Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024750.1 Corchorus olitorius cultivar O-4 contig24783, 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: 32840
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1090 original size:51 final size:51
Alignment explanation
Indices: 998--1183 Score: 266
Period size: 52 Copynumber: 3.6 Consensus size: 51
988 ATTGAAAACT
*
998 AAAACCTGGTGGGAACTTTCCCAATTTGCAAAAGAGCTAGATTGAATACTTTG
1 AAAA-CTGATGGGAACTTTCCCAATTTG-AAAAGAGCTAGATTGAATACTTTG
* * * *
1051 AAAACTGATGGAAACTTTCCCAAGTTGAAAAGAGGTAGATTGAATACTCTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAGATTGAATACTTTG
* * *
1102 AAAACTTGATGGGAACTTTCCCAATTTAAAAAGAGCTAAATTGAATAC-TTA
1 AAAAC-TGATGGGAACTTTCCCAATTTGAAAAGAGCTAGATTGAATACTTTG
1153 AAAACTGATGGGAACTTTCCCAATTTGAAAA
1 AAAACTGATGGGAACTTTCCCAATTTGAAAA
1184 CTTAAACATG
Statistics
Matches: 119, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
50 25 0.21
51 33 0.28
52 57 0.48
53 4 0.03
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (51 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAGATTGAATACTTTG
Found at i:3886 original size:51 final size:52
Alignment explanation
Indices: 3811--3912 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 52
3801 TATGTACTTA
* * *
3811 GTAATGACCAAAATGAAAAGGGATTTGAATTAAATGGAAGGTGTAGGAATTAG
1 GTAATGACC-AAAGGAAAAGGGATTTAAATTAAATGGAAGGTGGAGGAATTAG
3864 GTAATGACC-AAGGAAAAGGGATTTAAATTAAATGGAAGGTGGAGGAATT
1 GTAATGACCAAAGGAAAAGGGATTTAAATTAAATGGAAGGTGGAGGAATT
3913 GAAAGGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 37 0.80
53 9 0.20
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.24
Consensus pattern (52 bp):
GTAATGACCAAAGGAAAAGGGATTTAAATTAAATGGAAGGTGGAGGAATTAG
Found at i:6672 original size:25 final size:25
Alignment explanation
Indices: 6644--6726 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
6634 TAGATTCAAT
6644 TAGATTCAAAGTTGCTTGATTTGGC
1 TAGATTCAAAGTTGCTTGATTTGGC
* * **
6669 TAGATTC-AA-TTGCTGGCTCTTTATC
1 TAGATTCAAAGTTGCTTG--ATTTGGC
* *
6694 T-GCTTTAAAGTTGCTTGATTTGGC
1 TAGATTCAAAGTTGCTTGATTTGGC
6718 TAGATTCAA
1 TAGATTCAA
6727 TTAGATTTTC
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
23 6 0.15
24 10 0.24
25 19 0.46
26 6 0.15
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (25 bp):
TAGATTCAAAGTTGCTTGATTTGGC
Found at i:9686 original size:14 final size:14
Alignment explanation
Indices: 9667--9693 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9657 GAACACACTT
9667 AAAAACACTTTTGG
1 AAAAACACTTTTGG
9681 AAAAACACTTTTG
1 AAAAACACTTTTG
9694 ATTTTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (14 bp):
AAAAACACTTTTGG
Found at i:13651 original size:27 final size:27
Alignment explanation
Indices: 13585--13685 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
13575 AGTGGGCTTA
* * *
13585 AAATGACCACAATGCCCCTTGAGTGTGC
1 AAATGACCAAAATGCCCCTAGA-CGTGC
*
13613 AAATGACCAAAATGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTAGACGTGC
*
13640 AAATGACTAAAATGCCCCTAGACGTGC
1 AAATGACCAAAATGCCCCTAGACGTGC
*
13667 AAATGACTAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
13686 CTTTCAAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
27 48 0.71
28 20 0.29
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAGACGTGC
Found at i:14158 original size:39 final size:39
Alignment explanation
Indices: 14075--14168 Score: 93
Period size: 40 Copynumber: 2.4 Consensus size: 39
14065 ATTCTGCAGT
* *
14075 TAACTGACAAGCAATGATCCTGAACCAAGATCGAAATAA
1 TAACTGACAAGCAATAATCCTAAACCAAGATCGAAATAA
* * *
14114 AAACTGACAAAGCAATAATGCTAAATCAAGA-CTGAAAT-A
1 TAACTGAC-AAGCAATAATCCTAAACCAAGATC-GAAATAA
*
14153 TAACTGATGAAGCAAT
1 TAACTGA-CAAGCAAT
14169 GATCAAGATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
39 22 0.49
40 23 0.51
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (39 bp):
TAACTGACAAGCAATAATCCTAAACCAAGATCGAAATAA
Found at i:14300 original size:30 final size:30
Alignment explanation
Indices: 14264--14858 Score: 859
Period size: 30 Copynumber: 20.2 Consensus size: 30
14254 CTGATGAAGT
* *
14264 AATGATCCTAAACCAGGATTAAAACAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
* *
14294 AATGATCCTAAACCAGGATTAAAACAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
* *
14324 AATGATCCTCAACCATGACTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
* *
14354 AATGATCCTCAACTAGAATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
*
14384 AATGATCCTCAACTAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
* *
14414 AATGATCCTCAACCAGAATTGAAAT-AA-C
1 AATGATCCTCAACCAGGATTAAAATAAAGC
14442 ---GATCCTCAACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
14469 AATGATCCTCAACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
*
14499 AACGATCCTCAACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
14529 AATGATCCTCAACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
* *
14559 AATAATCCTCGACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
*
14589 AATGATCCTCGACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
* * * ** *
14619 AGTAATCCTAAACCAAAATTAAAATAGAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
* *
14649 AACGATCCTAAACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
*
14679 AATTATCCTCAACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
** *
14709 AACAATCCTCAACCAGGATTAAGATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
*
14739 AACGATCCTCAACCAGGATTAAAAT-----
1 AATGATCCTCAACCAGGATTAAAATAAAGC
14764 AATGATCCTCAACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
14794 AATGATCCTCAACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
*
14824 AACGATCCTCAACCAGGATTAAAATAAAGC
1 AATGATCCTCAACCAGGATTAAAATAAAGC
14854 AATGA
1 AATGA
14859 AGCAATGGTT
Statistics
Matches: 512, Mismatches: 43, Indels: 20
0.89 0.07 0.03
Matches are distributed among these distances:
25 44 0.09
26 2 0.00
27 1 0.00
28 1 0.00
29 2 0.00
30 462 0.90
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.19
Consensus pattern (30 bp):
AATGATCCTCAACCAGGATTAAAATAAAGC
Found at i:15368 original size:35 final size:35
Alignment explanation
Indices: 15115--15732 Score: 513
Period size: 35 Copynumber: 17.4 Consensus size: 35
15105 CAATTTGCGG
*
15115 TCAACTGAAATAAACTGCAGAACAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAA-AGATCGCCCTGGA
* * *
15151 TAAATTGAAATAAACTGAAGAAAGGATTGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
* *
15187 TCAACTGAAATGAACTGAAGAAAAGATCGCCTTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * *
15223 TCAACTGAAGTAAAATGAAGAAACGATCGCCCTGTA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
* * * *
15259 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGG
1 TC-AACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * * * *
15295 TCAACTAAAATTAATTGAATAAGAGATCTCCCTAGA
1 TCAACTGAAATAAACTGAAGAA-AGATCGCCCTGGA
* *
15331 TCAACTGAAATAATCTAAAGAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
*
15366 TCAACTGAAATAAACTG--GATAAGTATCGCCCTGGG
1 TCAACTGAAATAAACTGAAGA-AAG-ATCGCCCTGGA
* * * * *
15401 TCAACTTAAATGAATTGAAGAATAGATCTCCCTAGA
1 TCAACTGAAATAAACTGAAGAA-AGATCGCCCTGGA
* * * *
15437 TCAACTGAAATAATCTAAAGAAAAATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * * *
15472 TCAACTGAAATAAACTGGACAAGGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
15507 TCAACTGAAATGAATTGAAGAAGAGATCTCCCTAGA
1 TCAACTGAAATAAACTGAAGAA-AGATCGCCCTGGA
*
15543 TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * ** *
15578 TCAACTGAAATAAACTGAATAAGGACCAACCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
15613 TCAACTGAAATGAATTGAAGAAAGACCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * * * * * * * *
15648 TTAGCTGAAATGAATTGGAGAAAAACCACCTTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * *
15683 TCAGCTGGAATAAACTAAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* *
15719 TCAGCTGGAATAAA
1 TCAACTGAAATAAA
15733 ACTTTAGCAA
Statistics
Matches: 461, Mismatches: 107, Indels: 28
0.77 0.18 0.05
Matches are distributed among these distances:
33 2 0.00
34 3 0.01
35 234 0.51
36 199 0.43
37 23 0.05
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (35 bp):
TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
Found at i:15406 original size:106 final size:106
Alignment explanation
Indices: 15115--15634 Score: 675
Period size: 106 Copynumber: 4.9 Consensus size: 106
15105 CAATTTGCGG
** * * **
15115 TCAACTGAAATAAACTGCAGAACAGATCGCCCTGGATAAATTGAAATAAACTGAAGA-AAGGATT
1 TCAACTGAAATAAACTAAAGAA-AGATCGCCCTGGATCAACTGAAATAAACTG--GATAAGGACC
* * * * * *
15179 GCCCTGGATCAACTGAAATGAACTGAAGAAAAGATCGCCTTGGA
63 GCCCTGGGTCAACTGAAATGAATTGAAGAAGAGATCTCCCTAGA
* * * * *
15223 TCAACTGAAGTAAAATGAAGAAACGATCGCCCTGTATCAAACTGAAATAAACT-GAAATAGGACC
1 TCAACTGAAATAAACTAAAGAAA-GATCGCCCTGGATC-AACTGAAATAAACTGGATA-AGGACC
* * * *
15287 ACCCTGGGTCAACTAAAATTAATTGAATAAGAGATCTCCCTAGA
63 GCCCTGGGTCAACTGAAATGAATTGAAGAAGAGATCTCCCTAGA
* * *
15331 TCAACTGAAATAATCTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGGATAAGTATCGCC
1 TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGGATAAGGACCGCC
* *
15396 CTGGGTCAACTTAAATGAATTGAAGAATAGATCTCCCTAGA
66 CTGGGTCAACTGAAATGAATTGAAGAAGAGATCTCCCTAGA
* * * *
15437 TCAACTGAAATAATCTAAAGAAAAATCACCCTGGATCAACTGAAATAAACTGGACAAGGACCGCC
1 TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGGATAAGGACCGCC
15502 CTGGGTCAACTGAAATGAATTGAAGAAGAGATCTCCCTAGA
66 CTGGGTCAACTGAAATGAATTGAAGAAGAGATCTCCCTAGA
* **
15543 TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAATAAGGACCAAC
1 TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGGATAAGGACCGCC
15608 CTGGGTCAACTGAAATGAATTGAAGAA
66 CTGGGTCAACTGAAATGAATTGAAGAA
15635 AGACCACCCT
Statistics
Matches: 362, Mismatches: 45, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
106 243 0.67
107 18 0.05
108 88 0.24
109 13 0.04
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (106 bp):
TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGGATAAGGACCGCC
CTGGGTCAACTGAAATGAATTGAAGAAGAGATCTCCCTAGA
Found at i:15704 original size:70 final size:70
Alignment explanation
Indices: 15113--15732 Score: 308
Period size: 71 Copynumber: 8.7 Consensus size: 70
15103 ACCAATTTGC
** * ** * *
15113 GGTCAACTGAAATAAACTGCAGAACAGATCGCCCTGGATAAATTGAAATAAACTGAAGAAAGGAT
1 GGTCAACTGAAATAAACTAAAGAA-AGATCGCCCTGGATCAGCTGAAATAAACTGAAGAAA-AAC
***
15178 TGCCCTG
64 CAACCTG
* * * * * * * * *
15185 GATCAACTGAAATGAACTGAAGAAAAGATCGCCTTGGATCAACTGAAGTAAAATGAAGAAACGAT
1 GGTCAACTGAAATAAACTAAAG-AAAGATCGCCCTGGATCAGCTGAAATAAACTGAAGAAA-AAC
**
15250 CGCCCTG
64 CAACCTG
** * * * * * * * * * * *
15257 TATCAAACTGAAATAAACTGAAA-TAGGACCACCCTGGGTCAACTAAAATTAATTGAATAAGAGA
1 GGTC-AACTGAAATAAACT-AAAGAAAGATCGCCCTGGATCAGCTGAAATAAACTGAAGAA-AAA
* ** *
15321 TCTCCCTA
63 CCAACCTG
* * * * * ** * *
15329 GATCAACTGAAATAATCTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGGATAAGTATCG
1 GGTCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAGCTGAAATAAACTGAAGAAAAACCA
*
15394 CCCTG
66 ACCTG
* * * * * * * * * *
15399 GGTCAACTTAAATGAATTGAAGAATAGATCTCCCTAGATCAACTGAAATAATCTAAAGAAAAATC
1 GGTCAACTGAAATAAACTAAAGAA-AGATCGCCCTGGATCAGCTGAAATAAACTGAAGAAAAACC
*
15464 ACCCTG
65 AACCTG
* ** * * * * * * * * *
15470 GATCAACTGAAATAAACTGGACAAGGACCGCCCTGGGTCAACTGAAATGAATTGAAGAAGAGATC
1 GGTCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAGCTGAAATAAACTGAAGAA-AAACC
** *
15535 TCCCTA
65 AACCTG
* * * **
15541 GATCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAATAAGGACCA
1 GGTCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAGCTGAAATAAACTGAAGAAAAACCA
15606 ACCTG
66 ACCTG
* * * * * * * * *
15611 GGTCAACTGAAATGAATTGAAGAAAGACCACCCTGGATTAGCTGAAATGAATTGGAGAAAAACC-
1 GGTCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAGCTGAAATAAACTGAAGAAAAACCA
15675 ACCTTG
66 ACC-TG
* * *
15681 GGTCAGCTGGAATAAACTAAAGAAAAGATCGCCCTGGATCAGCTGGAATAAA
1 GGTCAACTGAAATAAACTAAAG-AAAGATCGCCCTGGATCAGCTGAAATAAA
15733 ACTTTAGCAA
Statistics
Matches: 427, Mismatches: 112, Indels: 19
0.77 0.20 0.03
Matches are distributed among these distances:
69 3 0.01
70 129 0.30
71 178 0.42
72 99 0.23
73 16 0.04
74 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (70 bp):
GGTCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAGCTGAAATAAACTGAAGAAAAACCA
ACCTG
Found at i:15716 original size:212 final size:212
Alignment explanation
Indices: 15115--15717 Score: 640
Period size: 212 Copynumber: 2.8 Consensus size: 212
15105 CAATTTGCGG
** * * * ***
15115 TCAACTGAAATAAACTGCAGAACAGATCGCCCTGGATAAATTGAAATAAACTGAAGAAAGGATTG
1 TCAACTGAAATAAACTAAAGAA-AGATCGCCCTGGATCAACTGAAATAAACTGAA-TAAGGACCA
* * * * * * * * * ** *
15180 CCCTGGATCAACTGAAATGAACTGAAGAAAAGATCGCCTTGGATCAACTGAAGTAAAATGAAGAA
64 ACCTGGGTCAACTGAAATGAATTGAAGAATAGACCACCCTAGATCAACTGAAATAATCTAAAGAA
* * * * * *
15245 ACGATCGCCCTGTATCAAACTGAAATAAACT-GA-AATAGGACCACCCTGGGTCAACTAAAATTA
129 A-AACCACCCTGGATC-AACTGAAATAAACTAGACAA-A-GACCGCCCTGGGTCAACTAAAATGA
*
15308 ATTGAATAAGAGATCTCCCTAGA
190 ATTGAAGAAGAGATCTCCCTAGA
* * * * **
15331 TCAACTGAAATAATCTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGGATAAGTATCGCC
1 TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAATAAGGACCAAC
* * *
15396 CTGGGTCAACTTAAATGAATTGAAGAATAGATCTCCCTAGATCAACTGAAATAATCTAAAGAAAA
66 CTGGGTCAACTGAAATGAATTGAAGAATAGACCACCCTAGATCAACTGAAATAATCTAAAGAAAA
* * * *
15461 ATCACCCTGGATCAACTGAAATAAACTGGACAAGGACCGCCCTGGGTCAACTGAAATGAATTGAA
131 ACCACCCTGGATCAACTGAAATAAACTAGACAAAGACCGCCCTGGGTCAACTAAAATGAATTGAA
15526 GAAGAGATCTCCCTAGA
196 GAAGAGATCTCCCTAGA
15543 TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAATAAGGACCAAC
1 TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAATAAGGACCAAC
* * * **
15608 CTGGGTCAACTGAAATGAATTGAAGAA-AGACCACCCTGGATTAGCTGAAATGAAT-TGGAGAAA
66 CTGGGTCAACTGAAATGAATTGAAGAATAGACCACCCTAGATCAACTGAAAT-AATCTAAAGAAA
* * * * *
15671 AACCACCTTGGGTCAGCTGGAATAAACTAAAGA-AAAGATCGCCCTGG
130 AACCACCCTGGATCAACTGAAATAAACT--AGACAAAGACCGCCCTGG
15718 ATCAGCTGGA
Statistics
Matches: 332, Mismatches: 50, Indels: 14
0.84 0.13 0.04
Matches are distributed among these distances:
211 48 0.14
212 158 0.48
213 15 0.05
214 63 0.19
215 29 0.09
216 19 0.06
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (212 bp):
TCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAATAAGGACCAAC
CTGGGTCAACTGAAATGAATTGAAGAATAGACCACCCTAGATCAACTGAAATAATCTAAAGAAAA
ACCACCCTGGATCAACTGAAATAAACTAGACAAAGACCGCCCTGGGTCAACTAAAATGAATTGAA
GAAGAGATCTCCCTAGA
Found at i:15717 original size:106 final size:105
Alignment explanation
Indices: 15144--15717 Score: 555
Period size: 106 Copynumber: 5.4 Consensus size: 105
15134 GAACAGATCG
* * ** * *
15144 CCCTGGATAAATTGAAATAAACTGAAGAAAGGATTGCCCTGGATCAACTGAAATGAACTGAAGAA
1 CCCTGGATCAACTGAAATAAACT-AAGAAAGGACCGCCCTGGGTCAACTGAAATGAATTGAAGAA
* * * * * * * * *
15209 AAGATCGCCTTGGATCAACTGAAGTAAAATGAAGAAACGATCG
65 GAGATCTCCCTAGATCAACTGAAAT-AATTAAAGAAA-AATCA
* * * * * *
15252 CCCTGTATCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGGTCAACTAAAATTAATTGAATA
1 CCCTGGATC-AACTGAAATAAACT-AAGAAAGGACCGCCCTGGGTCAACTGAAATGAATTGAAGA
* *
15316 AGAGATCTCCCTAGATCAACTGAAATAATCTAAAGAAAGATCG
64 AGAGATCTCCCTAGATCAACTGAAATAAT-TAAAGAAAAATCA
* * * *
15359 CCCTGGATCAACTGAAATAAACT-GGATAAGTATCGCCCTGGGTCAACTTAAATGAATTGAAGAA
1 CCCTGGATCAACTGAAATAAACTAAGA-AAGGACCGCCCTGGGTCAACTGAAATGAATTGAAGAA
*
15423 TAGATCTCCCTAGATCAACTGAAATAATCTAAAGAAAAATCA
65 GAGATCTCCCTAGATCAACTGAAATAAT-TAAAGAAAAATCA
*
15465 CCCTGGATCAACTGAAATAAACT-GGACAAGGACCGCCCTGGGTCAACTGAAATGAATTGAAGAA
1 CCCTGGATCAACTGAAATAAACTAAGA-AAGGACCGCCCTGGGTCAACTGAAATGAATTGAAGAA
* * *
15529 GAGATCTCCCTAGATCAACTGAAATAAACTAAAGAAAGATCG
65 GAGATCTCCCTAGATCAACTGAAAT-AATTAAAGAAAAATCA
* **
15571 CCCTGGATCAACTGAAATAAACTGAA-TAAGGACCAACCTGGGTCAACTGAAATGAATTGAAGAA
1 CCCTGGATCAACTGAAATAAACT-AAGAAAGGACCGCCCTGGGTCAACTGAAATGAATTGAAGAA
* * * * * ** *
15635 -AGACCACCCTGGATTAGCTGAAATGAATTGGAGAAAAACCA
65 GAGATCTCCCTAGATCAACTGAAAT-AATTAAAGAAAAATCA
* * * * * *
15676 CCTTGGGTCAGCTGGAATAAACTAAAGAAAAGATCGCCCTGG
1 CCCTGGATCAACTGAAATAAACT-AAGAAAGGACCGCCCTGG
15718 ATCAGCTGGA
Statistics
Matches: 393, Mismatches: 65, Indels: 18
0.83 0.14 0.04
Matches are distributed among these distances:
105 51 0.13
106 246 0.63
107 17 0.04
108 63 0.16
109 16 0.04
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (105 bp):
CCCTGGATCAACTGAAATAAACTAAGAAAGGACCGCCCTGGGTCAACTGAAATGAATTGAAGAAG
AGATCTCCCTAGATCAACTGAAATAATTAAAGAAAAATCA
Found at i:21642 original size:68 final size:65
Alignment explanation
Indices: 21414--22099 Score: 679
Period size: 67 Copynumber: 10.7 Consensus size: 65
21404 TGGAAAAGTT
* * * *** *
21414 GAAATTGACCCTTCGACCGAAAGGGCATTTTTGGAAAAAAGAAAGTACTAAACTGGGGTACAAAA
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGG-AAAAAGAAA-TACCAAA-T-TAATGCAAAA
21479 AGAC
62 AGAC
* * ** * * * *
21483 GAGAACGACCCTTTCGACCTTAAGGGCATTTTTGGAAACACAAA-A-CTAA--AATGCAAAAAGA
1 GAAAATGACCC-TTCGACCGAAAGGGTATTTTTGGAAAAAGAAATACCAAATTAATGCAAAAAGA
21544 C
65 C
* * *
21545 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAGATACTAAATGTATATGCAATAA
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAA-ATACCAAAT-TA-ATGCAAAAA
21610 GAC
63 GAC
*
21613 AAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAATGC-AAAA
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAG-AAATACCAAA-TT-AATGCAAAAA
21677 GAC
63 GAC
21680 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAATGC-AAAA
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAG-AAATACCAAA-TT-AATGCAAAAA
21744 GAC
63 GAC
* * * * *
21747 GAAAATAACCCTTCGACTGAAAGGGTATTTTTGGAAACACAAA-A-CTAA--AATGCAAAAAGAC
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAATACCAAATTAATGCAAAAAGAC
* * * * * * *
21808 GAAAACGACCCTTCGATCGGAAGGGCATTTTTGGAAACACAAA-ACC-AA--AATGCAAAAAAAC
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAATACCAAATTAATGCAAAAAGAC
*
21869 GAAAATGACCCTTCGACCGAAATGGTA-TTTTGGAAAAAGAAA-A-C------A-GC-AAAAGAC
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAATACCAAATTAATGCAAAAAGAC
21923 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAATGC-AAAA
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAG-AAATACCAAA-TT-AATGCAAAAA
21987 GAC
63 GAC
* *
21990 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGC-AAAA
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAG-AAATACCAAA-TT-AATGCAAAAA
22054 GAC
63 GAC
* *
22057 GAAAATAACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAA
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAA
22100 ATAGAGCTTT
Statistics
Matches: 540, Mismatches: 51, Indels: 55
0.84 0.08 0.09
Matches are distributed among these distances:
54 32 0.06
55 14 0.03
56 4 0.01
57 1 0.00
58 1 0.00
59 1 0.00
60 19 0.04
61 107 0.20
62 21 0.04
63 1 0.00
64 5 0.01
65 1 0.00
66 9 0.02
67 223 0.41
68 61 0.11
69 19 0.04
70 21 0.04
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.20
Consensus pattern (65 bp):
GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAATACCAAATTAATGCAAAAAGAC
Found at i:21716 original size:67 final size:67
Alignment explanation
Indices: 21525--22102 Score: 708
Period size: 67 Copynumber: 9.0 Consensus size: 67
21515 TGGAAACACA
* * *
21525 AAACTAAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAGAT
1 AAACTTAAATGC-AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAAT
*
21590 ACT
65 ACC
* *
21593 AAA-TGTATATGCAATAAGACAAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAA
1 AAACT-TAAATGCAA-AAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAA
21657 TACC
64 TACC
21661 AAACTTAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
1 AAACTTAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
21726 CC
66 CC
* * *
21728 AAACTTAAATGCAAAAGACGAAAATAACCCTTCGACTGAAAGGGTATTTTT-G-----G-AAACA
1 AAACTTAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
*
21786 CA
66 CC
* * * * * * *
21788 AAACTAAAATGCAAAAAGACGAAAACGACCCTTCGATCGGAAGGGCATTTTTGGAAACA-CAAA-
1 AAACTTAAATGC-AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAAT
21851 ACC
65 ACC
* *
21854 --A---AAATGCAAAAAAACGAAAATGACCCTTCGACCGAAATGGTA-TTTTGGAAAAAG-----
1 AAACTTAAATGC-AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAAT
21908 A--
65 ACC
21909 AAAC----A-GCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
1 AAACTTAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
21969 CC
66 CC
*
21971 AAACTTAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATA
1 AAACTTAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
*
22036 CT
66 CC
* *
22038 AAACTTAAATGCAAAAGACGAAAATAACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATA
1 AAACTTAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
22103 GAGCTTTACT
Statistics
Matches: 450, Mismatches: 32, Indels: 57
0.83 0.06 0.11
Matches are distributed among these distances:
54 32 0.07
55 14 0.03
56 1 0.00
57 2 0.00
60 27 0.06
61 69 0.15
62 5 0.01
64 1 0.00
66 4 0.01
67 226 0.50
68 68 0.15
69 1 0.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (67 bp):
AAACTTAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
CC
Found at i:21942 original size:54 final size:55
Alignment explanation
Indices: 21738--22033 Score: 234
Period size: 61 Copynumber: 5.0 Consensus size: 55
21728 AAACTTAAAT
* * * * *
21738 GCAAAAGACGAAAATAACCCTTCGACTGAAAGGGTATTTTTGGAAACACAAAACTAAAA
1 GCAAAAAACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA-A-AGAA--AACA
* * * * * *
21797 TGCAAAAAGACGAAAACGACCCTTCGATCGGAAGGGCATTTTTGGAAACACAAAACCAAAA
1 -GCAAAAA-ACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA-A-AGAA--AACA
*
21858 TGCAAAAAAACGAAAATGACCCTTCGACCGAAATGGTA-TTTTGGAAAAAGAAAACA
1 -GC-AAAAAACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAACA
*
21914 GCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAA
1 GCAAAAAACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAG-----A--AAAC----
21979 A
55 A
* *
21980 TGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAA
1 -GCAAAAAACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAA
22034 TACTAAACTT
Statistics
Matches: 203, Mismatches: 18, Indels: 30
0.81 0.07 0.12
Matches are distributed among these distances:
54 32 0.16
55 14 0.07
56 3 0.01
58 3 0.01
59 1 0.00
60 19 0.09
61 72 0.35
62 10 0.05
66 1 0.00
67 48 0.24
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.18
Consensus pattern (55 bp):
GCAAAAAACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAACA
Found at i:27318 original size:21 final size:22
Alignment explanation
Indices: 27292--27338 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
27282 TCAACGGATA
27292 TGGCACGG-GCATGGCCGGTGG
1 TGGCACGGTGCATGGCCGGTGG
* *
27313 TGGCACGGTGGATGGCCGGTTG
1 TGGCACGGTGCATGGCCGGTGG
27335 TGGC
1 TGGC
27339 TTGGTAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.09, C:0.21, G:0.51, T:0.19
Consensus pattern (22 bp):
TGGCACGGTGCATGGCCGGTGG
Found at i:29838 original size:22 final size:21
Alignment explanation
Indices: 29797--29843 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 21
29787 GCAGGGACAA
29797 AAATTTTTTTTTTTCATGACGC
1 AAATTTTTTTTTTT-ATGACGC
29819 AAATTTTTTTTTCCTT-TGACGC
1 AAATTTTTTTTT--TTATGACGC
29841 AAA
1 AAA
29844 ACACAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 21 0.91
24 2 0.09
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (21 bp):
AAATTTTTTTTTTTATGACGC
Done.