Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010190.1 Corchorus capsularis cultivar CVL-1 contig10211, 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: 67078
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:344 original size:29 final size:29
Alignment explanation
Indices: 302--404 Score: 144
Period size: 29 Copynumber: 3.7 Consensus size: 29
292 ACACTTTAAT
302 ATAGCGGCGTCTAGACGCCGCCAATCTAA
1 ATAGCGGCGTCTAGACGCCGCCAATCTAA
* * *
331 ATAGCAGCGTCTAGACGCCGACAATCTTA
1 ATAGCGGCGTCTAGACGCCGCCAATCTAA
360 ATAGCGGCGTCTAGACG-C-CC---CTAA
1 ATAGCGGCGTCTAGACGCCGCCAATCTAA
384 ATAGCGGCGTCTAGACGCCGC
1 ATAGCGGCGTCTAGACGCCGC
405 TATATATAGT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
24 20 0.30
25 1 0.02
26 1 0.02
27 1 0.02
28 1 0.02
29 42 0.64
ACGTcount: A:0.26, C:0.31, G:0.25, T:0.17
Consensus pattern (29 bp):
ATAGCGGCGTCTAGACGCCGCCAATCTAA
Found at i:4992 original size:27 final size:27
Alignment explanation
Indices: 4936--4993 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
4926 TTTGCTACTC
* **
4936 AACTTTTCCTACTCCTTTACATTACAA
1 AACTTTTCCTACTCCTTAACAACACAA
* *
4963 AACTTTTGCTACTCCTTAACAACACCA
1 AACTTTTCCTACTCCTTAACAACACAA
4990 AACT
1 AACT
4994 ACACCAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (27 bp):
AACTTTTCCTACTCCTTAACAACACAA
Found at i:7606 original size:11 final size:10
Alignment explanation
Indices: 7575--7622 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
7565 GAAGTTCGTG
7575 ATTGAAGATTA
1 ATTGAAGA-TA
7586 ATTGAAGATA
1 ATTGAAGATA
7596 ATTTGAAGAT-
1 A-TTGAAGATA
*
7606 A-TGAAGATC
1 ATTGAAGATA
7615 ATTGAAGA
1 ATTGAAGA
7623 ATTATATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 10 0.29
11 16 0.47
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (10 bp):
ATTGAAGATA
Found at i:8988 original size:19 final size:19
Alignment explanation
Indices: 8964--9000 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8954 TAGTTTATTG
*
8964 ATTGTTTTGAATTTAATTT
1 ATTGTTTTCAATTTAATTT
8983 ATTGTTTTCAATTTAATT
1 ATTGTTTTCAATTTAATT
9001 CTCAAAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (19 bp):
ATTGTTTTCAATTTAATTT
Found at i:24366 original size:35 final size:35
Alignment explanation
Indices: 24327--25215 Score: 1125
Period size: 35 Copynumber: 25.6 Consensus size: 35
24317 AGTAATAAGT
24327 AACTTAATTCAGGGTAATTAAGT-AGATCAGTGAAT-
1 AACTTAATTCAGGGTAATTAAGTAAG-TCAGT-AATC
*
24362 AACTTAATTCAGGGTAAATTAAGTAGGTCAGTGAAT-
1 AACTTAATTCAGGGT-AATTAAGTAAGTCAGT-AATC
* *
24398 AACTTAATTCAGGGTAATTAAGTAAGTTAGTAAGCC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-TC
*
24434 GGTAACTTAATTCAGGGTAATTAAGAAAGTCAGTAAAT-
1 ---AACTTAATTCAGGGTAATTAAGTAAGTCAGT-AATC
** *
24472 AACTTAATTTTGGGTAATTAAGCAAGTC---AA-C
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * *
24503 AACTTAATTCAGGATAATTAAGTAAGT-AATAGGT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTA-ATC
*
24537 AACTTAATTCAGGGTAATTAAGTCAGT-A--AAT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
24568 AGCTTAATTCAGGGTAATTAAGTAAAGTCAGTTAGT-
1 AACTTAATTCAGGGTAATTAAGT-AAGTCAG-TAATC
* * *
24604 AACTTAGTTCAGGGAAATTAAGTAAG---GCAAT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
24635 AACTTAATTCAAGGTAATTAAGTAAGTCTGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
24670 AATTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
24705 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
24740 AACTTAATTCAGGGTAATTAAGTAAATCGGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
24775 AGCTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
24810 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
24845 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * *
24880 AACTTAATACAGGGTAATTAAGTAATTTAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * *
24915 AACTTAATTCAGGGTAATTAAGTGAGTCAGCAGT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
24949 AACTTAATTCAGGTTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
24984 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATA
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
25019 AACTTAATTCAGGGTAATTAAGTAATTCAGTATTC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
25054 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
25089 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
25124 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * * * * *
25159 AACTTTAATTCGGGGTAATTAAGTGAGTTAATGATT
1 AAC-TTAATTCAGGGTAATTAAGTAAGTCAGTAATC
25195 AACTTAATTCAGGGTAATTAA
1 AACTTAATTCAGGGTAATTAA
25216 ATTTAGTAAG
Statistics
Matches: 752, Mismatches: 77, Indels: 50
0.86 0.09 0.06
Matches are distributed among these distances:
31 73 0.10
32 5 0.01
33 2 0.00
34 61 0.08
35 495 0.66
36 84 0.11
37 1 0.00
39 29 0.04
40 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.32
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
Found at i:24404 original size:21 final size:20
Alignment explanation
Indices: 24344--24404 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
24334 TTCAGGGTAA
24344 TTAAGTAGATCAGTGAATAAC
1 TTAAGTAG-TCAGTGAATAAC
* *
24365 TTAA-T--TCAG-G-GTAAA
1 TTAAGTAGTCAGTGAATAAC
24380 TTAAGTAGGTCAGTGAATAAC
1 TTAAGTA-GTCAGTGAATAAC
24401 TTAA
1 TTAA
24405 TTCAGGGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 7 0.23
16 2 0.07
17 4 0.13
19 4 0.13
20 2 0.07
21 11 0.37
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (20 bp):
TTAAGTAGTCAGTGAATAAC
Found at i:31082 original size:33 final size:33
Alignment explanation
Indices: 31040--31103 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
31030 CAATGTTATG
31040 ATCAACCAAAACAAA-TTTGTTTTCATCACAATT
1 ATCAACCAAAACAAATTTTG-TTTCATCACAATT
* *
31073 ATCATCCAAAACAGATTTTGTTTCATCACAA
1 ATCAACCAAAACAAATTTTGTTTCATCACAA
31104 ACAACACCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.33
Consensus pattern (33 bp):
ATCAACCAAAACAAATTTTGTTTCATCACAATT
Found at i:31117 original size:33 final size:33
Alignment explanation
Indices: 31080--31142 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
31070 ATTATCATCC
* *
31080 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
**
31113 AAAACAGATTTAGTGTCATTGCAAACAACA
1 AAAACAGATTTAGTGTCATCACAAACAACA
31143 TTCAAATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:34908 original size:30 final size:30
Alignment explanation
Indices: 34872--34957 Score: 145
Period size: 30 Copynumber: 2.9 Consensus size: 30
34862 TATAGGAGAG
34872 GATGGAATCGCACCAAAGATGCCATTAGGT
1 GATGGAATCGCACCAAAGATGCCATTAGGT
*
34902 GATGGAATCGCACCAAAGATGCTATTAGGT
1 GATGGAATCGCACCAAAGATGCCATTAGGT
* *
34932 GATGGAATCGTACCAAAGATGTCATT
1 GATGGAATCGCACCAAAGATGCCATT
34958 TGATCCTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (30 bp):
GATGGAATCGCACCAAAGATGCCATTAGGT
Found at i:63116 original size:39 final size:39
Alignment explanation
Indices: 63072--63447 Score: 264
Period size: 39 Copynumber: 9.6 Consensus size: 39
63062 TAACACAAAC
* * * *
63072 AGAGACCTCAAACAGGATTTTTTAGA-GAAAATCTTGAAT
1 AGAGACCTCAAACAGGA-TTTTGAAATGAAACTCTCGAAT
** * * *
63111 AGAGACCTTGAACAAGGGTTTTGAACT-TAACTCTCGAAT
1 AGAGACCTCAAAC-AGGATTTTGAAATGAAACTCTCGAAT
* * * * *
63150 AGGGATCTAAAACAGGATTTTGAAATGAAACTCACAAAT
1 AGAGACCTCAAACAGGATTTTGAAATGAAACTCTCGAAT
* ** ** *
63189 AGAGACCTCAAACAAGATTTTTTTAGCGAAAAC-CTTGAAT
1 AGAGACCTCAAACAGGA-TTTTGAAATG-AAACTCTCGAAT
** * *
63229 AGAGACCTTGAACAAGGGTTTT-AAACT-TAACTCTCGAAT
1 AGAGACCTCAAAC-AGGATTTTGAAA-TGAAACTCTCGAAT
* *
63268 AGAGACCTAAAACAGGATTTTGAAATGAAACTCTCAAAT
1 AGAGACCTCAAACAGGATTTTGAAATGAAACTCTCGAAT
** ** * *
63307 AGAGACCTCAAACAGGATTTTTTAGCGAAAATCTTGAAT
1 AGAGACCTCAAACAGGATTTTGAAATGAAACTCTCGAAT
** * * * *
63346 AGAGACCTTGAACAAGGGTTTT--AAGGTTAACTCTCAAAT
1 AGAGACCTCAAAC-AGGATTTTGAAATG-AAACTCTCGAAT
* *
63385 AGAGACCTAAAACAGGATTTTGAAATGAAACTCTCAAAT
1 AGAGACCTCAAACAGGATTTTGAAATGAAACTCTCGAAT
63424 AGAGACCTCAAACAGGA-TTTGAAA
1 AGAGACCTCAAACAGGATTTTGAAA
63448 AGAGCATGAT
Statistics
Matches: 257, Mismatches: 66, Indels: 29
0.73 0.19 0.08
Matches are distributed among these distances:
38 38 0.15
39 175 0.68
40 38 0.15
41 6 0.02
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.26
Consensus pattern (39 bp):
AGAGACCTCAAACAGGATTTTGAAATGAAACTCTCGAAT
Found at i:63210 original size:117 final size:116
Alignment explanation
Indices: 63065--63443 Score: 632
Period size: 117 Copynumber: 3.2 Consensus size: 116
63055 TTAAGCTTAA
* *
63065 CACAAACAGAGACCTCAAACAGGATTTTTTAGAGAAAATCTTGAATAGAGACCTTGAACAAGGGT
1 CACAAATAGAGACCTCAAACAGGATTTTTTAGCGAAAATCTTGAATAGAGACCTTGAACAAGGGT
* *
63130 TTTGAACTTAACTCTCGAATAGGGATCTAAAACAGGATTTTGAAATGAAACT
66 TTT-AACTTAACTCTCGAATAGAGACCTAAAACAGGATTTTGAAATGAAACT
* *
63182 CACAAATAGAGACCTCAAACAAGATTTTTTTAGCGAAAACCTTGAATAGAGACCTTGAACAAGGG
1 CACAAATAGAGACCTCAAACAGGA-TTTTTTAGCGAAAATCTTGAATAGAGACCTTGAACAAGGG
63247 TTTTAAACTTAACTCTCGAATAGAGACCTAAAACAGGATTTTGAAATGAAACT
65 TTTT-AACTTAACTCTCGAATAGAGACCTAAAACAGGATTTTGAAATGAAACT
*
63300 CTCAAATAGAGACCTCAAACAGGATTTTTTAGCGAAAATCTTGAATAGAGACCTTGAACAAGGGT
1 CACAAATAGAGACCTCAAACAGGATTTTTTAGCGAAAATCTTGAATAGAGACCTTGAACAAGGGT
* *
63365 TTTAAGGTTAACTCTCAAATAGAGACCTAAAACAGGATTTTGAAATGAAACT
66 TTTAA-CTTAACTCTCGAATAGAGACCTAAAACAGGATTTTGAAATGAAACT
*
63417 CTCAAATAGAGACCTCAAACAGGATTT
1 CACAAATAGAGACCTCAAACAGGATTT
63444 GAAAAGAGCA
Statistics
Matches: 248, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
116 2 0.01
117 136 0.55
118 110 0.44
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (116 bp):
CACAAATAGAGACCTCAAACAGGATTTTTTAGCGAAAATCTTGAATAGAGACCTTGAACAAGGGT
TTTAACTTAACTCTCGAATAGAGACCTAAAACAGGATTTTGAAATGAAACT
Found at i:63378 original size:78 final size:78
Alignment explanation
Indices: 62944--63431 Score: 337
Period size: 78 Copynumber: 6.3 Consensus size: 78
62934 TTTCAAACAA
** * * * ** * *
62944 AAACTCTCGAATAGAGACCTAAAAC-AGGATTTTGAAAC-GAAGCTCTCAACCAGACACTTAAAA
1 AAACTCTCGAATAGAGACCTTGAACAAGGGTTTT-AAGCTTAA-CTCTCAAATAGAGACCTAAAA
* *
63007 CAAGATTTTTGAAGTG
64 CAGGATTTTT-AAGCG
* * *
63023 AAACTCTCGAATAGAGACCTTGAACAAGGGTTTTAAGCTTAA--CACAAACAGAGACCTCAAACA
1 AAACTCTCGAATAGAGACCTTGAACAAGGGTTTTAAGCTTAACTCTCAAATAGAGACCTAAAACA
* *
63086 GGATTTTTTAGAG
66 GGATTTTTAAGCG
* * * * *
63099 AAAATCTTGAATAGAGACCTTGAACAAGGGTTTTGAA-CTTAACTCTCGAATAGGGATCTAAAAC
1 AAACTCTCGAATAGAGACCTTGAACAAGGGTTTT-AAGCTTAACTCTCAAATAGAGACCTAAAAC
* **
63163 AGGATTTTGAAATG
65 AGGATTTTTAAGCG
* * ** ** * ** ** **
63177 AAACTCACAAATAGAGACCTCAAACAAGATTTTTTTAGCGAAAAC-CTTGAATAGAGACCTTGAA
1 AAACTCTCGAATAGAGACCTTGAACAAG-GGTTTTAAGC-TTAACTCTCAAATAGAGACCTAAAA
* * *
63241 CAAGG-GTTTTAAACT
64 C-AGGATTTTTAAGCG
* ** * * * *
63256 TAACTCTCGAATAGAGACCTAAAAC-AGGATTTTGAA-ATGAAACTCTCAAATAGAGACCTCAAA
1 AAACTCTCGAATAGAGACCTTGAACAAGGGTTTT-AAGCT-TAACTCTCAAATAGAGACCTAAAA
*
63319 CAGGATTTTTTAGCG
64 CAGGATTTTTAAGCG
* * *
63334 AAAATCTTGAATAGAGACCTTGAACAAGGGTTTTAAGGTTAACTCTCAAATAGAGACCTAAAACA
1 AAACTCTCGAATAGAGACCTTGAACAAGGGTTTTAAGCTTAACTCTCAAATAGAGACCTAAAACA
* **
63399 GGATTTTGAAATG
66 GGATTTTTAAGCG
*
63412 AAACTCTCAAATAGAGACCT
1 AAACTCTCGAATAGAGACCT
63432 CAAACAGGAT
Statistics
Matches: 316, Mismatches: 78, Indels: 31
0.74 0.18 0.07
Matches are distributed among these distances:
76 40 0.13
77 36 0.11
78 144 0.46
79 81 0.26
80 15 0.05
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (78 bp):
AAACTCTCGAATAGAGACCTTGAACAAGGGTTTTAAGCTTAACTCTCAAATAGAGACCTAAAACA
GGATTTTTAAGCG
Found at i:63744 original size:190 final size:190
Alignment explanation
Indices: 63411--64255 Score: 1275
Period size: 190 Copynumber: 4.4 Consensus size: 190
63401 ATTTTGAAAT
* * * * * *
63411 GAAACTCTCAAATAGAGACCTCAAACAGGATTTGAAAAGAGCATGATTTTGGAATTGAAACAAGA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTGGAATTGAAACAAG-
* * * * * *
63476 AAAATCTCTATTAGAGACCTCAAGTAGGATTCGAAAACGAAACAAGATTTTAGATTAAAACAATA
65 AAACTCTCGACTAGAGACCTCAAGCAGGATTCGAAAATGAAACAAGATTTTAGATTAAAACAAGA
* *
63541 AACTCTTGACTAGTGGCCTGAAGCAGGATTTGAAACGAAACAAGACTTTAGATTGAAACAA
130 AACTCTCGACTAGTGACCTGAAGCAGGATTTGAAACGAAACAAGACTTTAGATTGAAACAA
* *
63602 GAAACTCTAGACTAGAGACCTTAAGCAGGATTTGAAATGAACAAGATTTTGGAATTGAAACAAGA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTGGAATTGAAACAAGA
* *
63667 AACTCTCGACTAGAGACCTCAAGTAGAATTCGAAAATGAAACAAGATTTTAGATTAAAACAAGAA
66 AACTCTCGACTAGAGACCTCAAGCAGGATTCGAAAATGAAACAAGATTTTAGATTAAAACAAGAA
* * *
63732 ACTGTCGACTAGTGACCTGAAGTAGGATTTGAAACGAAACAAAACTTTAGATTGAAACAA
131 ACTCTCGACTAGTGACCTGAAGCAGGATTTGAAACGAAACAAGACTTTAGATTGAAACAA
*
63792 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAAGGAACAAGATTTTGGAATTGAAACAAGA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTGGAATTGAAACAAGA
63857 AACTCTCGACTAGAGACCTCAAGCAGGATTCGAAAATGAAACAAGATTTTAGATTAAAACAAGAA
66 AACTCTCGACTAGAGACCTCAAGCAGGATTCGAAAATGAAACAAGATTTTAGATTAAAACAAGAA
63922 ACTCTCGACTAGTGACCTGAAGCAGGATTTGAAACGAAACAAGACTTTAGATTGAAACAA
131 ACTCTCGACTAGTGACCTGAAGCAGGATTTGAAACGAAACAAGACTTTAGATTGAAACAA
* *
63982 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGACTTTAG-ATTGAAACAAGA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTGGAATTGAAACAAGA
*** * * * *
64046 AAAAATCGACTAGAGACCTCAAGCAGGATTTG-AAATG-AACAGGATTTTTGAATTGAAACAAGA
66 AACTCTCGACTAGAGACCTCAAGCAGGATTCGAAAATGAAACAAGATTTTAG-ATTAAAACAAGA
** ** **
64109 AACTCTCGACTAGAAACCTCG-ATTAGGATTTGGAAGTGAAACAAGACTTTAGATTGAAACAA
130 AACTCTCGACTAGTGACCT-GAAGCAGGATTT-GAAACGAAACAAGACTTTAGATTGAAACAA
*
64171 GAAACTCTCGACTAGAGACCTCAAGTAGGATTTGAAATGAACAAGATTTTGGAATTGAAACAAGA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTGGAATTGAAACAAGA
*
64236 AACTCTTGACTAGAGACCTC
66 AACTCTCGACTAGAGACCTC
64256 GATTAGGAAA
Statistics
Matches: 600, Mismatches: 50, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
187 11 0.02
188 41 0.07
189 118 0.20
190 374 0.62
191 56 0.09
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (190 bp):
GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTGGAATTGAAACAAGA
AACTCTCGACTAGAGACCTCAAGCAGGATTCGAAAATGAAACAAGATTTTAGATTAAAACAAGAA
ACTCTCGACTAGTGACCTGAAGCAGGATTTGAAACGAAACAAGACTTTAGATTGAAACAA
Found at i:64263 original size:63 final size:63
Alignment explanation
Indices: 63411--64255 Score: 1036
Period size: 63 Copynumber: 13.3 Consensus size: 63
63401 ATTTTGAAAT
* * * * * * *
63411 GAAACTCTCAAATAGAGACCTCAAACAGGATTTGAAAAG-AGCATGATTTTGGAATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAG-ATTGAAACAA
* * * * * * *
63474 GAAAAATCTCTATTAGAGACCTCAAGTAGGATTCGAAAACGAAACAAGATTTTAGATTAAAACAA
1 G-AAACTCTCGACTAGAGACCTCAAGCAGGATTTG-AAATGAAACAAGATTTTAGATTGAAACAA
* * * * * * *
63539 TAAACTCTTGACTAGTGGCCTGAAGCAGGATTTGAAACGAAACAAGACTTTAGATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAGATTGAAACAA
* * *
63602 GAAACTCTAGACTAGAGACCTTAAGCAGGATTTGAAATG-AACAAGATTTTGGAATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAG-ATTGAAACAA
* * * *
63665 GAAACTCTCGACTAGAGACCTCAAGTAGAATTCGAAAATGAAACAAGATTTTAGATTAAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTG-AAATGAAACAAGATTTTAGATTGAAACAA
* * * * * * *
63729 GAAACTGTCGACTAGTGACCTGAAGTAGGATTTGAAACGAAACAAAACTTTAGATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAGATTGAAACAA
* *
63792 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAA-GGAACAAGATTTTGGAATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAG-ATTGAAACAA
* *
63855 GAAACTCTCGACTAGAGACCTCAAGCAGGATTCGAAAATGAAACAAGATTTTAGATTAAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTG-AAATGAAACAAGATTTTAGATTGAAACAA
* * * *
63919 GAAACTCTCGACTAGTGACCTGAAGCAGGATTTGAAACGAAACAAGACTTTAGATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAGATTGAAACAA
*
63982 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAAGACTTTAGATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAGATTGAAACAA
*** * *
64044 GAAAAAATCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAGGATTTTTGAATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAG-ATTGAAACAA
* * ** * *
64107 GAAACTCTCGACTAGAAACCTCGATTAGGATTTGGAAGTGAAACAAGACTTTAGATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTT-GAAATGAAACAAGATTTTAGATTGAAACAA
* *
64171 GAAACTCTCGACTAGAGACCTCAAGTAGGATTTGAAATG-AACAAGATTTTGGAATTGAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAG-ATTGAAACAA
*
64234 GAAACTCTTGACTAGAGACCTC
1 GAAACTCTCGACTAGAGACCTC
64256 GATTAGGAAA
Statistics
Matches: 677, Mismatches: 92, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
62 102 0.15
63 335 0.49
64 182 0.27
65 48 0.07
66 10 0.01
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (63 bp):
GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTAGATTGAAACAA
Found at i:64263 original size:127 final size:126
Alignment explanation
Indices: 63411--64255 Score: 1052
Period size: 127 Copynumber: 6.7 Consensus size: 126
63401 ATTTTGAAAT
* * * * * * *
63411 GAAACTCTCAAATAGAGACCTCAAACAGGATTTGAAAAGAGCATGATTTTGGAATTGAAACAAGA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTAGAATTGAAACAAG-
* * * * * * *
63476 AAAATCTCTATTAGAGACCTCAAGTAGGATTCGAAAACGAAACAAGATTTTAGATTAAAACAA
65 AAACTCTCGACTAGAGACCTCAAGTAGGATTTG-AAATGAAACAAGACTTTAGATTGAAACAA
* * * * * * *
63539 TAAACTCTTGACTAGTGGCCTGAAGCAGGATTTGAAACGAAACAAGACTTTAG-ATTGAAACAAG
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAAGATTTTAGAATTGAAACAAG
* * * * *
63603 AAACTCTAGACTAGAGACCTTAAGCAGGATTTGAAATG-AACAAGATTTTGGAATTGAAACAA
65 AAACTCTCGACTAGAGACCTCAAGTAGGATTTGAAATGAAACAAGACTTTAG-ATTGAAACAA
* * * *
63665 GAAACTCTCGACTAGAGACCTCAAGTAGAATTCGAAAATGAAACAAGATTTTAG-ATTAAAACAA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTG-AAATG-AACAAGATTTTAGAATTGAAACAA
* * * * *
63729 GAAACTGTCGACTAGTGACCTGAAGTAGGATTTGAAACGAAACAAAACTTTAGATTGAAACAA
64 GAAACTCTCGACTAGAGACCTCAAGTAGGATTTGAAATGAAACAAGACTTTAGATTGAAACAA
* *
63792 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAAGGAACAAGATTTTGGAATTGAAACAAGA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTAGAATTGAAACAAGA
* * * *
63857 AACTCTCGACTAGAGACCTCAAGCAGGATTCGAAAATGAAACAAGATTTTAGATTAAAACAA
66 AACTCTCGACTAGAGACCTCAAGTAGGATTTG-AAATGAAACAAGACTTTAGATTGAAACAA
* * * *
63919 GAAACTCTCGACTAGTGACCTGAAGCAGGATTTGAAACGAAACAAGACTTTAG-ATTGAAACAAG
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAAGATTTTAGAATTGAAACAAG
*
63983 AAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAAGACTTTAGATTGAAACAA
65 AAACTCTCGACTAGAGACCTCAAGTAGGATTTGAAATGAAACAAGACTTTAGATTGAAACAA
*** * *
64044 GAAAAAATCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAGGATTTTTGAATTGAAACAAGA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTAGAATTGAAACAAGA
* * * *
64109 AACTCTCGACTAGAAACCTCGATTAGGATTTGGAAGTGAAACAAGACTTTAGATTGAAACAA
66 AACTCTCGACTAGAGACCTCAAGTAGGATTT-GAAATGAAACAAGACTTTAGATTGAAACAA
* *
64171 GAAACTCTCGACTAGAGACCTCAAGTAGGATTTGAAATGAACAAGATTTTGGAATTGAAACAAGA
1 GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTAGAATTGAAACAAGA
*
64236 AACTCTTGACTAGAGACCTC
66 AACTCTCGACTAGAGACCTC
64256 GATTAGGAAA
Statistics
Matches: 619, Mismatches: 88, Indels: 21
0.85 0.12 0.03
Matches are distributed among these distances:
124 10 0.02
125 117 0.19
126 91 0.15
127 330 0.53
128 62 0.10
129 9 0.01
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (126 bp):
GAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTAGAATTGAAACAAGA
AACTCTCGACTAGAGACCTCAAGTAGGATTTGAAATGAAACAAGACTTTAGATTGAAACAA
Found at i:64626 original size:168 final size:169
Alignment explanation
Indices: 64325--64709 Score: 628
Period size: 168 Copynumber: 2.3 Consensus size: 169
64315 GTTATCAATT
* *
64325 CAAACTCTAAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAATTTTTGATGAAAAAAC
1 CAAACTCTGAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAAAC
* * * *
64390 TTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCTAGAGGACTTGTCTGAATTAATAC
66 TTGACGAAATGAAATGATACCCGGAGGTTTTACCAATTGCCTAGAGGACTTATCAGAATTAATAC
* *
64455 CCGGAGGTTTTTGAATTTGTGCCCGGAGGACTTACCATG
131 CCGGAGGTTTCTGAACTTGTGCCCGGAGGACTTACCATG
*
64494 CAAACTCTGAATAGAGACCTTTAACAAGGATTTTAGACTTAAACATGAATCTTTGATG-AAAAAC
1 CAAACTCTGAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAAAC
* *
64558 TTGACGAAATGAAATGATACCCGGAGGTTTTACCAATTGCCTGGAGGACTTATCAGAATTAGTAC
66 TTGACGAAATGAAATGATACCCGGAGGTTTTACCAATTGCCTAGAGGACTTATCAGAATTAATAC
**
64623 CCGGAGGTTTCTGAACTTGTGCTTGGAGGACTTACCATG
131 CCGGAGGTTTCTGAACTTGTGCCCGGAGGACTTACCATG
* *
64662 CAAACTTTGAATAAAGACCTTTAACAAGGATTTTAAACTTAAACATGA
1 CAAACTCTGAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGA
64710 TTAAAACTTG
Statistics
Matches: 200, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
168 145 0.73
169 55 0.28
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (169 bp):
CAAACTCTGAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAAAC
TTGACGAAATGAAATGATACCCGGAGGTTTTACCAATTGCCTAGAGGACTTATCAGAATTAATAC
CCGGAGGTTTCTGAACTTGTGCCCGGAGGACTTACCATG
Found at i:64829 original size:70 final size:70
Alignment explanation
Indices: 64716--64898 Score: 285
Period size: 70 Copynumber: 2.6 Consensus size: 70
64706 ATGATTAAAA
* *
64716 CTTGAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTTGTGGCTTGGATAGAAC
1 CTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTTGTAGCTTGGATAGAAC
*
64781 CGAGG
66 CAAGG
* *
64786 CTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCTTTGTATCTTGGATAGAAC
1 CTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTTGTAGCTTGGATAGAAC
64851 CAAGG
66 CAAGG
** * *
64856 CTTGAAGAGACTCGTATGGAAACGAGTTTGACTTATGGAAAAG
1 CTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
64899 TCAAAGTCTT
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 104 1.00
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (70 bp):
CTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTTGTAGCTTGGATAGAAC
CAAGG
Done.