size:36
Alignment explanation
Indices: 50199--50308 Score: 195
Period size: 36 Copynumber: 3.1 Consensus size: 36
50189 AAAAAGATTT
*
50199 AAAAGAGTAAAAATGGTATTCAGCAATTAAAGT-AA
1 AAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAAA
50234 AAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAAA
1 AAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAAA
*
50270 AAAAAAGTAAAAATGGTATTCAGTAATTAAAGTAAA
1 AAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAAA
50306 AAA
1 AAA
50309 GGCAAAAAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 32 0.44
36 40 0.56
ACGTcount: A:0.57, C:0.04, G:0.15, T:0.24
Consensus pattern (36 bp):
AAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAAA
Found at i:50329 original size:26 final size:26
Alignment explanation
Indices: 50300--50387 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
50290 CAGTAATTAA
*
50300 AGTAAAAAAGGCAAAAAATGGAAAAC
1 AGTAAAAAAGGTAAAAAATGGAAAAC
*
50326 AGTAAAAAAAGGTAAGAAAATGGTAATA-
1 AGT-AAAAAAGGTAA-AAAATGG-AAAAC
* * *
50354 AGT-AAAAAGAGTAAAAAATAGTAATC
1 AGTAAAAAAG-GTAAAAAATGGAAAAC
50380 AGTAAAAA
1 AGTAAAAA
50388 GAGTAAGGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
25 1 0.02
26 18 0.36
27 18 0.36
28 10 0.20
29 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.18, T:0.15
Consensus pattern (26 bp):
AGTAAAAAAGGTAAAAAATGGAAAAC
Found at i:50329 original size:71 final size:71
Alignment explanation
Indices: 50199--50330 Score: 194
Period size: 71 Copynumber: 1.9 Consensus size: 71
50189 AAAAAGATTT
* * * **
50199 AAAAGAGTAAAAATGGTATTCAGCAATTAAAGTAAAAAAGAGTAAAAATGGTATTCAGTAATTAA
1 AAAAAAGTAAAAATGGTATTCAGCAATTAAAGTAAAAAAGAGAAAAAATGGAAAACAGTAATTAA
50264 AGTAAA
66 AGTAAA
*
50270 AAAAAAGTAAAAATGGTATTCAGTAATTAAAGTAAAAAAG-GCAAAAAATGGAAAACAGTAA
1 AAAAAAGTAAAAATGGTATTCAGCAATTAAAGTAAAAAAGAG-AAAAAATGGAAAACAGTAA
50331 AAAAAGGTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 1 0.02
71 53 0.98
ACGTcount: A:0.58, C:0.05, G:0.17, T:0.21
Consensus pattern (71 bp):
AAAAAAGTAAAAATGGTATTCAGCAATTAAAGTAAAAAAGAGAAAAAATGGAAAACAGTAATTAA
AGTAAA
Found at i:50388 original size:26 final size:27
Alignment explanation
Indices: 50325--50394 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
50315 AAATGGAAAA
* *
50325 CAGTAAAAAAAGGTAAGAAAATGGTAAT
1 CAGTAAAAAGA-GTAAGAAAATAGTAAT
*
50353 AAGTAAAAAGAGTAA-AAAATAGTAAT
1 CAGTAAAAAGAGTAAGAAAATAGTAAT
50379 CAGTAAAAAGAGTAAG
1 CAGTAAAAAGAGTAAG
50395 GTGTAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 24 0.65
27 4 0.11
28 9 0.24
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (27 bp):
CAGTAAAAAGAGTAAGAAAATAGTAAT
Found at i:50510 original size:29 final size:28
Alignment explanation
Indices: 50453--50518 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 28
50443 AAGAAAAAGG
50453 AGAAGAGTAAACAATGGAAATAAAAAAAA
1 AGAAGAGTAAACAATGGAAAT-AAAAAAA
* * *
50482 AGAAGAGTAAACAATGGTAATCAATAAA
1 AGAAGAGTAAACAATGGAAATAAAAAAA
50510 A-AAGAGTAA
1 AGAAGAGTAA
50519 GAAAAGGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 8 0.24
28 6 0.18
29 20 0.59
ACGTcount: A:0.64, C:0.05, G:0.18, T:0.14
Consensus pattern (28 bp):
AGAAGAGTAAACAATGGAAATAAAAAAA
Found at i:51468 original size:22 final size:25
Alignment explanation
Indices: 51410--51475 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
51400 TAAAAATTAA
*
51410 AAACAGAAAATTTATTTTAATCGCAG
1 AAACA-AAAATTTTTTTTAATCGCAG
51436 AAACAAGAAATTTTTTTTAA-CGCA-
1 AAACAA-AAATTTTTTTTAATCGCAG
51460 AAA-AAAAATTTTTTTT
1 AAACAAAAATTTTTTTT
51476 TCGAAAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
22 11 0.29
23 2 0.05
24 3 0.08
25 5 0.13
26 17 0.45
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (25 bp):
AAACAAAAATTTTTTTTAATCGCAG
Found at i:60927 original size:10 final size:10
Alignment explanation
Indices: 60903--60931 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
60893 GCTCAACGAT
60903 ATCTCCATG-
1 ATCTCCATGC
60912 ATCTCCATGC
1 ATCTCCATGC
60922 ATCTCCATGC
1 ATCTCCATGC
60932 TTCCTTGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.31
Consensus pattern (10 bp):
ATCTCCATGC
Found at i:64559 original size:31 final size:31
Alignment explanation
Indices: 64489--64562 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
64479 GGTCTGATCA
* *
64489 CTTCCCTGACAAAAACAAGGAGAAAGTTTTC
1 CTTCCCCGGCAAAAACAAGGAGAAAGTTTTC
*
64520 CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
1 CTTCCCCGGCAAAAACAAGGAGAAAGTTTTC
64551 CTTCCCCGGCAA
1 CTTCCCCGGCAA
64563 CGGCGCCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (31 bp):
CTTCCCCGGCAAAAACAAGGAGAAAGTTTTC
Done.